From b1514ccb81a9f9b3a363e1519d579b23a4bc1354 Mon Sep 17 00:00:00 2001 From: patbel-pwr Date: Thu, 25 Feb 2021 21:54:18 +0100 Subject: [PATCH 0001/1193] Fix build error on old GCC --- .../b/Bison/Bison-3.7.1-old_gcc_fix.patch | 20 +++++++++++++++++++ easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb | 5 +++++ 2 files changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch new file mode 100644 index 000000000000..94e39a6c22ee --- /dev/null +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch @@ -0,0 +1,20 @@ +--- src/parse-simulation.c.orig 2020-08-02 07:59:31.000000000 +0200 ++++ src/parse-simulation.c 2021-02-24 11:12:02.385501723 +0100 +@@ -28,7 +28,7 @@ + #include "lssi.h" + #include "nullable.h" + +-typedef struct parse_state ++struct parse_state + { + // Path of state-items the parser has traversed. + struct si_chunk +@@ -58,7 +58,7 @@ + // Causes chunk contents to be freed when the reference count is + // one. Used when only the chunk metadata will be needed. + bool free_contents_early; +-} parse_state; ++} ; + + + static void diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb index c3cedc9436ed..f056aaf84221 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb @@ -21,6 +21,11 @@ builddependencies = [ ('M4', '1.4.18'), ] +# Uncomment if you encounter "error: redefinition of typedef 'parse_state'" during build +#patches = [ +# 'Bison-3.7.1-old_gcc_fix.patch' +#] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], 'dirs': [], From cacc2959d453481845a3c0e91c704933f1b5d218 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 18 May 2021 13:50:27 +0200 Subject: [PATCH 0002/1193] adding easyconfigs: Nipype-1.6.0-foss-2020b.eb --- .../n/Nipype/Nipype-1.6.0-foss-2020b.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb new file mode 100644 index 000000000000..b4ace4a20537 --- /dev/null +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -0,0 +1,87 @@ +easyblock = 'PythonBundle' + +name = 'Nipype' +version = '1.6.0' + +homepage = 'https://nipype.readthedocs.io' +description = """Nipype is a Python project that provides a uniform interface to existing neuroimaging software and + facilitates interaction between these packages within a single workflow.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('lxml', '4.6.2'), + ('networkx', '2.5'), + ('NiBabel', '3.2.1'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_SOURCE]} + +exts_list = [ + ('traits', '6.2.0', { + 'checksums': ['16fa1518b0778fd53bf0547e6a562b1787bf68c8f6b7995a13bd1902529fdb0c'], + }), + ('pydot', '1.4.2', { + 'checksums': ['248081a39bcb56784deb018977e428605c1c758f10897a339fce1dd728ff007d'], + }), + ('pydotplus', '2.0.2', { + 'checksums': ['91e85e9ee9b85d2391ead7d635e3d9c7f5f44fd60a60e59b13e2403fa66505c4'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('isodate', '0.6.0', { + 'checksums': ['2e364a3d5759479cdb2d37cce6b9376ea504db2ff90252a2e5b7cc89cc9ff2d8'], + }), + ('rdflib', '5.0.0', { + 'checksums': ['78149dd49d385efec3b3adfbd61c87afaf1281c30d3fcaf1b323b34f603fb155'], + }), + ('prov', '2.0.0', { + 'checksums': ['b6438f2195ecb9f6e8279b58971e02bc51814599b5d5383366eef91d867422ee'], + }), + ('simplejson', '3.17.2', { + 'checksums': ['75ecc79f26d99222a084fbdd1ce5aad3ac3a8bd535cd9059528452da38b68841'], + }), + ('pytest-forked', '1.3.0', { + 'modulename': 'pytest_forked', + 'checksums': ['6aa9ac7e00ad1a539c41bec6d21011332de671e938c7637378ec9710204e37ca'], + }), + ('apipkg', '1.5', { + 'checksums': ['37228cda29411948b422fae072f57e31d3396d2ee1c9783775980ee9c9990af6'], + }), + ('execnet', '1.8.0', { + 'checksums': ['b73c5565e517f24b62dea8a5ceac178c661c4309d3aa0c3e420856c072c411b4'], + }), + ('pytest-xdist', '2.2.1', { + 'modulename': 'xdist', + 'checksums': ['718887296892f92683f6a51f25a3ae584993b06f7076ce1e1fd482e59a8220a2'], + }), + ('ci-info', '0.2.0', { + 'checksums': ['dd70632c977feb8797b1e633507166b64ad5f57183cebb2b0ea56934abba4616'], + }), + ('filelock', '3.0.12', { + 'checksums': ['18d82244ee114f543149c66a6e0c14e9c4f8a1044b5cdaadd0f82159d6a6ff59'], + }), + ('etelemetry', '0.2.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3e304ea9070902e6367282369cb8eaae05f4beef9313820053cc03f611bd1e29'], + }), + ('nipype', version, { + 'preinstallopts': "sed -i'' 's/.*neurdflib.*//g' nipype/info.py && ", + 'checksums': ['bc56ce63f74c9a9a23c6edeaf77631377e8ad2bea928c898cc89527a47f101cf'], + }), +] + +sanity_check_paths = { + 'files': ['bin/nipypecli'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import nipype.interfaces'"] + +sanity_pip_check = True + +moduleclass = 'vis' From 8ac653864e0789ed23e82d2f9cb18a8c2be49049 Mon Sep 17 00:00:00 2001 From: Diego Lasa Date: Wed, 23 Jun 2021 15:26:49 +0200 Subject: [PATCH 0003/1193] adding easyconfigs: PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb --- ...CMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb new file mode 100644 index 000000000000..3fb0888f0eb9 --- /dev/null +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'PCMSolver' +version = '1.2.3' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://pcmsolver.readthedocs.org' +description = """An API for the Polarizable Continuum Model.""" + +toolchain = {'name': 'iimpi', 'version': '2020b'} +# we have to disable use of -march=native to ensure a correct build on recent Intel systems +# see also https://github.com/PCMSolver/pcmsolver/issues/159 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/PCMSolver/pcmsolver/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] + +builddependencies = [ + ('CMake', '3.18.4'), + ('Eigen', '3.3.8', '', ('GCCcore', '10.2.0')), +] + +dependencies = [ + ('Python', '3.8.6'), + ('zlib', '1.2.11'), + ('Boost', '1.74.0'), +] + +configopts = '-DEIGEN3_ROOT=$EBROOTEIGEN ' + +# The spherical test fails regardless of how it is compiled. +# Instead of patching the tests to skip it just don't run the tests for now. +# runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/run_pcm', 'lib/libpcm.a', 'lib/libpcm.%s' % SHLIB_EXT], + 'dirs': ['include/PCMSolver'] +} + +moduleclass = 'chem' From 3d91ae4cf5092ba2dd4c062b0bb49c70ee77a8c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?P=C3=A4r=20Axel=20Leonard=20Ros=C3=A9n?= Date: Wed, 30 Jun 2021 15:48:00 +0200 Subject: [PATCH 0004/1193] Julia for aarch64 --- .../j/Julia/Julia-1.6.0-linux-aarch64.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb new file mode 100644 index 000000000000..f6ac056dc63c --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb @@ -0,0 +1,25 @@ +## +# Author: Robert Mijakovic +## +# Updated by: rungitta +easyblock = 'Tarball' + +name = 'Julia' +version = '1.6.0' +versionsuffix = '-linux-aarch64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/aarch64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.so'], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lang' From dba95a0f91a631c950e766a987f13f73b31036f0 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Fri, 27 Aug 2021 16:10:38 +0200 Subject: [PATCH 0005/1193] adding easyconfigs: sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb --- .../sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb new file mode 100644 index 000000000000..03810b3b73cf --- /dev/null +++ b/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sinto' + +version = '0.7.3.1' + +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://timoast.github.io/sinto/index.html' + +description = """Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to: + + Subset reads from a BAM file by cell barcode + + Create a scATAC-seq fragments file from a BAM file + + Add read tags to a BAM file according to cell barcode information +""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['c4f3c1413a5c5e2d3587654f7bf53669df883e4d77bb64a846bcbc3c74757c53'] + +dependencies = [ + ('Python', '3.8.6'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2020.11'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'bio' From 3d452e074f02366ad4740c112a614dd026eafff1 Mon Sep 17 00:00:00 2001 From: Yann Sagon Date: Tue, 19 Jul 2022 08:11:31 +0200 Subject: [PATCH 0006/1193] cleanup and upgrade version and toolchain --- .../s/sinto/sinto-0.7.4-foss-2021a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb b/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb new file mode 100644 index 000000000000..2bade413d0cc --- /dev/null +++ b/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'sinto' + +version = '0.7.4' + +homepage = 'https://timoast.github.io/sinto/index.html' + +description = """Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to: + + Subset reads from a BAM file by cell barcode + + Create a scATAC-seq fragments file from a BAM file + + Add read tags to a BAM file according to cell barcode information +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a9bee81992939f6240643040551d9c69893ce07d23190e7e3a604eff254d775d'] + +dependencies = [ + ('Python', '3.9.5'), + ('Pysam', '0.16.0.1'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ['%(name)s --version'] + +moduleclass = 'bio' From 31ef1b936adc922a95b5283da040c9969db5c246 Mon Sep 17 00:00:00 2001 From: Sagon Date: Tue, 19 Jul 2022 10:34:51 +0200 Subject: [PATCH 0007/1193] Delete sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb obsolet version --- .../sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb deleted file mode 100644 index 03810b3b73cf..000000000000 --- a/easybuild/easyconfigs/s/sinto/sinto-0.7.3.1-foss-2020b-Python-3.8.6.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'sinto' - -version = '0.7.3.1' - -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://timoast.github.io/sinto/index.html' - -description = """Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to: - - Subset reads from a BAM file by cell barcode - - Create a scATAC-seq fragments file from a BAM file - - Add read tags to a BAM file according to cell barcode information -""" - -toolchain = {'name': 'foss', 'version': '2020b'} - -source_urls = [PYPI_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['c4f3c1413a5c5e2d3587654f7bf53669df883e4d77bb64a846bcbc3c74757c53'] - -dependencies = [ - ('Python', '3.8.6'), - ('Pysam', '0.16.0.1'), - ('SciPy-bundle', '2020.11'), -] - -download_dep_fail = True -use_pip = True - -sanity_check_commands = ['%(name)s --version'] - -moduleclass = 'bio' From b79e54339fa4faadc3cf6c570ed2d534040a0f18 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 2 Aug 2022 11:49:03 +0100 Subject: [PATCH 0008/1193] adding easyconfigs: pstoedit-3.78-GCCcore-11.3.0.eb --- .../pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..cd2f11ea34fb --- /dev/null +++ b/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'pstoedit' +version = '3.78' + +homepage = 'http://pstoedit.net/' +description = "pstoedit translates PostScript and PDF graphics into other vector formats" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8cc28e34bc7f88d913780f8074e813dd5aaa0ac2056a6b36d4bf004a0e90d801'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/pstoedit', 'lib/libpstoedit.%s' % SHLIB_EXT], + 'dirs': ['include/pstoedit', 'lib/pkgconfig', 'lib/pstoedit', 'share'], +} + +moduleclass = 'tools' From f9d212887f0954032530d864e8df46f6cf43fc94 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Aug 2022 12:39:45 +0100 Subject: [PATCH 0009/1193] More missing dependencies added, pushed to GCC, patch for ImageMagick added --- .../p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb | 50 +++++++++++++++++++ .../pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb | 22 -------- .../p/pstoedit/pstoedit-configure.patch | 16 ++++++ 3 files changed, 66 insertions(+), 22 deletions(-) create mode 100644 easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb delete mode 100644 easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pstoedit/pstoedit-configure.patch diff --git a/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb new file mode 100644 index 000000000000..a50dc8f4c8c3 --- /dev/null +++ b/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +# Updated version from the original one. +# Includes a patch so ImageMagick can be found, some missing +# dependencies included as well. +# libemf seems to be needed. +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'pstoedit' +version = '3.78' + +homepage = 'http://pstoedit.net/' +description = "pstoedit translates PostScript and PDF graphics into other vector formats" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = [('pstoedit-configure.patch')] + +checksums = [ + '8cc28e34bc7f88d913780f8074e813dd5aaa0ac2056a6b36d4bf004a0e90d801', # pstoedit-3.78.tar.gz + 'c81588eebf9c1dd344566654aae8e826b013c969057cffd8e2cc2cd0a93b90c3', # pstoedit-configure.patch +] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), + ('gawk', '5.1.1'), + ('Bison', '3.8.2'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('ImageMagick', '7.1.0-37'), + ('Zip', '3.0'), + ('libzip', '1.9.2'), + ('Ghostscript', '9.56.1'), +] + +osdependencies = [('libemf-dev', 'libEMF-devel', 'libplot-dev')] + +preconfigopts = "autoreconf -i &&" + +sanity_check_paths = { + 'files': ['bin/pstoedit', 'lib/libpstoedit.%s' % SHLIB_EXT], + 'dirs': ['include/pstoedit', 'lib/pkgconfig', 'lib/pstoedit', 'share'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb deleted file mode 100644 index cd2f11ea34fb..000000000000 --- a/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCCcore-11.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pstoedit' -version = '3.78' - -homepage = 'http://pstoedit.net/' -description = "pstoedit translates PostScript and PDF graphics into other vector formats" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_GZ] -checksums = ['8cc28e34bc7f88d913780f8074e813dd5aaa0ac2056a6b36d4bf004a0e90d801'] - -builddependencies = [('binutils', '2.38')] - -sanity_check_paths = { - 'files': ['bin/pstoedit', 'lib/libpstoedit.%s' % SHLIB_EXT], - 'dirs': ['include/pstoedit', 'lib/pkgconfig', 'lib/pstoedit', 'share'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pstoedit/pstoedit-configure.patch b/easybuild/easyconfigs/p/pstoedit/pstoedit-configure.patch new file mode 100644 index 000000000000..ccfc1947ed9c --- /dev/null +++ b/easybuild/easyconfigs/p/pstoedit/pstoedit-configure.patch @@ -0,0 +1,16 @@ +The original configure did not find ImageMagick and thus did not build it. +This patch fixes this. +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/pstoedit-3.78.orig/configure.ac b/pstoedit-3.78/configure.ac +index e8d9e59..4d188ad 100644 +--- a/pstoedit-3.78.orig/configure.ac ++++ b/pstoedit-3.78/configure.ac +@@ -313,7 +313,7 @@ if test "x${PSTOEDIT_GCC_OK}" = xno ; then + else + if test -n "$PKG_CONFIG"; then + AC_MSG_CHECKING(ImageMagick flags through pkg-config) +- PKG_CHECK_MODULES(LIBMAGICK, ImageMagick++, ++ PKG_CHECK_MODULES(LIBMAGICK, ImageMagick, + HAVE_LIBMAGICK=yes + LIBMAGICK_CFLAGS="-DHAVE_MAGIC $LIBMAGICK_CFLAGS" + LIBMAGICK_LDFLAGS="$LIBMAGICK_LIBS" , From 29689c01e1029229fd3177f3b3c9438a197e339f Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 14:14:06 +0100 Subject: [PATCH 0010/1193] adding easyconfigs: MATIO-1.5.22-GCCcore-11.2.0.eb, MATIO-1.5.23-GCCcore-12.1.0.eb --- .../m/MATIO/MATIO-1.5.22-GCCcore-11.2.0.eb | 36 +++++++++++++++++++ .../m/MATIO/MATIO-1.5.23-GCCcore-12.1.0.eb | 34 ++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.22-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.1.0.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.22-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.22-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..9e83706192f4 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.22-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.22' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['ac76efd240f982b779ba2b206349d7aeaa983c3d62b13b942006c8b1ff228472'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.37')] + +dependencies = [('zlib', '1.2.11')] + +sanity_check_commands = ['matdump --help'] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.1.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.1.0.eb new file mode 100644 index 000000000000..0e4dcad72d46 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.23-GCCcore-12.1.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.23' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.1.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['b3b29fb394e1cfa3f98cd57bac013c0cf7716ae7a085e398f2dfaff8f976f0c5'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.38')] + +dependencies = [('zlib', '1.2.12')] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 9d75d4e3225204284ba4a0de6900acfaa33a39cd Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 1 Sep 2022 17:42:02 +0200 Subject: [PATCH 0011/1193] adding easyconfigs: tox-3.25.1-GCCcore-10.2.0.eb, tox-3.25.1-GCCcore-11.3.0.eb --- .../t/tox/tox-3.25.1-GCCcore-10.2.0.eb | 24 +++++++++++++++++++ .../t/tox/tox-3.25.1-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..d6014a40f3bc --- /dev/null +++ b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-10.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'tox' +version = '3.25.1' + +homepage = 'https://tox.wiki' +description = "tox aims to automate and standardize testing in Python" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c138327815f53bc6da4fe56baec5f25f00622ae69ef3fe4e1e385720e22486f9'] + +builddependencies = [ + ('binutils', '2.35'), +] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..86664cd8be08 --- /dev/null +++ b/easybuild/easyconfigs/t/tox/tox-3.25.1-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'tox' +version = '3.25.1' + +homepage = 'https://tox.wiki' +description = "tox aims to automate and standardize testing in Python" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c138327815f53bc6da4fe56baec5f25f00622ae69ef3fe4e1e385720e22486f9'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 9765c203f95b6cc32b17c93247967a707788a56a Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 26 Sep 2022 15:50:18 -0700 Subject: [PATCH 0012/1193] missing pkg-config builddep --- easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb index 17bc1fb95191..2d6a713e0539 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb @@ -19,6 +19,7 @@ checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] builddependencies = [('binutils', '2.37')] dependencies = [ + ('pkg-config', '0.29.2'), ('libtasn1', '4.18.0'), ('libffi', '3.4.2'), ] From 706eacb6e16c410ef81bfa96b74d5df163491881 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 1 Nov 2022 15:17:32 +0000 Subject: [PATCH 0013/1193] adding easyconfigs: CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb and patches: CellBender-0.2.1-sphinxremoval.patch --- ...CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb | 60 +++++++++++++++++++ .../CellBender-0.2.1-sphinxremoval.patch | 15 +++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-sphinxremoval.patch diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..949da3f8a4ef --- /dev/null +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,60 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'CellBender' +version = '0.2.1' +versionsuffix = '-CUDA-%(cudaver)s' +local_pytorch_version = '1.10.0' + +homepage = 'https://github.com/broadinstitute/CellBender' +description = """CellBender is a software package for eliminating technical +artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), + ('PyTables', '3.6.1'), + ('CUDA', '11.3.1', '', SYSTEM), + ('PyTorch', local_pytorch_version, '-CUDA-%(cudaver)s'), + ('torchvision', '0.11.3', '-CUDA-%(cudaver)s'), + ('pyro-ppl', '1.8.0', '-CUDA-%(cudaver)s'), + ('h5py', '3.2.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('natsort', '7.1.1', { + 'checksums': ['00c603a42365830c4722a2eb7663a25919551217ec09a243d3399fa8dd4ac403'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + (name, version, { + 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'patches': ['%(name)s-%(version)s-sphinxremoval.patch'], + 'checksums': ['0f4c32c26a4f413d8852dea2a4d759cc754698bd40d076aa7c9191336752c46c', + # cellbender-0.2.1-sphinxremoval.patch + '0f6a342bac16f4ee80cd05d43923b4cc60d71999ea1bb5c80a75edb7290bbdec', + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/cellbender', 'bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "natsort --help", + "cellbender -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-sphinxremoval.patch b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-sphinxremoval.patch new file mode 100644 index 000000000000..0241bc741287 --- /dev/null +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-sphinxremoval.patch @@ -0,0 +1,15 @@ +Removes Sphinx from the build as it is not required +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/CellBender-0.2.1.orig/REQUIREMENTS.txt b/CellBender-0.2.1/REQUIREMENTS.txt +index 535e3e7..0646183 100644 +--- a/CellBender-0.2.1.orig/REQUIREMENTS.txt ++++ b/CellBender-0.2.1/REQUIREMENTS.txt +@@ -6,8 +6,3 @@ pandas + pyro-ppl>=0.3.2 + scikit-learn + matplotlib +-sphinx>=2.1 +-sphinx-rtd-theme +-sphinx-autodoc-typehints +-sphinxcontrib-programoutput +-sphinx-argparse From f78acaed0537565846287e38d0d254f68c2f9fb2 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Feb 2023 12:44:57 +0000 Subject: [PATCH 0014/1193] adding easyconfigs: poppunk-2.6.0-foss-2022a.eb --- .../p/poppunk/poppunk-2.6.0-foss-2022a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb new file mode 100644 index 000000000000..73309f8a306b --- /dev/null +++ b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb @@ -0,0 +1,60 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'poppunk' +version = '2.6.0' + +homepage = 'https://poppunk.readthedocs.io' +description = """PopPUNK is a tool for clustering genomes. +We refer to the clusters as variable-length-k-mer clusters, or VLKCs. +Biologically, these clusters typically represent distinct strains. +We refer to subclusters of strains as lineages.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('numba', '0.56.4'), + ('networkx', '2.8.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), + ('python-dateutil', '2.8.2'), + ('pandas', '1.5.3'), + ('Biopython', '1.79'), + ('matplotlib', '3.5.2'), + ('HDBSCAN', '0.8.29'), + ('h5py', '3.7.0'), + ('requests', '2.28.2'), + ('graph-tool', '2.45'), + ('X11', '20220504'), + ('pybind11', '2.9.2'), + ('Eigen', '3.4.0'), + ('Boost', '1.79.0'), + ('tqdm', '4.64.0'), + ('pp-sketchlib', '2.1.1'), + ('rapidNJ', '2.3.3'), + ('mandrake', '1.2.2'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('treeswift', '1.1.33', { + 'checksums': ['571cf2966b44bb1c64614cde7f0760e0c9c1b3d4579101d8191cff7272ff61fc'], + }), + (name, version, { + 'source_urls': ['https://github.com/bacpop/PopPUNK/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['9060e0f09e99c1cd34662fb4b6c4b28e4344c0e3d00e983a7be8b60591ad92ec'], + 'modulename': 'poppunk_refine', + }), +] + +moduleclass = 'bio' From 9663e3dfe687437c0ca197801f9ea48d48122b60 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 09:25:12 +0000 Subject: [PATCH 0015/1193] Pandas removed as already in SciPy --- easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb index 73309f8a306b..62498ace9e00 100644 --- a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb @@ -25,7 +25,6 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('scikit-learn', '1.1.2'), ('python-dateutil', '2.8.2'), - ('pandas', '1.5.3'), ('Biopython', '1.79'), ('matplotlib', '3.5.2'), ('HDBSCAN', '0.8.29'), From 99ee1a82280158829b6ec04a7c4eb7092ce59fbd Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 28 Feb 2023 09:39:30 +0000 Subject: [PATCH 0016/1193] Request removed as already in SciPy --- easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb index 62498ace9e00..5932f0cc8b7d 100644 --- a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb @@ -29,7 +29,6 @@ dependencies = [ ('matplotlib', '3.5.2'), ('HDBSCAN', '0.8.29'), ('h5py', '3.7.0'), - ('requests', '2.28.2'), ('graph-tool', '2.45'), ('X11', '20220504'), ('pybind11', '2.9.2'), From dd222aeca46b16f2d10bf03b780d51197e12516c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 Mar 2023 15:49:30 +0100 Subject: [PATCH 0017/1193] adding easyconfigs: Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb --- .../Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 000000000000..628af9a2b091 --- /dev/null +++ b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Vamb' +version = '3.0.9' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/RasmussenLab/vamb' +description = """Vamb is a metagenomic binner which feeds sequence +composition information from a contig catalogue and co-abundance +information from BAM files into a variational autoencoder and clusters +the latent representation.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pysam', '0.18.0'), + ('PyTorch', '1.12.1', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('setuptools', '59.6.0', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_allow_pytorch_1.12.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/RasmussenLab/vamb/archive'], + 'checksums': [ + {'v3.0.9.tar.gz': '3a9025ddc3e9e54e3debe65855ac2367335f920efbcb9e5ecc671a1036455d1e'}, + {'Vamb-3.0.9_allow_pytorch_1.12.patch': '52f909a91d7d63ead3dfa1314c66efb2918a3606212a8f3d8e3a9f7ee7b33c86'}, + ], + }), +] + +moduleclass = 'bio' From a468c3089d97a806a3507b086a05faf44bde7196 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 2 Mar 2023 16:47:38 +0100 Subject: [PATCH 0018/1193] add missing patch file --- .../v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch diff --git a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch new file mode 100644 index 000000000000..f19bf52595b7 --- /dev/null +++ b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9_allow_pytorch_1.12.patch @@ -0,0 +1,15 @@ +Drop requirement of pytorch to 1.12 to allow the use of foss/2021b toolchain + +Åke Sandgren, 2023-03-01 +diff -ru vamb-3.0.9.orig/setup.py vamb-3.0.9/setup.py +--- vamb-3.0.9.orig/setup.py 2022-11-24 11:02:48.000000000 +0100 ++++ vamb-3.0.9/setup.py 2023-03-01 08:26:12.432734868 +0100 +@@ -22,7 +22,7 @@ + "ext_modules": [Extension("vamb._vambtools", + sources=["src/_vambtools.pyx"], + language="c")], +- "install_requires": ["numpy>=1.20", "torch>=1.13", "pysam>=0.14"], ++ "install_requires": ["numpy>=1.20", "torch>=1.12", "pysam>=0.14"], + "setup_requires": ['Cython>=0.29', "setuptools>=58.0"], + "python_requires": ">=3.5", + "classifiers":[ From f8842f70296f93fba5262cf6606b70f4458df0ac Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 29 Mar 2023 17:38:23 +0100 Subject: [PATCH 0019/1193] Python-dateutil removed as already in Python --- easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb index 5932f0cc8b7d..113291caf709 100644 --- a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb @@ -24,7 +24,6 @@ dependencies = [ ('networkx', '2.8.4'), ('SciPy-bundle', '2022.05'), ('scikit-learn', '1.1.2'), - ('python-dateutil', '2.8.2'), ('Biopython', '1.79'), ('matplotlib', '3.5.2'), ('HDBSCAN', '0.8.29'), From 0e5b07bfd6fab0fbee859d664543573e5374c9e4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 7 Jul 2023 09:58:31 +0200 Subject: [PATCH 0020/1193] adding easyconfigs: rocm-smi-5.6.0-GCCcore-11.3.0.eb --- .../rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..2b102619380d --- /dev/null +++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'rocm-smi' +version = '5.6.0' + +homepage = 'https://github.com/RadeonOpenCompute/rocm_smi_lib' +description = """The ROCm System Management Interface Library, or ROCm SMI +library, is part of the Radeon Open Compute ROCm software stack. It is a C +library for Linux that provides a user space interface for applications to +monitor and control GPU applications.""" +docurls = ['https://rocmdocs.amd.com'] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ["https://github.com/RadeonOpenCompute/rocm_smi_lib/archive/"] +sources = ["rocm-%(version)s.tar.gz"] +checksums = ['88be875948a29454b8aacced8bb8ad967502a7a074ecbc579ed673c1650a2f7e'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +# This package hardcodes 'noexecheap' as a linker flag which is not supported +# by 'ld.gold', to get around we explicitly force 'ld.bfd' here +configopts = "-DCMAKE_CXX_FLAGS='-fuse-ld=bfd'" + +sanity_check_paths = { + 'files': ['bin/rocm-smi', 'libexec/rocm_smi/rocm_smi.py', 'lib/librocm_smi64.%s' % SHLIB_EXT, + 'libexec/rocm_smi/rsmiBindings.py'], + 'dirs': ['rocm_smi/include'], +} +sanity_check_commands = ['rocm-smi --help'] + +moduleclass = 'tools' From 96f7034156737cc04af5df7d9576fc79f4702ff7 Mon Sep 17 00:00:00 2001 From: fizwit Date: Mon, 10 Jul 2023 11:31:18 -0700 Subject: [PATCH 0021/1193] fix pkgconfig version --- .../easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb index 2d6a713e0539..54de0646472d 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] builddependencies = [('binutils', '2.37')] dependencies = [ - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ('libtasn1', '4.18.0'), ('libffi', '3.4.2'), ] From e1c4d0e44fe0e7e2ee3f4f27119d281e79f6513f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 21 Jul 2023 16:41:29 +0200 Subject: [PATCH 0022/1193] adding easyconfigs: OpenFOAM-v2306-foss-2022b.eb --- .../o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb new file mode 100644 index 000000000000..74cc6908afab --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -0,0 +1,47 @@ +name = 'OpenFOAM' +version = 'v2306' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'usempi': True, 'cstd': 'c++11', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2206-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + {'OpenFOAM-v2306.tgz': 'd7fba773658c0f06ad17f90199565f32e9bf502b7bb03077503642064e1f5344'}, + {'OpenFOAM-v2206-cleanup.patch': '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972'}, + {'OpenFOAM-v1906-wmake-ompi.patch': '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.24.3'), + ('flex', '2.6.4'), + ('CGAL', '5.5.2'), # header only +] + +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('KaHIP', '3.14'), + ('Boost', '1.81.0'), + ('ParaView', '5.11.0', '-mpi'), + ('gnuplot', '5.4.6'), +] + +moduleclass = 'cae' From a00a9af37725292183006aa60c355329840c6390 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 12 Aug 2023 10:45:39 +0100 Subject: [PATCH 0023/1193] demo of build_info_msg easyconfig parameter --- easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb index f0cf22b03b56..4255ed7b63b5 100644 --- a/easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.7-foss-2021b.eb @@ -24,6 +24,10 @@ local_nltk_data_install = [] # ] # modextravars = {'NLTK_DATA': local_nltk_data} +build_info_msg = """To install the NLTK data sets, and set the NLTK_DATA in the module file, during install set the + 'local_nltk_data' path and uncomment the 'local_nltk_data_install' and 'modextravars'. This can be done either by + having a local copy of the easyconfig or by using hooks.""" + use_pip = True sanity_pip_check = True From 9b27410398e600cfea3e87d1d841092b16233355 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 21 Aug 2023 11:31:10 +0200 Subject: [PATCH 0024/1193] Add furstj's updated patch --- .../o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch | 12 ++++++++++++ .../o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 4 ++-- 2 files changed, 14 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch new file mode 100644 index 000000000000..0cd23ac34f72 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2212-wmake-OpenMPI.patch @@ -0,0 +1,12 @@ +# - Add mplibEASYBUILDMPI configuration for wmake (OpenMPI version) +# +# author: Jiri Furst +--- /dev/null 2023-03-06 18:30:28.397302047 +0100 ++++ OpenFOAM-v2212/wmake/rules/General/mplibEASYBUILDMPI 2023-03-10 14:52:38.100740228 +0100 +@@ -0,0 +1,6 @@ ++#------------------------------------------------------------------------------ ++# Use openmpi mpicc to obtain settings - mpicc must be available ++ ++include $(GENERAL_RULES)/mpi-mpicc-openmpi ++ ++#------------------------------------------------------------------------------ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index 74cc6908afab..4aa214ced62f 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -17,12 +17,12 @@ source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ ('OpenFOAM-v2206-cleanup.patch', 1), - 'OpenFOAM-v1906-wmake-ompi.patch', + 'OpenFOAM-v2212-wmake-OpenMPI.patch', ] checksums = [ {'OpenFOAM-v2306.tgz': 'd7fba773658c0f06ad17f90199565f32e9bf502b7bb03077503642064e1f5344'}, {'OpenFOAM-v2206-cleanup.patch': '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972'}, - {'OpenFOAM-v1906-wmake-ompi.patch': '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '4f5110e98df1f057dc4b478a004e4ae2dc5cc763899f0d3ceb6773315c5c8ba9'}, ] builddependencies = [ From 3fb462214d4e9214619ff1a4dd066bd645120ee7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 21 Aug 2023 11:37:14 +0200 Subject: [PATCH 0025/1193] Fix patch level --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index 4aa214ced62f..0b40808465f4 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -17,7 +17,7 @@ source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] patches = [ ('OpenFOAM-v2206-cleanup.patch', 1), - 'OpenFOAM-v2212-wmake-OpenMPI.patch', + ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), ] checksums = [ {'OpenFOAM-v2306.tgz': 'd7fba773658c0f06ad17f90199565f32e9bf502b7bb03077503642064e1f5344'}, From 95c4abe63165e87ea2d16733f8cbd1f6d989075e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Aug 2023 15:09:13 +0200 Subject: [PATCH 0026/1193] adding easyconfigs: EpiSCORE-0.9.5-20220621-foss-2022a-R-4.2.1.eb --- ...SCORE-0.9.5-20220621-foss-2022a-R-4.2.1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/e/EpiSCORE/EpiSCORE-0.9.5-20220621-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/e/EpiSCORE/EpiSCORE-0.9.5-20220621-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/e/EpiSCORE/EpiSCORE-0.9.5-20220621-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..0f291cf43171 --- /dev/null +++ b/easybuild/easyconfigs/e/EpiSCORE/EpiSCORE-0.9.5-20220621-foss-2022a-R-4.2.1.eb @@ -0,0 +1,30 @@ +easyblock = 'RPackage' + +name = 'EpiSCORE' +local_commit = '4f7daef' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '0.9.5-20220621' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/aet21/EpiSCORE' +description = "Epigenetic cell-type deconvolution from Single-Cell Omic Reference profiles" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/aet21/EpiSCORE/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['85ce52efe0555295ceaab79518244bcbea8c3b7d454f84c74b99e577f56e1481'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('presto', '1.0.0-20230113', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 0b44bc2eef0811ff24cbf96b92b3e9e47b281f76 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 24 Aug 2023 17:24:48 +0200 Subject: [PATCH 0027/1193] Use C++14 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index 0b40808465f4..ced3f4fa1160 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2022b'} # Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. # Disabling vectorize was confirmed to fix the the known issues. # With no test suite, sticking to known working toolchain options until proven otherwise. -toolchainopts = {'usempi': True, 'cstd': 'c++11', 'vectorize': False} +toolchainopts = {'usempi': True, 'cstd': 'c++14', 'vectorize': False} source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] sources = [SOURCE_TGZ] From 3c6727cd07ad5ca5d97895c3f5fb8bf93ee4677c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 27 Sep 2023 11:07:38 +0200 Subject: [PATCH 0028/1193] adding easyconfigs: SciPy-bundle-2023.07-iimkl-2023a.eb --- .../SciPy-bundle-2023.07-iimkl-2023a.eb | 96 +++++++++++++++++++ 1 file changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb new file mode 100644 index 000000000000..ecebeee18f8b --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -0,0 +1,96 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2023.07' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'iimkl', 'version': '2023a'} +toolchainopts = {'pic': True, 'lowopt': True} + +builddependencies = [ + ('hypothesis', '6.82.0'), + ('UnZip', '6.0'), + # scipy >= 1.9.0 uses Meson/Ninja + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), # required by scipy +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('pybind11', '2.11.1'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.25.1', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.22.3_disable-broken-override-test.patch', + ], + 'checksums': [ + {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, + {'numpy-1.18.2-mkl.patch': 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf'}, + {'numpy-1.22.3_disable-broken-override-test.patch': + '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + ], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.4', { + 'checksums': ['9c270fe5f4b130969b54174de7db4e764b09b4f7f67ccfc32480e29f78348d97'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('pythran', '0.13.1', { + 'checksums': ['8aad08162f010e5425a7b254dd68d83311b430bb29f9252dce2eff3ba39497dd'], + }), + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + ('scipy', '1.11.1', { + 'patches': [ + 'scipy-1.11.1_disable-tests.patch', + 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + ], + 'checksums': [ + {'scipy-1.11.1.tar.gz': 'fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289'}, + {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, + {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': + '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + ], + 'enable_slow_tests': True, + 'ignore_test_result': False, + }), + ('numexpr', '2.8.4', { + 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], + }), + ('Bottleneck', '1.3.7', { + 'checksums': ['e1467e373ad469da340ed0ff283214d6531cc08bfdca2083361a3aa6470681f8'], + }), + ('tzdata', '2023.3', { + 'checksums': ['11ef1e08e54acb0d4f95bdb1be05da659673de4acbd21bf9c69e94cc5e907a3a'], + }), + ('pandas', '2.0.3', { + 'preinstallopts': "export PANDAS_CI=0 && ", + 'checksums': ['c02f372a88e0d17f36d3093a644c73cfc1788e876a7c4bcb4020a77512e2043c'], + }), + ('mpmath', '1.3.0', { + 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], + }), + ('deap', '1.4.0', { + 'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'], + 'modulename': 'deap.base', + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From ac0f77da746d1e5e51439cd02662fc2a22c802f3 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 27 Sep 2023 14:48:23 +0200 Subject: [PATCH 0029/1193] Fix FORTRAN test errors --- .../SciPy-bundle-2023.07-iimkl-2023a.eb | 6 ++++++ ...25.1_disable-broken-test_long_long_map.patch | 12 ++++++++++++ ...y-1.25.1_disable_fortran_callback_test.patch | 17 +++++++++++++++++ 3 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable_fortran_callback_test.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index ecebeee18f8b..829c1a6c5539 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -31,13 +31,19 @@ exts_list = [ ('numpy', '1.25.1', { 'patches': [ 'numpy-1.18.2-mkl.patch', + 'numpy-1.25.1_disable_fortran_callback_test.patch', 'numpy-1.22.3_disable-broken-override-test.patch', + 'numpy-1.25.1_disable-broken-test_long_long_map.patch', ], 'checksums': [ {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, {'numpy-1.18.2-mkl.patch': 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf'}, + {'numpy-1.25.1_disable_fortran_callback_test.patch': + '3c02bd9973b7082fde9f9d18edfeb05798226ccb5731a56f5677269200c345cf'}, {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, + {'numpy-1.25.1_disable-broken-test_long_long_map.patch': + 'c0f141b70938a46016a284c5eb7c76877ef0a3c9951fd8ffb148fa2a9143e91d'}, ], }), ('ply', '3.11', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch new file mode 100644 index 000000000000..fa78715ac797 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch @@ -0,0 +1,12 @@ +Disable test that imports a fortran function, it breaks on iimkl toolchain. +--- numpy-1.25.1/numpy/f2py/tests/test_value_attrspec.old 2023-07-08 21:25:45.000000000 +0200 ++++ numpy-1.25.1/numpy/f2py/tests/test_value_attrspec.py 2023-09-27 11:21:32.172791528 +0200 +@@ -7,7 +7,7 @@ + sources = [util.getpath("tests", "src", "value_attrspec", "gh21665.f90")] + + # gh-21665 +- def test_long_long_map(self): ++ def ignored_test_long_long_map(self): + inp = 2 + out = self.module.fortfuncs.square(inp) + exp_out = 4 diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable_fortran_callback_test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable_fortran_callback_test.patch new file mode 100644 index 000000000000..8bd095ba002b --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable_fortran_callback_test.patch @@ -0,0 +1,17 @@ +Disable TestF90Callback which fails when compiling the resulting code with ifort. +The resulting code is incorrect Fortran. +See https://github.com/numpy/numpy/issues/20157 + +Åke Sandgren, 20211021 +Updated: Jakob Schiøtz, 20230927 +--- numpy-1.25.1/numpy/f2py/tests/test_callback.old 2023-09-27 14:15:21.076625096 +0200 ++++ numpy-1.25.1/numpy/f2py/tests/test_callback.py 2023-09-27 14:15:46.401827839 +0200 +@@ -202,7 +202,7 @@ + options = ["-DF2PY_USE_PYTHON_TLS"] + + +-class TestF90Callback(util.F2PyTest): ++class Disabled_for_intel_TestF90Callback(util.F2PyTest): + sources = [util.getpath("tests", "src", "callback", "gh17797.f90")] + + def test_gh17797(self): From 0fd5037d34e3eb31b3036c56f7992bc3339e891b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 30 Sep 2023 16:26:54 +0200 Subject: [PATCH 0030/1193] adding easyconfigs: Perl-5.38.0.eb --- easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb | 91 +++++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb new file mode 100644 index 000000000000..059a04bfd90a --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb @@ -0,0 +1,91 @@ +name = 'Perl' +version = '5.38.0' + +homepage = 'https://www.perl.org/' +description = """Larry Wall's Practical Extraction and Report Language + +Includes a small selection of extra CPAN packages for core functionality. +""" + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['213ef58089d2f2c972ea353517dc60ec3656f050dcc027666e118b508423e517'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +# need to take care of $CFLAGS ourselves with SYSTEM toolchain +# we need to add -fPIC, but should also include -O* option to avoid +# compiling with -O0 (default for GCC) +configopts = '-Dccflags="-O2 -fPIC"' + +# !! order of extensions is important !! +# extensions updated on 2023-09-03 +# includes all dependencies for Autotools +exts_list = [ + ('threads', '2.21', { + 'source_tmpl': 'threads-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['28394c98a2bcae6f20ffb8a3d965a1c194b764c650169e2050ee38dbaa10f110'], + }), + ('constant', '1.33', { + 'source_tmpl': 'constant-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RJ/RJBS'], + 'checksums': ['79965d4130eb576670e27ca0ae6899ef0060c76da48b02b97682166882f1b504'], + }), + ('Getopt::Long', '2.54', { + 'source_tmpl': 'Getopt-Long-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JV/JV'], + 'checksums': ['584ba3c99bb2d6b341375212f9b874613f706cfb01cee21b8a2676a98ab985fe'], + }), + ('File::Path', '2.18', { + 'source_tmpl': 'File-Path-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], + 'checksums': ['980f0a17edb353df46e9cd7b357f9f5929cde0f80c45fd7a06cf7e0e8bd6addd'], + }), + ('File::Spec', '3.75', { + 'source_tmpl': 'PathTools-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['a558503aa6b1f8c727c0073339081a77888606aa701ada1ad62dd9d8c3f945a2'], + }), + ('IO::File', '1.51', { + 'source_tmpl': 'IO-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR/'], + 'checksums': ['5493ea55998728cd2b7ecb8234c58fb5d5df27098d0f07addca22444d7616ce0'], + }), + ('Thread::Queue', '3.13', { + 'source_tmpl': 'Thread-Queue-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JD/JDHEDDEN'], + 'checksums': ['6ba3dacddd2fbb66822b4aa1d11a0a5273cd04c825cb3ff31c20d7037cbfdce8'], + }), + ('Carp', '1.50', { + 'source_tmpl': 'Carp-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XS/XSAWYERX'], + 'checksums': ['f5273b4e1a6d51b22996c48cb3a3cbc72fd456c4038f5c20b127e2d4bcbcebd9'], + }), + ('Exporter', '5.77', { + 'source_tmpl': 'Exporter-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TO/TODDR'], + 'checksums': ['3892ee5c6ae6e482068d53b61e25cae4fc71ddc79cc47446e385df0a669bb8ed'], + }), + ('Text::ParseWords', '3.31', { + 'source_tmpl': 'Text-ParseWords-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NE/NEILB/'], + 'checksums': ['2ae555ba084d75b2b8feeeb8d1a00911276815ada86bccb1452236964d5a2fc7'], + }), + ('Data::Dumper', '2.183', { + 'source_tmpl': 'Data-Dumper-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/N/NW/NWCLARK/'], + 'checksums': ['e42736890b7dae1b37818d9c5efa1f1fdc52dec04f446a33a4819bf1d4ab5ad3'], + }), +] + +moduleclass = 'lang' From 83cb9e9c31f407100624f2e5d0919a5e38c062b2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 12:50:43 +0200 Subject: [PATCH 0031/1193] {bio}[foss/2023a] GTDB-Tk v2.3.2, DendroPy v4.6.1, prodigal v2.6.3, FastTree v2.1.11, pydantic v1.10.13 --- .../DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb | 43 ++++++++++++++++ .../FastTree-2.1.11-GCCcore-12.3.0.eb | 42 ++++++++++++++++ .../g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb | 49 +++++++++++++++++++ .../prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb | 46 +++++++++++++++++ .../pydantic-1.10.13-GCCcore-12.3.0.eb | 27 ++++++++++ 5 files changed, 207 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1241b1fec417 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.6.1-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2014 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'PythonPackage' + +name = 'DendroPy' +version = '4.6.1' + +homepage = 'https://dendropy.org/' +description = """A Python library for phylogenetics and phylogenetic computing: +reading, writing, simulation, processing and manipulation of phylogenetic trees +(phylogenies) and characters.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['26fcbe1cb5831301e8f1f2e15a0563620f0b8e29e6d409dd6a2a7c957dd64c16'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +use_pip = True + +fix_python_shebang_for = ['bin/*.py'] + +sanity_check_paths = { + 'files': ['bin/sumlabels.py', 'bin/sumtrees.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["sumtrees.py --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..24ad8b0638ce --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CmdCp' + +name = 'FastTree' +version = '2.1.11' + +homepage = 'http://www.microbesonline.org/fasttree/' +description = """FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide + or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of + time and memory. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +# HTTPS cert error: +# hostname 'www.microbesonline.org' doesn't match either of 'genomics.lbl.gov', 'mojave.qb3.berkeley.edu', ... +source_urls = ['http://www.microbesonline.org/fasttree/'] +sources = [{'filename': '%(name)s-%(version)s.c', 'extract_cmd': 'cp %s FastTree.c'}] +checksums = ['9026ae550307374be92913d3098f8d44187d30bea07902b9dcbfb123eaa2050f'] + +builddependencies = [('binutils', '2.40')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +# as FastTree is built with OpenMP, the correct binary is FastTreeMP +# the FastTree binary should normally be built without OpenMP, but let’s keep it as is for backward compatibility +# see http://www.microbesonline.org/fasttree/#OpenMP +postinstallcmds = ['cd %(installdir)s/bin && ln -s FastTree FastTreeMP'] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb new file mode 100644 index 000000000000..10f7db5d9fbb --- /dev/null +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb @@ -0,0 +1,49 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'GTDB-Tk' +version = '2.3.2' + +homepage = 'https://github.com/Ecogenomics/GTDBTk' +description = "A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('DendroPy', '4.6.1'), + ('matplotlib', '3.7.2'), + ('prodigal', '2.6.3'), + ('HMMER', '3.4'), + ('pplacer', '1.1.alpha19', '', SYSTEM), + ('FastANI', '1.34'), + ('FastTree', '2.1.11'), + ('Mash', '2.3'), + ('tqdm', '4.66.1'), + ('pydantic', '1.10.13'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://pypi.python.org/packages/source/g/gtdbtk'], + 'sources': ['gtdbtk-%(version)s.tar.gz'], + 'checksums': ['80efd31e10007d835f56a3d6fdf039a59db3b6ba4be26b234692da5e688aa99f'], + 'modulename': 'gtdbtk', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gtdbtk'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["gtdbtk --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..09e71ae37652 --- /dev/null +++ b/easybuild/easyconfigs/p/prodigal/prodigal-2.6.3-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +## +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: GPL-v3.0 +# +# Updated: Pavel Grochal (INUITS) +# +# Notes:: +## + +easyblock = 'MakeCp' + +name = 'prodigal' +version = '2.6.3' + +homepage = 'https://github.com/hyattpd/Prodigal/' + +description = """Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) + is a microbial (bacterial and archaeal) gene finding program developed + at Oak Ridge National Laboratory and the University of Tennessee.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/hyattpd/Prodigal/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['89094ad4bff5a8a8732d899f31cec350f5a4c27bcbdd12663f87c9d1f0ec599f'] + +builddependencies = [('binutils', '2.40')] + +files_to_copy = [ + (['prodigal'], 'bin'), + (['*.h'], 'include'), + (['LICENSE'], 'license'), +] + +sanity_check_paths = { + 'files': ['bin/prodigal'], + 'dirs': ['include', 'license'], +} + +sanity_check_commands = ["prodigal -h"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..399498e64575 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.13' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.8.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['32c8b48dcd3b2ac4e78b0ba4af3a2c2eb6048cb75202f0ea7b34feb740efc340'], + }), +] + +moduleclass = 'devel' From c78e004d19d8d2c79adfd63f808bcf98ed8e49cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 7 Oct 2023 12:52:13 +0200 Subject: [PATCH 0032/1193] add typing-extensions 4.8.0, required by pydantic --- .../typing-extensions-4.8.0-GCCcore-12.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b2f09550f851 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.8.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 2ba18257e03ed4dbd6a9c22ffde68eae6f85a4cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 9 Oct 2023 14:56:20 +0200 Subject: [PATCH 0033/1193] Update ParaView version --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb index ced3f4fa1160..74d81fdd5a11 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2306-foss-2022b.eb @@ -40,7 +40,7 @@ dependencies = [ ('SCOTCH', '7.0.3'), ('KaHIP', '3.14'), ('Boost', '1.81.0'), - ('ParaView', '5.11.0', '-mpi'), + ('ParaView', '5.11.1'), ('gnuplot', '5.4.6'), ] From e320922e5688735f2c540eec8c58d8a40f9dc6e5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 13 Oct 2023 09:56:47 +0200 Subject: [PATCH 0034/1193] adding easyconfigs: Bowtie2-2.5.1-GCC-10.3.0.eb --- .../b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb new file mode 100644 index 000000000000..b8a6bb85552f --- /dev/null +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.5.1-GCC-10.3.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Robert Schmidt +# Ottawa Hospital Research Institute - Bioinformatics Team +# Modified by: Adam Huffman +# The Francis Crick Institute +# Modified by: Kurt Lust, UAntwerp +# Modified by: Sebastien Moretti for non-x86_64 systems +# SIB Swiss Institute of Bioinformatics + +name = 'Bowtie2' +version = '2.5.1' +_simde_version = '20220504' +_simde_commit = 'cbef1c1' + +homepage = 'https://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +description = """ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads + to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s + of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. + Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, + its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'gnu++98'} + +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['cb6cbbbb5a7167a2f21a3d63cb9774336361f540e1ec3d8ff907f955c35f71b8'] + +# SIMD Everywhere implementations only, for non-x86_64 systems +if ARCH != 'x86_64': + source_urls += ['https://github.com/simd-everywhere/simde-no-tests/archive'] + sources += [ + {'download_filename': '%s.zip' % _simde_commit, + 'filename': 'simde-%s.zip' % _simde_version, + 'extract_cmd': 'unzip %%s && mv simde*-%s*/* %%(namelower)s-%%(version)s/third_party/simde/' % _simde_commit, + } + ] + checksums += ['d01f084ef5ff69b0a9b96370ae314fe1e55ef3339b25afcd3385958ac0e6ad68'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.32.1'), + ('Python', '3.9.5'), +] + +# to add script folder to path just uncomment this line +# modextrapaths = {'PATH': 'scripts'} + +sanity_check_commands = ['bowtie2 --help', 'bowtie2-build --help'] + +moduleclass = 'bio' From 8b65c6a306f02e837a586d7f76e55108da9b74d3 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Mon, 23 Oct 2023 16:16:40 +0200 Subject: [PATCH 0035/1193] Patches to make numpy build and pass self-test. --- .../SciPy-bundle-2023.07-iimkl-2023a.eb | 14 ++-- ...isable-broken-fortran-docstring-test.patch | 16 +++++ ....1_disable-broken-test_long_long_map.patch | 3 + ...y-1.25.1_fix_selected_kind_for_ifort.patch | 65 +++++++++++++++++++ 4 files changed, 94 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-fortran-docstring-test.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_fix_selected_kind_for_ifort.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 829c1a6c5539..1aea3e4f00f9 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -34,6 +34,8 @@ exts_list = [ 'numpy-1.25.1_disable_fortran_callback_test.patch', 'numpy-1.22.3_disable-broken-override-test.patch', 'numpy-1.25.1_disable-broken-test_long_long_map.patch', + 'numpy-1.25.1_fix_selected_kind_for_ifort.patch', + 'numpy-1.25.1_disable-broken-fortran-docstring-test.patch', ], 'checksums': [ {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, @@ -43,7 +45,11 @@ exts_list = [ {'numpy-1.22.3_disable-broken-override-test.patch': '9c589bb073b28b25ff45eb3c63c57966aa508dd8b318d0b885b6295271e4983c'}, {'numpy-1.25.1_disable-broken-test_long_long_map.patch': - 'c0f141b70938a46016a284c5eb7c76877ef0a3c9951fd8ffb148fa2a9143e91d'}, + 'fa0fb0a16c4f1339a974c1c84b79df21dc9bfdc14e3e68f6aebaf5e30bad3fe9'}, + {'numpy-1.25.1_fix_selected_kind_for_ifort.patch': + '4e6561f44de027edf498ac29ed93115f801348a3398700271ccbf048f433b2d3'}, + {'numpy-1.25.1_disable-broken-fortran-docstring-test.patch': + '8a4d36e3b3a9c9bf43df6e5214f3883234a069b80c5c1027a7c84bd5cb133457'}, ], }), ('ply', '3.11', { @@ -62,6 +68,8 @@ exts_list = [ 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], }), ('scipy', '1.11.1', { + 'enable_slow_tests': True, + 'ignore_test_result': False, 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', @@ -72,8 +80,6 @@ exts_list = [ {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, ], - 'enable_slow_tests': True, - 'ignore_test_result': False, }), ('numexpr', '2.8.4', { 'checksums': ['d5432537418d18691b9115d615d6daa17ee8275baef3edf1afbbf8bc69806147'], @@ -92,8 +98,8 @@ exts_list = [ 'checksums': ['7a28eb2a9774d00c7bc92411c19a89209d5da7c4c9a9e227be8330a23a25b91f'], }), ('deap', '1.4.0', { - 'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'], 'modulename': 'deap.base', + 'checksums': ['ffef2921932a0edbe634fcb6d156189e7a364bf638a2af4ae5d59931a9a4c8cc'], }), ] diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-fortran-docstring-test.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-fortran-docstring-test.patch new file mode 100644 index 000000000000..55cc2989ca9e --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-fortran-docstring-test.patch @@ -0,0 +1,16 @@ +Disable test for docstrings in fortran extension modules, as it fails due to an error +in autogenerated test code (int * versus npy_intp*). + +Author: Jakob Schiotz (Techn. Univ. Denmark) + +--- numpy/f2py/tests/test_module_doc.old 2023-10-23 15:49:00.858332420 +0200 ++++ numpy/f2py/tests/test_module_doc.py 2023-10-23 15:50:04.072826243 +0200 +@@ -7,7 +7,7 @@ + from numpy.testing import IS_PYPY + + +-class TestModuleDocString(util.F2PyTest): ++class Disabled_for_intel_TestModuleDocString(util.F2PyTest): + sources = [ + util.getpath("tests", "src", "module_data", + "module_data_docstring.f90") diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch index fa78715ac797..c79e894951a1 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_disable-broken-test_long_long_map.patch @@ -1,4 +1,7 @@ Disable test that imports a fortran function, it breaks on iimkl toolchain. + +Author: Jakob Schiotz (Techn. Univ. Denmark) + --- numpy-1.25.1/numpy/f2py/tests/test_value_attrspec.old 2023-07-08 21:25:45.000000000 +0200 +++ numpy-1.25.1/numpy/f2py/tests/test_value_attrspec.py 2023-09-27 11:21:32.172791528 +0200 @@ -7,7 +7,7 @@ diff --git a/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_fix_selected_kind_for_ifort.patch b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_fix_selected_kind_for_ifort.patch new file mode 100644 index 000000000000..6b20bc7fb274 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/numpy-1.25.1_fix_selected_kind_for_ifort.patch @@ -0,0 +1,65 @@ +Intel Fortran compiler does not support 10-byte reals, nor 16-byte integers. +The f2py module needs to know the supported types to reliably build Fortran extensions. + +This patch was inspired by the discussion at https://github.com/numpy/numpy/issues/13053 +in particular the comments at + https://github.com/numpy/numpy/issues/13053#issuecomment-470314843 +and + https://github.com/numpy/numpy/issues/13053#issuecomment-471008975 +by GitHub user @oleksandr-pavlyk + +Author: Jakob Schiotz (Tech. U. Denmark) + +--- numpy/f2py/crackfortran.py.old 2023-10-23 14:39:51.510964440 +0200 ++++ numpy/f2py/crackfortran.py 2023-10-23 15:10:21.963115914 +0200 +@@ -2385,7 +2385,8 @@ + return 'kind(' + string + ')' + + +-def _selected_int_kind_func(r): ++def _selected_int_kind_func_intel(r): ++ # Intel(R) Fortran compiler only supports kinds 1, 2, 4, 8. + # XXX: This should be processor dependent + m = 10 ** r + if m <= 2 ** 8: +@@ -2396,29 +2397,27 @@ + return 4 + if m <= 2 ** 63: + return 8 +- if m <= 2 ** 128: +- return 16 ++ # Not supported by ifort ++ #if m <= 2 ** 128: ++ # return 16 + return -1 + ++_selected_int_kind_func = _selected_int_kind_func_intel + +-def _selected_real_kind_func(p, r=0, radix=0): ++def _selected_real_kind_func_intel(p, r=0, radix=0): ++ # Intel(R) Fotran compiler only supports kinds 4, 8, 16 + # XXX: This should be processor dependent +- # This is only verified for 0 <= p <= 20, possibly good for p <= 33 and above ++ # This is only good for 0 <= p <= 20 + if p < 7: + return 4 + if p < 16: + return 8 +- machine = platform.machine().lower() +- if machine.startswith(('aarch64', 'arm64', 'power', 'ppc', 'riscv', 's390x', 'sparc')): +- if p <= 33: +- return 16 +- else: +- if p < 19: +- return 10 +- elif p <= 33: +- return 16 ++ if p <= 33: ++ return 16 + return -1 + ++_selected_real_kind_func = _selected_real_kind_func_intel ++ + + def get_parameters(vars, global_params={}): + params = copy.copy(global_params) From 47fbb7487a2b107dab77147367062c4a129c6162 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Mon, 23 Oct 2023 19:06:19 +0200 Subject: [PATCH 0036/1193] remove source_urls from exts_default_options since default value is used in Nipype-1.6.0-foss-2020b.eb --- easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb index b4ace4a20537..ce60ce71e31a 100644 --- a/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb +++ b/easybuild/easyconfigs/n/Nipype/Nipype-1.6.0-foss-2020b.eb @@ -18,8 +18,6 @@ dependencies = [ use_pip = True -exts_default_options = {'source_urls': [PYPI_SOURCE]} - exts_list = [ ('traits', '6.2.0', { 'checksums': ['16fa1518b0778fd53bf0547e6a562b1787bf68c8f6b7995a13bd1902529fdb0c'], From ef270cd87e647adaa01e715ec320ba6c22aca877 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 24 Oct 2023 09:28:45 +0200 Subject: [PATCH 0037/1193] Make scipy find MKL. --- .../SciPy-bundle-2023.07-iimkl-2023a.eb | 3 +++ .../scipy-1.11.1_meson-build-mkl-name.patch | 16 ++++++++++++++++ 2 files changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 1aea3e4f00f9..6330a31a5012 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -73,12 +73,15 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.11.1_meson-build-mkl-name.patch', ], 'checksums': [ {'scipy-1.11.1.tar.gz': 'fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289'}, {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.11.1_meson-build-mkl-name.patch': + 'c44a2d7991830928bc294f31a1fd6addda8b7f7bd89655457c79a656f6e83027'}, ], }), ('numexpr', '2.8.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch new file mode 100644 index 000000000000..df78b1592f53 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch @@ -0,0 +1,16 @@ +--- scipy/meson.build.old 2023-10-24 08:39:29.966344750 +0200 ++++ scipy/meson.build 2023-10-24 09:08:24.832773698 +0200 +@@ -153,6 +153,13 @@ + # https://github.com/mesonbuild/meson/issues/2835 + blas_name = get_option('blas') + lapack_name = get_option('lapack') ++# Hack for MKL in easybuild ++if blas_name == 'mkl' ++ blas_name = 'mkl-dynamic-lp64-seq' ++endif ++if lapack_name == 'mkl' ++ lapack_name = 'mkl-dynamic-lp64-seq' ++endif + # pkg-config uses a lower-case name while CMake uses a capitalized name, so try + # that too to make the fallback detection with CMake work + if blas_name == 'openblas' From 49292a8b3d4c4f1aee43c92e3be9d02401c2e225 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 24 Oct 2023 10:30:17 +0200 Subject: [PATCH 0038/1193] Add missing description to patch --- .../s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb | 2 +- .../s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch | 4 ++++ 2 files changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 6330a31a5012..b7c2b3fe051f 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -81,7 +81,7 @@ exts_list = [ {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, {'scipy-1.11.1_meson-build-mkl-name.patch': - 'c44a2d7991830928bc294f31a1fd6addda8b7f7bd89655457c79a656f6e83027'}, + '7d3ba117fe5874e96582f4a2ed991abd075a2f1998a9e339877f6a28377124bd'}, ], }), ('numexpr', '2.8.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch index df78b1592f53..baf731aa9fa2 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch @@ -1,3 +1,7 @@ +Meson tries to find MKL by using 'mkl' as a package name to pkg-config, that does not work. The real error is probably that -Dblas=mkl -Dlapack=mkl is passed to the meson build instead of -Dblas=mkl-dynamic-lp64-seq etc. The simplest fix is to hack the meson.build script. + +Author: Jakob Schiotz (Techn. Univ. Denmark) + --- scipy/meson.build.old 2023-10-24 08:39:29.966344750 +0200 +++ scipy/meson.build 2023-10-24 09:08:24.832773698 +0200 @@ -153,6 +153,13 @@ From a02ba9aff9ce700f4ab76a815d2a8769af30611c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 24 Oct 2023 15:38:32 +0200 Subject: [PATCH 0039/1193] fix dependencies and configure flags of GnuTLS 3.7.x --- .../g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb | 10 +++++++--- .../g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb | 10 +++++++--- .../g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb | 10 +++++++--- 3 files changed, 21 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb index fad3ae66a6f9..9f2970e7e9be 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb @@ -17,14 +17,17 @@ source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s sources = [SOURCELOWER_TAR_XZ] checksums = ['646e6c5a9a185faa4cea796d378a1ba8e1148dbb197ca6605f95986a25af2752'] -builddependencies = [('binutils', '2.36.1')] +builddependencies = [ + ('binutils', '2.36.1'), + ('pkgconf', '1.8.0'), +] dependencies = [ ('GMP', '6.2.1'), ('nettle', '3.7.2'), ('Guile', '2.2.7'), ('libtasn1', '4.17.0'), - ('libidn', '1.36'), + ('libidn2', '2.3.0'), ('p11-kit', '0.24.0'), ('zlib', '1.2.11'), ('zstd', '1.4.9'), @@ -32,7 +35,8 @@ dependencies = [ configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " -configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions" +configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions " +configopts += "--with-idn --with-p11-kit --without-tpm --without-tpm2" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb index ea03e7cd2dc8..bd61ab588dd2 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb @@ -17,14 +17,17 @@ source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s sources = [SOURCELOWER_TAR_XZ] checksums = ['fc59c43bc31ab20a6977ff083029277a31935b8355ce387b634fa433f8f6c49a'] -builddependencies = [('binutils', '2.37')] +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] dependencies = [ ('GMP', '6.2.1'), ('nettle', '3.7.3'), ('Guile', '3.0.7'), ('libtasn1', '4.18.0'), - ('libidn', '1.38'), + ('libidn2', '2.3.2'), ('p11-kit', '0.24.1'), ('zlib', '1.2.11'), ('zstd', '1.5.0'), @@ -32,7 +35,8 @@ dependencies = [ configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " -configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions" +configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions " +configopts += "--with-idn --with-p11-kit --without-tpm --without-tpm2" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb index 8660253cc57c..259078c22286 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb @@ -17,14 +17,17 @@ source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s sources = [SOURCELOWER_TAR_XZ] checksums = ['c58ad39af0670efe6a8aee5e3a8b2331a1200418b64b7c51977fb396d4617114'] -builddependencies = [('binutils', '2.38')] +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] dependencies = [ ('GMP', '6.2.1'), ('nettle', '3.8'), ('Guile', '3.0.8'), ('libtasn1', '4.19.0'), - ('libidn', '1.41'), + ('libidn2', '2.3.2'), ('p11-kit', '0.24.1'), ('zlib', '1.2.12'), ('zstd', '1.5.2'), @@ -32,7 +35,8 @@ dependencies = [ configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " -configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions" +configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions " +configopts += "--with-idn --with-p11-kit --with-zlib --with-zstd --without-brotli --without-tpm --without-tpm2" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', From d7b90afed86a398a51ad4344851c1e9369c0db54 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 24 Oct 2023 18:19:47 +0200 Subject: [PATCH 0040/1193] Build using easyblock patch. Skip two failing tests. Backport increased test tolerances. --- .../SciPy-bundle-2023.07-iimkl-2023a.eb | 9 +- .../scipy-1.11.1_disable-tests-iimkl.patch | 43 +++++++ .../scipy-1.11.1_meson-build-mkl-name.patch | 20 ---- .../scipy-1.11.1_relaxed_test_accuracy.patch | 110 ++++++++++++++++++ 4 files changed, 159 insertions(+), 23 deletions(-) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests-iimkl.patch delete mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_relaxed_test_accuracy.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index b7c2b3fe051f..314707a10f88 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -73,15 +73,18 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', - 'scipy-1.11.1_meson-build-mkl-name.patch', + 'scipy-1.11.1_disable-tests-iimkl.patch', + 'scipy-1.11.1_relaxed_test_accuracy.patch', ], 'checksums': [ {'scipy-1.11.1.tar.gz': 'fb5b492fa035334fd249f0973cc79ecad8b09c604b42a127a677b45a9a3d4289'}, {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, - {'scipy-1.11.1_meson-build-mkl-name.patch': - '7d3ba117fe5874e96582f4a2ed991abd075a2f1998a9e339877f6a28377124bd'}, + {'scipy-1.11.1_disable-tests-iimkl.patch': + 'e85cf95d343fa4fd9e0045df3a030209a8d7b32a47d6da64ae1efd7b8ef827e3'}, + {'scipy-1.11.1_relaxed_test_accuracy.patch': + '2b6a7f7f58a7a8391dff52ae9565270c20c8312558b482f526be5e474ad2e675'}, ], }), ('numexpr', '2.8.4', { diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests-iimkl.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests-iimkl.patch new file mode 100644 index 000000000000..6ec02dee408c --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_disable-tests-iimkl.patch @@ -0,0 +1,43 @@ +Skip tests that fail when compiling with iimkl/2023a: + +Disable PROPACK test for complex, as it appears to be broken when +using Intel compiler. The tests were already skipped in a few other +cases for similar reasons. + +Skip test test_x0_equals_Mb[bicgstab-nonsymposdef-F], it fails to +converge. Many other solvers are skipped with this test case for +similar reasons, although it is worrying that it works with OpenBLAS +and not with MKL. + +Author: Jakob Schiotz (Techn. Univ. Denmark) + +--- scipy/sparse/linalg/tests/test_propack.py.old 2023-10-24 12:12:17.722133108 +0200 ++++ scipy/sparse/linalg/tests/test_propack.py 2023-10-24 12:14:02.072938068 +0200 +@@ -34,14 +34,8 @@ + for dtype_flavour in TOLS.keys(): + marks = [] + if is_complex_type(dtype_flavour): +- if is_32bit(): +- # PROPACK has issues w/ complex on 32-bit; see gh-14433 +- marks = [pytest.mark.skip] +- elif is_windows() and np.dtype(dtype_flavour).itemsize == 16: +- # windows crashes for complex128 (so don't xfail); see gh-15108 +- marks = [pytest.mark.skip] +- else: +- marks = [pytest.mark.slow] # type: ignore[list-item] ++ # PROPACK crashes for complex with Intel compiler. ++ marks = [pytest.mark.skip] + _dtypes.append(pytest.param(dtype_flavour, marks=marks, + id=dtype_flavour.__name__)) + _dtypes = tuple(_dtypes) # type: ignore[assignment] +--- scipy/sparse/linalg/_isolve/tests/test_iterative.py.old 2023-10-24 17:07:24.697195558 +0200 ++++ scipy/sparse/linalg/_isolve/tests/test_iterative.py 2023-10-24 17:07:46.106361595 +0200 +@@ -162,7 +162,7 @@ + self.cases.append(Case("nonsymposdef", A, + skip=sym_solvers + [cgs, qmr, bicg, tfqmr])) + self.cases.append(Case("nonsymposdef-F", A.astype('F'), +- skip=sym_solvers + [cgs, qmr, bicg, tfqmr])) ++ skip=sym_solvers + [cgs, qmr, bicg, bicgstab, tfqmr])) + + # Symmetric, non-pd, hitting cgs/bicg/bicgstab/qmr/tfqmr breakdown + A = np.array([[0, 0, 0, 0, 0, 1, -1, -0, -0, -0, -0], diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch deleted file mode 100644 index baf731aa9fa2..000000000000 --- a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_meson-build-mkl-name.patch +++ /dev/null @@ -1,20 +0,0 @@ -Meson tries to find MKL by using 'mkl' as a package name to pkg-config, that does not work. The real error is probably that -Dblas=mkl -Dlapack=mkl is passed to the meson build instead of -Dblas=mkl-dynamic-lp64-seq etc. The simplest fix is to hack the meson.build script. - -Author: Jakob Schiotz (Techn. Univ. Denmark) - ---- scipy/meson.build.old 2023-10-24 08:39:29.966344750 +0200 -+++ scipy/meson.build 2023-10-24 09:08:24.832773698 +0200 -@@ -153,6 +153,13 @@ - # https://github.com/mesonbuild/meson/issues/2835 - blas_name = get_option('blas') - lapack_name = get_option('lapack') -+# Hack for MKL in easybuild -+if blas_name == 'mkl' -+ blas_name = 'mkl-dynamic-lp64-seq' -+endif -+if lapack_name == 'mkl' -+ lapack_name = 'mkl-dynamic-lp64-seq' -+endif - # pkg-config uses a lower-case name while CMake uses a capitalized name, so try - # that too to make the fallback detection with CMake work - if blas_name == 'openblas' diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_relaxed_test_accuracy.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_relaxed_test_accuracy.patch new file mode 100644 index 000000000000..df99f4a7389e --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.1_relaxed_test_accuracy.patch @@ -0,0 +1,110 @@ +Backported test from main branch of scipy on Github, relaxing the +tolerances of a few tests. Some of these fail with the Intel +compiler. + +The patch has been edited directly to backport it (np.double had been replaced +by np.float64 in the main branch), and one patch was to code that is not in +scipy-1.11.1. + +Backported by: Jakob Schiotz (Techn. Univ. Denmark) + +Original description: + +From a4fba82078d2e95005343150d821ccd33cb5de20 Mon Sep 17 00:00:00 2001 +From: Ralf Gommers +Date: Wed, 6 Sep 2023 15:08:59 +0200 +Subject: [PATCH] TST: test tolerance bumps to fix reported failures + +Closes gh-19117 + +The `test_sygst` one was reported in gh-19153. +--- + scipy/fft/_pocketfft/tests/test_real_transforms.py | 2 +- + scipy/linalg/tests/test_lapack.py | 2 +- + scipy/ndimage/tests/test_datatypes.py | 4 +++- + scipy/spatial/transform/tests/test_rotation.py | 8 ++++---- + scipy/special/tests/test_hyp2f1.py | 6 +++--- + 5 files changed, 12 insertions(+), 10 deletions(-) + +diff --git a/scipy/fft/_pocketfft/tests/test_real_transforms.py b/scipy/fft/_pocketfft/tests/test_real_transforms.py +index d1f4e1d..a217e75 100644 +--- a/scipy/fft/_pocketfft/tests/test_real_transforms.py ++++ b/scipy/fft/_pocketfft/tests/test_real_transforms.py +@@ -239,7 +239,7 @@ dec_map: DecMapType = { + (dst, np.float32, 3): 7, + + (dst, np.double, 4): 13, +- (dst, np.float32, 4): 6, ++ (dst, np.float32, 4): 5, + + # IDST + (idst, np.double, 1): 14, +diff --git a/scipy/linalg/tests/test_lapack.py b/scipy/linalg/tests/test_lapack.py +index 6c64a2a..2c994f6 100644 +--- a/scipy/linalg/tests/test_lapack.py ++++ b/scipy/linalg/tests/test_lapack.py +@@ -1031,7 +1031,7 @@ def test_sygst(): + + eig, _, info = syevd(a) + assert_(info == 0) +- assert_allclose(eig, eig_gvd, rtol=1e-4) ++ assert_allclose(eig, eig_gvd, rtol=1.2e-4) + + + def test_hegst(): +diff --git a/scipy/ndimage/tests/test_datatypes.py b/scipy/ndimage/tests/test_datatypes.py +index 327cc5a..1eb056b 100644 +--- a/scipy/ndimage/tests/test_datatypes.py ++++ b/scipy/ndimage/tests/test_datatypes.py +@@ -45,7 +45,7 @@ def test_map_coordinates_dts(): + assert_array_almost_equal(these_data, out) + + +-@pytest.mark.xfail(not sys.platform == 'darwin', reason="runs only on darwin") ++@pytest.mark.xfail(True, reason="Broken on many platforms") + def test_uint64_max(): + # Test interpolation respects uint64 max. Reported to fail at least on + # win32 (due to the 32 bit visual C compiler using signed int64 when +@@ -53,6 +53,8 @@ def test_uint64_max(): + # Interpolation is always done in double precision floating point, so + # we use the largest uint64 value for which int(float(big)) still fits + # in a uint64. ++ # This test was last enabled on macOS only, and there it started failing ++ # on arm64 as well (see gh-19117). + big = 2**64 - 1025 + arr = np.array([big, big, big], dtype=np.uint64) + # Tests geometric transform (map_coordinates, affine_transform) +diff --git a/scipy/special/tests/test_hyp2f1.py b/scipy/special/tests/test_hyp2f1.py +index 2fe732f..200d4bb 100644 +--- a/scipy/special/tests/test_hyp2f1.py ++++ b/scipy/special/tests/test_hyp2f1.py +@@ -474,7 +474,7 @@ class TestHyp2f1: + c=-15.5, + z=(1.1578947368421053-1.1578947368421053j), + expected=(0.9778506962676361+0.044083801141231616j), +- rtol=1e-12, ++ rtol=3e-12, + ), + ), + pytest.param( +@@ -1378,7 +1378,7 @@ class TestHyp2f1: + c=-7.949900487447654, + z=(0.4172413793103451-0.8724137931034484j), + expected=(-2258.1590330318213+8860.193389158803j), +- rtol=1e-10, ++ rtol=1.4e-10, + ), + ), + ] +@@ -1433,7 +1433,7 @@ class TestHyp2f1: + c=-15.964218273004214, + z=(0.6448275862068968+0.8724137931034486j), + expected=(85592537010.05054-8061416766688.324j), +- rtol=1e-14, ++ rtol=2e-14, + ), + ), + pytest.param( +-- +1.8.3.1 + From 67c28cb7dac6bb1080a9eee35044260a6ae3ff4d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 25 Oct 2023 15:58:25 +0200 Subject: [PATCH 0041/1193] adding easyconfigs: BiG-SCAPE-1.1.5-foss-2022a.eb --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb new file mode 100644 index 000000000000..d36acf49916f --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'BiG-SCAPE' +version = '1.1.5' + +homepage = 'https://bigscape-corason.secondarymetabolites.org/index.html' +description = """BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters +(BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene +cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'medema-group' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Biopython', '1.79'), + ('scikit-learn', '1.1.2'), + ('networkx', '2.8.4'), + ('HMMER', '3.3.2'), + ('FastTree', '2.1.11'), +] + +options = {'modulename': False} + +sanity_check_commands = [ + 'bigscape.py --help', +] + +moduleclass = 'bio' From f4c44979049b6c9991999de617945fe448f71d1d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 25 Oct 2023 16:38:02 +0200 Subject: [PATCH 0042/1193] Add missing use_pip/download_dep_fail/sanity_pip_check settings --- .../easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index d36acf49916f..845bcfd6d8c0 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -25,6 +25,10 @@ dependencies = [ ('FastTree', '2.1.11'), ] +use_pip = True +download_dep_fail = True +sanity_pip_check = True + options = {'modulename': False} sanity_check_commands = [ From 1aee365e0565390d8cabd9d8c17350a5916ce38c Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Thu, 26 Oct 2023 04:08:19 +0200 Subject: [PATCH 0043/1193] adding easyconfigs: UMI-tools-1.1.4-foss-2023a.eb, Pysam-0.22.0-GCC-12.3.0.eb --- .../p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb | 31 ++++++++++++++ .../u/UMI-tools/UMI-tools-1.1.4-foss-2023a.eb | 40 +++++++++++++++++++ 2 files changed, 71 insertions(+) create mode 100755 easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.1.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb new file mode 100755 index 000000000000..736831665244 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.22.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f'] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('ncurses', '6.4'), + ('cURL', '8.0.1'), + ('XZ', '5.4.2'), +] + +# https://github.com/pysam-developers/pysam/issues/1146#issuecomment-1309421979 +preinstallopts = """export CFLAGS="-fPIC $CFLAGS" && """ +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.1.4-foss-2023a.eb b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.1.4-foss-2023a.eb new file mode 100644 index 000000000000..1f6142bd5d2f --- /dev/null +++ b/easybuild/easyconfigs/u/UMI-tools/UMI-tools-1.1.4-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'UMI-tools' +version = '1.1.4' + +homepage = 'https://umi-tools.readthedocs.io' +description = "Tools for handling Unique Molecular Identifiers in NGS data sets" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('Pysam', '0.22.0'), +] + +use_pip = True + +exts_list = [ + ('regex', '2023.10.3', { + 'checksums': ['3fef4f844d2290ee0ba57addcec17eec9e3df73f10a2748485dfd6a3a188cc0f'], + }), + ('pybktree', '1.1', { + 'checksums': ['eec0037cdd3d7553e6d72435a4379bede64be17c6712f149e485169638154d2b'], + }), + (name, version, { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/CGATOxford/UMI-tools/archive/'], + 'checksums': ['945c4c98e2007369c301a7a009c6f9deb0fda74b0117cd14e14bd134164a4ff6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/umi_tools'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From f3f159a89e7c1b24a92ed302bf22f26163d1a0c6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 26 Oct 2023 13:02:57 +0200 Subject: [PATCH 0044/1193] remove numa configure option from hwloc 2.5+ --- easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb | 3 +-- 5 files changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb index 8f1e093450f0..273bef65c43a 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.5.0-GCCcore-11.2.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb index 6b7a745c08c4..15cba2b35a9c 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.7.1-GCCcore-11.3.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb index f6483901c2b3..e1493dc09533 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.17'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb index f3d054d78d2c..f454c0bc2636 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.1-GCCcore-12.3.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.17'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb index 274d96ba85df..e0816fd2d787 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.9.2-GCCcore-13.2.0.eb @@ -32,8 +32,7 @@ dependencies = [ ('libpciaccess', '0.17'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', From a0e014c084096a1134355468ca0009f6581062fd Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 26 Oct 2023 16:38:47 +0200 Subject: [PATCH 0045/1193] Re-add modloadmsg about Pfam database --- .../easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index 845bcfd6d8c0..ee064b78496e 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -35,4 +35,9 @@ sanity_check_commands = [ 'bigscape.py --help', ] +modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website" +modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " +modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" + moduleclass = 'bio' From 293f2e717e0f32448c4448759da09bca827343da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 27 Oct 2023 15:26:44 +0200 Subject: [PATCH 0046/1193] add env var to find MIBiG data files. --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 9 ++++++++- ...E-1.1.5_use_env_var_to_find-MIBiG-files.patch | 16 ++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index ee064b78496e..01cc4ccc8914 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -13,7 +13,14 @@ toolchain = {'name': 'foss', 'version': '2022a'} github_account = 'medema-group' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'] +patches = [ + '%(name)s-%(version)s_use_env_var_to_find-MIBiG-files.patch', +] +checksums = [ + {'v1.1.5.tar.gz': 'ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'}, + {'BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch': + 'f0602208765a2686a324a27ff6073aac01c230b6a81a00656269fd89c97cf370'}, +] dependencies = [ ('Python', '3.10.4'), diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch new file mode 100644 index 000000000000..cac184343709 --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch @@ -0,0 +1,16 @@ +Use MIBIG_PATH env var to locate MIBiG files instead of hardocded path +that isn't right in the first place. + +Åke Sandgren, 20231027 +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-10-27 14:15:41.385679191 +0200 +@@ -2336,6 +2336,8 @@ + + print("\n Trying to read bundled MIBiG BGCs as reference") + mibig_path = os.path.join(os.path.dirname(os.path.realpath(__file__)),"Annotated_MIBiG_reference") ++ # Use environment variable as first choice ++ mibig_path = os.getenv('MIBIG_PATH', mibig_path) + bgcs_path = os.path.join(mibig_path,mibig_zipfile_numbgcs[1]) + + # try to see if the zip file has already been decompressed From 9b874167ce1d4169a819ddf7e41ea48ea26106e7 Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Sun, 29 Oct 2023 17:02:02 +0100 Subject: [PATCH 0047/1193] Remove executable permission for Pysam easyconfig --- easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb old mode 100755 new mode 100644 From 77d7e1e12ef7503c379b5ce6838533a3b4f4a2f5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 30 Oct 2023 08:40:38 +0100 Subject: [PATCH 0048/1193] adding easyconfigs: nf-core-2.10-foss-2022b.eb, psycopg2-2.9.9-GCCcore-12.2.0.eb, pydantic-1.10.13-GCCcore-12.2.0.eb, pytest-workflow-2.0.1-GCCcore-12.2.0.eb, prompt-toolkit-3.0.36-foss-2022b.eb --- .../n/nf-core/nf-core-2.10-foss-2022b.eb | 126 ++++++++++++++++++ .../prompt-toolkit-3.0.36-foss-2022b.eb | 25 ++++ .../psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb | 27 ++++ .../pydantic-1.10.13-GCCcore-12.2.0.eb | 23 ++++ .../pytest-workflow-2.0.1-GCCcore-12.2.0.eb | 29 ++++ 5 files changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb b/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb new file mode 100644 index 000000000000..45142bfb4482 --- /dev/null +++ b/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb @@ -0,0 +1,126 @@ +easyblock = 'PythonBundle' + +name = 'nf-core' +version = '2.10' + +homepage = 'https://github.com/nf-core/tools' +description = """Python package with helper tools for the nf-core community.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('GitPython', '3.1.31'), + ('Greenlet', '2.0.2'), + ('prompt-toolkit', '3.0.36'), + ('psycopg2', '2.9.9'), + ('pydantic', '1.10.13'), + ('pyfaidx', '0.7.2.1'), + ('pytest-workflow', '2.0.1'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('url-normalize', '1.4.3', { + 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], + }), + ('cattrs', '23.1.2', { + 'checksums': ['db1c821b8c537382b2c7c66678c3790091ca0275ac486c76f3c8f3920e83c657'], + }), + ('requests-cache', '1.1.0', { + 'source_tmpl': 'requests_cache-%(version)s.tar.gz', + 'checksums': ['41b79166aa8e300cc4de982f7ab7c52af914a785160be1eda25c6e9265969a67'], + }), + ('ubiquerg', '0.6.3', { + 'checksums': ['025509c4ec77a5cde8e8be66dabfef2ca6e3cd99da3cb15066c66a6f2bc3b9b5'], + }), + ('oyaml', '1.0', { + 'checksums': ['ed8fc096811f4763e1907dce29c35895d6d5936c4d0400fe843a91133d4744ed'], + }), + ('attmap', '0.13.2', { + 'checksums': ['fdffa45f8671c13428eb8c3a1702bfdd1123badb99f7af14d72ad53cc7e770de'], + }), + ('yacman', '0.9.2', { + 'checksums': ['a98fee7ebf936330a9c249190f1f36eff9444cc744822800fe15f077e46ca867'], + }), + ('refgenconf', '0.12.2', { + 'checksums': ['6c9f9ecd8b91b4f75a535cfbdbdfb136f2dc9e9864142d07aa0352c61cf0cf78'], + }), + ('sqlalchemy2-stubs', '0.0.2a35', { + 'modulename': False, + 'checksums': ['bd5d530697d7e8c8504c7fe792ef334538392a5fb7aa7e4f670bfacdd668a19d'], + }), + ('SQLAlchemy', '1.4.49', { + 'checksums': ['06ff25cbae30c396c4b7737464f2a7fc37a67b7da409993b182b024cec80aed9'], + }), + ('sqlmodel', '0.0.10', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['10b3a312f66bed2b88a7b369cd06d1c0e89f62ad8e6303eefa1ea5b3e7b141f4'], + }), + ('logmuse', '0.2.7', { + 'checksums': ['a4692c44ddfa912c3cb149ca4c7545f80119aa7485868fd1412e7c647e9a7e7e'], + }), + ('peppy', '0.35.7', { + 'checksums': ['a7227ebb394f2af59e3efcd2f639928966654ad305cc113bedc67e20e2422687'], + }), + ('eido', '0.2.1', { + 'checksums': ['3e4cf582e854482980e4f54dee6e0259b7b866e677818d877573a6d3d2684fe2'], + }), + ('pipestat', '0.5.1', { + # https://github.com/pepkit/pipestat/issues/106 + 'preinstallopts': 'sed -i "s|psycopg2-binary|psycopg2|" requirements/requirements-all.txt && ', + 'checksums': ['b50541baf47151b107e1c2adea91c7571f24ca2b59e6bc85158d4957478e5125'], + }), + ('piper', '0.13.2', { + 'modulename': 'pypiper', + 'checksums': ['edc68583bf7925a44ed0cf439cd059bec51499cd70b4ff8a81ed67a9b0093867'], + }), + ('refgenie', '0.12.1', { + 'checksums': ['cfd007ed0981e00d019deb49aaea896952341096494165cb8378488850eec451'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('nodeenv', '1.8.0', { + 'checksums': ['d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2'], + }), + ('identify', '2.5.30', { + 'checksums': ['f302a4256a15c849b91cfcdcec052a8ce914634b2f77ae87dad29cd749f2d88d'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre-commit', '3.5.0', { + 'source_tmpl': 'pre_commit-%(version)s.tar.gz', + 'checksums': ['5804465c675b659b0862f07907f96295d490822a450c4c40e747d0b1c6ebcb32'], + }), + ('Markdown', '3.5', { + 'checksums': ['a807eb2e4778d9156c8f07876c6e4d50b5494c5665c4834f67b06459dfd877b3'], + }), + ('filetype', '1.2.0', { + 'checksums': ['66b56cd6474bf41d8c54660347d37afcc3f7d1970648de365c102ef77548aadb'], + }), + ('rich', '13.6.0', { + 'checksums': ['5c14d22737e6d5084ef4771b62d5d4363165b403455a30a1c8ca39dc7b644bef'], + }), + ('rich-click', '1.7.0', { + 'checksums': ['ab34e5d9f7733c4e6072f4de79eb3b35ac9ae78e692ea8a543f3b2828b30fee4'], + }), + (name, version, { + 'checksums': ['5d3b3d51844fd5b2cec73b84aa736980daac54eb548796243db39680ae39980d'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-foss-2022b.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-foss-2022b.eb new file mode 100644 index 000000000000..5bbf62b8f68f --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-foss-2022b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a8a12038088d --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'psycopg2' +version = '2.9.9' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d1454bde93fb1e224166811694d600e746430c006fbb031ea06ecc2ea41bf156'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('PostgreSQL', '15.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2e2c5db4c673 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'pydantic' +version = '1.10.13' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['32c8b48dcd3b2ac4e78b0ba4af3a2c2eb6048cb75202f0ea7b34feb740efc340'] + +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..94d158c4d708 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'pytest-workflow' +version = '2.0.1' + +homepage = 'https://github.com/LUMC/pytest-workflow' +description = """Configure workflow/pipeline tests using yaml files. + +pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by +using YAML files for the test configuration. +Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, +pytest-workflow makes testing easy. +pytest-workflow is build on top of the pytest test framework.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +sources = [SOURCE_TAR_GZ] +checksums = ['c4968baf2f3c5ff301e59e1f72dd2814c8dc7db950df7fcafbf358b495da7fa8'] + +moduleclass = 'tools' From c8736f22f11b96e4bcf90cb5d993da630301bd69 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 30 Oct 2023 09:12:05 +0100 Subject: [PATCH 0049/1193] Enable download_dep_fail --- .../easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb | 3 ++- .../p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb | 1 + 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb index 2e2c5db4c673..83cc65f4d053 100644 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb @@ -17,7 +17,8 @@ dependencies = [ sources = [SOURCE_TAR_GZ] checksums = ['32c8b48dcd3b2ac4e78b0ba4af3a2c2eb6048cb75202f0ea7b34feb740efc340'] -sanity_pip_check = True +download_dep_fail = True use_pip = True +sanity_pip_check = True moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb index 94d158c4d708..26f088cae6d7 100644 --- a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.0.1-GCCcore-12.2.0.eb @@ -20,6 +20,7 @@ dependencies = [ ('PyYAML', '6.0'), ] +download_dep_fail = True use_pip = True sanity_pip_check = True From c3cf4b52a5edcadd4ac734f25cb9735efc632bdd Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Wed, 1 Nov 2023 10:40:30 +0100 Subject: [PATCH 0050/1193] adding easyconfigs: scikit-learn-1.3.1-iimkl-2023a.eb --- .../scikit-learn-1.3.1-iimkl-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-iimkl-2023a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-iimkl-2023a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-iimkl-2023a.eb new file mode 100644 index 000000000000..365b2aaedd34 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.1-iimkl-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.3.1' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'iimkl', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['1a231cced3ee3fa04756b4a7ab532dc9417acd581a330adff5f2c01ac2831fcf'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From 71fdbd4cfdc1a67a8415a0aa5c032d23c61faf2f Mon Sep 17 00:00:00 2001 From: Neves-P Date: Mon, 6 Nov 2023 15:58:35 +0100 Subject: [PATCH 0051/1193] adding easyconfigs: QIIME2-2023.7.0-foss-2022a.eb --- .../q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb | 326 ++++++++++++++++++ 1 file changed, 326 insertions(+) create mode 100755 easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb new file mode 100755 index 000000000000..2149ad12c491 --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb @@ -0,0 +1,326 @@ +easyblock = 'PythonBundle' + +name = 'QIIME2' +version = '2023.7.0' + +homepage = 'https://qiime2.org' +description = """QIIME 2 is a powerful, extensible, and decentralized microbiome bioinformatics platform that is free, +open source, and community developed.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('IPython', '8.5.0'), + ('PyYAML', '6.0'), + ('Java', '11', '', SYSTEM), + ('Perl', '5.34.1'), + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', '-R-%(rver)s'), + ('Parsl', '2023.7.17'), + ('alsa-lib', '1.2.8'), + ('BLAST+', '2.13.0'), + ('bokeh', '2.4.3'), + ('Bowtie2', '2.4.5'), + ('bwidget', '1.9.15'), + ('bzip2', '1.0.8'), + ('cairo', '1.17.4'), + ('cURL', '7.83.0'), + ('cutadapt', '4.2'), + ('DendroPy', '4.5.2'), + ('expat', '2.4.8'), + ('FastTree', '2.1.11'), + ('fontconfig', '2.14.0'), + ('FriBidi', '1.0.12'), + ('giflib', '5.2.1'), + ('GLib', '2.72.1'), + ('GSL', '2.7'), + ('h5py', '3.7.0'), + ('HarfBuzz', '4.2.1'), + ('MAFFT', '7.505', '-with-extensions'), + ('scikit-bio', '0.5.7'), + ('scikit-learn', '1.1.2'), + ('Seaborn', '0.12.1'), + ('statsmodels', '0.13.1'), + ('umap-learn', '0.5.3'), + ('VSEARCH', '2.22.1'), + ('UniFrac', '1.3.2'), + ('attr', '2.5.1'), + ('Brotli-python', '1.0.9'), + ('SAMtools', '1.16.1'), + ('HTSlib', '1.15.1'), + ('HMMER', '3.3.2'), + ('networkx', '2.8.4'), +] + +use_pip = True + +# avoid that hidden (sub)directories like .config/q2cli are created in home directory +preinstallopts = "export HOME=%(builddir)s/home && " + +# avoid hatchling requirement to install altair +# (since installing it introduces conflicting version requirements with poetry included with Python) +# also copy missing vega-lite-schema.json to installdir +_preinstallopts = ' '.join([ + """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g'""", + """-e 's/^requires = .*/requires = ["setuptools"]/g'""", + """-e 's/^license-files = .*//g'""", + r"""-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'schemadir=%(installdir)s/lib/python%(pyshortver)s/site-packages/altair/vegalite/v5/schema/ && ', + 'mkdir -p $schemadir && cp altair/vegalite/v5/schema/vega-lite-schema.json $schemadir && ', +]) + +# versions of QIIME2 extensions taken from: +# https://github.com/qiime2/package-integration/blob/main/2023.7/staged/core/conda_build_config.yaml +exts_list = [ + ('unifrac', '1.1.1', { + 'patches': ['%(name)s-%(version)s_fix.patch'], + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/biocore/unifrac/archive/refs/tags'], + 'checksums': [ + {'1.1.1.tar.gz': '95aeb107d014ffd614fda5d3c58bfac860c1a6185a63e7cd6eb2462e4d4d4f06'}, + {'unifrac-1.1.1_fix.patch': '4f31e9e1f8c40a166d0a66852f6ae2434a95575664a69e49bb513997891d3806'}, + ], + }), + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('contourpy', '1.0.7', { + 'checksums': ['d8165a088d31798b59e91117d1f5fc3df8168d8b48c4acc10fc0df0d0bdbcc5e'], + }), + ('tzdata', '2022.7', { + 'checksums': ['fe5f866eddd8b96e9fcba978f8e503c909b19ea7efda11e52e39494bad3a7bfa'], + }), + ('pytz-deprecation-shim', '0.1.0.post0', { + 'source_tmpl': 'pytz_deprecation_shim-%(version)s.tar.gz', + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('tzlocal', '5.0.1', { + 'checksums': ['46eb99ad4bdb71f3f72b7d24f4267753e240944ecfc16f25d2719ba89827a803'], + }), + ('argon2-cffi-bindings', '21.2.0', { + 'modulename': '_argon2_cffi_bindings', + 'checksums': ['bb89ceffa6c791807d1305ceb77dbfacc5aa499891d2c55661c6459651fc39e3'], + }), + ('biom-format', '2.1.15', { + 'modulename': 'biom', + 'checksums': ['3bda2096e663dc1cb6f90f51b394da0838b9be5164a44370c134ce5b3b2a4dd3'], + }), + ('pylatexenc', '2.10', { + 'checksums': ['3dd8fd84eb46dc30bee1e23eaab8d8fb5a7f507347b23e5f38ad9675c84f40d3'], + }), + ('bibtexparser', '1.4.0', { + 'checksums': ['ca7ce2bc34e7c48a678dd49416429bb567441f26dbb13b3609082d8cd109ace6'], + }), + ('deblur', '1.1.0', { + 'checksums': ['78ca2c9946ed99c0d49352e92b63083ae10d04734af7682baddb2c31966c1674'], + }), + ('emperor', '1.0.4', { + 'checksums': ['8b57d6ee3709b62b4dfdd8e1f815dd88e5fee3a05947d72fa32191a16ac08854'], + }), + ('fastcluster', '1.2.6', { + 'checksums': ['aab886efa7b6bba7ac124f4498153d053e5a08b822d2254926b7206cdf5a8aa6'], + }), + ('gneiss', '0.4.6', { + 'preinstallopts': "sed -i '/nose/d' setup.py && ", + 'checksums': ['5ebf32148909cf74475e45682042c68224f002c1cbf723a5c96014a30f1cf323'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('ijson', '3.2.3', { + 'checksums': ['10294e9bf89cb713da05bc4790bdff616610432db561964827074898e174f917'], + }), + ('iow', '1.0.6', { + 'modulename': 'bp', + 'preinstallopts': """sed -i "/'nose /d" setup.py && """, + 'checksums': ['ac4f579a0881f1c827f75033a304341ae91d3a527cc6aed3fea53749f1b9951c'], + }), + ('atpublic', '4.0', { + 'modulename': 'public', + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['80057c55641253b86dcb68b524f82328172371b6547d4c7462a9127fbfbbabfc'], + }), + ('flufl-lock', '8.0.1', { + 'modulename': 'flufl.lock', + 'source_tmpl': 'flufl_lock-%(version)s-py3-none-any.whl', + 'checksums': ['a3df854d76173d59813fdcba91671234b59e2a14db3390793745c77a7bb92d9d'], + }), + ('astor', '0.8.1', { + 'checksums': ['6a6effda93f4e1ce9f618779b2dd1d9d84f1e32812c23a29b3fff6fd7f63fa5e'], + }), + ('interface_meta', '1.3.0', { + 'checksums': ['8a4493f8bdb73fb9655dcd5115bc897e207319e36c8835f39c516a2d7e9d79a1'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('formulaic', '0.4.0', { + 'checksums': ['087950518c53a2491deb52b8ddd66833f953882e517a42e476c007cc8f6892c5'], + }), + ('altair', '5.0.1', { + 'preinstallopts': """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' -e 's/^requires = .*/requires = ["setuptools"]/g' -e 's/^license-files = .*//g' -e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && schemadir=%(installdir)s/lib/python%(pyshortver)s/site-packages/altair/vegalite/v5/schema/ && mkdir -p $schemadir && cp altair/vegalite/v5/schema/vega-lite-schema.json $schemadir && """, + 'checksums': ['087d7033cb2d6c228493a053e12613058a5d47faf6a36aea3ff60305fd8b4cb0'], + }), + (name, version, { + 'patches': ['QIIME2-2023.5.1_fix.patch'], + 'source_urls': ['https://github.com/qiime2/qiime2/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': [ + {'QIIME2-2023.7.0.tar.gz': 'e812188bc2f658c556a3a9d4670c6d25595114726e975cff0b0cbc88e47318ec'}, + {'QIIME2-2023.5.1_fix.patch': '6148e5334f478bcdd6f5bf30fbe39426be71c391af1a384a529c49e658ada7a5'}, + ], + }), + ('q2cli', version, { + 'source_urls': ['https://github.com/qiime2/q2cli/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['2ee2f1f95bacaee8c8a3c4fbc43b20d01ab32bb8736a8d142216ba3ff6817487'], + }), + ('q2-alignment', version, { + 'source_urls': ['https://github.com/qiime2/q2-alignment/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8b93b0b5a156f0d318e984b2a9aff677e7de0426150019056266200c32b4b3c8'], + }), + ('q2-composition', version, { + 'source_urls': ['https://github.com/qiime2/q2-composition/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e884ce154fdc6e8ad3c77f2e799beab27a3de511836a9d0261cef56d96523721'], + }), + ('q2-cutadapt', version, { + 'source_urls': ['https://github.com/qiime2/q2-cutadapt/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['73c95ba387dd6f1612488cd8ad8ee4d483f6a85bb342b9b77dd8b075b1fde09d'], + }), + ('q2-dada2', version, { + 'source_urls': ['https://github.com/qiime2/q2-dada2/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['0597d81acea64f63b10a8e5061ae2acb4dd1cc04a77be243f921a70d3303ee93'], + }), + ('q2-deblur', version, { + 'source_urls': ['https://github.com/qiime2/q2-deblur/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['284ade6685e873642cf52d3d8625048a913fd218ec79427fc64d3825e5665578'], + }), + ('q2-demux', version, { + 'preinstallopts': "make all && ", + 'source_urls': ['https://github.com/qiime2/q2-demux/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ba3358e7af1f88dfbecb74aea31927b3b7208c534233f0691abea1df33445ce3'], + }), + ('q2-diversity', version, { + 'preinstallopts': "make all && ", + 'source_urls': ['https://github.com/qiime2/q2-diversity/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['30e1c3f72f6dbbd05752248f525950ba42d4c8e627c3b50599565848b969e7c4'], + }), + ('q2-diversity-lib', version, { + 'source_urls': ['https://github.com/qiime2/q2-diversity-lib/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['4c907b957e40356ac66bd9af2272051553491aaa8580be543da199f44e48f688'], + }), + ('q2-emperor', version, { + 'source_urls': ['https://github.com/qiime2/q2-emperor/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['d6581926a3038a3e8dbaad563281c4bb2b707ba2133329fb239af7fde0627a97'], + }), + ('q2-feature-classifier', version, { + 'source_urls': ['https://github.com/qiime2/q2-feature-classifier/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f802804dec72c29e2b2a6b8052858739fb5b3791d579e0020f4a0f4f92eb8587'], + }), + ('q2-feature-table', version, { + 'source_urls': ['https://github.com/qiime2/q2-feature-table/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['3175223586013da3b71cf982076aec4bc4548d13e9afa87422f35c6c9f7e009f'], + }), + ('q2-fragment-insertion', version, { + 'source_urls': ['https://github.com/qiime2/q2-fragment-insertion/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['bee91e55e4fce25475430c2f04f15a022850cc4c1f00d6872619a525c5ea568c'], + }), + ('q2-gneiss', version, { + 'source_urls': ['https://github.com/qiime2/q2-gneiss/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f495d0cfb9125325f85c39ba87a69ca843b856211c0b3250e34877cc5bdccb68'], + }), + ('q2-longitudinal', version, { + 'source_urls': ['https://github.com/qiime2/q2-longitudinal/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['141272036a032b29784101dd67f2537fc246b2ce0014189be8d48b48db7aa6b1'], + }), + ('q2-metadata', version, { + 'source_urls': ['https://github.com/qiime2/q2-metadata/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b3359c9660bfb2d913f0338c1d54633b197be7887f79d05e12930ab1e263044c'], + }), + ('q2-phylogeny', version, { + 'source_urls': ['https://github.com/qiime2/q2-phylogeny/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['c42361fb8878ed08c8cb130c3f6f894c0b35220a7d761b7d6e3f5c701bd19acc'], + }), + ('q2-quality-control', version, { + 'source_urls': ['https://github.com/qiime2/q2-quality-control/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8aacd517dc422dd429dc298f07f9bb324a2c1e261d6fce64b990b7d54e7216ce'], + }), + ('q2-quality-filter', version, { + 'source_urls': ['https://github.com/qiime2/q2-quality-filter/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['ed2abc58656585c1f7767f43b8a2f70e4c8e5a6f3393b4d05cce04a656b9418d'], + }), + ('q2-sample-classifier', version, { + 'source_urls': ['https://github.com/qiime2/q2-sample-classifier/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['8736b7fdd985ae6d33d74bde97a0500a2fc28e4d5d1349bcee3656ff9b354d1d'], + }), + ('q2-taxa', version, { + 'preinstallopts': "make all && ", + 'source_urls': ['https://github.com/qiime2/q2-taxa/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['df2fca8df1dfd2c795b2c7fd72a9ea2dd887813df468c9a9777fc902bddfdb1c'], + }), + ('q2-types', version, { + 'source_urls': ['https://github.com/qiime2/q2-types/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['eb646be101d499f92e60801f613ac54329f246936dd110c148d4381df4a0f64b'], + }), + ('q2-vsearch', version, { + 'source_urls': ['https://github.com/qiime2/q2-vsearch/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['4d67bfc97ff350538f07fd7aadc4a9ef7ad8dde8087052360dda937c13887aa1'], + }), + ('q2templates', version, { + 'source_urls': ['https://github.com/qiime2/q2templates/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['405a3f5e9146104ee6f16b6a164b317ee1c9692e8984c2fc54360b9bc267382d'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/biom', 'bin/qiime'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "qiime --help", + "qiime info", + "qiime tools validate " + "%(installdir)s/lib/python%(pyshortver)s/site-packages/q2_sample_classifier/tests/data/vaw.qza", +] + +modextrapaths = {'CONDA_PREFIX': ''} + +moduleclass = 'bio' + From f604af5d0462771e4ab2e95841a56c7a5c5ca743 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 7 Nov 2023 10:59:53 +0100 Subject: [PATCH 0052/1193] BiG-SCAPE: fix handling of domain files and html templates. --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 16 +++++++- ...E-1.1.5_use_env_var_for_domain_files.patch | 37 +++++++++++++++++++ ...BiG-SCAPE-1.1.5_use_env_var_for_html.patch | 33 +++++++++++++++++ 3 files changed, 85 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index 01cc4ccc8914..5c6c71a87211 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -15,11 +15,16 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_use_env_var_to_find-MIBiG-files.patch', + '%(name)s-%(version)s_use_env_var_for_domain_files.patch', + '%(name)s-%(version)s_use_env_var_for_html.patch', ] checksums = [ {'v1.1.5.tar.gz': 'ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'}, {'BiG-SCAPE-1.1.5_use_env_var_to_find-MIBiG-files.patch': 'f0602208765a2686a324a27ff6073aac01c230b6a81a00656269fd89c97cf370'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch': + '51337f22b2619ed38969f4ead5f7ce2f2df884f272793b47fb46d77e9c5e2aa2'}, + {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, ] dependencies = [ @@ -42,9 +47,18 @@ sanity_check_commands = [ 'bigscape.py --help', ] +modextravars = { + 'BIG_SCAPE_HTML_PATH': '%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE', +} + modloadmsg = "%(name)s needs processed Pfam database to work properly.\n" -modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website" +modloadmsg += "For this, download the latest 'Pfam-A.hmm.gz' file from the Pfam website " modloadmsg += "(http://ftp.ebi.ac.uk/pub/databases/Pfam/releases/), " modloadmsg += "uncompress it and process it using the `hmmpress` command.\n" +modloadmsg += "For data files, like the domains_color_file.tsv and domain_includelist.txt, " +modloadmsg += "one can set the environment variable BIG_SCAPE_DATA_PATH, if that is not set " +modloadmsg += "it will use the directory where the bigscape command is started from.\n" +modloadmsg += "One can copy the domains_color_file.tsv from " +modloadmsg += "%(installdir)s/lib/python%(pyshortver)s/site-packages/BiG-SCAPE/domains_color_file.tsv\n" moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch new file mode 100644 index 000000000000..afffdbb087bc --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch @@ -0,0 +1,37 @@ +Don't use domains_color_file.tsv and domain_includelist.txt from the install tree. +Use env var or current dir. + +Åke Sandgren, 2023-11-02 +diff -ru BiG-SCAPE-1.1.5.orig/ArrowerSVG.py BiG-SCAPE-1.1.5/ArrowerSVG.py +--- BiG-SCAPE-1.1.5.orig/ArrowerSVG.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/ArrowerSVG.py 2023-11-02 15:48:51.313247855 +0100 +@@ -27,7 +27,7 @@ + gene_contour_thickness = 2 # thickness grows outwards + stripe_thickness = 3 + +-domains_color_file = os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv") ++domains_color_file = os.path.join(os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()), "domains_color_file.tsv") + + + def read_color_domains_file(): +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-02 15:48:02.929621562 +0100 +@@ -2235,7 +2235,7 @@ + # Get domain_includelist + has_includelist = False + if options.domain_includelist: +- bigscape_path = os.path.dirname(os.path.realpath(__file__)) ++ bigscape_path = os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()) + if os.path.isfile(os.path.join(bigscape_path,"domain_includelist.txt")): + domain_includelist = set() + for line in open(os.path.join(bigscape_path,"domain_includelist.txt"), "r"): +@@ -2850,7 +2852,7 @@ + if not os.path.isfile(pfams_js_file): + with open(pfams_js_file, "w") as pfams_js: + pfam_json = {} +- pfam_colors = generatePfamColorsMatrix(os.path.join(os.path.dirname(os.path.realpath(__file__)), "domains_color_file.tsv")) ++ pfam_colors = generatePfamColorsMatrix(os.path.join(os.getenv('BIG_SCAPE_DATA_PATH', os.getcwd()), "domains_color_file.tsv")) + for pfam_code in pfam_info: + pfam_obj = {} + if pfam_code in pfam_colors: diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch new file mode 100644 index 000000000000..0f0da2a792ec --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_env_var_for_html.patch @@ -0,0 +1,33 @@ +Use EB specific env var to locate html_template + +Åke Sandgren, 20231106 +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-06 11:20:46.410872382 +0100 +@@ -1881,7 +1881,7 @@ + with open(os.path.join(module_html_path, "bs_data.js"), "w") as bs_data_js: + bs_data_js.write("var bs_data={};\n".format(json.dumps(bs_data, indent=4, separators=(',', ':'), sort_keys=True))) + bs_data_js.write("dataLoaded('bs_data');\n") +- shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "index_html"), os.path.join(module_html_path, "index.html")) ++ shutil.copy(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "index_html"), os.path.join(module_html_path, "index.html")) + + ## Write bgc_networks.js + with open(os.path.join(module_html_path, "bs_networks.js"), "w") as bs_networks_js: +@@ -2832,7 +2834,7 @@ + create_directory(network_files_folder, "Network Files", False) + + # copy html templates +- dir_util.copy_tree(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "output"), output_folder) ++ dir_util.copy_tree(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "output"), output_folder) + + # make a new run folder in the html output & copy the overview_html + network_html_folder = os.path.join(output_folder, "html_content", "networks", run_name) +@@ -2841,7 +2843,7 @@ + for cutoff in cutoff_list: + network_html_folder_cutoff = "{}_c{:.2f}".format(network_html_folder, cutoff) + create_directory(network_html_folder_cutoff, "Network HTML Files", False) +- shutil.copy(os.path.join(os.path.dirname(os.path.realpath(__file__)), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html")) ++ shutil.copy(os.path.join(os.getenv('BIG_SCAPE_HTML_PATH'), "html_template", "overview_html"), os.path.join(network_html_folder_cutoff, "overview.html")) + rundata_networks_per_run[network_html_folder_cutoff] = [] + html_subs_per_run[network_html_folder_cutoff] = [] + From 0c6ee78e6ab121aeb6cb666b861008c49129bcc8 Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Tue, 7 Nov 2023 11:31:51 +0100 Subject: [PATCH 0053/1193] Easyconfig added for DeepLabCut in foss/2022a --- ...DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..abd16842cec6 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,74 @@ +# Loosely based on PR #7680 +# J. Sassmannshausen (Imperial College London/UK) +# upgrade to version 2.3.6: J Hein, (LUNARC, Lund University, Sweden) + +easyblock = 'PythonBundle' + +name = 'DeepLabCut' +version = '2.3.6' +versionsuffix = '-CUDA-%(cudaver)s' +local_version = '%(versionsuffix)s-contrib' + +homepage = 'http://www.mousemotorlab.org/deeplabcut' +description = "Markerless tracking of user-defined features with deep learning" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('TensorFlow', '2.9.1', versionsuffix), + ('PyTorch', '1.12.0', versionsuffix), + ('scikit-image', '0.19.3'), + ('matplotlib', '3.5.2'), + ('numba', '0.56.4'), + ('scikit-learn', '1.1.2'), + ('FFmpeg', '4.4.2'), + ('PyZMQ', '24.0.1'), + ('tqdm', '4.64.0'), + ('imageio', '2.22.2'), + ('statsmodels', '0.13.1'), + ('PyTables', '3.8.0'), + ('ruamel.yaml', '0.17.21'), + ('imgaug', '0.4.0', versionsuffix), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('dlclibrary', '0.0.4', { + 'checksums': ['2b4ca078dc9cddb2a1f30d42cbc9d5c0e849e0f93f2b6781ca478baed0a829b8'], + }), + ('filterpy', '1.4.5', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], + }), + ('huggingface-hub', '0.17.3', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('imageio-ffmpeg', '0.4.9', { + 'checksums': ['39bcd1660118ef360fa4047456501071364661aa9d9021d3d26c58f1ee2081f5'], + }), + ('msgpack-numpy', '0.4.8', { + 'sources': ['msgpack-numpy-0.4.8.tar.gz'], + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + }), + ('tensorpack', '0.11', { + 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], + }), + ('tf_slim', '1.1.0', { + 'source_urls': ['https://github.com/google-research/tf-slim/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['964cde4b7728a408dcd5c841ab6b93d95137ab4b60db28b10400f86286bfeb8b'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['c4479f05b3c917a6198c1abbb6ea0ac580ce4b02fe1d068e0215b1984aa8e385'], + }), +] + + +moduleclass = 'lib' From 209f247a603145a6c5b29b0968407c211bdbc76c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 7 Nov 2023 13:43:39 +0100 Subject: [PATCH 0054/1193] {bio}[foss/2022a] cryoCARE v0.3.0 /w CUDA 11.7.0 --- .../cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..130fa01f271a --- /dev/null +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,62 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonBundle' + +name = 'cryoCARE' +version = '0.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/juglab/cryoCARE_pip' +description = """This package is a memory efficient implementation of cryoCARE. + +This setup trains a denoising U-Net for tomographic reconstruction according to + the Noise2Noise training paradigm. Therefore the user has to provide two +tomograms of the same sample. The simplest way to achieve this is with direct- +detector movie-frames. + +You can use Warp to generate two reconstructed tomograms based on the even/odd +frames. Alternatively, the movie-frames can be split in two halves (e.g. with +MotionCor2 -SplitSum 1 or with IMOD alignframes -debug 10000) from which two +identical, up to random noise, tomograms can be reconstructed. + +These two (even and odd) tomograms can be used as input to this cryoCARE +implementation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', True), + ('SciPy-bundle', '2022.05'), + ('TensorFlow', '2.11.0', versionsuffix), + ('mrcfile', '1.4.3'), + ('tqdm', '4.64.0'), + ('matplotlib', '3.5.2'), + ('CSBDeep', '0.7.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + (name, version, { + 'patches': ['%(name)s-%(version)s_relax_requirements.patch'], + 'checksums': [ + {'cryoCARE-0.3.0.tar.gz': '8885aeb03d1731de1958463bbf766fa9999f4480d71c3af09f711ee210ab9886'}, + {'cryoCARE-0.3.0_relax_requirements.patch': + 'a44814f6e568f5fb618cf789d21a6b5714fbda78b4170ec8e868e50fb0f2a5c0'}, + ], + }), +] + +sanity_check_commands = [ + 'cryoCARE_extract_train_data.py --help', + 'cryoCARE_train.py --help', + 'cryoCARE_predict.py --help', +] + +moduleclass = 'bio' + From 59d21337f8a9b045e5c81c0a6fedab24edcf6031 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 7 Nov 2023 18:13:03 +0100 Subject: [PATCH 0055/1193] adding easyconfigs: FDS-6.8.0-intel-2022b.eb --- .../f/FDS/FDS-6.8.0-intel-2022b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb diff --git a/easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb b/easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb new file mode 100644 index 000000000000..a8d35e94b263 --- /dev/null +++ b/easybuild/easyconfigs/f/FDS/FDS-6.8.0-intel-2022b.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'FDS' +version = '6.8.0' + +homepage = 'https://pages.nist.gov/fds-smv' +description = """Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, + with an emphasis on smoke and heat transport from fires.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': True} + +source_urls = ['https://github.com/firemodels/fds/archive/'] +sources = ['FDS-%(version)s.tar.gz'] +checksums = ['d8213d706bb36300ca5fdc9a7884fa4610e2820338de23212dd19de75d8e0704'] + +unpack_options = '--strip-components=1' + +start_dir = 'Build' + +# just run make in the install dir +skipsteps = ['configure', 'install'] +buildininstalldir = True + +buildopts = 'impi_intel_linux_openmp &&' +buildopts += 'cd %(installdir)s/Build && ln -s fds_impi_intel_linux_openmp fds' + +modextrapaths = {'PATH': 'Build'} + +sanity_check_paths = { + 'files': ['Build/fds'], + 'dirs': [], +} + +sanity_check_commands = [ + "fds 2>&1 | grep 'MPI Enabled;'", + "fds 2>&1 | grep 'OpenMP Enabled;'", +] + +moduleclass = 'phys' From 1bc26acd17723217942ba9dc727a2dc538e360dd Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 8 Nov 2023 09:32:56 +0100 Subject: [PATCH 0056/1193] add missing patch --- .../cryoCARE-0.3.0_relax_requirements.patch | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0_relax_requirements.patch diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0_relax_requirements.patch b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0_relax_requirements.patch new file mode 100644 index 000000000000..e35ce9f3a785 --- /dev/null +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0_relax_requirements.patch @@ -0,0 +1,16 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11 +# https://github.com/juglab/cryoCARE_pip/issues/47 +# The restriction to ~=1.19 has been introduced due to a conflict with +# Tensorflow 2.4. However, we are using TF 2.11 +diff -ru cryoCARE-0.3.0/setup.py cryoCARE-0.3.0_relax_requirements/setup.py +--- cryoCARE-0.3.0/setup.py 2023-06-15 15:33:40.000000000 +0200 ++++ cryoCARE-0.3.0_relax_requirements/setup.py 2023-11-07 11:01:24.464822422 +0100 +@@ -23,7 +23,7 @@ + ], + python_requires='>=3.8', + install_requires=[ +- "numpy~=1.19.2", ++ "numpy>=1.19.2", + "mrcfile", + "csbdeep>=0.7.0,<0.8.0", + "psutil" From c3ed2f8b77011e2d9b0b7fda9cbee7b6933c3b3c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 8 Nov 2023 10:29:57 +0100 Subject: [PATCH 0057/1193] Update cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb remove blank lines --- .../c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb index 130fa01f271a..4096518c32e9 100644 --- a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb @@ -59,4 +59,3 @@ sanity_check_commands = [ ] moduleclass = 'bio' - From 5bad7d6be08daa9cbbd5931ad0c6d373bdf594d5 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 8 Nov 2023 11:08:29 +0100 Subject: [PATCH 0058/1193] cuda dep SYSTEM --- .../c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb index 4096518c32e9..f7ea1e5bf2d2 100644 --- a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb @@ -26,7 +26,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('SciPy-bundle', '2022.05'), ('TensorFlow', '2.11.0', versionsuffix), ('mrcfile', '1.4.3'), From 32916375f727bc7e57935454640b74dabdd49718 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 8 Nov 2023 12:43:09 +0100 Subject: [PATCH 0059/1193] CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb --- .../c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb index f7ea1e5bf2d2..9e6d24ecafdb 100644 --- a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.3.0-foss-2022a-CUDA-11.7.0.eb @@ -32,16 +32,13 @@ dependencies = [ ('mrcfile', '1.4.3'), ('tqdm', '4.64.0'), ('matplotlib', '3.5.2'), - ('CSBDeep', '0.7.4'), + ('CSBDeep', '0.7.4', versionsuffix), ] use_pip = True sanity_pip_check = True exts_list = [ - ('tifffile', '2022.10.10', { - 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], - }), (name, version, { 'patches': ['%(name)s-%(version)s_relax_requirements.patch'], 'checksums': [ From e72478ffc80e89631ed08b3553be84f131bd679d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 8 Nov 2023 12:45:05 +0100 Subject: [PATCH 0060/1193] add CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb --- .../CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..fcd4c2441be9 --- /dev/null +++ b/easybuild/easyconfigs/c/CSBDeep/CSBDeep-0.7.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'CSBDeep' +version = '0.7.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://csbdeep.bioimagecomputing.com/" +description = """CSBDeep is a toolbox for Content-aware Image Restoration (CARE).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('TensorFlow', '2.11.0', versionsuffix), + ('matplotlib', '3.5.2'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2023.9.26', { + 'checksums': ['67e355e4595aab397f8405d04afe1b4ae7c6f62a44e22d933fee1a571a48c7ae'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['85d6fc360bb33253ba6f543d75cf0cf123595f0ea4dd1fa76b1e5bc8fc55b901'], + 'modulename': '%(namelower)s', + }), +] + +sanity_check_commands = ['care_predict'] + +moduleclass = 'bio' From f3891805aad23cdd5643b097b659b0d46afa5c2a Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 8 Nov 2023 16:04:09 +0100 Subject: [PATCH 0061/1193] Upgrade to TensorFlow 2.11.0 --- .../d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb index abd16842cec6..cec8160a27c9 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.3.6-foss-2022a-CUDA-11.7.0.eb @@ -18,7 +18,7 @@ toolchainopts = {'pic': True} dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), - ('TensorFlow', '2.9.1', versionsuffix), + ('TensorFlow', '2.11.0', versionsuffix), ('PyTorch', '1.12.0', versionsuffix), ('scikit-image', '0.19.3'), ('matplotlib', '3.5.2'), From 259e4d4b7994604dfd1dec8422e7d54cb56db3c0 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 7 Nov 2023 17:47:45 +0100 Subject: [PATCH 0062/1193] adding easyconfigs: f90nml-1.4.4-GCCcore-10.2.0.eb, f90nml-1.4.4-GCCcore-12.2.0.eb --- .../f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb | 27 +++++++++++++++++++ .../f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..5aff63728f98 --- /dev/null +++ b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'f90nml' +version = '1.4.4' + +homepage = 'https://github.com/marshallward/f90nml' +description = """A Python module and command line tool for parsing + Fortran namelist files""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65e8e135779895245238cbf6be5b1b80d6c2b8c9350c9cdce6183a31bdfd7622'] + +builddependencies = [ + ('binutils', '2.35'), +] +dependencies = [ + ('Python', '3.8.6'), + ('PyYAML', '5.3.1') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b554f52d3e93 --- /dev/null +++ b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'f90nml' +version = '1.4.4' + +homepage = 'https://github.com/marshallward/f90nml' +description = """A Python module and command line tool for parsing + Fortran namelist files""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65e8e135779895245238cbf6be5b1b80d6c2b8c9350c9cdce6183a31bdfd7622'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From fd201e8290d03db47d8238f818a7907448bf90fe Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 09:40:43 +0100 Subject: [PATCH 0063/1193] adding easyconfigs: numba-0.58.1-foss-2023a.eb, LLVM-14.0.3-GCCcore-12.3.0.eb and patches: llvmlite-0.41.1_static-linking-of-LLVM.patch --- .../l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb | 40 ++++++++++++++ ...vmlite-0.41.1_static-linking-of-LLVM.patch | 22 ++++++++ .../n/numba/numba-0.58.1-foss-2023a.eb | 55 +++++++++++++++++++ 3 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch create mode 100644 easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..09088210f919 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +name = 'LLVM' +version = '14.0.3' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] +checksums = ['1e09e8c26e1b67bc94a128b62e9b9c24b70c697a2436a479c9e5eedc4ae29654'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch b/easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch new file mode 100644 index 000000000000..9ead7b378205 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/llvmlite-0.41.1_static-linking-of-LLVM.patch @@ -0,0 +1,22 @@ +Link llvmlite statically to LLVM. This allows us to use the version of LLVM that is +officially supported by llvmlite (14.0.3) instead of the one that is default in the toolchain +(for 2023a, that is LLVM 16.0.6). This is a pragmatic solution that is much easier than patching +llvmlite to work with a different version of LLVM. + +Author: Jakob Schiotz, Techn. Univ. Denmark +Email: schiotz@fysik.dtu.dk +Date: 10. November 2023 + +diff --git a/ffi/build.py b/ffi/build.py +index f4f8c69..189a0e9 100755 +--- a/ffi/build.py ++++ b/ffi/build.py +@@ -174,7 +174,7 @@ def main_posix(kind, library_ext): + raise RuntimeError(msg) + + # Get LLVM information for building +- libs = run_llvm_config(llvm_config, "--system-libs --libs all".split()) ++ libs = run_llvm_config(llvm_config, "--link-static --system-libs --libs all".split()) + # Normalize whitespace (trim newlines) + os.environ['LLVM_LIBS'] = ' '.join(libs.split()) + diff --git a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb new file mode 100644 index 000000000000..d6beae0bc5de --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.58.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('LLVM', '14.0.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " + +exts_list = [ + ('llvmlite', '0.41.1', { + 'patches': ['llvmlite-0.41.1_static-linking-of-LLVM.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + {'llvmlite-0.41.1.tar.gz': 'f19f767a018e6ec89608e1f6b13348fa2fcde657151137cb64e56d48598a92db'}, + {'llvmlite-0.41.1_static-linking-of-LLVM.patch': + '0cb1fbe13db4ce8b697305229b6b6d79671a3ec5b93e95b4e059033ca626b43e'}, + ], + }), + (name, version, { + 'checksums': ['487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' From c564011ae4280907971ceef92568fd7a27ed57ca Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 09:54:19 +0100 Subject: [PATCH 0064/1193] Remove superfluous local variable (--inject-checksums moved the preinstallopts stuff around). --- easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb index d6beae0bc5de..233c86071ab5 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb @@ -23,8 +23,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -local_llvmlite_preinstallopts = "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && " - exts_list = [ ('llvmlite', '0.41.1', { 'patches': ['llvmlite-0.41.1_static-linking-of-LLVM.patch'], From 610d20fcaba5368423a8d9421e39b9ba268fa45a Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 15:45:38 +0100 Subject: [PATCH 0065/1193] Make special LLVM module with llvmlite specific patches applied. --- ...0.eb => LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb} | 14 +++++++++++--- .../easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb | 2 +- 2 files changed, 12 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/l/LLVM/{LLVM-14.0.3-GCCcore-12.3.0.eb => LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb} (76%) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb similarity index 76% rename from easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index 09088210f919..2f9a5d05bc90 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -1,5 +1,6 @@ name = 'LLVM' -version = '14.0.3' +version = '14.0.6' +versionsuffix = '-llvmlite' homepage = "https://llvm.org/" description = """The LLVM Core libraries provide a modern source- and target-independent @@ -13,9 +14,16 @@ description = """The LLVM Core libraries provide a modern source- and target-ind toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'cstd': 'gnu++11', 'pic': True} -source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +source_urls = [ + 'https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/', + 'https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/', + ] sources = ['llvm-%(version)s.src.tar.xz'] -checksums = ['1e09e8c26e1b67bc94a128b62e9b9c24b70c697a2436a479c9e5eedc4ae29654'] +patches = [ + 'llvm14-remove-use-of-clonefile.patch', + 'llvm14-clear-gotoffsetmap.patch', + 'llvm14-svml.patch', +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb index 233c86071ab5..f07c3608f254 100644 --- a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb +++ b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2023a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'pic': True} builddependencies = [ - ('LLVM', '14.0.3'), + ('LLVM', '14.0.6', '-llvmlite'), ] dependencies = [ From ee7d33ed3f95056449308c9ed7456f25b73ca2a3 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 16:00:22 +0100 Subject: [PATCH 0066/1193] Add the forgotten checksums. --- .../l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index 2f9a5d05bc90..6034a8bc8ed1 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -24,6 +24,12 @@ patches = [ 'llvm14-clear-gotoffsetmap.patch', 'llvm14-svml.patch', ] +checksums = [ + {'llvm-14.0.6.src.tar.xz': '050922ecaaca5781fdf6631ea92bc715183f202f9d2f15147226f023414f619a'}, + {'llvm14-remove-use-of-clonefile.patch': 'fd246e62292c6c7ad6ab4fa7626b7176f40b8141ec4cd78e811fea26bd29a1f1'}, + {'llvm14-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'}, + {'llvm14-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'}, +] builddependencies = [ ('binutils', '2.40'), From b9b15e0a541ca0d09beb312d1a2a7cdb6fb71473 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 10 Nov 2023 16:22:52 +0100 Subject: [PATCH 0067/1193] Fix bad indentation. --- .../easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index 6034a8bc8ed1..fe8f2a38ca22 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -17,7 +17,7 @@ toolchainopts = {'cstd': 'gnu++11', 'pic': True} source_urls = [ 'https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/', 'https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/', - ] +] sources = ['llvm-%(version)s.src.tar.xz'] patches = [ 'llvm14-remove-use-of-clonefile.patch', From 2b83a3d2e81b4670a7754f41d1b29c564fc17922 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Sat, 11 Nov 2023 09:36:55 +0100 Subject: [PATCH 0068/1193] Add patch files to EasyBuild instead of downloading (works, but test suite complains). --- .../LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb | 22 +- .../LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch | 31 + .../easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch | 2194 +++++++++++++++++ 3 files changed, 2236 insertions(+), 11 deletions(-) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb index fe8f2a38ca22..6ece6bfc09b2 100644 --- a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.3.0-llvmlite.eb @@ -9,26 +9,26 @@ description = """The LLVM Core libraries provide a modern source- and target-ind specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) - to use LLVM as an optimizer and code generator.""" + to use LLVM as an optimizer and code generator. + + This version include patches for llvmlite / numba.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'cstd': 'gnu++11', 'pic': True} -source_urls = [ - 'https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/', - 'https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/', -] +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] sources = ['llvm-%(version)s.src.tar.xz'] + +# Patches from https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/ but +# renamed to follow EasyBuild conventions. patches = [ - 'llvm14-remove-use-of-clonefile.patch', - 'llvm14-clear-gotoffsetmap.patch', - 'llvm14-svml.patch', + 'LLVM-14.0.6-clear-gotoffsetmap.patch', + 'LLVM-14.0.6-svml.patch', ] checksums = [ {'llvm-14.0.6.src.tar.xz': '050922ecaaca5781fdf6631ea92bc715183f202f9d2f15147226f023414f619a'}, - {'llvm14-remove-use-of-clonefile.patch': 'fd246e62292c6c7ad6ab4fa7626b7176f40b8141ec4cd78e811fea26bd29a1f1'}, - {'llvm14-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'}, - {'llvm14-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'}, + {'LLVM-14.0.6-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'}, + {'LLVM-14.0.6-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch new file mode 100644 index 000000000000..239f4ab20c1b --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-clear-gotoffsetmap.patch @@ -0,0 +1,31 @@ +From 322c79fff224389b4df9f24ac22965867007c2fa Mon Sep 17 00:00:00 2001 +From: Graham Markall +Date: Mon, 13 Mar 2023 21:35:11 +0000 +Subject: [PATCH] RuntimeDyldELF: Clear the GOTOffsetMap when finalizing the + load + +This needs resetting so that stale entries are not left behind when the +GOT section and index are reset. + +See llvm/llvm#61402: RuntimeDyldELF doesn't clear GOTOffsetMap in +finalizeLoad(), leading to invalid GOT relocations on AArch64 - +https://github.com/llvm/llvm-project/issues/61402. +--- + llvm/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp b/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp +index f92618afdff6..eb3c27a9406a 100644 +--- a/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp ++++ b/llvm-14.0.6.src/lib/ExecutionEngine/RuntimeDyld/RuntimeDyldELF.cpp +@@ -2345,6 +2345,7 @@ Error RuntimeDyldELF::finalizeLoad(const ObjectFile &Obj, + } + } + ++ GOTOffsetMap.clear(); + GOTSectionID = 0; + CurrentGOTIndex = 0; + +-- +2.34.1 + diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch new file mode 100644 index 000000000000..c753d3f5971a --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-svml.patch @@ -0,0 +1,2194 @@ +From 9de32f5474f1f78990b399214bdbb6c21f8f098e Mon Sep 17 00:00:00 2001 +From: Ivan Butygin +Date: Sun, 24 Jul 2022 20:31:29 +0200 +Subject: [PATCH] Fixes vectorizer and extends SVML support + +Fixes vectorizer and extends SVML support +Patch was updated to fix SVML calling convention issues uncovered by llvm 10. +In previous versions of patch SVML calling convention was selected based on +compilation settings. So if you try to call 256bit vector function from avx512 +code function will be called with avx512 cc which is incorrect. To fix this +SVML cc was separated into 3 different cc for 128, 256 and 512bit vector lengths +which are selected based on actual input vector length. + +Original patch merged several fixes: + +1. https://reviews.llvm.org/D47188 patch fixes the problem with improper calls +to SVML library as it has non-standard calling conventions. So accordingly it +has SVML calling conventions definitions and code to set CC to the vectorized +calls. As SVML provides several implementations for the math functions we also +took into consideration fast attribute and select more fast implementation in +such case. This work is based on original Matt Masten's work. +Author: Denis Nagorny + +2. https://reviews.llvm.org/D53035 patch implements support to legalize SVML +calls by breaking down the illegal vector call instruction into multiple legal +vector call instructions during code generation. Currently the vectorizer does +not check legality of the generated SVML (or any VECLIB) call instructions, and +this can lead to potential problems even during vector type legalization. This +patch addresses this issue by adding a legality check during code generation and +replaces the illegal SVML call with corresponding legalized instructions. +(RFC: http://lists.llvm.org/pipermail/llvm-dev/2018-June/124357.html) +Author: Karthik Senthil + +diff --git a/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h b/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h +index 17d1e3f770c14..110ff08189867 100644 +--- a/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h ++++ b/llvm-14.0.6.src/include/llvm/Analysis/TargetLibraryInfo.h +@@ -39,6 +39,12 @@ struct VecDesc { + NotLibFunc + }; + ++enum SVMLAccuracy { ++ SVML_DEFAULT, ++ SVML_HA, ++ SVML_EP ++}; ++ + /// Implementation of the target library information. + /// + /// This class constructs tables that hold the target library information and +@@ -157,7 +163,7 @@ class TargetLibraryInfoImpl { + /// Return true if the function F has a vector equivalent with vectorization + /// factor VF. + bool isFunctionVectorizable(StringRef F, const ElementCount &VF) const { +- return !getVectorizedFunction(F, VF).empty(); ++ return !getVectorizedFunction(F, VF, false).empty(); + } + + /// Return true if the function F has a vector equivalent with any +@@ -166,7 +172,10 @@ class TargetLibraryInfoImpl { + + /// Return the name of the equivalent of F, vectorized with factor VF. If no + /// such mapping exists, return the empty string. +- StringRef getVectorizedFunction(StringRef F, const ElementCount &VF) const; ++ std::string getVectorizedFunction(StringRef F, const ElementCount &VF, bool IsFast) const; ++ ++ Optional getVectorizedFunctionCallingConv( ++ StringRef F, const FunctionType &FTy, const DataLayout &DL) const; + + /// Set to true iff i32 parameters to library functions should have signext + /// or zeroext attributes if they correspond to C-level int or unsigned int, +@@ -326,8 +335,13 @@ class TargetLibraryInfo { + bool isFunctionVectorizable(StringRef F) const { + return Impl->isFunctionVectorizable(F); + } +- StringRef getVectorizedFunction(StringRef F, const ElementCount &VF) const { +- return Impl->getVectorizedFunction(F, VF); ++ std::string getVectorizedFunction(StringRef F, const ElementCount &VF, bool IsFast) const { ++ return Impl->getVectorizedFunction(F, VF, IsFast); ++ } ++ ++ Optional getVectorizedFunctionCallingConv( ++ StringRef F, const FunctionType &FTy, const DataLayout &DL) const { ++ return Impl->getVectorizedFunctionCallingConv(F, FTy, DL); + } + + /// Tests if the function is both available and a candidate for optimized code +diff --git a/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h b/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h +index 78ebb35e0ea4d..3ffb57db8b18b 100644 +--- a/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h ++++ b/llvm-14.0.6.src/include/llvm/AsmParser/LLToken.h +@@ -133,6 +133,9 @@ enum Kind { + kw_fastcc, + kw_coldcc, + kw_intel_ocl_bicc, ++ kw_intel_svmlcc128, ++ kw_intel_svmlcc256, ++ kw_intel_svmlcc512, + kw_cfguard_checkcc, + kw_x86_stdcallcc, + kw_x86_fastcallcc, +diff --git a/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt b/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt +index 0498fc269b634..23bb3de41bc1a 100644 +--- a/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt ++++ b/llvm-14.0.6.src/include/llvm/IR/CMakeLists.txt +@@ -20,3 +20,7 @@ tablegen(LLVM IntrinsicsX86.h -gen-intrinsic-enums -intrinsic-prefix=x86) + tablegen(LLVM IntrinsicsXCore.h -gen-intrinsic-enums -intrinsic-prefix=xcore) + tablegen(LLVM IntrinsicsVE.h -gen-intrinsic-enums -intrinsic-prefix=ve) + add_public_tablegen_target(intrinsics_gen) ++ ++set(LLVM_TARGET_DEFINITIONS SVML.td) ++tablegen(LLVM SVML.inc -gen-svml) ++add_public_tablegen_target(svml_gen) +diff --git a/llvm-14.0.6.src/include/llvm/IR/CallingConv.h b/llvm-14.0.6.src/include/llvm/IR/CallingConv.h +index fd28542465225..096eea1a8e19b 100644 +--- a/llvm-14.0.6.src/include/llvm/IR/CallingConv.h ++++ b/llvm-14.0.6.src/include/llvm/IR/CallingConv.h +@@ -252,6 +252,11 @@ namespace CallingConv { + /// M68k_INTR - Calling convention used for M68k interrupt routines. + M68k_INTR = 101, + ++ /// Intel_SVML - Calling conventions for Intel Short Math Vector Library ++ Intel_SVML128 = 102, ++ Intel_SVML256 = 103, ++ Intel_SVML512 = 104, ++ + /// The highest possible calling convention ID. Must be some 2^k - 1. + MaxID = 1023 + }; +diff --git a/llvm-14.0.6.src/include/llvm/IR/SVML.td b/llvm-14.0.6.src/include/llvm/IR/SVML.td +new file mode 100644 +index 0000000000000..5af710404c9d9 +--- /dev/null ++++ b/llvm-14.0.6.src/include/llvm/IR/SVML.td +@@ -0,0 +1,62 @@ ++//===-- Intel_SVML.td - Defines SVML call variants ---------*- tablegen -*-===// ++// ++// The LLVM Compiler Infrastructure ++// ++// This file is distributed under the University of Illinois Open Source ++// License. See LICENSE.TXT for details. ++// ++//===----------------------------------------------------------------------===// ++// ++// This file is used by TableGen to define the different typs of SVML function ++// variants used with -fveclib=SVML. ++// ++//===----------------------------------------------------------------------===// ++ ++class SvmlVariant; ++ ++def sin : SvmlVariant; ++def cos : SvmlVariant; ++def pow : SvmlVariant; ++def exp : SvmlVariant; ++def log : SvmlVariant; ++def acos : SvmlVariant; ++def acosh : SvmlVariant; ++def asin : SvmlVariant; ++def asinh : SvmlVariant; ++def atan2 : SvmlVariant; ++def atan : SvmlVariant; ++def atanh : SvmlVariant; ++def cbrt : SvmlVariant; ++def cdfnorm : SvmlVariant; ++def cdfnorminv : SvmlVariant; ++def cosd : SvmlVariant; ++def cosh : SvmlVariant; ++def erf : SvmlVariant; ++def erfc : SvmlVariant; ++def erfcinv : SvmlVariant; ++def erfinv : SvmlVariant; ++def exp10 : SvmlVariant; ++def exp2 : SvmlVariant; ++def expm1 : SvmlVariant; ++def hypot : SvmlVariant; ++def invsqrt : SvmlVariant; ++def log10 : SvmlVariant; ++def log1p : SvmlVariant; ++def log2 : SvmlVariant; ++def sind : SvmlVariant; ++def sinh : SvmlVariant; ++def sqrt : SvmlVariant; ++def tan : SvmlVariant; ++def tanh : SvmlVariant; ++ ++// TODO: SVML does not currently provide _ha and _ep variants of these fucnctions. ++// We should call the default variant of these functions in all cases instead. ++ ++// def nearbyint : SvmlVariant; ++// def logb : SvmlVariant; ++// def floor : SvmlVariant; ++// def fmod : SvmlVariant; ++// def ceil : SvmlVariant; ++// def trunc : SvmlVariant; ++// def rint : SvmlVariant; ++// def round : SvmlVariant; +diff --git a/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt b/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt +index aec84124129f4..98286e166fbe2 100644 +--- a/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt ++++ b/llvm-14.0.6.src/lib/Analysis/CMakeLists.txt +@@ -150,6 +150,7 @@ add_llvm_component_library(LLVMAnalysis + DEPENDS + intrinsics_gen + ${MLDeps} ++ svml_gen + + LINK_LIBS + ${MLLinkDeps} +diff --git a/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp b/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp +index 02923c2c7eb14..83abde28a62a4 100644 +--- a/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp ++++ b/llvm-14.0.6.src/lib/Analysis/TargetLibraryInfo.cpp +@@ -110,6 +110,11 @@ bool TargetLibraryInfoImpl::isCallingConvCCompatible(Function *F) { + F->getFunctionType()); + } + ++static std::string svmlMangle(StringRef FnName, const bool IsFast) { ++ std::string FullName = FnName.str(); ++ return IsFast ? FullName : FullName + "_ha"; ++} ++ + /// Initialize the set of available library functions based on the specified + /// target triple. This should be carefully written so that a missing target + /// triple gets a sane set of defaults. +@@ -1876,8 +1881,9 @@ void TargetLibraryInfoImpl::addVectorizableFunctionsFromVecLib( + } + case SVML: { + const VecDesc VecFuncs[] = { +- #define TLI_DEFINE_SVML_VECFUNCS +- #include "llvm/Analysis/VecFuncs.def" ++ #define GET_SVML_VARIANTS ++ #include "llvm/IR/SVML.inc" ++ #undef GET_SVML_VARIANTS + }; + addVectorizableFunctions(VecFuncs); + break; +@@ -1897,20 +1903,51 @@ bool TargetLibraryInfoImpl::isFunctionVectorizable(StringRef funcName) const { + return I != VectorDescs.end() && StringRef(I->ScalarFnName) == funcName; + } + +-StringRef +-TargetLibraryInfoImpl::getVectorizedFunction(StringRef F, +- const ElementCount &VF) const { ++std::string TargetLibraryInfoImpl::getVectorizedFunction(StringRef F, ++ const ElementCount &VF, ++ bool IsFast) const { ++ bool FromSVML = ClVectorLibrary == SVML; + F = sanitizeFunctionName(F); + if (F.empty()) +- return F; ++ return F.str(); + std::vector::const_iterator I = + llvm::lower_bound(VectorDescs, F, compareWithScalarFnName); + while (I != VectorDescs.end() && StringRef(I->ScalarFnName) == F) { +- if (I->VectorizationFactor == VF) +- return I->VectorFnName; ++ if (I->VectorizationFactor == VF) { ++ if (FromSVML) { ++ return svmlMangle(I->VectorFnName, IsFast); ++ } ++ return I->VectorFnName.str(); ++ } + ++I; + } +- return StringRef(); ++ return std::string(); ++} ++ ++static CallingConv::ID getSVMLCallingConv(const DataLayout &DL, const FunctionType &FType) ++{ ++ assert(isa(FType.getReturnType())); ++ auto *VecCallRetType = cast(FType.getReturnType()); ++ auto TypeBitWidth = DL.getTypeSizeInBits(VecCallRetType); ++ if (TypeBitWidth == 128) { ++ return CallingConv::Intel_SVML128; ++ } else if (TypeBitWidth == 256) { ++ return CallingConv::Intel_SVML256; ++ } else if (TypeBitWidth == 512) { ++ return CallingConv::Intel_SVML512; ++ } else { ++ llvm_unreachable("Invalid vector width"); ++ } ++ return 0; // not reachable ++} ++ ++Optional ++TargetLibraryInfoImpl::getVectorizedFunctionCallingConv( ++ StringRef F, const FunctionType &FTy, const DataLayout &DL) const { ++ if (F.startswith("__svml")) { ++ return getSVMLCallingConv(DL, FTy); ++ } ++ return {}; + } + + TargetLibraryInfo TargetLibraryAnalysis::run(const Function &F, +diff --git a/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp b/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp +index e3bf41c9721b6..4f9dccd4e0724 100644 +--- a/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp ++++ b/llvm-14.0.6.src/lib/AsmParser/LLLexer.cpp +@@ -603,6 +603,9 @@ lltok::Kind LLLexer::LexIdentifier() { + KEYWORD(spir_kernel); + KEYWORD(spir_func); + KEYWORD(intel_ocl_bicc); ++ KEYWORD(intel_svmlcc128); ++ KEYWORD(intel_svmlcc256); ++ KEYWORD(intel_svmlcc512); + KEYWORD(x86_64_sysvcc); + KEYWORD(win64cc); + KEYWORD(x86_regcallcc); +diff --git a/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp b/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp +index 432ec151cf8ae..3bd6ee61024b8 100644 +--- a/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp ++++ b/llvm-14.0.6.src/lib/AsmParser/LLParser.cpp +@@ -1781,6 +1781,9 @@ void LLParser::parseOptionalDLLStorageClass(unsigned &Res) { + /// ::= 'ccc' + /// ::= 'fastcc' + /// ::= 'intel_ocl_bicc' ++/// ::= 'intel_svmlcc128' ++/// ::= 'intel_svmlcc256' ++/// ::= 'intel_svmlcc512' + /// ::= 'coldcc' + /// ::= 'cfguard_checkcc' + /// ::= 'x86_stdcallcc' +@@ -1850,6 +1853,9 @@ bool LLParser::parseOptionalCallingConv(unsigned &CC) { + case lltok::kw_spir_kernel: CC = CallingConv::SPIR_KERNEL; break; + case lltok::kw_spir_func: CC = CallingConv::SPIR_FUNC; break; + case lltok::kw_intel_ocl_bicc: CC = CallingConv::Intel_OCL_BI; break; ++ case lltok::kw_intel_svmlcc128:CC = CallingConv::Intel_SVML128; break; ++ case lltok::kw_intel_svmlcc256:CC = CallingConv::Intel_SVML256; break; ++ case lltok::kw_intel_svmlcc512:CC = CallingConv::Intel_SVML512; break; + case lltok::kw_x86_64_sysvcc: CC = CallingConv::X86_64_SysV; break; + case lltok::kw_win64cc: CC = CallingConv::Win64; break; + case lltok::kw_webkit_jscc: CC = CallingConv::WebKit_JS; break; +diff --git a/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp b/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp +index 0ff045fa787e8..175651949ef85 100644 +--- a/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp ++++ b/llvm-14.0.6.src/lib/CodeGen/ReplaceWithVeclib.cpp +@@ -157,7 +157,7 @@ static bool replaceWithCallToVeclib(const TargetLibraryInfo &TLI, + // and the exact vector width of the call operands in the + // TargetLibraryInfo. + const std::string TLIName = +- std::string(TLI.getVectorizedFunction(ScalarName, VF)); ++ std::string(TLI.getVectorizedFunction(ScalarName, VF, CI.getFastMathFlags().isFast())); + + LLVM_DEBUG(dbgs() << DEBUG_TYPE << ": Looking up TLI mapping for `" + << ScalarName << "` and vector width " << VF << ".\n"); +diff --git a/llvm-14.0.6.src/lib/IR/AsmWriter.cpp b/llvm-14.0.6.src/lib/IR/AsmWriter.cpp +index 179754e275b03..c4e95752c97e8 100644 +--- a/llvm-14.0.6.src/lib/IR/AsmWriter.cpp ++++ b/llvm-14.0.6.src/lib/IR/AsmWriter.cpp +@@ -306,6 +306,9 @@ static void PrintCallingConv(unsigned cc, raw_ostream &Out) { + case CallingConv::X86_RegCall: Out << "x86_regcallcc"; break; + case CallingConv::X86_VectorCall:Out << "x86_vectorcallcc"; break; + case CallingConv::Intel_OCL_BI: Out << "intel_ocl_bicc"; break; ++ case CallingConv::Intel_SVML128: Out << "intel_svmlcc128"; break; ++ case CallingConv::Intel_SVML256: Out << "intel_svmlcc256"; break; ++ case CallingConv::Intel_SVML512: Out << "intel_svmlcc512"; break; + case CallingConv::ARM_APCS: Out << "arm_apcscc"; break; + case CallingConv::ARM_AAPCS: Out << "arm_aapcscc"; break; + case CallingConv::ARM_AAPCS_VFP: Out << "arm_aapcs_vfpcc"; break; +diff --git a/llvm-14.0.6.src/lib/IR/Verifier.cpp b/llvm-14.0.6.src/lib/IR/Verifier.cpp +index 989d01e2e3950..bae7382a36e13 100644 +--- a/llvm-14.0.6.src/lib/IR/Verifier.cpp ++++ b/llvm-14.0.6.src/lib/IR/Verifier.cpp +@@ -2457,6 +2457,9 @@ void Verifier::visitFunction(const Function &F) { + case CallingConv::Fast: + case CallingConv::Cold: + case CallingConv::Intel_OCL_BI: ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: + case CallingConv::PTX_Kernel: + case CallingConv::PTX_Device: + Assert(!F.isVarArg(), "Calling convention does not support varargs or " +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td b/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td +index 4dd8a6cdd8982..12e65521215e4 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td ++++ b/llvm-14.0.6.src/lib/Target/X86/X86CallingConv.td +@@ -498,6 +498,21 @@ def RetCC_X86_64 : CallingConv<[ + CCDelegateTo + ]>; + ++// Intel_SVML return-value convention. ++def RetCC_Intel_SVML : CallingConv<[ ++ // Vector types are returned in XMM0,XMM1 ++ CCIfType<[v4f32, v2f64], ++ CCAssignToReg<[XMM0,XMM1]>>, ++ ++ // 256-bit FP vectors ++ CCIfType<[v8f32, v4f64], ++ CCAssignToReg<[YMM0,YMM1]>>, ++ ++ // 512-bit FP vectors ++ CCIfType<[v16f32, v8f64], ++ CCAssignToReg<[ZMM0,ZMM1]>> ++]>; ++ + // This is the return-value convention used for the entire X86 backend. + let Entry = 1 in + def RetCC_X86 : CallingConv<[ +@@ -505,6 +520,10 @@ def RetCC_X86 : CallingConv<[ + // Check if this is the Intel OpenCL built-ins calling convention + CCIfCC<"CallingConv::Intel_OCL_BI", CCDelegateTo>, + ++ CCIfCC<"CallingConv::Intel_SVML128", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML256", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML512", CCDelegateTo>, ++ + CCIfSubtarget<"is64Bit()", CCDelegateTo>, + CCDelegateTo + ]>; +@@ -1064,6 +1083,30 @@ def CC_Intel_OCL_BI : CallingConv<[ + CCDelegateTo + ]>; + ++// X86-64 Intel Short Vector Math Library calling convention. ++def CC_Intel_SVML : CallingConv<[ ++ ++ // The SSE vector arguments are passed in XMM registers. ++ CCIfType<[v4f32, v2f64], ++ CCAssignToReg<[XMM0, XMM1, XMM2]>>, ++ ++ // The 256-bit vector arguments are passed in YMM registers. ++ CCIfType<[v8f32, v4f64], ++ CCAssignToReg<[YMM0, YMM1, YMM2]>>, ++ ++ // The 512-bit vector arguments are passed in ZMM registers. ++ CCIfType<[v16f32, v8f64], ++ CCAssignToReg<[ZMM0, ZMM1, ZMM2]>> ++]>; ++ ++def CC_X86_32_Intr : CallingConv<[ ++ CCAssignToStack<4, 4> ++]>; ++ ++def CC_X86_64_Intr : CallingConv<[ ++ CCAssignToStack<8, 8> ++]>; ++ + //===----------------------------------------------------------------------===// + // X86 Root Argument Calling Conventions + //===----------------------------------------------------------------------===// +@@ -1115,6 +1158,9 @@ def CC_X86_64 : CallingConv<[ + let Entry = 1 in + def CC_X86 : CallingConv<[ + CCIfCC<"CallingConv::Intel_OCL_BI", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML128", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML256", CCDelegateTo>, ++ CCIfCC<"CallingConv::Intel_SVML512", CCDelegateTo>, + CCIfSubtarget<"is64Bit()", CCDelegateTo>, + CCDelegateTo + ]>; +@@ -1227,3 +1273,27 @@ def CSR_SysV64_RegCall_NoSSE : CalleeSavedRegs<(add RBX, RBP, + (sequence "R%u", 12, 15))>; + def CSR_SysV64_RegCall : CalleeSavedRegs<(add CSR_SysV64_RegCall_NoSSE, + (sequence "XMM%u", 8, 15))>; ++ ++// SVML calling convention ++def CSR_32_Intel_SVML : CalleeSavedRegs<(add CSR_32_RegCall_NoSSE)>; ++def CSR_32_Intel_SVML_AVX512 : CalleeSavedRegs<(add CSR_32_Intel_SVML, ++ K4, K5, K6, K7)>; ++ ++def CSR_64_Intel_SVML_NoSSE : CalleeSavedRegs<(add RBX, RSI, RDI, RBP, RSP, R12, R13, R14, R15)>; ++ ++def CSR_64_Intel_SVML : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "XMM%u", 8, 15))>; ++def CSR_Win64_Intel_SVML : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "XMM%u", 6, 15))>; ++ ++def CSR_64_Intel_SVML_AVX : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "YMM%u", 8, 15))>; ++def CSR_Win64_Intel_SVML_AVX : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "YMM%u", 6, 15))>; ++ ++def CSR_64_Intel_SVML_AVX512 : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "ZMM%u", 16, 31), ++ K4, K5, K6, K7)>; ++def CSR_Win64_Intel_SVML_AVX512 : CalleeSavedRegs<(add CSR_64_Intel_SVML_NoSSE, ++ (sequence "ZMM%u", 6, 21), ++ K4, K5, K6, K7)>; +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp b/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp +index 8bb7e81e19bbd..1780ce3fc6467 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp ++++ b/llvm-14.0.6.src/lib/Target/X86/X86ISelLowering.cpp +@@ -3788,7 +3788,8 @@ void VarArgsLoweringHelper::forwardMustTailParameters(SDValue &Chain) { + // FIXME: Only some x86_32 calling conventions support AVX512. + if (Subtarget.useAVX512Regs() && + (is64Bit() || (CallConv == CallingConv::X86_VectorCall || +- CallConv == CallingConv::Intel_OCL_BI))) ++ CallConv == CallingConv::Intel_OCL_BI || ++ CallConv == CallingConv::Intel_SVML512))) + VecVT = MVT::v16f32; + else if (Subtarget.hasAVX()) + VecVT = MVT::v8f32; +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp b/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp +index 130cb61cdde24..9eec3b25ca9f2 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp ++++ b/llvm-14.0.6.src/lib/Target/X86/X86RegisterInfo.cpp +@@ -272,6 +272,42 @@ X86RegisterInfo::getRegPressureLimit(const TargetRegisterClass *RC, + } + } + ++namespace { ++std::pair getSVMLRegMaskAndSaveList( ++ bool Is64Bit, bool IsWin64, CallingConv::ID CC) { ++ assert(CC >= CallingConv::Intel_SVML128 && CC <= CallingConv::Intel_SVML512); ++ unsigned Abi = CC - CallingConv::Intel_SVML128 ; // 0 - 128, 1 - 256, 2 - 512 ++ ++ const std::pair Abi64[] = { ++ std::make_pair(CSR_64_Intel_SVML_RegMask, CSR_64_Intel_SVML_SaveList), ++ std::make_pair(CSR_64_Intel_SVML_AVX_RegMask, CSR_64_Intel_SVML_AVX_SaveList), ++ std::make_pair(CSR_64_Intel_SVML_AVX512_RegMask, CSR_64_Intel_SVML_AVX512_SaveList), ++ }; ++ ++ const std::pair AbiWin64[] = { ++ std::make_pair(CSR_Win64_Intel_SVML_RegMask, CSR_Win64_Intel_SVML_SaveList), ++ std::make_pair(CSR_Win64_Intel_SVML_AVX_RegMask, CSR_Win64_Intel_SVML_AVX_SaveList), ++ std::make_pair(CSR_Win64_Intel_SVML_AVX512_RegMask, CSR_Win64_Intel_SVML_AVX512_SaveList), ++ }; ++ ++ const std::pair Abi32[] = { ++ std::make_pair(CSR_32_Intel_SVML_RegMask, CSR_32_Intel_SVML_SaveList), ++ std::make_pair(CSR_32_Intel_SVML_RegMask, CSR_32_Intel_SVML_SaveList), ++ std::make_pair(CSR_32_Intel_SVML_AVX512_RegMask, CSR_32_Intel_SVML_AVX512_SaveList), ++ }; ++ ++ if (Is64Bit) { ++ if (IsWin64) { ++ return AbiWin64[Abi]; ++ } else { ++ return Abi64[Abi]; ++ } ++ } else { ++ return Abi32[Abi]; ++ } ++} ++} ++ + const MCPhysReg * + X86RegisterInfo::getCalleeSavedRegs(const MachineFunction *MF) const { + assert(MF && "MachineFunction required"); +@@ -327,6 +363,11 @@ X86RegisterInfo::getCalleeSavedRegs(const MachineFunction *MF) const { + return CSR_64_Intel_OCL_BI_SaveList; + break; + } ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: { ++ return getSVMLRegMaskAndSaveList(Is64Bit, IsWin64, CC).second; ++ } + case CallingConv::HHVM: + return CSR_64_HHVM_SaveList; + case CallingConv::X86_RegCall: +@@ -449,6 +490,11 @@ X86RegisterInfo::getCallPreservedMask(const MachineFunction &MF, + return CSR_64_Intel_OCL_BI_RegMask; + break; + } ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: { ++ return getSVMLRegMaskAndSaveList(Is64Bit, IsWin64, CC).first; ++ } + case CallingConv::HHVM: + return CSR_64_HHVM_RegMask; + case CallingConv::X86_RegCall: +diff --git a/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h b/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h +index 5d773f0c57dfb..6bdf5bc6f3fe9 100644 +--- a/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h ++++ b/llvm-14.0.6.src/lib/Target/X86/X86Subtarget.h +@@ -916,6 +916,9 @@ class X86Subtarget final : public X86GenSubtargetInfo { + case CallingConv::X86_ThisCall: + case CallingConv::X86_VectorCall: + case CallingConv::Intel_OCL_BI: ++ case CallingConv::Intel_SVML128: ++ case CallingConv::Intel_SVML256: ++ case CallingConv::Intel_SVML512: + return isTargetWin64(); + // This convention allows using the Win64 convention on other targets. + case CallingConv::Win64: +diff --git a/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp b/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp +index 047bf5569ded3..59897785f156c 100644 +--- a/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp ++++ b/llvm-14.0.6.src/lib/Transforms/Utils/InjectTLIMappings.cpp +@@ -92,7 +92,7 @@ static void addMappingsFromTLI(const TargetLibraryInfo &TLI, CallInst &CI) { + + auto AddVariantDecl = [&](const ElementCount &VF) { + const std::string TLIName = +- std::string(TLI.getVectorizedFunction(ScalarName, VF)); ++ std::string(TLI.getVectorizedFunction(ScalarName, VF, CI.getFastMathFlags().isFast())); + if (!TLIName.empty()) { + std::string MangledName = + VFABI::mangleTLIVectorName(TLIName, ScalarName, CI.arg_size(), VF); +diff --git a/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp b/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp +index 46ff0994e04e7..f472af5e1a835 100644 +--- a/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp ++++ b/llvm-14.0.6.src/lib/Transforms/Vectorize/LoopVectorize.cpp +@@ -712,6 +712,27 @@ class InnerLoopVectorizer { + virtual void printDebugTracesAtStart(){}; + virtual void printDebugTracesAtEnd(){}; + ++ /// Check legality of given SVML call instruction \p VecCall generated for ++ /// scalar call \p Call. If illegal then the appropriate legal instruction ++ /// is returned. ++ Value *legalizeSVMLCall(CallInst *VecCall, CallInst *Call); ++ ++ /// Returns the legal VF for a call instruction \p CI using TTI information ++ /// and vector type. ++ ElementCount getLegalVFForCall(CallInst *CI); ++ ++ /// Partially vectorize a given call \p Call by breaking it down into multiple ++ /// calls of \p LegalCall, decided by the variant VF \p LegalVF. ++ Value *partialVectorizeCall(CallInst *Call, CallInst *LegalCall, ++ unsigned LegalVF); ++ ++ /// Generate shufflevector instruction for a vector value \p V based on the ++ /// current \p Part and a smaller VF \p LegalVF. ++ Value *generateShuffleValue(Value *V, unsigned LegalVF, unsigned Part); ++ ++ /// Combine partially vectorized calls stored in \p CallResults. ++ Value *combinePartialVecCalls(SmallVectorImpl &CallResults); ++ + /// The original loop. + Loop *OrigLoop; + +@@ -4596,6 +4617,17 @@ static bool mayDivideByZero(Instruction &I) { + return !CInt || CInt->isZero(); + } + ++static void setVectorFunctionCallingConv(CallInst &CI, const DataLayout &DL, ++ const TargetLibraryInfo &TLI) { ++ Function *VectorF = CI.getCalledFunction(); ++ FunctionType *FTy = VectorF->getFunctionType(); ++ StringRef VFName = VectorF->getName(); ++ auto CC = TLI.getVectorizedFunctionCallingConv(VFName, *FTy, DL); ++ if (CC) { ++ CI.setCallingConv(*CC); ++ } ++} ++ + void InnerLoopVectorizer::widenCallInstruction(CallInst &I, VPValue *Def, + VPUser &ArgOperands, + VPTransformState &State) { +@@ -4664,9 +4696,246 @@ void InnerLoopVectorizer::widenCallInstruction(CallInst &I, VPValue *Def, + if (isa(V)) + V->copyFastMathFlags(CI); + ++ const DataLayout &DL = V->getModule()->getDataLayout(); ++ setVectorFunctionCallingConv(*V, DL, *TLI); ++ ++ // Perform legalization of SVML call instruction only if original call ++ // was not Intrinsic ++ if (!UseVectorIntrinsic && ++ (V->getCalledFunction()->getName()).startswith("__svml")) { ++ // assert((V->getCalledFunction()->getName()).startswith("__svml")); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Vector call inst:"; V->dump()); ++ auto *LegalV = cast(legalizeSVMLCall(V, CI)); ++ LLVM_DEBUG(dbgs() << "LV: Completed SVML legalization.\n LegalV: "; ++ LegalV->dump()); ++ State.set(Def, LegalV, Part); ++ addMetadata(LegalV, &I); ++ } else { + State.set(Def, V, Part); + addMetadata(V, &I); ++ } ++ } ++} ++ ++//===----------------------------------------------------------------------===// ++// Implementation of functions for SVML vector call legalization. ++//===----------------------------------------------------------------------===// ++// ++// Unlike other VECLIBs, SVML needs to be used with target-legal ++// vector types. Otherwise, link failures and/or runtime failures ++// will occur. A motivating example could be - ++// ++// double *a; ++// float *b; ++// #pragma clang loop vectorize_width(8) ++// for(i = 0; i < N; ++i) { ++// a[i] = sin(i); // Legal SVML VF must be 4 or below on AVX ++// b[i] = cosf(i); // VF can be 8 on AVX since 8 floats can fit in YMM ++// } ++// ++// Current implementation of vector code generation in LV is ++// driven based on a single VF (in InnerLoopVectorizer::VF). This ++// inhibits the flexibility of adjusting/choosing different VF ++// for different instructions. ++// ++// Due to this limitation it is much more straightforward to ++// first generate the illegal sin8 (svml_sin8 for SVML vector ++// library) call and then legalize it than trying to avoid ++// generating illegal code from the beginning. ++// ++// A solution for this problem is to check legality of the ++// call instruction right after generating it in vectorizer and ++// if it is illegal we split the call arguments and issue multiple ++// calls to match the legal VF. This is demonstrated currently for ++// the SVML vector library calls (non-intrinsic version only). ++// ++// Future directions and extensions: ++// 1) This legalization example shows us that a good direction ++// for the VPlan framework would be to model the vector call ++// instructions in a way that legal VF for each call is chosen ++// correctly within vectorizer and illegal code generation is ++// avoided. ++// 2) This logic can also be extended to general vector functions ++// i.e. legalization OpenMP decalre simd functions. The ++// requirements needed for this will be documented soon. ++ ++Value *InnerLoopVectorizer::legalizeSVMLCall(CallInst *VecCall, ++ CallInst *Call) { ++ ElementCount LegalVF = getLegalVFForCall(VecCall); ++ ++ assert(LegalVF.getKnownMinValue() > 1 && ++ "Legal VF for SVML call must be greater than 1 to vectorize"); ++ ++ if (LegalVF == VF) ++ return VecCall; ++ else if (LegalVF.getKnownMinValue() > VF.getKnownMinValue()) ++ // TODO: handle case when we are underfilling vectors ++ return VecCall; ++ ++ // Legal VF for this SVML call is smaller than chosen VF, break it down into ++ // smaller call instructions ++ ++ // Convert args, types and return type to match legal VF ++ SmallVector NewTys; ++ SmallVector NewArgs; ++ ++ for (Value *ArgOperand : Call->args()) { ++ Type *Ty = ToVectorTy(ArgOperand->getType(), LegalVF); ++ NewTys.push_back(Ty); ++ NewArgs.push_back(UndefValue::get(Ty)); + } ++ ++ // Construct legal vector function ++ const VFShape Shape = ++ VFShape::get(*Call, LegalVF /*EC*/, false /*HasGlobalPred*/); ++ Function *LegalVectorF = VFDatabase(*Call).getVectorizedFunction(Shape); ++ assert(LegalVectorF != nullptr && "Can't create legal vector function."); ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): LegalVectorF: "; LegalVectorF->dump()); ++ ++ SmallVector OpBundles; ++ Call->getOperandBundlesAsDefs(OpBundles); ++ auto LegalV = std::unique_ptr(CallInst::Create(LegalVectorF, NewArgs, OpBundles)); ++ ++ if (isa(LegalV)) ++ LegalV->copyFastMathFlags(Call); ++ ++ const DataLayout &DL = VecCall->getModule()->getDataLayout(); ++ // Set SVML calling conventions ++ setVectorFunctionCallingConv(*LegalV, DL, *TLI); ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): LegalV: "; LegalV->dump()); ++ ++ Value *LegalizedCall = partialVectorizeCall(VecCall, LegalV.get(), LegalVF.getKnownMinValue()); ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): LegalizedCall: "; LegalizedCall->dump()); ++ ++ // Remove the illegal call from Builder ++ VecCall->eraseFromParent(); ++ ++ return LegalizedCall; ++} ++ ++ElementCount InnerLoopVectorizer::getLegalVFForCall(CallInst *CI) { ++ const DataLayout DL = CI->getModule()->getDataLayout(); ++ FunctionType *CallFT = CI->getFunctionType(); ++ // All functions that need legalization should have a vector return type. ++ // This is true for all SVML functions that are currently supported. ++ assert(isa(CallFT->getReturnType()) && ++ "Return type of call that needs legalization is not a vector."); ++ auto *VecCallRetType = cast(CallFT->getReturnType()); ++ Type *ElemType = VecCallRetType->getElementType(); ++ ++ unsigned TypeBitWidth = DL.getTypeSizeInBits(ElemType); ++ unsigned VectorBitWidth = TTI->getRegisterBitWidth(TargetTransformInfo::RGK_FixedWidthVector); ++ unsigned LegalVF = VectorBitWidth / TypeBitWidth; ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): Type Bit Width: " << TypeBitWidth << "\n"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Current VL: " << VF << "\n"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Vector Bit Width: " << VectorBitWidth ++ << "\n"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): Legal Target VL: " << LegalVF << "\n"); ++ ++ return ElementCount::getFixed(LegalVF); ++} ++ ++// Partial vectorization of a call instruction is achieved by making clones of ++// \p LegalCall and overwriting its argument operands with shufflevector ++// equivalent decided based on \p LegalVF and current Part being filled. ++Value *InnerLoopVectorizer::partialVectorizeCall(CallInst *Call, ++ CallInst *LegalCall, ++ unsigned LegalVF) { ++ unsigned NumParts = VF.getKnownMinValue() / LegalVF; ++ LLVM_DEBUG(dbgs() << "LV(SVML): NumParts: " << NumParts << "\n"); ++ SmallVector CallResults; ++ ++ for (unsigned Part = 0; Part < NumParts; ++Part) { ++ auto *ClonedCall = cast(LegalCall->clone()); ++ ++ // Update the arg operand of cloned call to shufflevector ++ for (unsigned i = 0, ie = Call->arg_size(); i != ie; ++i) { ++ auto *NewOp = generateShuffleValue(Call->getArgOperand(i), LegalVF, Part); ++ ClonedCall->setArgOperand(i, NewOp); ++ } ++ ++ LLVM_DEBUG(dbgs() << "LV(SVML): ClonedCall: "; ClonedCall->dump()); ++ ++ auto *PartialVecCall = Builder.Insert(ClonedCall); ++ CallResults.push_back(PartialVecCall); ++ } ++ ++ return combinePartialVecCalls(CallResults); ++} ++ ++Value *InnerLoopVectorizer::generateShuffleValue(Value *V, unsigned LegalVF, ++ unsigned Part) { ++ // Example: ++ // Consider the following vector code - ++ // %1 = sitofp <4 x i32> %0 to <4 x double> ++ // %2 = call <4 x double> @__svml_sin4(<4 x double> %1) ++ // ++ // If the LegalVF is 2, we partially vectorize the sin4 call by invoking ++ // generateShuffleValue on the operand %1 ++ // If Part = 1, output value is - ++ // %shuffle = shufflevector <4 x double> %1, <4 x double> undef, <2 x i32> ++ // and if Part = 2, output is - ++ // %shuffle7 =shufflevector <4 x double> %1, <4 x double> undef, <2 x i32> ++ ++ assert(isa(V->getType()) && ++ "Cannot generate shuffles for non-vector values."); ++ SmallVector ShuffleMask; ++ Value *Undef = UndefValue::get(V->getType()); ++ ++ unsigned ElemIdx = Part * LegalVF; ++ ++ for (unsigned K = 0; K < LegalVF; K++) ++ ShuffleMask.push_back(static_cast(ElemIdx + K)); ++ ++ auto *ShuffleInst = ++ Builder.CreateShuffleVector(V, Undef, ShuffleMask, "shuffle"); ++ ++ return ShuffleInst; ++} ++ ++// Results of the calls executed by smaller legal call instructions must be ++// combined to match the original VF for later use. This is done by constructing ++// shufflevector instructions in a cumulative fashion. ++Value *InnerLoopVectorizer::combinePartialVecCalls( ++ SmallVectorImpl &CallResults) { ++ assert(isa(CallResults[0]->getType()) && ++ "Cannot combine calls with non-vector results."); ++ auto *CallType = cast(CallResults[0]->getType()); ++ ++ Value *CombinedShuffle; ++ unsigned NumElems = CallType->getElementCount().getKnownMinValue() * 2; ++ unsigned NumRegs = CallResults.size(); ++ ++ assert(NumRegs >= 2 && isPowerOf2_32(NumRegs) && ++ "Number of partial vector calls to combine must be a power of 2 " ++ "(atleast 2^1)"); ++ ++ while (NumRegs > 1) { ++ for (unsigned I = 0; I < NumRegs; I += 2) { ++ SmallVector ShuffleMask; ++ for (unsigned J = 0; J < NumElems; J++) ++ ShuffleMask.push_back(static_cast(J)); ++ ++ CombinedShuffle = Builder.CreateShuffleVector( ++ CallResults[I], CallResults[I + 1], ShuffleMask, "combined"); ++ LLVM_DEBUG(dbgs() << "LV(SVML): CombinedShuffle:"; ++ CombinedShuffle->dump()); ++ CallResults.push_back(CombinedShuffle); ++ } ++ ++ SmallVector::iterator Start = CallResults.begin(); ++ SmallVector::iterator End = Start + NumRegs; ++ CallResults.erase(Start, End); ++ ++ NumElems *= 2; ++ NumRegs /= 2; ++ } ++ ++ return CombinedShuffle; + } + + void LoopVectorizationCostModel::collectLoopScalars(ElementCount VF) { +diff --git a/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp b/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp +index 644372483edde..342f018b92184 100644 +--- a/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp ++++ b/llvm-14.0.6.src/lib/Transforms/Vectorize/SLPVectorizer.cpp +@@ -6322,6 +6322,17 @@ Value *BoUpSLP::vectorizeTree(ArrayRef VL) { + return Vec; + } + ++static void setVectorFunctionCallingConv(CallInst &CI, const DataLayout &DL, ++ const TargetLibraryInfo &TLI) { ++ Function *VectorF = CI.getCalledFunction(); ++ FunctionType *FTy = VectorF->getFunctionType(); ++ StringRef VFName = VectorF->getName(); ++ auto CC = TLI.getVectorizedFunctionCallingConv(VFName, *FTy, DL); ++ if (CC) { ++ CI.setCallingConv(*CC); ++ } ++} ++ + Value *BoUpSLP::vectorizeTree(TreeEntry *E) { + IRBuilder<>::InsertPointGuard Guard(Builder); + +@@ -6794,7 +6805,12 @@ Value *BoUpSLP::vectorizeTree(TreeEntry *E) { + + SmallVector OpBundles; + CI->getOperandBundlesAsDefs(OpBundles); +- Value *V = Builder.CreateCall(CF, OpVecs, OpBundles); ++ ++ CallInst *NewCall = Builder.CreateCall(CF, OpVecs, OpBundles); ++ const DataLayout &DL = NewCall->getModule()->getDataLayout(); ++ setVectorFunctionCallingConv(*NewCall, DL, *TLI); ++ ++ Value *V = NewCall; + + // The scalar argument uses an in-tree scalar so we add the new vectorized + // call to ExternalUses list to make sure that an extract will be +diff --git a/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll b/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll +index df8b7c498bd00..63a36549f18fd 100644 +--- a/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll ++++ b/llvm-14.0.6.src/test/CodeGen/Generic/replace-intrinsics-with-veclib.ll +@@ -10,7 +10,7 @@ target triple = "x86_64-unknown-linux-gnu" + define <4 x double> @exp_v4(<4 x double> %in) { + ; SVML-LABEL: define {{[^@]+}}@exp_v4 + ; SVML-SAME: (<4 x double> [[IN:%.*]]) { +-; SVML-NEXT: [[TMP1:%.*]] = call <4 x double> @__svml_exp4(<4 x double> [[IN]]) ++; SVML-NEXT: [[TMP1:%.*]] = call <4 x double> @__svml_exp4_ha(<4 x double> [[IN]]) + ; SVML-NEXT: ret <4 x double> [[TMP1]] + ; + ; LIBMVEC-X86-LABEL: define {{[^@]+}}@exp_v4 +@@ -37,7 +37,7 @@ declare <4 x double> @llvm.exp.v4f64(<4 x double>) #0 + define <4 x float> @exp_f32(<4 x float> %in) { + ; SVML-LABEL: define {{[^@]+}}@exp_f32 + ; SVML-SAME: (<4 x float> [[IN:%.*]]) { +-; SVML-NEXT: [[TMP1:%.*]] = call <4 x float> @__svml_expf4(<4 x float> [[IN]]) ++; SVML-NEXT: [[TMP1:%.*]] = call <4 x float> @__svml_expf4_ha(<4 x float> [[IN]]) + ; SVML-NEXT: ret <4 x float> [[TMP1]] + ; + ; LIBMVEC-X86-LABEL: define {{[^@]+}}@exp_f32 +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll +index a6e191c3d6923..d6e2e11106949 100644 +--- a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls-finite.ll +@@ -39,7 +39,8 @@ for.end: ; preds = %for.body + declare double @__exp_finite(double) #0 + + ; CHECK-LABEL: @exp_f64 +-; CHECK: <4 x double> @__svml_exp4 ++; CHECK: <2 x double> @__svml_exp2 ++; CHECK: <2 x double> @__svml_exp2 + ; CHECK: ret + define void @exp_f64(double* nocapture %varray) { + entry: +@@ -99,7 +100,8 @@ for.end: ; preds = %for.body + declare double @__log_finite(double) #0 + + ; CHECK-LABEL: @log_f64 +-; CHECK: <4 x double> @__svml_log4 ++; CHECK: <2 x double> @__svml_log2 ++; CHECK: <2 x double> @__svml_log2 + ; CHECK: ret + define void @log_f64(double* nocapture %varray) { + entry: +@@ -159,7 +161,8 @@ for.end: ; preds = %for.body + declare double @__pow_finite(double, double) #0 + + ; CHECK-LABEL: @pow_f64 +-; CHECK: <4 x double> @__svml_pow4 ++; CHECK: <2 x double> @__svml_pow2 ++; CHECK: <2 x double> @__svml_pow2 + ; CHECK: ret + define void @pow_f64(double* nocapture %varray, double* nocapture readonly %exp) { + entry: +@@ -190,7 +193,8 @@ declare float @__exp2f_finite(float) #0 + + define void @exp2f_finite(float* nocapture %varray) { + ; CHECK-LABEL: @exp2f_finite( +-; CHECK: call <4 x float> @__svml_exp2f4(<4 x float> %{{.*}}) ++; CHECK: call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> %{{.*}}) ++; CHECK: call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> %{{.*}}) + ; CHECK: ret void + ; + entry: +@@ -219,7 +223,8 @@ declare double @__exp2_finite(double) #0 + + define void @exp2_finite(double* nocapture %varray) { + ; CHECK-LABEL: @exp2_finite( +-; CHECK: call <4 x double> @__svml_exp24(<4 x double> {{.*}}) ++; CHECK: call intel_svmlcc128 <2 x double> @__svml_exp22_ha(<2 x double> {{.*}}) ++; CHECK: call intel_svmlcc128 <2 x double> @__svml_exp22_ha(<2 x double> {{.*}}) + ; CHECK: ret void + ; + entry: +@@ -276,7 +281,8 @@ for.end: ; preds = %for.body + declare double @__log2_finite(double) #0 + + ; CHECK-LABEL: @log2_f64 +-; CHECK: <4 x double> @__svml_log24 ++; CHECK: <2 x double> @__svml_log22 ++; CHECK: <2 x double> @__svml_log22 + ; CHECK: ret + define void @log2_f64(double* nocapture %varray) { + entry: +@@ -333,7 +339,8 @@ for.end: ; preds = %for.body + declare double @__log10_finite(double) #0 + + ; CHECK-LABEL: @log10_f64 +-; CHECK: <4 x double> @__svml_log104 ++; CHECK: <2 x double> @__svml_log102 ++; CHECK: <2 x double> @__svml_log102 + ; CHECK: ret + define void @log10_f64(double* nocapture %varray) { + entry: +@@ -390,7 +397,8 @@ for.end: ; preds = %for.body + declare double @__sqrt_finite(double) #0 + + ; CHECK-LABEL: @sqrt_f64 +-; CHECK: <4 x double> @__svml_sqrt4 ++; CHECK: <2 x double> @__svml_sqrt2 ++; CHECK: <2 x double> @__svml_sqrt2 + ; CHECK: ret + define void @sqrt_f64(double* nocapture %varray) { + entry: +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll +index 42c280df6ad02..088bbdcf1aa4a 100644 +--- a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-calls.ll +@@ -48,7 +48,7 @@ declare float @llvm.exp2.f32(float) #0 + + define void @sin_f64(double* nocapture %varray) { + ; CHECK-LABEL: @sin_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_sin4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -71,7 +71,7 @@ for.end: + + define void @sin_f32(float* nocapture %varray) { + ; CHECK-LABEL: @sin_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_sinf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_sinf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -94,7 +94,7 @@ for.end: + + define void @sin_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @sin_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_sin4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -117,7 +117,7 @@ for.end: + + define void @sin_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @sin_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_sinf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_sinf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -140,7 +140,7 @@ for.end: + + define void @cos_f64(double* nocapture %varray) { + ; CHECK-LABEL: @cos_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_cos4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -163,7 +163,7 @@ for.end: + + define void @cos_f32(float* nocapture %varray) { + ; CHECK-LABEL: @cos_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_cosf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_cosf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -186,7 +186,7 @@ for.end: + + define void @cos_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @cos_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_cos4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -209,7 +209,7 @@ for.end: + + define void @cos_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @cos_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_cosf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_cosf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -232,7 +232,7 @@ for.end: + + define void @pow_f64(double* nocapture %varray, double* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f64( +-; CHECK: [[TMP8:%.*]] = call <4 x double> @__svml_pow4(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -257,7 +257,7 @@ for.end: + + define void @pow_f64_intrinsic(double* nocapture %varray, double* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f64_intrinsic( +-; CHECK: [[TMP8:%.*]] = call <4 x double> @__svml_pow4(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP4:%.*]], <4 x double> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -282,7 +282,7 @@ for.end: + + define void @pow_f32(float* nocapture %varray, float* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f32( +-; CHECK: [[TMP8:%.*]] = call <4 x float> @__svml_powf4(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc128 <4 x float> @__svml_powf4_ha(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -307,7 +307,7 @@ for.end: + + define void @pow_f32_intrinsic(float* nocapture %varray, float* nocapture readonly %exp) { + ; CHECK-LABEL: @pow_f32_intrinsic( +-; CHECK: [[TMP8:%.*]] = call <4 x float> @__svml_powf4(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) ++; CHECK: [[TMP8:%.*]] = call intel_svmlcc128 <4 x float> @__svml_powf4_ha(<4 x float> [[TMP4:%.*]], <4 x float> [[WIDE_LOAD:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -332,7 +332,7 @@ for.end: + + define void @exp_f64(double* nocapture %varray) { + ; CHECK-LABEL: @exp_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -355,7 +355,7 @@ for.end: + + define void @exp_f32(float* nocapture %varray) { + ; CHECK-LABEL: @exp_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_expf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_expf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -378,7 +378,7 @@ for.end: + + define void @exp_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @exp_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -401,7 +401,7 @@ for.end: + + define void @exp_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @exp_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_expf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_expf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -424,7 +424,7 @@ for.end: + + define void @log_f64(double* nocapture %varray) { + ; CHECK-LABEL: @log_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -447,7 +447,7 @@ for.end: + + define void @log_f32(float* nocapture %varray) { + ; CHECK-LABEL: @log_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_logf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_logf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -470,7 +470,7 @@ for.end: + + define void @log_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @log_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -493,7 +493,7 @@ for.end: + + define void @log_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @log_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_logf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_logf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -516,7 +516,7 @@ for.end: + + define void @log2_f64(double* nocapture %varray) { + ; CHECK-LABEL: @log2_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -539,7 +539,7 @@ for.end: + + define void @log2_f32(float* nocapture %varray) { + ; CHECK-LABEL: @log2_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -562,7 +562,7 @@ for.end: + + define void @log2_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @log2_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -585,7 +585,7 @@ for.end: + + define void @log2_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @log2_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -608,7 +608,7 @@ for.end: + + define void @log10_f64(double* nocapture %varray) { + ; CHECK-LABEL: @log10_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log104(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log104_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -631,7 +631,7 @@ for.end: + + define void @log10_f32(float* nocapture %varray) { + ; CHECK-LABEL: @log10_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log10f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log10f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -654,7 +654,7 @@ for.end: + + define void @log10_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @log10_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_log104(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log104_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -677,7 +677,7 @@ for.end: + + define void @log10_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @log10_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_log10f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_log10f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -700,7 +700,7 @@ for.end: + + define void @sqrt_f64(double* nocapture %varray) { + ; CHECK-LABEL: @sqrt_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_sqrt4(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sqrt4_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -723,7 +723,7 @@ for.end: + + define void @sqrt_f32(float* nocapture %varray) { + ; CHECK-LABEL: @sqrt_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_sqrtf4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_sqrtf4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -746,7 +746,7 @@ for.end: + + define void @exp2_f64(double* nocapture %varray) { + ; CHECK-LABEL: @exp2_f64( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -769,7 +769,7 @@ for.end: + + define void @exp2_f32(float* nocapture %varray) { + ; CHECK-LABEL: @exp2_f32( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_exp2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -792,7 +792,7 @@ for.end: + + define void @exp2_f64_intrinsic(double* nocapture %varray) { + ; CHECK-LABEL: @exp2_f64_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x double> @__svml_exp24(<4 x double> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp24_ha(<4 x double> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -815,7 +815,7 @@ for.end: + + define void @exp2_f32_intrinsic(float* nocapture %varray) { + ; CHECK-LABEL: @exp2_f32_intrinsic( +-; CHECK: [[TMP5:%.*]] = call <4 x float> @__svml_exp2f4(<4 x float> [[TMP4:%.*]]) ++; CHECK: [[TMP5:%.*]] = call intel_svmlcc128 <4 x float> @__svml_exp2f4_ha(<4 x float> [[TMP4:%.*]]) + ; CHECK: ret void + ; + entry: +@@ -836,4 +836,44 @@ for.end: + ret void + } + ++; CHECK-LABEL: @atan2_finite ++; CHECK: intel_svmlcc256 <4 x double> @__svml_atan24( ++; CHECK: intel_svmlcc256 <4 x double> @__svml_atan24( ++; CHECK: ret ++ ++declare double @__atan2_finite(double, double) local_unnamed_addr #0 ++ ++define void @atan2_finite([100 x double]* nocapture %varray) local_unnamed_addr #0 { ++entry: ++ br label %for.cond1.preheader ++ ++for.cond1.preheader: ; preds = %for.inc7, %entry ++ %indvars.iv19 = phi i64 [ 0, %entry ], [ %indvars.iv.next20, %for.inc7 ] ++ %0 = trunc i64 %indvars.iv19 to i32 ++ %conv = sitofp i32 %0 to double ++ br label %for.body3 ++ ++for.body3: ; preds = %for.body3, %for.cond1.preheader ++ %indvars.iv = phi i64 [ 0, %for.cond1.preheader ], [ %indvars.iv.next, %for.body3 ] ++ %indvars.iv.next = add nuw nsw i64 %indvars.iv, 1 ++ %1 = trunc i64 %indvars.iv.next to i32 ++ %conv4 = sitofp i32 %1 to double ++ %call = tail call fast double @__atan2_finite(double %conv, double %conv4) ++ %arrayidx6 = getelementptr inbounds [100 x double], [100 x double]* %varray, i64 %indvars.iv19, i64 %indvars.iv ++ store double %call, double* %arrayidx6, align 8 ++ %exitcond = icmp eq i64 %indvars.iv.next, 100 ++ br i1 %exitcond, label %for.inc7, label %for.body3, !llvm.loop !5 ++ ++for.inc7: ; preds = %for.body3 ++ %indvars.iv.next20 = add nuw nsw i64 %indvars.iv19, 1 ++ %exitcond21 = icmp eq i64 %indvars.iv.next20, 100 ++ br i1 %exitcond21, label %for.end9, label %for.cond1.preheader ++ ++for.end9: ; preds = %for.inc7 ++ ret void ++} ++ + attributes #0 = { nounwind readnone } ++!5 = distinct !{!5, !6, !7} ++!6 = !{!"llvm.loop.vectorize.width", i32 8} ++!7 = !{!"llvm.loop.vectorize.enable", i1 true} +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-calls.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-calls.ll +new file mode 100644 +index 0000000000000..326c763994343 +--- /dev/null ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-calls.ll +@@ -0,0 +1,513 @@ ++; Check legalization of SVML calls, including intrinsic versions (like @llvm..). ++ ++; RUN: opt -vector-library=SVML -inject-tli-mappings -loop-vectorize -force-vector-width=8 -force-vector-interleave=1 -mattr=avx -S < %s | FileCheck %s ++ ++target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128" ++target triple = "x86_64-unknown-linux-gnu" ++ ++declare double @sin(double) #0 ++declare float @sinf(float) #0 ++declare double @llvm.sin.f64(double) #0 ++declare float @llvm.sin.f32(float) #0 ++ ++declare double @cos(double) #0 ++declare float @cosf(float) #0 ++declare double @llvm.cos.f64(double) #0 ++declare float @llvm.cos.f32(float) #0 ++ ++declare double @pow(double, double) #0 ++declare float @powf(float, float) #0 ++declare double @llvm.pow.f64(double, double) #0 ++declare float @llvm.pow.f32(float, float) #0 ++ ++declare double @exp(double) #0 ++declare float @expf(float) #0 ++declare double @llvm.exp.f64(double) #0 ++declare float @llvm.exp.f32(float) #0 ++ ++declare double @log(double) #0 ++declare float @logf(float) #0 ++declare double @llvm.log.f64(double) #0 ++declare float @llvm.log.f32(float) #0 ++ ++ ++define void @sin_f64(double* nocapture %varray) { ++; CHECK-LABEL: @sin_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @sin(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @sin_f32(float* nocapture %varray) { ++; CHECK-LABEL: @sin_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_sinf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @sinf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @sin_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @sin_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_sin4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.sin.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @sin_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @sin_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_sinf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.sin.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f64(double* nocapture %varray) { ++; CHECK-LABEL: @cos_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @cos(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f32(float* nocapture %varray) { ++; CHECK-LABEL: @cos_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_cosf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @cosf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @cos_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_cos4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.cos.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @cos_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @cos_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_cosf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.cos.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f64(double* nocapture %varray, double* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP2:%.*]], <4 x double> [[TMP3:%.*]]) ++; CHECK: [[TMP4:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP5:%.*]], <4 x double> [[TMP6:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %arrayidx = getelementptr inbounds double, double* %exp, i64 %iv ++ %tmp1 = load double, double* %arrayidx, align 4 ++ %tmp2 = tail call double @pow(double %conv, double %tmp1) ++ %arrayidx2 = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %tmp2, double* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f64_intrinsic(double* nocapture %varray, double* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP2:%.*]], <4 x double> [[TMP3:%.*]]) ++; CHECK: [[TMP4:%.*]] = call intel_svmlcc256 <4 x double> @__svml_pow4_ha(<4 x double> [[TMP5:%.*]], <4 x double> [[TMP6:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %arrayidx = getelementptr inbounds double, double* %exp, i64 %iv ++ %tmp1 = load double, double* %arrayidx, align 4 ++ %tmp2 = tail call double @llvm.pow.f64(double %conv, double %tmp1) ++ %arrayidx2 = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %tmp2, double* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f32(float* nocapture %varray, float* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_powf8_ha(<8 x float> [[TMP2:%.*]], <8 x float> [[WIDE_LOAD:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %arrayidx = getelementptr inbounds float, float* %exp, i64 %iv ++ %tmp1 = load float, float* %arrayidx, align 4 ++ %tmp2 = tail call float @powf(float %conv, float %tmp1) ++ %arrayidx2 = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %tmp2, float* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @pow_f32_intrinsic(float* nocapture %varray, float* nocapture readonly %exp) { ++; CHECK-LABEL: @pow_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_powf8_ha(<8 x float> [[TMP2:%.*]], <8 x float> [[TMP3:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %arrayidx = getelementptr inbounds float, float* %exp, i64 %iv ++ %tmp1 = load float, float* %arrayidx, align 4 ++ %tmp2 = tail call float @llvm.pow.f32(float %conv, float %tmp1) ++ %arrayidx2 = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %tmp2, float* %arrayidx2, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f64(double* nocapture %varray) { ++; CHECK-LABEL: @exp_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @exp(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f32(float* nocapture %varray) { ++; CHECK-LABEL: @exp_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_expf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @expf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @exp_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_exp4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.exp.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @exp_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @exp_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_expf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.exp.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f64(double* nocapture %varray) { ++; CHECK-LABEL: @log_f64( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @log(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f32(float* nocapture %varray) { ++; CHECK-LABEL: @log_f32( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_logf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @logf(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f64_intrinsic(double* nocapture %varray) { ++; CHECK-LABEL: @log_f64_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP2:%.*]]) ++; CHECK: [[TMP3:%.*]] = call intel_svmlcc256 <4 x double> @__svml_log4_ha(<4 x double> [[TMP4:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to double ++ %call = tail call double @llvm.log.f64(double %conv) ++ %arrayidx = getelementptr inbounds double, double* %varray, i64 %iv ++ store double %call, double* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++define void @log_f32_intrinsic(float* nocapture %varray) { ++; CHECK-LABEL: @log_f32_intrinsic( ++; CHECK: [[TMP1:%.*]] = call intel_svmlcc256 <8 x float> @__svml_logf8_ha(<8 x float> [[TMP2:%.*]]) ++; CHECK: ret void ++; ++entry: ++ br label %for.body ++ ++for.body: ++ %iv = phi i64 [ 0, %entry ], [ %iv.next, %for.body ] ++ %tmp = trunc i64 %iv to i32 ++ %conv = sitofp i32 %tmp to float ++ %call = tail call float @llvm.log.f32(float %conv) ++ %arrayidx = getelementptr inbounds float, float* %varray, i64 %iv ++ store float %call, float* %arrayidx, align 4 ++ %iv.next = add nuw nsw i64 %iv, 1 ++ %exitcond = icmp eq i64 %iv.next, 1000 ++ br i1 %exitcond, label %for.end, label %for.body ++ ++for.end: ++ ret void ++} ++ ++attributes #0 = { nounwind readnone } ++ +diff --git a/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-codegen.ll b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-codegen.ll +new file mode 100644 +index 0000000000000..9422653445dc2 +--- /dev/null ++++ b/llvm-14.0.6.src/test/Transforms/LoopVectorize/X86/svml-legal-codegen.ll +@@ -0,0 +1,61 @@ ++; Check that vector codegen splits illegal sin8 call to two sin4 calls on AVX for double datatype. ++; The C code used to generate this test: ++ ++; #include ++; ++; void foo(double *a, int N){ ++; int i; ++; #pragma clang loop vectorize_width(8) ++; for (i=0;i [[I0:%.*]] to <8 x double> ++; CHECK-NEXT: [[S1:%shuffle.*]] = shufflevector <8 x double> [[I1]], <8 x double> undef, <4 x i32> ++; CHECK-NEXT: [[I2:%.*]] = call fast intel_svmlcc256 <4 x double> @__svml_sin4(<4 x double> [[S1]]) ++; CHECK-NEXT: [[S2:%shuffle.*]] = shufflevector <8 x double> [[I1]], <8 x double> undef, <4 x i32> ++; CHECK-NEXT: [[I3:%.*]] = call fast intel_svmlcc256 <4 x double> @__svml_sin4(<4 x double> [[S2]]) ++; CHECK-NEXT: [[comb:%combined.*]] = shufflevector <4 x double> [[I2]], <4 x double> [[I3]], <8 x i32> ++; CHECK: store <8 x double> [[comb]], <8 x double>* [[TMP:%.*]], align 8 ++ ++ ++target datalayout = "e-m:e-i64:64-f80:128-n8:16:32:64-S128" ++target triple = "x86_64-unknown-linux-gnu" ++ ++; Function Attrs: nounwind uwtable ++define dso_local void @foo(double* nocapture %a, i32 %N) local_unnamed_addr #0 { ++entry: ++ %cmp5 = icmp sgt i32 %N, 0 ++ br i1 %cmp5, label %for.body.preheader, label %for.end ++ ++for.body.preheader: ; preds = %entry ++ %wide.trip.count = zext i32 %N to i64 ++ br label %for.body ++ ++for.body: ; preds = %for.body, %for.body.preheader ++ %indvars.iv = phi i64 [ 0, %for.body.preheader ], [ %indvars.iv.next, %for.body ] ++ %0 = trunc i64 %indvars.iv to i32 ++ %conv = sitofp i32 %0 to double ++ %call = tail call fast double @sin(double %conv) #2 ++ %arrayidx = getelementptr inbounds double, double* %a, i64 %indvars.iv ++ store double %call, double* %arrayidx, align 8, !tbaa !2 ++ %indvars.iv.next = add nuw nsw i64 %indvars.iv, 1 ++ %exitcond = icmp eq i64 %indvars.iv.next, %wide.trip.count ++ br i1 %exitcond, label %for.end, label %for.body, !llvm.loop !6 ++ ++for.end: ; preds = %for.body, %entry ++ ret void ++} ++ ++; Function Attrs: nounwind ++declare dso_local double @sin(double) local_unnamed_addr #1 ++ ++!2 = !{!3, !3, i64 0} ++!3 = !{!"double", !4, i64 0} ++!4 = !{!"omnipotent char", !5, i64 0} ++!5 = !{!"Simple C/C++ TBAA"} ++!6 = distinct !{!6, !7} ++!7 = !{!"llvm.loop.vectorize.width", i32 8} +diff --git a/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll b/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll +index e8c83c4d9bd1f..615fdc29176a2 100644 +--- a/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll ++++ b/llvm-14.0.6.src/test/Transforms/Util/add-TLI-mappings.ll +@@ -12,12 +12,12 @@ target triple = "x86_64-unknown-linux-gnu" + + ; COMMON-LABEL: @llvm.compiler.used = appending global + ; SVML-SAME: [6 x i8*] [ +-; SVML-SAME: i8* bitcast (<2 x double> (<2 x double>)* @__svml_sin2 to i8*), +-; SVML-SAME: i8* bitcast (<4 x double> (<4 x double>)* @__svml_sin4 to i8*), +-; SVML-SAME: i8* bitcast (<8 x double> (<8 x double>)* @__svml_sin8 to i8*), +-; SVML-SAME: i8* bitcast (<4 x float> (<4 x float>)* @__svml_log10f4 to i8*), +-; SVML-SAME: i8* bitcast (<8 x float> (<8 x float>)* @__svml_log10f8 to i8*), +-; SVML-SAME: i8* bitcast (<16 x float> (<16 x float>)* @__svml_log10f16 to i8*) ++; SVML-SAME: i8* bitcast (<2 x double> (<2 x double>)* @__svml_sin2_ha to i8*), ++; SVML-SAME: i8* bitcast (<4 x double> (<4 x double>)* @__svml_sin4_ha to i8*), ++; SVML-SAME: i8* bitcast (<8 x double> (<8 x double>)* @__svml_sin8_ha to i8*), ++; SVML-SAME: i8* bitcast (<4 x float> (<4 x float>)* @__svml_log10f4_ha to i8*), ++; SVML-SAME: i8* bitcast (<8 x float> (<8 x float>)* @__svml_log10f8_ha to i8*), ++; SVML-SAME: i8* bitcast (<16 x float> (<16 x float>)* @__svml_log10f16_ha to i8*) + ; MASSV-SAME: [2 x i8*] [ + ; MASSV-SAME: i8* bitcast (<2 x double> (<2 x double>)* @__sind2 to i8*), + ; MASSV-SAME: i8* bitcast (<4 x float> (<4 x float>)* @__log10f4 to i8*) +@@ -59,9 +59,9 @@ declare float @llvm.log10.f32(float) #0 + attributes #0 = { nounwind readnone } + + ; SVML: attributes #[[SIN]] = { "vector-function-abi-variant"= +-; SVML-SAME: "_ZGV_LLVM_N2v_sin(__svml_sin2), +-; SVML-SAME: _ZGV_LLVM_N4v_sin(__svml_sin4), +-; SVML-SAME: _ZGV_LLVM_N8v_sin(__svml_sin8)" } ++; SVML-SAME: "_ZGV_LLVM_N2v_sin(__svml_sin2_ha), ++; SVML-SAME: _ZGV_LLVM_N4v_sin(__svml_sin4_ha), ++; SVML-SAME: _ZGV_LLVM_N8v_sin(__svml_sin8_ha)" } + + ; MASSV: attributes #[[SIN]] = { "vector-function-abi-variant"= + ; MASSV-SAME: "_ZGV_LLVM_N2v_sin(__sind2)" } +diff --git a/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt b/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt +index 97df6a55d1b59..199e0285c9e5d 100644 +--- a/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt ++++ b/llvm-14.0.6.src/utils/TableGen/CMakeLists.txt +@@ -47,6 +47,7 @@ add_tablegen(llvm-tblgen LLVM + SearchableTableEmitter.cpp + SubtargetEmitter.cpp + SubtargetFeatureInfo.cpp ++ SVMLEmitter.cpp + TableGen.cpp + Types.cpp + X86DisassemblerTables.cpp +diff --git a/llvm-14.0.6.src/utils/TableGen/SVMLEmitter.cpp b/llvm-14.0.6.src/utils/TableGen/SVMLEmitter.cpp +new file mode 100644 +index 0000000000000..a5aeea48db28b +--- /dev/null ++++ b/llvm-14.0.6.src/utils/TableGen/SVMLEmitter.cpp +@@ -0,0 +1,110 @@ ++//===------ SVMLEmitter.cpp - Generate SVML function variants -------------===// ++// ++// The LLVM Compiler Infrastructure ++// ++// This file is distributed under the University of Illinois Open Source ++// License. See LICENSE.TXT for details. ++// ++//===----------------------------------------------------------------------===// ++// ++// This tablegen backend emits the scalar to svml function map for TLI. ++// ++//===----------------------------------------------------------------------===// ++ ++#include "CodeGenTarget.h" ++#include "llvm/Support/Format.h" ++#include "llvm/TableGen/Error.h" ++#include "llvm/TableGen/Record.h" ++#include "llvm/TableGen/TableGenBackend.h" ++#include ++#include ++ ++using namespace llvm; ++ ++#define DEBUG_TYPE "SVMLVariants" ++#include "llvm/Support/Debug.h" ++ ++namespace { ++ ++class SVMLVariantsEmitter { ++ ++ RecordKeeper &Records; ++ ++private: ++ void emitSVMLVariants(raw_ostream &OS); ++ ++public: ++ SVMLVariantsEmitter(RecordKeeper &R) : Records(R) {} ++ ++ void run(raw_ostream &OS); ++}; ++} // End anonymous namespace ++ ++/// \brief Emit the set of SVML variant function names. ++// The default is to emit the high accuracy SVML variants until a mechanism is ++// introduced to allow a selection of different variants through precision ++// requirements specified by the user. This code generates mappings to svml ++// that are in the scalar form of llvm intrinsics, math library calls, or the ++// finite variants of math library calls. ++void SVMLVariantsEmitter::emitSVMLVariants(raw_ostream &OS) { ++ ++ const unsigned MinSinglePrecVL = 4; ++ const unsigned MaxSinglePrecVL = 16; ++ const unsigned MinDoublePrecVL = 2; ++ const unsigned MaxDoublePrecVL = 8; ++ ++ OS << "#ifdef GET_SVML_VARIANTS\n"; ++ ++ for (const auto &D : Records.getAllDerivedDefinitions("SvmlVariant")) { ++ StringRef SvmlVariantNameStr = D->getName(); ++ // Single Precision SVML ++ for (unsigned VL = MinSinglePrecVL; VL <= MaxSinglePrecVL; VL *= 2) { ++ // Emit the scalar math library function to svml function entry. ++ OS << "{\"" << SvmlVariantNameStr << "f" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << "f" << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ ++ // Emit the scalar intrinsic to svml function entry. ++ OS << "{\"" << "llvm." << SvmlVariantNameStr << ".f32" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << "f" << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ ++ // Emit the finite math library function to svml function entry. ++ OS << "{\"__" << SvmlVariantNameStr << "f_finite" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << "f" << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ } ++ ++ // Double Precision SVML ++ for (unsigned VL = MinDoublePrecVL; VL <= MaxDoublePrecVL; VL *= 2) { ++ // Emit the scalar math library function to svml function entry. ++ OS << "{\"" << SvmlVariantNameStr << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << VL << "\", " << "ElementCount::getFixed(" << VL ++ << ")},\n"; ++ ++ // Emit the scalar intrinsic to svml function entry. ++ OS << "{\"" << "llvm." << SvmlVariantNameStr << ".f64" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << VL << "\", " << "ElementCount::getFixed(" << VL ++ << ")},\n"; ++ ++ // Emit the finite math library function to svml function entry. ++ OS << "{\"__" << SvmlVariantNameStr << "_finite" << "\", "; ++ OS << "\"" << "__svml_" << SvmlVariantNameStr << VL << "\", " ++ << "ElementCount::getFixed(" << VL << ")},\n"; ++ } ++ } ++ ++ OS << "#endif // GET_SVML_VARIANTS\n\n"; ++} ++ ++void SVMLVariantsEmitter::run(raw_ostream &OS) { ++ emitSVMLVariants(OS); ++} ++ ++namespace llvm { ++ ++void EmitSVMLVariants(RecordKeeper &RK, raw_ostream &OS) { ++ SVMLVariantsEmitter(RK).run(OS); ++} ++ ++} // End llvm namespace +diff --git a/llvm-14.0.6.src/utils/TableGen/TableGen.cpp b/llvm-14.0.6.src/utils/TableGen/TableGen.cpp +index 2d4a45f889be6..603d0c223b33a 100644 +--- a/llvm-14.0.6.src/utils/TableGen/TableGen.cpp ++++ b/llvm-14.0.6.src/utils/TableGen/TableGen.cpp +@@ -57,6 +57,7 @@ enum ActionType { + GenAutomata, + GenDirectivesEnumDecl, + GenDirectivesEnumImpl, ++ GenSVMLVariants, + }; + + namespace llvm { +@@ -138,7 +139,9 @@ cl::opt Action( + clEnumValN(GenDirectivesEnumDecl, "gen-directive-decl", + "Generate directive related declaration code (header file)"), + clEnumValN(GenDirectivesEnumImpl, "gen-directive-impl", +- "Generate directive related implementation code"))); ++ "Generate directive related implementation code"), ++ clEnumValN(GenSVMLVariants, "gen-svml", ++ "Generate SVML variant function names"))); + + cl::OptionCategory PrintEnumsCat("Options for -print-enums"); + cl::opt Class("class", cl::desc("Print Enum list for this class"), +@@ -272,6 +275,9 @@ bool LLVMTableGenMain(raw_ostream &OS, RecordKeeper &Records) { + case GenDirectivesEnumImpl: + EmitDirectivesImpl(Records, OS); + break; ++ case GenSVMLVariants: ++ EmitSVMLVariants(Records, OS); ++ break; + } + + return false; +diff --git a/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h b/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h +index 71db8dc77b052..86c3a3068c2dc 100644 +--- a/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h ++++ b/llvm-14.0.6.src/utils/TableGen/TableGenBackends.h +@@ -93,6 +93,7 @@ void EmitExegesis(RecordKeeper &RK, raw_ostream &OS); + void EmitAutomata(RecordKeeper &RK, raw_ostream &OS); + void EmitDirectivesDecl(RecordKeeper &RK, raw_ostream &OS); + void EmitDirectivesImpl(RecordKeeper &RK, raw_ostream &OS); ++void EmitSVMLVariants(RecordKeeper &RK, raw_ostream &OS); + + } // End llvm namespace + +diff --git a/llvm-14.0.6.src/utils/vim/syntax/llvm.vim b/llvm-14.0.6.src/utils/vim/syntax/llvm.vim +index 205db16b7d8cd..2572ab5a59e1b 100644 +--- a/llvm-14.0.6.src/utils/vim/syntax/llvm.vim ++++ b/llvm-14.0.6.src/utils/vim/syntax/llvm.vim +@@ -104,6 +104,7 @@ syn keyword llvmKeyword + \ inreg + \ intel_ocl_bicc + \ inteldialect ++ \ intel_svmlcc + \ internal + \ jumptable + \ linkonce From 448336815bd8b47afadf5a729ecde7870bd8739d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 13 Nov 2023 07:57:27 +0100 Subject: [PATCH 0069/1193] BiG-SCAPE: use correct name for the FastTree binary. --- .../b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb | 3 +++ ...CAPE-1.1.5_use_correct_name_for_FastTree.patch | 15 +++++++++++++++ 2 files changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb index 5c6c71a87211..54d08e2691ee 100644 --- a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5-foss-2022a.eb @@ -17,6 +17,7 @@ patches = [ '%(name)s-%(version)s_use_env_var_to_find-MIBiG-files.patch', '%(name)s-%(version)s_use_env_var_for_domain_files.patch', '%(name)s-%(version)s_use_env_var_for_html.patch', + '%(name)s-%(version)s_use_correct_name_for_FastTree.patch', ] checksums = [ {'v1.1.5.tar.gz': 'ec7cebbec8f83f4187c80e02ecbb37411a1898a2b83bb80088810f1600528ec7'}, @@ -25,6 +26,8 @@ checksums = [ {'BiG-SCAPE-1.1.5_use_env_var_for_domain_files.patch': '51337f22b2619ed38969f4ead5f7ce2f2df884f272793b47fb46d77e9c5e2aa2'}, {'BiG-SCAPE-1.1.5_use_env_var_for_html.patch': '540be22396ab982c2aeaaed4ce5acdb8ccb8ce2b31d36bc69d37be7a29c7c42a'}, + {'BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch': + 'e1572e4134c6163a3927ac32bd2a39b7f87cf01109f7913b3c55126e2381a771'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch new file mode 100644 index 000000000000..997ea971e5df --- /dev/null +++ b/easybuild/easyconfigs/b/BiG-SCAPE/BiG-SCAPE-1.1.5_use_correct_name_for_FastTree.patch @@ -0,0 +1,15 @@ +FastTree binary is not lowercase. + +Åke Sandgren, 2023-11-13 +diff -ru BiG-SCAPE-1.1.5.orig/bigscape.py BiG-SCAPE-1.1.5/bigscape.py +--- BiG-SCAPE-1.1.5.orig/bigscape.py 2022-11-14 17:04:47.000000000 +0100 ++++ BiG-SCAPE-1.1.5/bigscape.py 2023-11-13 07:52:23.064042200 +0100 +@@ -1644,7 +1644,7 @@ + # make tree + newick_file_path = os.path.join(gcf_trees_path, "GCF_c{:4.2f}_{:05d}.newick".format(cutoff,exemplar_idx)) + with open(newick_file_path, "w") as newick_file: +- command = ["fasttree", "-nopr", "-quiet", alignment_file_path] ++ command = ["FastTree", "-nopr", "-quiet", alignment_file_path] + p = subprocess.Popen(command, stdout=newick_file, shell=False) + p.wait() # only with process has terminated will the file be ready + From a595c584837353b12fc56a7028f5cbec35368b08 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 15 Nov 2023 10:33:40 +0000 Subject: [PATCH 0070/1193] adding easyconfigs: graph-tool-2.55-foss-2022a.eb --- .../graph-tool/graph-tool-2.55-foss-2022a.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/g/graph-tool/graph-tool-2.55-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/graph-tool/graph-tool-2.55-foss-2022a.eb b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.55-foss-2022a.eb new file mode 100644 index 000000000000..4abdda53cdfa --- /dev/null +++ b/easybuild/easyconfigs/g/graph-tool/graph-tool-2.55-foss-2022a.eb @@ -0,0 +1,57 @@ +# Author J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'graph-tool' +version = '2.55' + +homepage = 'https://graph-tool.skewed.de/' +description = """Graph-tool is an efficient Python module for manipulation and + statistical analysis of graphs (a.k.a. networks). Contrary to + most other python modules with similar functionality, the core + data structures and algorithms are implemented in C++, making + extensive use of template metaprogramming, based heavily on + the Boost Graph Library. This confers it a level of + performance that is comparable (both in memory usage and + computation time) to that of a pure C/C++ library.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://downloads.skewed.de/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['75728e55b774af734954cd48f3d80ba64cf08864ef6143408f3a7422474834b4'] + +builddependencies = [ + ('gawk', '5.1.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Boost.Python', '1.79.0'), + ('expat', '2.4.8'), + ('CGAL', '4.14.3'), + ('sparsehash', '2.0.4'), + ('matplotlib', '3.5.2'), + ('PyCairo', '1.21.0'), + ('cairomm', '1.16.2'), + ('PyGObject', '3.42.1'), + ('GTK3', '3.24.33'), +] + +configopts = '--enable-openmp --with-cgal=$EBROOTCGAL --with-boost=$EBROOTBOOST ' +configopts += '--with-boost-python=boost_python310 ' +configopts += '--with-python-module-path=%(installdir)s/lib/python%(pyshortver)s/site-packages ' + + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/graph_tool/all.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/graph_tool/include', 'share'], +} + +sanity_check_commands = ["python -c 'from graph_tool.all import graph_draw'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'math' From 57d633d419140ccb983cd507602775f2b7e1c2f9 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Thu, 16 Nov 2023 15:42:08 +0100 Subject: [PATCH 0071/1193] Build for new WIEN2k versions, include easybuild-easyblocks/pull/3035 --- .../w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 80 +++++++++++++++++++ .../WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch | 30 +++++++ ...k-23.2_fix_system_stderr_redirection.patch | 29 +++++++ 3 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch create mode 100644 easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb new file mode 100644 index 000000000000..a40da29ea437 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -0,0 +1,80 @@ +name = 'WIEN2k' +version = '23.2' + +homepage = 'http://www.wien2k.at/' +description = """The program package WIEN2k allows to perform electronic structure calculations of solids +using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave +((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. +WIEN2k is an all-electron scheme including relativistic effects and has many features.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +sources = ['%(name)s_%(version)s.tar'] +patches = [ + '%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch', + '%(name)s-%(version)s_fix_system_stderr_redirection.patch', +] +#checksums = [ +# '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11', # WIEN2k_21.1.tar +# '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch + # WIEN2k-21.1_fix_system_stderr_redirection.patch +# 'cdba467b0b6f2b310c2e1e2a3e6cabe75f8fd15ee0f7c14f8ef80c7e48073bdd', +#] + +download_instructions = """ +WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html. +""" + +builddependencies = [ + ('tcsh', '6.24.01') +] + +dependencies = [ + ('Python', '3.9.6'), + ('Perl', '5.34.0'), + ('DFT-D3', '3.2.0'), + ('ELPA', '2021.05.001'), + ('FFTW', '3.3.10'), + ('libxc', '5.1.6'), +] + +osdependencies = [ + ('glibc-devel', 'libc6-dev'), # required for libpthread.a +] + +# remote = 'pbsssh' +# If using a Slurm batch system it is highly recommended to use +# 'srun -n_NP_ _EXEC_' for wien_mpirun +wien_mpirun = 'mpirun -np _NP_ _EXEC_' +use_remote = False +mpi_remote = False +wien_granularity = True +taskset = 'no' + +# Change as needed, these are the defaults +# nmatmax = 19000 +# nume = 6000 + +fix_perl_shebang_for = [ + 'iniel_pressure_in2reader.pl_lapw', + 'iniel_pressure_reader.pl_lapw', + 'setrmt_lapw', + 'elast_setup_input.pl_lapw', + 'bashtime2csh.pl_lapw', +] + +tests = [ + # test case 1: NaCl +# ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']), + # test case 2: TiO2 + ('TiO2', + '-b -numk 1000 -rkmax 7.5', + '-in1ef -cc 0.00001 -fc 0.5 -i 100', + [ + r'^:ENE.*-4018.07', + r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', + r'^:FGL002.*15.*total forces', + ]), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch new file mode 100644 index 000000000000..473da9ef3789 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch @@ -0,0 +1,30 @@ +The Makefile.orig lapw0 is not updated according to how the Makefile works. +That causes a build failure for lapw0_mpi with libxc + +Åke Sandgren, 20210910 +diff -ru wien2k.orig/SRC_lapw0/Makefile.orig wien2k/SRC_lapw0/Makefile.orig +--- wien2k.orig/SRC_lapw0/Makefile.orig 2021-03-13 09:40:10.023772496 +0100 ++++ wien2k/SRC_lapw0/Makefile.orig 2021-09-10 14:53:07.875144996 +0200 +@@ -55,7 +55,9 @@ + #-------------- loader options ------------- + LDFLAGS = _LDFLAGS_ + R_LIBS = $(FFTW_LIBS) _R_LIBS_ $(LIBXC_LIBS) ++RR_LIBS = $(FFTW_LIBS) $(R_LIBS) $(LIBXC_LIBS) + RP_LIBS = $(FFTW_PLIBS) _RP_LIBS_ ++RPP_LIBS = $(FFTW_PLIBS) $(FFTW_LIBS) $(RP_LIBS) $(LIBXC_LIBS) + + ############################################################################### + # End of user defined variables # +@@ -128,10 +130,10 @@ + #.............................................................................. + + $(S_EXEC): $(OBJS) +- $(FORT) -o $(S_EXEC) $(OBJS) $(LDFLAGS) $(R_LIBS) ++ $(FORT) -o $(S_EXEC) $(OBJS) $(LDFLAGS) $(RR_LIBS) + + $(P_EXEC): $(OBJS) +- $(FORT) -o $(P_EXEC) $(OBJS) $(LDFLAGS) $(RP_LIBS) ++ $(FORT) -o $(P_EXEC) $(OBJS) $(LDFLAGS) $(RPP_LIBS) + + # sequential + keep_s_files: diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch new file mode 100644 index 000000000000..23b08d93cfb3 --- /dev/null +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch @@ -0,0 +1,29 @@ +--- SRC_Globals/W2kinit.F.orig 2023-11-08 17:54:06.183370012 +0100 ++++ SRC_Globals/W2kinit.F 2023-11-08 18:29:21.436975434 +0100 +@@ -403,7 +403,7 @@ + logical AVX512, AVX2, AVX, SSE + integer istat, system + AVX512=.false.; AVX2=.false.; AVX=.false.; SSE=.false. +- istat=system('ls /proc/cpuinfo > /dev/null') ++ istat=system('test -f /proc/cpuinfo') + if(istat.ne.0.and.myid.eq.0) then + print*, "Could not read your /proc/cpuinfo. The default kernel of your ELPA installation" + print*, "will be used." +@@ -413,13 +413,13 @@ + !_REAL print*, " ELPA_DEFAULT_real_kernel" + !_COMPLEX print*, " ELPA_DEFAULT_complex_kernel" + else +- istat=system('grep -i avx512 /proc/cpuinfo > /dev/null') ++ istat=system('grep -qi avx512 /proc/cpuinfo') + if(istat.eq.0) AVX512=.true. +- istat=system('grep -i avx2 /proc/cpuinfo > /dev/null') ++ istat=system('grep -qi avx2 /proc/cpuinfo') + if(istat.eq.0) AVX2=.true. +- istat=system('grep -i avx /proc/cpuinfo > /dev/null') ++ istat=system('grep -qi avx /proc/cpuinfo') + if(istat.eq.0) AVX=.true. +- istat=system('grep -i sse /proc/cpuinfo > /dev/null') ++ istat=system('grep -qi sse /proc/cpuinfo') + if(istat.eq.0) SSE=.true. + endif + return From 741ae8083a0f291146bd610a63d31a04f02f8e43 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 16 Nov 2023 16:56:56 +0100 Subject: [PATCH 0072/1193] Update WIEN2k-23.2-intel-2021b.eb --- .../easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index a40da29ea437..4e4c6e0714a8 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -14,21 +14,11 @@ patches = [ '%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch', '%(name)s-%(version)s_fix_system_stderr_redirection.patch', ] -#checksums = [ -# '32590778440a9280322bf2dc0d63f4f42a9fc48814fa6b8b7ee2d199c94bed11', # WIEN2k_21.1.tar -# '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-21.1_fix_libxc_for_lapw0_mpi.patch - # WIEN2k-21.1_fix_system_stderr_redirection.patch -# 'cdba467b0b6f2b310c2e1e2a3e6cabe75f8fd15ee0f7c14f8ef80c7e48073bdd', -#] download_instructions = """ WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html. """ -builddependencies = [ - ('tcsh', '6.24.01') -] - dependencies = [ ('Python', '3.9.6'), ('Perl', '5.34.0'), @@ -39,7 +29,8 @@ dependencies = [ ] osdependencies = [ - ('glibc-devel', 'libc6-dev'), # required for libpthread.a + ('glibc-devel', 'libc6-dev'), # required for libpthread. + ('tcsh', '6.24.01') ] # remote = 'pbsssh' From 41802cbe4d3a521772e7c89bcd44e4935b985493 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 16 Nov 2023 17:42:19 +0100 Subject: [PATCH 0073/1193] Update WIEN2k-23.2-intel-2021b.eb --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index 4e4c6e0714a8..2067f8abc667 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -56,13 +56,13 @@ fix_perl_shebang_for = [ tests = [ # test case 1: NaCl -# ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.14']), + ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), # test case 2: TiO2 ('TiO2', '-b -numk 1000 -rkmax 7.5', '-in1ef -cc 0.00001 -fc 0.5 -i 100', [ - r'^:ENE.*-4018.07', + r'^:ENE.*-4018.0', r'^:FGL001.*\s+[0.]+\s+[0.]+\s+[0.]+\s+total forces', r'^:FGL002.*15.*total forces', ]), From 1d2f6d3a6d09d2944bfbbe8e428bffcf75212f0d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 16 Nov 2023 18:36:21 +0100 Subject: [PATCH 0074/1193] Update WIEN2k-23.2-intel-2021b.eb --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index 2067f8abc667..cc8aed4ffbde 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -56,7 +56,7 @@ fix_perl_shebang_for = [ tests = [ # test case 1: NaCl - ('NaCl', '-b', '-i 3', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), + ('NaCl', '-b', '-i 100', [r'^:DIS.*0.1', r'^:ENE.*-1248.1']), # test case 2: TiO2 ('TiO2', '-b -numk 1000 -rkmax 7.5', From fe8d3102a545008b850247d3f9bee9ff5501c033 Mon Sep 17 00:00:00 2001 From: Jun Tang Date: Tue, 21 Nov 2023 21:16:34 +0000 Subject: [PATCH 0075/1193] disable tree-vectorize to reduce number of numerical errors for lapack-test --- .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 4 +++ ...-0.3.21_disable-tree-vectorize-cmake.patch | 26 +++++++++++++++++ ...S-0.3.21_disable-tree-vectorize-make.patch | 28 +++++++++++++++++++ 3 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-make.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index 7e7d8c4b75fa..083a42b7b699 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -21,6 +21,8 @@ patches = [ 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', + 'OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch', + 'OpenBLAS-0.3.21_disable-tree-vectorize-make.patch', ] checksums = [ {'v0.3.21.tar.gz': 'f36ba3d7a60e7c8bcc54cd9aaa9b1223dd42eaf02c811791c37e8ca707c241ca'}, @@ -36,6 +38,8 @@ checksums = [ {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': '9784e93567d100960a4c34d86e215bd7aa70bb28b0bc2c6bf1b22c6a05d56003'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, + {'OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch': 'd8fca9d3956e45d6b9e588159675aa198b6d02534b09e3e797fbf8aee824aed7'}, + {'OpenBLAS-0.3.21_disable-tree-vectorize-make.patch': '3040e30f752107111b23064b8b25514719d46daed7445ad4bca89d2f66ecf95a'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch new file mode 100644 index 000000000000..93e00ff90e61 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch @@ -0,0 +1,26 @@ +From 32566bfb44067e0c0459e94b53c9457613539eeb Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Thu, 13 Oct 2022 14:04:25 +0200 +Subject: [PATCH] Disable the gfortran tree vectorizer for netlib LAPACK + +--- + cmake/lapack.cmake | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/cmake/lapack.cmake b/cmake/lapack.cmake +index f8a27f5d4..3b221d420 100644 +--- a/cmake/lapack.cmake ++++ b/cmake/lapack.cmake +@@ -999,6 +999,9 @@ endforeach () + + if (NOT C_LAPACK) + set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_FFLAGS}") ++ if (${F_COMPILER} STREQUAL "GFORTRAN") ++ set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_FFLAGS} -fno-tree-vectorize") ++ endif() + else () + set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_CFLAGS}") + endif () +-- +2.25.1 + diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-make.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-make.patch new file mode 100644 index 000000000000..663bd5460742 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-make.patch @@ -0,0 +1,28 @@ +From 57809526c430ef0a07f5c5c39dce20c6d73a1f35 Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Thu, 13 Oct 2022 09:12:23 +0200 +Subject: [PATCH] Disable the gfortran tree vectorizer for lapack-netlib + +--- + Makefile | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/Makefile b/Makefile +index 289f0eca5..56af9847e 100644 +--- a/Makefile ++++ b/Makefile +@@ -278,7 +278,11 @@ prof_lapack : lapack_prebuild + lapack_prebuild : + ifeq ($(NO_LAPACK), $(filter 0,$(NO_LAPACK))) + -@echo "FC = $(FC)" > $(NETLIB_LAPACK_DIR)/make.inc ++ifeq ($(F_COMPILER), GFORTRAN) ++ -@echo "override FFLAGS = $(LAPACK_FFLAGS) -fno-tree-vectorize" >> $(NETLIB_LAPACK_DIR)/make.inc ++else + -@echo "override FFLAGS = $(LAPACK_FFLAGS)" >> $(NETLIB_LAPACK_DIR)/make.inc ++endif + -@echo "FFLAGS_DRV = $(LAPACK_FFLAGS)" >> $(NETLIB_LAPACK_DIR)/make.inc + -@echo "POPTS = $(LAPACK_FPFLAGS)" >> $(NETLIB_LAPACK_DIR)/make.inc + -@echo "FFLAGS_NOOPT = -O0 $(LAPACK_NOOPT)" >> $(NETLIB_LAPACK_DIR)/make.inc +-- +2.25.1 + From 142bc873b84310384ae505c9346cc6bffa929870 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Nov 2023 10:07:50 +0000 Subject: [PATCH 0076/1193] adding easyconfigs: json-fortran-8.3.0-intel-compilers-2022.1.0.eb, mctc-lib-0.3.1-intel-compilers-2022.1.0.eb, mstore-0.2.0-intel-compilers-2022.1.0.eb --- ...-fortran-8.3.0-intel-compilers-2022.1.0.eb | 31 ++++++++++++++ ...mctc-lib-0.3.1-intel-compilers-2022.1.0.eb | 41 +++++++++++++++++++ .../mstore-0.2.0-intel-compilers-2022.1.0.eb | 37 +++++++++++++++++ 3 files changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb create mode 100644 easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.1.0.eb diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb new file mode 100644 index 000000000000..b7db841c2ddb --- /dev/null +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb @@ -0,0 +1,31 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'json-fortran' +version = '8.3.0' + +homepage = 'https://github.com/jacobwilliams/json-fortran' +description = "JSON-Fortran: A Modern Fortran JSON API" + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} + +source_urls = ['https://github.com/jacobwilliams/json-fortran/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['5fe9ad709a726416cec986886503e0526419742e288c4e43f63c1c22026d1e8a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb new file mode 100644 index 000000000000..e996074a6268 --- /dev/null +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'mctc-lib' +version = '0.3.1' + +homepage = 'https://grimme-lab.github.io/mctc-lib' +description = """Common tool chain for working with molecular structure data in various +applications. This library provides a unified way to perform operations on +molecular structure data, like reading and writing to common geometry file +formats.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['03dc8ccba37413da70e55a07cef8e8de53bce33f5bb52c1f8db5fec326abe083'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('json-fortran', '8.3.0'), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mctc-convert --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.1.0.eb new file mode 100644 index 000000000000..fb04f173ae19 --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-intel-compilers-2022.1.0.eb @@ -0,0 +1,37 @@ +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'mstore' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/mstore' +description = """Molecular structure store for testing""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} +toolchainopts = {'pic': True} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/mstore-fortranize', 'bin/mstore-info', 'lib/libmstore.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["mstore-info --help"] + +moduleclass = 'chem' From 95463f59ec5ec8186a1b992791692bbedac5ae51 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 22 Nov 2023 12:44:48 +0000 Subject: [PATCH 0077/1193] Sanity check improved --- .../m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb index e996074a6268..3b10964597eb 100644 --- a/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/m/mctc-lib/mctc-lib-0.3.1-intel-compilers-2022.1.0.eb @@ -29,7 +29,7 @@ dependencies = [ configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] sanity_check_paths = { - 'files': ['bin/mctc-convert', 'lib/libmctc-lib.%s' % SHLIB_EXT], + 'files': ['bin/mctc-convert', 'lib/libmctc-lib.a', 'lib/libmctc-lib.%s' % SHLIB_EXT], 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], } From b081394713de226f4928ce36be319f092dcf9496 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Nov 2023 15:41:23 +0100 Subject: [PATCH 0078/1193] {ai}[foss/2022a] pytorch-3dunet v1.6.0 w/ CUDA 11.7.0 --- ...rch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..30a11ee99601 --- /dev/null +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,56 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'PythonBundle' + +name = 'pytorch-3dunet' +version = '1.6.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/wolny/pytorch-3dunet' +description = """ +PyTorch implementation of 3D U-Net and its variants: + - UNet3D: Standard 3D U-Net based on 3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation + - ResidualUNet3D: Residual 3D U-Net based on Superhuman Accuracy on the SNEMI3D + Connectomics Challenge + - ResidualUNetSE3D: Similar to ResidualUNet3D with the addition of Squeeze and + Excitation blocks based on Deep Learning Semantic Segmentation for High- + Resolution Medical Volumes. Original squeeze and excite paper: Squeeze-and- + Excitation Networks +The code allows for training the U-Net for both: semantic segmentation (binary +and multi-class) and regression problems (e.g. de-noising, learning +deconvolutions). +""" +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('cppy', '1.2.1') +] + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('CUDA', '11.7.0', '', SYSTEM), + ('h5py', '3.7.0'), + ('tensorboard', '2.10.0'), + ('scikit-image', '0.19.3') +] + +use_pip = True +sanity_pip_check = True + +github_account = 'wolny' +exts_list = [ + (name, version, { + 'modulename': 'pytorch3dunet', + 'source_urls': [GITHUB_SOURCE], + 'sources': '%(version)s.tar.gz', + 'checksums': ['5323eb8a31ad95c17a3e3d83e3de08b0d3cdd0841b28687aa41039355706b659'], + }), +] + +sanity_check_commands = [ + "train3dunet --help", + "predict3dunet --help" +] + +moduleclass = 'ai' From e24a81ac8a37aa5e64e4680b430bfc452c2af393 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 22 Nov 2023 16:01:05 +0100 Subject: [PATCH 0079/1193] fix src --- .../pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb index 30a11ee99601..e0ca7a4f166f 100644 --- a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -43,7 +43,7 @@ exts_list = [ (name, version, { 'modulename': 'pytorch3dunet', 'source_urls': [GITHUB_SOURCE], - 'sources': '%(version)s.tar.gz', + 'sources': ['%(version)s.tar.gz'], 'checksums': ['5323eb8a31ad95c17a3e3d83e3de08b0d3cdd0841b28687aa41039355706b659'], }), ] From 5e67ca569549f51718da85cdeddb7bc446180b15 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 22 Nov 2023 16:31:19 +0100 Subject: [PATCH 0080/1193] Add fortran modules to sanity check --- .../json-fortran-8.3.0-intel-compilers-2022.1.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb index b7db841c2ddb..ad4f0350f35a 100644 --- a/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/j/json-fortran/json-fortran-8.3.0-intel-compilers-2022.1.0.eb @@ -24,7 +24,8 @@ configopts = '-DUSE_GNU_INSTALL_CONVENTION=TRUE' runtest = 'check' sanity_check_paths = { - 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT], + 'files': ['lib/libjsonfortran.a', 'lib/libjsonfortran.%s' % SHLIB_EXT, + 'include/json_module.mod', 'include/json_parameters.mod'], 'dirs': ['include'], } From 62ac81c33dea0daae153b01d9ebe5cf6b33d302c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 23 Nov 2023 10:28:36 +0100 Subject: [PATCH 0081/1193] adding easyconfigs: InterOp-1.2.4-GCCcore-10.3.0.eb --- .../i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..36a6a7fe3c8b --- /dev/null +++ b/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb @@ -0,0 +1,48 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +easyblock = 'CMakeMake' + +name = 'InterOp' +version = '1.2.4' + +homepage = 'https://illumina.github.io/interop/' +description = """The Illumina InterOp libraries are a set of common routines used for +reading InterOp metric files produced by Illumina sequencers including NextSeq +1k/2k and NovaSeqX. These libraries are backwards compatible and capable of +supporting prior releases of the software, with one exception: GA systems have +been excluded.""" + +software_license = 'LicenseGPLv3' +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/Illumina/interop/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e10ee79f476d40f40a1d4c73074ea58088d82700239b1a2ae9633235afe894c3'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('SWIG', '4.0.2'), + ('Doxygen', '1.9.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05', '', ('foss', '2021a')), +] + +sanity_check_paths = { + 'files': ["lib64/libinterop_fpic_lib.a", "lib64/libinterop_lib.a", "README.md"], + 'dirs': ['bin', 'include', 'lib64', 'share', 'lib64/python'] +} + +sanity_check_commands = ["imaging_table"] + +moduleclass = 'bio' From bab7cdc551afe24df275c72694ead6326ff542a2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 23 Nov 2023 10:58:19 +0100 Subject: [PATCH 0082/1193] adding easyconfigs: tiny-cuda-nn-1.6-foss-2022a-CUDA-11.7.0.eb, CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb and patches: tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch --- .../CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb | 44 ++++++++++++ ...tiny-cuda-nn-1.6-foss-2022a-CUDA-11.7.0.eb | 55 +++++++++++++++ ...cuda-nn-1.6_use_external_fmt+cutlass.patch | 67 +++++++++++++++++++ 3 files changed, 166 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch diff --git a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..da5432a165c9 --- /dev/null +++ b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'CUTLASS' +version = '2.11.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cutlass' +description = """CUTLASS is a collection of CUDA C++ template +abstractions for implementing high-performance matrix-matrix +multiplication (GEMM) and related computations at all levels and scales +within CUDA. It incorporates strategies for hierarchical decomposition +and data movement similar to those used to implement cuBLAS and cuDNN. +CUTLASS decomposes these "moving parts" into reusable, modular software +components abstracted by C++ template classes. Primitives for different +levels of a conceptual parallelization hierarchy can be specialized and +tuned via custom tiling sizes, data types, and other algorithmic policy. +The resulting flexibility simplifies their use as building blocks within +custom kernels and applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b4394f1e080b63cfc54163069334096324c1262dfc66e67099880005d51b8af9'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.4'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), +] + +configopts = "-DCUTLASS_ENABLE_CUBLAS=1 -DCUTLASS_ENABLE_CUDNN=1 " + +sanity_check_paths = { + 'files': ['include/cutlass/cutlass.h', 'lib/libcutlass.%s' % SHLIB_EXT], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..d38b5962f490 --- /dev/null +++ b/easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonPackage' + +name = 'tiny-cuda-nn' +version = '1.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVlabs/tiny-cuda-nn' +description = """is a small, self-contained framework for training and +querying neural networks. Most notably, it contains a lightning fast +"fully fused" multi-layer perceptron (technical paper), a versatile +multiresolution hash encoding (technical paper), as well as support for +various other input encodings, losses, and optimizers.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'NVlabs' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use_external_fmt+cutlass.patch', +] +checksums = [ + {'v1.6.tar.gz': '490c944b58af1b376bfaaa3695f86d16eef81c3f903b67acdbd4d08612b099c5'}, + {'tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch': + 'ef01a927d6efe9c23cc83173a6fbebe3f597747c6d545a450f4928ed5971959f'}, +] + +builddependencies = [ + ('Ninja', '1.10.2'), + ('fmt', '9.1.0'), + ('CUTLASS', '2.11.0', versionsuffix), # tiny-cuda-nn is not compatible with CUTLASS 3.x yet +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.1', versionsuffix), +] + +start_dir = 'bindings/torch' + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# Even though CMake isn't a dependency the template value is still available +preinstallopts = 'export TCNN_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s" && ' + +options = {'modulename': 'tinycudann'} + +sanity_check_commands = [ + 'python -c "from tinycudann.modules import _C;"', +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch b/easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch new file mode 100644 index 000000000000..cfe7171ed179 --- /dev/null +++ b/easybuild/easyconfigs/t/tiny-cuda-nn/tiny-cuda-nn-1.6_use_external_fmt+cutlass.patch @@ -0,0 +1,67 @@ +Use external fmt and CUTLASS + +Åke Sandgren, 2023-11-23 +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 600bc41..c1bfba9 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -44,14 +44,6 @@ if (NOT CMAKE_BUILD_TYPE AND NOT CMAKE_CONFIGURATION_TYPES) + set_property(CACHE CMAKE_BUILD_TYPE PROPERTY STRINGS "Debug" "Release" "RelWithDebInfo") + endif() + +-if (NOT EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/dependencies/cutlass/CMakeLists.txt") +- message(FATAL_ERROR +- "Some tiny-cuda-nn dependencies are missing. " +- "If you forgot the \"--recursive\" flag when cloning this project, " +- "this can be fixed by calling \"git submodule update --init --recursive\"." +- ) +-endif() +- + if (APPLE) + set(CMAKE_MACOSX_RPATH ON) + endif() +@@ -187,7 +179,6 @@ find_library( + ) + + set(BUILD_SHARED_LIBS OFF) +-add_subdirectory("dependencies/fmt") + + ############################################################################### + # tiny-cuda-nn library, samples, and benchmarks +@@ -225,9 +216,6 @@ target_compile_options(tiny-cuda-nn PUBLIC $<$:${CUDA_NVC + target_include_directories(tiny-cuda-nn PUBLIC + "include" + "dependencies" +- "dependencies/cutlass/include" +- "dependencies/cutlass/tools/util/include" +- "dependencies/fmt/include" + ) + target_link_libraries(tiny-cuda-nn PUBLIC ${CUDA_LIBRARIES} cuda cublas fmt) + +diff --git a/bindings/torch/setup.py b/bindings/torch/setup.py +index 351a2ed..5a2886f 100644 +--- a/bindings/torch/setup.py ++++ b/bindings/torch/setup.py +@@ -89,8 +89,6 @@ bindings_dir = os.path.dirname(__file__) + root_dir = os.path.abspath(os.path.join(bindings_dir, "../..")) + source_files = [ + "tinycudann/bindings.cpp", +- "../../dependencies/fmt/src/format.cc", +- "../../dependencies/fmt/src/os.cc", + "../../src/cpp_api.cu", + "../../src/common.cu", + "../../src/common_device.cu", +@@ -115,12 +113,9 @@ ext = CUDAExtension( + include_dirs=[ + "%s/include" % root_dir, + "%s/dependencies" % root_dir, +- "%s/dependencies/cutlass/include" % root_dir, +- "%s/dependencies/cutlass/tools/util/include" % root_dir, +- "%s/dependencies/fmt/include" % root_dir, + ], + extra_compile_args={"cxx": cflags, "nvcc": nvcc_flags}, +- libraries=["cuda", "cudadevrt", "cudart_static"], ++ libraries=["cuda", "cudadevrt", "cudart_static", "fmt"], + ) + ext_modules = [ext] + From e7e57f1f29550086e6460230fc6a2150aba4cf90 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 23 Nov 2023 13:11:31 +0100 Subject: [PATCH 0083/1193] Only enable CUDA archs requested by cuda-compute-capabilities --- .../c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb index da5432a165c9..f534333fec7c 100644 --- a/easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CUTLASS/CUTLASS-2.11.0-foss-2022a-CUDA-11.7.0.eb @@ -34,7 +34,12 @@ dependencies = [ ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), ] -configopts = "-DCUTLASS_ENABLE_CUBLAS=1 -DCUTLASS_ENABLE_CUDNN=1 " +_copts = [ + '-DCUTLASS_NVCC_ARCHS="%(cuda_cc_cmake)s"', + '-DCUTLASS_ENABLE_CUBLAS=1', + '-DCUTLASS_ENABLE_CUDNN=1', +] +configopts = ' '.join(_copts) sanity_check_paths = { 'files': ['include/cutlass/cutlass.h', 'lib/libcutlass.%s' % SHLIB_EXT], From 0499e60894f2f2166d0f2762c13216651c8a3060 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Mon, 27 Nov 2023 13:16:26 +0100 Subject: [PATCH 0084/1193] adding easyconfigs: waLBerla-6.1-foss-2022b.eb, Boost.MPI-1.79.0-gompi-2022b.eb --- .../Boost.MPI/Boost.MPI-1.79.0-gompi-2022b.eb | 29 +++++++++++ .../w/waLBerla/waLBerla-6.1-foss-2022b.eb | 48 +++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022b.eb new file mode 100644 index 000000000000..e1d019dd676f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.79.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['273f1be93238a068aba4f9735a4a2b003019af067b9c183ed227780b8f36062c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('zstd', '1.5.2'), + ('ICU', '72.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb new file mode 100644 index 000000000000..5538d37e58b2 --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -0,0 +1,48 @@ +# easyconfig file for waLBerla v6.1 +easyblock = 'CMakeMake' + +name = 'waLBerla' +version = '6.1' + +homepage = "https://walberla.net/index.html" +description = """Widely applicable Lattics-Boltzmann from Erlangen is a +block-structured high-performance framework for multiphysics simulations""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] +sources = ['%(name)s-v%(version)s.tar.gz'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] +checksums = [ + {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': + '057066d07294e8f159c2545d2d5f9138d439dbb54bc70eb75eca1f82ae650c47'}, +] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('pybind11', '2.10.3'), + ('Python', '3.10.8'), + ('Boost.MPI', '1.79.0'), + ('SciPy-bundle', '2023.02'), +] + +parallel = 1 + +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " +configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " +configopts += "-DWALBERLA_BUILD_DOC=OFF " +configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " + +modextrapaths = {'PYTHONPATH': ['pythonmodule']} + +sanity_check_paths = { + 'files': ['waLBerlaDefinitions.h', 'pythonmodule/walberla_cpp.cpython-310-x86_64-linux-gnu.so'], + 'dirs': ['pythonmodule'] +} + +sanity_check_commands = [('python', "-c 'import waLBerla'")] + +moduleclass = 'chem' From 39e70d5563e0ac4ef0c7d78aadf24c09f9f0729e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 27 Nov 2023 12:45:03 +0000 Subject: [PATCH 0085/1193] adding easyconfigs: XCrySDen-1.6.2-intel-2021b.eb --- .../t/Togl/Togl-2.0-GCCcore-11.2.0.eb | 49 +++++++++++++++++++ .../x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb | 40 +++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb diff --git a/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..613a304992dc --- /dev/null +++ b/easybuild/easyconfigs/t/Togl/Togl-2.0-GCCcore-11.2.0.eb @@ -0,0 +1,49 @@ +# Last contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'Togl' +version = '2.0' + +homepage = 'https://sourceforge.net/projects/togl/' +description = """A Tcl/Tk widget for OpenGL rendering.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/%(namelower)s/%(name)s/%(version)s/'] +sources = ['%(name)s%(version)s-src.tar.gz'] +patches = [ + 'Togl-2.0_configure.patch', + 'Togl-2.0_decl.patch', +] +checksums = [ + 'b7d4a90bbad3aca618d505ee99e7fd8fb04c829f63231dda2360f557ba3f7610', # Togl2.0-src.tar.gz + 'da97f36b60cd107444cd92453809135b14dc1e8775146b3ba0731da8002e6f9f', # Togl-2.0_configure.patch + '05db6b3ca5139f60616d074903883a3070fcfb1eb8c965b0938779b4f9a6ec6a', # Togl-2.0_decl.patch +] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Mesa', '21.1.7'), + ('Tk', '8.6.11'), + ('Tcl', '8.6.11'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -DTOGL_USE_FONTS=0" && ' + +configopts = "--prefix=%(installdir)s --exec-prefix=%(installdir)s " +configopts += "--with-tcl=$EBROOTTCL/lib --with-tk=$EBROOTTK/lib" + +sanity_check_paths = { + 'files': [], + 'dirs': ['include', 'lib', 'lib/%(name)s%(version)s'], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': 'lib/%(name)s%(version)s', + 'LIBRARY_PATH': 'lib/%(name)s%(version)s', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb new file mode 100644 index 000000000000..1efe81bd1884 --- /dev/null +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb @@ -0,0 +1,40 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +name = 'XCrySDen' +version = '1.6.2' + +homepage = "http://www.xcrysden.org/" +docurls = "http://www.xcrysden.org/Documentation.html" +description = """ +XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces +and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. +It also possesses some tools for analysis of properties in reciprocal space such as interactive selection +of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. +""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +source_urls = ["http://www.xcrysden.org/download/"] +sources = [SOURCELOWER_TAR_GZ] +patches = ['XCrySDen-1.6.2-no-bwidget-tcl-download.patch'] +checksums = [ + '811736ee598bec1a5b427fd10e4e063a30dd7cadae96a43a50b36ce90a4f503f', # xcrysden-1.6.2.tar.gz + 'e5f79c77116c6faf441d63f62bb3d22c5520163995b28e505d2168424a587bac', # XCrySDen-1.6.2-no-bwidget-tcl-download.patch +] + +dependencies = [ + ('Togl', '2.0'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('bwidget', '1.9.15'), +] + +sanity_check_commands = [ + 'xcrysden --help', + # requires DISPLAY + # 'xcrysden --xsf $EBROOTXCRYSDEN/share/%(namelower)s-%(version)s/examples/XSF_Files/GaAsH.xsf --print output.png \ + # && rm output.png', +] + +moduleclass = 'vis' From 0a30199b0ffda1cfb308de5cd0c0ee787949ea04 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 27 Nov 2023 13:59:11 +0100 Subject: [PATCH 0086/1193] Update WIEN2k-23.2_fix_system_stderr_redirection.patch --- .../w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch index 23b08d93cfb3..4c0a3adaeef7 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2_fix_system_stderr_redirection.patch @@ -1,3 +1,5 @@ +This fix removes the assumption that tcsh is being used to run the software. + --- SRC_Globals/W2kinit.F.orig 2023-11-08 17:54:06.183370012 +0100 +++ SRC_Globals/W2kinit.F 2023-11-08 18:29:21.436975434 +0100 @@ -403,7 +403,7 @@ From bc197a8db5f1c0778e7b5fca1c2010f2d33fcf31 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 27 Nov 2023 14:06:04 +0100 Subject: [PATCH 0087/1193] Update WIEN2k-23.2-intel-2021b.eb --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index cc8aed4ffbde..256edac87852 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -14,6 +14,13 @@ patches = [ '%(name)s-%(version)s_fix_libxc_for_lapw0_mpi.patch', '%(name)s-%(version)s_fix_system_stderr_redirection.patch', ] +checksums = [ + '3a71565a4fb114a2f9af9a1710bd3160781a7566bb2746bef1ba8af372b4d7b0', # WIEN2k_23.2.tar + '1cc480a4824d9185ad5918dfc68c47bcb7826114626c8133d573be901bbdca84', # WIEN2k-23.2_fix_libxc_for_lapw0_mpi.patch + 'eb3f987b1f839b9f10c315d3f7a57e181e46bc98bec3a18e5b9942689b75fcc7', + # WIEN2k-23.2_fix_system_stderr_redirection.patch +] + download_instructions = """ WIEN2k can be ordered at http://susi.theochem.tuwien.ac.at/index.html. From 9cdd94a69154d0c976899ff6ec08a03a63fe83df Mon Sep 17 00:00:00 2001 From: Neves-P Date: Mon, 27 Nov 2023 14:53:30 +0100 Subject: [PATCH 0088/1193] Correct sanity check --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 5538d37e58b2..606418a8eb0b 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -43,6 +43,6 @@ sanity_check_paths = { 'dirs': ['pythonmodule'] } -sanity_check_commands = [('python', "-c 'import waLBerla'")] +sanity_check_commands = [('mpirun -np 1 python -c "import waLBerla"')] moduleclass = 'chem' From cde486fcbd77b25be2101cd03e56ebf64c3723f9 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Tue, 28 Nov 2023 15:03:24 +0100 Subject: [PATCH 0089/1193] First import MPI from mpi4py, then import walberla in sanity check --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 606418a8eb0b..b1ffd350698f 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -25,7 +25,7 @@ builddependencies = [('CMake', '3.24.3')] dependencies = [ ('pybind11', '2.10.3'), ('Python', '3.10.8'), - ('Boost.MPI', '1.79.0'), + ('Boost.MPI', '1.77.0'), ('SciPy-bundle', '2023.02'), ] @@ -43,6 +43,6 @@ sanity_check_paths = { 'dirs': ['pythonmodule'] } -sanity_check_commands = [('mpirun -np 1 python -c "import waLBerla"')] +sanity_check_commands = [('python -c "from mpi4py import MPI; import waLBerla"')] moduleclass = 'chem' From ed713aabf66aadf02cbf66033563d360c403b0c0 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Tue, 28 Nov 2023 21:09:28 +0100 Subject: [PATCH 0090/1193] Fix mpi4py dep, Boost.MPI version --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index b1ffd350698f..4a9284487765 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -25,8 +25,9 @@ builddependencies = [('CMake', '3.24.3')] dependencies = [ ('pybind11', '2.10.3'), ('Python', '3.10.8'), - ('Boost.MPI', '1.77.0'), + ('Boost.MPI', '1.79.0'), ('SciPy-bundle', '2023.02'), + ('mpi4py', '3.1.4'), ] parallel = 1 From 6b663b2626aa52c5426c74f376273b7b2f3280fd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 29 Nov 2023 22:35:47 +0000 Subject: [PATCH 0091/1193] graph-tool upgraded to v2.55 --- easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb index 113291caf709..d13f7fb7c81c 100644 --- a/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/poppunk/poppunk-2.6.0-foss-2022a.eb @@ -28,7 +28,7 @@ dependencies = [ ('matplotlib', '3.5.2'), ('HDBSCAN', '0.8.29'), ('h5py', '3.7.0'), - ('graph-tool', '2.45'), + ('graph-tool', '2.55'), ('X11', '20220504'), ('pybind11', '2.9.2'), ('Eigen', '3.4.0'), From 557f3f9ece8213bd977abde81b5c5bb299e76ea6 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 30 Nov 2023 14:08:34 +0100 Subject: [PATCH 0092/1193] Use foss/2021a toolchain instead --- ...Op-1.2.4-GCCcore-10.3.0.eb => InterOp-1.2.4-foss-2021a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/InterOp/{InterOp-1.2.4-GCCcore-10.3.0.eb => InterOp-1.2.4-foss-2021a.eb} (92%) diff --git a/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb similarity index 92% rename from easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb index 36a6a7fe3c8b..b963949f0deb 100644 --- a/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb @@ -19,7 +19,7 @@ supporting prior releases of the software, with one exception: GA systems have been excluded.""" software_license = 'LicenseGPLv3' -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/Illumina/interop/archive/refs/tags'] sources = ['v%(version)s.tar.gz'] @@ -35,7 +35,7 @@ builddependencies = [ dependencies = [ ('Python', '3.9.5'), - ('SciPy-bundle', '2021.05', '', ('foss', '2021a')), + ('SciPy-bundle', '2021.05'), ] sanity_check_paths = { From be367d2c019f412fcab87a98e75724f0c52983c2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 8 Dec 2023 14:24:57 +0100 Subject: [PATCH 0093/1193] adding easyconfigs: Philosopher-5.0.0-GCC-11.3.0.eb --- .../Philosopher-5.0.0-GCC-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..bd2ddaf1dc9d --- /dev/null +++ b/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'Philosopher' +version = '5.0.0' + +homepage = 'https://philosopher.nesvilab.org/' +description = """Philosopher is a fast, easy-to-use, scalable, and versatile + data analysis software for mass spectrometry-based proteomics. Philosopher + is dependency-free and can analyze both traditional database searches and + open searches for post-translational modification (PTM) discovery.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/Nesvilab/philosopher/archive/'] +sources = [{'download_filename': 'v%s.tar.gz' % version, 'filename': SOURCE_TAR_GZ}] +checksums = ['0c6895c60c1c2543f7b0ad7f8baae4be39c9c519d6035c8fdd2ad8a2f83a99cc'] + +builddependencies = [ + ('Go', '1.21.2', '', SYSTEM), +] + +# see https://github.com/Nesvilab/philosopher/wiki/How-to-Build +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" deploy && go build -o philosopher' + +files_to_copy = [ + (['%(namelower)s'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From e438e4ab5c1b834d3d418d85af02068595e4a481 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 11 Dec 2023 13:09:25 +0100 Subject: [PATCH 0094/1193] adding easyconfigs: devbio-napari-0.10.1-foss-2022a.eb, PyOpenCL-2023.1.4-foss-2022a.eb, autopep8-2.0.4-foss-2022a.eb, pycodestyle-2.11.1-foss-2022a.eb --- .../a/autopep8/autopep8-2.0.4-foss-2022a.eb | 23 ++ .../devbio-napari-0.10.1-foss-2022a.eb | 224 ++++++++++++++++++ .../PyOpenCL/PyOpenCL-2023.1.4-foss-2022a.eb | 33 +++ .../pycodestyle-2.11.1-foss-2022a.eb | 22 ++ 4 files changed, 302 insertions(+) create mode 100644 easybuild/easyconfigs/a/autopep8/autopep8-2.0.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/autopep8/autopep8-2.0.4-foss-2022a.eb b/easybuild/easyconfigs/a/autopep8/autopep8-2.0.4-foss-2022a.eb new file mode 100644 index 000000000000..ebf66aa504a6 --- /dev/null +++ b/easybuild/easyconfigs/a/autopep8/autopep8-2.0.4-foss-2022a.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonPackage' + +name = 'autopep8' +version = '2.0.4' + +homepage = "https://github.com/hhatto/autopep8" +description = """A tool that automatically formats Python code to conform to the PEP 8 style guide.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['2913064abd97b3419d1cc83ea71f042cb821f87e45b9c88cad5ad3c4ea87fe0c'] + +dependencies = [ + ('Python', '3.10.4'), + ('pycodestyle', '2.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb new file mode 100644 index 000000000000..df5816da9ef2 --- /dev/null +++ b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb @@ -0,0 +1,224 @@ +easyblock = 'PythonBundle' + +name = 'devbio-napari' +version = '0.10.1' + +homepage = 'https://github.com/haesleinhuepf/devbio-napari' +description = """A bundle of napari plugins useful for 3D+t image + processing and analysis for studying developmental biology.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('napari', '0.4.18'), + ('jupyter-server', '1.21.0'), + ('JupyterLab', '3.5.0'), + ('Seaborn', '0.12.1'), + ('scikit-learn', '1.1.2'), + ('SimpleITK', '2.1.1.2'), + ('PyQtGraph', '0.13.3'), + ('Deprecated', '1.2.13'), + ('imagecodecs', '2022.9.26'), + ('HDBSCAN', '0.8.29'), + ('umap-learn', '0.5.3'), + ('PyOpenCL', '2023.1.4'), + ('Mako', '1.2.0'), + ('autopep8', '2.0.4'), + ('Qt5', '5.15.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('napari-tools-menu', '0.1.19', { + 'checksums': ['6b58ac45d7fe84bc5975e7a53142340d5d62beff9ade0f2f58d7a3a4a0a8e8f8'], + }), + ('napari-assistant', '0.4.7', { + 'checksums': ['e18e0509c77907dae7b5ec66bebf33ca4fc5833553a3115ecca513f4702e3603'], + }), + ('napari-time-slicer', '0.5.0', { + 'checksums': ['950d3b35d9f1657178201da73de56d038e9bf4e257cf120882081f2707f1e074'], + }), + ('napari-workflows', '0.2.10', { + 'checksums': ['d48f2020693b4b8c1dd639668a3b1588115beac8f19f42394fc241fc1672be12'], + }), + ('pyclesperanto_prototype', '0.24.1', { + 'checksums': ['b2f2cd56bc382813b9477f07f75ce5afbf4cc24c6fd1734a577f602442f7c027'], + }), + ('stackview', '0.7.2', { + 'checksums': ['f417319e3c14384144198bc26cc0e5909a2262e8778f2d7e7b68396690ae797b'], + }), + ('reikna', '0.8.0', { + 'checksums': ['7e96b53dfa3910069f83b3e085ad7b1ba9391b5ddf744ae3725bf43a7fee6322'], + }), + ('pystackreg', '0.2.7', { + 'checksums': ['c3df8b42bb9f4d44ec7ba44b3c061d7ea7481ab62318c24a25ffdb22afbaf3ab'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('czifile', '2019.7.2', { + 'checksums': ['04c0e6bed3b24d1bf42bc2cf899a5a08986641379305ce88600fd1c710486436'], + }), + ('imageio-ffmpeg', '0.4.9', { + 'checksums': ['39bcd1660118ef360fa4047456501071364661aa9d9021d3d26c58f1ee2081f5'], + }), + ('apoc', '0.12.0', { + 'checksums': ['c6e5264f2ac0420e5f8e2b23ad16927126d75280bb12f0341480ef9853973263'], + }), + ('ipycanvas', '0.13.1', { + 'checksums': ['f9c3940681bc38383390f8c46ea5d8445d6e11c6da6484c37d89df5ae1dac131'], + }), + ('ipyevents', '2.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['60c2a9e992bdc41e8577aa27e57b124efafa48a59a3bff886029fe5700d546b3'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('transforms3d', '0.4.1', { + 'checksums': ['31c755266a0b0a222488b8d039f6f325cf486c52728c03e307ce047b2fad1179'], + }), + ('comm', '0.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2da8d9ebb8dd7bfc247adaff99f24dce705638a8042b85cb995066793e391001'], + }), + # overwrites installed version + ('debugpy', '1.8.0', { + 'source_tmpl': SOURCE_ZIP, + 'checksums': ['12af2c55b419521e33d5fb21bd022df0b5eb267c3e178f1d374a63a2a6bdccd0'], + }), + # overwrites installed version + ('ipykernel', '6.27.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['dab88b47f112f9f7df62236511023c9bdeef67abc73af7c652e4ce4441601686'], + }), + # overwrites installed version + ('platformdirs', '2.6.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['83c8f6d04389165de7c9b6f0c682439697887bca0aa2f1c87ef1826be3584490'], + }), + # overwrites installed version + ('jupyter_core', '5.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e11e02cd8ae0a9de5c6c44abf5727df9f2581055afe00b22183f621ba3585805'], + }), + # overwrites installed version + ('traitlets', '5.14.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['f14949d23829023013c47df20b4a76ccd1a85effb786dc060f34de7948361b33'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('mdit_py_plugins', '0.4.0', { + 'checksums': ['d8ab27e9aed6c38aa716819fedfde15ca275715955f8a185a8e1cf90fb1d2c1b'], + }), + ('jupytext', '1.15.2', { + 'checksums': ['c9976e24d834e991906c1de55af4b6d512d764f6372aabae45fc1ea72b589173'], + }), + ('napari-accelerated-pixel-and-object-classification', '0.14.1', { + 'checksums': ['2f626a9c2d671bf32cade62df74666eef328e6dc3f6d7f3ab6091a992131fb5c'], + }), + ('napari_animation', '0.0.7', { + 'preinstallopts': 'sed -i "s/__version__/version/g" napari_animation/animation.py && ', + 'checksums': ['301cce1d4629b18e618b7e1f1ea8885058171388ee0248f58ee78bdb25e8d72c'], + }), + ('napari-blob-detection', '0.0.2', { + 'checksums': ['a036c6f05e852ca0d332358249ec6c442c1ebdb83781e0609d9b146990e6f938'], + }), + ('napari-brightness-contrast', '0.1.8', { + 'checksums': ['88e0db47817a487b0db2b426ccfea88a57cbbf0185bf3ee0770fba81ed205dda'], + }), + ('napari-clusters-plotter', '0.7.3', { + 'checksums': ['3947e0c3e2335046526e6b92159c013e3e7b498eecd5b766cf1cbdd0239776df'], + }), + ('napari-crop', '0.1.9', { + 'checksums': ['54949ae74ab2fe118d33309d31b8c7eb7368de65428f1008038b82232d8856bd'], + }), + ('napari-curtain', '0.1.1', { + 'checksums': ['611bbabc2194ea749066bcd3cf6363174259c709dc3177142415400ba015f98c'], + }), + ('napari-czifile2', '0.2.7', { + 'checksums': ['67ca9b3d72aac804aba4ee3b34083f59d21134ee426de95a797733573ac2ffab'], + }), + ('napari-folder-browser', '0.1.3', { + 'checksums': ['c7144f8c0b321a30b64ad58928ed2efe65029f19670f0a650070506ae4551b76'], + }), + ('napari-layer-details-display', '0.1.5', { + 'checksums': ['cbee36e6bfa34415a2a102b60e5fb803e8f6b72d4ebc527b0cffc5dda10b2ae0'], + }), + ('napari-mouse-controls', '0.1.3', { + 'checksums': ['0dd9ee41146a3cb73ff8cf9378e242331d2ea9b0c4088188b4bce1650a45c7e6'], + }), + ('napari-plot-profile', '0.2.2', { + 'checksums': ['1a1f087b23eaa71a16f0ffde66e965fd7f6b69e5d52b3664c7db295f30fed501'], + }), + ('napari-plugin-search', '0.1.4', { + 'checksums': ['6dcc0793d072777c8d0cfebff89281252e57e13f8e13a8e0458a9ba7d86a06a0'], + }), + ('napari_pyclesperanto_assistant', '0.22.1', { + # import napari_pyclesperanto_assistant fails without GUI + # but it has been tested with GUI by `unset SESSION_MANAGER && python -c "import napari_pyclesperanto_assistant"` + 'modulename': False, + 'checksums': ['6df5e59e105d91f49826d57b2c61091271f62bba9d061dcb9c0c12d3ca000843'], + }), + ('napari_pystackreg', '0.1.4', { + 'checksums': ['ea3fb0b3ecc7b90b64f44c1ced4a85a6cf8231b07e5985ad59a6c1c152cd4cb3'], + }), + ('napari-roi', '0.1.8', { + 'checksums': ['0123238ee652931ed0bc90421ddf76d1d58c0d4c89790a8512c5649e88620729'], + }), + ('napari-segment-blobs-and-things-with-membranes', '0.3.7', { + 'checksums': ['7decc02f61d8499094a61cde6f69c1af5669815b5c8d4f1854ac1536c8e76862'], + }), + ('napari-simpleitk-image-processing', '0.4.5', { + 'checksums': ['b690d38aa67cdce3ae9e9b38f5ea98aa2bb3fcfb7b41943c56c68ed5df70ba3c'], + }), + ('napari-skimage-regionprops', '0.10.1', { + 'checksums': ['a25f8a84ad78f5d09074a32d84996fb6ff900bf82369dfb50501872d23dc22bc'], + }), + ('napari-tabu', '0.1.5', { + 'checksums': ['106be1897bb0670af06cb6dba90dc9a9faa3c5e7ba5017a8b216315749649ac7'], + }), + ('napari-workflow-inspector', '0.2.2', { + 'checksums': ['c7f1709ab537fc3b7c51bf353da305b4fe0adb025ec066df2cbaa4764810ec4f'], + }), + ('napari-workflow-optimizer', '0.1.4', { + 'checksums': ['e756ab013740cdc89fbb2626291386579ec8ce30ec30153a1b79517d7790f9c2'], + }), + ('PlatyMatch', '0.0.3', { + 'checksums': ['8fc7c437c1565c51744320ef09a91de72366beebdaa44780eaac2598eb3d810b'], + }), + ('RedLionfish', '0.9', { + 'modulename': 'RedLionfishDeconv', + 'checksums': ['82b76bf093851fc062448e8b764e846701bf890e64d7e82bf7cf11a7cf2c235b'], + }), + ('the-segmentation-game', '0.2.0', { + 'checksums': ['4bbf4deadecb84efc893c6cea2d51e90374181589f2034050aa3cf8fa65872f3'], + }), + (name, version, { + # reqired npe2 version limit is not necessary since 0.10.1 + # see https://github.com/haesleinhuepf/devbio-napari/issues/41#issuecomment-1594583026 + 'preinstallopts': "sed -i 's/npe2.*/npe2/g' requirements.txt setup.cfg &&", + 'checksums': ['c0bd80fbd3087128690259e25ecc5b13f42c09a99617229f97d6b696279d32a0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'from devbio_napari._viewer import devbio_napari_viewer'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a.eb new file mode 100644 index 000000000000..d640ea4b99f9 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2023.1.4' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('pocl', '1.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2023.1.1', { + 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], + }), + ('pyopencl', version, { + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + 'checksums': ['220174efca900e9d5de5aef2aa1b77a6f2550501de92b035a91013aeae4d4c5e'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022a.eb b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022a.eb new file mode 100644 index 000000000000..3b0f7de3367d --- /dev/null +++ b/easybuild/easyconfigs/p/pycodestyle/pycodestyle-2.11.1-foss-2022a.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'pycodestyle' +version = '2.11.1' + +homepage = "https://pycodestyle.readthedocs.io" +description = """pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['41ba0e7afc9752dfb53ced5489e89f8186be00e599e712660695b7a75ff2663f'] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 577237e110709454eab994e88e724dbff0b700e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 11 Dec 2023 15:00:02 +0100 Subject: [PATCH 0095/1193] fix line too long --- .../d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb index df5816da9ef2..5bb95d3c8ba5 100644 --- a/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb +++ b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb @@ -168,7 +168,8 @@ exts_list = [ }), ('napari_pyclesperanto_assistant', '0.22.1', { # import napari_pyclesperanto_assistant fails without GUI - # but it has been tested with GUI by `unset SESSION_MANAGER && python -c "import napari_pyclesperanto_assistant"` + # but it has been tested with GUI with following command: + # `unset SESSION_MANAGER && python -c "import napari_pyclesperanto_assistant"` 'modulename': False, 'checksums': ['6df5e59e105d91f49826d57b2c61091271f62bba9d061dcb9c0c12d3ca000843'], }), From 484dd1e327a9df1129f994e5178e14235bcc00e5 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 12 Dec 2023 11:32:30 +0000 Subject: [PATCH 0096/1193] use new DualSPHysics easyblock --- .../DualSPHysics-5.0.175-GCC-11.2.0.eb | 27 ++----------------- 1 file changed, 2 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb index 8f34229debc2..d16213507176 100644 --- a/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/d/DualSPHysics/DualSPHysics-5.0.175-GCC-11.2.0.eb @@ -2,8 +2,6 @@ # Authors: Eduardo Miguel Firvida Donestevez # Robert Mijakovic ## -easyblock = 'CMakeMake' - name = 'DualSPHysics' version = '5.0.175' @@ -22,31 +20,10 @@ source_urls = ['https://github.com/DualSPHysics/DualSPHysics/archive/refs/tags/' sources = ['v%(version)s.tar.gz'] checksums = ['d65bb7b8b4a21582091a534142348e46cff0a288a97ef86643bc2dde15637575'] -srcdir = 'src/source' - builddependencies = [ ('CMake', '3.21.1'), + # only needed if EasyBuild is configured with rpath: + ('patchelf', '0.13'), ] -separate_build_dir = True - -buildopts = " && chmod +x %(builddir)s/%(name)s-%(version)s/bin/linux/*_linux64" - -install_cmd = "mkdir -p %(installdir)s/bin && " -install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/bin/linux/* %(installdir)s/bin && " -install_cmd += "cp -r %(builddir)s/%(name)s-%(version)s/src/lib/linux_gcc %(installdir)s/lib" - -local_bins = ['GenCase', 'PartVTK', 'IsoSurface', 'MeasureTool', 'GenCase_MkWord', - 'DualSPHysics4.0_LiquidGas', 'DualSPHysics4.0_LiquidGasCPU', 'DualSPHysics5.0', - 'DualSPHysics5.0CPU', 'DualSPHysics5.0_NNewtonian', 'DualSPHysics5.0_NNewtonianCPU'] - - -sanity_check_paths = { - 'files': ['bin/%s_linux64' % x for x in local_bins], - 'dirs': ["lib"], -} - -sanity_check_commands = ['%s_linux64 -h' % x for x in local_bins] - - moduleclass = 'cae' From b7e81417f33092f0bc526aead0b772b50afe555c Mon Sep 17 00:00:00 2001 From: Neves-P Date: Tue, 12 Dec 2023 13:16:07 +0100 Subject: [PATCH 0097/1193] Remove mpi call in sanity check --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 4a9284487765..40852333bbec 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -44,6 +44,6 @@ sanity_check_paths = { 'dirs': ['pythonmodule'] } -sanity_check_commands = [('python -c "from mpi4py import MPI; import waLBerla"')] +sanity_check_commands = [('python -c "import waLBerla"')] moduleclass = 'chem' From c36168487eee8863d31d84523eb569dada06f522 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Dec 2023 16:46:44 +0000 Subject: [PATCH 0098/1193] adding easyconfigs: CREST-2.12-intel-2022a.eb --- .../c/CREST/CREST-2.12-intel-2022a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb new file mode 100644 index 000000000000..d2bf9b29cbd9 --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb @@ -0,0 +1,34 @@ +# Author: Jasper Grimm (UoY) +# Update to 2.12: +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'CREST' +version = '2.12' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['390f0ac0aedafbd6bb75974fcffefe7e0232ad6c4ea0ab4f1a77e656a3ce263d'] + +builddependencies = [('CMake', '3.24.3')] + +sanity_check_paths = { + 'files': ['bin/%s' % name.lower()], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' From 8426ba7ceb9e827a2000fbc3aaf318a2389d4eaa Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Dec 2023 16:55:10 +0000 Subject: [PATCH 0099/1193] adding easyconfigs: CENSO-1.2.0-intel-2022a.eb --- .../c/CENSO/CENSO-1.2.0-intel-2022a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-intel-2022a.eb b/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-intel-2022a.eb new file mode 100644 index 000000000000..106afeed1b5a --- /dev/null +++ b/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-intel-2022a.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'PythonBundle' + +name = 'CENSO' +version = '1.2.0' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/CENSO_docs/censo.html' +description = """Commandline Energetic SOrting (CENSO) is a sorting algorithm for +efficient evaluation of Structure Ensembles (SE). The input ensemble (or single +structure) originating from a CREST[SQM/FF] run can be ranked by free energy at +DFT level and/or geometries can be optimized using DFT.""" + +citing = """The main publication for the CENSO program can be found at J. Phys. Chem. A 2021 +https://pubs.acs.org/doi/10.1021/acs.jpca.1c00971""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('xtb', '6.6.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/grimme-lab/CENSO/archive'], + 'sources': ['v.%(version)s.tar.gz'], + 'checksums': ['f1d77d8eb9d25fe4157491a5d298321f84999123970411831b059cea39aecad2'], + 'modulename': 'censo_qm' + }), +] + +sanity_check_paths = { + 'files': ['bin/censo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["censo --help"] + +moduleclass = 'chem' From 94603d9f4f5d8a100bb2f34c200a3074f3be1dd2 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Dec 2023 17:52:44 +0000 Subject: [PATCH 0100/1193] Missing runtime xtb added --- easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb index d2bf9b29cbd9..53aabae810f7 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb @@ -24,6 +24,8 @@ checksums = ['390f0ac0aedafbd6bb75974fcffefe7e0232ad6c4ea0ab4f1a77e656a3ce263d'] builddependencies = [('CMake', '3.24.3')] +dependencies = [('xtb', '6.6.0')] # required to run the program + sanity_check_paths = { 'files': ['bin/%s' % name.lower()], 'dirs': [], From aca18a8160e2cbe198e7c831e690dc759f818b23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 13 Dec 2023 10:51:17 +0100 Subject: [PATCH 0101/1193] fix RPATH problem --- .../easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb index bd2ddaf1dc9d..c852b7dea6c3 100644 --- a/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb @@ -19,8 +19,8 @@ builddependencies = [ ('Go', '1.21.2', '', SYSTEM), ] -# see https://github.com/Nesvilab/philosopher/wiki/How-to-Build -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" deploy && go build -o philosopher' +prebuildopts = 'export CC="$CC" CFLAGS="$CFLAGS" && ' +buildopts = "deploy && make philosopher" files_to_copy = [ (['%(namelower)s'], 'bin'), From 8766a0e66d6ff7e02b2d65c0b78f5415c9d3e842 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 13 Dec 2023 11:21:18 +0000 Subject: [PATCH 0102/1193] Dryrun added --- easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb index 53aabae810f7..730906444ae3 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb @@ -33,4 +33,7 @@ sanity_check_paths = { sanity_check_commands = ["crest -h", "crest --cite"] +test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' +test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' + moduleclass = 'chem' From f38e444fd14b5436bd9029a10051f2d598dab39d Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 13 Dec 2023 11:23:19 +0000 Subject: [PATCH 0103/1193] Style cleanup --- easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb index 730906444ae3..e825fbace004 100644 --- a/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-intel-2022a.eb @@ -26,6 +26,10 @@ builddependencies = [('CMake', '3.24.3')] dependencies = [('xtb', '6.6.0')] # required to run the program +# Simple test command just to check if the program is working: +test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' +test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' + sanity_check_paths = { 'files': ['bin/%s' % name.lower()], 'dirs': [], @@ -33,7 +37,4 @@ sanity_check_paths = { sanity_check_commands = ["crest -h", "crest --cite"] -test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' -test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' - moduleclass = 'chem' From 3bbe11da38fb5262c5fc65cb07a20d432f11bfdb Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 18 Dec 2023 13:44:16 +0100 Subject: [PATCH 0104/1193] Update XCrySDen-1.6.2-intel-2021b.eb drop to intel-compilers --- easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb index 1efe81bd1884..94909a3276d7 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb @@ -13,7 +13,7 @@ It also possesses some tools for analysis of properties in reciprocal space such of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. """ -toolchain = {'name': 'intel', 'version': '2021b'} +toolchain = {'name': 'intel-compilers', 'version': '2021b'} source_urls = ["http://www.xcrysden.org/download/"] sources = [SOURCELOWER_TAR_GZ] From 94acfc4247efd37262219a63d12b30f8f5ba1b35 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 19 Dec 2023 10:54:05 +0000 Subject: [PATCH 0105/1193] add phonopy-2.20.0-foss-2023a.eb --- .../p/phono3py/phono3py-2.7.0-foss-2023a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb new file mode 100644 index 000000000000..3d8fa1685fb5 --- /dev/null +++ b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'phono3py' +version = '2.7.0' + +homepage = 'http://phonopy.github.io/phono3py/' +description = """A simulation package of phonon-phonon interaction related properties.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +#toolchainopts = {'pic': True} + +source_urls = ['https://github.com/phonopy/phono3py/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] + +dependencies = [ + ('Python', '3.11.3'), + ('phonopy', '2.20.0'), +] + +preinstallopts = 'echo "extra_compile_args = -fopenmp" > site.cfg && ' +preinstallopts += 'echo "extra_link_args = -lgomp -llapacke -lpthread" >> site.cfg && ' +#preinstallopts = "export LDLAGS='-lgomp -llapacke -lpthread ' && export CFLAGS='-fopenmp ' && " +installopts = " -vvv" + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phono3py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phono3py --help"] + +sanity_pip_check = True + +moduleclass = 'lib' From 93187e134c92247df9aec26be48b6ac489fcf920 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Wed, 20 Dec 2023 17:22:08 +0100 Subject: [PATCH 0106/1193] adding easyconfigs: Elmer-9.0-foss-2022b.eb and patches: Elmer-9.0-Qwt-6.2-Fix.patch, Elmer-9.0-renderarea-Qt5.patch --- .../e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch | 24 +++++++++ .../e/Elmer/Elmer-9.0-foss-2022b.eb | 53 +++++++++++++++++++ .../e/Elmer/Elmer-9.0-renderarea-Qt5.patch | 10 ++++ 3 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch create mode 100644 easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch new file mode 100644 index 000000000000..7fb7622038ac --- /dev/null +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch @@ -0,0 +1,24 @@ +--- ElmerGUI/Application/src/convergenceview.h.orig 2020-11-10 20:52:44.000000000 +0100 ++++ ElmerGUI/Application/src/convergenceview.h 2023-12-15 11:13:53.627242099 +0100 +@@ -51,8 +51,8 @@ + #include + #include + #include +-/*#include <-- deprecated in Qwt6, using qwt_compat.h instead*/ +-#include ++/*#include <-- deprecated in Qwt6, using qwt_compat.h instead ++#include <-- Removed in Qwt 6.2 */ + #include + #include + +@@ -76,8 +76,8 @@ + + private: + int d_count; +- QwtArray d_x; +- QwtArray d_y; ++ QVector d_x; ++ QVector d_y; + }; + + class Curve diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb new file mode 100644 index 000000000000..ef467e35e85a --- /dev/null +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'Elmer' +version = '9.0' + +homepage = 'https://www.csc.fi/web/elmer/elmer' +description = """Elmer is an open source multiphysical simulation software mainly developed by +CSC - IT Center for Science (CSC). Elmer includes physical models of fluid dynamics, structural +mechanics, electromagnetics, heat transfer and acoustics, for example. These are described by +partial differential equations which Elmer solves by the Finite Element Method (FEM).""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'opt': True, 'optarch': True} + +source_urls = ['https://github.com/ElmerCSC/elmerfem/archive/'] +sources = ['release-%(version)s.tar.gz'] +patches = ['Elmer-9.0-DCRComplexSolve.patch', 'Elmer-9.0-Qwt-6.2-Fix.patch', 'Elmer-9.0-renderarea-Qt5.patch'] +checksums = [ + {'release-9.0.tar.gz': '08c5bf261e87ff37456c1aa0372db3c83efabe4473ea3ea0b8ec66f5944d1aa0'}, + {'Elmer-9.0-DCRComplexSolve.patch': '6419890b32f556fc4d531c92abed5dafb5c0867c420b73ec6477507ea6466dd9'}, + {'Elmer-9.0-Qwt-6.2-Fix.patch': 'c831c2072f6ce8f9753074832b14a3be0c5733272991b12a5d3c69b601ccb2aa'}, + {'Elmer-9.0-renderarea-Qt5.patch': '6218e8669477a1352faf72e52c1e7764451c6765ab2082f263054024115b2018'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Hypre', '2.27.0'), + ('MUMPS', '5.6.1', '-metis'), + ('Qt5', '5.15.7'), + ('Qwt', '6.2.0'), + # ('Trilinos', '12.0.1', '-Python-2.7.9'), +] + +configopts = '-DWITH_ELMERGUI:BOOL=TRUE -DWITH_QT5:BOOL=TRUE ' +configopts += '-DWITH_MPI:BOOL=TRUE ' +configopts += '-DCMAKE_C_COMPILER=$(which $CC) ' +configopts += '-DCMAKE_Fortran_COMPILER=$(which $F90) ' +configopts += '-DCMAKE_CXX_COMPILER=$(which $CXX) ' +configopts += '-DBLAS_LIBRARIES="-L$EBVARBLAS_LAPACK_INC_DIR $EBVARLIBBLAS" ' +configopts += '-DLAPACK_LIBRARIES="-L$EBVARBLAS_LAPACK_INC_DIR $EBVARLIBLAPACK" ' +configopts += '-DSCALAPACK_LIBRARIES="-L$EBVARSCALAPACK_LIB_DIR $EBVARLIBSCALAPACK" ' + +sanity_check_paths = { + 'files': ['lib/elmersolver/libelmersolver.so'] + + ['bin/%s' % x for x in ['elmerf90', 'ElmerGrid', 'elmerld', 'ElmerSolver', + 'ElmerSolver_mpi', 'GebhardtFactors', 'matc', 'Mesh2D', 'ViewFactors']], + 'dirs': ['share/elmersolver/include'] +} + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch new file mode 100644 index 000000000000..cc7a876581a9 --- /dev/null +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch @@ -0,0 +1,10 @@ +--- ElmerGUI/Application/twod/renderarea.cpp.orig 2020-11-10 20:52:44.000000000 +0100 ++++ ElmerGUI/Application/twod/renderarea.cpp 2023-12-15 11:43:20.493498704 +0100 +@@ -38,6 +38,7 @@ + * * + *****************************************************************************/ + #include ++#include + #include + #include + #include From 9f7288d7e94562ae4eff71a553c3931ac8b9fc83 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Wed, 20 Dec 2023 17:25:51 +0100 Subject: [PATCH 0107/1193] Add missing patch --- .../e/Elmer/Elmer-9.0-DCRComplexSolve.patch | 427 ++++++++++++++++++ 1 file changed, 427 insertions(+) create mode 100644 easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch new file mode 100644 index 000000000000..0c9cb3682f50 --- /dev/null +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch @@ -0,0 +1,427 @@ +--- fem/src/modules/DCRComplexSolve.F90.orig 2023-12-15 10:28:53.729618181 +0100 ++++ fem/src/modules/DCRComplexSolve.F90 2023-12-15 10:28:58.846691361 +0100 +@@ -205,7 +205,7 @@ + CALL Info( 'DCRComplexSolve', Message, Level=4 ) + CALL Info( 'DCRComplexSolve', '-------------------------------------', Level=4 ) + CALL Info( 'DCRComplexSolve', ' ', Level=4 ) +- CALL Info( 'DCRComplexSolve', 'Starting Assmebly', Level=4 ) ++ CALL Info( 'DCRComplexSolve', 'Starting Assembly', Level=4 ) + + CALL InitializeToZero( StiffMatrix, ForceVector ) + ! +@@ -426,14 +426,14 @@ + SUBROUTINE InputTensor( Tensor, IsScalar, Name, Material, n, NodeIndexes ) + !------------------------------------------------------------------------------ + REAL(KIND=dp) :: Tensor(:,:,:) +- INTEGER :: n, NodeIndexes(:) ++ INTEGER :: i, n, NodeIndexes(:) + LOGICAL :: IsScalar + CHARACTER(LEN=*) :: Name + TYPE(ValueList_t), POINTER :: Material + !------------------------------------------------------------------------------ + LOGICAL :: FirstTime = .TRUE., stat + REAL(KIND=dp), POINTER :: Hwrk(:,:,:) +- ++ INTEGER :: n1,n2,t1 + SAVE FirstTime, Hwrk + !------------------------------------------------------------------------------ + IF ( FirstTime ) THEN +@@ -444,30 +444,33 @@ + Tensor = 0.0d0 + + CALL ListGetRealArray( Material, Name, Hwrk, n, NodeIndexes, stat ) +- IsScalar = SIZE(HWrk,1) == 1 .AND. SIZE(HWrk,2) == 1 ++ n1 = MIN(SIZE(HWrk,1),3) ++ n2 = MIN(SIZE(Hwrk,2),3) ++ IsScalar = (n1==1 .AND. n2==1) + + IF ( .NOT. stat ) RETURN + +- IF ( SIZE(Hwrk,1) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,2)) +- Tensor( i,i,1:n ) = Hwrk( 1,1,1:n ) +- END DO +- +- ELSE IF ( SIZE(Hwrk,2) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) +- Tensor(i,i,1:n) = Hwrk(i,1,1:n) +- END DO +- ++ IF ( IsScalar ) THEN ++ t1 = SIZE(Tensor,1) ++ DO i=1,t1 ++ Tensor(i,i,1:n) = Hwrk(1,1,1:n) ++ END DO + ELSE +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) +- DO j=1,MIN(3,SIZE(Hwrk,2)) ++ IF ( n1 == 1 ) THEN ++ DO i=1,n2 ++ Tensor( i,i,1:n ) = Hwrk( 1,i,1:n ) ++ END DO ++ ELSE IF ( n2 == 1 ) THEN ++ DO i=1,n1 ++ Tensor(i,i,1:n) = Hwrk(i,1,1:n) ++ END DO ++ ELSE ++ DO i=1,n1 ++ DO j=1,n2 + Tensor( i,j,1:n ) = Hwrk(i,j,1:n) +- END DO +- END DO +- ++ END DO ++ END DO ++ END IF + END IF + !------------------------------------------------------------------------------ + END SUBROUTINE InputTensor +@@ -485,7 +488,8 @@ + !------------------------------------------------------------------------------ + LOGICAL :: FirstTime = .TRUE., stat + REAL(KIND=dp), POINTER :: Hwrk(:,:,:) +- ++ INTEGER :: i ++ INTEGER :: n1,n2 + SAVE FirstTime, Hwrk + !------------------------------------------------------------------------------ + IF ( FirstTime ) THEN +@@ -496,22 +500,20 @@ + Tensor = 0.0d0 + + CALL ListGetRealArray( Material, Name, Hwrk, n, NodeIndexes, stat ) +- IsScalar = SIZE(HWrk,1) == 1 .AND. SIZE(HWrk,2) == 1 ++ n1 = MIN(SIZE(HWrk,1),3) ++ n2 = MIN(SIZE(HWrk,2),3) ++ IsScalar = (n1==1 .AND. n2==1) + + IF ( .NOT. stat ) RETURN +- +- IF ( SIZE(Hwrk,1) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,2)) +- Tensor( i,1:n ) = Hwrk( 1,1,1:n ) ++ ++ IF ( n1 == 1 ) THEN ++ DO i=1,n2 ++ Tensor( i,1:n ) = Hwrk( 1,i,1:n ) + END DO +- + ELSE +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) ++ DO i=1,n1 + Tensor( i,1:n ) = Hwrk( i,1,1:n ) + END DO +- + END IF + !------------------------------------------------------------------------------ + END SUBROUTINE InputVector +@@ -1061,20 +1063,20 @@ + + !------------------------------------------------------------------------------ + +-contains ++ CONTAINS + + !------------------------------------------------------------------------------ + SUBROUTINE InputVector( Tensor, IsScalar, Name, Material, n, NodeIndexes ) + !------------------------------------------------------------------------------ + REAL(KIND=dp) :: Tensor(:,:) +- INTEGER :: n, NodeIndexes(:) ++ INTEGER :: i, n, NodeIndexes(:) + LOGICAL :: IsScalar + CHARACTER(LEN=*) :: Name + TYPE(ValueList_t), POINTER :: Material + !------------------------------------------------------------------------------ + LOGICAL :: FirstTime = .TRUE., stat + REAL(KIND=dp), POINTER :: Hwrk(:,:,:) +- ++ INTEGER :: n1,n2 + SAVE FirstTime, Hwrk + !------------------------------------------------------------------------------ + IF ( FirstTime ) THEN +@@ -1085,22 +1087,20 @@ + Tensor = 0.0d0 + + CALL ListGetRealArray( Material, Name, Hwrk, n, NodeIndexes, stat ) +- IsScalar = SIZE(HWrk,1) == 1 .AND. SIZE(HWrk,2) == 1 ++ n1 = MIN(SIZE(HWrk,1),3) ++ n2 = MIN(SIZE(HWrk,2),3) ++ IsScalar = (n1==1 .AND. n2==1) + + IF ( .NOT. stat ) RETURN + +- IF ( SIZE(Hwrk,1) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,2)) ++ IF ( n1==1 ) THEN ++ DO i=1,n2 + Tensor( i,1:n ) = Hwrk( 1,1,1:n ) + END DO +- + ELSE +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) ++ DO i=1,n1 + Tensor( i,1:n ) = Hwrk( i,1,1:n ) + END DO +- + END IF + !------------------------------------------------------------------------------ + END SUBROUTINE InputVector +@@ -1127,7 +1127,6 @@ + + INTEGER :: i,j,k,l,n,t,DIM,En,Pn + LOGICAL :: stat, GotIt +-! REAL(KIND=dp), POINTER :: Hwrk(:,:,:) + + REAL(KIND=dp) :: Grad(3,3), Normal(3), EdgeLength, Jump, JumpReal, JumpImag, & + GradReal(3,3),GradImag(3,3) +@@ -1148,17 +1147,6 @@ + + TYPE(GaussIntegrationPoints_t), TARGET :: IntegStuff + +-! LOGICAL :: First = .TRUE. +-! SAVE Hwrk, First +-!------------------------------------------------------------------------------ +- +-! Initialize: +-! ----------- +- +-! IF ( First ) THEN +-! First = .FALSE. +-! NULLIFY( Hwrk ) +-! END IF + + SELECT CASE( CurrentCoordinateSystem() ) + CASE( AxisSymmetric, CylindricSymmetric ) +@@ -1361,20 +1349,20 @@ + Temperature, Pressure ) + !------------------------------------------------------------------------------ + +-contains ++ CONTAINS + + !------------------------------------------------------------------------------ + SUBROUTINE InputTensor( Tensor, IsScalar, Name, Material, n, NodeIndexes ) + !------------------------------------------------------------------------------ + REAL(KIND=dp) :: Tensor(:,:,:) +- INTEGER :: n, NodeIndexes(:) ++ INTEGER :: i, n, NodeIndexes(:) + LOGICAL :: IsScalar + CHARACTER(LEN=*) :: Name + TYPE(ValueList_t), POINTER :: Material + !------------------------------------------------------------------------------ + LOGICAL :: FirstTime = .TRUE., stat + REAL(KIND=dp), POINTER :: Hwrk(:,:,:) +- ++ INTEGER :: n1,n2 + SAVE FirstTime, Hwrk + !------------------------------------------------------------------------------ + IF ( FirstTime ) THEN +@@ -1385,30 +1373,27 @@ + Tensor = 0.0d0 + + CALL ListGetRealArray( Material, Name, Hwrk, n, NodeIndexes, stat ) +- IsScalar = SIZE(HWrk,1) == 1 .AND. SIZE(HWrk,2) == 1 + +- IF ( .NOT. stat ) RETURN ++ n1 = MIN(SIZE(HWrk,1),3) ++ n2 = MIN(SIZE(Hwrk,2),3) ++ IsScalar = (n1==1 .AND. n2==1) + +- IF ( SIZE(Hwrk,1) == 1 ) THEN ++ IF ( .NOT. stat ) RETURN + +- DO i=1,MIN(3,SIZE(Hwrk,2)) ++ IF ( n1 == 1 ) THEN ++ DO i=1,n2 + Tensor( i,i,1:n ) = Hwrk( 1,1,1:n ) + END DO +- +- ELSE IF ( SIZE(Hwrk,2) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) ++ ELSE IF ( n2 == 1 ) THEN ++ DO i=1,n1 + Tensor(i,i,1:n) = Hwrk(i,1,1:n) + END DO +- + ELSE +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) +- DO j=1,MIN(3,SIZE(Hwrk,2)) ++ DO i=1,n1 ++ DO j=1,n2 + Tensor( i,j,1:n ) = Hwrk(i,j,1:n) + END DO + END DO +- + END IF + !------------------------------------------------------------------------------ + END SUBROUTINE InputTensor +@@ -1419,14 +1404,14 @@ + SUBROUTINE InputVector( Tensor, IsScalar, Name, Material, n, NodeIndexes ) + !------------------------------------------------------------------------------ + REAL(KIND=dp) :: Tensor(:,:) +- INTEGER :: n, NodeIndexes(:) ++ INTEGER :: i, n, NodeIndexes(:) + LOGICAL :: IsScalar + CHARACTER(LEN=*) :: Name + TYPE(ValueList_t), POINTER :: Material + !------------------------------------------------------------------------------ + LOGICAL :: FirstTime = .TRUE., stat + REAL(KIND=dp), POINTER :: Hwrk(:,:,:) +- ++ INTEGER :: n1,n2 + SAVE FirstTime, Hwrk + !------------------------------------------------------------------------------ + IF ( FirstTime ) THEN +@@ -1437,22 +1422,20 @@ + Tensor = 0.0d0 + + CALL ListGetRealArray( Material, Name, Hwrk, n, NodeIndexes, stat ) +- IsScalar = SIZE(HWrk,1) == 1 .AND. SIZE(HWrk,2) == 1 ++ n1 = MIN(SIZE(HWrk,1),3) ++ n2 = MIN(SIZE(Hwrk,2),3) + ++ IsScalar = (n1==1 .AND. n2==1) + IF ( .NOT. stat ) RETURN + +- IF ( SIZE(Hwrk,1) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,2)) ++ IF ( n1 == 1 ) THEN ++ DO i=1,n2 + Tensor( i,1:n ) = Hwrk( 1,1,1:n ) + END DO +- + ELSE +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) ++ DO i=1,n1 + Tensor( i,1:n ) = Hwrk( i,1,1:n ) + END DO +- + END IF + !------------------------------------------------------------------------------ + END SUBROUTINE InputVector +@@ -1497,9 +1480,6 @@ + LOGICAL :: notScalar = .TRUE. + TYPE( ValueList_t ), POINTER :: Material + TYPE(GaussIntegrationPoints_t), TARGET :: IntegStuff +- +-! LOGICAL :: First = .TRUE. +-! SAVE Hwrk, First + !------------------------------------------------------------------------------ + + ! Initialize: +@@ -1720,14 +1700,14 @@ + SUBROUTINE InputTensor( Tensor, IsScalar, Name, Material, n, NodeIndexes ) + !------------------------------------------------------------------------------ + REAL(KIND=dp) :: Tensor(:,:,:) +- INTEGER :: n, NodeIndexes(:) ++ INTEGER :: i, n, NodeIndexes(:) + LOGICAL :: IsScalar + CHARACTER(LEN=*) :: Name + TYPE(ValueList_t), POINTER :: Material + !------------------------------------------------------------------------------ + LOGICAL :: FirstTime = .TRUE., stat + REAL(KIND=dp), POINTER :: Hwrk(:,:,:) +- ++ INTEGER :: n1,n2 + SAVE FirstTime, Hwrk + !------------------------------------------------------------------------------ + IF ( FirstTime ) THEN +@@ -1738,30 +1718,27 @@ + Tensor = 0.0d0 + + CALL ListGetRealArray( Material, Name, Hwrk, n, NodeIndexes, stat ) +- IsScalar = SIZE(HWrk,1) == 1 .AND. SIZE(HWrk,2) == 1 +- +- IF ( .NOT. stat ) RETURN + +- IF ( SIZE(Hwrk,1) == 1 ) THEN ++ n1 = MIN(SIZE(HWrk,1),3) ++ n2 = MIN(SIZE(HWrk,2),3) ++ IsScalar = (n1==1 .AND. n2==1) + +- DO i=1,MIN(3,SIZE(Hwrk,2)) ++ IF ( .NOT. stat ) RETURN ++ ++ IF ( n1 == 1 ) THEN ++ DO i=1,n2 + Tensor( i,i,1:n ) = Hwrk( 1,1,1:n ) + END DO +- +- ELSE IF ( SIZE(Hwrk,2) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) ++ ELSE IF ( n2 == 1 ) THEN ++ DO i=1,n1 + Tensor(i,i,1:n) = Hwrk(i,1,1:n) + END DO +- + ELSE +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) +- DO j=1,MIN(3,SIZE(Hwrk,2)) ++ DO i=1,n1 ++ DO j=1,n2 + Tensor( i,j,1:n ) = Hwrk(i,j,1:n) + END DO + END DO +- + END IF + !------------------------------------------------------------------------------ + END SUBROUTINE InputTensor +@@ -1772,14 +1749,14 @@ + SUBROUTINE InputVector( Tensor, IsScalar, Name, Material, n, NodeIndexes ) + !------------------------------------------------------------------------------ + REAL(KIND=dp) :: Tensor(:,:) +- INTEGER :: n, NodeIndexes(:) ++ INTEGER :: i, n, NodeIndexes(:) + LOGICAL :: IsScalar + CHARACTER(LEN=*) :: Name + TYPE(ValueList_t), POINTER :: Material + !------------------------------------------------------------------------------ + LOGICAL :: FirstTime = .TRUE., stat + REAL(KIND=dp), POINTER :: Hwrk(:,:,:) +- ++ INTEGER :: n1, n2 + SAVE FirstTime, Hwrk + !------------------------------------------------------------------------------ + IF ( FirstTime ) THEN +@@ -1790,22 +1767,20 @@ + Tensor = 0.0d0 + + CALL ListGetRealArray( Material, Name, Hwrk, n, NodeIndexes, stat ) +- IsScalar = SIZE(HWrk,1) == 1 .AND. SIZE(HWrk,2) == 1 ++ n1 = MIN(SIZE(HWrk,1),3) ++ n2 = MIN(SIZE(HWrk,2),3) + ++ IsScalar = (n1 == 1 .AND. n2 == 1 ) + IF ( .NOT. stat ) RETURN + +- IF ( SIZE(Hwrk,1) == 1 ) THEN +- +- DO i=1,MIN(3,SIZE(Hwrk,2)) ++ IF ( n1 == 1 ) THEN ++ DO i=1,n2 + Tensor( i,1:n ) = Hwrk( 1,1,1:n ) + END DO +- + ELSE +- +- DO i=1,MIN(3,SIZE(Hwrk,1)) ++ DO i=1,n1 + Tensor( i,1:n ) = Hwrk( i,1,1:n ) + END DO +- + END IF + !------------------------------------------------------------------------------ + END SUBROUTINE InputVector From 754664f8234f7f17194336a60edbdf17076dfe95 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Thu, 21 Dec 2023 08:43:32 +0100 Subject: [PATCH 0108/1193] Add missing patch --- .../q/Qwt/Qwt-6.2.0-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b37850e86e20 --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Qwt' +version = '6.2.0' + +homepage = 'https://qwt.sourceforge.io/' +description = """The Qwt library contains GUI Components and utility classes which are primarily useful for programs + with a technical background.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Qwt-6.2.0_fix-install-prefix.patch'] +checksums = [ + '9194f6513955d0fd7300f67158175064460197abab1a92fa127a67a4b0b71530', # qwt-6.2.0.tar.bz2 + 'ac5c329c0693d565b461cdd3b36c1b96b4d09885e1e0c10929fc7a9021c03bad', # Qwt-6.2.0_fix-install-prefix.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('Qt5', '5.15.7'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export QWT_PREFIX=%(installdir)s && ' +prebuildopts += "qmake qwt.pro && " + +sanity_check_paths = { + 'files': ['lib/libqwt.%s' % SHLIB_EXT, 'lib/pkgconfig/Qt5Qwt6.pc'], + 'dirs': ['doc', 'features', 'include', 'plugins'], +} + +moduleclass = 'lib' From 91e6ecf9f1dfb36ea9e46817f6957060f9275109 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 21 Dec 2023 13:02:44 +0100 Subject: [PATCH 0109/1193] adding easyconfigs: GIMIC-2.2.1-foss-2022a.eb and patches: GIMIC-2.2.1_fix-install-prefix.patch --- .../g/GIMIC/GIMIC-2.2.1-foss-2022a.eb | 49 +++++++++++++++++++ .../GIMIC-2.2.1_fix-install-prefix.patch | 10 ++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1_fix-install-prefix.patch diff --git a/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb new file mode 100644 index 000000000000..753e2426e13a --- /dev/null +++ b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = "CMakeMake" + +name = 'GIMIC' +version = '2.2.1' + +homepage = 'https://gimic.readthedocs.io' +description = """The GIMIC program calculates magnetically induced currents in molecules. + You need to provide this program with a density matrix in atomic-orbital (AO) basis + and three (effective) magnetically perturbed AO density matrices in the proper format. +Currently ACES2, Turbomole, G09, QChem, FERMION++, and LSDalton can produce these matrices.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'qmcurrents' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['GIMIC-%(version)s_fix-install-prefix.patch'] +checksums = [ + {'v2.2.1.tar.gz': '57672db21f4038b13743e9cca7861a877f8221e5929d931210fa7114284e0731'}, + {'GIMIC-2.2.1_fix-install-prefix.patch': '6e09bcebc2756a00a75ff6b16cde52124a339bdeb9781b1da004618837ee68b8'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), +] + +# allow mismatches (old GCC behaviour up to version 9) +preconfigopts = 'FCFLAGS="$FCFLAGS -fallow-argument-mismatch" ' +# enable OpenMP and disable MPI (see qmcurrents/gimic#169) +configopts = '-DENABLE_OPENMP=ON -DENABLE_MPI=OFF ' +# enable numerical libraries in this toolchain +configopts += '-DENABLE_MKL_FLAG=OFF -DENABLE_BLAS=ON -DENABLE_LAPACK=ON ' + +sanity_check_paths = { + 'files': ['bin/gimic', 'lib/libgimic2.a'], + 'dirs': ['include', 'bin/QCTools', 'lib/python/site-packages'], +} + +modextrapaths = { + 'PYTHONPATH': ['lib/python/site-packages', 'bin/QCTools'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1_fix-install-prefix.patch b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1_fix-install-prefix.patch new file mode 100644 index 000000000000..8a3a505b28c6 --- /dev/null +++ b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1_fix-install-prefix.patch @@ -0,0 +1,10 @@ +# Obey CMAKE_INSTALL_PREFIX +# July 10th 2018 by B. Hajgato (Free University Brussels - VUB) +--- cmake/custom/own.cmake.orig 2018-04-20 09:44:47.000000000 +0200 ++++ cmake/custom/own.cmake 2018-07-10 16:08:05.999455805 +0200 +@@ -1,4 +1,4 @@ +-set(CMAKE_INSTALL_PREFIX ${PROJECT_BINARY_DIR}) ++#set(CMAKE_INSTALL_PREFIX ${PROJECT_BINARY_DIR}) + + include(GNUInstallDirs) + From 20dec686c70e05f40329c77a8ef13613e19b582d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 15:08:56 +0100 Subject: [PATCH 0110/1193] Update and rename XCrySDen-1.6.2-intel-2021b.eb to XCrySDen-1.6.2-intel-compilers-2021.4.0.eb --- ...ntel-2021b.eb => XCrySDen-1.6.2-intel-compilers-2021.4.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/x/XCrySDen/{XCrySDen-1.6.2-intel-2021b.eb => XCrySDen-1.6.2-intel-compilers-2021.4.0.eb} (95%) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb similarity index 95% rename from easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb rename to easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb index 94909a3276d7..4cd4230723d7 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb @@ -13,7 +13,7 @@ It also possesses some tools for analysis of properties in reciprocal space such of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. """ -toolchain = {'name': 'intel-compilers', 'version': '2021b'} +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} source_urls = ["http://www.xcrysden.org/download/"] sources = [SOURCELOWER_TAR_GZ] From a88bdca43fe83d284a33ed16eca4942876994c64 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Thu, 21 Dec 2023 16:31:21 +0100 Subject: [PATCH 0111/1193] Update XCrySDen-1.6.2-intel-compilers-2021.4.0.eb --- .../x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb index 4cd4230723d7..1efe81bd1884 100644 --- a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb @@ -13,7 +13,7 @@ It also possesses some tools for analysis of properties in reciprocal space such of k-paths in the Brillouin zone for the band-structure plots, and visualisation of Fermi surfaces. """ -toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} +toolchain = {'name': 'intel', 'version': '2021b'} source_urls = ["http://www.xcrysden.org/download/"] sources = [SOURCELOWER_TAR_GZ] From 1bba3097286094aa6f9aa96b580aa50950177d82 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Thu, 21 Dec 2023 21:12:59 +0100 Subject: [PATCH 0112/1193] Add description to patches --- easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch | 1 + easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch | 1 + easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch | 1 + 3 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch index 0c9cb3682f50..744941d4d92a 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch @@ -1,3 +1,4 @@ +Backport to 9.0 to allow compile with foss/2022b compiler. --- fem/src/modules/DCRComplexSolve.F90.orig 2023-12-15 10:28:53.729618181 +0100 +++ fem/src/modules/DCRComplexSolve.F90 2023-12-15 10:28:58.846691361 +0100 @@ -205,7 +205,7 @@ diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch index 7fb7622038ac..4ab1d529f296 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch @@ -1,3 +1,4 @@ +Fix for recent Qwt --- ElmerGUI/Application/src/convergenceview.h.orig 2020-11-10 20:52:44.000000000 +0100 +++ ElmerGUI/Application/src/convergenceview.h 2023-12-15 11:13:53.627242099 +0100 @@ -51,8 +51,8 @@ diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch index cc7a876581a9..e91976f2ceb6 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch @@ -1,3 +1,4 @@ +Fix for recent Qt5 --- ElmerGUI/Application/twod/renderarea.cpp.orig 2020-11-10 20:52:44.000000000 +0100 +++ ElmerGUI/Application/twod/renderarea.cpp 2023-12-15 11:43:20.493498704 +0100 @@ -38,6 +38,7 @@ From b08ba66f7c6db32ba58c531309b4fd3f502bf8cf Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Fri, 22 Dec 2023 06:22:37 +0100 Subject: [PATCH 0113/1193] Update patches checksums --- easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb index ef467e35e85a..041ad527bbdc 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb @@ -17,9 +17,9 @@ sources = ['release-%(version)s.tar.gz'] patches = ['Elmer-9.0-DCRComplexSolve.patch', 'Elmer-9.0-Qwt-6.2-Fix.patch', 'Elmer-9.0-renderarea-Qt5.patch'] checksums = [ {'release-9.0.tar.gz': '08c5bf261e87ff37456c1aa0372db3c83efabe4473ea3ea0b8ec66f5944d1aa0'}, - {'Elmer-9.0-DCRComplexSolve.patch': '6419890b32f556fc4d531c92abed5dafb5c0867c420b73ec6477507ea6466dd9'}, - {'Elmer-9.0-Qwt-6.2-Fix.patch': 'c831c2072f6ce8f9753074832b14a3be0c5733272991b12a5d3c69b601ccb2aa'}, - {'Elmer-9.0-renderarea-Qt5.patch': '6218e8669477a1352faf72e52c1e7764451c6765ab2082f263054024115b2018'}, + {'Elmer-9.0-DCRComplexSolve.patch': '360d39251cd09423e4caa7cd7b150817fa17724c5eabc00b5427b113de9e4708'}, + {'Elmer-9.0-Qwt-6.2-Fix.patch': '9abf73537ee1053bd3e49c55fa19b83043ba51fb4a4176600964da0b5cd5a9ca'}, + {'Elmer-9.0-renderarea-Qt5.patch': '745b98335b5ba43bef7a4ee7123b00bdb4f784c875d138a16dea1d0797567cd9'}, ] builddependencies = [ From 8fac35abe3903b64446062ede88afa6f1e626b9e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 22 Dec 2023 15:17:24 +0100 Subject: [PATCH 0114/1193] adding easyconfigs: q2-krona-20220124-GCCcore-11.3.0.eb --- .../q2-krona-20220124-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1b0746297b38 --- /dev/null +++ b/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'q2-krona' +version = '20220124' +_commit = 'd34c526' + +homepage = 'https://library.qiime2.org/plugins/q2-krona/39/' +description = """QIIME2 plugin for creating Krona plots""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'sources': [{ + 'source_urls': ['https://github.com/kaanb93/q2-krona/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, + 'checksums': ['cf8f5bf6b10e89d35fbfa4fc401b965396c03ff86a964dead8634205171a1ed9'], + }], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From c11247eda068fcc7c10997fa868af10817190542 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 22 Dec 2023 15:21:15 +0100 Subject: [PATCH 0115/1193] fix checksum location --- .../easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb index 1b0746297b38..a3b32792201f 100644 --- a/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb @@ -25,8 +25,8 @@ exts_list = [ 'source_urls': ['https://github.com/kaanb93/q2-krona/archive'], 'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ, - 'checksums': ['cf8f5bf6b10e89d35fbfa4fc401b965396c03ff86a964dead8634205171a1ed9'], }], + 'checksums': ['cf8f5bf6b10e89d35fbfa4fc401b965396c03ff86a964dead8634205171a1ed9'], }), ] From 844fc7194b359c12e0a71363f3d6682cccc17536 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 26 Dec 2023 13:49:06 +0100 Subject: [PATCH 0116/1193] replace pyparsing with compatible version --- .../g/GIMIC/GIMIC-2.2.1-foss-2022a.eb | 24 +++++++++++++++---- 1 file changed, 20 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb index 753e2426e13a..f41a09d3499c 100644 --- a/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb @@ -36,14 +36,30 @@ preconfigopts = 'FCFLAGS="$FCFLAGS -fallow-argument-mismatch" ' configopts = '-DENABLE_OPENMP=ON -DENABLE_MPI=OFF ' # enable numerical libraries in this toolchain configopts += '-DENABLE_MKL_FLAG=OFF -DENABLE_BLAS=ON -DENABLE_LAPACK=ON ' +configopts += '-DPYTHON_VERSION=%(pyshortver)s ' -sanity_check_paths = { - 'files': ['bin/gimic', 'lib/libgimic2.a'], - 'dirs': ['include', 'bin/QCTools', 'lib/python/site-packages'], +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, } +exts_list = [ + ('pyparsing', '2.4.7', { + 'checksums': ['c203ec8783bf771a155b207279b9bccb8dea02d8f0c9e5f8ead507bc3246ecc1'], + }), +] modextrapaths = { - 'PYTHONPATH': ['lib/python/site-packages', 'bin/QCTools'], + 'PYTHONPATH': ['bin/QCTools', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bin/gimic', 'lib/libgimic2.a'], + 'dirs': ['include', 'bin/QCTools', 'lib/python%(pyshortver)s/site-packages'], } +sanity_check_commands = ['gimic --help'] + moduleclass = 'chem' From afa35ba031bb8f966d0bd52c42a62bbfbdc112cf Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Wed, 27 Dec 2023 15:24:10 +0100 Subject: [PATCH 0117/1193] Update patches with backport PR and commit references --- .../easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch | 3 +++ easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch | 2 ++ easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb | 6 +++--- .../easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch | 3 +++ 4 files changed, 11 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch index 744941d4d92a..e28233343265 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-DCRComplexSolve.patch @@ -1,4 +1,7 @@ Backport to 9.0 to allow compile with foss/2022b compiler. +See history of https://github.com/ElmerCSC/elmerfem/commits/devel/fem/src/modules/DCRComplexSolve.F90 +and commit "Try to fix some strange compile errors appearing after all these years in DCRComplexSolve.F90" +https://github.com/ElmerCSC/elmerfem/commit/54fd87054f687305644b92d0525a3f0cd4423a93 --- fem/src/modules/DCRComplexSolve.F90.orig 2023-12-15 10:28:53.729618181 +0100 +++ fem/src/modules/DCRComplexSolve.F90 2023-12-15 10:28:58.846691361 +0100 @@ -205,7 +205,7 @@ diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch index 4ab1d529f296..74e7c1458485 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-Qwt-6.2-Fix.patch @@ -1,4 +1,6 @@ Fix for recent Qwt +See PR https://github.com/ElmerCSC/elmerfem/pull/294 ( Compatibility with Qwt 6.2. Fix for #293 #294 ) +and commit https://github.com/ElmerCSC/elmerfem/commit/48e9430ccb858ca5bda28b967a0c84b51e2404b2 --- ElmerGUI/Application/src/convergenceview.h.orig 2020-11-10 20:52:44.000000000 +0100 +++ ElmerGUI/Application/src/convergenceview.h 2023-12-15 11:13:53.627242099 +0100 @@ -51,8 +51,8 @@ diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb index 041ad527bbdc..f477fdf3c2b9 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb @@ -17,9 +17,9 @@ sources = ['release-%(version)s.tar.gz'] patches = ['Elmer-9.0-DCRComplexSolve.patch', 'Elmer-9.0-Qwt-6.2-Fix.patch', 'Elmer-9.0-renderarea-Qt5.patch'] checksums = [ {'release-9.0.tar.gz': '08c5bf261e87ff37456c1aa0372db3c83efabe4473ea3ea0b8ec66f5944d1aa0'}, - {'Elmer-9.0-DCRComplexSolve.patch': '360d39251cd09423e4caa7cd7b150817fa17724c5eabc00b5427b113de9e4708'}, - {'Elmer-9.0-Qwt-6.2-Fix.patch': '9abf73537ee1053bd3e49c55fa19b83043ba51fb4a4176600964da0b5cd5a9ca'}, - {'Elmer-9.0-renderarea-Qt5.patch': '745b98335b5ba43bef7a4ee7123b00bdb4f784c875d138a16dea1d0797567cd9'}, + {'Elmer-9.0-DCRComplexSolve.patch': '456e9b255c4cebffd04c1243001a284fcdbda27cb586640f3f852c67511881eb'}, + {'Elmer-9.0-Qwt-6.2-Fix.patch': 'c21b83364e08d2cd8bf3f2d62dfd16ed4f9bc478b8808cf36ecffa5174247b32'}, + {'Elmer-9.0-renderarea-Qt5.patch': '66c185f4e15ce738b85887b138258e70d94d7ae786e52b863624a4b538761639'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch index e91976f2ceb6..643e538daac7 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-renderarea-Qt5.patch @@ -1,4 +1,7 @@ Fix for recent Qt5 +See https://github.com/ElmerCSC/elmerfem/issues/233 +and https://github.com/ElmerCSC/elmerfem/commit/e057b0d46a6d1708a0d322bc73d70594a63de447 +history for https://github.com/ElmerCSC/elmerfem/commits/devel/ElmerGUI/Application/twod/renderarea.cpp --- ElmerGUI/Application/twod/renderarea.cpp.orig 2020-11-10 20:52:44.000000000 +0100 +++ ElmerGUI/Application/twod/renderarea.cpp 2023-12-15 11:43:20.493498704 +0100 @@ -38,6 +38,7 @@ From 253636ff975467b7b911463f7cbef4ce753189d4 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Wed, 27 Dec 2023 15:41:35 +0100 Subject: [PATCH 0118/1193] Add sanity check command and remove Trilinos --- easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb index f477fdf3c2b9..eaea84ef6b4b 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb @@ -31,7 +31,6 @@ dependencies = [ ('MUMPS', '5.6.1', '-metis'), ('Qt5', '5.15.7'), ('Qwt', '6.2.0'), - # ('Trilinos', '12.0.1', '-Python-2.7.9'), ] configopts = '-DWITH_ELMERGUI:BOOL=TRUE -DWITH_QT5:BOOL=TRUE ' @@ -50,4 +49,6 @@ sanity_check_paths = { 'dirs': ['share/elmersolver/include'] } +sanity_check_commands = ["ElmerSolver -v"] + moduleclass = 'cae' From 155479a11dcfafe8bfaf6c058f4c9d6f68b87ce3 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Fri, 29 Dec 2023 13:10:35 +0000 Subject: [PATCH 0119/1193] add checksums --- easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb index 3d8fa1685fb5..fa82882d6c5d 100644 --- a/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://github.com/phonopy/phono3py/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] +checksums = ['8d2c6d52d4b9a25783d69fb3a502394ed02eba7d573c5f1a3e43fd74ac1e5ed3'] + dependencies = [ ('Python', '3.11.3'), ('phonopy', '2.20.0'), From 62eb3503d56e2b01c5f94428ba91598ccee7c1de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Dec 2023 21:57:07 +0100 Subject: [PATCH 0120/1193] adding easyconfigs: EasyBuild-4.9.0.eb --- .../e/EasyBuild/EasyBuild-4.9.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.0.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.0.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.0.eb new file mode 100644 index 000000000000..b719705413e8 --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.9.0.eb @@ -0,0 +1,44 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.9.0' + +homepage = 'https://easybuilders.github.io/easybuild' +description = """EasyBuild is a software build and installation framework + written in Python that allows you to install software in a structured, + repeatable and robust way.""" + +toolchain = SYSTEM + +source_urls = [ + # easybuild-framework + 'https://files.pythonhosted.org/packages/13/53/816fd9cabba920ab7457c4a9dba3225ede9cca7284ec910c5216e98ae3d2/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/6c/fb/86e8d0e3a7e7b4ec5c2953b369f0bcf452a024b2504fa1fa1b9065ab8955/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/6c/65/fb99bd1e1786d24c9bb93bffe7f534c147ff26e806f501b76677c541b861/', +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + {'easybuild-framework-4.9.0.tar.gz': 'a708437d49570b778ab7f98a0504ac4fa3185d93d31515becd8dee652a6919b2'}, + {'easybuild-easyblocks-4.9.0.tar.gz': 'feb930d927803ed10a26233051973ca016f17e4ff9df213228ff9f90ad96cc3d'}, + {'easybuild-easyconfigs-4.9.0.tar.gz': '767f8d1d03fd4b9eb4d063d5f386f4284136d3efa7ef0b11b3d3d34a2f2040f9'}, +] + +# order matters a lot, to avoid having dependencies auto-resolved (--no-deps easy_install option doesn't work?) +# EasyBuild is a (set of) Python packages, so it depends on Python +# usually, we want to use the system Python, so no actual Python dependency is listed +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +local_pyshortver = '.'.join(SYS_PYTHON_VERSION.split('.')[:2]) + +sanity_check_paths = { + 'files': ['bin/eb'], + 'dirs': ['lib/python%s/site-packages' % local_pyshortver], +} + +moduleclass = 'tools' From 2efd9b9ae5edee3c07a898a1dd523f17e2d3dec7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Dec 2023 22:33:31 +0100 Subject: [PATCH 0121/1193] bump version to 4.9.1dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 9f8a58a694dc..52ad359c69c8 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.0' +VERSION = '4.9.1.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From eed892900e529095ce9f7e60d0fe63f935962536 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 31 Dec 2023 19:09:53 +0100 Subject: [PATCH 0122/1193] adding easyconfigs: Ghostscript-10.02.1-GCCcore-13.2.0.eb, GTK3-3.24.39-GCCcore-13.2.0.eb --- .../g/GTK3/GTK3-3.24.39-GCCcore-13.2.0.eb | 72 +++++++++++++++++++ .../Ghostscript-10.02.1-GCCcore-13.2.0.eb | 56 +++++++++++++++ 2 files changed, 128 insertions(+) create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.39-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.39-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.39-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..a0bbb9d094a3 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.39-GCCcore-13.2.0.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.39' + +homepage = 'https://developer.gnome.org/gtk3/stable/' +description = """GTK+ is the primary library used to construct user interfaces in GNOME. It + provides all the user interface controls, or widgets, used in a common + graphical application. Its object-oriented API allows you to construct + user interfaces without dealing with the low-level details of drawing and + device interaction. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('Meson', '1.2.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('GObject-Introspection', '1.78.1'), +] + +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('cairo', '1.18.0'), + ('Gdk-Pixbuf', '2.42.10'), + ('GLib', '2.78.1'), + ('Pango', '1.51.0'), + ('libepoxy', '1.5.10'), + ('X11', '20231019'), + ('FriBidi', '1.0.13'), + ('Wayland', '1.22.0'), +] + +default_easyblock = 'MesonNinja' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + 'checksums': ['1cac3e566b9b2f3653a458c08c2dcdfdca9f908037ac03c9d8564b4295778d79'], + }), + ('hicolor-icon-theme', '0.17', { + 'easyblock': 'ConfigureMake', + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '45.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'checksums': ['2442bfb06f4e6cc95bf6e2682fdff98fa5eddc688751b9d6215c623cb4e42ff1'], + }), +] + +postinstallcmds = ['gtk-update-icon-cache'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gtk3-demo', 'gtk3-demo-application', 'gtk3-icon-browser', 'gtk3-widget-factory', + 'gtk-builder-tool', 'gtk-launch', 'gtk-query-immodules-3.0', 'gtk-query-settings', + 'gtk-update-icon-cache']] + + ['lib/%s-%%(version_major)s.%s' % (x, SHLIB_EXT) for x in ['libgailutil', 'libgdk', 'libgtk']], + 'dirs': ['include/%s-%%(version_major)s.0' % x for x in ['gail', 'gtk']] + + ['share/icons/hicolor', 'share/icons/Adwaita'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..5e464e9cb8d8 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.02.1' + +homepage = 'https://ghostscript.com' +description = """Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to + different targets. It used to be part of the cups printing stack, but is no longer used for that.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs10021'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e429e4f5b01615a4f0f93a4128e8a1a4d932dff983b1774174c79c0630717ad9'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('libpng', '1.6.40'), + ('freetype', '2.13.2'), + ('libjpeg-turbo', '3.0.1'), + ('expat', '2.5.0'), + ('GLib', '2.78.1'), + ('cairo', '1.18.0'), + ('LibTIFF', '4.6.0'), + ('GTK3', '3.24.39'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = 'mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && ' +preconfigopts += 'mv libpng libpng.no && export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' +configopts = "--with-system-libtiff --enable-dynamic --disable-hidden-visibility" + +# also build and install shared libs +build_cmd_targets = ['', 'so'] +installopts = 'soinstall' + +postinstallcmds = [ + # install header files + "mkdir -p %(installdir)s/include/%(namelower)s", + "install -v -m644 base/*.h %(installdir)s/include/%(namelower)s", + "install -v -m644 psi/*.h %(installdir)s/include/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/%(namelower)s', 'include/%(namelower)s', 'share/man'], +} + +sanity_check_commands = ["gs --help"] + +moduleclass = 'tools' From 2ef734474d06035fc57b0e4d550707caa9316626 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 31 Dec 2023 19:12:38 +0100 Subject: [PATCH 0123/1193] adding easyconfigs: HDF5-1.14.3-gompi-2023b.eb, HDF5-1.14.3-iimpi-2023b.eb, Szip-2.1.1-GCCcore-13.2.0.eb --- .../h/HDF5/HDF5-1.14.3-gompi-2023b.eb | 26 +++++++++++++++++ .../h/HDF5/HDF5-1.14.3-iimpi-2023b.eb | 26 +++++++++++++++++ .../s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb | 29 +++++++++++++++++++ 3 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb create mode 100644 easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb new file mode 100644 index 000000000000..f2aab3663a35 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-gompi-2023b.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.3' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] + +# replace src include path with installation dir for $H5BLD_CPPFLAGS +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + +dependencies = [ + ('zlib', '1.2.13'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb new file mode 100644 index 000000000000..77fa0c12ab96 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.14.3-iimpi-2023b.eb @@ -0,0 +1,26 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.14.3' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-%(version_major_minor)s/hdf5-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['09cdb287aa7a89148c1638dd20891fdbae08102cf433ef128fd345338aa237c7'] + +# replace src include path with installation dir for $H5BLD_CPPFLAGS +_regex = 's, -I[^[:space:]]+H5FDsubfiling , -I%(installdir)s/include ,g' +postinstallcmds = ['sed -i -r "%s" %%(installdir)s/bin/%s' % (_regex, x) for x in ['h5c++', 'h5pcc']] + +dependencies = [ + ('zlib', '1.2.13'), + ('Szip', '2.1.1'), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..8eb126706529 --- /dev/null +++ b/easybuild/easyconfigs/s/Szip/Szip-2.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'Szip' +version = '2.1.1' + +homepage = 'https://www.hdfgroup.org/doc_resource/SZIP/' + +description = """ + Szip compression software, providing lossless compression of scientific data +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.hdfgroup.org/ftp/lib-external/szip/%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['21ee958b4f2d4be2c9cabfa5e1a94877043609ce86fde5f286f105f7ff84d412'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ["lib/libsz.a", "lib/libsz.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["ricehdf.h", "szip_adpt.h", "szlib.h"]], + 'dirs': [], +} + +moduleclass = 'tools' From 2c1aab5b39e6ec5cea9308775377eba8d6445327 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 31 Dec 2023 19:14:29 +0100 Subject: [PATCH 0124/1193] adding easyconfigs: Blitz++-1.0.2-GCCcore-13.2.0.eb --- .../b/Blitz++/Blitz++-1.0.2-GCCcore-13.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..c38f1c9a588d --- /dev/null +++ b/easybuild/easyconfigs/b/Blitz++/Blitz++-1.0.2-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Blitz++' +version = '1.0.2' + +homepage = 'https://github.com/blitzpp/blitz' + +description = """ + Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation + in C++ with a speed comparable to Fortran implementations, while preserving an + object-oriented interface +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [('https://github.com/blitzpp/blitz/archive/')] +sources = ['%(version)s.tar.gz'] +patches = ['blitz-%(version)s_pkgconfig.patch'] +checksums = [ + {'1.0.2.tar.gz': '500db9c3b2617e1f03d0e548977aec10d36811ba1c43bb5ef250c0e3853ae1c2'}, + {'blitz-1.0.2_pkgconfig.patch': 'd15fb397e75eb009809ecacdd7f2f154ff05e6586895f3b0511d0b53a6e3b9fe'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6') +] + +sanity_check_paths = { + 'files': ['lib64/libblitz.a', 'lib64/libblitz.%s' % SHLIB_EXT], + 'dirs': ['include/blitz/array', 'include/blitz/meta', + 'include/random', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From bdf51b96ea7e51cb4b6748ed888ed93817ea8f94 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 2 Jan 2024 15:13:54 +0100 Subject: [PATCH 0125/1193] adding easyconfigs: Voro++-0.4.6-GCCcore-12.3.0.eb --- .../v/Voro++/Voro++-0.4.6-GCCcore-12.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..44fc3e502f61 --- /dev/null +++ b/easybuild/easyconfigs/v/Voro++/Voro++-0.4.6-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'Voro++' +version = '0.4.6' + +homepage = 'http://math.lbl.gov/voro++/' +description = """Voro++ is a software library for carrying out three-dimensional computations of the Voronoi +tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, +computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that +rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used +to analyze a system of particles.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://math.lbl.gov/voro++/download/dir/', + 'https://download.lammps.org/thirdparty', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef7970071ee2ce3800daa8723649ca069dc4c71cc25f0f7d22552387f3ea437e'] + +builddependencies = [('binutils', '2.40')] + + +# No configure +skipsteps = ['configure'] + +# Override CXX and CFLAGS variables from Makefile +buildopts = 'CXX="$CXX" CFLAGS="$CXXFLAGS"' + +# Override PREFIX variable from Makefile +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/voro++', 'lib/libvoro++.a', 'include/voro++/voro++.hh'], + 'dirs': [], +} + +moduleclass = 'math' From e01127cecc7a47ed55a47ca36ec312f0d3d0bb63 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 2 Jan 2024 15:43:32 +0100 Subject: [PATCH 0126/1193] adding easyconfigs: ScaFaCoS-1.0.4-foss-2023a.eb --- .../s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023a.eb b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023a.eb new file mode 100644 index 000000000000..4a1b88c83d2c --- /dev/null +++ b/easybuild/easyconfigs/s/ScaFaCoS/ScaFaCoS-1.0.4-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'ScaFaCoS' +version = '1.0.4' + +homepage = 'http://www.scafacos.de/' +description = """ScaFaCoS is a library of scalable fast coulomb solvers.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = [ + '6634c4202e825e771d1dd75bbe9cac5cee41136c87653fde98fbd634681c1be6', # scafacos-1.0.1.tar.gz +] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('GSL', '2.7'), +] + +preconfigopts = 'unset F77 && ' + +configopts = 'FCFLAGS="-fallow-argument-mismatch $FCFLAGS" ' +configopts += '--enable-shared --enable-static --disable-doc ' +# tell it where to find provided FFTW +configopts += '--without-internal-fftw --with-fftw3-includedir=$EBROOTFFTW/include --with-fftw3-libdir=$EBROOTFFTW/lib ' +# only include the solvers supported for LAMMPS +# (for p2nfft we need an additonal dependency) +configopts += '--enable-fcs-solvers=direct,ewald,fmm,p3m ' + +sanity_check_paths = { + 'files': ['lib/libfcs.a', 'include/fcs.h', 'include/fcs_module.mod'], + 'dirs': [], +} + +moduleclass = 'math' From 6f2980359d0cda0be198fea13c05c4274a300d72 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 2 Jan 2024 15:51:54 +0100 Subject: [PATCH 0127/1193] adding easyconfigs: LAMMPS-2Aug2023-foss-2023a-kokkos.eb --- .../LAMMPS-2Aug2023-foss-2023a-kokkos.eb | 167 ++++++++++++++++++ 1 file changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb new file mode 100644 index 000000000000..05ca147c95cd --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb @@ -0,0 +1,167 @@ +name = 'LAMMPS' +version = '2Aug2023' +versionsuffix = '-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s_update2.tar.gz'] +checksums = ['3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('archspec', '0.2.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('netCDF', '4.9.2'), + ('GSL', '2.7'), + ('zlib', '1.2.13'), + ('gzip', '1.12'), + ('cURL', '8.0.1'), + ('HDF5', '1.14.0'), + ('PCRE', '8.45'), + ('libxml2', '2.11.4'), + ('FFmpeg', '6.0'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.9.0'), + ('ScaFaCoS', '1.0.4'), + ('SciPy-bundle', '2023.07'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.3.0'), +] +if ARCH == 'x86_64': + # TBB is an optional dependency when building on Intel arch + dependencies += [('tbb', '2021.11.0'), ] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) +# 'INTEL' - if builing on Intel CPU +# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' + +# include the following extra packages into the build +general_packages = [ + 'AMOEBA', + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SPICA', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'LEPTON', + 'MACHDYN', + 'MANIFOLD', + 'MANYBODY', + 'MC', + 'MDI', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-POD', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPT', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + + +moduleclass = 'chem' From a829c8fd63bdb2460fd824634090159d5bfe6da4 Mon Sep 17 00:00:00 2001 From: vsc47063 Date: Tue, 2 Jan 2024 17:33:48 +0100 Subject: [PATCH 0128/1193] adding easyconfigs: PyopenCL-2023.1.4-foss-2023a.eb --- .../PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb b/easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb new file mode 100644 index 000000000000..1de93adbdac5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyopenCL' +version = '2023.1.4' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pocl', '4.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2023.1.1', { + 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], + }), + ('pyopencl', version, { + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + 'checksums': ['220174efca900e9d5de5aef2aa1b77a6f2550501de92b035a91013aeae4d4c5e'], + }), +] + +moduleclass = 'vis' From f44c578761a5f9a62950d0dd1da4ca5e9ad1ce3a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jan 2024 17:31:25 +0100 Subject: [PATCH 0129/1193] {geo}[foss/2023a] Cartopy v0.22.0, Fiona v1.9.5, Cython v3.0.7 --- .../c/Cartopy/Cartopy-0.22.0-foss-2023a.eb | 56 +++++++++++++++++++ .../c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb | 40 +++++++++++++ .../f/Fiona/Fiona-1.9.5-foss-2023a.eb | 48 ++++++++++++++++ 3 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.22.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.9.5-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.22.0-foss-2023a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.22.0-foss-2023a.eb new file mode 100644 index 000000000000..9dfe231d9e69 --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.22.0-foss-2023a.eb @@ -0,0 +1,56 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.22.0' + +homepage = 'https://scitools.org.uk/cartopy/docs/latest/' +description = """Cartopy is a Python package designed to make drawing maps for data analysis and visualisation easy.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + # sufficiently recent Cython is required, to fix issues like: + # pykdtree/kdtree.c:2437:76: error: PyArrayObject {aka struct tagPyArrayObject} has no member named data + # Cython included with Python-bundle-PyPI (0.29.35) is not sufficient + ('Cython', '3.0.7'), + ('Fiona', '1.9.5'), + ('GDAL', '3.7.1'), + ('GEOS', '3.12.0'), + ('matplotlib', '3.7.2'), + ('pyproj', '3.6.0'), + ('SciPy-bundle', '2023.07'), + ('Shapely', '2.0.1'), + ('lxml', '4.9.2'), + ('Pillow', '10.0.0'), + ('PROJ', '9.2.0'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('OWSLib', '0.29.3', { + 'checksums': ['3baf34058458b933767ee43e632174cb0baebf49d326da179faacb9772f98539'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.10', { + 'checksums': ['41e7c5d669cadc2188acc4bbb4b0b4dcaf492d84512f1e6517a7ab2d122c911d'], + }), + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + (name, version, { + 'checksums': ['b300f90120931d43f11ef87c064ea1dacec1b59a4940aa76ebf82cf09548bb49'], + 'preinstallopts': r"""sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9bc9168fac12 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.7' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['fb299acf3a578573c190c858d49e0cf9d75f4bc49c3f24c5a63804997ef09213'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cython --version"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.9.5-foss-2023a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.5-foss-2023a.eb new file mode 100644 index 000000000000..070bd33e7e9f --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.9.5-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.9.5' + +homepage = 'https://github.com/Toblerity/Fiona' +description = """Fiona is designed to be simple and dependable. It focuses on reading and writing data +in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, +mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using +multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS +packages such as pyproj, Rtree, and Shapely.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('GDAL', '3.7.1'), + ('Shapely', '2.0.1'), # optional for 'calc' extras +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '4.0.0', { + 'checksums': ['542cb151461263216a4e37c3fd9afc425feeaf38aaa3025cd2a981fadb422235'], + }), + ('fiona', version, { + 'use_pip_extras': 'calc', + 'checksums': ['99e2604332caa7692855c2ae6ed91e1fffdf9b59449aa8032dd18e070e59a2f7'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' From 2293219ba4440b54ed40744e6021cff656f85058 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jan 2024 17:50:41 +0100 Subject: [PATCH 0130/1193] adding easyconfigs: scikit-learn-1.3.2-gfbf-2023b.eb --- .../scikit-learn-1.3.2-gfbf-2023b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.2-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.2-gfbf-2023b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.2-gfbf-2023b.eb new file mode 100644 index 000000000000..e47d5155b2bb --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.3.2-gfbf-2023b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.3.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['a2f54c76accc15a34bfb9066e6c7a56c1e7235dda5762b990792330b52ccfb05'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From a9e1fe4c49125ced487d04d5788cf4a69cec26f4 Mon Sep 17 00:00:00 2001 From: vsc47063 Date: Tue, 2 Jan 2024 17:52:10 +0100 Subject: [PATCH 0131/1193] fix capital in name --- .../PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb new file mode 100644 index 000000000000..2e27afb78f07 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2023.1.4' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pocl', '4.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2023.1.1', { + 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], + }), + ('pyopencl', version, { + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + 'checksums': ['220174efca900e9d5de5aef2aa1b77a6f2550501de92b035a91013aeae4d4c5e'], + }), +] + +moduleclass = 'vis' From ebd24c1e6f18736a0efe6c2568b06f70c336da6c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jan 2024 21:41:51 +0100 Subject: [PATCH 0132/1193] remove PyopenCL easyconfig: incorrect name, should be PyOpenCL --- .../PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb | 33 ------------------- 1 file changed, 33 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb b/easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb deleted file mode 100644 index 1de93adbdac5..000000000000 --- a/easybuild/easyconfigs/p/PyopenCL/PyopenCL-2023.1.4-foss-2023a.eb +++ /dev/null @@ -1,33 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyopenCL' -version = '2023.1.4' - -homepage = "https://mathema.tician.de/software/pyopencl/" -description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('SciPy-bundle', '2023.07'), - ('pocl', '4.0'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('appdirs', '1.4.4', { - 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], - }), - ('pytools', '2023.1.1', { - 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], - }), - ('pyopencl', version, { - 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", - 'checksums': ['220174efca900e9d5de5aef2aa1b77a6f2550501de92b035a91013aeae4d4c5e'], - }), -] - -moduleclass = 'vis' From b811d4a4066762b0185bc7811ae7534c5800c96d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Jan 2024 21:43:47 +0100 Subject: [PATCH 0133/1193] remove appdirs from PyOpenCL easyconfig, already provided by Python-bundle-PyPI --- .../easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb index 2e27afb78f07..a89383bb849a 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a.eb @@ -18,9 +18,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('appdirs', '1.4.4', { - 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], - }), ('pytools', '2023.1.1', { 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], }), From 56d064dac99ad35331c5785ef5e42efa51bafffb Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 2 Jan 2024 21:51:30 +0100 Subject: [PATCH 0134/1193] adding easyconfigs: CapnProto-1.0.1.1-GCCcore-13.2.0.eb --- .../CapnProto-1.0.1.1-GCCcore-13.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..da2d96bc3574 --- /dev/null +++ b/easybuild/easyconfigs/c/CapnProto/CapnProto-1.0.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +# Contribution by +# DeepThought, Flinders University +# Updated to 0.9.1 +# R.QIAO + +easyblock = 'ConfigureMake' + +name = 'CapnProto' +version = '1.0.1.1' + +homepage = 'https://capnproto.org' +description = "Cap’n Proto is an insanely fast data interchange format and capability-based RPC system." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://capnproto.org/'] +sources = ['capnproto-c++-%(version)s.tar.gz'] +checksums = ['b224e61d5b46f13967b7189860a7373b96d0c105e0d6170f29acba09a2d31f57'] + +builddependencies = [('binutils', '2.40')] + +local_bins = ['capnp', 'capnpc', 'capnpc-c++', 'capnpc-capnp'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['include/capnp', 'include/kj', 'lib'], +} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +moduleclass = 'bio' From a45acea3037ae0690c4dbe8c63ff50ae724a502b Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 3 Jan 2024 12:59:09 +0800 Subject: [PATCH 0135/1193] adding easyconfigs: BerkeleyGW-3.1.0-foss-2022a.eb and patches: BerkeleyGW-3.1.0_tests.patch --- .../BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb | 34 +++++ .../b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch | 131 ++++++++++++++++++ 2 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb new file mode 100644 index 000000000000..4653db0fdb70 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb @@ -0,0 +1,34 @@ +name = 'BerkeleyGW' +version = '3.1.0' + +homepage = 'https://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://files.berkeleygw.org/'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'BerkeleyGW-3.1.0_tests.patch', + 'BerkeleyGW-3.0.1_makefile.patch', +] +checksums = [ + {'BerkeleyGW-3.1.0.tar.gz': '7e890a5faa5a6bb601aa665c73903b3af30df7bdd13ee09362b69793bbefa6d2'}, + {'BerkeleyGW-3.1.0_tests.patch': 'ef73cb7b69a6aad0da90538ef673e978e159d96e62147a304780b1ec25a4c156'}, + {'BerkeleyGW-3.0.1_makefile.patch': '56d90dc4e43db379441b6a1802e24f1f1356cd4aca4eb6d8b673f6c7926a7406'}, +] + +dependencies = [ + ('ELPA', '2021.11.001'), + ('Perl', '5.34.1'), + ('Python', '3.10.4'), + ('h5py', '3.7.0'), + ('fftlib', '20170628'), +] + +runtest = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch new file mode 100644 index 000000000000..924cfdf2b001 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch @@ -0,0 +1,131 @@ +* allow test scripts to inherit environment +* set stack size ulimit to unlimited +* slightly raise tolerance in some tests +author: Miguel Dias Costa (National University of Singapore) +--- testsuite/run_testsuite.sh.orig 2019-07-25 14:48:12.000000000 +0800 ++++ testsuite/run_testsuite.sh 2019-07-25 14:47:50.000000000 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + # + # Copyright (C) 2005-2009 Heiko Appel, David Strubbe + # +--- testsuite/run_testsuite.sh.orig 2021-01-14 13:52:07.312389000 +0800 ++++ testsuite/run_testsuite.sh 2021-01-14 14:00:31.592579000 +0800 +@@ -66,6 +66,8 @@ + # Run all tests. Takes as first argument a list of testfile names. + function run_testsuite() { + ++ulimit -s unlimited ++ + tests="$1" + + # Check for 'preserve working directories' flag. + +--- MeanField/Utilities/mf_convert_wrapper.sh.orig 2019-07-26 09:52:27.648341000 +0800 ++++ MeanField/Utilities/mf_convert_wrapper.sh 2019-07-26 09:52:39.922114228 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + + # David Strubbe, October 2010 + # Wrapper for mf_convert.x +--- testsuite/GaAs-EPM/GaAs.test.orig 2019-07-26 10:45:19.798520000 +0800 ++++ testsuite/GaAs-EPM/GaAs.test 2019-07-26 10:45:37.753775275 +0800 +@@ -32,7 +32,7 @@ + Output : WFN.out + Input : WFN.in PIPE + +-Precision : 8e-15 ++Precision : 9e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.2710614199849328 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.2565373697755460 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.1322637363008994 +--- testsuite/Si-EPM/Si.test.orig 2021-01-14 14:45:33.627112000 +0800 ++++ testsuite/Si-EPM/Si.test 2021-01-14 14:46:33.049539000 +0800 +@@ -16,7 +16,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_cplx_spin.test.orig 2019-07-17 07:20:29.000000000 +0800 ++++ testsuite/Si-EPM/Si_cplx_spin.test 2021-01-14 14:46:51.922928000 +0800 +@@ -17,7 +17,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace.test 2021-01-14 14:47:15.433562000 +0800 +@@ -20,7 +20,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace_cplx_spin.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace_cplx_spin.test 2021-01-14 14:47:30.610030000 +0800 +@@ -21,7 +21,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace_cplx.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace_cplx.test 2021-01-14 14:47:45.250225000 +0800 +@@ -20,7 +20,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_hdf5_cplx_spin.test.orig 2021-10-27 09:15:36.543399656 +0800 ++++ testsuite/Si-EPM/Si_hdf5_cplx_spin.test 2021-10-27 09:16:19.549009302 +0800 +@@ -17,7 +17,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_hdf5.test.orig 2021-10-27 09:17:11.134541236 +0800 ++++ testsuite/Si-EPM/Si_hdf5.test 2021-10-27 09:17:28.086387460 +0800 +@@ -16,7 +16,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/GaAs-EPM/GaAs.test.orig 2024-01-03 11:40:10.045425888 +0800 ++++ testsuite/GaAs-EPM/GaAs.test 2024-01-03 11:41:04.884166571 +0800 +@@ -32,7 +32,7 @@ + Output : WFN.out + Input : WFN.in PIPE + +-Precision : 9e-15 ++Precision : 9e-14 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.2710614199849328 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.2565373697755460 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.1322637363008994 From 398751c3d8dfa7d3299fb771486e82044dab35c7 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 3 Jan 2024 13:19:18 +0800 Subject: [PATCH 0136/1193] add fftlib easyconfig --- .../f/fftlib/fftlib-20170628-gompi-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2022a.eb diff --git a/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2022a.eb b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2022a.eb new file mode 100644 index 000000000000..9661081a3f25 --- /dev/null +++ b/easybuild/easyconfigs/f/fftlib/fftlib-20170628-gompi-2022a.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'fftlib' +version = '20170628' +local_commit = '44c5fa0' + +homepage = 'https://github.com/flwende/fftlib' +description = """A library that intercepts FFTW calls and adds features on top of it. + In particular, it enables FFT plan reuse when there are multiple calls for the same geometry.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'openmp': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/flwende/fftlib/archive/'] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': SOURCE_ZIP}] +checksums = ['f73dffeaf5c2e6972a5bc67d11ec28390f9eda281a7cb47edc1ee2fe394ed057'] + +dependencies = [('FFTW', '3.3.10')] + +local_options = "-DFFTLIB_THREADSAFE " # use this when multiple threads access fftlib +# local_options += "-DFFTLIB_USE_MKL " # use symbols from MKL's fft library +# local_options += "-DFFTLIB_BYPASS " # bypass fftlib's internal logic +# local_options += "-DFFTLIB_OWN_LOCK " # use fftlib's reader/writer lock +# local_options += "-DFFTLIB_UNSAFE_OPT " # activate unsafe optimizations in fftlib +# local_options += "-DFFTLIB_DEBUG " # print debug messages (infos and warnings) +# local_options += "-DFFTLIB_WARNINGS_ONLY " # print warnings only +# local_options += "-DFFTLIB_COMPOSED_FFT " # split 3d FFT computation into 2d+1d FFT + +start_dir = 'src' + +parallel = False + +build_cmd = "$CXX $CXXFLAGS -I../include -I$EBROOTFFTW/include %s -c fftlib.cpp -o fftlib.o" % local_options + +files_to_copy = [(['fftlib.o'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/fftlib.o'], + 'dirs': ["."] +} + +# this should be prepended to $LIBFFT(_MT) when building applications in order to intercept their FFT calls +modextravars = {'FFTLIB': "%(installdir)s/lib/fftlib.o -lgomp -lstdc++ -ldl"} + +moduleclass = 'lib' From 6f2dfeba50ca5b49e9695092df5464f57d3d9be9 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jan 2024 10:50:02 +0100 Subject: [PATCH 0137/1193] collapse patches for OpenBLAS v0.3.21 to disable -ftree-vectorize for LAPACK --- .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 7 +++-- ...-0.3.21_disable-tree-vectorize-cmake.patch | 26 ------------------- ...nBLAS-0.3.21_disable-tree-vectorize.patch} | 26 +++++++++++++++++++ 3 files changed, 29 insertions(+), 30 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch rename easybuild/easyconfigs/o/OpenBLAS/{OpenBLAS-0.3.21_disable-tree-vectorize-make.patch => OpenBLAS-0.3.21_disable-tree-vectorize.patch} (54%) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb index 083a42b7b699..ea28ea399a40 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -21,8 +21,7 @@ patches = [ 'OpenBLAS-0.3.21_fix-order-vectorization.patch', 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', - 'OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch', - 'OpenBLAS-0.3.21_disable-tree-vectorize-make.patch', + 'OpenBLAS-0.3.21_disable-tree-vectorize.patch', ] checksums = [ {'v0.3.21.tar.gz': 'f36ba3d7a60e7c8bcc54cd9aaa9b1223dd42eaf02c811791c37e8ca707c241ca'}, @@ -38,8 +37,8 @@ checksums = [ {'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch': '9784e93567d100960a4c34d86e215bd7aa70bb28b0bc2c6bf1b22c6a05d56003'}, {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, - {'OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch': 'd8fca9d3956e45d6b9e588159675aa198b6d02534b09e3e797fbf8aee824aed7'}, - {'OpenBLAS-0.3.21_disable-tree-vectorize-make.patch': '3040e30f752107111b23064b8b25514719d46daed7445ad4bca89d2f66ecf95a'}, + {'OpenBLAS-0.3.21_disable-tree-vectorize.patch': + '30abb2707ea5be5afcac53e12cc3febe66315b2bf84579142fdcd8f4fc0c23eb'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch deleted file mode 100644 index 93e00ff90e61..000000000000 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-cmake.patch +++ /dev/null @@ -1,26 +0,0 @@ -From 32566bfb44067e0c0459e94b53c9457613539eeb Mon Sep 17 00:00:00 2001 -From: Martin Kroeker -Date: Thu, 13 Oct 2022 14:04:25 +0200 -Subject: [PATCH] Disable the gfortran tree vectorizer for netlib LAPACK - ---- - cmake/lapack.cmake | 3 +++ - 1 file changed, 3 insertions(+) - -diff --git a/cmake/lapack.cmake b/cmake/lapack.cmake -index f8a27f5d4..3b221d420 100644 ---- a/cmake/lapack.cmake -+++ b/cmake/lapack.cmake -@@ -999,6 +999,9 @@ endforeach () - - if (NOT C_LAPACK) - set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_FFLAGS}") -+ if (${F_COMPILER} STREQUAL "GFORTRAN") -+ set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_FFLAGS} -fno-tree-vectorize") -+ endif() - else () - set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_CFLAGS}") - endif () --- -2.25.1 - diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-make.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize.patch similarity index 54% rename from easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-make.patch rename to easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize.patch index 663bd5460742..5085b51aff91 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize-make.patch +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-tree-vectorize.patch @@ -1,3 +1,29 @@ +From 32566bfb44067e0c0459e94b53c9457613539eeb Mon Sep 17 00:00:00 2001 +From: Martin Kroeker +Date: Thu, 13 Oct 2022 14:04:25 +0200 +Subject: [PATCH] Disable the gfortran tree vectorizer for netlib LAPACK + +--- + cmake/lapack.cmake | 3 +++ + 1 file changed, 3 insertions(+) + +diff --git a/cmake/lapack.cmake b/cmake/lapack.cmake +index f8a27f5d4..3b221d420 100644 +--- a/cmake/lapack.cmake ++++ b/cmake/lapack.cmake +@@ -999,6 +999,9 @@ endforeach () + + if (NOT C_LAPACK) + set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_FFLAGS}") ++ if (${F_COMPILER} STREQUAL "GFORTRAN") ++ set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_FFLAGS} -fno-tree-vectorize") ++ endif() + else () + set_source_files_properties(${LA_SOURCES} PROPERTIES COMPILE_FLAGS "${LAPACK_CFLAGS}") + endif () +-- +2.25.1 + From 57809526c430ef0a07f5c5c39dce20c6d73a1f35 Mon Sep 17 00:00:00 2001 From: Martin Kroeker Date: Thu, 13 Oct 2022 09:12:23 +0200 From b00ae1379d0cbeaa08e68f11902a7e05479aa5f4 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 3 Jan 2024 09:53:08 +0000 Subject: [PATCH 0138/1193] cleanup --- easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb index fa82882d6c5d..36a0c27b225b 100644 --- a/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb @@ -7,7 +7,6 @@ homepage = 'http://phonopy.github.io/phono3py/' description = """A simulation package of phonon-phonon interaction related properties.""" toolchain = {'name': 'foss', 'version': '2023a'} -#toolchainopts = {'pic': True} source_urls = ['https://github.com/phonopy/phono3py/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] @@ -19,9 +18,8 @@ dependencies = [ ('phonopy', '2.20.0'), ] -preinstallopts = 'echo "extra_compile_args = -fopenmp" > site.cfg && ' +preinstallopts = 'echo "extra_compile_args = -fopenmp" > site.cfg && ' preinstallopts += 'echo "extra_link_args = -lgomp -llapacke -lpthread" >> site.cfg && ' -#preinstallopts = "export LDLAGS='-lgomp -llapacke -lpthread ' && export CFLAGS='-fopenmp ' && " installopts = " -vvv" download_dep_fail = True From 8495557707dfd9b160f1b49cfab88512572d852a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jan 2024 12:24:33 +0100 Subject: [PATCH 0139/1193] adding easyconfigs: PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb --- ...yOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..eb7726440138 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2023.1.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('pocl', '4.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytools', '2023.1.1', { + 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], + }), + ('pyopencl', version, { + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + 'checksums': ['220174efca900e9d5de5aef2aa1b77a6f2550501de92b035a91013aeae4d4c5e'], + }), +] + +moduleclass = 'vis' From 586dbec032cf0975b2ad87996941b103a0ca696d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 3 Jan 2024 12:33:34 +0100 Subject: [PATCH 0140/1193] adding easyconfigs: PyTorch-2.1.2-foss-2023a.eb and patches: PyTorch-2.1.0_fix-test_numpy_torch_operators.patch --- ...2.1.0_fix-test_numpy_torch_operators.patch | 41 +++++ .../p/PyTorch/PyTorch-2.1.2-foss-2023a.eb | 161 ++++++++++++++++++ 2 files changed, 202 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_fix-test_numpy_torch_operators.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_fix-test_numpy_torch_operators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_fix-test_numpy_torch_operators.patch new file mode 100644 index 000000000000..acbb6b1ca727 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_fix-test_numpy_torch_operators.patch @@ -0,0 +1,41 @@ +From b03ef1d96909da213771c7590e36bbe1d258df53 Mon Sep 17 00:00:00 2001 +From: Oguz Ulgen +Date: Sat, 16 Sep 2023 07:37:04 +0000 +Subject: [PATCH] [Dynamo] Fix numpy error in test_numpy_torch_operators + (#109087) + +When you inplace matmul two one dimensional numpy arrays, numpy=="1.24.3" gives +``` +TypeError: In-place matrix multiplication is not (yet) supported. Use 'a = a @ b' instead of 'a @= b'. +``` +but numpy=="1.25.2" gives +``` +ValueError: inplace matrix multiplication requires the first operand to have at least one and the second at least two dimensions. +``` + +This diff makes it so that newer versions of numpy does not fail on this test because we do not catch ValueError. + +An alternative solution would be to update the test cases to be 2 dimensional, but that would have impact on other operators being tested. + +Pull Request resolved: https://github.com/pytorch/pytorch/pull/109087 +Approved by: https://github.com/jansel +--- + test/dynamo/test_misc.py | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/test/dynamo/test_misc.py b/test/dynamo/test_misc.py +index 311bffc3e5fba9..a0486278599dcf 100644 +--- a/test/dynamo/test_misc.py ++++ b/test/dynamo/test_misc.py +@@ -1339,6 +1339,11 @@ def fn(op, t1, t2): + # skip + # Did you know that tensor[ndarray_of_floats] works? + continue ++ if op is operator.imatmul and (t1_np or t2_np): ++ # skip ++ # in numpy, in place matmul does not work single ++ # dimensional arrays ++ continue + t1 = torch.rand(5) + if t1_np: + t1 = t1.numpy() diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb new file mode 100644 index 000000000000..fe23eab6738b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb @@ -0,0 +1,161 @@ +name = 'PyTorch' +version = '2.1.2' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', + 'PyTorch-1.13.1_fix-protobuf-dependency.patch', + 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', + 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_fix-skip-decorators.patch', + 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', + 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', + 'PyTorch-2.0.1_skip-failing-gradtest.patch', + 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', + 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', + 'PyTorch-2.1.0_disable-gcc12-warning.patch', + 'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch', + 'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch', + 'PyTorch-2.1.0_fix-validationError-output-test.patch', + 'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch', + 'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch', + 'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch', + 'PyTorch-2.1.0_remove-test-requiring-online-access.patch', + 'PyTorch-2.1.0_skip-diff-test-on-ppc.patch', + 'PyTorch-2.1.0_skip-dynamo-test_predispatch.patch', + 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', + 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', + 'PyTorch-2.1.0_skip-test_wrap_bad.patch', +] +checksums = [ + {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': + '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'}, + {'PyTorch-1.13.1_fix-protobuf-dependency.patch': + '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, + {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': + 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, + {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch': + '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': + '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'}, + {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': + '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, + {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, + {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'}, + {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch': + '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, + {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': + '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, + {'PyTorch-2.1.0_disable-gcc12-warning.patch': 'c858b8db0010f41005dc06f9a50768d0d3dc2d2d499ccbdd5faf8a518869a421'}, + {'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch': + 'b15b1291a3c37bf6a4982cfbb3483f693acb46a67bc0912b383fd98baf540ccf'}, + {'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch': + '84bb51a719abc677031a7a3dfe4382ff098b0cbd8b39b8bed2a7fa03f80ac1e9'}, + {'PyTorch-2.1.0_fix-validationError-output-test.patch': + '7eba0942afb121ed92fac30d1529447d892a89eb3d53c565f8e9d480e95f692b'}, + {'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch': + '3793b4b878be1abe7791efcbd534774b87862cfe7dc4774ca8729b6cabb39e7e'}, + {'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch': + 'aef38adf1210d0c5455e91d7c7a9d9e5caad3ae568301e0ba9fc204309438e7b'}, + {'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch': + '0ac36411e76506b3354c85a8a1260987f66af947ee52ffc64230aee1fa02ea8b'}, + {'PyTorch-2.1.0_remove-test-requiring-online-access.patch': + '35184b8c5a1b10f79e511cc25db3b8a5585a5d58b5d1aa25dd3d250200b14fd7'}, + {'PyTorch-2.1.0_skip-diff-test-on-ppc.patch': '394157dbe565ffcbc1821cd63d05930957412156cc01e949ef3d3524176a1dda'}, + {'PyTorch-2.1.0_skip-dynamo-test_predispatch.patch': + '6298daf9ddaa8542850eee9ea005f28594ab65b1f87af43d8aeca1579a8c4354'}, + {'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch': + '5229ca88a71db7667a90ddc0b809b2c817698bd6e9c5aaabd73d3173cf9b99fe'}, + {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': + '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, + {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.26.3'), + ('hypothesis', '6.82.0'), + # For tests + ('pytest-flakefinder', '1.1.0'), + ('pytest-rerunfailures', '12.0'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('Ninja', '1.11.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('protobuf', '24.0'), + ('protobuf-python', '4.24.0'), + ('pybind11', '2.11.1'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('MPFR', '4.2.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.16'), + ('FFmpeg', '6.0'), + ('Pillow', '10.0.0'), + ('expecttest', '0.1.5'), + ('networkx', '3.1'), + ('sympy', '1.12'), + ('Z3', '4.12.2', '-Python-%(pyver)s'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' From 0299897b4470dc11bd5d2060cc2040a59d030436 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jan 2024 12:45:25 +0100 Subject: [PATCH 0141/1193] add patch to fix flaky scipy build in SciPy-bundle v2023.11 --- .../SciPy-bundle-2023.11-gfbf-2023b.eb | 1 + .../scipy-1.11.4_fix-deps-ellip_harm_2.patch | 38 +++++++++++++++++++ 2 files changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.4_fix-deps-ellip_harm_2.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb index 5c21cbe94a78..23682b7b5ed6 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb @@ -67,6 +67,7 @@ exts_list = [ 'patches': [ 'scipy-1.11.1_disable-tests.patch', 'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch', + 'scipy-1.11.4_fix-deps-ellip_harm_2.patch', ], 'checksums': [ {'scipy-1.11.4.tar.gz': '90a2b78e7f5733b9de748f589f09225013685f9b218275257f8a8168ededaeaa'}, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.4_fix-deps-ellip_harm_2.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.4_fix-deps-ellip_harm_2.patch new file mode 100644 index 000000000000..22c2c22ae62d --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.11.4_fix-deps-ellip_harm_2.patch @@ -0,0 +1,38 @@ +fix for: 'scipy/special/cython_special.pxd' not found +see also https://github.com/scipy/scipy/issues/19167 + +From c4f6bdb78d1eac3e03399fbaacb2a1d4cf1167c8 Mon Sep 17 00:00:00 2001 +From: Ben Boeckel +Date: Thu, 31 Aug 2023 10:09:56 -0400 +Subject: [PATCH] BLD: special: fix dependencies for `_ellip_harm_2` + +Generating the source for `_ellip_harm_2` requires the +`cython_special.pxd` header to be generated. So add a dependency for +this. + +Closes gh-19167 + +Co-authored-by: Ralf Gommers +--- + scipy/special/meson.build | 4 ++-- + 1 file changed, 2 insertions(+), 2 deletions(-) + +diff --git a/scipy/special/meson.build b/scipy/special/meson.build +index e7e25aa54e83..900064410381 100644 +--- a/scipy/special/meson.build ++++ b/scipy/special/meson.build +@@ -318,12 +318,12 @@ cython_special_pxd = custom_target('_dummy_cython_special.pxd', + uf_cython_gen = generator(cython, + arguments : cython_args, + output : '@BASENAME@.c', +- depends : [_cython_tree, _ufuncs_pxi_pxd_sources]) ++ depends : [_cython_tree, _ufuncs_pxi_pxd_sources, cython_special_pxd]) + + uf_cython_gen_cpp = generator(cython, + arguments : cython_cplus_args, + output : '@BASENAME@.cpp', +- depends : [_cython_tree, _ufuncs_pxi_pxd_sources]) ++ depends : [_cython_tree, _ufuncs_pxi_pxd_sources, cython_special_pxd]) + + py3.extension_module('_ufuncs', + [ From 95eeb54f4a97ca3bc5697abd907b700743e498c9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 3 Jan 2024 12:51:02 +0100 Subject: [PATCH 0142/1193] Add pytest-shard & pytest-flakefinder --- ...pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb | 24 ++++++++++++++ .../pytest-shard-0.1.2-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5ebf016d64cf --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = """Runs tests multiple times to expose flakiness.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f5a4e364a1d7 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pytest-shard' +version = '0.1.2' + +homepage = 'https://github.com/AdamGleave/pytest-shard' +description = """pytest plugin to support parallelism across multiple machines. + +Shards tests based on a hash of their test name enabling easy parallelism across machines, +suitable for a wide variety of continuous integration services. +Tests are split at the finest level of granularity, individual test cases, +enabling parallelism even if all of your tests are in a single file +(or even single parameterized test method). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = False + +sources = [SOURCE_TAR_GZ] +checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] + +moduleclass = 'tools' From f511244a80c05ddeca9f3dda5ed2fba27f531da4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jan 2024 13:34:29 +0100 Subject: [PATCH 0143/1193] add checksum to easyconfig for SciPy-bundle 2023.11 for scipy-1.11.4_fix-deps-ellip_harm_2.patch --- .../s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb index 23682b7b5ed6..ae7ab11bbc43 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.11-gfbf-2023b.eb @@ -74,6 +74,8 @@ exts_list = [ {'scipy-1.11.1_disable-tests.patch': '906bfb03397d94882ccdc1b93bc2c8e854e0e060c2d107c83042992394e6a4af'}, {'scipy-1.11.1_xfail-aarch64_test_maxiter_worsening.patch': '918c8e6fa8215d459126f267764c961bde729ea4a116c7f6287cddfdc58ffcea'}, + {'scipy-1.11.4_fix-deps-ellip_harm_2.patch': + '5c3b4d4dab76cd4c9398c87e6a67b39e3806994ef955fa35781b49f9f99328a8'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, From 295a900b99f5a5fdb6ab86ee3413781c70fa4c85 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 3 Jan 2024 13:45:23 +0100 Subject: [PATCH 0144/1193] adding easyconfigs: angsd-0.940-GCC-12.3.0.eb --- .../a/angsd/angsd-0.940-GCC-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-12.3.0.eb b/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-12.3.0.eb new file mode 100644 index 000000000000..fdb6426d1ca7 --- /dev/null +++ b/easybuild/easyconfigs/a/angsd/angsd-0.940-GCC-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'angsd' +version = '0.940' + +homepage = 'http://www.popgen.dk/angsd' +description = """Program for analysing NGS data.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'ANGSD' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['73b43eb553892721c7d5db5d6d883a17074ee4e07536a32871c3b1ac5f701ad7'] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('HTSlib', '1.18'), +] + +buildopts = "HTSSRC=systemwide" + +files_to_copy = [ + (['angsd', 'misc/supersim', 'misc/thetaStat', 'misc/realSFS', 'misc/msToGlf', + 'misc/smartCount', 'misc/printIcounts', 'misc/contamination', 'misc/splitgl', + 'misc/NGSadmix', 'misc/contamination2', 'misc/haploToPlink', 'misc/ngsPSMC', + 'misc/ibs'], 'bin'), + 'doc', +] + +sanity_check_paths = { + 'files': ['bin/angsd'], + 'dirs': ['doc'], +} + +sanity_check_commands = ["angsd --help"] + +moduleclass = 'bio' From 55a85f9b8b92f4cc70b2406cb7e427399d1c405d Mon Sep 17 00:00:00 2001 From: vsc47063 Date: Wed, 3 Jan 2024 14:33:23 +0100 Subject: [PATCH 0145/1193] adding easyconfigs: dask-2023.12.1-foss-2023a.eb --- .../d/dask/dask-2023.12.1-foss-2023a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb b/easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb new file mode 100644 index 000000000000..156c0c2bf37c --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2023.12.1' + +homepage = 'https://dask.org/' +description = """Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance + at scale for the tools you love.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2023.07'), + ('bokeh', '3.2.2'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.4.0', { + 'checksums': ['aa0ff35dbbcc807ae374db56332f4c1b39b46f67bf2975f5151e0b4186aed0d5'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '3.0.0', { + 'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'], + }), + ('tblib', '2.0.0', { + 'checksums': ['a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7'], + }), + (name, version, { + 'checksums': ['0ac3acd5bdbfacb5ad6401ac7663a1135955b3fa051a118e1b8a88e87b6b44a2'], + }), + ('distributed', version, { + 'checksums': ['56e69d90c6099e066751907956144cf94d0bc7050bd69ef2ec8003e890c2540c'], + }), + ('dask-mpi', '2022.4.0', { + 'checksums': ['0a04f1d7d35a06cdff506593330d4414ea242c9172498ce191f5742eac499e17'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.2', { + 'checksums': ['d35407a05a0534347c5d958ae749b9f8535bec529857d013b6e5649cde43914a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/dask-%s' % x for x in ['mpi', 'scheduler', 'ssh', 'worker']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["dask-scheduler --help"] + +sanity_pip_check = True + +moduleclass = 'data' From 6443a39a8860e34affa0076a6e586ff8b73da433 Mon Sep 17 00:00:00 2001 From: vsc47063 Date: Wed, 3 Jan 2024 16:29:45 +0100 Subject: [PATCH 0146/1193] adding easyconfigs: radian-0.6.9-foss-2022b.eb --- .../r/radian/radian-0.6.9-foss-2022b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb diff --git a/easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb b/easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb new file mode 100644 index 000000000000..68f9bbf320c3 --- /dev/null +++ b/easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'radian' +version = '0.6.9' + +homepage = "https://github.com/randy3k/radian" +description = """radian is an alternative console for the R program with multiline editing and rich syntax highlight.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('R', '4.2.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['292cb074ffd37a6014e7c37490a182f61e1f6ab0ccd6d2313a0c25203833b774'], + }), + ('rchitect', '0.4.4', { + 'checksums': ['8762b47d8636774582c906891e5b0ec66ca4d48327fb7abf7db7d85d2c137df5'], + }), + ('prompt-toolkit', '3.0.43', { + 'sources': ['prompt_toolkit-%(version)s.tar.gz'], + 'checksums': ['3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d'], + }), +] + +moduleclass = 'devel' From 618306d4e194420db6a8b66b53e071e220d633a9 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 3 Jan 2024 19:08:04 +0100 Subject: [PATCH 0147/1193] adding easyconfigs: einops-0.7.0-GCCcore-12.3.0.eb, NiBabel-5.2.0-foss-2023a.eb, pydicom-2.4.4-GCCcore-12.3.0.eb --- .../e/einops/einops-0.7.0-GCCcore-12.3.0.eb | 30 ++++++++++++ .../n/NiBabel/NiBabel-5.2.0-foss-2023a.eb | 47 +++++++++++++++++++ .../p/pydicom/pydicom-2.4.4-GCCcore-12.3.0.eb | 26 ++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a18dab2ce621 --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.7.0' + +homepage = 'https://einops.rocks/' +description = """ +Flexible and powerful tensor operations for readable and reliable code. +Supports numpy, pytorch, tensorflow, jax, and others.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('hatchling', '1.18.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-foss-2023a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-foss-2023a.eb new file mode 100644 index 000000000000..ffc9dd60c3b5 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '5.2.0' + +homepage = 'https://nipy.github.io/nibabel' +description = """NiBabel provides read/write access to some common medical and neuroimaging file formats, + including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT + as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and + annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Pillow', '10.0.0'), + ('pydicom', '2.4.4'), + ('hatchling', '1.18.0'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['3df8f1ab981d1bd92f4331d565528d126ab9717fdbd4cfe68f43fcd1c2bf3f52'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nib-dicomfs', 'bin/nib-diff', 'bin/nib-ls', 'bin/nib-nifti-dx', 'bin/parrec2nii'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nib-diff --help", + "parrec2nii --help", +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..dc6774342011 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.4.4-GCCcore-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.4.4' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['42c06ed74331174111dd42c89db774a13fc472abe18015f22c5aba80cddb7843'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 86149154a6c5de618258ab5187efe3867c1400fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jan 2024 21:08:35 +0100 Subject: [PATCH 0148/1193] add missing SciPy-bundle dependency to TensorRT easyconfig --- .../t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb index d3862ffba615..02ef8ec6c804 100644 --- a/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/TensorRT/TensorRT-8.6.1-foss-2022a-CUDA-11.7.0.eb @@ -1,4 +1,3 @@ - name = 'TensorRT' version = '8.6.1' versionsuffix = '-CUDA-%(cudaver)s' @@ -18,6 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), ('CUDA', '11.7.0', '', SYSTEM), ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), ('protobuf-python', '3.19.4'), From c3c64a283f9b5e26052b3d6d2743bccfbe1a3498 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Jan 2024 22:03:53 +0100 Subject: [PATCH 0149/1193] adding easyconfigs: EggLib-3.3.0-GCC-13.2.0.eb --- .../e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb b/easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..7ccad4936f39 --- /dev/null +++ b/easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'EggLib' +version = '3.3.0' + +homepage = 'https://egglib.org' +description = """EggLib is a C++/Python library and program package for evolutionary genetics and genomics.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['781b8e01d16762026b18514687be40acf68f97cdd975ea670854d74d2f8bd5c5'] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From 2a6ad97e995f39edc8dbd642b3d463f93693295f Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 Jan 2024 06:38:31 +0800 Subject: [PATCH 0150/1193] update source url for BGW 3.1.0 --- .../easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb index 4653db0fdb70..66bc90e3a299 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb @@ -9,8 +9,8 @@ description = """The BerkeleyGW Package is a set of computer codes that calculat toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': True, 'openmp': True} -source_urls = ['https://files.berkeleygw.org/'] -sources = [SOURCE_TAR_GZ] +source_urls = ['https://app.box.com/shared/static/'] +sources = [{'download_filename': '2bik75lrs85zt281ydbup2xa7i5594gy.gz', 'filename': SOURCE_TAR_GZ}] patches = [ 'BerkeleyGW-3.1.0_tests.patch', 'BerkeleyGW-3.0.1_makefile.patch', From 0ef30d587692b8f5c9f3713adfeed5fbc8a7187c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 Jan 2024 11:25:04 +0800 Subject: [PATCH 0151/1193] update BerkeleyGW-3.1.0_makefile.patch --- .../BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb | 4 ++-- .../BerkeleyGW-3.1.0_makefile.patch | 24 +++++++++++++++++++ 2 files changed, 26 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb index 66bc90e3a299..a4a6cdb6e355 100644 --- a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-foss-2022a.eb @@ -13,12 +13,12 @@ source_urls = ['https://app.box.com/shared/static/'] sources = [{'download_filename': '2bik75lrs85zt281ydbup2xa7i5594gy.gz', 'filename': SOURCE_TAR_GZ}] patches = [ 'BerkeleyGW-3.1.0_tests.patch', - 'BerkeleyGW-3.0.1_makefile.patch', + 'BerkeleyGW-3.1.0_makefile.patch', ] checksums = [ {'BerkeleyGW-3.1.0.tar.gz': '7e890a5faa5a6bb601aa665c73903b3af30df7bdd13ee09362b69793bbefa6d2'}, {'BerkeleyGW-3.1.0_tests.patch': 'ef73cb7b69a6aad0da90538ef673e978e159d96e62147a304780b1ec25a4c156'}, - {'BerkeleyGW-3.0.1_makefile.patch': '56d90dc4e43db379441b6a1802e24f1f1356cd4aca4eb6d8b673f6c7926a7406'}, + {'BerkeleyGW-3.1.0_makefile.patch': '7a8b4bb593d75cf51ca42f94cd2b0ae5440b80e53e0cd00f183821539bc43fc6'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch new file mode 100644 index 000000000000..f5b9c258b23d --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch @@ -0,0 +1,24 @@ +* don't rebuild flavors when installing and checking, and check using MPI +author: Miguel Dias Costa (National University of Singapore) +--- Makefile.orig 2024-01-04 10:02:31.992454794 +0800 ++++ Makefile 2024-01-04 10:02:52.863330557 +0800 +@@ -130,7 +130,7 @@ + cp flavor_cplx.mk flavor.mk + $(MAKE) all + +-install: all ++install: + ifdef INSTDIR + mkdir -p $(INSTDIR)/bin + install bin/*.x $(INSTDIR)/bin/ +@@ -152,8 +152,8 @@ + $(error Error: Please define installation prefix INSTDIR via 'make install INSTDIR='.) + endif + +-check: all +- cd testsuite && $(MAKE) check ++check: ++ cd testsuite && $(MAKE) check-parallel + + check-save: all + cd testsuite && $(MAKE) check-save From c02f3ed366cfa4363341a2c5a1f39e6fcb00b6af Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jan 2024 09:37:08 +0100 Subject: [PATCH 0152/1193] add custom sanity check for EggLib 3.3.0 --- easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb b/easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb index 7ccad4936f39..e145d952fb95 100644 --- a/easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/e/EggLib/EggLib-3.3.0-GCC-13.2.0.eb @@ -19,6 +19,13 @@ dependencies = [ download_dep_fail = True use_pip = True +sanity_check_paths = { + 'files': ['bin/egglib-config', 'bin/egglib-test'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["egglib-config --help"] + sanity_pip_check = True moduleclass = 'bio' From 7cf28d00399725298a49d6d6cfac91bf1234c7d7 Mon Sep 17 00:00:00 2001 From: vsc47063 Date: Thu, 4 Jan 2024 11:25:53 +0100 Subject: [PATCH 0153/1193] update extensions versions --- easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb b/easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb index 156c0c2bf37c..149f0a916323 100644 --- a/easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb +++ b/easybuild/easyconfigs/d/dask/dask-2023.12.1-foss-2023a.eb @@ -26,8 +26,8 @@ exts_list = [ ('locket', '1.0.0', { 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], }), - ('partd', '1.4.0', { - 'checksums': ['aa0ff35dbbcc807ae374db56332f4c1b39b46f67bf2975f5151e0b4186aed0d5'], + ('partd', '1.4.1', { + 'checksums': ['56c25dd49e6fea5727e731203c466c6e092f308d8f0024e199d02f6aa2167f67'], }), ('HeapDict', '1.0.1', { 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], @@ -35,8 +35,8 @@ exts_list = [ ('zict', '3.0.0', { 'checksums': ['e321e263b6a97aafc0790c3cfb3c04656b7066e6738c37fffcca95d803c9fba5'], }), - ('tblib', '2.0.0', { - 'checksums': ['a6df30f272c08bf8be66e0775fad862005d950a6b8449b94f7c788731d70ecd7'], + ('tblib', '3.0.0', { + 'checksums': ['93622790a0a29e04f0346458face1e144dc4d32f493714c6c3dff82a4adb77e6'], }), (name, version, { 'checksums': ['0ac3acd5bdbfacb5ad6401ac7663a1135955b3fa051a118e1b8a88e87b6b44a2'], From 2f8a4179c5326f32e233cbcd190273296a02a486 Mon Sep 17 00:00:00 2001 From: vsc47063 Date: Thu, 4 Jan 2024 11:37:31 +0100 Subject: [PATCH 0154/1193] add sanity check + sort exts_list --- .../easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb b/easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb index 68f9bbf320c3..ffdcacd21d20 100644 --- a/easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb +++ b/easybuild/easyconfigs/r/radian/radian-0.6.9-foss-2022b.eb @@ -17,9 +17,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - (name, version, { - 'checksums': ['292cb074ffd37a6014e7c37490a182f61e1f6ab0ccd6d2313a0c25203833b774'], - }), ('rchitect', '0.4.4', { 'checksums': ['8762b47d8636774582c906891e5b0ec66ca4d48327fb7abf7db7d85d2c137df5'], }), @@ -27,6 +24,16 @@ exts_list = [ 'sources': ['prompt_toolkit-%(version)s.tar.gz'], 'checksums': ['3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d'], }), + (name, version, { + 'checksums': ['292cb074ffd37a6014e7c37490a182f61e1f6ab0ccd6d2313a0c25203833b774'], + }), ] +sanity_check_paths = { + 'files': ['bin/radian'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["radian --help"] + moduleclass = 'devel' From a7581e4afe6a332505923d95b7bf802c2b540f72 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jan 2024 14:00:51 +0100 Subject: [PATCH 0155/1193] adding easyconfigs: dorado-0.5.1-foss-2022a-CUDA-11.7.0.eb --- .../dorado-0.5.1-foss-2022a-CUDA-11.7.0.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/d/dorado/dorado-0.5.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/d/dorado/dorado-0.5.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/dorado/dorado-0.5.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..54b393227105 --- /dev/null +++ b/easybuild/easyconfigs/d/dorado/dorado-0.5.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,74 @@ +easyblock = 'CMakeMake' + +name = 'dorado' +version = '0.5.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/dorado' +description = """Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +# -Wno-error option is required to fix: +# error: void {anonymous}::convert_f32_to_f16_impl(c10::Half*, const float*, std::size_t) defined but not used +toolchainopts = {'usempi': True, 'extra_cxxflags': "-Wno-error=unused-function"} + +source_urls = ['https://github.com/nanoporetech/dorado/archive/'] +sources = [{ + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('HDF5', '1.12.2'), + ('zstd', '1.5.2'), + ('HTSlib', '1.15.1'), + ('kineto', '0.4.0'), + ('libaec', '1.0.6'), +] + +# don't link to OpenSSL static libraries +# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available) +preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../dorado/cmake/OpenSSL.cmake && " +preconfigopts += "export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && " +# link in the ssl and crypto libs, to fix: +# undefined reference to symbol 'SSL_get_peer_certificate@@OPENSSL_1_1_0' +preconfigopts += "sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../dorado/dorado/utils/CMakeLists.txt && " + +# don't use vendored HTSlib, use provided HTSlib dependency +preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i '/add_dependencies.*htslib_project/d' ../dorado/dorado/utils/CMakeLists.txt && " +preconfigopts += "sed -i '/Htslib.cmake/d' ../dorado/CMakeLists.txt && " +# link with -lhts, not -lhtslib +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/CMakeLists.txt && " +preconfigopts += "sed -i 's/htslib/hts/g' ../dorado/dorado/utils/CMakeLists.txt && " + +configopts = "-DDORADO_INSTALL_PATH=%(installdir)s " +configopts += "-DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc " +configopts += "-DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib " +# add -pthread flag (in addition to -lpthread) to avoid linking error: +# in function `_GLOBAL__sub_I_mutex.cc': mutex.cc:(.text.startup+0x17): undefined reference to `pthread_atfork' +configopts += '-DCMAKE_C_FLAGS="$CFLAGS -pthread" ' + +sanity_check_paths = { + 'files': ['bin/dorado'], + 'dirs': [], +} + +sanity_check_commands = ["dorado basecaller --help"] + +moduleclass = 'bio' From b4c306c797703ca1b5fadcab1ea110261d5cddff Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 4 Jan 2024 15:24:56 +0100 Subject: [PATCH 0156/1193] Build SUNDIAL using SuiteSparse and enable KLU --- .../s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb | 24 +++++++--- .../s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb | 24 +++++++--- ...ALS-6.6.0_fix_bad_find_library_calls.patch | 45 +++++++++++++++++++ 3 files changed, 83 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0_fix_bad_find_library_calls.patch diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb index 043d83c6d48e..47032021b89d 100755 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb @@ -12,11 +12,25 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['f90029b8da846c8faff5530fd1fa4847079188d040554f55c1d5d1e04743d29d'] - -builddependencies = [('CMake', '3.24.3')] - -configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" +patches = [ + '%(name)s-%(version)s_fix_bad_find_library_calls.patch', +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), +] + +_copts = [ + '-DENABLE_MPI=ON', + '-DENABLE_OPENMP=ON', + '-DENABLE_LAPACK=ON', + '-DENABLE_KLU=ON', +] +configopts = ' '.join(_copts) local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb index 02bb2f3f2fd2..ad6e8fa5b007 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb @@ -12,11 +12,25 @@ toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['f90029b8da846c8faff5530fd1fa4847079188d040554f55c1d5d1e04743d29d'] - -builddependencies = [('CMake', '3.26.3')] - -configopts = "-DMPI_ENABLE=ON -DOPENMP_ENABLE=ON -DLAPACK_ENABLE=ON" +patches = [ + '%(name)s-%(version)s_fix_bad_find_library_calls.patch', +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('SuiteSparse', '7.1.0'), +] + +_copts = [ + '-DENABLE_MPI=ON', + '-DENABLE_OPENMP=ON', + '-DENABLE_LAPACK=ON', + '-DENABLE_KLU=ON', +] +configopts = ' '.join(_copts) local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0_fix_bad_find_library_calls.patch b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0_fix_bad_find_library_calls.patch new file mode 100644 index 000000000000..a6b9d3fd5f81 --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0_fix_bad_find_library_calls.patch @@ -0,0 +1,45 @@ +Make FindKLU use default search paths so it finds our SuiteSparse installation. + +Åke Sandgren, 2023-12-20 +diff -ru sundials-6.6.0.orig/cmake/tpl/FindKLU.cmake sundials-6.6.0/cmake/tpl/FindKLU.cmake +--- sundials-6.6.0.orig/cmake/tpl/FindKLU.cmake 2023-07-20 20:47:41.062113287 +0200 ++++ sundials-6.6.0/cmake/tpl/FindKLU.cmake 2023-12-20 13:27:56.974985727 +0100 +@@ -55,25 +55,25 @@ + else () + # find library with user provided directory path + set(KLU_LIBRARY_NAME klu) +- find_library(KLU_LIBRARY ${KLU_LIBRARY_NAME} ${KLU_LIBRARY_DIR} NO_DEFAULT_PATH) ++ find_library(KLU_LIBRARY ${KLU_LIBRARY_NAME} ${KLU_LIBRARY_DIR}) + endif () + mark_as_advanced(KLU_LIBRARY) + + if (NOT AMD_LIBRARY) + set(AMD_LIBRARY_NAME amd) +- find_library(AMD_LIBRARY ${AMD_LIBRARY_NAME} ${KLU_LIBRARY_DIR} NO_DEFAULT_PATH) ++ find_library(AMD_LIBRARY ${AMD_LIBRARY_NAME} ${KLU_LIBRARY_DIR}) + mark_as_advanced(AMD_LIBRARY) + endif () + + if (NOT COLAMD_LIBRARY) + set(COLAMD_LIBRARY_NAME colamd) +- find_library(COLAMD_LIBRARY ${COLAMD_LIBRARY_NAME} ${KLU_LIBRARY_DIR} NO_DEFAULT_PATH) ++ find_library(COLAMD_LIBRARY ${COLAMD_LIBRARY_NAME} ${KLU_LIBRARY_DIR}) + mark_as_advanced(COLAMD_LIBRARY) + endif () + + if (NOT BTF_LIBRARY) + set(BTF_LIBRARY_NAME btf) +- find_library( BTF_LIBRARY ${BTF_LIBRARY_NAME} ${KLU_LIBRARY_DIR} NO_DEFAULT_PATH) ++ find_library( BTF_LIBRARY ${BTF_LIBRARY_NAME} ${KLU_LIBRARY_DIR}) + mark_as_advanced(BTF_LIBRARY) + endif () + +@@ -83,7 +83,7 @@ + if(WIN32 AND NOT MSYS) + set(CMAKE_FIND_LIBRARY_PREFIXES "") + endif() +- find_library( SUITESPARSECONFIG_LIBRARY ${SUITESPARSECONFIG_LIBRARY_NAME} ${KLU_LIBRARY_DIR} NO_DEFAULT_PATH) ++ find_library( SUITESPARSECONFIG_LIBRARY ${SUITESPARSECONFIG_LIBRARY_NAME} ${KLU_LIBRARY_DIR}) + mark_as_advanced(SUITESPARSECONFIG_LIBRARY) + endif () + From 0ed8dab455085eba55b0f4a2413bdaeab5149b5c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 Jan 2024 22:39:23 +0800 Subject: [PATCH 0157/1193] adding easyconfigs: BerkeleyGW-3.1.0-intel-2022a.eb --- .../BerkeleyGW-3.1.0-intel-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-intel-2022a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-intel-2022a.eb new file mode 100644 index 000000000000..52af177a2afb --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0-intel-2022a.eb @@ -0,0 +1,33 @@ +name = 'BerkeleyGW' +version = '3.1.0' + +homepage = 'https://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://app.box.com/shared/static/'] +sources = [{'download_filename': '2bik75lrs85zt281ydbup2xa7i5594gy.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'BerkeleyGW-3.1.0_tests.patch', + 'BerkeleyGW-3.1.0_makefile.patch', +] +checksums = [ + {'BerkeleyGW-3.1.0.tar.gz': '7e890a5faa5a6bb601aa665c73903b3af30df7bdd13ee09362b69793bbefa6d2'}, + {'BerkeleyGW-3.1.0_tests.patch': 'ef73cb7b69a6aad0da90538ef673e978e159d96e62147a304780b1ec25a4c156'}, + {'BerkeleyGW-3.1.0_makefile.patch': '7a8b4bb593d75cf51ca42f94cd2b0ae5440b80e53e0cd00f183821539bc43fc6'}, +] + +dependencies = [ + ('ELPA', '2021.11.001'), + ('Perl', '5.34.1'), + ('Python', '3.10.4'), + ('h5py', '3.7.0'), +] + +runtest = True + +moduleclass = 'phys' From 8db717f279b8f5a4564509ea3b2321eb344b3297 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 Jan 2024 22:51:05 +0800 Subject: [PATCH 0158/1193] add patches --- .../BerkeleyGW-3.1.0_makefile.patch | 24 ++++ .../b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch | 131 ++++++++++++++++++ 2 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch new file mode 100644 index 000000000000..f5b9c258b23d --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_makefile.patch @@ -0,0 +1,24 @@ +* don't rebuild flavors when installing and checking, and check using MPI +author: Miguel Dias Costa (National University of Singapore) +--- Makefile.orig 2024-01-04 10:02:31.992454794 +0800 ++++ Makefile 2024-01-04 10:02:52.863330557 +0800 +@@ -130,7 +130,7 @@ + cp flavor_cplx.mk flavor.mk + $(MAKE) all + +-install: all ++install: + ifdef INSTDIR + mkdir -p $(INSTDIR)/bin + install bin/*.x $(INSTDIR)/bin/ +@@ -152,8 +152,8 @@ + $(error Error: Please define installation prefix INSTDIR via 'make install INSTDIR='.) + endif + +-check: all +- cd testsuite && $(MAKE) check ++check: ++ cd testsuite && $(MAKE) check-parallel + + check-save: all + cd testsuite && $(MAKE) check-save diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch new file mode 100644 index 000000000000..924cfdf2b001 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-3.1.0_tests.patch @@ -0,0 +1,131 @@ +* allow test scripts to inherit environment +* set stack size ulimit to unlimited +* slightly raise tolerance in some tests +author: Miguel Dias Costa (National University of Singapore) +--- testsuite/run_testsuite.sh.orig 2019-07-25 14:48:12.000000000 +0800 ++++ testsuite/run_testsuite.sh 2019-07-25 14:47:50.000000000 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + # + # Copyright (C) 2005-2009 Heiko Appel, David Strubbe + # +--- testsuite/run_testsuite.sh.orig 2021-01-14 13:52:07.312389000 +0800 ++++ testsuite/run_testsuite.sh 2021-01-14 14:00:31.592579000 +0800 +@@ -66,6 +66,8 @@ + # Run all tests. Takes as first argument a list of testfile names. + function run_testsuite() { + ++ulimit -s unlimited ++ + tests="$1" + + # Check for 'preserve working directories' flag. + +--- MeanField/Utilities/mf_convert_wrapper.sh.orig 2019-07-26 09:52:27.648341000 +0800 ++++ MeanField/Utilities/mf_convert_wrapper.sh 2019-07-26 09:52:39.922114228 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + + # David Strubbe, October 2010 + # Wrapper for mf_convert.x +--- testsuite/GaAs-EPM/GaAs.test.orig 2019-07-26 10:45:19.798520000 +0800 ++++ testsuite/GaAs-EPM/GaAs.test 2019-07-26 10:45:37.753775275 +0800 +@@ -32,7 +32,7 @@ + Output : WFN.out + Input : WFN.in PIPE + +-Precision : 8e-15 ++Precision : 9e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.2710614199849328 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.2565373697755460 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.1322637363008994 +--- testsuite/Si-EPM/Si.test.orig 2021-01-14 14:45:33.627112000 +0800 ++++ testsuite/Si-EPM/Si.test 2021-01-14 14:46:33.049539000 +0800 +@@ -16,7 +16,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_cplx_spin.test.orig 2019-07-17 07:20:29.000000000 +0800 ++++ testsuite/Si-EPM/Si_cplx_spin.test 2021-01-14 14:46:51.922928000 +0800 +@@ -17,7 +17,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace.test 2021-01-14 14:47:15.433562000 +0800 +@@ -20,7 +20,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace_cplx_spin.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace_cplx_spin.test 2021-01-14 14:47:30.610030000 +0800 +@@ -21,7 +21,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM_subspace/Si_subspace_cplx.test.orig 2019-07-17 07:20:32.000000000 +0800 ++++ testsuite/Si-EPM_subspace/Si_subspace_cplx.test 2021-01-14 14:47:45.250225000 +0800 +@@ -20,7 +20,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_hdf5_cplx_spin.test.orig 2021-10-27 09:15:36.543399656 +0800 ++++ testsuite/Si-EPM/Si_hdf5_cplx_spin.test 2021-10-27 09:16:19.549009302 +0800 +@@ -17,7 +17,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/Si-EPM/Si_hdf5.test.orig 2021-10-27 09:17:11.134541236 +0800 ++++ testsuite/Si-EPM/Si_hdf5.test 2021-10-27 09:17:28.086387460 +0800 +@@ -16,7 +16,7 @@ + Output : WFN.out + Input : WFN.in PIPE NOCOPY + +-Precision : 6e-15 ++Precision : 7e-15 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.1283435360829054 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.3282472551260550 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.3490532646407310 +--- testsuite/GaAs-EPM/GaAs.test.orig 2024-01-03 11:40:10.045425888 +0800 ++++ testsuite/GaAs-EPM/GaAs.test 2024-01-03 11:41:04.884166571 +0800 +@@ -32,7 +32,7 @@ + Output : WFN.out + Input : WFN.in PIPE + +-Precision : 9e-15 ++Precision : 9e-14 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.2710614199849328 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.2565373697755460 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.1322637363008994 From e318e3b9380a716a9307775441ec31439b554a03 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 4 Jan 2024 15:55:48 +0100 Subject: [PATCH 0159/1193] adding easyconfigs: Boost.MPI-1.83.0-gompi-2022b.eb, Block-1.5.3-20200525-foss-2022b.eb and patches: Block-1.5.3_resolve_deprecated_Bind_placeholder.patch --- .../Block/Block-1.5.3-20200525-foss-2022b.eb | 56 +++++++ ..._resolve_deprecated_Bind_placeholder.patch | 151 ++++++++++++++++++ .../Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb | 29 ++++ 3 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb create mode 100644 easybuild/easyconfigs/b/Block/Block-1.5.3_resolve_deprecated_Bind_placeholder.patch create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb new file mode 100644 index 000000000000..524c89130952 --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb @@ -0,0 +1,56 @@ +easyblock = 'MakeCp' + +name = 'Block' +version = '1.5.3-20200525' +_commit = 'f95317b08043b7c531289576d59ad74a6d920741' + +homepage = 'https://sanshar.github.io/Block/' +description = """Block implements the density matrix renormalization group (DMRG) algorithm for +quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'cstd': 'c++11', 'pic': True} + +# Version 1.5 is a major rewrite of Block that was named at some point StackBlock +# sources are available in sanshar/StackBlock +# sources at sanshar/Block@b0e3671aad and pyscf/Block@db27636b76 correspond to version 1.1.1 +source_urls = ['https://github.com/sanshar/StackBlock/archive'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': '%(version)s.tar.gz'}] +patches = [ + 'Block-1.5.3_use-eb-environment.patch', + 'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch', + 'Block-1.5.3_resolve_deprecated_Bind_placeholder.patch' +] +checksums = [ + {'1.5.3-20200525.tar.gz': '8d793c5e460d7747a0adcb06ce4b457c6750cf2d42cead1d060db8b44643c3b1'}, + {'Block-1.5.3_use-eb-environment.patch': '7f3e8a52f28d251441d20dfde1f9cb8cdc0c34216defab61cc6980e540a6cf60'}, + {'Block-1.5.3_replace_mpi_cxx_binds_with_boost_mpi.patch': + 'f53f1f88cb7b12ab38d1313f93a9bbd31c745dca1beca7a8d51d00e0ae4e762f'}, + {'Block-1.5.3_resolve_deprecated_Bind_placeholder.patch': + '51d692f294e800e0a9e027ef35bf761612ecb9efe77ddb378ec973b55e39a1e8'}, +] + +dependencies = [ + ('Boost.MPI', '1.83.0'), +] + +buildopts = [ + # Multi-threaded build (block.spin_adapted-serial) + 'OPENMP="yes" EXECUTABLE="block.spin_adapted-serial"', + # MPI build (block.spin_adapted) + 'USE_MPI="yes"', +] + +files_to_copy = [(['block.spin_adapted*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/block.spin_adapted', 'bin/block.spin_adapted-serial'], + 'dirs': [], +} + +sanity_check_commands = [ + "block.spin_adapted-serial --version", + "%(mpi_cmd_prefix)s block.spin_adapted --version", +] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3_resolve_deprecated_Bind_placeholder.patch b/easybuild/easyconfigs/b/Block/Block-1.5.3_resolve_deprecated_Bind_placeholder.patch new file mode 100644 index 000000000000..9361e01827f0 --- /dev/null +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3_resolve_deprecated_Bind_placeholder.patch @@ -0,0 +1,151 @@ +resolve Error: "pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior." +define BOOST_BIND_GLOBAL_PLACEHOLDERS +replace #include with #include , +replace copy_option::overwrite_if_exists with copy_options::overwrite_existing +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/genetic/GAOptimize.C StackBlock-f95317b08043b7c531289576d59ad74a6d920741/genetic/GAOptimize.C +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/genetic/GAOptimize.C 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/genetic/GAOptimize.C 2024-01-04 15:22:29.874336000 +0100 +@@ -9,7 +9,7 @@ + using namespace std; + + #include +-#include ++#include + + #ifndef SERIAL + #include +@@ -18,6 +18,7 @@ + + #include + #include ++#include + + namespace genetic + { +@@ -58,7 +59,7 @@ + mpi::broadcast(world, ksum, 0); + #endif + +- Cell::Evaluate = boost::bind(genetic::Evaluate, 1.0/ksum, gainput.exponent, _1, K); ++ Cell::Evaluate = boost::bind(genetic::Evaluate, 1.0/ksum, gainput.exponent, std::placeholders::_1, K); + Cell best; + #ifndef SERIAL + int ntask = 1 + gainput.max_community / world.size(); +@@ -125,7 +126,7 @@ + mpi::broadcast(world, ksum, 0); + #endif + +- Cell::Evaluate = boost::bind(genetic::Evaluate, 1.0/ksum, gainput.exponent, _1, K); ++ Cell::Evaluate = boost::bind(genetic::Evaluate, 1.0/ksum, gainput.exponent, std::placeholders::_1, K); + Cell best; + #ifndef SERIAL + int ntask = 1 + gainput.max_community / world.size(); +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/genetic/GAOptimize.h StackBlock-f95317b08043b7c531289576d59ad74a6d920741/genetic/GAOptimize.h +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/genetic/GAOptimize.h 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/genetic/GAOptimize.h 2024-01-04 15:11:37.071030036 +0100 +@@ -1,6 +1,8 @@ + #ifndef GA_OPTIMIZE_H + #define GA_OPTIMIZE_H + ++#define BOOST_BIND_GLOBAL_PLACEHOLDERS ++ + #include + #include "Cell.h" + +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/modules/npdm/npdm_permutations.C StackBlock-f95317b08043b7c531289576d59ad74a6d920741/modules/npdm/npdm_permutations.C +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/modules/npdm/npdm_permutations.C 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/modules/npdm/npdm_permutations.C 2024-01-04 15:32:31.035358000 +0100 +@@ -13,6 +13,8 @@ + #include "Stackspinblock.h" + #include "pario.h" + ++#include ++ + namespace SpinAdapted{ + + //=========================================================================================================================================================== +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/StackMatrix.h StackBlock-f95317b08043b7c531289576d59ad74a6d920741/StackMatrix.h +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/StackMatrix.h 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/StackMatrix.h 2024-01-04 13:51:30.872835728 +0100 +@@ -1,6 +1,8 @@ + #ifndef SPIN_STACKMATRIX_HEADER + #define SPIN_STACKMATRIX_HEADER + ++#define BOOST_BIND_GLOBAL_PLACEHOLDERS ++ + #include + #include + #include +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/StackOperators.h StackBlock-f95317b08043b7c531289576d59ad74a6d920741/StackOperators.h +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/StackOperators.h 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/StackOperators.h 2024-01-04 13:48:49.790156000 +0100 +@@ -3,7 +3,7 @@ + #include "StackBaseOperator.h" + #include + #include +-#include ++#include + + typedef boost::function >)> FUNCTOR; + typedef boost::function)> FUNCTOR2; +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/Stackspinblock.C StackBlock-f95317b08043b7c531289576d59ad74a6d920741/Stackspinblock.C +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/Stackspinblock.C 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/Stackspinblock.C 2024-01-04 13:30:04.524917000 +0100 +@@ -23,7 +23,7 @@ + #include + #include + #include +-#include ++#include + #include + + #ifndef SERIAL +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/Stackspinblock.h StackBlock-f95317b08043b7c531289576d59ad74a6d920741/Stackspinblock.h +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/Stackspinblock.h 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/Stackspinblock.h 2024-01-04 13:41:28.043983000 +0100 +@@ -1,5 +1,6 @@ + #ifndef STACKSPINBLOCK_HEADER + #define STACKSPINBLOCK_HEADER ++#define BOOST_BIND_GLOBAL_PLACEHOLDERS + #include + #include + #include +diff -ru StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/Stackwavefunction.C StackBlock-f95317b08043b7c531289576d59ad74a6d920741/Stackwavefunction.C +--- StackBlock-f95317b08043b7c531289576d59ad74a6d920741.orig/Stackwavefunction.C 2020-05-25 15:51:59.000000000 +0200 ++++ StackBlock-f95317b08043b7c531289576d59ad74a6d920741/Stackwavefunction.C 2024-01-04 14:16:06.713200000 +0100 +@@ -224,7 +224,7 @@ + sprintf (fileout, "%s/%s", dmrginp.load_prefix().c_str() , outfile.c_str()); + boost::filesystem::path topath(fileout); + +- copy_file(frompath, topath,boost::filesystem::copy_option::overwrite_if_exists); ++ copy_file(frompath, topath,boost::filesystem::copy_options::overwrite_existing); + } + + string filename2 = itr->path().filename().string(); +@@ -242,7 +242,7 @@ + sprintf (fileout, "%s/%s", dmrginp.load_prefix().c_str() , outfile.c_str()); + boost::filesystem::path topath(fileout); + +- copy_file(frompath, topath,boost::filesystem::copy_option::overwrite_if_exists); ++ copy_file(frompath, topath,boost::filesystem::copy_options::overwrite_existing); + } + + } +@@ -284,7 +284,7 @@ + sprintf (fileout, "%s/%s", dmrginp.load_prefix().c_str() , outfile.c_str()); + boost::filesystem::path topath(fileout); + +- copy_file(frompath, topath,boost::filesystem::copy_option::overwrite_if_exists); ++ copy_file(frompath, topath,boost::filesystem::copy_options::overwrite_existing); + } + + string filename2 = itr->path().filename().string(); +@@ -302,7 +302,7 @@ + sprintf (fileout, "%s/%s", dmrginp.load_prefix().c_str() , outfile.c_str()); + boost::filesystem::path topath(fileout); + +- copy_file(frompath, topath,boost::filesystem::copy_option::overwrite_if_exists); ++ copy_file(frompath, topath,boost::filesystem::copy_options::overwrite_existing); + } + + } diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb new file mode 100644 index 000000000000..c0308757704f --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.83.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('zstd', '1.5.2'), + ('ICU', '72.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From f6dfb970144fe170294ea5eeabe7635bd24c0606 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 4 Jan 2024 14:59:25 +0000 Subject: [PATCH 0160/1193] include suggested changes --- .../easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb index 36a0c27b225b..0a8281d17083 100644 --- a/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phono3py/phono3py-2.7.0-foss-2023a.eb @@ -8,10 +8,11 @@ description = """A simulation package of phonon-phonon interaction related prope toolchain = {'name': 'foss', 'version': '2023a'} -source_urls = ['https://github.com/phonopy/phono3py/archive/refs/tags/'] +github_account = 'phonopy' +source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['8d2c6d52d4b9a25783d69fb3a502394ed02eba7d573c5f1a3e43fd74ac1e5ed3'] +checksums = ['26c91740bac42e7f654f2929033efa82c3751c8bebd2d861cbe37a573be86e8c'] dependencies = [ ('Python', '3.11.3'), From 256d9f5569050e878c0b551ba4bf6022573eb5d0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 4 Jan 2024 16:03:00 +0100 Subject: [PATCH 0161/1193] SUNDIALS: add missing checksums --- .../easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb | 5 +++++ .../easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb | 5 +++++ 2 files changed, 10 insertions(+) mode change 100755 => 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb old mode 100755 new mode 100644 index 47032021b89d..565de5bcd7ce --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2022b.eb @@ -15,6 +15,11 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-%(version)s_fix_bad_find_library_calls.patch', ] +checksums = [ + {'sundials-6.6.0.tar.gz': 'f90029b8da846c8faff5530fd1fa4847079188d040554f55c1d5d1e04743d29d'}, + {'SUNDIALS-6.6.0_fix_bad_find_library_calls.patch': + 'c5e3248bd036fee17436649280ff7156a2722698c33ec20a5e635e3a60d16823'}, +] builddependencies = [ ('CMake', '3.24.3'), diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb index ad6e8fa5b007..d3a8e2b177df 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a.eb @@ -15,6 +15,11 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-%(version)s_fix_bad_find_library_calls.patch', ] +checksums = [ + {'sundials-6.6.0.tar.gz': 'f90029b8da846c8faff5530fd1fa4847079188d040554f55c1d5d1e04743d29d'}, + {'SUNDIALS-6.6.0_fix_bad_find_library_calls.patch': + 'c5e3248bd036fee17436649280ff7156a2722698c33ec20a5e635e3a60d16823'}, +] builddependencies = [ ('CMake', '3.26.3'), From def2702cf047f961d50890117181b20bf889ee8f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 4 Jan 2024 16:57:26 +0100 Subject: [PATCH 0162/1193] fix lapack test failures in OpenBLAS 0.3.23/24 --- .../o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb | 8 +++--- ...AS-0.3.23_disable-xDRGES-LAPACK-test.patch | 26 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb | 8 +++--- 3 files changed, 32 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb index 490f623ac152..2cbbd45397e8 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23-GCC-12.3.0.eb @@ -19,10 +19,9 @@ patches = [ 'OpenBLAS-0.3.20_fix-x86-cpuid.patch', 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch', 'OpenBLAS-0.3.23_fix-parallel-build.patch', - 'OpenBLAS-0.3.23_fix-lapack-test.patch', 'OpenBLAS-0.3.23_fix-tests-hang.patch', - 'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch', ] checksums = [ {'v0.3.23.tar.gz': '5d9491d07168a5d00116cdc068a40022c3455bf9293c7cb86a65b1054d7e5114'}, @@ -35,11 +34,10 @@ checksums = [ '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch': + 'ab7e0af05f9b2a2ced32f3875e1e3767d9c3531a455421a38f7324350178a0ff'}, {'OpenBLAS-0.3.23_fix-parallel-build.patch': 'abe10ba3b0ca54772dbf235596e35325a5159018f6a60cfc88824c2c220d99d9'}, - {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, {'OpenBLAS-0.3.23_fix-tests-hang.patch': '9de1fdee6edf3b2bb55e4639fdd92d2877b5f0ac880f7df2cfea47ecebf16609'}, - {'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch': - '36a16b4d3b867897413b43b774f8b57d641ad9a1b452e9de33ced198ab25e461'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch new file mode 100644 index 000000000000..bdc1262873ab --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch @@ -0,0 +1,26 @@ +disable failing DDRGES3 test in LAPACK 3.10 test suite, fixes "Error code from DDRGES3 = 9"; +see also https://github.com/OpenMathLib/OpenBLAS/issues/4032 +author: Kenneth Hoste (HPC-UGent) +Similar for SDRGES: SGGES returned INFO= 9. +See https://github.com/OpenMathLib/OpenBLAS/issues/4415 +Author: Alexander Grund (TU Dresden) +--- OpenBLAS-0.3.23/lapack-netlib/TESTING/dgd.in.orig 2023-09-29 08:05:53.089031858 +0200 ++++ OpenBLAS-0.3.23/lapack-netlib/TESTING/dgd.in 2023-09-29 08:08:32.234680735 +0200 +@@ -1,6 +1,6 @@ + DGS Data for the Real Nonsymmetric Schur Form Driver + 5 Number of matrix dimensions +-2 6 10 12 20 30 Matrix dimensions ++2 10 12 20 30 Matrix dimensions + 1 1 1 2 1 Parameters NB, NBMIN, NXOVER, NS, NBCOL + 10 Threshold for test ratios + .TRUE. Put T to test the error exits +--- OpenBLAS-0.3.23/lapack-netlib/TESTING/sgd.in.orig 2023-06-06 11:01:50.512947527 +0000 ++++ OpenBLAS-0.3.23/lapack-netlib/TESTING/sgd.in 2023-06-06 11:02:05.318078733 +0000 +@@ -1,6 +1,6 @@ + SGS Data for the Real Nonsymmetric Schur Form Driver + 5 Number of matrix dimensions +-2 6 10 12 20 30 Matrix dimensions ++2 10 12 20 30 Matrix dimensions + 1 1 1 2 1 Parameters NB, NBMIN, NXOVER, NS, NBCOL + 10 Threshold for test ratios + .TRUE. Put T to test the error exits diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb index be80c46e97c0..4835813e357a 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.24-GCC-13.2.0.eb @@ -18,8 +18,7 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.20_use-xASUM-microkernels-on-new-intel-cpus.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', - 'OpenBLAS-0.3.23_fix-lapack-test.patch', - 'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch', + 'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch', 'OpenBLAS-0.3.24_fix-czasum.patch', ] checksums = [ @@ -32,9 +31,8 @@ checksums = [ '1dbd0f9473963dbdd9131611b455d8a801f1e995eae82896186d3d3ffe6d5f03'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, - {'OpenBLAS-0.3.23_fix-lapack-test.patch': 'f6b3d81061f136e34aaf5359bb80fb9d2bba28825cc1dd26179b8dd01a9a0054'}, - {'OpenBLAS-0.3.23_disable-DDRGES3-LAPACK-test.patch': - '36a16b4d3b867897413b43b774f8b57d641ad9a1b452e9de33ced198ab25e461'}, + {'OpenBLAS-0.3.23_disable-xDRGES-LAPACK-test.patch': + 'ab7e0af05f9b2a2ced32f3875e1e3767d9c3531a455421a38f7324350178a0ff'}, {'OpenBLAS-0.3.24_fix-czasum.patch': '8132b87c519fb08caa3bd7291fe8a1d0e1afe6fcb667d16f3020b46122afe20c'}, ] From 2e409e1dfc2d5cc3240656e4563fbe491c3e750b Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 4 Jan 2024 17:05:59 +0100 Subject: [PATCH 0163/1193] adding easyconfigs: RHEIA-1.1.6-foss-2022a.eb --- .../r/RHEIA/RHEIA-1.1.6-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.6-foss-2022a.eb b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.6-foss-2022a.eb new file mode 100644 index 000000000000..bf5b3e406ba6 --- /dev/null +++ b/easybuild/easyconfigs/r/RHEIA/RHEIA-1.1.6-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'RHEIA' +version = '1.1.6' + +homepage = 'https://github.com/rheia-framework/RHEIA' +description = "Robust design optimization of renewable Hydrogen and dErIved energy cArrier systems" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # deap, numpy, pandas, scipy + ('h5py', '3.7.0'), + ('matplotlib', '3.5.2'), +] + +use_pip = True + +exts_list = [ + ('pvlib', '0.10.3', { + 'checksums': ['024a1b523d73a633323612e7f315a1709cf06d1fd43ff0821901f66a4068b2d9'], + }), + ('pyDOE', '0.3.8', { + 'modulename': '%(name)s', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['cbd6f14ae26d3c9f736013205f53ea1191add4567033c3ee77b7dd356566c4b6'], + }), + ('SobolSequence', '0.2.1', { + 'modulename': 'sobol', + 'checksums': ['b2b4b57451b8d2e79ddb07efa23bc471dfdd436ea357d6368666bdc364df3eb1'], + }), + ('rheia', version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['4af382163ee3972881bc6ba59099c3f19965001d1c65eeeaea8343e0d3b77621'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 680f513a5dc5b52eee4b7308f3747a24b698392c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jan 2024 21:10:01 +0100 Subject: [PATCH 0164/1193] adding easyconfigs: medaka-1.11.3-foss-2022a.eb --- .../m/medaka/medaka-1.11.3-foss-2022a.eb | 79 +++++++++++++++++++ 1 file changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb new file mode 100644 index 000000000000..85c733711d19 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2022a.eb @@ -0,0 +1,79 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.11.3' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.24.3'), +] + +_minimap_ver = '2.24' +dependencies = [ + ('Python', '3.10.4'), # includes cffi + # tensorflow~=2.10.0 required by medaka 1.11.3, see requirements.txt + ('TensorFlow', '2.11.0'), + ('Pysam', '0.19.1'), + ('SAMtools', '1.16.1'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.15.1'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('python-parasail', '1.3.3'), + ('ont-fast5-api', '4.1.1'), + ('WhatsHap', '1.7'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.15.1'), + ('pybind11', '2.9.2'), + ('spoa', '4.0.7'), +] + +use_pip = True + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + # medaka 1.11.3 requires pyspoa >= 0.2.1 + ('pyspoa', '0.2.1', { + 'checksums': ['a8a7b7df3faa1b5bb16d6b4e82099b1c9aca604c8288bcf8ca4960d376f7ff8c'], + 'modulename': 'spoa', + }), + ('wurlitzer', '3.0.3', { + 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], + }), + (name, version, { + 'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'], + # remove TensorFlow version requirement which is too strict + 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' From 6cb05dc708bc818962ee6bf7e17f1e895d865850 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Jan 2024 21:32:24 +0100 Subject: [PATCH 0165/1193] adding easyconfigs: XlsxWriter-3.1.9-GCCcore-13.2.0.eb --- .../XlsxWriter-3.1.9-GCCcore-13.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.9-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.9-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..74d6a7ef4c52 --- /dev/null +++ b/easybuild/easyconfigs/x/XlsxWriter/XlsxWriter-3.1.9-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'XlsxWriter' +version = '3.1.9' + +homepage = 'https://xlsxwriter.readthedocs.io/' +description = "A Python module for creating Excel XLSX files" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['de810bf328c6a4550f4ffd6b0b34972aeb7ffcf40f3d285a0413734f9b63a929'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/vba_extract.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['vba_extract.py --help'] + +sanity_pip_check = True + +moduleclass = 'tools' From ee89bf66c7029eefae225eedf45e5c3065eb483a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 10:59:56 +0100 Subject: [PATCH 0166/1193] adding easyconfigs: Gerris-20131206-gompi-2023a.eb --- .../g/Gerris/Gerris-20131206-gompi-2023a.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gerris/Gerris-20131206-gompi-2023a.eb diff --git a/easybuild/easyconfigs/g/Gerris/Gerris-20131206-gompi-2023a.eb b/easybuild/easyconfigs/g/Gerris/Gerris-20131206-gompi-2023a.eb new file mode 100644 index 000000000000..935d3835a637 --- /dev/null +++ b/easybuild/easyconfigs/g/Gerris/Gerris-20131206-gompi-2023a.eb @@ -0,0 +1,67 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: David Quigley (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +## +easyblock = 'Bundle' + +name = 'Gerris' +version = '20131206' + +homepage = 'http://gfs.sourceforge.net/wiki/index.php/Main_Page' +description = """Gerris is a Free Software program for the solution of the partial + differential equations describing fluid flow""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GLib', '2.77.1'), # for GTS + ('gnuplot', '5.4.8'), # for gfsplot +] + +components = [ + ('GTS', '121130', { + 'easyblock': 'ConfigureMake', + 'source_urls': ['https://gts.sourceforge.net/tarballs/'], + 'sources': ['gts-snapshot-%(version)s.tar.gz'], + 'checksums': ['c23f72ab74bbf65599f8c0b599d6336fabe1ec2a09c19b70544eeefdc069b73b'], + 'start_dir': 'gts-snapshot-%(version)s', + }), + (name, version, { + 'easyblock': 'ConfigureMake', + 'source_urls': ['http://gerris.dalembert.upmc.fr/gerris/tarballs'], + 'sources': ['gerris-snapshot-131206.tar.gz'], + 'checksums': ['d5346a362b104ccc858c4b79938727d56c4654b103c268e54cf3aa56d0b55b39'], + 'start_dir': 'gerris-snapshot-%s' % version[2:], + 'preconfigopts': "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ", + 'prebuildopts': "sed -i 's/MPI_Errhandler_set/MPI_Comm_set_errhandler/g' src/init.c && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/gerris2D', 'bin/gerris3D', 'bin/gfscompare2D', 'bin/gfscompare3D', + 'bin/gfsjoin', 'bin/gfsjoin2D', 'bin/gfsjoin3D', + 'include/gfs.h', 'include/gts.h', 'include/gtsconfig.h', + 'lib/libgfs2D.a', 'lib/libgfs2D.%s' % SHLIB_EXT, + 'lib/libgfs3D.a', 'lib/libgfs3D.%s' % SHLIB_EXT, 'lib/libgts.%s' % SHLIB_EXT], + 'dirs': ['share/gerris', 'include/gerris'] +} + +sanity_check_commands = [ + "gerris2D -h", + "gerris3D -h", + "gfscompare2D -h", + "gfscompare3D -h", + "gfsjoin -h", + "gfsjoin2D -h", + "gfsjoin3D -h", +] + +moduleclass = 'cae' From 36b4ca08761b920fa93f704713561cd579711c74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 5 Jan 2024 11:18:16 +0100 Subject: [PATCH 0167/1193] adding easyconfigs: AMS-2023.104-iimpi-2022b-intelmpi.eb --- .../AMS/AMS-2023.104-iimpi-2022b-intelmpi.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMS/AMS-2023.104-iimpi-2022b-intelmpi.eb diff --git a/easybuild/easyconfigs/a/AMS/AMS-2023.104-iimpi-2022b-intelmpi.eb b/easybuild/easyconfigs/a/AMS/AMS-2023.104-iimpi-2022b-intelmpi.eb new file mode 100644 index 000000000000..95e08257026b --- /dev/null +++ b/easybuild/easyconfigs/a/AMS/AMS-2023.104-iimpi-2022b-intelmpi.eb @@ -0,0 +1,47 @@ +easyblock = 'Tarball' + +name = 'AMS' +version = '2023.104' +versionsuffix = '-intelmpi' + +homepage = 'https://www.scm.com/amsterdam-modeling-suite/' +description = """ +The Amsterdam Modeling Suite (AMS) provides a comprehensive set of modules for +computational chemistry and materials science, from quantum mechanics to fluid +thermodynamics. +""" + +toolchain = {'name': 'iimpi', 'version': '2022b'} + +sources = ['ams%(version)s.pc64_linux.intelmpi.bin.tgz'] +checksums = ['c977014f14291f7f210be7e48bc28f71ab0a076a5af257e92f2c873f54d208af'] + +dependencies = [('libGLU', '9.0.2')] + +keepsymlinks = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['atomicdata', 'bin', 'examples'], +} + +# check if license file is installed +# sanity_check_commands = ['dirac check'] + +modextrapaths = { + 'AMSHOME': '', + 'AMSBIN': 'bin', + 'AMSRESOURCES': 'atomicdata', +} + +modextravars = { + # use Intel MPI from EasyBuild + 'SCM_USE_LOCAL_IMPI': '1', +} + +modloadmsg = """These environment variables need to be defined before using AMS: + * $SCMLICENSE: path to AMS license file + * $SCM_TMPDIR: path to user scratch directory +""" + +moduleclass = 'chem' From 3fca2a0632f1185f72438c60edac931c2c010116 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 5 Jan 2024 12:16:11 +0100 Subject: [PATCH 0168/1193] Ghostscript v10.02.1: Improve style of EB file --- .../g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb index 5e464e9cb8d8..61620daade7b 100644 --- a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.02.1-GCCcore-13.2.0.eb @@ -10,7 +10,9 @@ description = """Ghostscript is a versatile processor for PostScript data with t toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs10021'] +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] sources = [SOURCELOWER_TAR_GZ] checksums = ['e429e4f5b01615a4f0f93a4128e8a1a4d932dff983b1774174c79c0630717ad9'] @@ -18,6 +20,7 @@ builddependencies = [ ('binutils', '2.40'), ('pkgconf', '2.0.3'), ] + dependencies = [ ('zlib', '1.2.13'), ('libpng', '1.6.40'), From e62ee26d6b0cbde3d63e57ffb04e24d20bbeaf3e Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 5 Jan 2024 15:33:44 +0100 Subject: [PATCH 0169/1193] f90nml: archive GCCcore/10.2.0 version and add GCCcore/13.2.0 version --- .../f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb | 0 .../f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb | 28 +++++++++++++++++++ 2 files changed, 28 insertions(+) rename easybuild/easyconfigs/{ => __archive__}/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb (100%) create mode 100644 easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/__archive__/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb similarity index 100% rename from easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb rename to easybuild/easyconfigs/__archive__/f/f90nml/f90nml-1.4.4-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..1e31e9ee12ec --- /dev/null +++ b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'f90nml' +version = '1.4.4' + +homepage = 'https://github.com/marshallward/f90nml' +description = """A Python module and command line tool for parsing + Fortran namelist files""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['65e8e135779895245238cbf6be5b1b80d6c2b8c9350c9cdce6183a31bdfd7622'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From b5707306432b2d29bcf9f0e47bdf285417051d19 Mon Sep 17 00:00:00 2001 From: Carsten Bauer Date: Fri, 5 Jan 2024 16:34:03 +0100 Subject: [PATCH 0170/1193] Add files via upload --- .../j/Julia/Julia-1.10.0-linux-x86_64.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb new file mode 100644 index 000000000000..c1f1080404a9 --- /dev/null +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb @@ -0,0 +1,23 @@ +easyblock = 'Tarball' + +name = 'Julia' +version = '1.10.0' +versionsuffix = '-linux-x86_64' + +homepage = 'https://julialang.org' +description = "Julia is a high-level, high-performance dynamic programming language for numerical computing" + +toolchain = SYSTEM + +source_urls = ['https://julialang-s3.julialang.org/bin/linux/x64/%(version_major_minor)s/'] +sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] +checksums = ['a7298207f72f2b27b2ab1ce392a6ea37afbd1fbee0f1f8d190b054dcaba878fe'] + +sanity_check_paths = { + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], + 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] +} + +sanity_check_commands = ['julia --help'] + +moduleclass = 'lang' From 542c8cb96a32ec50e37309dea0e96088fed67375 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 21:57:39 +0100 Subject: [PATCH 0171/1193] {lib}[GCC/12.2.0] SentencePiece v0.1.99, gperftools v2.14 --- .../gperftools-2.14-GCCcore-12.2.0.eb | 38 +++++++++++ .../SentencePiece-0.1.99-GCC-12.2.0.eb | 65 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/g/gperftools/gperftools-2.14-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.99-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gperftools/gperftools-2.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gperftools/gperftools-2.14-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..3b659f0b9c87 --- /dev/null +++ b/easybuild/easyconfigs/g/gperftools/gperftools-2.14-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'gperftools' +version = '2.14' + +homepage = 'https://github.com/gperftools/gperftools' +description = """ +gperftools is a collection of a high-performance multi-threaded malloc() +implementation, plus some pretty nifty performance analysis tools. +Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'gperftools' +source_urls = [GITHUB_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['ab456a74af2f57a3ee6c20462f73022d11f7ffc22e470fc06dec39692c0ee5f3'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] + +dependencies = [ + ('libunwind', '1.6.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = '--enable-libunwind' + +sanity_check_paths = { + 'files': ['bin/pprof', 'lib/libprofiler.a', 'lib/libprofiler.%s' % SHLIB_EXT, + 'lib/libtcmalloc.a', 'lib/libtcmalloc.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.99-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.99-GCC-12.2.0.eb new file mode 100644 index 000000000000..b0776f524b69 --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.99-GCC-12.2.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.99' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('gperftools', '2.14'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['63617eaf56c7a3857597dcd8780461f57dd21381b56a27716ef7d7e02e14ced4'], +} + +components = [ + (name, version, { + 'easyblock': 'CMakeMake', + 'separate_build_dir': True, + 'start_dir': '%(namelower)s-%(version)s', + }), + ('sentencepiece', version, { + 'easyblock': 'PythonPackage', + 'start_dir': '%(namelower)s-%(version)s/python', + 'prebuildopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'preinstallopts': 'export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && ', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + }), +] + +postinstallcmds = ['cp -a %(builddir)s/%(namelower)s-%(version)s/{data,doc} %(installdir)s/'] + +sanity_check_paths = { + 'files': ['bin/spm_%s' % x for x in ['decode', 'encode', 'export_vocab', 'normalize', 'train']] + + ['lib/libsentencepiece.%s' % SHLIB_EXT, 'lib/libsentencepiece_train.%s' % SHLIB_EXT] + + ['include/sentencepiece_processor.h', 'include/sentencepiece_trainer.h'], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'data', 'doc'], +} + +sanity_check_commands = [ + 'spm_train --help', + "python -c 'import sentencepiece'", +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'lib' From a7a41b9bf708040592061fb0a947d8e1524a4f1b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 21:59:54 +0100 Subject: [PATCH 0172/1193] {vis}[foss/2022b] torchvision v0.14.1, Pillow-SIMD v9.5.0 --- .../Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ .../torchvision-0.14.1-foss-2022b.eb | 21 ++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.14.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..cec85fa1ae6a --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Pillow-SIMD' +version = '9.5.0' + +homepage = 'https://github.com/uploadcare/pillow-simd' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/uploadcare/pillow-simd/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1a9819343b451b7faf34663156e2abca3ae69ab604f82e445478c8133422e4f0'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('LibTIFF', '4.4.0'), + ('freetype', '2.12.1'), + ('libwebp', '1.3.1'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'PIL'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/PIL'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.14.1-foss-2022b.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.14.1-foss-2022b.eb new file mode 100644 index 000000000000..4b7c687138c6 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.14.1-foss-2022b.eb @@ -0,0 +1,21 @@ +name = 'torchvision' +version = '0.14.1' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['ced67e1cf1f97e168cdf271851a4d0b6d382ab7936e7bcbb39aaa87239c324b6'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('Python', '3.10.8'), + ('Pillow-SIMD', '9.5.0'), + ('PyTorch', '1.13.1'), +] + +moduleclass = 'vis' From 524642617ea99549d8ced10092477d01c3d2950e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 22:00:35 +0100 Subject: [PATCH 0173/1193] adding easyconfigs: NLTK-3.8.1-foss-2022b.eb --- .../n/NLTK/NLTK-3.8.1-foss-2022b.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2022b.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2022b.eb new file mode 100644 index 000000000000..df522f5fd0a9 --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2022b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'NLTK' +version = '3.8.1' + +homepage = 'https://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('scikit-learn', '1.2.1'), + ('matplotlib', '3.7.0'), + ('tqdm', '4.64.1'), +] + +local_nltk_data_install = [] +# Install NLTK data sets (7.4 GB) +# local_nltk_data = '/path/to/database/nltk_data' +# local_nltk_data_install = [ +# "mkdir -p %s && NLTK_DATA=%s python -m nltk.downloader all" % (local_nltk_data, local_nltk_data) +# ] +# modextravars = {'NLTK_DATA': local_nltk_data} + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2023.12.25', { + 'checksums': ['29171aa128da69afdf4bde412d5bedc335f2ca8fcfe4489038577d05f16181e5'], + }), + ('python-crfsuite', '0.9.10', { + 'modulename': 'pycrfsuite', + 'checksums': ['f38524631e2b533341f10f2c77689270dc6ecd5985495dccf7aa37b1045bc2e5'], + }), + (name, version, { + 'postinstallcmds': [], + 'source_tmpl': '%(namelower)s-%(version)s.zip', + 'use_pip_extras': 'corenlp,machine_learning,plot,tgrep', + 'checksums': ['1834da3d0682cba4f2cede2f9aad6b0fafb6461ba451db0efb6f9c39798d64d3'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] + +moduleclass = 'devel' From 1b042331168af2fe31223c837952bd7e9e363d34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 22:01:15 +0100 Subject: [PATCH 0174/1193] adding easyconfigs: Sentence-Transformers-2.2.2-foss-2022b.eb --- .../Sentence-Transformers-2.2.2-foss-2022b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sentence-Transformers/Sentence-Transformers-2.2.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/s/Sentence-Transformers/Sentence-Transformers-2.2.2-foss-2022b.eb b/easybuild/easyconfigs/s/Sentence-Transformers/Sentence-Transformers-2.2.2-foss-2022b.eb new file mode 100644 index 000000000000..54f5df43bc66 --- /dev/null +++ b/easybuild/easyconfigs/s/Sentence-Transformers/Sentence-Transformers-2.2.2-foss-2022b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'Sentence-Transformers' +version = '2.2.2' + +homepage = 'https://github.com/UKPLab/sentence-transformers' +description = """Sentence Transformers provides an easy method to compute dense vector representations for sentences, + paragraphs, and images""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Transformers', '4.30.2'), + ('tqdm', '4.64.1'), + ('scikit-learn', '1.2.1'), + ('SentencePiece', '0.1.99'), + ('PyTorch', '1.13.1'), + ('torchvision', '0.14.1'), + ('NLTK', '3.8.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sentence-transformers', version, { + 'checksums': ['dbc60163b27de21076c9a30d24b5b7b6fa05141d68cf2553fa9a77bf79a29136'], + }), +] + +moduleclass = 'lib' From 7332864f8420e33b97c0d591c62346bb00562d95 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 22:17:12 +0100 Subject: [PATCH 0175/1193] adding easyconfigs: typing-extensions-4.9.0-GCCcore-12.2.0.eb --- .../typing-extensions-4.9.0-GCCcore-12.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..6d941d6f9713 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.9.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From d40ca3baf1f8a3974794c8d32f2ce52701503b1f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 22:17:42 +0100 Subject: [PATCH 0176/1193] adding easyconfigs: ONNX-Runtime-1.16.3-foss-2022b.eb, ONNX-1.15.0-foss-2022b.eb and patches: ONNX-1.15.0_fix-protobuf-linking.patch --- .../ONNX-Runtime-1.16.3-foss-2022b.eb | 50 +++++++++++++++ .../o/ONNX/ONNX-1.15.0-foss-2022b.eb | 64 +++++++++++++++++++ .../ONNX-1.15.0_fix-protobuf-linking.patch | 18 ++++++ 3 files changed, 132 insertions(+) create mode 100644 easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.16.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/o/ONNX/ONNX-1.15.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/o/ONNX/ONNX-1.15.0_fix-protobuf-linking.patch diff --git a/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.16.3-foss-2022b.eb b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.16.3-foss-2022b.eb new file mode 100644 index 000000000000..a94de01f28e8 --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX-Runtime/ONNX-Runtime-1.16.3-foss-2022b.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'ONNX-Runtime' +version = '1.16.3' + +homepage = 'https://onnxruntime.ai' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('ONNX', '1.15.0'), + ('flatbuffers-python', '23.1.4'), + ('sympy', '1.12'), +] + +use_pip = True + +local_whl_tmpl = 'onnxruntime-%%(version)s-cp310-cp310-manylinux_2_17_%s.manylinux2014_%s.whl' + +exts_list = [ + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + (name, version, { + 'source_urls': ['http://pypi.python.org/packages/source/o/onnxruntime'], + 'sources': [local_whl_tmpl % ('%(arch)s', '%(arch)s')], + 'checksums': [{ + local_whl_tmpl % ('x86_64', 'x86_64'): + 'ef2b1fc269cabd27f129fb9058917d6fdc89b188c49ed8700f300b945c81f889', + local_whl_tmpl % ('aarch64', 'aarch64'): + '5f91f5497fe3df4ceee2f9e66c6148d9bfeb320cd6a71df361c66c5b8bac985a', + }], + 'modulename': 'onnxruntime', + }), +] + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ONNX/ONNX-1.15.0-foss-2022b.eb b/easybuild/easyconfigs/o/ONNX/ONNX-1.15.0-foss-2022b.eb new file mode 100644 index 000000000000..0125931898cb --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX/ONNX-1.15.0-foss-2022b.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonPackage' + +name = 'ONNX' +version = '1.15.0' + +homepage = 'https://onnx.ai' +description = """ +Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI +developers to choose the right tools as their project evolves. ONNX provides an +open source format for AI models, both deep learning and traditional ML. It +defines an extensible computation graph model, as well as definitions of +built-in operators and standard data types. Currently we focus on the +capabilities needed for inferencing (scoring).""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCELOWER_TAR_GZ] +patches = ['ONNX-1.15.0_fix-protobuf-linking.patch'] +checksums = [ + {'onnx-1.15.0.tar.gz': 'b18461a7d38f286618ca2a6e78062a2a9c634ce498e631e708a8041b00094825'}, + {'ONNX-1.15.0_fix-protobuf-linking.patch': '5c11eca5275a25d69f989571fe1f387b84c7334478356577f6f6349c5954f54d'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + # more recent setuptools required to fix: AttributeError: editable_mode + ('setuptools', '64.0.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('protobuf-python', '4.23.0'), + ('typing-extensions', '4.9.0'), +] + +use_pip = True +download_dep_fail = True + +# hardcode version in pyproject.toml rather than determining it dynamically +preinstallopts = """sed -i 's/"version",//g' pyproject.toml && """ +preinstallopts += """sed -i 's/readme = .*/version = "%(version)s"/g' pyproject.toml && """ + +# specify C++17 standard and link to protobuf shared library (also requires patch to use -DPROTOBUF_USE_DLLS); +# required to fix "error: 'string_view' in namespace 'std' does not name a type", +# see also https://github.com/onnx/onnx/issues/5430 +preinstallopts += "export CMAKE_ARGS='-DCMAKE_CXX_STANDARD=17 -DONNX_USE_PROTOBUF_SHARED_LIBS=ON' && " + +preinstallopts += 'env MAX_JOBS="%(parallel)s"' + +sanity_check_paths = { + 'files': ['bin/check-model', 'bin/check-node', 'bin/backend-test-tools'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('check-model', '-h'), + ('check-node', '-h'), + ('backend-test-tools', '-h'), +] + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/ONNX/ONNX-1.15.0_fix-protobuf-linking.patch b/easybuild/easyconfigs/o/ONNX/ONNX-1.15.0_fix-protobuf-linking.patch new file mode 100644 index 000000000000..5368859cb537 --- /dev/null +++ b/easybuild/easyconfigs/o/ONNX/ONNX-1.15.0_fix-protobuf-linking.patch @@ -0,0 +1,18 @@ +fix for: undefined symbol: _ZN6google8protobuf8internal15ThreadSafeArena13thread_cache_E +see also https://bugs.archlinux.org/task/75242 +author: Kenneth Hoste (HPC-UGent) +--- onnx-1.15.0/CMakeLists.txt.orig 2024-01-05 21:11:09.060853188 +0100 ++++ onnx-1.15.0/CMakeLists.txt 2024-01-05 21:11:21.587828423 +0100 +@@ -46,10 +46,10 @@ + endif() + + if(ONNX_USE_PROTOBUF_SHARED_LIBS) +- if(MSVC) ++ #if(MSVC) + #TODO: if ONNX_USE_MSVC_STATIC_RUNTIME is ON, it may not work + add_definitions(-DPROTOBUF_USE_DLLS) +- endif() ++ #endif() + set(Protobuf_USE_STATIC_LIBS OFF) + else() + set(Protobuf_USE_STATIC_LIBS ON) From a6f997b463033124f9c8d7acfc2497f56fdeb6e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 22:18:34 +0100 Subject: [PATCH 0177/1193] adding easyconfigs: pydantic-2.5.3-GCCcore-12.2.0.eb, Rust-1.75.0-GCCcore-12.2.0.eb, maturin-1.4.0-GCCcore-12.2.0-Rust-1.75.0.eb --- ...aturin-1.4.0-GCCcore-12.2.0-Rust-1.75.0.eb | 647 ++++++++++++++++++ .../pydantic/pydantic-2.5.3-GCCcore-12.2.0.eb | 121 ++++ .../r/Rust/Rust-1.75.0-GCCcore-12.2.0.eb | 29 + 3 files changed, 797 insertions(+) create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.2.0-Rust-1.75.0.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.2.0-Rust-1.75.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.2.0-Rust-1.75.0.eb new file mode 100644 index 000000000000..7318a0d00fd2 --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.2.0-Rust-1.75.0.eb @@ -0,0 +1,647 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.4.0' +_rust_ver = '1.75.0' +versionsuffix = '-Rust-%s' % _rust_ver + +homepage = "https://github.com/pyo3/maturin" +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Python', '3.10.8'), + ('Rust', _rust_ver), +] + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.8.6'), + ('aho-corasick', '1.1.2'), + ('allocator-api2', '0.2.16'), + ('anstream', '0.3.2'), + ('anstream', '0.6.4'), + ('anstyle', '1.0.2'), + ('anstyle-parse', '0.2.1'), + ('anstyle-query', '1.0.0'), + ('anstyle-wincon', '1.0.2'), + ('anstyle-wincon', '3.0.1'), + ('anyhow', '1.0.75'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.5'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.1'), + ('block-buffer', '0.10.4'), + ('bstr', '1.8.0'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bytesize', '1.3.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', 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'1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.0.tar.gz': 'dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04'}, + {'winnow-0.5.19.tar.gz': '829846f3e3db426d4cee4510841b71a8e58aa2a76b1132579487ae430ccd9c7b'}, + {'xattr-1.0.1.tar.gz': 'f4686009f71ff3e5c4dbcf1a282d0a44db3f021ba69350cd42086b3e5f1c6985'}, + {'xwin-0.5.0.tar.gz': 'c43e0202f5457b48558096cb7b36d0e473f267551a89c82ed72d73b01dfd4007'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zerocopy-0.7.28.tar.gz': '7d6f15f7ade05d2a4935e34a457b936c23dc70a05cc1d97133dc99e7a3fe0f0e'}, + {'zerocopy-derive-0.7.28.tar.gz': 'dbbad221e3f78500350ecbd7dfa4e63ef945c05f4c61cb7f4d3f84cd0bba649b'}, + {'zeroize-1.7.0.tar.gz': '525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..da3ebeae4eb9 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.2.0.eb @@ -0,0 +1,121 @@ +easyblock = 'CargoPythonBundle' + +name = 'pydantic' +version = '2.5.3' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), + ('Rust', '1.75.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('typing-extensions', '4.9.0'), +] + +use_pip = True +sanity_pip_check = True + +crates = [ + ('ahash', '0.8.6'), + ('aho-corasick', '1.0.2'), + ('autocfg', '1.1.0'), + ('base64', '0.21.5'), + ('bitflags', '1.3.2'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('enum_dispatch', '0.3.12'), + ('equivalent', '1.0.1'), + ('form_urlencoded', '1.2.0'), + ('getrandom', '0.2.10'), + ('hashbrown', '0.14.0'), + ('heck', '0.4.1'), + ('idna', '0.4.0'), + ('indexmap', '2.0.0'), + ('indoc', '2.0.4'), + ('itoa', '1.0.8'), + ('jiter', '0.0.4'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memchr', '2.6.3'), + ('memoffset', '0.9.0'), + ('num-bigint', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.16'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('percent-encoding', '2.3.0'), + ('proc-macro2', '1.0.69'), + ('pyo3', '0.20.0'), + ('pyo3-build-config', '0.20.0'), + ('pyo3-ffi', '0.20.0'), + ('pyo3-macros', '0.20.0'), + ('pyo3-macros-backend', '0.20.0'), + ('python3-dll-a', '0.2.9'), + ('quote', '1.0.29'), + ('redox_syscall', '0.3.5'), + ('regex', '1.10.2'), + ('regex-automata', '0.4.3'), + ('regex-syntax', '0.8.2'), + ('rustversion', '1.0.13'), + ('ryu', '1.0.14'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.190'), + ('serde_derive', '1.0.190'), + ('serde_json', '1.0.108'), + ('smallvec', '1.11.1'), + ('speedate', '0.13.0'), + ('static_assertions', '1.1.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '2.0.38'), + ('target-lexicon', '0.12.9'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.10'), + ('unicode-normalization', '0.1.22'), + ('unindent', '0.2.3'), + ('url', '2.4.1'), + ('uuid', '1.5.0'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-targets', '0.48.1'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.48.0'), + ('zerocopy', '0.7.20'), + ('zerocopy-derive', '0.7.20'), +] + +exts_list = [ + ('annotated_types', '0.6.0', { + 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], + }), + ('pydantic_core', '2.14.6', { + 'checksums': ['1fd0c1d395372843fba13a51c28e3bb9d59bd7aebfeb17358ffaaa1e4dbbe948'], + }), + (name, version, { + 'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ", + 'checksums': ['b3ef57c62535b0941697cce638c08900d87fcb67e29cfa99e8a68f747f393f7a'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d9b3ab115e62 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +name = 'Rust' +version = '1.75.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.75.0-src.tar.gz': '5b739f45bc9d341e2d1c570d65d2375591e22c2d23ef5b8a37711a0386abc088'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'lang' From 679d9d829e41cfac4e1ddbeab03974bb08ec9f78 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 22:20:13 +0100 Subject: [PATCH 0178/1193] adding easyconfigs: PyTorch-Lightning-2.1.2-foss-2022b.eb, deepdiff-6.7.1-GCCcore-12.2.0.eb, tensorboardX-2.6.2.2-foss-2022b.eb, boto3-1.34.10-GCCcore-12.2.0.eb --- .../b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb | 39 +++++ .../deepdiff/deepdiff-6.7.1-GCCcore-12.2.0.eb | 34 ++++ .../PyTorch-Lightning-2.1.2-foss-2022b.eb | 156 ++++++++++++++++++ .../tensorboardX-2.6.2.2-foss-2022b.eb | 30 ++++ 4 files changed, 259 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb create mode 100644 easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..08804838492a --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.34.10' + +homepage = 'https://github.com/boto/boto3' +description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit +(SDK) for Python, which allows Python developers to write software that makes +use of services like Amazon S3 and Amazon EC2.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +exts_list = [ + ('botocore', '1.34.12', { + 'checksums': ['53dfc19d63f2b70821e9804b7ecfc5e50fc84d9bd6818359b27db629ef43ec59'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.0', { + 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], + }), + (name, version, { + 'checksums': ['ea14bc081d9cb40291133f89b3ad9070be360e152d6a98263af7b97a6534b669'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..948367bb91b6 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '6.7.1' + +homepage = 'https://zepworks.com/deepdiff/current/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsonpickle', '3.0.2', { + 'checksums': ['e37abba4bfb3ca4a4647d28bb9f4706436f7b46c8a8333b4a718abafa8e46b37'], + }), + ('ordered-set', '4.1.0', { + 'checksums': ['694a8e44c87657c59292ede72891eb91d34131f6531463aab3009191c77364a8'], + }), + (name, version, { + 'checksums': ['b367e6fa6caac1c9f500adc79ada1b5b1242c50d5f716a1a4362030197847d30'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb new file mode 100644 index 000000000000..b1d36af59482 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb @@ -0,0 +1,156 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '2.1.2' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.5'), + ('BeautifulSoup', '4.11.1'), + ('deepdiff', '6.7.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '1.13.1'), + ('tqdm', '4.64.1'), + ('tensorboardX', '2.6.2.2'), + ('pydantic', '2.5.3'), + ('boto3', '1.34.10'), + ('typing-extensions', '4.9.0'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + 'modulename': 'markdown_it', + }), + ('rich', '13.7.0', { + 'checksums': ['5cb5123b5cf9ee70584244246816e9114227e0b98ad9176eede6ad54bf5403fa'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('starlette', '0.32.0.post1', { + 'checksums': ['e54e2b7e2fb06dff9eac40133583f10dfa05913f5a85bf26f427c7a40a9a3d02'], + }), + ('fastapi', '0.108.0', { + 'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ", + 'checksums': ['5056e504ac6395bf68493d71fcfc5352fdbd5fda6f88c21f6420d80d81163296'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('exceptiongroup', '1.2.0', { + 'checksums': ['91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68'], + }), + ('anyio', '4.2.0', { + 'checksums': ['e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f'], + }), + ('websocket-client', '1.7.0', { + 'modulename': 'websocket', + 'checksums': ['10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6'], + }), + ('python_multipart', '0.0.6', { + 'checksums': ['e9925a80bb668529f1b67c7fdb0a5dacdd7cbfc6fb0bff3ea443fe22bdd62132'], + 'modulename': 'multipart', + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.25.0', { + 'checksums': ['6dddbad1d7ee0f5140aba5ec138ddc9612c5109399903828b4874c9937f009c2'], + }), + ('lightning_cloud', '0.5.57', { + 'checksums': ['1d30427a2935a367e0bd19873decb564425f1b648901abab2da9318a8b88c80b'], + }), + ('itsdangerous', version, { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '2.1.3', { + 'checksums': ['d20c5f277b64a86c16819f65ac50814ccdbd146776159e08c88b378b6612297d'], + }), + ('fsspec', '2023.12.2', { + 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], + }), + ('croniter', '2.0.1', { + 'checksums': ['d199b2ec3ea5e82988d1f72022433c5f9302b3b3ea9e6bfd6a1518f6ea5e700a'], + }), + ('traitlets', '5.14.1', { + 'checksums': ['8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e'], + }), + ('types-python-dateutil', '2.8.19.14', { + 'checksums': ['1f4f10ac98bb8b16ade9dbee3518d9ace017821d94b057a425b069f834737f4b'], + 'modulename': False, + }), + ('arrow', '1.3.0', { + 'preinstallopts': "PYTHONPATH=$PWD:$PYTHONPATH ", + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('lightning-utilities', '0.10.0', { + 'checksums': ['9e31617eccbbadc6b737a2432fd7076ff8e24957f9c63aeba2530b189e19319c'], + }), + ('blessed', '1.20.0', { + 'checksums': ['2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.5', { + 'checksums': ['08a456c2d7c1888cde3f4688b542621b676eb38cd6cfed7eb6cb2e2905ddc826'], + }), + ('runs', '1.2.0', { + 'checksums': ['8804271011b7a2eeb0d77c3e3f556e5ce5f602fa0dd2a31ed0c1222893be69b7'], + }), + ('xmod', '1.8.1', { + 'checksums': ['38c76486b9d672c546d57d8035df0beb7f4a9b088bc3fb2de5431ae821444377'], + }), + ('editor', '1.6.3', { + 'checksums': ['6d004f3087d7c587c111cc88a7ac0436df3539297c6b24243dd5aa5bc5bdcc08'], + }), + ('inquirer', '3.2.0', { + 'checksums': ['93f4beaad9b887cc3a068198c40837c67eb42b39ea87b3e80fff2a7773e8f29a'], + }), + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.9.0', { + 'preinstallopts': """sed -i "s/botocore>.*',/botocore',/g" setup.py && """, + 'checksums': ['4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e'], + }), + ('s3fs', '2023.12.2', { + 'checksums': ['b5ec07062481bbb45cb061b31984c7188d106e292c27033039e024e4ba5740dc'], + }), + ('torchmetrics', '1.2.1', { + 'checksums': ['217387738f84939c39b534b20d4983e737cc448d27aaa5340e0327948d97ca3e'], + }), + ('pytorch-lightning', version, { + 'checksums': ['58e26406215f3bfafe1b9b5b4bf37c9b8cff16494f7fd60e4db1ae37461b2b28'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/dateutil-stubs'], +} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2022b.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2022b.eb new file mode 100644 index 000000000000..2091399890c1 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2022b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'tensorboardX' +version = '2.6.2.2' + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'foss', 'version': '2022b'} + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('protobuf-python', '4.23.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'checksums': ['c6476d7cd0d529b0b72f4acadb1269f9ed8b22f441e87a84f2a3b940bb87b666'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From f76792b0f2c424e7633d36abe98d851e3449b7fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 5 Jan 2024 22:21:36 +0100 Subject: [PATCH 0179/1193] adding easyconfigs: DeepLoc-2.0-foss-2022b.eb, mygene-3.2.2-foss-2022b.eb, ESM-2-2.0.0-foss-2022b.eb --- .../d/DeepLoc/DeepLoc-2.0-foss-2022b.eb | 59 +++++++++++++++++++ .../e/ESM-2/ESM-2-2.0.0-foss-2022b.eb | 40 +++++++++++++ .../m/mygene/mygene-3.2.2-foss-2022b.eb | 31 ++++++++++ 3 files changed, 130 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022b.eb diff --git a/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2022b.eb b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2022b.eb new file mode 100644 index 000000000000..546c4bb876db --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLoc/DeepLoc-2.0-foss-2022b.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'DeepLoc' +version = '2.0' + +homepage = 'https://services.healthtech.dtu.dk/services/DeepLoc-2.0' +description = "DeepLoc 2.0 predicts the subcellular localization(s) of eukaryotic proteins" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('Biopython', '1.81'), + ('ONNX-Runtime', '1.16.3'), + ('ESM-2', '2.0.0'), # for fair-esm + ('PyTorch', '1.13.1'), + ('PyTorch-Lightning', '2.1.2'), + ('Transformers', '4.30.2'), + ('SentencePiece', '0.1.99'), + ('mygene', '3.2.2'), # required by bio +] + +use_pip = True + +local_deeploc_download_url = 'https://services.healthtech.dtu.dk/cgi-bin/sw_request?' +local_deeploc_download_url += 'software=deeploc&version=2.0&packageversion=2.0&platform=All' + +exts_list = [ + ('gprofiler-official', '1.0.0', { + 'checksums': ['5015b47f10fbdcb59c57e342e815c9c07afbe57cd3984154f75b845ddef2445d'], + 'modulename': 'gprofiler', + }), + ('bio', '1.6.2', { + 'sources': ['bio-%(version)s-py%(pymajver)s-none-any.whl'], + 'checksums': ['dcec8207f3993a7f41bd8205cde235218da3dc008175ae7bb7468276d8dacf71'], + 'modulename': 'biorun', + }), + (name, version, { + 'download_instructions': "Download via %s" % local_deeploc_download_url, + 'sources': ['deeploc-%(version)s.All.tar.gz'], + 'checksums': ['1741cf61cc38bba6307f1838c08ff9dd01386da09b8939610d15c27f98173651'], + 'modulename': 'DeepLoc2', + }), +] + +sanity_check_paths = { + 'files': ['bin/deeploc2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "deeploc2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2022b.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2022b.eb new file mode 100644 index 000000000000..0eca3505ba56 --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2022b.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'ESM-2' +version = '2.0.0' + +homepage = 'https://github.com/facebookresearch/esm' +description = """ESM-2 outperforms all tested single-sequence protein language models + across a range of structure prediction tasks. ESMFold harnesses the ESM-2 language model to generate + accurate structure predictions end to end directly from the sequence of a protein.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + +dependencies = [ + ('Python', '3.10.8'), + ('PyTorch', '1.13.1'), +] + +use_pip = True +sanity_pip_check = True + +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + ('fair-esm', version, { + 'modulename': "esm, esm.pretrained", + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022b.eb b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022b.eb new file mode 100644 index 000000000000..c849a2435063 --- /dev/null +++ b/easybuild/easyconfigs/m/mygene/mygene-3.2.2-foss-2022b.eb @@ -0,0 +1,31 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +easyblock = 'PythonBundle' + +name = 'mygene' +version = '3.2.2' + +homepage = 'https://github.com/biothings/mygene.py' +description = "Python Client for MyGene.Info services." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True + +exts_list = [ + ('biothings_client', '0.3.1', { + 'checksums': ['c972bf2e02b6f9cc78f7f2fbc5ef02cc56fe4f8a2adcb8801ec902f4ab7011e6'], + }), + (name, version, { + 'checksums': ['e729cabbc28cf5afb221bca1ab637883b375cb1a3e2f067587ec79f71affdaea'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From a3cd107dcedfe853c0101b1ce693b4c4269b832a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 6 Jan 2024 17:20:23 +0100 Subject: [PATCH 0180/1193] adding easyconfigs: wrf-python-1.3.4.1-foss-2023a.eb --- .../wrf-python-1.3.4.1-foss-2023a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb new file mode 100644 index 000000000000..26cf724496de --- /dev/null +++ b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'wrf-python' +version = '1.3.4.1' + +homepage = 'https://wrf-python.readthedocs.io' +description = """A collection of diagnostic and interpolation routines for use with output from + the Weather Research and Forecasting (WRF-ARW) Model.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('Python', '3.11.3'), + ('netcdf4-python', '1.6.4'), + ('xarray', '2023.9.0'), + ('matplotlib', '3.7.2'), + ('Cartopy', '0.22.0'), +] + +use_pip = True + +exts_list = [ + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + (name, version, { + 'modulename': 'wrf', + 'checksums': ['e349578da8c3f108b8169c19d2186e72d79f610561f2e11c59fbf6eda3f9a2e7'], + }), +] + +moduleclass = 'geo' From f6c52440544d48c4911971006e086ecc7c02488e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 Jan 2024 11:21:24 +0100 Subject: [PATCH 0181/1193] add missing basemap dependency + enable sanity_pip_check in easyconfig for wrf-python v1.3.4.1 --- .../b/basemap/basemap-1.3.9-foss-2023a.eb | 50 +++++++++++++++++++ .../wrf-python-1.3.4.1-foss-2023a.eb | 3 ++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/b/basemap/basemap-1.3.9-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.3.9-foss-2023a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.3.9-foss-2023a.eb new file mode 100644 index 000000000000..39b8785128d1 --- /dev/null +++ b/easybuild/easyconfigs/b/basemap/basemap-1.3.9-foss-2023a.eb @@ -0,0 +1,50 @@ +# The newer version require also the installation of basemap-data. +# Conveniently, the tarball contains that too, so that is the one +# being used here. +# Based on basemap-1.2.2-foss-2020a-Python-3.8.2.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'basemap' +version = '1.3.9' + +homepage = 'https://matplotlib.org/basemap/' +description = """The matplotlib basemap toolkit is a library for plotting +2D data on maps in Python""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('GEOS', '3.12.0'), + ('Pillow', '10.0.0'), + ('pyproj', '3.6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + ('basemap_data', version, { + 'modulename': 'mpl_toolkits.basemap_data', + 'preinstallopts': "cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS", + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['44ae3764595778077d4bc40b0756c90f483b816927e82206e9f376e31a2dc533'], + }), + (name, version, { + 'modulename': 'mpl_toolkits.basemap', + 'preinstallopts': "cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS", + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['44ae3764595778077d4bc40b0756c90f483b816927e82206e9f376e31a2dc533'], + }), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb index 26cf724496de..bc0634647b0f 100644 --- a/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb +++ b/easybuild/easyconfigs/w/wrf-python/wrf-python-1.3.4.1-foss-2023a.eb @@ -16,6 +16,7 @@ dependencies = [ ('xarray', '2023.9.0'), ('matplotlib', '3.7.2'), ('Cartopy', '0.22.0'), + ('basemap', '1.3.9'), ] use_pip = True @@ -30,4 +31,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'geo' From b268bac1a617e486cec5472a22e828b68c4336c6 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Sun, 7 Jan 2024 11:21:41 +0100 Subject: [PATCH 0182/1193] f90nml v1.4.4 for GCCcore/13.2.0: Remove default source_urls --- easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb index 1e31e9ee12ec..215dad71e8d9 100644 --- a/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/f/f90nml/f90nml-1.4.4-GCCcore-13.2.0.eb @@ -9,7 +9,6 @@ description = """A Python module and command line tool for parsing toolchain = {'name': 'GCCcore', 'version': '13.2.0'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['65e8e135779895245238cbf6be5b1b80d6c2b8c9350c9cdce6183a31bdfd7622'] From dd9ffb19d3c7060edb7327e29b9fe2c1cae49e2e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 7 Jan 2024 13:57:33 +0100 Subject: [PATCH 0183/1193] stick to usual order of easyconfig parameters in Cython easyconfig --- .../easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb index 9bc9168fac12..c051049f2e38 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.7-GCCcore-12.3.0.eb @@ -15,6 +15,9 @@ docurls = [ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +sources = [SOURCE_TAR_GZ] +checksums = ['fb299acf3a578573c190c858d49e0cf9d75f4bc49c3f24c5a63804997ef09213'] + builddependencies = [ ('binutils', '2.40'), ] @@ -23,9 +26,6 @@ dependencies = [ ('Python', '3.11.3'), ] -sources = [SOURCE_TAR_GZ] -checksums = ['fb299acf3a578573c190c858d49e0cf9d75f4bc49c3f24c5a63804997ef09213'] - download_dep_fail = True use_pip = True sanity_pip_check = True From bc9758d0cc533fb64a787c260c7b088832e8d12c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Mon, 8 Jan 2024 01:56:25 +0100 Subject: [PATCH 0184/1193] Rename XCrySDen-1.6.2-intel-compilers-2021.4.0.eb to XCrySDen-1.6.2-intel-2021b.eb --- ...-intel-compilers-2021.4.0.eb => XCrySDen-1.6.2-intel-2021b.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/x/XCrySDen/{XCrySDen-1.6.2-intel-compilers-2021.4.0.eb => XCrySDen-1.6.2-intel-2021b.eb} (100%) diff --git a/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb similarity index 100% rename from easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-compilers-2021.4.0.eb rename to easybuild/easyconfigs/x/XCrySDen/XCrySDen-1.6.2-intel-2021b.eb From 18aa7ea9b5dc939dc465e59fadf226688ff1d128 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 8 Jan 2024 10:50:45 +0100 Subject: [PATCH 0185/1193] Update pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb add SciPy-bundle dependency --- .../pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb index e0ca7a4f166f..4b306a76b674 100644 --- a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -32,7 +32,8 @@ dependencies = [ ('CUDA', '11.7.0', '', SYSTEM), ('h5py', '3.7.0'), ('tensorboard', '2.10.0'), - ('scikit-image', '0.19.3') + ('scikit-image', '0.19.3'), + ('SciPy-bundle', '2022.05'), ] use_pip = True From 5bbd7a398b104aebd802905acd31f555c94431a0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 8 Jan 2024 12:45:12 +0100 Subject: [PATCH 0186/1193] Update pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb reorder dependencies --- .../pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb index 4b306a76b674..7e56318d66d7 100644 --- a/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pytorch-3dunet/pytorch-3dunet-1.6.0-foss-2022a-CUDA-11.7.0.eb @@ -28,12 +28,12 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), - ('PyTorch', '1.12.0', versionsuffix), + ('SciPy-bundle', '2022.05'), ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), ('h5py', '3.7.0'), ('tensorboard', '2.10.0'), ('scikit-image', '0.19.3'), - ('SciPy-bundle', '2022.05'), ] use_pip = True From 5ecc30a07a10d141670b683a1b76975a9bf31cfc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 8 Jan 2024 13:03:47 +0100 Subject: [PATCH 0187/1193] SUNDIALS: Add CUDA version --- .../SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..500d7fdeab1c --- /dev/null +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'SUNDIALS' +version = '6.6.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://computing.llnl.gov/projects/sundials' + +description = "SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = ['https://github.com/LLNL/sundials/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_fix_bad_find_library_calls.patch', +] +checksums = [ + {'sundials-6.6.0.tar.gz': 'f90029b8da846c8faff5530fd1fa4847079188d040554f55c1d5d1e04743d29d'}, + {'SUNDIALS-6.6.0_fix_bad_find_library_calls.patch': + 'c5e3248bd036fee17436649280ff7156a2722698c33ec20a5e635e3a60d16823'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('SuiteSparse', '7.1.0'), +] + +_copts = [ + '-DENABLE_MPI=ON', + '-DENABLE_OPENMP=ON', + '-DENABLE_LAPACK=ON', + '-DENABLE_KLU=ON', + '-DENABLE_CUDA=ON', + '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"', +] +configopts = ' '.join(_copts) + +local_solvers = ['arkode', 'cvode', 'cvodes', 'ida', 'idas', 'kinsol'] + +sanity_check_paths = { + 'files': ['lib/libsundials_%s.a' % s for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']] + + ['lib/libsundials_%s.%s' % (s, SHLIB_EXT) for s in local_solvers + + ['nvecopenmp', 'nvecparallel', 'nvecserial']], + 'dirs': ['examples/%s' % s for s in local_solvers] + + ['include/%s' % s for s in local_solvers] + + ['examples/nvector', 'include/nvector', 'include/sundials'], +} + +moduleclass = 'math' From eb0263032056baa7752262910f1ee667e3be8653 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 8 Jan 2024 13:42:14 +0100 Subject: [PATCH 0188/1193] adding easyconfigs: MiXCR-4.6.0-Java-17.eb --- .../m/MiXCR/MiXCR-4.6.0-Java-17.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb new file mode 100644 index 000000000000..e8836a4b99d9 --- /dev/null +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb @@ -0,0 +1,28 @@ +easyblock = 'Tarball' + +name = 'MiXCR' +version = '4.6.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://milaboratory.com/software/mixcr' +description = """MiXCR is a universal software for fast and accurate extraction of T- and B- cell receptor repertoires +from any type of sequencing data.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/milaboratory/mixcr/releases/download/v%(version)s/'] +sources = [SOURCELOWER_ZIP] +checksums = ['05db1276951a2e656d0a7bf4e2b1fff326733a5f961a9d4829be139852fabe13'] + +dependencies = [('Java', '17')] + +sanity_check_paths = { + 'files': ['mixcr', 'mixcr.jar'], + 'dirs': [], +} + +sanity_check_commands = ["command -v mixcr"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 94204a04c90fe91f3a079d3bcf1a6da5c0277343 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 8 Jan 2024 13:54:27 +0100 Subject: [PATCH 0189/1193] adding easyconfigs: texinfo-7.1-GCCcore-12.3.0.eb --- .../t/texinfo/texinfo-7.1-GCCcore-12.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-7.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4622c62f424b --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-7.1-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +## +# Author: Robert Mijakovic +## +# Update: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '7.1' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['deeec9f19f159e046fdf8ad22231981806dac332cc372f1c763504ad82b30953'] + +builddependencies = [('binutils', '2.40')] + +osdependencies = ['texlive'] + +preinstallopts = "make TEXMF=%(installdir)s/texmf install-tex && " + +# This will overwrite a users $TEXMFHOME so this module is best used as a build dependency +modextravars = {'TEXMFHOME': '%(installdir)s/texmf'} +modloadmsg = "\n\nWARNING: This texinfo module has (re)defined the value for the environment variable $TEXMFHOME.\n" +modloadmsg += "If you use a custom texmf directory (such as ~/texmf) you should copy files found in the\n" +modloadmsg += "new $TEXMFHOME to your custom directory and reset the value of $TEXMFHOME to point to that space:\n" +modloadmsg += "\tcp -r $TEXMFHOME/* /path/to/your/texmf\n" +modloadmsg += "\texport TEXMFHOME=/path/to/your/texmf\n\n" + +sanity_check_paths = { + 'files': [ + 'texmf/tex/texinfo/texinfo.tex', + 'bin/install-info', 'bin/makeinfo', 'bin/pdftexi2dvi', 'bin/pod2texi', 'bin/texi2pdf' + ], + 'dirs': ['bin', 'share', 'texmf'], +} + +moduleclass = 'devel' From c6f55e5dd044cb46401f52f1d737c7572f54c2a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 8 Jan 2024 14:00:50 +0100 Subject: [PATCH 0190/1193] adding easyconfigs: PyInstaller-6.3.0-GCCcore-12.3.0.eb --- .../PyInstaller-6.3.0-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..2a4ccf880fff --- /dev/null +++ b/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'PyInstaller' +version = '6.3.0' + +homepage = 'https://pyinstaller.org/en/stable/' +description = """PyInstaller bundles a Python application and all its dependencies into a single package. + The user can run the packaged app without installing a Python interpreter or any modules.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), + ('makeinfo', '7.0.3'), +] + +use_pip = True +sanity_pip_check = True + + +exts_list = [ + ('altgraph', '0.17.4', { + 'checksums': ['1b5afbb98f6c4dcadb2e2ae6ab9fa994bbb8c1d75f4fa96d340f9437ae454406'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('pyinstaller-hooks-contrib', '2023.12', { + 'modulename': '_pyinstaller_hooks_contrib', + 'checksums': ['11a9d59d903723dd693e8c10b054f3ea1ecad390623c9fa527c731d715fc5b3f'], + }), + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'modulename': name, + 'checksums': ['914d4c96cc99472e37ac552fdd82fbbe09e67bb592d0717fcffaa99ea74273df'], + }), +] + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = 'devel' From aa29aba6c1c9f5f202d5056bf2d11c977bfa1fc8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 8 Jan 2024 14:20:50 +0100 Subject: [PATCH 0191/1193] add missing dependency --- .../p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb index 2a4ccf880fff..c89b4a0c04d8 100644 --- a/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb @@ -9,6 +9,8 @@ description = """PyInstaller bundles a Python application and all its dependenci toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [('binutils', '2.40')] + dependencies = [ ('Python', '3.11.3'), ('makeinfo', '7.0.3'), From 2e52e2b987b78ca59f4d0d01d08e1ba5c98f9a3f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 8 Jan 2024 16:00:49 +0100 Subject: [PATCH 0192/1193] adding easyconfigs: GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb --- .../GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/g/GATK/GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb new file mode 100644 index 000000000000..6f2cb5f51839 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.5.0.0-GCCcore-12.3.0-Java-17.eb @@ -0,0 +1,55 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 Cyprus Institute / CaSToRC, University of Luxembourg / LCSB +# Authors:: George Tsouloupas , Fotis Georgatos , +# Kenneth Hoste (UGent) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified for version 4.0.5.1 by: Ruben van Dijk, University of Groningen +# Modified for version 4.2.3.0 by: J. Sassmannshausen / GSTT +# Modified for version 4.4.0.0 by: Thomas Eylenbosch / Gluo NV +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.5.0.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://www.broadinstitute.org/gatk/' +description = """The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute + to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, + with a primary focus on variant discovery and genotyping as well as strong emphasis on + data quality assurance. Its robust architecture, powerful processing engine and + high-performance computing features make it capable of taking on projects of any size.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['dc1a4471e8bb566397db9894ca18acbf8f40f3fc312c8fad9a8c5390c218e916'] + +dependencies = [ + ('Java', '17', '', SYSTEM), + ('Python', '3.11.3'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} + +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' From c448437e2ff976401910159f8705296278e8947d Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 8 Jan 2024 16:32:39 +0000 Subject: [PATCH 0193/1193] adding easyconfigs: Hydra-1.3.2-GCCcore-12.3.0.eb --- .../h/Hydra/Hydra-1.3.2-GCCcore-12.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b337a4b9f63a --- /dev/null +++ b/easybuild/easyconfigs/h/Hydra/Hydra-1.3.2-GCCcore-12.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'Hydra' +version = '1.3.2' + +homepage = "https://hydra.cc/" +description = """ +Hydra is an open-source Python framework that simplifies the development of +research and other complex applications. The key feature is the ability to +dynamically create a hierarchical configuration by composition and override it +through config files and the command line. The name Hydra comes from its +ability to run multiple similar jobs - much like a Hydra with multiple heads. +""" + +github_account = 'facebookresearch' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Java', '17', '', SYSTEM), # needed by ANTLR runtime +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PyYAML', '6.0'), # needed by omegaconf +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('antlr4-python3-runtime', '4.9', { + 'modulename': 'antlr4', + 'checksums': ['02d9afb720c13c52b336234286966cdf5aff704f230a513e635adb0d94de97ae'], + }), + ('omegaconf', '2.3.0', { + 'checksums': ['d5d4b6d29955cc50ad50c46dc269bcd92c6e00f5f90d23ab5fee7bfca4ba4cc7'], + }), + + ('hydra', version, { + 'source_urls': ['https://github.com/%(github_account)s/%(namelower)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['3f0f14305e9c6ae4b1dbcba344fe09dd0fc79c0a0656470c249f4f7ca46bf471'], + }), +] + +moduleclass = 'data' From 7bcbb769de98a27ffbf062a402e9ce9b497cd332 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 8 Jan 2024 17:42:19 +0100 Subject: [PATCH 0194/1193] allow multiple versions of Rust as dependency if versionsuffix indicates alternate version being used --- test/easyconfigs/easyconfigs.py | 25 ++++++++++++++++++++++++- 1 file changed, 24 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f041f7f7b7dc..28cfc1d99ad0 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -456,7 +456,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # for some dependencies, we allow exceptions for software that depends on a particular version, # as long as that's indicated by the versionsuffix versionsuffix_deps = ['ASE', 'Boost', 'CUDA', 'CUDAcore', 'Java', 'Lua', - 'PLUMED', 'PyTorch', 'R', 'TensorFlow'] + 'PLUMED', 'PyTorch', 'R', 'Rust', 'TensorFlow'] if dep in versionsuffix_deps and len(dep_vars) > 1: # check for '-CUDA-*' versionsuffix for CUDAcore dependency @@ -824,6 +824,29 @@ def test_check_dep_vars(self): 'version: 2020.03; versionsuffix:': ['matplotlib-3.2.1-foss-2020a.eb'], })) + # multiple dependency variants of specific software is OK, but only if indicated via versionsuffix + self.assertTrue(self.check_dep_vars('2019b', 'TensorFlow', { + 'version: 1.15.2; versionsuffix: -TensorFlow-1.15.2': ['Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.2.eb'], + 'version: 2.2.0; versionsuffix: -TensorFlow-2.2.0-Python-3.7.4': + ['Horovod-0.19.5-fosscuda-2019b-TensorFlow-2.2.0-Python-3.7.4.eb'], + 'version: 2.1.0; versionsuffix: -Python-3.7.4': ['Keras-2.3.1-foss-2019b-Python-3.7.4.eb'], + })) + + self.assertFalse(self.check_dep_vars('2019b', 'TensorFlow', { + 'version: 1.15.2; versionsuffix: ': ['Horovod-0.18.2-fosscuda-2019b.eb'], + 'version: 2.1.0; versionsuffix: -Python-3.7.4': ['Keras-2.3.1-foss-2019b-Python-3.7.4.eb'], + })) + + self.assertTrue(self.check_dep_vars('2022b', 'Rust', { + 'version: 1.65.0; versionsuffix: ': ['maturin-1.1.0-GCCcore-12.2.0.eb'], + 'version: 1.75.0; versionsuffix: -Rust-1.75.0': ['maturin-1.4.0-GCCcore-12.2.0-Rust-1.75.0.eb'], + })) + + self.assertFalse(self.check_dep_vars('2022b', 'Rust', { + 'version: 1.65.0; versionsuffix: ': ['maturin-1.1.0-GCCcore-12.2.0.eb'], + 'version: 1.75.0; versionsuffix: ': ['maturin-1.4.0-GCCcore-12.2.0.eb'], + })) + def test_dep_versions_per_toolchain_generation(self): """ Check whether there's only one dependency version per toolchain generation actively used. From 83f5ed3dd6bb15357b2a591064996aa6f6677800 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Mon, 8 Jan 2024 18:28:26 +0100 Subject: [PATCH 0195/1193] remove empty line --- .../p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb index c89b4a0c04d8..04ff03940988 100644 --- a/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyInstaller/PyInstaller-6.3.0-GCCcore-12.3.0.eb @@ -19,7 +19,6 @@ dependencies = [ use_pip = True sanity_pip_check = True - exts_list = [ ('altgraph', '0.17.4', { 'checksums': ['1b5afbb98f6c4dcadb2e2ae6ab9fa994bbb8c1d75f4fa96d340f9437ae454406'], From 57943f5772b4afc0193b087eeaf582a132023d79 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Mon, 8 Jan 2024 21:46:24 +0100 Subject: [PATCH 0196/1193] fix line too long --- test/easyconfigs/easyconfigs.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 28cfc1d99ad0..76152b79d406 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -826,7 +826,8 @@ def test_check_dep_vars(self): # multiple dependency variants of specific software is OK, but only if indicated via versionsuffix self.assertTrue(self.check_dep_vars('2019b', 'TensorFlow', { - 'version: 1.15.2; versionsuffix: -TensorFlow-1.15.2': ['Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.2.eb'], + 'version: 1.15.2; versionsuffix: -TensorFlow-1.15.2': + ['Horovod-0.18.2-fosscuda-2019b-TensorFlow-1.15.2.eb'], 'version: 2.2.0; versionsuffix: -TensorFlow-2.2.0-Python-3.7.4': ['Horovod-0.19.5-fosscuda-2019b-TensorFlow-2.2.0-Python-3.7.4.eb'], 'version: 2.1.0; versionsuffix: -Python-3.7.4': ['Keras-2.3.1-foss-2019b-Python-3.7.4.eb'], From 09367456e4d1d2ea4d6279c581bc8d2b62884881 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 9 Jan 2024 10:51:20 +0100 Subject: [PATCH 0197/1193] adding easyconfigs: GPAW-24.1.0-foss-2023a.eb --- .../g/GPAW/GPAW-24.1.0-foss-2023a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb new file mode 100644 index 000000000000..9c555311a5b4 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.1.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.1.0.tar.gz': '14150bdc4b098060164b569699577ff57769a42783d79d37c9eb6cfe9cd506ea'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('ASE', '3.22.1'), + ('libxc', '6.2.2'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2023.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From 106a39ea4d50d5fab9ad1e3b3f184ecd695b3b1b Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 9 Jan 2024 11:15:20 +0100 Subject: [PATCH 0198/1193] set maxparallel = 1 to avoid build error --- easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb index f41a09d3499c..42e999a8fe0f 100644 --- a/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GIMIC/GIMIC-2.2.1-foss-2022a.eb @@ -62,4 +62,7 @@ sanity_check_paths = { sanity_check_commands = ['gimic --help'] +# Sometimes building in parallel leads to error +maxparallel = 1 + moduleclass = 'chem' From b8564760c7d097db8c9f69636fe582825d2b0dbd Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 9 Jan 2024 12:25:57 +0100 Subject: [PATCH 0199/1193] adding easyconfigs: GPAW-24.1.0-intel-2023a.eb --- .../g/GPAW/GPAW-24.1.0-intel-2023a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb new file mode 100644 index 000000000000..70ef81625bdb --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.1.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.1.0.tar.gz': '14150bdc4b098060164b569699577ff57769a42783d79d37c9eb6cfe9cd506ea'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('ASE', '3.22.1'), + ('libxc', '6.2.2'), + ('ELPA', '2023.05.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From 64cd56666dd273749a56dc4ecbf2de1619648cf0 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 9 Jan 2024 12:46:23 +0100 Subject: [PATCH 0200/1193] Add dependencies from PR #19079 - this obsoletes #19079. --- .../a/ASE/ASE-3.22.1-iimkl-2023a.eb | 64 +++++++++++++++ .../matplotlib-3.7.2-iimkl-2023a.eb | 82 +++++++++++++++++++ .../spglib-python-2.1.0-iimkl-2023a.eb | 40 +++++++++ 3 files changed, 186 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASE/ASE-3.22.1-iimkl-2023a.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb diff --git a/easybuild/easyconfigs/a/ASE/ASE-3.22.1-iimkl-2023a.eb b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-iimkl-2023a.eb new file mode 100644 index 000000000000..e5ade107d5cb --- /dev/null +++ b/easybuild/easyconfigs/a/ASE/ASE-3.22.1-iimkl-2023a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'ASE' +version = '3.22.1' + +homepage = 'https://wiki.fysik.dtu.dk/ase' +description = """ASE is a python package providing an open source Atomic Simulation Environment + in the Python scripting language. + +From version 3.20.1 we also include the ase-ext package, it contains optional reimplementations +in C of functions in ASE. ASE uses it automatically when installed.""" + +toolchain = {'name': 'iimkl', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('Tkinter', '%(pyver)s'), # Needed by GUI of ASE + ('spglib-python', '2.1.0'), # optional +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pytest-mock', '3.11.1', { + 'checksums': ['7f6b125602ac6d743e523ae0bfa71e1a697a2f5534064528c6ff84c2f7c2fc7f'], + }), + ('ase', version, { + 'patches': [ + 'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch', + 'ASE-3.22.1-Compatibility-with-pytest-part-2.patch', + 'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch', + 'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch', + ], + 'checksums': [ + {'ase-3.22.1.tar.gz': '004df6b0ea04b1114c790fadfe45d4125eb0e53125c66a93425af853d82ab432'}, + {'ASE-3.22.1-Compatibility-with-pytest-from-Python-3-10.patch': + '8184765ecc9e14081b183fee5c4470da716d77caa67c25164018ac1fdd225eac'}, + {'ASE-3.22.1-Compatibility-with-pytest-part-2.patch': + '3a3473912f5f96ffc625119d87227781ba4ea581de15d4af6a58ba960cdf4601'}, + {'ASE-3.22.1-Compatibility-with-Scipy-2022-05.patch': + 'c1cb07160b063d432f098efd40dd4b3c9f015b7966572c838a908613a482e0c8'}, + {'ASE-3.22.1-Compatibility-with-Flask-2-2-2.patch': + '2a05f98291dc970cb759904988783d1ecc3512ba6a0da852af1d3205667b398d'}, + ], + }), + ('ase-ext', '20.9.0', { + 'checksums': ['a348b0e42cf9fdd11f04b3df002b0bf150002c8df2698ff08d3c8fc7a1223aed'], + }), +] + +sanity_check_paths = { + 'files': ['bin/ase'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# make sure Tkinter is available, otherwise 'ase gui' will not work +sanity_check_commands = ["python -c 'import tkinter' "] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb new file mode 100644 index 000000000000..153096726af1 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb @@ -0,0 +1,82 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.7.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'iimkl', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('cppy', '1.2.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('libpng', '1.6.39'), + ('freetype', '2.13.0'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '10.0.0'), + ('Qhull', '2020.2'), + ('meson-python', '0.13.2'), +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +local_preinstallopts = "sed -e 's/#system_freetype = False/system_freetype = True/g' -e " +local_preinstallopts += "'s/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg" +local_preinstallopts += "&& export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.42.0', { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['614b1283dca88effd20ee48160518e6de275ce9b5456a3134d5f235523fc5065'], + 'modulename': 'fontTools', + }), + ('Cycler', '0.11.0', { + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + 'modulename': 'cycler', + }), + ('kiwisolver', '1.4.4', { + 'patches': ['kiwisolver-1.4.4-fix_version.patch'], + 'checksums': [ + {'kiwisolver-1.4.4.tar.gz': 'd41997519fcba4a1e46eb4a2fe31bc12f0ff957b2b81bac28db24744f333e955'}, + {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, + ], + }), + ('contourpy', '1.1.0', { + 'checksums': ['e53046c3863828d21d531cc3b53786e6580eb1ba02477e8681009b6aa0870b21'], + }), + (name, version, { + 'patches': ['matplotlib-3.7.2-fix_setup.patch'], + 'checksums': [ + {'matplotlib-3.7.2.tar.gz': 'a8cdb91dddb04436bd2f098b8fdf4b81352e68cf4d2c6756fcc414791076569b'}, + {'matplotlib-3.7.2-fix_setup.patch': '70b38f9fc9f26c67adc38440f5420d7c50d9438353ad08740cbb42a79358fb4f'}, + ], + 'preinstallopts': local_preinstallopts, + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb new file mode 100644 index 000000000000..5ecf2ab66d2c --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'spglib-python' +version = '2.1.0' + +homepage = 'https://pypi.python.org/pypi/spglib' +description = """Spglib for Python. + +Spglib is a library for finding and handling crystal symmetries written in C. +""" + +toolchain = {'name': 'iimkl', 'version': '2023a'} + +builddependencies = [ + ('scikit-build-core', '0.5.1') +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +sanity_pip_check = True + +exts_list = [ + ('pyproject-metadata', '0.7.1', { + 'checksums': ['0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67'], + }), + (name, version, { + 'modulename': 'spglib', + 'sources': ['spglib-%(version)s.tar.gz'], + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'], + 'checksums': ['8143545fdffc11fbcda4d705a6b6bcd4889de9bc3524b78df866a36dd0de0a4b'], + }), +] + +moduleclass = 'chem' From ea34fe86f8125f686c7ea7c1d9e2a654330bbaef Mon Sep 17 00:00:00 2001 From: Leonard Nielsen <55690238+lcniel@users.noreply.github.com> Date: Tue, 9 Jan 2024 13:10:19 +0100 Subject: [PATCH 0201/1193] Update WIEN2k-23.2-intel-2021b.eb --- easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb index 256edac87852..a8881dbe1180 100644 --- a/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb +++ b/easybuild/easyconfigs/w/WIEN2k/WIEN2k-23.2-intel-2021b.eb @@ -37,7 +37,7 @@ dependencies = [ osdependencies = [ ('glibc-devel', 'libc6-dev'), # required for libpthread. - ('tcsh', '6.24.01') + ('tcsh') ] # remote = 'pbsssh' From b2675413b409fe6ad91cf039d6e326a59bb1b685 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 9 Jan 2024 14:09:43 +0100 Subject: [PATCH 0202/1193] adding easyconfigs: netCDF-4.9.2-iimpi-2023b.eb --- .../n/netCDF/netCDF-4.9.2-iimpi-2023b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023b.eb new file mode 100644 index 000000000000..7d3a6e0f8ffd --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-iimpi-2023b.eb @@ -0,0 +1,59 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-4.9.0_skip-nasa-test.patch', +] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.27.6'), + ('Doxygen', '1.9.8'), +] + +dependencies = [ + ('HDF5', '1.14.3'), + ('cURL', '8.3.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.5'), + ('bzip2', '1.0.8'), + ('libxml2', '2.11.5'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/18523#issuecomment-1675313158 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 16 ./tst_parallel3|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' From bc49666794490f37b6eedc8d3567d5ad18596748 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 9 Jan 2024 15:20:31 +0100 Subject: [PATCH 0203/1193] adding easyconfigs: zlib-1.3-intel-2023a.eb --- .../z/zlib/zlib-1.3-intel-2023a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb new file mode 100644 index 000000000000..b3c10600d2a0 --- /dev/null +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'zlib' +version = '1.3' + +homepage = 'http://www.zlib.net/' +description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, + not covered by any patents -- lossless data-compression library for use on virtually any + computer hardware and operating system.""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.zlib.net/'] +sources = ['zlib-%(version)s.tar.gz'] +checksums = ['ff0ba4c292013dbc27530b3a81e1f9a813cd39de01ca5e0f8bf355702efa593e'] + +sanity_check_paths = { + 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 5f008b46d0b59fe8ff63a8f30a013a3e2515a089 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 9 Jan 2024 15:37:13 +0100 Subject: [PATCH 0204/1193] adding easyconfigs: SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb and patches: SOAPdenovo-Trans-1.0.5-fix-makefiles.patch --- .../SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb | 35 +++++++++++++++++++ ...SOAPdenovo-Trans-1.0.5-fix-makefiles.patch | 30 ++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb new file mode 100644 index 000000000000..901796573cc3 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'SOAPdenovo-Trans' +version = '1.0.5' + +homepage = 'http://soap.genomics.org.cn/SOAPdenovo-Trans.html' +description = """SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, +adapt to alternative splicing and different expression level among transcripts. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/aquaskyline/SOAPdenovo-Trans/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-1.0.5-fix-makefiles.patch'] +checksums = [ + {'1.0.5.tar.gz': 'c1903c0d81142270db95916e2833400f72c4841b5c9194f182c19ebda418936f'}, + {'SOAPdenovo-Trans-1.0.5-fix-makefiles.patch': '15c420a5e2c2a5a5837dbb1223a6b02b78f059b162e82952c7ceee83fdfdcffb'}, +] + +dependencies = [('zlib', '1.2.13')] + +start_dir = 'src' + +buildopts = ' && make 127mer=1' + +files_to_copy = [(['../SOAPdenovo-Trans-127mer', '../SOAPdenovo-Trans-31mer'], 'bin'), '../LICENSE', + '../README.md', '../VERSION'] + +sanity_check_paths = { + 'files': ['bin/SOAPdenovo-Trans-127mer', 'bin/SOAPdenovo-Trans-31mer'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch new file mode 100644 index 000000000000..edb305d00832 --- /dev/null +++ b/easybuild/easyconfigs/s/SOAPdenovo-Trans/SOAPdenovo-Trans-1.0.5-fix-makefiles.patch @@ -0,0 +1,30 @@ +# Fix makefile to use EB values +# Ward Poelmans +--- SOAPdenovo-Trans-src-v1.04.orig/src/Makefile 2014-04-15 04:37:16.000000000 +0200 ++++ SOAPdenovo-Trans-src-v1.04/src/Makefile 2017-08-23 07:54:58.108664416 +0200 +@@ -1,5 +1,5 @@ +-CC= gcc +-CFLAGS= -O3 -fomit-frame-pointer -static ++CC := $(CC) ++CFLAGS := -fomit-frame-pointer $(CFLAGS) + #CFLAGS= -O3 -g -D_DEBUG + DFLAGS= + +@@ -32,7 +32,7 @@ + INCLUDES= -Iinc + SUBDIRS= . + LIBPATH= +-LIBS= -pthread -lm -lrt -lbam -lz -L./inc ++LIBS := $(LIBS) -lrt -lbam -lz -L./inc + EXTRA_FLAGS= + + BIT_ERR = 0 +@@ -73,7 +73,7 @@ + @test $(BIT_ERR) != 1 || sh -c 'echo "Fatal: 64bit CPU and Operating System required!";false;' + + SOAPdenovo: envTest $(OBJS) +- @$(CC) $(CFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) ++ $(CC) $(CFLAGS) $(LDFLAGS) -o $(PROG) $(OBJS) $(LIBPATH) $(LIBS) $(ENTRAFLAGS) + @printf "Linking...\r" + @printf "$(PROG) compilation done.\n"; + From e61d3740af1c50a9d9c53d975db00cda37aadfb1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 9 Jan 2024 17:45:06 +0100 Subject: [PATCH 0205/1193] bug fix --- .../a/Arrow/Arrow-11.0.0-gfbf-2022b.eb | 7 +++++- .../a/Arrow/Arrow-8.0.0-foss-2021a.eb | 8 +++++-- .../a/Arrow/Arrow-8.0.0-foss-2022.05.eb | 7 +++++- .../a/Arrow/Arrow-8.0.0-foss-2022a.eb | 7 +++++- .../a/Arrow/Arrow-8.0.0_bugfix.patch | 24 +++++++++++++++++++ 5 files changed, 48 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb index 05a7cb4386eb..8b4d846b0ccf 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'gfbf', 'version': '2022b'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -checksums = ['2dd8f0ea0848a58785628ee3a57675548d509e17213a2f5d72b0d900b43f5430'] +patches = ['Arrow-8.0.0_bugfix.patch'] +checksums = [ + {'apache-arrow-11.0.0.tar.gz': '2dd8f0ea0848a58785628ee3a57675548d509e17213a2f5d72b0d900b43f5430'}, + {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, +] builddependencies = [ ('CMake', '3.24.3'), @@ -69,6 +73,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'from pyarrow.lib import BaseExtensionType; print(BaseExtensionType.__arrow_ext_class__)'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb index 8c7316d60a97..095ba852dc91 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb @@ -11,8 +11,11 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -checksums = ['ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'] - +patches = ['Arrow-8.0.0_bugfix.patch'] +checksums = [ + {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, + {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, +] builddependencies = [ ('CMake', '3.20.1'), ('Autotools', '20210128'), @@ -66,6 +69,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'from pyarrow.lib import BaseExtensionType; print(BaseExtensionType.__arrow_ext_class__)'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb index 63eb0955dd10..ce09420d0393 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'foss', 'version': '2022.05'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -checksums = ['ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'] +patches = ['Arrow-8.0.0_bugfix.patch'] +checksums = [ + {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, + {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, +] builddependencies = [ ('CMake', '3.23.1'), @@ -66,6 +70,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'from pyarrow.lib import BaseExtensionType; print(BaseExtensionType.__arrow_ext_class__)'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb index 63f8267f34fb..a8c4a18dc3ab 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb @@ -11,7 +11,11 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -checksums = ['ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'] +patches = ['Arrow-8.0.0_bugfix.patch'] +checksums = [ + {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, + {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, +] builddependencies = [ ('CMake', '3.23.1'), @@ -66,6 +70,7 @@ sanity_check_commands = [ "python -c 'import pyarrow'", "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", + "python -c 'from pyarrow.lib import BaseExtensionType; print(BaseExtensionType.__arrow_ext_class__)'", ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch new file mode 100644 index 000000000000..0b54d4c98495 --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch @@ -0,0 +1,24 @@ +patch fixes a bug mentioned here: https://github.com/vscentrum/vsc-software-stack/issues/150#issuecomment-1862807311 +the bug is fixed in Arrow version 14: https://github.com/apache/arrow/pull/33802 +diff -u python/pyarrow/types.pxi.orig python/pyarrow/types.pxi +--- python/pyarrow/types.pxi.orig 2022-05-03 18:59:12.000000000 +0200 ++++ python/pyarrow/types.pxi 2024-01-09 13:15:20.313755064 +0100 +@@ -760,6 +836,18 @@ + DataType.init(self, type) + self.ext_type = type.get() + ++ def __arrow_ext_class__(self): ++ """ ++ The associated array extension class ++ """ ++ return ExtensionArray ++ ++ def __arrow_ext_scalar_class__(self): ++ """ ++ The associated scalar class ++ """ ++ return ExtensionScalar ++ + @property + def extension_name(self): + """ From bc0b515c455e02544cb29ad53ae52459c58285d7 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 9 Jan 2024 22:02:09 +0100 Subject: [PATCH 0206/1193] adding easyconfigs: netCDF-4.9.2-gompi-2023b.eb --- .../n/netCDF/netCDF-4.9.2-gompi-2023b.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb new file mode 100644 index 000000000000..ec41aadb943f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb @@ -0,0 +1,57 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-4.9.0_skip-nasa-test.patch', +] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.27.6'), + ('Doxygen', '1.9.8'), +] + +dependencies = [ + ('HDF5', '1.14.3'), + ('cURL', '8.3.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.5'), + ('bzip2', '1.0.8'), + ('libxml2', '2.11.5'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' From 5fbba1dbafc7dbc4be5a610390dbc783023783cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 10 Jan 2024 09:24:04 +0100 Subject: [PATCH 0207/1193] use "mixcr -v" as sanity check command for MiXCR v4.6.0 Co-authored-by: Sam Moors --- easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb b/easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb index e8836a4b99d9..4c75c139e4e6 100644 --- a/easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb +++ b/easybuild/easyconfigs/m/MiXCR/MiXCR-4.6.0-Java-17.eb @@ -21,7 +21,7 @@ sanity_check_paths = { 'dirs': [], } -sanity_check_commands = ["command -v mixcr"] +sanity_check_commands = ["mixcr -v"] modextrapaths = {'PATH': ''} From 2213e88643b386ae6cb20b125f5239769e8f1491 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 10 Jan 2024 09:33:00 +0100 Subject: [PATCH 0208/1193] adding easyconfigs: netCDF-4.9.2-gompi-2023b.eb, netCDF-C++4-4.3.1-iimpi-2023b.eb, netCDF-C++4-4.3.1-gompi-2023b.eb, netCDF-Fortran-4.6.1-gompi-2023b.eb, netCDF-Fortran-4.6.1-iimpi-2023b.eb --- .../netCDF-C++4-4.3.1-gompi-2023b.eb | 25 ++++++++ .../netCDF-C++4-4.3.1-iimpi-2023b.eb | 25 ++++++++ .../netCDF-Fortran-4.6.1-gompi-2023b.eb | 28 +++++++++ .../netCDF-Fortran-4.6.1-iimpi-2023b.eb | 28 +++++++++ .../n/netCDF/netCDF-4.9.2-gompi-2023b.eb | 57 +++++++++++++++++++ 5 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2023b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023b.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023b.eb new file mode 100644 index 000000000000..272461e57c54 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2023b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.9.2')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2023b.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2023b.eb new file mode 100644 index 000000000000..66d3e5203956 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2023b.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.9.2')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023b.eb new file mode 100644 index 000000000000..375033b711ed --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2023b.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023b.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023b.eb new file mode 100644 index 000000000000..0fdc993e468d --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-iimpi-2023b.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb new file mode 100644 index 000000000000..ec41aadb943f --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb @@ -0,0 +1,57 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-4.9.0_skip-nasa-test.patch', +] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.27.6'), + ('Doxygen', '1.9.8'), +] + +dependencies = [ + ('HDF5', '1.14.3'), + ('cURL', '8.3.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.5'), + ('bzip2', '1.0.8'), + ('libxml2', '2.11.5'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " + +runtest = 'test' + +moduleclass = 'data' From 07999fd286d32cadc776310205136f94d5190951 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 10 Jan 2024 09:34:50 +0100 Subject: [PATCH 0209/1193] Update easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch index 0b54d4c98495..7c0dcc266f7c 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch @@ -1,5 +1,6 @@ -patch fixes a bug mentioned here: https://github.com/vscentrum/vsc-software-stack/issues/150#issuecomment-1862807311 -the bug is fixed in Arrow version 14: https://github.com/apache/arrow/pull/33802 +fix for: +AttributeError: 'pyarrow.lib.BaseExtensionType' object has no attribute '__arrow_ext_class__' +see https://github.com/apache/arrow/pull/33802 diff -u python/pyarrow/types.pxi.orig python/pyarrow/types.pxi --- python/pyarrow/types.pxi.orig 2022-05-03 18:59:12.000000000 +0200 +++ python/pyarrow/types.pxi 2024-01-09 13:15:20.313755064 +0100 From 704eeafd4167e45611ad5dd82580dc22b3ffa138 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 10 Jan 2024 09:39:07 +0100 Subject: [PATCH 0210/1193] use https instead of http --- easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb index b3c10600d2a0..425fb49cded9 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb @@ -11,7 +11,7 @@ description = """zlib is designed to be a free, general-purpose, legally unencum toolchain = {'name': 'intel', 'version': '2023a'} toolchainopts = {'pic': True} -source_urls = ['http://www.zlib.net/'] +source_urls = ['https://www.zlib.net/'] sources = ['zlib-%(version)s.tar.gz'] checksums = ['ff0ba4c292013dbc27530b3a81e1f9a813cd39de01ca5e0f8bf355702efa593e'] From a631d20638ce976be180671a9fb6f34a8b7e52fb Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Wed, 10 Jan 2024 09:40:15 +0100 Subject: [PATCH 0211/1193] https --- easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb index 425fb49cded9..e726074c7119 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'zlib' version = '1.3' -homepage = 'http://www.zlib.net/' +homepage = 'https://www.zlib.net/' description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.""" From b46d0df79b7a5df0cc992c2d196722d95cea692a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 10 Jan 2024 10:14:45 +0100 Subject: [PATCH 0212/1193] rename patch file, fix checksums --- easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb | 7 ++++--- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb | 6 ++++-- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb | 5 +++-- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb | 5 +++-- ...ow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch} | 0 5 files changed, 14 insertions(+), 9 deletions(-) rename easybuild/easyconfigs/a/Arrow/{Arrow-8.0.0_bugfix.patch => Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch} (100%) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb index 8b4d846b0ccf..f113c47c4313 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb @@ -11,10 +11,11 @@ toolchain = {'name': 'gfbf', 'version': '2022b'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-8.0.0_bugfix.patch'] +patches = ['Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch'] checksums = [ - {'apache-arrow-11.0.0.tar.gz': '2dd8f0ea0848a58785628ee3a57675548d509e17213a2f5d72b0d900b43f5430'}, - {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, + {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, + {'Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch': + '2db8a4c655e2a3f0ec7dac05e13bda6c2843203568873e736d2f1b8321b0dfc7'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb index 095ba852dc91..1ee3bb582e9d 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021a.eb @@ -11,11 +11,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-8.0.0_bugfix.patch'] +patches = ['Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch'] checksums = [ {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, - {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, + {'Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch': + '2db8a4c655e2a3f0ec7dac05e13bda6c2843203568873e736d2f1b8321b0dfc7'}, ] + builddependencies = [ ('CMake', '3.20.1'), ('Autotools', '20210128'), diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb index ce09420d0393..ab4fc5b05feb 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb @@ -11,10 +11,11 @@ toolchain = {'name': 'foss', 'version': '2022.05'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-8.0.0_bugfix.patch'] +patches = ['Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch'] checksums = [ {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, - {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, + {'Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch': + '2db8a4c655e2a3f0ec7dac05e13bda6c2843203568873e736d2f1b8321b0dfc7'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb index a8c4a18dc3ab..6f2ede07dd66 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb @@ -11,10 +11,11 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] sources = ['apache-arrow-%(version)s.tar.gz'] -patches = ['Arrow-8.0.0_bugfix.patch'] +patches = ['Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch'] checksums = [ {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, - {'Arrow-8.0.0_bugfix.patch': '5ee92dc353a4677782c5ff6a15601e01ece1068aeebc5c7ba65d96c64aefbfb5'}, + {'Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch': + '2db8a4c655e2a3f0ec7dac05e13bda6c2843203568873e736d2f1b8321b0dfc7'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch similarity index 100% rename from easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_bugfix.patch rename to easybuild/easyconfigs/a/Arrow/Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch From bb3644ba4a9b12452ad0af0dd7086b185b15d9a2 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 10 Jan 2024 10:15:24 +0100 Subject: [PATCH 0213/1193] adding easyconfigs: flatbuffers-23.5.26-GCCcore-13.2.0.eb --- .../flatbuffers-23.5.26-GCCcore-13.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..24ebbda011a4 --- /dev/null +++ b/easybuild/easyconfigs/f/flatbuffers/flatbuffers-23.5.26-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeNinja' + +name = 'flatbuffers' +version = '23.5.26' + +homepage = 'https://github.com/google/flatbuffers/' +description = """FlatBuffers: Memory Efficient Serialization Library""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/flatbuffers/archive/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1cce06b17cddd896b6d73cc047e36a254fb8df4d7ea18a46acf16c4c0cd3f3f3'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('Python', '3.11.5'), +] + +configopts = '-DFLATBUFFERS_ENABLE_PCH=ON ' + +sanity_check_paths = { + 'files': ['include/flatbuffers/flatbuffers.h', 'bin/flatc', 'lib/libflatbuffers.a'], + 'dirs': ['lib/cmake'], +} + +moduleclass = 'devel' From 24007c83819ae58870571be8f89bf1f09f8f0072 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 10 Jan 2024 10:24:10 +0100 Subject: [PATCH 0214/1193] adding easyconfigs: Redis-7.2.4-GCCcore-13.2.0.eb --- .../r/Redis/Redis-7.2.4-GCCcore-13.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/r/Redis/Redis-7.2.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.2.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.2.4-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..3ad4a7051a7e --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-7.2.4-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '7.2.4' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8d104c26a154b29fd67d6568b4f375212212ad41e0c2caa3d66480e78dbd3b59'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +skipsteps = ['configure'] + +# tests must be run from a local filesystem +# runtest = 'test' + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' From 415f6c2ce95a7e104f6f897adb2507a3a001eb27 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 10 Jan 2024 11:29:48 +0100 Subject: [PATCH 0215/1193] adding easyconfigs: VSCode-1.85.1-cli.eb --- .../easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb new file mode 100644 index 000000000000..937cc735ab6c --- /dev/null +++ b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'VSCode' +version = '1.85.1' +versionsuffix = '-cli' + +homepage = 'https://code.visualstudio.com/' +description = ''' + Visual Studio Code is a lightweight but powerful source code editor + which runs on your desktop and is available for Windows, macOS and + Linux. It comes with built-in support for JavaScript, TypeScript and + Node.js and has a rich ecosystem of extensions for other languages + and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin + your journey with VS Code with these introductory videos. +''' + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] +sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] + +sanity_check_paths = { + 'files': ['code'], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +moduleclass = 'devel' From e9c4d6041a6a859fbf40e304c258f4290c03a3bb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 10 Jan 2024 13:09:44 +0100 Subject: [PATCH 0216/1193] edit comment --- .../d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb index 5bb95d3c8ba5..11661fc52271 100644 --- a/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb +++ b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a.eb @@ -170,6 +170,9 @@ exts_list = [ # import napari_pyclesperanto_assistant fails without GUI # but it has been tested with GUI with following command: # `unset SESSION_MANAGER && python -c "import napari_pyclesperanto_assistant"` + # the `SESSION_MANAGER` needs to be unset to avoid the following message: + # `WARNING: Qt: Session management error: Authentication Rejected, reason : None of the + # authentication protocols specified are supported and host-based authentication failed` 'modulename': False, 'checksums': ['6df5e59e105d91f49826d57b2c61091271f62bba9d061dcb9c0c12d3ca000843'], }), From b6d002cf0deb31915cbf8aa004b149fd1687a339 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 10 Jan 2024 13:34:37 +0100 Subject: [PATCH 0217/1193] Chance Boost.MPI version from 1.83.0 to 1.81.0 --- .../Block/Block-1.5.3-20200525-foss-2022b.eb | 2 +- .../Boost.MPI/Boost.MPI-1.81.0-gompi-2022b.eb | 29 +++++++++++++++++++ 2 files changed, 30 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.81.0-gompi-2022b.eb diff --git a/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb index 524c89130952..4ab6f4db625f 100644 --- a/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb +++ b/easybuild/easyconfigs/b/Block/Block-1.5.3-20200525-foss-2022b.eb @@ -31,7 +31,7 @@ checksums = [ ] dependencies = [ - ('Boost.MPI', '1.83.0'), + ('Boost.MPI', '1.81.0'), ] buildopts = [ diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.81.0-gompi-2022b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.81.0-gompi-2022b.eb new file mode 100644 index 000000000000..1ab9827f302e --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.81.0-gompi-2022b.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.81.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['205666dea9f6a7cfed87c7a6dfbeb52a2c1b9de55712c9c1a87735d7181452b6'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('zstd', '1.5.2'), + ('ICU', '72.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From a2eb9d35ef940a7c26da6f00d9eef26be56890f6 Mon Sep 17 00:00:00 2001 From: lara Date: Wed, 10 Jan 2024 13:41:06 +0100 Subject: [PATCH 0218/1193] remove easy-config Boost.MPI-1.83.0-gompi-2022b.eb --- .../Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb deleted file mode 100644 index c0308757704f..000000000000 --- a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.83.0-gompi-2022b.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = 'EB_Boost' - -name = 'Boost.MPI' -version = '1.83.0' - -homepage = 'https://www.boost.org/' -description = """Boost provides free peer-reviewed portable C++ source libraries.""" - -toolchain = {'name': 'gompi', 'version': '2022b'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] -sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] -checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628'] - -dependencies = [ - ('bzip2', '1.0.8'), - ('zlib', '1.2.12'), - ('XZ', '5.2.7'), - ('zstd', '1.5.2'), - ('ICU', '72.1'), -] - -configopts = '--without-libraries=python' - -boost_mpi = True -tagged_layout = True - -moduleclass = 'devel' From c10569a3ceafa63605b84685344f7d896cebbe53 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 10 Jan 2024 13:50:40 +0100 Subject: [PATCH 0219/1193] adding easyconfigs: netcdf4-python-1.6.5-foss-2023b.eb, mpi4py-3.1.5-gompi-2023b.eb --- .../m/mpi4py/mpi4py-3.1.5-gompi-2023b.eb | 25 ++++++++ .../netcdf4-python-1.6.5-foss-2023b.eb | 57 +++++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.5-foss-2023b.eb diff --git a/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-gompi-2023b.eb b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-gompi-2023b.eb new file mode 100644 index 000000000000..a103eeb6eba5 --- /dev/null +++ b/easybuild/easyconfigs/m/mpi4py/mpi4py-3.1.5-gompi-2023b.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +name = 'mpi4py' +version = '3.1.5' + +homepage = 'https://github.com/mpi4py/mpi4py' +description = """MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for + the Python programming language, allowing any Python program to exploit multiple processors.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['a706e76db9255135c2fb5d1ef54cb4f7b0e4ad9e33cbada7de27626205f2a153'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.5-foss-2023b.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.5-foss-2023b.eb new file mode 100644 index 000000000000..b870f5e92a4b --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.5-foss-2023b.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.5' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('netCDF', '4.9.2'), + ('cURL', '8.3.0'), + ('mpi4py', '3.1.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cftime', '1.6.2', { + 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.1.8-avoid-diskless-test.patch', + 'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netCDF4-1.6.5.tar.gz': '824881d0aacfde5bd982d6adedd8574259c85553781e7b83e0ce82b890bfa0ef'}, + {'netcdf4-python-1.1.8-avoid-diskless-test.patch': + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72'}, + {'netcdf4-python-1.6.1_relax_tolerance_compression_test.patch': + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166'}, + ], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/nc3tonc4', 'bin/nc4tonc3', 'bin/ncinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "nc4tonc3 --help", + "nc3tonc4 --help", + "ncinfo --help", +] + +moduleclass = 'data' From 223b9766d3a2840171a5ced5677063440f4159c6 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Wed, 10 Jan 2024 13:58:38 +0100 Subject: [PATCH 0220/1193] adding easyconfigs: CppUnit-1.15.1-GCCcore-12.3.0.eb --- .../CppUnit/CppUnit-1.15.1-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..3e12be7a1d37 --- /dev/null +++ b/easybuild/easyconfigs/c/CppUnit/CppUnit-1.15.1-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'CppUnit' +version = '1.15.1' + +homepage = 'https://freedesktop.org/wiki/Software/cppunit/' + +description = """ + CppUnit is the C++ port of the famous JUnit framework for unit testing. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://dev-www.libreoffice.org/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['89c5c6665337f56fd2db36bc3805a5619709d51fb136e51937072f63fcc717a7'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['lib/libcppunit.a', 'lib/libcppunit.%s' % SHLIB_EXT, + 'lib/pkgconfig/cppunit.pc'], + 'dirs': ['bin', 'include/cppunit', 'share'], +} + +moduleclass = 'tools' From 745014179c902d7b2196da6b02a07c8c9d9448d7 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 10 Jan 2024 14:06:16 +0100 Subject: [PATCH 0221/1193] Use github_account --- easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb b/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb index b963949f0deb..6aa75a120c3f 100644 --- a/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb +++ b/easybuild/easyconfigs/i/InterOp/InterOp-1.2.4-foss-2021a.eb @@ -21,7 +21,8 @@ been excluded.""" software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = ['https://github.com/Illumina/interop/archive/refs/tags'] +github_account = 'Illumina' +source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['e10ee79f476d40f40a1d4c73074ea58088d82700239b1a2ae9633235afe894c3'] From 24f937d2ea51126b621cad0dad0933564f889c9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 10 Jan 2024 14:54:18 +0100 Subject: [PATCH 0222/1193] fix checksum typo --- easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb index f113c47c4313..ac85f87ad269 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-11.0.0-gfbf-2022b.eb @@ -13,7 +13,7 @@ source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(ve sources = ['apache-arrow-%(version)s.tar.gz'] patches = ['Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch'] checksums = [ - {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, + {'apache-arrow-11.0.0.tar.gz': '2dd8f0ea0848a58785628ee3a57675548d509e17213a2f5d72b0d900b43f5430'}, {'Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch': '2db8a4c655e2a3f0ec7dac05e13bda6c2843203568873e736d2f1b8321b0dfc7'}, ] From 8f81400ac84736f5d5f0fea49af269ecacff813f Mon Sep 17 00:00:00 2001 From: Neves-P Date: Wed, 10 Jan 2024 16:34:59 +0100 Subject: [PATCH 0223/1193] adding easyconfigs: OpenFOAM-11-foss-2023a.eb --- .../o/OpenFOAM/OpenFOAM-11-foss-2023a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100755 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb new file mode 100755 index 000000000000..1ce1045701de --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb @@ -0,0 +1,36 @@ +name = 'OpenFOAM' +version = '11' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-11-ThirdParty.patch'] +checksums = [ + {'version-%(version)s.tar.gz': 'ebc0f86ead699abba61290ba8aac5b730aa93256e675d1d93a5d5f116d51e0c0'}, + {'OpenFOAM-%(version)s-ThirdParty.patch': '7c526be93a0e241584c849cdcda682c23d1a87f23b1a06eae2fa8372a2cab415'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' From b958a4972235c1a514a3689fe1c88b5c940de361 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Wed, 10 Jan 2024 16:52:27 +0100 Subject: [PATCH 0224/1193] Fix easyconfig file permissions --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-11-foss-2023a.eb old mode 100755 new mode 100644 From 247d670cfaf782322be9a240acc39c4860551e51 Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Wed, 10 Jan 2024 16:10:16 +0000 Subject: [PATCH 0225/1193] adding easyconfigs: ESMF-8.4.2-foss-2022a.eb --- .../e/ESMF/ESMF-8.4.2-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.4.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.4.2-foss-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.4.2-foss-2022a.eb new file mode 100644 index 000000000000..cc9c6a7ad83d --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.4.2-foss-2022a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.4.2' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + {'v8.4.2.tar.gz': '969304efa518c7859567fa6e65efd960df2b4f6d72dbf2c3f29e39e4ab5ae594'}, + {'ESMF-6.1.1_libopts.patch': '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.6.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${ESMF_F90COMPILEOPTS} -fallow-argument-mismatch"' + +buildopts = 'ESMF_NETCDF_INCLUDE=$EBROOTNETCDFMINFORTRAN/include ' +buildopts += 'ESMF_NETCDF_LIBS="`nc-config --libs` `nf-config --flibs` `ncxx4-config --libs`"' + +# too parallel causes the build to become really slow +maxparallel = 8 + +moduleclass = 'geo' From 288788147d866d6960910cbf2f5924bc086c37cc Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 10 Jan 2024 17:47:17 +0100 Subject: [PATCH 0226/1193] add sanity check --- .../v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb new file mode 100644 index 000000000000..a60ef2004f82 --- /dev/null +++ b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'VSCode' +version = '1.85.1' +versionsuffix = '-cli-alpine-x64' + +homepage = 'https://code.visualstudio.com/' +description = ''' + Visual Studio Code is a lightweight but powerful source code editor + which runs on your desktop and is available for Windows, macOS and + Linux. It comes with built-in support for JavaScript, TypeScript and + Node.js and has a rich ecosystem of extensions for other languages + and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin + your journey with VS Code with these introductory videos. +''' + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] +sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['code'], + 'dirs': [] +} + +sanity_check_commands = ["code --help"] + +moduleclass = 'devel' From b4ffeb53a14c4e0378720cbfc9b637db7a5d244a Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 10 Jan 2024 17:49:50 +0100 Subject: [PATCH 0227/1193] change versionsuffix --- .../v/VSCode/VSCode-1.85.1-cli-x64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb new file mode 100644 index 000000000000..f1ba579749f0 --- /dev/null +++ b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'VSCode' +version = '1.85.1' +versionsuffix = '-cli-x64' + +homepage = 'https://code.visualstudio.com/' +description = ''' + Visual Studio Code is a lightweight but powerful source code editor + which runs on your desktop and is available for Windows, macOS and + Linux. It comes with built-in support for JavaScript, TypeScript and + Node.js and has a rich ecosystem of extensions for other languages + and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin + your journey with VS Code with these introductory videos. +''' + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] +sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['code'], + 'dirs': [] +} + +sanity_check_commands = ["code --help"] + +moduleclass = 'devel' From b2d33ea1e14980b508c802f58ae73ae0d3790c02 Mon Sep 17 00:00:00 2001 From: lara Date: Wed, 10 Jan 2024 17:53:29 +0100 Subject: [PATCH 0228/1193] remove SCode-1.85.1-cli-alpine-x64.eb VSCode-1.85.1-cli.eb --- .../v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb | 32 ------------------- .../easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb | 30 ----------------- 2 files changed, 62 deletions(-) delete mode 100644 easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb delete mode 100644 easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb deleted file mode 100644 index a60ef2004f82..000000000000 --- a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-alpine-x64.eb +++ /dev/null @@ -1,32 +0,0 @@ -easyblock = 'Tarball' - -name = 'VSCode' -version = '1.85.1' -versionsuffix = '-cli-alpine-x64' - -homepage = 'https://code.visualstudio.com/' -description = ''' - Visual Studio Code is a lightweight but powerful source code editor - which runs on your desktop and is available for Windows, macOS and - Linux. It comes with built-in support for JavaScript, TypeScript and - Node.js and has a rich ecosystem of extensions for other languages - and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin - your journey with VS Code with these introductory videos. -''' - -toolchain = {'name': 'system', 'version': 'system'} - -source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] -sources = ['vscode_cli_alpine_x64_cli.tar.gz'] -checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['code'], - 'dirs': [] -} - -sanity_check_commands = ["code --help"] - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb deleted file mode 100644 index 937cc735ab6c..000000000000 --- a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli.eb +++ /dev/null @@ -1,30 +0,0 @@ -easyblock = 'Tarball' - -name = 'VSCode' -version = '1.85.1' -versionsuffix = '-cli' - -homepage = 'https://code.visualstudio.com/' -description = ''' - Visual Studio Code is a lightweight but powerful source code editor - which runs on your desktop and is available for Windows, macOS and - Linux. It comes with built-in support for JavaScript, TypeScript and - Node.js and has a rich ecosystem of extensions for other languages - and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin - your journey with VS Code with these introductory videos. -''' - -toolchain = {'name': 'system', 'version': 'system'} - -source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] -sources = ['vscode_cli_alpine_x64_cli.tar.gz'] -checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] - -sanity_check_paths = { - 'files': ['code'], - 'dirs': [] -} - -modextrapaths = {'PATH': ''} - -moduleclass = 'devel' From 2ba41074c065770caf51b68878c628da6169b6b2 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 10 Jan 2024 18:34:18 +0100 Subject: [PATCH 0229/1193] adding easyconfigs: DETONATE-1.11-GCC-12.3.0.eb, SAMtools-0.1.20-GCC-12.3.0.eb, sparsehash-2.0.4-GCCcore-12.3.0.eb and patches: DETONATE-1.11_fix-deps.patch, DETONATE-1.11_include-fix.patch, DETONATE-1.11_Intel-fixes.patch, SAMtools-0.1.20_Makefile-ncurses.patch --- .../d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 60 ++++++++ .../DETONATE/DETONATE-1.11_Intel-fixes.patch | 48 ++++++ .../d/DETONATE/DETONATE-1.11_fix-deps.patch | 144 ++++++++++++++++++ .../DETONATE/DETONATE-1.11_include-fix.patch | 10 ++ .../s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb | 29 ++++ .../sparsehash-2.0.4-GCCcore-12.3.0.eb | 37 +++++ 6 files changed, 328 insertions(+) create mode 100644 easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_Intel-fixes.patch create mode 100644 easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_fix-deps.patch create mode 100644 easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_include-fix.patch create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb new file mode 100644 index 000000000000..1d03d30a2130 --- /dev/null +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'MakeCp' + +name = 'DETONATE' +version = '1.11' + +homepage = 'http://deweylab.biostat.wisc.edu/detonate/' +description = """DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) + consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used + to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds + of genomic sequences.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['http://deweylab.biostat.wisc.edu/detonate/'] +sources = ['detonate-1.11.tar.gz'] +patches = [ + 'DETONATE-%(version)s_fix-deps.patch', + 'DETONATE-%(version)s_Intel-fixes.patch', + 'DETONATE-%(version)s_include-fix.patch' +] +checksums = [ + {'detonate-1.11.tar.gz': 'e1d04af1b1d2504942a6941b346d430157da6117fac043b7ee83274717d99714'}, + {'DETONATE-1.11_fix-deps.patch': '0ab353f66d5459e1fa18fa214026589fe214365f3532a3b9ea182757c7547691'}, + {'DETONATE-1.11_Intel-fixes.patch': 'c72a18250857883e7075ac512bbbd532e61a1aab38868d0dc932ca4bdc412817'}, + {'DETONATE-1.11_include-fix.patch': '9071fc8dbc6bfc26a9c4bb60befca890a26acf9668df2815a7f0038d8bcdd9f6'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('SAMtools', '0.1.20'), + ] + +dependencies = [ + ('Boost', '1.82.0'), + ('sparsehash', '2.0.4'), + ('BamTools','2.5.2'), + ('zlib', '1.2.13'), +] + +start_dir = 'ref-eval' + +buildopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS -fopenmp" && cd ../rsem-eval && make CC="$CXX" CFLAGS="$CXXFLAGS"' + +runtest = 'test' + +files_to_copy = [(['ref-eval', 'ref-eval-estimate-true-assembly', '../rsem-eval/rsem-*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ref-eval', 'ref-eval-estimate-true-assembly', 'rsem-build-read-index', + 'rsem-eval-calculate-score', 'rsem-eval-estimate-transcript-length-distribution', + 'rsem-eval-run-em', 'rsem-extract-reference-transcripts', + 'rsem-parse-alignments', 'rsem-plot-model', 'rsem-preref', 'rsem-sam-validator', + 'rsem-scan-for-paired-end-reads', 'rsem-simulate-reads', + 'rsem-synthesis-reference-transcripts']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_Intel-fixes.patch b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_Intel-fixes.patch new file mode 100644 index 000000000000..150cb7a64012 --- /dev/null +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_Intel-fixes.patch @@ -0,0 +1,48 @@ +fix compilation issues that occur with Intel compilers +error: no suitable conversion function from "std::basic_istream>" to "bool" exists + +author: Kenneth Hoste (HPC-UGent), with a bit of help from Ward Poelmans +--- detonate-1.11/rsem-eval/SingleHit.h.orig 2018-01-23 11:01:34.269328898 +0100 ++++ detonate-1.11/rsem-eval/SingleHit.h 2018-01-23 11:01:55.859848244 +0100 +@@ -43,7 +43,7 @@ + + bool SingleHit::read(std::istream& in) { + conprb = 0.0; +- return (in>>sid>>pos); ++ return static_cast(in>>sid>>pos); + } + + void SingleHit::write(std::ostream& out) { +--- detonate-1.11/rsem-eval/PairedEndHit.h.orig 2018-01-23 11:07:46.838260187 +0100 ++++ detonate-1.11/rsem-eval/PairedEndHit.h 2018-01-23 11:08:12.628872625 +0100 +@@ -26,7 +26,7 @@ + + bool PairedEndHit::read(std::istream& in) { + conprb = 0.0; +- return (in>>sid>>pos>>insertL); ++ return static_cast(in>>pos>>insertL); + } + + void PairedEndHit::write(std::ostream& out) { +--- detonate-1.11/rsem-eval/buildReadIndex.cpp.orig 2018-01-23 13:58:46.313840541 +0100 ++++ detonate-1.11/rsem-eval/buildReadIndex.cpp 2018-01-23 13:59:51.375415745 +0100 +@@ -35,15 +35,15 @@ + streampos pos = fin.tellg(); + success = true; + +- success = (getline(fin, line)); ++ success = static_cast(getline(fin, line)); + if (!success) continue; +- success = (getline(fin, line)); ++ success = static_cast(getline(fin, line)); + if (!success) continue; + + if (hasQ) { +- success = (getline(fin, line)); ++ success = static_cast(getline(fin, line)); + if (!success) continue; +- success = (getline(fin, line)); ++ success = static_cast(getline(fin, line)); + if (!success) continue; + } + diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_fix-deps.patch b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_fix-deps.patch new file mode 100644 index 000000000000..ab19abb1ad67 --- /dev/null +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_fix-deps.patch @@ -0,0 +1,144 @@ +- fix compilation flags, use $CFLAGS passed by EasyBuild +- use Boost, SAMtools, sparsehash provided as dependencies via EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- detonate-1.11/rsem-eval/Makefile.orig 2016-06-22 23:34:39.000000000 +0200 ++++ detonate-1.11/rsem-eval/Makefile 2018-01-23 14:47:47.714929147 +0100 +@@ -7,18 +7,15 @@ + + all : $(PROGRAMS) + +-sam/libbam.a : +- cd sam ; ${MAKE} all +- + Transcript.h : utils.h + + Transcripts.h : utils.h my_assert.h Transcript.h + + rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp +- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts ++ $(CC) $(CFLAGS) extractRef.cpp -o rsem-extract-reference-transcripts + + rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp +- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts ++ $(CC) $(CFLAGS) synthesisRef.cpp -o rsem-synthesis-reference-transcripts + + BowtieRefSeqPolicy.h : RefSeqPolicy.h + +@@ -28,10 +25,10 @@ + + + rsem-preref : preRef.o +- $(CC) preRef.o -o rsem-preref ++ $(CC) $(CFLAGS) preRef.o -o rsem-preref + + preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp +- $(CC) $(COFLAGS) preRef.cpp ++ $(CC) -c -I $(CFLAGS) preRef.cpp + + + SingleRead.h : Read.h +@@ -49,14 +46,14 @@ + + SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h + +-rsem-parse-alignments : parseIt.o sam/libbam.a +- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread ++rsem-parse-alignments : parseIt.o ++ $(CC) -o rsem-parse-alignments parseIt.o ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread + + parseIt.o : utils.h RefSeq.h Refs.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp +- $(CC) -Wall -O2 -c -I. parseIt.cpp ++ $(CC) $(CFLAGS) -c -I. parseIt.cpp + + rsem-build-read-index : utils.h buildReadIndex.cpp +- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index ++ $(CC) $(CFLAGS) buildReadIndex.cpp -o rsem-build-read-index + + + simul.h : boost/random.hpp +@@ -85,23 +82,23 @@ + + CalcEvalScore.h : utils.h my_assert.h Refs.h GroupInfo.h Transcript.h Transcripts.h ContigLengthDist.h + +-rsem-eval-run-em : EM.o sam/libbam.a +- $(CC) -o rsem-eval-run-em EM.o sam/libbam.a -lz -lpthread ++rsem-eval-run-em : EM.o ++ $(CC) -o rsem-eval-run-em EM.o ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread + + EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h boost/math/distributions/negative_binomial.hpp ContigLengthDist.h CalcEvalScore.h EM.cpp +- $(CC) $(COFLAGS) EM.cpp ++ $(CC) -c -I $(CFLAGS) EM.cpp + + rsem-simulate-reads : simulation.o + $(CC) -o rsem-simulate-reads simulation.o + + simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp +- $(CC) $(COFLAGS) simulation.cpp ++ $(CC) -c -I $(CFLAGS) simulation.cpp + +-rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a +- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ ++rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp ++ $(CC) $(CFLAGS) samValidator.cpp ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread -o $@ + +-rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a +- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ ++rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp ++ $(CC) $(CFLAGS) scanForPairedEndReads.cpp ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread -o $@ + + clean : + rm -f *.o *~ $(PROGRAMS) +--- detonate-1.11/ref-eval/Makefile.orig 2016-06-22 23:34:39.000000000 +0200 ++++ detonate-1.11/ref-eval/Makefile 2018-01-23 15:10:47.078223944 +0100 +@@ -40,19 +40,19 @@ + + CXXFLAGS = -W -Wno-unused-parameter -g -O3 + CXXFLAGS_DEBUG = -g3 -fno-inline -O0 -Wall -Wextra +-BOOST_INC = -Iboost +-BOOST_LIB = boost/stage/lib/libboost_program_options.a boost/stage/lib/libboost_random.a ++BOOST_INC = -I${EBROOTBOOST}/include ++BOOST_LIB = ${EBROOTBOOST}/lib/libboost_program_options.a ${EBROOTBOOST}/lib/libboost_random.a + LEMON_INC = -Ilemon/build -Ilemon/lemon-main-473c71baff72 + LEMON_LIB = lemon/build/lemon/libemon.a -lpthread + CITY_INC = -Icity/install/include + CITY_LIB = city/install/lib/libcityhash.a + SAM_INC = -I. +-SAM_LIB = sam/libbam.a +-SH_INC = -Isparsehash/include ++SAM_LIB = ${EBROOTSAMTOOLS}/lib/libbam.a ++SH_INC = -I${EBROOTSPARSEHASH}/include + DL_INC = -Ideweylab + INC = $(BOOST_INC) $(LEMON_INC) $(CITY_INC) $(SAM_INC) $(SH_INC) $(DL_INC) + LIB = $(BOOST_LIB) $(LEMON_LIB) $(CITY_LIB) $(SAM_LIB) +-TEST_LIB = boost/stage/lib/libboost_unit_test_framework.a ++TEST_LIB = ${EBROOTBOOST}/lib/libboost_unit_test_framework.a -lboost_system + + ifeq (${NEED_CMAKE}, yes) + wd := $(shell pwd) +@@ -140,7 +140,7 @@ + @echo + cd sparsehash && $(MAKE) + +-ref-eval: ref-eval.cpp boost/finished lemon/finished city/finished sam/libbam.a sparsehash/finished ++ref-eval: ref-eval.cpp lemon/finished city/finished + @echo + @echo ----------------------------- + @echo - Building REF-EVAL itself. - +@@ -148,7 +148,7 @@ + @echo + $(CXX) $(OMP) $(CXXFLAGS) $(INC) ref-eval.cpp $(LIB) -o ref-eval + +-ref-eval-estimate-true-assembly: ref-eval-estimate-true-assembly.cpp boost/finished lemon/finished city/finished sam/libbam.a sparsehash/finished ++ref-eval-estimate-true-assembly: ref-eval-estimate-true-assembly.cpp lemon/finished city/finished + @echo + @echo --------------------------------------------------- + @echo - Building program to estimate the true assembly. - +@@ -170,7 +170,7 @@ + all_tests := test_lazycsv test_line_stream test_blast test_psl test_pairset test_mask test_alignment_segment test_re_matched test_re_kc + + .PHONY: test +-test: test_msg ${all_tests} boost/finished lemon/finished city/finished sparsehash/finished ++test: test_msg ${all_tests} lemon/finished city/finished + ./test_lazycsv + ./test_line_stream + ./test_blast diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_include-fix.patch b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_include-fix.patch new file mode 100644 index 000000000000..a7bcb389ea4f --- /dev/null +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_include-fix.patch @@ -0,0 +1,10 @@ +diff -u detonate-1.11/ref-eval/pairset.hh.orig detonate-1.11/ref-eval/pairset.hh +--- detonate-1.11/ref-eval/pairset.hh.orig 2016-06-22 23:34:39.000000000 +0200 ++++ detonate-1.11/ref-eval/pairset.hh 2024-01-08 18:31:58.579745141 +0100 +@@ -21,6 +21,7 @@ + #include + #include + #include ++#include + #include + #include \ No newline at end of file diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb new file mode 100644 index 000000000000..42f46e803a79 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +name = 'SAMtools' +version = '0.1.20' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +# toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['SAMtools-%(version)s_Makefile-ncurses.patch'] +checksums = [ + {'samtools-0.1.20.tar.gz': '500019b4d1886ad995513d5ce8b413b14b51f16f251ce76bc0b35a446b182a47'}, + {'SAMtools-0.1.20_Makefile-ncurses.patch': 'f01a05b73f28ff47e816d13a06b27083ec45a3ff93537378affeddf75f614bba'}, +] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + # ('bzip2', '1.0.8'), + # ('XZ', '5.4.2'), + # ('cURL', '8.0.1'), +] + +moduleclass = 'bio' \ No newline at end of file diff --git a/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b4dcdff4ce02 --- /dev/null +++ b/easybuild/easyconfigs/s/sparsehash/sparsehash-2.0.4-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +# Updated from previous easyconfig +# Author: Pavel Grochal (INUITS) +# Update: Pavel Tománek (INUITS) +# License: GPLv2 +# Updated to GCCcore-12.3.0 +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'sparsehash' +version = '2.0.4' + +homepage = 'https://github.com/sparsehash/sparsehash' +description = """ + An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! + The SparseHash library contains several hash-map implementations, including + implementations that optimize for space or speed. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8cd1a95827dfd8270927894eb77f62b4087735cbede953884647f16c521c7e58'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['include/google/type_traits.h'], + 'dirs': [], +} + +moduleclass = 'devel' From 5195fce3500c8294bbe6c564d054f44cf9debee4 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 10 Jan 2024 18:36:05 +0100 Subject: [PATCH 0230/1193] adding easyconfigs: SAMtools-1.13-GCC-12.3.0.eb --- .../s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb new file mode 100644 index 000000000000..7277c50ff97e --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb @@ -0,0 +1,25 @@ +name = 'SAMtools' +version = '1.13' + +homepage = 'https://www.htslib.org/' +description = """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating alignments in a per-position format.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['616ca2e051cc8009a1e9c01cfd8c7caf8b70916ddff66f3b76914079465f8c60'] + +# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. +# The latter is currently provided by XZ. +dependencies = [ + ('ncurses', '6.4'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('cURL', '8.0.1'), +] + +moduleclass = 'bio' \ No newline at end of file From 6c55f359231fd710c1b668e0b88f30e07a569495 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 10 Jan 2024 19:19:56 +0100 Subject: [PATCH 0231/1193] formatting --- .../easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 6 +++--- .../easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb | 2 +- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index 1d03d30a2130..75907087a7c5 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -28,14 +28,14 @@ checksums = [ ] builddependencies = [ - ('CMake', '3.26.3'), + ('CMake', '3.26.3'), ('SAMtools', '0.1.20'), - ] +] dependencies = [ ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), - ('BamTools','2.5.2'), + ('BamTools', '2.5.2'), ('zlib', '1.2.13'), ] diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb index 42f46e803a79..49aaba4b8449 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb @@ -26,4 +26,4 @@ dependencies = [ # ('cURL', '8.0.1'), ] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 0d8be9e29358819d8195eabd7e576a8987c1e8ed Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 10 Jan 2024 19:21:41 +0100 Subject: [PATCH 0232/1193] formatting --- easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb index 7277c50ff97e..7829fe976450 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-12.3.0.eb @@ -22,4 +22,4 @@ dependencies = [ ('cURL', '8.0.1'), ] -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 25cb9239098286a30b63d5a5ffc5985a97144bce Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 10 Jan 2024 19:29:54 +0100 Subject: [PATCH 0233/1193] cleaning --- .../easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb index 49aaba4b8449..e041e209606c 100644 --- a/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-0.1.20-GCC-12.3.0.eb @@ -6,7 +6,6 @@ description = """SAM Tools provide various utilities for manipulating alignments including sorting, merging, indexing and generating alignments in a per-position format.""" toolchain = {'name': 'GCC', 'version': '12.3.0'} -# toolchainopts = {'pic': True} source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/%(version)s'] sources = [SOURCELOWER_TAR_GZ] @@ -16,14 +15,9 @@ checksums = [ {'SAMtools-0.1.20_Makefile-ncurses.patch': 'f01a05b73f28ff47e816d13a06b27083ec45a3ff93537378affeddf75f614bba'}, ] -# The htslib component of SAMtools >= 1.4 uses zlib, bzip2 and lzma compression. -# The latter is currently provided by XZ. dependencies = [ ('ncurses', '6.4'), ('zlib', '1.2.13'), - # ('bzip2', '1.0.8'), - # ('XZ', '5.4.2'), - # ('cURL', '8.0.1'), ] moduleclass = 'bio' From a2ba1114dcf7cb07a8864fb97508b012537ddd2b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 11 Jan 2024 07:54:19 +0100 Subject: [PATCH 0234/1193] adding easyconfigs: Clustal-Omega-1.2.4-GCC-11.2.0.eb, argtable-2.13-GCCcore-11.2.0.eb --- .../argtable/argtable-2.13-GCCcore-11.2.0.eb | 30 ++++++++++++++++ .../Clustal-Omega-1.2.4-GCC-11.2.0.eb | 35 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..0eb9df1a37a2 --- /dev/null +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by: Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'argtable' +version = '2.13' + +homepage = 'https://argtable.sourceforge.io/' +description = """ Argtable is an ANSI C library for parsing GNU style + command line options with a minimum of fuss. """ + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] + +builddependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['include/argtable2.h', 'lib/libargtable2.%s' % SHLIB_EXT, 'lib/libargtable2.a'], + 'dirs': ['share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-11.2.0.eb b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-11.2.0.eb new file mode 100644 index 000000000000..1784c84bab0e --- /dev/null +++ b/easybuild/easyconfigs/c/Clustal-Omega/Clustal-Omega-1.2.4-GCC-11.2.0.eb @@ -0,0 +1,35 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel +# Modified by Adam Huffman +# Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'Clustal-Omega' +version = '1.2.4' + +homepage = 'http://www.clustal.org/omega/' +description = """ Clustal Omega is a multiple sequence alignment + program for proteins. It produces biologically meaningful multiple + sequence alignments of divergent sequences. Evolutionary relationships + can be seen via viewing Cladograms or Phylograms """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'openmp': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8683d2286d663a46412c12a0c789e755e7fd77088fb3bc0342bb71667f05a3ee'] + +dependencies = [('argtable', '2.13')] + +sanity_check_paths = { + 'files': ['bin/clustalo'], + 'dirs': [], +} + +sanity_check_commands = ["clustalo --help"] + +moduleclass = 'bio' From b03f45ae837799b4e97edb6bed9def7236bc0846 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 11 Jan 2024 09:03:39 +0100 Subject: [PATCH 0235/1193] Update easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb index f1ba579749f0..aa41c968952e 100644 --- a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb +++ b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb @@ -17,7 +17,10 @@ description = ''' toolchain = {'name': 'system', 'version': 'system'} source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] -sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +sources = [{ + 'download_filename': 'vscode_cli_alpine_x64_cli.tar.gz', + 'filename': 'vscode-%(version)s%(versionsuffix)s.tar.gz', +}] checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] modextrapaths = {'PATH': ''} From 1edc5c9b4c0e6d6d4c3da395c2f841cab43c8d34 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Jan 2024 09:06:25 +0100 Subject: [PATCH 0236/1193] adding easyconfigs: matplotlib-3.8.2-gfbf-2023b.eb, cppy-1.2.1-GCCcore-13.2.0.eb, Pillow-10.2.0-GCCcore-13.2.0.eb, Qhull-2020.2-GCCcore-13.2.0.eb and patches: matplotlib-3.8.2-fix_setup.patch --- .../c/cppy/cppy-1.2.1-GCCcore-13.2.0.eb | 32 ++++++++ .../matplotlib-3.8.2-fix_setup.patch | 13 +++ .../matplotlib/matplotlib-3.8.2-gfbf-2023b.eb | 82 +++++++++++++++++++ .../p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb | 42 ++++++++++ .../q/Qhull/Qhull-2020.2-GCCcore-13.2.0.eb | 40 +++++++++ 5 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-fix_setup.patch create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6fc757ce9c4f --- /dev/null +++ b/easybuild/easyconfigs/c/cppy/cppy-1.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'cppy' +version = '1.2.1' + +homepage = "https://github.com/nucleic/cppy" +description = """A small C++ header library which makes it easier to write +Python extension modules. The primary feature is a PyObject smart pointer +which automatically handles reference counting and provides convenience +methods for performing common object operations.""" + + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), +] + +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['cppy-1.2.1-manual_version.patch'] +checksums = [ + {'cppy-1.2.1.tar.gz': '83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'}, + {'cppy-1.2.1-manual_version.patch': '048aa0a86fd2e99c6896443b07ec83eaa369724297f639ef74c65c404b8f288f'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-fix_setup.patch b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-fix_setup.patch new file mode 100644 index 000000000000..da42051411f8 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-fix_setup.patch @@ -0,0 +1,13 @@ +Fix version (autoresolve fails) +S.D.Pinches, 10.01.2024 +diff -Nru matplotlib-3.8.2-orig/setup.py matplotlib-3.8.2/setup.py +--- matplotlib-3.8.2-orig/setup.py 2023-11-17 20:55:51.000000000 +0100 ++++ matplotlib-3.8.2/setup.py 2024-01-10 18:48:34.370649021 +0100 +@@ -279,6 +279,7 @@ + setup( # Finally, pass this all along to setuptools to do the heavy lifting. + name="matplotlib", + description="Python plotting package", ++ version="3.8.2", + author="John D. Hunter, Michael Droettboom", + author_email="matplotlib-users@python.org", + url="https://matplotlib.org", diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb new file mode 100644 index 000000000000..87330f4ad9b9 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb @@ -0,0 +1,82 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.8.2' + +homepage = 'https://matplotlib.org' +description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of + hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python + and ipython shell, web application servers, and six graphical user interface toolkits.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('cppy', '1.2.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('libpng', '1.6.40'), + ('freetype', '2.13.2'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '10.2.0'), + ('Qhull', '2020.2'), + ('meson-python', '0.15.0'), +] + +use_pip = True +sanity_pip_check = True + +# avoid that matplotlib downloads and builds its own copies of freetype and qhull +_fix_setup = "sed -e 's/#system_freetype = False/system_freetype = True/g' " +_fix_setup += "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +local_preinstallopts = "sed -e 's/#system_freetype = False/system_freetype = True/g' -e " +local_preinstallopts += "'s/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg" +local_preinstallopts += "&& export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('fonttools', '4.47.0', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['ec13a10715eef0e031858c1c23bfaee6cba02b97558e4a7bfa089dba4a8c2ebf'], + }), + ('Cycler', '0.12.1', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'checksums': ['88bb128f02ba341da8ef447245a9e138fae777f6a23943da4540077d3601eb1c'], + }), + ('kiwisolver', '1.4.5', { + 'patches': ['kiwisolver-1.4.4-fix_version.patch'], + 'checksums': [ + {'kiwisolver-1.4.5.tar.gz': 'e57e563a57fb22a142da34f38acc2fc1a5c864bc29ca1517a88abc963e60d6ec'}, + {'kiwisolver-1.4.4-fix_version.patch': '6753afbb3a88856493fcfa0b33989f35742f57bfd41ff3b7f71a98797e1bfbd0'}, + ], + }), + ('contourpy', '1.2.0', { + 'checksums': ['171f311cb758de7da13fc53af221ae47a5877be5a0843a9fe150818c51ed276a'], + }), + (name, version, { + 'patches': ['matplotlib-3.8.2-fix_setup.patch'], + 'preinstallopts': "sed -e 's/#system_freetype = False/system_freetype = True/g' -e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg&& export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'checksums': [ + {'matplotlib-3.8.2.tar.gz': '01a978b871b881ee76017152f1f1a0cbf6bd5f7b8ff8c96df0df1bd57d8755a1'}, + {'matplotlib-3.8.2-fix_setup.patch': '16e1610aec49af402e324e0b71c69d6b7ae106732088318e727b48282492a932'}, + ], + }), +] + +sanity_check_commands = [ + """python -c 'import matplotlib; matplotlib.use("Agg"); import matplotlib.pyplot' """, + "python -c 'from mpl_toolkits.mplot3d import Axes3D'", +] + +# use non-interactive plotting backend as default +# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend +modextravars = {'MPLBACKEND': 'Agg'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..124fdb2e5e26 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '10.2.0' + +homepage = 'https://pillow.readthedocs.org/' +description = """Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. + PIL is the Python Imaging Library by Fredrik Lundh and Contributors.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e87f0b2c78157e12d7686b27d63c070fd65d994e8ddae6f328e0dcf4a0cd007e'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), + ('LibTIFF', '4.6.0'), + ('freetype', '2.13.2') +] + +download_dep_fail = True + +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + +# avoid that hardcoded paths like /usr/include are used in build commands +installopts = "--global-option=build_ext --global-option='--disable-platform-guessing' " + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..0ae78992e08e --- /dev/null +++ b/easybuild/easyconfigs/q/Qhull/Qhull-2020.2-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'Qhull' +version = '2020.2' + +homepage = 'http://www.qhull.org' + +description = """ + Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, + halfspace intersection about a point, furthest-site Delaunay triangulation, + and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and + higher dimensions. Qhull implements the Quickhull algorithm for computing the + convex hull. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.qhull.org/download/'] +sources = ['%(namelower)s-%(version_major)s-src-8.0.2.tgz'] +checksums = ['b5c2d7eb833278881b952c8a52d20179eab87766b00b865000469a45c1838b7e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['bin/qhull', 'lib/libqhull_r.%s' % SHLIB_EXT, + 'lib/pkgconfig/qhull_r.pc'], + 'dirs': [], +} + +modextrapaths = { + 'CPATH': ['qhull/include'], +} + +parallel = 1 + +moduleclass = 'math' From f2396bf521e9ccb63d7b9e296e3f5307debdeb0b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Jan 2024 10:44:31 +0100 Subject: [PATCH 0237/1193] adding easyconfigs: QCG-PilotJob-0.13.1-gfbf-2023b.eb, PyZMQ-25.1.2-GCCcore-13.2.0.eb, Kaleido-0.2.1-GCCcore-13.2.0.eb, statsmodels-0.14.1-gfbf-2023b.eb, plotly.py-5.18.0-GCCcore-13.2.0.eb and patches: statsmodels-0.14.1_fix_setup.patch, trove-classifiers-2024.1.8_fix_setup.patch --- .../k/Kaleido/Kaleido-0.2.1-GCCcore-13.2.0.eb | 24 ++++++ .../p/PyZMQ/PyZMQ-25.1.2-GCCcore-13.2.0.eb | 29 ++++++++ .../plotly.py-5.18.0-GCCcore-13.2.0.eb | 37 ++++++++++ .../QCG-PilotJob-0.13.1-gfbf-2023b.eb | 73 +++++++++++++++++++ ...trove-classifiers-2024.1.8_fix_setup.patch | 11 +++ .../statsmodels-0.14.1-gfbf-2023b.eb | 33 +++++++++ .../statsmodels-0.14.1_fix_setup.patch | 11 +++ 7 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/plotly.py/plotly.py-5.18.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1_fix_setup.patch diff --git a/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..3332d0fc7f8c --- /dev/null +++ b/easybuild/easyconfigs/k/Kaleido/Kaleido-0.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Kaleido' +version = '0.2.1' + +homepage = 'https://github.com/plotly/Kaleido' +description = "Fast static image export for web-based visualization libraries with zero dependencies" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = ['kaleido-%(version)s-py2.py3-none-manylinux1_%(arch)s.whl'] +checksums = ['aa21cf1bf1c78f8fa50a9f7d45e1003c387bd3d6fe0a767cfbbf344b95bdc3a8'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..56cef4cbe67b --- /dev/null +++ b/easybuild/easyconfigs/p/PyZMQ/PyZMQ-25.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'PyZMQ' +version = '25.1.2' + +homepage = 'https://www.zeromq.org/bindings:python' +description = "Python bindings for ZeroMQ" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93f1aa311e8bb912e34f004cf186407a4e90eec4f0ecc0efd26056bf7eda0226'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('ZeroMQ', '4.3.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'zmq'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/plotly.py/plotly.py-5.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.18.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..22c68504cc40 --- /dev/null +++ b/easybuild/easyconfigs/p/plotly.py/plotly.py-5.18.0-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'plotly.py' +version = '5.18.0' + +homepage = 'https://plot.ly/python' +description = "An open-source, interactive graphing library for Python" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.5')] + +use_pip = True + +exts_list = [ + ('tenacity', '8.2.3', { + 'patches': ['tenacity-8.2.3-fix_version.patch'], + 'checksums': [ + {'tenacity-8.2.3.tar.gz': '5398ef0d78e63f40007c1fb4c0bff96e1911394d2fa8d194f77619c05ff6cc8a'}, + {'tenacity-8.2.3-fix_version.patch': 'eb066e8f70d2dc075fca18e04dbc2a6b0721285815470c602a16c599002b63f7'}, + ], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('plotly', version, { + 'checksums': ['360a31e6fbb49d12b007036eb6929521343d6bee2236f8459915821baefa2cbb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2023b.eb b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2023b.eb new file mode 100644 index 000000000000..e056461c26ab --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/QCG-PilotJob-0.13.1-gfbf-2023b.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'QCG-PilotJob' +version = '0.13.1' + +homepage = 'https://qcg-pilotjob.readthedocs.org' +description = """A python service for easy execution of many tasks inside a single allocation.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('PyZMQ', '25.1.2'), + ('Kaleido', '0.2.1'), + ('statsmodels', '0.14.1'), + ('plotly.py', '5.18.0'), +] + +use_pip = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + ('plotly_express', '0.4.1', { + 'checksums': ['ff73a41ce02fb43d1d8e8fa131ef3e6589857349ca216b941b8f3f862bce0278'], + }), + ('prompt_toolkit', '3.0.43', { + 'checksums': ['3527b7af26106cbc65a040bcc84839a3566ec1b051bb0bfe953631e704b0ff7d'], + }), + ('trove-classifiers', '2024.1.8', { + 'patches': ['trove-classifiers-2024.1.8_fix_setup.patch'], + 'checksums': [ + {'trove-classifiers-2024.1.8.tar.gz': '6e36caf430ff6485c4b57a4c6b364a13f6a898d16b9417c6c37467e59c14b05a'}, + {'trove-classifiers-2024.1.8_fix_setup.patch': + '90ef5954a558ece2e3d1bc0a9732224b397b8803f9cb8d8915cf2cf4b59498bc'}, + ], + }), + ('hatchling', '1.21.0', { + 'checksums': ['5c086772357a50723b825fd5da5278ac7e3697cdf7797d07541a6c90b6ff754c'], + }), + ('hatch_vcs', '0.4.0', { + 'checksums': ['093810748fe01db0d451fabcf2c1ac2688caefd232d4ede967090b1c1b07d9f7'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), + ('termcolor', '2.4.0', { + 'checksums': ['aab9e56047c8ac41ed798fa36d892a37aca6b3e9159f3e0c24bc64a9b3ac7b7a'], + }), + ('qcg-pilotjob', version, { + 'modulename': 'qcg.pilotjob', + 'patches': ['QCG-PilotJob-0.12.3_rename_zmq.patch'], + 'checksums': [ + {'qcg-pilotjob-0.13.1.tar.gz': '6aff74436edde78e8f584066a732298731e8ce1190f7fe69edfaab64a3ecc29d'}, + {'QCG-PilotJob-0.12.3_rename_zmq.patch': + '51cba1bfe1dcd33180dffe65941acdfa70823d6cae4b81182fd16a7debf907cd'}, + ], + }), + ('qcg-pilotjob-cmds', version, { + 'modulename': 'qcg.pilotjob.cmds', + 'checksums': ['dc7d4a30b65f2194cf68ec876401581647f683d766215a4fef32b438ec4cbffe'], + }), + ('qcg-pilotjob-executor-api', version, { + 'modulename': 'qcg.pilotjob.api', + 'checksums': ['9d7303199bcce1de35d480f96bc2da93b5259a5cac31476c486f790ccbdeebdf'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch new file mode 100644 index 000000000000..f21ac6f790a6 --- /dev/null +++ b/easybuild/easyconfigs/q/QCG-PilotJob/trove-classifiers-2024.1.8_fix_setup.patch @@ -0,0 +1,11 @@ +diff -Nru trove-classifiers-2024.1.8-orig/setup.py trove-classifiers-2024.1.8/setup.py +--- trove-classifiers-2024.1.8-orig/setup.py 2024-01-08 14:59:52.000000000 +0100 ++++ trove-classifiers-2024.1.8/setup.py 2024-01-11 10:37:27.552452000 +0100 +@@ -12,6 +12,7 @@ + setup( + name="trove-classifiers", + description="Canonical source for classifiers on PyPI (pypi.org).", ++ version="2024.1.8", + long_description=long_description, + long_description_content_type="text/markdown", + url="https://github.com/pypa/trove-classifiers", diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023b.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023b.eb new file mode 100644 index 000000000000..330f32a1d705 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023b.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.14.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + (name, version, { + 'patches': ['statsmodels-0.14.1_fix_setup.patch'], + 'checksums': [ + {'statsmodels-0.14.1.tar.gz': '2260efdc1ef89f39c670a0bd8151b1d0843567781bcafec6cda0534eb47a94f6'}, + {'statsmodels-0.14.1_fix_setup.patch': '27ea0e82b9cd1162490eb2bea9606b6ca79ed559bd7e793bbd073ec09c8b0f53'}, + ], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1_fix_setup.patch b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1_fix_setup.patch new file mode 100644 index 000000000000..4021d1c0750d --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1_fix_setup.patch @@ -0,0 +1,11 @@ +diff -Nru statsmodels-0.14.1-orig/setup.py statsmodels-0.14.1/setup.py +--- statsmodels-0.14.1-orig/setup.py 2023-12-07 14:22:55.000000000 +0100 ++++ statsmodels-0.14.1/setup.py 2024-01-11 09:13:32.010072459 +0100 +@@ -394,6 +394,7 @@ + ext_modules=extensions, + maintainer_email=MAINTAINER_EMAIL, + description=DESCRIPTION, ++ version="0.14.1", + license=LICENSE, + url=URL, + download_url=DOWNLOAD_URL, From 8867d4b0e03e2aacb956f2ced1a0ca4ca9d78d02 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 11 Jan 2024 11:07:36 +0100 Subject: [PATCH 0238/1193] {vis,lang}[GCCcore/12.3.0] PyQt5 v5.15.10, SIP v6.8.1 --- .../p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb | 121 ++++++++++++++++++ .../s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb | 39 ++++++ 2 files changed, 160 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..c0514cf60931 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb @@ -0,0 +1,121 @@ +# update 5.15.10, sip6: THEMBL +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.10' + +homepage = 'https://www.riverbankcomputing.com/software/pyqt' +description = """PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. +This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [ + ('binutils', '2.40'), + ('SIP', '6.8.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Qt5', '5.15.10'), +] + + +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%s:$PYTHONPATH && " % local_pylibdir + + +local_sip_configopts_common = [ + "--no-make", + "--jobs %(parallel)s", + "--qmake-setting 'QMAKE_CXXFLAGS+=$$(CFLAGS)'", + "--qmake-setting 'QMAKE_CFLAGS+=$$(CFLAGS)'", + "--qmake-setting 'QMAKE_LFLAGS+=$$(LDFLAGS)'", + "--api-dir %(installdir)s/qsci", + "--scripts-dir %(installdir)s/bin", + "--target-dir %s" % local_pylibdir, +] + +local_pyqt5_configopts = [ + "--confirm-license", + "--no-designer-plugin", + "--no-qml-plugin", +] + local_sip_configopts_common + +local_pyqtwebengine_configopts = local_sip_configopts_common + + +default_easyblock = 'PythonPackage' + +components = [ + ('PyQt-builder', '1.15.4', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + 'checksums': ['39f8c75db17d9ce17cb6bbf3df1650b5cebc1ea4e5bd73843d21cc96612b2ae1'], + }), + ('%s_sip' % name, '12.13.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'checksums': ['7f321daf84b9c9dbca61b80e1ef37bdaffc0e93312edae2cd7da25b953971d91'], + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMake', + 'configure_cmd': 'sip-build', + 'start_dir': '%(name)s-%(version)s', + 'configure_without_installdir': True, + 'preconfigopts': local_setup_env, + 'configopts': ' '.join(local_pyqt5_configopts), + 'prebuildopts': local_setup_env + 'cd build &&', + 'preinstallopts': 'cd build &&', + 'checksums': ['d46b7804b1b10a4ff91753f8113e5b5580d2b4462f3226288e2d84497334898a'], + }), + ('PyQtWebEngine', '5.15.6', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMake', + 'configure_cmd': 'sip-build', + 'start_dir': '%(name)s-%(version)s', + 'configure_without_installdir': True, + 'preconfigopts': local_setup_env, + 'configopts': ' '.join(local_pyqtwebengine_configopts), + 'prebuildopts': local_setup_env + 'cd build &&', + 'preinstallopts': 'cd build &&', + 'checksums': ['ae241ef2a61c782939c58b52c2aea53ad99b30f3934c8358d5e0a6ebb3fd0721'], + }) +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle']], + 'dirs': ['lib/python%(pyshortver)s/site-packages', 'qsci'], +} + +postinstallcmds = [ + 'mkdir %(installdir)s/share', + 'ln -s --relative %s/%%(name)s/bindings %s' % (local_pylibdir, local_sipdir) +] + +sanity_check_commands = [ + "python -c 'import %(name)s.QtCore'", + "python -c 'import %(name)s.QtWebEngineWidgets'", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..87f98d22087a --- /dev/null +++ b/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Bart Verleye +# Center for eResearch, Auckland +# update 6.8.1: THEMBL +easyblock = 'PythonPackage' + +name = 'SIP' +version = '6.8.1' + +homepage = 'http://www.riverbankcomputing.com/software/sip/' +description = """SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3002df415e168ac3ffe393942dbc7131cb82ade50000e1526f46a88ade26f598'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('PLY', '3.11'), +] + +use_pip = True +download_dep_fail = True +local_tools = ['build', 'distinfo', 'install', 'module', 'sdist', 'wheel'] +local_tools = [] +sanity_check_paths = { + 'files': ['bin/sip-%s' % x for x in local_tools], + 'dirs': ['lib/python%(pyshortver)s/site-packages/sipbuild'], +} + +sanity_check_commands = ['sip-%s --help' % x for x in local_tools] + +options = {'modulename': 'sipbuild'} +moduleclass = 'lang' From 1bce531195d49a834a3821a007bf949a9aeb2f5f Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Jan 2024 11:28:53 +0100 Subject: [PATCH 0239/1193] matplotlib/3.8.2: Fix formatting --- .../easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb index 87330f4ad9b9..93ec6abd3812 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb @@ -62,7 +62,9 @@ exts_list = [ }), (name, version, { 'patches': ['matplotlib-3.8.2-fix_setup.patch'], - 'preinstallopts': "sed -e 's/#system_freetype = False/system_freetype = True/g' -e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg&& export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", + 'preinstallopts': "sed -e 's/#system_freetype = False/system_freetype = True/g' " + "-e 's/#system_qhull = False/system_qhull = True/g' mplsetup.cfg.template >mplsetup.cfg" + "&& export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ", 'checksums': [ {'matplotlib-3.8.2.tar.gz': '01a978b871b881ee76017152f1f1a0cbf6bd5f7b8ff8c96df0df1bd57d8755a1'}, {'matplotlib-3.8.2-fix_setup.patch': '16e1610aec49af402e324e0b71c69d6b7ae106732088318e727b48282492a932'}, From caa52a705e766595102a2a750c987ea24ec40ef0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 11 Jan 2024 11:30:41 +0100 Subject: [PATCH 0240/1193] fix style; add sanity_pip_check --- easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb index 87f98d22087a..f97983ba89b4 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb @@ -27,12 +27,13 @@ dependencies = [ use_pip = True download_dep_fail = True local_tools = ['build', 'distinfo', 'install', 'module', 'sdist', 'wheel'] -local_tools = [] sanity_check_paths = { 'files': ['bin/sip-%s' % x for x in local_tools], 'dirs': ['lib/python%(pyshortver)s/site-packages/sipbuild'], } +sanity_pip_check = True + sanity_check_commands = ['sip-%s --help' % x for x in local_tools] options = {'modulename': 'sipbuild'} From 21c4edf11319dbf035cc516e293ffeccdbfb4687 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 11 Jan 2024 11:40:39 +0100 Subject: [PATCH 0241/1193] adding easyconfigs: Zeo++-0.3-intel-2021a.eb --- .../z/Zeo++/Zeo++-0.3-intel-2021a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-2021a.eb diff --git a/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-2021a.eb b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-2021a.eb new file mode 100644 index 000000000000..0879ff7c5047 --- /dev/null +++ b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-2021a.eb @@ -0,0 +1,51 @@ +easyblock = 'MakeCp' + +name = 'Zeo++' +version = '0.3' + +homepage = 'https://www.zeoplusplus.org/' +description = """ + Zeo++ is a software package for analysis of crystalline porous materials. + Zeo++ can be used to perform geometry-based analysis of structure and + topology of the void space inside a material, + to assemble or alternate structures as well as to generate structure + representations to be used in structure similarity calculations. + Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database. + """ + +toolchain = {'name': 'intel', 'version': '2021a'} + +source_urls = ['https://github.com/mharanczyk/zeoplusplus/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0361659094ec97add5d5846f14326863293e3d9a78997ba4890719f9ffae224a'] + +builddependencies = [('binutils', '2.36.1')] + +# try building libvoro in voro++ subdir, which is required by Zeo++ +prebuildopts = "cd voro++ && make && ls src/libvoro* && cd - && " + +buildopts = "all statlib" + +files_to_copy = [ + (['network', 'framework_builder', 'molecule_to_abstract'], 'bin'), + (['voro++/src/libvoro++.a', 'libzeo++.a'], 'lib') +] + +sanity_check_paths = { + 'files': [ + 'bin/network', + 'bin/framework_builder', + 'bin/molecule_to_abstract', + 'lib/libvoro++.a', + 'lib/libzeo++.a', + ], + 'dirs': [] +} + +sanity_check_commands = [ + "network --help", + "command -v framework_builder", + "command -v molecule_to_abstract", +] + +moduleclass = 'phys' From 662e93a7b0476768cc37edc3bdd1d8c0bc50ddf0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 11 Jan 2024 12:03:52 +0100 Subject: [PATCH 0242/1193] add PLY --- .../p/PLY/PLY-3.11-GCCcore-12.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1ce6d43a7754 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 445d98d30af54a1bd0291e436c890060b9819656 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 11 Jan 2024 12:32:30 +0100 Subject: [PATCH 0243/1193] adding easyconfigs: Flask-3.0.0-GCCcore-13.2.0.eb --- .../f/Flask/Flask-3.0.0-GCCcore-13.2.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flask/Flask-3.0.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/Flask/Flask-3.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/Flask/Flask-3.0.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..8050132f2f67 --- /dev/null +++ b/easybuild/easyconfigs/f/Flask/Flask-3.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'Flask' +version = '3.0.0' + +homepage = 'https://www.palletsprojects.com/p/flask/' +description = """ +Flask is a lightweight WSGI web application framework. It is designed to make +getting started quick and easy, with the ability to scale up to complex +applications. +This module includes the Flask extensions: Flask-Cors""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('werkzeug', '3.0.1', { + 'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'], + }), + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('blinker', '1.7.0', { + 'checksums': ['e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182'], + }), + ('flask', version, { + 'checksums': ['cfadcdb638b609361d29ec22360d6070a77d7463dcb3ab08d2c2f2f168845f58'], + }), + ('Flask-Cors', '4.0.0', { + 'checksums': ['f268522fcb2f73e2ecdde1ef45e2fd5c71cc48fe03cffb4b441c6d1b40684eb0'], + }), + ('cachelib', '0.10.2', { + 'checksums': ['593faeee62a7c037d50fc835617a01b887503f972fb52b188ae7e50e9cb69740'], + }), + ('Flask-Session', '0.5.0', { + 'checksums': ['190875e6aebf2953c6803d42379ef3b934bc209ef8ef006f97aecb08f5aaeb86'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'lib' From f8b880b9a5a94c70879163af736af7c4dd7e528c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Jan 2024 13:14:59 +0100 Subject: [PATCH 0244/1193] adding easyconfigs: spdlog-1.12.0-GCCcore-13.2.0.eb --- .../s/spdlog/spdlog-1.12.0-GCCcore-13.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/spdlog/spdlog-1.12.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/spdlog/spdlog-1.12.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/spdlog/spdlog-1.12.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..5e53029c10d1 --- /dev/null +++ b/easybuild/easyconfigs/s/spdlog/spdlog-1.12.0-GCCcore-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'spdlog' +version = '1.12.0' + +homepage = 'https://github.com/gabime/spdlog' +description = 'Very fast, header-only/compiled, C++ logging library.' +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/gabime/spdlog/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4dccf2d10f410c1e2feaff89966bfc49a1abb29ef6f08246335b110e001e09a9'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['include/spdlog/spdlog.h'], + 'dirs': ['lib64/cmake', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From a092fd13256c7d848e035859194f7d2bf65c6f2a Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Jan 2024 13:16:06 +0100 Subject: [PATCH 0245/1193] adding easyconfigs: fmt-10.2.0-GCCcore-13.2.0.eb --- .../f/fmt/fmt-10.2.0-GCCcore-13.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/f/fmt/fmt-10.2.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/f/fmt/fmt-10.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/f/fmt/fmt-10.2.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..718920c630a2 --- /dev/null +++ b/easybuild/easyconfigs/f/fmt/fmt-10.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'fmt' +version = '10.2.0' + +homepage = 'http://fmtlib.net/' +description = "fmt (formerly cppformat) is an open-source formatting library." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/fmtlib/fmt/releases/download/%(version)s/'] +sources = ['fmt-%(version)s.zip'] +checksums = ['8a942861a94f8461a280f823041cde8f620a6d8b0e0aacc98c15bb5a9dd92399'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['lib/libfmt.a'], + 'dirs': ['include/fmt', 'lib/cmake'], +} + +moduleclass = 'lib' From 674f898ed07f4bf029dc8708cdc1ba0160811d0c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Jan 2024 13:17:32 +0100 Subject: [PATCH 0246/1193] adding easyconfigs: libtirpc-1.3.4-GCCcore-13.2.0.eb --- .../libtirpc/libtirpc-1.3.4-GCCcore-13.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.4-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..25da96b4179a --- /dev/null +++ b/easybuild/easyconfigs/l/libtirpc/libtirpc-1.3.4-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libtirpc' +version = '1.3.4' + +homepage = 'https://sourceforge.net/projects/libtirpc/' +description = "Libtirpc is a port of Suns Transport-Independent RPC library to Linux." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['1e0b0c7231c5fa122e06c0609a76723664d068b0dba3b8219b63e6340b347860'] + +configopts = '--enable-static --enable-shared --disable-gssapi' + +builddependencies = [ + ('binutils', '2.40') +] + +sanity_check_paths = { + 'files': ['lib/libtirpc.%s' % (x,) for x in ['a', SHLIB_EXT]], + 'dirs': ['include/tirpc', 'lib'], +} + +modextrapaths = {'CPATH': 'include/tirpc'} + +moduleclass = 'lib' From 52234821f975e75c55edeba1368c18b3997ed1fa Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 11 Jan 2024 13:18:57 +0100 Subject: [PATCH 0247/1193] adding easyconfigs: libMemcached-1.0.18-GCCcore-13.2.0.eb --- .../libMemcached-1.0.18-GCCcore-13.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/l/libMemcached/libMemcached-1.0.18-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libMemcached/libMemcached-1.0.18-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libMemcached/libMemcached-1.0.18-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..83b4f18c5cf0 --- /dev/null +++ b/easybuild/easyconfigs/l/libMemcached/libMemcached-1.0.18-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'libMemcached' +version = '1.0.18' + +homepage = 'https://memcached.org' +description = """libMemcached is an open source C/C++ client library and tools for + the memcached server (http://danga.com/memcached). It has been designed to be light + on memory usage, thread safe, and provide full access to server side methods.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://launchpad.net/libmemcached/%(version_major_minor)s/%(version)s/+download/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['libMemcached-1.0.18-bugfix-comparison.patch'] +checksums = [ + 'e22c0bb032fde08f53de9ffbc5a128233041d9f33b5de022c0978a2149885f82', # libmemcached-1.0.18.tar.gz + '92a105c91bf0c6a7b3d7aa35a041a071db07f777f5b812ed2499ffc892c3fe5a', # libMemcached-1.0.18-bugfix-comparison.patch +] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['lib/libmemcached.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'tools' From 51eb7e7782bcb99acff2efe4806aabd730514316 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 11 Jan 2024 13:39:01 +0100 Subject: [PATCH 0248/1193] adding easyconfigs: OpenFOAM-v2312-foss-2023a.eb, KaHIP-3.16-gompi-2023a.eb and patches: OpenFOAM-v2312-cleanup.patch --- .../k/KaHIP/KaHIP-3.16-gompi-2023a.eb | 28 +++ .../o/OpenFOAM/OpenFOAM-v2312-cleanup.patch | 178 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb | 46 +++++ 3 files changed, 252 insertions(+) create mode 100644 easybuild/easyconfigs/k/KaHIP/KaHIP-3.16-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-cleanup.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb diff --git a/easybuild/easyconfigs/k/KaHIP/KaHIP-3.16-gompi-2023a.eb b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.16-gompi-2023a.eb new file mode 100644 index 000000000000..f631384b6804 --- /dev/null +++ b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.16-gompi-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'KaHIP' +version = '3.16' + +homepage = 'https://kahip.github.io/' +description = """The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/KaHIP/KaHIP/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b0ef72a26968d37d9baa1304f7a113b61e925966a15e86578d44e26786e76c75'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ["lib/libkahip_static.a", "lib/libkahip.%s" % SHLIB_EXT] + + ["lib/libparhip_interface_static.a", "lib/libparhip_interface.%s" % SHLIB_EXT] + + ["include/%s" % x for x in ["kaHIP_interface.h", "parhip_interface.h"]], + 'dirs': [], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-cleanup.patch new file mode 100644 index 000000000000..7d4add901e1b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-cleanup.patch @@ -0,0 +1,178 @@ +# Replaces OpenFOAM third-party libraries with EASYBUILD variants. +# Uses the OpenFOAM prefs mechanism and the FOAM_CONFIG_ETC variable +# to define the preferred settings without patching the original files +# +# Authors: Mark Olesen +# +# ChangeLog: +# - v2312 - activate METIS, KaHIP and readline support in etc/config.sh/setup +# author: Jiri Furst +# +# ------------------------------------------------------------------------- +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/prefs.sh 2020-12-14 10:02:26.488430802 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FOAM_CONFIG_ETC="etc/easybuild" ++ ++export WM_MPLIB=EASYBUILDMPI ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/CGAL 2020-12-14 10:10:55.991841204 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++export BOOST_ARCH_PATH="$EBROOTBOOST" ++export CGAL_ARCH_PATH="$EBROOTCGAL" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/FFTW 2020-12-14 10:10:53.735843322 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export FFTW_ARCH_PATH="$EBROOTFFTW" ++ ++##EasyBuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/metis 2020-12-11 21:23:28.774934024 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++METIS_VERSION="metis-$EBVERSIONMETIS" ++[ -d "$METIS_ARCH_PATH" ] || METIS_ARCH_PATH="$EBROOTMETIS" ++ ++##Easybuild## +--- /dev/null 2022-12-01 18:21:35.103878336 +0100 ++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip 2022-12-12 20:24:07.538408981 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++KAHIP_VERSION="kahip-$EBVERSIONKAHIP" ++export KAHIP_ARCH_PATH="$EBROOTKAHIP" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/readline 2020-12-11 21:23:22.534951043 +0100 +@@ -0,0 +1,5 @@ ++##Easybuild## settings -*- sh -*- ++ ++export READLINE_ARCH_PATH="$EBROOTLIBREADLINE" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/scotch 2020-12-11 21:23:17.586964539 +0100 +@@ -0,0 +1,7 @@ ++##Easybuild## settings -*- sh -*- ++ ++export SCOTCH_VERSION="scotch_$EBVERSIONSCOTCH" ++export SCOTCH_ARCH_PATH="$EBROOTSCOTCH" ++[ -d "$SCOTCH_ARCH_PATH" ] || SCOTCH_ARCH_PATH="$SCOTCH_ROOT" ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/vtk 2020-12-11 21:22:55.463024882 +0100 +@@ -0,0 +1,9 @@ ++##Easybuild## settings -*- sh -*- ++ ++export VTK_DIR="$EBROOTVTK" ++export MESA_ARCH_PATH="$EBROOTMESA" ++ ++# Define paraview-mesa directory as required ++unset ParaView_MESA_DIR ++ ++##Easybuild## +--- /dev/null 2020-12-14 09:05:45.272769166 +0100 ++++ OpenFOAM-v2012/etc/easybuild/config.sh/paraview 2020-12-14 10:13:53.583674383 +0100 +@@ -0,0 +1,75 @@ ++##Easybuild## settings -*- sh -*- ++# ++# Largely a knockoff of the OpenFOAM etc/config.sh/paraview-system ++# readjusted for easybuild ++# ++# Copyright (C) 2020 OpenCFD Ltd. ++# ++#------------------------------------------------------------------------------ ++# Compiler-specific location for ThirdParty installations ++archDir="$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER" ++ ++# Clean path and library path of previous settings ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++eval \ ++ "$($WM_PROJECT_DIR/bin/foamCleanPath -sh-env=LD_LIBRARY_PATH \ ++ $ParaView_DIR $archDir/ParaView- $archDir/qt-)" ++ ++ ++#------------------------------------------------------------------------------ ++ ++##Easybuild## settings ++ ++ParaView_VERSION="$EBVERSIONPARAVIEW" ++export ParaView_DIR="$EBROOTPARAVIEW" ++ ++#------------------------------------------------------------------------------ ++ ++unset PV_PLUGIN_PATH ++ ++# Set API to correspond to VERSION ++# pv_api is . from ParaView_VERSION ++#- ++# Extract API from VERSION ++pv_api=$(echo "$ParaView_VERSION" | \ ++ sed -ne 's/^[^0-9]*\([0-9][0-9]*\.[0-9][0-9]*\).*$/\1/p') ++ ++pv_plugin_dir="$FOAM_LIBBIN/paraview-$pv_api" ++ ++# Set paths if binaries are present ++if [ -r "$ParaView_DIR" ] ++then ++ export PATH="$ParaView_DIR/bin:$PATH" ++ ++ # ParaView libraries ++ # - 5.5 and later: lib/, but could also be lib64/ ++ for libDir in lib64 lib ++ do ++ pvLibDir="$libDir/paraview-$pv_api" ++ if [ -d "$ParaView_DIR/$pvLibDir" ] ++ then ++ export LD_LIBRARY_PATH="$ParaView_DIR/$libDir:$LD_LIBRARY_PATH" ++ break ++ fi ++ done ++ ++ # OpenFOAM plugin directory must be the first in PV_PLUGIN_PATH ++ # and have paraview-major.minor encoded in its name ++ if [ -d "$pv_plugin_dir" ] ++ then ++ export PV_PLUGIN_PATH="$pv_plugin_dir" ++ fi ++fi ++ ++ ++#------------------------------------------------------------------------------ ++ ++unset ParaView_VERSION ++ ++unset archDir libDir ++unset pv_api pv_plugin_dir pvLibDir ++ ++#------------------------------------------------------------------------------ +--- OpenFOAM-v2312/etc/config.sh/setup.orig 2024-01-11 09:49:24.823571481 +0100 ++++ OpenFOAM-v2312/etc/config.sh/setup 2024-01-11 09:51:40.545969774 +0100 +@@ -207,7 +207,9 @@ + _foamEtc -config CGAL + _foamEtc -config scotch + _foamEtc -config FFTW +- ++_foamEtc -config metis ++_foamEtc -config kahip ++_foamEtc -config readline + + # Finalize library paths + # ~~~~~~~~~~~~~~~~~~~~~~ + diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb new file mode 100644 index 000000000000..661327ff9a6e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2312-foss-2023a.eb @@ -0,0 +1,46 @@ +name = 'OpenFOAM' +version = 'v2312' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++14', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2312-cleanup.patch', 1), + ('OpenFOAM-v2212-wmake-OpenMPI.patch', 1), +] +checksums = [ + {'OpenFOAM-v2312.tgz': 'f113183a4d027c93939212af8967053c5f8fe76fb62e5848cb11bbcf8e829552'}, + {'OpenFOAM-v2312-cleanup.patch': 'f1389e5d89510209d99d35917a4a6bd727134121bbbaa12471235042e675dacf'}, + {'OpenFOAM-v2212-wmake-OpenMPI.patch': '4f5110e98df1f057dc4b478a004e4ae2dc5cc763899f0d3ceb6773315c5c8ba9'}, +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.26.3'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('ncurses', '6.4'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('KaHIP', '3.16'), + ('CGAL', '5.6'), + ('ParaView', '5.11.2'), + ('gnuplot', '5.4.8'), +] + +moduleclass = 'cae' From 8f2725f1c64a90e801d2ca18262997482f16c5e9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 11 Jan 2024 15:07:27 +0100 Subject: [PATCH 0249/1193] PyQt-builde as builddependency, not as component --- .../PyQt-builder-1.15.4-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ .../p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb | 24 ++++++-------- 2 files changed, 43 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..e54ad0fc4879 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/01 +easyblock = 'PythonBundle' + +name = 'PyQt-builder' +version = '1.15.4' + +homepage = 'http://www.example.com' +description = """ +PyQt-builder is the PEP 517 compliant build system for PyQt and projects that extend PyQt. It extends the SIP build system and uses Qt’s qmake to perform the actual compilation and installation of extension modules. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.3'), + ('SIP', '6.8.1'), +] + + +exts_list = [ + (name, version, {'modulename': 'pyqtbuild'}) +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb index c0514cf60931..877d70023535 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb @@ -1,5 +1,5 @@ # update 5.15.10, sip6: THEMBL -easyblock = 'Bundle' +easyblock = 'PythonBundle' name = 'PyQt5' version = '5.15.10' @@ -13,7 +13,8 @@ toolchainopts = {'cstd': 'c++11'} builddependencies = [ ('binutils', '2.40'), - ('SIP', '6.8.1'), + #('SIP', '6.8.1'), + ('PyQt-builder', '1.15.4'), ] dependencies = [ ('Python', '3.11.3'), @@ -52,13 +53,6 @@ local_pyqtwebengine_configopts = local_sip_configopts_common default_easyblock = 'PythonPackage' components = [ - ('PyQt-builder', '1.15.4', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'start_dir': 'PyQt-builder-%(version)s', - 'use_pip': True, - 'checksums': ['39f8c75db17d9ce17cb6bbf3df1650b5cebc1ea4e5bd73843d21cc96612b2ae1'], - }), ('%s_sip' % name, '12.13.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], @@ -94,16 +88,18 @@ components = [ }) ] +postinstallcmds = [ + 'mkdir %(installdir)s/share', + 'ln -s --relative %s/%%(name)s/bindings %s' % (local_pylibdir, local_sipdir) +] + sanity_check_paths = { 'files': ['bin/%s' % x for x in [ - 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle']], + 'pyrcc5', 'pyuic5', 'pylupdate5']], 'dirs': ['lib/python%(pyshortver)s/site-packages', 'qsci'], } -postinstallcmds = [ - 'mkdir %(installdir)s/share', - 'ln -s --relative %s/%%(name)s/bindings %s' % (local_pylibdir, local_sipdir) -] +sanity_pip_check = True sanity_check_commands = [ "python -c 'import %(name)s.QtCore'", From 6451ac106d71e5602986f7091c8ec52c7ccf363c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 11 Jan 2024 15:19:45 +0100 Subject: [PATCH 0250/1193] adding easyconfigs: GPAW-24.1.0-foss-2022a.eb, GPAW-24.1.0-intel-2022a.eb --- .../g/GPAW/GPAW-24.1.0-foss-2022a.eb | 49 +++++++++++++++++++ .../g/GPAW/GPAW-24.1.0-intel-2022a.eb | 48 ++++++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2022a.eb new file mode 100644 index 000000000000..42c48960ad76 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.1.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.1.0.tar.gz': '14150bdc4b098060164b569699577ff57769a42783d79d37c9eb6cfe9cd506ea'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('libvdwxc', '0.4.0'), + ('ELPA', '2021.11.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2022a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2022a.eb new file mode 100644 index 000000000000..739c9c2b18b0 --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2022a.eb @@ -0,0 +1,48 @@ +easyblock = "PythonPackage" + +name = 'GPAW' +version = '24.1.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) + method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or + atom-centered basis-functions.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': False} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('GPAW-20.1.0-Add-Easybuild-configuration-files.patch', 1), +] +checksums = [ + {'gpaw-24.1.0.tar.gz': '14150bdc4b098060164b569699577ff57769a42783d79d37c9eb6cfe9cd506ea'}, + {'GPAW-20.1.0-Add-Easybuild-configuration-files.patch': + '2b337399479bf018a86156ed073dd7a78ec8c0df1f28b015f9284c6bf9fa5f15'}, +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ASE', '3.22.1'), + ('libxc', '5.2.3'), + ('ELPA', '2021.11.001'), + ('PyYAML', '6.0'), + ('GPAW-setups', '0.9.20000', '', SYSTEM), +] + +prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' +preinstallopts = prebuildopts + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/gpaw%s' % x for x in ['', '-analyse-basis', '-basis', '-plot-parallel-timings', + '-runscript', '-setup', '-upfplot']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'chem' From 328e314a4484f7d4f1c8416b829d2ae635b7eb11 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 11 Jan 2024 15:24:26 +0100 Subject: [PATCH 0251/1193] fix style --- .../p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb | 5 +++-- .../easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb | 1 - 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb index e54ad0fc4879..afcc89671b77 100644 --- a/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb @@ -5,8 +5,9 @@ name = 'PyQt-builder' version = '1.15.4' homepage = 'http://www.example.com' -description = """ -PyQt-builder is the PEP 517 compliant build system for PyQt and projects that extend PyQt. It extends the SIP build system and uses Qt’s qmake to perform the actual compilation and installation of extension modules. +description = """PyQt-builder is the PEP 517 compliant build system for PyQt and projects that +extend PyQt. It extends the SIP build system and uses Qt’s qmake to perform the +actual compilation and installation of extension modules. """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb index 877d70023535..e131e085120e 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb @@ -13,7 +13,6 @@ toolchainopts = {'cstd': 'c++11'} builddependencies = [ ('binutils', '2.40'), - #('SIP', '6.8.1'), ('PyQt-builder', '1.15.4'), ] dependencies = [ From bb2ff68906788dd779387847d7fc4eb5b7416b66 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 11 Jan 2024 15:59:32 +0100 Subject: [PATCH 0252/1193] checksum --- .../p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb | 5 ++++- .../easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb | 3 ++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb index afcc89671b77..dfef8b1802c2 100644 --- a/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt-builder/PyQt-builder-1.15.4-GCCcore-12.3.0.eb @@ -20,7 +20,10 @@ dependencies = [ exts_list = [ - (name, version, {'modulename': 'pyqtbuild'}) + (name, version, { + 'modulename': 'pyqtbuild', + 'checksums': ['39f8c75db17d9ce17cb6bbf3df1650b5cebc1ea4e5bd73843d21cc96612b2ae1'], + }), ] use_pip = True diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb index e131e085120e..6d22a9bf0501 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb @@ -98,6 +98,8 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'qsci'], } +use_pip = True + sanity_pip_check = True sanity_check_commands = [ @@ -109,7 +111,6 @@ sanity_check_commands = [ ] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', 'QT_INSTALL_DATA': 'qsci', } From 72cd1a54c829587fd1fb5ce73403a7294f14fe22 Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Thu, 11 Jan 2024 16:15:35 +0100 Subject: [PATCH 0253/1193] adding easyconfigs: EnergyPlus-23.2.0-foss-2022a.eb --- .../EnergyPlus-23.2.0-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb b/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb new file mode 100644 index 000000000000..203938a54a60 --- /dev/null +++ b/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'EnergyPlus' +version = '23.2.0' + +homepage = 'https://energyplus.net/' + +description = """EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and water use in buildings.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': False, 'openmp': True} + +source_urls = ['https://github.com/NREL/%(name)s/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f4df81d8b233ee511276d471c5754b5e9de3080128b8162cf47d72349d549315'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('X11', '20220504'), +] + +configopts = '-DBUILD_FORTRAN=yes -DLINK_WITH_PYTHON=yes ' + +install_target_subdir = 'bin' + +postinstallcmds = ['ln -s ${EBROOTPYTHON}/lib/python%(pyshortver)s %(installdir)s/bin/python_standard_lib'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [ + 'bin', + 'bin/python_standard_lib', + ], +} + +moduleclass = 'phys' From 808f9f8a8cfcc9ffe6a9a0526ce24b889ade8eff Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Thu, 11 Jan 2024 16:37:38 +0100 Subject: [PATCH 0254/1193] Cleaned up formatting --- .../easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb b/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb index 203938a54a60..bb70a53dd72a 100644 --- a/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb @@ -5,7 +5,9 @@ version = '23.2.0' homepage = 'https://energyplus.net/' -description = """EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and water use in buildings.""" +description = """EnergyPlus is a whole building energy simulation program that engineers, architects, and researchers + use to model both energy consumption—for heating, cooling, ventilation, lighting and plug and process loads—and +water use in buildings.""" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'usempi': False, 'openmp': True} From 8e98d8a2131f1686135453912cccd8e94d3d9566 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 11 Jan 2024 18:48:24 +0100 Subject: [PATCH 0255/1193] adding easyconfigs: Dice-20240101-foss-2022b.eb and patches: Dice-20240101_deprecated-global-placeholders.patch --- .../d/Dice/Dice-20240101-foss-2022b.eb | 52 +++++++++++++++++++ ...40101_deprecated-global-placeholders.patch | 49 +++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb create mode 100644 easybuild/easyconfigs/d/Dice/Dice-20240101_deprecated-global-placeholders.patch diff --git a/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb b/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb new file mode 100644 index 000000000000..8e3d229477ab --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' + +name = 'Dice' +version = '20240101' +_commit = '823f303719efaee441b8bea3e5f9d5a159b58939' + +homepage = 'https://github.com/sanshar/Dice' +description = """Dice contains code for performing SHCI, VMC, GFMC, DMC, FCIQMC, stochastic MRCI +and SC-NEVPT2, and AFQMC calculations with a focus on ab initio systems.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'cstd': 'c++14'} + +github_account = 'sanshar' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = ['Dice-20221025_icpt-mkl-to-flexiblas.patch', 'Dice-20240101_deprecated-global-placeholders.patch'] +checksums = [ + {'Dice-20240101.tar.gz': 'f7a60c0df1ba1d27e60b478a15f9ef0e5282a030cc5acc520470eef4f55940b9'}, + {'Dice-20221025_icpt-mkl-to-flexiblas.patch': 'a712913e5b372017be0ea7508479094e96f06c0cfd46d0bfe61d85ef42cd1386'}, + {'Dice-20240101_deprecated-global-placeholders.patch': + 'b628e1883b033ec580aba272be427d10f3e54231f47d4d81eb0c878de24b49b1'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('git', '2.38.1', '-nodocs'), +] + +dependencies = [ + ('Boost.MPI', '1.81.0'), + ('HDF5', '1.14.0'), +] + +# Use build environment defined by EB +prebuildopts = "sed -i 's/^FLAGS_BASE =.*/FLAGS_BASE=$(CXXFLAGS) -g -w -I. $(CPPFLAGS)/' Makefile && " +buildopts = 'CXX="$MPICXX" USE_INTEL="no" HAS_AVX2="no" ' # avoid changes to -march +buildopts += 'INCLUDE_MKL="-I${EBROOTOPENBLAS}/include" LIB_MKL="${LIBBLAS}" ' # use OpenBLAS +buildopts += 'GIT_BRANCH="master" GIT_HASH="%s"' % _commit +buildopts += 'BOOST="${EBROOTBOOSTMPI}" ' +buildopts += 'EIGEN="${EBROOTEIGEN}/include" ' +buildopts += 'HDF5="${EBROOTHDF5}" ' + +files_to_copy = ['bin'] + +_binaries = ['Dice', 'DQMC', 'GFMC', 'ICPT', 'VMC', 'ZDice2', 'ZSHCI'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/d/Dice/Dice-20240101_deprecated-global-placeholders.patch b/easybuild/easyconfigs/d/Dice/Dice-20240101_deprecated-global-placeholders.patch new file mode 100644 index 000000000000..9a474df63c30 --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20240101_deprecated-global-placeholders.patch @@ -0,0 +1,49 @@ +resolve Error: "pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior." +define BOOST_BIND_GLOBAL_PLACEHOLDERS +replace #include with #include +diff -ru Dice.orig/ZSHCI/Hmult.h Dice/ZSHCI/Hmult.h +--- Dice.orig/ZSHCI/Hmult.h 2024-01-11 17:10:03.915355000 +0100 ++++ Dice/ZSHCI/Hmult.h 2024-01-11 17:20:04.223600142 +0100 +@@ -32,6 +32,7 @@ + #include + #include "SHCISortMpiUtils.h" + #include "SHCImake4cHamiltonian.h" ++#define BOOST_BIND_GLOBAL_PLACEHOLDERS + + using namespace Eigen; + using namespace std; +diff -ru Dice.orig/ZSHCI/iowrapper.h Dice/ZSHCI/iowrapper.h +--- Dice.orig/ZSHCI/iowrapper.h 2024-01-11 17:10:03.926065371 +0100 ++++ Dice/ZSHCI/iowrapper.h 2024-01-11 17:50:17.289606580 +0100 +@@ -18,6 +18,7 @@ + */ + #ifndef IOWRAPPER_HEADER_H + #define IOWRAPPER_HEADER_H ++#define BOOST_BIND_GLOBAL_PLACEHOLDERS + #include + #include + #include +diff -ru Dice.orig/ZSHCI/SHCI.cpp Dice/ZSHCI/SHCI.cpp +--- Dice.orig/ZSHCI/SHCI.cpp 2024-01-11 17:10:03.917251803 +0100 ++++ Dice/ZSHCI/SHCI.cpp 2024-01-11 17:19:30.845898274 +0100 +@@ -59,7 +59,7 @@ + #include "symmetry.h" + MatrixXd symmetry::product_table; + #include +-#include ++#include + + // Initialize + using namespace Eigen; +diff -ru Dice.orig/ZSHCI/symmetry.cpp Dice/ZSHCI/symmetry.cpp +--- Dice.orig/ZSHCI/symmetry.cpp 2024-01-11 17:10:03.927561000 +0100 ++++ Dice/ZSHCI/symmetry.cpp 2024-01-11 17:38:01.888632035 +0100 +@@ -25,7 +25,7 @@ + #include + #include + #include +-#include ++#include + #include + + #include "integral.h" From abbb804f7ce051154523e88d994f07d8eb737e25 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 11 Jan 2024 19:06:42 +0100 Subject: [PATCH 0256/1193] update checksums --- easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb b/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb index 8e3d229477ab..2ad0da886127 100644 --- a/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb +++ b/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb @@ -19,7 +19,7 @@ checksums = [ {'Dice-20240101.tar.gz': 'f7a60c0df1ba1d27e60b478a15f9ef0e5282a030cc5acc520470eef4f55940b9'}, {'Dice-20221025_icpt-mkl-to-flexiblas.patch': 'a712913e5b372017be0ea7508479094e96f06c0cfd46d0bfe61d85ef42cd1386'}, {'Dice-20240101_deprecated-global-placeholders.patch': - 'b628e1883b033ec580aba272be427d10f3e54231f47d4d81eb0c878de24b49b1'}, + 'fbf4037e928a57e737faed95dc7d6e1e5cdb8cee8db48503268d250a34c12ccc'}, ] builddependencies = [ From 8fd5285537344f4fcdfb1f43c9b9b12ad905f69f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 11 Jan 2024 19:20:14 +0100 Subject: [PATCH 0257/1193] adding easyconfigs: NECI-20230620-foss-2022b.eb --- .../n/NECI/NECI-20230620-foss-2022b.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb new file mode 100644 index 000000000000..02de75ee27ce --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMakeCp' +name = 'NECI' +version = '20230620' +_commit = '558e88c5ae6c30d0505a9badbc69111be0866ba1' + +homepage = 'https://github.com/ghb24/NECI_STABLE' +description = """Standalone NECI codebase designed for FCIQMC and other stochastic quantum +chemistry methods.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/ghb24', + 'repo_name': 'NECI_STABLE', + 'recursive': True, + 'commit': _commit, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['db8533219369600dcdb82b6d56f1f02a5e0058be6cc26bc26597d3471162d614'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +dependencies = [ + ('HDF5', '1.14.0'), +] + +# enable support for HDF5 +configopts = "-DENABLE_HDF5=ON" + +test_cmd = 'ctest' +runtest = '-j' + +files_to_copy = ['bin', 'lib', (['modules'], 'include')] + +_binaries = ['dneci', 'kdneci', 'kmneci', 'kneci', 'mneci', 'neci'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + ['lib/lib%s.a' % x for x in _binaries], + 'dirs': ['include'], +} + +moduleclass = 'chem' From 114fd43ca20ff95279a5110c15b65b870d7f89ec Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 11 Jan 2024 20:02:02 +0100 Subject: [PATCH 0258/1193] Delete netCDF-4.9.2-gompi-2023b.eb (was already merged) --- .../n/netCDF/netCDF-4.9.2-gompi-2023b.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb deleted file mode 100644 index ec41aadb943f..000000000000 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2023b.eb +++ /dev/null @@ -1,57 +0,0 @@ -name = 'netCDF' -version = '4.9.2' - -homepage = 'https://www.unidata.ucar.edu/software/netcdf/' -description = """NetCDF (network Common Data Form) is a set of software libraries - and machine-independent data formats that support the creation, access, and sharing of array-oriented - scientific data.""" - -toolchain = {'name': 'gompi', 'version': '2023b'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - 'netCDF-4.9.0_skip-nasa-test.patch', -] -checksums = [ - {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, - {'netCDF-4.9.0_skip-nasa-test.patch': '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, -] - -builddependencies = [ - ('Autotools', '20220317'), - ('CMake', '3.27.6'), - ('Doxygen', '1.9.8'), -] - -dependencies = [ - ('HDF5', '1.14.3'), - ('cURL', '8.3.0'), - ('Szip', '2.1.1'), - ('zstd', '1.5.5'), - ('bzip2', '1.0.8'), - ('libxml2', '2.11.5'), -] - -# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso -# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 -# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 -preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" - " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" - " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" - " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") - -# make sure both static and shared libs are built -# and disable "remote" tests that access a unreliable external test server over internet -configopts = [ - "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", - "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", -] - -# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests -pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " - -runtest = 'test' - -moduleclass = 'data' From 892d5e4383c3082cebc5b6b65f36b600204fa33e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 11 Jan 2024 20:14:13 +0100 Subject: [PATCH 0259/1193] change homepage for argtable (#19551) * change homepage * add missing checksum --- .../easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb | 2 +- .../easyconfigs/a/argtable/argtable-2.13-GCCcore-8.2.0.eb | 2 +- .../easyconfigs/a/argtable/argtable-2.13-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb | 3 ++- easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2018b.eb | 2 +- easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018a.eb | 2 +- easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb | 2 +- 8 files changed, 9 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb index 896c62218854..bf680a03bd20 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb index 3192e22d1106..916da386d287 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-10.3.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.2.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.2.0.eb index 61a92219cfba..6707d037e6d6 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.2.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.3.0.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.3.0.eb index fd585b367bd7..06fed40eb7b4 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-GCCcore-8.3.0.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb index 2eb391926ffb..389cfaf110a2 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2016b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ @@ -18,6 +18,7 @@ toolchain = {'name': 'foss', 'version': '2016b'} source_urls = [SOURCEFORGE_SOURCE] sources = ['%s%s.tar.gz' % (name, version.replace('.', '-'))] +checksums = ['8f77e8a7ced5301af6e22f47302fdbc3b1ff41f2b83c43c77ae5ca041771ddbf'] sanity_check_paths = { 'files': ['lib/libargtable2.so', 'lib/libargtable2.la'], diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2018b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2018b.eb index 8243740e61e0..dd5c88dcd040 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2018b.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-foss-2018b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018a.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018a.eb index 2aedcb78674e..d551fd9aed2a 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018a.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018a.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ diff --git a/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb b/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb index 0c9bb3bc28ee..fdeb13a11186 100644 --- a/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb +++ b/easybuild/easyconfigs/a/argtable/argtable-2.13-intel-2018b.eb @@ -10,7 +10,7 @@ easyblock = 'ConfigureMake' name = 'argtable' version = '2.13' -homepage = 'http://argtable.sourceforge.net/' +homepage = 'https://argtable.sourceforge.io/' description = """ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. """ From f3be72c4f45e14ef05f92753c0efa95a24b7ed81 Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Fri, 12 Jan 2024 10:30:03 +0100 Subject: [PATCH 0260/1193] Added sanity checks --- .../e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb b/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb index bb70a53dd72a..fd505046f573 100644 --- a/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EnergyPlus/EnergyPlus-23.2.0-foss-2022a.eb @@ -40,4 +40,10 @@ sanity_check_paths = { ], } +sanity_check_commands = [ + 'energyplus --help', + 'energyplus-%(version)s --help', + 'ConvertInputFormat --help', +] + moduleclass = 'phys' From 288e7452dbf93752621b8b3df0ef3db27c92411f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 12 Jan 2024 14:07:51 +0100 Subject: [PATCH 0261/1193] Change version of PyTorch to the one in the repo --- ...021b-CUDA-11.4.1.eb => Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/v/Vamb/{Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb => Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb} (97%) diff --git a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb similarity index 97% rename from easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb rename to easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb index 628af9a2b091..7f596a503167 100644 --- a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb @@ -13,7 +13,7 @@ the latent representation.""" toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ - ('CUDA', '11.4.1', '', SYSTEM), + ('CUDA', '11.5.2', '', SYSTEM), ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('Pysam', '0.18.0'), From 5179773a733e321adeb8228d3ce48c60281e0dc5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jan 2024 14:22:35 +0100 Subject: [PATCH 0262/1193] fix name for DETONATE in existing easyconfig --- .../DETONATE-1.11-intel-2017b.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/d/{detonate/detonate-1.11-intel-2017b.eb => DETONATE/DETONATE-1.11-intel-2017b.eb} (97%) diff --git a/easybuild/easyconfigs/d/detonate/detonate-1.11-intel-2017b.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-intel-2017b.eb similarity index 97% rename from easybuild/easyconfigs/d/detonate/detonate-1.11-intel-2017b.eb rename to easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-intel-2017b.eb index d15f2a4c8de5..a7078e2b055c 100644 --- a/easybuild/easyconfigs/d/detonate/detonate-1.11-intel-2017b.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-intel-2017b.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'detonate' +name = 'DETONATE' version = '1.11' homepage = 'http://deweylab.biostat.wisc.edu/detonate/' @@ -13,7 +13,7 @@ toolchain = {'name': 'intel', 'version': '2017b'} toolchainopts = {'cstd': 'c++11'} source_urls = ['http://deweylab.biostat.wisc.edu/detonate/'] -sources = [SOURCE_TAR_GZ] +sources = [SOURCELOWER_TAR_GZ] patches = [ 'detonate-%(version)s_fix-deps.patch', 'detonate-%(version)s_Intel-fixes.patch', From 5bae03fd53331fab8f279e63155e986390727be2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jan 2024 14:39:17 +0100 Subject: [PATCH 0263/1193] also move patch files for DETONATE --- .../d/{detonate => DETONATE}/detonate-1.11_Intel-fixes.patch | 0 .../d/{detonate => DETONATE}/detonate-1.11_fix-deps.patch | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/d/{detonate => DETONATE}/detonate-1.11_Intel-fixes.patch (100%) rename easybuild/easyconfigs/d/{detonate => DETONATE}/detonate-1.11_fix-deps.patch (100%) diff --git a/easybuild/easyconfigs/d/detonate/detonate-1.11_Intel-fixes.patch b/easybuild/easyconfigs/d/DETONATE/detonate-1.11_Intel-fixes.patch similarity index 100% rename from easybuild/easyconfigs/d/detonate/detonate-1.11_Intel-fixes.patch rename to easybuild/easyconfigs/d/DETONATE/detonate-1.11_Intel-fixes.patch diff --git a/easybuild/easyconfigs/d/detonate/detonate-1.11_fix-deps.patch b/easybuild/easyconfigs/d/DETONATE/detonate-1.11_fix-deps.patch similarity index 100% rename from easybuild/easyconfigs/d/detonate/detonate-1.11_fix-deps.patch rename to easybuild/easyconfigs/d/DETONATE/detonate-1.11_fix-deps.patch From 7a2564a7b19badd827f523a45cb83984d0eabc25 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 12 Jan 2024 14:53:06 +0100 Subject: [PATCH 0264/1193] adding easyconfigs: PASA-2.5.3-foss-2022b.eb, pblat-2.5.1-foss-2022b.eb --- .../p/PASA/PASA-2.5.3-foss-2022b.eb | 43 +++++++++++++++++++ .../p/pblat/pblat-2.5.1-foss-2022b.eb | 41 ++++++++++++++++++ 2 files changed, 84 insertions(+) create mode 100644 easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb new file mode 100644 index 000000000000..3dad7ad19d05 --- /dev/null +++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PASA' +version = '2.5.3' + +homepage = 'https://github.com/PASApipeline/PASApipeline' +description = """PASA, acronym for Program to Assemble Spliced Alignments (and pronounced 'pass-uh'), + is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript + sequences to automatically model gene structures, and to maintain gene structure annotation consistent + with the most recently available experimental sequence data. PASA also identifies and classifies all + splicing variations supported by the transcript alignments.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/PASApipeline/PASApipeline/archive/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['9b2f6a301b73fd8c713af0977cf6e97f3d928988d6b79715ebe81e19b51152eb'] + +dependencies = [ + ('SQLite', '3.39.4'), + ('GMAP-GSNAP', '2023-04-20'), + ('pblat', '2.5.1'), + ('minimap2', '2.26'), + ('FASTA', '36.3.8i'), +] + +buildininstalldir = True + +skipsteps = ['configure', 'install'] + +unpack_options = '--strip-components=1' + +local_bins = ['%(namelower)s', 'cdbfasta', 'cdbyank', 'cln2qual', 'mdust', + 'psx', 'seqclean', 'seqclean.psx', 'slclust', 'trimpoly'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['command -v %(namelower)s'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb new file mode 100644 index 000000000000..1fee4320100b --- /dev/null +++ b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'pblat' +version = '2.5.1' + +homepage = 'https://github.com/icebert/pblat' +description = """When the query file format is fasta, you can specify many threads to process it. + It can reduce run time linearly, and use almost equal memory as the original blat program. + This is useful when you blat a big query file to a huge reference like human whole genome sequence.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'icebert' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['e85a4d752b8e159502d529f0f9e47579851a6b466b6c2f1f4d49f598642bc615'] + +dependencies = [ + ('HTSlib', '1.17'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# use HTSlib dependency provided through EasyBuild +prebuildopts = "sed -i '5s/.\/htslib/$\{EBROOTHTSLIB\}\/include\/htslib/' Makefile && " +prebuildopts += "sed -i '40s/ htslib\/libhts.a//' Makefile && " +prebuildopts += "sed -i '41s/htslib\/libhts.a/-lhts -lcurl/' Makefile && " +prebuildopts += "sed -i -e '/htslib\/libhts.a:/,+2d' Makefile && " + +files_to_copy = [ + (['%(name)s'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [] +} + +sanity_check_commands = ["command -v %(name)s"] + +moduleclass = 'bio' From 202e516dc7f9bba5c89f5f39bc6663af6316cba1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 12 Jan 2024 14:58:38 +0100 Subject: [PATCH 0265/1193] fix PEP8 syntax --- easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb index 1fee4320100b..f832a56d7b26 100644 --- a/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/pblat/pblat-2.5.1-foss-2022b.eb @@ -22,10 +22,10 @@ dependencies = [ ] # use HTSlib dependency provided through EasyBuild -prebuildopts = "sed -i '5s/.\/htslib/$\{EBROOTHTSLIB\}\/include\/htslib/' Makefile && " -prebuildopts += "sed -i '40s/ htslib\/libhts.a//' Makefile && " -prebuildopts += "sed -i '41s/htslib\/libhts.a/-lhts -lcurl/' Makefile && " -prebuildopts += "sed -i -e '/htslib\/libhts.a:/,+2d' Makefile && " +prebuildopts = "sed -i '5s/.\\/htslib/$\\{EBROOTHTSLIB\\}\\/include\\/htslib/' Makefile && " +prebuildopts += "sed -i '40s/ htslib\\/libhts.a//' Makefile && " +prebuildopts += "sed -i '41s/htslib\\/libhts.a/-lhts -lcurl/' Makefile && " +prebuildopts += "sed -i -e '/htslib\\/libhts.a:/,+2d' Makefile && " files_to_copy = [ (['%(name)s'], 'bin'), From 313acd31568becd2d60d6800f73e164892f1406c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 12 Jan 2024 15:20:29 +0100 Subject: [PATCH 0266/1193] fix PEP8 syntax --- .../easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb | 14 ++++++++++++-- 1 file changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb index 3dad7ad19d05..ee1d056b0346 100644 --- a/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PASA/PASA-2.5.3-foss-2022b.eb @@ -30,8 +30,18 @@ skipsteps = ['configure', 'install'] unpack_options = '--strip-components=1' -local_bins = ['%(namelower)s', 'cdbfasta', 'cdbyank', 'cln2qual', 'mdust', - 'psx', 'seqclean', 'seqclean.psx', 'slclust', 'trimpoly'] +local_bins = [ + '%(namelower)s', + 'cdbfasta', + 'cdbyank', + 'cln2qual', + 'mdust', + 'psx', + 'seqclean', + 'seqclean.psx', + 'slclust', + 'trimpoly', +] sanity_check_paths = { 'files': ['bin/%s' % x for x in local_bins], From f38c0cd018ed008f32e088ab8f8623e94f406f59 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 12 Jan 2024 15:33:54 +0100 Subject: [PATCH 0267/1193] Improve PyTorch-2.1.2-foss-2022a for non-x86 --- .../p/PyTorch/PyTorch-2.1.2-foss-2022a.eb | 21 ++++ ...ension_backend-without-vectorization.patch | 39 +++++++ ...Torch-2.1.2_fix-test_memory_profiler.patch | 19 ++++ ....1.2_fix-test_torchinductor-rounding.patch | 87 +++++++++++++++ .../PyTorch-2.1.2_fix-vsx-vector-abs.patch | 47 ++++++++ .../PyTorch-2.1.2_fix-vsx-vector-div.patch | 104 ++++++++++++++++++ ...cpu_repro-test-without-vectorization.patch | 88 +++++++++++++++ ...around_dynamo_failure_without_nnpack.patch | 32 ++++++ 8 files changed, 437 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb index f38a49fcfee1..0f6d51fd1bb4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022a.eb @@ -40,6 +40,13 @@ patches = [ 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', 'PyTorch-2.1.0_skip-test_wrap_bad.patch', + 'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch', + 'PyTorch-2.1.2_fix-test_memory_profiler.patch', + 'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch', + 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', + 'PyTorch-2.1.2_fix-vsx-vector-div.patch', + 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, @@ -94,6 +101,18 @@ checksums = [ {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, + {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch': + 'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'}, + {'PyTorch-2.1.2_fix-test_memory_profiler.patch': + '30b0c9355636c0ab3dedae02399789053825dc3835b4d7dac6e696767772b1ce'}, + {'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch': + 'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'}, + {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'}, + {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, + {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': + '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': + 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -128,6 +147,8 @@ dependencies = [ ('Z3', '4.10.2', '-Python-%(pyver)s'), ] +use_pip = True + excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch new file mode 100644 index 000000000000..eacc92b9e84b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch @@ -0,0 +1,39 @@ +The test checks for a substring "loadu" in generated code. +On AVX systems that line is: +> auto tmp0 = at::vec::Vectorized::loadu(in_ptr0 + static_cast(i0)) +however on non-AVX systems it is +> auto tmp0 = in_ptr0[static_cast(i0)]; + +the difference depends on `codecache.valid_vec_isa_list()` being non-empty. +See torch/_inductor/codegen/cpp.py:2639 + +Modify the test to account for that. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_extension_backend.py b/test/inductor/test_extension_backend.py +index 7d6f35d7b74..decc61d62d7 100644 +--- a/test/inductor/test_extension_backend.py ++++ b/test/inductor/test_extension_backend.py +@@ -20,7 +20,7 @@ except ImportError: + ) + + from torch._C import FileCheck +-from torch._inductor import metrics ++from torch._inductor import codecache, metrics + from torch._inductor.codegen.common import ( + get_scheduling_for_device, + get_wrapper_codegen_for_device, +@@ -130,7 +130,11 @@ class ExtensionBackendTests(TestCase): + metrics.reset() + opt_fn = torch.compile()(fn) + code = run_and_get_cpp_code(opt_fn, x, y, z) +- FileCheck().check("void kernel").check("loadu").check("extension_device").run( ++ if codecache.valid_vec_isa_list(): ++ load_expr = 'loadu' ++ else: ++ load_expr = ' = in_ptr0[static_cast(i0)];' ++ FileCheck().check("void kernel").check(load_expr).check("extension_device").run( + code + ) + opt_fn(x, y, z) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch new file mode 100644 index 000000000000..163c474053b6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch @@ -0,0 +1,19 @@ +The test seems to be too sensitive and may fail due to a small temporary allocation. +Increase the filter size to make it pass. +See https://github.com/pytorch/pytorch/issues/109592 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/profiler/test_memory_profiler.py b/test/profiler/test_memory_profiler.py +index 243d109693b..3f46ea6ac58 100644 +--- a/test/profiler/test_memory_profiler.py ++++ b/test/profiler/test_memory_profiler.py +@@ -1480,7 +1480,7 @@ class TestMemoryProfilerE2E(TestCase): + + # We generally don't care about tiny allocations during memory + # profiling and they add a lot of noise to the unit test. +- if size > 512 ++ if size > 1024 + ] + + self.assertExpectedInline( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch new file mode 100644 index 000000000000..18ce6456a0e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch @@ -0,0 +1,87 @@ +test_round_correctness_dynamic_shapes_cpu in test_torchinductor_dynamic_shapes.py +and test_comprehensive_round_cpu_float16 in test_torchinductor_opinfo +may fail, e.g. on PPC, due to unsafe math optimizations changing the rounding. +In particular it does not round halfway cases to even leading to a diff of 1.0: + +Mismatched elements: 6 / 200 (3.0%) +Greatest absolute difference: 1.0 at index (15,) (up to 1e-07 allowed) +Greatest relative difference: 0.5 at index (75,) (up to 1e-07 allowed) + +See https://github.com/pytorch/pytorch/issues/117346 +Fix by disabling -funsafe-math-optimizations for these tests. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_torchinductor.py b/test/inductor/test_torchinductor.py +index e6f1ea5a056..d6922da0289 100644 +--- a/test/inductor/test_torchinductor.py ++++ b/test/inductor/test_torchinductor.py +@@ -81,7 +81,7 @@ from torch._inductor import config, test_operators + from torch._inductor.compile_fx import compile_fx, compile_fx_inner + from torch._inductor.utils import has_torchvision_roi_align + +-from torch.testing._internal.common_utils import slowTest ++from torch.testing._internal.common_utils import slowTest, disable_unsafe_math_optimizations + from torch.testing._internal.inductor_utils import HAS_CPU, HAS_CUDA + + HAS_MULTIGPU = HAS_CUDA and torch.cuda.device_count() >= 2 +@@ -1287,6 +1287,7 @@ class CommonTemplate: + # with *100 we are always getting a number exactly at .5 which we don't do right in half + self.common(fn, (torch.randn(8, 8) * 100, torch.randn(8, 8) * 10)) + ++ @disable_unsafe_math_optimizations + def test_round_correctness(self): + if self.device == "cuda": + raise unittest.SkipTest("need to debug tl.libdevice on A100/V100") +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 5f6fa9e3eda..b25d5663b4e 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -16,7 +16,7 @@ from torch import inf, nan + from typing import Any, Dict, List, Tuple, Union, Sequence + from torch.testing import make_tensor + from torch.testing._internal.common_dtype import ( +- _dispatch_dtypes, floating_types, floating_types_and, complex_types, floating_and_complex_types, ++ _dispatch_dtypes, floating_types, floating_types_and, floating_types_and_half, complex_types, floating_and_complex_types, + floating_and_complex_types_and, all_types_and_complex_and, all_types_and, all_types_and_complex, integral_types_and, + all_types, empty_types, complex_types_and, integral_types + ) +@@ -30,6 +30,7 @@ from torch.testing._internal.common_cuda import ( + _get_torch_cuda_version, _get_torch_rocm_version, + ) + from torch.testing._internal.common_utils import ( ++ disable_unsafe_math_optimizations, + make_fullrank_matrices_with_distinct_singular_values, + TEST_WITH_ROCM, IS_WINDOWS, IS_MACOS, TEST_SCIPY, + torch_to_numpy_dtype_dict, TEST_WITH_ASAN, +@@ -14353,6 +14354,11 @@ op_db: List[OpInfo] = [ + 'TestNNCOpInfo', + 'test_nnc_correctness', + dtypes=(torch.bfloat16,)), ++ DecorateInfo(disable_unsafe_math_optimizations, ++ 'TestInductorOpInfo', ++ 'test_comprehensive', ++ dtypes=floating_types_and_half(), ++ device_type='cpu'), + ), + supports_sparse=True, + supports_sparse_csr=True, +diff --git a/torch/testing/_internal/common_utils.py b/torch/testing/_internal/common_utils.py +index 1e18ca2afec..fe183bbc736 100644 +--- a/torch/testing/_internal/common_utils.py ++++ b/torch/testing/_internal/common_utils.py +@@ -999,6 +999,14 @@ def is_avx512_vnni_supported(): + + IS_AVX512_VNNI_SUPPORTED = is_avx512_vnni_supported() + ++def disable_unsafe_math_optimizations(method): ++ @wraps(method) ++ def wrapper(*args, **kwargs): ++ flags = torch._inductor.codecache.optimization_flags() + ' -fno-unsafe-math-optimizations' ++ with unittest.mock.patch("torch._inductor.codecache.optimization_flags", return_value=flags): ++ method(*args, **kwargs) ++ return wrapper ++ + if IS_WINDOWS: + @contextmanager + def TemporaryFileName(*args, **kwargs): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch new file mode 100644 index 000000000000..ee7baf51f3d4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch @@ -0,0 +1,47 @@ +VSX: Fix vectorized abs function for complex tensors + +Use a similar approach with Sleef as in #99550 +to improve the precision and extremal value handling of the `abs` +function for complex tensors. + +This fixes +- test_reference_numerics_extremal__refs_abs_cpu_float64 +- test_reference_numerics_extremal__refs_abs_cpu_float128 +which failed on PPC. + +See https://github.com/pytorch/pytorch/pull/116859 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +index b80f7b79fca..382f32c0305 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +@@ -226,8 +226,9 @@ class Vectorized { + } + + Vectorized abs_() const { +- auto ret = abs_2_(); +- return ret.elwise_sqrt(); ++ auto vi = el_mergeo(); ++ auto vr = el_mergee(); ++ return {Sleef_hypotd2_u05vsx(vr._vec0, vi._vec0), Sleef_hypotd2_u05vsx(vr._vec1, vi._vec1)}; + } + + Vectorized abs() const { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 7efffa76c3a..0e30742eb9b 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -274,8 +274,9 @@ class Vectorized { + } + + Vectorized abs_() const { +- auto ret = abs_2_(); +- return ret.elwise_sqrt(); ++ auto vi = el_mergeo(); ++ auto vr = el_mergee(); ++ return {Sleef_hypotf4_u05vsx(vr._vec0, vi._vec0), Sleef_hypotf4_u05vsx(vr._vec1, vi._vec1)}; + } + + Vectorized abs() const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch new file mode 100644 index 000000000000..5e7330f21c2f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch @@ -0,0 +1,104 @@ +Fix overflow (to inf) in division of large complex values leading to failures in e.g. +test_reference_numerics_extremal__refs_abs_cpu_complex64 (test_unary_ufuncs) +See https://github.com/pytorch/pytorch/pull/116972 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 0e30742eb9b..5bff72e6874 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -238,18 +238,14 @@ class Vectorized { + return loadu(tmp); + } + +- static Vectorized horizontal_add_permD8( ++ static Vectorized horizontal_add( + Vectorized& first, + Vectorized& second) { +- // we will simulate it differently with 6 instructions total +- // lets permute second so that we can add it getting horizontal sums +- auto first_perm = first.el_swapped(); // 2perm +- auto second_perm = second.el_swapped(); // 2perm +- // sum +- auto first_ret = first + first_perm; // 2add +- auto second_ret = second + second_perm; // 2 add +- // now lets choose evens +- return el_mergee(first_ret, second_ret); // 2 mergee's ++ // Operates on individual floats, see _mm_hadd_ps ++ // {f0+f1, s0+s1, f2+f3, s2+s3, ...} ++ // i.e. it sums the re and im of each value and interleaves first and second: ++ // {f_re0 + f_im0, s_re0 + s_im0, f_re1 + f_im1, s_re1 + s_im1, ...} ++ return el_mergee(first, second) + el_mergeo(first, second); + } + + static Vectorized horizontal_sub_permD8( +@@ -353,12 +349,19 @@ class Vectorized { + static Vectorized el_mergee( + Vectorized& first, + Vectorized& second) { +- // as mergee phased in , we can use vec_perm with mask + return { + vec_mergee(first._vecb0, second._vecb0), + vec_mergee(first._vecb1, second._vecb1)}; + } + ++ static Vectorized el_mergeo( ++ Vectorized& first, ++ Vectorized& second) { ++ return { ++ vec_mergeo(first._vecb0, second._vecb0), ++ vec_mergeo(first._vecb1, second._vecb1)}; ++ } ++ + Vectorized angle_() const { + // angle = atan2(b/a) + // auto b_a = _mm256_permute_ps(values, 0xB1); // b a +@@ -485,25 +488,20 @@ class Vectorized { + // re + im*i = (a + bi) / (c + di) + // re = (ac + bd)/abs_2() + // im = (bc - ad)/abs_2() +-#if 1 +- auto vi = b.el_mergeo(); +- auto vr = b.el_mergee(); +- auto abs_b = b.abs_2_(); +- vi = vi ^ isign_mask; +- auto ret = elwise_mult(vr); +- auto vx_swapped = el_swapped(); +- ret = vx_swapped.el_madd(vi, ret); +- ret = ret.elwise_div(abs_b); +-#else +- // Vectorized x86 simulation +- auto ac_bd = elwise_mult(b); +- auto d_c = b.el_swapped(); +- d_c = d_c ^ rsign_mask; +- auto ad_bc = elwise_mult(d_c); +- auto abs_b = b.abs_2_(); +- auto re_im = horizontal_add_permD8(ac_bd, ad_bc); +- auto ret = re_im.elwise_div(abs_b); +-#endif ++ auto fabs_cd = Vectorized{ ++ vec_andc(b._vec0, sign_mask), ++ vec_andc(b._vec1, sign_mask)}; // |c| |d| ++ auto fabs_dc = fabs_cd.el_swapped(); // |d| |c| ++ auto scale = fabs_cd.elwise_max(fabs_dc); // sc = max(|c|, |d|) ++ auto a2 = elwise_div(scale); // a/sc b/sc ++ auto b2 = b.elwise_div(scale); // c/sc d/sc ++ auto acbd2 = a2.elwise_mult(b2); // ac/sc^2 bd/sc^2 ++ auto dc2 = b2.el_swapped(); // d/sc c/sc ++ dc2 = dc2 ^ rsign_mask; // -d/sc c/sc ++ auto adbc2 = a2.elwise_mult(dc2); // -ad/sc^2 bc/sc^2 ++ auto ret = horizontal_add(acbd2, adbc2); // (ac+bd)/sc^2 (bc-ad)/sc^2 ++ auto denom2 = b2.abs_2_(); // (c^2+d^2)/sc^2 (c^2+d^2)/sc^2 ++ ret = ret.elwise_div(denom2); + return ret; + } + +@@ -628,6 +626,7 @@ class Vectorized { + DEFINE_MEMBER_OP(elwise_ge, ComplexFlt, vec_cmpge) + DEFINE_MEMBER_OP(elwise_lt, ComplexFlt, vec_cmplt) + DEFINE_MEMBER_OP(elwise_le, ComplexFlt, vec_cmple) ++ DEFINE_MEMBER_OP(elwise_max, ComplexFlt, vec_max) + }; + + template <> diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch new file mode 100644 index 000000000000..cb6028e1b062 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch @@ -0,0 +1,88 @@ +test_cpu_repro fails on e.g. PPC where no AVX is available +Failures are all of the kind + + assert metrics.generated_cpp_vec_kernel_count == 1 +AssertionError + +As this is expected, skip the affected tests. +See https://github.com/pytorch/pytorch/pull/117262 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_cpu_repro.py b/test/inductor/test_cpu_repro.py +index 102c5af5168..3bc107b960b 100644 +--- a/test/inductor/test_cpu_repro.py ++++ b/test/inductor/test_cpu_repro.py +@@ -56,6 +56,8 @@ TestCase = test_torchinductor.TestCase + aten = torch.ops.aten + check_model = test_torchinductor.check_model + ++requires_vectorization = unittest.skipUnless(codecache.valid_vec_isa_list(), ++ "Does not support vectorization") + + class LstmModule(torch.nn.Module): + def __init__( +@@ -2165,6 +2167,7 @@ class CPUReproTests(TestCase): + self.assertEqual(metrics.generated_kernel_count, 1) + self.assertTrue(same(fn(a, b, c, idx), opt_fn(a, b, c, idx))) + ++ @requires_vectorization + def test_lowp_fp_neg_abs(self): + def fn(x): + return x.neg().abs() +@@ -2177,6 +2180,7 @@ class CPUReproTests(TestCase): + assert metrics.cpp_to_dtype_count == 0 + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_transpose_non_contiguous(self): + def fn(a): + # From part of timm HaloAttn: +@@ -2214,6 +2218,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x,)) + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_non_contiguous_index_with_constant_stride(self): + def fn(x): + x1 = x[:, :, :, ::2] +@@ -2252,6 +2257,7 @@ class CPUReproTests(TestCase): + fn(torch.randn([8, 128])) + self.assertGreater(len(strings), 3) + ++ @requires_vectorization + def test_vertical_sum_cpu_only(self): + def fn1(a): + return a.sum(dim=0) +@@ -2269,6 +2275,7 @@ class CPUReproTests(TestCase): + self.common(fn2, (x,)) + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_transpose_vertical_sum_cpu_only(self): + def fn(a, b): + c = a * b +@@ -2280,6 +2287,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x, y)) + assert metrics.generated_cpp_vec_kernel_count == 2 + ++ @requires_vectorization + def test_transpose_sum2d_cpu_only(self): + def fn(a, b): + c = a * b +@@ -2291,6 +2299,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x, y)) + assert metrics.generated_cpp_vec_kernel_count == 2 + ++ @requires_vectorization + def test_transpose_sum_outer(self): + # https://github.com/pytorch/pytorch/issues/98573 + def fn(a): +@@ -2417,6 +2426,7 @@ class CPUReproTests(TestCase): + ) + self.assertEqual(metrics.generated_kernel_count, 1) + ++ @requires_vectorization + def test_scalar_mul_bfloat16(self): + def f(x): + return torch.ops.aten.mul.Tensor(x, 1.7015043497085571) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch new file mode 100644 index 000000000000..2386210fd235 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch @@ -0,0 +1,32 @@ +test_module_partitioner_functional_conv_relu_conv in test_fx.py fails with an IndexError +on e.g. POWER systems. + +Last part of the stacktrace: + File "/sympy/printing/printer.py", line 331, in _print + return printmethod(expr, **kwargs) + File "/torch/fx/experimental/symbolic_shapes.py", line 1575, in _print_Symbol + return self.print_source(self.symbol_to_source[expr][0]) +IndexError: list index out of range + +One cause is the missing MKLDNN and NNPACK (unavailable on PPC) making it skip some checks. +A workaround here is adding a check that has side effects but doesn't change the result. +That makes at least the test pass. +Another change in PyTorch 2.2.x also avoids that issue but is to large to backport. + +See https://github.com/pytorch/pytorch/issues/117033 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/Convolution.cpp b/aten/src/ATen/native/Convolution.cpp +index 7af281a7cd9..3709d27b2bb 100644 +--- a/aten/src/ATen/native/Convolution.cpp ++++ b/aten/src/ATen/native/Convolution.cpp +@@ -543,7 +543,7 @@ struct ConvParams { + #endif + ; + #endif +- return false; ++ return (at::symint::size(weight, 2) < 17) && (at::symint::size(weight, 3) < 17) && false; + } + bool use_xnnpack(const at::Tensor& input, const at::Tensor& weight, + const at::OptionalArrayRef bias_sizes_opt) const { From 4e0cb064755d47993e63abe5e39a8f96065b5dc8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 12 Jan 2024 15:34:56 +0100 Subject: [PATCH 0268/1193] Improve PyTorch-2.1.2-foss-2022b for non-x86 --- .../p/PyTorch/PyTorch-2.1.2-foss-2022b.eb | 21 ++++ ...ension_backend-without-vectorization.patch | 39 +++++++ ...Torch-2.1.2_fix-test_memory_profiler.patch | 19 ++++ ....1.2_fix-test_torchinductor-rounding.patch | 87 +++++++++++++++ .../PyTorch-2.1.2_fix-vsx-vector-abs.patch | 47 ++++++++ .../PyTorch-2.1.2_fix-vsx-vector-div.patch | 104 ++++++++++++++++++ ...cpu_repro-test-without-vectorization.patch | 88 +++++++++++++++ ...around_dynamo_failure_without_nnpack.patch | 32 ++++++ 8 files changed, 437 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb index 85f9942c63e2..146e42cb2b82 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2022b.eb @@ -41,6 +41,13 @@ patches = [ 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', 'PyTorch-2.1.0_skip-test_wrap_bad.patch', + 'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch', + 'PyTorch-2.1.2_fix-test_memory_profiler.patch', + 'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch', + 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', + 'PyTorch-2.1.2_fix-vsx-vector-div.patch', + 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, @@ -96,6 +103,18 @@ checksums = [ {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, + {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch': + 'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'}, + {'PyTorch-2.1.2_fix-test_memory_profiler.patch': + '30b0c9355636c0ab3dedae02399789053825dc3835b4d7dac6e696767772b1ce'}, + {'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch': + 'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'}, + {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'}, + {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, + {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': + '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': + 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -128,6 +147,8 @@ dependencies = [ ('Z3', '4.12.2', '-Python-%(pyver)s'), ] +use_pip = True + excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch new file mode 100644 index 000000000000..eacc92b9e84b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch @@ -0,0 +1,39 @@ +The test checks for a substring "loadu" in generated code. +On AVX systems that line is: +> auto tmp0 = at::vec::Vectorized::loadu(in_ptr0 + static_cast(i0)) +however on non-AVX systems it is +> auto tmp0 = in_ptr0[static_cast(i0)]; + +the difference depends on `codecache.valid_vec_isa_list()` being non-empty. +See torch/_inductor/codegen/cpp.py:2639 + +Modify the test to account for that. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_extension_backend.py b/test/inductor/test_extension_backend.py +index 7d6f35d7b74..decc61d62d7 100644 +--- a/test/inductor/test_extension_backend.py ++++ b/test/inductor/test_extension_backend.py +@@ -20,7 +20,7 @@ except ImportError: + ) + + from torch._C import FileCheck +-from torch._inductor import metrics ++from torch._inductor import codecache, metrics + from torch._inductor.codegen.common import ( + get_scheduling_for_device, + get_wrapper_codegen_for_device, +@@ -130,7 +130,11 @@ class ExtensionBackendTests(TestCase): + metrics.reset() + opt_fn = torch.compile()(fn) + code = run_and_get_cpp_code(opt_fn, x, y, z) +- FileCheck().check("void kernel").check("loadu").check("extension_device").run( ++ if codecache.valid_vec_isa_list(): ++ load_expr = 'loadu' ++ else: ++ load_expr = ' = in_ptr0[static_cast(i0)];' ++ FileCheck().check("void kernel").check(load_expr).check("extension_device").run( + code + ) + opt_fn(x, y, z) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch new file mode 100644 index 000000000000..163c474053b6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch @@ -0,0 +1,19 @@ +The test seems to be too sensitive and may fail due to a small temporary allocation. +Increase the filter size to make it pass. +See https://github.com/pytorch/pytorch/issues/109592 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/profiler/test_memory_profiler.py b/test/profiler/test_memory_profiler.py +index 243d109693b..3f46ea6ac58 100644 +--- a/test/profiler/test_memory_profiler.py ++++ b/test/profiler/test_memory_profiler.py +@@ -1480,7 +1480,7 @@ class TestMemoryProfilerE2E(TestCase): + + # We generally don't care about tiny allocations during memory + # profiling and they add a lot of noise to the unit test. +- if size > 512 ++ if size > 1024 + ] + + self.assertExpectedInline( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch new file mode 100644 index 000000000000..18ce6456a0e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch @@ -0,0 +1,87 @@ +test_round_correctness_dynamic_shapes_cpu in test_torchinductor_dynamic_shapes.py +and test_comprehensive_round_cpu_float16 in test_torchinductor_opinfo +may fail, e.g. on PPC, due to unsafe math optimizations changing the rounding. +In particular it does not round halfway cases to even leading to a diff of 1.0: + +Mismatched elements: 6 / 200 (3.0%) +Greatest absolute difference: 1.0 at index (15,) (up to 1e-07 allowed) +Greatest relative difference: 0.5 at index (75,) (up to 1e-07 allowed) + +See https://github.com/pytorch/pytorch/issues/117346 +Fix by disabling -funsafe-math-optimizations for these tests. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_torchinductor.py b/test/inductor/test_torchinductor.py +index e6f1ea5a056..d6922da0289 100644 +--- a/test/inductor/test_torchinductor.py ++++ b/test/inductor/test_torchinductor.py +@@ -81,7 +81,7 @@ from torch._inductor import config, test_operators + from torch._inductor.compile_fx import compile_fx, compile_fx_inner + from torch._inductor.utils import has_torchvision_roi_align + +-from torch.testing._internal.common_utils import slowTest ++from torch.testing._internal.common_utils import slowTest, disable_unsafe_math_optimizations + from torch.testing._internal.inductor_utils import HAS_CPU, HAS_CUDA + + HAS_MULTIGPU = HAS_CUDA and torch.cuda.device_count() >= 2 +@@ -1287,6 +1287,7 @@ class CommonTemplate: + # with *100 we are always getting a number exactly at .5 which we don't do right in half + self.common(fn, (torch.randn(8, 8) * 100, torch.randn(8, 8) * 10)) + ++ @disable_unsafe_math_optimizations + def test_round_correctness(self): + if self.device == "cuda": + raise unittest.SkipTest("need to debug tl.libdevice on A100/V100") +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 5f6fa9e3eda..b25d5663b4e 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -16,7 +16,7 @@ from torch import inf, nan + from typing import Any, Dict, List, Tuple, Union, Sequence + from torch.testing import make_tensor + from torch.testing._internal.common_dtype import ( +- _dispatch_dtypes, floating_types, floating_types_and, complex_types, floating_and_complex_types, ++ _dispatch_dtypes, floating_types, floating_types_and, floating_types_and_half, complex_types, floating_and_complex_types, + floating_and_complex_types_and, all_types_and_complex_and, all_types_and, all_types_and_complex, integral_types_and, + all_types, empty_types, complex_types_and, integral_types + ) +@@ -30,6 +30,7 @@ from torch.testing._internal.common_cuda import ( + _get_torch_cuda_version, _get_torch_rocm_version, + ) + from torch.testing._internal.common_utils import ( ++ disable_unsafe_math_optimizations, + make_fullrank_matrices_with_distinct_singular_values, + TEST_WITH_ROCM, IS_WINDOWS, IS_MACOS, TEST_SCIPY, + torch_to_numpy_dtype_dict, TEST_WITH_ASAN, +@@ -14353,6 +14354,11 @@ op_db: List[OpInfo] = [ + 'TestNNCOpInfo', + 'test_nnc_correctness', + dtypes=(torch.bfloat16,)), ++ DecorateInfo(disable_unsafe_math_optimizations, ++ 'TestInductorOpInfo', ++ 'test_comprehensive', ++ dtypes=floating_types_and_half(), ++ device_type='cpu'), + ), + supports_sparse=True, + supports_sparse_csr=True, +diff --git a/torch/testing/_internal/common_utils.py b/torch/testing/_internal/common_utils.py +index 1e18ca2afec..fe183bbc736 100644 +--- a/torch/testing/_internal/common_utils.py ++++ b/torch/testing/_internal/common_utils.py +@@ -999,6 +999,14 @@ def is_avx512_vnni_supported(): + + IS_AVX512_VNNI_SUPPORTED = is_avx512_vnni_supported() + ++def disable_unsafe_math_optimizations(method): ++ @wraps(method) ++ def wrapper(*args, **kwargs): ++ flags = torch._inductor.codecache.optimization_flags() + ' -fno-unsafe-math-optimizations' ++ with unittest.mock.patch("torch._inductor.codecache.optimization_flags", return_value=flags): ++ method(*args, **kwargs) ++ return wrapper ++ + if IS_WINDOWS: + @contextmanager + def TemporaryFileName(*args, **kwargs): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch new file mode 100644 index 000000000000..ee7baf51f3d4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch @@ -0,0 +1,47 @@ +VSX: Fix vectorized abs function for complex tensors + +Use a similar approach with Sleef as in #99550 +to improve the precision and extremal value handling of the `abs` +function for complex tensors. + +This fixes +- test_reference_numerics_extremal__refs_abs_cpu_float64 +- test_reference_numerics_extremal__refs_abs_cpu_float128 +which failed on PPC. + +See https://github.com/pytorch/pytorch/pull/116859 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +index b80f7b79fca..382f32c0305 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +@@ -226,8 +226,9 @@ class Vectorized { + } + + Vectorized abs_() const { +- auto ret = abs_2_(); +- return ret.elwise_sqrt(); ++ auto vi = el_mergeo(); ++ auto vr = el_mergee(); ++ return {Sleef_hypotd2_u05vsx(vr._vec0, vi._vec0), Sleef_hypotd2_u05vsx(vr._vec1, vi._vec1)}; + } + + Vectorized abs() const { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 7efffa76c3a..0e30742eb9b 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -274,8 +274,9 @@ class Vectorized { + } + + Vectorized abs_() const { +- auto ret = abs_2_(); +- return ret.elwise_sqrt(); ++ auto vi = el_mergeo(); ++ auto vr = el_mergee(); ++ return {Sleef_hypotf4_u05vsx(vr._vec0, vi._vec0), Sleef_hypotf4_u05vsx(vr._vec1, vi._vec1)}; + } + + Vectorized abs() const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch new file mode 100644 index 000000000000..5e7330f21c2f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch @@ -0,0 +1,104 @@ +Fix overflow (to inf) in division of large complex values leading to failures in e.g. +test_reference_numerics_extremal__refs_abs_cpu_complex64 (test_unary_ufuncs) +See https://github.com/pytorch/pytorch/pull/116972 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 0e30742eb9b..5bff72e6874 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -238,18 +238,14 @@ class Vectorized { + return loadu(tmp); + } + +- static Vectorized horizontal_add_permD8( ++ static Vectorized horizontal_add( + Vectorized& first, + Vectorized& second) { +- // we will simulate it differently with 6 instructions total +- // lets permute second so that we can add it getting horizontal sums +- auto first_perm = first.el_swapped(); // 2perm +- auto second_perm = second.el_swapped(); // 2perm +- // sum +- auto first_ret = first + first_perm; // 2add +- auto second_ret = second + second_perm; // 2 add +- // now lets choose evens +- return el_mergee(first_ret, second_ret); // 2 mergee's ++ // Operates on individual floats, see _mm_hadd_ps ++ // {f0+f1, s0+s1, f2+f3, s2+s3, ...} ++ // i.e. it sums the re and im of each value and interleaves first and second: ++ // {f_re0 + f_im0, s_re0 + s_im0, f_re1 + f_im1, s_re1 + s_im1, ...} ++ return el_mergee(first, second) + el_mergeo(first, second); + } + + static Vectorized horizontal_sub_permD8( +@@ -353,12 +349,19 @@ class Vectorized { + static Vectorized el_mergee( + Vectorized& first, + Vectorized& second) { +- // as mergee phased in , we can use vec_perm with mask + return { + vec_mergee(first._vecb0, second._vecb0), + vec_mergee(first._vecb1, second._vecb1)}; + } + ++ static Vectorized el_mergeo( ++ Vectorized& first, ++ Vectorized& second) { ++ return { ++ vec_mergeo(first._vecb0, second._vecb0), ++ vec_mergeo(first._vecb1, second._vecb1)}; ++ } ++ + Vectorized angle_() const { + // angle = atan2(b/a) + // auto b_a = _mm256_permute_ps(values, 0xB1); // b a +@@ -485,25 +488,20 @@ class Vectorized { + // re + im*i = (a + bi) / (c + di) + // re = (ac + bd)/abs_2() + // im = (bc - ad)/abs_2() +-#if 1 +- auto vi = b.el_mergeo(); +- auto vr = b.el_mergee(); +- auto abs_b = b.abs_2_(); +- vi = vi ^ isign_mask; +- auto ret = elwise_mult(vr); +- auto vx_swapped = el_swapped(); +- ret = vx_swapped.el_madd(vi, ret); +- ret = ret.elwise_div(abs_b); +-#else +- // Vectorized x86 simulation +- auto ac_bd = elwise_mult(b); +- auto d_c = b.el_swapped(); +- d_c = d_c ^ rsign_mask; +- auto ad_bc = elwise_mult(d_c); +- auto abs_b = b.abs_2_(); +- auto re_im = horizontal_add_permD8(ac_bd, ad_bc); +- auto ret = re_im.elwise_div(abs_b); +-#endif ++ auto fabs_cd = Vectorized{ ++ vec_andc(b._vec0, sign_mask), ++ vec_andc(b._vec1, sign_mask)}; // |c| |d| ++ auto fabs_dc = fabs_cd.el_swapped(); // |d| |c| ++ auto scale = fabs_cd.elwise_max(fabs_dc); // sc = max(|c|, |d|) ++ auto a2 = elwise_div(scale); // a/sc b/sc ++ auto b2 = b.elwise_div(scale); // c/sc d/sc ++ auto acbd2 = a2.elwise_mult(b2); // ac/sc^2 bd/sc^2 ++ auto dc2 = b2.el_swapped(); // d/sc c/sc ++ dc2 = dc2 ^ rsign_mask; // -d/sc c/sc ++ auto adbc2 = a2.elwise_mult(dc2); // -ad/sc^2 bc/sc^2 ++ auto ret = horizontal_add(acbd2, adbc2); // (ac+bd)/sc^2 (bc-ad)/sc^2 ++ auto denom2 = b2.abs_2_(); // (c^2+d^2)/sc^2 (c^2+d^2)/sc^2 ++ ret = ret.elwise_div(denom2); + return ret; + } + +@@ -628,6 +626,7 @@ class Vectorized { + DEFINE_MEMBER_OP(elwise_ge, ComplexFlt, vec_cmpge) + DEFINE_MEMBER_OP(elwise_lt, ComplexFlt, vec_cmplt) + DEFINE_MEMBER_OP(elwise_le, ComplexFlt, vec_cmple) ++ DEFINE_MEMBER_OP(elwise_max, ComplexFlt, vec_max) + }; + + template <> diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch new file mode 100644 index 000000000000..cb6028e1b062 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch @@ -0,0 +1,88 @@ +test_cpu_repro fails on e.g. PPC where no AVX is available +Failures are all of the kind + + assert metrics.generated_cpp_vec_kernel_count == 1 +AssertionError + +As this is expected, skip the affected tests. +See https://github.com/pytorch/pytorch/pull/117262 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_cpu_repro.py b/test/inductor/test_cpu_repro.py +index 102c5af5168..3bc107b960b 100644 +--- a/test/inductor/test_cpu_repro.py ++++ b/test/inductor/test_cpu_repro.py +@@ -56,6 +56,8 @@ TestCase = test_torchinductor.TestCase + aten = torch.ops.aten + check_model = test_torchinductor.check_model + ++requires_vectorization = unittest.skipUnless(codecache.valid_vec_isa_list(), ++ "Does not support vectorization") + + class LstmModule(torch.nn.Module): + def __init__( +@@ -2165,6 +2167,7 @@ class CPUReproTests(TestCase): + self.assertEqual(metrics.generated_kernel_count, 1) + self.assertTrue(same(fn(a, b, c, idx), opt_fn(a, b, c, idx))) + ++ @requires_vectorization + def test_lowp_fp_neg_abs(self): + def fn(x): + return x.neg().abs() +@@ -2177,6 +2180,7 @@ class CPUReproTests(TestCase): + assert metrics.cpp_to_dtype_count == 0 + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_transpose_non_contiguous(self): + def fn(a): + # From part of timm HaloAttn: +@@ -2214,6 +2218,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x,)) + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_non_contiguous_index_with_constant_stride(self): + def fn(x): + x1 = x[:, :, :, ::2] +@@ -2252,6 +2257,7 @@ class CPUReproTests(TestCase): + fn(torch.randn([8, 128])) + self.assertGreater(len(strings), 3) + ++ @requires_vectorization + def test_vertical_sum_cpu_only(self): + def fn1(a): + return a.sum(dim=0) +@@ -2269,6 +2275,7 @@ class CPUReproTests(TestCase): + self.common(fn2, (x,)) + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_transpose_vertical_sum_cpu_only(self): + def fn(a, b): + c = a * b +@@ -2280,6 +2287,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x, y)) + assert metrics.generated_cpp_vec_kernel_count == 2 + ++ @requires_vectorization + def test_transpose_sum2d_cpu_only(self): + def fn(a, b): + c = a * b +@@ -2291,6 +2299,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x, y)) + assert metrics.generated_cpp_vec_kernel_count == 2 + ++ @requires_vectorization + def test_transpose_sum_outer(self): + # https://github.com/pytorch/pytorch/issues/98573 + def fn(a): +@@ -2417,6 +2426,7 @@ class CPUReproTests(TestCase): + ) + self.assertEqual(metrics.generated_kernel_count, 1) + ++ @requires_vectorization + def test_scalar_mul_bfloat16(self): + def f(x): + return torch.ops.aten.mul.Tensor(x, 1.7015043497085571) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch new file mode 100644 index 000000000000..2386210fd235 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch @@ -0,0 +1,32 @@ +test_module_partitioner_functional_conv_relu_conv in test_fx.py fails with an IndexError +on e.g. POWER systems. + +Last part of the stacktrace: + File "/sympy/printing/printer.py", line 331, in _print + return printmethod(expr, **kwargs) + File "/torch/fx/experimental/symbolic_shapes.py", line 1575, in _print_Symbol + return self.print_source(self.symbol_to_source[expr][0]) +IndexError: list index out of range + +One cause is the missing MKLDNN and NNPACK (unavailable on PPC) making it skip some checks. +A workaround here is adding a check that has side effects but doesn't change the result. +That makes at least the test pass. +Another change in PyTorch 2.2.x also avoids that issue but is to large to backport. + +See https://github.com/pytorch/pytorch/issues/117033 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/Convolution.cpp b/aten/src/ATen/native/Convolution.cpp +index 7af281a7cd9..3709d27b2bb 100644 +--- a/aten/src/ATen/native/Convolution.cpp ++++ b/aten/src/ATen/native/Convolution.cpp +@@ -543,7 +543,7 @@ struct ConvParams { + #endif + ; + #endif +- return false; ++ return (at::symint::size(weight, 2) < 17) && (at::symint::size(weight, 3) < 17) && false; + } + bool use_xnnpack(const at::Tensor& input, const at::Tensor& weight, + const at::OptionalArrayRef bias_sizes_opt) const { From f346ffda44e960bde61c00771a7d8197b5cb242b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 12 Jan 2024 15:36:04 +0100 Subject: [PATCH 0269/1193] Improve PyTorch-2.1.2-foss-2023a for non-x86 --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a.eb | 21 ++++ ...ension_backend-without-vectorization.patch | 39 +++++++ ...Torch-2.1.2_fix-test_memory_profiler.patch | 19 ++++ ....1.2_fix-test_torchinductor-rounding.patch | 87 +++++++++++++++ .../PyTorch-2.1.2_fix-vsx-vector-abs.patch | 47 ++++++++ .../PyTorch-2.1.2_fix-vsx-vector-div.patch | 104 ++++++++++++++++++ ...cpu_repro-test-without-vectorization.patch | 88 +++++++++++++++ ...around_dynamo_failure_without_nnpack.patch | 32 ++++++ 8 files changed, 437 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb index fe23eab6738b..31d433c30740 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb @@ -42,6 +42,13 @@ patches = [ 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', 'PyTorch-2.1.0_skip-test_wrap_bad.patch', + 'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch', + 'PyTorch-2.1.2_fix-test_memory_profiler.patch', + 'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch', + 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', + 'PyTorch-2.1.2_fix-vsx-vector-div.patch', + 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, @@ -99,6 +106,18 @@ checksums = [ {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, + {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch': + 'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'}, + {'PyTorch-2.1.2_fix-test_memory_profiler.patch': + '30b0c9355636c0ab3dedae02399789053825dc3835b4d7dac6e696767772b1ce'}, + {'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch': + 'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'}, + {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'}, + {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, + {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': + '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': + 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -132,6 +151,8 @@ dependencies = [ ('Z3', '4.12.2', '-Python-%(pyver)s'), ] +use_pip = True + excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch new file mode 100644 index 000000000000..eacc92b9e84b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch @@ -0,0 +1,39 @@ +The test checks for a substring "loadu" in generated code. +On AVX systems that line is: +> auto tmp0 = at::vec::Vectorized::loadu(in_ptr0 + static_cast(i0)) +however on non-AVX systems it is +> auto tmp0 = in_ptr0[static_cast(i0)]; + +the difference depends on `codecache.valid_vec_isa_list()` being non-empty. +See torch/_inductor/codegen/cpp.py:2639 + +Modify the test to account for that. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_extension_backend.py b/test/inductor/test_extension_backend.py +index 7d6f35d7b74..decc61d62d7 100644 +--- a/test/inductor/test_extension_backend.py ++++ b/test/inductor/test_extension_backend.py +@@ -20,7 +20,7 @@ except ImportError: + ) + + from torch._C import FileCheck +-from torch._inductor import metrics ++from torch._inductor import codecache, metrics + from torch._inductor.codegen.common import ( + get_scheduling_for_device, + get_wrapper_codegen_for_device, +@@ -130,7 +130,11 @@ class ExtensionBackendTests(TestCase): + metrics.reset() + opt_fn = torch.compile()(fn) + code = run_and_get_cpp_code(opt_fn, x, y, z) +- FileCheck().check("void kernel").check("loadu").check("extension_device").run( ++ if codecache.valid_vec_isa_list(): ++ load_expr = 'loadu' ++ else: ++ load_expr = ' = in_ptr0[static_cast(i0)];' ++ FileCheck().check("void kernel").check(load_expr).check("extension_device").run( + code + ) + opt_fn(x, y, z) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch new file mode 100644 index 000000000000..163c474053b6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_memory_profiler.patch @@ -0,0 +1,19 @@ +The test seems to be too sensitive and may fail due to a small temporary allocation. +Increase the filter size to make it pass. +See https://github.com/pytorch/pytorch/issues/109592 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/profiler/test_memory_profiler.py b/test/profiler/test_memory_profiler.py +index 243d109693b..3f46ea6ac58 100644 +--- a/test/profiler/test_memory_profiler.py ++++ b/test/profiler/test_memory_profiler.py +@@ -1480,7 +1480,7 @@ class TestMemoryProfilerE2E(TestCase): + + # We generally don't care about tiny allocations during memory + # profiling and they add a lot of noise to the unit test. +- if size > 512 ++ if size > 1024 + ] + + self.assertExpectedInline( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch new file mode 100644 index 000000000000..18ce6456a0e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-test_torchinductor-rounding.patch @@ -0,0 +1,87 @@ +test_round_correctness_dynamic_shapes_cpu in test_torchinductor_dynamic_shapes.py +and test_comprehensive_round_cpu_float16 in test_torchinductor_opinfo +may fail, e.g. on PPC, due to unsafe math optimizations changing the rounding. +In particular it does not round halfway cases to even leading to a diff of 1.0: + +Mismatched elements: 6 / 200 (3.0%) +Greatest absolute difference: 1.0 at index (15,) (up to 1e-07 allowed) +Greatest relative difference: 0.5 at index (75,) (up to 1e-07 allowed) + +See https://github.com/pytorch/pytorch/issues/117346 +Fix by disabling -funsafe-math-optimizations for these tests. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_torchinductor.py b/test/inductor/test_torchinductor.py +index e6f1ea5a056..d6922da0289 100644 +--- a/test/inductor/test_torchinductor.py ++++ b/test/inductor/test_torchinductor.py +@@ -81,7 +81,7 @@ from torch._inductor import config, test_operators + from torch._inductor.compile_fx import compile_fx, compile_fx_inner + from torch._inductor.utils import has_torchvision_roi_align + +-from torch.testing._internal.common_utils import slowTest ++from torch.testing._internal.common_utils import slowTest, disable_unsafe_math_optimizations + from torch.testing._internal.inductor_utils import HAS_CPU, HAS_CUDA + + HAS_MULTIGPU = HAS_CUDA and torch.cuda.device_count() >= 2 +@@ -1287,6 +1287,7 @@ class CommonTemplate: + # with *100 we are always getting a number exactly at .5 which we don't do right in half + self.common(fn, (torch.randn(8, 8) * 100, torch.randn(8, 8) * 10)) + ++ @disable_unsafe_math_optimizations + def test_round_correctness(self): + if self.device == "cuda": + raise unittest.SkipTest("need to debug tl.libdevice on A100/V100") +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 5f6fa9e3eda..b25d5663b4e 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -16,7 +16,7 @@ from torch import inf, nan + from typing import Any, Dict, List, Tuple, Union, Sequence + from torch.testing import make_tensor + from torch.testing._internal.common_dtype import ( +- _dispatch_dtypes, floating_types, floating_types_and, complex_types, floating_and_complex_types, ++ _dispatch_dtypes, floating_types, floating_types_and, floating_types_and_half, complex_types, floating_and_complex_types, + floating_and_complex_types_and, all_types_and_complex_and, all_types_and, all_types_and_complex, integral_types_and, + all_types, empty_types, complex_types_and, integral_types + ) +@@ -30,6 +30,7 @@ from torch.testing._internal.common_cuda import ( + _get_torch_cuda_version, _get_torch_rocm_version, + ) + from torch.testing._internal.common_utils import ( ++ disable_unsafe_math_optimizations, + make_fullrank_matrices_with_distinct_singular_values, + TEST_WITH_ROCM, IS_WINDOWS, IS_MACOS, TEST_SCIPY, + torch_to_numpy_dtype_dict, TEST_WITH_ASAN, +@@ -14353,6 +14354,11 @@ op_db: List[OpInfo] = [ + 'TestNNCOpInfo', + 'test_nnc_correctness', + dtypes=(torch.bfloat16,)), ++ DecorateInfo(disable_unsafe_math_optimizations, ++ 'TestInductorOpInfo', ++ 'test_comprehensive', ++ dtypes=floating_types_and_half(), ++ device_type='cpu'), + ), + supports_sparse=True, + supports_sparse_csr=True, +diff --git a/torch/testing/_internal/common_utils.py b/torch/testing/_internal/common_utils.py +index 1e18ca2afec..fe183bbc736 100644 +--- a/torch/testing/_internal/common_utils.py ++++ b/torch/testing/_internal/common_utils.py +@@ -999,6 +999,14 @@ def is_avx512_vnni_supported(): + + IS_AVX512_VNNI_SUPPORTED = is_avx512_vnni_supported() + ++def disable_unsafe_math_optimizations(method): ++ @wraps(method) ++ def wrapper(*args, **kwargs): ++ flags = torch._inductor.codecache.optimization_flags() + ' -fno-unsafe-math-optimizations' ++ with unittest.mock.patch("torch._inductor.codecache.optimization_flags", return_value=flags): ++ method(*args, **kwargs) ++ return wrapper ++ + if IS_WINDOWS: + @contextmanager + def TemporaryFileName(*args, **kwargs): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch new file mode 100644 index 000000000000..ee7baf51f3d4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-abs.patch @@ -0,0 +1,47 @@ +VSX: Fix vectorized abs function for complex tensors + +Use a similar approach with Sleef as in #99550 +to improve the precision and extremal value handling of the `abs` +function for complex tensors. + +This fixes +- test_reference_numerics_extremal__refs_abs_cpu_float64 +- test_reference_numerics_extremal__refs_abs_cpu_float128 +which failed on PPC. + +See https://github.com/pytorch/pytorch/pull/116859 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +index b80f7b79fca..382f32c0305 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h +@@ -226,8 +226,9 @@ class Vectorized { + } + + Vectorized abs_() const { +- auto ret = abs_2_(); +- return ret.elwise_sqrt(); ++ auto vi = el_mergeo(); ++ auto vr = el_mergee(); ++ return {Sleef_hypotd2_u05vsx(vr._vec0, vi._vec0), Sleef_hypotd2_u05vsx(vr._vec1, vi._vec1)}; + } + + Vectorized abs() const { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 7efffa76c3a..0e30742eb9b 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -274,8 +274,9 @@ class Vectorized { + } + + Vectorized abs_() const { +- auto ret = abs_2_(); +- return ret.elwise_sqrt(); ++ auto vi = el_mergeo(); ++ auto vr = el_mergee(); ++ return {Sleef_hypotf4_u05vsx(vr._vec0, vi._vec0), Sleef_hypotf4_u05vsx(vr._vec1, vi._vec1)}; + } + + Vectorized abs() const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch new file mode 100644 index 000000000000..5e7330f21c2f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-vsx-vector-div.patch @@ -0,0 +1,104 @@ +Fix overflow (to inf) in division of large complex values leading to failures in e.g. +test_reference_numerics_extremal__refs_abs_cpu_complex64 (test_unary_ufuncs) +See https://github.com/pytorch/pytorch/pull/116972 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +index 0e30742eb9b..5bff72e6874 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h +@@ -238,18 +238,14 @@ class Vectorized { + return loadu(tmp); + } + +- static Vectorized horizontal_add_permD8( ++ static Vectorized horizontal_add( + Vectorized& first, + Vectorized& second) { +- // we will simulate it differently with 6 instructions total +- // lets permute second so that we can add it getting horizontal sums +- auto first_perm = first.el_swapped(); // 2perm +- auto second_perm = second.el_swapped(); // 2perm +- // sum +- auto first_ret = first + first_perm; // 2add +- auto second_ret = second + second_perm; // 2 add +- // now lets choose evens +- return el_mergee(first_ret, second_ret); // 2 mergee's ++ // Operates on individual floats, see _mm_hadd_ps ++ // {f0+f1, s0+s1, f2+f3, s2+s3, ...} ++ // i.e. it sums the re and im of each value and interleaves first and second: ++ // {f_re0 + f_im0, s_re0 + s_im0, f_re1 + f_im1, s_re1 + s_im1, ...} ++ return el_mergee(first, second) + el_mergeo(first, second); + } + + static Vectorized horizontal_sub_permD8( +@@ -353,12 +349,19 @@ class Vectorized { + static Vectorized el_mergee( + Vectorized& first, + Vectorized& second) { +- // as mergee phased in , we can use vec_perm with mask + return { + vec_mergee(first._vecb0, second._vecb0), + vec_mergee(first._vecb1, second._vecb1)}; + } + ++ static Vectorized el_mergeo( ++ Vectorized& first, ++ Vectorized& second) { ++ return { ++ vec_mergeo(first._vecb0, second._vecb0), ++ vec_mergeo(first._vecb1, second._vecb1)}; ++ } ++ + Vectorized angle_() const { + // angle = atan2(b/a) + // auto b_a = _mm256_permute_ps(values, 0xB1); // b a +@@ -485,25 +488,20 @@ class Vectorized { + // re + im*i = (a + bi) / (c + di) + // re = (ac + bd)/abs_2() + // im = (bc - ad)/abs_2() +-#if 1 +- auto vi = b.el_mergeo(); +- auto vr = b.el_mergee(); +- auto abs_b = b.abs_2_(); +- vi = vi ^ isign_mask; +- auto ret = elwise_mult(vr); +- auto vx_swapped = el_swapped(); +- ret = vx_swapped.el_madd(vi, ret); +- ret = ret.elwise_div(abs_b); +-#else +- // Vectorized x86 simulation +- auto ac_bd = elwise_mult(b); +- auto d_c = b.el_swapped(); +- d_c = d_c ^ rsign_mask; +- auto ad_bc = elwise_mult(d_c); +- auto abs_b = b.abs_2_(); +- auto re_im = horizontal_add_permD8(ac_bd, ad_bc); +- auto ret = re_im.elwise_div(abs_b); +-#endif ++ auto fabs_cd = Vectorized{ ++ vec_andc(b._vec0, sign_mask), ++ vec_andc(b._vec1, sign_mask)}; // |c| |d| ++ auto fabs_dc = fabs_cd.el_swapped(); // |d| |c| ++ auto scale = fabs_cd.elwise_max(fabs_dc); // sc = max(|c|, |d|) ++ auto a2 = elwise_div(scale); // a/sc b/sc ++ auto b2 = b.elwise_div(scale); // c/sc d/sc ++ auto acbd2 = a2.elwise_mult(b2); // ac/sc^2 bd/sc^2 ++ auto dc2 = b2.el_swapped(); // d/sc c/sc ++ dc2 = dc2 ^ rsign_mask; // -d/sc c/sc ++ auto adbc2 = a2.elwise_mult(dc2); // -ad/sc^2 bc/sc^2 ++ auto ret = horizontal_add(acbd2, adbc2); // (ac+bd)/sc^2 (bc-ad)/sc^2 ++ auto denom2 = b2.abs_2_(); // (c^2+d^2)/sc^2 (c^2+d^2)/sc^2 ++ ret = ret.elwise_div(denom2); + return ret; + } + +@@ -628,6 +626,7 @@ class Vectorized { + DEFINE_MEMBER_OP(elwise_ge, ComplexFlt, vec_cmpge) + DEFINE_MEMBER_OP(elwise_lt, ComplexFlt, vec_cmplt) + DEFINE_MEMBER_OP(elwise_le, ComplexFlt, vec_cmple) ++ DEFINE_MEMBER_OP(elwise_max, ComplexFlt, vec_max) + }; + + template <> diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch new file mode 100644 index 000000000000..cb6028e1b062 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch @@ -0,0 +1,88 @@ +test_cpu_repro fails on e.g. PPC where no AVX is available +Failures are all of the kind + + assert metrics.generated_cpp_vec_kernel_count == 1 +AssertionError + +As this is expected, skip the affected tests. +See https://github.com/pytorch/pytorch/pull/117262 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/inductor/test_cpu_repro.py b/test/inductor/test_cpu_repro.py +index 102c5af5168..3bc107b960b 100644 +--- a/test/inductor/test_cpu_repro.py ++++ b/test/inductor/test_cpu_repro.py +@@ -56,6 +56,8 @@ TestCase = test_torchinductor.TestCase + aten = torch.ops.aten + check_model = test_torchinductor.check_model + ++requires_vectorization = unittest.skipUnless(codecache.valid_vec_isa_list(), ++ "Does not support vectorization") + + class LstmModule(torch.nn.Module): + def __init__( +@@ -2165,6 +2167,7 @@ class CPUReproTests(TestCase): + self.assertEqual(metrics.generated_kernel_count, 1) + self.assertTrue(same(fn(a, b, c, idx), opt_fn(a, b, c, idx))) + ++ @requires_vectorization + def test_lowp_fp_neg_abs(self): + def fn(x): + return x.neg().abs() +@@ -2177,6 +2180,7 @@ class CPUReproTests(TestCase): + assert metrics.cpp_to_dtype_count == 0 + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_transpose_non_contiguous(self): + def fn(a): + # From part of timm HaloAttn: +@@ -2214,6 +2218,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x,)) + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_non_contiguous_index_with_constant_stride(self): + def fn(x): + x1 = x[:, :, :, ::2] +@@ -2252,6 +2257,7 @@ class CPUReproTests(TestCase): + fn(torch.randn([8, 128])) + self.assertGreater(len(strings), 3) + ++ @requires_vectorization + def test_vertical_sum_cpu_only(self): + def fn1(a): + return a.sum(dim=0) +@@ -2269,6 +2275,7 @@ class CPUReproTests(TestCase): + self.common(fn2, (x,)) + assert metrics.generated_cpp_vec_kernel_count == 1 + ++ @requires_vectorization + def test_transpose_vertical_sum_cpu_only(self): + def fn(a, b): + c = a * b +@@ -2280,6 +2287,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x, y)) + assert metrics.generated_cpp_vec_kernel_count == 2 + ++ @requires_vectorization + def test_transpose_sum2d_cpu_only(self): + def fn(a, b): + c = a * b +@@ -2291,6 +2299,7 @@ class CPUReproTests(TestCase): + self.common(fn, (x, y)) + assert metrics.generated_cpp_vec_kernel_count == 2 + ++ @requires_vectorization + def test_transpose_sum_outer(self): + # https://github.com/pytorch/pytorch/issues/98573 + def fn(a): +@@ -2417,6 +2426,7 @@ class CPUReproTests(TestCase): + ) + self.assertEqual(metrics.generated_kernel_count, 1) + ++ @requires_vectorization + def test_scalar_mul_bfloat16(self): + def f(x): + return torch.ops.aten.mul.Tensor(x, 1.7015043497085571) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch new file mode 100644 index 000000000000..2386210fd235 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch @@ -0,0 +1,32 @@ +test_module_partitioner_functional_conv_relu_conv in test_fx.py fails with an IndexError +on e.g. POWER systems. + +Last part of the stacktrace: + File "/sympy/printing/printer.py", line 331, in _print + return printmethod(expr, **kwargs) + File "/torch/fx/experimental/symbolic_shapes.py", line 1575, in _print_Symbol + return self.print_source(self.symbol_to_source[expr][0]) +IndexError: list index out of range + +One cause is the missing MKLDNN and NNPACK (unavailable on PPC) making it skip some checks. +A workaround here is adding a check that has side effects but doesn't change the result. +That makes at least the test pass. +Another change in PyTorch 2.2.x also avoids that issue but is to large to backport. + +See https://github.com/pytorch/pytorch/issues/117033 + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/native/Convolution.cpp b/aten/src/ATen/native/Convolution.cpp +index 7af281a7cd9..3709d27b2bb 100644 +--- a/aten/src/ATen/native/Convolution.cpp ++++ b/aten/src/ATen/native/Convolution.cpp +@@ -543,7 +543,7 @@ struct ConvParams { + #endif + ; + #endif +- return false; ++ return (at::symint::size(weight, 2) < 17) && (at::symint::size(weight, 3) < 17) && false; + } + bool use_xnnpack(const at::Tensor& input, const at::Tensor& weight, + const at::OptionalArrayRef bias_sizes_opt) const { From f67580105bc1dc157f5922a522d046c3c448ea8d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 12 Jan 2024 15:39:02 +0100 Subject: [PATCH 0270/1193] adding easyconfigs: gcsfs-2023.12.2-foss-2023a.post1.eb --- .../gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb diff --git a/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb b/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb new file mode 100644 index 000000000000..1d010a873c3a --- /dev/null +++ b/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb @@ -0,0 +1,91 @@ +easyblock = "PythonBundle" + +name = 'gcsfs' +version = '2023.12.2' +versionsuffix = '.post1' + +homepage = 'https://github.com/fsspec/gcsfs' +description = """Pythonic file-system interface for Google Cloud Storage.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# builddependencies = [('protobuf', '24.0')] + +dependencies = [ + ('Python', '3.11.3'), + ('aiohttp', '3.8.5'), + ('poetry', '1.5.1'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('googleapis-common-protos', '1.62.0', { + 'modulename': 'google.api.annotations_pb2', + 'checksums': ['83f0ece9f94e5672cced82f592d2a5edf527a96ed1794f0bab36d5735c996277'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.3.0', { + 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-resumable-media', '2.7.0', { + 'modulename': 'google.resumable_media', + 'checksums': ['5f18f5fa9836f4b083162064a1c2c98c17239bfda9ca50ad970ccf905f3e625b'], + }), + ('google-crc32c', '1.5.0', { + 'modulename': 'google_crc32c', + 'checksums': ['89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7'], + }), + ('g', '0.0.3', { + 'checksums': ['988738c40b80bc382a2bfc776e86b616867601a882729296a1902c9c9e7cc4d6'], + }), + ('google-cloud-core', '2.4.1', { + 'modulename': 'google.cloud.environment_vars', + 'checksums': ['9b7749272a812bde58fff28868d0c5e2f585b82f37e09a1f6ed2d4d10f134073'], + }), + ('google-api-core', '2.15.0', { + 'modulename': 'google.api_core', + 'checksums': ['abc978a72658f14a2df1e5e12532effe40f94f868f6e23d95133bd6abcca35ca'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('fsspec', version, { + 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], + }), + ('google-auth', '2.26.2', { + 'modulename': 'google.auth', + 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], + }), + ('google-auth-oauthlib', '1.2.0', { + # 'modulename': 'google.auth.oauthlib', + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('google-cloud-storage', '2.14.0', { + 'modulename': 'google.cloud.storage', + 'checksums': ['2d23fcf59b55e7b45336729c148bb1c464468c69d5efbaee30f7201dd90eb97e'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s%(versionsuffix)s.tar.gz', + 'checksums': ['e38b7e59580a1e490d62d55a47cba33b49a941b01917c3d6f6cfd2563371ab7b'], + }), +] + +moduleclass = 'tools' From 7c12fb95c99f83f99233204f4bfd40775ef6c140 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 12 Jan 2024 15:48:24 +0100 Subject: [PATCH 0271/1193] adding easyconfigs: OpenFOAM-v2206-foss-2022a-64bitint.eb, METIS-5.1.0-GCCcore-11.3.0-64bitint.eb, SCOTCH-7.0.1-gompi-2022a-64bitint.eb --- .../METIS-5.1.0-GCCcore-11.3.0-64bitint.eb | 42 +++++++++++++++++ .../OpenFOAM-v2206-foss-2022a-64bitint.eb | 46 +++++++++++++++++++ .../SCOTCH-7.0.1-gompi-2022a-64bitint.eb | 26 +++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-64bitint.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-64bitint.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-64bitint.eb diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-64bitint.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-64bitint.eb new file mode 100644 index 000000000000..94ac2d3888fa --- /dev/null +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-64bitint.eb @@ -0,0 +1,42 @@ +name = 'METIS' +version = '5.1.0' +versionsuffix = '-64bitint' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' + +description = """ + METIS is a set of serial programs for partitioning graphs, partitioning + finite element meshes, and producing fill reducing orderings for sparse + matrices. The algorithms implemented in METIS are based on the multilevel + recursive-bisection, multilevel k-way, and multi-constraint partitioning + schemes. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] + +# We use 32bit for indices and 64bit for content +patches = [ + '%(name)s-%(version)s-use-doubles.patch', + '%(name)s_IDXTYPEWIDTH.patch', +] +checksums = [ + {'metis-5.1.0.tar.gz': '76faebe03f6c963127dbb73c13eab58c9a3faeae48779f049066a21c087c5db2'}, + {'METIS-5.1.0-use-doubles.patch': '7e38a3ec8f2b8e3d189239bade5b28c0dd1c564485050109164fa71a6a767c67'}, + {'METIS_IDXTYPEWIDTH.patch': 'e68cdbdd3b537d135d2bb487cf6f74a8e6410e204f019ad33d1afde6e242ce34'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = ['', 'shared=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-64bitint.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-64bitint.eb new file mode 100644 index 000000000000..ac8c13f3b097 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-64bitint.eb @@ -0,0 +1,46 @@ +name = 'OpenFOAM' +version = 'v2206' +versionsuffix = '-64bitint' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++11', 'vectorize': False, 'i8': True} + + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2206-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + 'db95eda4afb97ca870733b2d4201ef539099d0778e3f3eca9a075d4f1a0eea46', # OpenFOAM-v2206.tgz + '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972', # OpenFOAM-v2206-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + ('METIS', '5.1.0', '-64bitint'), + ('SCOTCH', '7.0.1', '-64bitint'), + ('KaHIP', '3.14'), + ('CGAL', '4.14.3'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-64bitint.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-64bitint.eb new file mode 100644 index 000000000000..d6d973678846 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-64bitint.eb @@ -0,0 +1,26 @@ +name = 'SCOTCH' +version = '7.0.1' +versionsuffix = '-64bitint' + +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' +description = """Software package and libraries for sequential and parallel graph partitioning, +static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'i8': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['0618e9bc33c02172ea7351600fce4fccd32fe00b3359c4aabb5e415f17c06fed'] +threadedmpi = False + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +moduleclass = 'math' From c33f11a72cb0bf8fa7fe22e594bc4bbe17b9f8bc Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 12 Jan 2024 16:12:25 +0100 Subject: [PATCH 0272/1193] adding easyconfigs: s3fs-2023.12.2-foss-2023a.eb --- .../s/s3fs/s3fs-2023.12.2-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/s/s3fs/s3fs-2023.12.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/s3fs/s3fs-2023.12.2-foss-2023a.eb b/easybuild/easyconfigs/s/s3fs/s3fs-2023.12.2-foss-2023a.eb new file mode 100644 index 000000000000..8f4065fc9832 --- /dev/null +++ b/easybuild/easyconfigs/s/s3fs/s3fs-2023.12.2-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 's3fs' +version = '2023.12.2' + +homepage = 'https://github.com/fsspec/s3fs/' +description = """S3FS builds on aiobotocore to provide a convenient Python filesystem interface for S3..""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('aiohttp', '3.8.5'), + ('wrapt', '1.15.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.33.13', { + 'checksums': ['fb577f4cb175605527458b04571451db1bd1a2036976b626206036acd4496617'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.9.0', { + 'checksums': ['4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e'], + }), + ('fsspec', version, { + 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], + }), + (name, version, { + 'checksums': ['b5ec07062481bbb45cb061b31984c7188d106e292c27033039e024e4ba5740dc'], + }), +] + +moduleclass = 'tools' From 7f96c443fa1154ce6f1e1c3b2bad162df6360fff Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Fri, 12 Jan 2024 16:22:41 +0100 Subject: [PATCH 0273/1193] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-12.3.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..85eb10386d6f --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('zlib', '1.2.13'), +] +dependencies = [ + ('Python', '3.11.3'), + ('bzip2', '1.0.8'), + ('gzip', '1.12'), +] + + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + +moduleclass = 'bio' From ef0cc1c301061b28cd8f38e92dc0122b314e1151 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 12 Jan 2024 17:28:04 +0100 Subject: [PATCH 0274/1193] rename DETONATE patch files rather than copying them --- .../d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb | 4 +- .../d/DETONATE/DETONATE-1.11-intel-2017b.eb | 8 +- ...atch => DETONATE-1.11_fix-cast-bool.patch} | 0 .../DETONATE/detonate-1.11_Intel-fixes.patch | 48 ------ .../d/DETONATE/detonate-1.11_fix-deps.patch | 144 ------------------ 5 files changed, 6 insertions(+), 198 deletions(-) rename easybuild/easyconfigs/d/DETONATE/{DETONATE-1.11_Intel-fixes.patch => DETONATE-1.11_fix-cast-bool.patch} (100%) delete mode 100644 easybuild/easyconfigs/d/DETONATE/detonate-1.11_Intel-fixes.patch delete mode 100644 easybuild/easyconfigs/d/DETONATE/detonate-1.11_fix-deps.patch diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb index 75907087a7c5..c1457cc041cd 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-GCC-12.3.0.eb @@ -17,13 +17,13 @@ source_urls = ['http://deweylab.biostat.wisc.edu/detonate/'] sources = ['detonate-1.11.tar.gz'] patches = [ 'DETONATE-%(version)s_fix-deps.patch', - 'DETONATE-%(version)s_Intel-fixes.patch', + 'DETONATE-%(version)s_fix-cast-bool.patch', 'DETONATE-%(version)s_include-fix.patch' ] checksums = [ {'detonate-1.11.tar.gz': 'e1d04af1b1d2504942a6941b346d430157da6117fac043b7ee83274717d99714'}, {'DETONATE-1.11_fix-deps.patch': '0ab353f66d5459e1fa18fa214026589fe214365f3532a3b9ea182757c7547691'}, - {'DETONATE-1.11_Intel-fixes.patch': 'c72a18250857883e7075ac512bbbd532e61a1aab38868d0dc932ca4bdc412817'}, + {'DETONATE-1.11_fix-cast-bool.patch': 'c72a18250857883e7075ac512bbbd532e61a1aab38868d0dc932ca4bdc412817'}, {'DETONATE-1.11_include-fix.patch': '9071fc8dbc6bfc26a9c4bb60befca890a26acf9668df2815a7f0038d8bcdd9f6'}, ] diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-intel-2017b.eb b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-intel-2017b.eb index a7078e2b055c..1b493a4e5db2 100644 --- a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-intel-2017b.eb +++ b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11-intel-2017b.eb @@ -15,13 +15,13 @@ toolchainopts = {'cstd': 'c++11'} source_urls = ['http://deweylab.biostat.wisc.edu/detonate/'] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'detonate-%(version)s_fix-deps.patch', - 'detonate-%(version)s_Intel-fixes.patch', + 'DETONATE-%(version)s_fix-deps.patch', + 'DETONATE-%(version)s_fix-cast-bool.patch', ] checksums = [ 'e1d04af1b1d2504942a6941b346d430157da6117fac043b7ee83274717d99714', # detonate-1.11.tar.gz - '0ab353f66d5459e1fa18fa214026589fe214365f3532a3b9ea182757c7547691', # detonate-1.11_fix-deps.patch - 'c72a18250857883e7075ac512bbbd532e61a1aab38868d0dc932ca4bdc412817', # detonate-1.11_Intel-fixes.patch + '0ab353f66d5459e1fa18fa214026589fe214365f3532a3b9ea182757c7547691', # DETONATE-1.11_fix-deps.patch + 'c72a18250857883e7075ac512bbbd532e61a1aab38868d0dc932ca4bdc412817', # DETONATE-1.11_fix-cast-bool.patch ] builddependencies = [('CMake', '3.10.1')] diff --git a/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_Intel-fixes.patch b/easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_fix-cast-bool.patch similarity index 100% rename from easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_Intel-fixes.patch rename to easybuild/easyconfigs/d/DETONATE/DETONATE-1.11_fix-cast-bool.patch diff --git a/easybuild/easyconfigs/d/DETONATE/detonate-1.11_Intel-fixes.patch b/easybuild/easyconfigs/d/DETONATE/detonate-1.11_Intel-fixes.patch deleted file mode 100644 index 150cb7a64012..000000000000 --- a/easybuild/easyconfigs/d/DETONATE/detonate-1.11_Intel-fixes.patch +++ /dev/null @@ -1,48 +0,0 @@ -fix compilation issues that occur with Intel compilers -error: no suitable conversion function from "std::basic_istream>" to "bool" exists - -author: Kenneth Hoste (HPC-UGent), with a bit of help from Ward Poelmans ---- detonate-1.11/rsem-eval/SingleHit.h.orig 2018-01-23 11:01:34.269328898 +0100 -+++ detonate-1.11/rsem-eval/SingleHit.h 2018-01-23 11:01:55.859848244 +0100 -@@ -43,7 +43,7 @@ - - bool SingleHit::read(std::istream& in) { - conprb = 0.0; -- return (in>>sid>>pos); -+ return static_cast(in>>sid>>pos); - } - - void SingleHit::write(std::ostream& out) { ---- detonate-1.11/rsem-eval/PairedEndHit.h.orig 2018-01-23 11:07:46.838260187 +0100 -+++ detonate-1.11/rsem-eval/PairedEndHit.h 2018-01-23 11:08:12.628872625 +0100 -@@ -26,7 +26,7 @@ - - bool PairedEndHit::read(std::istream& in) { - conprb = 0.0; -- return (in>>sid>>pos>>insertL); -+ return static_cast(in>>pos>>insertL); - } - - void PairedEndHit::write(std::ostream& out) { ---- detonate-1.11/rsem-eval/buildReadIndex.cpp.orig 2018-01-23 13:58:46.313840541 +0100 -+++ detonate-1.11/rsem-eval/buildReadIndex.cpp 2018-01-23 13:59:51.375415745 +0100 -@@ -35,15 +35,15 @@ - streampos pos = fin.tellg(); - success = true; - -- success = (getline(fin, line)); -+ success = static_cast(getline(fin, line)); - if (!success) continue; -- success = (getline(fin, line)); -+ success = static_cast(getline(fin, line)); - if (!success) continue; - - if (hasQ) { -- success = (getline(fin, line)); -+ success = static_cast(getline(fin, line)); - if (!success) continue; -- success = (getline(fin, line)); -+ success = static_cast(getline(fin, line)); - if (!success) continue; - } - diff --git a/easybuild/easyconfigs/d/DETONATE/detonate-1.11_fix-deps.patch b/easybuild/easyconfigs/d/DETONATE/detonate-1.11_fix-deps.patch deleted file mode 100644 index ab19abb1ad67..000000000000 --- a/easybuild/easyconfigs/d/DETONATE/detonate-1.11_fix-deps.patch +++ /dev/null @@ -1,144 +0,0 @@ -- fix compilation flags, use $CFLAGS passed by EasyBuild -- use Boost, SAMtools, sparsehash provided as dependencies via EasyBuild -author: Kenneth Hoste (HPC-UGent) ---- detonate-1.11/rsem-eval/Makefile.orig 2016-06-22 23:34:39.000000000 +0200 -+++ detonate-1.11/rsem-eval/Makefile 2018-01-23 14:47:47.714929147 +0100 -@@ -7,18 +7,15 @@ - - all : $(PROGRAMS) - --sam/libbam.a : -- cd sam ; ${MAKE} all -- - Transcript.h : utils.h - - Transcripts.h : utils.h my_assert.h Transcript.h - - rsem-extract-reference-transcripts : utils.h my_assert.h GTFItem.h Transcript.h Transcripts.h extractRef.cpp -- $(CC) -Wall -O3 extractRef.cpp -o rsem-extract-reference-transcripts -+ $(CC) $(CFLAGS) extractRef.cpp -o rsem-extract-reference-transcripts - - rsem-synthesis-reference-transcripts : utils.h my_assert.h Transcript.h Transcripts.h synthesisRef.cpp -- $(CC) -Wall -O3 synthesisRef.cpp -o rsem-synthesis-reference-transcripts -+ $(CC) $(CFLAGS) synthesisRef.cpp -o rsem-synthesis-reference-transcripts - - BowtieRefSeqPolicy.h : RefSeqPolicy.h - -@@ -28,10 +25,10 @@ - - - rsem-preref : preRef.o -- $(CC) preRef.o -o rsem-preref -+ $(CC) $(CFLAGS) preRef.o -o rsem-preref - - preRef.o : utils.h RefSeq.h Refs.h PolyARules.h RefSeqPolicy.h AlignerRefSeqPolicy.h preRef.cpp -- $(CC) $(COFLAGS) preRef.cpp -+ $(CC) -c -I $(CFLAGS) preRef.cpp - - - SingleRead.h : Read.h -@@ -49,14 +46,14 @@ - - SamParser.h : sam/sam.h sam/bam.h utils.h my_assert.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h Transcripts.h - --rsem-parse-alignments : parseIt.o sam/libbam.a -- $(CC) -o rsem-parse-alignments parseIt.o sam/libbam.a -lz -lpthread -+rsem-parse-alignments : parseIt.o -+ $(CC) -o rsem-parse-alignments parseIt.o ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread - - parseIt.o : utils.h RefSeq.h Refs.h GroupInfo.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h HitContainer.h SamParser.h Transcripts.h sam/sam.h sam/bam.h parseIt.cpp -- $(CC) -Wall -O2 -c -I. parseIt.cpp -+ $(CC) $(CFLAGS) -c -I. parseIt.cpp - - rsem-build-read-index : utils.h buildReadIndex.cpp -- $(CC) -O3 buildReadIndex.cpp -o rsem-build-read-index -+ $(CC) $(CFLAGS) buildReadIndex.cpp -o rsem-build-read-index - - - simul.h : boost/random.hpp -@@ -85,23 +82,23 @@ - - CalcEvalScore.h : utils.h my_assert.h Refs.h GroupInfo.h Transcript.h Transcripts.h ContigLengthDist.h - --rsem-eval-run-em : EM.o sam/libbam.a -- $(CC) -o rsem-eval-run-em EM.o sam/libbam.a -lz -lpthread -+rsem-eval-run-em : EM.o -+ $(CC) -o rsem-eval-run-em EM.o ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread - - EM.o : utils.h my_assert.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleHit.h PairedEndHit.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h GroupInfo.h HitContainer.h ReadIndex.h ReadReader.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h ModelParams.h RefSeq.h RefSeqPolicy.h PolyARules.h Profile.h NoiseProfile.h Transcript.h Transcripts.h HitWrapper.h BamWriter.h sam/bam.h sam/sam.h simul.h sam_rsem_aux.h sampling.h boost/random.hpp WriteResults.h boost/math/distributions/negative_binomial.hpp ContigLengthDist.h CalcEvalScore.h EM.cpp -- $(CC) $(COFLAGS) EM.cpp -+ $(CC) -c -I $(CFLAGS) EM.cpp - - rsem-simulate-reads : simulation.o - $(CC) -o rsem-simulate-reads simulation.o - - simulation.o : utils.h Read.h SingleRead.h SingleReadQ.h PairedEndRead.h PairedEndReadQ.h SingleModel.h SingleQModel.h PairedEndModel.h PairedEndQModel.h Refs.h RefSeq.h GroupInfo.h Transcript.h Transcripts.h Orientation.h LenDist.h RSPD.h QualDist.h QProfile.h NoiseQProfile.h Profile.h NoiseProfile.h simul.h boost/random.hpp WriteResults.h simulation.cpp -- $(CC) $(COFLAGS) simulation.cpp -+ $(CC) -c -I $(CFLAGS) simulation.cpp - --rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp sam/libbam.a -- $(CC) -O3 -Wall samValidator.cpp sam/libbam.a -lz -lpthread -o $@ -+rsem-sam-validator : sam/bam.h sam/sam.h my_assert.h samValidator.cpp -+ $(CC) $(CFLAGS) samValidator.cpp ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread -o $@ - --rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp sam/libbam.a -- $(CC) -O3 -Wall scanForPairedEndReads.cpp sam/libbam.a -lz -lpthread -o $@ -+rsem-scan-for-paired-end-reads : sam/bam.h sam/sam.h my_assert.h scanForPairedEndReads.cpp -+ $(CC) $(CFLAGS) scanForPairedEndReads.cpp ${EBROOTSAMTOOLS}/lib/libbam.a -lz -lpthread -o $@ - - clean : - rm -f *.o *~ $(PROGRAMS) ---- detonate-1.11/ref-eval/Makefile.orig 2016-06-22 23:34:39.000000000 +0200 -+++ detonate-1.11/ref-eval/Makefile 2018-01-23 15:10:47.078223944 +0100 -@@ -40,19 +40,19 @@ - - CXXFLAGS = -W -Wno-unused-parameter -g -O3 - CXXFLAGS_DEBUG = -g3 -fno-inline -O0 -Wall -Wextra --BOOST_INC = -Iboost --BOOST_LIB = boost/stage/lib/libboost_program_options.a boost/stage/lib/libboost_random.a -+BOOST_INC = -I${EBROOTBOOST}/include -+BOOST_LIB = ${EBROOTBOOST}/lib/libboost_program_options.a ${EBROOTBOOST}/lib/libboost_random.a - LEMON_INC = -Ilemon/build -Ilemon/lemon-main-473c71baff72 - LEMON_LIB = lemon/build/lemon/libemon.a -lpthread - CITY_INC = -Icity/install/include - CITY_LIB = city/install/lib/libcityhash.a - SAM_INC = -I. --SAM_LIB = sam/libbam.a --SH_INC = -Isparsehash/include -+SAM_LIB = ${EBROOTSAMTOOLS}/lib/libbam.a -+SH_INC = -I${EBROOTSPARSEHASH}/include - DL_INC = -Ideweylab - INC = $(BOOST_INC) $(LEMON_INC) $(CITY_INC) $(SAM_INC) $(SH_INC) $(DL_INC) - LIB = $(BOOST_LIB) $(LEMON_LIB) $(CITY_LIB) $(SAM_LIB) --TEST_LIB = boost/stage/lib/libboost_unit_test_framework.a -+TEST_LIB = ${EBROOTBOOST}/lib/libboost_unit_test_framework.a -lboost_system - - ifeq (${NEED_CMAKE}, yes) - wd := $(shell pwd) -@@ -140,7 +140,7 @@ - @echo - cd sparsehash && $(MAKE) - --ref-eval: ref-eval.cpp boost/finished lemon/finished city/finished sam/libbam.a sparsehash/finished -+ref-eval: ref-eval.cpp lemon/finished city/finished - @echo - @echo ----------------------------- - @echo - Building REF-EVAL itself. - -@@ -148,7 +148,7 @@ - @echo - $(CXX) $(OMP) $(CXXFLAGS) $(INC) ref-eval.cpp $(LIB) -o ref-eval - --ref-eval-estimate-true-assembly: ref-eval-estimate-true-assembly.cpp boost/finished lemon/finished city/finished sam/libbam.a sparsehash/finished -+ref-eval-estimate-true-assembly: ref-eval-estimate-true-assembly.cpp lemon/finished city/finished - @echo - @echo --------------------------------------------------- - @echo - Building program to estimate the true assembly. - -@@ -170,7 +170,7 @@ - all_tests := test_lazycsv test_line_stream test_blast test_psl test_pairset test_mask test_alignment_segment test_re_matched test_re_kc - - .PHONY: test --test: test_msg ${all_tests} boost/finished lemon/finished city/finished sparsehash/finished -+test: test_msg ${all_tests} lemon/finished city/finished - ./test_lazycsv - ./test_line_stream - ./test_blast From 6edb19a45df06bed0b57be8266c4a87c7f0b9508 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 12:01:54 +0100 Subject: [PATCH 0275/1193] adding easyconfigs: KronaTools-2.8.1-GCCcore-12.2.0.eb --- .../KronaTools-2.8.1-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..13e81b38941f --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# by Easybuild when it is tidying up +# This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder +# so users can install their own Taxonomy database + +easyblock = 'Tarball' + +name = 'KronaTools' +version = '2.8.1' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from +several Bioinformatics tools as well as from text and XML files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['f3ab44bf172e1f846e8977c7443d2e0c9676b421b26c50e91fa996d70a6bfd10'] + +dependencies = [('Perl', '5.36.0')] + +postinstallcmds = [ + "cd %(installdir)s && ./install.pl --prefix=%(installdir)s;", + "cd %(installdir)s/bin && ln -s ../updateAccessions.sh . && ln -s ../updateTaxonomy.sh .", +] + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], +} + +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + +moduleclass = 'bio' From 7e69ddd0929866b4e3b0b97e1b7172bd7053d11e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 12:03:38 +0100 Subject: [PATCH 0276/1193] adding easyconfigs: openpyxl-3.1.2-GCCcore-13.2.0.eb --- .../openpyxl/openpyxl-3.1.2-GCCcore-13.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..f2b7ecdd0447 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.1.2' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('lxml', '4.9.3'), + ('Pillow', '10.2.0'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['a6f5977418eff3b2d5500d54d9db50c8277a368436f4e4f8ddb1be3422870184'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 4ae056c360f0f353d9045202df21321cc257bd41 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 13 Jan 2024 12:28:19 +0100 Subject: [PATCH 0277/1193] adding easyconfigs: GROMACS-2023.3-foss-2023a-CUDA-12.1.1-PLUMED-2.9.0.eb and patches: GROMACS-2023.3_skip_test_for_plumed.patch --- ...3.3-foss-2023a-CUDA-12.1.1-PLUMED-2.9.0.eb | 101 ++++++++++++++++++ .../GROMACS-2023.3_skip_test_for_plumed.patch | 26 +++++ 2 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-CUDA-12.1.1-PLUMED-2.9.0.eb create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3_skip_test_for_plumed.patch diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-CUDA-12.1.1-PLUMED-2.9.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-CUDA-12.1.1-PLUMED-2.9.0.eb new file mode 100644 index 000000000000..0dd91c1da838 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2023a-CUDA-12.1.1-PLUMED-2.9.0.eb @@ -0,0 +1,101 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.3' +_plumedver = '2.9.0' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = _cuda_suffix + '-PLUMED-%s' % _plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI builds +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build +next to PLUMED.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True, 'extra_cxxflags': '-fpermissive'} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + '%(name)s-2023.1_fix_tests_for_gmx_thread_mpi.patch', + '%(name)s-%(version)s_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), + ('Doxygen', '1.9.7'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', _cuda_suffix), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), + ('PLUMED', _plumedver), +] + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -fpermissive" ' + +# PLUMED 2.9.0 is compatible with GROMACS 2023; 2023.3 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3_skip_test_for_plumed.patch b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3_skip_test_for_plumed.patch new file mode 100644 index 000000000000..d50dc00f45c5 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3_skip_test_for_plumed.patch @@ -0,0 +1,26 @@ +Skip test checking output of 'mdrun -h' when patched with PLUMED +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur gromacs-2023.3.orig/src/programs/mdrun/tests/CMakeLists.txt gromacs-2023.3/src/programs/mdrun/tests/CMakeLists.txt +--- gromacs-2023.3.orig/src/programs/mdrun/tests/CMakeLists.txt 2023-10-19 10:40:01.000000000 +0200 ++++ gromacs-2023.3/src/programs/mdrun/tests/CMakeLists.txt 2024-01-13 12:01:40.289374738 +0100 +@@ -49,20 +49,6 @@ + # To avoid running into test timeouts, some end-to-end tests of mdrun + # functionality are split off. This can be rearranged in future as we + # see fit. +-set(testname "MdrunOutputTests") +-set(exename "mdrun-output-test") +- +-gmx_add_gtest_executable(${exename} +- CPP_SOURCE_FILES +- compressed_x_output.cpp +- helpwriting.cpp +- outputfiles.cpp +- trajectory_writing.cpp +- # pseudo-library for code for mdrun +- $ +- ) +-target_link_libraries(${exename} PRIVATE mdrun_test_infrastructure) +-gmx_register_gtest_test(${testname} ${exename} OPENMP_THREADS 2 INTEGRATION_TEST IGNORE_LEAKS QUICK_GPU_TEST) + + set(testname "MdrunModulesTests") + set(exename "mdrun-modules-test") From 0b21f2dc5d18acda151097b117147e74fdeb98f4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 13:54:32 +0100 Subject: [PATCH 0278/1193] adding easyconfigs: remake-4.3+dbg-1.6-GCCcore-11.3.0.eb --- .../remake-4.3+dbg-1.6-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..e43ec77c556f --- /dev/null +++ b/easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'remake' +version = '4.3+dbg-1.6' + +homepage = 'https://bashdb.sourceforge.net/remake' +description = """remake is an enhanced version of GNU Make that adds improved error reporting, better tracing, + profiling and a debugger""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/rocky/remake/releases/download/remake-%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['f6a0c6179cd92524ad5dd04787477c0cd45afb5822d977be93d083b810647b87'] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['bin/remake'], + 'dirs': ['share'], +} + +sanity_check_commands = [ + "remake --help", +] + +moduleclass = 'tools' From f7881d8ef562fe084842b3894371d370d2af4e12 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 14:47:18 +0100 Subject: [PATCH 0279/1193] {vis}[foss/2022a] PyOpenCL v2023.1.4, pocl v1.8 w/ CUDA 11.7.0 --- ...yOpenCL-2023.1.4-foss-2022a-CUDA-11.7.0.eb | 39 +++++++++++++++ .../p/pocl/pocl-1.8-GCC-11.3.0-CUDA-11.7.0.eb | 48 +++++++++++++++++++ 2 files changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..83b28565e3f3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenCL' +version = '2023.1.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://mathema.tician.de/software/pyopencl/" +description = """PyOpenCL lets you access GPUs and other massively parallel compute devices from Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('pocl', '1.8', versionsuffix), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('appdirs', '1.4.4', { + 'checksums': ['7d5d0167b2b1ba821647616af46a749d1c653740dd0d2415100fe26e27afdf41'], + }), + ('pytools', '2023.1.1', { + 'checksums': ['80637873d206f6bcedf7cdb46ad93e868acb4ea2256db052dfcca872bdd0321f'], + }), + ('pyopencl', version, { + 'preinstallopts': "./configure.py --cl-pretend-version=1.2 && ", + 'checksums': ['220174efca900e9d5de5aef2aa1b77a6f2550501de92b035a91013aeae4d4c5e'], + }), +] + +sanity_check_commands = [ + "python -c 'import pyopencl as cl; platform = cl.get_platforms()[0]; print(platform.get_devices())'", +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 000000000000..28bc17ce36f3 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '1.8' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://portablecl.org' +description = "Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['pocl-%(version)s_fix-header-install.patch'] +checksums = [ + '0f63377ae1826e16e90038fc8e7f65029be4ff6f9b059f6907174b5c0d1f8ab2', # v1.8.tar.gz + '97dc45437ae7464bda9f13088720482804b8a19a4e71067196daa86af487222d', # pocl-1.8_fix-header-install.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Clang', '13.0.1', versionsuffix), + ('hwloc', '2.7.1'), + ('libtool', '2.4.7'), + ('libxml2', '2.9.13'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 5ef14d153e5c5f0ed0dd6897182f06c7013685b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 15:14:47 +0100 Subject: [PATCH 0280/1193] adding easyconfigs: nichenetr-2.0.4-foss-2022b-R-4.2.2.eb --- .../nichenetr-2.0.4-foss-2022b-R-4.2.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/n/nichenetr/nichenetr-2.0.4-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/n/nichenetr/nichenetr-2.0.4-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/n/nichenetr/nichenetr-2.0.4-foss-2022b-R-4.2.2.eb new file mode 100644 index 000000000000..f7e62cf08dd1 --- /dev/null +++ b/easybuild/easyconfigs/n/nichenetr/nichenetr-2.0.4-foss-2022b-R-4.2.2.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'nichenetr' +version = '2.0.4' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/saeyslab/nichenetr' +description = """R implementation of the NicheNet method, + to predict active ligand-target links between interacting cells""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/saeyslab/nichenetr/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['52239f245802bdb2bc1822099896dd1776d9cec9d62c85caa2a97264347adde2'] + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From e89d81e27f2ee0b87941c20d328dba9ad5f43caf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 16:28:53 +0100 Subject: [PATCH 0281/1193] install required newer boto3 version as extension in PyTorch-Lightning v2.1.2 with foss/2022b --- .../b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb | 39 ------------------- .../PyTorch-Lightning-2.1.2-foss-2022b.eb | 14 ++++++- 2 files changed, 13 insertions(+), 40 deletions(-) delete mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb deleted file mode 100644 index 08804838492a..000000000000 --- a/easybuild/easyconfigs/b/boto3/boto3-1.34.10-GCCcore-12.2.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'boto3' -version = '1.34.10' - -homepage = 'https://github.com/boto/boto3' -description = """Boto3 is the Amazon Web Services (AWS) Software Development Kit -(SDK) for Python, which allows Python developers to write software that makes -use of services like Amazon S3 and Amazon EC2.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -builddependencies = [ - ('binutils', '2.39'), -] - -dependencies = [ - ('Python', '3.10.8'), -] - -exts_list = [ - ('botocore', '1.34.12', { - 'checksums': ['53dfc19d63f2b70821e9804b7ecfc5e50fc84d9bd6818359b27db629ef43ec59'], - }), - ('jmespath', '1.0.1', { - 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], - }), - ('s3transfer', '0.10.0', { - 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], - }), - (name, version, { - 'checksums': ['ea14bc081d9cb40291133f89b3ad9070be360e152d6a98263af7b97a6534b669'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb index b1d36af59482..0696a5bcb676 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.2-foss-2022b.eb @@ -19,7 +19,6 @@ dependencies = [ ('tqdm', '4.64.1'), ('tensorboardX', '2.6.2.2'), ('pydantic', '2.5.3'), - ('boto3', '1.34.10'), ('typing-extensions', '4.9.0'), ] @@ -135,6 +134,19 @@ exts_list = [ 'preinstallopts': """sed -i "s/botocore>.*',/botocore',/g" setup.py && """, 'checksums': ['4dc1e20da4561ae662219ca95b20f923328c3106764a741bec00e98eb6680f7e'], }), + # s3fs requires recent botocore + ('botocore', '1.34.18', { + 'checksums': ['85a77e72560a45b0dfdad94f92f5e114c82be07a51bb2d19dd310dab8be158cf'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.0', { + 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], + }), + ('boto3', '1.34.18', { + 'checksums': ['5e38ca63007e903a7efe0a1751a0374d287b50d7bc148b9d3d495cdf74a0b712'], + }), ('s3fs', '2023.12.2', { 'checksums': ['b5ec07062481bbb45cb061b31984c7188d106e292c27033039e024e4ba5740dc'], }), From cdf92ebbcbe180a4c1189f61ff0e76bd3cfe552b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 18:02:05 +0100 Subject: [PATCH 0282/1193] make sure we get a static binary for Philosopher by setting $CGO_ENABLED to 0 before running 'go build' --- .../easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb index c852b7dea6c3..cb66397c2247 100644 --- a/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/Philosopher/Philosopher-5.0.0-GCC-11.3.0.eb @@ -20,7 +20,9 @@ builddependencies = [ ] prebuildopts = 'export CC="$CC" CFLAGS="$CFLAGS" && ' -buildopts = "deploy && make philosopher" +# we want to make sure we get a static binary, +# see also https://mt165.co.uk/blog/static-link-go +buildopts = "deploy && export CGO_ENABLED=0 && make philosopher" files_to_copy = [ (['%(namelower)s'], 'bin'), From 3aac781e68e32d46b7ff9920f155aa3cadfc3b76 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 20:12:50 +0100 Subject: [PATCH 0283/1193] apply suggested changes in easyconfig for sinto MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb | 15 ++------------- 1 file changed, 2 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb b/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb index 2bade413d0cc..8a7ac5cfae14 100644 --- a/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb +++ b/easybuild/easyconfigs/s/sinto/sinto-0.7.4-foss-2021a.eb @@ -1,19 +1,10 @@ easyblock = 'PythonPackage' name = 'sinto' - version = '0.7.4' homepage = 'https://timoast.github.io/sinto/index.html' - -description = """Sinto is a toolkit for processing aligned single-cell data. Sinto includes functions to: - - Subset reads from a BAM file by cell barcode - - Create a scATAC-seq fragments file from a BAM file - - Add read tags to a BAM file according to cell barcode information -""" +description = """Sinto is a toolkit for processing aligned single-cell data.""" toolchain = {'name': 'foss', 'version': '2021a'} @@ -26,10 +17,8 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ] -download_dep_fail = True - use_pip = True - +download_dep_fail = True sanity_pip_check = True sanity_check_commands = ['%(name)s --version'] From e2981ed6cf9e4126488e383efcfe5cd3e4aa20fd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 20:22:26 +0100 Subject: [PATCH 0284/1193] remove Python versionsuffix for PCMSolver with iimpi/2020b --- ...pi-2020b-Python-3.8.6.eb => PCMSolver-1.2.3-iimpi-2020b.eb} | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) rename easybuild/easyconfigs/p/PCMSolver/{PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb => PCMSolver-1.2.3-iimpi-2020b.eb} (92%) diff --git a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb similarity index 92% rename from easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb rename to easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb index 3fb0888f0eb9..2ee4d8e8eb51 100644 --- a/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b-Python-3.8.6.eb +++ b/easybuild/easyconfigs/p/PCMSolver/PCMSolver-1.2.3-iimpi-2020b.eb @@ -2,7 +2,6 @@ easyblock = 'CMakeMake' name = 'PCMSolver' version = '1.2.3' -versionsuffix = '-Python-%(pyver)s' homepage = 'https://pcmsolver.readthedocs.org' description = """An API for the Polarizable Continuum Model.""" @@ -18,7 +17,7 @@ checksums = ['d1ef6bdc268a2e719b36c85125c3543df7a26e1a738daf4483f4ded0c76f5b60'] builddependencies = [ ('CMake', '3.18.4'), - ('Eigen', '3.3.8', '', ('GCCcore', '10.2.0')), + ('Eigen', '3.3.8'), ] dependencies = [ From 7dab8a140f62293e1a37db159de9896dc1a2c32f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 20:42:58 +0100 Subject: [PATCH 0285/1193] use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 --- ...Clang-16.0.6-GCCcore-12.3.0-CUDA-12.1.1.eb | 59 +++++++++++++++++++ ...yOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb | 6 +- .../p/pocl/pocl-4.0-GCC-12.3.0-CUDA-12.1.1.eb | 50 ++++++++++++++++ 3 files changed, 114 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 000000000000..10a89a27b240 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang/Clang-16.0.6-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,59 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2015 Dmitri Gribenko, Ward Poelmans +# Authors:: Dmitri Gribenko +# Authors:: Ward Poelmans +# License:: GPLv2 or later, MIT, three-clause BSD. +# $Id$ +## + +name = 'Clang' +version = '16.0.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://clang.llvm.org/' +description = """C, C++, Objective-C compiler, based on LLVM. Does not + include C++ standard library -- use libstdc++ from GCC.""" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s"] +sources = [ + 'llvm-project-%(version)s.src.tar.xz', +] +checksums = ['ce5e71081d17ce9e86d7cbcfa28c4b04b9300f8fb7e78422b1feb6bc52c3028e'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Perl', '5.36.1'), + # Including Python bindings would require this as a runtime dep + ('Python', '3.11.3'), +] +dependencies = [ + # since Clang is a compiler, binutils is a runtime dependency too + ('binutils', '2.40'), + ('hwloc', '2.9.1'), + ('libxml2', '2.11.4'), + ('ncurses', '6.4'), + ('GMP', '6.2.1'), + ('Z3', '4.12.2'), + ('CUDA', '12.1.1', '', SYSTEM), +] + +# enabling RTTI makes the flang compiler need to link to libc++ so instead of +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 +# you would need +# flang-new -flang-experimental-exec -fopenmp hello_openmp.f90 -l c++ +enable_rtti = False + +assertions = True +python_bindings = False +skip_all_tests = True + +llvm_runtimes = ['libunwind', 'libcxx', 'libcxxabi'] +llvm_projects = ['polly', 'lld', 'lldb', 'clang-tools-extra', 'flang'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb index eb7726440138..57cb3d5be997 100644 --- a/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyOpenCL/PyOpenCL-2023.1.4-foss-2023a-CUDA-12.1.1.eb @@ -13,7 +13,7 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), - ('pocl', '4.0'), + ('pocl', '4.0', versionsuffix), ] use_pip = True @@ -29,4 +29,8 @@ exts_list = [ }), ] +sanity_check_commands = [ + "python -c 'import pyopencl as cl; platform = cl.get_platforms()[0]; print(platform.get_devices())'", +] + moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 000000000000..7632513ead63 --- /dev/null +++ b/easybuild/easyconfigs/p/pocl/pocl-4.0-GCC-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,50 @@ +# https://github.com/pocl/pocl/issues/1219 +# "PoCL 3.1 supports LLVM only up to 15", so need 4.0 for working with Clang 16 +easyblock = 'CMakeNinja' + +name = 'pocl' +version = '4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://portablecl.org' +description = """PoCL is a portable open source (MIT-licensed) implementation +of the OpenCL standard (1.2 with some 2.0 features supported).""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pocl/pocl/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [] +checksums = [ + '7f4e8ab608b3191c2b21e3f13c193f1344b40aba7738f78762f7b88f45e8ce03', # v4.0.tar.gz +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Clang', '16.0.6', versionsuffix), + ('hwloc', '2.9.1'), + ('libtool', '2.4.7'), + ('libxml2', '2.11.4'), +] + +separate_build_dir = True + +# disable attempt to find an ICD loader, always build libOpenCL.so, enable CUDA +configopts = "-DENABLE_ICD=0 -DINSTALL_OPENCL_HEADERS=1 -DENABLE_CUDA=1 " +# make sure we use the easybuild Clang +configopts += "-DWITH_LLVM_CONFIG=$EBROOTCLANG/bin/llvm-config -DSTATIC_LLVM=ON " +# avoid host CPU auto-detection (which may fail on recent CPUs) +configopts += "-DLLC_HOST_CPU=native " + +sanity_check_paths = { + 'files': ['bin/poclcc', 'lib64/libOpenCL.%s' % SHLIB_EXT], + 'dirs': ['include/CL', 'lib64/pkgconfig'], +} + +moduleclass = 'lib' From 6cace47299e75952a678acd7f3d4348c022ca584 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 13 Jan 2024 21:02:56 +0100 Subject: [PATCH 0286/1193] consistently add pkgconf build dependency to recent p11-kit easyconfigs --- .../easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb | 5 ++++- .../easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb | 6 ++++-- .../easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb | 5 ++++- 3 files changed, 12 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb index d6be94570068..3f422baafaad 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.0-GCCcore-10.3.0.eb @@ -16,7 +16,10 @@ source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version) sources = [SOURCE_TAR_XZ] checksums = ['81e6140584f635e4e956a1b93a32239acf3811ff5b2d3a5c6094e94e99d2c685'] -builddependencies = [('binutils', '2.36.1')] +builddependencies = [ + ('binutils', '2.36.1'), + ('pkgconf', '1.8.0'), +] dependencies = [ ('libtasn1', '4.17.0'), diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb index 54de0646472d..62561fca6530 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.2.0.eb @@ -16,10 +16,12 @@ source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version) sources = [SOURCE_TAR_XZ] checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] -builddependencies = [('binutils', '2.37')] +builddependencies = [ + ('binutils', '2.37'), + ('pkgconf', '1.8.0'), +] dependencies = [ - ('pkgconf', '1.8.0'), ('libtasn1', '4.18.0'), ('libffi', '3.4.2'), ] diff --git a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb index 4a07aaf936cd..08cb956cf61c 100644 --- a/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb @@ -16,7 +16,10 @@ source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version) sources = [SOURCE_TAR_XZ] checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] -builddependencies = [('binutils', '2.38')] +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] dependencies = [ ('libtasn1', '4.19.0'), From ee5f51175fdbb63b4add831a184e91a980f2b99e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 Jan 2024 09:52:46 +0100 Subject: [PATCH 0287/1193] add description to patch for Bison 3.7.1 --- easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb | 9 +++++---- ...d_gcc_fix.patch => Bison-3.7.1_fix-parse-state.patch} | 3 +++ 2 files changed, 8 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/b/Bison/{Bison-3.7.1-old_gcc_fix.patch => Bison-3.7.1_fix-parse-state.patch} (81%) diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb b/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb index f056aaf84221..41ecce369aa8 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1.eb @@ -15,16 +15,17 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -checksums = ['1dd952839cf0d5a8178c691eeae40dc48fa50d18dcce648b1ad9ae0195367d13'] +patches = ['Bison-3.7.1_fix-parse-state.patch'] +checksums = [ + {'bison-3.7.1.tar.gz': '1dd952839cf0d5a8178c691eeae40dc48fa50d18dcce648b1ad9ae0195367d13'}, + {'Bison-3.7.1_fix-parse-state.patch': 'd2f27ee047e380240c1e787e75ab70a465f973a39b28ab1a8be13e7bb1a99416'}, +] builddependencies = [ ('M4', '1.4.18'), ] # Uncomment if you encounter "error: redefinition of typedef 'parse_state'" during build -#patches = [ -# 'Bison-3.7.1-old_gcc_fix.patch' -#] sanity_check_paths = { 'files': ['bin/%s' % x for x in ['bison', 'yacc']] + [('lib/liby.a', 'lib64/liby.a')], diff --git a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch b/easybuild/easyconfigs/b/Bison/Bison-3.7.1_fix-parse-state.patch similarity index 81% rename from easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch rename to easybuild/easyconfigs/b/Bison/Bison-3.7.1_fix-parse-state.patch index 94e39a6c22ee..a71de14a6d91 100644 --- a/easybuild/easyconfigs/b/Bison/Bison-3.7.1-old_gcc_fix.patch +++ b/easybuild/easyconfigs/b/Bison/Bison-3.7.1_fix-parse-state.patch @@ -1,3 +1,6 @@ +fix for: +src/parse-simulation.c:61: error: redefinition of typedef 'parse_state' +author: Patryk Belzak (Wroclaw University) --- src/parse-simulation.c.orig 2020-08-02 07:59:31.000000000 +0200 +++ src/parse-simulation.c 2021-02-24 11:12:02.385501723 +0100 @@ -28,7 +28,7 @@ From af6228f58c59b8fc1d765ed098d09301bf06f0ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 Jan 2024 10:19:40 +0100 Subject: [PATCH 0288/1193] add sanity check command for Julia + also set `$JULIA_DEPOT_PATH` --- .../easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb | 11 ++++++++++- 1 file changed, 10 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb index f6ac056dc63c..225d86de75a2 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.6.0-linux-aarch64.eb @@ -18,8 +18,17 @@ sources = ['%(namelower)s-%(version)s%(versionsuffix)s.tar.gz'] checksums = ['0f496972d26cea88151204d03e6bd87702aa1ff983de3b1e4f320c48ef67325f'] sanity_check_paths = { - 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.so'], + 'files': ['bin/julia', 'include/julia/julia.h', 'lib/libjulia.%s' % SHLIB_EXT], 'dirs': ['bin', 'etc', 'include', 'lib', 'share'] } +sanity_check_commands = ['julia --help'] + +modextravars = { + # Use default DEPOT_PATH where first entry is user's depot + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths + 'JULIA_DEPOT_PATH': ':', +} + moduleclass = 'lang' From d6717f5246a7e13e8124ac6c32cd17555a5031c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 14 Jan 2024 15:56:37 +0100 Subject: [PATCH 0289/1193] trivial style fixes in PyQt5 v5.15.10 and SIP v6.8.1 easyconfigs --- .../p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb | 12 ++++-------- .../easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb | 4 +++- 2 files changed, 7 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb index 6d22a9bf0501..531882e6f565 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.10-GCCcore-12.3.0.eb @@ -19,8 +19,6 @@ dependencies = [ ('Python', '3.11.3'), ('Qt5', '5.15.10'), ] - - local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' @@ -47,8 +45,6 @@ local_pyqt5_configopts = [ ] + local_sip_configopts_common local_pyqtwebengine_configopts = local_sip_configopts_common - - default_easyblock = 'PythonPackage' components = [ @@ -68,8 +64,8 @@ components = [ 'configure_without_installdir': True, 'preconfigopts': local_setup_env, 'configopts': ' '.join(local_pyqt5_configopts), - 'prebuildopts': local_setup_env + 'cd build &&', - 'preinstallopts': 'cd build &&', + 'prebuildopts': local_setup_env + "cd build && ", + 'preinstallopts': "cd build && ", 'checksums': ['d46b7804b1b10a4ff91753f8113e5b5580d2b4462f3226288e2d84497334898a'], }), ('PyQtWebEngine', '5.15.6', { @@ -81,8 +77,8 @@ components = [ 'configure_without_installdir': True, 'preconfigopts': local_setup_env, 'configopts': ' '.join(local_pyqtwebengine_configopts), - 'prebuildopts': local_setup_env + 'cd build &&', - 'preinstallopts': 'cd build &&', + 'prebuildopts': local_setup_env + "cd build && ", + 'preinstallopts': "cd build && ", 'checksums': ['ae241ef2a61c782939c58b52c2aea53ad99b30f3934c8358d5e0a6ebb3fd0721'], }) ] diff --git a/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb index f97983ba89b4..266456f2dc19 100644 --- a/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/SIP/SIP-6.8.1-GCCcore-12.3.0.eb @@ -24,8 +24,9 @@ dependencies = [ ('PLY', '3.11'), ] -use_pip = True download_dep_fail = True +use_pip = True + local_tools = ['build', 'distinfo', 'install', 'module', 'sdist', 'wheel'] sanity_check_paths = { 'files': ['bin/sip-%s' % x for x in local_tools], @@ -37,4 +38,5 @@ sanity_pip_check = True sanity_check_commands = ['sip-%s --help' % x for x in local_tools] options = {'modulename': 'sipbuild'} + moduleclass = 'lang' From 4d2188778bed679bbb3708a71ebaa6eb710ff2ca Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 15 Jan 2024 07:31:11 +0100 Subject: [PATCH 0290/1193] Change version of Pysam to match the default for the toolchain. --- .../easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb index 7f596a503167..6d8e9f256971 100644 --- a/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb +++ b/easybuild/easyconfigs/v/Vamb/Vamb-3.0.9-foss-2021b-CUDA-11.5.2.eb @@ -16,7 +16,7 @@ dependencies = [ ('CUDA', '11.5.2', '', SYSTEM), ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), - ('Pysam', '0.18.0'), + ('Pysam', '0.17.0'), ('PyTorch', '1.12.1', versionsuffix), ] From 69056f7c75a2f4cb2f312f90bb22b4a081bbf20e Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 15 Jan 2024 09:55:00 +0100 Subject: [PATCH 0291/1193] adding easyconfigs: VSCode-cli-1.85.1-x64.eb --- .../v/VSCode-cli/VSCode-cli-1.85.1-x64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb diff --git a/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb b/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb new file mode 100644 index 000000000000..9ad26dcede50 --- /dev/null +++ b/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'VSCode-cli' +version = '1.85.1' +versionsuffix = '-x64' + +homepage = 'https://code.visualstudio.com/' +description = ''' + Visual Studio Code is a lightweight but powerful source code editor + which runs on your desktop and is available for Windows, macOS and + Linux. It comes with built-in support for JavaScript, TypeScript and + Node.js and has a rich ecosystem of extensions for other languages + and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin + your journey with VS Code with these introductory videos. +''' + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] +sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['code'], + 'dirs': [] +} + +sanity_check_commands = ["code --help"] + +moduleclass = 'devel' From 809c9dda9a2ab1cdceaf287ffcf452885031fb33 Mon Sep 17 00:00:00 2001 From: lara Date: Mon, 15 Jan 2024 09:58:12 +0100 Subject: [PATCH 0292/1193] change name and location of VSCode-1.85.1-cli-x64.eb to VSCode-cli-1.85.1-x64.eb --- .../v/VSCode/VSCode-1.85.1-cli-x64.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb deleted file mode 100644 index aa41c968952e..000000000000 --- a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.1-cli-x64.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'Tarball' - -name = 'VSCode' -version = '1.85.1' -versionsuffix = '-cli-x64' - -homepage = 'https://code.visualstudio.com/' -description = ''' - Visual Studio Code is a lightweight but powerful source code editor - which runs on your desktop and is available for Windows, macOS and - Linux. It comes with built-in support for JavaScript, TypeScript and - Node.js and has a rich ecosystem of extensions for other languages - and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin - your journey with VS Code with these introductory videos. -''' - -toolchain = {'name': 'system', 'version': 'system'} - -source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] -sources = [{ - 'download_filename': 'vscode_cli_alpine_x64_cli.tar.gz', - 'filename': 'vscode-%(version)s%(versionsuffix)s.tar.gz', -}] -checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['code'], - 'dirs': [] -} - -sanity_check_commands = ["code --help"] - -moduleclass = 'devel' From 7e4849f3c046baa207e850a672505f1a06490a78 Mon Sep 17 00:00:00 2001 From: lara Date: Mon, 15 Jan 2024 10:00:45 +0100 Subject: [PATCH 0293/1193] specify version in downloaded file --- easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb b/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb index 9ad26dcede50..69c007bebba1 100644 --- a/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb +++ b/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb @@ -17,7 +17,10 @@ description = ''' toolchain = {'name': 'system', 'version': 'system'} source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] -sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +sources = [{ + 'download_filename': 'vscode_cli_alpine_x64_cli.tar.gz', + 'filename': 'vscode-%(version)s%(versionsuffix)s.tar.gz', +}] checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] modextrapaths = {'PATH': ''} From 0d270439df0ccb5915d49efb8f255cb96398c65b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 15 Jan 2024 10:37:10 +0100 Subject: [PATCH 0294/1193] change in version, cleaned --- .../gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb b/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb new file mode 100644 index 000000000000..44cc04085aec --- /dev/null +++ b/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb @@ -0,0 +1,86 @@ +easyblock = "PythonBundle" + +name = 'gcsfs' +version = '2023.12.2.post1' + +homepage = 'https://github.com/fsspec/gcsfs' +description = """Pythonic file-system interface for Google Cloud Storage.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('aiohttp', '3.8.5'), + ('poetry', '1.5.1'), + ('protobuf-python', '4.24.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('googleapis-common-protos', '1.62.0', { + 'modulename': 'google.api.annotations_pb2', + 'checksums': ['83f0ece9f94e5672cced82f592d2a5edf527a96ed1794f0bab36d5735c996277'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('pyasn1-modules', '0.3.0', { + 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-resumable-media', '2.7.0', { + 'modulename': 'google.resumable_media', + 'checksums': ['5f18f5fa9836f4b083162064a1c2c98c17239bfda9ca50ad970ccf905f3e625b'], + }), + ('google-crc32c', '1.5.0', { + 'modulename': 'google_crc32c', + 'checksums': ['89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7'], + }), + ('g', '0.0.3', { + 'checksums': ['988738c40b80bc382a2bfc776e86b616867601a882729296a1902c9c9e7cc4d6'], + }), + ('google-cloud-core', '2.4.1', { + 'modulename': 'google.cloud.environment_vars', + 'checksums': ['9b7749272a812bde58fff28868d0c5e2f585b82f37e09a1f6ed2d4d10f134073'], + }), + ('google-api-core', '2.15.0', { + 'modulename': 'google.api_core', + 'checksums': ['abc978a72658f14a2df1e5e12532effe40f94f868f6e23d95133bd6abcca35ca'], + }), + ('decorator', '5.1.1', { + 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], + }), + ('fsspec', '2023.12.2', { + 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], + }), + ('google-auth', '2.26.2', { + 'modulename': 'google.auth', + 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('google-cloud-storage', '2.14.0', { + 'modulename': 'google.cloud.storage', + 'checksums': ['2d23fcf59b55e7b45336729c148bb1c464468c69d5efbaee30f7201dd90eb97e'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + (name, version, { + 'checksums': ['e38b7e59580a1e490d62d55a47cba33b49a941b01917c3d6f6cfd2563371ab7b'], + }), +] + +moduleclass = 'tools' From 5b473e654b60459b9308c8452f7a85eba1fe1599 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 15 Jan 2024 11:11:37 +0100 Subject: [PATCH 0295/1193] adding easyconfigs: devbio-napari-0.10.1-foss-2022a-CUDA-11.7.0.eb --- ...io-napari-0.10.1-foss-2022a-CUDA-11.7.0.eb | 230 ++++++++++++++++++ 1 file changed, 230 insertions(+) create mode 100644 easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..6d8faf24fe6f --- /dev/null +++ b/easybuild/easyconfigs/d/devbio-napari/devbio-napari-0.10.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,230 @@ +easyblock = 'PythonBundle' + +name = 'devbio-napari' +version = '0.10.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/haesleinhuepf/devbio-napari' +description = """A bundle of napari plugins useful for 3D+t image + processing and analysis for studying developmental biology.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('napari', '0.4.18'), + ('jupyter-server', '1.21.0'), + ('JupyterLab', '3.5.0'), + ('Seaborn', '0.12.1'), + ('scikit-learn', '1.1.2'), + ('SimpleITK', '2.1.1.2'), + ('PyQtGraph', '0.13.3'), + ('Deprecated', '1.2.13'), + ('imagecodecs', '2022.9.26'), + ('HDBSCAN', '0.8.29'), + ('umap-learn', '0.5.3'), + ('PyOpenCL', '2023.1.4', versionsuffix), + ('Mako', '1.2.0'), + ('autopep8', '2.0.4'), + ('Qt5', '5.15.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('napari-tools-menu', '0.1.19', { + 'checksums': ['6b58ac45d7fe84bc5975e7a53142340d5d62beff9ade0f2f58d7a3a4a0a8e8f8'], + }), + ('napari-assistant', '0.4.7', { + 'checksums': ['e18e0509c77907dae7b5ec66bebf33ca4fc5833553a3115ecca513f4702e3603'], + }), + ('napari-time-slicer', '0.5.0', { + 'checksums': ['950d3b35d9f1657178201da73de56d038e9bf4e257cf120882081f2707f1e074'], + }), + ('napari-workflows', '0.2.10', { + 'checksums': ['d48f2020693b4b8c1dd639668a3b1588115beac8f19f42394fc241fc1672be12'], + }), + ('pyclesperanto_prototype', '0.24.1', { + 'checksums': ['b2f2cd56bc382813b9477f07f75ce5afbf4cc24c6fd1734a577f602442f7c027'], + }), + ('stackview', '0.7.2', { + 'checksums': ['f417319e3c14384144198bc26cc0e5909a2262e8778f2d7e7b68396690ae797b'], + }), + ('reikna', '0.8.0', { + 'checksums': ['7e96b53dfa3910069f83b3e085ad7b1ba9391b5ddf744ae3725bf43a7fee6322'], + }), + ('pystackreg', '0.2.7', { + 'checksums': ['c3df8b42bb9f4d44ec7ba44b3c061d7ea7481ab62318c24a25ffdb22afbaf3ab'], + }), + ('loguru', '0.7.2', { + 'checksums': ['e671a53522515f34fd406340ee968cb9ecafbc4b36c679da03c18fd8d0bd51ac'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('czifile', '2019.7.2', { + 'checksums': ['04c0e6bed3b24d1bf42bc2cf899a5a08986641379305ce88600fd1c710486436'], + }), + ('imageio-ffmpeg', '0.4.9', { + 'checksums': ['39bcd1660118ef360fa4047456501071364661aa9d9021d3d26c58f1ee2081f5'], + }), + ('apoc', '0.12.0', { + 'checksums': ['c6e5264f2ac0420e5f8e2b23ad16927126d75280bb12f0341480ef9853973263'], + }), + ('ipycanvas', '0.13.1', { + 'checksums': ['f9c3940681bc38383390f8c46ea5d8445d6e11c6da6484c37d89df5ae1dac131'], + }), + ('ipyevents', '2.0.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['60c2a9e992bdc41e8577aa27e57b124efafa48a59a3bff886029fe5700d546b3'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('transforms3d', '0.4.1', { + 'checksums': ['31c755266a0b0a222488b8d039f6f325cf486c52728c03e307ce047b2fad1179'], + }), + ('comm', '0.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2da8d9ebb8dd7bfc247adaff99f24dce705638a8042b85cb995066793e391001'], + }), + # overwrites installed version + ('debugpy', '1.8.0', { + 'source_tmpl': SOURCE_ZIP, + 'checksums': ['12af2c55b419521e33d5fb21bd022df0b5eb267c3e178f1d374a63a2a6bdccd0'], + }), + # overwrites installed version + ('ipykernel', '6.27.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['dab88b47f112f9f7df62236511023c9bdeef67abc73af7c652e4ce4441601686'], + }), + # overwrites installed version + ('platformdirs', '2.6.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['83c8f6d04389165de7c9b6f0c682439697887bca0aa2f1c87ef1826be3584490'], + }), + # overwrites installed version + ('jupyter_core', '5.5.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['e11e02cd8ae0a9de5c6c44abf5727df9f2581055afe00b22183f621ba3585805'], + }), + # overwrites installed version + ('traitlets', '5.14.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['f14949d23829023013c47df20b4a76ccd1a85effb786dc060f34de7948361b33'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('mdit_py_plugins', '0.4.0', { + 'checksums': ['d8ab27e9aed6c38aa716819fedfde15ca275715955f8a185a8e1cf90fb1d2c1b'], + }), + ('jupytext', '1.15.2', { + 'checksums': ['c9976e24d834e991906c1de55af4b6d512d764f6372aabae45fc1ea72b589173'], + }), + ('napari-accelerated-pixel-and-object-classification', '0.14.1', { + 'checksums': ['2f626a9c2d671bf32cade62df74666eef328e6dc3f6d7f3ab6091a992131fb5c'], + }), + ('napari_animation', '0.0.7', { + 'preinstallopts': 'sed -i "s/__version__/version/g" napari_animation/animation.py && ', + 'checksums': ['301cce1d4629b18e618b7e1f1ea8885058171388ee0248f58ee78bdb25e8d72c'], + }), + ('napari-blob-detection', '0.0.2', { + 'checksums': ['a036c6f05e852ca0d332358249ec6c442c1ebdb83781e0609d9b146990e6f938'], + }), + ('napari-brightness-contrast', '0.1.8', { + 'checksums': ['88e0db47817a487b0db2b426ccfea88a57cbbf0185bf3ee0770fba81ed205dda'], + }), + ('napari-clusters-plotter', '0.7.3', { + 'checksums': ['3947e0c3e2335046526e6b92159c013e3e7b498eecd5b766cf1cbdd0239776df'], + }), + ('napari-crop', '0.1.9', { + 'checksums': ['54949ae74ab2fe118d33309d31b8c7eb7368de65428f1008038b82232d8856bd'], + }), + ('napari-curtain', '0.1.1', { + 'checksums': ['611bbabc2194ea749066bcd3cf6363174259c709dc3177142415400ba015f98c'], + }), + ('napari-czifile2', '0.2.7', { + 'checksums': ['67ca9b3d72aac804aba4ee3b34083f59d21134ee426de95a797733573ac2ffab'], + }), + ('napari-folder-browser', '0.1.3', { + 'checksums': ['c7144f8c0b321a30b64ad58928ed2efe65029f19670f0a650070506ae4551b76'], + }), + ('napari-layer-details-display', '0.1.5', { + 'checksums': ['cbee36e6bfa34415a2a102b60e5fb803e8f6b72d4ebc527b0cffc5dda10b2ae0'], + }), + ('napari-mouse-controls', '0.1.3', { + 'checksums': ['0dd9ee41146a3cb73ff8cf9378e242331d2ea9b0c4088188b4bce1650a45c7e6'], + }), + ('napari-plot-profile', '0.2.2', { + 'checksums': ['1a1f087b23eaa71a16f0ffde66e965fd7f6b69e5d52b3664c7db295f30fed501'], + }), + ('napari-plugin-search', '0.1.4', { + 'checksums': ['6dcc0793d072777c8d0cfebff89281252e57e13f8e13a8e0458a9ba7d86a06a0'], + }), + ('napari_pyclesperanto_assistant', '0.22.1', { + # import napari_pyclesperanto_assistant fails without GUI + # but it has been tested with GUI with following command: + # `unset SESSION_MANAGER && python -c "import napari_pyclesperanto_assistant"` + # the `SESSION_MANAGER` needs to be unset to avoid the following message: + # `WARNING: Qt: Session management error: Authentication Rejected, reason : None of the + # authentication protocols specified are supported and host-based authentication failed` + 'modulename': False, + 'checksums': ['6df5e59e105d91f49826d57b2c61091271f62bba9d061dcb9c0c12d3ca000843'], + }), + ('napari_pystackreg', '0.1.4', { + 'checksums': ['ea3fb0b3ecc7b90b64f44c1ced4a85a6cf8231b07e5985ad59a6c1c152cd4cb3'], + }), + ('napari-roi', '0.1.8', { + 'checksums': ['0123238ee652931ed0bc90421ddf76d1d58c0d4c89790a8512c5649e88620729'], + }), + ('napari-segment-blobs-and-things-with-membranes', '0.3.7', { + 'checksums': ['7decc02f61d8499094a61cde6f69c1af5669815b5c8d4f1854ac1536c8e76862'], + }), + ('napari-simpleitk-image-processing', '0.4.5', { + 'checksums': ['b690d38aa67cdce3ae9e9b38f5ea98aa2bb3fcfb7b41943c56c68ed5df70ba3c'], + }), + ('napari-skimage-regionprops', '0.10.1', { + 'checksums': ['a25f8a84ad78f5d09074a32d84996fb6ff900bf82369dfb50501872d23dc22bc'], + }), + ('napari-tabu', '0.1.5', { + 'checksums': ['106be1897bb0670af06cb6dba90dc9a9faa3c5e7ba5017a8b216315749649ac7'], + }), + ('napari-workflow-inspector', '0.2.2', { + 'checksums': ['c7f1709ab537fc3b7c51bf353da305b4fe0adb025ec066df2cbaa4764810ec4f'], + }), + ('napari-workflow-optimizer', '0.1.4', { + 'checksums': ['e756ab013740cdc89fbb2626291386579ec8ce30ec30153a1b79517d7790f9c2'], + }), + ('PlatyMatch', '0.0.3', { + 'checksums': ['8fc7c437c1565c51744320ef09a91de72366beebdaa44780eaac2598eb3d810b'], + }), + ('RedLionfish', '0.9', { + 'modulename': 'RedLionfishDeconv', + 'checksums': ['82b76bf093851fc062448e8b764e846701bf890e64d7e82bf7cf11a7cf2c235b'], + }), + ('the-segmentation-game', '0.2.0', { + 'checksums': ['4bbf4deadecb84efc893c6cea2d51e90374181589f2034050aa3cf8fa65872f3'], + }), + (name, version, { + # reqired npe2 version limit is not necessary since 0.10.1 + # see https://github.com/haesleinhuepf/devbio-napari/issues/41#issuecomment-1594583026 + 'preinstallopts': "sed -i 's/npe2.*/npe2/g' requirements.txt setup.cfg &&", + 'checksums': ['c0bd80fbd3087128690259e25ecc5b13f42c09a99617229f97d6b696279d32a0'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'from devbio_napari._viewer import devbio_napari_viewer'"] + +moduleclass = 'vis' From f9245d2495183a45534d4dfeccebee9d1fcbfebc Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 15 Jan 2024 14:04:52 +0100 Subject: [PATCH 0296/1193] adding easyconfigs: PostgreSQL-16.1-GCCcore-13.2.0.eb --- .../PostgreSQL-16.1-GCCcore-13.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..a2b79b4e50a8 --- /dev/null +++ b/easybuild/easyconfigs/p/PostgreSQL/PostgreSQL-16.1-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'PostgreSQL' +version = '16.1' + +homepage = 'https://www.postgresql.org/' +description = """PostgreSQL is a powerful, open source object-relational database system. + It is fully ACID compliant, has full support for foreign keys, + joins, views, triggers, and stored procedures (in multiple languages). + It includes most SQL:2008 data types, including INTEGER, + NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. + It also supports storage of binary large objects, including pictures, + sounds, or video. It has native programming interfaces for C/C++, Java, + .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['http://ftp.postgresql.org/pub/source/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bf0564725613f7c57f1c3ebf5c909b3ec58b9cfb3d81b4bb1209d88767065a87'] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Perl', '5.38.0'), + ('Python', '3.11.5'), +] + +dependencies = [ + ('libreadline', '8.2'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-python --with-openssl --without-icu' + +sanity_check_paths = { + 'files': ['bin/psql', 'bin/pg_config', 'lib/libpq.a', 'lib/libpq.%s' % SHLIB_EXT], + 'dirs': ['share/postgresql'], +} + +moduleclass = 'data' From 5db3e109d7cd2bdec81fa3d2aa08463401c3a5ad Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 15 Jan 2024 14:41:28 +0100 Subject: [PATCH 0297/1193] adding easyconfigs: Brotli-python-1.1.0-GCCcore-13.2.0.eb --- .../Brotli-python-1.1.0-GCCcore-13.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.1.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.1.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..5e9aae8b0256 --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli-python/Brotli-python-1.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Brotli-python' +version = '1.1.0' + +homepage = 'https://github.com/google/brotli' +description = """Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination + of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio + comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate + but offers more dense compression. +The specification of the Brotli Compressed Data Format is defined in RFC 7932.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/B/Brotli'] +sources = ['Brotli-%(version)s.tar.gz'] +checksums = ['81de08ac11bcb85841e440c13611c00b67d3bf82698314928d0b676362546724'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Brotli', '1.1.0'), + ('Python', '3.11.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'brotli'} + +moduleclass = 'tools' From 2ac3146af821f136c7f4ecff9ebdde6c854fd7ac Mon Sep 17 00:00:00 2001 From: sam Date: Mon, 15 Jan 2024 16:25:05 +0100 Subject: [PATCH 0298/1193] add exception and change versionsuffix to int64 --- ...int.eb => METIS-5.1.0-GCCcore-11.3.0-int64.eb} | 2 +- ...tint.eb => OpenFOAM-v2206-foss-2022a-int64.eb} | 6 +++--- ...itint.eb => SCOTCH-7.0.1-gompi-2022a-int64.eb} | 2 +- test/easyconfigs/easyconfigs.py | 15 +++++++++++++++ 4 files changed, 20 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/METIS/{METIS-5.1.0-GCCcore-11.3.0-64bitint.eb => METIS-5.1.0-GCCcore-11.3.0-int64.eb} (97%) rename easybuild/easyconfigs/o/OpenFOAM/{OpenFOAM-v2206-foss-2022a-64bitint.eb => OpenFOAM-v2206-foss-2022a-int64.eb} (93%) rename easybuild/easyconfigs/s/SCOTCH/{SCOTCH-7.0.1-gompi-2022a-64bitint.eb => SCOTCH-7.0.1-gompi-2022a-int64.eb} (96%) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-64bitint.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb similarity index 97% rename from easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-64bitint.eb rename to easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb index 94ac2d3888fa..2c2187c05807 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-64bitint.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb @@ -1,6 +1,6 @@ name = 'METIS' version = '5.1.0' -versionsuffix = '-64bitint' +versionsuffix = '-int64' homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/metis/overview' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-64bitint.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb similarity index 93% rename from easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-64bitint.eb rename to easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb index ac8c13f3b097..60bf0d8cf75e 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-64bitint.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb @@ -1,6 +1,6 @@ name = 'OpenFOAM' version = 'v2206' -versionsuffix = '-64bitint' +versionsuffix = '-int64' homepage = 'https://www.openfoam.com/' description = """OpenFOAM is a free, open source CFD software package. @@ -36,8 +36,8 @@ builddependencies = [ dependencies = [ ('libreadline', '8.1.2'), ('ncurses', '6.3'), - ('METIS', '5.1.0', '-64bitint'), - ('SCOTCH', '7.0.1', '-64bitint'), + ('METIS', '5.1.0', versionsuffix), + ('SCOTCH', '7.0.1', versionsuffix), ('KaHIP', '3.14'), ('CGAL', '4.14.3'), ('gnuplot', '5.4.4'), diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-64bitint.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-int64.eb similarity index 96% rename from easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-64bitint.eb rename to easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-int64.eb index d6d973678846..20ccbdb5deff 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-64bitint.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-gompi-2022a-int64.eb @@ -1,6 +1,6 @@ name = 'SCOTCH' version = '7.0.1' -versionsuffix = '-64bitint' +versionsuffix = '-int64' homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 76152b79d406..32450f7df66b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -484,6 +484,21 @@ def check_dep_vars(self, gen, dep, dep_vars): if len(dep_vars) == 1: break + # for some dependencies, we allow exceptions for software with the same version + # but with a -64bit-int versionsuffix in both the dependency and all its dependents + int_64bit_deps = ['SCOTCH', 'METIS'] + if dep in int_64bit_deps and len(dep_vars) > 1: + unique_dep_vers = {version_regex.search(x).group('version') for x in list(dep_vars)} + if len(unique_dep_vers) == 1: + for key in list(dep_vars): + if all(re.search('-64bit-int', v) for v in dep_vars[key]) and re.search( + '; versionsuffix: .*-64bit-int', key + ): + dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break + # filter out variants that are specific to a particular version of CUDA cuda_dep_vars = [v for v in dep_vars.keys() if '-CUDA' in v] if len(dep_vars) >= len(cuda_dep_vars) and len(dep_vars) > 1: From 58af1e7aa71b5818ea38614d4728d1047d094efa Mon Sep 17 00:00:00 2001 From: sam Date: Mon, 15 Jan 2024 16:30:26 +0100 Subject: [PATCH 0299/1193] fix exception --- test/easyconfigs/easyconfigs.py | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 32450f7df66b..41a322acdb46 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -485,14 +485,14 @@ def check_dep_vars(self, gen, dep, dep_vars): break # for some dependencies, we allow exceptions for software with the same version - # but with a -64bit-int versionsuffix in both the dependency and all its dependents - int_64bit_deps = ['SCOTCH', 'METIS'] - if dep in int_64bit_deps and len(dep_vars) > 1: + # but with a -int64 versionsuffix in both the dependency and all its dependents + int64_deps = ['SCOTCH', 'METIS'] + if dep in int64_deps and len(dep_vars) > 1: unique_dep_vers = {version_regex.search(x).group('version') for x in list(dep_vars)} if len(unique_dep_vers) == 1: for key in list(dep_vars): - if all(re.search('-64bit-int', v) for v in dep_vars[key]) and re.search( - '; versionsuffix: .*-64bit-int', key + if all(re.search('-int64', v) for v in dep_vars[key]) and re.search( + '; versionsuffix: .*-int64', key ): dep_vars.pop(key) # always retain at least one dep variant From 2caf366f475c9c82b47d4292b2a65279e7c3b91d Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 15 Jan 2024 16:37:45 +0100 Subject: [PATCH 0300/1193] Update OpenFOAM-v2206-foss-2022a-int64.eb Add Paraview dependency --- .../easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb index 60bf0d8cf75e..b830cfdf044d 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a-int64.eb @@ -40,6 +40,7 @@ dependencies = [ ('SCOTCH', '7.0.1', versionsuffix), ('KaHIP', '3.14'), ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), ('gnuplot', '5.4.4'), ] From c3931edc5dd98b2a091204f700eb0382550cd721 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 15 Jan 2024 16:40:36 +0100 Subject: [PATCH 0301/1193] Update METIS-5.1.0-GCCcore-11.3.0-int64.eb Fix comment --- .../easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb index 2c2187c05807..a413a69cd5bc 100644 --- a/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb +++ b/easybuild/easyconfigs/m/METIS/METIS-5.1.0-GCCcore-11.3.0-int64.eb @@ -21,7 +21,7 @@ source_urls = [ ] sources = [SOURCELOWER_TAR_GZ] -# We use 32bit for indices and 64bit for content +# We use 64 bit for indices and for content patches = [ '%(name)s-%(version)s-use-doubles.patch', '%(name)s_IDXTYPEWIDTH.patch', From fcd6e0eceabe90af1a32784963b7df3c5b8c57b9 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 15 Jan 2024 19:42:41 +0100 Subject: [PATCH 0302/1193] adding easyconfigs: Biopython-1.83-foss-2023a.eb --- .../b/Biopython/Biopython-1.83-foss-2023a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb new file mode 100644 index 000000000000..de31433aa3de --- /dev/null +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb @@ -0,0 +1,46 @@ +# Updated from previous easyconfig +# Author: Robert Mijakovic +# Update: Pavel Tománek (INUITS) + +easyblock = 'PythonPackage' + +name = 'Biopython' +version = '1.83' + +homepage = 'https://www.biopython.org' +description = """Biopython is a set of freely available tools for biological + computation written in Python by an international team of developers. It is + a distributed collaborative effort to develop Python libraries and + applications which address the needs of current and future work in + bioinformatics. """ + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://biopython.org/DIST'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['78e6bfb78de63034037afd35fe77cb6e0a9e5b62706becf78a7d922b16ed83f7'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# Run only tests that don't require internet connection +runtest = 'python setup.py test --offline' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/Bio', + 'lib/python%(pyshortver)s/site-packages/BioSQL'] +} + +# extra check to ensure numpy dependency is available +sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' \ No newline at end of file From 8e9bf8ab24b4e3ad04a094e6caea2740a79daf08 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 15 Jan 2024 19:44:34 +0100 Subject: [PATCH 0303/1193] Added end newline --- easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb b/easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb index de31433aa3de..70b13923d394 100644 --- a/easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb +++ b/easybuild/easyconfigs/b/Biopython/Biopython-1.83-foss-2023a.eb @@ -43,4 +43,4 @@ sanity_check_commands = ["python -c 'import Bio.MarkovModel'"] options = {'modulename': 'Bio'} -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 2b568042d7fed16dfdd1536c6b46d22fea03290c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Jan 2024 10:47:39 +0100 Subject: [PATCH 0304/1193] {chem}[foss/2023a] ESPResSo v4.2.1, Boost.MPI v1.82.0, Pint v0.23, typing-extensions v4.9.0 --- .../Boost.MPI/Boost.MPI-1.82.0-gompi-2023a.eb | 29 ++++++++++ .../e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb | 55 +++++++++++++++++++ .../p/Pint/Pint-0.23-GCCcore-12.3.0.eb | 31 +++++++++++ .../typing-extensions-4.9.0-GCCcore-12.3.0.eb | 22 ++++++++ 4 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.82.0-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.23-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.82.0-gompi-2023a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.82.0-gompi-2023a.eb new file mode 100644 index 000000000000..c40cdfadf46d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.82.0-gompi-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.82.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['66a469b6e608a51f8347236f4912e27dc5c60c60d7d53ae9bfe4683316c6f04c'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('zstd', '1.5.5'), + ('ICU', '73.2'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb new file mode 100644 index 000000000000..6d4ef208058b --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'ESPResSo' +version = '4.2.1' + +homepage = 'https://espressomd.org/wordpress' +description = """A software package for performing and analyzing scientific Molecular Dynamics simulations.""" + +source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'] + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost.MPI', '1.82.0'), + ('HDF5', '1.14.0'), + ('Mesa', '23.1.4'), + ('GSL', '2.7'), + ('IPython', '8.14.0'), + ('Pint', '0.23'), +] + +configopts = ' -DCMAKE_SKIP_RPATH=OFF -DWITH_TESTS=ON -DWITH_CUDA=OFF' +# make sure the right Python is used (note: -DPython3_EXECUTABLE or -DPython_EXECUTABLE does not work!) +configopts += ' -DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +runtest = 'check_unit_tests && make check_python' + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +_binaries = ['ipypresso', 'pypresso'] +_libs = [ + 'Espresso_config', 'Espresso_core', 'Espresso_script_interface', 'Espresso_shapes', + '_init', 'analyze', 'code_info', 'electrokinetics', 'galilei', + 'integrate', 'interactions', 'lb', 'particle_data', 'polymer', 'profiler', + 'script_interface', 'system', 'thermostat', 'utils', 'version', +] + +_lib_path = 'lib/python%(pyshortver)s/site-packages/espressomd' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries] + + [_lib_path + '/%s.' % x + SHLIB_EXT for x in _libs], + 'dirs': ['bin', 'lib'] +} + +sanity_check_commands = ['pypresso -h', 'ipypresso -h'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.23-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.23-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d0b98ea01021 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.23-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.23' + +homepage = 'https://github.com/hgrecco/pint' +description = """Pint is a Python package to define, operate and +manipulate physical quantities: the product of a numerical value and a +unit of measurement. It allows arithmetic operations between them and +conversions from and to different units.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1509b91606dbc52527c600a4ef74ffac12fff70688aff20e9072409346ec9b4'] + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.9.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..44a057a01fd9 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.9.0' + +homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' +description = 'Typing Extensions – Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 70ed1fee112a6e3db9da5dd184c613ed4659306a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 16 Jan 2024 12:03:33 +0100 Subject: [PATCH 0305/1193] adding easyconfigs: rMATS-turbo-4.2.0-gfbf-2023a.eb and patches: rMATS-turbo-4.2.0_bamtools_as_dependency.patch --- .../rMATS-turbo-4.2.0-gfbf-2023a.eb | 70 +++++++++++++++++++ ...S-turbo-4.2.0_bamtools_as_dependency.patch | 37 ++++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0-gfbf-2023a.eb b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0-gfbf-2023a.eb new file mode 100644 index 000000000000..6d1ce5784b5c --- /dev/null +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0-gfbf-2023a.eb @@ -0,0 +1,70 @@ +easyblock = 'Bundle' + +name = 'rMATS-turbo' +version = '4.2.0' + +homepage = 'https://github.com/Xinglab/rmats-turbo' +description = """rMATS turbo is the C/Cython version of rMATS (refer to https://rnaseq-mats.sourceforge.io).""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'openmp': True} + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('GSL', '2.7'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11a'), + ('BamTools', '2.5.2'), +] + +local_ldflags = " -lm -lgsl -lgslcblas $LIBLAPACK" +local_buildopts = ' CC="$CC" CXX="$CXX" FC="$FC" LDFLAGS="%s"' % local_ldflags + +default_component_specs = { + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/Xinglab/%(name)s/archive/refs/tags/'], + 'checksums': ['80fd32ffa00190b2eb3fcefcd4efb0d466a808c5e80bc91419a71bc033cdbd72'], +} + +components = [ + (name, version, { + 'easyblock': 'MakeCp', + 'start_dir': 'rmats-turbo-%(version)s/rMATS_C', + 'buildopts': "%s" % local_buildopts, + 'files_to_copy': [(['rMATSexe', '../rmats.py', '../rMATS_C', '../rMATS_R', '../rMATS_P'], 'bin')] + }), + ('rmats-turbo-python', version, { + 'easyblock': 'PythonPackage', + 'patches': ['rMATS-turbo-%(version)s_bamtools_as_dependency.patch'], + 'checksums': [ + '80fd32ffa00190b2eb3fcefcd4efb0d466a808c5e80bc91419a71bc033cdbd72', + 'a4c70e3d8ef9723fcb801d39a62c132f8f1903fb3a60dad330de895c12f5f7e7', + ], + 'start_dir': 'rmats-turbo-%(version)s/rMATS_pipeline', + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'options': {'modulename': 'rmatspipeline'}, + }), +] + +modextrapaths = { + 'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages'] +} + +postinstallcmds = ["chmod a+x %(installdir)s/bin/rmats.py"] + +sanity_check_commands = [ + 'rmats.py --version', +] + +sanity_check_paths = { + 'files': ['bin/rMATSexe', 'bin/rmats.py'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch new file mode 100644 index 000000000000..a1d613184c2f --- /dev/null +++ b/easybuild/easyconfigs/r/rMATS-turbo/rMATS-turbo-4.2.0_bamtools_as_dependency.patch @@ -0,0 +1,37 @@ +# author: Denis Kristak +# this patch makes rMATS take bamtools from official dependencies, not from the downloaded folder +# updated for new version by Samuel Moors (Vrije Universiteit Brussel) +diff -ur rmats-turbo-4.2.0.orig/rMATS_pipeline/setup.py rmats-turbo-4.2.0/rMATS_pipeline/setup.py +--- rmats-turbo-4.2.0.orig/rMATS_pipeline/setup.py 2023-10-18 18:33:06.000000000 +0200 ++++ rmats-turbo-4.2.0/rMATS_pipeline/setup.py 2024-01-16 10:59:40.272152202 +0100 +@@ -5,15 +5,16 @@ + from Cython.Build import cythonize + from Cython.Distutils import build_ext + +-bamtools_include = [os.path.abspath('../bamtools/include'),] +-bamtools_lib = [os.path.abspath('../bamtools/lib'),] ++bamtools_root = os.environ['EBROOTBAMTOOLS'] ++bamtools_include = bamtools_root + '/include/bamtools' ++bamtools_lib = bamtools_root + '/lib' + source_pattern = 'rmatspipeline/%s.pyx' + + asevent_ext = [ +- Extension('rmats.rmatspipeline', sources=[source_pattern % "rmatspipeline"], +- include_dirs=bamtools_include, ++ Extension('rmatspipeline', sources=[source_pattern % "rmatspipeline"], ++ include_dirs=[bamtools_include,], + libraries=['m','stdc++','bamtools','z'], +- library_dirs=bamtools_lib, ++ library_dirs=[bamtools_lib,], + extra_compile_args = ['-O3', '-funroll-loops', + '-std=c++11', '-fopenmp', + '-D__STDC_CONSTANT_MACROS', +@@ -31,7 +32,7 @@ + compiler_directives['legacy_implicit_noexcept'] = True + + setup( +- name = 'rmats.rmatspipeline', ++ name = 'rmatspipeline', + ext_modules = cythonize(asevent_ext, compiler_directives=compiler_directives), + cmdclass = {'build_ext': build_ext}, + ) From 33997eadf8786358d268caf287b15d6562921ee9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 16 Jan 2024 12:43:35 +0100 Subject: [PATCH 0306/1193] adding easyconfigs: freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb, vcflib-1.0.9-gfbf-2023a-R-4.3.2.eb and patches: freebayes-1.3.7_fix-includes.patch, freebayes-1.3.7_find-external-libs.patch, vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch --- .../b/BWA/BWA-0.7.17-GCCcore-12.3.0.eb | 50 +++++ .../fastahack-1.0.0-GCCcore-12.3.0.eb | 36 ++++ .../fermi-lite-20190320-GCCcore-12.3.0.eb | 48 +++++ .../filevercmp-20191210-GCCcore-12.3.0.eb | 37 ++++ .../freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb | 48 +++++ .../freebayes-1.3.7_find-external-libs.patch | 48 +++++ .../freebayes-1.3.7_fix-includes.patch | 174 +++++++++++++++ .../f/fsom/fsom-20151117-GCCcore-12.3.0.eb | 43 ++++ .../intervaltree-0.1-GCCcore-12.3.0.eb | 38 ++++ .../multichoose-1.0.3-GCCcore-12.3.0.eb | 32 +++ .../s/SSW/SSW-1.1-GCCcore-12.3.0.eb | 48 +++++ .../s/SeqLib/SeqLib-1.2.0-GCC-12.3.0.eb | 49 +++++ .../smithwaterman-20160702-GCCcore-12.3.0.eb | 34 +++ .../t/tabixpp/tabixpp-1.1.2-GCC-12.3.0.eb | 41 ++++ .../vcflib/vcflib-1.0.9-gfbf-2023a-R-4.3.2.eb | 82 +++++++ ...use-external-deps_and_fix_shared_lib.patch | 204 ++++++++++++++++++ .../w/WFA2/WFA2-2.3.4-GCCcore-12.3.0.eb | 30 +++ 17 files changed, 1042 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_find-external-libs.patch create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_fix-includes.patch create mode 100644 easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-gfbf-2023a-R-4.3.2.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch create mode 100644 easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..df988c782617 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..caaa9fc53ffd --- /dev/null +++ b/easybuild/easyconfigs/f/fastahack/fastahack-1.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fastahack' +version = '1.0.0' + +homepage = 'https://github.com/ekg/fastahack' +description = """Utilities for indexing and sequence extraction from FASTA files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + 'cc1c04729b0c8ba3647cbb7e15e2b490ce701d73773f30f5892d68c36a1dceae', # v1.0.0.tar.gz + '7f804486c6bafd9b1572cb5f86ff28dbebb4d6da551bde1091d6ff8f82748bf4', # fastahack-1.0.0_build-libs.patch +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfastahack.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b816dabffd91 --- /dev/null +++ b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'fermi-lite' +version = '20190320' +local_commit = 'b499514' + +homepage = 'https://github.com/lh3/fermi-lite' +description = """Standalone C library for assembling Illumina short reads in small regions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = [ + '%(name)s-20190320_avoid-bwa-namespace-conflict.patch', + '%(name)s-20190320_build-shared-lib.patch', +] +checksums = [ + 'ea1230e298b8e7193a996b5aceeff7fea44ef00852b0b87d4fcb504bdca0e712', # b499514.tar.gz + # fermi-lite-20190320_avoid-bwa-namespace-conflict.patch + '27600733f1cea8b1d1503b1a67b9d41526e907c1b6321313ff51194e166c1842', + '43398559fbb3910d6d3d1a41af3fb16bf8f26bd7cc34176dfc9a068a551c3f50', # fermi-lite-20190320_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +prebuildopts = 'CFLAGS="$CFLAGS -fcommon"' + +parallel = 1 + +files_to_copy = [ + (['fml-asm'], 'bin'), + (['*.a', '*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/fml'), + 'test', +] + +sanity_check_paths = { + 'files': ['bin/fml-asm', 'lib/libfml.a', 'lib/libfml.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..caddc6c090f0 --- /dev/null +++ b/easybuild/easyconfigs/f/filevercmp/filevercmp-20191210-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'filevercmp' +version = '20191210' +local_commit = 'df20dcc' + +homepage = 'https://github.com/ekg/filevercmp' +description = """filevercmp function as in sort --version-sort.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-libs.patch'] +checksums = [ + '89835829a7829f7a25783b2cf9d482f1e3c794703343c9214c15c66a8c7f4aae', # df20dcc.tar.gz + '051438f76dd04219abfb283f61101c04d748407031e180b7ae3841344416ec4f', # filevercmp-20191210_build-libs.patch +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = 'DESTDIR="" PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfilevercmp.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s abca bcac'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..5e1a919fcec2 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb @@ -0,0 +1,48 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.7' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/freebayes/freebayes' +description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.3.7_find-external-libs.patch', + '%(name)s-1.3.7_fix-includes.patch', + '%(name)s-1.3.6_install-libs-headers.patch', +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('R', '4.3.2'), + ('parallel', '20230722'), + ('libffi', '3.4.4'), + ('VCFtools', '0.1.16'), + ('vcflib', '1.0.9', versionsuffix), + ('SeqLib', '1.2.0'), +] + +configopts = "-Dprefer_system_deps=true --buildtype release" + +sanity_check_paths = { + 'files': ['bin/freebayes', 'bin/bamleftalign', 'scripts/freebayes-parallel'], + 'dirs': [], +} + +sanity_check_commands = ["freebayes --help"] + +modextrapaths = {'PATH': ['scripts']} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_find-external-libs.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_find-external-libs.patch new file mode 100644 index 000000000000..fd806aa0735c --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_find-external-libs.patch @@ -0,0 +1,48 @@ +Author: Jasper Grimm (UoY) +Switch to cc.find_library to search for libraries in LD_LIBRARY_PATH +Add dependencies on fastahack, smithwaterman +diff -Nru freebayes-1.3.6.orig/meson.build freebayes-1.3.6_p1/meson.build +--- freebayes-1.3.6.orig/meson.build 2022-01-21 09:38:32.000000000 +0000 ++++ freebayes-1.3.6_p1/meson.build 2022-03-29 12:46:15.000000000 +0100 +@@ -32,8 +32,10 @@ + if get_option('prefer_system_deps') + htslib_dep = dependency('htslib', static: static_build, required: false) + tabixpp_dep = cc.find_library('tabixpp', static: static_build, required: false) +- vcflib_dep = dependency('libvcflib', static: static_build, required: false) +- seqlib_dep = dependency('libseqlib', static: static_build, required: false) ++ vcflib_dep = cc.find_library('vcflib', static: static_build, required: false) ++ seqlib_dep = cc.find_library('seqlib', static: static_build, required: false) ++ fastahack_dep = cc.find_library('fastahack', required : false) ++ sw_dep = cc.find_library('sw', required : false) + else + # uses the local git submodules + htslib_dep = dependency('', required : false) +@@ -221,7 +223,7 @@ + include_directories : incdir, + cpp_args : extra_cpp_args, + dependencies : [zlib_dep, lzma_dep, thread_dep, htslib_dep, tabixpp_dep, +- vcflib_dep, seqlib_dep], ++ vcflib_dep, seqlib_dep, fastahack_dep, sw_dep], + install : false, + ) + +@@ -237,7 +239,8 @@ + cpp_args : extra_cpp_args, + link_args: link_arguments, + dependencies: [zlib_dep, lzma_dep, thread_dep, +- htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep], ++ htslib_dep, tabixpp_dep, vcflib_dep, seqlib_dep, ++ fastahack_dep, sw_dep], + link_with : freebayes_lib, + install: true + ) +@@ -248,7 +251,8 @@ + cpp_args : extra_cpp_args, + link_args: link_arguments, + dependencies: [zlib_dep, lzma_dep, thread_dep, +- htslib_dep, vcflib_dep, seqlib_dep], ++ htslib_dep, vcflib_dep, seqlib_dep, ++ fastahack_dep, sw_dep], + link_with : freebayes_lib, + install: true + ) diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_fix-includes.patch b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_fix-includes.patch new file mode 100644 index 000000000000..1a84f0489b19 --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7_fix-includes.patch @@ -0,0 +1,174 @@ +Created by Jasper Grimm (UoY) +Patch include statements to match installed include hierarchy + +Adapted to 1.3.7, Åke Sandgren +diff -ru freebayes-1.3.7.orig/src/Allele.cpp freebayes-1.3.7/src/Allele.cpp +--- freebayes-1.3.7.orig/src/Allele.cpp 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/Allele.cpp 2024-01-15 14:13:47.699765112 +0100 +@@ -1,5 +1,5 @@ + #include "Allele.h" +-#include "multichoose.h" ++#include "multichoose/multichoose.h" + #include "TryCatch.h" + + +diff -ru freebayes-1.3.7.orig/src/AlleleParser.cpp freebayes-1.3.7/src/AlleleParser.cpp +--- freebayes-1.3.7.orig/src/AlleleParser.cpp 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/AlleleParser.cpp 2024-01-15 14:14:31.443396494 +0100 +@@ -1,9 +1,9 @@ + #include "AlleleParser.h" +-#include "multichoose.h" // includes generic functions, so it must be included here ++#include "multichoose/multichoose.h" // includes generic functions, so it must be included here + // otherwise we will get a linker error + // see: http://stackoverflow.com/questions/36039/templates-spread-across-multiple-files + // http://www.cplusplus.com/doc/tutorial/templates/ "Templates and Multi-file projects" +-#include "multipermute.h" ++#include "multichoose/multipermute.h" + #include "Logging.h" + + using namespace std; +diff -ru freebayes-1.3.7.orig/src/AlleleParser.h freebayes-1.3.7/src/AlleleParser.h +--- freebayes-1.3.7.orig/src/AlleleParser.h 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/AlleleParser.h 2024-01-15 14:15:03.027130346 +0100 +@@ -13,7 +13,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + #include // XXX workaround for a missing include in vcflib's join.h + #include "join.h" + +diff -ru freebayes-1.3.7.orig/src/BedReader.cpp freebayes-1.3.7/src/BedReader.cpp +--- freebayes-1.3.7.orig/src/BedReader.cpp 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/BedReader.cpp 2024-01-15 14:15:34.242867296 +0100 +@@ -7,11 +7,11 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + #include "Utility.h" + #include "BedReader.h" + #include "Logging.h" +-#include "../intervaltree/IntervalTree.h" ++#include "intervaltree/IntervalTree.h" + + using namespace std; + +diff -ru freebayes-1.3.7.orig/src/BedReader.h freebayes-1.3.7/src/BedReader.h +--- freebayes-1.3.7.orig/src/BedReader.h 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/BedReader.h 2024-01-15 14:15:57.538658059 +0100 +@@ -9,8 +9,8 @@ + #include + #include + #include +-#include "../intervaltree/IntervalTree.h" +-#include "split.h" ++#include "intervaltree/IntervalTree.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -ru freebayes-1.3.7.orig/src/Bias.h freebayes-1.3.7/src/Bias.h +--- freebayes-1.3.7.orig/src/Bias.h 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/Bias.h 2024-01-15 14:16:09.778547984 +0100 +@@ -7,7 +7,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -ru freebayes-1.3.7.orig/src/CNV.h freebayes-1.3.7/src/CNV.h +--- freebayes-1.3.7.orig/src/CNV.h 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/CNV.h 2024-01-15 14:16:27.602387691 +0100 +@@ -10,7 +10,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -ru freebayes-1.3.7.orig/src/Contamination.h freebayes-1.3.7/src/Contamination.h +--- freebayes-1.3.7.orig/src/Contamination.h 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/Contamination.h 2024-01-15 14:16:44.546235315 +0100 +@@ -8,7 +8,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + + using namespace std; + +diff -ru freebayes-1.3.7.orig/src/DataLikelihood.cpp freebayes-1.3.7/src/DataLikelihood.cpp +--- freebayes-1.3.7.orig/src/DataLikelihood.cpp 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/DataLikelihood.cpp 2024-01-15 14:17:30.629820891 +0100 +@@ -1,6 +1,6 @@ + #include "DataLikelihood.h" +-#include "multichoose.h" +-#include "multipermute.h" ++#include "multichoose/multichoose.h" ++#include "multichoose/multipermute.h" + #include "Logging.h" + + long double +diff -ru freebayes-1.3.7.orig/src/FBFasta.h freebayes-1.3.7/src/FBFasta.h +--- freebayes-1.3.7.orig/src/FBFasta.h 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/FBFasta.h 2024-01-15 14:17:54.405607067 +0100 +@@ -16,10 +16,10 @@ + #include + #include + #include +-#include "LargeFileSupport.h" ++#include "fastahack/LargeFileSupport.h" + #include "Utility.h" + #include +-#include "split.h" ++#include "fastahack/split.h" + #include + #include + #include +diff -ru freebayes-1.3.7.orig/src/freebayes.cpp freebayes-1.3.7/src/freebayes.cpp +--- freebayes-1.3.7.orig/src/freebayes.cpp 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/freebayes.cpp 2024-01-15 14:18:13.669433822 +0100 +@@ -30,8 +30,8 @@ + #include "Utility.h" + #include "SegfaultHandler.h" + +-#include "multichoose.h" +-#include "multipermute.h" ++#include "multichoose/multichoose.h" ++#include "multichoose/multipermute.h" + + #include "Genotype.h" + #include "DataLikelihood.h" +diff -ru freebayes-1.3.7.orig/src/Genotype.cpp freebayes-1.3.7/src/Genotype.cpp +--- freebayes-1.3.7.orig/src/Genotype.cpp 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/Genotype.cpp 2024-01-15 14:18:31.973269211 +0100 +@@ -1,6 +1,6 @@ + #include "Genotype.h" +-#include "multichoose.h" +-#include "multipermute.h" ++#include "multichoose/multichoose.h" ++#include "multichoose/multipermute.h" + + + vector Genotype::uniqueAlleles(void) { +diff -ru freebayes-1.3.7.orig/src/Parameters.h freebayes-1.3.7/src/Parameters.h +--- freebayes-1.3.7.orig/src/Parameters.h 2023-02-12 04:55:52.000000000 +0100 ++++ freebayes-1.3.7/src/Parameters.h 2024-01-15 14:18:55.093061290 +0100 +@@ -9,7 +9,7 @@ + #include + #include + #include +-#include "split.h" ++#include "fastahack/split.h" + #include "version_git.h" + #include "Utility.h" + diff --git a/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..e35176f1207e --- /dev/null +++ b/easybuild/easyconfigs/f/fsom/fsom-20151117-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'fsom' +version = '20151117' +local_commit = '56695e1' + +homepage = 'https://github.com/ekg/fsom' +description = """A tiny C library for managing SOM (Self-Organizing Maps) neural networks.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ekg' + +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] + +patches = [ + '%(name)s-%(version)s_build-libs.patch', + '%(name)s-20141119_fix-abs-overload.patch' +] + +checksums = [ + '1ba3360985be781bb9f79d974705c86e7bb0719cb83638955e113b5dd83ec8dd', # 56695e1.tar.gz + 'd4e19b2db054cc5d3153ceba88ad2b11e5143e3a3c243103ce1e6994a83c43fe', # fsom-20151117_build-libs.patch + '54dd6ae76033535fe1b0231142d8bd41a815950dc3fd269dc321f698d4973639', # fsom-20141119_fix-abs-overload.patch +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libfsom.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..3e6a69dcf983 --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree/intervaltree-0.1-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'intervaltree' +version = '0.1' + +homepage = 'https://github.com/ekg/intervaltree' +description = """An interval tree can be used to efficiently find a set of numeric intervals + overlapping or containing another interval. This library provides a basic implementation of an + interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-numeric_limits.patch'] +checksums = [ + '7ba41f164a98bdcd570f1416fde1634b23d3b0d885b11ccebeec76f58810c307', # v0.1.tar.gz + '1d69caf35af86c0a55000e1bde3f9a0f19dd63d1d2b6bd48e4e5fecbb1aaa6b0', # intervaltree-0.1_fix-numeric_limits.patch +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +preinstallopts = 'DESTDIR="" PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/interval_tree_test', 'include/intervaltree/IntervalTree.h'], + 'dirs': [], +} +sanity_check_commands = ["interval_tree_test"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b876c3bad74c --- /dev/null +++ b/easybuild/easyconfigs/m/multichoose/multichoose-1.0.3-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'multichoose' +version = '1.0.3' + +homepage = 'https://github.com/ekg/multichoose' +description = """generate multiset combinations (n multichoose k).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_improve-build-system.patch'] +checksums = [ + '74f0a223c670f5aa81b14191c53ad8d84281838a47471c10253ae391f736c877', # v1.0.3.tar.gz + '96abf6ac1105ee596be078d6e8fb478f870a4ae33fffe70f93e627c0360cfc77', # multichoose-1.0.3_improve-build-system.patch +] + +builddependencies = [('binutils', '2.40')] + +local_bins = [name, 'multipermute'] +files_to_copy = [(local_bins, 'bin'), (['*.h'], 'include/%(name)s')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s 1 a'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..03f67550dacd --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-12.3.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'MakeCp' + +name = 'SSW' +version = '1.1' + +homepage = 'https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library' +description = """SSW is a fast implementation of the Smith-Waterman algorithm, which uses the + Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the + instruction level. SSW library provides an API that can be flexibly used by programs written in + C, C++ and other languages. We also provide a software that can do protein and genome alignment + directly. Current version of our implementation is ~50 times faster than an ordinary + Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path + (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and + location heuristically. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-1.1_build-cpp-lib.patch'] +checksums = [ + 'cdbc20740daeb188ed39413ea5ff9ae4cf72c4d7ccff1d2de2cac0446d64d99f', # v1.1.tar.gz + 'fe0d1f536ecd526dda8879b2f41b62c3c82b39d236f023ee735c1c18d584f06a', # SSW-1.1_build-cpp-lib.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +start_dir = 'src' + +buildopts = 'default' + +files_to_copy = [ + (['ssw_test'], 'bin'), + (['*.%s*' % SHLIB_EXT], 'lib'), + (['*.h'], 'include/ssw'), +] + +sanity_check_paths = { + 'files': ['bin/ssw_test', 'lib/libssw.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..fe0fb357d28d --- /dev/null +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-12.3.0.eb @@ -0,0 +1,49 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'SeqLib' +version = '1.2.0' + +homepage = 'https://github.com/walaj/SeqLib' +description = """C++ interface to HTSlib, BWA-MEM and Fermi.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'walaj' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version_major_minor)s.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-%(version_major_minor)s.0_use-external-deps.patch', +] +checksums = [ + '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz + # SeqLib-1.2.0_avoid-bwa-fml-namespace-conflict.patch + '9be9229bcf34db8e4bd1fd49614bb55d84c12df263ca7174980f7f4b1bd63da9', + '413f0ad8e0963d8922205d31e0c361cfa98a10f93e7d3e0506e0bed539ec70eb', # SeqLib-1.2.0_use-external-deps.patch +] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('bzip2', '1.0.8'), + ('JsonCpp', '1.9.5'), + ('BWA', '0.7.17'), + ('HTSlib', '1.18'), + ('fermi-lite', '20190320'), + ('SSW', '1.1'), + ('PCRE', '8.45'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/seqtools', 'lib/libseqlib.%s' % SHLIB_EXT], + 'dirs': [], +} +sanity_check_commands = ["seqtools"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..141312e7775e --- /dev/null +++ b/easybuild/easyconfigs/s/smithwaterman/smithwaterman-20160702-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'ConfigureMake' + +name = 'smithwaterman' +version = '20160702' +local_commit = '2610e25' + +homepage = 'https://github.com/ekg/smithwaterman' +description = """smith-waterman-gotoh alignment algorithm.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +patches = ['%(name)s-%(version)s_build-shared-lib.patch'] +checksums = [ + '8e1b37ab0e8cd9d3d5cbfdba80258c0ebd0862749b531e213f44cdfe2fc541d8', # 2610e25.tar.gz + '2aa63ec5cd0260efcab002eaf4bbf62497b91afc0e3f82d8290496803c35e582', # smithwaterman-20160702_build-shared-lib.patch +] + +builddependencies = [('binutils', '2.40')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/libsw.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.3.0.eb b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.3.0.eb new file mode 100644 index 000000000000..2d1b9e045312 --- /dev/null +++ b/easybuild/easyconfigs/t/tabixpp/tabixpp-1.1.2-GCC-12.3.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'ConfigureMake' + +name = 'tabixpp' +version = '1.1.2' + +homepage = 'https://github.com/ekg/tabixpp' +description = """C++ wrapper to tabix indexer""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'ekg' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use-external-HTSlib.patch'] + +checksums = [ + 'c850299c3c495221818a85c9205c60185c8ed9468d5ec2ed034470bb852229dc', # v1.1.2.tar.gz + 'a4684b6c3a69258d0686f601564b635ae3dc098e712783b46d9ca5b7ff996906', # tabixpp-1.1.2_use-external-HTSlib.patch +] + +dependencies = [ + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.2'), + ('HTSlib', '1.18'), + ('PCRE', '8.45'), +] + +skipsteps = ['configure'] + +preinstallopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/tabix++', 'lib/libtabixpp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-gfbf-2023a-R-4.3.2.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-gfbf-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..3d7ab00d6ded --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9-gfbf-2023a-R-4.3.2.eb @@ -0,0 +1,82 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +# Updated: Petr Král (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/vcflib/vcflib' +description = """vcflib provides methods to manipulate and interpret sequence variation as it can be + described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended + to concisely describe reference-indexed genetic variations between individuals.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch', +] +checksums = [ + {'v1.0.9.tar.gz': 'd17fcf8a34d65f1dfecf4b4290d058be744422b6baf34ecdef8ea912d59a4569'}, + {'vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch': + '82f622a6b4bac1501b10bbc82c4e6567e095869c17b7d34d92b8c4836816b5a1'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('R', '4.3.2'), + ('XZ', '5.4.2'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.18'), + ('tabixpp', '1.1.2'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20151117'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), + ('WFA2', '2.3.4'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f " +preconfigopts += r"-regextype egrep -regex '.*\.(h|cpp)' -exec sed -i" +preconfigopts += " -e 's|SmithWatermanGotoh.h|smithwaterman/SmithWatermanGotoh.h|g'" +preconfigopts += " -e 's|IntervalTree.h|intervaltree/IntervalTree.h|g'" +preconfigopts += " -e 's|multichoose.h|multichoose/multichoose.h|g' -e 's|filevercmp.h|filevercmp/filevercmp.h|g'" +preconfigopts += " -e 's|tabix.hpp|tabixpp/tabix.hpp|g' -e 's|Fasta.h|fastahack/Fasta.h|g'" +preconfigopts += r" -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +configopts = "-DZIG=OFF -DWFA_GITMODULE=OFF -DWFA_INCLUDE_DIRS=$EBROOTWFA2/include/wfa2lib " +configopts += "-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python" + +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = { + 'PATH': 'scripts', + 'PYTHONPATH': 'lib', +} + +sanity_check_paths = { + 'files': ['bin/vcffilter', 'bin/vcfcombine', 'lib/libvcflib.a', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': ['scripts', 'include'], +} + +sanity_check_commands = [ + "python -c 'import pyvcflib'", + "vcfwave --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch new file mode 100644 index 000000000000..17f1f91c75d5 --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.9_use-external-deps_and_fix_shared_lib.patch @@ -0,0 +1,204 @@ +Use external deps for as much as possible +Add shared library +Update VERSION +Based on patches from 1.0.3 and old 1.0.9 + +Åke Sandgren, 2024-01-16 +diff -ru vcflib-1.0.9.orig/CMakeLists.txt vcflib-1.0.9/CMakeLists.txt +--- vcflib-1.0.9.orig/CMakeLists.txt 2023-02-11 17:41:26.000000000 +0100 ++++ vcflib-1.0.9/CMakeLists.txt 2024-01-16 08:10:32.112086067 +0100 +@@ -45,6 +45,12 @@ + + set(EXTRA_FLAGS " ") # otherwise it injects OFF + ++# ---- Get version ++ ++file (STRINGS "VERSION" BUILD_NUMBER) ++add_definitions(-DVCFLIB_VERSION="${BUILD_NUMBER}") ++add_definitions(-DVERSION="${BUILD_NUMBER}") ++ + # ---- Dependencies + + if(OPENMP) +@@ -59,7 +65,7 @@ + set_package_properties(Threads PROPERTIES TYPE REQUIRED) + + pkg_check_modules(HTSLIB htslib) # Optionally builds from contrib/ +-pkg_check_modules(TABIXPP tabixpp) # Optionally builds from contrib/ ++#pkg_check_modules(TABIXPP tabixpp) # Optionally builds from contrib/ + + # ---- Build switches + set(CMAKE_POSITION_INDEPENDENT_CODE ON) +@@ -109,25 +115,25 @@ + # ---- Include files + + include_directories(include) +-include_directories(contrib/fastahack) +-include_directories(contrib/intervaltree) +-include_directories(contrib/smithwaterman) +-include_directories(contrib/multichoose) +-include_directories(contrib/filevercmp) ++# include_directories(contrib/fastahack) ++# include_directories(contrib/intervaltree) ++# include_directories(contrib/smithwaterman) ++# include_directories(contrib/multichoose) ++# include_directories(contrib/filevercmp) + include_directories(contrib/c-progress-bar) + +-if(NOT HTSLIB_FOUND) +- set(HTSLIB_LOCAL contrib/tabixpp/htslib) +- set(TABIX_FOUND OFF) # also build tabixpp if htslib is missing +-endif() +- +-if (NOT TABIX_FOUND) +- set(TABIXPP_LOCAL contrib/tabixpp) +- include_directories(contrib/tabixpp) +- set(tabixpp_SOURCE +- contrib/tabixpp/tabix.cpp +- ) +-endif() ++# if(NOT HTSLIB_FOUND) ++# set(HTSLIB_LOCAL contrib/tabixpp/htslib) ++# set(TABIX_FOUND OFF) # also build tabixpp if htslib is missing ++#endif() ++ ++#if (NOT TABIX_FOUND) ++# set(TABIXPP_LOCAL contrib/tabixpp) ++# include_directories(contrib/tabixpp) ++# set(tabixpp_SOURCE ++# contrib/tabixpp/tabix.cpp ++# ) ++#endif() + + if(WFA_GITMODULE) + set(WFA_LOCAL contrib/WFA2-lib) +@@ -135,14 +141,14 @@ + + file(GLOB INCLUDES + src/*.h* +- contrib/multichoose/*.h* +- contrib/intervaltree/*.h* +- contrib/smithwaterman/*.h* +- contrib/fastahack/*.h* +- contrib/filevercmp/*.h* +- ) ++# contrib/multichoose/*.h* ++# contrib/intervaltree/*.h* ++# contrib/smithwaterman/*.h* ++# contrib/fastahack/*.h* ++# contrib/filevercmp/*.h* ++) + +-set(vcflib_SOURCE ++set(SOURCES + src/vcf-c-api.cpp + src/legacy.cpp + src/vcf-wfa.cpp +@@ -158,14 +164,14 @@ + src/LeftAlign.cpp + src/cigar.cpp + src/allele.cpp +- contrib/fastahack/Fasta.cpp +- contrib/smithwaterman/SmithWatermanGotoh.cpp +- contrib/smithwaterman/Repeats.cpp +- contrib/smithwaterman/IndelAllele.cpp +- contrib/smithwaterman/disorder.cpp +- contrib/smithwaterman/LeftAlign.cpp +- contrib/fsom/fsom.c +- contrib/filevercmp/filevercmp.c ++# contrib/fastahack/Fasta.cpp ++# contrib/smithwaterman/SmithWatermanGotoh.cpp ++# contrib/smithwaterman/Repeats.cpp ++# contrib/smithwaterman/IndelAllele.cpp ++# contrib/smithwaterman/disorder.cpp ++# contrib/smithwaterman/LeftAlign.cpp ++# contrib/fsom/fsom.c ++# contrib/filevercmp/filevercmp.c + contrib/c-progress-bar/progress.c + ) + +@@ -173,10 +179,6 @@ + list(APPEND vcflib_SOURCE ${tabixpp_SOURCE}) + endif() + +-add_library(vcflib STATIC +- ${vcflib_SOURCE} +- ) +- + set(BINS + vcfecho + dumpContigsFromHeader +@@ -304,12 +306,6 @@ + vcfvarstats + ) + +-# ---- Get version +- +-file (STRINGS "VERSION" BUILD_NUMBER) +-add_definitions(-DVCFLIB_VERSION="${BUILD_NUMBER}") +-add_definitions(-DVERSION="${BUILD_NUMBER}") +- + # ---- Build htslib + # + # Note by default we use the distributed htslib! These are +@@ -363,7 +359,7 @@ + add_subdirectory(${WFA_LOCAL} EXCLUDE_FROM_ALL) + set(WFALIB wfa2) # pick up the wfa2 lib target from the included CMakeLists.txt + else(WFA_GITMODULE) +- set(WFA_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib) ++ # set(WFA_INCLUDE_DIRS ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_INCLUDEDIR}/wfa2lib) + find_library(WFALIB wfa2 wfa) # distro search for shared lib + if(NOT WFALIB) + message(STATUS "ERROR: Can not find libfwa! Make sure it is installed or use the git submodule instead") +@@ -419,9 +415,9 @@ + ${ZLIB_LIBRARIES} + ${LIBLZMA_LIBRARIES} + ${BZIP2_LIBRARIES} +- ${TABIXPP_LIBRARIES} ++ tabixpp + ${CMAKE_THREAD_LIBS_INIT} +- ${WFA_LINK_LIBRARIES} ++ ${WFALIB} + ${HTSLIB_LINK_LIBRARIES} + ) + +@@ -429,7 +425,14 @@ + list(APPEND vcflib_LIBS ${ZIG_LINK_LIBRARIES}) + endif() + ++add_library(vcflib_static STATIC ${SOURCES}) ++set_target_properties(vcflib_static PROPERTIES OUTPUT_NAME vcflib) ++add_library(vcflib SHARED ${SOURCES}) ++set_target_properties(vcflib PROPERTIES VERSION ${BUILD_NUMBER} SOVERSION 1) ++target_link_libraries(vcflib tabixpp fastahack sw fsom filevercmp ${WFALIB} ${LDFLAGS} ${LIBS}) ++ + add_dependencies(vcflib ${vcflib_DEPS}) ++add_dependencies(vcflib_static ${vcflib_DEPS}) + + # ---- Build all + +@@ -437,7 +440,7 @@ + foreach(BIN ${BINS}) + add_executable(${BIN} src/${BIN}.cpp) + add_dependencies(${BIN} vcflib) +- target_link_libraries(${BIN} PUBLIC ${vcflib_LIBS} vcflib) ++ target_link_libraries(${BIN} PUBLIC vcflib ${vcflib_LIBS}) + endforeach(BIN ${BINS}) + # These binaries include WFALIB + target_link_libraries(vcfallelicprimitives PUBLIC ${WFALIB}) +@@ -576,7 +579,8 @@ + + # ---- Install + +-install(TARGETS vcflib ARCHIVE DESTINATION ${CMAKE_INSTALL_BINDIR}) ++install(TARGETS vcflib LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}) ++install(TARGETS vcflib_static ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) + + install(FILES ${INCLUDES} DESTINATION include) + +diff -ru vcflib-1.0.9.orig/VERSION vcflib-1.0.9/VERSION +--- vcflib-1.0.9.orig/VERSION 2023-02-11 17:41:26.000000000 +0100 ++++ vcflib-1.0.9/VERSION 2024-01-15 16:33:28.640523913 +0100 +@@ -1 +1 @@ +-1.0.7 ++1.0.9 diff --git a/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..90cdfd83d9c8 --- /dev/null +++ b/easybuild/easyconfigs/w/WFA2/WFA2-2.3.4-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'WFA2' +version = '2.3.4' + +homepage = 'https://github.com/smarco/WFA2-lib' +description = """The wavefront alignment (WFA) algorithm is an exact + gap-affine algorithm that takes advantage of homologous regions + between the sequences to accelerate the alignment process.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/smarco/WFA2-lib/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['3a02d19b45c7efcdcabdd956421b1e449e771fca0b0f072e02d7aa65ebb29f23'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), +] + +configopts = "-DOPENMP=ON" + +sanity_check_paths = { + 'files': ['lib/libwfa2.a'], + 'dirs': ['include/wfa2lib'], +} + +moduleclass = 'bio' From d4b59fb0c012c8e22d4cea39543016fc41dd4a81 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 16 Jan 2024 13:02:34 +0100 Subject: [PATCH 0307/1193] adding easyconfigs: fastp-0.23.4-GCC-12.3.0.eb --- .../f/fastp/fastp-0.23.4-GCC-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.3.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.3.0.eb new file mode 100644 index 000000000000..8e423ebec0f7 --- /dev/null +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.4-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'fastp' +version = '0.23.4' + +homepage = 'https://github.com/OpenGene/fastp' +description = """A tool designed to provide fast all-in-one preprocessing for FastQ files. + This tool is developed in C++ with multithreading supported to afford high performance.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +# https://github.com/OpenGene/fastp +github_account = 'OpenGene' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4fad6db156e769d46071add8a778a13a5cb5186bc1e1a5f9b1ffd499d84d72b5'] + +dependencies = [ + ('zlib', '1.2.13'), + ('libdeflate', '1.18'), + ('ISA-L', '2.30.0'), +] + +skipsteps = ['configure'] + +buildopts = ' CXX=${CXX}' + +preinstallopts = 'mkdir -p %(installdir)s/bin && ' + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/fastp'], + 'dirs': [], +} + +sanity_check_commands = [('fastp', '--help')] + +moduleclass = 'bio' From 3926be52b369ec1bf21da1c169adc899385445f4 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 16 Jan 2024 13:14:37 +0100 Subject: [PATCH 0308/1193] adding easyconfigs: PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0.eb --- ...ometric-2.1.0-foss-2022a-PyTorch-1.12.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0.eb new file mode 100644 index 000000000000..c8dbbb4853e2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2022a-PyTorch-1.12.0.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.1.0' +local_pytorchver = '1.12.0' +versionsuffix = '-PyTorch-%s' % local_pytorchver + +homepage = 'https://github.com/rusty1s/pytorch_geometric' +description = "PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', local_pytorchver), + ('scikit-learn', '1.1.2'), + ('scikit-image', '0.19.3'), + ('numba', '0.56.4'), + ('h5py', '3.7.0'), + ('tqdm', '4.64.0'), + ('RDFlib', '6.2.0'), + ('ASE', '3.22.1'), + ('YACS', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('googledrivedownloader', '0.4', { + 'modulename': 'google_drive_downloader', + 'checksums': ['4b34c1337b2ff3bf2bd7581818efbdcaea7d50ffd484ccf80809688f5ca0e204'], + }), + ('plyfile', '0.7.4', { + 'checksums': ['9e9a18d22a3158fcd74df38761d43a7facc6df75126f2ab9f4e9a5d4d2188652'], + }), + ('torch_scatter', version, { + 'checksums': ['3a7124c2a033552febbdc72407f7d4d8cb6dce465720e84ab831512e81c1d208'], + }), + ('torch_sparse', '0.6.15', { + 'checksums': ['3a741ae8a7cc19247a44de549fa4d593c4257b5f741e1eb5110b712a14209dd9'], + }), + ('torch_cluster', '1.6.0', { + 'checksums': ['249c1bd8c33a887b22bf569a59d0868545804032123594dd8c76ba1885859c39'], + }), + ('torch_spline_conv', '1.2.1', { + 'checksums': ['364f658e0ecb4c5263a728c2961553e022fc44c11a633d5a1bf986cf169ab438'], + }), + ('python-louvain', '0.16', { + 'modulename': 'community.community_louvain', + 'checksums': ['b7ba2df5002fd28d3ee789a49532baad11fe648e4f2117cf0798e7520a1da56b'], + }), + ('torch_geometric', version, { + 'checksums': ['72653deca925885e4d613eb5c72268bb9710325d9c717516922499fbe1197079'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 47b94fb756f2ef1e96f30c579914419b7818cb18 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 16 Jan 2024 13:21:09 +0100 Subject: [PATCH 0309/1193] adding easyconfigs: MONAI-1.3.0-foss-2023a.eb, PyTorch-Ignite-0.4.11-foss-2023a.eb, tensorboard-2.15.1-foss-2023a.eb, torchvision-0.16.0-foss-2023a.eb and patches: PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch, torchvision-0.16.0_fix-build-with-FFmpeg6.patch --- .../m/MONAI/MONAI-1.3.0-foss-2023a.eb | 76 +++++++++++++++++ .../PyTorch-Ignite-0.4.11-foss-2023a.eb | 35 ++++++++ ...0.4.11_fix_error_on_importing_Events.patch | 19 +++++ .../tensorboard-2.15.1-foss-2023a.eb | 82 +++++++++++++++++++ .../torchvision-0.16.0-foss-2023a.eb | 31 +++++++ ...vision-0.16.0_fix-build-with-FFmpeg6.patch | 25 ++++++ 6 files changed, 268 insertions(+) create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb new file mode 100644 index 000000000000..fd4274ac696a --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.3.0' + +homepage = 'https://monai.io/' +description = """ +MONAI is a PyTorch-based, open-source framework for deep learning in healthcare +imaging, part of PyTorch Ecosystem. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyTorch-Ignite', '0.4.11'), # Monai 1.3.0 requires PyTorch-Ignite==0.4.11 + ('einops', '0.7.0'), + ('ITK', '5.3.0'), + ('NiBabel', '5.2.0'), + ('scikit-image', '0.22.0'), + ('tensorboard', '2.15.1'), + ('torchvision', '0.16.0'), + ('tqdm', '4.66.1'), + ('Pillow', '10.0.0'), + ('openslide-python', '1.3.1'), + ('BeautifulSoup', '4.12.2'), + ('hatchling', '1.18.0'), +] + +# install MONAI with list of 'extras', which require additional dependencies +local_pip_extras = "nibabel,skimage,pillow,tensorboard,gdown,ignite,torchvision,itk,tqdm,lmdb,psutil,openslide,fire" + +exts_list = [ + ('gdown', '4.7.1', { + 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], + }), + ('lmdb', '1.4.1', { + 'checksums': ['1f4c76af24e907593487c904ef5eba1993beb38ed385af82adb25a858f2d658d'], + }), + ('termcolor', '2.3.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['3afb05607b89aed0ffe25202399ee0867ad4d3cb4180d98aaf8eefa6a5f7d475'], + }), + ('fire', '0.5.0', { + 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], + }), + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['%(version)s.tar.gz'], + 'use_pip_extras': local_pip_extras, + 'checksums': ['67e0f55678faad4bd38b1ea69d5de94586b20b551b8ad745415623a8b6c1c5e2'], + }), +] + +use_pip = True + +sanity_pip_check = True + +# 'pip check' does not verify whether all optional dependencies required to support 'extras' +# are actually available, so we do it here via an import check; +# Pillow is a special case, since there we need to use 'import PIL' +sanity_check_commands = [ + "python -c 'import monai; monai.config.print_config()'", + "python -c 'import PIL'", # for Pillow required dependency +] + ["python -c 'import %s'" % x for x in local_pip_extras.split(',') if x != 'pillow'] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb new file mode 100644 index 000000000000..f73933e70143 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Ignite' +version = '0.4.11' + +homepage = 'https://pytorch-ignite.ai/' +description = """ +Ignite is a high-level library to help with training and evaluating neural +networks in PyTorch flexibly and transparently.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), +] + +exts_list = [ + ('pytorch-ignite', version, { + 'modulename': 'ignite', + 'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'], + 'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s'], + 'sources': ['pytorch-ignite-%(version)s.tar.gz'], + 'checksums': [ + {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'}, + {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch': + 'd481a1cb8e4cb668802cb29fe301129fbf10cec056cfdc81402a2d1764448ca3'}, + ], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch new file mode 100644 index 000000000000..f0b9f9f59e46 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch @@ -0,0 +1,19 @@ +Fix bug error on importing Events in python 3.11 +as in https://github.com/pytorch/ignite/pull/2907 +Author: Cintia Willemyns (Vrije Universiteit Brussel) + +--- ignite/engine/events.py.orig 2024-01-03 16:37:16.972475097 +0100 ++++ ignite/engine/events.py 2024-01-03 16:39:03.703040949 +0100 +@@ -248,8 +248,10 @@ + # ... + """ + +- pass +- ++ def __new__(cls, value: str) -> "EventEnum": ++ obj = CallableEventWithFilter.__new__(cls) ++ obj._value_ = value ++ return obj + + class Events(EventEnum): + """Events that are fired by the :class:`~ignite.engine.engine.Engine` during execution. Built-in events: diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb new file mode 100644 index 000000000000..350ba1d68b88 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb @@ -0,0 +1,82 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.15.1' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and understanding +your TensorFlow runs and graphs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('protobuf-python', '4.24.0'), + ('poetry', '1.5.1'), # for rsa +] + +exts_list = [ + ('absl-py', '2.0.0', { + 'modulename': 'absl', + 'checksums': ['d9690211c5fcfefcdd1a45470ac2b5c5acd45241c3af71eed96bc5441746c0d5'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('pyasn1_modules', '0.3.0', { + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.26.0', { + 'modulename': 'google.auth', + 'checksums': ['5d8bf0a5143baa45368c3d08bf157babda468db1c5dd987cd2c824b788524196'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('grpcio', '1.60.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['2199165a1affb666aa24adf0c97436686d0a61bc5fc113c037701fb7c7fceb96'], + }), + ('Markdown', '3.5.1', { + 'checksums': ['b65d7beb248dc22f2e8a31fb706d93798093c308dc1aba295aedeb9d41a813bd'], + }), + ('tensorboard_data_server', '0.7.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('Werkzeug', '3.0.1', { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c46c1d1cf13a458c429868a78b2531d8ff5f682058d69ec0840b0bc7a38f1c0f'], + }), +] + +# Relax restriction on protobuf dependency as issue was fixed +# in https://github.com/protocolbuffers/upb/pull/1514 +postinstallcmds = [ + 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + + '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb new file mode 100644 index 000000000000..7610052afb69 --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb @@ -0,0 +1,31 @@ +name = 'torchvision' +version = '0.16.0' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'cstd': 'c++17'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix-build-with-FFmpeg6.patch', +] +checksums = [ + {'v0.16.0.tar.gz': '79b30b082237e3ead21e74587cedf4a4d832f977cf7dfeccfb65f67988b12ceb'}, + {'torchvision-0.16.0_fix-build-with-FFmpeg6.patch': + '14039456cd10f2ea1281eaaa908429958f6c72d7b2041f23cf9bd43b8b810d2f'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Pillow-SIMD', '9.5.0'), + ('PyTorch', '2.1.2'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch new file mode 100644 index 000000000000..4220434d610b --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch @@ -0,0 +1,25 @@ +Make torchvision 0.16.0 build with ffmpeg 6.0 (from https://github.com/pytorch/vision/issues/7998) +Author: Cintia Willemyns (Vrije Universiteit Brussel) + +diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp +index 0d625ef211..8c91405058 100644 +--- a/torchvision/csrc/io/decoder/stream.cpp ++++ b/torchvision/csrc/io/decoder/stream.cpp +@@ -63,15 +63,8 @@ int Stream::openCodec(std::vector* metadata, int num_threads) { + codecCtx_->thread_count = num_threads; + } else { + // otherwise set sensible defaults +- // with the special case for the different MPEG4 codecs +- // that don't have threading context functions +- if (codecCtx_->codec->capabilities & AV_CODEC_CAP_INTRA_ONLY) { +- codecCtx_->thread_type = FF_THREAD_FRAME; +- codecCtx_->thread_count = 2; +- } else { +- codecCtx_->thread_count = 8; +- codecCtx_->thread_type = FF_THREAD_SLICE; +- } ++ codecCtx_->thread_count = 8; ++ codecCtx_->thread_type = FF_THREAD_SLICE; + } + + int ret; From 62b69a08c6f741bf7345c80ff9502750565ee6d2 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 16 Jan 2024 13:30:48 +0100 Subject: [PATCH 0310/1193] Update checksum of NECI v20230620 --- easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb index 02de75ee27ce..aa2e6188e2dd 100644 --- a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb @@ -19,7 +19,7 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = ['db8533219369600dcdb82b6d56f1f02a5e0058be6cc26bc26597d3471162d614'] +checksums = ['c8057259fc5c6cf5a3141f013eff52fc94401f47563fbbd86cdc9e56fcff5153'] builddependencies = [ ('CMake', '3.24.3'), From cd4eb9f054d0f1b8a878b60daec508adfb144b99 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 16 Jan 2024 13:32:25 +0100 Subject: [PATCH 0311/1193] adding easyconfigs: YODA-1.9.9-GCC-12.3.0.eb --- .../y/YODA/YODA-1.9.9-GCC-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb new file mode 100644 index 000000000000..f05a5831f164 --- /dev/null +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'YODA' +version = '1.9.9' + +homepage = 'https://yoda.hepforge.org/' +description = """ +Yet more Objects for (High Energy Physics) Data Analysis +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://yoda.hepforge.org/downloads?f='] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['79054152ef806f26e646b89f14834e5c'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Python', '3.11.3') +] +configopts = "--disable-root --enable-pyext --disable-static" +buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" +installopts = buildopts + +sanity_check_paths = { + 'files': ['bin/yoda-config', 'lib/libYODA.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} +sanity_check_commands = ["python -c 'import yoda'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +moduleclass = 'phys' From bbdc3cec82a7730ac278ca59ad16d48dad5fd978 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 16 Jan 2024 13:47:36 +0100 Subject: [PATCH 0312/1193] freebayes: Add missing checksums --- .../f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb index 5e1a919fcec2..9c7ff736b2ec 100644 --- a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.7-gfbf-2023a-R-4.3.2.eb @@ -16,6 +16,12 @@ patches = [ '%(name)s-1.3.7_fix-includes.patch', '%(name)s-1.3.6_install-libs-headers.patch', ] +checksums = [ + {'v1.3.7.tar.gz': '89c2202aaa82925bc6a49e04df593e5ef3b1547b3b514efcbd490a54d8ad200b'}, + {'freebayes-1.3.7_find-external-libs.patch': 'ef1acb874b51e6efe077e2d2769892082c38f880e09eac1b0987b02ee4a59beb'}, + {'freebayes-1.3.7_fix-includes.patch': '7a3f8ab89f59ed77150ca5d70eb5dc6fe5780f9a17229c69c762288eafc935b7'}, + {'freebayes-1.3.6_install-libs-headers.patch': '5ba006ca6956905bbd81107a17e02287c515890ee25884c444ebf5b95da1caae'}, +] builddependencies = [ ('CMake', '3.26.3'), From 1f9f1b42c6477c696a2a3e272345ac0d73886791 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Tue, 16 Jan 2024 15:10:38 +0100 Subject: [PATCH 0313/1193] use FlexiBlas instead of OpenBlas Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb b/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb index 2ad0da886127..201cdb4bf25f 100644 --- a/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb +++ b/easybuild/easyconfigs/d/Dice/Dice-20240101-foss-2022b.eb @@ -35,7 +35,7 @@ dependencies = [ # Use build environment defined by EB prebuildopts = "sed -i 's/^FLAGS_BASE =.*/FLAGS_BASE=$(CXXFLAGS) -g -w -I. $(CPPFLAGS)/' Makefile && " buildopts = 'CXX="$MPICXX" USE_INTEL="no" HAS_AVX2="no" ' # avoid changes to -march -buildopts += 'INCLUDE_MKL="-I${EBROOTOPENBLAS}/include" LIB_MKL="${LIBBLAS}" ' # use OpenBLAS +buildopts += 'INCLUDE_MKL="-I${EBROOTFLEXIBLAS}/include" LIB_MKL="${LIBBLAS}" ' # use FlexiBLAS buildopts += 'GIT_BRANCH="master" GIT_HASH="%s"' % _commit buildopts += 'BOOST="${EBROOTBOOSTMPI}" ' buildopts += 'EIGEN="${EBROOTEIGEN}/include" ' From 18bbbb47dc481eba541d83d6a237dac17b2bc3e5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 16 Jan 2024 15:11:15 +0100 Subject: [PATCH 0314/1193] Remove osdependencies from GCCcore ccache --- .../easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb | 6 ++---- .../easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb | 6 ++---- 2 files changed, 4 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb index 355a2da891f3..5b623f231cc6 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.1-GCCcore-11.2.0.eb @@ -14,17 +14,15 @@ caching previous compilations and detecting when the same compilation is being d toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +source_urls = [GITHUB_RELEASE] sources = [SOURCE_TAR_GZ] checksums = ['59b28a57c3a45e48d6049001999c9f94cd4d3e9b0196994bed9a6a7437ffa3bc'] -osdependencies = [('glibc-static', 'libc6-dev', 'glibc-devel')] - builddependencies = [ ('binutils', '2.37'), ('CMake', '3.22.1'), ('Ninja', '1.10.2'), - ('zstd', '1.5.0', ), + ('zstd', '1.5.0'), ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb index 770822d93b69..30f7490b38bf 100644 --- a/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/ccache/ccache-4.6.3-GCCcore-11.3.0.eb @@ -14,17 +14,15 @@ caching previous compilations and detecting when the same compilation is being d toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://github.com/ccache/ccache/releases/download/v%(version)s/'] +source_urls = [GITHUB_RELEASE] sources = [SOURCE_TAR_GZ] checksums = ['f46ba3706ad80c30d4d5874dee2bf9227a7fcd0ccaac31b51919a3053d84bd05'] -osdependencies = [('glibc-static', 'libc6-dev', 'glibc-devel')] - builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), ('Ninja', '1.10.2'), - ('zstd', '1.5.2', ), + ('zstd', '1.5.2'), ('pkgconf', '1.8.0'), ] From 9a495e9aff62e77fd6483ed142abfba3ba80ac5b Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 16 Jan 2024 15:12:07 +0100 Subject: [PATCH 0315/1193] adding easyconfigs: OpenFOAM-v2112-foss-2022a.eb --- .../o/OpenFOAM/OpenFOAM-v2112-foss-2022a.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2022a.eb new file mode 100644 index 000000000000..c98556c09829 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2112-foss-2022a.eb @@ -0,0 +1,45 @@ +name = 'OpenFOAM' +version = 'v2112' + +homepage = 'https://www.openfoam.com/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +# Users have found that vectorizion caused OpenFOAM to produce some very incorrect results. +# Disabling vectorize was confirmed to fix the the known issues. +# With no test suite, sticking to known working toolchain options until proven otherwise. +toolchainopts = {'cstd': 'c++11', 'vectorize': False} + +source_urls = ['https://sourceforge.net/projects/openfoam/files/%(version)s/'] +sources = [SOURCE_TGZ] +patches = [ + ('OpenFOAM-v2012-cleanup.patch', 1), + 'OpenFOAM-v1906-wmake-ompi.patch', +] +checksums = [ + '3e838731e79db1c288acc27aad8cc8a43d9dac1f24e5773e3b9fa91419a8c3f7', # OpenFOAM-v2112.tgz + 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('CGAL', '4.14.3'), + ('ParaView', '5.10.1', '-mpi'), + ('gnuplot', '5.4.4'), +] + +moduleclass = 'cae' From e518795c5b3a0f2dc919f4e3adf6e543f9bbe4b0 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 16 Jan 2024 15:15:28 +0100 Subject: [PATCH 0316/1193] adding easyconfigs: OpenFOAM-7-foss-2022a-20200508.eb --- .../OpenFOAM-7-foss-2022a-20200508.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508.eb new file mode 100644 index 000000000000..299b51f57b82 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508.eb @@ -0,0 +1,48 @@ +name = 'OpenFOAM' +local_commit = '3bcbaf9' +version = '7' +versionsuffix = '-20200508' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': 'OpenFOAM-%(version)s%(versionsuffix)s.tar.gz', +}] +patches = [ + 'OpenFOAM-7-20200508-cleanup.patch', + 'OpenFOAM-%(version)s-mpi-compilation.patch', +] +checksums = [ + 'e91cc1355cdfc21b953e704d22ccd0e01a32bb11775cbbdd8105cf4364b498af', # OpenFOAM-7-20200508.tar.gz + '91f78714058a020da314b1311beb2c3cc2f4a817d02b1495c43b57156774cfa6', # OpenFOAM-7-20200508-cleanup.patch + '9f2af8f67a57a187f68aadaa99bc99f1cfbfe41086e5839a57e1bb4e41b3762c', # OpenFOAM-7-mpi-compilation.patch +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('CGAL', '4.14.3'), + ('gnuplot', '5.4.4'), +] +# Paraview is not included in here as it is an optional dependecy and +# OpenFOAM 7 is only compatible with old versions of Paraview (< 5.7) + +moduleclass = 'cae' From 626ed34b139ef0c2e41185a028d808ca748ead59 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 16 Jan 2024 15:19:36 +0100 Subject: [PATCH 0317/1193] adding easyconfigs: OpenFOAM-7-foss-2022a-20200508-int64.eb --- .../OpenFOAM-7-foss-2022a-20200508-int64.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508-int64.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508-int64.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508-int64.eb new file mode 100644 index 000000000000..2bf9648d00c6 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-7-foss-2022a-20200508-int64.eb @@ -0,0 +1,47 @@ +name = 'OpenFOAM' +local_commit = '3bcbaf9' +version = '7' +versionsuffix = '-20200508-int64' + +homepage = 'https://www.openfoam.org/' +description = """OpenFOAM is a free, open source CFD software package. + OpenFOAM has an extensive range of features to solve anything from complex fluid flows + involving chemical reactions, turbulence and heat transfer, + to solid dynamics and electromagnetics.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++11', 'i8': True} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': 'OpenFOAM-%(version)s%(versionsuffix)s.tar.gz', +}] +patches = [ + 'OpenFOAM-7-20200508-cleanup.patch', + 'OpenFOAM-%(version)s-mpi-compilation.patch', +] +checksums = [ + 'e91cc1355cdfc21b953e704d22ccd0e01a32bb11775cbbdd8105cf4364b498af', # OpenFOAM-7-20200508.tar.gz + '91f78714058a020da314b1311beb2c3cc2f4a817d02b1495c43b57156774cfa6', # OpenFOAM-7-20200508-cleanup.patch + '9f2af8f67a57a187f68aadaa99bc99f1cfbfe41086e5839a57e1bb4e41b3762c', # OpenFOAM-7-mpi-compilation.patch +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1.2'), + ('ncurses', '6.3'), + ('METIS', '5.1.0', '-int64'), + ('SCOTCH', '7.0.1', '-int64'), + ('CGAL', '4.14.3'), + ('gnuplot', '5.4.4'), +] +# Paraview is not included in here as it is an optional dependecy and +# OpenFOAM 7 is only compatible with old versions of Paraview (< 5.7) + +moduleclass = 'cae' From 1b8f25ea3f704c89569b7bb90f6c24ee5787bde3 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 16 Jan 2024 15:32:30 +0100 Subject: [PATCH 0318/1193] Switch md5 to sha256 --- easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb index f05a5831f164..f94434b4fb5b 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb @@ -16,7 +16,7 @@ toolchainopts = {'optarch': True, 'pic': True} source_urls = ['https://yoda.hepforge.org/downloads?f='] sources = ['%(name)s-%(version)s.tar.bz2'] -checksums = ['79054152ef806f26e646b89f14834e5c'] +checksums = ['ebcad55369a1cedcee3a2de059407c851652ba44495113f5c09d8c2e57f516aa'] builddependencies = [ ('Autotools', '20220317'), From 173f22ac7fee37d2668ca5ba5686e870007dde86 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 16 Jan 2024 16:03:50 +0100 Subject: [PATCH 0319/1193] adding easyconfigs: ccache-4.9-GCCcore-12.3.0.eb --- .../c/ccache/ccache-4.9-GCCcore-12.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..6ba94b8786d2 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.3.0.eb @@ -0,0 +1,49 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.9' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['866b2223d59333640f0e7a003cbb85b32d9ca3c9445bd9e3cf142942e69dd3ec'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + ('zstd', '1.5.5'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('hiredis', '1.2.0'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link most libraries statically + '-DSTATIC_LINK=ON', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' From cb0a7bf586b27d036bc189c9a5269e788210df2f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 16 Jan 2024 16:06:24 +0100 Subject: [PATCH 0320/1193] adding easyconfigs: ccache-4.9-GCCcore-12.2.0.eb, hiredis-1.2.0-GCCcore-12.2.0.eb --- .../c/ccache/ccache-4.9-GCCcore-12.2.0.eb | 49 +++++++++++++++++++ .../h/hiredis/hiredis-1.2.0-GCCcore-12.2.0.eb | 41 ++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..713f314a2dd1 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-12.2.0.eb @@ -0,0 +1,49 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.9' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['866b2223d59333640f0e7a003cbb85b32d9ca3c9445bd9e3cf142942e69dd3ec'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Ninja', '1.11.1'), + ('zstd', '1.5.2'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('hiredis', '1.2.0'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link most libraries statically + '-DSTATIC_LINK=ON', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..81201ae4c9bd --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.2.0' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 5bac3fc0011a90b8ee8e88763d80f6210938e2d1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 16 Jan 2024 16:06:36 +0100 Subject: [PATCH 0321/1193] adding easyconfigs: ccache-4.9-GCCcore-13.2.0.eb, hiredis-1.2.0-GCCcore-13.2.0.eb --- .../c/ccache/ccache-4.9-GCCcore-13.2.0.eb | 49 +++++++++++++++++++ .../h/hiredis/hiredis-1.2.0-GCCcore-13.2.0.eb | 41 ++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..15153cb27473 --- /dev/null +++ b/easybuild/easyconfigs/c/ccache/ccache-4.9-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL + +easyblock = 'CMakeNinja' + +name = 'ccache' +version = '4.9' + +homepage = 'https://ccache.dev/' +description = """Ccache (or “ccache”) is a compiler cache. It speeds up recompilation by +caching previous compilations and detecting when the same compilation is being done again""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['866b2223d59333640f0e7a003cbb85b32d9ca3c9445bd9e3cf142942e69dd3ec'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('zstd', '1.5.5'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('hiredis', '1.2.0'), +] + +# use BFD linker rather than default ld.gold (required on CentOS 8) +preconfigopts = 'LDFLAGS="-fuse-ld=bfd"' +configopts = ' '.join([ + '-DENABLE_DOCUMENTATION=OFF', + '-DENABLE_IPO=ON', + # Link most libraries statically + '-DSTATIC_LINK=ON', + # Disable downloading dependencies + '-DZSTD_FROM_INTERNET=OFF -DHIREDIS_FROM_INTERNET=OFF', +]) + +sanity_check_paths = { + 'files': ['bin/ccache'], + 'dirs': [] +} +sanity_check_commands = ['ccache --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..c8967f81a57b --- /dev/null +++ b/easybuild/easyconfigs/h/hiredis/hiredis-1.2.0-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +# Author: Alexander Grund (TU Dresden) +# Based on EC by J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'hiredis' +version = '1.2.0' + +homepage = 'https://github.com/redis/hiredis' +description = """Hiredis is a minimalistic C client library for the Redis database. + +It is minimalistic because it just adds minimal support for the protocol, +but at the same time it uses a high level printf-alike API in order to +make it much higher level than otherwise suggested by its minimal code base +and the lack of explicit bindings for every Redis command.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'redis' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['82ad632d31ee05da13b537c124f819eb88e18851d9cb0c30ae0552084811588c'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = ['-DBUILD_SHARED_LIBS=ON', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['lib/libhiredis.a', 'lib/libhiredis.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 68e42e98b278d497efdb31812450388a0936a75f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 16 Jan 2024 16:28:00 +0100 Subject: [PATCH 0322/1193] delete old easyconfig for gcsfs --- .../gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb | 91 ------------------- 1 file changed, 91 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb diff --git a/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb b/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb deleted file mode 100644 index 1d010a873c3a..000000000000 --- a/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2-foss-2023a.post1.eb +++ /dev/null @@ -1,91 +0,0 @@ -easyblock = "PythonBundle" - -name = 'gcsfs' -version = '2023.12.2' -versionsuffix = '.post1' - -homepage = 'https://github.com/fsspec/gcsfs' -description = """Pythonic file-system interface for Google Cloud Storage.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -# builddependencies = [('protobuf', '24.0')] - -dependencies = [ - ('Python', '3.11.3'), - ('aiohttp', '3.8.5'), - ('poetry', '1.5.1'), - ('protobuf-python', '4.24.0'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('oauthlib', '3.2.2', { - 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], - }), - ('googleapis-common-protos', '1.62.0', { - 'modulename': 'google.api.annotations_pb2', - 'checksums': ['83f0ece9f94e5672cced82f592d2a5edf527a96ed1794f0bab36d5735c996277'], - }), - ('rsa', '4.9', { - 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], - }), - ('pyasn1-modules', '0.3.0', { - 'source_tmpl': 'pyasn1_modules-%(version)s.tar.gz', - 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], - }), - ('cachetools', '5.3.2', { - 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], - }), - ('requests-oauthlib', '1.3.1', { - 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], - }), - ('google-resumable-media', '2.7.0', { - 'modulename': 'google.resumable_media', - 'checksums': ['5f18f5fa9836f4b083162064a1c2c98c17239bfda9ca50ad970ccf905f3e625b'], - }), - ('google-crc32c', '1.5.0', { - 'modulename': 'google_crc32c', - 'checksums': ['89284716bc6a5a415d4eaa11b1726d2d60a0cd12aadf5439828353662ede9dd7'], - }), - ('g', '0.0.3', { - 'checksums': ['988738c40b80bc382a2bfc776e86b616867601a882729296a1902c9c9e7cc4d6'], - }), - ('google-cloud-core', '2.4.1', { - 'modulename': 'google.cloud.environment_vars', - 'checksums': ['9b7749272a812bde58fff28868d0c5e2f585b82f37e09a1f6ed2d4d10f134073'], - }), - ('google-api-core', '2.15.0', { - 'modulename': 'google.api_core', - 'checksums': ['abc978a72658f14a2df1e5e12532effe40f94f868f6e23d95133bd6abcca35ca'], - }), - ('decorator', '5.1.1', { - 'checksums': ['637996211036b6385ef91435e4fae22989472f9d571faba8927ba8253acbc330'], - }), - ('fsspec', version, { - 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], - }), - ('google-auth', '2.26.2', { - 'modulename': 'google.auth', - 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], - }), - ('google-auth-oauthlib', '1.2.0', { - # 'modulename': 'google.auth.oauthlib', - 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], - }), - ('google-cloud-storage', '2.14.0', { - 'modulename': 'google.cloud.storage', - 'checksums': ['2d23fcf59b55e7b45336729c148bb1c464468c69d5efbaee30f7201dd90eb97e'], - }), - ('requests', '2.31.0', { - 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], - }), - (name, version, { - 'source_tmpl': '%(name)s-%(version)s%(versionsuffix)s.tar.gz', - 'checksums': ['e38b7e59580a1e490d62d55a47cba33b49a941b01917c3d6f6cfd2563371ab7b'], - }), -] - -moduleclass = 'tools' From cc3c1cacbb36b42ef0374f586316399f56c0217e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 16 Jan 2024 17:03:26 +0100 Subject: [PATCH 0323/1193] add new ec with intel-compilers + delete old one --- ...a.eb => Zeo++-0.3-intel-compilers-2023.1.0.eb} | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) rename easybuild/easyconfigs/z/Zeo++/{Zeo++-0.3-intel-2021a.eb => Zeo++-0.3-intel-compilers-2023.1.0.eb} (78%) diff --git a/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-2021a.eb b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb similarity index 78% rename from easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-2021a.eb rename to easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb index 0879ff7c5047..b025b7f26bbe 100644 --- a/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-2021a.eb +++ b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb @@ -13,15 +13,13 @@ description = """ Zeo++ can be used to either analyze a single structure or perform high-throughput analysis of a large database. """ -toolchain = {'name': 'intel', 'version': '2021a'} +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} source_urls = ['https://github.com/mharanczyk/zeoplusplus/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['0361659094ec97add5d5846f14326863293e3d9a78997ba4890719f9ffae224a'] -builddependencies = [('binutils', '2.36.1')] - -# try building libvoro in voro++ subdir, which is required by Zeo++ +# first build libvoro in voro++ subdir, which is required by Zeo++ prebuildopts = "cd voro++ && make && ls src/libvoro* && cd - && " buildopts = "all statlib" @@ -32,13 +30,8 @@ files_to_copy = [ ] sanity_check_paths = { - 'files': [ - 'bin/network', - 'bin/framework_builder', - 'bin/molecule_to_abstract', - 'lib/libvoro++.a', - 'lib/libzeo++.a', - ], + 'files': ['bin/network', 'bin/framework_builder', 'bin/molecule_to_abstract', + 'lib/libvoro++.a', 'lib/libzeo++.a'], 'dirs': [] } From 6e65b151695f0669c4e3619c1b10e46d35c68423 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 16 Jan 2024 18:06:09 +0100 Subject: [PATCH 0324/1193] set chesum to none, see https://github.com/easybuilders/easybuild-easyconfigs/pull/16751 --- easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb index aa2e6188e2dd..c91d417c90f5 100644 --- a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2022b.eb @@ -19,7 +19,7 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = ['c8057259fc5c6cf5a3141f013eff52fc94401f47563fbbd86cdc9e56fcff5153'] +checksums = [None] builddependencies = [ ('CMake', '3.24.3'), From b8802c252a4e4bc58e5350e8689bb1161293d3fa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Jan 2024 19:11:33 +0100 Subject: [PATCH 0325/1193] add patch to fix broken 'decorators' test in ESPResSo 4.2.1 on top of Python 3.11.3 --- .../e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb | 7 +- ...o-4.2.1_fix-setuptools-pkg_resources.patch | 79 +++++++++++++++++++ 2 files changed, 85 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1_fix-setuptools-pkg_resources.patch diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb index 6d4ef208058b..de6eaa16c9a8 100644 --- a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1-foss-2023a.eb @@ -8,7 +8,12 @@ description = """A software package for performing and analyzing scientific Mole source_urls = ['https://github.com/espressomd/espresso/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] -checksums = ['f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'] +patches = ['ESPResSo-4.2.1_fix-setuptools-pkg_resources.patch'] +checksums = [ + {'4.2.1.tar.gz': 'f7264d78fe1fd7774b89972fe10d5b15d2e9d620d406158dab90df5df0b9f255'}, + {'ESPResSo-4.2.1_fix-setuptools-pkg_resources.patch': + '0c528ab36dee10c6f310910269427e409ca40730ddaa7a9fe93ec135b3031fc4'}, +] toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = {'usempi': True, 'pic': True} diff --git a/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1_fix-setuptools-pkg_resources.patch b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1_fix-setuptools-pkg_resources.patch new file mode 100644 index 000000000000..98594dc1702e --- /dev/null +++ b/easybuild/easyconfigs/e/ESPResSo/ESPResSo-4.2.1_fix-setuptools-pkg_resources.patch @@ -0,0 +1,79 @@ +fix for failing 'decorators' test: +AttributeError: module 'setuptools.version' has no attribute 'pkg_resources' + +see https://github.com/espressomd/espresso/pull/4709 + +From 111283a0e0184e1674ef29ec0bd873a099574096 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Jean-No=C3=ABl=20Grad?= +Date: Tue, 18 Apr 2023 10:46:51 +0200 +Subject: [PATCH] python: Update deprecated setuptools functionality + +Starting with setuptools v67.3.0, the pkg_resources module is being +progressively phased out from the setuptools main module. +--- + doc/tutorials/constant_pH/constant_pH.ipynb | 4 ++-- + maintainer/benchmarks/mc_acid_base_reservoir.py | 4 ++-- + testsuite/python/unittest_decorators.py | 4 ++-- + 3 files changed, 6 insertions(+), 6 deletions(-) + +diff --git a/doc/tutorials/constant_pH/constant_pH.ipynb b/doc/tutorials/constant_pH/constant_pH.ipynb +index bcfd5bdf993..ca4029465a4 100644 +--- a/doc/tutorials/constant_pH/constant_pH.ipynb ++++ b/doc/tutorials/constant_pH/constant_pH.ipynb +@@ -137,10 +137,10 @@ + "plt.rcParams.update({'font.size': 18})\n", + "\n", + "import numpy as np\n", +- "import setuptools\n", ++ "import pkg_resources\n", + "import pint # module for working with units and dimensions\n", + "import time\n", +- "assert setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \\\n", ++ "assert pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \\\n", + " f'pint version {pint.__version__} is too old: several numpy operations can cast away the unit'\n", + "\n", + "import espressomd\n", +diff --git a/maintainer/benchmarks/mc_acid_base_reservoir.py b/maintainer/benchmarks/mc_acid_base_reservoir.py +index 97e465e8c70..a7a7a965f73 100644 +--- a/maintainer/benchmarks/mc_acid_base_reservoir.py ++++ b/maintainer/benchmarks/mc_acid_base_reservoir.py +@@ -24,7 +24,7 @@ + import espressomd + import espressomd.electrostatics + import espressomd.reaction_methods +-import setuptools ++import pkg_resources + import argparse + + parser = argparse.ArgumentParser(description="Benchmark MC simulations in the grand-reaction ensemble. " +@@ -45,7 +45,7 @@ + # process and check arguments + assert args.particles_per_core >= 100, "you need to use at least 100 particles per core to avoid finite-size effects in the simulation" + espressomd.assert_features(['WCA', 'ELECTROSTATICS']) +-assert setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \ ++assert pkg_resources.packaging.specifiers.SpecifierSet('>=0.10.1').contains(pint.__version__), \ + f'pint version {pint.__version__} is too old: several numpy operations can cast away the unit' + + +diff --git a/testsuite/python/unittest_decorators.py b/testsuite/python/unittest_decorators.py +index 109f89cc8d7..a9a0e5200c4 100644 +--- a/testsuite/python/unittest_decorators.py ++++ b/testsuite/python/unittest_decorators.py +@@ -19,7 +19,7 @@ + + import sys + import importlib +-import setuptools ++import pkg_resources + import unittest + + import espressomd +@@ -74,7 +74,7 @@ def skipIfUnmetModuleVersionRequirement(module, version_requirement): + _module = importlib.import_module(module) + except ImportError: + return skipIfMissingModules(module) +- if not setuptools.version.pkg_resources.packaging.specifiers.SpecifierSet( ++ if not pkg_resources.packaging.specifiers.SpecifierSet( + version_requirement).contains(_module.__version__): + return unittest.skip( + "Skipping test: version requirement not met for module {}".format(module)) From 29b12f61baf7f5910c91e290ff162f98893624c3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Jan 2024 19:13:38 +0100 Subject: [PATCH 0326/1193] fix indent in Zeo++ easyconfig --- .../easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb index b025b7f26bbe..f15685f3b31e 100644 --- a/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb @@ -31,7 +31,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ['bin/network', 'bin/framework_builder', 'bin/molecule_to_abstract', - 'lib/libvoro++.a', 'lib/libzeo++.a'], + 'lib/libvoro++.a', 'lib/libzeo++.a'], 'dirs': [] } From ab8870d73a72aabb7f419dd3f39a117c5ec6214b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Jan 2024 19:54:53 +0100 Subject: [PATCH 0327/1193] fix indent in Zeo++ easyconfig --- .../easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb index f15685f3b31e..0246ec88d36a 100644 --- a/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/z/Zeo++/Zeo++-0.3-intel-compilers-2023.1.0.eb @@ -31,7 +31,7 @@ files_to_copy = [ sanity_check_paths = { 'files': ['bin/network', 'bin/framework_builder', 'bin/molecule_to_abstract', - 'lib/libvoro++.a', 'lib/libzeo++.a'], + 'lib/libvoro++.a', 'lib/libzeo++.a'], 'dirs': [] } From 6ca0e3c4ab1a1cef42ea9b66d680cb06b008889c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 16 Jan 2024 20:10:11 +0100 Subject: [PATCH 0328/1193] adding easyconfigs: texlive-20230313-GCC-12.3.0.eb --- .../t/texlive/texlive-20230313-GCC-12.3.0.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-12.3.0.eb b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-12.3.0.eb new file mode 100644 index 000000000000..0cf99eed71c5 --- /dev/null +++ b/easybuild/easyconfigs/t/texlive/texlive-20230313-GCC-12.3.0.eb @@ -0,0 +1,78 @@ +# Based off the 2017 version by John Dey jfdey@fredhutch.org +# https://github.com/easybuilders/easybuild-easyconfigs/pull/5085 +easyblock = 'Tarball' + +name = 'texlive' +version = '20230313' +local_ver_year = version[:4] + +homepage = 'https://tug.org' +description = """TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript + text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a + PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to + be a representation of the final typeset output, and so can be easily edited and manipulated.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = [ + 'ftp://tug.org/texlive/historic/%s/' % local_ver_year, + 'https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/' % local_ver_year, +] +sources = [ + { + 'download_filename': 'install-tl-unx.tar.gz', + 'filename': 'install-tl-unx-%(version)s.tar.gz' + } +] +checksums = ['d97bdb3b1903428e56373e70861b24db448243d74d950cdff96f4e888f008605'] + +dependencies = [ + ('X11', '20230603'), + ('libpng', '1.6.39'), + ('libGLU', '9.0.3'), + ('Perl', '5.36.1'), + ('HarfBuzz', '5.3.1'), + ('poppler', '23.09.0'), + ('cairo', '1.17.8'), + ('fontconfig', '2.14.2'), + ('zlib', '1.2.13'), + ('graphite2', '1.3.14'), +] + +# For the latest release, the tlnet-final repository isn't available yet, so we use the default +# But, the default can _not_ be used for the historic releases. The only way to write an EasyConfig +# that will work today and in the future, is to try one by one. +# Similarly, ftp is not available on all HPC systems, hence providing fallback to https +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/17871 +local_install_tl = "%%(builddir)s/install-tl-%%(version)s/install-tl -profile %%(installdir)s/texlive.profile %s" +local_ftp = '-repository ftp://ftp.math.utah.edu/pub/tex/historic/systems/textlive/%s/tlnet-final' % local_ver_year +local_https = '-repository https://ftp.math.utah.edu/pub/tex/historic/systems/texlive/%s/tlnet-final' % local_ver_year +local_install_tl_or = ( + ' || '.join([ + local_install_tl % '', + local_install_tl % local_ftp, + local_install_tl % local_https, + ]) +) +postinstallcmds = [ + 'echo "TEXDIR %%(installdir)s/" > %%(installdir)s/texlive.profile && ' + 'echo "TEXMFLOCAL %%(installdir)s/texmf-local" >> %%(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSCONFIG %%(installdir)s/texmf-config" >> %%(installdir)s/texlive.profile && ' + 'echo "TEXMFSYSVAR %%(installdir)s/texmf-var" >> %%(installdir)s/texlive.profile && ' + '%s' % local_install_tl_or +] + +sanity_check_paths = { + 'files': ['bin/%(arch)s-linux/tex', 'bin/%(arch)s-linux/latex'], + 'dirs': ['bin/%(arch)s-linux', 'texmf-dist'], +} + +modextrapaths = { + 'INFOPATH': 'texmf-dist/doc/info', + 'MANPATH': 'texmf-dist/doc/man', + 'PATH': 'bin/%(arch)s-linux', +} + +modextravars = {'TEXMFHOME': '%(installdir)s/texmf-dist'} + +moduleclass = 'devel' From 0dbff2eaf9895b4d03618fbe1a7dd84baedd179e Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 17 Jan 2024 09:42:28 +0100 Subject: [PATCH 0329/1193] adding easyconfigs: Wannier90-3.1.0-intel-2022b.eb --- .../Wannier90/Wannier90-3.1.0-intel-2022b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022b.eb diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022b.eb new file mode 100644 index 000000000000..c696e0ffde03 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-intel-2022b.eb @@ -0,0 +1,32 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From 4bfe39a005b9f61d6413348b4ce4e2a462354040 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 11:31:21 +0100 Subject: [PATCH 0330/1193] adding easyconfigs: Ruby-3.3.0-GCCcore-12.3.0.eb --- .../r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..3059ed91825a --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb @@ -0,0 +1,23 @@ +name = 'Ruby' +version = '3.3.0' + +homepage = 'https://www.ruby-lang.org' +description = """Ruby is a dynamic, open source programming language with + a focus on simplicity and productivity. It has an elegant syntax that is + natural to read and easy to write.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['96518814d9832bece92a85415a819d4893b307db5921ae1f0f751a9a89a56b7d'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('libyaml', '0.2.5'), +] + +moduleclass = 'lang' From a714f21cb38e7ae31e9913646b5e90aa8160b859 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 17 Jan 2024 12:23:00 +0100 Subject: [PATCH 0331/1193] adding easyconfigs: Rust-1.75.0-GCCcore-12.3.0.eb --- .../r/Rust/Rust-1.75.0-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..2d2e5e8c3879 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.75.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.75.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.75.0-src.tar.gz': '5b739f45bc9d341e2d1c570d65d2375591e22c2d23ef5b8a37711a0386abc088'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Python', '3.11.3'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'lang' From 427c02c6ff7dfdd861725282d8e8894dac374153 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Jan 2024 13:15:53 +0100 Subject: [PATCH 0332/1193] adding easyconfigs: archspec-0.2.2-GCCcore-13.2.0.eb --- .../archspec/archspec-0.2.2-GCCcore-13.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.2.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.2.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..5af93d472ee5 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.2.2' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d922c9fd80a5234d8cef883fbe0e146b381c449062c0405f91714ebad1edc035'] + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] + +dependencies = [('Python', '3.11.5')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from archspec.cpu import host; print(host())'"] + +moduleclass = 'tools' From 8819425f219f759f083f0a2c711503d968c32853 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 13:26:44 +0100 Subject: [PATCH 0333/1193] adding easyconfigs: psmc-0.6.5_20221121-GCC-12.3.0.eb --- .../p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb b/easybuild/easyconfigs/p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb new file mode 100644 index 000000000000..d59f8ed5d78e --- /dev/null +++ b/easybuild/easyconfigs/p/psmc/psmc-0.6.5_20221121-GCC-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MakeCp' + +name = 'psmc' +version = '0.6.5_20221121' +_commit = '8bd902f' + +homepage = 'https://github.com/lh3/psmc' +description = """This software package infers population size history from a diploid sequence +using the Pairwise Sequentially Markovian Coalescent (PSMC) model.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/lh3/psmc/archive/'] +sources = [{ + 'source_urls': ['https://github.com/lh3/psmc/archive/'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['24a79addd863d91c7f19bcd2dc2cb16bb3d7b303d5ff44e48b8b89c975cf1c49'] + +dependencies = [('Perl', '5.36.1')] + +buildopts = '&& cd utils && make' + +local_utils = [ + 'avg.pl', 'calD', 'cntcpg', 'ctime_plot.pl', 'dec2ctime.pl', 'decode2bed.pl', 'fq2psmcfa', 'history2ms.pl', + 'ms2psmcfa.pl', 'mutDiff', 'pcnt_bezier.lua', 'psmc2history.pl', 'psmc_plot.pl', 'psmc_trunc.pl', 'splitfa', +] + +files_to_copy = [ + (['psmc'], 'bin'), + (['utils/%s' % x for x in local_utils], 'bin') +] + +postinstallcmds = [ + # recommended help, see perldoc Getopt::Std + "sed -i '/use Getopt::Std;/a $Getopt::Std::STANDARD_HELP_VERSION = 1;' %(installdir)s/bin/*.pl", +] + +fix_perl_shebang_for = ['bin/*.pl'] + +sanity_check_paths = { + 'files': ['bin/psmc'] + ['bin/%s' % x for x in local_utils], + 'dirs': [], +} + +sanity_check_commands = [ + 'psmc 2>&1 |grep "Usage:"', + 'calD 2>&1 |grep "Usage:"', + 'avg.pl --help', + 'ctime_plot.pl --help', +] + +moduleclass = 'bio' From 5496f24cd8c42294cf77b10d4ee4fbbb844b283c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 17 Jan 2024 13:52:29 +0100 Subject: [PATCH 0334/1193] fix trivial (style) differences with QIIME2 v2023.5.1 easyconfig --- easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb index 2149ad12c491..37d299ece5ea 100755 --- a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb @@ -8,6 +8,7 @@ description = """QIIME 2 is a powerful, extensible, and decentralized microbiome open source, and community developed.""" toolchain = {'name': 'foss', 'version': '2022a'} + dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), @@ -146,6 +147,7 @@ exts_list = [ 'preinstallopts': """sed -i "/'nose /d" setup.py && """, 'checksums': ['ac4f579a0881f1c827f75033a304341ae91d3a527cc6aed3fea53749f1b9951c'], }), + # using prebuilt wheels for atpublic and flufl.lock because building them requires pdm ('atpublic', '4.0', { 'modulename': 'public', 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', @@ -169,7 +171,7 @@ exts_list = [ 'checksums': ['087950518c53a2491deb52b8ddd66833f953882e517a42e476c007cc8f6892c5'], }), ('altair', '5.0.1', { - 'preinstallopts': """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' -e 's/^requires = .*/requires = ["setuptools"]/g' -e 's/^license-files = .*//g' -e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && schemadir=%(installdir)s/lib/python%(pyshortver)s/site-packages/altair/vegalite/v5/schema/ && mkdir -p $schemadir && cp altair/vegalite/v5/schema/vega-lite-schema.json $schemadir && """, + 'preinstallopts': _preinstallopts, 'checksums': ['087d7033cb2d6c228493a053e12613058a5d47faf6a36aea3ff60305fd8b4cb0'], }), (name, version, { @@ -323,4 +325,3 @@ sanity_check_commands = [ modextrapaths = {'CONDA_PREFIX': ''} moduleclass = 'bio' - From 128bc04644406d5f4db206129fa45637a17bf9ea Mon Sep 17 00:00:00 2001 From: Neves-P Date: Wed, 17 Jan 2024 14:39:16 +0100 Subject: [PATCH 0335/1193] Fix file permissions --- easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2023.7.0-foss-2022a.eb old mode 100755 new mode 100644 From 880c3a6504dad754e0352486c2ce756cc0485bba Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 15:53:36 +0100 Subject: [PATCH 0336/1193] adding easyconfigs: BioPerl-1.7.8-GCCcore-12.3.0.eb --- .../b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..066042c93e83 --- /dev/null +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb @@ -0,0 +1,57 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchinson Cancer Research Center +# Thomas Eylenbosch - Gluo NV + +easyblock = 'PerlModule' + +name = 'BioPerl' +version = '1.7.8' + +homepage = 'https://bioperl.org/' +description = """Bioperl is the product of a community effort to produce Perl code which is useful in biology. + Examples include Sequence objects, Alignment objects and database searching objects.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('XML-LibXML', '2.0209'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('XML::Writer', '0.900', { + 'source_tmpl': 'XML-Writer-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JO/JOSEPHW'], + 'checksums': ['73c8f5bd3ecf2b350f4adae6d6676d52e08ecc2d7df4a9f089fa68360d400d1f'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['c490a3be7715ea6e4305efd9710e5edab82dabc55fd786b6505b550a30d71738'], + }), + ('Bio::Procedural', '1.7.4', { + 'source_tmpl': 'Bio-Procedural-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CJ/CJFIELDS/'], + 'checksums': ['d2bd9cfbb091eee2d80ed6cf812ac3813b1c8a1aaca20671037f5f225d31d1da'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/perl5/site_perl/%(perlver)s/Bio'], +} + +moduleclass = 'bio' From 1fb433cc523b0e52a71345300834c0aa3a50a28b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 16:06:45 +0100 Subject: [PATCH 0337/1193] adding easyconfigs: ClustalW2-2.1-GCC-12.3.0.eb, PRANK-170427-GCC-12.3.0.eb --- .../c/ClustalW2/ClustalW2-2.1-GCC-12.3.0.eb | 38 +++++++++++++++++++ .../p/PRANK/PRANK-170427-GCC-12.3.0.eb | 36 ++++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..85a6b9a43949 --- /dev/null +++ b/easybuild/easyconfigs/c/ClustalW2/ClustalW2-2.1-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# https://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## +# foss-2016b modified by: +# Adam Huffman +# The Francis Crick Institute + +easyblock = 'ConfigureMake' + +name = 'ClustalW2' +version = '2.1' + +homepage = 'https://www.ebi.ac.uk/Tools/msa/clustalw2/' +description = """ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.clustal.org/download/%(version)s'] +sources = ['clustalw-%(version)s.tar.gz'] +checksums = ['e052059b87abfd8c9e695c280bfba86a65899138c82abccd5b00478a80f49486'] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = ['(echo H; echo X; echo X) | clustalw2'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-12.3.0.eb new file mode 100644 index 000000000000..4d5f9b5fae7f --- /dev/null +++ b/easybuild/easyconfigs/p/PRANK/PRANK-170427-GCC-12.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'MakeCp' + +name = 'PRANK' +version = '170427' + +homepage = 'http://wasabiapp.org/software/prank/' +description = """ PRANK is a probabilistic multiple alignment program for DNA, + codon and amino-acid sequences. PRANK is based on a novel algorithm that treats + insertions correctly and avoids over-estimation of the number of deletion events.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://wasabiapp.org/download/prank/'] +sources = ['%(namelower)s.source.%(version)s.tgz'] +checksums = ['623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859'] + +# PRANK uses MAFFT as external tool to construct guide tree +dependencies = [('MAFFT', '7.520', '-with-extensions')] + +start_dir = 'src' + +files_to_copy = [(['prank'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/prank'], + 'dirs': [], +} + +sanity_check_commands = ['prank -help'] + +moduleclass = 'bio' From 4887f1cd566d4ac32658a7c8dadf649dbe13c211 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 16:32:13 +0100 Subject: [PATCH 0338/1193] adding easyconfigs: MUSCLE-5.1.0-GCCcore-12.3.0.eb --- .../m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..8482b40b846b --- /dev/null +++ b/easybuild/easyconfigs/m/MUSCLE/MUSCLE-5.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MakeCp' + +name = 'MUSCLE' +version = '5.1.0' + +homepage = 'https://drive5.com/muscle/' +description = """MUSCLE is one of the best-performing multiple alignment programs + according to published benchmark tests, with accuracy and speed that are consistently + better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users + learn everything they need to know about MUSCLE in a few minutes-only a handful of + command-line options are needed to perform common alignment tasks.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'rcedgar' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['2bba8b06e3ccabf6465fa26f459763b2029d7e7b9596881063e3aaba60d9e87d'] + +builddependencies = [ + ('binutils', '2.40'), +] + +start_dir = 'src' + +# Use build environment defined by EasyBuild +prebuildopts = "sed -i 's/$(CPPOPTS)/$(CPPOPTS) $(CXXFLAGS) $(CPPFLAGS)/g' Makefile &&" +buildopts = "CPP=${CXX} CC=${CC}" + +files_to_copy = [(['Linux/muscle'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/muscle'], + 'dirs': [], +} + +sanity_check_commands = ["muscle -h"] + +moduleclass = 'bio' From 4f792bb565fecfdbeafb3b91b96a2b0d82af9223 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Wed, 17 Jan 2024 16:32:33 +0100 Subject: [PATCH 0339/1193] Depend on Boost.MPI-1.81, not Boost.MPI-1.79 --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 40852333bbec..0509b1144b80 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -25,7 +25,7 @@ builddependencies = [('CMake', '3.24.3')] dependencies = [ ('pybind11', '2.10.3'), ('Python', '3.10.8'), - ('Boost.MPI', '1.79.0'), + ('Boost.MPI', '1.81.0'), ('SciPy-bundle', '2023.02'), ('mpi4py', '3.1.4'), ] From 9542ea038022db1a2f30db5f5739db83ba0c3d24 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 17:04:19 +0100 Subject: [PATCH 0340/1193] add XML-LibXML dep --- .../XML-LibXML-2.0209-GCCcore-12.3.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9b61bb47ce17 --- /dev/null +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb @@ -0,0 +1,65 @@ +# updated toolchain, version, and dependency versions +# Thomas Eylenbosch 5-Jun-23 + +easyblock = 'Bundle' + +name = 'XML-LibXML' +version = '2.0209' + +homepage = 'https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod' +description = "Perl binding for libxml2" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('Perl-bundle-CPAN', '5.36.1'), + ('libxml2', '2.11.4'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('File::chdir', '0.1011', { + 'source_tmpl': 'File-chdir-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], + 'checksums': ['31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79'], + }), + ('Alien::Base', '2.80', { + 'source_tmpl': 'Alien-Build-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/'], + 'checksums': ['d9edc936b06705bb5cb5ee5a2ea8bcf6111a3e8815914f177e15e3c0fed301f3'], + }), + ('Alien::Build::Plugin::Download::GitLab', '0.01', { + 'source_tmpl': 'Alien-Build-Plugin-Download-GitLab-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['c1f089c8ea152a789909d48a83dbfcf2626f773daf30431c8622582b26aba902'], + }), + ('Alien::Libxml2', '0.19', { + 'source_tmpl': 'Alien-Libxml2-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PL/PLICEASE'], + 'checksums': ['f4a674099bbd5747c0c3b75ead841f3b244935d9ef42ba35368024bd611174c9'], + }), + ('XML::LibXML', version, { + 'source_tmpl': 'XML-LibXML-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/S/SH/SHLOMIF/'], + 'checksums': ['b4a5abbcd689aa2fbbc8b7b45339e961c4984e48108494eb6c282b4748222425'], + }), +] + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], +} + +moduleclass = 'data' From 8d836f292059426db5bc7611f14c11a8dcbd4a5f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 17:14:38 +0100 Subject: [PATCH 0341/1193] adding easyconfigs: GUIDANCE-2.02-GCC-12.3.0.eb --- .../g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb new file mode 100644 index 000000000000..1a801d890904 --- /dev/null +++ b/easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'GUIDANCE' +version = '2.02' + +homepage = 'https://taux.evolseq.net/guidance/' +description = """ +GUIDANCE is a software package for aligning biological sequences (DNA or +amino acids) using either MAFFT, PRANK, or CLUSTALW, and calculating +confidence scores for each column, sequence and residue in the alignment.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://taux.evolseq.net/guidance/static/download/'] +sources = ['%(namelower)s.v%(version)s.tar.gz'] +checksums = ['825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844'] + +dependencies = [ + ('Perl', '5.36.1'), + ('BioPerl', '1.7.8'), + ('Ruby', '3.3.0'), + ('MAFFT', '7.520', '-with-extensions'), + ('PRANK', '170427'), + ('ClustalW2', '2.1'), + ('MUSCLE', '5.1.0'), + ('PAGAN2', '1.53_20230824', '-linux64', SYSTEM), +] + +_bins = ['isEqualTree', 'msa_set_score', 'removeTaxa', 'semphy'] + +files_to_copy = [(['programs/%s/%s' % (x, x) for x in _bins], 'bin'), 'www'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': [], +} + +sanity_check_commands = ['msa_set_score -h', 'semphy -h'] + +moduleclass = 'bio' From 5708fb6882810a5c081056e02c9eaf6e897cbde6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 17:16:28 +0100 Subject: [PATCH 0342/1193] adding easyconfigs: PAGAN2-1.53_20230824-linux64.eb --- .../p/PAGAN2/PAGAN2-1.53_20230824-linux64.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/PAGAN2/PAGAN2-1.53_20230824-linux64.eb diff --git a/easybuild/easyconfigs/p/PAGAN2/PAGAN2-1.53_20230824-linux64.eb b/easybuild/easyconfigs/p/PAGAN2/PAGAN2-1.53_20230824-linux64.eb new file mode 100644 index 000000000000..58d8d806b588 --- /dev/null +++ b/easybuild/easyconfigs/p/PAGAN2/PAGAN2-1.53_20230824-linux64.eb @@ -0,0 +1,39 @@ +easyblock = 'PackedBinary' + +name = 'PAGAN2' +version = '1.53_20230824' +versionsuffix = '-linux64' +_commit = 'c7fa56d' + +homepage = 'https://github.com/ariloytynoja/pagan2-msa' +description = """ +PAGAN2 is a general-purpose method for the alignment of DNA, codon and +amino-acid sequences as graphs. It aligns sequences either with pileup or, when +related by a tree, using phylogeny-aware progressive alignment algorithm. In +both cases it uses graphs to describe the uncertainty in the presence of +characters at certain sequence positions. PAGAN2 is largely compatible with +PAGAN but implements new algorithms for alignment anchoring and memory handling. +As a result, PAGAN2 can align sequences of several hundreds of kilobases in +length.""" + +toolchain = SYSTEM + +sources = [{ + 'source_urls': ['https://github.com/ariloytynoja/pagan2-msa/archive'], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['e4368d6a271fd527aae8bed93c38d9b3ed66f7d781f0509c01486f7b5ffc683e'] + +install_cmds = [ + 'cd %(installdir)s && mkdir -p bin && cp %(builddir)s/pagan2*/bin/pagan2 bin/', +] + +sanity_check_paths = { + 'files': ['bin/pagan2'], + 'dirs': [], +} + +sanity_check_commands = ['pagan2 --help'] + +moduleclass = 'bio' From eca6fcc6b2d27a927fe0e677659bcb699ce79bec Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 17 Jan 2024 18:14:22 +0100 Subject: [PATCH 0343/1193] add missing DB_File dep --- .../b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb | 1 + .../d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 2 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb index 066042c93e83..b47216124f89 100644 --- a/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/BioPerl/BioPerl-1.7.8-GCCcore-12.3.0.eb @@ -22,6 +22,7 @@ dependencies = [ ('Perl', '5.36.1'), ('Perl-bundle-CPAN', '5.36.1'), ('XML-LibXML', '2.0209'), + ('DB_File', '1.859'), ] exts_defaultclass = 'PerlModule' diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ceaba6014167 --- /dev/null +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'DB_File' +version = '1.859' + +homepage = 'https://perldoc.perl.org/DB_File.html' +description = """Perl5 access to Berkeley DB version 1.x.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://www.cpan.org/modules/by-module/DB_File/PMQS'] +sources = [SOURCE_TAR_GZ] +checksums = ['5674e0d2cd0b060c4d1253670ea022c64d842a55257f9eb8edb19c0f53e2565c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Perl', '5.36.1'), + ('DB', '18.1.40'), +] + +preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'dirs': [], +} + +moduleclass = 'data' From 044c6c2490ce55216cfeb415e679667133a7cd72 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 17 Jan 2024 19:13:47 +0100 Subject: [PATCH 0344/1193] adding easyconfigs: ant-1.10.14-Java-21.eb --- .../easyconfigs/a/ant/ant-1.10.14-Java-21.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/a/ant/ant-1.10.14-Java-21.eb diff --git a/easybuild/easyconfigs/a/ant/ant-1.10.14-Java-21.eb b/easybuild/easyconfigs/a/ant/ant-1.10.14-Java-21.eb new file mode 100644 index 000000000000..815383ca5c0d --- /dev/null +++ b/easybuild/easyconfigs/a/ant/ant-1.10.14-Java-21.eb @@ -0,0 +1,27 @@ +easyblock = 'PackedBinary' + +name = 'ant' +version = '1.10.14' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://ant.apache.org/' +description = """Apache Ant is a Java library and command-line tool whose mission is to drive processes described in + build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of + Java applications.""" + +toolchain = SYSTEM + +source_urls = ['https://archive.apache.org/dist/ant/binaries/'] +sources = ['apache-%(name)s-%(version)s-bin.tar.gz'] +checksums = ['e2852fddaaddc1ab76a099ca0d7b2ee47a907b8a91a64f70f6aa9e6a3d0dd504'] + +dependencies = [('Java', '21')] + +sanity_check_paths = { + 'files': ['bin/ant', 'lib/ant.jar'], + 'dirs': [], +} + +modextravars = {'ANT_HOME': '%(installdir)s'} + +moduleclass = 'devel' From ba0e904ca440917ca40ad63663425be2086829b9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Jan 2024 19:20:34 +0100 Subject: [PATCH 0345/1193] adding easyconfigs: OpenSSL-3.eb --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb | 40 ++++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb new file mode 100644 index 000000000000..8c5991c16269 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb @@ -0,0 +1,40 @@ +easyblock = 'EB_OpenSSL_wrapper' + +name = 'OpenSSL' +version = '3' +minimum_openssl_version = '3.0.0' + +homepage = 'https://www.openssl.org/' +description = """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, + and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) + protocols as well as a full-strength general purpose cryptography library. """ + +toolchain = SYSTEM +toolchainopts = {'pic': True} + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Perl', '5.38.0'), +] + +# This easyconfig will wrap the OpenSSL installation in the host system. +# If the system provides the required binary, header files, and libraries for +# this version of OpenSSL, the installation directory of this module will be +# populated with symlinks to the system files. The minimum required version of +# OpenSSL can be finely controled with 'minimum_openssl_version' (defaults to +# easyconfig version). +# If the host system does not have this version of OpenSSL (or with the option +# wrap_system_openssl = False), EasyBuild will fall back to the following +# component list, which will be build and installed as usual. + +components = [ + (name, '3.2.0', { + 'easyblock': 'EB_OpenSSL', + 'source_urls': ['https://www.openssl.org/source/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['14c826f07c7e433706fb5c69fa9e25dab95684844b4c962a2cf1bf183eb4690e'], + 'start_dir': '%(namelower)s-%(version)s', + }), +] + +moduleclass = 'system' From 893ed0203618b0623e542cb42a38800e0e6fce97 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 17 Jan 2024 19:25:20 +0100 Subject: [PATCH 0346/1193] adding easyconfigs: Saxon-HE-12.4-Java-21.eb --- .../s/Saxon-HE/Saxon-HE-12.4-Java-21.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb new file mode 100644 index 000000000000..3024279f7ab0 --- /dev/null +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'Saxon-HE' +version = '12.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'http://saxon.sourceforge.net' +description = """Open Source SAXON XSLT processor developed by Saxonica Limited.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/Saxonica/Saxon-HE/releases/download/SaxonHE12-4/'] +sources = ['SaxonHE%sJ.zip' % version.replace('.', '-')] +checksums = ['44ab28ea945090983196f0b6479596a27fd57a341e8465b6db7fc2eca8c3ddce'] + +dependencies = [('Java', '21')] + +local_jarfiles = [ + '%(namelower)s-%(version)s.jar', '%(namelower)s-test-%(version)s.jar', '%(namelower)s-xqj-%(version)s.jar' +] + +sanity_check_paths = { + 'files': local_jarfiles, + 'dirs': [], +} + +modextrapaths = {'CLASSPATH': local_jarfiles} + +moduleclass = 'devel' From 5866d338e0dd48036f4fc1a631ae499f5695c116 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 17 Jan 2024 22:09:14 +0100 Subject: [PATCH 0347/1193] adding easyconfigs: GSL-2.7-GCC-13.2.0.eb --- .../easyconfigs/g/GSL/GSL-2.7-GCC-13.2.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-13.2.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-13.2.0.eb new file mode 100644 index 000000000000..0b2ef39668bb --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-GCC-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' From 50f87173b54b8015b618f03f509b6d2d86df3290 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 18 Jan 2024 12:13:33 +0100 Subject: [PATCH 0348/1193] adding easyconfigs: PyCheMPS2-1.8.12-foss-2022b.eb, PyBerny-0.6.3-foss-2022b.eb, XCFun-2.1.1-GCCcore-12.2.0.eb, libcint-5.4.0-gfbf-2022b.eb, CPPE-0.3.1-GCC-12.2.0.eb, PySCF-2.4.0-foss-2022b.eb --- .../c/CPPE/CPPE-0.3.1-GCC-12.2.0.eb | 47 +++++++ .../l/libcint/libcint-5.4.0-gfbf-2022b.eb | 37 ++++++ .../p/PyBerny/PyBerny-0.6.3-foss-2022b.eb | 38 ++++++ .../PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb | 34 +++++ .../p/PySCF/PySCF-2.4.0-foss-2022b.eb | 123 ++++++++++++++++++ .../x/XCFun/XCFun-2.1.1-GCCcore-12.2.0.eb | 27 ++++ 6 files changed, 306 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb create mode 100644 easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.2.0.eb b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.2.0.eb new file mode 100644 index 000000000000..cb04681be996 --- /dev/null +++ b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-12.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'CPPE' +version = '0.3.1' + +homepage = 'https://github.com/maxscheurer/cppe' +description = """CPPE is an open-source, light-weight C++ and Python library for Polarizable +Embedding (PE)1,2 calculations. It provides an easy-to-use API to implement PE +for ground-state self-consistent field (SCF) calculations and post-SCF methods. +A convenient Python interface is also available.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +github_account = 'maxscheurer' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['38d4230ba3ace78936049c23ad4b1fe9e704fd250ec57cc9733cb3904b62cf7c'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pybind11', '2.10.3'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} +exts_list = [ + ('cppe', version, { + 'source_urls': [PYPI_SOURCE], + 'checksums': ['b0aef578d6919f8c103d4d4a9fcd3db481bd73c59c157985f52bf62477425d6c'], + }), +] + +sanity_check_paths = { + 'files': ['lib/libcppe.%s' % SHLIB_EXT], + 'dirs': ['include/cppe', 'lib/python%(pyshortver)s/site-packages', 'share/cmake'], +} + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb new file mode 100644 index 000000000000..8a1e3005861f --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '5.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = "libcint is an open source library for analytical Gaussian integrals." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/sunqm/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] +checksums = [ + {'v5.4.0.tar.gz': '42a8f2e9244e4575437e426e32cd1e60ef9559971c42a41f860c870efc745d99'}, + {'libcint-4.4.0_remove_pyscftest.patch': '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +configopts = "-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on" + +buildopts = 'VERBOSE=1' + +runtest = "test " +separate_build_dir = False # Must use the same directory for tests + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/%(name)s.so'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022b.eb b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022b.eb new file mode 100644 index 000000000000..570de2838b1b --- /dev/null +++ b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022b.eb @@ -0,0 +1,38 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'PyBerny' +version = '0.6.3' + +homepage = 'https://github.com/jhrmnn/pyberny' +description = """PyBerny is an optimizer of molecular geometries with respect to the total energy, +using nuclear gradient information.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True + +exts_list = [ + ('pyberny', version, { + 'modulename': 'berny', + 'checksums': ['b4bd9d3d2d58261e8f1d91b8204cc563617044d4b9daf6aae8feee31893cb336'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/berny'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["berny -h"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb new file mode 100644 index 000000000000..8b8ff5ae60e2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'PyCheMPS2' +version = '1.8.12' + +homepage = 'https://sebwouters.github.io/CheMPS2' +description = """PyCheMPS2 is a python interface to CheMPS2, for compilation without +MPI. CheMPS2 is a scientific library which contains a spin-adapted +implementation of the density matrix renormalization group (DMRG) +for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('CheMPS2', version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'], + 'install_src': './%(name)s', + }), +] + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb new file mode 100644 index 000000000000..64c2ec531760 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb @@ -0,0 +1,123 @@ +easyblock = 'CMakeMakeCp' +name = 'PySCF' +version = '2.4.0' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['cc76440b9a7bf6a4969559b61eceb67c25760d211e6f59fc540209b1ea359d8d'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pybind11', '2.10.3'), # needed by zquatev +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), # for numpy, scipy + ('h5py', '3.8.0'), + ('libcint', '5.4.0'), + ('libxc', '6.1.0'), + ('XCFun', '2.1.1'), + ('CPPE', '0.3.1'), # extra + ('PyBerny', '0.6.3'), # extra + ('PyCheMPS2', '1.8.12'), # needed by dmrgscf + ('Block', '1.5.3-20200525'), # needed by dmrgscf + ('NECI', '20230620'), # needed by fciqmc + ('Dice', '20240101'), # needed by icmpspt +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'modulename': 'pyscf.%(name)s', + 'source_urls': ['https://github.com/pyscf/%(name)s/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], +} + +# The following list of extensions is equivalent to installing PySCF with extras: +# all + dmrgscf + fciqmcscf + hci + mbd + tblis + zquatev +exts_list = [ + ('dftd3', '94091d8', { + 'checksums': ['a69ae44b3d02d2c06fd531373f20ee1251ef27fc932d40a7cafea6c09d8784fc'], + }), + ('doci', '08079a9', { + 'checksums': ['f492ba45dfe50c9b459e53a946a677528af0dc2097ff77ea3767aa4f46c5d9ba'], + }), + ('icmpspt', '50c386e', { + 'checksums': ['08029863ae8740939a730fe5e104661c67d8dd0b8a8555b603fc8a0777096d48'], + }), + ('properties', '92a4df7', { + 'modulename': 'pyscf.prop', + 'checksums': ['df5456315855c7a4f5858b244461793f2cbc21f6a6c0328039838ad85913c79d'], + }), + ('qsdopt', '3ad2c02', { + 'checksums': ['cc639150e5f9efad8ffe496b3dccd2952a1f60fdad51f611cffba701892b384e'], + }), + ('semiempirical', '470d716', { + 'checksums': ['0bbe304867fd053ed647445ac84c4c76787ad23def9f72415aec297740121eef'], + }), + ('shciscf', 'e8985e7', { + 'checksums': ['a017ffcf54601ccb3e95a273eff47289905c81d7fd590f9b51e22a69e141b592'], + }), + ('MCfun', '0.2.2', { + 'modulename': 'mcfun', + 'source_urls': ['https://github.com/Multi-collinear/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['1cb6b36be86bcf13c15ecc9934d13dc67eb15834a7a6545e73f82f53835e278d'], + }), + ('pyqmc', '0.6.0', { + 'modulename': 'pyqmc', + 'source_urls': ['https://github.com/WagnerGroup/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6e9f612c2d0bf2198154520e01dce57cf3a6e474840c1892466de3171eaeb7db'], + }), + ('dmrgscf', '4ff57bf', { + 'checksums': ['0683cfc2e6676aa11da7b2eee66e96442a64a37b72f65057779718c5fdb43c5f'], + }), + ('fciqmc', 'ee98fb4', { + 'modulename': 'pyscf.fciqmcscf', + 'checksums': ['b2f081ac295df0e622c6d1b3bff6d7834f97131f1f0fc87ec8bcff2137ef4199'], + }), + ('mbd', '485c18c', { + 'checksums': ['de1fb14650fcb87909cae33dc318d2e213653ac4393ced7e070dfa6308d95846'], + }), + ('naive-hci', '0c28d6e', { + 'modulename': 'pyscf.hci', + 'checksums': ['de247d17b80133655df5966341e5adb691b0df150cd9b0f1980cf62ec55229d5'], + }), + ('tblis', '0d4dfd2', { + 'modulename': 'pyscf.tblis_einsum', + 'source_urls': ['https://github.com/pyscf/pyscf-tblis/archive/'], + 'checksums': ['5e0e5840b78451085420b333cd4b5ee06fd659df06f142fa854de65b3f73fc5e'], + }), + ('zquatev', '4eb41b1', { + 'modulename': 'zquatev', + 'preinstallopts': "sed -i 's/add_subdirectory(pybind11)/find_package(pybind11 REQUIRED)/' CMakeLists.txt && ", + 'source_urls': ['https://github.com/sunqm/%(name)s/archive/'], + 'checksums': ['4caf08e3831a5d86e6bc22f3b4028cc159101cb9658d09de16e382e268a5a2e9'], + }), +] + +start_dir = 'pyscf/lib' +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +_py_site_packages = 'lib/python%(pyshortver)s/site-packages' +files_to_copy = [(['pyscf'], _py_site_packages)] + +sanity_check_paths = { + 'files': [_py_site_packages + '/pyscf/__init__.py'], + 'dirs': [_py_site_packages + d for d in ['/pyscf/data', '/pyscf/lib']], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': _py_site_packages} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..60e7b3d6bd21 --- /dev/null +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'XCFun' +version = '2.1.1' + +homepage = 'https://xcfun.readthedocs.io' +description = """Arbitrary order exchange-correlation functional library""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/dftlibs/xcfun/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b602df74c7be83d501532565deafd1b7881946d94789122f24c309a669298ab'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3') +] + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' From a9bf01191ac1098e8f334769dee9365169b7b8ce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jan 2024 12:16:15 +0100 Subject: [PATCH 0349/1193] use https source URL for alsa-lib --- .../easyconfigs/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb | 2 +- .../easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb | 2 +- .../easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb | 2 +- .../easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb index 8c428e9d3cbb..af83ab6b0ff2 100644 --- a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.4-GCCcore-9.3.0.eb @@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and toolchain = {'name': 'GCCcore', 'version': '9.3.0'} -source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] sources = [SOURCE_TAR_BZ2] checksums = ['f7554be1a56cdff468b58fc1c29b95b64864c590038dd309c7a978c7116908f7'] diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb index a96a6a054dd9..e679e4629886 100644 --- a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-10.2.0.eb @@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and toolchain = {'name': 'GCCcore', 'version': '10.2.0'} -source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] sources = [SOURCE_TAR_BZ2] checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb index ae379c9ac316..2e943babc7ff 100644 --- a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb @@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] sources = [SOURCE_TAR_BZ2] checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] diff --git a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb index 1476c3783663..0db6c912f2cf 100644 --- a/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb @@ -9,7 +9,7 @@ description = """The Advanced Linux Sound Architecture (ALSA) provides audio and toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +source_urls = ['https://www.alsa-project.org/files/pub/lib/'] sources = [SOURCE_TAR_BZ2] checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] From 79df1fd37ad2fe57128701c2e60727e20522bb1f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 18 Jan 2024 12:38:21 +0100 Subject: [PATCH 0350/1193] append ':' to JULIA_DEPOT_PATH --- .../easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb index c1f1080404a9..ffd968fc0d96 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb @@ -20,4 +20,12 @@ sanity_check_paths = { sanity_check_commands = ['julia --help'] +modextrapaths_append = { + # Use default DEPOT_PATH where first entry is user's depot. + # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have + # those installations appended to DEPOT_PATH without disabling any of the default paths. + # Appending ':' to make sure we don't override the user's JULIA_DEPOT_PATH. + 'JULIA_DEPOT_PATH': ':', +} + moduleclass = 'lang' From 0e78cc6898126f27b5f79d2727f48f76d3126320 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 18 Jan 2024 12:40:08 +0100 Subject: [PATCH 0351/1193] adding easyconfigs: CheMPS2-1.8.12-foss-2022b.eb, PyCheMPS2-1.8.12-foss-2022b.eb --- .../c/CheMPS2/CheMPS2-1.8.12-foss-2022b.eb | 30 ++++++++++++++++ .../PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb | 34 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022b.eb create mode 100644 easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022b.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022b.eb new file mode 100644 index 000000000000..a485b6d6e596 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022b.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CheMPS2' +version = '1.8.12' + +homepage = 'https://github.com/SebWouters/CheMPS2' +description = """CheMPS2 is a scientific library which contains a spin-adapted implementation of the +density matrix renormalization group (DMRG) for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'] + +builddependencies = [('CMake', '3.24.3')] + +dependencies = [ + ('HDF5', '1.14.0') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], + 'dirs': ['include/chemps2'] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb new file mode 100644 index 000000000000..8b8ff5ae60e2 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'PyCheMPS2' +version = '1.8.12' + +homepage = 'https://sebwouters.github.io/CheMPS2' +description = """PyCheMPS2 is a python interface to CheMPS2, for compilation without +MPI. CheMPS2 is a scientific library which contains a spin-adapted +implementation of the density matrix renormalization group (DMRG) +for ab initio quantum chemistry.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('CheMPS2', version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'checksums': ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'], + 'install_src': './%(name)s', + }), +] + +sanity_pip_check = True + +moduleclass = 'chem' From 39d95d89324617e8438558f274ba455e23d4be69 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 18 Jan 2024 12:41:24 +0100 Subject: [PATCH 0352/1193] slight rephrase --- easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb index ffd968fc0d96..6671e1cd4ff5 100644 --- a/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb +++ b/easybuild/easyconfigs/j/Julia/Julia-1.10.0-linux-x86_64.eb @@ -24,7 +24,7 @@ modextrapaths_append = { # Use default DEPOT_PATH where first entry is user's depot. # JULIA_DEPOT_PATH must be set to be able to load other JuliaPackage modules and have # those installations appended to DEPOT_PATH without disabling any of the default paths. - # Appending ':' to make sure we don't override the user's JULIA_DEPOT_PATH. + # Appending ':' to make sure we don't override the user's custom JULIA_DEPOT_PATH if set. 'JULIA_DEPOT_PATH': ':', } From c8dc6da62a869e610bf4f2a2bd4823cb624a04ff Mon Sep 17 00:00:00 2001 From: lara Date: Thu, 18 Jan 2024 12:42:30 +0100 Subject: [PATCH 0353/1193] remove PyCheMPS2-1.8.12-foss-2022b.eb and opened in new pr --- .../PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb deleted file mode 100644 index 8b8ff5ae60e2..000000000000 --- a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022b.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyCheMPS2' -version = '1.8.12' - -homepage = 'https://sebwouters.github.io/CheMPS2' -description = """PyCheMPS2 is a python interface to CheMPS2, for compilation without -MPI. CheMPS2 is a scientific library which contains a spin-adapted -implementation of the density matrix renormalization group (DMRG) -for ab initio quantum chemistry.""" - -toolchain = {'name': 'foss', 'version': '2022b'} - -dependencies = [ - ('Python', '3.10.8'), - ('SciPy-bundle', '2023.02'), - ('CheMPS2', version), -] - -use_pip = True - -exts_list = [ - (name, version, { - 'modulename': '%(name)s', - 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], - 'source_tmpl': 'v%(version)s.tar.gz', - 'checksums': ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'], - 'install_src': './%(name)s', - }), -] - -sanity_pip_check = True - -moduleclass = 'chem' From b912e7a838ceb7d0cfb7cfaba1ea50732615c67a Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 18 Jan 2024 12:55:20 +0100 Subject: [PATCH 0354/1193] use arch --- .../x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb | 2 +- .../x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb index 23fbad63969d..3172f2c2daa3 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0208-GCCcore-12.2.0.eb @@ -58,7 +58,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb index 9b61bb47ce17..38708f32b6a7 100644 --- a/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/XML-LibXML/XML-LibXML-2.0209-GCCcore-12.3.0.eb @@ -59,7 +59,7 @@ modextrapaths = { sanity_check_paths = { 'files': [], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/XML/LibXML'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/XML/LibXML'], } moduleclass = 'data' From b6bfba8af2ebfc5f05cce04b01737f92cb688a13 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Thu, 18 Jan 2024 12:55:36 +0100 Subject: [PATCH 0355/1193] adding easyconfigs: Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb, HepMC3-3.2.6-GCC-12.3.0.eb, fastjet-3.4.2-gompi-2023a.eb, fastjet-contrib-1.053-gompi-2023a.eb, siscone-3.0.6-GCCcore-12.3.0.eb --- .../fastjet-contrib-1.053-gompi-2023a.eb | 32 ++++++++++++ .../f/fastjet/fastjet-3.4.2-gompi-2023a.eb | 43 +++++++++++++++ .../h/HepMC3/HepMC3-3.2.6-GCC-12.3.0.eb | 36 +++++++++++++ .../Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb | 52 +++++++++++++++++++ .../s/siscone/siscone-3.0.6-GCCcore-12.3.0.eb | 27 ++++++++++ 5 files changed, 190 insertions(+) create mode 100644 easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.053-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/f/fastjet/fastjet-3.4.2-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.6-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb create mode 100644 easybuild/easyconfigs/s/siscone/siscone-3.0.6-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.053-gompi-2023a.eb b/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.053-gompi-2023a.eb new file mode 100644 index 000000000000..94b820e6902b --- /dev/null +++ b/easybuild/easyconfigs/f/fastjet-contrib/fastjet-contrib-1.053-gompi-2023a.eb @@ -0,0 +1,32 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'fastjet-contrib' +version = '1.053' + +homepage = 'https://fastjet.hepforge.org/contrib/' +description = """3rd party extensions of FastJet""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://fastjet.hepforge.org/contrib/downloads/'] +sources = ['fjcontrib-' + version + '.tar.gz'] +checksums = ['b12a248e0b143934c99e3b7c8dd83265122f6c6c09533c2a03df44f5eff1e6fa'] + +dependencies = [ + ('fastjet', '3.4.2') +] + +build_cmd_targets = ['', 'fragile-shared'] +install_cmd = "make install && make fragile-shared-install" + +sanity_check_paths = { + 'files': ['lib/libfastjetcontribfragile.%s' % SHLIB_EXT], + 'dirs': ['include/fastjet/contrib'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/f/fastjet/fastjet-3.4.2-gompi-2023a.eb b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.2-gompi-2023a.eb new file mode 100644 index 000000000000..36cf015e3927 --- /dev/null +++ b/easybuild/easyconfigs/f/fastjet/fastjet-3.4.2-gompi-2023a.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'fastjet' +version = '3.4.2' + +homepage = 'https://fastjet.fr/' +description = """A software package for jet finding in pp and e+e- collisions""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://fastjet.fr/repo/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['fastjet-3.4.0_excludeSISCone.patch'] +checksums = [ + {'fastjet-3.4.2.tar.gz': 'b3d33155b55ce43f420cd6d99b525acf7bdc2593a7bb7ea898a9ddb3d8ca38e3'}, + {'fastjet-3.4.0_excludeSISCone.patch': '698902b4c4d54873d640239461cccc036234986ae8d6a33ceb649462ade971d3'}, +] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('siscone', '3.0.6'), + ('CGAL', '5.6'), +] +configopts = '--enable-cgal-header-only --enable-pyext --enable-allplugins --enable-allcxxplugins ' +configopts += "--enable-shared" + +sanity_check_paths = { + 'files': ['lib/libfastjet.%s' % SHLIB_EXT, 'bin/fastjet-config'], + 'dirs': ['include/fastjet'], +} +sanity_check_commands = ["python -c 'import fastjet'"] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.6-GCC-12.3.0.eb b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.6-GCC-12.3.0.eb new file mode 100644 index 000000000000..294a54e451d2 --- /dev/null +++ b/easybuild/easyconfigs/h/HepMC3/HepMC3-3.2.6-GCC-12.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'CMakeMake' + +name = 'HepMC3' +version = '3.2.6' + +homepage = 'http://hepmc.web.cern.ch/hepmc/' +description = """HepMC is a standard for storing Monte Carlo event data.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://hepmc.web.cern.ch/hepmc/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['248f3b5b36dd773844cbe73d51f60891458334b986b259754c59dbf4bbf1d525'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3') +] + +configopts = '-DHEPMC3_ENABLE_ROOTIO=OFF -Dmomentum=GEV -Dlength=MM ' +configopts += '-DHEPMC3_ENABLE_PYTHON=ON ' +configopts += '-DHEPMC3_Python_SITEARCH311=%(installdir)s/lib/python%(pyshortver)s/site-packages' + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libHepMC3.%s' % SHLIB_EXT], + 'dirs': ['include/HepMC3'] +} +sanity_check_commands = ["python -c 'import pyHepMC3'"] + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb new file mode 100644 index 000000000000..b347de870f9d --- /dev/null +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb @@ -0,0 +1,52 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'Rivet' +version = '3.1.9' +local_hepmc = "HepMC3" +local_hepmcver = "3.2.6" +versionsuffix = '-%s-%s' % (local_hepmc, local_hepmcver) + +homepage = 'https://gitlab.com/hepcedar/rivet' +description = """ +Rivet toolkit (Robust Independent Validation of Experiment and Theory) + +To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['https://www.hepforge.org/archive/rivet/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ddf0f13f722d0b4fc61969f3db06416b6b68f721dba36ca5d2a85c2759bf9fd7'] + +dependencies = [ + ('Python', '3.11.3'), + ('YODA', '1.9.9'), + ('fastjet', '3.4.2'), + ('fastjet-contrib', '1.053'), + ('HepMC3', '3.2.6'), + ('GSL', '2.7'), +] + +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" + +sanity_check_paths = { + 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], + 'dirs': ['share/Rivet', 'lib/Rivet'] +} +sanity_check_commands = ["python -c 'import rivet'"] + +modloadmsg = """ +To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. +You might want to load `texlive` or `matplotlib` if you want to create plots. +""" +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + # 'RIVET_ANALYSIS_PATH': '/path/to/share/Rivet/', # please adapt for system-wided shared non-default analysis +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/s/siscone/siscone-3.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/siscone/siscone-3.0.6-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a6a381868f74 --- /dev/null +++ b/easybuild/easyconfigs/s/siscone/siscone-3.0.6-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'siscone' +version = '3.0.6' + +homepage = 'https://siscone.hepforge.org/' +description = """Hadron Seedless Infrared-Safe Cone jet algorithm""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://siscone.hepforge.org/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9f19e87433305d073e5715a175d8ef0a56101f97203e5bd36a09b3eeb5cb04a'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ["lib/libsiscone.so"], + 'dirs': ["include/siscone"], +} + +moduleclass = 'phys' From eb080309e00183fae83650f6d9a70d8d11f6b283 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jan 2024 13:42:30 +0100 Subject: [PATCH 0356/1193] don't set `optarch` toolchain to `True` in `Rivert` easyconfigs, since that's the default --- .../easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb index b347de870f9d..3cdde9f0f492 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb @@ -17,7 +17,7 @@ To use your own analysis you must append the path to `RIVET_ANALYSIS_PATH`. """ toolchain = {'name': 'gompi', 'version': '2023a'} -toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'pic': True} source_urls = ['https://www.hepforge.org/archive/rivet/'] sources = [SOURCE_TAR_GZ] From 8692ba176e2c2f8c71c7f59140577fe1a9bee508 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 18 Jan 2024 14:51:57 +0100 Subject: [PATCH 0357/1193] adding easyconfigs: imutils-0.5.4-foss-2022a-CUDA-11.7.0.eb --- .../imutils-0.5.4-foss-2022a-CUDA-11.7.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imutils/imutils-0.5.4-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/i/imutils/imutils-0.5.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..7fe7ef3814e3 --- /dev/null +++ b/easybuild/easyconfigs/i/imutils/imutils-0.5.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'imutils' +version = '0.5.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/jrosebr1/imutils' +description = """A series of convenience functions to make basic image processing operations such as translation, +rotation, resizing, skeletonization, and displaying Matplotlib images easier with OpenCV and Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['03827a9fca8b5c540305c0844a62591cf35a0caec199cb0f2f0a4a0fb15d8f24'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'vis' From fa5bfe0f48b67f064a96db9e364c5a7c753bd680 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 18 Jan 2024 15:47:46 +0100 Subject: [PATCH 0358/1193] add missing KronaTools dep to q2-krona --- .../easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb index a3b32792201f..7666fd54d3bd 100644 --- a/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/q/q2-krona/q2-krona-20220124-GCCcore-11.3.0.eb @@ -15,6 +15,7 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), + ('KronaTools', '2.8.1'), ] use_pip = True From dfbda07996caf7fdfb6e5c2e844aaaa0ab0bd364 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 18 Jan 2024 18:29:12 +0100 Subject: [PATCH 0359/1193] adding easyconfigs: maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb --- ...aturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb | 648 ++++++++++++++++++ 1 file changed, 648 insertions(+) create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb new file mode 100644 index 000000000000..c3d3986de93a --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb @@ -0,0 +1,648 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.4.0' +_rust_ver = '1.75.0' +versionsuffix = '-Rust-%s' % _rust_ver + +homepage = "https://github.com/pyo3/maturin" +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Rust', _rust_ver), + ('setuptools-rust', '1.6.0'), +] + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.8.6'), + ('aho-corasick', '1.1.2'), + ('allocator-api2', '0.2.16'), + ('anstream', '0.3.2'), + ('anstream', '0.6.4'), + ('anstyle', '1.0.2'), + ('anstyle-parse', '0.2.1'), + ('anstyle-query', '1.0.0'), + ('anstyle-wincon', '1.0.2'), + ('anstyle-wincon', '3.0.1'), + ('anyhow', '1.0.75'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.5'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.1'), + ('block-buffer', '0.10.4'), + ('bstr', '1.8.0'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bytesize', '1.3.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.6'), + ('cargo-config2', '0.1.16'), + ('cargo-options', '0.7.2'), + ('cargo-platform', '0.1.5'), + ('cargo-xwin', '0.16.2'), + ('cargo-zigbuild', '0.18.0'), + ('cargo_metadata', '0.18.1'), + ('cbindgen', '0.26.0'), + ('cc', '1.0.83'), + ('cfb', '0.9.0'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.3'), + ('clap', '4.3.24'), + ('clap_builder', '4.3.24'), + ('clap_complete', '4.3.2'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_fig', '4.3.1'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.3.12'), + ('clap_lex', '0.5.0'), + ('cli-table', '0.4.7'), + ('colorchoice', '1.0.0'), + ('configparser', '3.0.3'), + ('console', '0.15.7'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.4'), + ('cpufeatures', '0.2.11'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.8'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.15'), + ('crossbeam-utils', '0.8.16'), + ('crypto-common', '0.1.6'), + ('data-encoding', '2.5.0'), + ('deranged', '0.3.9'), + ('dialoguer', '0.11.0'), + ('diff', '0.1.13'), + ('digest', '0.10.7'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('dissimilar', '1.0.7'), + ('dunce', '1.0.4'), + ('either', '1.9.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.33'), + ('equivalent', '1.0.1'), + ('errno', '0.3.8'), + ('expect-test', '1.4.1'), + ('fastrand', '2.0.1'), + ('fat-macho', '0.4.7'), + ('filetime', '0.2.22'), + ('flate2', '1.0.28'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.1'), + ('fs-err', '2.11.0'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.11'), + ('glob', '0.3.1'), + ('globset', '0.4.14'), + ('goblin', '0.7.1'), + ('hashbrown', '0.12.3'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.3'), + ('home', '0.5.5'), + ('humantime', '2.1.0'), + ('humantime-serde', '1.1.1'), + ('idna', '0.5.0'), + ('ignore', '0.4.20'), + ('indexmap', '1.9.3'), + ('indexmap', '2.1.0'), + ('indicatif', '0.17.7'), + ('indoc', '2.0.4'), + ('instant', '0.1.12'), + ('io-lifetimes', '1.0.11'), + ('is-terminal', '0.4.9'), + ('itertools', '0.11.0'), + ('itertools', '0.12.0'), + ('itoa', '1.0.9'), + ('keyring', '2.0.5'), + ('lazy_static', '1.4.0'), + ('lddtree', '0.3.3'), + ('libc', '0.2.150'), + ('libredox', '0.0.1'), + ('linux-keyutils', '0.2.3'), + ('linux-raw-sys', '0.3.8'), + ('linux-raw-sys', '0.4.11'), + ('lock_api', '0.4.11'), + ('log', '0.4.20'), + ('lzxd', '0.1.4'), + ('mailparse', '0.14.0'), + ('matchers', '0.1.0'), + ('memchr', '2.6.4'), + ('memoffset', '0.9.0'), + ('mime', '0.3.17'), + ('mime_guess', '2.0.4'), + ('minijinja', '1.0.10'), + ('minimal-lexical', '0.2.1'), + ('miniz_oxide', '0.7.1'), + ('msi', '0.7.0'), + ('multipart', '0.18.0'), + ('native-tls', '0.2.11'), + ('nom', '7.1.3'), + ('normalize-line-endings', '0.3.0'), + ('normpath', '1.1.1'), + ('nu-ansi-term', '0.46.0'), + 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'1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.0.tar.gz': 'dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04'}, + {'winnow-0.5.19.tar.gz': '829846f3e3db426d4cee4510841b71a8e58aa2a76b1132579487ae430ccd9c7b'}, + {'xattr-1.0.1.tar.gz': 'f4686009f71ff3e5c4dbcf1a282d0a44db3f021ba69350cd42086b3e5f1c6985'}, + {'xwin-0.5.0.tar.gz': 'c43e0202f5457b48558096cb7b36d0e473f267551a89c82ed72d73b01dfd4007'}, + {'yansi-0.5.1.tar.gz': '09041cd90cf85f7f8b2df60c646f853b7f535ce68f85244eb6731cf89fa498ec'}, + {'zerocopy-0.7.28.tar.gz': '7d6f15f7ade05d2a4935e34a457b936c23dc70a05cc1d97133dc99e7a3fe0f0e'}, + {'zerocopy-derive-0.7.28.tar.gz': 'dbbad221e3f78500350ecbd7dfa4e63ef945c05f4c61cb7f4d3f84cd0bba649b'}, + {'zeroize-1.7.0.tar.gz': '525b4ec142c6b68a2d10f01f7bbf6755599ca3f81ea53b8431b7dd348f5fdb2d'}, + {'zip-0.6.6.tar.gz': '760394e246e4c28189f19d488c058bf16f564016aefac5d32bb1f3b51d5e9261'}, +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'tools' \ No newline at end of file From af13c63459134cba0c644676aa9e262bcefd2360 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 18 Jan 2024 19:16:52 +0100 Subject: [PATCH 0360/1193] Update maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb newline --- .../m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb index c3d3986de93a..33c5facbf0ea 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.4.0-GCCcore-12.3.0-Rust-1.75.0.eb @@ -645,4 +645,4 @@ use_pip = True sanity_pip_check = True download_dep_fail = True -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' From 13d79d08bffcb7d10f277ade5c941df82c8c71cf Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 18 Jan 2024 19:32:41 +0100 Subject: [PATCH 0361/1193] adding easyconfigs: libxc-6.2.2-GCC-13.2.0.eb --- .../l/libxc/libxc-6.2.2-GCC-13.2.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb new file mode 100644 index 000000000000..e04565bf6ec8 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Perl', '5.38.0'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' From b95024f0bea7cff4b8516acaf2b130e3d74f4348 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 18 Jan 2024 21:40:32 +0000 Subject: [PATCH 0362/1193] adding easyconfigs: umap-learn-0.5.5-foss-2023a.eb --- .../umap-learn/umap-learn-0.5.5-foss-2023a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.5-foss-2023a.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.5-foss-2023a.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.5-foss-2023a.eb new file mode 100644 index 000000000000..061f83b7adec --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.5-foss-2023a.eb @@ -0,0 +1,42 @@ +# Author: Denis Krišťák (INUITS) +# This is a contribution from HPCNow! (http://hpcnow.com) +# Update: Erica Bianco +# License:: GPL-v3.0 +easyblock = "PythonBundle" + +name = 'umap-learn' +version = '0.5.5' + +homepage = 'https://umap-learn.readthedocs.io/en/latest/' +description = """ +Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique +that can be used for visualisation similarly to t-SNE, but also for general non-linear +dimension reduction. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('numba', '0.58.1'), + ('LLVM', '16.0.6'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +exts_list = [ + ('pynndescent', '0.5.11', { + 'checksums': ['6f44ced9d5a9da2c87d9b2fff30bb5308540c0657605e4d5cde7ed3275bbad50'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['c54d607364413eade968b73ba07c8b3ea14412817f53cd07b6f720ac957293c4'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From ed67033859e63ef024f22cac02d4ca0698983ae8 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 18 Jan 2024 21:41:04 +0000 Subject: [PATCH 0363/1193] adding easyconfigs: gflags-2.2.2-GCCcore-12.3.0.eb --- .../g/gflags/gflags-2.2.2-GCCcore-12.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..576ab189247a --- /dev/null +++ b/easybuild/easyconfigs/g/gflags/gflags-2.2.2-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'gflags' +version = '2.2.2' + +homepage = 'https://github.com/gflags/gflags' +description = """ +The gflags package contains a C++ library that implements commandline flags +processing. It includes built-in support for standard types such as string +and the ability to define flags in the source file in which they are used. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/gflags/gflags/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['34af2f15cf7367513b352bdcd2493ab14ce43692d2dcd9dfc499492966c64dcf'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_STATIC_LIBS=ON' + +sanity_check_paths = { + 'files': ['bin/gflags_completions.sh'] + + ['lib/%s' % x for x in ['libgflags.%s' % SHLIB_EXT, 'libgflags_nothreads.%s' % SHLIB_EXT, + 'libgflags.a', 'libgflags_nothreads.a']] + + ['include/gflags/gflags_completions.h'], + 'dirs': [], +} + +moduleclass = 'devel' From cb4ef9a7ce32d0cdbae0f9303878678ade6fa6d9 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 18 Jan 2024 21:41:21 +0000 Subject: [PATCH 0364/1193] adding easyconfigs: mrcfile-1.5.0-foss-2023a.eb --- .../m/mrcfile/mrcfile-1.5.0-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.5.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.5.0-foss-2023a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.5.0-foss-2023a.eb new file mode 100644 index 000000000000..604c8259c91b --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.5.0-foss-2023a.eb @@ -0,0 +1,41 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/11 +easyblock = 'PythonPackage' + +name = 'mrcfile' +version = '1.5.0' + +homepage = 'https://github.com/ccpem/mrcfile' +description = """mrcfile is a Python implementation of the MRC2014 file format, which is used in +structural biology to store image and volume data. + +It allows MRC files to be created and opened easily using a very simple API, +which exposes the file’s header and data as numpy arrays. The code runs in +Python 2 and 3 and is fully unit-tested. + +This library aims to allow users and developers to read and write standard- +compliant MRC files in Python as easily as possible, and with no dependencies on +any compiled libraries except numpy. You can use it interactively to inspect +files, correct headers and so on, or in scripts and larger software packages to +provide basic MRC file I/O functions. """ + + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9e8196b8a33aa5b5237b43336cb9d08b6058b8127ea668d63b84d58bca795ec1'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'bio' From 33b9adfe8ed8e4ee189a51912502ed7a65118921 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 18 Jan 2024 23:15:12 +0100 Subject: [PATCH 0365/1193] adding easyconfigs: libxc-6.2.2-intel-compilers-2023.2.1.eb --- .../libxc-6.2.2-intel-compilers-2023.2.1.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb new file mode 100644 index 000000000000..41d6760191c7 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' + +homepage = 'https://www.tddft.org/programs/libxc' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'} + +source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Perl', '5.38.0'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# perform iterative build to get both static and shared libraries +configopts = [ + local_common_configopts + ' -DBUILD_SHARED_LIBS=OFF', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' From a37cff7c7c8fe3353aa97b519f8bd9c1def35d76 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 18 Jan 2024 23:16:43 +0100 Subject: [PATCH 0366/1193] adding easyconfigs: ELPA-2023.11.001-foss-2023b.eb, ELPA-2023.11.001-intel-2023b.eb --- .../e/ELPA/ELPA-2023.11.001-foss-2023b.eb | 49 +++++++++++++++++ .../e/ELPA/ELPA-2023.11.001-intel-2023b.eb | 53 +++++++++++++++++++ 2 files changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-foss-2023b.eb create mode 100644 easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-intel-2023b.eb diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-foss-2023b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-foss-2023b.eb new file mode 100644 index 000000000000..e0c5b2588350 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-foss-2023b.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2023.11.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = [ + '%(name)s-2023.05.001_fix_hardcoded_perl_path.patch', + '%(name)s-2023.05.001_fix_AVX512_support.patch', +] +checksums = [ + {'%(namelower)s-new_release_%(version)s.tar.gz': + 'b8dd04e238dac23c1e910e8862370b1779b239eae4b871c9966bee578d40c750'}, + {'%(name)s-2023.05.001_fix_hardcoded_perl_path.patch': + '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, + {'%(name)s-2023.05.001_fix_AVX512_support.patch': + 'ecf08b64fe1da432a218040fa45d4ecfbb3269d58cb018b12da5a2d854bf96be'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.11.5'), + ('Perl', '5.38.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-intel-2023b.eb b/easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-intel-2023b.eb new file mode 100644 index 000000000000..c0e9fe260803 --- /dev/null +++ b/easybuild/easyconfigs/e/ELPA/ELPA-2023.11.001-intel-2023b.eb @@ -0,0 +1,53 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Inge Gutheil , Alan O'Cais +# License:: MIT/GPL +# +## + +name = 'ELPA' +version = '2023.11.001' + +homepage = 'https://elpa.mpcdf.mpg.de/' +description = """Eigenvalue SoLvers for Petaflop-Applications.""" + +toolchain = {'name': 'intel', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://gitlab.mpcdf.mpg.de/elpa/elpa/-/archive/new_release_%(version)s/'] +sources = ['elpa-new_release_%(version)s.tar.gz'] +patches = [ + '%(name)s-2023.05.001_fix_hardcoded_perl_path.patch', + '%(name)s-2023.05.001_fix_AVX512_support.patch', +] +checksums = [ + {'%(namelower)s-new_release_%(version)s.tar.gz': + 'b8dd04e238dac23c1e910e8862370b1779b239eae4b871c9966bee578d40c750'}, + {'%(name)s-2023.05.001_fix_hardcoded_perl_path.patch': + '0548105065777a2ed07dde306636251c4f96e555a801647564de37d1ddd7b0b5'}, + {'%(name)s-2023.05.001_fix_AVX512_support.patch': + 'ecf08b64fe1da432a218040fa45d4ecfbb3269d58cb018b12da5a2d854bf96be'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + # remove_xcompiler script requires 'python' command, + ('Python', '3.11.5'), + ('Perl', '5.38.0'), +] + +preconfigopts = './autogen.sh && ' +preconfigopts += 'export LDFLAGS="-lm $LDFLAGS" && ' +preconfigopts += 'autoreconf && ' +# If the build is running in a batch job, make sure Intel libmpi does +# not try to use Slurm to run the MPI_THREAD test code that ELPA's +# configure is running without "mpirun". +preconfigopts += 'unset SLURM_JOBID && unset SLURM_NODELIST && unset I_MPI_PMI_LIBRARY && ' + +# When building in parallel, the file test_setup_mpi.mod is sometimes +# used before it is built, leading to an error. This must be a bug in +# the makefile affecting parallel builds. +maxparallel = 1 + +moduleclass = 'math' From 8a8ede101a5072de1d49f83341e9cbe6a5236c05 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 19 Jan 2024 11:05:46 +0100 Subject: [PATCH 0367/1193] adding easyconfigs: code-cli-1.85.1-x64.eb --- .../c/code-cli/code-cli-1.85.1-x64.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb diff --git a/easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb b/easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb new file mode 100644 index 000000000000..004b570f4484 --- /dev/null +++ b/easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb @@ -0,0 +1,32 @@ +easyblock = 'Tarball' + +name = 'code-cli' +version = '1.85.1' +versionsuffix = '-x64' + +homepage = 'https://code.visualstudio.com/' +description = ''' + Visual Studio Code is a lightweight but powerful source code editor + which runs on your desktop and is available for Windows, macOS and + Linux. It comes with built-in support for JavaScript, TypeScript and + Node.js and has a rich ecosystem of extensions for other languages + and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin + your journey with VS Code with these introductory videos. +''' + +toolchain = {'name': 'system', 'version': 'system'} + +source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] +sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['code'], + 'dirs': [] +} + +sanity_check_commands = ["code --help"] + +moduleclass = 'devel' From d2e2c1558f76d19775c0bf06922b3a6ac89c728e Mon Sep 17 00:00:00 2001 From: lara Date: Fri, 19 Jan 2024 11:12:13 +0100 Subject: [PATCH 0368/1193] replace VSCode-cli with code-cli --- .../v/VSCode-cli/VSCode-cli-1.85.1-x64.eb | 35 ------------------- 1 file changed, 35 deletions(-) delete mode 100644 easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb diff --git a/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb b/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb deleted file mode 100644 index 69c007bebba1..000000000000 --- a/easybuild/easyconfigs/v/VSCode-cli/VSCode-cli-1.85.1-x64.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'Tarball' - -name = 'VSCode-cli' -version = '1.85.1' -versionsuffix = '-x64' - -homepage = 'https://code.visualstudio.com/' -description = ''' - Visual Studio Code is a lightweight but powerful source code editor - which runs on your desktop and is available for Windows, macOS and - Linux. It comes with built-in support for JavaScript, TypeScript and - Node.js and has a rich ecosystem of extensions for other languages - and runtimes (such as C++, C#, Java, Python, PHP, Go, .NET). Begin - your journey with VS Code with these introductory videos. -''' - -toolchain = {'name': 'system', 'version': 'system'} - -source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] -sources = [{ - 'download_filename': 'vscode_cli_alpine_x64_cli.tar.gz', - 'filename': 'vscode-%(version)s%(versionsuffix)s.tar.gz', -}] -checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] - -modextrapaths = {'PATH': ''} - -sanity_check_paths = { - 'files': ['code'], - 'dirs': [] -} - -sanity_check_commands = ["code --help"] - -moduleclass = 'devel' From 7cd11db2bcd0a5d3b1cb9bb75e67c972a3bba0b2 Mon Sep 17 00:00:00 2001 From: lara Date: Fri, 19 Jan 2024 11:14:19 +0100 Subject: [PATCH 0369/1193] fix sources --- easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb b/easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb index 004b570f4484..71e7200c0cea 100644 --- a/easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb +++ b/easybuild/easyconfigs/c/code-cli/code-cli-1.85.1-x64.eb @@ -17,7 +17,10 @@ description = ''' toolchain = {'name': 'system', 'version': 'system'} source_urls = ['https://update.code.visualstudio.com/%(version)s/cli-alpine-x64/stable#'] -sources = ['vscode_cli_alpine_x64_cli.tar.gz'] +sources = [{ + 'download_filename': 'vscode_cli_alpine_x64_cli.tar.gz', + 'filename': 'vscode-%(version)s%(versionsuffix)s.tar.gz', +}] checksums = ['cc469ba0461141fc3a58f589262c6e7d2bfa43044dd267267e794e8d89b831d1'] modextrapaths = {'PATH': ''} From ec233efc880553e41c17474eecfdc523195ff8f4 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Fri, 19 Jan 2024 11:35:19 +0100 Subject: [PATCH 0370/1193] adding easyconfigs: snakemake-8.2.1-foss-2023a.eb --- .../c/Cbc/Cbc-2.10.11-foss-2023a.eb | 63 ++++++++ .../c/Cgl/Cgl-0.60.8-foss-2023a.eb | 50 ++++++ .../c/Clp/Clp-1.17.9-foss-2023a.eb | 61 ++++++++ .../CoinUtils/CoinUtils-2.11.10-GCC-12.3.0.eb | 36 +++++ .../o/Osi/Osi-0.108.9-GCC-12.3.0.eb | 48 ++++++ .../p/PuLP/PuLP-2.8.0-foss-2023a.eb | 36 +++++ .../s/snakemake/snakemake-8.2.1-foss-2023a.eb | 144 ++++++++++++++++++ 7 files changed, 438 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb create mode 100644 easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb create mode 100644 easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb create mode 100644 easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/snakemake/snakemake-8.2.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb new file mode 100644 index 000000000000..a1daf137fead --- /dev/null +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb @@ -0,0 +1,63 @@ +easyblock = "ConfigureMake" + +name = 'Cbc' +version = '2.10.11' + +homepage = "https://github.com/coin-or/Cbc" +description = """Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming +solver written in C++. It can be used as a callable library or using a +stand-alone executable.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Cbc/archive/refs/tags/releases'] +sources = ['%(version)s.tar.gz'] +checksums = ['1fb591dd88336fdaf096b8e42e46111e41671a5eb85d4ee36e45baff1678bd33'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('Clp', '1.17.9'), + ('Cgl', '0.60.8'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' +# Use METIS AND MUMPS from EB +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord" ' +# Disable GLPK, dependencies have to be built with it as well +configopts += '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' +# Use Cgl from EB +configopts += '--with-cgl-lib="-lCgl" ' +configopts += '--with-cgl-datadir=$EBROOTCGL/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/cbc'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Cbc', 'CbcSolver', 'OsiCbc']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb new file mode 100644 index 000000000000..9e5a23290e4a --- /dev/null +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = "ConfigureMake" + +name = 'Cgl' +version = '0.60.8' + +homepage = "https://github.com/coin-or/Cgl" +description = """The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that +can be used with other COIN-OR packages that make use of cuts, such as, among +others, the linear solver Clp or the mixed integer linear programming solvers +Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or +communicate with a solver. It does not directly call a solver.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Cgl/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['1482ba38afb783d124df8d5392337f79fdd507716e9f1fb6b98fc090acd1ad96'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('Clp', '1.17.9'), +] + +# Use CoinUtils from EB +configopts = '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +# Use Clp from EB +configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' +configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' +# Use Osi from EB (also needs links to Clp due to OsiClpSolver) +configopts += '--with-osi-lib="-lOsiClp -lClpSolver -lClp -lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['lib/libCgl.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb new file mode 100644 index 000000000000..8b4fedf45da3 --- /dev/null +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb @@ -0,0 +1,61 @@ +easyblock = 'ConfigureMake' + +name = 'Clp' +version = '1.17.9' + +homepage = "https://github.com/coin-or/Clp" +description = """Clp (Coin-or linear programming) is an open-source linear programming solver. +It is primarily meant to be used as a callable library, but a basic, +stand-alone executable version is also available.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/coin-or/Clp/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['b02109be54e2c9c6babc9480c242b2c3c7499368cfca8c0430f74782a694a49f'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('METIS', '5.1.0'), + ('MUMPS', '5.6.1', '-metis'), + ('CoinUtils', '2.11.10'), + ('Osi', '0.108.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# Use BLAS/LAPACK from OpenBLAS +configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' + +# Use METIS AND MUMPS from EB +# --with-metis-lib is ignored +configopts += '--with-metis-lib="-lmetis" ' +configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' + +# Disable GLPK because Clp requires headers from its sources +configopts += '--without-glpk ' + +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +# Use Osi from EB +configopts += '--with-osi-lib="-lOsi" ' +configopts += '--with-osi-datadir=$EBROOTOSI/share/coin/Data ' + +sanity_check_paths = { + 'files': ['bin/clp'] + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['Clp', 'ClpSolver', 'OsiClp']], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-12.3.0.eb b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-12.3.0.eb new file mode 100644 index 000000000000..642d353e5d84 --- /dev/null +++ b/easybuild/easyconfigs/c/CoinUtils/CoinUtils-2.11.10-GCC-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'CoinUtils' +version = '2.11.10' + +homepage = "https://github.com/coin-or/CoinUtils" +description = """CoinUtils (Coin-OR Utilities) is an open-source collection of classes and +functions that are generally useful to more than one COIN-OR project.""" + +source_urls = ['https://github.com/coin-or/CoinUtils/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['80c7c215262df8d6bd2ba171617c5df844445871e9891ec6372df12ccbe5bcfd'] + +# NOTE: this esyconfig for CoinUtils provides a minimal build not using BLAS/LAPACK or MPI +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['lib/libCoinUtils.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-12.3.0.eb b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-12.3.0.eb new file mode 100644 index 000000000000..4be65c422ec8 --- /dev/null +++ b/easybuild/easyconfigs/o/Osi/Osi-0.108.9-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'ConfigureMake' + +name = 'Osi' +version = '0.108.9' + +homepage = "https://github.com/coin-or/Osi" +description = """Osi (Open Solver Interface) provides an abstract base class to a generic linear +programming (LP) solver, along with derived classes for specific solvers. Many +applications may be able to use the Osi to insulate themselves from a specific +LP solver. That is, programs written to the OSI standard may be linked to any +solver with an OSI interface and should produce correct results. The OSI has +been significantly extended compared to its first incarnation. Currently, the +OSI supports linear programming solvers and has rudimentary support for integer +programming.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/coin-or/Osi/archive/refs/tags/releases/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8b09802960d7d4fd9579b3e4320bfb36e7f8dca5e5094bf1f5edf1b7003f5562'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Doxygen', '1.9.7'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('CoinUtils', '2.11.10'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +# Disable GLPK because Osi requires GLPK<=4.48 +configopts = '--without-glpk ' +# Use CoinUtils from EB +configopts += '--with-coinutils-lib="-lCoinUtils" --with-coinutils-incdir=$EBROOTCOINUTILS/include/coin ' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' + +sanity_check_paths = { + 'files': ['lib/libOsi.%s' % SHLIB_EXT, 'lib/libOsiCommonTests.%s' % SHLIB_EXT], + 'dirs': ['include/coin', 'lib/pkgconfig', 'share/coin'] +} + +# other coin-or projects expect instead of +modextrapaths = {'CPATH': 'include/coin'} + +moduleclass = "math" diff --git a/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2023a.eb b/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2023a.eb new file mode 100644 index 000000000000..63aeec327a82 --- /dev/null +++ b/easybuild/easyconfigs/p/PuLP/PuLP-2.8.0-foss-2023a.eb @@ -0,0 +1,36 @@ +# Contribution by +# DeepThought, Flinders University +# R.QIAO +# Updated: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'PuLP' +version = '2.8.0' + +homepage = 'https://github.com/coin-or/pulp' +description = """ +PuLP is an LP modeler written in Python. PuLP can generate MPS or LP files and +call GLPK, COIN-OR CLP/CBC, CPLEX, GUROBI, MOSEK, XPRESS, CHOCO, MIPCL, SCIP to +solve linear problems. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125'] + +dependencies = [ + ('Python', '3.11.3'), + ('GLPK', '5.0'), + ('Cbc', '2.10.11'), + # Gurobi requires a seperate license + # ('Gurobi', '9.5.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.2.1-foss-2023a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.2.1-foss-2023a.eb new file mode 100644 index 000000000000..c0caaff39e29 --- /dev/null +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.2.1-foss-2023a.eb @@ -0,0 +1,144 @@ +easyblock = 'PythonBundle' + +name = 'snakemake' +version = '8.2.1' + +homepage = 'https://snakemake.readthedocs.io' +description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('GitPython', '3.1.40'), + ('IPython', '8.14.0'), + ('PyYAML', '6.0'), + ('wrapt', '1.15.0'), + ('PuLP', '2.8.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('datrie', '0.8.2', { + 'checksums': ['525b08f638d5cf6115df6ccd818e5a01298cd230b2dac91c8ff2e6499d18765d'], + }), + ('plac', '1.4.2', { + 'checksums': ['b0d04d9bc4875625df45982bc900e9d9826861c221850dbfda096eab82fe3330'], + }), + ('dpath', '2.1.6', { + 'checksums': ['f1e07c72e8605c6a9e80b64bc8f42714de08a789c7de417e49c3f87a19692e47'], + }), + ('yte', '1.5.4', { + 'checksums': ['d2d77e53eafca74f58234fcd3fea28cc0a719e4f3784911511e35e86594bc880'], + }), + ('toposort', '1.10', { + 'checksums': ['bfbb479c53d0a696ea7402601f4e693c97b0367837c8898bc6471adfca37a6bd'], + }), + ('throttler', '1.2.2', { + 'checksums': ['d54db406d98e1b54d18a9ba2b31ab9f093ac64a0a59d730c1cf7bb1cdfc94a58'], + }), + ('stopit', '1.1.2', { + 'checksums': ['f7f39c583fd92027bd9d06127b259aee7a5b7945c1f1fa56263811e1e766996d'], + }), + ('ConfigArgParse', '1.7', { + 'checksums': ['e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1'], + }), + ('argparse-dataclass', '2.0.0', { + 'modulename': 'argparse_dataclass', + 'source_tmpl': 'argparse_dataclass-%(version)s.tar.gz', + 'checksums': ['09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f'], + }), + ('snakemake-interface-common', '1.15.1', { + 'modulename': 'snakemake_interface_common', + 'source_tmpl': 'snakemake_interface_common-%(version)s.tar.gz', + 'checksums': ['5a779c7a0f27412bce26e1dfe4ccc712d04e0c0b9ceaa1640335a35d02509732'], + }), + ('reretry', '0.11.8', { + 'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'], + }), + ('snakemake-interface-storage-plugins', '3.0.0', { + 'modulename': 'snakemake_interface_storage_plugins', + 'source_tmpl': 'snakemake_interface_storage_plugins-%(version)s.tar.gz', + 'checksums': ['f20d85ee7e86a1e2ffa3f72e2385dd5abb17fa7b58a26cba8ba59096872fe169'], + }), + ('snakemake-interface-executor-plugins', '8.2.0', { + 'modulename': 'snakemake_interface_executor_plugins', + 'source_tmpl': 'snakemake_interface_executor_plugins-%(version)s.tar.gz', + 'checksums': ['4c74e3e1751bab6b266baf8688e854b8b4c5c5e10f5e34c581f42d69af4ff13b'], + }), + ('smart-open', '6.4.0', { + 'sources': ['smart_open-%(version)s.tar.gz'], + 'checksums': ['be3c92c246fbe80ebce8fbacb180494a481a77fcdcb7c1aadb2ea5b9c2bee8b9'], + }), + ('jupyter-core', '5.7.1', { + 'modulename': 'jupyter_core', + 'source_tmpl': 'jupyter_core-%(version)s.tar.gz', + 'checksums': ['de61a9d7fc71240f688b2fb5ab659fbb56979458dc66a71decd098e03c79e218'], + }), + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + ('nbformat', '5.9.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['1c5172d786a41b82bcfd0c23f9e6b6f072e8fb49c39250219e4acfff1efe89e9'], + }), + ('immutables', '0.20', { + 'checksums': ['1d2f83e6a6a8455466cd97b9a90e2b4f7864648616dfa6b19d18f49badac3876'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('connection-pool', '0.0.3', { + 'sources': ['connection_pool-%(version)s.tar.gz'], + 'checksums': ['bf429e7aef65921c69b4ed48f3d48d3eac1383b05d2df91884705842d974d0dc'], + }), + ('conda-inject', '1.3.1', { + 'sources': ['conda_inject-%(version)s.tar.gz'], + 'checksums': ['9e8d902230261beba74083aae12c2c5a395e29b408469fefadc8aaf51ee441e5'], + }), + (name, version, { + 'checksums': ['f177ada98188a10602aa2ed758fc9b7ff13e7107c5e582463ae681c525c28f0c'], + }), + # Also install some of the snakemake executors + ('snakemake-executor-plugin-slurm-jobstep', '0.1.10', { + 'modulename': 'snakemake_executor_plugin_slurm_jobstep', + 'source_tmpl': 'snakemake_executor_plugin_slurm_jobstep-%(version)s.tar.gz', + 'checksums': ['321b6bdf7883a8fb40ff4aeeb88633502e4db8394e40b6628db41a430c2eae2b'], + }), + ('snakemake-executor-plugin-flux', '0.1.0', { + 'modulename': 'snakemake_executor_plugin_flux', + 'source_tmpl': 'snakemake_executor_plugin_flux-%(version)s.tar.gz', + 'checksums': ['92b1944dcf9ea163519a8879d4d638df2b3d0cd83ea6e8397d26046897811214'], + }), + ('snakemake-executor-plugin-slurm', '0.2.1', { + 'modulename': 'snakemake_executor_plugin_slurm', + 'source_tmpl': 'snakemake_executor_plugin_slurm-%(version)s.tar.gz', + 'checksums': ['dd484fcb136612a3f2bdcccf15ca4ebffc2f5fcdfa7f1fcc14416dd272812999'], + }), + ('snakemake-executor-plugin-cluster-sync', '0.1.3', { + 'modulename': 'snakemake_executor_plugin_cluster_sync', + 'source_tmpl': 'snakemake_executor_plugin_cluster_sync-%(version)s.tar.gz', + 'checksums': ['c30fca6ccb98a3f7ca52ca8a95414c71360a3d4a835bd4a097a13445d6fce2ac'], + }), + ('snakemake-executor-plugin-cluster-generic', '1.0.7', { + 'modulename': 'snakemake_executor_plugin_cluster_generic', + 'source_tmpl': 'snakemake_executor_plugin_cluster_generic-%(version)s.tar.gz', + 'checksums': ['093808e63cc48294a9d1eb0b620cdff8cc970806294a2f6ba127a49f8a81d473'], + }), +] + +sanity_check_paths = { + 'files': ['bin/snakemake'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/snakemake'], +} + +sanity_check_commands = ['snakemake --help'] + +moduleclass = 'tools' From dda23feef2ab1fbcd3ab6dea7b763608ddf03a4d Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 19 Jan 2024 13:16:47 +0100 Subject: [PATCH 0371/1193] update version the specify update --- ...MMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 167 ++++++++++++++++++ 1 file changed, 167 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb new file mode 100644 index 000000000000..50f05a3b61c4 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -0,0 +1,167 @@ +name = 'LAMMPS' +version = '2Aug2023_update2' +versionsuffix = '-kokkos' + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s_update2.tar.gz'] +checksums = ['3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('archspec', '0.2.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('netCDF', '4.9.2'), + ('GSL', '2.7'), + ('zlib', '1.2.13'), + ('gzip', '1.12'), + ('cURL', '8.0.1'), + ('HDF5', '1.14.0'), + ('PCRE', '8.45'), + ('libxml2', '2.11.4'), + ('FFmpeg', '6.0'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.9.0'), + ('ScaFaCoS', '1.0.4'), + ('SciPy-bundle', '2023.07'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.3.0'), +] +if ARCH == 'x86_64': + # TBB is an optional dependency when building on Intel arch + dependencies += [('tbb', '2021.11.0'), ] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) +# 'INTEL' - if builing on Intel CPU +# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' + +# include the following extra packages into the build +general_packages = [ + 'AMOEBA', + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SPICA', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'LEPTON', + 'MACHDYN', + 'MANIFOLD', + 'MANYBODY', + 'MC', + 'MDI', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-POD', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPT', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + + +moduleclass = 'chem' From ea4a63537ae4434978e03d12deab139c8474ec87 Mon Sep 17 00:00:00 2001 From: lara Date: Fri, 19 Jan 2024 13:26:27 +0100 Subject: [PATCH 0372/1193] remove old config LAMMPS-2Aug2023-foss-2023a-kokkos.eb --- .../LAMMPS-2Aug2023-foss-2023a-kokkos.eb | 167 ------------------ 1 file changed, 167 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb deleted file mode 100644 index 05ca147c95cd..000000000000 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023-foss-2023a-kokkos.eb +++ /dev/null @@ -1,167 +0,0 @@ -name = 'LAMMPS' -version = '2Aug2023' -versionsuffix = '-kokkos' - -homepage = 'https://www.lammps.org' -description = """LAMMPS is a classical molecular dynamics code, and an acronym -for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has -potentials for solid-state materials (metals, semiconductors) and soft matter -(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be -used to model atoms or, more generically, as a parallel particle simulator at -the atomic, meso, or continuum scale. LAMMPS runs on single processors or in -parallel using message-passing techniques and a spatial-decomposition of the -simulation domain. The code is designed to be easy to modify or extend with new -functionality. -""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'openmp': True, 'usempi': True} - -# 'https://github.com/lammps/lammps/archive/' -source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s_update2.tar.gz'] -checksums = ['3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'] - -builddependencies = [ - ('CMake', '3.26.3'), - ('pkgconf', '1.9.5'), - ('archspec', '0.2.1'), -] -dependencies = [ - ('Python', '3.11.3'), - ('libpng', '1.6.39'), - ('libjpeg-turbo', '2.1.5.1'), - ('netCDF', '4.9.2'), - ('GSL', '2.7'), - ('zlib', '1.2.13'), - ('gzip', '1.12'), - ('cURL', '8.0.1'), - ('HDF5', '1.14.0'), - ('PCRE', '8.45'), - ('libxml2', '2.11.4'), - ('FFmpeg', '6.0'), - ('Voro++', '0.4.6'), - ('kim-api', '2.3.0'), - ('Eigen', '3.4.0'), - ('PLUMED', '2.9.0'), - ('ScaFaCoS', '1.0.4'), - ('SciPy-bundle', '2023.07'), - # VTK package is auto-disabled if this dep is not available - ('VTK', '9.3.0'), -] -if ARCH == 'x86_64': - # TBB is an optional dependency when building on Intel arch - dependencies += [('tbb', '2021.11.0'), ] - -# To use additional custom configuration options, use the 'configopts' easyconfig parameter -# See docs and lammps easyblock for more information. -# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options - -# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, -# which is claimed to be faster in pure MPI calculations -# configopts = "-DKokkos_ENABLE_SERIAL=yes " - - -# packages auto-enabled by easyblock -# 'GPU' - if cuda package is present and kokkos is disabled -# 'KOKKOS' - if kokkos is enabled (by default) -# 'INTEL' - if builing on Intel CPU -# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' - -# include the following extra packages into the build -general_packages = [ - 'AMOEBA', - 'ASPHERE', - 'ATC', - 'AWPMD', - 'BOCS', - 'BODY', - 'BPM', - 'BROWNIAN', - 'CG-DNA', - 'CG-SPICA', - 'CLASS2', - 'COLLOID', - 'COLVARS', - 'COMPRESS', - 'CORESHELL', - 'DIELECTRIC', - 'DIFFRACTION', - 'DIPOLE', - 'DPD-BASIC', - 'DPD-MESO', - 'DPD-REACT', - 'DPD-SMOOTH', - 'DRUDE', - 'EFF', - 'ELECTRODE', - 'EXTRA-COMPUTE', - 'EXTRA-DUMP', - 'EXTRA-FIX', - 'EXTRA-MOLECULE', - 'EXTRA-PAIR', - 'FEP', - 'GRANULAR', - 'H5MD', - 'INTERLAYER', - 'KIM', - 'KSPACE', - 'LATBOLTZ', - 'LEPTON', - 'MACHDYN', - 'MANIFOLD', - 'MANYBODY', - 'MC', - 'MDI', - 'MEAM', - 'MGPT', - 'MISC', - 'ML-IAP', - 'ML-PACE', - 'ML-POD', - 'ML-RANN', - 'ML-SNAP', - 'MOFFF', - 'MOLECULE', - 'MOLFILE', - 'MPIIO', - 'NETCDF', - 'OPT', - 'ORIENT', - 'PERI', - 'PHONON', - 'PLUGIN', - 'PLUMED', - 'POEMS', - 'PTM', - 'PYTHON', - 'QEQ', - 'QTB', - 'REACTION', - 'REAXFF', - 'REPLICA', - 'RIGID', - 'SCAFACOS', - 'SHOCK', - 'SMTBQ', - 'SPH', - 'SPIN', - 'SRD', - 'TALLY', - 'UEF', - 'VORONOI', - 'VTK', - 'YAFF', -] - -# Excluded packages due to requiring additional (non-trivial) deps -# - ADIOS -# - LATTE -# - MESONT (requires very large files downloaded during build) -# - ML-HDNNP (requires N2P2) -# - ML-QUIP -# - MSCG -# - QMMM (setup seems complex) - - -moduleclass = 'chem' From 5c0a830bd6244c1fa308422277e0cd847cf7c66f Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 19 Jan 2024 14:07:55 +0100 Subject: [PATCH 0373/1193] fix source --- .../l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb index 50f05a3b61c4..b51db79bc457 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -19,7 +19,7 @@ toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] -sources = ['stable_%(version)s_update2.tar.gz'] +sources = ['stable_%(version)s.tar.gz'] checksums = ['3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'] builddependencies = [ From f9e66cfd7046548870439671d693112f35f99399 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Jan 2024 15:43:36 +0100 Subject: [PATCH 0374/1193] {lib}[foss/2023a] PyTorch-Lightning v2.1.3, deepdiff v6.7.1, tensorboardX v2.6.2.2 --- .../deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb | 36 ++++ .../PyTorch-Lightning-2.1.3-foss-2023a.eb | 169 ++++++++++++++++++ .../tensorboardX-2.6.2.2-foss-2023a.eb | 26 +++ 3 files changed, 231 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..557a3af6db10 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '6.7.1' + +homepage = 'https://zepworks.com/deepdiff/current/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), # for setuptools-scm +] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('jsonpickle', '3.0.2', { + 'checksums': ['e37abba4bfb3ca4a4647d28bb9f4706436f7b46c8a8333b4a718abafa8e46b37'], + }), + ('ordered-set', '4.1.0', { + 'checksums': ['694a8e44c87657c59292ede72891eb91d34131f6531463aab3009191c77364a8'], + }), + (name, version, { + 'checksums': ['b367e6fa6caac1c9f500adc79ada1b5b1242c50d5f716a1a4362030197847d30'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb new file mode 100644 index 000000000000..a3de9a847a71 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb @@ -0,0 +1,169 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '2.1.3' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('flit', '3.9.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.5'), + ('BeautifulSoup', '4.12.2'), + ('deepdiff', '6.7.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '2.1.2'), + ('tqdm', '4.66.1'), + ('tensorboardX', '2.6.2.2'), + ('pydantic', '2.5.3'), + ('typing-extensions', '4.9.0'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.7.0', { + 'checksums': ['5cb5123b5cf9ee70584244246816e9114227e0b98ad9176eede6ad54bf5403fa'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('starlette', '0.35.1', { + 'checksums': ['3e2639dac3520e4f58734ed22553f950d3f3cb1001cd2eaac4d57e8cdc5f66bc'], + }), + ('fastapi', '0.109.0', { + 'checksums': ['b978095b9ee01a5cf49b19f4bc1ac9b8ca83aa076e770ef8fd9af09a2b88d191'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('exceptiongroup', '1.2.0', { + 'checksums': ['91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68'], + }), + ('anyio', '4.2.0', { + 'checksums': ['e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f'], + }), + ('websocket-client', '1.7.0', { + 'modulename': 'websocket', + 'checksums': ['10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6'], + }), + ('python_multipart', '0.0.6', { + 'modulename': 'multipart', + 'checksums': ['e9925a80bb668529f1b67c7fdb0a5dacdd7cbfc6fb0bff3ea443fe22bdd62132'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.26.0', { + 'checksums': ['48bfd350fce3c5c57af5fb4995fded8fb50da3b4feb543eb18ad7e0d54589602'], + }), + ('lightning_cloud', '0.5.61', { + 'checksums': ['bd57f0921022a0603a0da08bdee1108f98fdc55eee59f3b99f6cead2e98c74fb'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '2.1.2', { + 'checksums': ['7e028b7b06a5b7f8ac4fe7894eb609941f96d137bc9d6cc6b6d86ae4724d7e36'], + }), + ('fsspec', '2023.12.2', { + 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], + }), + ('croniter', '2.0.1', { + 'checksums': ['d199b2ec3ea5e82988d1f72022433c5f9302b3b3ea9e6bfd6a1518f6ea5e700a'], + }), + ('traitlets', '5.14.1', { + 'checksums': ['8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e'], + }), + ('types-python-dateutil', '2.8.19.20240106', { + 'modulename': False, + 'checksums': ['1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f'], + }), + ('arrow', '1.3.0', { + 'preinstallopts': "PYTHONPATH=$PWD:$PYTHONPATH ", + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('lightning-utilities', '0.10.1', { + 'checksums': ['362755023dcf93b8fa519bc002ae41794943a3ffbc5318e40804d36aa14bf1fd'], + }), + ('blessed', '1.20.0', { + 'checksums': ['2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.5', { + 'checksums': ['08a456c2d7c1888cde3f4688b542621b676eb38cd6cfed7eb6cb2e2905ddc826'], + }), + ('runs', '1.2.0', { + 'checksums': ['8804271011b7a2eeb0d77c3e3f556e5ce5f602fa0dd2a31ed0c1222893be69b7'], + }), + ('xmod', '1.8.1', { + 'checksums': ['38c76486b9d672c546d57d8035df0beb7f4a9b088bc3fb2de5431ae821444377'], + }), + ('editor', '1.6.5', { + 'checksums': ['5a8ad611d2a05de34994df3781605e26e63492f82f04c2e93abdd330eed6fa8d'], + }), + ('inquirer', '3.2.1', { + 'checksums': ['d5ff9bb8cd07bd3f076eabad8ae338280886e93998ff10461975b768e3854fbc'], + }), + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('botocore', '1.33.13', { + 'checksums': ['fb577f4cb175605527458b04571451db1bd1a2036976b626206036acd4496617'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.8.2', { + 'checksums': ['368ac6876a9e9ed91f6bc86581e319be08188dc60d50e0d56308ed5765446283'], + }), + ('boto3', '1.33.13', { + 'checksums': ['0e966b8a475ecb06cc0846304454b8da2473d4c8198a45dfb2c5304871986883'], + }), + ('aiobotocore', '2.9.1', { + 'checksums': ['24daf4f1ce86e2fb5aee146cdc944736ef76791635ec3a9b6f3d5755b1ac3c46'], + }), + ('s3fs', '2023.12.2', { + 'checksums': ['b5ec07062481bbb45cb061b31984c7188d106e292c27033039e024e4ba5740dc'], + }), + ('torchmetrics', '1.3.0.post0', { + 'checksums': ['6d31aeabee964ff539425800164790b8670293f2fade9fcfee6fabbe3f45dd7e'], + }), + ('pytorch-lightning', version, { + 'checksums': ['2500b002fa09cb37b0e12f879876bf30a2d260b0f04783d33264dab175f0c966'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/dateutil-stubs'], +} + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb new file mode 100644 index 000000000000..3bc7840841c4 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'tensorboardX' +version = '2.6.2.2' + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'foss', 'version': '2023a'} + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('protobuf-python', '4.24.0'), +] + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'checksums': ['c6476d7cd0d529b0b72f4acadb1269f9ed8b22f441e87a84f2a3b940bb87b666'], + }), +] + +moduleclass = 'vis' From 1a6718d02362a896e05ba76948f5e8576162e915 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Fri, 19 Jan 2024 15:51:15 +0000 Subject: [PATCH 0375/1193] adding easyconfigs: napari-0.4.18-foss-2023a.eb, pydantic-1.10.13-GCCcore-12.3.0.eb, Qtconsole-5.5.1-GCCcore-12.3.0.eb, QtPy-2.4.1-GCCcore-12.3.0.eb, VisPy-0.12.2-gfbf-2023a.eb --- .../n/napari/napari-0.4.18-foss-2023a.eb | 123 ++++++++++++++++++ .../pydantic-1.10.13-GCCcore-12.3.0.eb | 41 ++++++ .../q/QtPy/QtPy-2.4.1-GCCcore-12.3.0.eb | 29 +++++ .../Qtconsole-5.5.1-GCCcore-12.3.0.eb | 32 +++++ .../v/VisPy/VisPy-0.12.2-gfbf-2023a.eb | 46 +++++++ 5 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.5.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb new file mode 100644 index 000000000000..f450bff7ed2b --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb @@ -0,0 +1,123 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2023/08 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.18' + +homepage = 'https://napari.org/' +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +designed for browsing, annotating, and analyzing large multi-dimensional images. +It's built on top of Qt (for the GUI), vispy (for performant GPU-based +rendering), and the scientific Python stack (numpy, scipy).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyQt5', '5.15.10'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('pydantic', '1.10.13'), + ('dask', '2023.9.2'), + ('PyOpenGL', '3.1.7'), + ('imageio', '2.33.1'), + ('tqdm', '4.66.1'), + ('IPython', '8.14.0'), + ('VisPy', '0.12.2'), # vispy<0.13,>=0.12.1 + ('scikit-image', '0.22.0'), + ('matplotlib', '3.7.2'), + ('Qtconsole', '5.5.1'), + ('Pint', '0.23'), + ('wrapt', '1.15.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('in_n_out', '0.1.9', { + 'checksums': ['89feb944e420faf42d3c2542145681b4d57144355932c2b859695fcdc4f9a2da'], + }), + ('pydantic_compat', '0.1.2', { + 'checksums': ['c5c5bca39ca2d22cad00c02898e400e1920e5127649a8e860637f15566739373'], + }), + ('app_model', '0.2.4', { + 'checksums': ['127cda637003a34b26371c9c68ae5b24d7012682f071a10657a94900c8cd439d'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('lazy_loader', '0.3', { + 'checksums': ['3b68898e34f5b2a29daaaac172c6555512d0f32074f147e2254e4a6d9d838f37'], + }), + ('docstring_parser', '0.15', { + 'checksums': ['48ddc093e8b1865899956fcc03b03e66bb7240c310fac5af81814580c55bf682'], + }), + ('magicgui', '0.8.1', { + 'checksums': ['43553d8f11002a79dd5fee57caff3ba9d3e37d7d50e8ed40efe79b360adc806a'], + }), + ('numpydoc', '1.6.0', { + 'checksums': ['ae7a5380f0a06373c3afe16ccd15bd79bc6b07f2704cbc6f1e7ecc94b4f5fc0d'], + }), + ('psygnal', '0.9.5', { + 'checksums': ['4956ea6c36a75f7fc457558935b67dd8be2594661b4d08eeb3357d69c509c55f'], + }), + ('superqt', '0.6.1', { + 'checksums': ['f1a9e0499c4bbcef34b6f895eb57cd41301b3799242cd030029238124184dade'], + }), + ('napari-console', '0.0.9', { + 'checksums': ['3bc86dd96cf94b1af96bba1043f90a39b1369bb978a8df9038a1ac422e66b532'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.10', { + 'checksums': ['18e642c888a71e09c9d1097f25bced1e7ef5dde1771469647bcd77975800f77d'], + }), + ('typer', '0.9.0', { + 'checksums': ['50922fd79aea2f4751a8e0408ff10d2662bd0c8bbfa84755a699f3bada2978b2'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + ('build', '1.0.3', { + 'checksums': ['538aab1b64f9828977f84bc63ae570b060a8ed1be419e7870b8b4fc5e6ea553b'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.7.0', { + 'checksums': ['5cb5123b5cf9ee70584244246816e9114227e0b98ad9176eede6ad54bf5403fa'], + }), + ('npe2', '0.7.3', { + 'checksums': ['4bbb45577a7c60e1aa15636040ef4cf7690d22470e08717af689f50ddeffc807'], + }), + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + (name, version, { + 'checksums': ['daea9ab94124140fc0f715e945dd1dd6dc3056a1cb2f2cc31fc29b80162943e4'], + 'preinstallopts': "sed -i 's|sphinx.*|sphinx|g' setup.cfg && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = [ + '%(name)s --help', + 'pyrcc5 -version 2>&1 |grep pyrcc5' # make sure PyQt5 module was not built with --no-tools +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..96ad7fb45129 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.13' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('typing_extensions', '4.9.0', { + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + }), + ('annotated-types', '0.6.0', { + 'source_tmpl': 'annotated_types-%(version)s.tar.gz', + 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], + }), + ('pydantic-core', '2.14.6', { + 'source_tmpl': 'pydantic_core-%(version)s.tar.gz', + 'checksums': ['1fd0c1d395372843fba13a51c28e3bb9d59bd7aebfeb17358ffaaa1e4dbbe948'], + }), + (name, version, { + 'checksums': ['32c8b48dcd3b2ac4e78b0ba4af3a2c2eb6048cb75202f0ea7b34feb740efc340'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..91aea4a371f8 --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '2.4.1' + +homepage = "https://github.com/spyder-ide/qtpy" +description = """QtPy is a small abstraction layer that lets you write applications using a single API call to + either PyQt or PySide. It provides support for PyQt5, PyQt4, PySide2 and PySide.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a5a15ffd519550a1361bdc56ffc07fda56a6af7292f17c7b395d4083af632987'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyQt5', '5.15.10'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.5.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..61694a5b190e --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.5.1' + +homepage = 'https://jupyter.org/' +description = """A rich Qt-based console for working with Jupyter kernels, supporting rich media +output, session export, and more. +The Qtconsole is a very lightweight application that largely feels like a +terminal, but provides a number of enhancements only possible in a GUI, such as +inline figures, proper multiline editing with syntax highlighting, graphical +calltips, and more.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a0e806c6951db9490628e4df80caec9669b65149c7ba40f9bf033c025a5b56bc'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), + ('QtPy', '2.4.1'), + ('Jupyter-bundle', '20230823'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb new file mode 100644 index 000000000000..3b3f8920ab15 --- /dev/null +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'VisPy' +version = '0.12.2' + +homepage = 'https://vispy.org' +description = """VisPy is a high-performance interactive 2D/3D data visualization library + leveraging the computational power of modern Graphics Processing Units (GPUs) through the + OpenGL library to display very large datasets.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('PyQt5', '5.15.10'), + ('matplotlib', '3.7.2'), # for kiwisolver + ('freetype', '2.13.0'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +download_dep_fail = True + +# setuptools-scm needs the .git dir to determine the version, otherwise it shows as 0.0.0 +_fix_pip_version = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ + +exts_list = [ + ('freetype_py', '2.4.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-2.4.0.zip'], + 'checksums': ['8ad81195d2f8f339aba61700cebfbd77defad149c51f59b75a2a5e37833ae12e'], + 'preinstallopts': _fix_pip_version, + }), + ('hsluv', '5.0.4', { + 'checksums': ['2281f946427a882010042844a38c7bbe9e0d0aaf9d46babe46366ed6f169b72e'], + }), + ('vispy', version, { + 'checksums': ['141c2ddccc1158555bc89f09010c4b1d754487e816357333f31e795a7146a024'], + 'preinstallopts': _fix_pip_version, + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 9f991412a4a9d346861ed5af707df75f32bc253f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 19 Jan 2024 16:52:44 +0100 Subject: [PATCH 0376/1193] add missing dm-tree dependency for dm-reverb 0.2.0 --- easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb index aa3a70ea80f7..39199d15af2f 100644 --- a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.2.0-foss-2020b.eb @@ -27,6 +27,7 @@ dependencies = [ ('Python', '3.8.6'), ('TensorFlow', '2.4.1'), ('protobuf', '3.14.0'), + ('dm-tree', '0.1.5'), ('snappy', '1.1.8'), ('zlib', '1.2.11'), ] From 4f24b5d39d35136cde36dc67bb6b1b609220baea Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 19 Jan 2024 16:18:11 +0000 Subject: [PATCH 0377/1193] adding easyconfigs: motif-2.3.8-GCCcore-12.3.0.eb --- .../m/motif/motif-2.3.8-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4af5309341a9 --- /dev/null +++ b/easybuild/easyconfigs/m/motif/motif-2.3.8-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'motif' +version = '2.3.8' + +homepage = 'https://motif.ics.com/' +description = """Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building + applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. + It was the standard toolkit for the Common Desktop Environment and thus for Unix.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['859b723666eeac7df018209d66045c9853b50b4218cecadb794e2359619ebce7'] + +builddependencies = [ + ('Autotools', '20220317'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('binutils', '2.40'), + ('util-linux', '2.39'), +] + +dependencies = [ + ('X11', '20230603'), + ('libpng', '1.6.39'), + ('freetype', '2.13.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('bzip2', '1.0.8'), +] + +# makefile is not parallel safe +parallel = 1 + +sanity_check_paths = { + 'files': ['lib/libMrm.a', 'lib/libUil.a', 'lib/libXm.a', 'bin/mwm', 'bin/uil', 'bin/xmbind'], + 'dirs': ['include/Mrm', 'include/uil', 'include/X11', 'include/Xm'], +} + +moduleclass = 'vis' From 508e40fcb9bd38e30ede688484b1e0bb941364d6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 20 Jan 2024 08:43:38 +0000 Subject: [PATCH 0378/1193] update comment in ncurses and zlib for dummy -> SYSTEM toolchain --- easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb | 2 +- easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb | 2 +- easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb | 2 +- 8 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb index 8f2c950f72be..18dd57e1d6e1 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-5.9.eb @@ -34,7 +34,7 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb index 244ea3bdd800..85438274955d 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.1.eb @@ -22,7 +22,7 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb index 26cb42a20bfc..14b48372eed9 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.2.eb @@ -22,7 +22,7 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb index 3d144c5ab1ac..83969aa9fa57 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.3.eb @@ -25,7 +25,7 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' diff --git a/easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb b/easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb index 7edecb90d1b7..a5d4b191e8a4 100644 --- a/easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb +++ b/easybuild/easyconfigs/n/ncurses/ncurses-6.4.eb @@ -25,7 +25,7 @@ configopts = [ local_common_configopts + "--enable-ext-colors --enable-widec --includedir=%(installdir)s/include/ncursesw/", ] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb index 38e3bed9d4ab..2fad13cb84d1 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.11.eb @@ -18,7 +18,7 @@ source_urls = ['https://zlib.net/fossils/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid # compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb index 75f1815ef62b..f6b625eac3df 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.12.eb @@ -22,7 +22,7 @@ checksums = [ 'f35eb05334a4f8d7b40b6c5610a6369f654863b5fa1a19c2507888f918025238', # zlib-1.2.12_fix-CC-logic-in-configure.patch ] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid # compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb index 397dbe63b578..1e59f99d6a0e 100644 --- a/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb +++ b/easybuild/easyconfigs/z/zlib/zlib-1.2.13.eb @@ -18,7 +18,7 @@ source_urls = ['https://zlib.net/fossils/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b3a24de97a8fdbc835b9833169501030b8977031bcb54b3b3ac13740f846ab30'] -# need to take care of $CFLAGS ourselves with dummy toolchain +# need to take care of $CFLAGS ourselves with SYSTEM toolchain # we need to add -fPIC, but should also include -O* option to avoid # compiling with -O0 (default for GCC) buildopts = 'CFLAGS="-O2 -fPIC"' From fb36bfb6f255649c8b034d44aeebf5416f3656d8 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 21 Jan 2024 14:45:08 +0000 Subject: [PATCH 0379/1193] add libyaml import check to PyYAML and fix builds since split to minimal Python --- easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb | 2 ++ easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb | 2 ++ easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb | 3 +++ .../easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb | 6 ++++++ 4 files changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb index 0c55d6c41a2e..a715d91e5302 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-11.3.0.eb @@ -24,4 +24,6 @@ sanity_pip_check = True use_pip = True options = {'modulename': 'yaml'} +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb index 6f216f2874f7..a9baad89a068 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb @@ -24,4 +24,6 @@ sanity_pip_check = True use_pip = True options = {'modulename': 'yaml'} +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb index a1f8e4ff4f65..b373b0c8033e 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.3.0.eb @@ -17,6 +17,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('libyaml', '0.2.5'), + ('Python-bundle-PyPI', '2023.06'), ] download_dep_fail = True @@ -24,4 +25,6 @@ sanity_pip_check = True use_pip = True options = {'modulename': 'yaml'} +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb index caa66c5b231d..23133f20f022 100644 --- a/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0.1-GCCcore-13.2.0.eb @@ -17,11 +17,17 @@ builddependencies = [ dependencies = [ ('Python', '3.11.5'), ('libyaml', '0.2.5'), + ('Python-bundle-PyPI', '2023.10'), ] +# Use Cython old_build_ext, as PyYAML does not support the new build_ext in Cython 3 +preinstallopts = 'sed -i "s/Cython.Distutils import /Cython.Distutils.old_build_ext import old_/" setup.py &&' + download_dep_fail = True sanity_pip_check = True use_pip = True options = {'modulename': 'yaml'} +sanity_check_commands = ["python -c 'import yaml; yaml.CLoader'"] + moduleclass = 'lib' From a92f5112a57a7d724b6c712ed11e91d2c2d16dd1 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 10:39:01 +0000 Subject: [PATCH 0380/1193] drop download_dep_fail --- easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb b/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb index 3b3f8920ab15..ea5153042cc4 100644 --- a/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/v/VisPy/VisPy-0.12.2-gfbf-2023a.eb @@ -20,7 +20,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True # setuptools-scm needs the .git dir to determine the version, otherwise it shows as 0.0.0 _fix_pip_version = """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ From b7a91e074fcafd43ea2e5b8305945216cbd9e269 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 22 Jan 2024 12:12:01 +0100 Subject: [PATCH 0381/1193] adding easyconfigs: GRASP-suite-2022.7.4-Java-17.eb --- .../GRASP-suite-2022.7.4-Java-17.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb diff --git a/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb new file mode 100644 index 000000000000..cbbaa4f6f5ea --- /dev/null +++ b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb @@ -0,0 +1,33 @@ +easyblock = 'JAR' + +name = 'GRASP-suite' +version = '2022.7.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://bodenlab.github.io/GRASP-suite/' +description = """GRASP-suite is a collection of tools and tutorials to perform and +analyse ancestral sequence reconstruction.""" + +toolchain = SYSTEM + +source_urls = ['https://bodenlab.github.io/GRASP-suite/project/graspcmd/archive/'] +sources = ['bnkit.jar'] +checksums = ['7ee4cbc9f23857c8c7cf3e6bd0dde962d9a244974d955aac92212b5b5e29a385'] + +dependencies = [('Java', '17')] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + "echo '#!/bin/sh' > %(installdir)s/bin/grasp", + "echo 'java -jar -Xmx16g %(installdir)s/bnkit.jar $@' >> %(installdir)s/bin/grasp", + "chmod a+rx %(installdir)s/bin/grasp" +] + +sanity_check_commands = ["grasp -h"] + +sanity_check_paths = { + 'files': ['bin/grasp', 'bnkit.jar'], + 'dirs': [], +} + +moduleclass = 'bio' From 8d0677d562b9f1bc5dba3dd2ff53893605f70141 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 12:16:38 +0000 Subject: [PATCH 0382/1193] adding easyconfigs: PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb --- .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 163 ++++++++++++++++++ 1 file changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..102b2735fec0 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,163 @@ +name = 'PyTorch' +version = '2.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', + 'PyTorch-1.13.1_fix-protobuf-dependency.patch', + 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', + 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_fix-skip-decorators.patch', + 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', + 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', + 'PyTorch-2.0.1_skip-failing-gradtest.patch', + 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', + 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', + 'PyTorch-2.1.0_disable-gcc12-warning.patch', + 'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch', + 'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch', + 'PyTorch-2.1.0_fix-validationError-output-test.patch', + 'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch', + 'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch', + 'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch', + 'PyTorch-2.1.0_remove-test-requiring-online-access.patch', + 'PyTorch-2.1.0_skip-diff-test-on-ppc.patch', + 'PyTorch-2.1.0_skip-dynamo-test_predispatch.patch', + 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', + 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', + 'PyTorch-2.1.0_skip-test_wrap_bad.patch', +] +checksums = [ + {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': + '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'}, + {'PyTorch-1.13.1_fix-protobuf-dependency.patch': + '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, + {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': + 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, + {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch': + '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': + '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'}, + {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': + '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, + {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, + {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'}, + {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch': + '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, + {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': + '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, + {'PyTorch-2.1.0_disable-gcc12-warning.patch': 'c858b8db0010f41005dc06f9a50768d0d3dc2d2d499ccbdd5faf8a518869a421'}, + {'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch': + 'b15b1291a3c37bf6a4982cfbb3483f693acb46a67bc0912b383fd98baf540ccf'}, + {'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch': + '84bb51a719abc677031a7a3dfe4382ff098b0cbd8b39b8bed2a7fa03f80ac1e9'}, + {'PyTorch-2.1.0_fix-validationError-output-test.patch': + '7eba0942afb121ed92fac30d1529447d892a89eb3d53c565f8e9d480e95f692b'}, + {'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch': + '3793b4b878be1abe7791efcbd534774b87862cfe7dc4774ca8729b6cabb39e7e'}, + {'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch': + 'aef38adf1210d0c5455e91d7c7a9d9e5caad3ae568301e0ba9fc204309438e7b'}, + {'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch': + '0ac36411e76506b3354c85a8a1260987f66af947ee52ffc64230aee1fa02ea8b'}, + {'PyTorch-2.1.0_remove-test-requiring-online-access.patch': + '35184b8c5a1b10f79e511cc25db3b8a5585a5d58b5d1aa25dd3d250200b14fd7'}, + {'PyTorch-2.1.0_skip-diff-test-on-ppc.patch': '394157dbe565ffcbc1821cd63d05930957412156cc01e949ef3d3524176a1dda'}, + {'PyTorch-2.1.0_skip-dynamo-test_predispatch.patch': + '6298daf9ddaa8542850eee9ea005f28594ab65b1f87af43d8aeca1579a8c4354'}, + {'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch': + '5229ca88a71db7667a90ddc0b809b2c817698bd6e9c5aaabd73d3173cf9b99fe'}, + {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': + '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, + {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.26.3'), + ('hypothesis', '6.82.0'), + # For tests + ('pytest-flakefinder', '1.1.0'), + ('pytest-rerunfailures', '12.0'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Ninja', '1.11.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('protobuf', '24.0'), + ('protobuf-python', '4.24.0'), + ('pybind11', '2.11.1'), + ('SciPy-bundle', '2023.07'), + ('PyYAML', '6.0'), + ('MPFR', '4.2.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.16'), + ('FFmpeg', '6.0'), + ('Pillow', '10.0.0'), + ('expecttest', '0.1.5'), + ('networkx', '3.1'), + ('sympy', '1.12'), + ('Z3', '4.12.2', '-Python-%(pyver)s'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' From 1a315828b8e11b70eac751b10f3de8b0260c1eff Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 12:19:24 +0000 Subject: [PATCH 0383/1193] add PyOpenGL 3.1.7 --- .../PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..132e708af8e7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenGL' +version = '3.1.7' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Mesa', '23.1.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'OpenGL', + 'checksums': ['eef31a3888e6984fd4d8e6c9961b184c9813ca82604d37fe3da80eb000a76c86'], + }), +] + +moduleclass = 'vis' From 8af337d315a647182fe1e78fedcdb6e73ff6797a Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 12:23:35 +0000 Subject: [PATCH 0384/1193] demote meson-python to a build dep in matplotlib --- .../easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb | 2 +- .../easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb index 50cd58acdfdb..c15e4a6a5fe7 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-gfbf-2023a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ ('pkgconf', '1.9.5'), ('cppy', '1.2.1'), + ('meson-python', '0.13.2'), ] dependencies = [ @@ -23,7 +24,6 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ('Pillow', '10.0.0'), ('Qhull', '2020.2'), - ('meson-python', '0.13.2'), ] use_pip = True diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb index 93ec6abd3812..b69859542f79 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.8.2-gfbf-2023b.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'gfbf', 'version': '2023b'} builddependencies = [ ('pkgconf', '2.0.3'), ('cppy', '1.2.1'), + ('meson-python', '0.15.0'), ] dependencies = [ @@ -23,7 +24,6 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ('Pillow', '10.2.0'), ('Qhull', '2020.2'), - ('meson-python', '0.15.0'), ] use_pip = True From cdc853747d0df9153ca9ca74ca92d5e7b691a05e Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 14:06:07 +0000 Subject: [PATCH 0385/1193] patch upb CopyFrom error in protobuf-python 4.24.0 --- .../protobuf-python-4.24.0-GCCcore-12.3.0.eb | 7 +++- ...tobuf-python-4.24.0_fix-upb-copyfrom.patch | 39 +++++++++++++++++++ 2 files changed, 45 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0_fix-upb-copyfrom.patch diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb index 0a299aea4807..4606b18567e7 100644 --- a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb @@ -10,7 +10,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] sources = ['protobuf-%(version)s.tar.gz'] -checksums = ['5d0ceb9de6e08311832169e601d1fc71bd8e8c779f3ee38a97a78554945ecb85'] +patches = ['%(name)s-%(version)s_fix-upb-copyfrom.patch'] +checksums = [ + {'protobuf-4.24.0.tar.gz': '5d0ceb9de6e08311832169e601d1fc71bd8e8c779f3ee38a97a78554945ecb85'}, + {'protobuf-python-4.24.0_fix-upb-copyfrom.patch': + '9afea4c68ee54d7278ec61a7e7d91c0aad2e7b0d63ba22f2200d0df2fac34de7'}, +] builddependencies = [('binutils', '2.40')] diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0_fix-upb-copyfrom.patch b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0_fix-upb-copyfrom.patch new file mode 100644 index 000000000000..85d4ba67fe49 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0_fix-upb-copyfrom.patch @@ -0,0 +1,39 @@ +From 57636ce03ac1e2aab3a362a61a6664981e21cda5 Mon Sep 17 00:00:00 2001 +From: Jie Luo +Date: Thu, 24 Aug 2023 14:27:41 -0700 +Subject: [PATCH] upb CopyFrom the default empty message should just clear + instead of deep copy from memory + +fix https://github.com/protocolbuffers/protobuf/issues/13485 + +PiperOrigin-RevId: 559870202 +--- + python/message.c | 15 +++++++++------ + 1 file changed, 9 insertions(+), 6 deletions(-) + +diff --git a/python/message.c b/python/message.c +index afdd4311a..e61eebb23 100644 +--- a/python/message.c ++++ b/python/message.c +@@ -1237,12 +1237,15 @@ static PyObject* PyUpb_Message_CopyFrom(PyObject* _self, PyObject* arg) { + PyUpb_Message* other = (void*)arg; + PyUpb_Message_EnsureReified(self); + +- PyObject* tmp = PyUpb_Message_Clear(self); +- Py_DECREF(tmp); +- +- upb_Message_DeepCopy(self->ptr.msg, other->ptr.msg, +- upb_MessageDef_MiniTable(other->def), +- PyUpb_Arena_Get(self->arena)); ++ const upb_Message* other_msg = PyUpb_Message_GetIfReified((PyObject*)other); ++ if (other_msg) { ++ upb_Message_DeepCopy(self->ptr.msg, other_msg, ++ upb_MessageDef_MiniTable(other->def), ++ PyUpb_Arena_Get(self->arena)); ++ } else { ++ PyObject* tmp = PyUpb_Message_Clear(self); ++ Py_DECREF(tmp); ++ } + PyUpb_Message_SyncSubobjs(self); + + Py_RETURN_NONE; From 1777a370f076d7eaf50cc6d25fe3c36eeb5b420d Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 14:58:43 +0000 Subject: [PATCH 0386/1193] adding easyconfigs: tensorboard-2.15.1-gfbf-2023a.eb --- .../tensorboard-2.15.1-gfbf-2023a.eb | 82 +++++++++++++++++++ 1 file changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb new file mode 100644 index 000000000000..a6d266f6b199 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb @@ -0,0 +1,82 @@ +easyblock = 'PythonBundle' + +name = 'tensorboard' +version = '2.15.1' + +homepage = 'https://github.com/tensorflow/tensorboard' +description = """TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs +and graphs.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('protobuf-python', '4.24.0'), +] + +# upper constraint can be removed if protobuf-python is patched +# see https://github.com/easybuilders/easybuild-easyconfigs/pull/19671 +postinstallcmds = ["sed -i 's/protobuf <4.24,>=3.19.6/protobuf >=3.19.6/g' " + "%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA"] + +exts_list = [ + ('absl-py', '2.1.0', { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), + ('cachetools', '5.3.2', { + 'checksums': ['086ee420196f7b2ab9ca2db2520aca326318b68fe5ba8bc4d49cca91add450f2'], + }), + ('pyasn1_modules', '0.3.0', { + 'checksums': ['5bd01446b736eb9d31512a30d46c1ac3395d676c6f3cafa4c03eb54b9925631c'], + }), + ('rsa', '4.9', { + 'checksums': ['e38464a49c6c85d7f1351b0126661487a7e0a14a50f1675ec50eb34d4f20ef21'], + }), + ('google-auth', '2.26.2', { + 'modulename': 'google.auth', + 'checksums': ['97327dbbf58cccb58fc5a1712bba403ae76668e64814eb30f7316f7e27126b81'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('google-auth-oauthlib', '1.2.0', { + 'checksums': ['292d2d3783349f2b0734a0a0207b1e1e322ac193c2c09d8f7c613fb7cc501ea8'], + }), + ('grpcio', '1.60.0', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['2199165a1affb666aa24adf0c97436686d0a61bc5fc113c037701fb7c7fceb96'], + }), + ('Markdown', '3.5.2', { + 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], + }), + ('tensorboard_data_server', '0.7.2', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['7e0610d205889588983836ec05dc098e80f97b7e7bbff7e994ebb78f578d0ddb'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('werkzeug', '3.0.1', { + 'checksums': ['507e811ecea72b18a404947aded4b3390e1db8f826b494d76550ef45bb3b1dcc'], + }), + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c46c1d1cf13a458c429868a78b2531d8ff5f682058d69ec0840b0bc7a38f1c0f'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 67f030e44447adf2c55562b3186a2e33d4492acf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 22 Jan 2024 16:50:44 +0100 Subject: [PATCH 0387/1193] adding easyconfigs: geopandas-0.14.2-foss-2023a.eb, psycopg2-2.9.9-GCCcore-12.3.0.eb, SQLAlchemy-2.0.25-GCCcore-12.3.0.eb --- .../geopandas/geopandas-0.14.2-foss-2023a.eb | 43 ++++++++++++++++++ .../psycopg2/psycopg2-2.9.9-GCCcore-12.3.0.eb | 33 ++++++++++++++ .../SQLAlchemy-2.0.25-GCCcore-12.3.0.eb | 44 +++++++++++++++++++ 3 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.14.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.14.2-foss-2023a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.14.2-foss-2023a.eb new file mode 100644 index 000000000000..5ba4ab4b6124 --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.14.2-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.14.2' + +homepage = 'https://geopandas.org' +description = """GeoPandas is a project to add support for geographic data to pandas objects. +It currently implements GeoSeries and GeoDataFrame types which are subclasses of pandas.Series +and pandas.DataFrame respectively. GeoPandas objects can act on shapely geometry objects and +perform geometric operations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('Shapely', '2.0.1'), + ('Fiona', '1.9.5'), + ('pyproj', '3.6.0'), + ('matplotlib', '3.7.2'), # optional + ('psycopg2', '2.9.9'), # optional + ('SQLAlchemy', '2.0.25'), # optional + ('networkx', '3.1'), # needed by mapclassify + ('scikit-learn', '1.3.1'), # needed by mapclassify + ('numba', '0.58.1'), # optional, numba extra in mapclassify +] + +use_pip = True + +exts_list = [ + ('mapclassify', '2.6.1', { + 'checksums': ['4441798d55a051e75206bf46dccfc8a8f8323aac8596d19961d11660c98677ca'], + 'use_pip_extras': 'numba', + }), + (name, version, { + 'checksums': ['6e71d57b8376f9fdc9f1c3aa3170e7e420e91778de854f51013ae66fd371ccdb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..2f6b6ba35f1f --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'psycopg2' +version = '2.9.9' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PostgreSQL', '16.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['d1454bde93fb1e224166811694d600e746430c006fbb031ea06ecc2ea41bf156'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..442398989587 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'SQLAlchemy' +version = '2.0.25' + +homepage = 'https://www.sqlalchemy.org/' +description = """SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives +application developers the full power and flexibility of SQL. SQLAlchemy +provides a full suite of well known enterprise-level persistence patterns, +designed for efficient and high-performing database access, adapted into a +simple and Pythonic domain language.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('psycopg2', '2.9.9'), # optional, postgresql extra +] + +use_pip = True + +exts_list = [ + ('greenlet', '3.0.3', { + 'checksums': ['43374442353259554ce33599da8b692d5aa96f8976d567d4badf263371fbe491'], + }), + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('asyncpg', '0.29.0', { + 'checksums': ['d1c49e1f44fffafd9a55e1a9b101590859d881d639ea2922516f5d9c512d354e'], + }), + (name, version, { + 'use_pip_extras': 'asyncio,postgresql,postgresql_asyncpg', + 'checksums': ['a2c69a7664fb2d54b8682dd774c3b54f67f84fa123cf84dda2a5f40dcaa04e08'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From d84e316bd1efaf1ad6b0d421c62e8e3d73681bb6 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 16:22:06 +0000 Subject: [PATCH 0388/1193] demote poetry to build dep in expecttest --- .../easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb index f7a501bcaa2f..a32a4481faee 100644 --- a/easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.1.5-GCCcore-12.3.0.eb @@ -16,10 +16,10 @@ checksums = ['5b3a6a165250860f5a14199f9c59461752beb3b45d48b93347d9afc7293a611c'] builddependencies = [ ('binutils', '2.40'), + ('poetry', '1.5.1'), ] dependencies = [ ('Python', '3.11.3'), - ('poetry', '1.5.1'), ] download_dep_fail = True From dd13a68cccc9561281addecc444cb7ed51727e69 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 16:36:43 +0000 Subject: [PATCH 0389/1193] adding easyconfigs: Meson-1.3.1-GCCcore-12.3.0.eb, meson-python-0.15.0-GCCcore-12.3.0.eb --- .../m/Meson/Meson-1.3.1-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ .../meson-python-0.15.0-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-1.3.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/meson-python/meson-python-0.15.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-1.3.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/Meson/Meson-1.3.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..06dea8648879 --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-1.3.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '1.3.1' + +homepage = 'https://mesonbuild.com' +description = "Meson is a cross-platform build system designed to be both as fast and as user friendly as possible." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6020568bdede1643d4fb41e28215be38eff5d52da28ac7d125457c59e0032ad7'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), # includes required 'wheel' package + ('Ninja', '1.11.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'mesonbuild'} + +sanity_check_paths = { + 'files': ['bin/meson'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["meson --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.15.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.15.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..0e087e824684 --- /dev/null +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.15.0-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'meson-python' +version = '0.15.0' + +homepage = 'https://github.com/mesonbuild/meson-python' +description = "Python build backend (PEP 517) for Meson projects" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # provides 'packaging' + ('Meson', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('pyproject-metadata', '0.7.1', { + 'checksums': ['0a94f18b108b9b21f3a26a3d541f056c34edcb17dc872a144a15618fed7aef67'], + }), + (name, version, { + 'modulename': 'mesonpy', + 'sources': ['meson_python-%(version)s.tar.gz'], + 'checksums': ['fddb73eecd49e89c1c41c87937cd89c2d0b65a1c63ba28238681d4bd9484d26f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 81d4c080220ee59a27d2672bd99becf0c7038887 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 22 Jan 2024 16:52:47 +0000 Subject: [PATCH 0390/1193] adding easyconfigs: PBZIP2-1.1.13-GCCcore-12.3.0.eb and patches: PBZIP2-1.1.13_makefile-hardening.patch --- .../p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb | 40 +++++++++++++++++++ .../PBZIP2-1.1.13_makefile-hardening.patch | 29 ++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13_makefile-hardening.patch diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4f000f843774 --- /dev/null +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'ConfigureMake' + +name = 'PBZIP2' +version = '1.1.13' + +homepage = 'http://compression.great-site.net/pbzip2' +description = """PBZIP2 is a parallel implementation of the bzip2 block-sorting + file compressor that uses pthreads and achieves near-linear speedup on SMP + machines. The output of this version is fully compatible with bzip2 v1.0.2 or + newer (ie: anything compressed with pbzip2 can be decompressed with bzip2). + PBZIP2 should work on any system that has a pthreads compatible C++ compiler + (such as gcc). It has been tested on: Linux, Windows (cygwin & MinGW), Solaris, + Tru64/OSF1, HP-UX, OS/2, OSX, and Irix. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://launchpad.net/pbzip2/1.1/1.1.13/+download'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_makefile-hardening.patch'] +checksums = [ + {'pbzip2-1.1.13.tar.gz': '8fd13eaaa266f7ee91f85c1ea97c86d9c9cc985969db9059cdebcb1e1b7bdbe6'}, + {'PBZIP2-1.1.13_makefile-hardening.patch': 'd493c0757c445f91960c62f735b90f83951b2e26f0b7359aa5898a95024dbcef'}, +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('bzip2', '1.0.8')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/pbzip2', 'share/man/man1/pbzip2.1'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13_makefile-hardening.patch b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13_makefile-hardening.patch new file mode 100644 index 000000000000..c8f65024b4c1 --- /dev/null +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13_makefile-hardening.patch @@ -0,0 +1,29 @@ +Author: William Grzybowski +Subject: Fix build for debug and hardening, do not install symlinks. +Last-Update: 2019-07-10 +--- pbzip2.orig/Makefile 2019-07-08 18:46:10.382725910 -0300 ++++ pbzip2/Makefile 2019-07-08 18:46:24.886865907 -0300 +@@ -19,3 +19,3 @@ + # Optimization flags +-CXXFLAGS = -O2 ++CXXFLAGS += $(CPPFLAGS) + +@@ -49,9 +49,6 @@ + CXXFLAGS += $(CXXFLAGS_PTHREAD) + + +-# Linker flags +-LDFLAGS = +- + + # External libraries + LDLIBS = -lbz2 +@@ -81,8 +81,6 @@ + if ( test ! -d $(DESTDIR)$(PREFIX)/share/man/man1 ) ; then mkdir -p $(DESTDIR)$(PREFIX)/share/man/man1 ; fi + cp -f pbzip2 $(DESTDIR)$(PREFIX)/bin/pbzip2 + chmod a+x $(DESTDIR)$(PREFIX)/bin/pbzip2 +- ln -s -f pbzip2 $(DESTDIR)$(PREFIX)/bin/pbunzip2 +- ln -s -f pbzip2 $(DESTDIR)$(PREFIX)/bin/pbzcat + cp -f pbzip2.1 $(DESTDIR)$(PREFIX)/share/man/man1 + chmod a+r $(DESTDIR)$(PREFIX)/share/man/man1/pbzip2.1 + From 07529298616eb41e5408f464267d4463024734ff Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 22 Jan 2024 19:49:02 +0100 Subject: [PATCH 0391/1193] Add zlib dependency to YODA and Rivet --- .../r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb | 5 +++-- .../r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb | 3 ++- easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb | 5 +++-- easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb | 5 +++-- 4 files changed, 11 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb index 530bb5151e9c..d1d00c698f8e 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb @@ -31,10 +31,11 @@ dependencies = [ ('fastjet', '3.4.0'), ('fastjet-contrib', '1.049'), ('HepMC3', '3.2.5'), - ('GSL', '2.7') + ('GSL', '2.7'), + ('zlib', '1.2.12') ] -configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 --with-zlib=$EBROOTZLIB" sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb index 3cdde9f0f492..154442dfb5c5 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb @@ -30,9 +30,10 @@ dependencies = [ ('fastjet-contrib', '1.053'), ('HepMC3', '3.2.6'), ('GSL', '2.7'), + ('zlib', '1.2.13') ] -configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 --with-zlib=$EBROOTZLIB" sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb index 31487c94983d..778f39d14f67 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb @@ -23,10 +23,11 @@ builddependencies = [ ] dependencies = [ - ('Python', '3.10.4') + ('Python', '3.10.4'), + ('zlib', '1.2.12') ] -configopts = "--disable-root --enable-pyext --disable-static" +configopts = "--disable-root --enable-pyext --disable-static --with-zlib=$EBROOTZLIB" buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" installopts = buildopts diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb index f94434b4fb5b..8a977f5b4c1d 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb @@ -23,9 +23,10 @@ builddependencies = [ ] dependencies = [ - ('Python', '3.11.3') + ('Python', '3.11.3'), + ('zlib', '1.2.13') ] -configopts = "--disable-root --enable-pyext --disable-static" +configopts = "--disable-root --enable-pyext --disable-static --with-zlib=$EBROOTZLIB" buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" installopts = buildopts From 5b82ff23f52c53f21e3e593646c84d9c69452471 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 22 Jan 2024 20:18:20 +0100 Subject: [PATCH 0392/1193] Remove double space --- .../easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb index 154442dfb5c5..0f3e627b995a 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb @@ -33,7 +33,7 @@ dependencies = [ ('zlib', '1.2.13') ] -configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 --with-zlib=$EBROOTZLIB" +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 --with-zlib=$EBROOTZLIB" sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], From 8988c44838ffceb0c34e1f19be635b453f83cdc4 Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 23 Jan 2024 10:05:33 +0100 Subject: [PATCH 0393/1193] {bio}[GCCcore/12.3.0] AreTomo2 v1.0.0 and MotionCor3 v1.0.1 w/CUDA 12.1.1 --- ...eTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb | 55 ++++++++++++++++++ .../a/AreTomo2/AreTomo2-1.0.0_makefile.patch | 46 +++++++++++++++ ...onCor3-1.0.1-GCCcore-12.3.0-CUDA-12.1.1.eb | 57 +++++++++++++++++++ .../MotionCor3-1.0.1_makefile.patch | 54 ++++++++++++++++++ 4 files changed, 212 insertions(+) create mode 100644 easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0_makefile.patch create mode 100644 easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1-GCCcore-12.3.0-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1_makefile.patch diff --git a/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 000000000000..4864dbcbee3d --- /dev/null +++ b/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,55 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/1 +easyblock = 'MakeCp' + +name = 'AreTomo2' +version = '1.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/czimaginginstitute/AreTomo2' + +description = """AreTomo2, a multi-GPU accelerated software package that fully automates motion- +corrected marker-free tomographic alignment and reconstruction, now includes +robust GPU-accelerated CTF (Contrast Transfer Function) estimation in a single +package. AreTomo2 is part of our endeavor to build a fully-automated high- +throughput processing pipeline that enables real-time reconstruction of +tomograms in parallel with tomographic data collection. It strives to be fast +and accurate, as well as provides for easy integration into subtomogram +processing workflows by generating IMod compatible files containing alignment +and CTF parameters needed to bootstrap subtomogram averaging. AreTomo2 can also +be used for on-the-fly reconstruction of tomograms and CTF estimation in +parallel with tilt series collection, enabling real-time assessment of sample +quality and adjustment of collection parameters""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + {'v1.0.0.tar.gz': '5518cd5d7bc13a6dbb6d9310b22c301e73a0c91dc059da403445d79ca0ff8892'}, + {'AreTomo2-1.0.0_makefile.patch': '8595b2fc55e0b5e1bf7c077c93c09503b4e8f95123c6aaf0a5fbe44dda871c73'}, +] + +github_account = 'czimaginginstitute' + +build_cmd = 'make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"' + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), +] + +files_to_copy = [(['%(name)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['bin'], +} + +sanity_check_commands = ['%(name)s -h'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0_makefile.patch b/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0_makefile.patch new file mode 100644 index 000000000000..ebef90dd5d2e --- /dev/null +++ b/easybuild/easyconfigs/a/AreTomo2/AreTomo2-1.0.0_makefile.patch @@ -0,0 +1,46 @@ +# Thomas Hoffmann, EBML Heidelberg, structures-it@embl.de, 2023/10 +# allow to inject cuda compute capabilities and cfalgs +diff -ru AreTomo2-1.0.0/makefile11 AreTomo2-1.0.0_makefile/makefile11 +--- AreTomo2-1.0.0/makefile11 2023-10-26 19:49:07.000000000 +0200 ++++ AreTomo2-1.0.0_makefile/makefile11 2023-10-30 19:00:07.212270395 +0100 +@@ -156,18 +156,21 @@ + $(CUCPPS) + OBJS = $(patsubst %.cpp, %.o, $(SRCS)) + #------------------------------------- +-CC = g++ -std=c++11 +-CFLAG = -c -g -pthread -m64 ++#CC = g++ -std=c++11 ++CFLAG = -c -g -pthread -m64 $(CFLAGS) + NVCC = $(CUDAHOME)/bin/nvcc -std=c++11 +-CUFLAG = -Xptxas -dlcm=ca -O2 \ +- -gencode arch=compute_80,code=sm_80 \ +- -gencode arch=compute_75,code=sm_75 \ +- -gencode arch=compute_70,code=sm_70 \ +- -gencode arch=compute_61,code=sm_61 \ +- -gencode arch=compute_60,code=sm_60 \ +- -gencode arch=compute_53,code=sm_53 \ +- -gencode arch=compute_52,code=sm_52 \ +- -gencode arch=compute_86,code=sm_86 ++SPACE= ' ' ++SEMI= ; ++GENCODES = $(foreach x,$(subst $(SEMI),$(SPACE),$(CUDACC)),-gencode arch=compute_$x,code=sm_$x) ++CUFLAG = -Xptxas -dlcm=ca -O2 $(GENCODES) ++# -gencode arch=compute_80,code=sm_80 \ ++# -gencode arch=compute_75,code=sm_75 \ ++# -gencode arch=compute_70,code=sm_70 \ ++# -gencode arch=compute_61,code=sm_61 \ ++# -gencode arch=compute_60,code=sm_60 \ ++# -gencode arch=compute_53,code=sm_53 \ ++# -gencode arch=compute_52,code=sm_52 \ ++# -gencode arch=compute_86,code=sm_86 + #------------------------------------------ + cuda: $(CUCPPS) + +@@ -183,6 +186,7 @@ + -lcufft -lcudart -lcuda -lc -lm -lpthread \ + -o AreTomo2 + @echo AreTomo2 has been generated. ++ @echo used cuda gencodes: $(GENCODES) + + %.o: %.cu + @$(NVCC) -c $(CUFLAG) -I$(PRJINC) -I$(CUPRJINC) $< -o $@ diff --git a/easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 000000000000..fc4fec158f3c --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,57 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/1 +easyblock = 'MakeCp' + +name = 'MotionCor3' +version = '1.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/czimaginginstitute/MotionCor3' + +description = """Anisotropic correction of beam induced motion for cryo-electron microscopy and +cryo-electron tomography images. +MotionCor3, an improved implementation of MotionCor2 with addition of CTF +(Contrast Transfer Function) estimation, is a multi-GPU accelerated software +package that enables single-pixel level correction of anisotropic beam induced +sample motion for cryo-electron microscopy and cryo-electron tomography images. +The iterative, patch-based motion detection combined with spatial and temporal +constraints and dose weighting provides robust and accurate correction. By +refining the measurement of early motion, MotionCor3 further improves correction +on tilted samples. The efficiency achieved by multi-GPU acceleration and +parallelization enables correction to keep pace with automated data collection. +The recent addition of a very robust GPU-accelerated CTF estimation makes +MotionCor3 more versatile in cryoEM and cryoET processing pipeline.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + {'v1.0.1.tar.gz': '9b1eaa43f67c6ca54c1cea6ad53ee78726a14a87a3c5d91e7820786ebe0786a3'}, + {'MotionCor3-1.0.1_makefile.patch': 'd047c1f097eead3173a60fd3ae821ee7b285728bf8470f496021580f11875d12'}, +] + +github_account = 'czimaginginstitute' + +build_cmd = 'make exe -f makefile11 CUDAHOME=$CUDA_HOME CUDACC="%(cuda_cc_cmake)s"' + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('LibTIFF', '4.5.0'), +] + +files_to_copy = [(['%(name)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['bin'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1_makefile.patch b/easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1_makefile.patch new file mode 100644 index 000000000000..0a99204e2dde --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor3/MotionCor3-1.0.1_makefile.patch @@ -0,0 +1,54 @@ +# Thomas Hoffmann, EBML Heidelberg, structures-it@embl.de, 2023/10 +# allow to inject cuda compute capabilities and cfalgs +diff -ru MotionCor3-1.0.1/makefile11 MotionCor3-1.0.1_makefile/makefile11 +--- MotionCor3-1.0.1/makefile11 2023-10-25 23:59:50.000000000 +0200 ++++ MotionCor3-1.0.1_makefile/makefile11 2023-10-31 14:24:25.377992618 +0100 +@@ -1,6 +1,6 @@ + PRJHOME = $(shell pwd) + CONDA = $(HOME)/miniconda3 +-CUDAHOME = $(HOME)/nvidia/cuda-12.1 ++#CUDAHOME = $(HOME)/nvidia/cuda-12.1 + CUDAINC = $(CUDAHOME)/include + CUDALIB = $(CUDAHOME)/lib64 + PRJINC = $(PRJHOME)/Include +@@ -139,18 +139,21 @@ + $(CUCPPS) + OBJS = $(patsubst %.cpp, %.o, $(SRCS)) + #------------------------------------- +-CC = g++ -std=c++11 +-CFLAG = -c -g -pthread -m64 ++#CC = g++ -std=c++11 ++CFLAG = -c -g -pthread -m64 $(CFLAGS) + NVCC = $(CUDAHOME)/bin/nvcc -std=c++11 +-CUFLAG = -Xptxas -dlcm=ca -O2 \ +- -gencode arch=compute_86,code=sm_86 \ +- -gencode arch=compute_80,code=sm_80 \ +- -gencode arch=compute_75,code=sm_75 \ +- -gencode arch=compute_70,code=sm_70 \ +- -gencode arch=compute_52,code=sm_52 \ +- -gencode arch=compute_53,code=sm_53 \ +- -gencode arch=compute_60,code=sm_60 \ +- -gencode arch=compute_61,code=sm_61 ++SPACE= ' ' ++SEMI= ; ++GENCODES = $(foreach x,$(subst $(SEMI),$(SPACE),$(CUDACC)),-gencode arch=compute_$x,code=sm_$x) ++CUFLAG = -Xptxas -dlcm=ca -O2 $(GENCODES) ++# -gencode arch=compute_86,code=sm_86 \ ++# -gencode arch=compute_80,code=sm_80 \ ++# -gencode arch=compute_75,code=sm_75 \ ++# -gencode arch=compute_70,code=sm_70 \ ++# -gencode arch=compute_52,code=sm_52 \ ++# -gencode arch=compute_53,code=sm_53 \ ++# -gencode arch=compute_60,code=sm_60 \ ++# -gencode arch=compute_61,code=sm_61 + #------------------------------------------ + cuda: $(CUCPPS) + +@@ -165,6 +168,7 @@ + -lcufft -lcudart -lcuda -lnvToolsExt -ltiff -lc -lm -lpthread \ + -o MotionCor3 + @echo MotionCor3 has been generated. ++ @echo used cuda gencodes: $(GENCODES) + + %.cpp: %.cu + @echo "-----------------------------------------------" From 88e7d49b7fb69da5e620ceb373614d04413585f7 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 23 Jan 2024 10:43:13 +0000 Subject: [PATCH 0394/1193] adding easyconfigs: poetry-1.7.1-GCCcore-12.3.0.eb --- .../p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb | 173 ++++++++++++++++++ 1 file changed, 173 insertions(+) create mode 100755 easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb new file mode 100755 index 000000000000..acc1b0fcb8cd --- /dev/null +++ b/easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,173 @@ +easyblock = 'PythonBundle' + +name = 'poetry' +version = '1.7.1' + +homepage = 'https://python-poetry.org' +description = """Python packaging and dependency management made easy. Poetry helps you declare, manage and install + dependencies of Python projects, ensuring you have the right stack everywhere.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('scikit-build', '0.17.6'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('hatchling', '1.18.0'), + ('cryptography', '41.0.1'), + ('virtualenv', '20.23.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('idna', '3.6', { + 'checksums': ['9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca'], + }), + ('certifi', '2023.11.17', { + 'checksums': ['9b469f3a900bf28dc19b8cfbf8019bf47f7fdd1a65a1d4ffb98fc14166beb4d1'], + }), + ('urllib3', '2.1.0', { + 'checksums': ['df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54'], + }), + 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['ee7d41123f3c9911050ea2c2dac107568dc43b2d3b0c7557a33212c398ead30f'], + }), + ('jsonschema_specifications', '2023.12.1', { + 'checksums': ['48a76787b3e70f5ed53f1160d2b81f586e4ca6d1548c5de7085d1682674764cc'], + }), + ('referencing', '0.32.1', { + 'checksums': ['3c57da0513e9563eb7e203ebe9bb3a1b509b042016433bd1e45a2853466c3dd3'], + }), + ('rpds_py', '0.17.1', { + 'modulename': 'rpds', + 'checksums': ['0210b2668f24c078307260bf88bdac9d6f1093635df5123789bfee4d8d7fc8e7'], + }), + ('jsonschema', '4.21.0', { + 'checksums': ['3ba18e27f7491ea4a1b22edce00fb820eec968d397feb3f9cb61d5894bb38167'], + }), + ('platformdirs', '3.11.0', { + 'checksums': ['cf8ee52a3afdb965072dcc652433e0c7e3e40cf5ea1477cd4b3b1d2eb75495b3'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('tomlkit', '0.12.3', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['b0a645a9156dc7cb5d3a1f0d4bab66db287fcb8e0430bdd4664a095ea16414ba'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('msgpack', '1.0.7', { + 'checksums': ['572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87'], + }), + ('CacheControl', '0.13.1', { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['f012366b79d2243a6118309ce73151bf52a38d4a5dac8ea57f09bd29087e506b'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('fastjsonschema', '2.19.1', { + 'checksums': ['e3126a94bdc4623d3de4485f8d468a12f02a67921315ddc87836d6e456dc789d'], + }), + ('poetry_core', '1.8.1', { + 'modulename': 'poetry.core', + 'checksums': ['67a76c671da2a70e55047cddda83566035b701f7e463b32a2abfeac6e2a16376'], + }), + ('poetry_plugin_export', '1.6.0', { + 'checksums': ['091939434984267a91abf2f916a26b00cff4eee8da63ec2a24ba4b17cf969a59'], + }), + (name, version, { + 'checksums': ['b348a70e7d67ad9c0bd3d0ea255bc6df84c24cf4b16f8d104adb30b425d6ff32'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +moduleclass = 'tools' From 4c26448e220789b49841054f44b24b5f06c1db84 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 23 Jan 2024 12:17:52 +0100 Subject: [PATCH 0395/1193] adding easyconfigs: PETSc-3.20.3-foss-2023a.eb, SuperLU_DIST-8.1.2-foss-2023a.eb, SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb, ParMETIS-4.0.3-gompi-2023a.eb --- .../p/PETSc/PETSc-3.20.3-foss-2023a.eb | 45 +++++++++++++++++++ .../p/ParMETIS/ParMETIS-4.0.3-gompi-2023a.eb | 29 ++++++++++++ ...iteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb | 31 +++++++++++++ .../SuperLU_DIST-8.1.2-foss-2023a.eb | 40 +++++++++++++++++ 4 files changed, 145 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb create mode 100644 easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb new file mode 100644 index 000000000000..de6c5d13631c --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb @@ -0,0 +1,45 @@ +## +# Author: Robert Mijakovic +# Author: Jasper Grimm (UoY) +## +name = 'PETSc' +version = '3.20.3' + +homepage = 'https://www.mcs.anl.gov/petsc' +description = """PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the + scalable (parallel) solution of scientific applications modeled by partial differential equations.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://web.cels.anl.gov/projects/petsc/download/release-snapshots', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['75a94fb44df0512f51ad093fa784e56b61f51b7ead5956fbe49185c203f8c245'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.3'), + ('MUMPS', '5.6.1', '-metis'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('Hypre', '2.29.0'), + ('ParMETIS', '4.0.3'), + ('SuperLU_DIST', '8.1.2'), + ('mpi4py', '3.1.4'), +] + +configopts = '--LIBS="$LIBS -lrt" --with-mpi4py=0 ' + +shared_libs = 1 + +# only required when building PETSc in a SLURM job environment +# configopts += '--with-batch=1 --known-mpi-shared-libraries=1 --known-64-bit-blas-indices=0 ' +# prebuildopts = "srun ./conftest-arch-linux2-c-opt && ./reconfigure-arch-linux2-c-opt.py && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023a.eb new file mode 100644 index 000000000000..f7b833028734 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2023a.eb @@ -0,0 +1,29 @@ +## +# Author: Robert Mijakovic +## +name = 'ParMETIS' +version = '4.0.3' + +homepage = 'http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview' +description = """ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning + unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the + functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and + large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way + graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +source_urls = [ + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis', + 'http://glaros.dtc.umn.edu/gkhome/fetch/sw/parmetis/OLD', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f2d9a231b7cf97f1fee6e8c9663113ebf6c240d407d3c118c55b3633d6be6e5f'] + +builddependencies = [('CMake', '3.26.3')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb new file mode 100644 index 000000000000..5d4c41b2f4d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb @@ -0,0 +1,31 @@ +name = 'SuiteSparse' +version = '5.13.0' +local_metis_ver = '5.1.0' +versionsuffix = '-METIS-%s' % local_metis_ver + +homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' +description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['59c6ca2959623f0c69226cf9afb9a018d12a37fab3a8869db5f6d7f83b6b147d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('METIS', local_metis_ver), + ('MPFR', '4.2.0'), +] + +# make sure that bin/demo can find libsuitesparseconfig.so.5 during build +prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " +# remove broken symlink +prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb new file mode 100644 index 000000000000..d71b00777fc5 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "EB_SuperLU" + +name = 'SuperLU_DIST' +version = '8.1.2' + +homepage = 'https://crd-legacy.lbl.gov/~xiaoye/SuperLU/' +description = """SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems + of linear equations on high performance machines.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['7b16c442bb01ea8b298c0aab9a2584aa4615d09786aac968cb2f3118c058206b'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('ParMETIS', '4.0.3'), +] + +configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' +configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' + +# Some tests run longer than default 1500s timeout on fairly big machine (36 cores). +# Include only first four tests, which should be fairly small to run +pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' + +postinstallcmds = [ + "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a +] + +sanity_check_paths = { + 'files': ['lib64/libsuperlu_dist.a'], + 'dirs': ['include'] +} + +moduleclass = 'numlib' From b32132e05bd47bf5cf3134aa8ddb24d209fd856a Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 23 Jan 2024 11:28:51 +0000 Subject: [PATCH 0396/1193] fix missing spaces in Graphviz configure options --- .../Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb | 26 +++++++++++-------- .../Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb | 26 +++++++++++-------- .../Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb | 26 +++++++++++-------- 3 files changed, 45 insertions(+), 33 deletions(-) diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb index a2f44ff0ff81..10a270e5598d 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-5.0.0-GCCcore-11.3.0.eb @@ -51,17 +51,21 @@ dependencies = [ preconfigopts = './autogen.sh NOCONFIG && ' -configopts = '--enable-python%s=yes ' % local_pyver_major -configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' -configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' -# Use ltdl from libtool in EB -configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' -configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' -# Override the hardcoded paths to Java libraries -configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' -configopts += '--with-javalibdir=$JAVA_HOME/lib' -configopts += '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib' -configopts += '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib' +_copts = [ + '--enable-python%s=yes' % local_pyver_major, + '--enable-guile=no --enable-lua=no --enable-ocaml=no', + '--enable-r=no --enable-ruby=no --enable-php=no', + # Use ltdl from libtool in EB + '--enable-ltdl --without-included-ltdl --disable-ltdl-install', + '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib', + # Override the hardcoded paths to Java libraries + '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux', + '--with-javalibdir=$JAVA_HOME/lib', + '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib', + '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib', +] + +configopts = ' '.join(_copts) prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb index aa04b6e837cb..c21c34aba1d5 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.2.0.eb @@ -50,17 +50,21 @@ dependencies = [ preconfigopts = './autogen.sh NOCONFIG && ' -configopts = '--enable-python%s=yes ' % local_pyver_major -configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' -configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' -# Use ltdl from libtool in EB -configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' -configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' -# Override the hardcoded paths to Java libraries -configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' -configopts += '--with-javalibdir=$JAVA_HOME/lib' -configopts += '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib' -configopts += '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib' +_copts = [ + '--enable-python%s=yes' % local_pyver_major, + '--enable-guile=no --enable-lua=no --enable-ocaml=no', + '--enable-r=no --enable-ruby=no --enable-php=no', + # Use ltdl from libtool in EB + '--enable-ltdl --without-included-ltdl --disable-ltdl-install', + '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib', + # Override the hardcoded paths to Java libraries + '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux', + '--with-javalibdir=$JAVA_HOME/lib', + '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib', + '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib', +] + +configopts = ' '.join(_copts) prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' diff --git a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb index 9f0b7753a7f5..f6cb40952659 100644 --- a/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/Graphviz/Graphviz-8.1.0-GCCcore-12.3.0.eb @@ -50,17 +50,21 @@ dependencies = [ preconfigopts = './autogen.sh NOCONFIG && ' -configopts = '--enable-python%s=yes ' % local_pyver_major -configopts += '--enable-guile=no --enable-lua=no --enable-ocaml=no ' -configopts += '--enable-r=no --enable-ruby=no --enable-php=no ' -# Use ltdl from libtool in EB -configopts += '--enable-ltdl --without-included-ltdl --disable-ltdl-install ' -configopts += '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib ' -# Override the hardcoded paths to Java libraries -configopts += '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux ' -configopts += '--with-javalibdir=$JAVA_HOME/lib' -configopts += '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib' -configopts += '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib' +_copts = [ + '--enable-python%s=yes' % local_pyver_major, + '--enable-guile=no --enable-lua=no --enable-ocaml=no', + '--enable-r=no --enable-ruby=no --enable-php=no', + # Use ltdl from libtool in EB + '--enable-ltdl --without-included-ltdl --disable-ltdl-install', + '--with-ltdl-include=$EBROOTLIBTOOL/include --with-ltdl-lib=$EBROOTLIBTOOL/lib', + # Override the hardcoded paths to Java libraries + '--with-javaincludedir=$JAVA_HOME/include --with-javaincludedir=$JAVA_HOME/include/linux', + '--with-javalibdir=$JAVA_HOME/lib', + '--with-expatincludedir=$EBROOTEXPAT/include --with-expatlibdir=$EBROOTEXPAT/lib', + '--with-zincludedir=$EBROOTZLIB/include --with-zlibdir=$EBROOTZLIB/lib', +] + +configopts = ' '.join(_copts) prebuildopts = 'qmake -o cmd/gvedit/qMakefile cmd/gvedit/gvedit.pro && ' From c95fda7f2cb922df67b7af98317e194f687cc50d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 23 Jan 2024 13:08:50 +0100 Subject: [PATCH 0397/1193] add patch PyTorch-2.1.0_skip-test-linalg-svd-complex.patch --- ...h-2.1.0_skip-test-linalg-svd-complex.patch | 19 +++++++++++++++++++ .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 3 +++ 2 files changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_skip-test-linalg-svd-complex.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_skip-test-linalg-svd-complex.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_skip-test-linalg-svd-complex.patch new file mode 100644 index 000000000000..92ea36337ebb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_skip-test-linalg-svd-complex.patch @@ -0,0 +1,19 @@ +Skip test_python_ref_meta__refs_linalg_svd_cpu_complex +Result varies depending on underlying device +see https://github.com/pytorch/pytorch/issues/105068 +author: Alex Domingo (Vrije Universiteit Brussel) +--- test/test_ops.py.orig 2024-01-16 15:37:02.596411122 +0100 ++++ test/test_ops.py 2024-01-16 15:39:02.824489395 +0100 +@@ -311,6 +311,12 @@ + return out + return x + ++ # Skip test_python_ref_meta__refs_linalg_svd_cpu_complex ++ # Result varies depending on underlying device ++ # see https://github.com/pytorch/pytorch/issues/105068 ++ if op.name == '_refs.linalg.svd' and dtype in (torch.complex64, torch.complex128): ++ self.skipTest("Unreliable on certain devices, see issue #105068") ++ + # TODO: iterate over requires_grad true/false + for sample in op.reference_inputs(device, dtype, requires_grad=False): + result = op(sample.input, *sample.args, **sample.kwargs) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 102b2735fec0..0c46fa6a22e1 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -43,6 +43,7 @@ patches = [ 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', 'PyTorch-2.1.0_skip-test_wrap_bad.patch', + 'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch', ] checksums = [ {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, @@ -100,6 +101,8 @@ checksums = [ {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, + {'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch': + '5ba7e0b4203ea8c27b55b5231de024004697aca7bbae30aa248524babb451dc7'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From df898b67c668fda7bc1ae3b3c2028226f41eecea Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 23 Jan 2024 13:13:22 +0100 Subject: [PATCH 0398/1193] add patch PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch --- ...able-cudnn-tf32-for-too-strict-tests.patch | 56 +++++++++++++++++++ .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 3 + 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch new file mode 100644 index 000000000000..f991b44530b4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch @@ -0,0 +1,56 @@ +Disallow TF32 on tests with thresholds too strict for this data type. Nvidia +GPUs with TF32 support default to this data type instead of regular FP32 to +improve performance at the expense of precision. +author: Alex Domingo (Vrije Universiteit Brussel) +--- test/test_nn.py.orig 2024-01-15 14:07:35.421908795 +0100 ++++ test/test_nn.py 2024-01-15 14:54:00.867537101 +0100 +@@ -3762,6 +3761,7 @@ + self.assertEqual(weight_data, all_vars[4].data) + + @unittest.skipIf(not TEST_CUDNN, 'CUDNN not available') ++ @torch.backends.cudnn.flags(enabled=True, allow_tf32=False) + def test_cudnn_weight_tying(self): + rnns = [ + nn.LSTM(10, 20, batch_first=True, bidirectional=True), +@@ -4461,6 +4461,7 @@ + self._test_RNN_cpu_vs_cudnn(1) + + @unittest.skipIf(not TEST_CUDNN, "needs cudnn") ++ @torch.backends.cudnn.flags(enabled=True, allow_tf32=False) + def test_RNN_cudnn_weight_norm(self): + input_size = 10 + hidden_size = 6 +@@ -4492,6 +4493,7 @@ + check_weight_norm(nn.LSTM(input_size, hidden_size, num_layers, proj_size=3), 'weight_hr_l0') + + @unittest.skipIf(not TEST_CUDA, 'CUDA not available') ++ @torch.backends.cudnn.flags(enabled=True, allow_tf32=False) + def test_partial_flat_weights(self): + input_size = 10 + hidden_size = 6 +--- test/jit/test_freezing.py.orig 2024-01-15 14:38:11.054125484 +0100 ++++ test/jit/test_freezing.py 2024-01-15 14:49:41.689011617 +0100 +@@ -2733,7 +2733,11 @@ + else: + FileCheck().check("aten::cudnn_convolution_relu").run(frozen_mod.graph) + +- self.assertEqual(mod_eager(inp), frozen_mod(inp)) ++ if not TEST_WITH_ROCM: ++ with torch.backends.cudnn.flags(enabled=True, allow_tf32=False): ++ self.assertEqual(mod_eager(inp), frozen_mod(inp)) ++ else: ++ self.assertEqual(mod_eager(inp), frozen_mod(inp)) + + @unittest.skipIf(not (TEST_CUDNN or TEST_WITH_ROCM), "requires CUDNN") + def test_freeze_conv_relu_fusion_not_forward(self): +--- ../PyTorch/2.1.2/foss-2023a-CUDA-12.1.1/pytorch-v2.1.2/test/nn/test_convolution.py 2023-12-15 03:03:27.000000000 +0100 ++++ test/nn/test_convolution.py 2024-01-15 15:03:15.606208376 +0100 +@@ -518,7 +518,7 @@ + # Covering special case when group > 1, input-channel / group < 16 and output-channel is multiple of 16 + # See also https://github.com/pytorch/pytorch/pull/18463#issuecomment-476563686 + # and https://github.com/pytorch/pytorch/pull/18463#issuecomment-477001024 +- @torch.backends.cudnn.flags(enabled=True, benchmark=False) ++ @torch.backends.cudnn.flags(enabled=True, benchmark=False, allow_tf32=False) + def test_Conv2d_groups_nobias_v2(self): + torch.manual_seed(123) + dev_dtypes = [("cpu", torch.float)] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 0c46fa6a22e1..6ffe56d33ed2 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -44,6 +44,7 @@ patches = [ 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', 'PyTorch-2.1.0_skip-test_wrap_bad.patch', 'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch', + 'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch', ] checksums = [ {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, @@ -103,6 +104,8 @@ checksums = [ {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, {'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch': '5ba7e0b4203ea8c27b55b5231de024004697aca7bbae30aa248524babb451dc7'}, + {'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch': + '7abccc94f0ae6c317d5d08d4db4e3724eedde8d1d00707e78cf57d8cbf858be5'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From ad64b4abb0c1a314c06dc6151231d1e3c76c1c54 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 23 Jan 2024 15:43:02 +0100 Subject: [PATCH 0399/1193] adding easyconfigs: medaka-1.9.1-foss-2022b.eb --- ...ntervaltree-python-3.1.0-GCCcore-12.2.0.eb | 34 +++++++++ .../m/medaka/medaka-1.9.1-foss-2022b.eb | 71 +++++++++++++++++++ .../r/Racon/Racon-1.5.0-GCCcore-12.2.0.eb | 28 ++++++++ .../w/WhatsHap/WhatsHap-2.1-foss-2022b.eb | 54 ++++++++++++++ 4 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022b.eb create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5888f2f29d0d --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'intervaltree-python' +_modname = 'intervaltree' +version = '3.1.0' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = """A mutable, self-balancing interval tree. Queries may be by + point, by range overlap, or by range containment. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname] +sources = ['%s-%s.tar.gz' % (_modname, version)] +checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': _modname} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022b.eb b/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022b.eb new file mode 100644 index 000000000000..c536e4bfc247 --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.9.1-foss-2022b.eb @@ -0,0 +1,71 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.9.1' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.10.8'), # includes cffi + # tensorflow~=2.10.0 required by medaka 1.11.3, see requirements.txt + ('TensorFlow', '2.13.0'), + ('Pysam', '0.21.0'), + ('SAMtools', '1.17'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.17'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.0.9'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.1'), + ('WhatsHap', '2.1'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.17'), +] + +use_pip = True + +_sedcmds = [ + "sed -i -e 's/tensorflow.*/tensorflow/g' -e 's/cffi.*/cffi/' requirements.txt", + "sed -i -e 's/cffi==1.15.0/cffi/' pyproject.toml", +] + +exts_list = [ + ('mappy', '2.26', { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + (name, version, { + 'preinstallopts': " && ".join(_sedcmds) + " && ", + 'checksums': ['1018c07267d24cb4607ae823ced01a1789939b5f8143d1c240ce243dc1160ef5'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..333d4b2bfac8 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.1-foss-2022b.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.1-foss-2022b.eb new file mode 100644 index 000000000000..6aff37fd8512 --- /dev/null +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.1-foss-2022b.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'PythonBundle' + +name = 'WhatsHap' +version = '2.1' + +homepage = 'https://whatshap.readthedocs.io' +description = """WhatsHap is a software for phasing genomic variants using DNA +sequencing reads, also called read-based phasing or haplotype assembly. It is +especially suitable for long reads, but works also well with short reads.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('Python', '3.10.8'), + ('Pysam', '0.21.0'), + ('networkx', '3.0'), + ('SciPy-bundle', '2023.02'), + ('Biopython', '1.81'), + ('Yasm', '1.3.0'), + ('pyfaidx', '0.7.2.1'), + ('python-isal', '1.1.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('xopen', '1.7.0', { + 'preinstallopts': """sed -i -e 's/^dynamic = \\["version"\\]/version = "%(version)s"/' """ + + "%(start_dir)s/pyproject.toml && ", + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('pulp', '2.8.0', { + 'source_tmpl': 'PuLP-%(version)s.tar.gz', + 'checksums': ['4903bf96110bbab8ed2c68533f90565ebb76aa367d9e4df38e51bf727927c125'], + }), + (name, version, { + 'preinstallopts': """sed -i -e 's/^dynamic = \\["version",/version = "%(version)s"\\ndynamic = \\[/' """ + + "%(start_dir)s/pyproject.toml && ", + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['9b61812eda1dd5251ba8d02db16d7ddda152ccc813cb3db6a1ec796f1865fe8d'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From 15ec9edab49d2d0a58cb2e69d73e426047fcbacb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 23 Jan 2024 15:52:34 +0100 Subject: [PATCH 0400/1193] add NGSpeciesID-0.3.0 --- .../NGSpeciesID-0.3.0-foss-2022b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb new file mode 100644 index 000000000000..2ef782e31992 --- /dev/null +++ b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'NGSpeciesID' +version = '0.3.0' + +homepage = 'https://github.com/ksahlin/NGSpeciesID' +description = "NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads." + +toolchain = {'name': 'foss', 'version': '2022b'} + +sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.10.8'), + ('python-parasail', '1.3.4'), + ('edlib', '1.3.9'), + ('spoa', '4.0.7'), + ('Racon', '1.5.0'), + ('minimap2', '2.26'), + ('medaka', '1.9.1'), +] + +download_dep_fail = True +use_pip = True + +# strip away too strict version requirement for parasail +preinstallopts = "sed -i 's/parasail==[0-9.]*/parasail/g' setup.py && " + +# no proper namespace for NGSpeciesID +options = {'modulename': 'modules.consensus'} + +sanity_check_paths = { + 'files': ['bin/NGSpeciesID'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NGSpeciesID --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 37453bcb805c38efcbe874bdeeb07e7daf5f2162 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 23 Jan 2024 16:19:10 +0100 Subject: [PATCH 0401/1193] Drop --with-zlib path due to incompatiblilty with EESSI --- .../easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb | 2 +- .../easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb | 2 +- easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb | 2 +- easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb index d1d00c698f8e..2f34240eb524 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb @@ -35,7 +35,7 @@ dependencies = [ ('zlib', '1.2.12') ] -configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 --with-zlib=$EBROOTZLIB" +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb index 0f3e627b995a..0ce992612863 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb @@ -33,7 +33,7 @@ dependencies = [ ('zlib', '1.2.13') ] -configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 --with-zlib=$EBROOTZLIB" +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb index 778f39d14f67..af8619886260 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb @@ -27,7 +27,7 @@ dependencies = [ ('zlib', '1.2.12') ] -configopts = "--disable-root --enable-pyext --disable-static --with-zlib=$EBROOTZLIB" +configopts = "--disable-root --enable-pyext --disable-static" buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" installopts = buildopts diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb index 8a977f5b4c1d..af9f9f997906 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ ('Python', '3.11.3'), ('zlib', '1.2.13') ] -configopts = "--disable-root --enable-pyext --disable-static --with-zlib=$EBROOTZLIB" +configopts = "--disable-root --enable-pyext --disable-static" buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" installopts = buildopts From bd1a140058e4f5bbfe86d6593310852181f22476 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 23 Jan 2024 16:54:47 +0100 Subject: [PATCH 0402/1193] add missing checksum for NGSpeciesID-0.3.0 --- .../easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb index 2ef782e31992..9fe367ad885f 100644 --- a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb +++ b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2022b.eb @@ -9,6 +9,7 @@ description = "NGSpeciesID is a tool for clustering and consensus forming of tar toolchain = {'name': 'foss', 'version': '2022b'} sources = [SOURCE_TAR_GZ] +checksums = ['71663ce280220d4e692cc6c3aea44f91e40b3143ed09a9462bdf2feb1d94aa9f'] dependencies = [ ('Python', '3.10.8'), From 1f3c72ef411a17693a18c85c398de7e7829c3818 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 23 Jan 2024 17:11:48 +0100 Subject: [PATCH 0403/1193] adding easyconfigs: sktime-0.25.0-gfbf-2023a.eb --- .../s/sktime/sktime-0.25.0-gfbf-2023a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb new file mode 100644 index 000000000000..b5e07a105c36 --- /dev/null +++ b/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'sktime' +version = '0.25.0' +homepage = 'https://www.sktime.net/en/stable/' +description = """sktime is a library for time series analysis in Python. +It provides a unified interface for multiple time series learning tasks. +Currently, this includes time series classification, regression, clustering, +annotation, and forecasting. It comes with time series algorithms and +scikit-learn compatible tools to build, tune and validate time series models.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1') +] + + +exts_list = [ + ('scikit-base', '0.6.2', { + 'modulename': 'skbase', + 'checksums': ['ac7c1dd9b1006e1e466d8269074f7fb02b7f5143c615f7fdf6a1e0c7565431fe'], + }), + (name, version, { + 'checksums': ['b687d44608e5d2fd6b3c631b2608f4cf7bc581e22c1131ac78d59cea7687b589'], + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From d9bc2c79568b94a371c9d2f57aeda42889843bec Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 23 Jan 2024 17:24:32 +0100 Subject: [PATCH 0404/1193] adding easyconfigs: fugue-0.8.7-foss-2022a.eb --- .../f/fugue/fugue-0.8.7-foss-2022a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb new file mode 100644 index 000000000000..894765fac9ed --- /dev/null +++ b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'fugue' +version = '0.8.7' +homepage = 'https://github.com/fugue-project/fugue' +description = """Fugue is a unified interface for distributed computing that lets users execute Python, Pandas, and SQL code on Spark, Dask, and Ray with minimal rewrites. + +Fugue is most commonly used for: + +Parallelizing or scaling existing Python and Pandas code by bringing it to Spark, Dask, or Ray with minimal rewrites. +Using FugueSQL to define end-to-end workflows on top of Pandas, Spark, and Dask DataFrames. FugueSQL is an enhanced SQL interface that can invoke Python code. +""" +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Cython', '0.29.33'), + ('Arrow', '8.0.0'), +] + + +exts_list = [ +# ('scikit-base', '0.6.2', { +# 'modulename': 'skbase', +# 'checksums': ['ac7c1dd9b1006e1e466d8269074f7fb02b7f5143c615f7fdf6a1e0c7565431fe'], +# }), + ('adagio', '0.2.4'), + ('fugue-sql-antlr', '0.2.0'), + ('antlr4-python3-runtime', '4.11.1', { + 'modulename': 'antlr4', + }), + ('fs', '2.4.16'), + ('fsspec', '2023.12.2'), + ('qpd', '0.4.4'), + ('sqlglot', '20.9.0'), + ('triad', '0.9.4'), + (name, version, { + }), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From 45999fca8b27d8afdf67d2f3576289fd2bdf51bc Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 23 Jan 2024 17:27:28 +0100 Subject: [PATCH 0405/1193] remove useless option --- easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb index b5e07a105c36..86d063a85c30 100644 --- a/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb @@ -29,7 +29,6 @@ exts_list = [ }), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 7c09b52fe7053fe73b950e846d9aa97651d5f16e Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 23 Jan 2024 17:30:42 +0100 Subject: [PATCH 0406/1193] remove useless option and change file name --- easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb index 894765fac9ed..de329a4abfe8 100644 --- a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb +++ b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb @@ -42,7 +42,6 @@ exts_list = [ }), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From db5fbecfa99722ec0dcacb812cc3ddd23480665b Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 23 Jan 2024 16:55:18 +0000 Subject: [PATCH 0407/1193] strip iconv from libarchive pkgconfig file --- .../easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb index 3126faae1c50..1ac7a59be8ab 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb @@ -25,6 +25,8 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] +postinstallcmds = ["sed -i 's/iconv//g' %(installdir)s/lib/pkgconfig/libarchive.pc"] + sanity_check_paths = { 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], 'dirs': ['bin', 'share/man/man3'], From cb52621234ad6265c4014b2102f05f272e6d09d8 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 23 Jan 2024 16:56:41 +0000 Subject: [PATCH 0408/1193] adding easyconfigs: enchant-2-2.6.5-GCCcore-12.3.0.eb, hunspell-1.7.2-GCCcore-12.3.0.eb, ITSTool-2.0.7-GCCcore-12.3.0.eb, libxml2-python-2.11.4-GCCcore-12.3.0.eb, Vala-0.56.14-GCCcore-12.3.0.eb --- .../enchant-2-2.6.5-GCCcore-12.3.0.eb | 49 ++++++++++++++++++ .../hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb | 42 ++++++++++++++++ .../i/ITSTool/ITSTool-2.0.7-GCCcore-12.3.0.eb | 28 +++++++++++ .../libxml2-python-2.11.4-GCCcore-12.3.0.eb | 50 +++++++++++++++++++ .../v/Vala/Vala-0.56.14-GCCcore-12.3.0.eb | 40 +++++++++++++++ 5 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/Vala/Vala-0.56.14-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..af01c6213280 --- /dev/null +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.6.5-GCCcore-12.3.0.eb @@ -0,0 +1,49 @@ +# Updated from enchant-1.6.1-intel-2017a.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'enchant-2' +version = '2.6.5' + +homepage = 'https://github.com/AbiWord/enchant' +description = """Enchant aims to provide a simple but comprehensive abstraction for dealing +with different spell checking libraries in a consistent way. A client, such +as a text editor or word processor, need not know anything about a specific +spell-checker, and since all back-ends are plugins, new spell-checkers can +be added without needing any change to the program using Enchant.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s'] +sources = ['enchant-%(version)s.tar.gz'] +checksums = ['9e8fd28cb65a7b6da3545878a5c2f52a15f03c04933a5ff48db89fe86845728e'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('M4', '1.4.19'), + ('pkgconf', '1.9.5'), +] + +preconfigopts = "autoreconf -vfi && " + +dependencies = [ + ('hunspell', '1.7.2'), + ('GLib', '2.77.1'), +] + +buildopts = "LIBTOOL='libtool --tag=CC'" + +sanity_check_commands = [ + 'enchant-2 -v', + 'enchant-lsmod-2 -v', +] + +sanity_check_paths = { + 'files': ['bin/enchant-2', 'bin/enchant-lsmod-2', + 'lib/libenchant-2.a', 'lib/libenchant-2.%s' % SHLIB_EXT], + 'dirs': ['include/enchant-2', 'lib/enchant-2'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b34936b9ab16 --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +# Contribution from Imperial College London/UK +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.7.2' + +homepage = 'https://hunspell.github.io/' +description = """Hunspell is a spell checker and morphological analyzer +library and program designed for languageswith rich morphology and +complex word compounding or character encoding.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['69fa312d3586c988789266eaf7ffc9861d9f6396c31fc930a014d551b59bbd6e'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('gettext', '0.21.1'), +] + +preconfigopts = "autoreconf -vfi && " + +sanity_check_commands = [ + 'hunspell -h', +] + +sanity_check_paths = { + 'files': ['bin/hunspell', 'lib/libhunspell-%(version_major_minor)s.a', + 'lib/libhunspell-%%(version_major_minor)s.%s' % SHLIB_EXT, 'lib/pkgconfig/hunspell.pc'], + 'dirs': ['include/hunspell'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..6e664d898081 --- /dev/null +++ b/easybuild/easyconfigs/i/ITSTool/ITSTool-2.0.7-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'ITSTool' +version = '2.0.7' + +homepage = 'http://itstool.org/' +description = "ITS Tool allows you to translate your XML documents with PO files" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://files.itstool.org/itstool/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['6b9a7cd29a12bb95598f5750e8763cee78836a1a207f85b74d8b3275b27e87ca'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('libxml2-python', '2.11.4'), +] + +sanity_check_paths = { + 'files': ['bin/itstool'], + 'dirs': ['share/itstool/its', 'share/man'], +} +sanity_check_commands = ["itstool --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4f84efd5bc46 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonPackage' + +name = 'libxml2-python' +version = '2.11.4' + +homepage = 'http://xmlsoft.org/' +description = """ + Libxml2 is the XML C parser and toolchain developed for the Gnome project + (but usable outside of the Gnome platform). This is the Python binding.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = ['libxml2-%(version)s.tar.xz'] +patches = ['%(name)s-2.11.4_fix-hardcoded-paths.patch'] +checksums = [ + {'libxml2-2.11.4.tar.xz': '737e1d7f8ab3f139729ca13a2494fd17bf30ddb4b7a427cf336252cab57f57f7'}, + {'libxml2-2.11.4_fix-hardcoded-paths.patch': 'b8069b149ab7e0e3a96ca1462c07d0bf1d7c7434eb434eb1b0ec824074b70f6a'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('XZ', '5.4.2'), + ('Python', '3.11.3'), + ('libxml2', version), + ('libiconv', '1.17'), + ('ICU', '73.2'), +] + +start_dir = 'python' + +# need to run a configure first, since there is only a setup.py.in +preinstallopts = 'cd .. && ./configure --prefix=%(installdir)s && cd python && ' + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'libxml2'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/v/Vala/Vala-0.56.14-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/Vala/Vala-0.56.14-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..26fa6d03ef8a --- /dev/null +++ b/easybuild/easyconfigs/v/Vala/Vala-0.56.14-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Vala' +version = '0.56.14' + +homepage = 'https://wiki.gnome.org/Projects/Vala' +description = """Vala is a programming language using modern high level abstractions without imposing additional runtime +requirements and without using a different ABI compared to applications and libraries written in C.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://download.gnome.org/sources/vala/%(version_major_minor)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['9382c268ca9bdc02aaedc8152a9818bf3935273041f629c56de410e360a3f557'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('Graphviz', '8.1.0'), +] + +dependencies = [ + ('GLib', '2.77.1'), +] + +sanity_check_paths = { + 'files': ['bin/vala', 'bin/valac', 'bin/valadoc', 'lib/libvala-%%(version_major_minor)s.%s' % SHLIB_EXT, + 'lib/libvaladoc-%%(version_major_minor)s.%s' % SHLIB_EXT], + 'dirs': ['include/vala-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "vala --help", + "valac --help", + "valadoc --help", +] + +moduleclass = 'lang' From 195054017a2514402f6423aef41751c945cd4904 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 23 Jan 2024 16:57:38 +0000 Subject: [PATCH 0409/1193] add missing patch --- ...l2-python-2.11.4_fix-hardcoded-paths.patch | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4_fix-hardcoded-paths.patch diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4_fix-hardcoded-paths.patch b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4_fix-hardcoded-paths.patch new file mode 100644 index 000000000000..2c8ab7442c50 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4_fix-hardcoded-paths.patch @@ -0,0 +1,20 @@ +# Add easybuild locations of dependencies +# December 13th 2018 by B. Hajgato (Free University Brussels - VUB) +# updated for 2.11.4 by Jasper Grimm (University of York) +diff -Nru libxml2-2.11.4.orig/python/setup.py.in libxml2-2.11.4/python/setup.py.in +--- libxml2-2.11.4.orig/python/setup.py.in 2024-01-23 14:42:40.321205584 +0000 ++++ libxml2-2.11.4/python/setup.py.in 2024-01-23 14:54:31.558212220 +0000 +@@ -71,11 +71,8 @@ + # - libxml2/libxml/tree.h + # - libxslt/xsltconfig.h + includes_dir = [ +-"/usr/include", +-"/usr/local/include", +-"/opt/include", +-os.path.join(ROOT,'include'), +-HOME ++ os.path.join(os.getenv("EBROOTLIBXML2"),"include"), ++ os.path.join(os.getenv("EBROOTLIBICONV"),"include"), + ]; + + xml_includes="" From 179b7d2cee1892e3f3f9805befe69b89a413bba2 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 23 Jan 2024 16:58:17 +0000 Subject: [PATCH 0410/1193] adding easyconfigs: evince-45.0-GCC-12.3.0.eb, libgxps-0.3.2-GCCcore-12.3.0.eb, libspectre-0.2.12-GCCcore-12.3.0.eb, gspell-1.12.2-GCCcore-12.3.0.eb, GI-DocGen-2023.3-GCCcore-12.3.0.eb --- .../e/evince/evince-45.0-GCC-12.3.0.eb | 62 +++++++++++++++++++ .../GI-DocGen-2023.3-GCCcore-12.3.0.eb | 49 +++++++++++++++ .../g/gspell/gspell-1.12.2-GCCcore-12.3.0.eb | 36 +++++++++++ .../l/libgxps/libgxps-0.3.2-GCCcore-12.3.0.eb | 43 +++++++++++++ .../libspectre-0.2.12-GCCcore-12.3.0.eb | 33 ++++++++++ 5 files changed, 223 insertions(+) create mode 100644 easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/gspell/gspell-1.12.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgxps/libgxps-0.3.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/l/libspectre/libspectre-0.2.12-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..1a866acab696 --- /dev/null +++ b/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb @@ -0,0 +1,62 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MesonNinja' + +name = 'evince' +version = '45.0' + +homepage = 'https://wiki.gnome.org/Apps/Evince' +description = """Evince is a document viewer for multiple document formats. The + goal of evince is to replace the multiple document viewers that exist on the + GNOME Desktop with a single simple application. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://ftp.gnome.org/pub/GNOME/sources/%(name)s/45'] +sources = [SOURCE_TAR_XZ] +checksums = ['d18647d4275cbddf0d32817b1d04e307342a85be914ec4dad2d8082aaf8aa4a8'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('GI-DocGen', '2023.3'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('GLib', '2.77.1'), + ('GTK3', '3.24.37'), + ('libhandy', '1.8.2'), + ('ITSTool', '2.0.7'), + ('Gdk-Pixbuf', '2.42.10'), + ('cairo', '1.17.8'), + ('zlib', '1.2.13'), + ('GObject-Introspection', '1.76.1'), + ('GStreamer', '1.22.5'), + ('gspell', '1.12.2'), + ('libspectre', '0.2.12'), + ('libarchive', '3.6.2'), + ('poppler', '23.09.0'), + ('Ghostscript', '10.01.2'), + ('LibTIFF', '4.5.0'), + ('libgxps', '0.3.2'), + ('DBus', '1.15.4'), + # ddjvuapi + # kpathsea +] + +_bins = ['bin/%%(name)s%s' % x for x in ['', '-previewer', '-thumbnailer']] +_incs = ['include/evince', 'lib/evince', 'lib/pkgconfig'] +_libs = ['lib/%s.%s' % (x, SHLIB_EXT) for x in ['libevdocument3', 'libevview3']] + ['libexec/evinced'] + +sanity_check_paths = { + 'files': _bins + _libs, + 'dirs': _incs, +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..104de3f6a1df --- /dev/null +++ b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb @@ -0,0 +1,49 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'PythonBundle' + +name = 'GI-DocGen' +version = '2023.3' + +homepage = 'https://gitlab.gnome.org/GNOME/gi-docgen' +description = """ +GI-DocGen is a document generator for GObject-based libraries. GObject is +the base type system of the GNOME project. GI-Docgen reuses the +introspection data generated by GObject-based libraries to generate the API +reference of these libraries, as well as other ancillary documentation. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'use_pip': True, +} + +exts_list = [ + ('Markdown', '3.5.2', { + 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], + }), + ('typogrify', '2.0.7', { + 'checksums': ['8be4668cda434163ce229d87ca273a11922cb1614cb359970b7dc96eed13cb38'], + }), + ('smartypants', '1.8.3', { + 'checksums': ['36dd37a573c74b68ba3614f52ebab0ec7a7ffe4255b7da9c4de46cda3c2e9e68'], + }), + ('gi-docgen', version, { + 'modulename': 'gidocgen', + 'checksums': ['977616bcc0e2735bb596c71e8eb34533526680740c666e87f9dfc323acd488f0'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gspell/gspell-1.12.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/gspell/gspell-1.12.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d8589535afb9 --- /dev/null +++ b/easybuild/easyconfigs/g/gspell/gspell-1.12.2-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'ConfigureMake' + +name = 'gspell' +version = '1.12.2' + +homepage = 'https://gitlab.gnome.org/GNOME/gspell' +description = "gspell provides a flexible API to add spell-checking to a GTK application." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['b4e993bd827e4ceb6a770b1b5e8950fce3be9c8b2b0cbeb22fdf992808dd2139'] + +builddependencies = [ + ('binutils', '2.40'), + ('Vala', '0.56.14'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('GTK3', '3.24.37'), + ('GObject-Introspection', '1.76.1'), + ('enchant-2', '2.6.5'), +] + +configopts = '--enable-introspection --enable-vala' + +sanity_check_paths = { + 'files': ['bin/%(name)s-app1', 'lib/lib%%(name)s-1.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s-1'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libgxps/libgxps-0.3.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libgxps/libgxps-0.3.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..715e0f3b46b2 --- /dev/null +++ b/easybuild/easyconfigs/l/libgxps/libgxps-0.3.2-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MesonNinja' + +name = 'libgxps' +version = '0.3.2' + +homepage = 'https://wiki.gnome.org/Projects/libgxps' +description = "libgxps is a GObject based library for handling and rendering XPS documents." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCE_TAR_XZ] +checksums = ['6d27867256a35ccf9b69253eb2a88a32baca3b97d5f4ef7f82e3667fa435251c'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.5'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('GLib', '2.77.1'), + ('GObject-Introspection', '1.76.1'), + ('cairo', '1.17.8'), + ('libarchive', '3.6.2'), + ('freetype', '2.13.0'), + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), + ('libpng', '1.6.39'), + ('zlib', '1.2.13'), + ('LittleCMS', '2.15'), + ('GTK3', '3.24.37'), +] + +sanity_check_paths = { + 'files': ['lib/%%(name)s.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libspectre/libspectre-0.2.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libspectre/libspectre-0.2.12-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a2425353846a --- /dev/null +++ b/easybuild/easyconfigs/l/libspectre/libspectre-0.2.12-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'ConfigureMake' + +name = 'libspectre' +version = '0.2.12' + +homepage = 'https://www.freedesktop.org/wiki/Software/libspectre/' +description = """libspectre is a small library for rendering Postscript + documents. It provides a convenient easy to use API for handling and + rendering Postscript documents. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://libspectre.freedesktop.org/releases'] +sources = [SOURCE_TAR_GZ] +checksums = ['55a7517cd3572bd2565df0cf450944a04d5273b279ebb369a895391957f0f960'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Ghostscript', '10.01.2'), + ('cairo', '1.17.8'), +] + +sanity_check_paths = { + 'files': ['lib/%%(name)s.%s' % x for x in [SHLIB_EXT, 'a', 'la']], + 'dirs': ['include/%(name)s'], +} + +moduleclass = 'lib' From 63dbbdf6251784b2f8fd13dcc183fef04fb211b0 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 23 Jan 2024 18:02:24 +0100 Subject: [PATCH 0411/1193] fix indent --- .../easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb index de329a4abfe8..ca542ff2d403 100644 --- a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb +++ b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb @@ -3,12 +3,15 @@ easyblock = 'PythonBundle' name = 'fugue' version = '0.8.7' homepage = 'https://github.com/fugue-project/fugue' -description = """Fugue is a unified interface for distributed computing that lets users execute Python, Pandas, and SQL code on Spark, Dask, and Ray with minimal rewrites. +description = """Fugue is a unified interface for distributed computing that +lets users execute Python, Pandas, and SQL code on Spark, Dask, and Ray with minimal rewrites. Fugue is most commonly used for: -Parallelizing or scaling existing Python and Pandas code by bringing it to Spark, Dask, or Ray with minimal rewrites. -Using FugueSQL to define end-to-end workflows on top of Pandas, Spark, and Dask DataFrames. FugueSQL is an enhanced SQL interface that can invoke Python code. +Parallelizing or scaling existing Python and Pandas code by bringing it to +Spark, Dask, or Ray with minimal rewrites. +Using FugueSQL to define end-to-end workflows on top of Pandas, Spark, and Dask DataFrames. +FugueSQL is an enhanced SQL interface that can invoke Python code. """ toolchain = {'name': 'foss', 'version': '2022a'} @@ -24,15 +27,11 @@ dependencies = [ exts_list = [ -# ('scikit-base', '0.6.2', { -# 'modulename': 'skbase', -# 'checksums': ['ac7c1dd9b1006e1e466d8269074f7fb02b7f5143c615f7fdf6a1e0c7565431fe'], -# }), ('adagio', '0.2.4'), ('fugue-sql-antlr', '0.2.0'), ('antlr4-python3-runtime', '4.11.1', { 'modulename': 'antlr4', - }), + }), ('fs', '2.4.16'), ('fsspec', '2023.12.2'), ('qpd', '0.4.4'), From 68f3fadda3aec477ede23c1f2072bff072b19be5 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 23 Jan 2024 17:03:36 +0000 Subject: [PATCH 0412/1193] fix perms --- easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/poetry/poetry-1.7.1-GCCcore-12.3.0.eb old mode 100755 new mode 100644 From e5c38b7518b8185915ff36bdf35f321aa76b78ba Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 23 Jan 2024 18:54:24 +0100 Subject: [PATCH 0413/1193] inject-checksums --- .../f/fugue/fugue-0.8.7-foss-2022a.eb | 30 ++++++++++++++----- 1 file changed, 23 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb index ca542ff2d403..d4b64dc0341b 100644 --- a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb +++ b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb @@ -27,17 +27,33 @@ dependencies = [ exts_list = [ - ('adagio', '0.2.4'), - ('fugue-sql-antlr', '0.2.0'), + ('adagio', '0.2.4', { + 'checksums': ['e58abc4539184a65faf9956957d3787616bedeb1303ac5c9b1a201d8af6b87d7'], + }), + ('fugue-sql-antlr', '0.2.0', { + 'checksums': ['e15433aaf09502c5b0423019d9fa93e161172ceb08e7bd27af0175dadf3cf552'], + }), ('antlr4-python3-runtime', '4.11.1', { 'modulename': 'antlr4', + 'checksums': ['a53de701312f9bdacc5258a6872cd6c62b90d3a90ae25e494026f76267333b60'], + }), + ('fs', '2.4.16', { + 'checksums': ['ae97c7d51213f4b70b6a958292530289090de3a7e15841e108fbe144f069d313'], + }), + ('fsspec', '2023.12.2', { + 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], + }), + ('qpd', '0.4.4', { + 'checksums': ['e0ed05b88e321ea9935874377bda11339c90f1469f34344e9b41d16b8088e136'], + }), + ('sqlglot', '20.9.0', { + 'checksums': ['0b62ea136dcd5835d1a003e598d834ace36dfc1104d5cbabf5a1429993105de4'], + }), + ('triad', '0.9.4', { + 'checksums': ['580658b7b88f7a1f71be5e69282d2e13dcbfacbb126a4a576187be2b2e673e20'], }), - ('fs', '2.4.16'), - ('fsspec', '2023.12.2'), - ('qpd', '0.4.4'), - ('sqlglot', '20.9.0'), - ('triad', '0.9.4'), (name, version, { + 'checksums': ['4c56946de46083778cdd6ec5b91ac5d37a847164c80790771edc6832bb9a260d'], }), ] From 02fa8eedfeb10fd947681aff01de80eceee4e883 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 23 Jan 2024 18:37:43 +0000 Subject: [PATCH 0414/1193] Use separate bcrypt easyconfig (using CargoPythonPackage) --- .../j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb index 6e978bce8690..a83e3042286d 100644 --- a/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterHub/JupyterHub-4.0.2-GCCcore-12.3.0.eb @@ -11,8 +11,6 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), - ('setuptools-rust', '1.6.0'), # Needed for bcrypt - ('Rust', '1.70.0'), # Needed for bcrypt ] dependencies = [ ('Python', '3.11.3'), @@ -21,6 +19,7 @@ dependencies = [ ('configurable-http-proxy', '4.5.6'), ('OpenSSL', '1.1', '', SYSTEM), ('tornado', '6.3.2'), + ('bcrypt', '4.0.1'), ('PycURL', '7.45.2'), # optional, recommended with large number of users ] @@ -111,9 +110,6 @@ exts_list = [ ('onetimepass', '1.0.1', { 'checksums': ['a569dac076d6e3761cbc55e36952144a637ca1b075c6d509de1c1dbc5e7f6a27'], }), - ('bcrypt', '4.0.1', { - 'checksums': ['27d375903ac8261cfe4047f6709d16f7d18d39b1ec92aaf72af989552a650ebd'], - }), ('jupyterhub-nativeauthenticator', '1.2.0', { 'modulename': 'nativeauthenticator', 'checksums': ['826228e6e9ca37736361e2e60c5723e245ec72e34fdc42cc218fc54a67f968e1'], From 1f7b94ee433a4b0339d8b1d2eee9c60aab5c3e74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 23 Jan 2024 19:19:53 +0000 Subject: [PATCH 0415/1193] fastparquet: use maturin CargoPythonPackage as a dep --- .../f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb | 7 +------ 1 file changed, 1 insertion(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb index edfd1ab8d112..2320c4b7539b 100644 --- a/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/f/fastparquet/fastparquet-2023.4.0-gfbf-2022b.eb @@ -12,23 +12,18 @@ toolchain = {'name': 'gfbf', 'version': '2022b'} builddependencies = [ ('patchelf', '0.17.2'), - ('Rust', '1.65.0'), # needed by maturin ] dependencies = [ ('Python', '3.10.8'), ('SciPy-bundle', '2023.02'), + ('maturin', '1.1.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('maturin', '1.1.0', { - 'easyblock': 'CargoPythonPackage', - 'offline': False, - 'checksums': ['4650aeaa8debd004b55aae7afb75248cbd4d61cd7da2dcf4ead8b22b58cecae0'], - }), ('thrift', '0.16.0', { 'checksums': ['2b5b6488fcded21f9d312aa23c9ff6a0195d0f6ae26ddbd5ad9e3e25dfc14408'], }), From 98bfd40dc341a3d30cdbdfad601de94b06ff7699 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 23 Jan 2024 21:43:48 +0100 Subject: [PATCH 0416/1193] Try bash fallback --- .../r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb | 3 ++- .../r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb | 3 ++- easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb | 3 ++- easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb | 3 ++- 4 files changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb index 2f34240eb524..e45a6645d009 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.7-gompi-2022a-HepMC3-3.2.5.eb @@ -35,7 +35,8 @@ dependencies = [ ('zlib', '1.2.12') ] -configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 " +configopts += "--with-zlib=${EBROOTZLIB:-%(sysroot)s/usr}" sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb index 0ce992612863..e1ab9fdf4c08 100644 --- a/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb +++ b/easybuild/easyconfigs/r/Rivet/Rivet-3.1.9-gompi-2023a-HepMC3-3.2.6.eb @@ -33,7 +33,8 @@ dependencies = [ ('zlib', '1.2.13') ] -configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3" +configopts = "--with-yoda=$EBROOTYODA --with-fastjet=$EBROOTFASTJET --with-hepmc3=$EBROOTHEPMC3 " +configopts += "--with-zlib=${EBROOTZLIB:-%(sysroot)s/usr}" sanity_check_paths = { 'files': ['bin/rivet-config', 'lib/libRivet.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb index af8619886260..56d2cc9a2753 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.7-GCC-11.3.0.eb @@ -27,7 +27,8 @@ dependencies = [ ('zlib', '1.2.12') ] -configopts = "--disable-root --enable-pyext --disable-static" +configopts = "--disable-root --enable-pyext --disable-static " +configopts += "--with-zlib=${EBROOTZLIB:-%(sysroot)s/usr}" buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" installopts = buildopts diff --git a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb index af9f9f997906..61927358ec28 100644 --- a/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/y/YODA/YODA-1.9.9-GCC-12.3.0.eb @@ -26,7 +26,8 @@ dependencies = [ ('Python', '3.11.3'), ('zlib', '1.2.13') ] -configopts = "--disable-root --enable-pyext --disable-static" +configopts = "--disable-root --enable-pyext --disable-static " +configopts += "--with-zlib=${EBROOTZLIB:-%(sysroot)s/usr}" buildopts = "YODA_PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages" installopts = buildopts From 93af32606279202eaf1ca6e7c8beb991c77ce186 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 24 Jan 2024 09:56:02 +0000 Subject: [PATCH 0417/1193] Remove trailing whitespace From 907f90ae4e8166eab23cf39ce50c868364756591 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Jan 2024 11:05:02 +0100 Subject: [PATCH 0418/1193] adding easyconfigs: CmdStanR-0.7.1-foss-2023a-R-4.3.2.eb --- .../CmdStanR-0.7.1-foss-2023a-R-4.3.2.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.7.1-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.7.1-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.7.1-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..9c87742f5037 --- /dev/null +++ b/easybuild/easyconfigs/c/CmdStanR/CmdStanR-0.7.1-foss-2023a-R-4.3.2.eb @@ -0,0 +1,28 @@ +easyblock = 'RPackage' + +name = 'CmdStanR' +version = '0.7.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://mc-stan.org/cmdstanr' +description = "CmdStanR is a lightweight interface to Stan for R users" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/stan-dev/cmdstanr/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62e552c641c4faaf64edaf0951a8c39dde8758193154bb79c6b7df114bce233c'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'bio' From 376cad9f441077042f6597b74f9ad66dbc14808b Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 24 Jan 2024 11:14:24 +0000 Subject: [PATCH 0419/1193] add binutils build dep to GI-DocGen --- .../easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb index 104de3f6a1df..d098c3c3cbc0 100644 --- a/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GI-DocGen/GI-DocGen-2023.3-GCCcore-12.3.0.eb @@ -14,6 +14,8 @@ reference of these libraries, as well as other ancillary documentation. toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [('binutils', '2.40')] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), From e8f595bf50495248ed7ca3fe3faf3e771fd7e8a5 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 24 Jan 2024 11:15:54 +0000 Subject: [PATCH 0420/1193] set download_dep_fail in libxml2-python --- .../l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb index 4f84efd5bc46..2d0cb13e73b4 100644 --- a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb @@ -38,6 +38,7 @@ start_dir = 'python' preinstallopts = 'cd .. && ./configure --prefix=%(installdir)s && cd python && ' use_pip = True +download_dep_fail = True sanity_pip_check = True sanity_check_paths = { From acef85a2f9cd4d18f235a3727f19d6d1d5e0d72e Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 24 Jan 2024 11:16:35 +0000 Subject: [PATCH 0421/1193] strip trailing whitespace --- .../easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb index 1ac7a59be8ab..8460682342fd 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -postinstallcmds = ["sed -i 's/iconv//g' %(installdir)s/lib/pkgconfig/libarchive.pc"] +postinstallcmds = ["sed -i 's/iconv//g' %(installdir)s/lib/pkgconfig/libarchive.pc"] sanity_check_paths = { 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], From a27a479eade0d24fd2b3afa3e251ce0267eecbb9 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 24 Jan 2024 11:42:08 +0000 Subject: [PATCH 0422/1193] checksums --- .../l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb index 2d0cb13e73b4..66e8634cd6db 100644 --- a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.11.4-GCCcore-12.3.0.eb @@ -16,7 +16,8 @@ sources = ['libxml2-%(version)s.tar.xz'] patches = ['%(name)s-2.11.4_fix-hardcoded-paths.patch'] checksums = [ {'libxml2-2.11.4.tar.xz': '737e1d7f8ab3f139729ca13a2494fd17bf30ddb4b7a427cf336252cab57f57f7'}, - {'libxml2-2.11.4_fix-hardcoded-paths.patch': 'b8069b149ab7e0e3a96ca1462c07d0bf1d7c7434eb434eb1b0ec824074b70f6a'}, + {'libxml2-python-2.11.4_fix-hardcoded-paths.patch': + 'b8069b149ab7e0e3a96ca1462c07d0bf1d7c7434eb434eb1b0ec824074b70f6a'}, ] builddependencies = [ From 0bc786f828d22e7d86cb5bca30321977fba8dcbd Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 24 Jan 2024 13:32:40 +0100 Subject: [PATCH 0423/1193] adding easyconfigs: bx-python-0.10.0-foss-2023a.eb --- .../bx-python/bx-python-0.10.0-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb b/easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb new file mode 100644 index 000000000000..da5a1cb4e5bb --- /dev/null +++ b/easybuild/easyconfigs/b/bx-python/bx-python-0.10.0-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'bx-python' +version = '0.10.0' + +homepage = 'https://github.com/bxlab/bx-python' +description = """The bx-python project is a Python library and associated set of scripts to allow for rapid + implementation of genome scale analyses.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('LZO', '2.10'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('python-lzo', '1.15', { + 'modulename': 'lzo', + 'preinstallopts': "export PREFIX=$EBROOTLZO && ", + 'checksums': ['a57aaa00c5c3a0515dd9f7426ba2cf601767dc19dc023d8b99d4a13b0a327b49'], + }), + (name, version, { + 'modulename': 'bx', + 'checksums': ['bfe9541d7b18a98e907b085e31f58d3989fbca4dc667c4ae48c33b753e0e2da8'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 7c1eb272ac24b85ff9208e384472712c021824b1 Mon Sep 17 00:00:00 2001 From: Turakar Date: Wed, 24 Jan 2024 14:07:50 +0100 Subject: [PATCH 0424/1193] Add Java version 8u402b06 --- easybuild/easyconfigs/j/Java/Java-8.402.eb | 31 ++++++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-8.402.eb diff --git a/easybuild/easyconfigs/j/Java/Java-8.402.eb b/easybuild/easyconfigs/j/Java/Java-8.402.eb new file mode 100644 index 000000000000..d130041813b0 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-8.402.eb @@ -0,0 +1,31 @@ +name = 'Java' +version = '8.402' +local_build = 'b06' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK8U-jdk_%s_linux_hotspot_%%(version_major)su%%(version_minor)s%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin8-binaries/releases/download/' + 'jdk%%(version_major)su%%(version_minor)s-%s/' % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + 'fcfd08abe39f18e719e391f2fc37b8ac1053075426d10efac4cbf8969e7aa55e', + local_tarball_tmpl % ('aarch64', local_build): + '241a72d6f0051de30c71e7ade95b34cd85a249c8e5925bcc7a95872bee81fd84', + local_tarball_tmpl % ('ppc64le', local_build): + '64bc05cdffe827c84000177dca2eb4ff0a8ff0021889bb75abff3639d4f51838', + + } +] + +moduleclass = 'lang' From 6df559acf615f7ed48973fd670ffd0660724d715 Mon Sep 17 00:00:00 2001 From: Turakar Date: Wed, 24 Jan 2024 14:18:11 +0100 Subject: [PATCH 0425/1193] Add Java version 21.0.2 --- easybuild/easyconfigs/j/Java/Java-21.0.2.eb | 30 +++++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-21.0.2.eb diff --git a/easybuild/easyconfigs/j/Java/Java-21.0.2.eb b/easybuild/easyconfigs/j/Java/Java-21.0.2.eb new file mode 100644 index 000000000000..55747f0a8921 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-21.0.2.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '21.0.2' +local_build = '13' + +homepage = 'http://openjdk.java.net' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '454bebb2c9fe48d981341461ffb6bf1017c7b7c6e15c6b0c29b959194ba3aaa5', + local_tarball_tmpl % ('aarch64', local_build): + '3ce6a2b357e2ef45fd6b53d6587aa05bfec7771e7fb982f2c964f6b771b7526a', + local_tarball_tmpl % ('ppc64le', local_build): + 'd08de863499d8851811c893e8915828f2cd8eb67ed9e29432a6b4e222d80a12f', + } +] + +moduleclass = 'lang' From 6963751805b691dde2cdd693b0705f9bd0a19fc7 Mon Sep 17 00:00:00 2001 From: thoffman Date: Wed, 24 Jan 2024 14:32:26 +0100 Subject: [PATCH 0426/1193] {vis}[GCCcore/12.3.0]xpdf v4.04 --- .../x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..42036e63751c --- /dev/null +++ b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb @@ -0,0 +1,38 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2023/11 +easyblock = 'CMakeMake' + +name = 'xpdf' +version = '4.04' + +homepage = 'https://www.xpdfreader.com/' +description = """Xpdf was first released in 1995. It was written, and is still developed, by +Derek Noonburg. +Xpdf is a free PDF viewer and toolkit, including a text extractor, image +converter, HTML converter, and more. Most of the tools are available as open source.""" + + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://dl.xpdfreader.com/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['63ce23fcbf76048f524c40be479ac3840d7a2cbadb6d1e0646ea77926656bade'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('freetype', '2.13.0'), + ('libpng', '1.6.39'), + ('Qt5', '5.15.10'), + ('LittleCMS', '2.15') +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin'], +} + +moduleclass = 'vis' From f78e833409a220fe5f3ccd9e37666310c1fc1e6c Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 24 Jan 2024 14:41:45 +0000 Subject: [PATCH 0427/1193] add test exception for muliple meson versions for meson-python --- test/easyconfigs/easyconfigs.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 41a322acdb46..eb7336feb664 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -394,6 +394,15 @@ def check_dep_vars(self, gen, dep, dep_vars): if all(ec.startswith('%s-%s-' % (parent_name, dep_ver)) for ec in ecs) and len(dep_vars) > 1: dep_vars.pop(key) + # multiple variants of Meson is OK as long as they are deps for meson-python, since meson-python should only be + # a build dependency elsewhere + if dep == 'Meson' and len(dep_vars) >1: + for key in list(dep_vars): + ecs = dep_vars[key] + # filter out Meson variants that are only used as a dependency for meson-python + if all(ec.startswith('meson-python-') for ec in ecs): + dep_vars.pop(key) + # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python if dep == 'Boost' and len(dep_vars) > 1: for key in list(dep_vars): From d770faafe86d6afd2455f024f33332d9d6d532b6 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 24 Jan 2024 14:44:19 +0000 Subject: [PATCH 0428/1193] linting --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index eb7336feb664..2b1b2bc61f0e 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -396,7 +396,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # multiple variants of Meson is OK as long as they are deps for meson-python, since meson-python should only be # a build dependency elsewhere - if dep == 'Meson' and len(dep_vars) >1: + if dep == 'Meson' and len(dep_vars) > 1: for key in list(dep_vars): ecs = dep_vars[key] # filter out Meson variants that are only used as a dependency for meson-python From 1785a207231593ca879d17594c75f720ee98226f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 24 Jan 2024 15:20:31 +0000 Subject: [PATCH 0429/1193] retain at least one variant --- test/easyconfigs/easyconfigs.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 2b1b2bc61f0e..26a5643ce0f9 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -402,6 +402,9 @@ def check_dep_vars(self, gen, dep, dep_vars): # filter out Meson variants that are only used as a dependency for meson-python if all(ec.startswith('meson-python-') for ec in ecs): dep_vars.pop(key) + # always retain at least one dep variant + if len(dep_vars) == 1: + break # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python if dep == 'Boost' and len(dep_vars) > 1: From 157a952f523f7ff02d838e22d36d252c9bcd1fe3 Mon Sep 17 00:00:00 2001 From: garadar Date: Wed, 24 Jan 2024 18:05:47 +0100 Subject: [PATCH 0430/1193] Update easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb index d4b64dc0341b..fd5d8ef5c479 100644 --- a/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb +++ b/easybuild/easyconfigs/f/fugue/fugue-0.8.7-foss-2022a.eb @@ -21,7 +21,6 @@ builddependencies = [ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('Cython', '0.29.33'), ('Arrow', '8.0.0'), ] From b1d41d5ecf636893fbe9fb7060fc0bf390e6f281 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Jan 2024 19:35:32 +0100 Subject: [PATCH 0431/1193] add tidybayes to R-bundle-CRAN v2023.12 --- .../R-bundle-CRAN-2023.12-foss-2023a.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index 61f2a58a16ab..9d48ee9ea592 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -3383,6 +3383,18 @@ exts_list = [ ('ridge', '3.3', { 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], }), + ('ggdist', '3.3.1', { + 'checksums': ['6705e8a252701bc162bbbe26f7cbb3e95e93a11af6288456ab711f5d0c0df929'], + }), + ('svUnit', '1.0.6', { + 'checksums': ['263e6c03d6c2717dfd25b96d25f8019c9c98120de280a17224e0d79adba2d522'], + }), + ('arrayhelpers', '1.1-0', { + 'checksums': ['5fddd5dd4fb8237bcb24465ef823bc8715ba53e6e5fd7a716c31c48ec128340b'], + }), + ('tidybayes', '3.0.6', { + 'checksums': ['706044e17855a684a5ad1aeb582963dd3c7192a4a8ad0584358d0ea7c7aadb90'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From ed40138ed3454358097cb247c295ac4775d1d14d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 24 Jan 2024 20:13:17 +0100 Subject: [PATCH 0432/1193] adding easyconfigs: igvShiny-20240112-foss-2022a-R-4.2.1.eb --- .../igvShiny-20240112-foss-2022a-R-4.2.1.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/i/igvShiny/igvShiny-20240112-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/i/igvShiny/igvShiny-20240112-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/i/igvShiny/igvShiny-20240112-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..b91cc438bab8 --- /dev/null +++ b/easybuild/easyconfigs/i/igvShiny/igvShiny-20240112-foss-2022a-R-4.2.1.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'igvShiny' +local_commit = '5bcdc51' +version = '20240112' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/gladkia/igvShiny' +description = "An htmlwidget version of igv, for RStudio and Shiny apps" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/gladkia/igvShiny/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ad28f7bfc7b355fb6d2593f7fbe31068f9bdfa14244719df959b91f0a0057ddc'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +options = {'modulename': name} + +moduleclass = 'vis' From 929917729c803cd1acd435018e1c7e03e2158777 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 25 Jan 2024 08:36:49 +0100 Subject: [PATCH 0433/1193] Update easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb index 42036e63751c..8475e41b9ac2 100644 --- a/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb @@ -31,8 +31,10 @@ dependencies = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ['bin'], + 'files': ['bin/%(name)s'], + 'dirs': [], } +sanity_check_commands = ["pdfinfo --help 2>&1 | grep 'pdfinfo version %(version)s'"] + moduleclass = 'vis' From ca73ed7622f4e6d85393e0d783abf77d30cb2019 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 25 Jan 2024 08:37:06 +0100 Subject: [PATCH 0434/1193] Update easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb Co-authored-by: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb index 8475e41b9ac2..15d45b69a39e 100644 --- a/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb @@ -9,8 +9,6 @@ description = """Xpdf was first released in 1995. It was written, and is still d Derek Noonburg. Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source.""" - - toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://dl.xpdfreader.com/'] From a871bf5aef091dbeb1961b9253814f71e29a295f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 09:44:32 +0100 Subject: [PATCH 0435/1193] adding easyconfigs: pydantic-2.5.3-GCCcore-12.3.0.eb --- .../pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb | 122 ++++++++++++++++++ 1 file changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..23955f5d21d5 --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-2.5.3-GCCcore-12.3.0.eb @@ -0,0 +1,122 @@ +easyblock = 'CargoPythonBundle' + +name = 'pydantic' +version = '2.5.3' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('maturin', '1.4.0', '-Rust-1.75.0'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.9.0'), +] + +use_pip = True +sanity_pip_check = True + +crates = [ + ('ahash', '0.8.6'), + ('aho-corasick', '1.0.2'), + ('autocfg', '1.1.0'), + ('base64', '0.21.5'), + ('bitflags', '1.3.2'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('enum_dispatch', '0.3.12'), + ('equivalent', '1.0.1'), + ('form_urlencoded', '1.2.0'), + ('getrandom', '0.2.10'), + ('hashbrown', '0.14.0'), + ('heck', '0.4.1'), + ('idna', '0.4.0'), + ('indexmap', '2.0.0'), + ('indoc', '2.0.4'), + ('itoa', '1.0.8'), + ('jiter', '0.0.4'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memchr', '2.6.3'), + ('memoffset', '0.9.0'), + ('num-bigint', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.16'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('percent-encoding', '2.3.0'), + ('proc-macro2', '1.0.69'), + ('pyo3', '0.20.0'), + ('pyo3-build-config', '0.20.0'), + ('pyo3-ffi', '0.20.0'), + ('pyo3-macros', '0.20.0'), + ('pyo3-macros-backend', '0.20.0'), + ('python3-dll-a', '0.2.9'), + ('quote', '1.0.29'), + ('redox_syscall', '0.3.5'), + ('regex', '1.10.2'), + ('regex-automata', '0.4.3'), + ('regex-syntax', '0.8.2'), + ('rustversion', '1.0.13'), + ('ryu', '1.0.14'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.190'), + ('serde_derive', '1.0.190'), + ('serde_json', '1.0.108'), + ('smallvec', '1.11.1'), + ('speedate', '0.13.0'), + ('static_assertions', '1.1.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '2.0.38'), + ('target-lexicon', '0.12.9'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.10'), + ('unicode-normalization', '0.1.22'), + ('unindent', '0.2.3'), + ('url', '2.4.1'), + ('uuid', '1.5.0'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-targets', '0.48.1'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.48.0'), + ('zerocopy', '0.7.20'), + ('zerocopy-derive', '0.7.20'), +] + +exts_list = [ + ('annotated_types', '0.6.0', { + 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], + }), + ('pydantic_core', '2.14.6', { + 'checksums': ['1fd0c1d395372843fba13a51c28e3bb9d59bd7aebfeb17358ffaaa1e4dbbe948'], + }), + (name, version, { + 'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ", + 'checksums': ['b3ef57c62535b0941697cce638c08900d87fcb67e29cfa99e8a68f747f393f7a'], + }), +] + +moduleclass = 'devel' From f0d3c91961d59bfb751dffee15a0c9c74fb3b546 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 09:47:03 +0100 Subject: [PATCH 0436/1193] adding easyconfigs: Greenlet-2.0.2-foss-2023a.eb --- .../g/Greenlet/Greenlet-2.0.2-foss-2023a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb new file mode 100644 index 000000000000..29d04a9e7b50 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '2.0.2' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'] + +moduleclass = 'devel' From a061826121782dc0d5b80f19c7affae25fdc774d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Dec 2023 19:26:09 +0000 Subject: [PATCH 0437/1193] adding easyconfigs: coverage-7.2.3-GCCcore-12.3.0.eb, molmod-1.4.8-foss-2023a.eb, nose3-1.3.8-GCCcore-12.3.0.eb, yaff-1.6.0-foss-2023a.eb --- .../coverage/coverage-7.2.3-GCCcore-12.3.0.eb | 33 ++ .../m/molmod/molmod-1.4.8-foss-2023a.eb | 37 +++ ...lmod-1.4.8-foss-2023a_fix-np-unicode.patch | 38 +++ .../n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb | 36 +++ .../y/yaff/yaff-1.6.0-foss-2023a.eb | 60 ++++ .../yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch | 293 ++++++++++++++++++ .../yaff-1.6.0-foss-2023a_fix-nose-dep.patch | 13 + ...f-1.6.0-foss-2023a_fix-random-import.patch | 14 + 8 files changed, 524 insertions(+) create mode 100644 easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch create mode 100644 easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch create mode 100644 easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f75075ae45e7 --- /dev/null +++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'coverage' +version = '7.2.3' + +homepage = 'https://coverage.readthedocs.io' +description = """ Coverage.py is a tool for measuring code coverage of Python programs. + It monitors your program, noting which parts of the code have been executed, + then analyzes the source to identify code that could have been executed but was not. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d298c2815fa4891edd9abe5ad6e6cb4207104c7dd9fd13aea3fdebf6f9b91259'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/coverage%s' % x for x in ['', '3', '-%(pyshortver)s']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb new file mode 100644 index 000000000000..eb570fc10780 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'molmod' +version = '1.4.8' + +homepage = 'https://molmod.github.io/molmod/' +description = "MolMod is a Python library with many compoments that are useful to write molecular modeling programs." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8-foss-2023a_fix-np-unicode.patch'] +checksums = [ + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8-foss-2023a_fix-np-unicode.patch': + '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" +runtest += "python setup.py build_ext -i; pytest -ra" + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch new file mode 100644 index 000000000000..278ec6a95ad2 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch @@ -0,0 +1,38 @@ +Fixes use of `np.unicode` instead of `np.unicode_`. + ++++ 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/test/test_chk.py 2023-12-11 14:55:11.534543922 +0000 +--- 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/test/test_chk.py.orig 2023-12-11 14:53:00.080194283 +0000 +@@ -62,7 +62,7 @@ + + + def test_strings_array_unicode(): ++ data = {'values': np.array(['foo', 'bar'], dtype=np.unicode_)} +- data = {'values': np.array(['foo', 'bar'], dtype=np.unicode)} + check_data_array('test_strings_array', data, np.dtype('U22')) + + +@@ -90,8 +90,8 @@ + + + def test_strings(): ++ check_data('test_strings_array', {'values': 'foo'}, (str, np.unicode_)) ++ check_data('test_strings_array', {'values': 'foo bar'}, (str, np.unicode_)) +- check_data('test_strings_array', {'values': 'foo'}, (str, np.unicode)) +- check_data('test_strings_array', {'values': 'foo bar'}, (str, np.unicode)) + + + def test_floats(): + +--- 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/chk.py.orig 2023-12-11 15:11:10.785959605 +0000 ++++ 1.4.8/foss-2023a/molmod-1.4.8/molmod/io/chk.py 2023-12-11 15:12:24.978584525 +0000 +@@ -141,8 +141,8 @@ + if value.dtype.fields is not None: + raise TypeError('Arrays with fields are not supported.') + shape_str = ','.join(str(i) for i in value.shape) +- if issubclass(value.dtype.type, (str, np.unicode, np.bytes_)): +- value = value.astype(np.unicode) ++ if issubclass(value.dtype.type, (str, np.unicode_, np.bytes_)): ++ value = value.astype(np.unicode_) + for cell in value.flat: + if len(cell) >= 22: + raise ValueError('In case of string arrays, a string may contain at most 21 characters.') diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..46f4f2d26692 --- /dev/null +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'nose3' +version = '1.3.8' + +homepage = 'https://nose.readthedocs.io/' +description = """Nose extends unittest to make testing easier.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('coverage', '7.2.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/nosetests'], + 'dirs': [], +} + +options = {'modulename': 'nose'} + +sanity_check_commands = ["nosetests --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb new file mode 100644 index 000000000000..4bc49223ce2e --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb @@ -0,0 +1,60 @@ +# Updated from previous config +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# +# Building this in interactive Slurm session will result in freeze during either +# runtest phase or sanity_check_commands phase (python -c 'import yaff') +# +# If you submit this as non-interactive Slurm job, it will build just fine. +# Possibly root cause: https://github.com/h5py/h5py/issues/917 +# +easyblock = 'PythonBundle' + +name = 'yaff' +version = '1.6.0' + +homepage = 'https://molmod.github.io/yaff/' +description = """Yaff stands for 'Yet another force field'. It is a pythonic force-field code.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconfig', '1.5.5', '-python')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('molmod', '1.4.8'), + ('nose3', '1.3.8') +] + +use_pip = True +sanity_pip_check = True + +local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " +local_runtest += "python setup.py build_ext -i; nosetests -v" + +exts_list = [ + (name, version, { + 'patches': [ + 'yaff-1.6.0-foss-2023a_fix-random-import.patch', + 'yaff-1.6.0-foss-2023a_fix-h5py.patch', + 'yaff-1.6.0-foss-2023a_fix-nose-dep.patch', + ], + 'runtest': ("export MATPLOTLIBRC=$PWD; " + "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " + "python setup.py build_ext -i; nosetests -v"), + 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], + 'checksums': [ + {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, + {'yaff-1.6.0-foss-2023a_fix-random-import.patch': + 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, + {'yaff-1.6.0-foss-2023a_fix-h5py.patch': + 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, + {'yaff-1.6.0-foss-2023a_fix-nose-dep.patch': + '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, + ], + }), +] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch new file mode 100644 index 000000000000..13476202a1a4 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch @@ -0,0 +1,293 @@ +Adds write mode to ensure h5 files are created as intended. + +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_rdf.py.orig 2023-12-11 16:49:03.170062363 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_rdf.py 2023-12-11 16:54:57.393259317 +0000 +@@ -54,7 +54,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File(__name__ + 'test_rdf1_online.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + 'test_rdf1_online.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + select = ff.system.get_indexes('O') + rdf0 = RDF(4.5*angstrom, 0.1*angstrom, f, select0=select) +@@ -85,7 +85,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File(__name__ + '.test_rdf2_online.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_rdf2_online.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + select0 = ff.system.get_indexes('O') + select1 = ff.system.get_indexes('H') +@@ -156,7 +156,7 @@ + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/chloro_pos.xyz') + fn_vol = pkg_resources.resource_filename(__name__, '../../data/test/chloro_vol.txt') + system = System.from_file(fn_xyz, rvecs=np.diag([48.877]*3)) +- with h5.File(__name__ + '.test_rdf_from_file_variable_cell', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_rdf_from_file_variable_cell', mode='w', driver='core', backing_store=False) as f: + # Prepare in-memory HDF5 file + system.to_hdf5(f) + xyz_to_hdf5(f, fn_xyz) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_spectrum.py.orig 2023-12-11 16:56:45.254710284 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_spectrum.py 2023-12-11 16:57:01.733626405 +0000 +@@ -58,7 +58,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_online_%i.h5' % bsize, driver='core', backing_store=False) as f: ++ with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_online_%i.h5' % bsize, mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + spectrum0 = Spectrum(f, bsize=bsize) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=[hdf5, spectrum0]) +@@ -95,7 +95,7 @@ + + + def test_spectrum_iter_indexes(): +- with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_iter_indexes.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.analysis.test.test_spectrum.test_spectrum_iter_indexes.h5', mode='w', driver='core', backing_store=False) as f: + spectrum = Spectrum(f, bsize=10) + l = list(spectrum._iter_indexes(np.zeros((10, 5, 3), float))) + assert l == [(0, 0), (0, 1), (0, 2), (1, 0), (1, 1), (1, 2), (2, 0), (2, 1), +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_cp2k.py.orig 2023-12-11 16:58:37.780137513 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_cp2k.py 2023-12-11 16:58:51.184069284 +0000 +@@ -33,7 +33,7 @@ + + + def test_cp2k_ener_to_hdf5(): +- with h5.File(__name__ + '.test_xyz_to_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_xyz_to_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, twice + for i in range(2): +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_dlpoly.py.orig 2023-12-11 17:01:09.540364868 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_dlpoly.py 2023-12-11 17:01:36.290228634 +0000 +@@ -33,7 +33,7 @@ + + + def test_dlpoly_history_uo(): +- with h5.File(__name__ + '.test_dlpoly_history_uo.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_dlpoly_history_uo.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, twice + for i in range(2): +@@ -60,7 +60,7 @@ + + + def test_dlpoly_history_sam(): +- with h5.File(__name__ + '.test_dlpoly_history_sam.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_dlpoly_history_sam.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, twice + for i in range(2): +@@ -84,7 +84,7 @@ + + def test_dlpoly_history_an(): + raise SkipTest('Fails, ask An why because dlpoly_history_sam does work') +- with h5.File(__name__ + '.test_dlpoly_history_an.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_dlpoly_history_an.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. The trajectory file has no system directory... + # Actual trajectory conversion, par1 + fn = pkg_resources.resource_filename(__name__, '../../data/test/dlpoly_HISTORY_an1') +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_gaussian.py.orig 2023-12-11 17:03:12.986736177 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_gaussian.py 2023-12-11 17:03:28.326658047 +0000 +@@ -85,7 +85,7 @@ + vel_unit = np.sqrt(amu)/second + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/gaussian_sioh4_md.xyz') + fn_log = pkg_resources.resource_filename(__name__, '../../data/test/gaussian_sioh4_md.log') +- with h5.File('yaff.conversion.test.test_gaussian.test_to_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.conversion.test.test_gaussian.test_to_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + system = System.from_file(fn_xyz) + system.to_hdf5(f) + # Actual trajectory conversion, twice +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_xyz.py.orig 2023-12-11 17:04:41.964283021 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/conversion/test/test_xyz.py 2023-12-11 17:04:52.624228732 +0000 +@@ -34,7 +34,7 @@ + + + def test_xyz_to_hdf5(): +- with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. Proper use is to initialize the system object from a + # different XYZ (or yet something else) with a single geometry. + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/water_trajectory.xyz') +@@ -55,7 +55,7 @@ + + + def test_xyz_to_hdf5_alt(): +- with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5_alt.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.conversion.test.test_xyz.test_xyz_to_hdf5_alt.h5', mode='w', driver='core', backing_store=False) as f: + # Bad practice. Proper use is to initialize the system object from a + # different XYZ (or yet something else) with a single geometry. + fn_xyz = pkg_resources.resource_filename(__name__, '../../data/test/water_trajectory.xyz') +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/examples/001_tutorial_bks/nvt/analysis.py.orig 2023-12-11 17:16:05.373802516 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/examples/001_tutorial_bks/nvt/analysis.py 2023-12-11 17:16:27.458690041 +0000 +@@ -48,7 +48,7 @@ + p_unit = 1e9*pascal + + # Open the trajectory file for post-processing the MD simulation +-with h5.File('traj_%s.h5' % suffix) as f: ++with h5.File('traj_%s.h5' % suffix, mode='r+') as f: + # Get the isotropic pressure. This is the trace of the time-dependent virial + # stress divided by three. + press = np.array(f['trajectory/press'][nskip:]) + +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_verlet.py.orig 2023-12-11 17:37:15.223312935 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_verlet.py 2023-12-11 17:37:28.158245974 +0000 +@@ -77,7 +77,7 @@ + + + def test_hdf5(): +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(get_ff_water32(), 1.0*femtosecond, hooks=hdf5) + nve.run(15) +@@ -88,7 +88,7 @@ + + + def test_hdf5_start(): +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f, start=2) + nve = VerletIntegrator(get_ff_water32(), 1.0*femtosecond, hooks=hdf5) + nve.run(5) +@@ -99,7 +99,7 @@ + + + def test_hdf5_step(): +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_step.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_step.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f, step=2) + nve = VerletIntegrator(get_ff_water32(), 1.0*femtosecond, hooks=hdf5) + nve.run(5) +@@ -113,7 +113,7 @@ + # This test does not write all possible outputs + sys = get_system_water() + ff = ForceField.generate(sys, pkg_resources.resource_filename(__name__, '../../data/test/parameters_water_bondharm.txt')) +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_simple.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_simple.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5) + nve.run(15) +@@ -138,7 +138,7 @@ + part_bias.add_term(bias1) + cv_tracker = CVStateItem([cv0,cv1]) + bias_tracker = BiasStateItem(part_bias) +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_cvs.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_cvs.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5, state=[cv_tracker, bias_tracker]) + nve.run(5) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/common.py.orig 2023-12-11 17:47:09.632235821 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/common.py 2023-12-11 17:47:19.706183672 +0000 +@@ -40,7 +40,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + nve = VerletIntegrator(ff, 1.0*femtosecond, hooks=hdf5) + nve.run(5) +@@ -55,7 +55,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + thermostat = LangevinThermostat(temp=300) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[hdf5, thermostat]) +@@ -71,7 +71,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + opt = CGOptimizer(FullCellDOF(ff), hooks=hdf5) + opt.run(5) +@@ -94,7 +94,7 @@ + # Dihedral angles are periodic, this has to be taken into account! + periodicities = np.array([2.0*np.pi,2.0*np.pi]) + # Run a test simulation +- with h5.File('%s/output.h5' % dn_tmp) as f: ++ with h5.File('%s/output.h5' % dn_tmp, mode='w') as f: + hdf5 = HDF5Writer(f) + mtd = MTDHook(ff, [cv0,cv1], sigmas, K, f=f, start=pace, step=pace, + periodicities=periodicities) +53c53 +< with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', driver='core', backing_store=False) as f: +--- +> with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', mode='w', driver='core', backing_store=False) as f: +140c140 +< driver='core', backing_store=False) as f0: +--- +> mode='w', driver='core', backing_store=False) as f0: +148c148 +< driver='core', backing_store=False) as f1: +--- +> mode='w', driver='core', backing_store=False) as f1: +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_diffusion.py.orig 2023-12-11 17:54:24.258996848 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/test/test_diffusion.py 2023-12-11 17:54:35.027941887 +0000 +@@ -53,7 +53,7 @@ + # Setup a test FF + ff = get_ff_water32() + # Run a test simulation +- with h5.File('yaff.analysis.test.test_diffusion.test_diff_online.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.analysis.test.test_diffusion.test_diff_online.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + select = ff.system.get_indexes('O') + diff0 = Diffusion(f, select=select) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_enhanced.py.orig 2023-12-11 17:55:55.676530269 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_enhanced.py 2023-12-11 17:56:12.271445571 +0000 +@@ -50,7 +50,7 @@ + # Construct metadynamics as a Yaff hook + ff = get_alaninedipeptide_amber99ff() + cv = CVInternalCoordinate(ff.system, DihedAngle(4,6,8,14)) +- with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_enhanced.test_mtd_alanine.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + mtd = MTDHook(ff, cv, sigma, K, f = f, start=pace, step=pace, periodicities=2*np.pi) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[mtd]) +@@ -137,7 +137,7 @@ + ff = get_alaninedipeptide_amber99ff() + cv = CVInternalCoordinate(ff.system, DihedAngle(4,6,8,14)) + with h5.File('yaff.sampling.test.test_enhanced.test_mtd_restart.h5', +- driver='core', backing_store=False) as f0: ++ mode='w', driver='core', backing_store=False) as f0: + hdf5 = HDF5Writer(f0) + mtd = MTDHook(ff, cv, sigma, K, f = f0, start=pace, step=pace, periodicities=2*np.pi) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[mtd]) +@@ -145,7 +145,7 @@ + nvt.run(12) + ff = get_alaninedipeptide_amber99ff() + with h5.File('yaff.sampling.test.test_enhanced.test_mtd_restarted.h5', +- driver='core', backing_store=False) as f1: ++ mode='w', driver='core', backing_store=False) as f1: + mtd_restart = MTDHook(ff, cv, sigma, K, f=f1, start=pace, + step=pace, restart_file=f0, periodicities=2*np.pi) + nvt = VerletIntegrator(ff, 1.0*femtosecond, hooks=[mtd_restart]) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_mc.py.orig 2023-12-11 17:57:03.929181919 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_mc.py 2023-12-11 17:57:38.412005932 +0000 +@@ -110,7 +110,7 @@ + fn_host = pkg_resources.resource_filename(__name__, '../../data/test/CAU_13.chk') + fn_pars = pkg_resources.resource_filename(__name__, '../../data/test/parameters_CAU-13_xylene.txt') + fn_guest = pkg_resources.resource_filename(__name__, '../../data/test/xylene.chk') +- with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', driver='core', backing_store=False) as f: ++ with h5.File('yaff.sampling.test.test_verlet.test_hdf5_start.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = MCHDF5Writer(f) + gcmc = GCMC.from_files(fn_guest, fn_pars, host=fn_host, hooks=[hdf5]) + gcmc.set_external_conditions(200*kelvin, 1000*bar) +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_opt.py.orig 2023-12-11 18:10:36.504037548 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/sampling/test/test_opt.py 2023-12-11 18:10:48.346977460 +0000 +@@ -120,7 +120,7 @@ + + + def test_cg_hdf5(): +- with h5.File(__name__ + '.test_cg_hdf5.h5', driver='core', backing_store=False) as f: ++ with h5.File(__name__ + '.test_cg_hdf5.h5', mode='w', driver='core', backing_store=False) as f: + hdf5 = HDF5Writer(f) + opt = CGOptimizer(CartesianDOF(get_ff_water32()), hooks=hdf5) + opt.run(15) diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch new file mode 100644 index 000000000000..eae5fd3999f4 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch @@ -0,0 +1,13 @@ +This patch replaces the dependency on nose with a dependency on nose3. + +--- 1.6.0/foss-2023a/yaff/yaff-1.6.0/setup.py.orig 2023-12-11 18:18:12.215725329 +0000 ++++ 1.6.0/foss-2023a/yaff/yaff-1.6.0/setup.py 2023-12-11 18:19:04.794458554 +0000 +@@ -90,7 +90,7 @@ + include_package_data=True, + zip_safe=False, + setup_requires=['numpy>=1.5', 'cython>=0.26'], +- install_requires=['numpy>=1.5', 'nose>=0.11', 'cython>=0.26', 'matplotlib>1.0.0', ++ install_requires=['numpy>=1.5', 'nose3', 'cython>=0.26', 'matplotlib>1.0.0', + 'h5py>=2.0.0', 'molmod>=1.4.1', 'scipy>=0.17.1'], + ext_modules=[ + Extension("yaff.pes.ext", diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch new file mode 100644 index 000000000000..787c1d31a840 --- /dev/null +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch @@ -0,0 +1,14 @@ +Replaces import of scipy.random with numpy.random. + +--- /dev/shm/yaff/1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/pca.py.orig 2023-12-11 16:29:17.807097965 +0000 ++++ /dev/shm/yaff/1.6.0/foss-2023a/yaff/yaff-1.6.0/yaff/analysis/pca.py 2023-12-11 16:29:46.094953909 +0000 +@@ -30,7 +30,7 @@ + import numpy as np + import scipy.linalg as spla + import matplotlib.pyplot as pt +-from scipy import random ++from numpy import random + + from molmod.units import * + from molmod.constants import boltzmann + From 9ecebfe4e1f5a0170ead7c91b2bf2bb92fdb0a99 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 23 Jan 2024 10:58:35 +0100 Subject: [PATCH 0438/1193] Remove toolchain suffix from patch files --- .../easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb | 4 ++-- ...icode.patch => molmod-1.4.8_fix-np-unicode.patch} | 0 .../easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb | 12 ++++++------ ...023a_fix-h5py.patch => yaff-1.6.0_fix-h5py.patch} | 0 ...-nose-dep.patch => yaff-1.6.0_fix-nose-dep.patch} | 0 ...port.patch => yaff-1.6.0_fix-random-import.patch} | 0 6 files changed, 8 insertions(+), 8 deletions(-) rename easybuild/easyconfigs/m/molmod/{molmod-1.4.8-foss-2023a_fix-np-unicode.patch => molmod-1.4.8_fix-np-unicode.patch} (100%) rename easybuild/easyconfigs/y/yaff/{yaff-1.6.0-foss-2023a_fix-h5py.patch => yaff-1.6.0_fix-h5py.patch} (100%) rename easybuild/easyconfigs/y/yaff/{yaff-1.6.0-foss-2023a_fix-nose-dep.patch => yaff-1.6.0_fix-nose-dep.patch} (100%) rename easybuild/easyconfigs/y/yaff/{yaff-1.6.0-foss-2023a_fix-random-import.patch => yaff-1.6.0_fix-random-import.patch} (100%) diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb index eb570fc10780..6d091b4f23b3 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb @@ -10,10 +10,10 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['molmod-1.4.8-foss-2023a_fix-np-unicode.patch'] +patches = ['molmod-1.4.8_fix-np-unicode.patch'] checksums = [ {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, - {'molmod-1.4.8-foss-2023a_fix-np-unicode.patch': + {'molmod-1.4.8_fix-np-unicode.patch': '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'}, ] diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch b/easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-np-unicode.patch similarity index 100% rename from easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a_fix-np-unicode.patch rename to easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-np-unicode.patch diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb index 4bc49223ce2e..743974c697c5 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb @@ -37,9 +37,9 @@ local_runtest += "python setup.py build_ext -i; nosetests -v" exts_list = [ (name, version, { 'patches': [ - 'yaff-1.6.0-foss-2023a_fix-random-import.patch', - 'yaff-1.6.0-foss-2023a_fix-h5py.patch', - 'yaff-1.6.0-foss-2023a_fix-nose-dep.patch', + 'yaff-1.6.0_fix-random-import.patch', + 'yaff-1.6.0_fix-h5py.patch', + 'yaff-1.6.0_fix-nose-dep.patch', ], 'runtest': ("export MATPLOTLIBRC=$PWD; " "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " @@ -47,11 +47,11 @@ exts_list = [ 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], 'checksums': [ {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, - {'yaff-1.6.0-foss-2023a_fix-random-import.patch': + {'yaff-1.6.0_fix-random-import.patch': 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, - {'yaff-1.6.0-foss-2023a_fix-h5py.patch': + {'yaff-1.6.0_fix-h5py.patch': 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, - {'yaff-1.6.0-foss-2023a_fix-nose-dep.patch': + {'yaff-1.6.0_fix-nose-dep.patch': '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, ], }), diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-h5py.patch similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-h5py.patch rename to easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-h5py.patch diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-nose-dep.patch similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-nose-dep.patch rename to easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-nose-dep.patch diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch b/easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-random-import.patch similarity index 100% rename from easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a_fix-random-import.patch rename to easybuild/easyconfigs/y/yaff/yaff-1.6.0_fix-random-import.patch From 649f0ae9932bce46d1924c3d3715cec826bc6e87 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 24 Jan 2024 11:10:28 +0100 Subject: [PATCH 0439/1193] Convert some ECs to PythonPackage and improve formatting --- .../coverage/coverage-7.2.3-GCCcore-12.3.0.eb | 9 +-- .../n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb | 4 +- .../y/yaff/yaff-1.6.0-foss-2023a.eb | 58 ++++++++----------- 3 files changed, 27 insertions(+), 44 deletions(-) diff --git a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb index f75075ae45e7..66cdb2b6ec48 100644 --- a/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/coverage/coverage-7.2.3-GCCcore-12.3.0.eb @@ -13,13 +13,8 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['d298c2815fa4891edd9abe5ad6e6cb4207104c7dd9fd13aea3fdebf6f9b91259'] -builddependencies = [ - ('binutils', '2.40'), -] - -dependencies = [ - ('Python', '3.11.3'), -] +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.3')] use_pip = True sanity_pip_check = True diff --git a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb index 46f4f2d26692..bc5d8e115864 100644 --- a/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/n/nose3/nose3-1.3.8-GCCcore-12.3.0.eb @@ -11,9 +11,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} sources = [SOURCE_TAR_GZ] checksums = ['762aae22cadb898b00b9d4f4bbb9f8e87f8e0dde6c49a88cd0c554f4e5925b76'] -builddependencies = [ - ('binutils', '2.40'), -] +builddependencies = [('binutils', '2.40')] dependencies = [ ('Python', '3.11.3'), diff --git a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb index 743974c697c5..47eba698998f 100644 --- a/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb +++ b/easybuild/easyconfigs/y/yaff/yaff-1.6.0-foss-2023a.eb @@ -1,14 +1,7 @@ # Updated from previous config # Author: Pavel Grochal (INUITS) # License: GPLv2 -# -# Building this in interactive Slurm session will result in freeze during either -# runtest phase or sanity_check_commands phase (python -c 'import yaff') -# -# If you submit this as non-interactive Slurm job, it will build just fine. -# Possibly root cause: https://github.com/h5py/h5py/issues/917 -# -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'yaff' version = '1.6.0' @@ -19,7 +12,6 @@ description = """Yaff stands for 'Yet another force field'. It is a pythonic for toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [('pkgconfig', '1.5.5', '-python')] - dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), @@ -28,33 +20,31 @@ dependencies = [ ('nose3', '1.3.8') ] +source_urls = ['https://github.com/molmod/yaff/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'yaff-1.6.0_fix-random-import.patch', + 'yaff-1.6.0_fix-h5py.patch', + 'yaff-1.6.0_fix-nose-dep.patch', +] +checksums = [ + {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, + {'yaff-1.6.0_fix-random-import.patch': + 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, + {'yaff-1.6.0_fix-h5py.patch': + 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, + {'yaff-1.6.0_fix-nose-dep.patch': + '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, +] + use_pip = True +download_dep_fail = True sanity_pip_check = True -local_runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " -local_runtest += "python setup.py build_ext -i; nosetests -v" - -exts_list = [ - (name, version, { - 'patches': [ - 'yaff-1.6.0_fix-random-import.patch', - 'yaff-1.6.0_fix-h5py.patch', - 'yaff-1.6.0_fix-nose-dep.patch', - ], - 'runtest': ("export MATPLOTLIBRC=$PWD; " - "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc; " - "python setup.py build_ext -i; nosetests -v"), - 'source_urls': ['https://github.com/molmod/yaff/releases/download/%(version)s'], - 'checksums': [ - {'yaff-1.6.0.tar.gz': 'a266ab032778e37bb2e93152aefb67f396827aa728151651403984429c74ceaa'}, - {'yaff-1.6.0_fix-random-import.patch': - 'a38afacbcbfbf16a80742ae8253852e725e656c9d684310894c806f689362840'}, - {'yaff-1.6.0_fix-h5py.patch': - 'bd2a73f375910360fd5dd22b3ec006344527476e80dea549f4d82297257105f9'}, - {'yaff-1.6.0_fix-nose-dep.patch': - '2314c487c4a847d7740d7dfc97052cf7efd764ced726d098def0a1aef0b498e0'}, - ], - }), -] +runtest = ' '.join([ + "export MATPLOTLIBRC=$PWD;", + "echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;", + "python setup.py build_ext -i; nosetests -v", +]) moduleclass = 'chem' From 85f2271efcf1efdf58ad5a3124ca6d1a1179159c Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Dec 2023 19:26:09 +0000 Subject: [PATCH 0440/1193] adding easyconfigs: Blosc-1.21.5-GCCcore-12.3.0.eb, Blosc2-2.8.0-GCCcore-12.3.0.eb --- .../b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb | 28 +++++++++++++++++ .../b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 2 files changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..60fb8a755d19 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.5' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['32e61961bbf81ffea6ff30e9d70fca36c86178afd3e3cfa13376adec8c687509'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..58f563af452a --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.8.0' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['be608cdf68deb02e0d3ee62e183942a0fe5d5d3185375b9b6566e2ae35a9bdbd'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 4d826445400ecb15b34eafcbae3d315463875038 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 24 Jan 2024 11:07:44 +0100 Subject: [PATCH 0441/1193] Remove explicit C++ standard from Blosc/Blosc2 Not required for newer GCC versions and can cause trouble --- easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb index 60fb8a755d19..8ec9141c86c2 100644 --- a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-12.3.0.eb @@ -8,7 +8,7 @@ homepage = 'https://www.blosc.org/' description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/Blosc/c-blosc/archive/'] sources = ['v%(version)s.tar.gz'] diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb index 58f563af452a..9cebfb5a167e 100644 --- a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.8.0-GCCcore-12.3.0.eb @@ -11,7 +11,7 @@ homepage = 'https://www.blosc.org/' description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -toolchainopts = {'pic': True, 'cstd': 'c++11'} +toolchainopts = {'pic': True} source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] sources = ['v%(version)s.tar.gz'] From 4a37b764ab1470f111b3aa581d3b21d356b08b25 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 10:25:13 +0100 Subject: [PATCH 0442/1193] adding easyconfigs: pymatgen-2023.12.18-foss-2023a.eb and patches: emmet-core-0.75.0-fix-readme.patch --- .../emmet-core-0.75.0-fix-readme.patch | 13 ++ .../pymatgen-2023.12.18-foss-2023a.eb | 138 ++++++++++++++++++ 2 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/p/pymatgen/emmet-core-0.75.0-fix-readme.patch create mode 100644 easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pymatgen/emmet-core-0.75.0-fix-readme.patch b/easybuild/easyconfigs/p/pymatgen/emmet-core-0.75.0-fix-readme.patch new file mode 100644 index 000000000000..2ed9d7c4983d --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/emmet-core-0.75.0-fix-readme.patch @@ -0,0 +1,13 @@ +Fixes attempt to open nonexistent README.md. + +--- 0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py.orig 2023-12-21 18:58:49.428075405 +0000 ++++ 0.5.1/foss-2023a/emmetcore/emmet-core-0.75.0/setup.py 2023-12-21 18:59:10.200024324 +0000 +@@ -7,8 +7,6 @@ + description="Core Emmet Library", + author="The Materials Project", + author_email="feedback@materialsproject.org", +- long_description=open("../README.md").read(), # noqa: SIM115 +- long_description_content_type="text/markdown", + url="https://github.com/materialsproject/emmet", + packages=find_namespace_packages(include=["emmet.*"]), + package_data={ diff --git a/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb new file mode 100644 index 000000000000..5432a146d044 --- /dev/null +++ b/easybuild/easyconfigs/p/pymatgen/pymatgen-2023.12.18-foss-2023a.eb @@ -0,0 +1,138 @@ +easyblock = 'PythonBundle' + +name = 'pymatgen' +version = '2023.12.18' + +homepage = 'https://pymatgen.org/' +description = """Python Materials Genomics is a robust materials analysis code that defines core object + representations for structures and molecules with support for many electronic structure codes.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('hypothesis', '6.82.0'), # required for tests + ('maturin', '1.1.0'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('PyZMQ', '25.1.1'), + ('bcrypt', '4.0.1'), + ('boto3', '1.28.70'), + ('Flask', '2.3.3'), + ('matplotlib', '3.7.2'), + ('networkx', '3.1'), + ('paramiko', '3.2.0'), + ('plotly.py', '5.16.0'), + ('pydantic', '2.5.3'), + ('ruamel.yaml', '0.17.32'), + ('spglib-python', '2.1.0'), + ('sympy', '1.12'), + ('tqdm', '4.66.1'), + ('uncertainties', '3.1.7'), +] + +use_pip = True + +exts_list = [ + ('palettable', '3.3.0', { + 'checksums': ['72feca71cf7d79830cd6d9181b02edf227b867d503bec953cf9fa91bf44896bd'], + }), + ('latexcodec', '2.0.1', { + 'checksums': ['2aa2551c373261cefe2ad3a8953a6d6533e68238d180eb4bb91d7964adb3fe9a'], + }), + ('pybtex', '0.24.0', { + 'checksums': ['818eae35b61733e5c007c3fcd2cfb75ed1bc8b4173c1f70b56cc4c0802d34755'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.25.0', { + 'checksums': ['6dddbad1d7ee0f5140aba5ec138ddc9612c5109399903828b4874c9937f009c2'], + }), + ('sshtunnel', '0.4.0', { + 'checksums': ['e7cb0ea774db81bf91844db22de72a40aae8f7b0f9bb9ba0f666d474ef6bf9fc'], + }), + ('dnspython', '2.4.2', { + 'modulename': False, + 'checksums': ['8dcfae8c7460a2f84b4072e26f1c9f4101ca20c071649cb7c34e8b6a93d58984'], + }), + ('pymongo', '4.6.1', { + 'checksums': ['31dab1f3e1d0cdd57e8df01b645f52d43cc1b653ed3afd535d2891f4fc4f9712'], + }), + ('pydash', '7.0.6', { + 'checksums': ['7d9df7e9f36f2bbb08316b609480e7c6468185473a21bdd8e65dda7915565a26'], + }), + ('python-dotenv', '1.0.0', { + 'modulename': 'dotenv', + 'checksums': ['a8df96034aae6d2d50a4ebe8216326c61c3eb64836776504fcca410e5937a3ba'], + }), + ('pydantic-settings', '2.1.0', { + 'sources': {'source_urls': ['https://github.com/pydantic/pydantic-settings/archive/refs/tags/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ}, + 'checksums': ['be83f7a7da10a0686a00da1b9e62856072bbcfb7d6a420ea3c78c66b145fcd93'], + }), + ('emmet-core', '0.75.0', { + 'modulename': 'emmet', + 'patches': ['emmet-core-0.75.0-fix-readme.patch'], + 'checksums': [ + {'emmet-core-0.75.0.tar.gz': '2d4b20d542e56c97009d05d03f5595be9395ac27c2fe9809d617f28596c40640'}, + {'emmet-core-0.75.0-fix-readme.patch': + 'd299f388044fdcff32fc246b0215ae4b656bc20d9d3c759d545cbe3167df08b8'}, + ], + }), + ('orjson', '3.9.10', { + 'checksums': ['9ebbdbd6a046c304b1845e96fbcc5559cd296b4dfd3ad2509e33c4d9ce07d6a1'], + }), + ('monty', '2023.11.3', { + 'checksums': ['d961c14b0b20901c7603aa00d275e62dee8333fbdaf1179f5d862c6fb3f3c52f'], + }), + ('sentinels', '1.0.0', { + 'checksums': ['7be0704d7fe1925e397e92d18669ace2f619c92b5d4eb21a89f31e026f9ff4b1'], + }), + ('mongomock', '4.1.2', { + 'checksums': ['f06cd62afb8ae3ef63ba31349abd220a657ef0dd4f0243a29587c5213f931b7d'], + }), + ('mongogrant', '0.3.3', { + 'checksums': ['ad494b8638adfa840cdd5568af44448dd43771b58102550cf7c61402b1620ab4'], + }), + ('sniffio', '1.3.0', { # Same version as in jupyter-server + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.7.1', { # Same version as in jupyter-server + 'checksums': ['44a3c9aba0f5defa43261a8b3efb97891f2bd7d804e0e1f56419befa1adfc780'], + }), + ('starlette', '0.27.0', { + 'checksums': ['6a6b0d042acb8d469a01eba54e9cda6cbd24ac602c4cd016723117d6a7e73b75'], + }), + ('fastapi', '0.105.0', { + 'checksums': ['4d12838819aa52af244580675825e750ad67c9df4614f557a769606af902cf22'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('maggma', '0.60.2', { + 'checksums': ['12e8da1f80505f39432b972cbe47fb378cd9aa51fab968877a2d3b2588c96c69'], + }), + ('mp-api', '0.39.4', { + 'checksums': ['692abefd6adec36eb4fa193f914e08167ed33a5a3a9714ec3c15606839649f32'], + }), + (name, version, { + 'checksums': ['56c0041fe5431ac1b8f8c0c17d06091c4d61082c3a99924f3940d73ebb6656eb'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pmg'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pmg --help"] + +sanity_pip_check = True + +moduleclass = 'chem' From 28bbb82dfb44447f11b9de692c02b322d40eec65 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 10:45:48 +0100 Subject: [PATCH 0443/1193] Add uncertainties-3.1.7 --- .../uncertainties-3.1.7-foss-2023a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb diff --git a/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb new file mode 100644 index 000000000000..2b643d74ce64 --- /dev/null +++ b/easybuild/easyconfigs/u/uncertainties/uncertainties-3.1.7-foss-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'uncertainties' +version = '3.1.7' + +homepage = 'http://uncertainties-python-package.readthedocs.io' +description = """Transparent calculations with uncertainties on the quantities involved (aka error propagation); + fast calculation of derivatives""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['80111e0839f239c5b233cb4772017b483a0b7a1573a581b92ab7746a35e6faab'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From abd4a4b1134070144fec8b4291848440190f2ff0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 25 Jan 2024 11:38:44 +0100 Subject: [PATCH 0444/1193] adding easyconfigs: OBITools3-3.0.1b26-GCCcore-12.3.0.eb --- .../OBITools3-3.0.1b26-GCCcore-12.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..2d5ba362a086 --- /dev/null +++ b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb @@ -0,0 +1,44 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'OBITools3' +version = '3.0.1b26' + +homepage = 'https://metabarcoding.org/obitools3' +description = """A package for the management of analyses and data in DNA metabarcoding.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d53d60b6b0d4f242a14a9c3da5934805f1ee26e889540add02dc066490a6aba7'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3') +] + +dependencies = [ + ('Python', '3.11.3'), + ('IPython', '8.14.0'), +] + +use_pip = True + +preinstallopts = "sed -i \"s|get_python_lib()|get_python_lib(prefix='%(installdir)s')|g\" setup.py &&" + +fix_python_shebang_for = ['bin/obi'] + +sanity_check_paths = { + 'files': ['bin/obi'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "obi --help", + "obi --version", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 33f32d61b066969af7ebf0a7f873066b1f710b81 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 25 Jan 2024 11:59:36 +0000 Subject: [PATCH 0445/1193] depend on typing-extensions easyconfig --- .../easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb index 96ad7fb45129..359b3f1f1a3b 100644 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb @@ -16,15 +16,13 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), + ('typing-extensions', '4.9.0',), ] sanity_pip_check = True use_pip = True exts_list = [ - ('typing_extensions', '4.9.0', { - 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], - }), ('annotated-types', '0.6.0', { 'source_tmpl': 'annotated_types-%(version)s.tar.gz', 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], From 955d25e222455d4bb567f3033a0eef3981e15753 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 13:21:46 +0100 Subject: [PATCH 0446/1193] adding easyconfigs: TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb, TAMkin-1.2.6-foss-2020b.eb, TAMkin-1.2.6-foss-2021a.eb, TAMkin-1.2.6-foss-2021b.eb --- .../TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb | 42 +++++++++++++++++++ .../t/TAMkin/TAMkin-1.2.6-foss-2020b.eb | 41 ++++++++++++++++++ .../t/TAMkin/TAMkin-1.2.6-foss-2021a.eb | 41 ++++++++++++++++++ .../t/TAMkin/TAMkin-1.2.6-foss-2021b.eb | 41 ++++++++++++++++++ 4 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb new file mode 100644 index 000000000000..f16feb95b9f0 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2020a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['TAMkin-1.2.6_fix-python38.patch'] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, +] + +dependencies = [ + ('Python', '3.8.2'), + ('matplotlib', '3.2.1', versionsuffix), + ('molmod', '1.4.5', versionsuffix), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb new file mode 100644 index 000000000000..1287bce55994 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['TAMkin-1.2.6_fix-python38.patch'] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, +] + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.5.1'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb new file mode 100644 index 000000000000..95ac548b7497 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['TAMkin-1.2.6_fix-python38.patch'] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, +] + +dependencies = [ + ('Python', '3.9.5'), + ('matplotlib', '3.4.2'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb new file mode 100644 index 000000000000..a4dd316d17cf --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonPackage' + +name = 'TAMkin' +version = '1.2.6' + +homepage = 'https://molmod.github.io/tamkin/' +description = """TAMkin is a post-processing toolkit for normal mode analysis, + thermochemistry and reaction kinetics. It uses a Hessian computation from a + standard computational chemistry program as its input.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +patches = ['TAMkin-1.2.6_fix-python38.patch'] +checksums = [ + {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, + {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, +] + +dependencies = [ + ('Python', '3.9.6'), + ('matplotlib', '3.4.3'), + ('molmod', '1.4.8'), +] + +download_dep_fail = True +use_pip = True + +# disable tests that require X11 by specifying "backend: agg" in matplotlibrc +runtest = 'export MATPLOTLIBRC=$PWD; echo "backend: agg" > $MATPLOTLIBRC/matplotlibrc; ' +runtest += 'export OMP_NUM_THREADS=1; nosetests -v tamkin' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'chem' From abbfae56637c8ef2d8a9d83276965b274ea95533 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 25 Jan 2024 13:54:19 +0100 Subject: [PATCH 0447/1193] Use matplotlib 3.3.3 for 2020b --- easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb index 1287bce55994..022abda9c0d5 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -20,7 +20,7 @@ checksums = [ dependencies = [ ('Python', '3.8.6'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ('molmod', '1.4.8'), ] From befc6582a10eb12dfcf30a5d0d2baef7b2ba8d31 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 25 Jan 2024 14:00:05 +0000 Subject: [PATCH 0448/1193] backport pydantic 2 compat for napari 0.4.18 --- .../n/napari/napari-0.4.18-foss-2023a.eb | 14 +- ...apari-0.4.18_pydantic2-compatibility.patch | 827 ++++++++++++++++++ .../pydantic-1.10.13-GCCcore-12.3.0.eb | 39 - 3 files changed, 837 insertions(+), 43 deletions(-) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.18_pydantic2-compatibility.patch delete mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb index f450bff7ed2b..b6ecb0109d35 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb @@ -5,9 +5,9 @@ name = 'napari' version = '0.4.18' homepage = 'https://napari.org/' -description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's +description = """napari is a fast, interactive, multi-dimensional image viewer for Python. It's designed for browsing, annotating, and analyzing large multi-dimensional images. -It's built on top of Qt (for the GUI), vispy (for performant GPU-based +It's built on top of Qt (for the GUI), vispy (for performant GPU-based rendering), and the scientific Python stack (numpy, scipy).""" toolchain = {'name': 'foss', 'version': '2023a'} @@ -22,7 +22,8 @@ dependencies = [ ('PyQt5', '5.15.10'), ('SciPy-bundle', '2023.07'), ('PyYAML', '6.0'), - ('pydantic', '1.10.13'), + # ('pydantic', '1.10.13'), + ('pydantic', '2.5.3'), ('dask', '2023.9.2'), ('PyOpenGL', '3.1.7'), ('imageio', '2.33.1'), @@ -105,8 +106,13 @@ exts_list = [ 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], }), (name, version, { - 'checksums': ['daea9ab94124140fc0f715e945dd1dd6dc3056a1cb2f2cc31fc29b80162943e4'], + 'patches': ['%(name)s-0.4.18_pydantic2-compatibility.patch'], 'preinstallopts': "sed -i 's|sphinx.*|sphinx|g' setup.cfg && ", + 'checksums': [ + {'napari-0.4.18.tar.gz': 'daea9ab94124140fc0f715e945dd1dd6dc3056a1cb2f2cc31fc29b80162943e4'}, + {'napari-0.4.18_pydantic2-compatibility.patch': + '4f4b828dc2ff680c21428c427d44cebbdfa490233cbbaffe51b9548ab4e2c999'}, + ], }), ] diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18_pydantic2-compatibility.patch b/easybuild/easyconfigs/n/napari/napari-0.4.18_pydantic2-compatibility.patch new file mode 100644 index 000000000000..c78f0c3c77ed --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18_pydantic2-compatibility.patch @@ -0,0 +1,827 @@ +Backport pydantic 2.x compatibility from 0.4.19 release candidates to napari 0.4.18 +Based on: https://github.com/napari/napari/commit/e9ea8d06d5f9f8e029f464b3938e6a60df3f6bb8 +diff -Nru napari-0.4.18.orig/napari/components/camera.py napari-0.4.18/napari/components/camera.py +--- napari-0.4.18.orig/napari/components/camera.py 2024-01-25 13:30:10.975544424 +0000 ++++ napari-0.4.18/napari/components/camera.py 2024-01-25 13:30:22.482507550 +0000 +@@ -2,9 +2,9 @@ + from typing import Optional, Tuple + + import numpy as np +-from pydantic import validator + from scipy.spatial.transform import Rotation as R + ++from napari._pydantic_compat import validator + from napari.utils.events import EventedModel + from napari.utils.misc import ensure_n_tuple + from napari.utils.translations import trans +diff -Nru napari-0.4.18.orig/napari/components/dims.py napari-0.4.18/napari/components/dims.py +--- napari-0.4.18.orig/napari/components/dims.py 2024-01-25 13:30:10.976544421 +0000 ++++ napari-0.4.18/napari/components/dims.py 2024-01-25 13:30:22.482507550 +0000 +@@ -7,8 +7,8 @@ + ) + + import numpy as np +-from pydantic import root_validator, validator + ++from napari._pydantic_compat import root_validator, validator + from napari.utils.events import EventedModel + from napari.utils.misc import argsort, reorder_after_dim_reduction + from napari.utils.translations import trans +diff -Nru napari-0.4.18.orig/napari/components/viewer_model.py napari-0.4.18/napari/components/viewer_model.py +--- napari-0.4.18.orig/napari/components/viewer_model.py 2024-01-25 13:30:10.977544418 +0000 ++++ napari-0.4.18/napari/components/viewer_model.py 2024-01-25 13:30:22.483507547 +0000 +@@ -20,9 +20,9 @@ + ) + + import numpy as np +-from pydantic import Extra, Field, PrivateAttr, validator + + from napari import layers ++from napari._pydantic_compat import Extra, Field, PrivateAttr, validator + from napari.components._viewer_mouse_bindings import dims_scroll + from napari.components.camera import Camera + from napari.components.cursor import Cursor +diff -Nru napari-0.4.18.orig/napari/layers/points/_tests/test_points.py napari-0.4.18/napari/layers/points/_tests/test_points.py +--- napari-0.4.18.orig/napari/layers/points/_tests/test_points.py 2024-01-25 13:30:10.979544411 +0000 ++++ napari-0.4.18/napari/layers/points/_tests/test_points.py 2024-01-25 13:30:22.483507547 +0000 +@@ -6,9 +6,9 @@ + import pandas as pd + import pytest + from psygnal.containers import Selection +-from pydantic import ValidationError + from vispy.color import get_colormap + ++from napari._pydantic_compat import ValidationError + from napari._tests.utils import ( + assert_colors_equal, + assert_layer_state_equal, +diff -Nru napari-0.4.18.orig/napari/layers/shapes/_tests/test_shapes.py napari-0.4.18/napari/layers/shapes/_tests/test_shapes.py +--- napari-0.4.18.orig/napari/layers/shapes/_tests/test_shapes.py 2024-01-25 13:30:10.980544408 +0000 ++++ napari-0.4.18/napari/layers/shapes/_tests/test_shapes.py 2024-01-25 13:30:22.483507547 +0000 +@@ -5,8 +5,8 @@ + import numpy as np + import pandas as pd + import pytest +-from pydantic import ValidationError + ++from napari._pydantic_compat import ValidationError + from napari._tests.utils import ( + assert_colors_equal, + check_layer_world_data_extent, +diff -Nru napari-0.4.18.orig/napari/layers/_source.py napari-0.4.18/napari/layers/_source.py +--- napari-0.4.18.orig/napari/layers/_source.py 2024-01-25 13:30:10.977544418 +0000 ++++ napari-0.4.18/napari/layers/_source.py 2024-01-25 13:30:22.483507547 +0000 +@@ -6,8 +6,8 @@ + from typing import Optional, Tuple + + from magicgui.widgets import FunctionGui +-from pydantic import BaseModel, validator + ++from napari._pydantic_compat import BaseModel, validator + from napari.layers.base.base import Layer + + +diff -Nru napari-0.4.18.orig/napari/layers/surface/normals.py napari-0.4.18/napari/layers/surface/normals.py +--- napari-0.4.18.orig/napari/layers/surface/normals.py 2024-01-25 13:30:10.980544408 +0000 ++++ napari-0.4.18/napari/layers/surface/normals.py 2024-01-25 13:30:22.483507547 +0000 +@@ -1,7 +1,6 @@ + from enum import Enum, auto + +-from pydantic import Field +- ++from napari._pydantic_compat import Field + from napari.utils.color import ColorValue + from napari.utils.events import EventedModel + +diff -Nru napari-0.4.18.orig/napari/layers/_tests/test_source.py napari-0.4.18/napari/layers/_tests/test_source.py +--- napari-0.4.18.orig/napari/layers/_tests/test_source.py 2024-01-25 13:30:10.977544418 +0000 ++++ napari-0.4.18/napari/layers/_tests/test_source.py 2024-01-25 13:30:22.483507547 +0000 +@@ -1,6 +1,6 @@ +-import pydantic + import pytest + ++from napari._pydantic_compat import ValidationError + from napari.layers import Points + from napari.layers._source import Source, current_source, layer_source + +@@ -46,7 +46,7 @@ + + def test_source_assert_parent(): + assert current_source() == Source() +- with pytest.raises(pydantic.error_wrappers.ValidationError): ++ with pytest.raises(ValidationError): + with layer_source(parent=''): + current_source() + assert current_source() == Source() +diff -Nru napari-0.4.18.orig/napari/layers/utils/color_encoding.py napari-0.4.18/napari/layers/utils/color_encoding.py +--- napari-0.4.18.orig/napari/layers/utils/color_encoding.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/color_encoding.py 2024-01-25 13:30:22.484507544 +0000 +@@ -9,8 +9,8 @@ + ) + + import numpy as np +-from pydantic import Field, parse_obj_as, validator + ++from napari._pydantic_compat import Field, parse_obj_as, validator + from napari.layers.utils.color_transformations import ColorType + from napari.layers.utils.style_encoding import ( + StyleEncoding, +diff -Nru napari-0.4.18.orig/napari/layers/utils/color_manager.py napari-0.4.18/napari/layers/utils/color_manager.py +--- napari-0.4.18.orig/napari/layers/utils/color_manager.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/color_manager.py 2024-01-25 13:30:22.484507544 +0000 +@@ -3,8 +3,8 @@ + from typing import Any, Dict, Optional, Tuple, Union + + import numpy as np +-from pydantic import Field, root_validator, validator + ++from napari._pydantic_compat import Field, root_validator, validator + from napari.layers.utils._color_manager_constants import ColorMode + from napari.layers.utils.color_manager_utils import ( + _validate_colormap_mode, +diff -Nru napari-0.4.18.orig/napari/layers/utils/plane.py napari-0.4.18/napari/layers/utils/plane.py +--- napari-0.4.18.orig/napari/layers/utils/plane.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/plane.py 2024-01-25 13:30:22.484507544 +0000 +@@ -1,8 +1,8 @@ + from typing import Tuple + + import numpy as np +-from pydantic import validator + ++from napari._pydantic_compat import validator + from napari.utils.events import EventedModel, SelectableEventedList + from napari.utils.geometry import intersect_line_with_plane_3d + from napari.utils.translations import trans +diff -Nru napari-0.4.18.orig/napari/layers/utils/string_encoding.py napari-0.4.18/napari/layers/utils/string_encoding.py +--- napari-0.4.18.orig/napari/layers/utils/string_encoding.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/string_encoding.py 2024-01-25 13:30:22.484507544 +0000 +@@ -2,8 +2,8 @@ + from typing import Any, Literal, Protocol, Sequence, Union, runtime_checkable + + import numpy as np +-from pydantic import parse_obj_as + ++from napari._pydantic_compat import parse_obj_as + from napari.layers.utils.style_encoding import ( + StyleEncoding, + _ConstantStyleEncoding, +diff -Nru napari-0.4.18.orig/napari/layers/utils/_tests/test_color_manager.py napari-0.4.18/napari/layers/utils/_tests/test_color_manager.py +--- napari-0.4.18.orig/napari/layers/utils/_tests/test_color_manager.py 2024-01-25 13:30:10.980544408 +0000 ++++ napari-0.4.18/napari/layers/utils/_tests/test_color_manager.py 2024-01-25 13:30:22.483507547 +0000 +@@ -3,8 +3,8 @@ + + import numpy as np + import pytest +-from pydantic import ValidationError + ++from napari._pydantic_compat import ValidationError + from napari.layers.utils.color_manager import ColorManager, ColorProperties + from napari.utils.colormaps.categorical_colormap import CategoricalColormap + from napari.utils.colormaps.standardize_color import transform_color +diff -Nru napari-0.4.18.orig/napari/layers/utils/_tests/test_plane.py napari-0.4.18/napari/layers/utils/_tests/test_plane.py +--- napari-0.4.18.orig/napari/layers/utils/_tests/test_plane.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/_tests/test_plane.py 2024-01-25 13:30:22.483507547 +0000 +@@ -1,7 +1,7 @@ + import numpy as np + import pytest +-from pydantic import ValidationError + ++from napari._pydantic_compat import ValidationError + from napari.layers.utils.plane import ClippingPlaneList, Plane, SlicingPlane + + +diff -Nru napari-0.4.18.orig/napari/layers/utils/_tests/test_style_encoding.py napari-0.4.18/napari/layers/utils/_tests/test_style_encoding.py +--- napari-0.4.18.orig/napari/layers/utils/_tests/test_style_encoding.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/_tests/test_style_encoding.py 2024-01-25 13:30:22.483507547 +0000 +@@ -13,8 +13,8 @@ + import numpy as np + import pandas as pd + import pytest +-from pydantic import Field + ++from napari._pydantic_compat import Field + from napari.layers.utils.style_encoding import ( + _ConstantStyleEncoding, + _DerivedStyleEncoding, +diff -Nru napari-0.4.18.orig/napari/layers/utils/_tests/test_text_manager.py napari-0.4.18/napari/layers/utils/_tests/test_text_manager.py +--- napari-0.4.18.orig/napari/layers/utils/_tests/test_text_manager.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/_tests/test_text_manager.py 2024-01-25 13:30:22.484507544 +0000 +@@ -1,8 +1,8 @@ + import numpy as np + import pandas as pd + import pytest +-from pydantic import ValidationError + ++from napari._pydantic_compat import ValidationError + from napari._tests.utils import assert_colors_equal + from napari.layers.utils.string_encoding import ( + ConstantStringEncoding, +diff -Nru napari-0.4.18.orig/napari/layers/utils/text_manager.py napari-0.4.18/napari/layers/utils/text_manager.py +--- napari-0.4.18.orig/napari/layers/utils/text_manager.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/layers/utils/text_manager.py 2024-01-25 13:30:22.484507544 +0000 +@@ -4,8 +4,8 @@ + + import numpy as np + import pandas as pd +-from pydantic import PositiveInt, validator + ++from napari._pydantic_compat import PositiveInt, validator + from napari.layers.base._base_constants import Blending + from napari.layers.utils._text_constants import Anchor + from napari.layers.utils._text_utils import get_text_anchors +diff -Nru napari-0.4.18.orig/napari/plugins/_plugin_manager.py napari-0.4.18/napari/plugins/_plugin_manager.py +--- napari-0.4.18.orig/napari/plugins/_plugin_manager.py 2024-01-25 13:30:10.981544405 +0000 ++++ napari-0.4.18/napari/plugins/_plugin_manager.py 2024-01-25 13:30:22.484507544 +0000 +@@ -22,9 +22,9 @@ + PluginManager as PluginManager, + ) + from napari_plugin_engine.hooks import HookCaller +-from pydantic import ValidationError + from typing_extensions import TypedDict + ++from napari._pydantic_compat import ValidationError + from napari.plugins import hook_specifications + from napari.settings import get_settings + from napari.types import AugmentedWidget, LayerData, SampleDict, WidgetCallable +diff -Nru napari-0.4.18.orig/napari/_pydantic_compat.py napari-0.4.18/napari/_pydantic_compat.py +--- napari-0.4.18.orig/napari/_pydantic_compat.py 1970-01-01 01:00:00.000000000 +0100 ++++ napari-0.4.18/napari/_pydantic_compat.py 2024-01-25 13:30:22.482507550 +0000 +@@ -0,0 +1,97 @@ ++try: ++ # pydantic v2 ++ from pydantic.v1 import ( ++ BaseModel, ++ BaseSettings, ++ Extra, ++ Field, ++ PositiveInt, ++ PrivateAttr, ++ ValidationError, ++ color, ++ conlist, ++ constr, ++ errors, ++ main, ++ parse_obj_as, ++ root_validator, ++ types, ++ utils, ++ validator, ++ ) ++ from pydantic.v1.env_settings import ( ++ EnvSettingsSource, ++ SettingsError, ++ SettingsSourceCallable, ++ ) ++ from pydantic.v1.error_wrappers import ErrorWrapper, display_errors ++ from pydantic.v1.fields import SHAPE_LIST, ModelField ++ from pydantic.v1.generics import GenericModel ++ from pydantic.v1.main import ClassAttribute, ModelMetaclass ++ from pydantic.v1.utils import ROOT_KEY, sequence_like ++except ImportError: ++ # pydantic v1 ++ from pydantic import ( ++ BaseModel, ++ BaseSettings, ++ Extra, ++ Field, ++ PositiveInt, ++ PrivateAttr, ++ ValidationError, ++ color, ++ conlist, ++ constr, ++ errors, ++ main, ++ parse_obj_as, ++ root_validator, ++ types, ++ utils, ++ validator, ++ ) ++ from pydantic.env_settings import ( ++ EnvSettingsSource, ++ SettingsError, ++ SettingsSourceCallable, ++ ) ++ from pydantic.error_wrappers import ErrorWrapper, display_errors ++ from pydantic.fields import SHAPE_LIST, ModelField ++ from pydantic.generics import GenericModel ++ from pydantic.main import ClassAttribute, ModelMetaclass ++ from pydantic.utils import ROOT_KEY, sequence_like ++ ++Color = color.Color ++ ++__all__ = ( ++ 'BaseModel', ++ 'BaseSettings', ++ 'ClassAttribute', ++ 'Color', ++ 'EnvSettingsSource', ++ 'ErrorWrapper', ++ 'Extra', ++ 'Field', ++ 'ModelField', ++ 'GenericModel', ++ 'ModelMetaclass', ++ 'PositiveInt', ++ 'PrivateAttr', ++ 'ROOT_KEY', ++ 'SettingsError', ++ 'SettingsSourceCallable', ++ 'SHAPE_LIST', ++ 'ValidationError', ++ 'color', ++ 'conlist', ++ 'constr', ++ 'display_errors', ++ 'errors', ++ 'main', ++ 'parse_obj_as', ++ 'root_validator', ++ 'sequence_like', ++ 'types', ++ 'utils', ++ 'validator', ++) +diff -Nru napari-0.4.18.orig/napari/_qt/dialogs/preferences_dialog.py napari-0.4.18/napari/_qt/dialogs/preferences_dialog.py +--- napari-0.4.18.orig/napari/_qt/dialogs/preferences_dialog.py 2024-01-25 13:30:10.968544447 +0000 ++++ napari-0.4.18/napari/_qt/dialogs/preferences_dialog.py 2024-01-25 13:30:22.482507550 +0000 +@@ -2,7 +2,6 @@ + from enum import EnumMeta + from typing import TYPE_CHECKING, Tuple, cast + +-from pydantic.main import BaseModel, ModelMetaclass + from qtpy.QtCore import QSize, Qt, Signal + from qtpy.QtWidgets import ( + QDialog, +@@ -14,10 +13,10 @@ + QVBoxLayout, + ) + ++from napari._pydantic_compat import BaseModel, ModelField, ModelMetaclass + from napari.utils.translations import trans + + if TYPE_CHECKING: +- from pydantic.fields import ModelField + from qtpy.QtGui import QCloseEvent, QKeyEvent + + +diff -Nru napari-0.4.18.orig/napari/_qt/dialogs/_tests/test_preferences_dialog.py napari-0.4.18/napari/_qt/dialogs/_tests/test_preferences_dialog.py +--- napari-0.4.18.orig/napari/_qt/dialogs/_tests/test_preferences_dialog.py 2024-01-25 13:30:10.968544447 +0000 ++++ napari-0.4.18/napari/_qt/dialogs/_tests/test_preferences_dialog.py 2024-01-25 13:30:22.482507550 +0000 +@@ -1,7 +1,7 @@ + import pytest +-from pydantic import BaseModel + from qtpy.QtCore import Qt + ++from napari._pydantic_compat import BaseModel + from napari._qt.dialogs.preferences_dialog import ( + PreferencesDialog, + QMessageBox, +diff -Nru napari-0.4.18.orig/napari/settings/_appearance.py napari-0.4.18/napari/settings/_appearance.py +--- napari-0.4.18.orig/napari/settings/_appearance.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_appearance.py 2024-01-25 13:30:22.484507544 +0000 +@@ -1,5 +1,4 @@ +-from pydantic import Field +- ++from napari._pydantic_compat import Field + from napari.settings._fields import Theme + from napari.utils.events.evented_model import EventedModel + from napari.utils.theme import available_themes +diff -Nru napari-0.4.18.orig/napari/settings/_application.py napari-0.4.18/napari/settings/_application.py +--- napari-0.4.18.orig/napari/settings/_application.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_application.py 2024-01-25 13:30:22.484507544 +0000 +@@ -3,8 +3,8 @@ + from typing import List, Optional, Tuple + + from psutil import virtual_memory +-from pydantic import Field, validator + ++from napari._pydantic_compat import Field, validator + from napari.settings._constants import LoopMode + from napari.settings._fields import Language + from napari.utils._base import _DEFAULT_LOCALE +diff -Nru napari-0.4.18.orig/napari/settings/_base.py napari-0.4.18/napari/settings/_base.py +--- napari-0.4.18.orig/napari/settings/_base.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_base.py 2024-01-25 13:30:22.484507544 +0000 +@@ -9,10 +9,13 @@ + from typing import TYPE_CHECKING, Dict, List, Optional, Sequence, Tuple, cast + from warnings import warn + +-from pydantic import BaseModel, BaseSettings, ValidationError +-from pydantic.env_settings import SettingsError +-from pydantic.error_wrappers import display_errors +- ++from napari._pydantic_compat import ( ++ BaseModel, ++ BaseSettings, ++ SettingsError, ++ ValidationError, ++ display_errors, ++) + from napari.settings._yaml import PydanticYamlMixin + from napari.utils.events import EmitterGroup, EventedModel + from napari.utils.misc import deep_update +@@ -23,8 +26,10 @@ + if TYPE_CHECKING: + from typing import AbstractSet, Any, Union + +- from pydantic.env_settings import EnvSettingsSource, SettingsSourceCallable +- ++ from napari._pydantic_compat import ( ++ EnvSettingsSource, ++ SettingsSourceCallable, ++ ) + from napari.utils.events import Event + + IntStr = Union[int, str] +@@ -33,7 +38,7 @@ + MappingIntStrAny = Mapping[IntStr, Any] + + +-class EventedSettings(BaseSettings, EventedModel): # type: ignore[misc] ++class EventedSettings(BaseSettings, EventedModel): + """A variant of EventedModel designed for settings. + + Pydantic's BaseSettings model will attempt to determine the values of any +@@ -116,7 +121,7 @@ + """Return the path to/from which settings be saved/loaded.""" + return self._config_path + +- def dict( # type: ignore [override] ++ def dict( + self, + *, + include: Union[AbstractSetIntStr, MappingIntStrAny] = None, # type: ignore +@@ -241,7 +246,7 @@ + the return list to change the priority of sources. + """ + cls._env_settings = nested_env_settings(env_settings) +- return ( # type: ignore [return-value] ++ return ( + init_settings, + cls._env_settings, + cls._config_file_settings_source, +diff -Nru napari-0.4.18.orig/napari/settings/_experimental.py napari-0.4.18/napari/settings/_experimental.py +--- napari-0.4.18.orig/napari/settings/_experimental.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_experimental.py 2024-01-25 13:30:22.484507544 +0000 +@@ -1,7 +1,6 @@ + from typing import Union + +-from pydantic import Field +- ++from napari._pydantic_compat import Field + from napari.settings._base import EventedSettings + from napari.utils.translations import trans + +diff -Nru napari-0.4.18.orig/napari/settings/_napari_settings.py napari-0.4.18/napari/settings/_napari_settings.py +--- napari-0.4.18.orig/napari/settings/_napari_settings.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_napari_settings.py 2024-01-25 13:30:22.484507544 +0000 +@@ -2,8 +2,7 @@ + from pathlib import Path + from typing import Any, Optional + +-from pydantic import Field +- ++from napari._pydantic_compat import Field + from napari.settings._appearance import AppearanceSettings + from napari.settings._application import ApplicationSettings + from napari.settings._base import ( +diff -Nru napari-0.4.18.orig/napari/settings/_plugins.py napari-0.4.18/napari/settings/_plugins.py +--- napari-0.4.18.orig/napari/settings/_plugins.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_plugins.py 2024-01-25 13:30:22.484507544 +0000 +@@ -1,8 +1,8 @@ + from typing import Dict, List, Set + +-from pydantic import Field + from typing_extensions import TypedDict + ++from napari._pydantic_compat import Field + from napari.settings._base import EventedSettings + from napari.utils.translations import trans + +diff -Nru napari-0.4.18.orig/napari/settings/_shortcuts.py napari-0.4.18/napari/settings/_shortcuts.py +--- napari-0.4.18.orig/napari/settings/_shortcuts.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_shortcuts.py 2024-01-25 13:30:22.484507544 +0000 +@@ -1,7 +1,6 @@ + from typing import Dict, List + +-from pydantic import Field, validator +- ++from napari._pydantic_compat import Field, validator + from napari.utils.events.evented_model import EventedModel + from napari.utils.shortcuts import default_shortcuts + from napari.utils.translations import trans +diff -Nru napari-0.4.18.orig/napari/settings/_tests/test_settings.py napari-0.4.18/napari/settings/_tests/test_settings.py +--- napari-0.4.18.orig/napari/settings/_tests/test_settings.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_tests/test_settings.py 2024-01-25 13:30:22.484507544 +0000 +@@ -2,11 +2,11 @@ + import os + from pathlib import Path + +-import pydantic + import pytest + from yaml import safe_load + + from napari import settings ++from napari._pydantic_compat import Field, ValidationError + from napari.settings import CURRENT_SCHEMA_VERSION, NapariSettings + from napari.utils.theme import get_theme, register_theme + +@@ -74,7 +74,7 @@ + data = "appearance:\n theme: 1" + fake_path = tmp_path / 'fake_path.yml' + fake_path.write_text(data) +- with pytest.raises(pydantic.ValidationError): ++ with pytest.raises(ValidationError): + NapariSettings(fake_path) + + +@@ -108,8 +108,8 @@ + fake_path = tmp_path / 'fake_path.yml' + fake_path.write_text(data) + +- settings = NapariSettings(fake_path) +- assert getattr(settings, "non_existing_section", None) is None ++ settings_ = NapariSettings(fake_path) ++ assert getattr(settings_, "non_existing_section", None) is None + + + def test_settings_to_dict(test_settings): +@@ -145,11 +145,11 @@ + + + def test_settings_model(test_settings): +- with pytest.raises(pydantic.error_wrappers.ValidationError): ++ with pytest.raises(ValidationError): + # Should be string + test_settings.appearance.theme = 1 + +- with pytest.raises(pydantic.error_wrappers.ValidationError): ++ with pytest.raises(ValidationError): + # Should be a valid string + test_settings.appearance.theme = "vaporwave" + +@@ -159,7 +159,7 @@ + custom_theme_name = "_test_blue_" + + # No theme registered yet, this should fail +- with pytest.raises(pydantic.error_wrappers.ValidationError): ++ with pytest.raises(ValidationError): + test_settings.appearance.theme = custom_theme_name + + blue_theme = get_theme('dark', True) +@@ -219,7 +219,7 @@ + + def test_settings_env_variables_fails(monkeypatch): + monkeypatch.setenv('NAPARI_APPEARANCE_THEME', 'FOOBAR') +- with pytest.raises(pydantic.ValidationError): ++ with pytest.raises(ValidationError): + NapariSettings() + + +@@ -228,7 +228,7 @@ + from napari.settings._base import EventedSettings + + class Sub(EventedSettings): +- x: int = pydantic.Field(1, env='varname') ++ x: int = Field(1, env='varname') + + class T(NapariSettings): + sub: Sub +diff -Nru napari-0.4.18.orig/napari/settings/_yaml.py napari-0.4.18/napari/settings/_yaml.py +--- napari-0.4.18.orig/napari/settings/_yaml.py 2024-01-25 13:30:10.984544395 +0000 ++++ napari-0.4.18/napari/settings/_yaml.py 2024-01-25 13:30:22.485507540 +0000 +@@ -3,9 +3,9 @@ + from enum import Enum + from typing import TYPE_CHECKING, Type + +-from pydantic import BaseModel + from yaml import SafeDumper, dump_all + ++from napari._pydantic_compat import BaseModel + from napari.settings._fields import Version + + if TYPE_CHECKING: +@@ -77,7 +77,7 @@ + exclude_none=exclude_none, + ) + if self.__custom_root_type__: +- from pydantic.utils import ROOT_KEY ++ from napari._pydantic_compat import ROOT_KEY + + data = data[ROOT_KEY] + return self._yaml_dump(data, dumper, **dumps_kwargs) +diff -Nru napari-0.4.18.orig/napari/utils/colormaps/colormap.py napari-0.4.18/napari/utils/colormaps/colormap.py +--- napari-0.4.18.orig/napari/utils/colormaps/colormap.py 2024-01-25 13:30:10.985544392 +0000 ++++ napari-0.4.18/napari/utils/colormaps/colormap.py 2024-01-25 13:33:20.714011699 +0000 +@@ -2,7 +2,7 @@ + from typing import Optional + + import numpy as np +-from pydantic import PrivateAttr, validator ++from napari._pydantic_compat import Field, PrivateAttr, validator + + from napari.utils.color import ColorArray + from napari.utils.colormaps.colorbars import make_colorbar +diff -Nru napari-0.4.18.orig/napari/utils/events/containers/_selection.py napari-0.4.18/napari/utils/events/containers/_selection.py +--- napari-0.4.18.orig/napari/utils/events/containers/_selection.py 2024-01-25 13:30:10.986544389 +0000 ++++ napari-0.4.18/napari/utils/events/containers/_selection.py 2024-01-25 13:30:22.485507540 +0000 +@@ -5,7 +5,7 @@ + from napari.utils.translations import trans + + if TYPE_CHECKING: +- from pydantic.fields import ModelField ++ from napari._pydantic_compat import ModelField + + _T = TypeVar("_T") + _S = TypeVar("_S") +@@ -140,7 +140,7 @@ + @classmethod + def validate(cls, v, field: 'ModelField'): + """Pydantic validator.""" +- from pydantic.utils import sequence_like ++ from napari._pydantic_compat import sequence_like + + if isinstance(v, dict): + data = v.get("selection", []) +@@ -180,7 +180,7 @@ + errors.append(error) + + if errors: +- from pydantic import ValidationError ++ from napari._pydantic_compat import ValidationError + + raise ValidationError(errors, cls) # type: ignore + obj = cls(data=data) +diff -Nru napari-0.4.18.orig/napari/utils/events/containers/_set.py napari-0.4.18/napari/utils/events/containers/_set.py +--- napari-0.4.18.orig/napari/utils/events/containers/_set.py 2024-01-25 13:30:10.986544389 +0000 ++++ napari-0.4.18/napari/utils/events/containers/_set.py 2024-01-25 13:30:22.485507540 +0000 +@@ -8,7 +8,7 @@ + _T = TypeVar("_T") + + if TYPE_CHECKING: +- from pydantic.fields import ModelField ++ from napari._pydantic_compat import ModelField + + + class EventedSet(MutableSet[_T]): +@@ -165,7 +165,7 @@ + @classmethod + def validate(cls, v, field: ModelField): + """Pydantic validator.""" +- from pydantic.utils import sequence_like ++ from napari._pydantic_compat import sequence_like + + if not sequence_like(v): + raise TypeError( +@@ -185,7 +185,7 @@ + if error: + errors.append(error) + if errors: +- from pydantic import ValidationError ++ from napari._pydantic_compat import ValidationError + + raise ValidationError(errors, cls) # type: ignore + return cls(v) +diff -Nru napari-0.4.18.orig/napari/utils/events/custom_types.py napari-0.4.18/napari/utils/events/custom_types.py +--- napari-0.4.18.orig/napari/utils/events/custom_types.py 2024-01-25 13:30:10.986544389 +0000 ++++ napari-0.4.18/napari/utils/events/custom_types.py 2024-01-25 13:30:22.485507540 +0000 +@@ -11,12 +11,13 @@ + ) + + import numpy as np +-from pydantic import errors, types ++ ++from napari._pydantic_compat import errors, types + + if TYPE_CHECKING: + from decimal import Decimal + +- from pydantic.fields import ModelField ++ from napari._pydantic_compat import ModelField + + Number = Union[int, float, Decimal] + +diff -Nru napari-0.4.18.orig/napari/utils/events/debugging.py napari-0.4.18/napari/utils/events/debugging.py +--- napari-0.4.18.orig/napari/utils/events/debugging.py 2024-01-25 13:30:10.986544389 +0000 ++++ napari-0.4.18/napari/utils/events/debugging.py 2024-01-25 13:30:22.485507540 +0000 +@@ -4,8 +4,7 @@ + from textwrap import indent + from typing import TYPE_CHECKING, ClassVar, Set + +-from pydantic import BaseSettings, Field, PrivateAttr +- ++from napari._pydantic_compat import BaseSettings, Field, PrivateAttr + from napari.utils.misc import ROOT_DIR + from napari.utils.translations import trans + +@@ -39,8 +38,12 @@ + # to include/exclude when printing events. + include_emitters: Set[str] = Field(default_factory=set) + include_events: Set[str] = Field(default_factory=set) +- exclude_emitters: Set[str] = {'TransformChain', 'Context'} +- exclude_events: Set[str] = {'status', 'position'} ++ exclude_emitters: Set[str] = Field( ++ default_factory=lambda: {'TransformChain', 'Context'} ++ ) ++ exclude_events: Set[str] = Field( ++ default_factory=lambda: {'status', 'position'} ++ ) + # stack depth to show + stack_depth: int = 20 + # how many sub-emit nesting levels to show +diff -Nru napari-0.4.18.orig/napari/utils/events/evented_model.py napari-0.4.18/napari/utils/events/evented_model.py +--- napari-0.4.18.orig/napari/utils/events/evented_model.py 2024-01-25 13:30:10.986544389 +0000 ++++ napari-0.4.18/napari/utils/events/evented_model.py 2024-01-25 13:30:22.485507540 +0000 +@@ -5,8 +5,14 @@ + from typing import Any, Callable, ClassVar, Dict, Set, Union + + import numpy as np +-from pydantic import BaseModel, PrivateAttr, main, utils + ++from napari._pydantic_compat import ( ++ BaseModel, ++ ModelMetaclass, ++ PrivateAttr, ++ main, ++ utils, ++) + from napari.utils.events.event import EmitterGroup, Event + from napari.utils.misc import pick_equality_operator + from napari.utils.translations import trans +@@ -63,7 +69,7 @@ + main.ClassAttribute = utils.ClassAttribute + + +-class EventedMetaclass(main.ModelMetaclass): ++class EventedMetaclass(ModelMetaclass): + """pydantic ModelMetaclass that preps "equality checking" operations. + + A metaclass is the thing that "constructs" a class, and ``ModelMetaclass`` +diff -Nru napari-0.4.18.orig/napari/utils/events/_tests/test_evented_model.py napari-0.4.18/napari/utils/events/_tests/test_evented_model.py +--- napari-0.4.18.orig/napari/utils/events/_tests/test_evented_model.py 2024-01-25 13:30:10.986544389 +0000 ++++ napari-0.4.18/napari/utils/events/_tests/test_evented_model.py 2024-01-25 13:30:22.485507540 +0000 +@@ -9,8 +9,8 @@ + import pytest + from dask import delayed + from dask.delayed import Delayed +-from pydantic import Field + ++from napari._pydantic_compat import Field + from napari.utils.events import EmitterGroup, EventedModel + from napari.utils.events.custom_types import Array + from napari.utils.misc import StringEnum +diff -Nru napari-0.4.18.orig/napari/utils/events/_tests/test_selection.py napari-0.4.18/napari/utils/events/_tests/test_selection.py +--- napari-0.4.18.orig/napari/utils/events/_tests/test_selection.py 2024-01-25 13:30:10.986544389 +0000 ++++ napari-0.4.18/napari/utils/events/_tests/test_selection.py 2024-01-25 13:30:22.485507540 +0000 +@@ -1,8 +1,8 @@ + from unittest.mock import Mock + + import pytest +-from pydantic import ValidationError + ++from napari._pydantic_compat import ValidationError + from napari.utils.events import EventedModel, Selection + + +diff -Nru napari-0.4.18.orig/napari/utils/_tests/test_theme.py napari-0.4.18/napari/utils/_tests/test_theme.py +--- napari-0.4.18.orig/napari/utils/_tests/test_theme.py 2024-01-25 13:30:10.985544392 +0000 ++++ napari-0.4.18/napari/utils/_tests/test_theme.py 2024-01-25 13:30:22.485507540 +0000 +@@ -5,8 +5,8 @@ + from npe2 import PluginManager, PluginManifest, __version__ as npe2_version + from npe2.manifest.schema import ContributionPoints + from packaging.version import parse as parse_version +-from pydantic import ValidationError + ++from napari._pydantic_compat import ValidationError + from napari.resources._icons import PLUGIN_FILE_NAME + from napari.settings import get_settings + from napari.utils.theme import ( +diff -Nru napari-0.4.18.orig/napari/utils/theme.py napari-0.4.18/napari/utils/theme.py +--- napari-0.4.18.orig/napari/utils/theme.py 2024-01-25 13:30:10.987544386 +0000 ++++ napari-0.4.18/napari/utils/theme.py 2024-01-25 13:30:22.485507540 +0000 +@@ -8,9 +8,8 @@ + from typing import List, Union + + import npe2 +-from pydantic import validator +-from pydantic.color import Color + ++from napari._pydantic_compat import Color, validator + from napari._vendor import darkdetect + from napari.resources._icons import ( + PLUGIN_FILE_NAME, +diff -Nru napari-0.4.18.orig/setup.cfg napari-0.4.18/setup.cfg +--- napari-0.4.18.orig/setup.cfg 2024-01-25 13:30:10.988544382 +0000 ++++ napari-0.4.18/setup.cfg 2024-01-25 13:34:10.674857084 +0000 +@@ -63,7 +63,7 @@ + pint>=0.17 + psutil>=5.0 + psygnal>=0.3.4 +- pydantic>=1.9.0,<2 ++ pydantic>=1.9.0 + pygments>=2.6.0 + PyOpenGL>=3.1.0 + PyYAML>=5.1 diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb deleted file mode 100644 index 359b3f1f1a3b..000000000000 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb +++ /dev/null @@ -1,39 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pydantic' -version = '1.10.13' - -homepage = 'https://github.com/samuelcolvin/pydantic' -description = """Data validation and settings management using Python type hinting.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('binutils', '2.40'), - ('hatchling', '1.18.0'), - ('maturin', '1.4.0', '-Rust-1.75.0'), -] - -dependencies = [ - ('Python', '3.11.3'), - ('typing-extensions', '4.9.0',), -] - -sanity_pip_check = True -use_pip = True - -exts_list = [ - ('annotated-types', '0.6.0', { - 'source_tmpl': 'annotated_types-%(version)s.tar.gz', - 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], - }), - ('pydantic-core', '2.14.6', { - 'source_tmpl': 'pydantic_core-%(version)s.tar.gz', - 'checksums': ['1fd0c1d395372843fba13a51c28e3bb9d59bd7aebfeb17358ffaaa1e4dbbe948'], - }), - (name, version, { - 'checksums': ['32c8b48dcd3b2ac4e78b0ba4af3a2c2eb6048cb75202f0ea7b34feb740efc340'], - }), -] - -moduleclass = 'devel' From 9f6ea8613e63d3250db26353dfdc58177c385a86 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 25 Jan 2024 16:02:13 +0100 Subject: [PATCH 0449/1193] wandb should not specify urllib3 since it does not need a newer version then the one in Python-bundle-PyPI --- easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb index 5c06dc3de1be..878f6cc3f726 100644 --- a/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/w/wandb/wandb-0.16.1-GCC-12.3.0.eb @@ -26,9 +26,6 @@ exts_list = [ 'modulename': 'dockerpycreds', 'checksums': ['6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4'], }), - ('urllib3', '2.1.0', { - 'checksums': ['df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54'], - }), ('sentry-sdk', '1.39.1', { 'checksums': ['320a55cdf9da9097a0bead239c35b7e61f53660ef9878861824fd6d9b2eaf3b5'], }), From ef1c47dc64559ef43bb2dc995971706c7352df8a Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 25 Jan 2024 15:51:10 +0000 Subject: [PATCH 0450/1193] set download_dep_fail in OBITools3 --- .../easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb index 2d5ba362a086..c2ae09ce8536 100644 --- a/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/OBITools3/OBITools3-3.0.1b26-GCCcore-12.3.0.eb @@ -24,6 +24,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True preinstallopts = "sed -i \"s|get_python_lib()|get_python_lib(prefix='%(installdir)s')|g\" setup.py &&" From c75eb407d6ccb5c2dfa0cf4c0d3ced65f96f5cd2 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Thu, 25 Jan 2024 16:27:32 +0000 Subject: [PATCH 0451/1193] missing space in description Co-authored-by: Adam Huffman --- .../easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb index b34936b9ab16..785dc7f23200 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.2-GCCcore-12.3.0.eb @@ -8,7 +8,7 @@ version = '1.7.2' homepage = 'https://hunspell.github.io/' description = """Hunspell is a spell checker and morphological analyzer -library and program designed for languageswith rich morphology and +library and program designed for languages with rich morphology and complex word compounding or character encoding.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} From 1e1458486f5310939b556c82b0660946687c8e47 Mon Sep 17 00:00:00 2001 From: Leon Kos Date: Thu, 25 Jan 2024 22:37:28 +0100 Subject: [PATCH 0452/1193] Remove compiler selectors --- easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb index eaea84ef6b4b..8b541bcdd0e8 100644 --- a/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb +++ b/easybuild/easyconfigs/e/Elmer/Elmer-9.0-foss-2022b.eb @@ -35,9 +35,6 @@ dependencies = [ configopts = '-DWITH_ELMERGUI:BOOL=TRUE -DWITH_QT5:BOOL=TRUE ' configopts += '-DWITH_MPI:BOOL=TRUE ' -configopts += '-DCMAKE_C_COMPILER=$(which $CC) ' -configopts += '-DCMAKE_Fortran_COMPILER=$(which $F90) ' -configopts += '-DCMAKE_CXX_COMPILER=$(which $CXX) ' configopts += '-DBLAS_LIBRARIES="-L$EBVARBLAS_LAPACK_INC_DIR $EBVARLIBBLAS" ' configopts += '-DLAPACK_LIBRARIES="-L$EBVARBLAS_LAPACK_INC_DIR $EBVARLIBLAPACK" ' configopts += '-DSCALAPACK_LIBRARIES="-L$EBVARSCALAPACK_LIB_DIR $EBVARLIBSCALAPACK" ' From e8233156a52b8979049b83b5cc7c8c56bd887305 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Jan 2024 10:52:34 +0100 Subject: [PATCH 0453/1193] adding easyconfigs: scikit-learn-1.4.0-gfbf-2023b.eb --- .../scikit-learn-1.4.0-gfbf-2023b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.4.0-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.4.0-gfbf-2023b.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.4.0-gfbf-2023b.eb new file mode 100644 index 000000000000..75efad093b78 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.4.0-gfbf-2023b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.4.0' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'checksums': ['d4373c984eba20e393216edd51a3e3eede56cbe93d4247516d205643c3b93121'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 4dab87b7855643d4cb034b693a248f842f223fb8 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Jan 2024 10:33:09 +0000 Subject: [PATCH 0454/1193] Patched to work on Debian Bookworm --- .../Perl-bundle-5.36.1-debian-release.patch | 73 ++++++++ .../Perl-bundle-5.36.1-pod.patch | 159 ++++++++++++++++++ .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 26 ++- 3 files changed, 256 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-debian-release.patch create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-pod.patch diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-debian-release.patch b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-debian-release.patch new file mode 100644 index 000000000000..e738ee0fa5cd --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-debian-release.patch @@ -0,0 +1,73 @@ +From a1c14cce4121862bb12fe34f294b5ab1d3dce7da Mon Sep 17 00:00:00 2001 +From: Vincent Lefevre +Date: Tue, 8 Oct 2019 17:06:57 +0200 +Subject: [PATCH] Update for Debian 8.0 (jessie), 9.0 (stretch) and 10.0 + (buster). + +Also removed the obsolete debian_version and debian_release lines, +as Distribution.pm no longer supports multiple release files and +they made the tests fail (fixes issue #2 for Debian). + +Bug: https://github.com/burak/CPAN-Sys-Info-Driver-Linux/pull/3 + +Added bullseye and bookworm as well. + +--- + lib/Sys/Info/Driver/Linux/OS/Distribution/Conf.pm | 8 ++++++-- + 1 file changed, 6 insertions(+), 2 deletions(-) + +--- a/lib/Sys/Info/Driver/Linux/OS/Distribution/Conf.pm ++++ b/lib/Sys/Info/Driver/Linux/OS/Distribution/Conf.pm +@@ -31,8 +31,6 @@ + + manufacturer = Debian Project + version_match = (.+) +- release = debian_version +- release = debian_release + + 1.1 = buzz + 1.2 = rex +@@ -46,21 +44,31 @@ + 5.0 = lenny + 6.0 = squeeze + 7.0 = wheezy ++ 8.0 = jessie ++ 9.0 = stretch ++ 10.0 = buster ++ 11.0 = bullseye ++ 12.0 = bookworm + + # we get the version as "lenny/sid" for example + +- buzz = 1.1 +- rex = 1.2 +- bo = 1.3 +- hamm = 2.0 +- slink = 2.1 +- potato = 2.2 +- woody = 3.0 +- sarge = 3.1 +- etch = 4.0 +- lenny = 5.0 +- squeeze = 6.0 +- wheezy = 7.0 ++ buzz = 1.1 ++ rex = 1.2 ++ bo = 1.3 ++ hamm = 2.0 ++ slink = 2.1 ++ potato = 2.2 ++ woody = 3.0 ++ sarge = 3.1 ++ etch = 4.0 ++ lenny = 5.0 ++ squeeze = 6.0 ++ wheezy = 7.0 ++ jessie = 8.0 ++ stretch = 9.0 ++ buster = 10.0 ++ bullseye = 11.0 ++ bookworm = 12.0 + + + diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-pod.patch b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-pod.patch new file mode 100644 index 000000000000..0f21a1395d95 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-5.36.1-pod.patch @@ -0,0 +1,159 @@ +Description: remove duplicate NAME sections, keep the one with a synopsis +Origin: vendor +Author: gregor herrmann +Last-Update: 2019-10-25 + +--- a/lib/Sys/Info/Driver/Linux.pm ++++ b/lib/Sys/Info/Driver/Linux.pm +@@ -29,7 +29,7 @@ + + =head1 NAME + +-Sys::Info::Driver::Linux ++Sys::Info::Driver::Linux - Linux driver for Sys::Info + + =head1 VERSION + +@@ -43,10 +43,6 @@ + + This is the main module in the C driver collection. + +-=head1 NAME +- +-Sys::Info::Driver::Linux - Linux driver for Sys::Info +- + =head1 METHODS + + None. +--- a/lib/Sys/Info/Driver/Linux/Constants.pm ++++ b/lib/Sys/Info/Driver/Linux/Constants.pm +@@ -74,7 +74,7 @@ + + =head1 NAME + +-Sys::Info::Driver::Linux::Constants ++Sys::Info::Driver::Linux::Constants - Constants for Linux driver + + =head1 VERSION + +@@ -86,10 +86,6 @@ + + Constants for Linux driver. + +-=head1 NAME +- +-Sys::Info::Driver::Linux::Constants - Constants for Linux driver +- + =head1 METHODS + + None. +--- a/lib/Sys/Info/Driver/Linux/Device.pm ++++ b/lib/Sys/Info/Driver/Linux/Device.pm +@@ -13,7 +13,7 @@ + + =head1 NAME + +-Sys::Info::Driver::Linux::Device ++Sys::Info::Driver::Linux::Device - Base class for Linux device drivers + + =head1 VERSION + +@@ -27,10 +27,6 @@ + + Base class for Linux device drivers. + +-=head1 NAME +- +-Sys::Info::Driver::Linux::Device - Base class for Linux device drivers +- + =head1 METHODS + + None. +--- a/lib/Sys/Info/Driver/Linux/Device/CPU.pm ++++ b/lib/Sys/Info/Driver/Linux/Device/CPU.pm +@@ -94,7 +94,7 @@ + + =head1 NAME + +-Sys::Info::Driver::Linux::Device::CPU ++Sys::Info::Driver::Linux::Device::CPU - Linux CPU Device Driver + + =head1 VERSION + +@@ -108,10 +108,6 @@ + + Identifies the CPU with L, L and C<< /proc >>. + +-=head1 NAME +- +-Sys::Info::Driver::Linux::Device::CPU - Linux CPU Device Driver +- + =head1 METHODS + + =head2 identify +--- a/lib/Sys/Info/Driver/Linux/OS.pm ++++ b/lib/Sys/Info/Driver/Linux/OS.pm +@@ -263,7 +263,7 @@ + + =head1 NAME + +-Sys::Info::Driver::Linux::OS ++Sys::Info::Driver::Linux::OS - Linux backend + + =head1 VERSION + +@@ -277,10 +277,6 @@ + + - + +-=head1 NAME +- +-Sys::Info::Driver::Linux::OS - Linux backend +- + =head1 METHODS + + Please see L for definitions of these methods and more. +--- a/lib/Sys/Info/Driver/Linux/OS/Distribution.pm ++++ b/lib/Sys/Info/Driver/Linux/OS/Distribution.pm +@@ -360,7 +360,7 @@ + + =head1 NAME + +-Sys::Info::Driver::Linux::OS::Distribution ++Sys::Info::Driver::Linux::OS::Distribution - Linux distribution probe + + =head1 VERSION + +@@ -394,10 +394,6 @@ + redflag and ubuntu(lsb). People running unsupported distro's are greatly + encouraged to submit patches. + +-=head1 NAME +- +-Sys::Info::Driver::Linux::OS::Distribution - Linux distribution probe +- + =head1 METHODS + + =head2 build +--- a/lib/Sys/Info/Driver/Linux/OS/Distribution/Conf.pm ++++ b/lib/Sys/Info/Driver/Linux/OS/Distribution/Conf.pm +@@ -259,7 +259,7 @@ + + =head1 NAME + +-Sys::Info::Driver::Linux::OS::Distribution::Conf ++Sys::Info::Driver::Linux::OS::Distribution::Conf - Distro configuration + + =head1 VERSION + +@@ -269,10 +269,6 @@ + + =head1 DESCRIPTION + +-=head1 NAME +- +-Sys::Info::Driver::Linux::OS::Distribution::Conf - Distro configuration +- + =head1 AUTHOR + + Burak Gursoy diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 9c5ab28d7b70..b67a4de71773 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -2053,7 +2053,18 @@ exts_list = [ ('Sys::Info::Driver::Linux::Device::CPU', '0.7905', { 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], - 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + 'patches': [ + ('Perl-bundle-5.36.1-debian-release.patch'), + ('Perl-bundle-5.36.1-pod.patch'), + ], + 'checksums': [ + {'Sys-Info-Driver-Linux-%(version)s.tar.gz': + '899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'}, + {'Perl-bundle-5.36.1-debian-release.patch': + '18b8d876db5b3abe7e5a1bb8c6abf8b5fef481b56294472fcf9f96f974c56c48'}, + {'Perl-bundle-5.36.1-pod.patch': + '7c70bd91a06c256a8d85845e011e53a1a9d4f8a250d9f06bd06f5004596f271a'}, + ], }), ('Sys::Info', '0.7811', { 'source_tmpl': 'Sys-Info-%(version)s.tar.gz', @@ -2103,7 +2114,18 @@ exts_list = [ ('Sys::Info::Driver::Linux', '0.7905', { 'source_tmpl': 'Sys-Info-Driver-Linux-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/B/BU/BURAK'], - 'checksums': ['899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'], + 'patches': [ + ('Perl-bundle-5.36.1-debian-release.patch'), + ('Perl-bundle-5.36.1-pod.patch'), + ], + 'checksums': [ + {'Sys-Info-Driver-Linux-%(version)s.tar.gz': + '899c329bd3508ec5849ad0e5dadfa7c3679bbacaea9dda12404a7893032e8b7b'}, + {'Perl-bundle-5.36.1-debian-release.patch': + '18b8d876db5b3abe7e5a1bb8c6abf8b5fef481b56294472fcf9f96f974c56c48'}, + {'Perl-bundle-5.36.1-pod.patch': + '7c70bd91a06c256a8d85845e011e53a1a9d4f8a250d9f06bd06f5004596f271a'}, + ], }), ('Unix::Processors', '2.046', { 'source_tmpl': 'Unix-Processors-%(version)s.tar.gz', From 622cd993b426ce875c34dcb1ad863750ab5ad5b7 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 26 Jan 2024 12:26:35 +0100 Subject: [PATCH 0455/1193] update PySCF v2.4.0 --- .../p/PySCF/PySCF-2.4.0-foss-2022b.eb | 24 ++++++++++++++----- 1 file changed, 18 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb index 64c2ec531760..3485580284d2 100644 --- a/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb @@ -49,12 +49,16 @@ exts_list = [ ('doci', '08079a9', { 'checksums': ['f492ba45dfe50c9b459e53a946a677528af0dc2097ff77ea3767aa4f46c5d9ba'], }), - ('icmpspt', '50c386e', { - 'checksums': ['08029863ae8740939a730fe5e104661c67d8dd0b8a8555b603fc8a0777096d48'], + ('icmpspt', 'f26062b', { + 'patches': [('PySCF-2.1.1_icmpspt-exe-path.patch', 0)], + 'checksums': [ + {'icmpspt-f26062b.tar.gz': '8f44b317da209882e0353d2731d8bc907de450af02429e962ae9b8d3f8c95a47'}, + {'PySCF-2.1.1_icmpspt-exe-path.patch': 'e972e377b34b964c48a99909301bf21a9c73d8eb9ecb96a889621d71471c56c9'}, + ], }), - ('properties', '92a4df7', { + ('properties', '8b94d8d', { 'modulename': 'pyscf.prop', - 'checksums': ['df5456315855c7a4f5858b244461793f2cbc21f6a6c0328039838ad85913c79d'], + 'checksums': ['b40e071472a6bdfcaec8cd358c7c58c58748c59d8b188fdca09d6eca63329914'], }), ('qsdopt', '3ad2c02', { 'checksums': ['cc639150e5f9efad8ffe496b3dccd2952a1f60fdad51f611cffba701892b384e'], @@ -78,14 +82,22 @@ exts_list = [ 'checksums': ['6e9f612c2d0bf2198154520e01dce57cf3a6e474840c1892466de3171eaeb7db'], }), ('dmrgscf', '4ff57bf', { - 'checksums': ['0683cfc2e6676aa11da7b2eee66e96442a64a37b72f65057779718c5fdb43c5f'], + 'patches': [('PySCF-2.1.1_dmrgscf-settings.patch', 0)], + 'checksums': [ + {'dmrgscf-4ff57bf.tar.gz': '0683cfc2e6676aa11da7b2eee66e96442a64a37b72f65057779718c5fdb43c5f'}, + {'PySCF-2.1.1_dmrgscf-settings.patch': 'a0310a2a90e96bd64d1560b2cc73a805717e129d2921e91cc5e6038b9f153677'}, + ], }), ('fciqmc', 'ee98fb4', { 'modulename': 'pyscf.fciqmcscf', 'checksums': ['b2f081ac295df0e622c6d1b3bff6d7834f97131f1f0fc87ec8bcff2137ef4199'], }), ('mbd', '485c18c', { - 'checksums': ['de1fb14650fcb87909cae33dc318d2e213653ac4393ced7e070dfa6308d95846'], + 'patches': [('PySCF-2.1.1_mbd-fix-init.patch', 0)], + 'checksums': [ + {'mbd-485c18c.tar.gz': 'de1fb14650fcb87909cae33dc318d2e213653ac4393ced7e070dfa6308d95846'}, + {'PySCF-2.1.1_mbd-fix-init.patch': '4f8e4b2e39b77428187851c4b6ced39401561bc81f4f3a4605da5d5c7b798cbc'}, + ], }), ('naive-hci', '0c28d6e', { 'modulename': 'pyscf.hci', From a612b0ed7206a3dae9877481d6ec0d27a3309d9f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Jan 2024 12:25:12 +0000 Subject: [PATCH 0456/1193] Checksum updated as tarball had minor changes done --- .../CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb index 949da3f8a4ef..b455f7c9a677 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -39,11 +39,13 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], 'sources': ['v%(version)s.tar.gz'], - 'patches': ['%(name)s-%(version)s-sphinxremoval.patch'], - 'checksums': ['0f4c32c26a4f413d8852dea2a4d759cc754698bd40d076aa7c9191336752c46c', - # cellbender-0.2.1-sphinxremoval.patch - '0f6a342bac16f4ee80cd05d43923b4cc60d71999ea1bb5c80a75edb7290bbdec', - ], + 'patches': ['cellbender-0.2.1-sphinxremoval.patch'], + 'checksums': [ + {'%(version)s.tar.gz': + '309f6245585d9741ba7099690a10a8f496756c4827d100100130be589b797ba4'}, + {'cellbender-0.2.1-sphinxremoval.patch': + '0f6a342bac16f4ee80cd05d43923b4cc60d71999ea1bb5c80a75edb7290bbdec'}, + ], }), ] From 3ab1cd0cf86efeb1b8a28a0a726c5d8ed86fdfb1 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Jan 2024 12:38:50 +0000 Subject: [PATCH 0457/1193] Typo corrected --- .../c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb index b455f7c9a677..db39ff14dca9 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -39,11 +39,11 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], 'sources': ['v%(version)s.tar.gz'], - 'patches': ['cellbender-0.2.1-sphinxremoval.patch'], + 'patches': ['Cellbender-0.2.1-sphinxremoval.patch'], 'checksums': [ {'%(version)s.tar.gz': '309f6245585d9741ba7099690a10a8f496756c4827d100100130be589b797ba4'}, - {'cellbender-0.2.1-sphinxremoval.patch': + {'Cellbender-0.2.1-sphinxremoval.patch': '0f6a342bac16f4ee80cd05d43923b4cc60d71999ea1bb5c80a75edb7290bbdec'}, ], }), From dd8ddd06cf549af976e0f7f279e49e1de87a2d2f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Jan 2024 12:51:39 +0000 Subject: [PATCH 0458/1193] Another typo corrected --- .../c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb index db39ff14dca9..0976e7eed105 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -39,11 +39,11 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], 'sources': ['v%(version)s.tar.gz'], - 'patches': ['Cellbender-0.2.1-sphinxremoval.patch'], + 'patches': ['CellBender-0.2.1-sphinxremoval.patch'], 'checksums': [ {'%(version)s.tar.gz': '309f6245585d9741ba7099690a10a8f496756c4827d100100130be589b797ba4'}, - {'Cellbender-0.2.1-sphinxremoval.patch': + {'CellBender-0.2.1-sphinxremoval.patch': '0f6a342bac16f4ee80cd05d43923b4cc60d71999ea1bb5c80a75edb7290bbdec'}, ], }), From 048ee08735ec1210ff973a3256ea12e2e84591c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Jan 2024 14:07:13 +0100 Subject: [PATCH 0459/1193] add spdep extension to R-bundle-CRAN v2023.12 --- .../r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index 9d48ee9ea592..c17dfda0cf1d 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -3395,6 +3395,9 @@ exts_list = [ ('tidybayes', '3.0.6', { 'checksums': ['706044e17855a684a5ad1aeb582963dd3c7192a4a8ad0584358d0ea7c7aadb90'], }), + ('spdep', '1.3-1', { + 'checksums': ['36062ccd094f9110a43cd51902c794242311fd23b861dde22c450446dce85396'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 802c8208aad8104fd169cf84614aae4e26acea1f Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 26 Jan 2024 14:51:33 +0100 Subject: [PATCH 0460/1193] adding easyconfigs: cclib-1.8-foss-2023a.eb --- .../c/cclib/cclib-1.8-foss-2023a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/cclib/cclib-1.8-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/cclib/cclib-1.8-foss-2023a.eb b/easybuild/easyconfigs/c/cclib/cclib-1.8-foss-2023a.eb new file mode 100644 index 000000000000..9ab78e650e91 --- /dev/null +++ b/easybuild/easyconfigs/c/cclib/cclib-1.8-foss-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'cclib' +version = '1.8' + +homepage = 'https://cclib.github.io/' + +description = """ + cclib is a Python library that provides parsers for computational chemistry log files. + It also provides a platform to implement algorithms in a package-independent manner. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('periodictable', '1.6.1', { + 'checksums': ['7c501c9f73d77b1fb28cb51e85b28429c2c44a99ce3d1274894564c72d712603'], + }), + (name, version, { + 'checksums': ['12b7a7ed8191f02fa12320dbdc830546ee1615e8b4737e3d766f34622abbd521'], + }), +] + +_bins = ['ccframe', 'ccget', 'ccwrite', 'cda'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%s --help' % x for x in _bins] + +moduleclass = 'chem' From 82523f9ce5acacca03754e70081b8e3dd99cbdc4 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 26 Jan 2024 15:18:47 +0100 Subject: [PATCH 0461/1193] tag vesion of libcint to v4.5.0 --- .../l/libcint/libcint-5.5.0-gfbf-2022b.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb b/easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb new file mode 100644 index 000000000000..32f2622348ab --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '5.5.0' + +homepage = 'https://github.com/sunqm/libcint' +description = "libcint is an open source library for analytical Gaussian integrals." + +toolchain = {'name': 'gfbf', 'version': '2022b'} + +source_urls = ['https://github.com/sunqm/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] +checksums = [ + {'v5.4.0.tar.gz': '42a8f2e9244e4575437e426e32cd1e60ef9559971c42a41f860c870efc745d99'}, + {'libcint-4.4.0_remove_pyscftest.patch': '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +configopts = "-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on" + +buildopts = 'VERBOSE=1' + +runtest = "test " +separate_build_dir = False # Must use the same directory for tests + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/%(name)s.so'], + 'dirs': [], +} + +moduleclass = 'chem' From e419a563fbafaa28158681a87dca9dd5bd258de1 Mon Sep 17 00:00:00 2001 From: lara Date: Fri, 26 Jan 2024 15:24:03 +0100 Subject: [PATCH 0462/1193] remove libcint-5.4.0-gfbf-2022b.eb --- .../l/libcint/libcint-5.4.0-gfbf-2022b.eb | 37 ------------------- 1 file changed, 37 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb b/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb deleted file mode 100644 index 8a1e3005861f..000000000000 --- a/easybuild/easyconfigs/l/libcint/libcint-5.4.0-gfbf-2022b.eb +++ /dev/null @@ -1,37 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'libcint' -version = '5.4.0' - -homepage = 'https://github.com/sunqm/libcint' -description = "libcint is an open source library for analytical Gaussian integrals." - -toolchain = {'name': 'gfbf', 'version': '2022b'} - -source_urls = ['https://github.com/sunqm/%(name)s/archive/'] -sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] -checksums = [ - {'v5.4.0.tar.gz': '42a8f2e9244e4575437e426e32cd1e60ef9559971c42a41f860c870efc745d99'}, - {'libcint-4.4.0_remove_pyscftest.patch': '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d'}, -] - -builddependencies = [ - ('CMake', '3.24.3'), - ('Python', '3.10.8'), - ('SciPy-bundle', '2023.02'), -] - -configopts = "-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on" - -buildopts = 'VERBOSE=1' - -runtest = "test " -separate_build_dir = False # Must use the same directory for tests - -sanity_check_paths = { - 'files': ['include/cint.h', 'lib/%(name)s.so'], - 'dirs': [], -} - -moduleclass = 'chem' From f6fb2fb4e250ccd08e5040cb2bf61bca42cfdb1e Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 26 Jan 2024 15:26:23 +0100 Subject: [PATCH 0463/1193] tag vesion of libcint to v4.5.0 --- easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb index 3485580284d2..5a3844f6a3c5 100644 --- a/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.4.0-foss-2022b.eb @@ -20,7 +20,7 @@ dependencies = [ ('Python', '3.10.8'), ('SciPy-bundle', '2023.02'), # for numpy, scipy ('h5py', '3.8.0'), - ('libcint', '5.4.0'), + ('libcint', '5.5.0'), ('libxc', '6.1.0'), ('XCFun', '2.1.1'), ('CPPE', '0.3.1'), # extra From 80c2502a42375115a1ecc98f375ca8932d44bd36 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 26 Jan 2024 15:37:59 +0100 Subject: [PATCH 0464/1193] Add 'strict' to toolchain options. --- .../s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 314707a10f88..31e8bcc16d45 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -7,7 +7,7 @@ homepage = 'https://python.org/' description = "Bundle of Python packages for scientific software" toolchain = {'name': 'iimkl', 'version': '2023a'} -toolchainopts = {'pic': True, 'lowopt': True} +toolchainopts = {'pic': True, 'lowopt': True, 'strict': True} builddependencies = [ ('hypothesis', '6.82.0'), From b30cfd888abd0e5cd7a3f95d76fecca216c06068 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Fri, 26 Jan 2024 16:01:56 +0100 Subject: [PATCH 0465/1193] tag vesion of libcint to v4.5.0 --- easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb b/easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb index 32f2622348ab..c8d70b5db4e7 100644 --- a/easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb +++ b/easybuild/easyconfigs/l/libcint/libcint-5.5.0-gfbf-2022b.eb @@ -12,7 +12,7 @@ source_urls = ['https://github.com/sunqm/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] patches = ['%(name)s-4.4.0_remove_pyscftest.patch'] checksums = [ - {'v5.4.0.tar.gz': '42a8f2e9244e4575437e426e32cd1e60ef9559971c42a41f860c870efc745d99'}, + {'v5.5.0.tar.gz': 'c822a9a454587d935287de0f64a2c2cf5338323a554a3f34bcfb4a2892daf477'}, {'libcint-4.4.0_remove_pyscftest.patch': '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d'}, ] From cfa86811fb214600186c15ed9c605c69193158eb Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Jan 2024 15:23:25 +0000 Subject: [PATCH 0466/1193] emf added as dependency --- .../easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb index a50dc8f4c8c3..ec4f248d6dba 100644 --- a/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pstoedit/pstoedit-3.78-GCC-11.3.0.eb @@ -17,10 +17,9 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCE_TAR_GZ] patches = [('pstoedit-configure.patch')] - checksums = [ - '8cc28e34bc7f88d913780f8074e813dd5aaa0ac2056a6b36d4bf004a0e90d801', # pstoedit-3.78.tar.gz - 'c81588eebf9c1dd344566654aae8e826b013c969057cffd8e2cc2cd0a93b90c3', # pstoedit-configure.patch + {'pstoedit-3.78.tar.gz': '8cc28e34bc7f88d913780f8074e813dd5aaa0ac2056a6b36d4bf004a0e90d801'}, + {'pstoedit-configure.patch': 'c81588eebf9c1dd344566654aae8e826b013c969057cffd8e2cc2cd0a93b90c3'}, ] builddependencies = [ @@ -36,10 +35,10 @@ dependencies = [ ('Zip', '3.0'), ('libzip', '1.9.2'), ('Ghostscript', '9.56.1'), + ('libemf', '1.0.13'), + ('plotutils', '2.6'), ] -osdependencies = [('libemf-dev', 'libEMF-devel', 'libplot-dev')] - preconfigopts = "autoreconf -i &&" sanity_check_paths = { From add48e27d24ef3929c143ac5a6bda151e6690fcb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Jan 2024 17:51:51 +0100 Subject: [PATCH 0467/1193] add patch to fix numpy's test_cpu_features on Intel Sapphire Rapids Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb index 31e8bcc16d45..95d1e9f41c41 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.07-iimkl-2023a.eb @@ -36,6 +36,7 @@ exts_list = [ 'numpy-1.25.1_disable-broken-test_long_long_map.patch', 'numpy-1.25.1_fix_selected_kind_for_ifort.patch', 'numpy-1.25.1_disable-broken-fortran-docstring-test.patch', + 'numpy-1.25.1_fix-test_features.patch' ], 'checksums': [ {'numpy-1.25.1.tar.gz': '9a3a9f3a61480cc086117b426a8bd86869c213fc4072e606f01c4e4b66eb92bf'}, @@ -50,6 +51,8 @@ exts_list = [ '4e6561f44de027edf498ac29ed93115f801348a3398700271ccbf048f433b2d3'}, {'numpy-1.25.1_disable-broken-fortran-docstring-test.patch': '8a4d36e3b3a9c9bf43df6e5214f3883234a069b80c5c1027a7c84bd5cb133457'}, + {'numpy-1.25.1_fix-test_features.patch': + '1c05ee5d105fe2f824416dd6dd5c64ed0c1cd710a002b4e6dbfafff19203adc5'}, ], }), ('ply', '3.11', { From 75cfaa755d299a70e74aa377bacee47701439fb5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Jan 2024 18:13:43 +0100 Subject: [PATCH 0468/1193] enable use_pip and sanity_pip_check in easyconfig for tensorboardX v2.6.2.2 --- .../t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb index 3bc7840841c4..c6f2278fae05 100644 --- a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.6.2.2-foss-2023a.eb @@ -16,11 +16,15 @@ dependencies = [ ('protobuf-python', '4.24.0'), ] +use_pip = True + exts_list = [ (name, version, { - 'modulename': '%(name)s', 'checksums': ['c6476d7cd0d529b0b72f4acadb1269f9ed8b22f441e87a84f2a3b940bb87b666'], + 'modulename': '%(name)s', }), ] +sanity_pip_check = True + moduleclass = 'vis' From fcb1ef2599f2cad83fc50d1477019adda780a1d5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Jan 2024 18:44:07 +0100 Subject: [PATCH 0469/1193] add missing poetry build dependency for PyTorch-Lightning v2.1.3 with foss/2023a --- .../p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb index a3de9a847a71..33266d03c517 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ ('flit', '3.9.0'), + ('poetry', '1.5.1'), ] dependencies = [ From 09074592e26b29a5106fa7b4c25fe34d8dbc648c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Jan 2024 19:07:22 +0100 Subject: [PATCH 0470/1193] adding easyconfigs: Sambamba-1.0.1-GCC-11.3.0.eb --- .../s/Sambamba/Sambamba-1.0.1-GCC-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sambamba/Sambamba-1.0.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Sambamba/Sambamba-1.0.1-GCC-11.3.0.eb b/easybuild/easyconfigs/s/Sambamba/Sambamba-1.0.1-GCC-11.3.0.eb new file mode 100644 index 000000000000..6614cdcf8fd9 --- /dev/null +++ b/easybuild/easyconfigs/s/Sambamba/Sambamba-1.0.1-GCC-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Sambamba' +version = '1.0.1' + +homepage = 'https://lomereiter.github.io/sambamba/' +description = """Sambamba is a high performance modern robust and fast tool + (and library), written in the D programming language, for working with SAM + and BAM files. Current functionality is an important subset of samtools + functionality, including view, index, sort, markdup, and depth.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/biod/sambamba/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['955a51a00be9122aa9b0c27796874bfdda85de58aa0181148ef63548ea5192b0'] + +builddependencies = [ + ('LDC', '1.30.0'), + ('Python', '3.10.4'), + ('lz4', '1.9.3'), +] + +files_to_copy = [(['bin/sambamba-%(version)s'], 'bin')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s sambamba-%(version)s sambamba"] + +sanity_check_paths = { + 'files': ['bin/sambamba'], + 'dirs': [], +} + +sanity_check_commands = ["sambamba 2>&1 | grep '^sambamba %(version)s'"] + +moduleclass = 'bio' From 49612baf5bedadc9731c6c662e212b4cbbf0518e Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 26 Jan 2024 18:17:10 +0000 Subject: [PATCH 0471/1193] Typo for source-tarball corrected --- .../c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb index 0976e7eed105..3203da29108c 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -41,7 +41,7 @@ exts_list = [ 'sources': ['v%(version)s.tar.gz'], 'patches': ['CellBender-0.2.1-sphinxremoval.patch'], 'checksums': [ - {'%(version)s.tar.gz': + {'v%(version)s.tar.gz': '309f6245585d9741ba7099690a10a8f496756c4827d100100130be589b797ba4'}, {'CellBender-0.2.1-sphinxremoval.patch': '0f6a342bac16f4ee80cd05d43923b4cc60d71999ea1bb5c80a75edb7290bbdec'}, From f74e8407018f3d483ea027ec43c3a6f22371be57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 26 Jan 2024 19:21:39 +0100 Subject: [PATCH 0472/1193] {bio}[foss/2022b] MACS3 v3.0.0, Cython v3.0.8 --- .../c/Cython/Cython-3.0.8-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ .../m/MACS3/MACS3-3.0.0-foss-2022b.eb | 39 ++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2a288dcb2349 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.8' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['8333423d8fd5765e7cceea3a9985dd1e0a5dfeb2734629e1a2ed2d6233d39de6'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cython --version"] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb new file mode 100644 index 000000000000..08020a2ce4b3 --- /dev/null +++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.0-foss-2022b.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'MACS3' +version = '3.0.0' + +homepage = 'https://macs3-project.github.io/MACS/' +description = """Model Based Analysis for ChIP-Seq data""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +builddependencies = [ + ('pybind11', '2.10.3'), +] + +dependencies = [ + ('Python', '3.10.8'), + # MACS3 3.0 requires Cython 3.x + ('Cython', '3.0.8'), + ('SciPy-bundle', '2023.02'), + ('matplotlib', '3.7.0'), + ('hmmlearn', '0.3.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cykhash', '2.0.1', { + 'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'], + }), + (name, version, { + 'modulename': 'MACS3', + 'checksums': ['57271e060c0f2c41f3aa6de44245c6db7fd0b1945ebfba115a6841628f75770e'], + }), +] + +sanity_check_commands = ["macs3 --help"] + +moduleclass = 'bio' From c7a9c709a0e3d2c483fa672ca25fb87c67e8b4a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Jan 2024 21:41:44 +0100 Subject: [PATCH 0473/1193] add -DgFortran to CPPFLAGS --- easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb | 3 +++ easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 3 +++ easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb | 3 +++ easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb | 3 +++ 4 files changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb index 78745e7806b5..2169f07b3ef8 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.5-gompi-2021b.eb @@ -42,6 +42,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + sanity_check_paths = { 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb index 2cca13754df1..124d47abae6d 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -43,6 +43,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + sanity_check_paths = { 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb index 33b3ae569e7e..864efb1aae42 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb @@ -43,6 +43,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + sanity_check_paths = { 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb index 0adb6ba2358f..77cac651f2bb 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023a.eb @@ -43,6 +43,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + sanity_check_paths = { 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], 'dirs': ['include'], From 055b2bc5bbeeae2131aab6559b4413fed94af449 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Fri, 26 Jan 2024 23:10:33 +0100 Subject: [PATCH 0474/1193] Change version of scikit-build-core to match what is in toolchain. --- .../s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb index 5ecf2ab66d2c..cc5ea96be97b 100644 --- a/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-2.1.0-iimkl-2023a.eb @@ -12,7 +12,7 @@ Spglib is a library for finding and handling crystal symmetries written in C. toolchain = {'name': 'iimkl', 'version': '2023a'} builddependencies = [ - ('scikit-build-core', '0.5.1') + ('scikit-build-core', '0.5.0') ] dependencies = [ From b93c1936f8e095065f5867832c15feae3622c625 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Sat, 27 Jan 2024 14:15:11 +0100 Subject: [PATCH 0475/1193] Update PETSc to use SuiteSparse-7.1.0 --- .../p/PETSc/PETSc-3.20.3-foss-2023a.eb | 3 +- ...iteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb | 31 ------------------- 2 files changed, 1 insertion(+), 33 deletions(-) delete mode 100644 easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb index de6c5d13631c..7b23fa6d644a 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb @@ -16,7 +16,6 @@ source_urls = [ 'https://web.cels.anl.gov/projects/petsc/download/release-snapshots', ] sources = [SOURCELOWER_TAR_GZ] -checksums = ['75a94fb44df0512f51ad093fa784e56b61f51b7ead5956fbe49185c203f8c245'] builddependencies = [('CMake', '3.26.3')] @@ -27,7 +26,7 @@ dependencies = [ ('METIS', '5.1.0'), ('SCOTCH', '7.0.3'), ('MUMPS', '5.6.1', '-metis'), - ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('SuiteSparse', '7.1.0'), ('Hypre', '2.29.0'), ('ParMETIS', '4.0.3'), ('SuperLU_DIST', '8.1.2'), diff --git a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb b/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb deleted file mode 100644 index 5d4c41b2f4d1..000000000000 --- a/easybuild/easyconfigs/s/SuiteSparse/SuiteSparse-5.13.0-foss-2023a-METIS-5.1.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -name = 'SuiteSparse' -version = '5.13.0' -local_metis_ver = '5.1.0' -versionsuffix = '-METIS-%s' % local_metis_ver - -homepage = 'https://faculty.cse.tamu.edu/davis/suitesparse.html' -description = """SuiteSparse is a collection of libraries manipulate sparse matrices.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'unroll': True, 'pic': True} - -source_urls = ['https://github.com/DrTimothyAldenDavis/SuiteSparse/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['59c6ca2959623f0c69226cf9afb9a018d12a37fab3a8869db5f6d7f83b6b147d'] - -builddependencies = [ - ('CMake', '3.26.3'), - ('M4', '1.4.19'), -] - -dependencies = [ - ('METIS', local_metis_ver), - ('MPFR', '4.2.0'), -] - -# make sure that bin/demo can find libsuitesparseconfig.so.5 during build -prebuildopts = "export LD_LIBRARY_PATH=%(builddir)s/SuiteSparse-%(version)s/lib:$LD_LIBRARY_PATH && " -# remove broken symlink -prebuildopts += "rm GraphBLAS/CUDA/test/graphblascuda_test && " - -moduleclass = 'numlib' From 1c16f6f2c2f0f0a65edf2f049227755bbfbc8004 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Sat, 27 Jan 2024 14:33:46 +0100 Subject: [PATCH 0476/1193] Add missing checksums --- easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb index 7b23fa6d644a..7c4db8a3646c 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.20.3-foss-2023a.eb @@ -16,6 +16,7 @@ source_urls = [ 'https://web.cels.anl.gov/projects/petsc/download/release-snapshots', ] sources = [SOURCELOWER_TAR_GZ] +checksums = ['75a94fb44df0512f51ad093fa784e56b61f51b7ead5956fbe49185c203f8c245'] builddependencies = [('CMake', '3.26.3')] From a2165493378199fbcd27e0f87b4549c9e3601ec9 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Sat, 27 Jan 2024 22:10:59 +0000 Subject: [PATCH 0477/1193] Add patch for jupyter_core to set jupyter path by `EB_ENV_JUPYTER_ROOT` --- .../JupyterLab-4.0.3-GCCcore-12.2.0.eb | 5 +--- .../JupyterNotebook-7.0.3-GCCcore-12.2.0.eb | 5 +--- ...pyter-server-proxy-3.2.2-GCCcore-12.2.0.eb | 5 +--- .../jupyter-core-5.3.1_fix_jupyter_path.patch | 26 +++++++++++++++++++ .../jupyter-server-2.7.0-GCCcore-12.2.0.eb | 6 ++--- 5 files changed, 31 insertions(+), 16 deletions(-) create mode 100644 easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb index ce74a8838029..aa4cce7aaca7 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.3-GCCcore-12.2.0.eb @@ -68,10 +68,7 @@ exts_list = [ sanity_check_commands = ["jupyter lab --help"] -modextrapaths = { - 'JUPYTER_PATH': 'share/jupyter', - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} modextravars = { # only one path allowed as JUPYTERLAB_DIR 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', diff --git a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb index 2202fae1e72a..afe231a13cf4 100644 --- a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.3-GCCcore-12.2.0.eb @@ -36,9 +36,6 @@ sanity_check_paths = { sanity_check_commands = ['jupyter notebook --help'] -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb index 2b029331d33c..c2b3d7a52c4d 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-3.2.2-GCCcore-12.2.0.eb @@ -38,9 +38,6 @@ exts_list = [ }), ] -modextrapaths = { - 'JUPYTER_PATH': 'share/jupyter', - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch b/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch new file mode 100644 index 000000000000..b2c4039e7022 --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch @@ -0,0 +1,26 @@ +diff --git a/jupyter_core/paths.py b/jupyter_core/paths.py +index a7bf051..b38589c 100644 +--- a/jupyter_core/paths.py ++++ b/jupyter_core/paths.py +@@ -225,7 +225,10 @@ else: + ] + + ENV_JUPYTER_PATH: List[str] = [os.path.join(sys.prefix, "share", "jupyter")] +- ++if os.environ.get("EB_ENV_JUPYTER_ROOT"): ++ EB_ENV_JUPYTER_ROOT = [p.rstrip(os.sep) for p in os.environ["EB_ENV_JUPYTER_ROOT"].split(os.pathsep)] ++ ENV_JUPYTER_PATH = [str(Path(p, "share", "jupyter")) for p in EB_ENV_JUPYTER_ROOT] ++ + + def jupyter_path(*subdirs: str) -> List[str]: + """Return a list of directories to search for data files +@@ -303,6 +306,9 @@ else: + "/etc/jupyter", + ] + ENV_CONFIG_PATH: List[str] = [os.path.join(sys.prefix, "etc", "jupyter")] ++if os.environ.get("EB_ENV_JUPYTER_ROOT"): ++ EB_ENV_JUPYTER_ROOT = [p.rstrip(os.sep) for p in os.environ["EB_ENV_JUPYTER_ROOT"].split(os.pathsep)] ++ ENV_CONFIG_PATH = [str(Path(p, "etc", "jupyter")) for p in EB_ENV_JUPYTER_ROOT] + + + def jupyter_config_path() -> List[str]: diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb index 371d6d3a26f2..cbc9ac27fbf3 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb @@ -61,6 +61,7 @@ exts_list = [ 'checksums': ['8b97c6c1e1681b78cbc9424b138d880f0803c2254c5ebaabdde57bb6c62093f2'], }), ('jupyter_core', '5.3.1', { + 'patches': ['jupyter-core-5.3.1_fix_jupyter_path.patch'], 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], }), ('fastjsonschema', '2.17.1', { @@ -168,10 +169,7 @@ exts_list = [ }), ] -modextrapaths = { - 'JUPYTER_PATH': 'share/jupyter', - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} sanity_check_paths = { 'files': [ From 84dc9cb2a970e665f56c6051b7dac14527d828aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Sun, 28 Jan 2024 15:00:32 +0100 Subject: [PATCH 0478/1193] adding easyconfigs: CalculiX-CrunchiX-2.20-foss-2023a.eb, SPOOLES-2.2-gompi-2023a.eb --- .../CalculiX-CrunchiX-2.20-foss-2023a.eb | 50 ++++++++++++++++++ .../s/SPOOLES/SPOOLES-2.2-gompi-2023a.eb | 51 +++++++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2023a.eb diff --git a/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2023a.eb b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2023a.eb new file mode 100644 index 000000000000..4f246716c095 --- /dev/null +++ b/easybuild/easyconfigs/c/CalculiX-CrunchiX/CalculiX-CrunchiX-2.20-foss-2023a.eb @@ -0,0 +1,50 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'CalculiX-CrunchiX' +version = '2.20' + +homepage = 'http://www.calculix.de' +description = 'A Free Software Three-Dimensional Structural Finite Element Program' + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['http://www.dhondt.de'] +sources = ['ccx_%(version)s.src.tar.bz2'] +patches = ['CalculiX-CrunchiX-2.20_improve-makefile.patch'] +checksums = [ + {'ccx_2.20.src.tar.bz2': '63bf6ea09e7edcae93e0145b1bb0579ea7ae82e046f6075a27c8145b72761bcf'}, + {'CalculiX-CrunchiX-2.20_improve-makefile.patch': + 'ada15598029d231f804f61d959ce91e2bb3a58749fe5955398f42fbe87dc970c'}, +] + +builddependencies = [ + ('Perl', '5.36.1'), +] + +dependencies = [ + ('arpack-ng', '3.9.0'), + ('SPOOLES', '2.2'), +] + +start_dir = 'CalculiX/ccx_%(version)s/src' + +prebuildopts = 'CFLAGS="$CFLAGS $CPPFLAGS" FFLAGS="$FFLAGS -fallow-argument-mismatch"' +buildopts = 'SPOOLES_INC_DIR="$EBROOTSPOOLES/include/spooles"' + +files_to_copy = [(['ccx_%(version)s'], 'bin')] + +postinstallcmds = ['cd %(installdir)s/bin && ln -sf ccx_%(version)s ccx'] + +sanity_check_paths = { + 'files': ['bin/ccx'], + 'dirs': [], +} + +sanity_check_commands = [ + # ccx {,-v} exit with code 201 + "ccx | grep 'Usage: CalculiX.exe -i jobname'", + "ccx -v | grep 'Version %(version)s'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2023a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2023a.eb new file mode 100644 index 000000000000..b62a968bd10c --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2023a.eb @@ -0,0 +1,51 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'SPOOLES' +version = '2.2' + +homepage = 'https://netlib.org/linalg/spooles/spooles.2.2.html' +description = """SPOOLES is a library for solving sparse real and complex linear + systems of equations, written in the C language using object oriented design. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://netlib.org/linalg/spooles'] +sources = ['%(namelower)s.%(version)s.tgz'] +patches = [ + '%(name)s-2.2_build-mpi-mt.patch', + '%(name)s-2.2_shared-libs.patch', +] +checksums = [ + {'spooles.2.2.tgz': 'a84559a0e987a1e423055ef4fdf3035d55b65bbe4bf915efaa1a35bef7f8c5dd'}, + {'SPOOLES-2.2_build-mpi-mt.patch': 'c983c7f37eb0904959cd2f6dff0b1fdb6a36440ca2a044fb2d324fd301e3dd7c'}, + {'SPOOLES-2.2_shared-libs.patch': 'bca50e13e3c552240f7494c4d9f69be8725054c9f79ebc82dbe6b7531588d09e'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.36.1'), +] + +build_cmd_targets = 'lib' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="-L$MPI_LIB_DIR" MPI_INCLUDE_DIR="-I$MPI_INC_DIR"' + +files_to_copy = [ + (['libspooles*'], 'lib'), +] + +# install header files, keeping relative subdirectories +_install_headers = " ".join([ + "cd %(builddir)s && mkdir -p %(installdir)s/include/spooles &&", + r"find . -name '*.h' -print -exec install -D {} %(installdir)s/include/spooles/{} \;" +]) + +postinstallcmds = [_install_headers] + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/spooles'], +} + +moduleclass = 'math' From 0a0388dbb5ed20b4f4353f47d4a22baa4c11ac9c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:09:25 +0100 Subject: [PATCH 0479/1193] update PyTorch-Ignite on foss/2023a to version 0.4.13 --- .../PyTorch-Ignite-0.4.11-foss-2023a.eb | 35 ------------------- .../PyTorch-Ignite-0.4.13-foss-2023a.eb | 28 +++++++++++++++ 2 files changed, 28 insertions(+), 35 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.13-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb deleted file mode 100644 index f73933e70143..000000000000 --- a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11-foss-2023a.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyTorch-Ignite' -version = '0.4.11' - -homepage = 'https://pytorch-ignite.ai/' -description = """ -Ignite is a high-level library to help with training and evaluating neural -networks in PyTorch flexibly and transparently.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('PyTorch', '2.1.2'), -] - -exts_list = [ - ('pytorch-ignite', version, { - 'modulename': 'ignite', - 'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'], - 'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s'], - 'sources': ['pytorch-ignite-%(version)s.tar.gz'], - 'checksums': [ - {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'}, - {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch': - 'd481a1cb8e4cb668802cb29fe301129fbf10cec056cfdc81402a2d1764448ca3'}, - ], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.13-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.13-foss-2023a.eb new file mode 100644 index 000000000000..d11672d31f9f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.13-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Ignite' +version = '0.4.13' + +homepage = 'https://pytorch-ignite.ai/' +description = """Ignite is a high-level library to help with training and evaluating neural +networks in PyTorch flexibly and transparently.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), +] + +use_pip = True + +exts_list = [ + ('pytorch-ignite', version, { + 'modulename': 'ignite', + 'checksums': ['f334dd65161cc4f4a77da5d0ed3b1e8bc08235be832016515f8a33c249dac060'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 8f7e6ce32ad77c05361efa046358066a8b0c5c22 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:10:10 +0100 Subject: [PATCH 0480/1193] remove dependency on poetry from tensorboard-2.15.1-foss-2023a.eb --- .../easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb index 350ba1d68b88..5d34e2966cfb 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb @@ -13,7 +13,6 @@ dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('protobuf-python', '4.24.0'), - ('poetry', '1.5.1'), # for rsa ] exts_list = [ From b538b1a3ed27382f3dde50a697103f0c91f62d6e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:11:23 +0100 Subject: [PATCH 0481/1193] lower toolchain of tensorboard v2.15.1 to gfbf/2023a --- ....15.1-foss-2023a.eb => tensorboard-2.15.1-gfbf-2023a.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/t/tensorboard/{tensorboard-2.15.1-foss-2023a.eb => tensorboard-2.15.1-gfbf-2023a.eb} (96%) diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb similarity index 96% rename from easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb rename to easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb index 5d34e2966cfb..7eadb5543caf 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb @@ -4,10 +4,10 @@ name = 'tensorboard' version = '2.15.1' homepage = 'https://github.com/tensorflow/tensorboard' -description = """TensorBoard is a suite of web applications for inspecting and understanding -your TensorFlow runs and graphs.""" +description = """TensorBoard is a suite of web applications for inspecting and +understanding your TensorFlow runs and graphs.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} dependencies = [ ('Python', '3.11.3'), From 3bbdad0eff3a3f1dce8c87312796ac339a36017d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:13:18 +0100 Subject: [PATCH 0482/1193] update patch torchvision-0.16.0_fix-build-with-FFmpeg6.patch with upstream version --- .../torchvision-0.16.0-foss-2023a.eb | 2 +- ...vision-0.16.0_fix-build-with-FFmpeg6.patch | 19 +++++++++++++++---- 2 files changed, 16 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb index 7610052afb69..404a5a480be1 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb @@ -15,7 +15,7 @@ patches = [ checksums = [ {'v0.16.0.tar.gz': '79b30b082237e3ead21e74587cedf4a4d832f977cf7dfeccfb65f67988b12ceb'}, {'torchvision-0.16.0_fix-build-with-FFmpeg6.patch': - '14039456cd10f2ea1281eaaa908429958f6c72d7b2041f23cf9bd43b8b810d2f'}, + 'a49336e7bfa1c950e886852bff37a3ea2146ac7bda87241e3ffb31c5cb869cce'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch index 4220434d610b..7a3637f3adc9 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0_fix-build-with-FFmpeg6.patch @@ -1,8 +1,19 @@ -Make torchvision 0.16.0 build with ffmpeg 6.0 (from https://github.com/pytorch/vision/issues/7998) -Author: Cintia Willemyns (Vrije Universiteit Brussel) +From 86620bd84b872b76db0acafec167949dca03a29e Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Zolt=C3=A1n=20B=C3=B6sz=C3=B6rm=C3=A9nyi?= + +Date: Tue, 7 Nov 2023 10:43:11 +0100 +Subject: [PATCH] Fix build with ffmpeg 6.0 +MIME-Version: 1.0 +Content-Type: text/plain; charset=UTF-8 +Content-Transfer-Encoding: 8bit + +Signed-off-by: Zoltán Böszörményi +--- + torchvision/csrc/io/decoder/stream.cpp | 11 ++--------- + 1 file changed, 2 insertions(+), 9 deletions(-) diff --git a/torchvision/csrc/io/decoder/stream.cpp b/torchvision/csrc/io/decoder/stream.cpp -index 0d625ef211..8c91405058 100644 +index 0d625ef211c..8c914050587 100644 --- a/torchvision/csrc/io/decoder/stream.cpp +++ b/torchvision/csrc/io/decoder/stream.cpp @@ -63,15 +63,8 @@ int Stream::openCodec(std::vector* metadata, int num_threads) { @@ -22,4 +33,4 @@ index 0d625ef211..8c91405058 100644 + codecCtx_->thread_type = FF_THREAD_SLICE; } - int ret; + int ret; From 36f5c2b185f682de3f561167a944b519a10d1a61 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:16:22 +0100 Subject: [PATCH 0483/1193] add direct dependency on FFmpeg to torchvision v0.16.0 --- .../easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb index 404a5a480be1..f9988fed3feb 100644 --- a/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.16.0-foss-2023a.eb @@ -24,6 +24,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), + ('FFmpeg', '6.0'), ('Pillow-SIMD', '9.5.0'), ('PyTorch', '2.1.2'), ] From 0047082792557eb4c46b19833d2ea7cd07647081 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:24:44 +0100 Subject: [PATCH 0484/1193] update patch PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch with upstream version --- ...0.4.11_fix_error_on_importing_Events.patch | 47 ++++++++++++++++--- 1 file changed, 40 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch index f0b9f9f59e46..ddfd065cf6e4 100644 --- a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch +++ b/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch @@ -1,19 +1,52 @@ -Fix bug error on importing Events in python 3.11 -as in https://github.com/pytorch/ignite/pull/2907 -Author: Cintia Willemyns (Vrije Universiteit Brussel) +From 136306c9d00c997a425f1840128847c7529b8415 Mon Sep 17 00:00:00 2001 +From: Sadra Barikbin +Date: Sat, 1 Apr 2023 14:54:40 +0330 +Subject: [PATCH 1/2] Fix the issue ---- ignite/engine/events.py.orig 2024-01-03 16:37:16.972475097 +0100 -+++ ignite/engine/events.py 2024-01-03 16:39:03.703040949 +0100 -@@ -248,8 +248,10 @@ +--- + ignite/engine/events.py | 8 +++++++- + 1 file changed, 7 insertions(+), 1 deletion(-) + +diff --git a/ignite/engine/events.py b/ignite/engine/events.py +index a80277c525d..213dd8a9878 100644 +--- a/ignite/engine/events.py ++++ b/ignite/engine/events.py +@@ -237,7 +237,13 @@ def function_before_backprop(engine): # ... """ - pass -- + def __new__(cls, value: str) -> "EventEnum": + obj = CallableEventWithFilter.__new__(cls) + obj._value_ = value + return obj ++ ++ def __repr__(self) -> str: ++ return CallableEventWithFilter.__repr__(self) + + + class Events(EventEnum): + +From 2fd992774017fe2d603bc456c5dcca0f83167018 Mon Sep 17 00:00:00 2001 +From: Sadra Barikbin +Date: Thu, 13 Apr 2023 06:28:38 +0330 +Subject: [PATCH 2/2] Remove unnecessary __repr__ + +--- + ignite/engine/events.py | 3 --- + 1 file changed, 3 deletions(-) + +diff --git a/ignite/engine/events.py b/ignite/engine/events.py +index 213dd8a9878..9dd99348492 100644 +--- a/ignite/engine/events.py ++++ b/ignite/engine/events.py +@@ -242,9 +242,6 @@ def __new__(cls, value: str) -> "EventEnum": + obj._value_ = value + return obj + +- def __repr__(self) -> str: +- return CallableEventWithFilter.__repr__(self) +- class Events(EventEnum): """Events that are fired by the :class:`~ignite.engine.engine.Engine` during execution. Built-in events: From ada74974788f583a18f0ab9861a566afacc0c2f0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:32:46 +0100 Subject: [PATCH 0485/1193] bundle PyTorch-Ignite v0.4.11 as an extension of MONAI v1.3.0 --- .../easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb | 15 ++++++++++++--- ...ite-0.4.11_fix_error_on_importing_Events.patch | 0 2 files changed, 12 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/{p/PyTorch-Ignite => m/MONAI}/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch (100%) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb index fd4274ac696a..63de4904eaa8 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb @@ -16,7 +16,6 @@ github_account = 'Project-MONAI' dependencies = [ ('Python', '3.11.3'), ('PyTorch', '2.1.2'), - ('PyTorch-Ignite', '0.4.11'), # Monai 1.3.0 requires PyTorch-Ignite==0.4.11 ('einops', '0.7.0'), ('ITK', '5.3.0'), ('NiBabel', '5.2.0'), @@ -30,9 +29,12 @@ dependencies = [ ('hatchling', '1.18.0'), ] +use_pip = True + # install MONAI with list of 'extras', which require additional dependencies local_pip_extras = "nibabel,skimage,pillow,tensorboard,gdown,ignite,torchvision,itk,tqdm,lmdb,psutil,openslide,fire" +# PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it exts_list = [ ('gdown', '4.7.1', { 'checksums': ['347f23769679aaf7efa73e5655270fcda8ca56be65eb84a4a21d143989541045'], @@ -47,6 +49,15 @@ exts_list = [ ('fire', '0.5.0', { 'checksums': ['a6b0d49e98c8963910021f92bba66f65ab440da2982b78eb1bbf95a0a34aacc6'], }), + ('pytorch-ignite', '0.4.11', { + 'modulename': 'ignite', + 'patches': ['PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch'], + 'checksums': [ + {'pytorch-ignite-0.4.11.tar.gz': 'ee31096a58679417097ef7f3f27d88bec40b789ac5e13cd9ed08bc89ca8ce2e2'}, + {'PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch': + 'd45c0da30c01f7ce47b7be49a6d5d6eb9529c94a0b9de89260d4b07d9d2359e0'}, + ], + }), (name, version, { 'preinstallopts': 'BUILD_MONAI=1', 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], @@ -56,8 +67,6 @@ exts_list = [ }), ] -use_pip = True - sanity_pip_check = True # 'pip check' does not verify whether all optional dependencies required to support 'extras' diff --git a/easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch b/easybuild/easyconfigs/m/MONAI/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch similarity index 100% rename from easybuild/easyconfigs/p/PyTorch-Ignite/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch rename to easybuild/easyconfigs/m/MONAI/PyTorch-Ignite-0.4.11_fix_error_on_importing_Events.patch From c8c3e7b43c1fe64910f9205074d473b5eb4a1c74 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:35:29 +0100 Subject: [PATCH 0486/1193] add Ninja and move hatchling as build dependencies of MONAI v1.3.0 --- easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb index 63de4904eaa8..bd20d5218e61 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb @@ -13,6 +13,11 @@ toolchain = {'name': 'foss', 'version': '2023a'} github_account = 'Project-MONAI' +builddependencies = [ + ('hatchling', '1.18.0'), + ('Ninja', '1.11.1'), +] + dependencies = [ ('Python', '3.11.3'), ('PyTorch', '2.1.2'), @@ -26,7 +31,6 @@ dependencies = [ ('Pillow', '10.0.0'), ('openslide-python', '1.3.1'), ('BeautifulSoup', '4.12.2'), - ('hatchling', '1.18.0'), ] use_pip = True From 53c1d2ca39086fc48c4371542883b9365dc071c4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 11:44:32 +0100 Subject: [PATCH 0487/1193] add missing installation extras to MONAI-1.3.0-foss-2023a.eb --- .../m/MONAI/MONAI-1.3.0-foss-2023a.eb | 20 ++++++++++++------- 1 file changed, 13 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb index bd20d5218e61..c00b11caf83c 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.3.0-foss-2023a.eb @@ -20,6 +20,8 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), ('PyTorch', '2.1.2'), ('einops', '0.7.0'), ('ITK', '5.3.0'), @@ -36,7 +38,9 @@ dependencies = [ use_pip = True # install MONAI with list of 'extras', which require additional dependencies -local_pip_extras = "nibabel,skimage,pillow,tensorboard,gdown,ignite,torchvision,itk,tqdm,lmdb,psutil,openslide,fire" +local_pip_extras = "einops,fire,gdown,ignite,itk,jsonschema,lmdb,nibabel," +local_pip_extras += "openslide,pandas,pillow,psutil,pydicom,pyyaml,scipy," +local_pip_extras += "skimage,tensorboard,torchvision,tqdm" # PyTorch-Ignite v0.4.11 bundled as an extension because MONAI v1.3.0 has a strict requirement on it exts_list = [ @@ -75,15 +79,17 @@ sanity_pip_check = True # 'pip check' does not verify whether all optional dependencies required to support 'extras' # are actually available, so we do it here via an import check; -# Pillow is a special case, since there we need to use 'import PIL' -sanity_check_commands = [ - "python -c 'import monai; monai.config.print_config()'", - "python -c 'import PIL'", # for Pillow required dependency -] + ["python -c 'import %s'" % x for x in local_pip_extras.split(',') if x != 'pillow'] +local_extra_mod_check = {x: x for x in local_pip_extras.split(",")} +# Some special cases with different module name than extra name +local_extra_mod_check['pillow'] = 'PIL' +local_extra_mod_check['pyyaml'] = 'yaml' + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] +sanity_check_commands += ["python -c 'import %s'" % local_extra_mod_check[x] for x in local_extra_mod_check] sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/ignite'], } moduleclass = 'vis' From add4c09e2fb8985338c5e6ac0b00e53462069143 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 29 Jan 2024 13:49:58 +0100 Subject: [PATCH 0488/1193] adding easyconfigs: maturin-1.3.2-GCCcore-11.3.0.eb, timm-0.9.7-foss-2022a-CUDA-11.7.0.eb --- .../m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb | 616 ++++++++++++++++++ .../timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb | 474 ++++++++++++++ 2 files changed, 1090 insertions(+) create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1cf2893b0443 --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb @@ -0,0 +1,616 @@ +# easyblock = 'CargoPythonPackage' +easyblock = 'CargoPythonBundle' + +name = 'maturin' +version = '1.3.2' +homepage = 'https://github.com/pyo3/maturin' +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('Rust', '1.65.0'), +] + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.7.7'), + ('aho-corasick', '0.7.20'), + ('anstream', '0.3.2'), + ('anstyle', '1.0.1'), + ('anstyle-parse', '0.2.1'), + ('anstyle-query', '1.0.0'), + ('anstyle-wincon', '1.0.2'), + ('anyhow', '1.0.75'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.2'), + ('bitflags', '1.3.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.6.0'), + ('byteorder', '1.4.3'), + ('bytes', '1.4.0'), + ('bytesize', '1.2.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.6'), + ('cargo-config2', '0.1.9'), + ('cargo-options', '0.6.0'), + ('cargo-platform', '0.1.3'), + ('cargo-xwin', '0.14.8'), + ('cargo-zigbuild', '0.17.5'), + ('cargo_metadata', '0.18.0'), + ('cbindgen', '0.26.0'), + ('cc', '1.0.82'), + ('cfb', '0.7.3'), + ('cfg-expr', '0.15.4'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.2'), + ('clap', '4.1.14'), + ('clap_builder', '4.1.14'), + ('clap_complete', '4.2.3'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_fig', '4.2.0'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.1.14'), + ('clap_lex', '0.4.1'), + ('cli-table', '0.4.7'), + ('colorchoice', '1.0.0'), + ('configparser', '3.0.2'), + ('console', '0.15.7'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.4'), + ('cpufeatures', '0.2.9'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.8'), + ('crossbeam-deque', '0.8.3'), + ('crossbeam-epoch', '0.9.15'), + ('crossbeam-utils', '0.8.16'), + ('crypto-common', '0.1.6'), + ('data-encoding', '2.4.0'), + ('deranged', '0.3.9'), + ('dialoguer', '0.11.0'), + ('diff', '0.1.13'), + ('digest', '0.10.7'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('dissimilar', '1.0.7'), + ('dunce', '1.0.4'), + ('either', '1.9.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.32'), + ('errno', '0.3.2'), + ('errno-dragonfly', '0.1.2'), + ('expect-test', '1.4.1'), + ('fastrand', '1.9.0'), + ('fat-macho', '0.4.7'), + ('filetime', '0.2.22'), + ('flate2', '1.0.27'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.0'), + ('fs-err', '2.9.0'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.10'), + ('glob', '0.3.1'), + ('globset', '0.4.10'), + ('goblin', '0.7.1'), + ('hashbrown', '0.12.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.2'), + ('home', '0.5.5'), + ('humantime', '2.1.0'), + ('humantime-serde', '1.1.1'), + ('idna', '0.4.0'), + ('ignore', '0.4.20'), + ('indexmap', '1.9.3'), + ('indicatif', '0.17.6'), + ('indoc', '2.0.3'), + ('instant', '0.1.12'), + ('io-lifetimes', 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b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..afb2da239876 --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,474 @@ +easyblock = 'CargoPythonBundle' + +name = 'timm' +version = '0.9.7' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), + ('torchvision', '0.13.1', versionsuffix), + ('maturin', '1.3.2'), +] + +builddependencies = [ + ('Rust', '1.65.0'), # for safetensors +] + +crates = [ + # crates for PyO3 + ('ahash', '0.8.7'), + ('allocator-api2', '0.2.16'), + ('android-tzdata', '0.1.1'), + ('android_system_properties', '0.1.5'), + ('anyhow', '1.0.79'), + ('arrayvec', '0.7.4'), + ('assert_approx_eq', '1.1.0'), + ('autocfg', '1.1.0'), + ('basic-toml', '0.1.8'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('bumpalo', '3.14.0'), + ('cc', '1.0.83'), + ('cfg-if', '1.0.0'), + ('chrono', '0.4.33'), + ('core-foundation-sys', '0.8.6'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('either', '1.9.0'), + ('equivalent', '1.0.1'), + ('eyre', '0.6.11'), + ('getrandom', '0.2.12'), + ('glob', '0.3.1'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('iana-time-zone', '0.1.59'), + ('iana-time-zone-haiku', '0.1.2'), + ('indenter', '0.3.3'), + ('indexmap', '2.1.0'), + ('indoc', '2.0.4'), + ('inventory', '0.3.15'), + ('itoa', '1.0.10'), + ('js-sys', '0.3.67'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.152'), + ('libm', '0.2.8'), + ('lock_api', '0.4.11'), + ('log', '0.4.20'), + ('memoffset', '0.9.0'), + ('num-bigint', '0.4.4'), + ('num-complex', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.17'), + ('once_cell', '1.19.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.78'), + ('proptest', '1.4.0'), + ('python3-dll-a', '0.2.9'), + ('quote', '1.0.35'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xorshift', '0.3.0'), + ('rayon', '1.8.1'), + ('rayon-core', '1.12.1'), + ('redox_syscall', '0.4.1'), + ('regex-syntax', '0.8.2'), + ('rust_decimal', '1.33.1'), + ('ryu', '1.0.16'), + ('scopeguard', '1.2.0'), + ('send_wrapper', '0.6.0'), + ('serde', '1.0.195'), + ('serde_derive', '1.0.195'), + ('serde_json', '1.0.111'), + ('smallvec', '1.13.1'), + ('syn', '2.0.48'), + ('target-lexicon', '0.12.13'), + ('termcolor', '1.4.1'), + ('trybuild', '1.0.89'), + ('unarray', '0.1.4'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.90'), + ('wasm-bindgen-backend', '0.2.90'), + ('wasm-bindgen-macro', '0.2.90'), + ('wasm-bindgen-macro-support', '0.2.90'), + ('wasm-bindgen-shared', '0.2.90'), + ('widestring', '0.5.1'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.0'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), + # crates for safetensors + ('aho-corasick', '1.1.2'), + ('anes', '0.1.6'), + ('atty', '0.2.14'), + ('autocfg', '1.1.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('bumpalo', '3.14.0'), + ('cast', '0.3.0'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '3.2.25'), + ('clap_lex', '0.2.4'), + ('criterion', '0.4.0'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('crunchy', '0.2.2'), + ('either', '1.9.0'), + ('errno', '0.3.8'), + ('fastrand', '2.0.1'), + ('fnv', '1.0.7'), + ('getrandom', '0.2.12'), + ('half', '2.3.1'), + ('hashbrown', '0.12.3'), + ('hermit-abi', '0.1.19'), + ('indexmap', '1.9.3'), + ('itertools', '0.10.5'), + ('itoa', '1.0.10'), + ('js-sys', '0.3.67'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.152'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.13'), + ('log', '0.4.20'), + ('memchr', '2.7.1'), + ('memmap2', '0.5.10'), + ('num-traits', '0.2.17'), + ('once_cell', '1.19.0'), + ('oorandom', '11.1.3'), + ('os_str_bytes', '6.6.1'), + ('plotters', '0.3.5'), + ('plotters-backend', '0.3.5'), + ('plotters-svg', '0.3.5'), + ('ppv-lite86', '0.2.17'), + ('proc-macro2', '1.0.78'), + ('proptest', '1.4.0'), + ('pyo3', '0.20.2'), + ('pyo3-build-config', '0.20.2'), + ('pyo3-ffi', '0.20.2'), + ('pyo3-macros', '0.20.2'), + ('pyo3-macros-backend', '0.20.2'), + ('quick-error', '1.2.3'), + ('quote', '1.0.35'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xorshift', '0.3.0'), + ('rayon', '1.8.1'), + ('rayon-core', '1.12.1'), + ('redox_syscall', '0.4.1'), + ('regex', '1.10.3'), + ('regex-automata', '0.4.4'), + ('regex-syntax', '0.8.2'), + ('rustix', '0.38.30'), + ('rusty-fork', '0.3.0'), + ('ryu', '1.0.16'), + ('same-file', '1.0.6'), + ('serde', '1.0.195'), + ('serde_derive', '1.0.195'), + ('serde_json', '1.0.111'), + ('syn', '2.0.48'), + ('tempfile', '3.9.0'), + ('textwrap', '0.16.0'), + ('tinytemplate', '1.2.1'), + ('unarray', '0.1.4'), + ('unicode-ident', '1.0.12'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.4.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.90'), + ('wasm-bindgen-backend', '0.2.90'), + ('wasm-bindgen-macro', '0.2.90'), + ('wasm-bindgen-macro-support', '0.2.90'), + ('wasm-bindgen-shared', '0.2.90'), + ('web-sys', '0.3.67'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.52.0'), +] +sources = [SOURCE_TAR_GZ] +checksums = [ + {'timm-0.9.7.tar.gz': '2bfb1029e90b72e65eb9c75556169815f2e82257eaa1f6ebd623a4b4a52867a2'}, + {'ahash-0.8.7.tar.gz': '77c3a9648d43b9cd48db467b3f87fdd6e146bcc88ab0180006cef2179fe11d01'}, + {'allocator-api2-0.2.16.tar.gz': '0942ffc6dcaadf03badf6e6a2d0228460359d5e34b57ccdc720b7382dfbd5ec5'}, + {'android-tzdata-0.1.1.tar.gz': 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'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.6.tar.gz': 'f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-targets-0.52.0.tar.gz': '8a18201040b24831fbb9e4eb208f8892e1f50a37feb53cc7ff887feb8f50e7cd'}, + {'windows_aarch64_gnullvm-0.52.0.tar.gz': 'cb7764e35d4db8a7921e09562a0304bf2f93e0a51bfccee0bd0bb0b666b015ea'}, + {'windows_aarch64_msvc-0.52.0.tar.gz': 'bbaa0368d4f1d2aaefc55b6fcfee13f41544ddf36801e793edbbfd7d7df075ef'}, + {'windows_i686_gnu-0.52.0.tar.gz': 'a28637cb1fa3560a16915793afb20081aba2c92ee8af57b4d5f28e4b3e7df313'}, + {'windows_i686_msvc-0.52.0.tar.gz': 'ffe5e8e31046ce6230cc7215707b816e339ff4d4d67c65dffa206fd0f7aa7b9a'}, + {'windows_x86_64_gnu-0.52.0.tar.gz': '3d6fa32db2bc4a2f5abeacf2b69f7992cd09dca97498da74a151a3132c26befd'}, + {'windows_x86_64_gnullvm-0.52.0.tar.gz': '1a657e1e9d3f514745a572a6846d3c7aa7dbe1658c056ed9c3344c4109a6949e'}, + {'windows_x86_64_msvc-0.52.0.tar.gz': 'dff9641d1cd4be8d1a070daf9e3773c5f67e78b4d9d42263020c057706765c04'}, +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.17.3', { + 'checksums': ['40439632b211311f788964602bf8b0d9d6b7a2314fba4e8d67b2ce3ecea0e3fd'], + }), + ('safetensors', '0.4.2', { + 'checksums': ['acc85dcb09ec5e8aa787f588d7ad4d55c103f31e4ff060e17d92cc0e8b8cac73'], + }), + (name, version, { + 'checksums': ['2bfb1029e90b72e65eb9c75556169815f2e82257eaa1f6ebd623a4b4a52867a2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From ce81f774be9ad0225923917090746ce0f5933a2d Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 29 Jan 2024 13:51:12 +0100 Subject: [PATCH 0489/1193] remove comment maturin-1.3.2-GCCcore-11.3.0.eb --- easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb index 1cf2893b0443..c11f63a2ddd8 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb @@ -1,4 +1,3 @@ -# easyblock = 'CargoPythonPackage' easyblock = 'CargoPythonBundle' name = 'maturin' From 86a073db208e4da886e4d902bf8c79140345beee Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 29 Jan 2024 14:14:31 +0100 Subject: [PATCH 0490/1193] remove "download_dep_fail" in maturin-1.3.2-GCCcore-11.3.0.eb remove "download_dep_fail" since PythonBundle easyblock is used --- easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb index c11f63a2ddd8..db238831f5f7 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb @@ -610,6 +610,5 @@ exts_list = [ sanity_pip_check = True use_pip = True -download_dep_fail = True moduleclass = 'tools' From 3347a6aee2f9cf95e1b250918368d98f43ec9607 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 29 Jan 2024 15:43:45 +0100 Subject: [PATCH 0491/1193] Add Rust version suffix to maturin-1.3.2-GCCcore-11.3.0-Rust-1.65.0.eb --- ...1.3.0.eb => maturin-1.3.2-GCCcore-11.3.0-Rust-1.65.0.eb} | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/m/maturin/{maturin-1.3.2-GCCcore-11.3.0.eb => maturin-1.3.2-GCCcore-11.3.0-Rust-1.65.0.eb} (99%) diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0-Rust-1.65.0.eb similarity index 99% rename from easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb rename to easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0-Rust-1.65.0.eb index db238831f5f7..e96036f787bc 100644 --- a/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/maturin/maturin-1.3.2-GCCcore-11.3.0-Rust-1.65.0.eb @@ -1,7 +1,11 @@ easyblock = 'CargoPythonBundle' + name = 'maturin' version = '1.3.2' +_rust_ver = '1.65.0' +versionsuffix = '-Rust-%s' % _rust_ver + homepage = 'https://github.com/pyo3/maturin' description = """This project is meant as a zero configuration replacement for setuptools-rust and milksnake. It supports building @@ -14,7 +18,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('Python', '3.10.4'), - ('Rust', '1.65.0'), + ('Rust', _rust_ver), ] crates = [ From 12713558edc5165cca588afff50299876ccb9571 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 29 Jan 2024 15:44:58 +0100 Subject: [PATCH 0492/1193] Add version suffix to maturin dependency in timm-0.9.7-foss-2022a-CUDA-11.7.0.eb --- .../easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb index afb2da239876..5268f5637706 100644 --- a/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('PyYAML', '6.0'), ('tqdm', '4.64.0'), ('torchvision', '0.13.1', versionsuffix), - ('maturin', '1.3.2'), + ('maturin', '1.3.2', '-Rust-1.65.0'), ] builddependencies = [ From 6be17db844e80acff9bb52ac67f380923cccf9be Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jan 2024 15:51:49 +0100 Subject: [PATCH 0493/1193] fix jar file name --- .../g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb | 12 ++++++++---- 1 file changed, 8 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb index cbbaa4f6f5ea..afbd964816bb 100644 --- a/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb +++ b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb @@ -4,14 +4,18 @@ name = 'GRASP-suite' version = '2022.7.4' versionsuffix = '-Java-%(javaver)s' -homepage = 'https://bodenlab.github.io/GRASP-suite/' +homepage = 'https://github.com/bodenlab/GRASP-suite/' + description = """GRASP-suite is a collection of tools and tutorials to perform and analyse ancestral sequence reconstruction.""" toolchain = SYSTEM source_urls = ['https://bodenlab.github.io/GRASP-suite/project/graspcmd/archive/'] -sources = ['bnkit.jar'] +sources = [{ + "download_filename": "bnkit.jar", + "filename": "%(name)s-%(version)s.jar", + }] checksums = ['7ee4cbc9f23857c8c7cf3e6bd0dde962d9a244974d955aac92212b5b5e29a385'] dependencies = [('Java', '17')] @@ -19,14 +23,14 @@ dependencies = [('Java', '17')] postinstallcmds = [ "mkdir -p %(installdir)s/bin", "echo '#!/bin/sh' > %(installdir)s/bin/grasp", - "echo 'java -jar -Xmx16g %(installdir)s/bnkit.jar $@' >> %(installdir)s/bin/grasp", + "echo 'java -jar -Xmx16g %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/grasp", "chmod a+rx %(installdir)s/bin/grasp" ] sanity_check_commands = ["grasp -h"] sanity_check_paths = { - 'files': ['bin/grasp', 'bnkit.jar'], + 'files': ['bin/grasp', '%(name)s-%(version)s.jar'], 'dirs': [], } From 10c48fb45128cfc0388a4bac84e6672cf7b15a43 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 29 Jan 2024 16:04:01 +0100 Subject: [PATCH 0494/1193] fix style --- .../easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb index afbd964816bb..0e5afae691a0 100644 --- a/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb +++ b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb @@ -15,7 +15,7 @@ source_urls = ['https://bodenlab.github.io/GRASP-suite/project/graspcmd/archive/ sources = [{ "download_filename": "bnkit.jar", "filename": "%(name)s-%(version)s.jar", - }] +}] checksums = ['7ee4cbc9f23857c8c7cf3e6bd0dde962d9a244974d955aac92212b5b5e29a385'] dependencies = [('Java', '17')] From 3afa26a3bb7c4f53d3724b18291de2f9066246dd Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 29 Jan 2024 16:18:01 +0100 Subject: [PATCH 0495/1193] Set maturin as builddependency in timm-0.9.7-foss-2022a-CUDA-11.7.0.eb --- .../easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb index 5268f5637706..f97e02d9b160 100644 --- a/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/t/timm/timm-0.9.7-foss-2022a-CUDA-11.7.0.eb @@ -21,11 +21,10 @@ dependencies = [ ('PyYAML', '6.0'), ('tqdm', '4.64.0'), ('torchvision', '0.13.1', versionsuffix), - ('maturin', '1.3.2', '-Rust-1.65.0'), ] builddependencies = [ - ('Rust', '1.65.0'), # for safetensors + ('maturin', '1.3.2', '-Rust-1.65.0'), ] crates = [ From 6496e5faace10f81262e3a3bb3ee3a8169782312 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 29 Jan 2024 16:53:37 +0100 Subject: [PATCH 0496/1193] add build dependency on poetry to tensorboard-2.15.1-gfbf-2023a.eb --- .../t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb index 7eadb5543caf..dd45e0d7f73d 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb @@ -9,6 +9,10 @@ understanding your TensorFlow runs and graphs.""" toolchain = {'name': 'gfbf', 'version': '2023a'} +builddependencies = [ + ('poetry', '1.5.1'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From f6c5b53dbd6b7ab39230c6d8c2af8dfbee40b9c5 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 29 Jan 2024 17:09:06 +0000 Subject: [PATCH 0497/1193] adding easyconfigs: Blosc2-2.4.3-GCCcore-11.2.0.eb --- .../b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..c2404f648b97 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.4.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d4aa5e0794598794f20ab950e973d44f0d0d9c133ea1a5a07cb200fa54d2e036'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.22.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From d2a92960f9345e15f0745936f84e84b3227750c5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 29 Jan 2024 20:31:15 +0100 Subject: [PATCH 0498/1193] minor style fixes --- easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb b/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb index 86d063a85c30..5090b62f7625 100644 --- a/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/sktime/sktime-0.25.0-gfbf-2023a.eb @@ -3,6 +3,7 @@ easyblock = 'PythonBundle' name = 'sktime' version = '0.25.0' homepage = 'https://www.sktime.net/en/stable/' + description = """sktime is a library for time series analysis in Python. It provides a unified interface for multiple time series learning tasks. Currently, this includes time series classification, regression, clustering, @@ -11,14 +12,12 @@ scikit-learn compatible tools to build, tune and validate time series models.""" toolchain = {'name': 'gfbf', 'version': '2023a'} - dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), - ('scikit-learn', '1.3.1') + ('scikit-learn', '1.3.1'), ] - exts_list = [ ('scikit-base', '0.6.2', { 'modulename': 'skbase', From 0413b50a64eb249acf4f1612325a27b9b1a58e4d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 29 Jan 2024 20:44:38 +0000 Subject: [PATCH 0499/1193] stop using custom easyblock for Doxygen --- .../d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb | 9 +++++++++ .../d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb | 9 +++++++++ .../d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb | 9 +++++++++ .../d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb | 9 +++++++++ .../d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb | 9 +++++++++ .../d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb | 9 +++++++++ .../d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb | 9 +++++++++ .../d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb | 9 +++++++++ 8 files changed, 72 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb index 3d72f0970bd3..065a4b2b89a4 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.17-GCCcore-9.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.8.17' @@ -25,4 +27,11 @@ dependencies = [('libiconv', '1.16')] configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb index f972f6c1aab2..245da2674609 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.8.20-GCCcore-10.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.8.20' @@ -25,4 +27,11 @@ dependencies = [('libiconv', '1.16')] configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb index 1601d6a560fb..1c7a82223dc2 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.9.1' @@ -25,4 +27,11 @@ dependencies = [('libiconv', '1.16')] configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb index 394f61d368ac..cc7368fa6541 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.9.1' @@ -25,4 +27,11 @@ dependencies = [('libiconv', '1.16')] configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb index b66694660858..2131eb73ee5e 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.9.4' @@ -28,4 +30,11 @@ dependencies = [ configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb index 35b262f3df87..a3156c6174e5 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.9.5' @@ -28,4 +30,11 @@ dependencies = [ configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb index 26007e7a8236..4ea9de048212 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.9.7' @@ -28,4 +30,11 @@ dependencies = [ configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb index e6c21e1dd18b..f880a5094989 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb @@ -1,3 +1,5 @@ +easyblock = 'CMakeMake' + name = 'Doxygen' version = '1.9.8' @@ -28,4 +30,11 @@ dependencies = [ configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" +sanity_check_paths = { + 'files': ["bin/doxygen"], + 'dirs': [], +} + +sanity_check_commands = ["doxygen --help"] + moduleclass = 'devel' From d6317bd5390d0bc440f8f4f34398dc2aa911e0c1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Mon, 29 Jan 2024 21:28:59 +0000 Subject: [PATCH 0500/1193] Update easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb index 4f000f843774..03088bf2860a 100644 --- a/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PBZIP2/PBZIP2-1.1.13-GCCcore-12.3.0.eb @@ -37,4 +37,5 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['pbzip2 -h 2>&1 | grep "Parallel BZIP2 v%(version)s"'] moduleclass = 'tools' From f3c2f7ac0d20721169352b1caf4f4f24ecdb3453 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 29 Jan 2024 21:30:53 +0000 Subject: [PATCH 0501/1193] add Python build depenency to 1.9.x Doxygen --- easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb | 1 + easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb | 1 + easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb | 1 + easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb | 1 + easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb | 1 + easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb | 1 + 6 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb index 1601d6a560fb..3929603f8c81 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-10.3.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('CMake', '3.20.1'), ('flex', '2.6.4'), ('pkg-config', '0.29.2'), + ('Python', '3.9.5', '-bare'), ] dependencies = [('libiconv', '1.16')] diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb index 394f61d368ac..16fc33537147 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.1-GCCcore-11.2.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('CMake', '3.21.1'), ('flex', '2.6.4'), ('pkg-config', '0.29.2'), + ('Python', '3.9.6', '-bare'), ] dependencies = [('libiconv', '1.16')] diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb index b66694660858..c535e4f1ea6c 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.4-GCCcore-11.3.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('CMake', '3.23.1'), ('flex', '2.6.4'), ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), ] dependencies = [ diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb index 35b262f3df87..d72907d1e8da 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('CMake', '3.24.3'), ('flex', '2.6.4'), ('pkgconf', '1.9.3'), + ('Python', '3.10.8', '-bare'), ] dependencies = [ diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb index 26007e7a8236..38b9d8962d4d 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.7-GCCcore-12.3.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('CMake', '3.26.3'), ('flex', '2.6.4'), ('pkgconf', '1.9.5'), + ('Python', '3.11.3'), ] dependencies = [ diff --git a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb index e6c21e1dd18b..b2a8de9a12f2 100644 --- a/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.8-GCCcore-13.2.0.eb @@ -20,6 +20,7 @@ builddependencies = [ ('CMake', '3.27.6'), ('flex', '2.6.4'), ('pkgconf', '2.0.3'), + ('Python', '3.11.5'), ] dependencies = [ From 10fb64344f14980ac78cd9d751a88a9fbdaa473c Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Tue, 30 Jan 2024 10:31:27 +0100 Subject: [PATCH 0502/1193] adding easyconfigs: ASAP3-3.13.3-intel-2023a.eb, ASAP3-3.13.3-foss-2023a.eb, kim-api-2.3.0-intel-compilers-2023.1.0.eb, openkim-models-20210811-intel-compilers-2023.1.0.eb --- .../a/ASAP3/ASAP3-3.13.3-foss-2023a.eb | 36 +++++++++++++ .../a/ASAP3/ASAP3-3.13.3-intel-2023a.eb | 42 ++++++++++++++++ .../kim-api-2.3.0-intel-compilers-2023.1.0.eb | 43 ++++++++++++++++ ...odels-20210811-intel-compilers-2023.1.0.eb | 50 +++++++++++++++++++ 4 files changed, 171 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-intel-2023a.eb create mode 100644 easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-intel-compilers-2023.1.0.eb create mode 100644 easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-intel-compilers-2023.1.0.eb diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-foss-2023a.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-foss-2023a.eb new file mode 100644 index 000000000000..4315122d3cb4 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = "PythonPackage" + +name = 'ASAP3' +version = '3.13.3' + +homepage = 'https://wiki.fysik.dtu.dk/asap/' +description = """ASAP is a calculator for doing large-scale classical molecular +dynamics within the Campos Atomic Simulation Environment (ASE).""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True, 'openmp': False} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['78aa4c9ee11315b6e7f8cd9b1fda6ab9a240cc4f4ff418972ea079612e26d369'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ASE', '3.22.1'), + ('kim-api', '2.3.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-intel-2023a.eb b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-intel-2023a.eb new file mode 100644 index 000000000000..0fc1bd1708f5 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP3/ASAP3-3.13.3-intel-2023a.eb @@ -0,0 +1,42 @@ +easyblock = "PythonPackage" + +name = 'ASAP3' +version = '3.13.3' + +homepage = 'https://wiki.fysik.dtu.dk/asap/' +description = """ASAP is a calculator for doing large-scale classical molecular +dynamics within the Campos Atomic Simulation Environment (ASE).""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = { + 'pic': True, + 'usempi': True, + 'openmp': False, + 'extra_cflags': '-fp-speculation=fast -fp-model fast' +} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['78aa4c9ee11315b6e7f8cd9b1fda6ab9a240cc4f4ff418972ea079612e26d369'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('ASE', '3.22.1'), + ('kim-api', '2.3.0'), +] + +installopts = '--verbose' +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'] +} + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-intel-compilers-2023.1.0.eb new file mode 100644 index 000000000000..0f7148a4b8df --- /dev/null +++ b/easybuild/easyconfigs/k/kim-api/kim-api-2.3.0-intel-compilers-2023.1.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'kim-api' +version = '2.3.0' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +KIM is an API and OpenKIM is a collection of interatomic models (potentials) for +atomistic simulations. This is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild only installs the API, the models can be installed with the +package openkim-models, or the user can install them manually by running + kim-api-collections-management install user MODELNAME +or + kim-api-collections-management install user OpenKIM +to install them all. + """ + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +source_urls = ['https://s3.openkim.org/kim-api/'] +sources = ['%(name)s-%(version)s.txz'] +checksums = ['93673bb8fbc0625791f2ee67915d1672793366d10cabc63e373196862c14f991'] + +dependencies = [ + ('CMake', '3.26.3'), # Also needed to install models, thus not just a builddependency. +] + +parallel = 1 +separate_build_dir = True + +modextravars = { + 'KIM_API_CMAKE_PREFIX_DIR': '%(installdir)s/lib64' +} + +sanity_check_paths = { + 'files': ['bin/kim-api-collections-management', 'lib64/libkim-api.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-intel-compilers-2023.1.0.eb new file mode 100644 index 000000000000..e26d2ec61f0b --- /dev/null +++ b/easybuild/easyconfigs/o/openkim-models/openkim-models-20210811-intel-compilers-2023.1.0.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'openkim-models' +version = '20210811' + +homepage = 'https://openkim.org/' +description = """Open Knowledgebase of Interatomic Models. + +OpenKIM is an API and a collection of interatomic models (potentials) for +atomistic simulations. It is a library that can be used by simulation programs +to get access to the models in the OpenKIM database. + +This EasyBuild installs the models. The API itself is in the kim-api +package. + """ + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('kim-api', '2.3.0'), +] + +source_urls = ['https://s3.openkim.org/archives/collection/'] +sources = ['openkim-models-2021-08-11.txz'] +checksums = ['f42d241969787297d839823bdd5528bc9324cd2d85f5cf2054866e654ce576da'] + +separate_build_dir = True +abs_path_compilers = True # Otherwise some KIM-API magic breaks cmake. +configopts = '-DKIM_API_INSTALL_COLLECTION=SYSTEM ' +configopts += '-DKIM_API_PORTABLE_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/portable-models ' +configopts += '-DKIM_API_SIMULATOR_MODEL_INSTALL_PREFIX=%(installdir)s/lib/kim-api/simulator-models ' +configopts += '-DKIM_API_MODEL_DRIVER_INSTALL_PREFIX=%(installdir)s/lib/kim-api/model-drivers ' + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/kim-api/model-drivers', 'lib/kim-api/portable-models', 'lib/kim-api/simulator-models'] +} + +modextravars = { + 'KIM_API_MODEL_DRIVERS_DIR': '%(installdir)s/lib/kim-api/model-drivers', + 'KIM_API_PORTABLE_MODELS_DIR': '%(installdir)s/lib/kim-api/portable-models', + 'KIM_API_SIMULATOR_MODELS_DIR': '%(installdir)s/lib/kim-api/simulator-models', +} + + +moduleclass = 'chem' From 09e5d63dfac79c7de6a2d002982036bac622df4e Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 30 Jan 2024 12:31:27 +0000 Subject: [PATCH 0503/1193] Fix the missing checksum --- .../j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb index cbc9ac27fbf3..fcf403d82f9e 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb @@ -62,7 +62,11 @@ exts_list = [ }), ('jupyter_core', '5.3.1', { 'patches': ['jupyter-core-5.3.1_fix_jupyter_path.patch'], - 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + 'checksums': [ + {'jupyter_core-5.3.1.tar.gz': '5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'}, + {'jupyter-core-5.3.1_fix_jupyter_path.patch': + '4684b1270559e6d67b3839fd7d2f88e584ae1428b47e035e0aa8ae63ac896458'}, + ], }), ('fastjsonschema', '2.17.1', { 'checksums': ['f4eeb8a77cef54861dbf7424ac8ce71306f12cbb086c45131bcba2c6a4f726e3'], From 5d6f07a16c29120045c4198085a989cde460051b Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 30 Jan 2024 12:38:12 +0000 Subject: [PATCH 0504/1193] Make same changes for GCCcore-12.3.0 toolchain --- .../j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb | 5 +---- .../JupyterNotebook-7.0.2-GCCcore-12.3.0.eb | 5 +---- .../jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb | 2 +- .../jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb | 5 +---- .../jupyter-server-2.7.2-GCCcore-12.3.0.eb | 12 +++++++----- .../jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb | 5 +---- 6 files changed, 12 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb index 19c7e8a67101..cc3dbfb5a129 100644 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-4.0.5-GCCcore-12.3.0.eb @@ -63,10 +63,7 @@ sanity_check_paths = { sanity_check_commands = ['jupyter lab --help'] -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} diff --git a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb index 8fb29542706e..ce1d02d63c1a 100644 --- a/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterNotebook/JupyterNotebook-7.0.2-GCCcore-12.3.0.eb @@ -36,9 +36,6 @@ sanity_check_paths = { sanity_check_commands = ['jupyter notebook --help'] -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb index 02d3f79c0cb6..0eadab83cb03 100644 --- a/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-resource-usage/jupyter-resource-usage-1.0.0-GCCcore-12.3.0.eb @@ -35,6 +35,6 @@ sanity_check_paths = { } # Add the notebook extension to the search path for jupyter notebooks -modextrapaths = {'JUPYTER_PATH': 'share/jupyter/'} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb index 5c1a64b90902..96efada62189 100644 --- a/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server-proxy/jupyter-server-proxy-4.0.0-GCCcore-12.3.0.eb @@ -37,9 +37,6 @@ exts_list = [ }), ] -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb index 76b36f7551f4..0af996d6771e 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -53,7 +53,12 @@ exts_list = [ 'checksums': ['9502a3cca51f4fac40b5feca985b6703a5c1f6ad815588a7ca9e285b9dca6757'], }), ('jupyter_core', '5.3.1', { - 'checksums': ['5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'], + 'patches': ['jupyter-core-5.3.1_fix_jupyter_path.patch'], + 'checksums': [ + {'jupyter_core-5.3.1.tar.gz': '5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'}, + {'jupyter-core-5.3.1_fix_jupyter_path.patch': + '4684b1270559e6d67b3839fd7d2f88e584ae1428b47e035e0aa8ae63ac896458'}, + ], }), ('fastjsonschema', '2.18.0', { 'checksums': ['e820349dd16f806e4bd1467a138dced9def4bc7d6213a34295272a6cac95b5bd'], @@ -182,9 +187,6 @@ sanity_check_paths = { sanity_check_commands = ['jupyter --help'] -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb index f3a22452bde7..f096b4542faf 100644 --- a/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyterlmod/jupyterlmod-4.0.3-GCCcore-12.3.0.eb @@ -37,9 +37,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages', 'share/jupyter'], } -modextrapaths = { - 'JUPYTER_CONFIG_PATH': 'etc/jupyter', - 'JUPYTER_PATH': 'share/jupyter', -} +modextrapaths = {'EB_ENV_JUPYTER_ROOT': ''} moduleclass = 'tools' From a0801f9b9b5ec2622d079a6261aa1a4edee2132b Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 30 Jan 2024 13:28:30 +0000 Subject: [PATCH 0505/1193] Fix style --- .../j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb | 2 +- .../j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb index fcf403d82f9e..1ec1509cb4a9 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb @@ -64,7 +64,7 @@ exts_list = [ 'patches': ['jupyter-core-5.3.1_fix_jupyter_path.patch'], 'checksums': [ {'jupyter_core-5.3.1.tar.gz': '5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'}, - {'jupyter-core-5.3.1_fix_jupyter_path.patch': + {'jupyter-core-5.3.1_fix_jupyter_path.patch': '4684b1270559e6d67b3839fd7d2f88e584ae1428b47e035e0aa8ae63ac896458'}, ], }), diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb index 0af996d6771e..d487875e2861 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -56,7 +56,7 @@ exts_list = [ 'patches': ['jupyter-core-5.3.1_fix_jupyter_path.patch'], 'checksums': [ {'jupyter_core-5.3.1.tar.gz': '5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'}, - {'jupyter-core-5.3.1_fix_jupyter_path.patch': + {'jupyter-core-5.3.1_fix_jupyter_path.patch': '4684b1270559e6d67b3839fd7d2f88e584ae1428b47e035e0aa8ae63ac896458'}, ], }), From 88a1b6b7c5ce09fb535d4a9be5d93d847fbd2a3b Mon Sep 17 00:00:00 2001 From: nicolas Date: Tue, 30 Jan 2024 14:39:27 +0100 Subject: [PATCH 0506/1193] adding easyconfigs: R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb, arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb, semla-1.1.6-foss-2023a-R-4.3.2.eb --- .../arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb | 35 + ...le-Bioconductor-3.18-foss-2023a-R-4.3.2.eb | 1352 +++++++++++++++++ .../s/semla/semla-1.1.6-foss-2023a-R-4.3.2.eb | 31 + 3 files changed, 1418 insertions(+) create mode 100644 easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb create mode 100644 easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb create mode 100644 easybuild/easyconfigs/s/semla/semla-1.1.6-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..260e080346cd --- /dev/null +++ b/easybuild/easyconfigs/a/arrow-R/arrow-R-14.0.0.2-foss-2023a-R-4.3.2.eb @@ -0,0 +1,35 @@ +easyblock = 'RPackage' + +name = 'arrow-R' +version = '14.0.0.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://cran.r-project.org/src/contrib/Archive/arrow', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages +] +sources = ['arrow_%(version)s.tar.gz'] +checksums = ['7138a52d66f1b94ec31c25e8929d6f92b1640df852a10817600a82ab68ba8ab7'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('Arrow', '14.0.1'), +] + +preinstallopts = "export LIBARROW_BINARY=true && " + +sanity_check_paths = { + 'files': [], + 'dirs': ['arrow'], +} + +options = {'modulename': 'arrow'} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..19c0cf74fe1c --- /dev/null +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -0,0 +1,1352 @@ +easyblock = 'Bundle' + +name = 'R-bundle-Bioconductor' +version = '3.18' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://bioconductor.org' +description = """Bioconductor provides tools for the analysis and coprehension + of high-throughput genomic data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('pkgconf', '1.9.5')] + +dependencies = [ + ('R', '4.3.2'), + ('Boost', '1.82.0'), # for mzR + ('GSL', '2.7'), # for flowClust + ('HDF5', '1.14.0'), # for rhdf5 + ('arrow-R', '14.0.0.2', versionsuffix), # required by RcisTarget +] + +exts_default_options = { + 'source_urls': [ + 'https://bioconductor.org/packages/3.18/bioc/src/contrib/', + 'https://bioconductor.org/packages/3.18/bioc/src/contrib/Archive/%(name)s', + 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/', + 'https://bioconductor.org/packages/3.18/data/experiment/src/contrib/', + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz' +} + +exts_defaultclass = 'RPackage' + +# check whether correct version is installed in extension filter +# (some versions in this bundle may be newer than the ones provided by R) +local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver != '%(ext_version)s') " +local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" +exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) + +# CRAN packages on which these Bioconductor packages depend are available in R module on which this depends +# !! order of packages is important !! +# packages updated on 18th March 2023 +exts_list = [ + ('BiocGenerics', '0.48.0', { + 'checksums': ['f413b2a812c5cbb219fc799d04fe36e4c88faa7ff946f643afcf5fdba312e44f'], + }), + ('Biobase', '2.62.0', { + 'checksums': ['ef753acc499c2504e226bf76e0acc08b7aa370fc60cc369bb8ebc1913f57d37e'], + }), + ('S4Vectors', '0.40.2', { + 'checksums': ['4cd9a63b3b41b08fca8121dc5b8f43d6f7d580842b1b000055dee90b68f49982'], + }), + ('IRanges', '2.36.0', { + 'checksums': ['58c05c3c4eb7fdee64cb027ba849de0ec57f2e4150b9aa645b62549da1401066'], + }), + ('GenomeInfoDbData', '1.2.11', { + 'checksums': ['311fe287842e6161f24fc1faaa824a6d5ce88afcbf4c0203f5e309456e667bc2'], + }), + ('GenomeInfoDb', '1.38.5', { + 'checksums': ['2cf2ebbeca6d05a71d0eb2f25dbf56e4c19b67b26bba5e0ad3a08b7977fe859f'], + }), + ('zlibbioc', '1.48.0', { + 'checksums': 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['eff1ae8d7f4ed5c6bed335de63a758be593750fb0b3483c01cf50402688d244d'], + }), + ('WGCNA', '1.72-5', { + 'checksums': ['03439143ff235c17f0dbca7dd6362afa8ddb5a72594f5c2df1c6df1caca2e79d'], + }), + ('DNABarcodes', '1.32.0', { + 'checksums': ['09263a219f974c60eeb384fc391a47d967eac19d6ffe81e8f77c433d4b99a48b'], + }), + ('GenomicInteractions', '1.36.0', { + 'checksums': ['8c50e4b566f2d9f24a45fb076cb0295c15963227951f3cf69ffe29215eec368f'], + }), + ('CAGEfightR', '1.22.0', { + 'checksums': ['80fd09e31d654bac277962dfee644c4b09ef3a0148c14b8ee51147f2f4cf7d41'], + }), + ('CAGEr', '2.8.0', { + 'checksums': ['78f0d302723f0fd6bb7ab86aaf545857576767359a45215e457c4fe65a5a2a8c'], + }), + ('SPOTlight', '1.6.7', { + 'checksums': ['58f1dc14f94d2009952543306c5cb9da86ca2b98729941af93c1975d836e7af6'], + }), + ('CGHcall', '2.64.0', { + 'checksums': ['9efe61577fe85ccde939e205ef871a0287cfc65f974bba42fb82d40548765ff4'], + }), + ('QDNAseq', '1.38.0', { + 'checksums': ['7a5681d90baeeb8dc5878163b5692b8851cdd1bb564fa67dd80e0e8ef1b358d8'], + }), + ('HiCcompare', '1.24.0', { + 'checksums': ['4dbca074754c4aea7f95e1a4483943d955fa7584b69d37865a90ffde7edb68ac'], + }), + ('ROntoTools', '2.30.0', { + 'checksums': ['b1033239dc62910eb2227b8bd37c86c5fb19a2214c20b8e37079ca970485fbdc'], + }), + ('scDblFinder', '1.16.0', { + 'checksums': ['48d905de681d1731f926962eb2ba8b2249ad43999f52292a2f2675e94c0d76b8'], + }), + ('treeio', '1.26.0', { + 'checksums': ['393ea7c7df0e5d40df43b63f78f4b889701ed0b359b7d6f9232793c37d6e7fcf'], + }), + ('ggtree', '3.10.0', { + 'checksums': ['0eb3445c924b852fd52312cf1932c42dcaaadfe60468ea4ab35f150670a0828b'], + }), + ('scistreer', '1.2.0', { + 'checksums': ['6c445f61042866d1aef2e8ccae402d79dab657f880a1b07d02db9819cf25cd0e'], + }), + ('numbat', '1.3.2-1', { + 'checksums': ['0413b538e9e7e88dfd5a5328ca26da57b527007962fbe2e742eafcc1dff42bad'], + }), + ('HiCBricks', '1.20.0', { + 'checksums': ['efffffa51ff278b92110f1d3afe0bd56c34a84bfb44a52a42b2bf0aa398c2015'], + }), + ('dir.expiry', '1.10.0', { + 'checksums': ['38b5c0460b8022e1c801d574fd3aaea0d74603730e304113e07af74621462ba4'], + }), + ('basilisk.utils', '1.14.1', { + 'checksums': ['474007e52f5a18e9e76c7e0fad7121cba2a77aed02c649e98fd5cc994182a4a6'], + }), + ('basilisk', '1.14.2', { + 'checksums': ['afe999c64bcf0faee0e3a518e43411f17e6cdf61137fc11758eabb734310233a'], + }), + ('zellkonverter', '1.12.1', { + 'checksums': ['19e5093c1898bbe6232cd271d9d341efdadf1cd8ab33f5f6a30a245684c52b09'], + }), + ('DO.db', '2.9', { + 'checksums': ['762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881'], + }), + ('GOSemSim', '2.28.1', { + 'checksums': ['bd27320fdadd709002a19f80e7b230b1411a4413f32a74430d6645a22232035d'], + }), + ('HDO.db', '0.99.1', { + 'checksums': ['c17cf28d06621d91148a64d47fdeaa906d8621aba7a688715fb9571a55f7cf92'], + }), + ('DOSE', '3.28.2', { + 'checksums': ['ee22b726664304643116a88c40eb8b2032e2a4faa92c2b2523986ddf19a2644e'], + }), + ('enrichplot', '1.22.0', { + 'checksums': ['9d52274b4a0b2e31c448a343f35dcd54426660a89f3a5c414490d8d59449fa16'], + }), + ('gson', '0.1.0', { + 'checksums': ['14ddbee5be66d0b1dc178e41175a50ab6ed9ffed04d4361ecf5eef3548d9a381'], + }), + ('clusterProfiler', '4.10.0', { + 'checksums': ['58401c819244b196cb907715e7c215791424a4f06082c22d2e91b9cffcf299ee'], + }), + ('reactome.db', '1.86.2', { + 'checksums': ['0c319b4164ab7e590233437ab715dd9a0092287611ac588b74ec42a01b8ce80a'], + }), + ('graphite', '1.48.0', { + 'checksums': ['5678e693530ed9e5727e45b938ff830db24efc1bbac59f8deefa0bd0250812c1'], + }), + ('ReactomePA', '1.46.0', { + 'checksums': ['4cf764415b9361d776e57a5ebed52c783a79e8adda1dd851ded14fe62be5d44d'], + }), + ('flowClean', '1.40.0', { + 'checksums': ['0a0029fd76fd2f9dd2ba7bd5ccabeeebb53438a947143e6bae79d96c55a00325'], + }), + ('flowAI', '1.32.0', { + 'checksums': ['7ffe8ec5e2736ad644cc24174b6350a5bd9f382086ea70a2a2c78883911b21ae'], + }), + ('flowFP', '1.60.0', { + 'checksums': ['f58cf1d0947a64f04a101b74eedead6dc441d465c6cf4abad1a8831e4711d834'], + }), + ('simplifyEnrichment', '1.12.0', { + 'checksums': ['fc86227bb20671fbb242983e9a6b1c9509b70003817860c116b106841ca41962'], + }), + ('RPMG', '2.2-7', { + 'checksums': ['c413de3c126bc377fe31a948887d27f404a9637c57fe0e07b087d5509cb99f11'], + }), + ('Rwave', '2.6-5', { + 'checksums': ['6c9ef75bb376f2e3f5c5dcd3b3fdca7d86797ce809da34f444632657189be2e4'], + }), + ('RSEIS', '4.1-6', { + 'checksums': ['6a4a3e57fb4935676a3105597e879ff79839bba86349fca35aba7bab13e87aed'], + }), + ('splancs', '2.01-44', { + 'checksums': ['08d46df9b56488925cc1b66261cf1134292ce4b5174b45e066eeb1e951dec171'], + }), + ('MBA', '0.1-0', { + 'checksums': ['78039905c5b98be2bb79a5f292187a2aca21ef449daeefea58b0cac53a5283af'], + }), + ('GEOmap', '2.5-5', { + 'checksums': ['8a17a78926cda3f885584f797db6765d218f89b39eda512ff8af379651fb483f'], + }), + ('RFOC', '3.4-10', { + 'checksums': ['b1211db8960b482ebb516233c86b075d1a1f006a88191a72fa98babd5a8e2100'], + }), + ('flowDensity', '1.36.1', { + 'checksums': ['e2b9102bc7c67cd450d340602fc88d2ef8736266b7ff9386974192fae6d65570'], + }), + ('flowPeaks', '1.48.0', { + 'checksums': ['84baaf3c7e8c2cd9790dfd086bf56ce07d448be6255285330dfc92b0b2fafafb'], + }), + ('SamSPECTRAL', '1.56.0', { + 'checksums': ['49814844e37282fde405c3217ae222637583a0a0ca4f3008194b148f576b74f0'], + }), + ('ddPCRclust', '1.22.0', { + 'checksums': ['4c745a4fbe80d7827e24e9ccfbb911a61aa636fba5a46aadf6de862667f1cd31'], + }), + ('feature', '1.2.15', { + 'checksums': ['de38292b7e800068a20824e2a9e7d5d4d0b465b7925db0d165346aa5030ff67b'], + }), + ('flowMerge', '2.50.0', { + 'checksums': ['cbd7a2e4ffdac86fb0fe36fa1f9b5adb277fd882a8fb3ea793031546f1dd6701'], + }), + ('SpatialExperiment', '1.12.0', { + 'checksums': ['c49efa705e32d385b9bdcf3f8d205bf4e55cb1016ed59f0614c6b892f09782e8'], + }), + ('TrajectoryUtils', '1.10.0', { + 'checksums': ['bba459c730a76780adab71dd1f130e2e025c0fb8990c45bb7320611336a00d5f'], + }), + ('slingshot', '2.10.0', { + 'checksums': ['2d30c816b11d7f32ed87afcdf3a30cb9e130a1abac28d8c792d556c2ae047260'], + }), + ('TreeSummarizedExperiment', '2.10.0', { + 'checksums': ['cf7cd38f3199dc9324b6dbedd40ce2fae4c910abd0b11c41d7eaaa1d698f78fb'], + }), + ('decontam', '1.22.0', { + 'checksums': ['736b270861e029e47b7b9958fe38bda6c6b833ebe8e98b54e2e766ddb1699f54'], + }), + ('DECIPHER', '2.30.0', { + 'checksums': ['e9d06fe494792d31c2c547c04a409c26fe739c1000fc3aec7697e1367aa328e6'], + }), + ('mia', '1.10.0', { + 'checksums': ['b7b3c20dd45e2a376fe90b62a77f01af323f1b676324009795b11fa7bbbb9a10'], + }), + ('ANCOMBC', '2.4.0', { + 'checksums': ['874699e6662d2624d174fe877e0e81024ecc5aa636d5b23ed9b5c09e5698c3d4'], + }), + ('decoupleR', '2.8.0', { + 'checksums': ['09b6d3398eec6e5aa6eacd41c8d025488e6acc771e04e43040cb8ea1feccd4ee'], + }), + ('UCell', '2.6.2', { + 'checksums': ['ad8c56756ac2645f02cfbb00e6aec756528ebc729413ba9af57ff8e3425a6403'], + }), + ('intervals', '0.15.4', { + 'checksums': ['50c0e1e3aab3e7b72cc1f0a6559d96caa3a360e969c38538479907e6cbe39f8f'], + }), + ('oompaBase', '3.2.9', { + 'checksums': ['14ca2b8e713a6a7ce13758f7f5c183dbc4fdfedc4f1244ca31bbdadf8a16bcb2'], + }), + ('oompaData', '3.1.3', { + 'checksums': ['aeb932f75d3de2101d2e1b387fe76677f2d38d4819710320c0e3df07df3ab73d'], + }), + ('TailRank', '3.2.2', { + 'checksums': ['21ed95ea47d21155f08ae2ad7bca9547f89f492000bc1defe1cc5ec172739d09'], + }), + ('RnBeads', '2.20.0', { + 'checksums': ['1797f32b209a122fac0b416cc98dd52e0fc7ed11f4849342ed01f85b2da1e797'], + }), + ('RnBeads.hg19', '1.34.0', { + 'checksums': ['26b2c7cd893c78a9475aa812cf2dfa7b5e1b0f4ba702d8c4c18d470e27be6657'], + }), + ('RnBeads.hg38', '1.34.0', { + 'checksums': ['454c1a34cb3c9c1ebc66f792626b6aaf19258ca35506e054b056da386c3988a6'], + }), + ('RnBeads.mm9', '1.34.0', { + 'checksums': ['eecf24c99996e6e7ffd2bd3fb3633a231a201ac16815472227f6235526d4f4b4'], + }), + ('RnBeads.mm10', '2.10.0', { + 'checksums': ['28b28ad3b3521da37bd630b3c540dd2ad539435c34ba5cd3988234c5dbeb3674'], + }), + ('RnBeads.rn5', '1.34.0', { + 'checksums': ['1ad1e5a37a018e6e53e7d7f84333dda5ceae3368c2e44076c9e4ef66a26b57a0'], + }), + ('log4r', '0.4.3', { + 'checksums': ['dfe3d49d35a8d8f3ad63f156d18e860540a01bd0af0e343cbab3e31a2cf5904c'], + }), + ('MSstatsConvert', '1.12.0', { + 'checksums': ['8c284b086736f4eba4035a95c5bdd5163b9d3102f1644fc7f0cd1209dc3de5f6'], + }), + ('MSstats', '4.10.0', { + 'checksums': ['cd1ca2161c6554906e33c76a6af0f63de624abcb87335f5d9a9494f8677a7b94'], + }), + ('MSstatsTMT', '2.10.0', { + 'checksums': ['e4eff0f7d684c8aefd1d3d2efa87f4b902029dbdae318a23ffba84cebf7dd303'], + }), + ('MSstatsPTM', '2.4.2', { + 'checksums': ['3cd199935444e7e4e7af0586cfbe415d0b5702dd8dc4d7687d38cb163830d507'], + }), + ('factoextra', '1.0.7', { + 'checksums': ['624ff01c74933352aca55966f8a052b1ccc878f52c2c307e47f88e0665db94aa'], + }), + ('MSstatsLiP', '1.8.1', { + 'checksums': ['b64eb9a2021720205da3f0124152d5ff7159e6c6f8a7c076dcf4cd99630f3fd9'], + }), + ('babelgene', '22.9', { + 'checksums': ['ce6601dcb78352516d3b0355042c52a20e154b39d3b27b93ff52150a59c885e2'], + }), + ('msigdbr', '7.5.1', { + 'checksums': ['dc30487bdf3594425ae9faec1ca0d7d0cd7278f4f177689133f92880e74acaca'], + }), + ('escape', '1.12.0', { + 'checksums': ['d69dda267e9346b1d3f10274fb0985409d23060abba609d4e8859eae92b1b12e'], + }), +] + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': [], + 'dirs': ['AnnotationDbi', 'BiocManager', 'GenomicFeatures'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/semla/semla-1.1.6-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/s/semla/semla-1.1.6-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..e214778d526a --- /dev/null +++ b/easybuild/easyconfigs/s/semla/semla-1.1.6-foss-2023a-R-4.3.2.eb @@ -0,0 +1,31 @@ +easyblock = 'RPackage' + +name = 'semla' +version = '1.1.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/arrow' +description = "R interface to the Apache Arrow C++ library" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://github.com/ludvigla/semla/releases/download/v%(version)s', +] +sources = ['semla_%(version)s.tar.gz'] +checksums = ['845b7af52a1d7f74ef3158936c1bcaa0f81724e1d0938c6326ced6128d6fbec3'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), +] + + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + + +moduleclass = 'bio' From 63b871c31f59193cc471b29e62fd5905569b9cfc Mon Sep 17 00:00:00 2001 From: Ehsan Moravveji Date: Tue, 30 Jan 2024 15:14:16 +0100 Subject: [PATCH 0507/1193] Starting with the first GenomeComb easyconfig --- .../g/GenomeComb/GenomeComb-0.106.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb diff --git a/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb b/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb new file mode 100644 index 000000000000..9a46a9a3d423 --- /dev/null +++ b/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PackedBinary' + +name = 'GenomeComb' +version = '0.106.0' + +homepage = 'https://github.com/derijkp/genomecomb' +description = 'Genomecomb is a package designed to analyze, combine, annotate and query genome as well as transcriptome sequencing data.' + +toolchain = SYSTEM + +source_urls = ['https://github.com/derijkp/genomecomb/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-Linux-x86_64.tar.gz'] +checksums = ['bf238688b8f060e5f93a748941e80f024e8c24e760906a6bc6e050de1cd9a2ae'] + +sanity_check_paths = { + 'files': ['cg', 'cedit', 'ctable', 'tclsh8.5', 'apps/cg/cg.tcl'], + 'dirs': ['bin', 'exts/genomecomb0.x', ] +} + +sanity_check_commands = [ + ('cg', 'help'), + ('cg', 'version samtools') +] + +moduleclass = 'bio' From 7acea6d2223b21cac4cd7e239c6c4f8c7affff9d Mon Sep 17 00:00:00 2001 From: Ehsan Moravveji Date: Tue, 30 Jan 2024 15:37:43 +0100 Subject: [PATCH 0508/1193] fixing long description --- easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb b/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb index 9a46a9a3d423..d995f6b94e56 100644 --- a/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb +++ b/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb @@ -3,8 +3,11 @@ easyblock = 'PackedBinary' name = 'GenomeComb' version = '0.106.0' +description = """ +Genomecomb is a package designed to analyze, combine, annotate and query genome +as well as transcriptome sequencing data. +""" homepage = 'https://github.com/derijkp/genomecomb' -description = 'Genomecomb is a package designed to analyze, combine, annotate and query genome as well as transcriptome sequencing data.' toolchain = SYSTEM From b1d766f2c5fa42faba70336c885f3b4acab30449 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 30 Jan 2024 15:49:06 +0100 Subject: [PATCH 0509/1193] adding easyconfigs: atools-1.5.1-GCCcore-12.3.0.eb --- .../a/atools/atools-1.5.1-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1124e45ce7b5 --- /dev/null +++ b/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'atools' +version = '1.5.1' + +homepage = 'https://github.com/gjbex/atools' +description = """Tools to make using job arrays a lot more convenient.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/gjbex/atools/archive'] +sources = [SOURCE_TAR_GZ] +checksums = ['540714c39aa83dd5f1a7367d76f8d6f491336fa5fc00077591a22151ef5d31f4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +# to enable SLURM integration (site-specific) (options are torque, moab, sge, slurm) +configopts = '--with-batchsystem=slurm' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acreate', 'aenv', 'aload', 'alog', 'arange', 'areduce']], + 'dirs': ['lib/vsc/atools'] +} + +sanity_check_commands = [ + 'acreate -h', + 'aenv -h', + 'aload -h', + 'alog -h', + 'arange -h', + 'areduce -h', +] + +moduleclass = 'tools' From fe22bf99dce85b1644f66b15c27e0d5671a8ed9c Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 30 Jan 2024 14:56:07 +0000 Subject: [PATCH 0510/1193] fix indentation --- test/easyconfigs/easyconfigs.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 26a5643ce0f9..1cda82901702 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -403,8 +403,8 @@ def check_dep_vars(self, gen, dep, dep_vars): if all(ec.startswith('meson-python-') for ec in ecs): dep_vars.pop(key) # always retain at least one dep variant - if len(dep_vars) == 1: - break + if len(dep_vars) == 1: + break # multiple versions of Boost is OK as long as they are deps for a matching Boost.Python if dep == 'Boost' and len(dep_vars) > 1: From 28bfbc8ec117d1abe3c28fb3a2f4748f09df1e9e Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 30 Jan 2024 16:21:24 +0100 Subject: [PATCH 0511/1193] add MDI dependency --- ...MMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 1 + .../m/MDI/MDI-1.4.26-gompi-2023a.eb | 47 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb index b51db79bc457..8d594686fa29 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -46,6 +46,7 @@ dependencies = [ ('PLUMED', '2.9.0'), ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2023.07'), + ('MDI', '1.4.26'), # VTK package is auto-disabled if this dep is not available ('VTK', '9.3.0'), ] diff --git a/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb new file mode 100644 index 000000000000..aa11e702a52f --- /dev/null +++ b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb @@ -0,0 +1,47 @@ +# MDI package for LAMMPS +# Author: J. Saßmannshausen (Imperial College London) + +easyblock = 'CMakeMake' +name = 'MDI' +version = '1.4.26' + +homepage = 'https://github.com/MolSSI-MDI/MDI_Library' +description = """The MolSSI Driver Interface (MDI) project provides a +standardized API for fast, on-the-fly communication between computational +chemistry codes. This greatly simplifies the process of implementing +methods that require the cooperation of multiple software packages and +enables developers to write a single implementation that works across +many different codes. The API is sufficiently general to support a wide +variety of techniques, including QM/MM, ab initio MD, machine learning, +advanced sampling, and path integral MD, while also being straightforwardly +extensible. Communication between codes is handled by the MDI Library, which +enables tight coupling between codes using either the MPI or TCP/IP methods. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/MolSSI-MDI/MDI_Library/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8cbd80ae9adf44394b693fe812b8e4e8ca506173b3ca1f31002adbe7eaf61362'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +# perform iterative build to get both static and shared libraries +local_common_configopts = '-DCMAKE_POSITION_INDEPENDENT_CODE=ON ' +configopts = [ + local_common_configopts + ' -Dlibtype=STATIC', + local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', +] + +sanity_check_paths = { + 'files': ['lib/mdi/libmdi.a', 'lib/mdi/libmdi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'chem' From 7f80087ca199b568ce43f0ea1bdf629dbc054d78 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 30 Jan 2024 15:47:33 +0000 Subject: [PATCH 0512/1193] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-12.2.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ca99945c383b --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'MEGAHIT' +version = '1.2.9' + +homepage = 'https://github.com/voutcn/megahit' +description = """An ultra-fast single-node solution for large and complex +metagenomics assembly via succinct de Bruijn graph""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('zlib', '1.2.12'), +] +dependencies = [ + ('Python', '3.10.8'), + ('bzip2', '1.0.8'), + ('gzip', '1.12'), +] + + +sanity_check_paths = { + 'files': [ + 'bin/%(namelower)s', + 'bin/%(namelower)s_core', + 'bin/%(namelower)s_core_no_hw_accel', + 'bin/%(namelower)s_core_popcnt', + 'bin/%(namelower)s_toolkit', + ], + 'dirs': [], +} + +sanity_check_commands = [ + "megahit --version", + "megahit --test", +] + +moduleclass = 'bio' From e1d0086dcfda2b654d7823d2bd64a8871f2d17d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Jan 2024 16:59:56 +0100 Subject: [PATCH 0513/1193] adding easyconfigs: PHYLIP-3.697-GCC-12.3.0.eb --- .../p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb new file mode 100644 index 000000000000..cb261efb52ce --- /dev/null +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'MakeCp' + +name = 'PHYLIP' +version = '3.697' + +homepage = 'https://evolution.genetics.washington.edu/phylip' +description = "PHYLIP is a free package of programs for inferring phylogenies." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +# -fcommon is required to avoid 'multiple definitions' linking error +toolchainopts = {'extra_cflags': "-fcommon"} + +source_urls = ['https://evolution.gs.washington.edu/phylip/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1'] + +buildopts = '-Csrc -fMakefile.unx all CFLAGS="$CFLAGS" && make -Csrc -fMakefile.unx install' + +files_to_copy = [(['exe/*'], 'bin'), (['src/libdrawgram.%s' % SHLIB_EXT, 'src/libdrawtree.%s' % SHLIB_EXT], 'lib')] + +sanity_check_paths = { + 'files': ['bin/dnapars', 'bin/fitch', 'bin/gendist', 'bin/penny', 'bin/seqboot', + 'lib/libdrawgram.%s' % SHLIB_EXT, 'lib/libdrawtree.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +moduleclass = 'bio' From 086f7d0fb940dd76c73c9c9e3c8f7bcc6d6fa483 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Jan 2024 17:38:14 +0100 Subject: [PATCH 0514/1193] fix source URL for PHYLIP 3.697 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb index cb261efb52ce..90a44d6fc01a 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCC', 'version': '12.3.0'} # -fcommon is required to avoid 'multiple definitions' linking error toolchainopts = {'extra_cflags': "-fcommon"} -source_urls = ['https://evolution.gs.washington.edu/phylip/download/'] +source_urls = ['https://phylipweb.github.io/phylip/download/'] sources = [SOURCELOWER_TAR_GZ] checksums = ['9a26d8b08b8afea7f708509ef41df484003101eaf4beceb5cf7851eb940510c1'] From 412d32dfbd09a9ab05a4f29481a41046cf22ff5e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Jan 2024 17:40:39 +0100 Subject: [PATCH 0515/1193] fix homepage for PHYLIP 3.697 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb index 90a44d6fc01a..435d189659dc 100644 --- a/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/p/PHYLIP/PHYLIP-3.697-GCC-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'MakeCp' name = 'PHYLIP' version = '3.697' -homepage = 'https://evolution.genetics.washington.edu/phylip' +homepage = 'https://phylipweb.github.io/phylip' description = "PHYLIP is a free package of programs for inferring phylogenies." toolchain = {'name': 'GCC', 'version': '12.3.0'} From 1a76e4146e0eba0d3431e8e6b6215fda8a8fc771 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Jan 2024 17:40:52 +0000 Subject: [PATCH 0516/1193] adding easyconfigs: yt-4.3.0-foss-2022a.eb --- .../easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb new file mode 100644 index 000000000000..dc5a4057e2a2 --- /dev/null +++ b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb @@ -0,0 +1,54 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'yt' +version = '4.3.0' + +homepage = 'https://yt-project.org' +description = """yt is an open-source, permissively-licensed python package for +analyzing and visualizing volumetric data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('astropy', '5.1.1'), + ('h5py', '3.7.0'), + ('SciPy-bundle', '2022.05'), + ('IPython','8.5.0'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cmyt', '2.0.0', { + 'checksums': ['4beef670f488818efc6ac30491bae81b63a71590936e8cdd3dc3fc9027ab4bfd'], + }), + ('ewah-bool-utils', '1.1.0', { + 'source_tmpl': 'ewah_bool_utils-%(version)s.tar.gz', + 'checksums': ['7050b5a25f4df14f05f8898fd9e797cd0a0f7103207c618e0467a450d3dee987'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('unyt', '2.9.5', { + 'checksums': ['99892f33b5c6bf97053beac84c8a136747631828f030725e9a01147d48377337'], + }), + ('typing-extensions', '4.9.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + }), + (name, version, { + 'checksums': ['cdcab7c07d8c46fe87d94fcec4bbac750394aa40b88cb7381abc843dcdce30ee'], + }), +] + +sanity_check_commands = [ + "python -c 'import yt'", +] + +moduleclass = 'vis' From c8c3be8f362a18fdb460a8f96e04a9282e0c027e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 30 Jan 2024 21:07:57 +0100 Subject: [PATCH 0517/1193] adding easyconfigs: rethinking-2.40-20230914-foss-2023a-R-4.3.2.eb --- ...inking-2.40-20230914-foss-2023a-R-4.3.2.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/r/rethinking/rethinking-2.40-20230914-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/r/rethinking/rethinking-2.40-20230914-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/rethinking/rethinking-2.40-20230914-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..2f61ca5e87bc --- /dev/null +++ b/easybuild/easyconfigs/r/rethinking/rethinking-2.40-20230914-foss-2023a-R-4.3.2.eb @@ -0,0 +1,32 @@ +easyblock = 'RPackage' + +name = 'rethinking' +# see DESCRIPTION file for version + add datestamp of commit +local_commit = 'f3ac8de' +version = '2.40-20230914' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/rmcelreath/rethinking' +description = """R package that contains tools for conducting both quick quadratic approximation of the posterior + distribution as well as Hamiltonian Monte Carlo.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/rmcelreath/rethinking/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['831b6bebc861615aee94415c42ec37000e74b00242b30830af17bb5a126fd786'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('CmdStanR', '0.7.1', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +options = {'modulename': '%(namelower)s'} + +moduleclass = 'math' From 8c103801a1c76d8b488023594e4fa002493c49d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 30 Jan 2024 22:45:12 +0100 Subject: [PATCH 0518/1193] add blank line and remove double blank line --- easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb index ca99945c383b..476de3749c79 100644 --- a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-12.2.0.eb @@ -18,13 +18,13 @@ builddependencies = [ ('CMake', '3.24.3'), ('zlib', '1.2.12'), ] + dependencies = [ ('Python', '3.10.8'), ('bzip2', '1.0.8'), ('gzip', '1.12'), ] - sanity_check_paths = { 'files': [ 'bin/%(namelower)s', From 14bec48a5aeb17ad7a7005380ccd96687740af02 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Jan 2024 21:52:27 +0000 Subject: [PATCH 0519/1193] adding easyconfigs: Cython-3.0.8-GCCcore-11.3.0.eb --- .../c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..77f401f157e9 --- /dev/null +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'Cython' +version = '3.0.8' + +homepage = 'https://cython.org/' +description = """ +Cython is an optimising static compiler for both the Python programming +language and the extended Cython programming language (based on Pyrex). +""" +docurls = [ + 'https://cython.org/#documentation', + 'https://github.com/cython/cython', +] + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sources = [SOURCE_TAR_GZ] +checksums = ['8333423d8fd5765e7cceea3a9985dd1e0a5dfeb2734629e1a2ed2d6233d39de6'] + +sanity_check_paths = { + 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'cython --version', +] + +moduleclass = 'lang' From 512fe66dc5599ad427957dc0c4ff9ae72f5b6be8 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Jan 2024 21:57:12 +0000 Subject: [PATCH 0520/1193] Problem fixed by adding Cython --- .../easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb | 39 ++++++++++++++++--- 1 file changed, 33 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb index dc5a4057e2a2..699cfdf39dc4 100644 --- a/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb @@ -11,14 +11,21 @@ analyzing and visualizing volumetric data.""" toolchain = {'name': 'foss', 'version': '2022a'} +builddependencies = [ + ('Cython', '3.0.8'), +] + dependencies = [ + ('Python', '3.10.4'), ('astropy', '5.1.1'), ('h5py', '3.7.0'), ('SciPy-bundle', '2022.05'), - ('IPython','8.5.0'), + ('IPython', '8.5.0'), ('matplotlib', '3.5.2'), ('Pillow', '9.1.1'), ('tqdm', '4.64.0'), + ('sympy', '1.11.1'), + ('poetry', '1.2.2'), ] use_pip = True @@ -32,15 +39,35 @@ exts_list = [ 'source_tmpl': 'ewah_bool_utils-%(version)s.tar.gz', 'checksums': ['7050b5a25f4df14f05f8898fd9e797cd0a0f7103207c618e0467a450d3dee987'], }), - ('packaging', '23.2', { - 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], - }), ('unyt', '2.9.5', { 'checksums': ['99892f33b5c6bf97053beac84c8a136747631828f030725e9a01147d48377337'], }), - ('typing-extensions', '4.9.0', { + ('typing-extensions', '4.6.3', { 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', - 'checksums': ['23478f88c37f27d76ac8aee6c905017a143b0b1b886c3c9f66bc2fd94f9f5783'], + 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], + }), + ('traitlets', '5.14.1', { + 'checksums': ['8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e'], + }), + ('comm', '0.2.1', { + 'checksums': ['0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a'], + }), + ('deprecation', '2.1.0', { + 'checksums': ['72b3bde64e5d778694b0cf68178aed03d15e15477116add3fb773e581f9518ff'], + }), + ('jupyter-packaging', '0.12.3', { + 'source_tmpl': 'jupyter_packaging-%(version)s.tar.gz', + 'checksums': ['9d9b2b63b97ffd67a8bc5391c32a421bc415b264a32c99e4d8d8dd31daae9cf4'], + }), + ('jupyterlab-widgets', '3.0.9', { + 'source_tmpl': 'jupyterlab_widgets-%(version)s.tar.gz', + 'checksums': ['6005a4e974c7beee84060fdfba341a3218495046de8ae3ec64888e5fe19fdb4c'], + }), + ('widgetsnbextension', '4.0.9', { + 'checksums': ['3c1f5e46dc1166dfd40a42d685e6a51396fd34ff878742a3e47c6f0cc4a2a385'], + }), + ('ipywidgets', '8.1.1', { + 'checksums': ['40211efb556adec6fa450ccc2a77d59ca44a060f4f9f136833df59c9f538e6e8'], }), (name, version, { 'checksums': ['cdcab7c07d8c46fe87d94fcec4bbac750394aa40b88cb7381abc843dcdce30ee'], From 57bfaf7c358525055fcbb297a21331c01f7b534e Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Jan 2024 23:37:29 +0000 Subject: [PATCH 0521/1193] Binutils version corrected --- easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb index c2404f648b97..8a13072d93ba 100644 --- a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.2.0.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['d4aa5e0794598794f20ab950e973d44f0d0d9c133ea1a5a07cb200fa54d2e036'] builddependencies = [ - ('binutils', '2.38'), + ('binutils', '2.37'), ('CMake', '3.22.1'), ] From 30a71e74e427637c5b2c808c49d3da77717c703e Mon Sep 17 00:00:00 2001 From: maximm Date: Wed, 31 Jan 2024 10:31:11 +0100 Subject: [PATCH 0522/1193] adding easyconfigs: MCR-R2023a.eb --- easybuild/easyconfigs/m/MCR/MCR-R2023a.eb | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCR/MCR-R2023a.eb diff --git a/easybuild/easyconfigs/m/MCR/MCR-R2023a.eb b/easybuild/easyconfigs/m/MCR/MCR-R2023a.eb new file mode 100644 index 000000000000..85e10cd81157 --- /dev/null +++ b/easybuild/easyconfigs/m/MCR/MCR-R2023a.eb @@ -0,0 +1,17 @@ +name = 'MCR' +version = 'R2023a' # runtime version 9.14 +local_update = '0' + +homepage = 'https://www.mathworks.com/products/compiler/mcr/' +description = """The MATLAB Runtime is a standalone set of shared libraries + that enables the execution of compiled MATLAB applications + or components on computers that do not have MATLAB installed.""" + +toolchain = SYSTEM + +source_urls = ['https://ssd.mathworks.com/supportfiles/downloads/%%(version)s/Release/%s/deployment_files/' + 'installer/complete/glnxa64/' % local_update] +sources = ['MATLAB_Runtime_%(version)s_glnxa64.zip'] +checksums = ['dbeae03ae5b8a00e1cf4c863b69e376fccb3ba16e40d705a18f891dd38e51d28'] + +moduleclass = 'math' From 286d341ea645c19e299d27b3fdc8217d228fa647 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 31 Jan 2024 11:37:41 +0100 Subject: [PATCH 0523/1193] adding easyconfigs: DeltaLake-0.15.1-gfbf-2023a.eb and patches: DeltaLake-0.15.1_remove-obsolete-pyarrow-hotfix.patch --- .../DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb | 872 ++++++++++++++++++ ....15.1_remove-obsolete-pyarrow-hotfix.patch | 43 + 2 files changed, 915 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1_remove-obsolete-pyarrow-hotfix.patch diff --git a/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb new file mode 100644 index 000000000000..7894b46cf3e7 --- /dev/null +++ b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb @@ -0,0 +1,872 @@ +easyblock = 'CargoPythonPackage' + +name = 'DeltaLake' +version = '0.15.1' + +homepage = 'https://delta-io.github.io/delta-rs/' +description = """Native Delta Lake Python binding based on delta-rs with Pandas integration. +The Delta Lake project aims to unlock the power of the Deltalake for as many +users and projects as possible by providing native low-level APIs aimed at +developers and integrators, as well as a high-level operations API that lets +you query, inspect, and operate your Delta Lake with ease.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +patches = ['DeltaLake-0.15.1_remove-obsolete-pyarrow-hotfix.patch'] +checksums = [ + {'deltalake-0.15.1.tar.gz': '77ca8e239297c7db99ae0dd4c13097550f4dca64d6b6f9bd493d9084fdf25fb3'}, + {'addr2line-0.21.0.tar.gz': '8a30b2e23b9e17a9f90641c7ab1549cd9b44f296d3ccbf309d2863cfe398a0cb'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'ahash-0.8.7.tar.gz': '77c3a9648d43b9cd48db467b3f87fdd6e146bcc88ab0180006cef2179fe11d01'}, + {'aho-corasick-1.1.2.tar.gz': 'b2969dcb958b36655471fc61f7e416fa76033bdd4bfed0678d8fee1e2d07a1f0'}, + {'alloc-no-stdlib-2.0.4.tar.gz': 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('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.1'), + ('fs_extra', '1.3.0'), + ('futures', '0.3.30'), + ('futures-channel', '0.3.30'), + ('futures-core', '0.3.30'), + ('futures-executor', '0.3.30'), + ('futures-io', '0.3.30'), + ('futures-macro', '0.3.30'), + ('futures-sink', '0.3.30'), + ('futures-task', '0.3.30'), + ('futures-util', '0.3.30'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.11'), + ('gimli', '0.28.1'), + ('glob', '0.3.1'), + ('h2', '0.3.22'), + ('half', '1.8.2'), + ('half', '2.3.1'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('hermit-abi', '0.3.3'), + ('hex', '0.4.3'), + ('hmac', '0.11.0'), + ('hmac', '0.12.1'), + ('http', '0.2.11'), + ('http-body', '0.4.6'), + ('httparse', '1.8.0'), + ('httpdate', '1.0.3'), + ('humantime', '2.1.0'), + ('hyper', '0.14.28'), + ('hyper-rustls', '0.22.1'), + ('hyper-rustls', '0.24.2'), + ('hyper-tls', '0.5.0'), + ('iana-time-zone', '0.1.59'), + ('iana-time-zone-haiku', '0.1.2'), + ('idna', '0.5.0'), + ('indexmap', '2.1.0'), + ('indoc', '2.0.4'), + ('instant', '0.1.12'), + ('integer-encoding', '3.0.4'), + ('ipnet', '2.9.0'), + ('is-terminal', '0.4.10'), + ('itertools', '0.10.5'), + ('itertools', '0.11.0'), + ('itertools', '0.12.0'), + ('itoa', '1.0.10'), + ('jobserver', '0.1.27'), + ('js-sys', '0.3.66'), + ('lazy_static', '1.4.0'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.152'), + ('libm', '0.2.8'), + ('libredox', '0.0.1'), + ('linux-raw-sys', '0.4.12'), + ('lock_api', '0.4.11'), + ('log', '0.4.20'), + ('lz4_flex', '0.11.1'), + ('lzma-sys', '0.1.20'), + ('maplit', '1.0.2'), + ('md-5', '0.9.1'), + ('md-5', '0.10.6'), + ('memchr', '2.7.1'), + ('memoffset', '0.9.0'), + ('mime', '0.3.17'), + ('miniz_oxide', '0.7.1'), + ('mio', '0.8.10'), + ('native-tls', '0.2.11'), + ('num', '0.4.1'), + ('num-bigint', '0.4.4'), + ('num-complex', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-iter', '0.1.43'), + ('num-rational', '0.4.1'), + ('num-traits', '0.2.17'), + ('num_cpus', '1.16.0'), + ('object', '0.32.2'), + ('object_store', '0.8.0'), + ('once_cell', '1.19.0'), + ('oorandom', '11.1.3'), + ('opaque-debug', '0.3.0'), + ('openssl', '0.10.62'), + ('openssl-macros', '0.1.1'), + ('openssl-probe', '0.1.5'), + ('openssl-src', '300.2.1+3.2.0'), + ('openssl-sys', '0.9.98'), + ('ordered-float', '2.10.1'), + ('outref', '0.5.1'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.9'), + ('parquet', '49.0.0'), + ('parse-zoneinfo', '0.3.0'), + ('paste', '1.0.14'), + ('percent-encoding', '2.3.1'), + ('petgraph', '0.6.4'), + ('phf', '0.11.2'), + ('phf_codegen', '0.11.2'), + ('phf_generator', '0.11.2'), + ('phf_shared', '0.11.2'), + ('pin-project-lite', '0.2.13'), + ('pin-utils', '0.1.0'), + ('pkg-config', '0.3.28'), + ('plotters', '0.3.5'), + ('plotters-backend', '0.3.5'), + ('plotters-svg', '0.3.5'), + ('powerfmt', '0.2.0'), + ('ppv-lite86', '0.2.17'), + ('pretty_assertions', '1.4.0'), + ('pretty_env_logger', '0.5.0'), + ('proc-macro2', '1.0.76'), + ('prost', '0.12.3'), + ('prost-derive', '0.12.3'), + ('pyo3', '0.20.2'), + ('pyo3-build-config', '0.20.2'), + ('pyo3-ffi', '0.20.2'), + ('pyo3-macros', '0.20.2'), + ('pyo3-macros-backend', '0.20.2'), + ('quick-xml', '0.31.0'), + ('quote', '1.0.35'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rayon', '1.8.0'), + ('rayon-core', '1.12.0'), + ('redox_syscall', '0.4.1'), + ('redox_users', '0.4.4'), + ('regex', '1.10.2'), + ('regex-automata', '0.4.3'), + ('regex-lite', '0.1.5'), + ('regex-syntax', '0.8.2'), + ('reqwest', '0.11.23'), + ('retain_mut', '0.1.7'), + ('ring', '0.16.20'), + ('ring', '0.17.7'), + ('roaring', '0.10.2'), + ('rusoto_core', '0.47.0'), + ('rusoto_credential', '0.47.0'), + ('rusoto_dynamodb', '0.47.0'), + ('rusoto_signature', '0.47.0'), + ('rusoto_sts', '0.47.0'), + ('rustc-demangle', '0.1.23'), + ('rustc_version', '0.4.0'), + ('rustix', '0.38.28'), + ('rustls', '0.19.1'), + ('rustls', '0.21.10'), + ('rustls-native-certs', '0.5.0'), + ('rustls-native-certs', '0.6.3'), + ('rustls-pemfile', '1.0.4'), + ('rustls-webpki', '0.101.7'), + ('rustversion', '1.0.14'), + ('ryu', '1.0.16'), + ('same-file', '1.0.6'), + ('schannel', '0.1.23'), + ('scopeguard', '1.2.0'), + ('sct', '0.6.1'), + ('sct', '0.7.1'), + ('security-framework', '2.9.2'), + ('security-framework-sys', '2.9.1'), + ('semver', '1.0.21'), + ('seq-macro', '0.3.5'), + ('serde', '1.0.195'), + ('serde_derive', '1.0.195'), + ('serde_json', '1.0.111'), + ('serde_urlencoded', '0.7.1'), + ('serial_test', '2.0.0'), + ('serial_test_derive', '2.0.0'), + ('sha2', '0.9.9'), + ('sha2', '0.10.8'), + ('shlex', '1.2.0'), + ('signal-hook-registry', '1.4.1'), + ('siphasher', '0.3.11'), + ('slab', '0.4.9'), + ('smallvec', '1.11.2'), + ('snafu', '0.7.5'), + ('snafu-derive', '0.7.5'), + ('snap', '1.1.1'), + ('socket2', '0.5.5'), + ('spin', '0.5.2'), + ('spin', '0.9.8'), + ('sqlparser', '0.40.0'), + ('sqlparser_derive', '0.2.2'), + ('static_assertions', '1.1.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('subtle', '2.4.1'), + ('syn', '1.0.109'), + ('syn', '2.0.48'), + ('system-configuration', '0.5.1'), + ('system-configuration-sys', '0.5.0'), + ('target-lexicon', '0.12.13'), + ('tempfile', '3.9.0'), + ('termcolor', '1.4.0'), + ('thiserror', '1.0.56'), + ('thiserror-impl', '1.0.56'), + ('thrift', '0.17.0'), + ('time', '0.3.31'), + ('time-core', '0.1.2'), + ('time-macros', '0.2.16'), + ('tiny-keccak', '2.0.2'), + ('tinytemplate', '1.2.1'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('tokio', '1.35.1'), + ('tokio-macros', '2.2.0'), + ('tokio-native-tls', '0.3.1'), + ('tokio-rustls', '0.22.0'), + ('tokio-rustls', '0.24.1'), + ('tokio-util', '0.7.10'), + ('tower-service', '0.3.2'), + ('tracing', '0.1.40'), + ('tracing-attributes', '0.1.27'), + ('tracing-core', '0.1.32'), + ('try-lock', '0.2.5'), + ('twox-hash', '1.6.3'), + ('typenum', '1.17.0'), + ('unicode-bidi', '0.3.14'), + ('unicode-ident', '1.0.12'), + ('unicode-normalization', '0.1.22'), + ('unicode-segmentation', '1.10.1'), + ('unicode-width', '0.1.11'), + ('unindent', '0.2.3'), + ('untrusted', '0.7.1'), + ('untrusted', '0.9.0'), + ('url', '2.5.0'), + ('urlencoding', '2.1.3'), + ('utime', '0.3.1'), + ('uuid', '1.6.1'), + ('vcpkg', '0.2.15'), + ('version_check', '0.9.4'), + ('vsimd', '0.8.0'), + ('walkdir', '2.4.0'), + ('want', '0.3.1'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.89'), + ('wasm-bindgen-backend', '0.2.89'), + ('wasm-bindgen-futures', '0.4.39'), + ('wasm-bindgen-macro', '0.2.89'), + ('wasm-bindgen-macro-support', '0.2.89'), + ('wasm-bindgen-shared', '0.2.89'), + ('wasm-streams', '0.3.0'), + ('web-sys', '0.3.66'), + ('webpki', '0.21.4'), + ('webpki-roots', '0.25.3'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.6'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('windows-core', '0.52.0'), + ('windows-sys', '0.48.0'), + ('windows-sys', '0.52.0'), + ('windows-targets', '0.48.5'), + ('windows-targets', '0.52.0'), + ('windows_aarch64_gnullvm', '0.48.5'), + ('windows_aarch64_gnullvm', '0.52.0'), + ('windows_aarch64_msvc', '0.48.5'), + ('windows_aarch64_msvc', '0.52.0'), + ('windows_i686_gnu', '0.48.5'), + ('windows_i686_gnu', '0.52.0'), + ('windows_i686_msvc', '0.48.5'), + ('windows_i686_msvc', '0.52.0'), + ('windows_x86_64_gnu', '0.48.5'), + ('windows_x86_64_gnu', '0.52.0'), + ('windows_x86_64_gnullvm', '0.48.5'), + ('windows_x86_64_gnullvm', '0.52.0'), + ('windows_x86_64_msvc', '0.48.5'), + ('windows_x86_64_msvc', '0.52.0'), + ('winreg', '0.50.0'), + ('xml-rs', '0.8.19'), + ('xmlparser', '0.13.6'), + ('xz2', '0.1.7'), + ('yansi', '0.5.1'), + ('z85', '3.0.5'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), + ('zeroize', '1.7.0'), + ('zstd', '0.13.0'), + ('zstd-safe', '7.0.0'), + ('zstd-sys', '2.0.9+zstd.1.5.5'), +] + +builddependencies = [ + ('maturin', '1.4.0', '-Rust-1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Arrow', '14.0.1'), +] + +use_pip = True +use_pip_extras = "pandas" +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1_remove-obsolete-pyarrow-hotfix.patch b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1_remove-obsolete-pyarrow-hotfix.patch new file mode 100644 index 000000000000..89e3f66ddead --- /dev/null +++ b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1_remove-obsolete-pyarrow-hotfix.patch @@ -0,0 +1,43 @@ +Security vulnerability CVE-2023-47248 is already fixed upstream since Arrow 14.0.1 +see https://github.com/pitrou/pyarrow-hotfix?tab=readme-ov-file#description +author: Alex Domingo (Vrije Universiteit Brussel) +--- PKG-INFO.orig 2024-01-31 10:24:17.114114000 +0100 ++++ PKG-INFO 2024-01-31 10:22:43.428088000 +0100 +@@ -8,7 +8,6 @@ + Classifier: Programming Language :: Python :: 3.11 + Classifier: Programming Language :: Python :: 3.12 + Requires-Dist: pyarrow >=8 +-Requires-Dist: pyarrow-hotfix + Requires-Dist: pandas ; extra == 'pandas' + Requires-Dist: mypy ; extra == 'devel' + Requires-Dist: ruff >=0.1.5 ; extra == 'devel' +--- pyproject.toml.orig 2024-01-31 10:24:37.004732357 +0100 ++++ pyproject.toml 2024-01-31 01:13:56.729671621 +0100 +@@ -19,7 +19,6 @@ + ] + dependencies = [ + "pyarrow>=8", +- "pyarrow-hotfix", + ] + + [project.optional-dependencies] +--- deltalake/table.py.orig 2024-01-31 10:25:17.340707000 +0100 ++++ deltalake/table.py 2024-01-31 10:22:13.865436632 +0100 +@@ -25,7 +25,6 @@ + import pyarrow + import pyarrow.dataset as ds + import pyarrow.fs as pa_fs +-import pyarrow_hotfix # noqa: F401; addresses CVE-2023-47248; # type: ignore + from pyarrow.dataset import ( + Expression, + FileSystemDataset, +--- python/deltalake/table.py.orig 2024-01-31 10:25:28.723000000 +0100 ++++ python/deltalake/table.py 2024-01-31 10:22:00.855595977 +0100 +@@ -25,7 +25,6 @@ + import pyarrow + import pyarrow.dataset as ds + import pyarrow.fs as pa_fs +-import pyarrow_hotfix # noqa: F401; addresses CVE-2023-47248; # type: ignore + from pyarrow.dataset import ( + Expression, + FileSystemDataset, From 2ac7cf4da1287a4c6dc4c376d78f1d39efe73c3c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 31 Jan 2024 11:39:54 +0100 Subject: [PATCH 0524/1193] use extension to install pyarrow in Arrow-14.0.1-gfbf-2023a.eb --- .../a/Arrow/Arrow-14.0.1-gfbf-2023a.eb | 36 ++++++++++++------- 1 file changed, 24 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb index 40327535b8b5..85715fef4954 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-14.0.1-gfbf-2023a.eb @@ -44,18 +44,30 @@ configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " configopts += "-DZSTD_ROOT=$EBROOTZSTD " -# also install Python bindings -local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " -local_install_pyarrow_cmds += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " -local_install_pyarrow_cmds += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && " -local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " -local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT -local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " -local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." -postinstallcmds = [local_install_pyarrow_cmds] +# install Python bindings +_pyarrow_preinstall_opts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +_pyarrow_preinstall_opts += "export Arrow_DIR=%(installdir)s && export ArrowDataset_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export ArrowAcero_DIR=%(installdir)s && export Parquet_DIR=%(installdir)s && " +_pyarrow_preinstall_opts += "export XDG_CACHE_HOME=$TMPDIR && " +_pyarrow_preinstall_opts += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +_pyarrow_preinstall_opts += "Python3_ROOT_DIR=$EBROOTPYTHON " +_pyarrow_preinstall_opts += "PYARROW_CMAKE_OPTIONS='-DZSTD_LIB=$EBROOTZSTD/lib/libzstd.%s ' " % SHLIB_EXT +_pyarrow_preinstall_opts += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('pyarrow', version, { + 'sources': ['apache-arrow-%(version)s.tar.gz'], + 'checksums': ['5c70eafb1011f9d124bafb328afe54f62cc5b9280b7080e1e3d668f78c0e407e'], + 'start_dir': '%(builddir)s/apache-arrow-%(version)s/python', + 'preinstallopts': _pyarrow_preinstall_opts, + }), +] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 01b9ef4b871065b1e959fe1c199bdf42d07504ec Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 31 Jan 2024 11:54:39 +0000 Subject: [PATCH 0525/1193] undo change to description --- .../t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb index 5a21ff78eb02..9845a9c7d2ed 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb @@ -4,8 +4,8 @@ name = 'tensorboard' version = '2.15.1' homepage = 'https://github.com/tensorflow/tensorboard' -description = """TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs -and graphs.""" +description = """TensorBoard is a suite of web applications for inspecting and +understanding your TensorFlow runs and graphs.""" toolchain = {'name': 'gfbf', 'version': '2023a'} From 9e09c9023ca34570691b9a2bc61b86f67cef140f Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 31 Jan 2024 11:55:43 +0000 Subject: [PATCH 0526/1193] reinsert blank line --- .../easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb index 9845a9c7d2ed..9c74e1a8f87d 100644 --- a/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/t/tensorboard/tensorboard-2.15.1-gfbf-2023a.eb @@ -79,6 +79,7 @@ postinstallcmds = [ 'sed -i "s/Requires-Dist: protobuf.*/Requires-Dist: protobuf >=3.19.6/g" ' + '%(installdir)s/lib/python%(pyshortver)s/site-packages/%(name)s-%(version)s.dist-info/METADATA', ] + use_pip = True sanity_pip_check = True From 3c8e037db5345fd3232599848126bd5f69fd735d Mon Sep 17 00:00:00 2001 From: Ehsan Moravveji Date: Wed, 31 Jan 2024 14:12:56 +0100 Subject: [PATCH 0527/1193] Including versionsuffix --- .../{GenomeComb-0.106.0.eb => GenomeComb-0.106.0-x86_64.eb} | 1 + 1 file changed, 1 insertion(+) rename easybuild/easyconfigs/g/GenomeComb/{GenomeComb-0.106.0.eb => GenomeComb-0.106.0-x86_64.eb} (96%) diff --git a/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb b/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0-x86_64.eb similarity index 96% rename from easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb rename to easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0-x86_64.eb index d995f6b94e56..ac7291f9249b 100644 --- a/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0.eb +++ b/easybuild/easyconfigs/g/GenomeComb/GenomeComb-0.106.0-x86_64.eb @@ -2,6 +2,7 @@ easyblock = 'PackedBinary' name = 'GenomeComb' version = '0.106.0' +versionsuffix = '-x86_64' description = """ Genomecomb is a package designed to analyze, combine, annotate and query genome From 62ebe9f1e294ad1715c76a7056e93790be249984 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 14:18:11 +0100 Subject: [PATCH 0528/1193] add missing spaces in configopts in Cbc, Cgl, Clp + use $LIBSCALAPACK in Clp easyconfig --- easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb | 4 ++-- easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb | 2 +- easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb | 6 +++--- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb index a1daf137fead..1f52c6bdfc2f 100644 --- a/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Cbc/Cbc-2.10.11-foss-2023a.eb @@ -32,7 +32,7 @@ dependencies = [ ('zlib', '1.2.13'), ] -# Use BLAS/LAPACK from OpenBLAS +# Use BLAS/LAPACK from toolchain configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' # Use METIS AND MUMPS from EB configopts += '--with-metis-lib="-lmetis" ' @@ -41,7 +41,7 @@ configopts += '--with-mumps-lib="-lcmumps -ldmumps -lsmumps -lzmumps -lmumps_com configopts += '--without-glpk ' # Use CoinUtils from EB configopts += '--with-coinutils-lib="-lCoinUtils" ' -configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' # Use Clp from EB configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' diff --git a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb index 9e5a23290e4a..e77e6950d69e 100644 --- a/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Cgl/Cgl-0.60.8-foss-2023a.eb @@ -31,7 +31,7 @@ dependencies = [ # Use CoinUtils from EB configopts = '--with-coinutils-lib="-lCoinUtils" ' -configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' # Use Clp from EB configopts += '--with-clp-lib="-lOsiClp -lClpSolver -lClp" ' configopts += '--with-clp-datadir=$EBROOTCLP/share/coin/Data ' diff --git a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb index 8b4fedf45da3..b87d2708941b 100644 --- a/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Clp/Clp-1.17.9-foss-2023a.eb @@ -30,21 +30,21 @@ dependencies = [ ('zlib', '1.2.13'), ] -# Use BLAS/LAPACK from OpenBLAS +# Use BLAS/LAPACK from toolchain configopts = '--with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK" ' # Use METIS AND MUMPS from EB # --with-metis-lib is ignored configopts += '--with-metis-lib="-lmetis" ' configopts += '--with-mumps-lib="-lesmumps -lcmumps -ldmumps -lsmumps -lzmumps -lmumps_common -lpord -lmpi_mpifh ' -configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr -lscalapack" ' +configopts += '-lmetis -lscotch -lptscotch -lptscotcherr -lscotcherrexit -lscotcherr $LIBSCALAPACK" ' # Disable GLPK because Clp requires headers from its sources configopts += '--without-glpk ' # Use CoinUtils from EB configopts += '--with-coinutils-lib="-lCoinUtils" ' -configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data' +configopts += '--with-coinutils-datadir=$EBROOTCOINUTILS/share/coin/Data ' # Use Osi from EB configopts += '--with-osi-lib="-lOsi" ' From 908a70a4adee1afc38aba01a0d45a04fbe319f83 Mon Sep 17 00:00:00 2001 From: benjamic Date: Wed, 31 Jan 2024 14:21:46 +0100 Subject: [PATCH 0529/1193] adding easyconfigs: pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb --- .../pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb new file mode 100644 index 000000000000..a2cff6e2c34b --- /dev/null +++ b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'pmt' +version = '1.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('binutils', '2.38') +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM) +] + + +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['98faf305c60cc4d39d3b8ada1dcb7c87c49bf6f01a3cd2800b413d21d5df1a38'] + +configopts = '-DBUILD_NVML_PMT=1' + +sanity_check_paths = { + 'files': ["bin/Rapl-test"], + 'files': ["bin/NVML-test"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'lib' From 1f73421fc31e95c6426f0dad3c162dfa9862f923 Mon Sep 17 00:00:00 2001 From: benjamic Date: Wed, 31 Jan 2024 14:25:14 +0100 Subject: [PATCH 0530/1193] adding easyconfigs: pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb --- .../pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb new file mode 100644 index 000000000000..74892696975d --- /dev/null +++ b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'pmt' +version = '1.2.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM) +] + + +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['98faf305c60cc4d39d3b8ada1dcb7c87c49bf6f01a3cd2800b413d21d5df1a38'] + +configopts = '-DBUILD_NVML_PMT=1' + +sanity_check_paths = { + 'files': ["bin/Rapl-test"], + 'files': ["bin/NVML-test"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'lib' From 6d76b3200344a555c9c2fce131e6ad8bd50678c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 15:22:44 +0100 Subject: [PATCH 0531/1193] adding easyconfigs: CellBender-0.3.1-foss-2022a.eb --- .../CellBender/CellBender-0.3.1-foss-2022a.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb new file mode 100644 index 000000000000..1cb1e03789df --- /dev/null +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'CellBender' +local_commit = 'e2fb597' +version = '0.3.1' + +homepage = 'http://github.com/broadinstitute/CellBender' +description = """ +CellBender is a software package for eliminating technical artifacts from +high-throughput single-cell RNA sequencing (scRNA-seq) data. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('PyTorch', '1.12.0'), + ('IPython', '8.5.0'), + ('anndata', '0.8.0'), + ('jupyter-contrib-nbextensions', '0.7.0'), + ('pyro-ppl', '1.8.4'), + ('loompy', '3.0.7'), + ('PyTables', '3.8.0'), + ('Qtconsole', '5.4.0'), +] + +use_pip = True + +local_comm_preinstallopts = """sed -i -e 's/^requires.*hatchling.*/requires = ["setuptools"]/g' """ +local_comm_preinstallopts += """-e 's/^build-backend.*/build-backend = "setuptools.build_meta"/g' """ +local_comm_preinstallopts += """-e 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """ + +exts_list = [ + ('setuptools', '69.0.3', { + 'checksums': ['be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78'], + }), + ('comm', '0.2.1', { + 'checksums': ['0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a'], + 'preinstallopts': local_comm_preinstallopts, + }), + # jupyter-console 6.6.3 requires ipykernel>=6.14 + ('ipykernel', '6.20.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5d0675d5f48bf6a95fd517d7b70bcb3b2c5631b2069949b5c2d6e1d7477fb5a0'], + }), + # jupyter-console 6.6.3 requires jupyter-core!=5.0.*,>=4.12 + ('jupyter_core', '4.12.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a54672c539333258495579f6964144924e0aa7b07f7069947bef76d7ea5cb4c1'], + }), + # jupyter-console 6.6.3 requires traitlets>=5.4 + ('traitlets', '5.14.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('cellbender', version, { + 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], + 'sources': [{'download_filename': 'e2fb597.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['7eb67837d28495adb82147e80a2ab58eeb406c5d91aa69dd0cc120d9cb3d6396'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 25fa2f069cbddea440da16f7cad517b304303e62 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 15:27:51 +0100 Subject: [PATCH 0532/1193] updte to snakemake 8.4.2 --- ...-8.2.1-foss-2023a.eb => snakemake-8.4.2-foss-2023a.eb} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/s/snakemake/{snakemake-8.2.1-foss-2023a.eb => snakemake-8.4.2-foss-2023a.eb} (95%) diff --git a/easybuild/easyconfigs/s/snakemake/snakemake-8.2.1-foss-2023a.eb b/easybuild/easyconfigs/s/snakemake/snakemake-8.4.2-foss-2023a.eb similarity index 95% rename from easybuild/easyconfigs/s/snakemake/snakemake-8.2.1-foss-2023a.eb rename to easybuild/easyconfigs/s/snakemake/snakemake-8.4.2-foss-2023a.eb index c0caaff39e29..2bfe0da0595b 100644 --- a/easybuild/easyconfigs/s/snakemake/snakemake-8.2.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/snakemake/snakemake-8.4.2-foss-2023a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'snakemake' -version = '8.2.1' +version = '8.4.2' homepage = 'https://snakemake.readthedocs.io' description = "The Snakemake workflow management system is a tool to create reproducible and scalable data analyses." @@ -55,10 +55,10 @@ exts_list = [ 'source_tmpl': 'argparse_dataclass-%(version)s.tar.gz', 'checksums': ['09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f'], }), - ('snakemake-interface-common', '1.15.1', { + ('snakemake-interface-common', '1.15.2', { 'modulename': 'snakemake_interface_common', 'source_tmpl': 'snakemake_interface_common-%(version)s.tar.gz', - 'checksums': ['5a779c7a0f27412bce26e1dfe4ccc712d04e0c0b9ceaa1640335a35d02509732'], + 'checksums': ['f2a4908a5ec5d6e657723f90221da3c136e70a1c5897b4e1d65a703bc08e8d7a'], }), ('reretry', '0.11.8', { 'checksums': ['f2791fcebe512ea2f1d153a2874778523a8064860b591cd90afc21a8bed432e3'], @@ -104,7 +104,7 @@ exts_list = [ 'checksums': ['9e8d902230261beba74083aae12c2c5a395e29b408469fefadc8aaf51ee441e5'], }), (name, version, { - 'checksums': ['f177ada98188a10602aa2ed758fc9b7ff13e7107c5e582463ae681c525c28f0c'], + 'checksums': ['ea9273d7a27706b635fafae87bb21100dad02275570e138fdcff125cb3cba4f4'], }), # Also install some of the snakemake executors ('snakemake-executor-plugin-slurm-jobstep', '0.1.10', { From 4f3f43e14d49adf79582b5ff0d4c3c4531874be1 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Wed, 31 Jan 2024 16:09:37 +0000 Subject: [PATCH 0533/1193] Add patch description --- .../jupyter-core-5.3.1_fix_jupyter_path.patch | 8 ++++++++ .../jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb | 2 +- .../jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb | 2 +- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch b/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch index b2c4039e7022..3ad978d96463 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-core-5.3.1_fix_jupyter_path.patch @@ -1,3 +1,11 @@ +# Patch jupyter_core to help jupyter find the correct installation path. +# +# If jupyter is installed by EasyBuild, jupyter is not in the same place as python. +# `EB_ENV_JUPYTER_ROOT` is used to indicate where jupyter are and should be set to +# the instllation path in easyconfigs. +# Avoid using `ENV_JUPYTER_PATH` and `ENV_CONFIG_PATH`. Otherwise user configuration +# has lower priority and cannot save their own settings. +# Author: Chia-Jung Hsu, 2024-01-31 diff --git a/jupyter_core/paths.py b/jupyter_core/paths.py index a7bf051..b38589c 100644 --- a/jupyter_core/paths.py diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb index 1ec1509cb4a9..77484efe933b 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.0-GCCcore-12.2.0.eb @@ -65,7 +65,7 @@ exts_list = [ 'checksums': [ {'jupyter_core-5.3.1.tar.gz': '5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'}, {'jupyter-core-5.3.1_fix_jupyter_path.patch': - '4684b1270559e6d67b3839fd7d2f88e584ae1428b47e035e0aa8ae63ac896458'}, + '030f1beb91987eb7519360c6d0b5c999f8843f00bca6a170f9ea5d3667ee61e5'}, ], }), ('fastjsonschema', '2.17.1', { diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb index d487875e2861..53722e2f4cb9 100644 --- a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-2.7.2-GCCcore-12.3.0.eb @@ -57,7 +57,7 @@ exts_list = [ 'checksums': [ {'jupyter_core-5.3.1.tar.gz': '5ba5c7938a7f97a6b0481463f7ff0dbac7c15ba48cf46fa4035ca6e838aa1aba'}, {'jupyter-core-5.3.1_fix_jupyter_path.patch': - '4684b1270559e6d67b3839fd7d2f88e584ae1428b47e035e0aa8ae63ac896458'}, + '030f1beb91987eb7519360c6d0b5c999f8843f00bca6a170f9ea5d3667ee61e5'}, ], }), ('fastjsonschema', '2.18.0', { From cb7e4115ddb058cab36dc2040b8d3344d878e10e Mon Sep 17 00:00:00 2001 From: x0139045 Date: Wed, 31 Jan 2024 17:27:38 +0100 Subject: [PATCH 0534/1193] adding easyconfigs: Archive-Zip-1.68-GCCcore-12.2.0.eb, Bio-DB-HTS-3.01-GCC-12.2.0.eb, Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb, DBD-mysql-4.050-GCC-12.2.0.eb, VEP-111-GCC-12.2.0.eb --- .../Archive-Zip-1.68-GCCcore-12.2.0.eb | 32 ++++++++++++++++ .../Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb | 32 ++++++++++++++++ .../Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb | 31 +++++++++++++++ .../d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb | 29 ++++++++++++++ .../easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb | 38 +++++++++++++++++++ 5 files changed, 162 insertions(+) create mode 100644 easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..088d0a56de6f --- /dev/null +++ b/easybuild/easyconfigs/a/Archive-Zip/Archive-Zip-1.68-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Archive-Zip' +version = '1.68' + +homepage = 'https://metacpan.org/pod/Archive::Zip' +description = "Provide an interface to ZIP archive files." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PH/PHRED/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['984e185d785baf6129c6e75f8eb44411745ac00bf6122fb1c8e822a3861ec650'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('UnZip', '6.0'), + ('Zip', '3.0'), +] + +options = {'modulename': 'Archive::Zip'} + +sanity_check_paths = { + 'files': ['bin/crc32'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/Archive/Zip'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb new file mode 100644 index 000000000000..a3de8e7098bd --- /dev/null +++ b/easybuild/easyconfigs/b/Bio-DB-HTS/Bio-DB-HTS-3.01-GCC-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PerlModule' + +name = 'Bio-DB-HTS' +version = '3.01' + +homepage = 'https://metacpan.org/release/Bio-DB-HTS' +description = "Read files using HTSlib including BAM/CRAM, Tabix and BCF database files" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/A/AV/AVULLO/'] +sources = ['Bio-DB-HTS-%(version)s.tar.gz'] +checksums = ['12a6bc1f579513cac8b9167cce4e363655cc8eba26b7d9fe1170dfe95e044f42'] + +builddependencies = [('pkgconf', '1.9.3')] + +dependencies = [ + ('Perl', '5.36.0'), + ('BioPerl', '1.7.8'), + ('HTSlib', '1.17'), +] + +preconfigopts = "env HTSLIB_DIR=$EBROOTHTSLIB" + +options = {'modulename': 'Bio::DB::HTS'} + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/perl5/site_perl/%(perlver)s', 'man/man3'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..c3c856455fb3 --- /dev/null +++ b/easybuild/easyconfigs/c/Compress-Raw-Zlib/Compress-Raw-Zlib-2.202-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PerlModule' + +name = 'Compress-Raw-Zlib' +version = '2.202' + +homepage = 'https://metacpan.org/pod/Compress::Raw::Zlib' +description = "Low-Level Interface to zlib or zlib-ng compression library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/P/PM/PMQS/'] +sources = ['%(name)s-%(version)s.tar.gz'] +checksums = ['96e20946eb457a32d2d7a0050b922e37b5ada41246bcdc824196d3f7c4da91b7'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Perl', '5.36.0'), + ('zlib', '1.2.12'), +] + +options = {'modulename': 'Compress::Raw::Zlib'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/Compress/Raw/Zlib.pm'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb new file mode 100644 index 000000000000..1cdd942d323b --- /dev/null +++ b/easybuild/easyconfigs/d/DBD-mysql/DBD-mysql-4.050-GCC-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PerlModule' + +name = 'DBD-mysql' +version = '4.050' + +homepage = 'https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm' +description = "Perl binding for MySQL" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://cpan.metacpan.org/authors/id/D/DV/DVEEDEN'] +sources = [SOURCE_TAR_GZ] +checksums = ['4f48541ff15a0a7405f76adc10f81627c33996fbf56c95c26c094444c0928d78'] + +dependencies = [ + ('Perl', '5.36.0'), + ('MariaDB', '10.11.2'), + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +options = {'modulename': 'DBD::mysql'} + +sanity_check_paths = { + 'files': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql.pm' % ARCH], + 'dirs': ['lib/perl5/site_perl/%%(perlver)s/%s-linux-thread-multi/DBD/mysql' % ARCH], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb new file mode 100644 index 000000000000..12e3b0d4bc8d --- /dev/null +++ b/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb @@ -0,0 +1,38 @@ +name = 'VEP' +version = '111' + +homepage = 'https://www.ensembl.org/info/docs/tools/vep' +description = """Variant Effect Predictor (VEP) determines the effect of your + variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, + transcripts, and protein sequence, as well as regulatory regions. + Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently + used routines in VEP.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/Ensembl/ensembl-vep/archive/release/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4e46a81640e8527e2717d6684fca13e6766fe7970c0410589195d77e19bd2971'] + +dependencies = [ + ('Perl', '5.36.0'), + ('Archive-Zip', '1.68'), + ('DBD-mysql', '4.050'), + ('BioPerl', '1.7.8'), + ('Bio-DB-HTS', '3.01'), + # VEP requires Compress::Raw::Zlib >= 2.103 + ('Compress-Raw-Zlib', '2.202'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perl -e 'require %(ext_name)s'", "") + +exts_list = [ + ('Bio::EnsEMBL::XS', '2.3.2', { + 'source_urls': ['https://github.com/Ensembl/ensembl-xs/archive'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['aafc59568cd1042259196575e99cdfeef9c0fb7966e5f915cfaf38c70885ffa5'], + }), +] + +moduleclass = 'bio' From f5a8f7e85dacb9dc5d242ad9a944f7727a644634 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 17:42:07 +0100 Subject: [PATCH 0535/1193] {bio}[foss/2022a] CellBender v0.3.1, pyro-ppl v1.8.4 w/ CUDA 11.7.0 --- ...CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb | 76 +++++++++++++++++++ .../pyro-ppl-1.8.4-foss-2022a-CUDA-11.7.0.eb | 46 +++++++++++ 2 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..36e5fb160927 --- /dev/null +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'CellBender' +local_commit = 'e2fb597' +version = '0.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://github.com/broadinstitute/CellBender' +description = """ +CellBender is a software package for eliminating technical artifacts from +high-throughput single-cell RNA sequencing (scRNA-seq) data. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('PyTorch', '1.12.0', versionsuffix), + ('IPython', '8.5.0'), + ('anndata', '0.8.0'), + ('jupyter-contrib-nbextensions', '0.7.0'), + ('pyro-ppl', '1.8.4', versionsuffix), + ('loompy', '3.0.7'), + ('PyTables', '3.8.0'), + ('Qtconsole', '5.4.0'), +] + +use_pip = True + +local_comm_preinstallopts = """sed -i -e 's/^requires.*hatchling.*/requires = ["setuptools"]/g' """ +local_comm_preinstallopts += """-e 's/^build-backend.*/build-backend = "setuptools.build_meta"/g' """ +local_comm_preinstallopts += """-e 's/^dynamic = .*version.*/version = "%(version)s"/g' pyproject.toml && """ + +exts_list = [ + ('setuptools', '69.0.3', { + 'checksums': ['be1af57fc409f93647f2e8e4573a142ed38724b8cdd389706a867bb4efcf1e78'], + }), + ('comm', '0.2.1', { + 'checksums': ['0bc91edae1344d39d3661dcbc36937181fdaddb304790458f8b044dbc064b89a'], + 'preinstallopts': local_comm_preinstallopts, + }), + # jupyter-console 6.6.3 requires ipykernel>=6.14 + ('ipykernel', '6.20.2', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['5d0675d5f48bf6a95fd517d7b70bcb3b2c5631b2069949b5c2d6e1d7477fb5a0'], + }), + # jupyter-console 6.6.3 requires jupyter-core!=5.0.*,>=4.12 + ('jupyter_core', '4.12.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['a54672c539333258495579f6964144924e0aa7b07f7069947bef76d7ea5cb4c1'], + }), + # jupyter-console 6.6.3 requires traitlets>=5.4 + ('traitlets', '5.14.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2e5a030e6eff91737c643231bfcf04a65b0132078dad75e4936700b213652e74'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + ('jupyter', '1.0.0', { + 'checksums': ['d9dc4b3318f310e34c82951ea5d6683f67bed7def4b259fafbfe4f1beb1d8e5f'], + }), + ('cellbender', version, { + 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], + 'sources': [{'download_filename': 'e2fb597.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['7eb67837d28495adb82147e80a2ab58eeb406c5d91aa69dd0cc120d9cb3d6396'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..3b186c8a4204 --- /dev/null +++ b/easybuild/easyconfigs/p/pyro-ppl/pyro-ppl-1.8.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,46 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'PythonBundle' + +name = 'pyro-ppl' +version = '1.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/pyro-ppl/pyro' +description = "Pyro is a flexible, scalable deep probabilistic programming library built on PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + (name, version, { + 'modulename': 'pyro', + 'checksums': ['766fad61e52df48885de96d41213da1f8e8c1b79ecf308ad53189fcd15c1cb41'], + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'from pyroapi import distributions as dist'", + "python -c 'from pyroapi import infer, ops, optim, pyro, pyro_backend'", + "python -c 'from pyro import infer, nn, distributions'", +] + +moduleclass = 'tools' From 681df9b700dda60bc54535905e03cf907d98f210 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 19:53:42 +0100 Subject: [PATCH 0536/1193] {bio}[foss/2022a] SemiBin v2.0.2, FragGeneScan v1.31 --- .../FragGeneScan-1.31-GCCcore-11.3.0.eb | 38 +++++++++++++ .../s/SemiBin/SemiBin-2.0.2-foss-2022a.eb | 55 +++++++++++++++++++ 2 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..915a307b6e70 --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'MakeCp' + +name = 'FragGeneScan' +version = '1.31' + +homepage = 'https://omics.informatics.indiana.edu/FragGeneScan/' +description = "FragGeneScan is an application for finding (fragmented) genes in short reads." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Perl', '5.34.1')] + +fix_perl_shebang_for = ['*.pl'] + +prebuildopts = "make clean && " +buildopts = 'CC="$CC" CFLAG="$CFLAGS" fgs && chmod -R go+rx *.pl train example' + +files_to_copy = ['FragGeneScan', 'run_FragGeneScan.pl', 'example', 'train'] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['FragGeneScan', 'run_FragGeneScan.pl'], + 'dirs': ['example', 'train'], +} + +sanity_check_commands = [ + './run_FragGeneScan.pl help', + './run_FragGeneScan.pl -genome=./example/NC_000913.fna -out=./example/NC_000913-fgs -complete=1 -train=complete' +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a.eb new file mode 100644 index 000000000000..140669ba7d89 --- /dev/null +++ b/easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'SemiBin' +version = '2.0.2' + +homepage = 'https://semibin.readthedocs.io' +description = "SemiBin: Metagenomic Binning Using Siamese Neural Networks for short and long reads" + +toolchain = {'name': 'foss', 'version': '2022a'} + +local_pytorch_ver = '1.12.0' + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), + ('scikit-learn', '1.1.2'), + ('python-igraph', '0.10.3'), + ('PyTorch', local_pytorch_ver), + ('torchvision', '0.13.1'), + ('torchaudio', '0.12.0', '-PyTorch-%s' % local_pytorch_ver), + ('BEDTools', '2.30.0'), + ('HMMER', '3.3.2'), + ('MMseqs2', '14-7e284'), + ('prodigal', '2.6.3'), + ('FragGeneScan', '1.31'), + ('SAMtools', '1.16.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/BigDataBiology/SemiBin/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['12541eaadb1f8ed841a713ede7fa4b85624e3ddbc3ee005e41de368e359c70fd'], + 'preinstallopts': "sed -i 's/python-igraph/igraph/g' setup.py && ", + 'modulename': 'SemiBin', + }), +] + +sanity_check_paths = { + 'files': ['bin/SemiBin', 'bin/SemiBin2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "SemiBin --help", + "SemiBin2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 991e016b4c0665d9511df49a390a2d077947180f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 20:17:20 +0100 Subject: [PATCH 0537/1193] adding easyconfigs: SemiBin-2.0.2-foss-2022a-CUDA-11.7.0.eb --- .../SemiBin-2.0.2-foss-2022a-CUDA-11.7.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..8c9f5d9c8951 --- /dev/null +++ b/easybuild/easyconfigs/s/SemiBin/SemiBin-2.0.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'SemiBin' +version = '2.0.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://semibin.readthedocs.io' +description = "SemiBin: Metagenomic Binning Using Siamese Neural Networks for short and long reads" + +toolchain = {'name': 'foss', 'version': '2022a'} + +local_pytorch_ver = '1.12.0' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), + ('scikit-learn', '1.1.2'), + ('python-igraph', '0.10.3'), + ('PyTorch', local_pytorch_ver, versionsuffix), + ('torchvision', '0.13.1', versionsuffix), + ('torchaudio', '0.12.0', '-PyTorch-%s' % local_pytorch_ver + versionsuffix), + ('BEDTools', '2.30.0'), + ('HMMER', '3.3.2'), + ('MMseqs2', '14-7e284'), + ('prodigal', '2.6.3'), + ('FragGeneScan', '1.31'), + ('SAMtools', '1.16.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/BigDataBiology/SemiBin/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['12541eaadb1f8ed841a713ede7fa4b85624e3ddbc3ee005e41de368e359c70fd'], + 'preinstallopts': "sed -i 's/python-igraph/igraph/g' setup.py && ", + 'modulename': 'SemiBin', + }), +] + +sanity_check_paths = { + 'files': ['bin/SemiBin', 'bin/SemiBin2'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "SemiBin --help", + "SemiBin2 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 789030b2eb708762e7a19e5126a4eed9355bc56e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 20:19:15 +0100 Subject: [PATCH 0538/1193] adding easyconfigs: Concorde-20031219-GCC-12.3.0.eb and patches: Concorde-20031219_fix-h_addr.patch --- .../Concorde/Concorde-20031219-GCC-12.3.0.eb | 40 +++++++++++++++++++ .../Concorde-20031219_fix-h_addr.patch | 13 ++++++ 2 files changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/c/Concorde/Concorde-20031219-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/Concorde/Concorde-20031219_fix-h_addr.patch diff --git a/easybuild/easyconfigs/c/Concorde/Concorde-20031219-GCC-12.3.0.eb b/easybuild/easyconfigs/c/Concorde/Concorde-20031219-GCC-12.3.0.eb new file mode 100644 index 000000000000..05e2c345c513 --- /dev/null +++ b/easybuild/easyconfigs/c/Concorde/Concorde-20031219-GCC-12.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'Concorde' +version = '20031219' + +homepage = 'https://www.math.uwaterloo.ca/tsp/concorde.html' +description = """Concorde is a computer code for the symmetric traveling salesman problem (TSP) + and some related network optimization problems""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://www.math.uwaterloo.ca/tsp/concorde/downloads/codes/src/'] +sources = ['co%s.tgz' % version[2:]] +patches = ['Concorde-20031219_fix-h_addr.patch'] +checksums = [ + {'co031219.tgz': 'c3650a59c8d57e0a00e81c1288b994a99c5aa03e5d96a314834c2d8f9505c724'}, + {'Concorde-20031219_fix-h_addr.patch': '1632e45d68c6d3806d2d56eae6d84b02ab0aa526f557b0ae1210385b0f00b8ae'}, +] + +with_configure = True + +local_binaries = ['CUT/mincut', 'EDGEGEN/edgegen', 'FMATCH/fmatch', 'LINKERN/linkern', 'LOCALCUT/localcut', + 'TOOLS/fconvert', 'TOOLS/edg2len', 'TOOLS/edgunion', 'TOOLS/prob2tsp', 'TOOLS/showres', + 'TOOLS/tourchk', 'TOOLS/tourlen', 'TSP/concorde'] + +files_to_copy = [ + (['concorde.a'], 'lib'), + (['concorde.h'], 'include'), + (local_binaries, 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/concorde', 'bin/edgegen', 'bin/edg2len', 'bin/fconvert', 'bin/fmatch', 'bin/linkern', 'bin/showres', + 'include/concorde.h', 'lib/concorde.a'], + 'dirs': [], +} + +sanity_check_commands = ["concorde 2>&1 | grep '^Usage: concorde'"] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/c/Concorde/Concorde-20031219_fix-h_addr.patch b/easybuild/easyconfigs/c/Concorde/Concorde-20031219_fix-h_addr.patch new file mode 100644 index 000000000000..96430079869c --- /dev/null +++ b/easybuild/easyconfigs/c/Concorde/Concorde-20031219_fix-h_addr.patch @@ -0,0 +1,13 @@ +fix for: error: ‘struct hostent’ has no member named ‘h_addr’ +author: Kenneth Hoste (HPC-UGent) +--- concorde/UTIL/safe_io.c.orig 2024-01-31 19:51:20.865401391 +0100 ++++ concorde/UTIL/safe_io.c 2024-01-31 19:51:40.452228752 +0100 +@@ -1248,7 +1248,7 @@ + fprintf (stderr, "cannot get host info for %s\n", hname); + return (CC_SFILE *) NULL; + } +- memcpy ((void *) &hsock.sin_addr, (void *) h->h_addr, h->h_length); ++ memcpy ((void *) &hsock.sin_addr, (void *) h->h_addr_list[0], h->h_length); + hsock.sin_family = AF_INET; + hsock.sin_port = htons(p); + From 0766eaac6f7944e64cec35e2650a4b3e084f2665 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Jan 2024 21:55:36 +0100 Subject: [PATCH 0539/1193] move sources and checksums up a bit --- .../easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb index 77f401f157e9..43149d5a83b2 100644 --- a/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/Cython/Cython-3.0.8-GCCcore-11.3.0.eb @@ -15,6 +15,9 @@ docurls = [ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +sources = [SOURCE_TAR_GZ] +checksums = ['8333423d8fd5765e7cceea3a9985dd1e0a5dfeb2734629e1a2ed2d6233d39de6'] + builddependencies = [('binutils', '2.38')] dependencies = [('Python', '3.10.4')] @@ -23,8 +26,6 @@ download_dep_fail = True use_pip = True sanity_pip_check = True -sources = [SOURCE_TAR_GZ] -checksums = ['8333423d8fd5765e7cceea3a9985dd1e0a5dfeb2734629e1a2ed2d6233d39de6'] sanity_check_paths = { 'files': ['bin/cygdb', 'bin/cython', 'bin/cythonize'], From 1e6d41de5b4b4ff2e4af76f6a89d8aafc3c1a835 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 22:15:18 +0100 Subject: [PATCH 0540/1193] add custom sanity check for CellBender v0.3.1 --- .../CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb index 36e5fb160927..11c144346953 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb @@ -71,6 +71,15 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': ['bin/cellbender'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cellbender --help", +] + sanity_pip_check = True moduleclass = 'bio' From fd5557f17fa0fd80bce301bb47309142aaddd7bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 31 Jan 2024 22:16:25 +0100 Subject: [PATCH 0541/1193] add custom sanity check for CellBender v0.3.1 --- .../c/CellBender/CellBender-0.3.1-foss-2022a.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb index 1cb1e03789df..f24dd8e7518b 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb @@ -69,6 +69,15 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': ['bin/cellbender'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cellbender --help", +] + sanity_pip_check = True moduleclass = 'bio' From 07c5bb13f9e84f56e5ba6ea796c2fffedea4d907 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 1 Feb 2024 10:50:09 +0100 Subject: [PATCH 0542/1193] adding easyconfigs: numba-0.58.1-foss-2022b.eb, LLVM-14.0.6-GCCcore-12.2.0-llvmlite.eb --- .../LLVM-14.0.6-GCCcore-12.2.0-llvmlite.eb | 54 +++++++++++++++++++ .../n/numba/numba-0.58.1-foss-2022b.eb | 53 ++++++++++++++++++ 2 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.2.0-llvmlite.eb create mode 100644 easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2022b.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.2.0-llvmlite.eb b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.2.0-llvmlite.eb new file mode 100644 index 000000000000..fd2c5562a406 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-14.0.6-GCCcore-12.2.0-llvmlite.eb @@ -0,0 +1,54 @@ +name = 'LLVM' +version = '14.0.6' +versionsuffix = '-llvmlite' + +homepage = "https://llvm.org/" +description = """The LLVM Core libraries provide a modern source- and target-independent + optimizer, along with code generation support for many popular CPUs + (as well as some less common ones!) These libraries are built around a well + specified code representation known as the LLVM intermediate representation + ("LLVM IR"). The LLVM Core libraries are well documented, and it is + particularly easy to invent your own language (or port an existing compiler) + to use LLVM as an optimizer and code generator. + + This version include patches for llvmlite / numba.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'cstd': 'gnu++11', 'pic': True} + +source_urls = ['https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/'] +sources = ['llvm-%(version)s.src.tar.xz'] + +# Patches from https://github.com/numba/llvmlite/raw/v0.41.1/conda-recipes/ but +# renamed to follow EasyBuild conventions. +patches = [ + 'LLVM-14.0.6-clear-gotoffsetmap.patch', + 'LLVM-14.0.6-svml.patch', +] +checksums = [ + {'llvm-14.0.6.src.tar.xz': '050922ecaaca5781fdf6631ea92bc715183f202f9d2f15147226f023414f619a'}, + {'LLVM-14.0.6-clear-gotoffsetmap.patch': '690c96dcbd0a81e11d87f02e740c4ef34a0c578be741aaa6559cc00a5349fabf'}, + {'LLVM-14.0.6-svml.patch': '59df18ea4af3479de42ecbc1c524d4106f4a55f23335a64c0f0d5433daaba1b7'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Python', '3.10.8'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/llvm-ar', 'bin/FileCheck'], + 'dirs': ['include/llvm', 'include/llvm-c'], +} + +sanity_check_commands = ["llvm-ar --help"] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2022b.eb b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2022b.eb new file mode 100644 index 000000000000..c9540b4de8c7 --- /dev/null +++ b/easybuild/easyconfigs/n/numba/numba-0.58.1-foss-2022b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'numba' +version = '0.58.1' + +homepage = 'https://numba.pydata.org/' +description = """Numba is an Open Source NumPy-aware optimizing compiler for +Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM +compiler infrastructure to compile Python syntax to machine code.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('LLVM', '14.0.6', '-llvmlite'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('llvmlite', '0.41.1', { + 'patches': ['llvmlite-0.41.1_static-linking-of-LLVM.patch'], + 'preinstallopts': "export LLVM_CONFIG=${EBROOTLLVM}/bin/llvm-config && ", + 'checksums': [ + {'llvmlite-0.41.1.tar.gz': 'f19f767a018e6ec89608e1f6b13348fa2fcde657151137cb64e56d48598a92db'}, + {'llvmlite-0.41.1_static-linking-of-LLVM.patch': + '0cb1fbe13db4ce8b697305229b6b6d79671a3ec5b93e95b4e059033ca626b43e'}, + ], + }), + (name, version, { + 'checksums': ['487ded0633efccd9ca3a46364b40006dbdaca0f95e99b8b83e778d1195ebcbaa'], + }), +] + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/numba'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -m llvmlite.tests", + "numba --help", +] + +moduleclass = 'lang' From 1d4fbe43cebadd3c0cfa7910d5d03462debf79bd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 12:12:09 +0100 Subject: [PATCH 0543/1193] adding easyconfigs: anvio-8-foss-2022b.eb, ETE-3.1.3-foss-2022b.eb, Levenshtein-0.24.0-GCCcore-12.2.0.eb and patches: anvio-8_fix-rU.patch --- .../easyconfigs/a/anvio/anvio-8-foss-2022b.eb | 111 ++++ .../easyconfigs/a/anvio/anvio-8_fix-rU.patch | 484 ++++++++++++++++++ .../easyconfigs/e/ETE/ETE-3.1.3-foss-2022b.eb | 38 ++ .../Levenshtein-0.24.0-GCCcore-12.2.0.eb | 35 ++ 4 files changed, 668 insertions(+) create mode 100644 easybuild/easyconfigs/a/anvio/anvio-8-foss-2022b.eb create mode 100644 easybuild/easyconfigs/a/anvio/anvio-8_fix-rU.patch create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/anvio/anvio-8-foss-2022b.eb b/easybuild/easyconfigs/a/anvio/anvio-8-foss-2022b.eb new file mode 100644 index 000000000000..c13c2a6a213a --- /dev/null +++ b/easybuild/easyconfigs/a/anvio/anvio-8-foss-2022b.eb @@ -0,0 +1,111 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'anvio' +version = '8' + +homepage = 'https://merenlab.org/software/anvio/' +description = """An analysis and visualization platform for 'omics data.""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +github_account = 'merenlab' + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('Pysam', '0.21.0'), + ('matplotlib', '3.7.0'), + ('scikit-learn', '1.2.1'), + ('prodigal', '2.6.3'), + ('Biopython', '1.81'), + ('h5py', '3.8.0'), + ('HMMER', '3.3.2'), + ('networkx', '3.0'), + ('numba', '0.58.1'), + ('statsmodels', '0.14.0'), + ('snakemake', '7.32.3'), + ('ETE', '3.1.3'), + ('dill', '0.3.7'), + ('Seaborn', '0.12.2'), + ('Levenshtein', '0.24.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bottle', '0.12.25', { + 'checksums': ['e1a9c94970ae6d710b3fb4526294dfeb86f2cb4a81eff3a4b98dc40fb0e5e021'], + }), + ('colored', '2.2.4', { + 'checksums': ['595e1dd7f3b472ea5f12af21d2fec8a2ea2cf8f9d93e67180197330b26df9b61'], + }), + ('asgiref', '3.7.2', { + 'checksums': ['9e0ce3aa93a819ba5b45120216b23878cf6e8525eb3848653452b4192b92afed'], + }), + ('sqlparse', '0.4.4', { + 'checksums': ['d446183e84b8349fa3061f0fe7f06ca94ba65b426946ffebe6e3e8295332420c'], + }), + ('Django', '5.0.1', { + 'checksums': ['8c8659665bc6e3a44fefe1ab0a291e5a3fb3979f9a8230be29de975e57e8f854'], + }), + ('illumina-utils', '2.13', { + 'checksums': ['e688ca221ea6178614073b72205fce7b4a54695237c7aa96713492ecd99bd56e'], + # python-Levenshtein was renamed to Levenshtein + 'preinstallopts': "sed -i 's/python-Levenshtein/Levenshtein/g' requirements.txt && ", + 'modulename': 'IlluminaUtils', + }), + ('mistune', '3.0.2', { + 'checksums': ['fc7f93ded930c92394ef2cb6f04a8aabab4117a91449e72dcc8dfa646a508be8'], + }), + ('multiprocess', '0.70.15', { + 'checksums': ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'], + }), + ('Paste', '3.7.1', { + 'checksums': ['6d07a8e1c7fa72b8cf403762a002f80d12c0384056956dd0a87cb9a3be64749a'], + }), + ('plotext', '5.2.8', { + 'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'], + }), + ('pyani', '0.2.12', { + 'checksums': ['4f56b217656f53416b333b69495a4ba8cde782e64e475e1481cb2213ce6b9388'], + }), + ('rich_argparse', '1.4.0', { + 'checksums': ['c275f34ea3afe36aec6342c2a2298893104b5650528941fb53c21067276dba19'], + }), + (name, version, { + 'source_urls': ['https://github.com/merenlab/anvio/releases/download/v%(version)s/'], + 'patches': ['anvio-8_fix-rU.patch'], + 'checksums': [ + {'anvio-8.tar.gz': '13da84d48d7266a8986815efb024772fa26ad1c8a951d42897c3a51e3d924feb'}, + {'anvio-8_fix-rU.patch': '5eafa5962f59b563cfc3913fb688963b5fe052714c7d7c66b013af065e7a2fea'}, + ], + # remove too strict requirements for Python packages anvio depends on + 'preinstallopts': "sed -i -e 's/==.*//g' -e 's/<=.*//g' requirements.txt && ", + }), +] + +local_binaries_list = [ + 'anvi-pan-genome', + 'anvi-script-reformat-fasta', + 'anvi-profile', + 'anvi-help', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries_list], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "anvi-self-test --suite mini --no-interactive", + "anvi-pan-genome --help", + "anvi-script-reformat-fasta --help", + "anvi-profile --version", + "anvi-help --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/a/anvio/anvio-8_fix-rU.patch b/easybuild/easyconfigs/a/anvio/anvio-8_fix-rU.patch new file mode 100644 index 000000000000..e34f180be1fe --- /dev/null +++ b/easybuild/easyconfigs/a/anvio/anvio-8_fix-rU.patch @@ -0,0 +1,484 @@ +fix for: ValueError: invalid mode: 'rU' +see also https://github.com/merenlab/anvio/commit/a974118fc6f1b53c846892fc6dee0a86e6658963 +and https://github.com/merenlab/anvio/commit/ac5908eac71809b31f3bd0ff92bbb573cc17f730 + +From a974118fc6f1b53c846892fc6dee0a86e6658963 Mon Sep 17 00:00:00 2001 +From: "A. Murat Eren" +Date: Wed, 25 Oct 2023 16:09:42 +0200 +Subject: [PATCH] rU -> r. + +we will see tonight if things explode and we will blame meren for that. +--- + anvio/cogs.py | 6 +++--- + anvio/dbops.py | 4 ++-- + anvio/drivers/emapper.py | 2 +- + anvio/fastalib.py | 2 +- + anvio/filesnpaths.py | 8 ++++---- + anvio/interactive.py | 2 +- + anvio/kegg.py | 14 +++++++------- + anvio/mcgclassifier.py | 4 ++-- + anvio/merger.py | 2 +- + anvio/panops.py | 2 +- + anvio/parsers/kaiju.py | 2 +- + anvio/profiler.py | 2 +- + anvio/programs.py | 2 +- + anvio/samplesops.py | 4 ++-- + anvio/structureops.py | 2 +- + anvio/variabilityops.py | 2 +- + anvio/workflows/__init__.py | 2 +- + bin/anvi-export-structures | 2 +- + bin/anvi-get-sequences-for-hmm-hits | 2 +- + 19 files changed, 33 insertions(+), 33 deletions(-) + +diff --git a/anvio/cogs.py b/anvio/cogs.py +index c14041a710..1700af254d 100644 +--- a/anvio/cogs.py ++++ b/anvio/cogs.py +@@ -702,7 +702,7 @@ def raise_error(line_num, line_content, fields, e): + p_id_without_cog_id = set([]) + + line_counter = 0 +- for line in open(input_file_path, 'rU').readlines(): ++ for line in open(input_file_path, 'r').readlines(): + line_counter += 1 + + if line_counter % 500 == 0: +@@ -823,7 +823,7 @@ def format_categories(self, input_file_path, output_file_path): + progress.update('...') + + output = open(output_file_path, 'w') +- for line in open(input_file_path, 'rU').readlines(): ++ for line in open(input_file_path, 'r').readlines(): + if line.startswith('#'): + continue + +@@ -951,7 +951,7 @@ def check_raw_data_hash_and_existence(self, input_file_path, output_file_path): + + # Get a dictionnary of checksums, the file is formatted as "checksum filename" per line + checksums = {} +- for line in open(input_file_path, 'rU').readlines(): ++ for line in open(input_file_path, 'r').readlines(): + stripped = line.strip('\n').split(' ') + file_name = stripped[-1].strip('*') + checksums[file_name] = stripped[0] +diff --git a/anvio/dbops.py b/anvio/dbops.py +index 34e3198a8a..ce700b784d 100644 +--- a/anvio/dbops.py ++++ b/anvio/dbops.py +@@ -4335,7 +4335,7 @@ def create(self, args): + + if description_file_path: + filesnpaths.is_file_plain_text(description_file_path) +- description = open(os.path.abspath(description_file_path), 'rU').read() ++ description = open(os.path.abspath(description_file_path), 'r').read() + else: + description = '' + +@@ -4957,7 +4957,7 @@ def get_description_in_db(anvio_db_path, run=run): + + def update_description_in_db_from_file(anvio_db_path, description_file_path, run=run): + filesnpaths.is_file_plain_text(description_file_path) +- description = open(os.path.abspath(description_file_path), 'rU').read() ++ description = open(os.path.abspath(description_file_path), 'r').read() + + update_description_in_db(anvio_db_path, description, run=run) + +diff --git a/anvio/drivers/emapper.py b/anvio/drivers/emapper.py +index 7ea2d8fa53..dd94e9baa8 100644 +--- a/anvio/drivers/emapper.py ++++ b/anvio/drivers/emapper.py +@@ -357,7 +357,7 @@ def populate_annotations_dict(self, annotations_file_path): + + num_entries_processed = 0 + self.progress.new('Parsing the annotations file') +- for line in open(annotations_file_path, 'rU').readlines(): ++ for line in open(annotations_file_path, 'r').readlines(): + if line.startswith('#') or line == '\n': + continue + +diff --git a/anvio/fastalib.py b/anvio/fastalib.py +index 2da45c16f0..0980098ae7 100644 +--- a/anvio/fastalib.py ++++ b/anvio/fastalib.py +@@ -97,7 +97,7 @@ def __init__(self, fasta_file_path, lazy_init=True, unique=False, allow_mixed_ca + if self.compressed: + self.file_pointer = gzip.open(self.fasta_file_path, mode="rt") + else: +- self.file_pointer = io.open(self.fasta_file_path, 'rU', newline='') ++ self.file_pointer = io.open(self.fasta_file_path, 'r', newline='') + + if not self.file_pointer.read(1) == '>': + self.file_pointer.close() +diff --git a/anvio/filesnpaths.py b/anvio/filesnpaths.py +index 93327207de..a9d7939cbc 100644 +--- a/anvio/filesnpaths.py ++++ b/anvio/filesnpaths.py +@@ -73,7 +73,7 @@ def is_proper_external_gene_calls_file(file_path): + headers_proper = ['gene_callers_id', 'contig', 'start', 'stop', 'direction', 'partial', 'call_type', 'source', 'version', 'aa_sequence'] + call_types_allowed = set(list(constants.gene_call_types.values())) + +- with open(file_path, 'rU') as input_file: ++ with open(file_path, 'r') as input_file: + headers = input_file.readline().strip().split('\t') + + if len(headers) == 10: +@@ -196,7 +196,7 @@ def is_file_empty(file_path): + + def is_file_tab_delimited(file_path, separator='\t', expected_number_of_fields=None, dont_raise=False): + is_file_exists(file_path) +- f = open(file_path, 'rU') ++ f = open(file_path, 'r') + + try: + while True: +@@ -246,7 +246,7 @@ def is_file_json_formatted(file_path): + is_file_exists(file_path) + + try: +- json.load(open(file_path, 'rU')) ++ json.load(open(file_path, 'r')) + except ValueError as e: + raise FilesNPathsError("File '%s' does not seem to be a properly formatted JSON " + "file ('%s', cries the library)." % (file_path, e)) +@@ -272,7 +272,7 @@ def is_file_plain_text(file_path, dont_raise=False): + is_file_exists(file_path) + + try: +- open(os.path.abspath(file_path), 'rU').read(512) ++ open(os.path.abspath(file_path), 'r').read(512) + except IsADirectoryError: + if dont_raise: + return False +diff --git a/anvio/interactive.py b/anvio/interactive.py +index f397c0e56d..1564353064 100644 +--- a/anvio/interactive.py ++++ b/anvio/interactive.py +@@ -546,7 +546,7 @@ def process_external_item_order(self): + + filesnpaths.is_file_exists(self.item_order_path) + +- item_order = [l.strip() for l in open(self.item_order_path, 'rU').readlines()] ++ item_order = [l.strip() for l in open(self.item_order_path, 'r').readlines()] + self.run.info('Items order', 'An items order with %d items is found at %s.' % (len(item_order), self.item_order_path), mc='cyan') + + self.progress.new('External items order') +diff --git a/anvio/kegg.py b/anvio/kegg.py +index 13fbaf57b1..4f25761453 100644 +--- a/anvio/kegg.py ++++ b/anvio/kegg.py +@@ -924,7 +924,7 @@ def process_pathway_file(self): + filesnpaths.is_file_exists(self.kegg_pathway_file) + filesnpaths.is_file_plain_text(self.kegg_pathway_file) + +- f = open(self.kegg_pathway_file, 'rU') ++ f = open(self.kegg_pathway_file, 'r') + self.progress.new("Parsing KEGG Pathway file") + + current_category = None +@@ -998,7 +998,7 @@ def get_accessions_from_htext_file(self, htext_file): + filesnpaths.is_file_exists(htext_file) + filesnpaths.is_file_plain_text(htext_file) + +- f = open(htext_file, 'rU') ++ f = open(htext_file, 'r') + self.progress.new(f"Parsing KEGG htext file: {htext_file}") + + target_level = None +@@ -1077,7 +1077,7 @@ def download_generic_flat_file(self, accession, download_dir="./"): + utils.download_file(self.kegg_rest_api_get + '/' + accession, + file_path, progress=self.progress, run=self.run) + # verify entire file has been downloaded +- f = open(file_path, 'rU') ++ f = open(file_path, 'r') + f.seek(0, os.SEEK_END) + f.seek(f.tell() - 4, os.SEEK_SET) + last_line = f.readline().strip('\n') +@@ -1146,7 +1146,7 @@ def download_pathways(self): + utils.download_file(self.kegg_rest_api_get + '/' + konum, + file_path, progress=self.progress, run=self.run) + # verify entire file has been downloaded +- f = open(file_path, 'rU') ++ f = open(file_path, 'r') + f.seek(0, os.SEEK_END) + f.seek(f.tell() - 4, os.SEEK_SET) + last_line = f.readline().strip('\n') +@@ -1528,7 +1528,7 @@ def process_module_file(self): + filesnpaths.is_file_exists(self.kegg_module_file) + filesnpaths.is_file_plain_text(self.kegg_module_file) + +- f = open(self.kegg_module_file, 'rU') ++ f = open(self.kegg_module_file, 'r') + self.progress.new("Parsing KEGG Module file") + + current_module_type = None +@@ -1641,7 +1641,7 @@ def confirm_downloaded_modules(self): + f"on your computer. Very sorry to tell you this, but you need to re-download the KEGG " + f"data. We recommend the --reset flag.") + # verify entire file has been downloaded +- f = open(file_path, 'rU') ++ f = open(file_path, 'r') + f.seek(0, os.SEEK_END) + f.seek(f.tell() - 4, os.SEEK_SET) + last_line = f.readline().strip('\n') +@@ -6677,7 +6677,7 @@ def create(self): + for mnum in self.module_dict.keys(): + self.progress.update("Parsing Module %s" % mnum) + mod_file_path = os.path.join(self.module_data_directory, mnum) +- f = open(mod_file_path, 'rU') ++ f = open(mod_file_path, 'r') + + prev_data_name_field = None + module_has_annotation_source = False +diff --git a/anvio/mcgclassifier.py b/anvio/mcgclassifier.py +index 2d9f0b0bb3..bd38770778 100644 +--- a/anvio/mcgclassifier.py ++++ b/anvio/mcgclassifier.py +@@ -92,7 +92,7 @@ def __init__(self, args, run=run, progress=progress): + if self.exclude_samples: + # check that there is a file like this + filesnpaths.is_file_exists(self.exclude_samples) +- self.samples_to_exclude = set([l.split('\t')[0].strip() for l in open(self.exclude_samples, 'rU').readlines()]) ++ self.samples_to_exclude = set([l.split('\t')[0].strip() for l in open(self.exclude_samples, 'r').readlines()]) + + if not self.samples_to_exclude: + raise ConfigError("You asked to exclude samples, but provided an empty list.") +@@ -102,7 +102,7 @@ def __init__(self, args, run=run, progress=progress): + if self.include_samples: + # check that there is a file like this + filesnpaths.is_file_exists(self.include_samples) +- self.samples_to_include = set([l.split('\t')[0].strip() for l in open(self.include_samples, 'rU').readlines()]) ++ self.samples_to_include = set([l.split('\t')[0].strip() for l in open(self.include_samples, 'r').readlines()]) + + if not self.samples_to_include: + raise ConfigError("You provided an empty list of samples to include.") +diff --git a/anvio/merger.py b/anvio/merger.py +index 0e2aa44480..440f07a592 100644 +--- a/anvio/merger.py ++++ b/anvio/merger.py +@@ -334,7 +334,7 @@ def sanity_check(self): + # do we have a description file? + if self.description_file_path: + filesnpaths.is_file_plain_text(self.description_file_path) +- self.description = open(os.path.abspath(self.description_file_path), 'rU').read() ++ self.description = open(os.path.abspath(self.description_file_path), 'r').read() + + + def set_sample_id(self): +diff --git a/anvio/panops.py b/anvio/panops.py +index 5cf700d29a..824c2d5ac8 100644 +--- a/anvio/panops.py ++++ b/anvio/panops.py +@@ -234,7 +234,7 @@ def check_params(self): + + if self.description_file_path: + filesnpaths.is_file_plain_text(self.description_file_path) +- self.description = open(os.path.abspath(self.description_file_path), 'rU').read() ++ self.description = open(os.path.abspath(self.description_file_path), 'r').read() + + self.pan_db_path = self.get_output_file_path(self.project_name + '-PAN.db') + +diff --git a/anvio/parsers/kaiju.py b/anvio/parsers/kaiju.py +index 4d8f60e60b..057320a42a 100644 +--- a/anvio/parsers/kaiju.py ++++ b/anvio/parsers/kaiju.py +@@ -62,7 +62,7 @@ def fix_input_file(self, input_file_path): + + corrected_temp_file_path = filesnpaths.get_temp_file_path() + corrected_temp_file = open(corrected_temp_file_path, 'w') +- input_file = open(input_file_path, 'rU') ++ input_file = open(input_file_path, 'r') + + num_correct_lines = 0 + for line in input_file.readlines(): +diff --git a/anvio/profiler.py b/anvio/profiler.py +index 2a25ec3592..d2facf2a25 100644 +--- a/anvio/profiler.py ++++ b/anvio/profiler.py +@@ -450,7 +450,7 @@ def init_dirs_and_dbs(self): + + if self.description_file_path: + filesnpaths.is_file_plain_text(self.description_file_path) +- self.description = open(os.path.abspath(self.description_file_path), 'rU').read() ++ self.description = open(os.path.abspath(self.description_file_path), 'r').read() + + if self.output_directory: + self.output_directory = filesnpaths.check_output_directory(self.output_directory, ok_if_exists=self.overwrite_output_destinations) +diff --git a/anvio/programs.py b/anvio/programs.py +index b404d470a9..230f4c248d 100644 +--- a/anvio/programs.py ++++ b/anvio/programs.py +@@ -55,7 +55,7 @@ def get_until_blank(output): + + + def get_meta_information_from_file(file_path, meta_tag): +- all_lines = [l.strip() for l in open(file_path, 'rU').readlines()] ++ all_lines = [l.strip() for l in open(file_path, 'r').readlines()] + + meta_tag_content = '' + +diff --git a/anvio/samplesops.py b/anvio/samplesops.py +index f603df9779..814b0d96f4 100644 +--- a/anvio/samplesops.py ++++ b/anvio/samplesops.py +@@ -50,7 +50,7 @@ def process_samples_information_file(self, samples_information_path): + self.sample_names_in_samples_information_file = filesnpaths.is_proper_samples_information_file(samples_information_path) + + self.samples_information_dict, self.aliases_to_attributes_dict = self.convert_samples_information_dict(utils.get_TAB_delimited_file_as_dictionary(samples_information_path)) +- self.samples_information_default_layer_order = open(samples_information_path, 'rU').readline().strip().split('\t')[1:] ++ self.samples_information_default_layer_order = open(samples_information_path, 'r').readline().strip().split('\t')[1:] + + self.run.info('Samples information', 'Loaded for %d samples' % len(self.samples_information_dict), quiet=self.quiet) + +@@ -122,7 +122,7 @@ def process_single_order_data(self, single_order_path, single_order_name): + + filesnpaths.is_file_plain_text(single_order_path) + +- single_order_file_content = [l.strip('\n') for l in open(single_order_path, 'rU').readlines()] ++ single_order_file_content = [l.strip('\n') for l in open(single_order_path, 'r').readlines()] + + if len(single_order_file_content) != 1: + raise SamplesError("The single order file should contain a single line of information. It can't have nothing,\ +diff --git a/anvio/structureops.py b/anvio/structureops.py +index aa47125fe2..d9a41fcaca 100755 +--- a/anvio/structureops.py ++++ b/anvio/structureops.py +@@ -1968,7 +1968,7 @@ def get_path(self, gene_callers_id): + + def is_header_ok(self): + headers_proper = ['gene_callers_id', 'path'] +- with open(self.path, 'rU') as input_file: ++ with open(self.path, 'r') as input_file: + headers = input_file.readline().strip().split('\t') + missing_headers = [h for h in headers_proper if h not in headers] + +diff --git a/anvio/variabilityops.py b/anvio/variabilityops.py +index c116469a15..deb19b14e3 100644 +--- a/anvio/variabilityops.py ++++ b/anvio/variabilityops.py +@@ -764,7 +764,7 @@ def sanity_check(self): + filesnpaths.is_file_tab_delimited(self.genes_of_interest_path, expected_number_of_fields=1) + + try: +- self.gene_caller_ids = [int(g.strip()) for g in open(self.genes_of_interest_path, 'rU').readlines()] ++ self.gene_caller_ids = [int(g.strip()) for g in open(self.genes_of_interest_path, 'r').readlines()] + except: + raise ConfigError("The gene caller ids anvi'o found in that file does not seem like gene caller " + "ids anvi'o would use. There is something wrong here :(") +diff --git a/anvio/workflows/__init__.py b/anvio/workflows/__init__.py +index ffae6b78dd..828dab9af0 100644 +--- a/anvio/workflows/__init__.py ++++ b/anvio/workflows/__init__.py +@@ -333,7 +333,7 @@ def dry_run(self, workflow_graph_output_file_path_prefix='workflow'): + # we are (it still may be better to do it elsewhere more appropriate .. so + # we can look more decent or whatever): + if self.save_workflow_graph: +- lines = open(log_file_path, 'rU').readlines() ++ lines = open(log_file_path, 'r').readlines() + + try: + line_of_interest = [line_no for line_no in range(0, len(lines)) if lines[line_no].startswith('digraph')][0] +diff --git a/bin/anvi-export-structures b/bin/anvi-export-structures +index 147f82c346..0f059b74ed 100755 +--- a/bin/anvi-export-structures ++++ b/bin/anvi-export-structures +@@ -38,7 +38,7 @@ def main(args): + raise ConfigError("Pick one of --gene-caller-ids and --genes-of-interest") + elif genes_of_interest_path: + filesnpaths.is_file_exists(args.genes_of_interest) +- genes_of_interest = set(int(g.strip()) for g in open(args.genes_of_interest, 'rU').readlines()) ++ genes_of_interest = set(int(g.strip()) for g in open(args.genes_of_interest, 'r').readlines()) + elif gene_caller_ids: + genes_of_interest = set(int(g) for g in gene_caller_ids.split(',')) + else: +diff --git a/bin/anvi-get-sequences-for-hmm-hits b/bin/anvi-get-sequences-for-hmm-hits +index b18183737d..f2fec99652 100755 +--- a/bin/anvi-get-sequences-for-hmm-hits ++++ b/bin/anvi-get-sequences-for-hmm-hits +@@ -166,7 +166,7 @@ def main(args): + + # figure out gene names.. if the user provided a file, use that, otherwhise parse gene names out of the comma-separated text + if args.gene_names and filesnpaths.is_file_exists(args.gene_names, dont_raise=True): +- gene_names = [g.strip() for g in open(args.gene_names, 'rU').readlines()] if args.gene_names else [] ++ gene_names = [g.strip() for g in open(args.gene_names, 'r').readlines()] if args.gene_names else [] + else: + gene_names = [g.strip() for g in args.gene_names.split(',')] if args.gene_names else [] + +From ac5908eac71809b31f3bd0ff92bbb573cc17f730 Mon Sep 17 00:00:00 2001 +From: "A. Murat Eren" +Date: Wed, 25 Oct 2023 16:06:15 +0200 +Subject: [PATCH] rU is deprecated for a long time + +--- + anvio/utils.py | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/anvio/utils.py b/anvio/utils.py +index 4e599aaa3..c52888934 100644 +--- a/anvio/utils.py ++++ b/anvio/utils.py +@@ -850,7 +850,7 @@ def transpose_tab_delimited_file(input_file_path, output_file_path, remove_after + filesnpaths.is_file_tab_delimited(input_file_path) + filesnpaths.is_output_file_writable(output_file_path) + +- file_content = [line.strip('\n').split('\t') for line in open(input_file_path, 'rU').readlines()] ++ file_content = [line.strip('\n').split('\t') for line in open(input_file_path, 'r').readlines()] + + output_file = open(output_file_path, 'w') + for entry in zip(*file_content): +@@ -1048,7 +1048,7 @@ def get_column_data_from_TAB_delim_file(input_file_path, column_indices=[], expe + for index in column_indices: + d[index] = [] + +- with open(input_file_path, "rU") as input_file: ++ with open(input_file_path, "r") as input_file: + for line in input_file.readlines(): + fields = line.strip('\n').split(separator) + +@@ -1066,9 +1066,9 @@ def get_columns_of_TAB_delim_file(file_path, include_first_column=False): + filesnpaths.is_file_exists(file_path) + + if include_first_column: +- return open(file_path, 'rU').readline().strip('\n').split('\t') ++ return open(file_path, 'r').readline().strip('\n').split('\t') + else: +- return open(file_path, 'rU').readline().strip('\n').split('\t')[1:] ++ return open(file_path, 'r').readline().strip('\n').split('\t')[1:] + + + def get_names_order_from_newick_tree(newick_tree, newick_format=1, reverse=False, names_with_only_digits_ok=False): +@@ -1095,7 +1095,7 @@ def get_vectors_from_TAB_delim_matrix(file_path, cols_to_return=None, rows_to_re + id_to_sample_dict = {} + sample_to_id_dict = {} + +- input_matrix = open(file_path, 'rU') ++ input_matrix = open(file_path, 'r') + columns = input_matrix.readline().strip('\n').split('\t')[1:] + + fields_of_interest = [] +@@ -1489,7 +1489,7 @@ def get_gene_caller_ids_from_args(gene_caller_ids, delimiter=','): + gene_caller_ids_set = set([]) + if gene_caller_ids: + if os.path.exists(gene_caller_ids): +- gene_caller_ids_set = set([g.strip() for g in open(gene_caller_ids, 'rU').readlines()]) ++ gene_caller_ids_set = set([g.strip() for g in open(gene_caller_ids, 'r').readlines()]) + else: + gene_caller_ids_set = set([g.strip() for g in gene_caller_ids.split(delimiter)]) + +@@ -1764,7 +1764,7 @@ def concatenate_files(dest_file, file_list, remove_concatenated_files=False): + + dest_file_obj = open(dest_file, 'w') + for chunk_path in file_list: +- for line in open(chunk_path, 'rU'): ++ for line in open(chunk_path, 'r'): + dest_file_obj.write(line) + + dest_file_obj.close() +@@ -3547,7 +3547,7 @@ def get_TAB_delimited_file_as_dictionary(file_path, expected_fields=None, dict_t + failed_lines = [] + column_mapping_for_line_failed = None + +- f = open(file_path, 'rU') ++ f = open(file_path, 'r') + + # learn the number of fields and reset the file: + num_fields = len(f.readline().strip('\n').split(separator)) diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2022b.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2022b.eb new file mode 100644 index 000000000000..1a1837b76f16 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2022b.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.3' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2022b'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +patches = ['ETE-3.1.2-foss-2021b_fix_binpath.patch'] +checksums = [ + {'ete3-3.1.3.tar.gz': '06a3b7fa8ed90187b076a8dbbe5b1b62acee94201d3c6e822f55f449601ef6f2'}, + {'ETE-3.1.2-foss-2021b_fix_binpath.patch': 'f71d1135e87e1035736f67b92ebcfebd2ae4d57e48f45e25c1a6144c60f11fbd'}, +] + +dependencies = [ + ('Python', '3.10.8'), + ('SciPy-bundle', '2023.02'), + ('lxml', '4.9.2'), + ('PyQt5', '5.15.7'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..fffd5d3635f1 --- /dev/null +++ b/easybuild/easyconfigs/l/Levenshtein/Levenshtein-0.24.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Levenshtein' +version = '0.24.0' + +homepage = 'https://pypi.org/project/python-Levenshtein/' +description = 'Python extension for computing string edit distances and similarities.' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), + ('scikit-build', '0.17.2'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.8'), +] + +use_pip = True + +exts_list = [ + ('rapidfuzz', '3.6.1', { + 'checksums': ['35660bee3ce1204872574fa041c7ad7ec5175b3053a4cb6e181463fc07013de7'], + }), + (name, version, { + 'modulename': 'Levenshtein', + 'checksums': ['0cbcf3c9a7c77de3a405bfc857ab94341b4049e8c5c6b917f5ffcd5a92ff169a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 02ae134cb33cada15ee348b7d580a38ba5bfdcef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 12:13:20 +0100 Subject: [PATCH 0544/1193] adding easyconfigs: Seaborn-0.13.2-gfbf-2023a.eb --- .../s/Seaborn/Seaborn-0.13.2-gfbf-2023a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023a.eb new file mode 100644 index 000000000000..3168e1c38439 --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.13.2-gfbf-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.13.2' + +homepage = 'https://seaborn.pydata.org/' +description = """ Seaborn is a Python visualization library based on matplotlib. + It provides a high-level interface for drawing attractive statistical graphics. """ + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7'] + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From d067d63c0f506bdfdb2c29c2122d7624d61b9296 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 12:14:56 +0100 Subject: [PATCH 0545/1193] adding easyconfigs: statsmodels-0.14.1-gfbf-2023a.eb --- .../statsmodels-0.14.1-gfbf-2023a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023a.eb new file mode 100644 index 000000000000..6c62326b90d4 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.14.1-gfbf-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.14.1' + +homepage = 'https://www.statsmodels.org/' +description = """Statsmodels is a Python module that allows users to explore data, estimate statistical models, +and perform statistical tests.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.6', { + 'checksums': ['95c6d47a7222535f84bff7f63d7303f2e297747a598db89cf5c67f0c0c7d2cdb'], + }), + (name, version, { + 'checksums': ['2260efdc1ef89f39c670a0bd8151b1d0843567781bcafec6cda0534eb47a94f6'], + 'preinstallopts': """sed -i 's/name=DISTNAME/name=DISTNAME, version = "%(version)s"/g' setup.py && """, + }), +] + +moduleclass = 'math' From 26ceb6387d1676e2b9f0148c0e47f98402b9dae3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 12:17:32 +0100 Subject: [PATCH 0546/1193] adding easyconfigs: Pysam-0.22.0-GCC-12.3.0.eb --- .../p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100755 easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb new file mode 100755 index 000000000000..684f68062454 --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.22.0' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f'] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('ncurses', '6.4'), + ('cURL', '8.0.1'), + ('XZ', '5.4.2'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' From 5edb74d935daf7507eb8e0cd935b3168df078fcd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 12:17:48 +0100 Subject: [PATCH 0547/1193] adding easyconfigs: ETE-3.1.3-foss-2023a.eb --- .../easyconfigs/e/ETE/ETE-3.1.3-foss-2023a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2023a.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2023a.eb new file mode 100644 index 000000000000..be10b6336336 --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.3-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.3' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +patches = ['ETE-3.1.2-foss-2021b_fix_binpath.patch'] +checksums = [ + {'ete3-3.1.3.tar.gz': '06a3b7fa8ed90187b076a8dbbe5b1b62acee94201d3c6e822f55f449601ef6f2'}, + {'ETE-3.1.2-foss-2021b_fix_binpath.patch': 'f71d1135e87e1035736f67b92ebcfebd2ae4d57e48f45e25c1a6144c60f11fbd'}, +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lxml', '4.9.2'), + ('PyQt5', '5.15.10'), +] + +download_dep_fail = True +use_pip = True + +options = {'modulename': 'ete3'} + +sanity_check_paths = { + 'files': ['bin/ete3'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'vis' From 479ecec53a1ac285392b1072181d7ea256d76fa8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 13:23:59 +0100 Subject: [PATCH 0548/1193] use existing typing-extensions 4.9.0 as dependency for pydantic v1.10.13 --- .../pydantic-1.10.13-GCCcore-12.3.0.eb | 2 +- .../typing-extensions-4.8.0-GCCcore-12.3.0.eb | 22 ------------------- 2 files changed, 1 insertion(+), 23 deletions(-) delete mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb index 399498e64575..d49023624260 100644 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.3.0.eb @@ -12,7 +12,7 @@ builddependencies = [('binutils', '2.40')] dependencies = [ ('Python', '3.11.3'), - ('typing-extensions', '4.8.0'), + ('typing-extensions', '4.9.0'), ] sanity_pip_check = True diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb deleted file mode 100644 index b2f09550f851..000000000000 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.8.0-GCCcore-12.3.0.eb +++ /dev/null @@ -1,22 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'typing-extensions' -version = '4.8.0' - -homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' -description = 'Typing Extensions – Backported and Experimental Type Hints for Python' - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = ['typing_extensions-%(version)s.tar.gz'] -checksums = ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [('Python', '3.11.3')] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'devel' From 1291d4643f210855ed8cd1071005bbad4f679fd2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 13:24:20 +0100 Subject: [PATCH 0549/1193] use gtdbtk as name for extension in GTDB-Tk easyconfig --- easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb index 10f7db5d9fbb..7bc18e6624c9 100644 --- a/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GTDB-Tk/GTDB-Tk-2.3.2-foss-2023a.eb @@ -29,11 +29,8 @@ dependencies = [ use_pip = True exts_list = [ - (name, version, { - 'source_urls': ['https://pypi.python.org/packages/source/g/gtdbtk'], - 'sources': ['gtdbtk-%(version)s.tar.gz'], + ('gtdbtk', version, { 'checksums': ['80efd31e10007d835f56a3d6fdf039a59db3b6ba4be26b234692da5e688aa99f'], - 'modulename': 'gtdbtk', }), ] From 5f745491bd464be1543ad5d09d38e1edd80fdcdb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 13:26:20 +0100 Subject: [PATCH 0550/1193] remove exec permissions for Pysam-0.22.0-GCC-12.3.0.eb --- easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb old mode 100755 new mode 100644 From 486266c420da616a10aacd50205f16142a244300 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 13:24:39 +0100 Subject: [PATCH 0551/1193] add exception for pydantic 1.x dependency that is required by GTDB-Tk v2.3.2 --- test/easyconfigs/easyconfigs.py | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 1cda82901702..ef9393046fb4 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -599,6 +599,10 @@ def check_dep_vars(self, gen, dep, dep_vars): # OpenFOAM 5.0 requires older ParaView, CFDEMcoupling depends on OpenFOAM 5.0 (r'5\.4\.1', [r'CFDEMcoupling-3\.8\.0', r'OpenFOAM-5\.0-20180606']), ], + 'pydantic': [ + # GTDB-Tk v2.3.2 requires pydantic 1.x + ('1.10.13;', ['GTDB-Tk-2.3.2-']), + ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, # which is newer than what others use as dependency w.r.t. Pysam version in 2019b generation; # decona 0.1.2 and NGSpeciesID 0.1.1.1 depend on medaka 1.1.3 From 88ddb2d02700f048dd8a4139204aec5842f407a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 13:54:02 +0100 Subject: [PATCH 0552/1193] add reference to GTDB-Tk PR that shows why pydantic 1.x must be used --- test/easyconfigs/easyconfigs.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index ef9393046fb4..fb128fdbf200 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -600,7 +600,7 @@ def check_dep_vars(self, gen, dep, dep_vars): (r'5\.4\.1', [r'CFDEMcoupling-3\.8\.0', r'OpenFOAM-5\.0-20180606']), ], 'pydantic': [ - # GTDB-Tk v2.3.2 requires pydantic 1.x + # GTDB-Tk v2.3.2 requires pydantic 1.x (see https://github.com/Ecogenomics/GTDBTk/pull/530) ('1.10.13;', ['GTDB-Tk-2.3.2-']), ], # medaka 1.1.*, 1.2.*, 1.4.* requires Pysam 0.16.0.1, From 9329c569a3570f65b312e3e43b65574924be53f1 Mon Sep 17 00:00:00 2001 From: x0139045 Date: Thu, 1 Feb 2024 14:57:44 +0100 Subject: [PATCH 0553/1193] Set species to install as an option in VEP easyconfig --- easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb index 12e3b0d4bc8d..4a03b0fa6e33 100644 --- a/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb @@ -24,6 +24,8 @@ dependencies = [ ('Compress-Raw-Zlib', '2.202'), ] +species = 'cyprinus_carpio_carpio' + exts_defaultclass = 'PerlModule' exts_filter = ("perl -e 'require %(ext_name)s'", "") From 1245f433f7cc2af1088c7ca463a6da2d68814312 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 1 Feb 2024 15:34:06 +0100 Subject: [PATCH 0554/1193] add Perl as build dependency of DeltaLake-0.15.1-gfbf-2023a.eb --- easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb index 7894b46cf3e7..a0e60d3e0e2d 100644 --- a/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb @@ -856,6 +856,7 @@ crates = [ builddependencies = [ ('maturin', '1.4.0', '-Rust-1.75.0'), + ('Perl', '5.36.1'), # needed by crate openssl-sys ] dependencies = [ From 969ef926a01e26defccfdc4f41b086cbde86ee6d Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 1 Feb 2024 15:45:56 +0000 Subject: [PATCH 0555/1193] add cudnn, magma, nccl --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 6ffe56d33ed2..6b2ab3b4970c 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -138,6 +138,9 @@ dependencies = [ ('networkx', '3.1'), ('sympy', '1.12'), ('Z3', '4.12.2', '-Python-%(pyver)s'), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('magma', '2.7.2', versionsuffix), + ('NCCL', '2.18.3', versionsuffix), ] excluded_tests = { From 88380e57f74d5e0f414cb295f0170e66ce99efff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 16:57:35 +0100 Subject: [PATCH 0556/1193] remove trailing whitespace in DeltaLake easyconfig --- .../easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb index a0e60d3e0e2d..e3342fac4f60 100644 --- a/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/d/DeltaLake/DeltaLake-0.15.1-gfbf-2023a.eb @@ -856,7 +856,7 @@ crates = [ builddependencies = [ ('maturin', '1.4.0', '-Rust-1.75.0'), - ('Perl', '5.36.1'), # needed by crate openssl-sys + ('Perl', '5.36.1'), # needed by crate openssl-sys ] dependencies = [ From 05b89d3c9e4f6821d1bfe4613728a69f02e39a6a Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 1 Feb 2024 16:10:32 +0000 Subject: [PATCH 0557/1193] add extra patches from non-CUDA 2.1.2 PyTorch --- .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 6b2ab3b4970c..97f308a3d555 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -43,6 +43,13 @@ patches = [ 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', 'PyTorch-2.1.0_skip-test_wrap_bad.patch', + 'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch', + 'PyTorch-2.1.2_fix-test_memory_profiler.patch', + 'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch', + 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', + 'PyTorch-2.1.2_fix-vsx-vector-div.patch', + 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', 'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch', 'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch', ] @@ -102,6 +109,18 @@ checksums = [ {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, + {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch': + 'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'}, + {'PyTorch-2.1.2_fix-test_memory_profiler.patch': + '30b0c9355636c0ab3dedae02399789053825dc3835b4d7dac6e696767772b1ce'}, + {'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch': + 'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'}, + {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'}, + {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, + {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': + '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': + 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, {'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch': '5ba7e0b4203ea8c27b55b5231de024004697aca7bbae30aa248524babb451dc7'}, {'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch': From 6c368c6fae5d1ff6bffe4645f0ed739e7e165d78 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 1 Feb 2024 18:33:54 +0100 Subject: [PATCH 0558/1193] Update easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb --- easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb b/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb index 4a03b0fa6e33..3266a41274cf 100644 --- a/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/v/VEP/VEP-111-GCC-12.2.0.eb @@ -24,6 +24,8 @@ dependencies = [ ('Compress-Raw-Zlib', '2.202'), ] +# To select all species use 'all' (but this was broken as of 2024.02.01 and species need to explicitly listed +# with comma separation, see https://github.com/Ensembl/ensembl-vep/issues/1364#issuecomment-1753080504) species = 'cyprinus_carpio_carpio' exts_defaultclass = 'PerlModule' From 855a92391f3b1224996748597b83078696e3889c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 18:51:33 +0100 Subject: [PATCH 0559/1193] fix download of RcisTarget 1.22.0 in R-bundle-Bioconductor 3.18 --- .../R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 19c0cf74fe1c..3b75c5285b6e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -30,7 +30,7 @@ exts_default_options = { 'https://cran.r-project.org/src/contrib/', # current version of packages 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages ], - 'source_tmpl': '%(name)s_%(version)s.tar.gz' + 'sources': ['%(name)s_%(version)s.tar.gz'], } exts_defaultclass = 'RPackage' @@ -1080,7 +1080,12 @@ exts_list = [ 'checksums': ['202ecaf0f3c1ab6ce11bb73ccb69e85f1dbd4126f6a64d0fd3bc9e88f06231b4'], }), ('RcisTarget', '1.22.0', { - 'checksums': ['661cc189b281284eec9ed518db018eefff2b18ed8a8608108803ba7422ad82a4'], + # download of source tarball via Bioconductor doesn't work, + # see https://github.com/aertslab/RcisTarget/issues/39 + 'source_urls': ['https://code.bioconductor.org/browse/RcisTarget/tarball/'], + 'sources': [{'download_filename': 'RELEASE_3_18', 'filename': '%(name)s_%(version)s.tar.gz'}], + # download via code.bioconductor.org is not consistent, so can't use a checksum... + 'checksums': [None], }), ('NMF', '0.26', { 'checksums': ['8d44562ef5f33f3811929f944c9d029ec25526d2ddddfe7c8a5b6e23adbc2ec0'], From 5264095563df30f6c3cbf1277c62237cdde287a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 19:24:38 +0100 Subject: [PATCH 0560/1193] restore use of local_commit in CellBender easyconfig MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb index 11c144346953..88f92ec75ab2 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a-CUDA-11.7.0.eb @@ -66,7 +66,7 @@ exts_list = [ }), ('cellbender', version, { 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], - 'sources': [{'download_filename': 'e2fb597.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['7eb67837d28495adb82147e80a2ab58eeb406c5d91aa69dd0cc120d9cb3d6396'], }), ] From 9ee5a531d5e99b0813d645892d9b1ac522a079e6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Feb 2024 19:25:34 +0100 Subject: [PATCH 0561/1193] restore use of local_commit in CellBender easyconfig --- .../easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb index f24dd8e7518b..798e18442ab9 100644 --- a/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CellBender/CellBender-0.3.1-foss-2022a.eb @@ -64,7 +64,7 @@ exts_list = [ }), ('cellbender', version, { 'source_urls': ['https://github.com/broadinstitute/CellBender/archive'], - 'sources': [{'download_filename': 'e2fb597.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'sources': [{'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['7eb67837d28495adb82147e80a2ab58eeb406c5d91aa69dd0cc120d9cb3d6396'], }), ] From 1413fdc7c492bbaf9dab78188ddb3c417d930478 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 2 Feb 2024 09:27:22 +0100 Subject: [PATCH 0562/1193] RcisTarget sources is .tar, not .tar.gz --- .../R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 3b75c5285b6e..607e5edebb44 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1083,7 +1083,7 @@ exts_list = [ # download of source tarball via Bioconductor doesn't work, # see https://github.com/aertslab/RcisTarget/issues/39 'source_urls': ['https://code.bioconductor.org/browse/RcisTarget/tarball/'], - 'sources': [{'download_filename': 'RELEASE_3_18', 'filename': '%(name)s_%(version)s.tar.gz'}], + 'sources': [{'download_filename': 'RELEASE_3_18', 'filename': '%(name)s_%(version)s.tar'}], # download via code.bioconductor.org is not consistent, so can't use a checksum... 'checksums': [None], }), From b55c612ec899e2cc465b9a52f9dff67acd56c799 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 2 Feb 2024 09:51:56 +0100 Subject: [PATCH 0563/1193] move setuptools_scm from hatchling to Python easyconfig in develop --- .../h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb | 12 ------------ .../h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb | 12 ------------ .../Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb | 3 --- .../Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb | 3 --- .../p/Python/Python-3.11.3-GCCcore-12.3.0.eb | 12 ++++++++++++ .../p/Python/Python-3.11.5-GCCcore-13.2.0.eb | 12 ++++++++++++ 6 files changed, 24 insertions(+), 30 deletions(-) diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb index 85919d3f2b7d..5f163a171371 100644 --- a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-12.3.0.eb @@ -21,18 +21,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('packaging', '23.1', { - 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], - }), - ('setuptools_scm', '7.1.0', { - 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], - }), - ('typing_extensions', '4.6.3', { - 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], - }), ('pathspec', '0.11.1', { 'checksums': ['2798de800fa92780e33acca925945e9a19a133b715067cf165b8866c15a31687'], }), diff --git a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb index 765badccfffa..c12f3b9d9654 100644 --- a/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/h/hatchling/hatchling-1.18.0-GCCcore-13.2.0.eb @@ -21,18 +21,6 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('packaging', '23.2', { - 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], - }), - ('setuptools-scm', '8.0.4', { - 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], - }), - ('typing_extensions', '4.8.0', { - 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], - }), ('pathspec', '0.11.2', { 'checksums': ['e0d8d0ac2f12da61956eb2306b69f9469b42f4deb0f3cb6ed47b9cce9996ced3'], }), diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb index 642b6fed3793..6a91bcca5e41 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.06-GCCcore-12.3.0.eb @@ -105,9 +105,6 @@ exts_list = [ ('semantic_version', '2.10.0', { 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('typing_extensions', '4.6.3', { - 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], - }), ('pyasn1', '0.5.0', { 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], }), diff --git a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb index f1c29800a58a..d551945f5e7d 100644 --- a/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python-bundle-PyPI/Python-bundle-PyPI-2023.10-GCCcore-13.2.0.eb @@ -105,9 +105,6 @@ exts_list = [ ('semantic_version', '2.10.0', { 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('typing_extensions', '4.8.0', { - 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], - }), ('pyasn1', '0.5.0', { 'checksums': ['97b7290ca68e62a832558ec3976f15cbf911bf5d7c7039d8b861c2a0ece69fde'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb index 2bea26aa47d5..092c0b628d78 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.11.3-GCCcore-12.3.0.eb @@ -50,6 +50,18 @@ exts_list = [ ('setuptools', '67.7.2', { 'checksums': ['f104fa03692a2602fa0fec6c6a9e63b6c8a968de13e17c026957dd1f53d80990'], }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.1', { + 'checksums': ['a392980d2b6cffa644431898be54b0045151319d1e7ec34f0cfed48767dd334f'], + }), + ('typing_extensions', '4.6.3', { + 'checksums': ['d91d5919357fe7f681a9f2b5b4cb2a5f1ef0a1e9f59c4d8ff0d3491e05c0ffd5'], + }), + ('setuptools_scm', '7.1.0', { + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), ('pip', '23.1.2', { 'checksums': ['0e7c86f486935893c708287b30bd050a36ac827ec7fe5e43fe7cb198dd835fba'], }), diff --git a/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb index 2a132b975957..5ad7ceb101b6 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.11.5-GCCcore-13.2.0.eb @@ -47,6 +47,18 @@ exts_list = [ ('wheel', '0.41.2', { 'checksums': ['0c5ac5ff2afb79ac23ab82bab027a0be7b5dbcf2e54dc50efe4bf507de1f7985'], }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('typing_extensions', '4.8.0', { + 'checksums': ['df8e4339e9cb77357558cbdbceca33c303714cf861d1eef15e1070055ae8b7ef'], + }), + ('setuptools-scm', '8.0.4', { + 'checksums': ['b5f43ff6800669595193fd09891564ee9d1d7dcb196cab4b2506d53a2e1c95c7'], + }), ('setuptools', '68.2.2', { 'checksums': ['4ac1475276d2f1c48684874089fefcd83bd7162ddaafb81fac866ba0db282a87'], }), From cbda2474826435b81ec31a3063f6f4b1ff8a4acb Mon Sep 17 00:00:00 2001 From: benjamic Date: Fri, 2 Feb 2024 10:36:47 +0100 Subject: [PATCH 0564/1193] Update easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Following suggestion adding files to same line. Co-authored-by: Bob Dröge --- .../easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb index 74892696975d..aa84200c49e8 100644 --- a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -27,8 +27,7 @@ checksums = ['98faf305c60cc4d39d3b8ada1dcb7c87c49bf6f01a3cd2800b413d21d5df1a38'] configopts = '-DBUILD_NVML_PMT=1' sanity_check_paths = { - 'files': ["bin/Rapl-test"], - 'files': ["bin/NVML-test"], +'files': ["bin/Rapl-test", "bin/NVML-test"], 'dirs': ["lib", "include"], } From 51ebd253543b177404958ed03f7109d34db24136 Mon Sep 17 00:00:00 2001 From: benjamic Date: Fri, 2 Feb 2024 10:37:15 +0100 Subject: [PATCH 0565/1193] Update easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb index aa84200c49e8..9485900e4dea 100644 --- a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -10,6 +10,10 @@ description = """PMT is a high-level software library capable of toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['98faf305c60cc4d39d3b8ada1dcb7c87c49bf6f01a3cd2800b413d21d5df1a38'] + builddependencies = [ ('CMake', '3.26.3'), ('binutils', '2.40'), @@ -19,11 +23,6 @@ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM) ] - -source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] -sources = ['pmt-%(version)s.tar.gz'] -checksums = ['98faf305c60cc4d39d3b8ada1dcb7c87c49bf6f01a3cd2800b413d21d5df1a38'] - configopts = '-DBUILD_NVML_PMT=1' sanity_check_paths = { From a3dd14a3e0af471d31a838448c361f6865919147 Mon Sep 17 00:00:00 2001 From: benjamic Date: Fri, 2 Feb 2024 10:38:18 +0100 Subject: [PATCH 0566/1193] Update easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Following style correction suggestion Co-authored-by: Bob Dröge --- .../p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb index a2cff6e2c34b..3375c4c69e35 100644 --- a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -10,20 +10,19 @@ description = """PMT is a high-level software library capable of toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['98faf305c60cc4d39d3b8ada1dcb7c87c49bf6f01a3cd2800b413d21d5df1a38'] + builddependencies = [ ('CMake', '3.23.1'), - ('binutils', '2.38') + ('binutils', '2.38'), ] dependencies = [ - ('CUDA', '11.7.0', '', SYSTEM) + ('CUDA', '11.7.0', '', SYSTEM), ] - -source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] -sources = ['pmt-%(version)s.tar.gz'] -checksums = ['98faf305c60cc4d39d3b8ada1dcb7c87c49bf6f01a3cd2800b413d21d5df1a38'] - configopts = '-DBUILD_NVML_PMT=1' sanity_check_paths = { From f6545b1aefd5b1e5ed755eae28e6930d845dfb0b Mon Sep 17 00:00:00 2001 From: benjamic Date: Fri, 2 Feb 2024 10:38:32 +0100 Subject: [PATCH 0567/1193] Update easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- .../easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb index 3375c4c69e35..d486de9b7b37 100644 --- a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -26,8 +26,7 @@ dependencies = [ configopts = '-DBUILD_NVML_PMT=1' sanity_check_paths = { - 'files': ["bin/Rapl-test"], - 'files': ["bin/NVML-test"], + 'files': ["bin/Rapl-test", "bin/NVML-test"], 'dirs': ["lib", "include"], } From 0123b1756df230c3e6fbb57ed80bd7120cc19ed5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 2 Feb 2024 10:43:58 +0100 Subject: [PATCH 0568/1193] adding easyconfigs: IQ-TREE-2.2.2.7-gompi-2023a.eb, LSD2-2.4.1-GCCcore-12.3.0.eb --- .../i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb | 57 +++++++++++++++++++ .../l/LSD2/LSD2-2.4.1-GCCcore-12.3.0.eb | 40 +++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb new file mode 100644 index 000000000000..eeb83687517d --- /dev/null +++ b/easybuild/easyconfigs/i/IQ-TREE/IQ-TREE-2.2.2.7-gompi-2023a.eb @@ -0,0 +1,57 @@ +# Updated to v2.1.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'IQ-TREE' +version = '2.2.2.7' + +# HTTPS is not working +homepage = 'http://www.iqtree.org/' +description = """Efficient phylogenomic software by maximum likelihood""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +# Including 'usempi' will take precedence and override IQTREE_FLAGS and produces only 'iqtree-mpi' binary + +source_urls = ['https://github.com/iqtree/iqtree2/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'IQ-TREE-2.1.2_use_EB_LSD2.patch', + 'IQ-TREE-2.2.1_fix-mpi.patch', +] +checksums = [ + {'v2.2.2.7.tar.gz': '407a1a56d352ba9c2152a1d708cd29db872a41c252fbdc7acd8e0de0da8af008'}, + {'IQ-TREE-2.1.2_use_EB_LSD2.patch': 'daa2ab12d44e26eb5607c4ed6acb9d970e230a83dabcf21461f37bc48263b816'}, + {'IQ-TREE-2.2.1_fix-mpi.patch': '9ead6808efd11d4c01dd265cca6094cffd6377746d3b2fc84b43d2faeee0777c'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('LSD2', '2.4.1'), +] + +local_conf_opts = ' -DUSE_LSD2=ON ' +configopts = [ + '-DIQTREE_FLAGS=omp' + local_conf_opts, + '-DIQTREE_FLAGS=mpi -DCMAKE_C_COMPILER="$MPICC" -DCMAKE_CXX_COMPILER="$MPICXX"' + local_conf_opts, +] + +sanity_check_paths = { + 'files': ['bin/iqtree2', 'bin/iqtree2-mpi'], + 'dirs': [], +} + +sanity_check_commands = [ + "iqtree2 --help", + "mkdir -p $TMPDIR/{test-omp,test-mpi}", + "cd $TMPDIR/test-omp && cp -a %(installdir)s/example.phy . && iqtree2 -s example.phy -redo", + "cd $TMPDIR/test-mpi && cp -a %(installdir)s/example.phy . && mpirun -np 1 iqtree2-mpi -s example.phy -redo", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..07a7015b5b8f --- /dev/null +++ b/easybuild/easyconfigs/l/LSD2/LSD2-2.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,40 @@ +# Updated to v2.3 by +# R.QIAO +# DeepThought, Flinders University + +easyblock = 'CMakeMake' + +name = 'LSD2' +version = '2.4.1' + +homepage = 'https://github.com/tothuhien/lsd2' +description = "Least-squares methods to estimate rates and dates from phylogenies" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'tothuhien' + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v.%(version)s.tar.gz'] +patches = ['%(name)s-1.9.7_fix_cmake_to_build_lib_and_binary.patch'] +checksums = [ + {'v.2.4.1.tar.gz': '3d0921c96edb8f30498dc8a27878a76d785516043fbede4a72eefd84b5955458'}, + {'LSD2-1.9.7_fix_cmake_to_build_lib_and_binary.patch': + '8ef6e8c3a9a5aa2099678ed84a7e54ef687e3900894694c4eec1f5399f0487f6'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['bin/lsd2', 'lib/liblsd2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['lsd2 -h'] + +moduleclass = 'bio' From d246f5988a1654cd4108aaf4da55f8e9d1d4db75 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 11:08:27 +0100 Subject: [PATCH 0569/1193] adding easyconfigs: phyluce-1.7.3-foss-2023a.eb and patches: phyluce-1.7.3_fix-config-paths.patch, phyluce-1.7.3_removal-Bio-Alphabet.patch --- .../p/phyluce/phyluce-1.7.3-foss-2023a.eb | 139 ++++++++++++++++++ .../phyluce-1.7.3_fix-config-paths.patch | 51 +++++++ .../phyluce-1.7.3_removal-Bio-Alphabet.patch | 19 +++ 3 files changed, 209 insertions(+) create mode 100644 easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch create mode 100644 easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb new file mode 100644 index 000000000000..cc34f7ad8477 --- /dev/null +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -0,0 +1,139 @@ +easyblock = 'PythonBundle' + +name = 'phyluce' +version = '1.7.3' + +homepage = 'https://github.com/faircloth-lab/phyluce' +description = """ +phyluce is a software package for working with data generated from sequence capture of UCE +(ultra-conserved element) loci, as first published in [BCF2012]. Specifically, phyluce is a suite of programs to: +1) assemble raw sequence reads from Illumina platforms into contigs +2) determine which contigs represent UCE loci +3) filter potentially paralagous UCE loci +4) generate different sets of UCE loci across taxa of interest +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Biopython', '1.83'), + ('Python-bundle-PyPI', '2023.06'), + ('snakemake', '8.2.1'), + ('DendroPy', '4.6.1'), + ('bx-python', '0.10.0'), + ('ABySS', '2.3.7'), + ('BCFtools', '1.18'), + ('BEDTools', '2.31.0'), + ('BWA', '0.7.17'), + ('Gblocks', '0.91b','',SYSTEM), + ('LASTZ', '1.04.22'), + ('MAFFT', '7.520', '-with-extensions'), + ('MUSCLE', '5.1.0'), + ('Pilon', '1.23', '-Java-11-wrapped', SYSTEM), + ('RAxML-NG', '1.2.0'), + ('SAMtools', '1.18'), + ('seqtk', '1.4'), + ('SPAdes', '3.15.4'), + ('trimAl', '1.4.1'), + ('Velvet', '1.2.10', '-mt-kmer_191') +] + +use_pip = True + +exts_list = [ + (name, version, { + 'patches': [ + '%(name)s-%(version)s_fix-config-paths.patch', + '%(name)s-%(version)s_removal-Bio-Alphabet.patch', + ], + 'source_urls': ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'], + 'sources': 'v%(version)s.tar.gz', + 'checksums': [ + {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, + {'phyluce-1.7.3_fix-config-paths.patch': + '2abfec1856ba2900bb6788838cebc296d66cc7fe11c7c97076133bbca176ae1e'}, + {'phyluce-1.7.3_removal-Bio-Alphabet.patch': + 'd92fa984f25f3e1bd7ea735b6e50beefc6b5c5e645dddd93fde551306767926e'}, + ], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["%s --help" % x for x in [ + "phyluce_align_extract_taxa_from_alignments", + "phyluce_align_extract_taxon_fasta_from_alignments", + "phyluce_align_filter_alignments", + "phyluce_align_format_concatenated_phylip_for_paml", + "phyluce_align_get_align_summary_data", + "phyluce_align_get_gblocks_trimmed_alignments_from_untrimmed", + "phyluce_align_get_incomplete_matrix_estimates", + "phyluce_align_get_informative_sites", + "phyluce_align_get_only_loci_with_min_taxa", + "phyluce_align_get_ry_recoded_alignments", + "phyluce_align_get_smilogram_from_alignments", + "phyluce_align_get_taxon_locus_counts_in_alignments", + "phyluce_align_get_trimal_trimmed_alignments_from_untrimmed", + "phyluce_align_move_align_by_conf_file", + "phyluce_align_randomly_sample_and_concatenate", + "phyluce_align_reduce_alignments_with_raxml", + "phyluce_align_remove_empty_taxa", + "phyluce_align_remove_locus_name_from_files", + "phyluce_align_screen_alignments_for_problems", + "phyluce_align_seqcap_align", + "phyluce_align_split_concat_nexus_to_loci", + "phyluce_assembly_assemblo_abyss", + "phyluce_assembly_assemblo_spades", + "phyluce_assembly_assemblo_velvet", + "phyluce_assembly_explode_get_fastas_file", + "phyluce_assembly_extract_contigs_to_barcodes", + "phyluce_assembly_get_bed_from_lastz", + "phyluce_assembly_get_fasta_lengths", + "phyluce_assembly_get_fastas_from_match_counts", + "phyluce_assembly_get_fastq_lengths", + "phyluce_assembly_get_match_counts", + "phyluce_assembly_match_contigs_to_barcodes", + "phyluce_genetrees_get_mean_bootrep_support", + "phyluce_genetrees_generate_multilocus_bootstrap_count", + "phyluce_genetrees_rename_tree_leaves", + "phyluce_genetrees_sort_multilocus_bootstraps", + "phyluce_genetrees_get_tree_counts", + "phyluce_ncbi_chunk_fasta_for_ncbi", + "phyluce_ncbi_prep_uce_align_files_for_ncbi", + "phyluce_probe_easy_lastz", + "phyluce_probe_get_genome_sequences_from_bed", + "phyluce_probe_get_locus_bed_from_lastz_files", + "phyluce_probe_get_multi_fasta_table", + "phyluce_probe_get_multi_merge_table", + "phyluce_probe_get_probe_bed_from_lastz_files", + "phyluce_probe_get_screened_loci_by_proximity", + "phyluce_probe_get_subsets_of_tiled_probes", + "phyluce_probe_get_tiled_probe_from_multiple_inputs", + "phyluce_probe_get_tiled_probes", + "phyluce_probe_query_multi_fasta_table", + "phyluce_probe_query_multi_merge_table", + "phyluce_probe_reconstruct_uce_from_probe", + "phyluce_probe_remove_duplicate_hits_from_probes_using_lastz", + "phyluce_probe_remove_overlapping_probes_given_config", + "phyluce_probe_run_multiple_lastzs_sqlite", + "phyluce_probe_slice_sequence_from_genomes", + "phyluce_probe_strip_masked_loci_from_set", + "phyluce_utilities_combine_reads", + "phyluce_utilities_filter_bed_by_fasta", + "phyluce_utilities_get_bed_from_fasta", + "phyluce_utilities_merge_multiple_gzip_files", + "phyluce_utilities_merge_next_seq_gzip_files", + "phyluce_utilities_replace_many_links", + "phyluce_utilities_unmix_fasta_reads", + "phyluce_workflow", +]] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/phyluce'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch new file mode 100644 index 000000000000..47396dba7d82 --- /dev/null +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch @@ -0,0 +1,51 @@ +--- config/phyluce.conf.orig 2024-02-01 11:38:15.279943701 +0100 ++++ config/phyluce.conf 2024-02-01 14:52:31.565662528 +0100 +@@ -1,27 +1,27 @@ + [binaries] +-abyss:$CONDA/bin/ABYSS +-abyss-pe:$CONDA/bin/abyss-pe +-bcftools:$CONDA/bin/bcftools +-bedtools:$CONDA/bin/bedtools +-bwa:$CONDA/bin/bwa +-gblocks:$CONDA/bin/Gblocks +-lastz:$CONDA/bin/lastz +-mafft:$CONDA/bin/mafft +-muscle:$CONDA/bin/muscle +-pilon:$CONDA/bin/pilon +-raxml-ng:$CONDA/bin/raxml-ng +-samtools:$CONDA/bin/samtools +-seqtk:$CONDA/bin/seqtk +-spades:$CONDA/bin/spades.py +-trimal:$CONDA/bin/trimal +-velvetg:$CONDA/bin/velvetg +-velveth:$CONDA/bin/velveth +-snakemake:$CONDA/bin/Snakemake ++abyss:$EBROOTABYSS/bin/ABYSS ++abyss-pe:$EBROOTABYSS/bin/abyss-pe ++bcftools:$EBROOTBCFTOOLS/bin/bcftools ++bedtools:$EBROOTBEDTOOLS/bin/bedtools ++bwa:$EBROOTBWA/bin/bwa ++gblocks:$EBROOTGBLOCKS/Gblocks ++lastz:$EBROOTLASTZ/bin/lastz ++mafft:$EBROOTMAFFT/bin/mafft ++muscle:$EBROOTMUSCLE/bin/muscle ++pilon:$EBROOTPILON/bin/pilon ++raxml-ng:$EBROOTRAXMLMINNG/bin/raxml-ng ++samtools:$EBROOTSAMTOOLS/bin/samtools ++seqtk:$EBROOTSEQTK/bin/seqtk ++spades:$EBROOTSPADES/bin/spades.py ++trimal:$EBROOTTRIMAL/bin/trimal ++velvetg:$EBROOTVELVET/bin/velvetg ++velveth:$EBROOTVELVET/bin/velveth ++snakemake:$EBROOTSNAKEMAKE/bin/snakemake + + [workflows] +-mapping:$WORKFLOWS/mapping/Snakefile +-correction:$WORKFLOWS/contig-correction/Snakefile +-phasing:$WORKFLOWS/phasing/Snakefile ++mapping:$EBROOTPHYLUCE/phyluce/workflows/mapping/Snakefile ++correction:$EBROOTPHYLUCE/phyluce/workflows/contig-correction/Snakefile ++phasing:$EBROOTPHYLUCE/phyluce/workflows/phasing/Snakefile + + #---------------- + # Advanced diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch new file mode 100644 index 000000000000..32d9d8964a89 --- /dev/null +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch @@ -0,0 +1,19 @@ +--- bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi.orig 2024-02-01 15:53:37.732931000 +0100 ++++ bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi 2024-02-01 16:16:42.885167000 +0100 +@@ -18,7 +18,6 @@ + from Bio import AlignIO + from Bio.Seq import Seq + from Bio.SeqRecord import SeqRecord +-from Bio.Alphabet import IUPAC + + from phyluce import ncbi + from phyluce.log import setup_logging +@@ -127,7 +126,7 @@ + .upper() + ) + new_record = SeqRecord( +- Seq(new_seq, IUPAC.IUPACAmbiguousDNA()), ++ Seq(new_seq), + id=new_id, + name="", + description="", From cd9ecd36450a8d75f54db3d39bd9f2860d407e7e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 11:10:46 +0100 Subject: [PATCH 0570/1193] add deps 1 --- .../a/ABySS/ABySS-2.3.7-foss-2023a.eb | 35 +++++++++++++++ .../b/btllib/btllib-1.7.0-GCC-12.3.0.eb | 43 +++++++++++++++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb create mode 100644 easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb new file mode 100644 index 000000000000..c8fcbae9bce2 --- /dev/null +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'ABySS' +version = '2.3.7' + +homepage = 'https://www.bcgsc.ca/platform/bioinfo/software/abyss' +description = """Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'cstd': 'c++17'} + +source_urls = ['http://github.com/bcgsc/abyss/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ba37780e79ec3aa359b6003e383caef13479a87f4d0022af01b86398f9ffca1f'] + +dependencies = [ + ('Autoconf', '2.71'), + ('Automake', '1.16.5'), + ('Boost', '1.82.0'), + ('sparsehash', '2.0.4'), + ('OpenMPI', '4.1.5'), + ('btllib', '1.7.0'), +] + +preconfigopts = "./autogen.sh && " +configopts = 'CXXFLAGS="$CXXFLAGS -Wno-error"' + +sanity_check_paths = { + 'files': ["bin/ABYSS", "bin/ABYSS-P"], + 'dirs': [] +} + +sanity_check_commands = ['ABYSS --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..448b9f163b58 --- /dev/null +++ b/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'CmdCp' + +name = 'btllib' +version = '1.7.0' + +homepage = 'https://github.com/bcgsc/btllib' +description = """Bioinformatics Technology Lab common code library""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +sources = [{ + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/bcgsc', + 'repo_name': 'btllib', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = ['62936bf7b136c1628736d5b69ba9b7f738417fa19802e4e5e36c2bf35e7aa9fa'] + +dependencies = [ + ('Python', '3.11.3'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('CMake', '3.26.3'), + ('SAMtools', '1.18'), +] + +cmds_map = [('.*', "./compile")] + +files_to_copy = [(['install/bin/*'], 'bin'), (['install/lib/*'], 'lib'), (['install/include/*'], 'include'),] + +sanity_check_paths = { + 'files': ['bin/randseq', 'bin/indexlr', 'bin/mi_bf_generate' ], + 'dirs': [], +} + +sanity_check_commands = ['randseq --help', 'indexlr --help'] + +moduleclass = 'lang' From 3aab2934e00eb9a907dec2e65c9fe336f16c8c8a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 11:12:11 +0100 Subject: [PATCH 0571/1193] add deps 2 --- .../l/LASTZ/LASTZ-1.04.22-foss-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-foss-2023a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-foss-2023a.eb new file mode 100644 index 000000000000..6dd3a06101b7 --- /dev/null +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-foss-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'LASTZ' +version = '1.04.22' + +homepage = 'https://github.com/lastz/lastz' +description = """ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle + sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS + sequencing technologies such as Roche 454. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['4c829603ba4aed7ddf64255b528cd88850e4557382fca29580d3576c25c5054a'] + +skipsteps = ['configure'] + +buildopts = "allowBackToBackGaps=ON" + +installopts = 'installDir=%(installdir)s/bin' + +sanity_check_paths = { + 'files': ['bin/lastz', 'bin/lastz_D'], + 'dirs': [], +} + +moduleclass = 'bio' From b57d3eacd4c1c7877c71887c622cfef48e508981 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 11:17:13 +0100 Subject: [PATCH 0572/1193] add deps 3 --- .../p/Pilon/Pilon-1.23-Java-11-wrapped.eb | 31 ++++++++++++ .../s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb | 48 +++++++++++++++++++ .../s/seqtk/seqtk-1.4-GCC-12.3.0.eb | 36 ++++++++++++++ .../t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb | 37 ++++++++++++++ .../Velvet-1.2.10-foss-2023a-mt-kmer_191.eb | 35 ++++++++++++++ 5 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb create mode 100644 easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2023a-mt-kmer_191.eb diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb new file mode 100644 index 000000000000..4275740264a8 --- /dev/null +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb @@ -0,0 +1,31 @@ +easyblock = 'JAR' + +name = 'Pilon' +version = '1.23' +versionsuffix = '-Java-%(javaver)s-wrapped' + +homepage = 'https://github.com/broadinstitute/pilon' +description = " Pilon is an automated genome assembly improvement and variant detection tool" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.jar'] +checksums = ['bde1d3c8da5537abbc80627f0b2a4165c2b68551690e5733a6adf62413b87185'] + +dependencies = [('Java', '11')] + +sanity_check_paths = { + 'files': ['pilon-%(version)s.jar'], + 'dirs': [], +} + +postinstallcmds = [ + "cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar", + "mkdir -p %(installdir)s/bin", + "echo '#!/bin/sh' > %(installdir)s/bin/%(namelower)s", + "echo 'java -jar -Xmx8G %(installdir)s/%(namelower)s-%(version)s.jar $@' >> %(installdir)s/bin/%(namelower)s", + "chmod a+rx %(installdir)s/bin/%(namelower)s" +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb new file mode 100644 index 000000000000..63a20e129998 --- /dev/null +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb @@ -0,0 +1,48 @@ +# This file is an EasyBuild reciPY as per https://easybuilders.github.io/easybuild/ +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# Modified by: +# Adam Huffman +# The Francis Crick Institute +# Updated by: +# Filip Kružík (INUITS) +# Pavel Tománek (INUIS) + +easyblock = 'CMakeMake' + +name = 'SPAdes' +version = '3.15.4' + +homepage = 'https://cab.spbu.ru/software/spades/' +description = "Genome assembler for single-cell and isolates data sets" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['3b241c528a42a8bdfdf23e5bf8f0084834790590d08491decea9f0f009d8589f'] + +builddependencies = [ + ('CMake', '3.26.3'), +] +dependencies = [ + ('Python', '3.11.3'), + ('zlib', '1.2.13'), + ('bzip2', '1.0.8'), + ('libreadline', '8.2'), +] + +start_dir = 'src' + +configopts = " -DBoost_NO_BOOST_CMAKE=ON" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['spades-bwa', 'spades-core', 'spades-gbuilder', 'spades-hammer', + 'spades-ionhammer', 'spades-kmercount', 'spades.py']], + 'dirs': [], +} + +sanity_check_commands = [('%(namelower)s.py', '--test')] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.3.0.eb b/easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.3.0.eb new file mode 100644 index 000000000000..d19790ad481a --- /dev/null +++ b/easybuild/easyconfigs/s/seqtk/seqtk-1.4-GCC-12.3.0.eb @@ -0,0 +1,36 @@ +## +# created by Thomas Eylenbosch +# updated by Pavel Tománek (INUITS) +## + +easyblock = 'ConfigureMake' + +name = 'seqtk' +version = '1.4' + +homepage = 'https://github.com/lh3/seqtk/' +description = """Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. + It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'lh3' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d124604ec24f29ed14ce127426ab90e0f3a2c0280c80d1a3ff8b1c09feede19c'] + +dependencies = [('zlib', '1.2.13')] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CFLAGS="$CLFAGS"' + +preinstallopts = "mkdir %(installdir)s/bin && " +installopts = 'BINDIR=%(installdir)s/bin/' + +sanity_check_paths = { + 'files': ['bin/seqtk'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f9e630d1b3bb --- /dev/null +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated by: +# R.QIAO +# DeepThought, Flinders University +# and +# Pavel Tománek (INUITS) + +easyblock = 'MakeCp' + +name = 'trimAl' +version = '1.4.1' + +homepage = 'https://github.com/scapella/trimal' +description = """EVB, FEP and LIE simulator.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +github_account = 'scapella' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cb8110ca24433f85c33797b930fa10fe833fa677825103d6e7f81dd7551b9b4e'] + +builddependencies = [ + ('binutils', '2.40'), + +] +start_dir = 'source' + +files_to_copy = [(['trimal', 'readal', 'statal'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/trimal', 'bin/readal', 'bin/statal'], + 'dirs': [] +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2023a-mt-kmer_191.eb b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2023a-mt-kmer_191.eb new file mode 100644 index 000000000000..3b712ec8ed1a --- /dev/null +++ b/easybuild/easyconfigs/v/Velvet/Velvet-1.2.10-foss-2023a-mt-kmer_191.eb @@ -0,0 +1,35 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA, 2012-2013 The Cyprus Institute +# Authors:: Cedric Laczny , Fotis Georgatos , +# Thekla Loizou , Andreas Panteli +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +name = 'Velvet' +version = '1.2.10' +versionsuffix = '-mt-kmer_191' + +homepage = 'https://github.com/dzerbino/velvet/' +description = """Sequence assembler for very short reads""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'pic': True} + +github_account = 'dzerbino' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4615e52dc2e8a05f1009daf2c0978c218860be364afa044f73677cd298f10c7b'] + +dependencies = [('zlib', '1.2.13')] + +buildopts = "OPENMP=1 MAXKMERLENGTH=%s LONGSEQUENCES=1" % versionsuffix.split('_')[1] + +postinstallcmds = ["cd contrib/MetaVelvet-1.* && make && cd ../../ && cp -a contrib %(installdir)s/"] + +moduleclass = 'bio' From d44229e1b5d7f8fb721a754d118b4bb39af63ba0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 23 Jan 2024 15:57:31 +0100 Subject: [PATCH 0573/1193] adding easyconfigs: geocube-0.4.3-foss-2023a.eb, rasterio-1.3.9-foss-2023a.eb, rioxarray-0.15.0-foss-2023a.eb --- .../g/geocube/geocube-0.4.3-foss-2023a.eb | 42 ++++++++++++++ .../r/rasterio/rasterio-1.3.9-foss-2023a.eb | 55 +++++++++++++++++++ .../rioxarray/rioxarray-0.15.0-foss-2023a.eb | 30 ++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/r/rasterio/rasterio-1.3.9-foss-2023a.eb create mode 100644 easybuild/easyconfigs/r/rioxarray/rioxarray-0.15.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb b/easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb new file mode 100644 index 000000000000..d31bb78f395d --- /dev/null +++ b/easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'geocube' +version = '0.4.3' + +homepage = 'https://corteva.github.io/geocube' +description = "Tool to convert geopandas vector data into rasterized xarray data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('geopandas', '0.14.2'), + ('rasterio', '1.3.9'), + ('rioxarray', '0.15.0'), +] + +use_pip = True + +exts_list = [ + ('cachetools', '5.3.1', { + 'checksums': ['dce83f2d9b4e1f732a8cd44af8e8fab2dbe46201467fc98b3ef8f269092bf62b'], + }), + ('odc-geo', '0.4.1', { + 'modulename': 'odc.geo', + 'checksums': ['0b04d0835e783685f128453e4b4169d86d322632887bfee9c7dbde364a3c324d'], + }), + (name, version, { + 'checksums': ['d0deebbcd2cd169d466ef8f9e6419c8ee23914d10e00b8f7bd73f9bed468a0fb'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.3.9-foss-2023a.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.9-foss-2023a.eb new file mode 100644 index 000000000000..443760ece32c --- /dev/null +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.9-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'rasterio' +version = '1.3.9' + +homepage = 'https://github.com/mapbox/rasterio' +description = "Rasterio reads and writes geospatial raster data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('GDAL', '3.7.1'), + ('matplotlib', '3.7.2'), # plot extra + ('boto3', '1.28.70'), # s3 extra +] + +use_pip = True + +exts_list = [ + ('affine', '2.4.0', { + 'checksums': ['a24d818d6a836c131976d22f8c27b8d3ca32d0af64c1d8d29deb7bafa4da1eea'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + (name, version, { + 'use_pip_extras': 'plot,s3', + 'checksums': ['fc6d0d290492fa1a5068711cfebb21cc936968891b7ed9da0690c8a7388885c5'], + }), +] + +fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "jp.py --help", + "rio --help", +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rioxarray/rioxarray-0.15.0-foss-2023a.eb b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.15.0-foss-2023a.eb new file mode 100644 index 000000000000..602dfef53870 --- /dev/null +++ b/easybuild/easyconfigs/r/rioxarray/rioxarray-0.15.0-foss-2023a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'rioxarray' +version = '0.15.0' + +homepage = 'https://corteva.github.io/rioxarray' +description = "Geospatial xarray extension powered by rasterio" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('rasterio', '1.3.9'), + ('pyproj', '3.6.0'), + ('xarray', '2023.9.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'use_pip_extras': 'interp', + 'checksums': ['d2a8429a5b6405913c7b6f515ef2992b05139c96eb39a2dc1c9f475ce0848c9c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From ffc504733971c25319e02ca17c629e5e45ffc01b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 11:36:13 +0100 Subject: [PATCH 0574/1193] fix format --- easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb | 4 ++-- easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb index 448b9f163b58..5b6f08028d8f 100644 --- a/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb @@ -31,10 +31,10 @@ dependencies = [ cmds_map = [('.*', "./compile")] -files_to_copy = [(['install/bin/*'], 'bin'), (['install/lib/*'], 'lib'), (['install/include/*'], 'include'),] +files_to_copy = [(['install/bin/*'], 'bin'), (['install/lib/*'], 'lib'), (['install/include/*'], 'include')] sanity_check_paths = { - 'files': ['bin/randseq', 'bin/indexlr', 'bin/mi_bf_generate' ], + 'files': ['bin/randseq', 'bin/indexlr', 'bin/mi_bf_generate'], 'dirs': [], } diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index cc34f7ad8477..3c8a51917c58 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -26,7 +26,7 @@ dependencies = [ ('BCFtools', '1.18'), ('BEDTools', '2.31.0'), ('BWA', '0.7.17'), - ('Gblocks', '0.91b','',SYSTEM), + ('Gblocks', '0.91b', '', SYSTEM), ('LASTZ', '1.04.22'), ('MAFFT', '7.520', '-with-extensions'), ('MUSCLE', '5.1.0'), From b367f72f9fcabcfce6a673f7349072de61415d84 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 12:07:16 +0100 Subject: [PATCH 0575/1193] fix snakemake version --- easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index 3c8a51917c58..1cd9d97138e1 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -19,7 +19,7 @@ dependencies = [ ('Python', '3.11.3'), ('Biopython', '1.83'), ('Python-bundle-PyPI', '2023.06'), - ('snakemake', '8.2.1'), + ('snakemake', '8.4.2'), ('DendroPy', '4.6.1'), ('bx-python', '0.10.0'), ('ABySS', '2.3.7'), From e6f34a65222a726e718b37399a88b77ed93ebd9f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 12:30:20 +0100 Subject: [PATCH 0576/1193] add patches descriptions --- .../easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch | 1 + .../p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch | 2 ++ 2 files changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch index 47396dba7d82..3bfd7955fea8 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch @@ -1,3 +1,4 @@ +# fix path of binaries in config file --- config/phyluce.conf.orig 2024-02-01 11:38:15.279943701 +0100 +++ config/phyluce.conf 2024-02-01 14:52:31.565662528 +0100 @@ -1,27 +1,27 @@ diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch index 32d9d8964a89..82e9c87c44fe 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch @@ -1,3 +1,5 @@ +# removal of the Bio.Alphabet - it is not part of Biopython anymore (since v1.78) +# https://biopython.org/wiki/Alphabet --- bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi.orig 2024-02-01 15:53:37.732931000 +0100 +++ bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi 2024-02-01 16:16:42.885167000 +0100 @@ -18,7 +18,6 @@ From 16b20441662b20d6e9294ca1ae6575dc780dc863 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 2 Feb 2024 11:53:44 +0000 Subject: [PATCH 0577/1193] exclude pipeline/sync tests and increase max_failed_tests to 30 --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 97f308a3d555..29559cf73d1a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -176,6 +176,9 @@ excluded_tests = { # intermittent failures on various systems # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 'distributed/rpc/test_tensorpipe_agent', + # failures on OmniPath systems, which don't support some optional InfiniBand features + # See https://github.com/pytorch/tensorpipe/issues/413 + 'distributed/pipeline/sync', ] } @@ -184,7 +187,7 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # Especially test_quantization has a few corner cases that are triggered by the random input values, # those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 # So allow a low number of tests to fail as the tests "usually" succeed -max_failed_tests = 2 +max_failed_tests = 30 tests = ['PyTorch-check-cpp-extension.py'] From 71f8671d93cee7485422b68f41e8de5c419a02d9 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 13:01:22 +0100 Subject: [PATCH 0578/1193] fix patches cheksums --- easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index 1cd9d97138e1..dad12086b5bb 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -52,9 +52,9 @@ exts_list = [ 'checksums': [ {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, {'phyluce-1.7.3_fix-config-paths.patch': - '2abfec1856ba2900bb6788838cebc296d66cc7fe11c7c97076133bbca176ae1e'}, + '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a'}, {'phyluce-1.7.3_removal-Bio-Alphabet.patch': - 'd92fa984f25f3e1bd7ea735b6e50beefc6b5c5e645dddd93fde551306767926e'}, + 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171'}, ], }), ] From e790d05832e6f342e0ef1d496aad30b6f2a59b0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 2 Feb 2024 13:58:26 +0100 Subject: [PATCH 0579/1193] fix indentation --- .../easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb index 9485900e4dea..4d46849355e6 100644 --- a/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/pmt/pmt-1.2.0-GCCcore-12.3.0-CUDA-12.1.1.eb @@ -26,7 +26,7 @@ dependencies = [ configopts = '-DBUILD_NVML_PMT=1' sanity_check_paths = { -'files': ["bin/Rapl-test", "bin/NVML-test"], + 'files': ["bin/Rapl-test", "bin/NVML-test"], 'dirs': ["lib", "include"], } From 1dfbf8ea0d98ce44c2d59b72c54a61719cf8a4a8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 14:20:48 +0100 Subject: [PATCH 0580/1193] changed to PythonPavkage easyblock --- .../p/phyluce/phyluce-1.7.3-foss-2023a.eb | 33 ++++++++----------- 1 file changed, 13 insertions(+), 20 deletions(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index dad12086b5bb..2ad1884d43d3 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonBundle' +easyblock = 'PythonPackage' name = 'phyluce' version = '1.7.3' @@ -15,6 +15,18 @@ phyluce is a software package for working with data generated from sequence capt toolchain = {'name': 'foss', 'version': '2023a'} +source_urls = ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_fix-config-paths.patch', + '%(name)s-%(version)s_removal-Bio-Alphabet.patch', +] +checksums = [ + {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, + {'phyluce-1.7.3_fix-config-paths.patch': '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a'}, + {'phyluce-1.7.3_removal-Bio-Alphabet.patch': 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171'}, +] + dependencies = [ ('Python', '3.11.3'), ('Biopython', '1.83'), @@ -40,25 +52,6 @@ dependencies = [ ] use_pip = True - -exts_list = [ - (name, version, { - 'patches': [ - '%(name)s-%(version)s_fix-config-paths.patch', - '%(name)s-%(version)s_removal-Bio-Alphabet.patch', - ], - 'source_urls': ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'], - 'sources': 'v%(version)s.tar.gz', - 'checksums': [ - {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, - {'phyluce-1.7.3_fix-config-paths.patch': - '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a'}, - {'phyluce-1.7.3_removal-Bio-Alphabet.patch': - 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171'}, - ], - }), -] - sanity_pip_check = True sanity_check_paths = { From bf06a6c074877ac3cf393a05db0823b7205a6d46 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Fri, 2 Feb 2024 13:32:32 +0000 Subject: [PATCH 0581/1193] exactly specify excluded distributed/pipeline/sync tests --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 29559cf73d1a..665750b5fb6f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -178,7 +178,12 @@ excluded_tests = { 'distributed/rpc/test_tensorpipe_agent', # failures on OmniPath systems, which don't support some optional InfiniBand features # See https://github.com/pytorch/tensorpipe/issues/413 - 'distributed/pipeline/sync', + 'distributed/pipeline/sync/skip/test_gpipe', + 'distributed/pipeline/sync/skip/test_leak', + 'distributed/pipeline/sync/test_bugs', + 'distributed/pipeline/sync/test_inplace', + 'distributed/pipeline/sync/test_pipe', + 'distributed/pipeline/sync/test_transparency', ] } From 018bcd73e1fdb04ef8dd9c5312ba5c29e86d6dd2 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 14:50:38 +0100 Subject: [PATCH 0582/1193] fix indents --- easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index 2ad1884d43d3..1f8f8f1877e4 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -18,8 +18,8 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] patches = [ - '%(name)s-%(version)s_fix-config-paths.patch', - '%(name)s-%(version)s_removal-Bio-Alphabet.patch', + '%(name)s-%(version)s_fix-config-paths.patch', + '%(name)s-%(version)s_removal-Bio-Alphabet.patch', ] checksums = [ {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, From b0c3a8692d53a8910ead83373d24868716de87b5 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 2 Feb 2024 13:54:29 +0000 Subject: [PATCH 0583/1193] sympy version changed to 1.10.1 --- easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb index 699cfdf39dc4..627e71bea0df 100644 --- a/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb @@ -24,7 +24,7 @@ dependencies = [ ('matplotlib', '3.5.2'), ('Pillow', '9.1.1'), ('tqdm', '4.64.0'), - ('sympy', '1.11.1'), + ('sympy', '1.10.1'), ('poetry', '1.2.2'), ] From 56c0a8de7a072e2bb3a3a46f0ac5bdc15466661a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 14:55:09 +0100 Subject: [PATCH 0584/1193] adding easyconfigs: OrfM-0.7.1-GCCcore-12.3.0.eb --- .../o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..26f32136b066 --- /dev/null +++ b/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OrfM' +version = '0.7.1' + +homepage = 'https://github.com/wwood/OrfM' +description = "A simple and not slow open reading frame (ORF) caller." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/wwood/OrfM/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['19f39c72bcc48127b757613c5eef4abae95ee6c82dccf96b041db527b27f319a'] + +dependencies = [('zlib', '1.2.13')] + +sanity_check_paths = { + 'files': ['bin/orfm'], + 'dirs': [], +} + +sanity_check_commands = ["orfm -h"] + +moduleclass = 'bio' From 5910ef75d725640f6095fbf66bd0083aadb4acd2 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 2 Feb 2024 13:57:12 +0000 Subject: [PATCH 0585/1193] sanity check command removed as requested --- easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb index 627e71bea0df..d0d113b80ef5 100644 --- a/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb +++ b/easybuild/easyconfigs/y/yt/yt-4.3.0-foss-2022a.eb @@ -74,8 +74,4 @@ exts_list = [ }), ] -sanity_check_commands = [ - "python -c 'import yt'", -] - moduleclass = 'vis' From d28994dcd035bf3d5330d0d52955dd367c3d3ba2 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 15:17:46 +0100 Subject: [PATCH 0586/1193] GCC toolchain --- .../o/OrfM/OrfM-0.7.1-GCC-12.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..260970f668b0 --- /dev/null +++ b/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCC-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'OrfM' +version = '0.7.1' + +homepage = 'https://github.com/wwood/OrfM' +description = "A simple and not slow open reading frame (ORF) caller." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/wwood/OrfM/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['19f39c72bcc48127b757613c5eef4abae95ee6c82dccf96b041db527b27f319a'] + +dependencies = [('zlib', '1.2.13')] + +sanity_check_paths = { + 'files': ['bin/orfm'], + 'dirs': [], +} + +sanity_check_commands = ["orfm -h"] + +moduleclass = 'bio' From 34b83016f6e3dbf4b1c07db41f2caaca8c82e987 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 15:38:55 +0100 Subject: [PATCH 0587/1193] adding easyconfigs: mfqe-0.5.0-GCCcore-12.3.0.eb --- .../m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb | 233 ++++++++++++++++++ 1 file changed, 233 insertions(+) create mode 100644 easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4265a486aa36 --- /dev/null +++ b/easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,233 @@ +easyblock = 'Cargo' + +name = 'mfqe' +version = '0.5.0' + +homepage = 'https://github.com/wwood/mfqe' +description = 'extract one or more sets of reads from a FASTQ (or FASTA) file by specifying their read names.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/wwood/mfqe/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + {'v0.5.0.tar.gz': 'dbbafb84e2b40f319735fd9c61b6c60401e311d2dd23fad6e5669f66e0610abf'}, + {'adler32-1.0.4.tar.gz': '5d2e7343e7fc9de883d1b0341e0b13970f764c14101234857d2ddafa1cb1cac2'}, + {'aho-corasick-0.7.6.tar.gz': '58fb5e95d83b38284460a5fda7d6470aa0b8844d283a0b614b8535e880800d2d'}, + {'ansi_term-0.11.0.tar.gz': 'ee49baf6cb617b853aa8d93bf420db2383fab46d314482ca2803b40d5fde979b'}, + {'approx-0.1.1.tar.gz': '08abcc3b4e9339e33a3d0a5ed15d84a687350c05689d825e0f6655eef9e76a94'}, + {'arrayvec-0.4.12.tar.gz': 'cd9fd44efafa8690358b7408d253adf110036b88f55672a933f01d616ad9b1b9'}, + 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'8093091eeb260906a183e6ae1abdba2ef5ef2257a21801128899c3fc699229c6'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.2.tar.gz': '7168bab6e1daee33b4557efd0e95d5ca70a03706d39fa5f3fe7a236f584b03c9'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, + {'wincolor-1.0.2.tar.gz': '96f5016b18804d24db43cebf3c77269e7569b8954a8464501c216cc5e070eaa9'}, + {'winconsole-0.10.0.tar.gz': '3ef84b96d10db72dd980056666d7f1e7663ce93d82fa33b63e71c966f4cf5032'}, +] + +builddependencies = [ + ('Rust', '1.75.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +crates = [ + ('adler32', '1.0.4'), + ('aho-corasick', '0.7.6'), + ('ansi_term', '0.11.0'), + ('approx', '0.1.1'), + ('arrayvec', '0.4.12'), + ('assert_cli', '0.6.3'), + ('atty', '0.2.13'), + ('autocfg', '0.1.7'), + ('backtrace', '0.3.40'), + ('backtrace-sys', '0.1.32'), + ('bitflags', '1.2.1'), + ('buf_redux', '0.7.1'), + ('c2-chacha', '0.2.3'), + ('cc', '1.0.46'), + ('cfg-if', '0.1.10'), + ('cgmath', '0.16.1'), + ('clap', '2.33.0'), + ('cloudabi', '0.0.3'), + ('colored', '1.8.0'), + ('crc32fast', '1.2.0'), + ('crossbeam', '0.4.1'), + ('crossbeam-channel', '0.2.6'), + ('crossbeam-deque', '0.5.2'), + ('crossbeam-epoch', '0.5.2'), + ('crossbeam-epoch', '0.6.1'), + ('crossbeam-utils', '0.5.0'), + ('crossbeam-utils', '0.6.6'), + ('difference', '2.0.0'), + ('env_logger', '0.7.1'), + ('environment', '0.1.1'), + ('failure', '0.1.6'), + ('failure_derive', '0.1.6'), + ('flate2', '1.0.12'), + ('fuchsia-cprng', '0.1.1'), + ('getrandom', '0.1.13'), + ('humantime', '1.3.0'), + ('itoa', '0.4.4'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.65'), + ('lock_api', '0.1.5'), + ('log', '0.4.8'), + ('mach', '0.2.3'), + ('memchr', '2.2.1'), + ('memoffset', '0.2.1'), + ('miniz_oxide', '0.3.5'), + ('nodrop', '0.1.14'), + ('num-traits', '0.1.43'), + ('num-traits', '0.2.8'), + ('owning_ref', '0.4.0'), + ('parking_lot', '0.6.4'), + ('parking_lot_core', '0.3.1'), + ('ppv-lite86', '0.2.6'), + ('proc-macro2', '1.0.6'), + ('quick-error', '1.2.2'), + ('quote', '1.0.2'), + ('rand', '0.4.6'), + ('rand', '0.5.6'), + ('rand', '0.7.2'), + ('rand_chacha', '0.2.1'), + ('rand_core', '0.3.1'), + ('rand_core', '0.4.2'), + ('rand_core', '0.5.1'), + ('rand_hc', '0.2.0'), + ('rdrand', '0.4.0'), + ('redox_syscall', '0.1.56'), + ('regex', '1.3.1'), + ('regex-syntax', '0.6.12'), + ('remove_dir_all', '0.5.2'), + ('rgb', '0.8.14'), + ('rustc-demangle', '0.1.16'), + ('rustc_version', '0.2.3'), + ('ryu', '1.0.2'), + ('safemem', '0.2.0'), + ('scoped_threadpool', '0.1.9'), + ('scopeguard', '0.3.3'), + ('semver', '0.9.0'), + ('semver-parser', '0.7.0'), + ('seq_io', '0.3.0'), + ('serde', '1.0.102'), + ('serde_derive', '1.0.102'), + ('serde_json', '1.0.41'), + ('slice-deque', '0.1.16'), + ('smallvec', '0.6.12'), + ('stable_deref_trait', '1.1.1'), + ('strsim', '0.8.0'), + ('syn', '1.0.7'), + ('synstructure', '0.12.1'), + ('tempfile', '3.1.0'), + ('termcolor', '1.0.5'), + ('textwrap', '0.11.0'), + ('thread_local', '0.3.6'), + ('unicode-width', '0.1.6'), + ('unicode-xid', '0.2.0'), + ('vec_map', '0.8.1'), + ('wasi', '0.7.0'), + ('winapi', '0.3.8'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-util', '0.1.2'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), + ('wincolor', '1.0.2'), + ('winconsole', '0.10.0'), +] + +moduleclass = 'bio' From 8976e5414fc0f86901ef90a357ec754364c4c91f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 15:46:17 +0100 Subject: [PATCH 0588/1193] adding easyconfigs: KronaTools-2.8.1-GCCcore-12.3.0.eb --- .../KronaTools-2.8.1-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5de20f3fd779 --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +# Contribution from the Crick HPC team +# uploaded by J. Sassmannshausen +# this is a bug fix to make sure the symlinks in bin are not getting destroyed +# by Easybuild when it is tidying up +# This build also links updateTaxonomy.sh and updateAccessions.sh in the bin folder +# so users can install their own Taxonomy database + +easyblock = 'Tarball' + +name = 'KronaTools' +version = '2.8.1' + +homepage = 'https://github.com/marbl/Krona/wiki/KronaTools' +description = """Krona Tools is a set of scripts to create Krona charts from +several Bioinformatics tools as well as from text and XML files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['f3ab44bf172e1f846e8977c7443d2e0c9676b421b26c50e91fa996d70a6bfd10'] + +dependencies = [('Perl', '5.36.1')] + +postinstallcmds = [ + "cd %(installdir)s && ./install.pl --prefix=%(installdir)s;", + "cd %(installdir)s/bin && ln -s ../updateAccessions.sh . && ln -s ../updateTaxonomy.sh .", +] + +sanity_check_paths = { + 'files': ['bin/ktClassifyBLAST', 'bin/ktImportBLAST', 'bin/ktImportTaxonomy', + 'bin/updateAccessions.sh', 'bin/updateTaxonomy.sh'], + 'dirs': ['data', 'img', 'scripts'], +} + +sanity_check_commands = [ + "updateAccessions.sh --help", + "ktImportText", +] + +moduleclass = 'bio' From 6d8dce8e4f05571e67b34d384381c02fbb7f3f96 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 2 Feb 2024 16:36:40 +0100 Subject: [PATCH 0589/1193] adding easyconfigs: SRA-Toolkit-3.0.10-gompi-2023a.eb, ncbi-vdb-3.0.10-gompi-2023a.eb, file-5.43-GCCcore-12.3.0.eb --- .../f/file/file-5.43-GCCcore-12.3.0.eb | 28 ++++++++ .../n/ncbi-vdb/ncbi-vdb-3.0.10-gompi-2023a.eb | 38 +++++++++++ .../SRA-Toolkit-3.0.10-gompi-2023a.eb | 68 +++++++++++++++++++ 3 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.43-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.10-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9c5e6cc35917 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'file' +version = '5.43' + +homepage = 'https://www.darwinsys.com/file/' +description = """The file command is 'a file type guesser', that is, a command-line tool + that tells you in words what kind of data a file contains.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/file', 'include/magic.h', 'lib/libmagic.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.10-gompi-2023a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.10-gompi-2023a.eb new file mode 100644 index 000000000000..f070a7bab5f3 --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.10-gompi-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.0.10' + +homepage = 'https://github.com/ncbi/ncbi-vdb' +description = """The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for + using data in the INSDC Sequence Read Archives.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['2e088a8542e6c3bc1aad01a5d2fca2ef5b745c36a3aafd3b0b42cb53b42b345d'] + +builddependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('HDF5', '1.14.0'), + ('libxml2', '2.11.4'), + ('bzip2', '1.0.8'), +] + +configopts = "-DHDF5_INCDIR=$EBROOTHDF5/include -DHDF5_LIBDIR=$EBROOTHDF5/lib " +configopts += "-DXML2_INCDIR=$EBROOTLIBXML2/include -DXML2_LIBDIR=$EBROOTLIBXML2/lib " + +sanity_check_paths = { + 'files': ['include/ncbi/ncbi.h', 'include/ncbi/vdb-blast.h'] + + [('lib/libncbi-%s.%s' % (k, e)) for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb new file mode 100644 index 000000000000..450b5339baa8 --- /dev/null +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb @@ -0,0 +1,68 @@ +# updated: Denis Kristak (INUITS) +# updated: Sebastien Moretti (SIB - Vital-IT) +# updated: Pavel Tománek (INUITS) +easyblock = 'CMakeMake' + +name = 'SRA-Toolkit' +version = '3.0.10' + +homepage = 'https://github.com/ncbi/sra-tools' +description = """The SRA Toolkit, and the source-code SRA System Development + Kit (SDK), will allow you to programmatically access data housed within SRA + and convert it from the SRA format""" +github_account = 'ncbi' + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'extra_cflags': '-DH5_USE_110_API'} + +source_urls = ['https://github.com/ncbi/sra-tools/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['93cfa802938506866b9d565a18a31ac84fd26f2929636b23f1f8dd9f39cf977d'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('Perl', '5.36.1'), + ('Python', '3.11.3'), +] + +dependencies = [ + ('Java', '11', '', SYSTEM), + ('OpenSSL', '1.1', '', SYSTEM), + ('ncbi-vdb', version), + ('bzip2', '1.0.8'), + ('file', '5.43'), + ('HDF5', '1.14.0'), + ('libxml2', '2.11.4'), + ('zlib', '1.2.13'), +] + +configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" ' +configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' + +_sra_bin = [ + 'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump', + 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'pacbio-load', + 'prefetch', 'rcexplain', 'sam-dump', 'sff-dump', 'sff-load', 'srapath', 'sra-pileup', 'sra-sort', 'sra-stat', + 'sratools', 'srf-load', 'test-sra', 'vdb-config', 'vdb-copy', 'vdb-decrypt', 'vdb-dump', 'vdb-encrypt', 'vdb-lock', + 'vdb-unlock', 'vdb-validate', +] + +_ngs_libs = ['libncbi-ngs.a', 'libncbi-ngs-c++.a', 'libncbi-ngs.%s' % SHLIB_EXT, + 'libngs-c++.a', 'libngs-c++.%s' % SHLIB_EXT] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _sra_bin] + ['lib/%s' % l for l in _ngs_libs], + 'dirs': ['jar', 'include/ncbi-vdb', 'include/ngs'] +} + +sanity_check_commands = [ + "abi-dump --help", + "kar --help", + "sra-sort --help", +] + +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} + +moduleclass = 'bio' From 0e82edf87d4f6fcec7723a66b4e5c9b1517bfb30 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 3 Feb 2024 12:41:14 +0100 Subject: [PATCH 0590/1193] adding easyconfigs: NAMD-2.14-foss-2023a-mpi.eb --- .../n/NAMD/NAMD-2.14-foss-2023a-mpi.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2023a-mpi.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2023a-mpi.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2023a-mpi.eb new file mode 100644 index 000000000000..5fd06c84ff9c --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2023a-mpi.eb @@ -0,0 +1,37 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-mpi' + +homepage = 'https://www.ks.uiuc.edu/Research/namd/' +description = """NAMD is a parallel molecular dynamics code designed for high-performance simulation of + large biomolecular systems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = ['NAMD_%(version)s_Source.tar.gz'] +patches = [ + 'NAMD-2.14_fix-constant-pH.patch', + 'NAMD-2.14_fix-LJCorrection.patch', +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + '864c6941b7cf52b78d26f2311236ec717f29399aa71436904930706d5d8b61de', # NAMD-2.14_fix-constant-pH.patch + '7b54cc62c893f00f491d8ff75685c8877d78a9471fa3db6fc70974edba09e70a', # NAMD-2.14_fix-LJCorrection.patch +] + +dependencies = [ + ('Tcl', '8.6.13'), +] + +# /bin/csh is required by 'config' script +builddependencies = [ + ('tcsh', '6.24.10'), +] + +# Hard to make charm build the mpi version with gcc on POWER, so we don't currently try +charm_arch = 'mpi-linux-x86_64' +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From 6685ed1b1c8efe5d07bf990976dad594519b9486 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Sat, 3 Feb 2024 11:59:32 +0000 Subject: [PATCH 0591/1193] strip trailing whitespace --- .../easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb index 450b5339baa8..90c6bda7d375 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb @@ -30,7 +30,7 @@ builddependencies = [ dependencies = [ ('Java', '11', '', SYSTEM), ('OpenSSL', '1.1', '', SYSTEM), - ('ncbi-vdb', version), + ('ncbi-vdb', version), ('bzip2', '1.0.8'), ('file', '5.43'), ('HDF5', '1.14.0'), From 05f96b6913d9dac0ecbc10931de1b634c2f4af70 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 3 Feb 2024 21:53:28 +0100 Subject: [PATCH 0592/1193] adding easyconfigs: NVHPC-24.1-CUDA-12.3.0.eb --- .../n/NVHPC/NVHPC-24.1-CUDA-12.3.0.eb | 75 +++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-24.1-CUDA-12.3.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-24.1-CUDA-12.3.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.1-CUDA-12.3.0.eb new file mode 100644 index 000000000000..2bab93e8ab3c --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.1-CUDA-12.3.0.eb @@ -0,0 +1,75 @@ +name = 'NVHPC' +version = '24.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2024_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + '8c2ce561d5901a03eadce7f07dce5fbc55e8e88c87b74cf60e01e2eca231c41c', + local_tarball_tmpl % 'ppc64le': + 'e7330eb35e23dcd9b0b3bedc67c0d5443c4fd76b59caa894a76ecb0d17f71f43', + local_tarball_tmpl % 'x86_64': + '27992e5fd56af8738501830daddc5e9510ebd553326fea8730236fee4f0f1dd8', + } +] + +local_gccver = '13.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.40', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.16', '', ('GCCcore', local_gccver)), + ('CUDA', '12.3.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 2923bc1b1c72ea82b6ff38cd34d8dd19c1e1e0be Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Feb 2024 13:55:54 +0000 Subject: [PATCH 0593/1193] adding easyconfigs: Go-1.21.6.eb --- easybuild/easyconfigs/g/Go/Go-1.21.6.eb | 29 +++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.21.6.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.21.6.eb b/easybuild/easyconfigs/g/Go/Go-1.21.6.eb new file mode 100644 index 000000000000..7db3587245f9 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.21.6.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.21.6' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': '3f934f40ac360b9c01f616a9aa1796d227d8b0328bf64cb045c7b8c4ee9caea4', + 'go%(version)s.linux-arm64.tar.gz': 'e2e8aa88e1b5170a0d495d7d9c766af2b2b6c6925a8f8956d834ad6b4cacbd9a', +}] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' From eaea4038fdccc2c5047c6c6d4feb6f7a0f550dea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 4 Feb 2024 16:42:30 +0000 Subject: [PATCH 0594/1193] adding easyconfigs: git-lfs-3.4.1.eb --- .../easyconfigs/g/git-lfs/git-lfs-3.4.1.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb new file mode 100644 index 000000000000..78d81235b601 --- /dev/null +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'git-lfs' +version = '3.4.1' + +homepage = 'https://git-lfs.github.com' +description = """Git Large File Storage (LFS) replaces large files such as audio + samples, videos, datasets, and graphics with text pointers inside Git, while + storing the file contents on a remote server like GitHub.com""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/git-lfs/git-lfs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa93f65cc5c15b96037a72cf243bc2cc04c94ea5cccc346664425d6d4bac66c2'] + +builddependencies = [('Go', '1.21.6')] + +files_to_copy = [(['bin/%(name)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/git-lfs'], + 'dirs': [], +} + +sanity_check_commands = ["git-lfs --version"] + +moduleclass = 'tools' From c309998cf89a21f8cd4b73506cdf3e0c73775d08 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 5 Feb 2024 09:54:46 +0100 Subject: [PATCH 0595/1193] add download_dep_fail --- easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index 1f8f8f1877e4..aa14b674a10a 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -53,6 +53,7 @@ dependencies = [ use_pip = True sanity_pip_check = True +download_dep_fail = True sanity_check_paths = { 'files': [], From 7028ffe964b2cb977c683b73c3c9f3cde1e6dc92 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Mon, 5 Feb 2024 12:34:34 +0000 Subject: [PATCH 0596/1193] {data}[gompi/2023b] CDO v2.2.2, UDUNITS v2.2.28 , PROJ v9.3.1, ecCodes v2.31.0 , libaec v1.0.6, nlohmann_json v3.11.3, pkgconfig v1.5.5 --- .../c/CDO/CDO-2.2.2-gompi-2023b.eb | 53 +++++++++++++++++++ .../e/ecCodes/ecCodes-2.31.0-gompi-2023b.eb | 46 ++++++++++++++++ .../l/libaec/libaec-1.0.6-GCCcore-13.2.0.eb | 34 ++++++++++++ .../nlohmann_json-3.11.3-GCCcore-13.2.0.eb | 25 +++++++++ .../p/PROJ/PROJ-9.3.1-GCCcore-13.2.0.eb | 49 +++++++++++++++++ .../pkgconfig-1.5.5-GCCcore-13.2.0-python.eb | 31 +++++++++++ .../UDUNITS/UDUNITS-2.2.28-GCCcore-13.2.0.eb | 44 +++++++++++++++ 7 files changed, 282 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PROJ/PROJ-9.3.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.2.0-python.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb new file mode 100644 index 000000000000..bb45409b1469 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb @@ -0,0 +1,53 @@ +# updated to version 2.0.6, based on the previous 2.0.5 version +# J. Sassmannshausen (Imperial College London, UK) +# Alex Domingo (Vrije Universiteit Brussel, BE) +# Maxim Masterov (SURF, NL) + +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.2.2' + +homepage = 'https://code.zmaw.de/projects/cdo' +description = """CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'cstd': 'c++17', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/28882/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['419c77315244019af41a296c05066f474cccbf94debfaae9e2106da51bc7c937'] + +builddependencies = [ + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('cURL', '8.3.0'), + ('ecCodes', '2.31.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.14.3'), + ('libxml2', '2.11.5'), + ('netCDF', '4.9.2'), + ('PROJ', '9.3.1'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.39'), +] + +# Build libcdi +configopts = "--enable-cdi-lib " + +# Use dependencies from EasyBuild +configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw3 --with-hdf5=$EBROOTHDF5 " +configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " +configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'Climate Data Operators version %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023b.eb new file mode 100644 index 000000000000..298c5b7134a7 --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.31.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/ecmwf/eccodes/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}] +checksums = ['cb4cd3bab9cebd85a00397e12ce8e4a579b2f0a25aaf6df763436cf37db063e1'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('ecBuild', '3.8.0', '', SYSTEM), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), + ('libaec', '1.0.6'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF -DENABLE_JPG=ON " +configopts += "-DENABLE_JPG_LIBJASPER=ON -DENABLE_ECCODES_THREADS=ON" + + +sanity_check_paths = { + 'files': ['bin/bufr_compare', 'bin/bufr_copy', 'bin/bufr_dump', 'bin/bufr_filter', 'bin/bufr_get', 'bin/bufr_ls', + 'bin/grib_compare', 'bin/grib_copy', 'bin/grib_dump', 'bin/grib_filter', 'bin/grib_get', 'bin/grib_ls', + 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', + 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', + 'bin/metar_ls', 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', + 'lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..c458b8ac4117 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['bin/aec', 'include/%(name)s.h', 'include/szlib.h', + 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ['aec --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..4928eeab1045 --- /dev/null +++ b/easybuild/easyconfigs/n/nlohmann_json/nlohmann_json-3.11.3-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'CMakeMake' + +name = 'nlohmann_json' +version = '3.11.3' + +homepage = 'https://github.com/nlohmann/json' +description = """JSON for Modern C++""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/nlohmann/json/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0d8ef5af7f9794e3263480193c491549b2ba6cc74bb018906202ada498a79406'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['include/nlohmann/json.hpp'], + 'dirs': ['share/cmake', 'share/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PROJ/PROJ-9.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PROJ/PROJ-9.3.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..4b2f17e16ad0 --- /dev/null +++ b/easybuild/easyconfigs/p/PROJ/PROJ-9.3.1-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'CMakeMake' + +name = 'PROJ' +version = '9.3.1' + +homepage = 'https://proj.org' +description = """Program proj is a standard Unix filter function which converts +geographic longitude and latitude coordinates into cartesian coordinates""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/proj/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b0f919cb9e1f42f803a3e616c2b63a78e4d81ecfaed80978d570d3a5e29d10bc'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('googletest', '1.14.0'), +] + +dependencies = [ + ('SQLite', '3.43.1'), + ('LibTIFF', '4.6.0'), + ('cURL', '8.3.0'), + ('XZ', '5.4.4'), + ('nlohmann_json', '3.11.3'), +] + +# build twice, once for static, once for shared libraries +configopts = ['', '-DBUILD_SHARED_LIBS=OFF'] + +sanity_check_paths = { + 'files': ['bin/cct', 'bin/cs2cs', 'bin/geod', 'bin/gie', 'bin/proj', 'bin/projinfo', + 'lib/libproj.a', 'lib/libproj.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.2.0-python.eb b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.2.0-python.eb new file mode 100644 index 000000000000..b26e6146bdc5 --- /dev/null +++ b/easybuild/easyconfigs/p/pkgconfig/pkgconfig-1.5.5-GCCcore-13.2.0-python.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pkgconfig' +version = '1.5.5' +# The -python versionsuffix is used to avoid confusion between +# pkg-config (the tool) and pkgconfig (the Python wrappers) +versionsuffix = '-python' + +homepage = 'https://github.com/matze/pkgconfig' +description = """pkgconfig is a Python module to interface with the pkg-config command line tool""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['deb4163ef11f75b520d822d9505c1f462761b4309b1bb713d08689759ea8b899'] + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('pkgconf', '2.0.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..1170be53a332 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('expat', '2.5.0')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 2707ec6ec43dbc206fbb644b8283fd917aa2b048 Mon Sep 17 00:00:00 2001 From: Ehsan Moravveji Date: Mon, 5 Feb 2024 14:07:20 +0100 Subject: [PATCH 0597/1193] easyconfig for latest Flye v2.9.3 with 2021a toolchain --- .../f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..1aa8c30f5d80 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.3' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['09580390ed0558c131ca0b836a2374d3cc7993cba2a6500024c2ee1d96666edc'] + +dependencies = [('Python', '3.9.5')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From 0e0d88695a588f4950de4a1e3eeea42e9a228b32 Mon Sep 17 00:00:00 2001 From: Ehsan Moravveji Date: Mon, 5 Feb 2024 14:50:04 +0100 Subject: [PATCH 0598/1193] using GCC instead of GCCcore --- .../{Flye-2.9.3-GCCcore-10.3.0.eb => Flye-2.9.3-GCC-10.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/f/Flye/{Flye-2.9.3-GCCcore-10.3.0.eb => Flye-2.9.3-GCC-10.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCC-10.3.0.eb similarity index 93% rename from easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCC-10.3.0.eb index 1aa8c30f5d80..906ac5fc08cf 100644 --- a/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCC-10.3.0.eb @@ -7,7 +7,7 @@ homepage = 'https://github.com/fenderglass/Flye' description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies.""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://github.com/fenderglass/Flye/archive/'] sources = ['%(version)s.tar.gz'] From 3545676c4ffeb9f7801b1e2ec32ec9b2498d9a06 Mon Sep 17 00:00:00 2001 From: Frederik Himpe Date: Mon, 5 Feb 2024 19:35:32 +0100 Subject: [PATCH 0599/1193] adding easyconfigs: cuDNN-8.9.7.29-CUDA-12.3.0.eb --- .../c/cuDNN/cuDNN-8.9.7.29-CUDA-12.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.7.29-CUDA-12.3.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.7.29-CUDA-12.3.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.7.29-CUDA-12.3.0.eb new file mode 100644 index 000000000000..448f36baf3cb --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.9.7.29-CUDA-12.3.0.eb @@ -0,0 +1,40 @@ +name = 'cuDNN' +version = '8.9.7.29' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '12' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = [{ + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '8574d291b299f9cc0134304473c9933bd098cc717e8d0876f4aba9f9eebe1b76', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'e98b7c80010785e5d5ca01ee4ce9b5b0c8c73587ea6f8648be34d3f8d1d47bd1', + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '475333625c7e42a7af3ca0b2f7506a106e30c93b1aa0081cd9c13efb6e21e3bb', +}] + +dependencies = [('CUDA', '12.3.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_infer_static.a', 'lib64/libcudnn_adv_train_static.a', + 'lib64/libcudnn_cnn_infer_static.a', 'lib64/libcudnn_cnn_train_static.a', + 'lib64/libcudnn_ops_infer_static.a', 'lib64/libcudnn_ops_train_static.a', + 'lib64/libcudnn.%s' % SHLIB_EXT + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' From c551d7c576cf710108d06e4ae7635843df7fe417 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Feb 2024 10:54:09 +0100 Subject: [PATCH 0600/1193] delete version with GCCcore --- .../o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb | 24 ------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb deleted file mode 100644 index 26f32136b066..000000000000 --- a/easybuild/easyconfigs/o/OrfM/OrfM-0.7.1-GCCcore-12.3.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'OrfM' -version = '0.7.1' - -homepage = 'https://github.com/wwood/OrfM' -description = "A simple and not slow open reading frame (ORF) caller." - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -source_urls = ['https://github.com/wwood/OrfM/releases/download/v%(version)s/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['19f39c72bcc48127b757613c5eef4abae95ee6c82dccf96b041db527b27f319a'] - -dependencies = [('zlib', '1.2.13')] - -sanity_check_paths = { - 'files': ['bin/orfm'], - 'dirs': [], -} - -sanity_check_commands = ["orfm -h"] - -moduleclass = 'bio' From 5161dca55b2eaa65218f2ea1e20303aa56515b48 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Feb 2024 10:56:33 +0100 Subject: [PATCH 0601/1193] replace toolchain to GCC --- .../{mfqe-0.5.0-GCCcore-12.3.0.eb => mfqe-0.5.0-GCC-12.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/m/mfqe/{mfqe-0.5.0-GCCcore-12.3.0.eb => mfqe-0.5.0-GCC-12.3.0.eb} (99%) diff --git a/easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCC-12.3.0.eb similarity index 99% rename from easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCC-12.3.0.eb index 4265a486aa36..c69398631fc0 100644 --- a/easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/m/mfqe/mfqe-0.5.0-GCC-12.3.0.eb @@ -6,7 +6,7 @@ version = '0.5.0' homepage = 'https://github.com/wwood/mfqe' description = 'extract one or more sets of reads from a FASTQ (or FASTA) file by specifying their read names.' -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/wwood/mfqe/archive/'] sources = ['v%(version)s.tar.gz'] From 81c9a54352358e70a38cec447c1c453958676a06 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Feb 2024 12:32:24 +0100 Subject: [PATCH 0602/1193] fix btllib checksum --- easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb index 5b6f08028d8f..960f1b09253a 100644 --- a/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/b/btllib/btllib-1.7.0-GCC-12.3.0.eb @@ -19,7 +19,7 @@ sources = [{ 'keep_git_dir': True, } }] -checksums = ['62936bf7b136c1628736d5b69ba9b7f738417fa19802e4e5e36c2bf35e7aa9fa'] +checksums = [None] dependencies = [ ('Python', '3.11.3'), From 2b6125a655bd7cf51fc3a522b98a00178d0aa61f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Feb 2024 15:50:51 +0100 Subject: [PATCH 0603/1193] get bnkit.jar from a commit --- ...2022.7.4-Java-17.eb => GRASP-suite-2023-05-09-Java-17.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/GRASP-suite/{GRASP-suite-2022.7.4-Java-17.eb => GRASP-suite-2023-05-09-Java-17.eb} (84%) diff --git a/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2023-05-09-Java-17.eb similarity index 84% rename from easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb rename to easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2023-05-09-Java-17.eb index 0e5afae691a0..8182799823d3 100644 --- a/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2022.7.4-Java-17.eb +++ b/easybuild/easyconfigs/g/GRASP-suite/GRASP-suite-2023-05-09-Java-17.eb @@ -1,7 +1,8 @@ easyblock = 'JAR' name = 'GRASP-suite' -version = '2022.7.4' +version = '2023-05-09' +local_commit = '97cceec' versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/bodenlab/GRASP-suite/' @@ -11,7 +12,7 @@ analyse ancestral sequence reconstruction.""" toolchain = SYSTEM -source_urls = ['https://bodenlab.github.io/GRASP-suite/project/graspcmd/archive/'] +source_urls = ['https://github.com/bodenlab/GRASP-suite/raw/%s/content/project/graspcmd/archive/' % local_commit] sources = [{ "download_filename": "bnkit.jar", "filename": "%(name)s-%(version)s.jar", From b3648a6b1f9b8576a6f8017836844ae5f5cf312e Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 6 Feb 2024 18:56:48 +0100 Subject: [PATCH 0604/1193] ngs added --- .../s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb index 90c6bda7d375..76f0b841a22c 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb @@ -24,10 +24,10 @@ builddependencies = [ ('flex', '2.6.4'), ('Bison', '3.8.2'), ('Perl', '5.36.1'), - ('Python', '3.11.3'), ] dependencies = [ + ('Python', '3.11.3'), ('Java', '11', '', SYSTEM), ('OpenSSL', '1.1', '', SYSTEM), ('ncbi-vdb', version), @@ -41,6 +41,10 @@ dependencies = [ configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBIMINVDB/lib" ' configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' +postinstallcmds = [ + "cp -r %(builddir)s/sra-tools-3.0.10/ngs/ngs-python/ %(installdir)s/", +] + _sra_bin = [ 'abi-dump', 'abi-load', 'align-info', 'bam-load', 'cache-mgr', 'cg-load', 'copycat', 'fasterq-dump', 'fastq-dump', 'fastq-load', 'helicos-load', 'illumina-dump', 'illumina-load', 'kar', 'kdbmeta', 'latf-load', 'pacbio-load', @@ -61,8 +65,9 @@ sanity_check_commands = [ "abi-dump --help", "kar --help", "sra-sort --help", + "python -c 'import ngs'", ] -modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar'} +modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar', 'PYTHONPATH': 'ngs-python'} moduleclass = 'bio' From 20853e5b57ece5ade6be364d3e942beaf7ff6389 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 6 Feb 2024 19:46:58 +0100 Subject: [PATCH 0605/1193] Update Gblocks-0.91b.eb Update source url --- easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb b/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb index efb17d72c5d5..aa6af8aad5d9 100644 --- a/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb +++ b/easybuild/easyconfigs/g/Gblocks/Gblocks-0.91b.eb @@ -3,12 +3,12 @@ easyblock = 'Tarball' name = 'Gblocks' version = '0.91b' -homepage = 'http://molevol.cmima.csic.es/castresana/Gblocks.html' +homepage = 'https://www.biologiaevolutiva.org/jcastresana/Gblocks.html' description = "Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis" toolchain = SYSTEM -source_urls = ['http://molevol.cmima.csic.es/castresana/Gblocks/'] +source_urls = ['https://www.biologiaevolutiva.org/jcastresana/Gblocks/'] sources = [{ 'filename': 'Gblocks_Linux64_%(version)s.tar.Z', 'extract_cmd': 'tar xfz %s' From 0f37f63ffb138a96c4de5e96888584334e4c2923 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Feb 2024 21:22:22 +0000 Subject: [PATCH 0606/1193] adding easyconfigs: buildenv-default-foss-2023b.eb, buildenv-default-intel-2023b.eb --- .../b/buildenv/buildenv-default-foss-2023b.eb | 13 +++++++++++++ .../b/buildenv/buildenv-default-intel-2023b.eb | 13 +++++++++++++ 2 files changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b.eb create mode 100644 easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023b.eb diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b.eb new file mode 100644 index 000000000000..5508687d00a4 --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-foss-2023b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'foss', 'version': '2023b'} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023b.eb b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023b.eb new file mode 100644 index 000000000000..558beb36286a --- /dev/null +++ b/easybuild/easyconfigs/b/buildenv/buildenv-default-intel-2023b.eb @@ -0,0 +1,13 @@ +easyblock = 'BuildEnv' + +name = 'buildenv' +version = 'default' + +homepage = 'None' +description = """This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that + you can use to easily transition between toolchains when building your software. To query the variables being set + please use: module show """ + +toolchain = {'name': 'intel', 'version': '2023b'} + +moduleclass = 'devel' From f55b5f12725afec1f85eaac44529614914a5c479 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Feb 2024 10:41:21 +0100 Subject: [PATCH 0607/1193] easyblock PythonBundle --- .../p/phyluce/phyluce-1.7.3-foss-2023a.eb | 30 +++++++++++-------- 1 file changed, 17 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index aa14b674a10a..06621496a09a 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'phyluce' version = '1.7.3' @@ -15,18 +15,6 @@ phyluce is a software package for working with data generated from sequence capt toolchain = {'name': 'foss', 'version': '2023a'} -source_urls = ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'] -sources = ['v%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_fix-config-paths.patch', - '%(name)s-%(version)s_removal-Bio-Alphabet.patch', -] -checksums = [ - {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, - {'phyluce-1.7.3_fix-config-paths.patch': '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a'}, - {'phyluce-1.7.3_removal-Bio-Alphabet.patch': 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171'}, -] - dependencies = [ ('Python', '3.11.3'), ('Biopython', '1.83'), @@ -51,6 +39,22 @@ dependencies = [ ('Velvet', '1.2.10', '-mt-kmer_191') ] +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'patches': [ + '%(name)s-%(version)s_fix-config-paths.patch', + '%(name)s-%(version)s_removal-Bio-Alphabet.patch', + ], + 'checksums': [ + '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11', # v1.7.3.tar.gz + '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a', # phyluce-1.7.3_fix-config-paths.patch + 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171', # phyluce-1.7.3_removal-Bio-Alphabet.patch + ], + }), +] + use_pip = True sanity_pip_check = True download_dep_fail = True From 42140df5ba1d68d009ff3f15d4f6d96fa9377ed8 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Feb 2024 12:36:57 +0100 Subject: [PATCH 0608/1193] fix too long line --- .../easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index 06621496a09a..9d7654bdf702 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -48,9 +48,12 @@ exts_list = [ '%(name)s-%(version)s_removal-Bio-Alphabet.patch', ], 'checksums': [ - '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11', # v1.7.3.tar.gz - '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a', # phyluce-1.7.3_fix-config-paths.patch - 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171', # phyluce-1.7.3_removal-Bio-Alphabet.patch + # v1.7.3.tar.gz + '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11', + # phyluce-1.7.3_fix-config-paths.patch + '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a', + # phyluce-1.7.3_removal-Bio-Alphabet.patch + 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171', ], }), ] From 4fb6728cb2647566249f1ea947466420c9f0801c Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 7 Feb 2024 14:08:57 +0100 Subject: [PATCH 0609/1193] remove download_dep_fail --- easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index 9d7654bdf702..aa2423273b02 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -60,7 +60,6 @@ exts_list = [ use_pip = True sanity_pip_check = True -download_dep_fail = True sanity_check_paths = { 'files': [], From d38ef973c0355b07c8a6cd7237c6755a26192d22 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 7 Feb 2024 14:58:55 +0100 Subject: [PATCH 0610/1193] adding easyconfigs: WhatsHap-2.2-foss-2023a.eb, pyfaidx-0.8.1.1-GCCcore-12.3.0.eb --- .../pyfaidx/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb | 42 ++++++++++++++++ .../w/WhatsHap/WhatsHap-2.2-foss-2023a.eb | 50 +++++++++++++++++++ 2 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b476b81ba380 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'pyfaidx' +version = '0.8.1.1' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.3')] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('zipp', '3.17.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0e923e726174922dce09c53c59ad483ff7bbb8e572e00c7f7c46b88556409f31'], + }), + ('importlib_metadata', '7.0.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4805911c3a4ec7c3966410053e9ec6a1fecd629117df5adee56dfc9432a1081e'], + }), + (name, version, { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['2694af8e3f35f1890a03f04c0f89ba245caf24ff9e435f2c494b132f537e70f6'], + }), +] + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.2-foss-2023a.eb b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.2-foss-2023a.eb new file mode 100644 index 000000000000..7ea2d4357588 --- /dev/null +++ b/easybuild/easyconfigs/w/WhatsHap/WhatsHap-2.2-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'WhatsHap' +version = '2.2' + +homepage = 'https://whatshap.readthedocs.io' +description = """WhatsHap is a software for phasing genomic variants using DNA +sequencing reads, also called read-based phasing or haplotype assembly. It is +especially suitable for long reads, but works also well with short reads.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.3'), + ('Pysam', '0.22.0'), + ('networkx', '3.1'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Yasm', '1.3.0'), + ('pyfaidx', '0.8.1.1'), + ('python-isal', '1.1.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('xopen', '1.7.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['c4c6c978bb5f6f2a4364438da09f4f8fde078b6df4de18e3f72fccc472d1ee33'], + }), + ('PuLP', '2.8.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['4a19814a5b0a4392d788ac2315263435293579b0583c3469943fe0c6a586f263'], + }), + ('whatshap', version, { + 'checksums': ['4cd34e9b82930c4f42e9e6b7dce2e321e4c81f934fdb980b6093ad91a06ae30a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From cc4bb982a1fd50f913298b887ee150e3de85a95d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 7 Feb 2024 16:13:43 +0100 Subject: [PATCH 0611/1193] adding easyconfigs: python-parasail-1.3.4-foss-2023a.eb, parasail-2.6.2-GCC-12.3.0.eb --- .../p/parasail/parasail-2.6.2-GCC-12.3.0.eb | 26 +++++++++++++++ .../python-parasail-1.3.4-foss-2023a.eb | 32 +++++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.3.0.eb b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.3.0.eb new file mode 100644 index 000000000000..25f71f7e3aa8 --- /dev/null +++ b/easybuild/easyconfigs/p/parasail/parasail-2.6.2-GCC-12.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'parasail' +version = '2.6.2' + +homepage = 'https://github.com/jeffdaily/parasail' +description = """parasail is a SIMD C (C99) library containing implementations + of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global + pairwise sequence alignment algorithms. """ + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'jeffdaily' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9057041db8e1cde76678f649420b85054650414e5de9ea84ee268756c7ea4b4b'] + +builddependencies = [('CMake', '3.26.3')] + +sanity_check_paths = { + 'files': ['bin/parasail_aligner', 'bin/parasail_stats', + 'lib/libparasail.%s' % SHLIB_EXT, 'include/parasail.h'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb new file mode 100644 index 000000000000..26796f9e0d9e --- /dev/null +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'python-parasail' +version = '1.3.4' + +homepage = 'https://github.com/jeffdaily/parasail-python' +description = "Python Bindings for the Parasail C Library" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = ['parasail-%(version)s.tar.gz'] +checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'] + +builddependencies = [ + ('parasail', '2.6.2'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# make sure setup.py finds the parasail library +preinstallopts = "ln -s $EBROOTPARASAIL/lib/libparasail.so parasail/libparasail.%s && " % SHLIB_EXT + +options = {'modulename': 'parasail'} + +moduleclass = 'bio' From 52295fa673ba3bd8261ada81f10a7ab7199c4981 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Wed, 7 Feb 2024 17:22:17 +0100 Subject: [PATCH 0612/1193] add patch for installing lammps python package and timestep balance --- ...Aug2023_fix-timestep-balance-example.patch | 32 +++++++++++++++ ...python_pachage_in_eb_software_module.patch | 41 +++++++++++++++++++ ...MMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 16 +++++++- 3 files changed, 87 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_fix-timestep-balance-example.patch create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_fix-timestep-balance-example.patch b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_fix-timestep-balance-example.patch new file mode 100644 index 000000000000..0c56cd2b7d0e --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_fix-timestep-balance-example.patch @@ -0,0 +1,32 @@ +reduce timestep to fix sanity check commands, +see https://github.com/lammps/lammps/commit/9b88ba595d0f05e384cbe6c94cd42870ad15f3bc + https://github.com/lammps/lammps/pull/3950 +diff -ru lammps-stable_2Aug2023_update2.orig/examples/balance/in.balance lammps-stable_2Aug2023_update2/examples/balance/in.balance +--- lammps-stable_2Aug2023_update2.orig/examples/balance/in.balance 2023-12-15 03:09:30.000000000 +0100 ++++ lammps-stable_2Aug2023_update2/examples/balance/in.balance 2024-02-07 14:53:43.792799526 +0100 +@@ -50,5 +50,6 @@ + + thermo_style custom step temp epair press f_10[3] f_10 + thermo 100 ++timestep 0.001 + + run 10000 +diff -ru lammps-stable_2Aug2023_update2.orig/examples/balance/in.balance.bond.fast lammps-stable_2Aug2023_update2/examples/balance/in.balance.bond.fast +--- lammps-stable_2Aug2023_update2.orig/examples/balance/in.balance.bond.fast 2023-12-15 03:09:30.000000000 +0100 ++++ lammps-stable_2Aug2023_update2/examples/balance/in.balance.bond.fast 2024-02-07 14:55:03.844643449 +0100 +@@ -59,5 +59,6 @@ + + thermo_style custom step temp epair press f_10[3] f_10 + thermo 100 ++timestep 0.001 + + run 10000 +diff -ru lammps-stable_2Aug2023_update2.orig/examples/balance/in.balance.bond.slow lammps-stable_2Aug2023_update2/examples/balance/in.balance.bond.slow +--- lammps-stable_2Aug2023_update2.orig/examples/balance/in.balance.bond.slow 2023-12-15 03:09:30.000000000 +0100 ++++ lammps-stable_2Aug2023_update2/examples/balance/in.balance.bond.slow 2024-02-07 14:55:29.673468900 +0100 +@@ -58,5 +58,6 @@ + + thermo_style custom step temp epair press f_10[3] f_10 + thermo 100 ++timestep 0.001 + + run 40000 \ No newline at end of file diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch new file mode 100644 index 000000000000..7f32721a36e2 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch @@ -0,0 +1,41 @@ +Add option in install.py to install lammps python packages in the site-packages of the easubuild software module +diff -ru lammps-stable_2Aug2023_update2.orig/python/install.py lammps-stable_2Aug2023_update2/python/install.py +--- lammps-stable_2Aug2023_update2.orig/python/install.py 2023-12-15 03:09:30.000000000 +0100 ++++ lammps-stable_2Aug2023_update2/python/install.py 2024-02-07 11:07:35.404221000 +0100 +@@ -27,6 +27,8 @@ + help="path to a directory where the created wheel will be stored") + parser.add_argument("-v", "--versionfile", required=True, + help="path to the LAMMPS version.h source file") ++parser.add_argument("-i", "--installdir", required=True, ++ help= "path to site-packages in lammps module") + + args = parser.parse_args() + +@@ -70,6 +72,14 @@ + else: + args.versionfile = os.path.abspath(args.versionfile) + ++if args.installdir: ++ if not os.path.exists(args.installdir): ++ print("\nERROR: LAMMPS site-packages file at %s does not exist\n" % args.installdir) ++ parser.print_help() ++ sys.exit(1) ++ else: ++ args.installdir = os.path.abspath(args.installdir) ++ + olddir = os.path.abspath('.') + pythondir = os.path.abspath(os.path.join(args.package,'..')) + os.putenv('LAMMPS_VERSION_FILE',os.path.abspath(args.versionfile)) +@@ -145,6 +155,12 @@ + py_exe = sys.executable + + try: ++ txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel, '--target', args.installdir], stderr=subprocess.STDOUT, shell=False) ++ print(txt) ++ sys.exit(0) ++except subprocess.CalledProcessError as err: ++ sys.exit(0) ++try: + txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False) + print(txt.decode('UTF-8')) + sys.exit(0) \ No newline at end of file diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb index 8d594686fa29..31ec777be167 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -20,7 +20,17 @@ toolchainopts = {'openmp': True, 'usempi': True} # 'https://github.com/lammps/lammps/archive/' source_urls = [GITHUB_LOWER_SOURCE] sources = ['stable_%(version)s.tar.gz'] -checksums = ['3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'] +patches = [ + 'LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch', + 'LAMMPS-2Aug2023_fix-timestep-balance-example.patch', +] +checksums = [ + {'stable_2Aug2023_update2.tar.gz': '3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'}, + {'LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch': + '33968fa2b6f545a7aaf9a8ef418add8913d89824197e19f0f9564b418a79fc65'}, + {'LAMMPS-2Aug2023_fix-timestep-balance-example.patch': + '6f68387ced2b4bd0a06e4c3d31b0ffd47042476777d87d8a0ca6b19a4e6a1777'}, +] builddependencies = [ ('CMake', '3.26.3'), @@ -46,9 +56,10 @@ dependencies = [ ('PLUMED', '2.9.0'), ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2023.07'), - ('MDI', '1.4.26'), # VTK package is auto-disabled if this dep is not available ('VTK', '9.3.0'), + # We use a custom build of MDI + ('MDI', '1.4.26'), ] if ARCH == 'x86_64': # TBB is an optional dependency when building on Intel arch @@ -164,5 +175,6 @@ general_packages = [ # - MSCG # - QMMM (setup seems complex) +#install_cmd = 'make install && python %(builddir)s/lammps-stable_%(version)s/python/install.py -p %(installdir)s/lib -l %(installdir)s/lib/liblammps.so -v %(builddir)s/src/version.h' moduleclass = 'chem' From d65b48b29f9ec5d402c21d0dda2d6e463bff6c91 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 18:49:57 +0100 Subject: [PATCH 0613/1193] make sure that Brunsli libraries are installed into /lib (#19805) --- .../easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb | 9 ++++++--- .../easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb | 9 ++++++--- .../easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb | 9 ++++++--- .../easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb | 9 ++++++--- .../easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb | 9 ++++++--- 5 files changed, 30 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb index f90442fc544f..22f38cbf5f96 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.2.0.eb @@ -27,7 +27,10 @@ dependencies = [ # skip use of third_party directory, since we provide Brotli via a proper dependency preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " -configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" @@ -35,8 +38,8 @@ buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" postinstallcmds = [ "mkdir %(installdir)s/bin", "cp dbrunsli %(installdir)s/bin/", - "cp libbrunsli*.a %(installdir)s/lib*/", - "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb index 20cd4b20aef4..301194a32a4d 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -28,7 +28,10 @@ dependencies = [ # skip use of third_party directory, since we provide Brotli via a proper dependency preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " -configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" @@ -36,8 +39,8 @@ buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" postinstallcmds = [ "mkdir %(installdir)s/bin", "cp dbrunsli %(installdir)s/bin/", - "cp libbrunsli*.a %(installdir)s/lib*/", - "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb index 35fa3a03359f..7522f1025e33 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-11.3.0.eb @@ -28,7 +28,10 @@ dependencies = [ # skip use of third_party directory, since we provide Brotli via a proper dependency preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " -configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" @@ -36,8 +39,8 @@ buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" postinstallcmds = [ "mkdir %(installdir)s/bin", "cp dbrunsli %(installdir)s/bin/", - "cp libbrunsli*.a %(installdir)s/lib*/", - "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb index 68552f70d3a8..cc914cae6cd4 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.2.0.eb @@ -28,7 +28,10 @@ dependencies = [ # skip use of third_party directory, since we provide Brotli via a proper dependency preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " -configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" @@ -36,8 +39,8 @@ buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" postinstallcmds = [ "mkdir %(installdir)s/bin", "cp dbrunsli %(installdir)s/bin/", - "cp libbrunsli*.a %(installdir)s/lib*/", - "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb index e9d6adbb76fd..22917f651e9a 100644 --- a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-12.3.0.eb @@ -28,7 +28,10 @@ dependencies = [ # skip use of third_party directory, since we provide Brotli via a proper dependency preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " -configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon" ' + +# make sure that libraries end up in /lib (not lib64) +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" @@ -36,8 +39,8 @@ buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" postinstallcmds = [ "mkdir %(installdir)s/bin", "cp dbrunsli %(installdir)s/bin/", - "cp libbrunsli*.a %(installdir)s/lib*/", - "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, + "cp libbrunsli*.a %(installdir)s/lib/", + "cp libbrunsli*.%s %%(installdir)s/lib/" % SHLIB_EXT, ] sanity_check_paths = { From e59c85cf4ce67469b103ebc569f68d9d0c9004f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 19:41:26 +0100 Subject: [PATCH 0614/1193] stick to GCC toolchain for LASTZ --- ...{LASTZ-1.04.22-foss-2023a.eb => LASTZ-1.04.22-GCC-12.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/LASTZ/{LASTZ-1.04.22-foss-2023a.eb => LASTZ-1.04.22-GCC-12.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-foss-2023a.eb b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb similarity index 93% rename from easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-foss-2023a.eb rename to easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb index 6dd3a06101b7..bd9b31a13aca 100644 --- a/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-foss-2023a.eb +++ b/easybuild/easyconfigs/l/LASTZ/LASTZ-1.04.22-GCC-12.3.0.eb @@ -9,7 +9,7 @@ description = """ LASTZ is a program for aligning DNA sequences, a pairwise alig sequencing technologies such as Roche 454. """ -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = [GITHUB_LOWER_SOURCE] sources = ['%(version)s.tar.gz'] From f6e5f3f2724377900796b1626575d3299ce641d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 19:44:46 +0100 Subject: [PATCH 0615/1193] add pilon wrapper script to existing Pilon easyconfig --- .../p/Pilon/Pilon-1.23-Java-11-wrapped.eb | 31 ------------------- .../easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb | 24 +++++++++----- .../p/phyluce/phyluce-1.7.3-foss-2023a.eb | 2 +- 3 files changed, 17 insertions(+), 40 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb deleted file mode 100644 index 4275740264a8..000000000000 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11-wrapped.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'JAR' - -name = 'Pilon' -version = '1.23' -versionsuffix = '-Java-%(javaver)s-wrapped' - -homepage = 'https://github.com/broadinstitute/pilon' -description = " Pilon is an automated genome assembly improvement and variant detection tool" - -toolchain = SYSTEM - -source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] -sources = ['%(namelower)s-%(version)s.jar'] -checksums = ['bde1d3c8da5537abbc80627f0b2a4165c2b68551690e5733a6adf62413b87185'] - -dependencies = [('Java', '11')] - -sanity_check_paths = { - 'files': ['pilon-%(version)s.jar'], - 'dirs': [], -} - -postinstallcmds = [ - "cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar", - "mkdir -p %(installdir)s/bin", - "echo '#!/bin/sh' > %(installdir)s/bin/%(namelower)s", - "echo 'java -jar -Xmx8G %(installdir)s/%(namelower)s-%(version)s.jar $@' >> %(installdir)s/bin/%(namelower)s", - "chmod a+rx %(installdir)s/bin/%(namelower)s" -] - -moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb index d53818870559..e0e3a41e14ff 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb @@ -2,7 +2,7 @@ easyblock = 'JAR' name = 'Pilon' version = '1.23' -versionsuffix = '-Java-%(javaver)s' +versionsuffix = '-Java-%(javaver)s-wrapped' homepage = 'https://github.com/broadinstitute/pilon' description = " Pilon is an automated genome assembly improvement and variant detection tool" @@ -10,21 +10,29 @@ description = " Pilon is an automated genome assembly improvement and variant de toolchain = SYSTEM source_urls = ['https://github.com/broadinstitute/pilon/releases/download/v%(version)s/'] -sources = ['%(namelower)s-%(version)s.jar'] +sources = ['pilon-%(version)s.jar'] checksums = ['bde1d3c8da5537abbc80627f0b2a4165c2b68551690e5733a6adf62413b87185'] dependencies = [('Java', '11')] -sanity_check_paths = { - 'files': ['pilon-%(version)s.jar'], - 'dirs': [], -} - -postinstallcmds = ['cd %(installdir)s && ln -s %(namelower)s-%(version)s.jar pilon.jar'] +postinstallcmds = [ + "cd %(installdir)s && ln -s pilon-%(version)s.jar pilon.jar", + "mkdir -p %(installdir)s/bin", + "echo '#!/bin/sh' > %(installdir)s/bin/pilon", + "echo 'java -jar -Xmx8G %(installdir)s/pilon-%(version)s.jar $@' >> %(installdir)s/bin/pilon", + "chmod a+rx %(installdir)s/bin/pilon" +] modloadmsg = """ To execute Pilon run: java -Xmx8G -jar $EBROOTPILON/pilon.jar Adjust the memory value according to the size of your input files """ +sanity_check_paths = { + 'files': ['bin/pilon', 'pilon.jar'], + 'dirs': [], +} + +sanity_check_commands = ["pilon --help"] + moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index aa2423273b02..c9ee0a99bae5 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -30,7 +30,7 @@ dependencies = [ ('LASTZ', '1.04.22'), ('MAFFT', '7.520', '-with-extensions'), ('MUSCLE', '5.1.0'), - ('Pilon', '1.23', '-Java-11-wrapped', SYSTEM), + ('Pilon', '1.23', '-Java-11', SYSTEM), ('RAxML-NG', '1.2.0'), ('SAMtools', '1.18'), ('seqtk', '1.4'), From c43ff54c33d75d50967054da9c438293f105312d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 19:45:35 +0100 Subject: [PATCH 0616/1193] add sanity check command for trimAl --- easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb index f9e630d1b3bb..ab4fbb5db3db 100644 --- a/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/trimAl/trimAl-1.4.1-GCCcore-12.3.0.eb @@ -34,4 +34,6 @@ sanity_check_paths = { 'dirs': [] } +sanity_check_commands = ["trimal -h"] + moduleclass = 'bio' From ebc0b9ade2a290b622f1baa2d4ee14021f71fef3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 19:45:49 +0100 Subject: [PATCH 0617/1193] remove explicit OpenMPI dependency in ABySS easyconfig --- easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb b/easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb index c8fcbae9bce2..b7ed9556e62d 100644 --- a/easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb +++ b/easybuild/easyconfigs/a/ABySS/ABySS-2.3.7-foss-2023a.eb @@ -18,7 +18,6 @@ dependencies = [ ('Automake', '1.16.5'), ('Boost', '1.82.0'), ('sparsehash', '2.0.4'), - ('OpenMPI', '4.1.5'), ('btllib', '1.7.0'), ] From 73802aa4e4f5dcb5cb84580794e3cf9e9988f23e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 20:13:01 +0100 Subject: [PATCH 0618/1193] add missing authorship in patches for phyluce --- .../p/phyluce/phyluce-1.7.3-foss-2023a.eb | 13 ++++++------- .../p/phyluce/phyluce-1.7.3_fix-config-paths.patch | 3 ++- .../phyluce-1.7.3_removal-Bio-Alphabet.patch | 5 +++-- 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb index c9ee0a99bae5..527d3deae71d 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3-foss-2023a.eb @@ -42,18 +42,17 @@ dependencies = [ exts_list = [ (name, version, { 'source_urls': ['https://github.com/faircloth-lab/phyluce/archive/refs/tags/'], - 'source_tmpl': 'v%(version)s.tar.gz', + 'sources': ['v%(version)s.tar.gz'], 'patches': [ '%(name)s-%(version)s_fix-config-paths.patch', '%(name)s-%(version)s_removal-Bio-Alphabet.patch', ], 'checksums': [ - # v1.7.3.tar.gz - '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11', - # phyluce-1.7.3_fix-config-paths.patch - '543daee90e1422a7a43c304d6f33e5f16411cc7b85c522b847388feff8cc402a', - # phyluce-1.7.3_removal-Bio-Alphabet.patch - 'f6c5237552fde5a3bf24105781a9001ee5e87bbd825015fc1aa6b5c6a147e171', + {'v1.7.3.tar.gz': '931fd512730bb101266b27728576df00277858d256e1ab30d64b474588362e11'}, + {'phyluce-1.7.3_fix-config-paths.patch': + '22d5467d7498a9b2b718660e9580fb41986964e122e4c3baf851a324a968ae5d'}, + {'phyluce-1.7.3_removal-Bio-Alphabet.patch': + '9401f8b8052924476d2a73d8ac2672e750eadf11618c672d9679f3c99234049d'}, ], }), ] diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch index 3bfd7955fea8..1d0cbcdbb078 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_fix-config-paths.patch @@ -1,4 +1,5 @@ -# fix path of binaries in config file +fix path of binaries in config file +author: Pavel Tomanek (INUITS) --- config/phyluce.conf.orig 2024-02-01 11:38:15.279943701 +0100 +++ config/phyluce.conf 2024-02-01 14:52:31.565662528 +0100 @@ -1,27 +1,27 @@ diff --git a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch index 82e9c87c44fe..05063f88ea17 100644 --- a/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch +++ b/easybuild/easyconfigs/p/phyluce/phyluce-1.7.3_removal-Bio-Alphabet.patch @@ -1,5 +1,6 @@ -# removal of the Bio.Alphabet - it is not part of Biopython anymore (since v1.78) -# https://biopython.org/wiki/Alphabet +removal of the Bio.Alphabet - it is not part of Biopython anymore (since v1.78) +see also https://biopython.org/wiki/Alphabet +author: Pavel Tomanek (INUITS) --- bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi.orig 2024-02-01 15:53:37.732931000 +0100 +++ bin/ncbi/phyluce_ncbi_prep_uce_align_files_for_ncbi 2024-02-01 16:16:42.885167000 +0100 @@ -18,7 +18,6 @@ From c56968a43231a0859c499824a5980952b5d0a14c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 20:17:15 +0100 Subject: [PATCH 0619/1193] fix versionsuffix for Pilon --- easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb index e0e3a41e14ff..1423f7b4e540 100644 --- a/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb +++ b/easybuild/easyconfigs/p/Pilon/Pilon-1.23-Java-11.eb @@ -2,7 +2,7 @@ easyblock = 'JAR' name = 'Pilon' version = '1.23' -versionsuffix = '-Java-%(javaver)s-wrapped' +versionsuffix = '-Java-%(javaver)s' homepage = 'https://github.com/broadinstitute/pilon' description = " Pilon is an automated genome assembly improvement and variant detection tool" From b59956ae805a0726fa0b430eee259c936ec11e8e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 20:28:05 +0100 Subject: [PATCH 0620/1193] don't hardcode version number in postinstallcmds for SRA-Toolkit to copy ngs-python --- .../easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb index 76f0b841a22c..ce9e693a0f52 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb @@ -42,7 +42,7 @@ configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBI configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' postinstallcmds = [ - "cp -r %(builddir)s/sra-tools-3.0.10/ngs/ngs-python/ %(installdir)s/", + "cp -r %(startdir)s/ngs/ngs-python/ %(installdir)s/", ] _sra_bin = [ From 7b3622f9cd63d5b0382c67eed80523c9a8692658 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Feb 2024 20:28:29 +0100 Subject: [PATCH 0621/1193] use one environment variable per line in modextrapaths in SRA-Toolkit easyconfig --- .../s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb index ce9e693a0f52..7d8797766bed 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb @@ -68,6 +68,9 @@ sanity_check_commands = [ "python -c 'import ngs'", ] -modextrapaths = {'CLASSPATH': 'jar/ngs-java.jar', 'PYTHONPATH': 'ngs-python'} +modextrapaths = { + 'CLASSPATH': 'jar/ngs-java.jar', + 'PYTHONPATH': 'ngs-python', +} moduleclass = 'bio' From e08ba7374f0928be0e96ab33a4d4def5a4fe0e37 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Feb 2024 02:06:00 +0100 Subject: [PATCH 0622/1193] adding easyconfigs: geopy-2.4.1-GCCcore-12.3.0.eb, contextily-1.5.0-foss-2023a.eb --- .../contextily/contextily-1.5.0-foss-2023a.eb | 39 +++++++++++++++++++ .../g/geopy/geopy-2.4.1-GCCcore-12.3.0.eb | 35 +++++++++++++++++ 2 files changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/c/contextily/contextily-1.5.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/geopy/geopy-2.4.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/contextily/contextily-1.5.0-foss-2023a.eb b/easybuild/easyconfigs/c/contextily/contextily-1.5.0-foss-2023a.eb new file mode 100644 index 000000000000..afde40726ac2 --- /dev/null +++ b/easybuild/easyconfigs/c/contextily/contextily-1.5.0-foss-2023a.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'contextily' +version = '1.5.0' + +homepage = 'https://contextily.readthedocs.io/' +description = """contextily is a small Python 3 package to retrieve tile maps from the internet. +It can add those tiles as basemap to matplotlib figures or write tile maps to +disk into geospatial raster files. Bounding boxes can be passed in both WGS84 +(EPSG:4326) and Spheric Mercator (EPSG:3857).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('geopy', '2.4.1'), + ('matplotlib', '3.7.2'), + ('Pillow', '10.0.0'), + ('rasterio', '1.3.9'), +] + +use_pip = True + +exts_list = [ + ('xyzservices', '2023.7.0', { + 'checksums': ['0ec928742227d6f5d4367ea7b457fcfed943429f4de2949b5b02a82cdf5569d6'], + }), + ('mercantile', '1.2.1', { + 'checksums': ['fa3c6db15daffd58454ac198b31887519a19caccee3f9d63d17ae7ff61b3b56b'], + }), + (name, version, { + 'checksums': ['295b2d8097f8f6e80e1cb5e6e77538d1cdf729f827ec54eedc57f613c0a3ce0e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/geopy/geopy-2.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/geopy/geopy-2.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..c04a5817a0cf --- /dev/null +++ b/easybuild/easyconfigs/g/geopy/geopy-2.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'geopy' +version = '2.4.1' + +homepage = 'https://geopy.readthedocs.io/' +description = """geopy is a Python client for several popular geocoding web services. +geopy makes it easy for Python developers to locate the coordinates of +addresses, cities, countries, and landmarks across the globe using third-party +geocoders and other data sources.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + ('geographiclib', '2.0', { + 'checksums': ['f7f41c85dc3e1c2d3d935ec86660dc3b2c848c83e17f9a9e51ba9d5146a15859'], + }), + (name, version, { + 'checksums': ['50283d8e7ad07d89be5cb027338c6365a32044df3ae2556ad3f52f4840b3d0d1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 6b35b294a16c4bcbd0e05e5dde8fba58b85ec2a4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Feb 2024 08:54:00 +0100 Subject: [PATCH 0623/1193] use correct %(start_dir)s template in postinstallcmds of SRA-Toolkit to copy ngs-python --- .../easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb index 7d8797766bed..b7658b73c234 100644 --- a/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb +++ b/easybuild/easyconfigs/s/SRA-Toolkit/SRA-Toolkit-3.0.10-gompi-2023a.eb @@ -42,7 +42,7 @@ configopts = '-DVDB_INCDIR="$EBROOTNCBIMINVDB/include" -DVDB_LIBDIR="$EBROOTNCBI configopts += '-DBUILD_TOOLS_LOADERS=ON -DBUILD_TOOLS_INTERNAL=ON' postinstallcmds = [ - "cp -r %(startdir)s/ngs/ngs-python/ %(installdir)s/", + "cp -r %(start_dir)s/ngs/ngs-python/ %(installdir)s/", ] _sra_bin = [ From 1bf54a59e5c73a270551af9cb387dd358a68e034 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 09:23:22 +0100 Subject: [PATCH 0624/1193] adding easyconfigs: pyspoa-0.2.1-GCC-12.3.0.eb and patches: pyspoa-0.2.1_use-spoa-dep.patch --- .../p/pyspoa/pyspoa-0.2.1-GCC-12.3.0.eb | 62 +++++++++++++++++++ .../p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch | 24 +++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-12.3.0.eb b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..96e58f230909 --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1-GCC-12.3.0.eb @@ -0,0 +1,62 @@ +easyblock = 'PythonPackage' + +name = 'pyspoa' +version = '0.2.1' + +local_cereal_version = '1.3.2' + +homepage = 'https://github.com/nanoporetech/pyspoa' +description = "Python bindings to spoa." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +toolchainopts = {'extra_cflags': "-fpermissive"} + +sources = [ + { + 'filename': '%(name)s-%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/nanoporetech', + 'repo_name': 'pyspoa', + 'tag': 'v%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } + }, + { + 'source_urls': ['https://github.com/USCiLab/cereal/archive/'], + 'download_filename': 'v%s.tar.gz' % local_cereal_version, + 'filename': 'cereal-%s.tar.gz' % local_cereal_version, + }, +] + +patches = ['pyspoa-%(version)s_use-spoa-dep.patch'] + +checksums = [ + None, + '16a7ad9b31ba5880dac55d62b5d6f243c3ebc8d46a3514149e56b5e7ea81f85f', + 'dffd946e3b36e4872846fe983d287f992b5bf177798e11141bf0d645cfc0664d', +] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Python', '3.11.3'), + ('pybind11', '2.11.1'), + ('spoa', '4.1.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +preinstallopts = "mkdir -p src/vendor/cereal && ln -s %(builddir)s/cereal-*/include src/vendor/cereal/include && " +# strip out cmake requirements, since we provide that as proper dependency +preinstallopts += "sed -i 's/.cmake==[0-9.]*.//g' setup.py && " +preinstallopts += "export libspoa=$EBROOTSPOA/lib/libspoa.a && " + +options = {'modulename': 'spoa'} + +sanity_check_commands = ["cd %(builddir)s/*/tests && python test_pyspoa.py"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch new file mode 100644 index 000000000000..37a309bd217c --- /dev/null +++ b/easybuild/easyconfigs/p/pyspoa/pyspoa-0.2.1_use-spoa-dep.patch @@ -0,0 +1,24 @@ +use spoa dependency provided through EasyBuild + +author: Kenneth Hoste (HPC-UGent) +updated by: Petr Král (Inuits) +diff --git a/pyspoa-0.2.1/setup.py.orig b/pyspoa-0.2.1/setup.py +--- a/pyspoa-0.2.1/setup.py.orig 2023-11-27 14:48:14.661356275 +0100 ++++ b/pyspoa-0.2.1/setup.py 2023-11-27 14:52:53.880656275 +0100 +@@ -119,14 +119,14 @@ + 'spoa', + ['pyspoa.cpp'], + include_dirs=[ +- 'src/include/spoa', ++ os.path.join(os.getenv('EBROOTSPOA'), 'include/spoa'), + 'src/vendor/cereal/include', + get_pybind_include(), + get_pybind_include(user=True), + ], + language='c++', + extra_objects=[ +- LIB_SPOA ++ os.path.join(os.getenv('EBROOTSPOA'), 'lib64/libspoa.a'), + ], + + ), From 252661bcd2e33c5c320a9bea9729c5097ae0297f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 09:29:38 +0100 Subject: [PATCH 0625/1193] adding easyconfigs: ont-fast5-api-4.1.2-foss-2023a.eb --- .../ont-fast5-api-4.1.2-foss-2023a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.2-foss-2023a.eb b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.2-foss-2023a.eb new file mode 100644 index 000000000000..6850f3a6d994 --- /dev/null +++ b/easybuild/easyconfigs/o/ont-fast5-api/ont-fast5-api-4.1.2-foss-2023a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '4.1.2' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'checksums': ['c7c59c6100e992ef8bc239cdf91f7a8ab46abf57ecd689f94b2b98e72a9e9472'], + }), +] + +sanity_check_paths = { + 'files': [ + 'bin/compress_fast5', + 'bin/fast5_subset', + 'bin/multi_to_single_fast5', + 'bin/single_to_multi_fast5' + ], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 656d671578446071741d587f9266b52677878739 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 09:32:38 +0100 Subject: [PATCH 0626/1193] adding easyconfigs: minimap2-2.26-GCCcore-12.3.0.eb --- .../minimap2/minimap2-2.26-GCCcore-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..180de6104311 --- /dev/null +++ b/easybuild/easyconfigs/m/minimap2/minimap2-2.26-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Adam Huffman +# DeepThought, Flinders University +# Updated to 2.22 +# R.QIAO + +# Update Petr Král (INUITS) +easyblock = 'MakeCp' + +name = 'minimap2' +version = '2.26' + +homepage = 'https://github.com/lh3/minimap2' +description = """Minimap2 is a fast sequence mapping and alignment +program that can find overlaps between long noisy reads, or map long +reads or their assemblies to a reference genome optionally with detailed +alignment (i.e. CIGAR). At present, it works efficiently with query +sequences from a few kilobases to ~100 megabases in length at an error +rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited +test data sets, minimap2 is over 20 times faster than most other +long-read aligners. It will replace BWA-MEM for long reads and contig +alignment.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/lh3/%(name)s/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar.bz2'] +checksums = ['6a588efbd273bff4f4808d5190957c50272833d2daeb4407ccf4c1b78143624c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +buildopts = 'CC="${CC}" CFLAGS="${CFLAGS}" INCLUDES="${CPPFLAGS}"' + +files_to_copy = [ + (['%(name)s'], 'bin'), + (['lib%(name)s.a'], 'lib'), + (['*.h'], 'include'), + 'LICENSE.txt', 'NEWS.md', 'README.md', + (['%(name)s.1'], 'share/man/man1') +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'lib/lib%(name)s.a'], + 'dirs': ['include'] +} + +sanity_check_commands = [ + "minimap2 --help", + "cd %(builddir)s/minimap2-%(version)s && minimap2 -a test/MT-human.fa test/MT-orang.fa > test.sam", +] + +moduleclass = 'bio' From 5175816ec9772a8a3649c0168f6c907d8f542626 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 09:41:47 +0100 Subject: [PATCH 0627/1193] add missing dependency --- .../s/spoa/spoa-4.1.0-GCC-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-12.3.0.eb b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..b85132ee1097 --- /dev/null +++ b/easybuild/easyconfigs/s/spoa/spoa-4.1.0-GCC-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'spoa' +version = '4.1.0' + +homepage = 'https://github.com/rvaser/spoa' +description = """Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm + which is used to generate consensus sequences""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rvaser/spoa/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['43238356f00bce2ad9698fc18b3e320024172a82182dcff24d57c5cf19e342c8'] + +builddependencies = [('CMake', '3.26.3')] + +configopts = "-Dspoa_build_executable=ON" + +sanity_check_paths = { + 'files': ['bin/spoa'] + ['include/spoa/%s' % x for x in ['alignment_engine.hpp', 'graph.hpp', 'spoa.hpp']] + + ['lib/libspoa.a'], + 'dirs': [], +} + +sanity_check_commands = ["spoa --help"] + +moduleclass = 'bio' From 81382eb30e0dc993b2e59a5083d4c484aebcfed5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 10:05:54 +0100 Subject: [PATCH 0628/1193] adding easyconfigs: MSFragger-4.0-Java-11.eb --- .../m/MSFragger/MSFragger-4.0-Java-11.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/m/MSFragger/MSFragger-4.0-Java-11.eb diff --git a/easybuild/easyconfigs/m/MSFragger/MSFragger-4.0-Java-11.eb b/easybuild/easyconfigs/m/MSFragger/MSFragger-4.0-Java-11.eb new file mode 100644 index 000000000000..3e1805a31126 --- /dev/null +++ b/easybuild/easyconfigs/m/MSFragger/MSFragger-4.0-Java-11.eb @@ -0,0 +1,39 @@ +easyblock = 'Tarball' + +name = 'MSFragger' +version = '4.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://msfragger.nesvilab.org/' +description = """MSFragger is an ultrafast database search tool for peptide identification + in mass spectrometry-based proteomics. It has demonstrated excellent performance across a wide + range of datasets and applications. MSFragger is suitable for standard shotgun proteomics + analyses as well as large datasets (including timsTOF PASEF data), enzyme unconstrained + searches (e.g., peptidome), open database searches (e.g., precursor mass tolerance set + to hundreds of Daltons) for identification of modified peptides, and glycopeptide + identification (N-linked and O-linked).""" + +toolchain = SYSTEM + +sources = ['%(name)s-%(version)s.zip'] +checksums = ['25bdab705c4ac97729d1da8d7a075e3920d8a447596fa52eff8e564606d1720e'] + +download_instructions = 'Manual download required, see http://msfragger-upgrader.nesvilab.org/upgrader/' + +dependencies = [('Java', '11')] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + "echo '#!/bin/sh' > %(installdir)s/bin/%(namelower)s", + "echo 'java -jar %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/%(namelower)s", + "chmod a+rx %(installdir)s/bin/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['%(name)s-%(version)s.jar'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From bd2618199eb7b4028564ae1f4049f089f38a1829 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 10:07:47 +0100 Subject: [PATCH 0629/1193] adding easyconfigs: IonQuant-1.10.12-Java-11.eb --- .../i/IonQuant/IonQuant-1.10.12-Java-11.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/IonQuant/IonQuant-1.10.12-Java-11.eb diff --git a/easybuild/easyconfigs/i/IonQuant/IonQuant-1.10.12-Java-11.eb b/easybuild/easyconfigs/i/IonQuant/IonQuant-1.10.12-Java-11.eb new file mode 100644 index 000000000000..31a90a213913 --- /dev/null +++ b/easybuild/easyconfigs/i/IonQuant/IonQuant-1.10.12-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'IonQuant' +version = '1.10.12' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://ionquant.nesvilab.org/' +description = """IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based + quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free + quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used + for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar + labelling strategies. IonQuant is available as part of FragPipe.""" + +toolchain = SYSTEM + +sources = ['%(name)s-%(version)s.zip'] +checksums = ['861a633ab815a34ea54e6e26f318e19b510b25cb8955f3daeb83d6d10c6938ea'] + +download_instructions = 'Manual download required, see https://msfragger.arsci.com/ionquant/' + +dependencies = [('Java', '11')] + +postinstallcmds = [ + "mkdir -p %(installdir)s/bin", + "echo '#!/bin/sh' > %(installdir)s/bin/%(namelower)s", + "echo 'java -jar %(installdir)s/%(name)s-%(version)s.jar $@' >> %(installdir)s/bin/%(namelower)s", + "chmod a+rx %(installdir)s/bin/%(namelower)s", +] + +sanity_check_paths = { + 'files': ['%(name)s-%(version)s.jar'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s | grep '^Usage'"] + +moduleclass = 'bio' From 4a24fda35081fa4536a42b2ed93e0d3db642d6f7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 10:16:30 +0100 Subject: [PATCH 0630/1193] adding easyconfigs: edlib-1.3.9-GCC-12.3.0.eb --- .../e/edlib/edlib-1.3.9-GCC-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.3.0.eb new file mode 100644 index 000000000000..5eb1f74e9d27 --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'edlib' +version = '1.3.9' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cogapp', '3.3.0', { + 'checksums': ['1be95183f70282422d594fa42426be6923070a4bd8335621f6347f3aeee81db0'], + }), + (name, version, { + 'source_urls': ['https://github.com/Martinsos/edlib/archive/'], + 'source_tmpl': 'python-%(version)s.tar.gz', + # fixes `edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory` + # see https://github.com/Martinsos/edlib/issues/217#issuecomment-1736234091 + 'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ', + 'checksums': ['6506eee9b93bf461ccc3cd239096707d0b86a5cbe5af08e82e7bd616271d55c6'], + }), +] + +moduleclass = 'bio' From a4fa2450a76ffd34f36e865d6fc03005c8563961 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 10:42:33 +0100 Subject: [PATCH 0631/1193] adding easyconfigs: medaka-1.11.3-foss-2023a.eb, Racon-1.5.0-GCCcore-12.3.0.eb, intervaltree-python-3.1.0-GCCcore-12.3.0.eb --- ...ntervaltree-python-3.1.0-GCCcore-12.3.0.eb | 34 +++++++++ .../m/medaka/medaka-1.11.3-foss-2023a.eb | 72 +++++++++++++++++++ .../r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb | 28 ++++++++ 3 files changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4934ceb72f3b --- /dev/null +++ b/easybuild/easyconfigs/i/intervaltree-python/intervaltree-python-3.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# Author: Jasper Grimm (UoY) +# Update: Petr Král (INUITS) + +easyblock = 'PythonPackage' + +name = 'intervaltree-python' +_modname = 'intervaltree' +version = '3.1.0' + +homepage = 'https://github.com/chaimleib/intervaltree' +description = """A mutable, self-balancing interval tree. Queries may be by + point, by range overlap, or by range containment. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://pypi.python.org/packages/source/i/%s' % _modname] +sources = ['%s-%s.tar.gz' % (_modname, version)] +checksums = ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': _modname} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb new file mode 100644 index 000000000000..989d24aff32d --- /dev/null +++ b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb @@ -0,0 +1,72 @@ +# This is a contribution from HPCNow! (http://hpcnow.com) +# Copyright:: HPCNow! +# Authors:: Danilo Gonzalez +# License:: GPL-v3.0 +# Updated to foss-2020b to use with artic tool +# J. Sassmannshausen (GSTT/NHS UK) +# Updated to 1.5.0 +# Jasper Grimm (UoY) +# Updated: Petr Král (INUITS) + +easyblock = 'PythonBundle' + +name = 'medaka' +version = '1.11.3' + +homepage = 'https://github.com/nanoporetech/medaka' +description = "medaka is a tool to create a consensus sequence from nanopore sequencing data." + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +builddependencies = [('Autotools', '20220317')] + +_minimap_ver = '2.26' +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # includes cffi + # tensorflow~=2.10.0 required by medaka 1.9.1, see requirements.txt + ('TensorFlow', '2.13.0'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('minimap2', _minimap_ver), + ('HTSlib', '1.18'), # for tabix, bgzip + ('Racon', '1.5.0'), + ('edlib', '1.3.9'), + ('pyspoa', '0.2.1'), + ('python-parasail', '1.3.4'), + ('ont-fast5-api', '4.1.2'), + ('WhatsHap', '2.1'), + ('intervaltree-python', '3.1.0'), + ('BCFtools', '1.18'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('mappy', _minimap_ver, { + 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], + }), + ('wurlitzer', '3.0.3', { + 'checksums': ['224f5fe70618be3872c05dfddc8c457191ec1870654596279fcc1edadebe3e5b'], + }), + (name, version, { + 'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'], + # Some requirements are too strict. + 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && " + + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py && ", + }), +] + +sanity_check_paths = { + 'files': ['bin/medaka', 'bin/medaka_consensus', 'bin/medaka_version_report'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "medaka --help", + "medaka_version_report", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d75d2f0ac0e6 --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From 0297925efc2d60f416720788711502c99219e122 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 10:48:09 +0100 Subject: [PATCH 0632/1193] adding easyconfigs: NGSpeciesID-0.3.0-foss-2023a.eb --- .../NGSpeciesID-0.3.0-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb new file mode 100644 index 000000000000..ad912110bf76 --- /dev/null +++ b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonPackage' + +name = 'NGSpeciesID' +version = '0.3.0' + +homepage = 'https://github.com/ksahlin/NGSpeciesID' +description = "NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads." + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['71663ce280220d4e692cc6c3aea44f91e40b3143ed09a9462bdf2feb1d94aa9f'] + +dependencies = [ + ('Python', '3.11.3'), + ('python-parasail', '1.3.4'), + ('edlib', '1.3.9'), + ('medaka', '1.11.3'), + ('spoa', '4.1.0'), + ('Racon', '1.5.0'), + ('minimap2', '2.26'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +# no proper namespace for NGSpeciesID +options = {'modulename': 'modules.consensus'} + +# parasail requirements are too strict +preinstallopts = "sed -i 's/parasail==/parasail>=/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NGSpeciesID'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NGSpeciesID --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From d549705c37e64ffb8a851658d47d4a937552b7d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 8 Feb 2024 11:16:21 +0100 Subject: [PATCH 0633/1193] fix preinstallopts --- .../easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb index 989d24aff32d..d2dd82d498e8 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb @@ -44,6 +44,12 @@ dependencies = [ use_pip = True sanity_pip_check = True +local_sed_commands = [ + "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==1.15.0/cffi/g' requirements.txt pyproject.toml", + # Python 3.11 support + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py", +] + exts_list = [ ('mappy', _minimap_ver, { 'checksums': ['e53fbe9a3ea8762a64b8103f4f779c9fb16d418eaa0a731f45cebc83867a9b71'], @@ -54,8 +60,7 @@ exts_list = [ (name, version, { 'checksums': ['940568212d152f573270967b02f6e841561cc43138b6aa15783c371457fef7b9'], # Some requirements are too strict. - 'preinstallopts': "sed -i 's/tensorflow.*/tensorflow/g;s/cffi==/cffi>=/g' requirements.txt && " - + "sed -i 's/8, 9, 10/8, 9, 10, 11/g;s/,<3.11//g' setup.py && ", + 'preinstallopts': " && ".join(local_sed_commands) + " && ", }), ] From 3f7fd32c7358302a10ca77992f77b000007f08b4 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Thu, 8 Feb 2024 11:24:35 +0000 Subject: [PATCH 0634/1193] adding easyconfigs: EDirect-20.5.20231006-GCCcore-12.2.0.eb --- .../EDirect-20.5.20231006-GCCcore-12.2.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.2.0.eb b/easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d055a8c9798f --- /dev/null +++ b/easybuild/easyconfigs/e/EDirect/EDirect-20.5.20231006-GCCcore-12.2.0.eb @@ -0,0 +1,57 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## +easyblock = 'Binary' + +name = 'EDirect' +version = '20.5.20231006' + +homepage = 'https://www.ncbi.nlm.nih.gov/books/NBK25501/' +# See also https://dataguide.nlm.nih.gov/edirect/install.html +description = """Entrez Direct (EDirect) provides access to the NCBI's suite of +interconnected databases from a Unix terminal window. Search terms are entered +as command-line arguments. Individual operations are connected with Unix pipes +to construct multi-step queries. Selected records can then be retrieved in a +variety of formats.""" +# software_license = 'Public Domain' + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/versions/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abb7a7c2d7dd4bf80b5f951211d20bf432fe9b787f6ad093feba2f5cb46d62dd'] + +builddependencies = [ + ('Go', '1.21.2', '', SYSTEM), +] + +dependencies = [ + ('Python', '3.10.8'), + ('Perl', '5.36.0'), +] + +extract_sources = True + +postinstallcmds = [ + "cd cmd/ && " + "sed -i 's@target=\"\\$HOME/Misc/scripts/\"@target=\"%(installdir)s/\"@' build.sh && " + "./build.sh install && cd %(installdir)s/ && rm -rf cmd/ eutils/" +] + +sanity_check_paths = { + 'files': ['einfo', 'README'], + 'dirs': ['help'], +} + +sanity_check_commands = [ + "esearch -version && " + "xtract -version && " + "esearch -db pubmed -query 'Babalobi OO[au] AND 2008[pdat]' | efetch -format xml | " + "xtract -pattern Author -if Affiliation -contains Medicine -element Initials" +] + +moduleclass = 'bio' From 5d57daff77f6393d9fa64d77e1d6d916ba712cdb Mon Sep 17 00:00:00 2001 From: torri Date: Thu, 8 Feb 2024 14:08:50 +0100 Subject: [PATCH 0635/1193] adding easyconfigs: BWA-0.7.17.20220923-GCCcore-12.3.0.eb --- .../BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..380dd41df28c --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb @@ -0,0 +1,59 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Cyprus Institute / CaSToRC, Uni.Lu/LCSB, NTUA +# Authors:: George Tsouloupas , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +# +# Version >= 0.7.15 +# Author: Adam Huffman +# The Francis Crick Institute +# +# Note that upstream development is mainly at: https://github.com/lh3/bwa +## + +name = 'BWA' +version = '0.7.17.20220923' + +homepage = 'http://bio-bwa.sourceforge.net/' + +description = """ + Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively + short nucleotide sequences against a long reference sequence such as the human + genome. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +local_commit = '139f68f' + +sources = [{ + 'filename': '%s-%s-%s.tar.gz' % (name, version, local_commit), + 'git_config': { + 'url': 'https://github.com/lh3', + 'repo_name': 'bwa', + 'commit': local_commit, + 'recursive': True, + }, +}] +checksums = ['127d3f82ccc3bf7e918d2e64cafc0ffc49ff841b0955327f4666ca448364859f'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Perl', '5.36.1'), + ('zlib', '1.2.13'), +] + +# Allow use of x86 intrinsics on PPC +prebuildopts = 'export CFLAGS="$CFLAGS -fcommon -DNO_WARN_X86_INTRINSICS" && ' +prebuildopts += "sed -i 's|^CC=|#CC=|g' Makefile && " +prebuildopts += "sed -i 's|^CFLAGS=|#CFLAGS=|g' Makefile && " +prebuildopts += "sed -i 's|^LIBS=|LIBS= $(LDFLAGS) |g' Makefile && " + +moduleclass = 'bio' From 68b0231dfdb82376b3af51a57b9e8e69b89009cb Mon Sep 17 00:00:00 2001 From: ariel Date: Thu, 8 Feb 2024 15:05:37 +0100 Subject: [PATCH 0636/1193] fix dependency with libidn.so.11 --- .../t/tbl2asn/tbl2asn-20220427-linux64.eb | 42 +++++++++++++------ .../t/tbl2asn/tbl2asn-20230713-linux64.eb | 42 +++++++++++++------ 2 files changed, 58 insertions(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb index 8cb78e848ca3..c1d2f495db61 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20220427-linux64.eb @@ -2,8 +2,9 @@ # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano -easyblock = 'CmdCp' +easyblock = 'Bundle' name = 'tbl2asn' version = '20220427' @@ -14,27 +15,42 @@ description = """Tbl2asn is a command-line program that automates the creation o sequence records for submission to GenBank""" toolchain = SYSTEM +builddependencies = [ + ('binutils', '2.35'), +] + +default_easyblock = 'CmdCp' # It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, # reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 # checksums. -source_urls = ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % - (version[:4] + '-' + version[4:6] + '-' + version[6:])] -sources = [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], - 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] -checksums = ['c76481700e196ebd98a83f4174e0146569db9d6fe5753ac18691e9836d5c6a75'] - -cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] -files_to_copy = [ - (['tbl2asn'], 'bin'), +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['c76481700e196ebd98a83f4174e0146569db9d6fe5753ac18691e9836d5c6a75'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), ] +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + sanity_check_paths = { - 'files': ['bin/tbl2asn'], - 'dirs': [], + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], } -postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] +sanity_check_commands = ['tbl2asn --help'] moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb index 1f682d08a358..71b750650ba0 100644 --- a/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb +++ b/easybuild/easyconfigs/t/tbl2asn/tbl2asn-20230713-linux64.eb @@ -2,8 +2,9 @@ # Author: Pablo Escobar Lopez # sciCORE - University of Basel # SIB Swiss Institute of Bioinformatics +# revised by Ariel Lozano -easyblock = 'CmdCp' +easyblock = 'Bundle' name = 'tbl2asn' version = '20230713' @@ -14,27 +15,42 @@ description = """Tbl2asn is a command-line program that automates the creation o sequence records for submission to GenBank""" toolchain = SYSTEM +builddependencies = [ + ('binutils', '2.35'), +] + +default_easyblock = 'CmdCp' # It is not entirely clean how long NCBI keeps "older" versions. At April 29, 2022, we had six timestamps/versions, # reporiting the same verion (tbl2asn --help -> 25.8) but 5 out of 6 (gunzipped) executables have different sha256 # checksums. -source_urls = ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % - (version[:4] + '-' + version[4:6] + '-' + version[6:])] -sources = [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], - 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}] -checksums = ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'] - -cmds_map = [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")] -files_to_copy = [ - (['tbl2asn'], 'bin'), +components = [ + ('libidn', '1.34', { + 'easyblock': 'ConfigureMake', + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': '%(namelower)s-%(version)s', + 'checksums': ['3719e2975f2fb28605df3479c380af2cf4ab4e919e1506527e4c7670afff6e3c'], + }), + (name, version, { + 'source_urls': ['https://ftp.ncbi.nih.gov/toolbox/ncbi_tools/converters/versions/%s/all/' % + (version[:4] + '-' + version[4:6] + '-' + version[6:])], + 'sources': [{'download_filename': 'tbl2asn.%s.gz' % versionsuffix[1:], + 'filename': '%(name)s-%(version)s%(versionsuffix)s.gz'}], + 'checksums': ['544c4a2a53f2121fd21c44778fc61980a701ce852ea0142979241c0465c38a0c'], + 'cmds_map': [('.*', "cp %(name)s-%(version)s%(versionsuffix)s tbl2asn")], + 'files_to_copy': [(['tbl2asn'], 'bin')], + }), ] +postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] + sanity_check_paths = { - 'files': ['bin/tbl2asn'], - 'dirs': [], + 'files': ['bin/tbl2asn', 'bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], } -postinstallcmds = ["chmod +x %(installdir)s/bin/tbl2asn"] +sanity_check_commands = ['tbl2asn --help'] moduleclass = 'bio' From 7ef9c60813e8b07606b3e1c371ed69b8f34dcb98 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Feb 2024 16:22:20 +0100 Subject: [PATCH 0637/1193] don't use git_config for BWA + use - to separate datestamp from version when using specific commit --- ... => BWA-0.7.17-20220923-GCCcore-12.3.0.eb} | 19 +++++-------------- 1 file changed, 5 insertions(+), 14 deletions(-) rename easybuild/easyconfigs/b/BWA/{BWA-0.7.17.20220923-GCCcore-12.3.0.eb => BWA-0.7.17-20220923-GCCcore-12.3.0.eb} (79%) diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-20220923-GCCcore-12.3.0.eb similarity index 79% rename from easybuild/easyconfigs/b/BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/b/BWA/BWA-0.7.17-20220923-GCCcore-12.3.0.eb index 380dd41df28c..6f701c63b85b 100644 --- a/easybuild/easyconfigs/b/BWA/BWA-0.7.17.20220923-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-20220923-GCCcore-12.3.0.eb @@ -17,10 +17,10 @@ ## name = 'BWA' -version = '0.7.17.20220923' +local_commit = '139f68f' +version = '0.7.17-20220923' homepage = 'http://bio-bwa.sourceforge.net/' - description = """ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human @@ -30,18 +30,9 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} -local_commit = '139f68f' - -sources = [{ - 'filename': '%s-%s-%s.tar.gz' % (name, version, local_commit), - 'git_config': { - 'url': 'https://github.com/lh3', - 'repo_name': 'bwa', - 'commit': local_commit, - 'recursive': True, - }, -}] -checksums = ['127d3f82ccc3bf7e918d2e64cafc0ffc49ff841b0955327f4666ca448364859f'] +source_urls = ['https://github.com/lh3/bwa/archive'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['be460d6e13ddf34896aafae00bad71e05a0b9f7e23490eeeca8ad257065f5e60'] builddependencies = [('binutils', '2.40')] From d5f78ab05a3356dded3bb9bf11a3397aad462973 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 8 Feb 2024 17:39:13 +0100 Subject: [PATCH 0638/1193] adding easyconfigs: FFAVES-2022.11.1-foss-2022a.eb --- .../f/FFAVES/FFAVES-2022.11.1-foss-2022a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFAVES/FFAVES-2022.11.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/f/FFAVES/FFAVES-2022.11.1-foss-2022a.eb b/easybuild/easyconfigs/f/FFAVES/FFAVES-2022.11.1-foss-2022a.eb new file mode 100644 index 000000000000..27f977391e0d --- /dev/null +++ b/easybuild/easyconfigs/f/FFAVES/FFAVES-2022.11.1-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'FFAVES' +version = '2022.11.1' +local_commit = '2c1fa89' + +homepage = 'https://github.com/aradley/FFAVES' +description = """Functional Feature Amplification Via Entropy Sorting (FFAVES). +Use FFAVES to amplify the signal of groups of co-regulating genes in an unsupervised, multivariate manner. +By amplifying the signal of genes with correlated expression, while filtering out genes that are randomly expressed, +we can identify a subset of genes more predictive of different cell types. +The output of FFAVES can then be used in our second algorithm, entropy sort feature weighting (ESFW), +to create a ranked list of genes that are most likely to pertain to distinct +sub-populations of cells in an scRNA-seq dataset. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('dill', '0.3.8', { + 'checksums': ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'], + }), + ('multiprocess', '0.70.16', { + 'checksums': ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'], + }), + (name, version, { + 'preinstallopts': "sed -i 's/==/>=/' requirements.txt && ", + 'source_urls': ['https://github.com/aradley/FFAVES/archive/'], + 'sources': [{'download_filename': '2c1fa89.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b833cc26cc60ad44c48d1b5712ce32b0ceb7f8d7876c06466514f79d357e4f83'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ffaves.py', 'get_gprof', 'get_objgraph', 'undill']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +moduleclass = 'bio' From 26a736fe4ed5ec8ca0e4f676f2be0a0587b344b4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Feb 2024 15:34:06 +0100 Subject: [PATCH 0639/1193] adding easyconfigs: CENSO-1.2.0-GCCcore-12.3.0.eb, CREST-2.12-gfbf-2023a.eb --- .../c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb | 45 +++++++++++++++++++ .../c/CREST/CREST-2.12-gfbf-2023a.eb | 41 +++++++++++++++++ 2 files changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..eb81c834cb81 --- /dev/null +++ b/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'PythonBundle' + +name = 'CENSO' +version = '1.2.0' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/CENSO_docs/censo.html' +description = """Commandline Energetic SOrting (CENSO) is a sorting algorithm for +efficient evaluation of Structure Ensembles (SE). The input ensemble (or single +structure) originating from a CREST[SQM/FF] run can be ranked by free energy at +DFT level and/or geometries can be optimized using DFT.""" + +citing = """The main publication for the CENSO program can be found at J. Phys. Chem. A 2021 +https://pubs.acs.org/doi/10.1021/acs.jpca.1c00971""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# CENSO interfaces with QM codes like xtb, crest, TURBOMOLE and ORCA. +# User can load any of those at runtime +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/grimme-lab/CENSO/archive'], + 'sources': ['v.%(version)s.tar.gz'], + 'checksums': ['f1d77d8eb9d25fe4157491a5d298321f84999123970411831b059cea39aecad2'], + 'modulename': 'censo_qm' + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/censo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["censo --help"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023a.eb b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023a.eb new file mode 100644 index 000000000000..8c77a302032a --- /dev/null +++ b/easybuild/easyconfigs/c/CREST/CREST-2.12-gfbf-2023a.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +# Update to 2.12: +# Author: J. Sassmannshausen (Imperial College London) + +easyblock = 'CMakeMake' + +name = 'CREST' +version = '2.12' + +homepage = 'https://xtb-docs.readthedocs.io/en/latest/crest.html' +description = """CREST is an utility/driver program for the xtb program. Originally it was designed + as conformer sampling program, hence the abbreviation Conformer–Rotamer Ensemble Sampling Tool, + but now offers also some utility functions for calculations with the GFNn–xTB methods. Generally + the program functions as an IO based OMP scheduler (i.e., calculations are performed by the xtb + program) and tool for the creation and analysation of structure ensembles. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'opt': True, 'optarch': True, 'extra_fflags': '-ffree-line-length-none'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['390f0ac0aedafbd6bb75974fcffefe7e0232ad6c4ea0ab4f1a77e656a3ce263d'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [('xtb', '6.6.1')] # required to run the program + +# Simple test command just to check if the program is working: +test_cmd = 'export PATH=%(builddir)s/easybuild_obj:$PATH && ' +test_cmd += 'cd %(builddir)s/%(namelower)s-%(version)s/examples/expl-0/ && ./run.sh ' + +sanity_check_paths = { + 'files': ['bin/%s' % name.lower()], + 'dirs': [], +} + +sanity_check_commands = ["crest -h", "crest --cite"] + +moduleclass = 'chem' From 1e6c888cd55d5147dfc552649326b96efcec19d3 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Feb 2024 15:36:51 +0100 Subject: [PATCH 0640/1193] downgrade xtb v6.6.1 from foss/2023a to gfbf/2023a --- .../x/xtb/{xtb-6.6.1-foss-2023a.eb => xtb-6.6.1-gfbf-2023a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/x/xtb/{xtb-6.6.1-foss-2023a.eb => xtb-6.6.1-gfbf-2023a.eb} (95%) diff --git a/easybuild/easyconfigs/x/xtb/xtb-6.6.1-foss-2023a.eb b/easybuild/easyconfigs/x/xtb/xtb-6.6.1-gfbf-2023a.eb similarity index 95% rename from easybuild/easyconfigs/x/xtb/xtb-6.6.1-foss-2023a.eb rename to easybuild/easyconfigs/x/xtb/xtb-6.6.1-gfbf-2023a.eb index 2c7121360de1..7b92e5920d52 100644 --- a/easybuild/easyconfigs/x/xtb/xtb-6.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/x/xtb/xtb-6.6.1-gfbf-2023a.eb @@ -6,7 +6,7 @@ version = '6.6.1' homepage = 'https://xtb-docs.readthedocs.io' description = """ xtb - An extended tight-binding semi-empirical program package. """ -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} github_account = 'grimme-lab' source_urls = [GITHUB_LOWER_SOURCE] From da8b731a9dde458b8fe905b3f62a4ab734ced51b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Feb 2024 16:00:07 +0100 Subject: [PATCH 0641/1193] add build dependency on binutils to CENSO-1.2.0-GCCcore-12.3.0.eb --- easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb index eb81c834cb81..4482c3a592bc 100644 --- a/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/CENSO/CENSO-1.2.0-GCCcore-12.3.0.eb @@ -16,6 +16,10 @@ https://pubs.acs.org/doi/10.1021/acs.jpca.1c00971""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40'), +] + # CENSO interfaces with QM codes like xtb, crest, TURBOMOLE and ORCA. # User can load any of those at runtime dependencies = [ From bac989728011acb5a43accd6d772edab809d83f2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Feb 2024 16:19:57 +0100 Subject: [PATCH 0642/1193] add alembic to SQLAlchemy-2.0.25-GCCcore-12.3.0.eb --- .../s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb index 442398989587..352d4e5fd08a 100644 --- a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.25-GCCcore-12.3.0.eb @@ -19,6 +19,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), ('psycopg2', '2.9.9'), # optional, postgresql extra + ('Mako', '1.2.4'), # needed by alembic ] use_pip = True @@ -37,6 +38,9 @@ exts_list = [ 'use_pip_extras': 'asyncio,postgresql,postgresql_asyncpg', 'checksums': ['a2c69a7664fb2d54b8682dd774c3b54f67f84fa123cf84dda2a5f40dcaa04e08'], }), + ('alembic', '1.13.1', { + 'checksums': ['4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595'], + }), ] sanity_pip_check = True From 7a466ef0b736892be66e391165497f6abe91a914 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Sat, 10 Feb 2024 13:11:45 +0000 Subject: [PATCH 0643/1193] add libhandy --- .../libhandy/libhandy-1.8.2-GCCcore-12.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libhandy/libhandy-1.8.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/libhandy/libhandy-1.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libhandy/libhandy-1.8.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b5adc2d9fad4 --- /dev/null +++ b/easybuild/easyconfigs/l/libhandy/libhandy-1.8.2-GCCcore-12.3.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MesonNinja' + +name = 'libhandy' +version = '1.8.2' + +homepage = 'https://gnome.pages.gitlab.gnome.org/libhandy/' +description = "Building blocks for modern adaptive GNOME apps" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/%(name)s/-/archive/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['2c551aae128dff918b84943a93a58bc9be84f42a709b9e43c8d074538e68c10e'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Vala', '0.56.14'), +] + +dependencies = [ + ('GObject-Introspection', '1.76.1'), + ('GTK3', '3.24.37'), + ('FriBidi', '1.0.12'), +] + +configopts = '-Dgtk_doc=false' + +sanity_check_paths = { + 'files': ['bin/handy-1-demo', 'lib/%%(name)s-1.%s' % SHLIB_EXT, 'lib/pkgconfig/libhandy-1.pc'], + 'dirs': ['include/libhandy-1'], +} + +moduleclass = 'lib' From c14a849395cf1ba70d5e1d8942b5e1ee4e433548 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Feb 2024 16:10:50 +0000 Subject: [PATCH 0644/1193] adding easyconfigs: build-1.0.3-foss-2023a.eb --- .../b/build/build-1.0.3-foss-2023a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb b/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb new file mode 100644 index 000000000000..f91a0c87e9e4 --- /dev/null +++ b/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'build' +version = '1.0.3' + +homepage = 'https://github.com/pypa/build' +description = """A simple, correct Python build frontend.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_list = [ + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + (name, version, { + 'checksums': ['538aab1b64f9828977f84bc63ae570b060a8ed1be419e7870b8b4fc5e6ea553b'], + }), +] + +sanity_check_commands = [ + "python3 -m build -V", +] + +moduleclass = 'devel' From 62aa3b0477424ea7e75c0c96b754a49ab80d426a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 11 Feb 2024 16:23:55 +0000 Subject: [PATCH 0645/1193] remember eb4 options --- easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb b/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb index f91a0c87e9e4..ddde55757bd4 100644 --- a/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb +++ b/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023a.eb @@ -12,6 +12,9 @@ dependencies = [ ('Python', '3.11.3'), ] +use_pip = True +sanity_pip_check = True + exts_list = [ ('pyproject_hooks', '1.0.0', { 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], From 211a0a3cebb08abaa4cbb034bcc7f1f81e54065a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Feb 2024 21:32:41 +0100 Subject: [PATCH 0646/1193] add missing dependencies for fslpy in easyconfig for FSL v6.0.5.1 --- .../f/FSL/FSL-6.0.5.1-foss-2021a.eb | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb index 490c55164b60..8a3d4685ce6a 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb @@ -52,30 +52,40 @@ dependencies = [ ('GSL', '2.7'), ('Qwt', '6.2.0'), ('h5py', '3.2.1'), + ('NiBabel', '3.2.1'), ] modextrapaths = {'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages']} -# The executable files 'imglob' and 'imcp' come from fslpy exts_defaultclass = 'PythonPackage' exts_default_options = { + 'buildininstalldir': False, + 'source_urls': [PYPI_LOWER_SOURCE], 'download_dep_fail': True, 'use_pip': True, } exts_list = [ + ('dataclasses', '0.8', { + 'checksums': ['8479067f342acf957dc82ec415d355ab5edb7e7646b90dc6e2fd1d96ad084c97'], + 'preinstallopts': "sed -i '/python_requires/d' setup.py && ", + }), + # The executable files 'imglob' and 'imcp' come from fslpy ('fslpy', '3.5.3', { - 'installopts': '--prefix=%(installdir)s/fsl', - 'source_urls': ['https://pypi.python.org/packages/source/f/fslpy/'], 'checksums': ['f80ef8b7b49f475bfb71946619d33c118a7cbbe106c72f7777aaf14d9e261530'], + 'installopts': '--prefix=%(installdir)s/fsl', }), ] +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + modextravars = { 'FSLOUTPUTTYPE': 'NIFTI_GZ', 'FSLMULTIFILEQUIT': 'TRUE', 'FSLTCLSH': 'tclsh', - 'FSLWISH': 'wish8.6' + 'FSLWISH': 'wish8.6', } moduleclass = 'bio' From 6fe0d6bbfa2cb5a6458404a7d4206b2331d9a543 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Feb 2024 22:54:13 +0100 Subject: [PATCH 0647/1193] fix duplicate modextrapaths in FSL easyconfig --- easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb index 8a3d4685ce6a..418940cf74a6 100644 --- a/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb +++ b/easybuild/easyconfigs/f/FSL/FSL-6.0.5.1-foss-2021a.eb @@ -55,8 +55,6 @@ dependencies = [ ('NiBabel', '3.2.1'), ] -modextrapaths = {'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages']} - exts_defaultclass = 'PythonPackage' exts_default_options = { 'buildininstalldir': False, @@ -78,7 +76,7 @@ exts_list = [ ] modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'PYTHONPATH': ['fsl/lib/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages'], } modextravars = { From 56793bccdb8f0ad1b9b575e8e549ccafd7eb329e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sun, 11 Feb 2024 23:09:30 +0100 Subject: [PATCH 0648/1193] bump OpenSSL 3 wrapper fallback to 3.2.1 --- easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb index 8c5991c16269..13b0f8437a92 100644 --- a/easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb +++ b/easybuild/easyconfigs/o/OpenSSL/OpenSSL-3.eb @@ -28,11 +28,11 @@ builddependencies = [ # component list, which will be build and installed as usual. components = [ - (name, '3.2.0', { + (name, '3.2.1', { 'easyblock': 'EB_OpenSSL', 'source_urls': ['https://www.openssl.org/source/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['14c826f07c7e433706fb5c69fa9e25dab95684844b4c962a2cf1bf183eb4690e'], + 'checksums': ['83c7329fe52c850677d75e5d0b0ca245309b97e8ecbcfdc1dfdc4ab9fac35b39'], 'start_dir': '%(namelower)s-%(version)s', }), ] From 6182446308b0960accd211672e4e174f008057b9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 12 Feb 2024 11:48:11 +0100 Subject: [PATCH 0649/1193] fix dependency version --- easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb index d2dd82d498e8..dffdad4341fc 100644 --- a/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb +++ b/easybuild/easyconfigs/m/medaka/medaka-1.11.3-foss-2023a.eb @@ -36,7 +36,7 @@ dependencies = [ ('pyspoa', '0.2.1'), ('python-parasail', '1.3.4'), ('ont-fast5-api', '4.1.2'), - ('WhatsHap', '2.1'), + ('WhatsHap', '2.2'), ('intervaltree-python', '3.1.0'), ('BCFtools', '1.18'), ] From 155104fda55aa9d8cd76818b70b67387309cfb3a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 13:38:42 +0100 Subject: [PATCH 0650/1193] adding easyconfigs: CubeLib-4.8.2-GCCcore-13.2.0.eb, CubeWriter-4.8.2-GCCcore-13.2.0.eb, OPARI2-2.0.8-GCCcore-13.2.0.eb, OTF2-3.0.3-GCCcore-13.2.0.eb, PAPI-7.1.0-GCCcore-13.2.0.eb, PDT-3.25.2-GCCcore-13.2.0.eb, Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb, Score-P-8.3-gompi-2023b.eb, SIONlib-1.7.7-GCCcore-13.2.0-tools.eb --- .../c/CubeLib/CubeLib-4.8.2-GCCcore-13.2.0.eb | 51 +++++++++++++++++ .../CubeWriter-4.8.2-GCCcore-13.2.0.eb | 51 +++++++++++++++++ .../o/OPARI2/OPARI2-2.0.8-GCCcore-13.2.0.eb | 44 ++++++++++++++ .../o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb | 50 ++++++++++++++++ .../p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb | 49 ++++++++++++++++ .../p/PDT/PDT-3.25.2-GCCcore-13.2.0.eb | 40 +++++++++++++ .../SIONlib-1.7.7-GCCcore-13.2.0-tools.eb | 51 +++++++++++++++++ .../Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb | 57 +++++++++++++++++++ .../s/Score-P/Score-P-8.3-gompi-2023b.eb | 54 ++++++++++++++++++ 9 files changed, 447 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6fcd6c4bd018 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8.2-GCCcore-13.2.0.eb @@ -0,0 +1,51 @@ +# Copyright 2019 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeLib' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube general purpose C++ library component and + command-line tools. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d6fdef57b1bc9594f1450ba46cf08f431dd0d4ae595c47e2f3454e17e4ae74f4'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubelib-config', + 'lib/libcube4.a', 'lib/libcube4.%s' % SHLIB_EXT], + 'dirs': ['include/cubelib'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..d3ca6064df93 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8.2-GCCcore-13.2.0.eb @@ -0,0 +1,51 @@ +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Copyright 2023-2024 TU Dresden, Germany +# Authors:: Markus Geimer +# Alexander Grund +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ + +easyblock = 'EB_Score_minus_P' + +name = 'CubeWriter' +version = '4.8.2' + +homepage = 'https://www.scalasca.org/software/cube-4.x/download.html' +description = """ + Cube, which is used as performance report explorer for Scalasca and Score-P, + is a generic tool for displaying a multi-dimensional performance space + consisting of the dimensions (i) performance metric, (ii) call path, and + (iii) system resource. Each dimension can be represented as a tree, where + non-leaf nodes of the tree can be collapsed or expanded to achieve the + desired level of granularity. + + This module provides the Cube high-performance C writer library component. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['4f3bcf0622c2429b8972b5eb3f14d79ec89b8161e3c1cc5862ceda417d7975d2'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +configopts = '--enable-shared' + +sanity_check_paths = { + 'files': ['bin/cubew-config', + 'lib/libcube4w.a', 'lib/libcube4w.%s' % SHLIB_EXT], + 'dirs': ['include/cubew'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..627b4923cd79 --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.8-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'ConfigureMake' + +name = 'OPARI2' +version = '2.0.8' + +homepage = 'https://www.score-p.org' +description = """ + OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a + source-to-source instrumentation tool for OpenMP and hybrid codes. + It surrounds OpenMP directives and runtime library calls with calls + to the POMP2 measurement interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['196e59a2a625e6c795a6124c61e784bad142f9f38df0b4fa4d435ba9b9c19721'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['bin/opari2', 'include/opari2/pomp2_lib.h'], + 'dirs': [], +} + +sanity_check_commands = ['opari2-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..48cbf931ec51 --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.3-GCCcore-13.2.0.eb @@ -0,0 +1,50 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +easyblock = 'EB_Score_minus_P' + +name = 'OTF2' +version = '3.0.3' + +homepage = 'https://www.score-p.org' +description = """ + The Open Trace Format 2 is a highly scalable, memory efficient event trace + data format plus support library. It is the new standard trace format for + Scalasca, Vampir, and TAU and is open for other tools. + +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['18a3905f7917340387e3edc8e5766f31ab1af41f4ecc5665da6c769ca21c4ee8'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + # SIONlib container support (optional): + ('SIONlib', '1.7.7', '-tools'), +] + +configopts = '--enable-shared' + + +sanity_check_paths = { + 'files': ['bin/otf2-config', 'include/otf2/otf2.h', + 'lib/libotf2.a', 'lib/libotf2.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s-config --help'] + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..fafbe94664c4 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +## +# Author: Robert Mijakovic +# Updated: Alexander Grund +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.1.0' + +homepage = 'https://icl.cs.utk.edu/projects/papi/' +description = """ + PAPI provides the tool designer and application engineer with a consistent + interface and methodology for use of the performance counter hardware found + in most major microprocessors. PAPI enables software engineers to see, in near + real time, the relation between software performance and processor events. + In addition Component PAPI provides access to a collection of components + that expose performance measurement opportunites across the hardware and + software stack. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://icl.utk.edu/projects/papi/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5818afb6dba3ece57f51e65897db5062f8e3464e6ed294b654ebf34c3991bc4f'] + +builddependencies = [ + ('binutils', '2.40'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +# There is also "fulltest" that is a superset of "test" but hangs on some processors +# indefinitely with a defunct `make` process. So use only "test". +runtest = 'test' + +sanity_check_paths = { + 'files': ["bin/papi_%s" % x + for x in ["avail", "clockres", "command_line", "component_avail", + "cost", "decode", "error_codes", "event_chooser", + "mem_info", "multiplex_cost", "native_avail", + "version", "xml_event_info"]], + 'dirs': [], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..182c5d920a02 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.2-GCCcore-13.2.0.eb @@ -0,0 +1,40 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2013-2019 Juelich Supercomputing Centre, Germany +# Authors:: Bernd Mohr +# Markus Geimer +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +# # + +name = 'PDT' +version = '3.25.2' + +homepage = 'https://www.cs.uoregon.edu/research/pdt/' +description = """ + Program Database Toolkit (PDT) is a framework for analyzing source code + written in several programming languages and for making rich program + knowledge accessible to developers of static and dynamic analysis tools. + PDT implements a standard program representation, the program database + (PDB), that can be accessed in a uniform way through a class library + supporting common PDB operations. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +# Might now be available as direct download although e.g. http://tau.uoregon.edu/pdt.tgz may work +download_instructions = ("Download from https://www.cs.uoregon.edu/research/pdt/downloads.php " + + "and rename to " + sources[0]) +checksums = ['01c2d403bc6672b2b264a182c325806541066c5ed5713878eb598f5506428cbe'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb new file mode 100644 index 000000000000..4ac7b2ae50d1 --- /dev/null +++ b/easybuild/easyconfigs/s/SIONlib/SIONlib-1.7.7-GCCcore-13.2.0-tools.eb @@ -0,0 +1,51 @@ +# # +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2016-2019 Juelich Supercomputing Centre, Germany +# Authors:: Markus Geimer +# Modified 2017 by Andreas Henkel +# License:: 3-clause BSD +# # + +easyblock = 'ConfigureMake' + +name = 'SIONlib' +version = '1.7.7' +# Provide a stripped-down version with renamed symbols for tools, +# see description for further details +versionsuffix = '-tools' + +homepage = 'https://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html' +description = """ + SIONlib is a scalable I/O library for parallel access to task-local files. + The library not only supports writing and reading binary data to or from + several thousands of processors into a single or a small number of physical + files, but also provides global open and close functions to access SIONlib + files in parallel. This package provides a stripped-down installation of + SIONlib for use with performance tools (e.g., Score-P), with renamed symbols + to avoid conflicts when an application using SIONlib itself is linked against + a tool requiring a different SIONlib version. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://apps.fz-juelich.de/jsc/%(namelower)s/download.php?version=%(version)sl'] +sources = ['%(namelower)s-%(version)sl.tar.gz'] +checksums = ['3b5072d8a32a9e9858d85dfe4dc01e7cfdbf54cdaa60660e760b634ee08d8a4c'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = '--disable-cxx --disable-fortran --disable-ompi ' + +# Comment it out if you have Xeon Phi: +configopts += '--disable-mic ' + +sanity_check_paths = { + 'files': ['bin/sionconfig'] + + ['lib/lib%s_64.a' % x for x in ['lsioncom', 'lsiongen', 'lsionser']], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb new file mode 100644 index 000000000000..cc589f1caa9e --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['76c914e6319221c059234597a3bc53da788ed679179ac99c147284dcefb1574a'] + +dependencies = [ + ('CUDA', '12.3.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b.eb new file mode 100644 index 000000000000..7d56fa199bb9 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b.eb @@ -0,0 +1,54 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.3' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['76c914e6319221c059234597a3bc53da788ed679179ac99c147284dcefb1574a'] + +dependencies = [ + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 47d1b5d5dd20491db1ec2c54e9b486293990eba5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:09:56 +0100 Subject: [PATCH 0651/1193] remove numa configure option from hwloc 2.2+ --- easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.4.1-GCCcore-10.3.0.eb | 3 +-- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb index ddabd3a73812..f3d9db107b45 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-10.2.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb index a109e5d7a9b0..a4faff0a4288 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.2.0-GCCcore-9.3.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.4.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.4.1-GCCcore-10.3.0.eb index d107ffdc713f..c073323d16af 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.4.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.4.1-GCCcore-10.3.0.eb @@ -38,8 +38,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', From 78d48913b8900e9ebf31b36882fdd764e88b4bfb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:12:17 +0100 Subject: [PATCH 0652/1193] remove numa configure option from hwloc 2+ --- easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb | 3 +-- easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb | 3 +-- 3 files changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb index 72e874914ceb..8cfa41cb0c5e 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.2-GCCcore-8.2.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.14'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb index 78cc42f4ed76..c9c64f7bbfc1 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.0.3-GCCcore-8.3.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.14'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', diff --git a/easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb b/easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb index ed6d9b15b312..4abf2d989abc 100644 --- a/easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.1.0-GCCcore-9.2.0.eb @@ -35,8 +35,7 @@ dependencies = [ ('libpciaccess', '0.16'), ] -configopts = "--enable-libnuma=$EBROOTNUMACTL " -configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " +configopts = "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " sanity_check_paths = { 'files': ['bin/lstopo', 'include/hwloc/linux.h', From cbcc136a5dc740ebe2bf88df26c7180f7abf6830 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:28:25 +0100 Subject: [PATCH 0653/1193] Add more patches and sort them --- ...able-cudnn-tf32-for-too-strict-tests.patch | 15 ----- .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 24 +++++-- .../PyTorch-2.1.2_add-cuda-skip-markers.patch | 59 +++++++++++++++++ ....1.2_fix-conj-mismatch-test-failures.patch | 66 +++++++++++++++++++ .../PyTorch-2.1.2_fix-device-mesh-check.patch | 22 +++++++ .../PyTorch-2.1.2_relax-cuda-tolerances.patch | 22 +++++++ ...ve-nccl-backend-default-without-gpus.patch | 41 ++++++++++++ ...ip-failing-test_dtensor_ops-subtests.patch | 36 ++++++++++ 8 files changed, 264 insertions(+), 21 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_add-cuda-skip-markers.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-device-mesh-check.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_relax-cuda-tolerances.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch index f991b44530b4..e40b2cccf535 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch @@ -28,21 +28,6 @@ author: Alex Domingo (Vrije Universiteit Brussel) def test_partial_flat_weights(self): input_size = 10 hidden_size = 6 ---- test/jit/test_freezing.py.orig 2024-01-15 14:38:11.054125484 +0100 -+++ test/jit/test_freezing.py 2024-01-15 14:49:41.689011617 +0100 -@@ -2733,7 +2733,11 @@ - else: - FileCheck().check("aten::cudnn_convolution_relu").run(frozen_mod.graph) - -- self.assertEqual(mod_eager(inp), frozen_mod(inp)) -+ if not TEST_WITH_ROCM: -+ with torch.backends.cudnn.flags(enabled=True, allow_tf32=False): -+ self.assertEqual(mod_eager(inp), frozen_mod(inp)) -+ else: -+ self.assertEqual(mod_eager(inp), frozen_mod(inp)) - - @unittest.skipIf(not (TEST_CUDNN or TEST_WITH_ROCM), "requires CUDNN") - def test_freeze_conv_relu_fusion_not_forward(self): --- ../PyTorch/2.1.2/foss-2023a-CUDA-12.1.1/pytorch-v2.1.2/test/nn/test_convolution.py 2023-12-15 03:03:27.000000000 +0100 +++ test/nn/test_convolution.py 2024-01-15 15:03:15.606208376 +0100 @@ -518,7 +518,7 @@ diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 665750b5fb6f..9aee7924a4f8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -31,6 +31,7 @@ patches = [ 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', 'PyTorch-2.1.0_disable-gcc12-warning.patch', + 'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch', 'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch', 'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch', 'PyTorch-2.1.0_fix-validationError-output-test.patch', @@ -43,15 +44,19 @@ patches = [ 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', 'PyTorch-2.1.0_skip-test_wrap_bad.patch', + 'PyTorch-2.1.2_add-cuda-skip-markers.patch', + 'PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch', + 'PyTorch-2.1.2_fix-device-mesh-check.patch', 'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch', 'PyTorch-2.1.2_fix-test_memory_profiler.patch', 'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch', 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', + 'PyTorch-2.1.2_relax-cuda-tolerances.patch', + 'PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', - 'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch', - 'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch', ] checksums = [ {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, @@ -87,6 +92,8 @@ checksums = [ {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, {'PyTorch-2.1.0_disable-gcc12-warning.patch': 'c858b8db0010f41005dc06f9a50768d0d3dc2d2d499ccbdd5faf8a518869a421'}, + {'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch': + 'd895018ebdfd46e65d9f7645444a3b4c5bbfe3d533a08db559a04be34e01e478'}, {'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch': 'b15b1291a3c37bf6a4982cfbb3483f693acb46a67bc0912b383fd98baf540ccf'}, {'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch': @@ -109,6 +116,10 @@ checksums = [ {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, + {'PyTorch-2.1.2_add-cuda-skip-markers.patch': 'd007d6d0cdb533e7d01f503e9055218760123a67c1841c57585385144be18c9a'}, + {'PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch': + 'c164357efa4ce88095376e590ba508fc1daa87161e1e59544eda56daac7f2847'}, + {'PyTorch-2.1.2_fix-device-mesh-check.patch': 'c0efc288bf3d9a9a3c8bbd2691348a589a2677ea43880a8c987db91c8de4806b'}, {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch': 'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'}, {'PyTorch-2.1.2_fix-test_memory_profiler.patch': @@ -117,14 +128,15 @@ checksums = [ 'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'}, {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'}, {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, + {'PyTorch-2.1.2_relax-cuda-tolerances.patch': '554ad09787f61080fafdb84216e711e32327aa357e2a9c40bb428eb6503dee6e'}, + {'PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch': + 'e6a1efe3d127fcbf4723476a7a1c01cfcf2ccb16d1fb250f478192623e8b6a15'}, {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch': + '6cf711bf26518550903b09ed4431de9319791e79d61aab065785d6608fd5cc88'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, - {'PyTorch-2.1.0_skip-test-linalg-svd-complex.patch': - '5ba7e0b4203ea8c27b55b5231de024004697aca7bbae30aa248524babb451dc7'}, - {'PyTorch-2.1.0_disable-cudnn-tf32-for-too-strict-tests.patch': - '7abccc94f0ae6c317d5d08d4db4e3724eedde8d1d00707e78cf57d8cbf858be5'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_add-cuda-skip-markers.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_add-cuda-skip-markers.patch new file mode 100644 index 000000000000..4bf18dde7375 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_add-cuda-skip-markers.patch @@ -0,0 +1,59 @@ +distributed/test_inductor_collectives & distributed/test_dynamo_distributed fail when run without GPUs +with "RuntimeError: ProcessGroupNCCL is only supported with GPUs, no GPUs found!" +Skip those in that case. +See https://github.com/pytorch/pytorch/pull/117741 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/test_dynamo_distributed.py b/test/distributed/test_dynamo_distributed.py +index c8fae62bd62..6220b62a9a9 100644 +--- a/test/distributed/test_dynamo_distributed.py ++++ b/test/distributed/test_dynamo_distributed.py +@@ -30,6 +30,7 @@ from torch.testing._internal.common_distributed import ( + requires_nccl, + _dynamo_dist_per_rank_init, + ) ++from torch.testing._internal.common_utils import requires_cuda + import torch._dynamo.logging + from torch._dynamo.comptime import comptime + +@@ -452,6 +453,7 @@ class TestMultiProc(DynamoDistributedMultiProcTestCase): + + + @requires_nccl() ++@requires_cuda + class TestSingleProc(DynamoDistributedSingleProcTestCase): + """ + Test harness initializes dist process group. +diff --git a/test/distributed/test_inductor_collectives.py b/test/distributed/test_inductor_collectives.py +index 9183e2e9ce4..37149865fd9 100644 +--- a/test/distributed/test_inductor_collectives.py ++++ b/test/distributed/test_inductor_collectives.py +@@ -19,6 +19,7 @@ from torch.testing._internal.common_distributed import ( + requires_nccl, + skip_if_lt_x_gpu, + ) ++from torch.testing._internal.common_utils import requires_cuda + from torch._inductor.compile_fx import compile_fx as inductor_compile_fx + from torch._inductor.utils import has_triton, run_and_get_triton_code + import torch._dynamo.logging +@@ -216,6 +217,7 @@ class TestCollectivesMultiProc(DynamoDistributedMultiProcTestCase): + + + @requires_nccl() ++@requires_cuda + class TestCollectivesInductor(DynamoDistributedSingleProcTestCase): + """ + Prefer single-proc test runner for basic tests as it is easier to work with. +diff --git a/torch/testing/_internal/common_utils.py b/torch/testing/_internal/common_utils.py +index 1e18ca2afec..bad5af5212f 100644 +--- a/torch/testing/_internal/common_utils.py ++++ b/torch/testing/_internal/common_utils.py +@@ -1111,6 +1111,7 @@ if TEST_CUDA and 'NUM_PARALLEL_PROCS' in os.environ: + # other libraries take up about 11% of space per process + torch.cuda.set_per_process_memory_fraction(round(1 / num_procs - .11, 2)) + ++requires_cuda = unittest.skipUnless(torch.cuda.is_available(), "Requires CUDA") + + def skipIfCrossRef(fn): + @wraps(fn) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch new file mode 100644 index 000000000000..0fcb86b16249 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch @@ -0,0 +1,66 @@ +In test_ops.py the tests test_python_ref_meta__refs_linalg_svd_cpu_complex* fail +when PyTorch is compiled with CUDA support with +> RuntimeError: Conj mismatch! is_conj is set to False and True + +This is a known issue (https://github.com/pytorch/pytorch/issues/105068) +so don't check the flag in the test. + +diff --git a/test/test_ops.py b/test/test_ops.py +index 08a8185d346..dc98e7c7439 100644 +--- a/test/test_ops.py ++++ b/test/test_ops.py +@@ -302,6 +302,10 @@ class TestCommon(TestCase): + @ops(python_ref_db) + @skipIfTorchInductor("Takes too long for inductor") + def test_python_ref_meta(self, device, dtype, op): ++ CHECK_CONJ_SKIPS = { ++ torch._refs.linalg.svd, ++ } ++ + with FakeTensorMode() as mode: + pass + +@@ -328,12 +332,12 @@ class TestCommon(TestCase): + + if isinstance(result, torch.Tensor): + self.assertTrue(isinstance(meta_result, FakeTensor)) +- prims.utils.compare_tensor_meta(result, meta_result) ++ prims.utils.compare_tensor_meta(result, meta_result, check_conj=op.op not in CHECK_CONJ_SKIPS) + elif isinstance(result, Sequence): + for a, b in zip(result, meta_result): + if isinstance(a, torch.Tensor) or isinstance(b, torch.Tensor): + self.assertTrue(isinstance(b, FakeTensor)) +- prims.utils.compare_tensor_meta(a, b) ++ prims.utils.compare_tensor_meta(a, b, check_conj=op.op not in CHECK_CONJ_SKIPS) + + def _ref_test_helper( + self, +diff --git a/torch/_prims_common/__init__.py b/torch/_prims_common/__init__.py +index d60931162da..da217470930 100644 +--- a/torch/_prims_common/__init__.py ++++ b/torch/_prims_common/__init__.py +@@ -90,7 +90,7 @@ def same_shape(a: ShapeType, b: ShapeType) -> bool: + + # TODO: look at using torch.testing.assert_close instead with an option + # to just compare metadata +-def compare_tensor_meta(a: TensorLikeType, b: TensorLikeType, check_strides=False): ++def compare_tensor_meta(a: TensorLikeType, b: TensorLikeType, check_strides=False, check_conj=True): + """ + Checks that two tensor likes have the same shape, + dtype and device. +@@ -131,10 +131,11 @@ def compare_tensor_meta(a: TensorLikeType, b: TensorLikeType, check_strides=Fals + msg = f"Storage offset mismatch! Storage offsets are {a.storage_offset()} and {b.storage_offset()}!" + raise RuntimeError(msg) + +- if a.is_conj() != b.is_conj(): +- raise RuntimeError( +- f"Conj mismatch! is_conj is set to {a.is_conj()} and {b.is_conj()}" +- ) ++ if check_conj: ++ if a.is_conj() != b.is_conj(): ++ raise RuntimeError( ++ f"Conj mismatch! is_conj is set to {a.is_conj()} and {b.is_conj()}" ++ ) + + if a.is_neg() != b.is_neg(): + raise RuntimeError( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-device-mesh-check.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-device-mesh-check.patch new file mode 100644 index 000000000000..e34583414360 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-device-mesh-check.patch @@ -0,0 +1,22 @@ +Fix error when there are more GPUs than ranks: +> RuntimeError: DeviceMesh only support homogeneous hardware, but found 4 ranks and 8 cuda devices! + +See https://github.com/pytorch/pytorch/pull/111091 + +diff --git a/torch/distributed/_tensor/device_mesh.py b/torch/distributed/_tensor/device_mesh.py +index b5e30eeca82..21ba82503a8 100644 +--- a/torch/distributed/_tensor/device_mesh.py ++++ b/torch/distributed/_tensor/device_mesh.py +@@ -165,7 +165,10 @@ class DeviceMesh: + # automatically set the current cuda/cuda-like device base on num of gpu devices available in each host + # NOTE: This device selection would only work for homogeneous hardware. + num_devices_per_host = device_handle.device_count() +- if world_size % num_devices_per_host != 0: ++ if ( ++ world_size > num_devices_per_host ++ and world_size % num_devices_per_host != 0 ++ ): + raise RuntimeError( + f"DeviceMesh only support homogeneous hardware, but found " + f"{world_size} ranks and {num_devices_per_host} {self.device_type} devices!" + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_relax-cuda-tolerances.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_relax-cuda-tolerances.patch new file mode 100644 index 000000000000..7301efcdd109 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_relax-cuda-tolerances.patch @@ -0,0 +1,22 @@ +test_jit fails in test_freeze_conv_relu_fusion with +Mismatched elements: 7 / 30 (23.3%) +Greatest absolute difference: 3.053247928619385e-05 at index (1, 1, 0, 0, 0) (up to 1e-05 allowed) +Greatest relative difference: 0.0004548609140329063 at index (3, 1, 0, 0, 0) (up to 1.3e-06 allowed) + +Increase the tolerance to allow this to pass. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/jit/test_freezing.py b/test/jit/test_freezing.py +index c8c1441adbf..e0feffd6bb5 100644 +--- a/test/jit/test_freezing.py ++++ b/test/jit/test_freezing.py +@@ -2733,7 +2733,7 @@ class TestFrozenOptimizations(JitTestCase): + else: + FileCheck().check("aten::cudnn_convolution_relu").run(frozen_mod.graph) + +- self.assertEqual(mod_eager(inp), frozen_mod(inp)) ++ self.assertEqual(mod_eager(inp), frozen_mod(inp), atol=1e-4, rtol=4e-3) + + @unittest.skipIf(not (TEST_CUDNN or TEST_WITH_ROCM), "requires CUDNN") + def test_freeze_conv_relu_fusion_not_forward(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch new file mode 100644 index 000000000000..6506508c9169 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch @@ -0,0 +1,41 @@ +In some code paths the ProcessGroupNCCL is created when PyTorch was compiled with NCCL. +However without any GPUs present at runtime the creation will fail with +> RuntimeError: ProcessGroupNCCL is only supported with GPUs, no GPUs found! + +Remove NCCL as a available default backend if CUDA isn't available. +See https://github.com/pytorch/pytorch/issues/117746 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/distributed/distributed_c10d.py b/torch/distributed/distributed_c10d.py +index 098e209264c..80962466bff 100644 +--- a/torch/distributed/distributed_c10d.py ++++ b/torch/distributed/distributed_c10d.py +@@ -271,9 +271,11 @@ class BackendConfig: + if backend == Backend.UNDEFINED: + # default config when backend is not specified + # supported since PyTorch 2.0 +- for device in Backend.default_device_backend_map: +- if is_backend_available(Backend.default_device_backend_map[device]): +- self.device_backend_map[device] = Backend.default_device_backend_map[device] ++ for device, default_backend in Backend.default_device_backend_map.items(): ++ if is_backend_available(default_backend): ++ if default_backend == Backend.NCCL and not torch.cuda.is_available(): ++ continue ++ self.device_backend_map[device] = default_backend + elif backend.lower() in Backend.backend_list: + # Cases for when backend is a single string (without device types) + # e.g. "nccl", "gloo", "ucc", "mpi" +diff --git a/test/distributed/test_c10d_common.py b/test/distributed/test_c10d_common.py +index a717c875e76..b382ba760f4 100644 +--- a/test/distributed/test_c10d_common.py ++++ b/test/distributed/test_c10d_common.py +@@ -1775,7 +1775,7 @@ class ProcessGroupWithDispatchedCollectivesTests(MultiProcessTestCase): + if not dist.is_mpi_available(): + continue + elif backend == dist.Backend.NCCL: +- if not dist.is_nccl_available(): ++ if not dist.is_nccl_available() or not torch.cuda.is_available(): + continue + elif backend == dist.Backend.GLOO: + if not dist.is_gloo_available(): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch new file mode 100644 index 000000000000..41bf36603018 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch @@ -0,0 +1,36 @@ +test_dtensor_op_db_nn_functional_pad_circular_cpu_float32 may unexpectatly succeed, just skip it. +Failure is expected until https://github.com/pytorch/pytorch/commit/9378a2ceda8 +test_dtensor_op_db_nn_functional_multi_head_attention_forward_cpu_float32 fails with +> NotImplementedError: Operator aten.constant_pad_nd.default does not have a sharding strategy registered. +Marked xfail in https://github.com/pytorch/pytorch/commit/49d826bcd3de952eb84a33c89ed399a1a2821c15 +test_dtensor_op_db_empty_strided_cpu_float32 doesn't make sense to run in the first place, +see https://github.com/pytorch/pytorch/issues/118094 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/_tensor/test_dtensor_ops.py b/test/distributed/_tensor/test_dtensor_ops.py +index b7d453e56be..5a27c7f84da 100644 +--- a/test/distributed/_tensor/test_dtensor_ops.py ++++ b/test/distributed/_tensor/test_dtensor_ops.py +@@ -147,6 +147,7 @@ dtensor_fails = { + xfail("dot"), + xfail("einsum"), + xfail("empty"), ++ skip("empty_strided"), + xfail("empty_like"), + xfail("empty_permuted"), + xfail("exponential"), +@@ -359,11 +360,12 @@ dtensor_fails = { + xfail("nn.functional.mish"), + xfail("nn.functional.mse_loss"), + xfail("nn.functional.multi_margin_loss"), ++ skip("nn.functional.multi_head_attention_forward"), + xfail("nn.functional.multilabel_margin_loss"), + xfail("nn.functional.multilabel_soft_margin_loss"), + xfail("nn.functional.nll_loss"), + xfail("nn.functional.normalize"), +- xfail("nn.functional.pad", "circular"), ++ skip("nn.functional.pad", "circular"), + xfail("nn.functional.pad", "constant"), + xfail("nn.functional.pad", "reflect"), + xfail("nn.functional.pad", "replicate"), From 7bc4243cbf3fdc957e9627b4005db3df8b105ed5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:29:04 +0100 Subject: [PATCH 0654/1193] Put CUDA dependencies together --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 9aee7924a4f8..379219b20f1d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -152,6 +152,9 @@ builddependencies = [ dependencies = [ ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.7.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.18.3', '-CUDA-%(cudaver)s'), ('Ninja', '1.11.1'), # Required for JIT compilation of C++ extensions ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), @@ -169,9 +172,6 @@ dependencies = [ ('networkx', '3.1'), ('sympy', '1.12'), ('Z3', '4.12.2', '-Python-%(pyver)s'), - ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), - ('magma', '2.7.2', versionsuffix), - ('NCCL', '2.18.3', versionsuffix), ] excluded_tests = { From 1482e78fc839321939d7e5aba26c0b36c18a038c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:29:41 +0100 Subject: [PATCH 0655/1193] Add sanity check for CUDA stub libs --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 379219b20f1d..b88302f9a685 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -206,6 +206,13 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # So allow a low number of tests to fail as the tests "usually" succeed max_failed_tests = 30 +# The readelf sanity check command can be taken out once the TestRPATH test from +# https://github.com/pytorch/pytorch/pull/109493 is accepted, since it is then checked as part of the PyTorch test suite +local_libcaffe2 = "$EBROOTPYTORCH/lib/python%%(pyshortver)s/site-packages/torch/lib/libcaffe2_nvrtc.%s" % SHLIB_EXT +sanity_check_commands = [ + "readelf -d %s | egrep 'RPATH|RUNPATH' | grep -v stubs" % local_libcaffe2, +] + tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'ai' From 7bb4b36642381858efb48a2afdde8b173e9fbd50 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:29:58 +0100 Subject: [PATCH 0656/1193] Use pip to install --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index b88302f9a685..9416d4cf12ce 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -174,6 +174,9 @@ dependencies = [ ('Z3', '4.12.2', '-Python-%(pyver)s'), ] +use_pip = True +buildcmd = '%(python)s setup.py build' # Run the (long) build in the build step + excluded_tests = { '': [ # This test seems to take too long on NVIDIA Ampere at least. From a9efd81e24a8bf0d6fe234b14f39ef28bf39f8fe Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 14:33:02 +0100 Subject: [PATCH 0657/1193] Reduce allowed test failures --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 9416d4cf12ce..a1419a04b134 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -207,7 +207,7 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # Especially test_quantization has a few corner cases that are triggered by the random input values, # those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 # So allow a low number of tests to fail as the tests "usually" succeed -max_failed_tests = 30 +max_failed_tests = 4 # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/109493 is accepted, since it is then checked as part of the PyTorch test suite From 230d530479ee5c9f6063e926dd5a7b9546aa90d3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 15:20:03 +0100 Subject: [PATCH 0658/1193] Remove CUDA variant --- .../Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb | 57 ------------------- 1 file changed, 57 deletions(-) delete mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb deleted file mode 100644 index cc589f1caa9e..000000000000 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.3.0.eb +++ /dev/null @@ -1,57 +0,0 @@ -# Copyright 2013-2020 Juelich Supercomputing Centre, Germany -# Copyright 2020-2024 TU Dresden, Germany -# Authors:: -# * Bernd Mohr -# * Markus Geimer -# * Alexander Grund -# * Robert Mijakovic -# License:: 3-clause BSD - -name = 'Score-P' -version = '8.3' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://www.score-p.org' -description = """ - The Score-P measurement infrastructure is a highly scalable and easy-to-use - tool suite for profiling, event tracing, and online analysis of HPC - applications. -""" - -toolchain = {'name': 'gompi', 'version': '2023b'} - -source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] -sources = ['scorep-%(version)s.tar.gz'] -checksums = ['76c914e6319221c059234597a3bc53da788ed679179ac99c147284dcefb1574a'] - -dependencies = [ - ('CUDA', '12.3.0', '', SYSTEM), - ('UCX-CUDA', '1.15.0', versionsuffix), - ('CubeLib', '4.8.2'), - ('CubeWriter', '4.8.2'), - ('libunwind', '1.6.2'), - ('OPARI2', '2.0.8'), - ('OTF2', '3.0.3'), - # Hardware counter support (optional): - ('PAPI', '7.1.0'), - # PDT source-to-source instrumentation support (optional): - ('PDT', '3.25.2'), -] - -configopts = '--enable-shared' - -local_adapters = [ - 'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' -] -sanity_check_paths = { - 'files': - ['bin/scorep', 'include/scorep/SCOREP_User.h'] + - ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], - 'dirs': [], -} -sanity_check_commands = ['scorep-config --help'] - -# Ensure that local metric documentation is found by CubeGUI -modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} - -moduleclass = 'perf' From 3e17ad2a5fd51585e599cf2b524c0c91ec46ba00 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 15:26:51 +0000 Subject: [PATCH 0659/1193] avoid spurious test failure in Perl --- .../p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb | 7 ++++- ...est-failure-due-to-PATH-line-1000-ch.patch | 27 +++++++++++++++++++ 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Perl/Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb index 0d05c82ee82a..cc172f108369 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb @@ -12,7 +12,12 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'] +patches = ['%(name)s-%(version)s_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch b/easybuild/easyconfigs/p/Perl/Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch new file mode 100644 index 000000000000..b63b2c1692bc --- /dev/null +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch @@ -0,0 +1,27 @@ +From https://github.com/perl/perl5/issues/15544#issuecomment-544083477 + +From b197f9a55e2ae877b3089282cfe07f3647d240f9 Mon Sep 17 00:00:00 2001 +From: James E Keenan +Date: Mon, 22 Aug 2016 09:25:08 -0400 +Subject: [PATCH] Avoid spurious test failure due to PATH line > 1000 + characters. + +--- + lib/perlbug.t | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/lib/perlbug.t b/lib/perlbug.t +index ed32c04..8ff8991 100644 +--- a/lib/perlbug.t ++++ b/lib/perlbug.t +@@ -148,7 +148,7 @@ my $maxlen1 = 0; # body + my $maxlen2 = 0; # attachment + for (split(/\n/, $contents)) { + my $len = length; +- $maxlen1 = $len if $len > $maxlen1 and !/$B/; ++ $maxlen1 = $len if $len > $maxlen1 and ! (/(?:$B|PATH)/); + $maxlen2 = $len if $len > $maxlen2 and /$B/; + } + ok($maxlen1 < 1000, "[perl #128020] long body lines are wrapped: maxlen $maxlen1"); +-- +2.7.4 From d3d3739234d1e1b52ec8af82939de3e6047580ca Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 15:29:56 +0000 Subject: [PATCH 0660/1193] add missing Python deps and packages in PSI4 --- .../easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb | 26 ++++++++++++++----- 1 file changed, 20 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb index a45e9eb8eb68..9e98b3b9c6ee 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb @@ -19,9 +19,9 @@ patches = [ 'PSI4-%(version)s_fix_snsmp2_version.patch', ] checksums = [ - '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366', # v1.7.tar.gz - 'a8af68947fb4d632d16adb3341b90990d9129d3fe9a28dee733b67bcd2aeff08', # PSI4-1.3.1_fix_cmake_release.patch - '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9', # PSI4-1.7_fix_snsmp2_version.patch + {'v1.7.tar.gz': '85a2772a148d57423a909fd91f3f9b068ae393b161510e78e7a824fbe3997366'}, + {'PSI4-1.7_fix_cmake_release.patch': 'a8af68947fb4d632d16adb3341b90990d9129d3fe9a28dee733b67bcd2aeff08'}, + {'PSI4-1.7_fix_snsmp2_version.patch': '064dcf60e74e0c449f77bb6e4dcf4b3338edad7d9a046089ecc2979aed1a00f9'}, ] dependencies = [ @@ -32,6 +32,7 @@ dependencies = [ ('psutil', '5.9.4'), ('pytest', '7.1.3'), ('Boost', '1.77.0'), + ('PyYAML', '5.4.1'), ] builddependencies = [ @@ -58,8 +59,6 @@ exts_defaultclass = 'PythonPackage' exts_filter = ("python -c 'import %(ext_name)s'", '') exts_default_options = { 'source_urls': [PYPI_SOURCE], - 'download_dep_fail': True, - 'use_pip': True, } exts_list = [ @@ -76,10 +75,25 @@ exts_list = [ 'modulename': 'msgpack', 'checksums': ['378cc8a6d3545b532dfd149da715abae4fda2a3adb6d74e525d0d5e51f46909b'], }), + ('qcelemental', '0.25.1', { + 'checksums': ['e3e0e53fe047d14756718441040a5d737135f0bdb33efb1d63a1935b95821a74'], + }), + ('qcengine', '0.26.0', { + 'checksums': ['8c10377b11ffab311a2997ae9af80a0f4b4a9c3a6d65d96fd4aca4c941ecf018'], + }), + ('OptKing', '0.2.1', { + 'source_urls': ['https://github.com/psi-rking/optking/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['7c4a2ea83b61fa91a178d2470612069eb9968ed3157336694c77805752ba545d'], + }), + ('snsmp2', '1.0.0', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['acfc95f8eb40e18d9d0c737b42fc8dfa786c381a5510a3094772b82538d211ed'], + }), ('py-cpuinfo', '9.0.0', { 'modulename': 'cpuinfo', 'checksums': ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'], - }) + }), ] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 6fc82794cdd158000076886e9967398a8a498750 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 15:44:14 +0000 Subject: [PATCH 0661/1193] revert accidental EB5 change in develop --- easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb index 9e98b3b9c6ee..8f23ffda6099 100644 --- a/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb +++ b/easybuild/easyconfigs/p/PSI4/PSI4-1.7-foss-2021b.eb @@ -59,6 +59,8 @@ exts_defaultclass = 'PythonPackage' exts_filter = ("python -c 'import %(ext_name)s'", '') exts_default_options = { 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, } exts_list = [ From c7a23fde4c82b934f59822c2451b1b638ada18a2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 12 Feb 2024 16:46:36 +0100 Subject: [PATCH 0662/1193] fix MS_RDONLY error in OpenMPI 4.0.5 --- .../o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb | 2 + .../o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb | 2 + .../OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb | 2 + .../o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb | 2 + .../OpenMPI-4.0.5-iccifort-2020.4.304.eb | 2 + .../OpenMPI-4.0.5_fix-MS_RDONLY-error.patch | 47 +++++++++++++++++++ 6 files changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb index 1536146190d3..184de98e3315 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-10.2.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -20,6 +21,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb index c399450ab49a..c62a1b54501d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-GCC-9.3.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -20,6 +21,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb index 383370dd6f52..bb1fb2730aca 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-NVHPC-21.2-CUDA-11.2.1.eb @@ -14,6 +14,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -22,6 +23,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb index 3746daadf8e7..838b2563b31f 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-gcccuda-2020b.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -20,6 +21,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb index de0f5b3d2e19..08a4dbccb2d6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5-iccifort-2020.4.304.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '572e777441fd47d7f06f1b8a166e7f44b8ea01b8b2e79d1e299d509725d1bd05', # openmpi-4.0.5.tar.gz @@ -20,6 +21,7 @@ checksums = [ '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch # OpenMPI-4.0.5-6-pml-ucx-datatype-memleak.patch '7d8695f0d23453c82638ad33b18e41690274d5c7784291213e98335b42c54578', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch new file mode 100644 index 000000000000..89df2e3ff365 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch @@ -0,0 +1,47 @@ +From 5b525b251c3433bf50b44b05c84937a39fb10074 Mon Sep 17 00:00:00 2001 +From: Bert Wesarg +Date: Tue, 23 Feb 2021 08:21:22 +0100 +Subject: [PATCH] fs/lustre: Remove unneeded includes + +The functionality was migrated to `fs/base/fs_base_get_parent_dir.c` long +ago, but the includes stayed. Though in lustre 2.14 `lustre_user.h` +moved the inclusion of `linux/fs.h` outside the `__KERNEL__` guard. This +triggered now Debian bug #898743 [1], which states that including +`sys/mount.h` after `linux/fs.h` breaks compilation. Thus the include +removal also avoids this breakage. + +Closes #8508. + +[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=898743 + +Signed-off-by: Bert Wesarg +--- + ompi/mca/fs/lustre/fs_lustre.c | 15 --------------- + 1 file changed, 15 deletions(-) + +diff --git a/ompi/mca/fs/lustre/fs_lustre.c b/ompi/mca/fs/lustre/fs_lustre.c +index df2c7c3ac7c..20fdfc76991 100644 +--- a/ompi/mca/fs/lustre/fs_lustre.c ++++ b/ompi/mca/fs/lustre/fs_lustre.c +@@ -32,21 +32,6 @@ + #include "ompi/mca/fs/base/base.h" + #include "ompi/mca/fs/lustre/fs_lustre.h" + +-#ifdef HAVE_SYS_STATFS_H +-#include /* or */ +-#endif +-#ifdef HAVE_SYS_PARAM_H +-#include +-#endif +-#ifdef HAVE_SYS_MOUNT_H +-#include +-#endif +-#ifdef HAVE_SYS_STAT_H +-#include +-#endif +- +-#include +- + /* + * ******************************************************************* + * ************************ actions structure ************************ From 490f37597e6c6d005e16c31c610e41652ad8b334 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 16:04:26 +0000 Subject: [PATCH 0663/1193] also 5.36.0 --- .../p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb | 7 ++++++- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 7 ++++++- 2 files changed, 12 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb index c426d66b7eb6..15256f12d966 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb @@ -13,7 +13,12 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 157d352765f2..cd326152ab68 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -9,7 +9,12 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] -checksums = ['e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.39'), From 332e092cc73e7b91f51cc8cefe92164cd3296df9 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 16:09:05 +0000 Subject: [PATCH 0664/1193] also Perl for .1 GCCcores --- .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 8 +++++++- .../easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 8 +++++++- 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 78044193927a..bfaa95762e01 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -9,7 +9,13 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] -checksums = ['e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] + builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index 929a2807a020..aad04c751199 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -12,7 +12,13 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'] +patches = ['%(name)s-5(version)s_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] + builddependencies = [ ('binutils', '2.40'), From 2af9d2600d9c53ba116d2c09e6ab1f5879f17b32 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 16:20:36 +0000 Subject: [PATCH 0665/1193] typo --- easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index aad04c751199..807b44bc75cf 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-5(version)s_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +patches = ['%(name)s-%(version)s_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] checksums = [ {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': From d3fddfa3b04da27cee83b81c8ad8d8afb439b1d4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 18:44:51 +0000 Subject: [PATCH 0666/1193] all but the latest Perls --- .../p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 2 +- .../p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb | 2 +- .../p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 2 +- .../p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 2 +- .../p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 2 +- .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 6 ------ .../p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb | 5 ----- .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 5 ----- .../easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb | 7 +------ .../easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 8 +------- .../easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb | 2 +- easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb | 2 +- 18 files changed, 15 insertions(+), 42 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb index 865360a39d34..a9df2ef78e7a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.34'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index a0b67405467e..7a27b1d747fc 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -9,7 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.34'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb index 882c2de9022e..bd93ea380e4e 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index 34e3a3e297dd..f24535bf5c2c 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -9,7 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb index 6b718496c02e..8e1e777214a7 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb index 123f7022a08d..503eb90daabf 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index 264dc8a3d153..b394c6e11eaa 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb index 75ba2d908fa5..e37edd051cea 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.37'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 2a9ef4add3da..079db35cb8fa 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -9,7 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] -checksums = ['551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.37'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb index 727f35d6cc4e..fbb45fa3fd06 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb @@ -13,7 +13,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['357951a491b0ba1ce3611263922feec78ccd581dddc24a446b033e25acf242a1'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index 142a6d159172..cc78df60c5c8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -9,7 +9,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] -checksums = ['357951a491b0ba1ce3611263922feec78ccd581dddc24a446b033e25acf242a1'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index bfaa95762e01..73f61c5e20b8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -10,12 +10,6 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] - builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb index 15256f12d966..5e0fb7283cd8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb @@ -14,11 +14,6 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index cd326152ab68..2fc6a8e78354 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -10,11 +10,6 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb index cc172f108369..6a75f9bff082 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb @@ -12,12 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index 807b44bc75cf..fc5e0849d3dd 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -12,13 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-%(version)s_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] -checksums = [ - {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, - {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': - '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, -] - +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb index 1620e4f9dfa6..eee2a6d077b3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['213ef58089d2f2c972ea353517dc60ec3656f050dcc027666e118b508423e517'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb index 059a04bfd90a..217e18d54aa3 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['213ef58089d2f2c972ea353517dc60ec3656f050dcc027666e118b508423e517'] +patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] builddependencies = [ ('binutils', '2.40'), From 1d5b506e403e20cf4471b1f657e211840d8c4cb6 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:48:33 +0000 Subject: [PATCH 0667/1193] remove accidental change --- easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb index 217e18d54aa3..059a04bfd90a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = ['213ef58089d2f2c972ea353517dc60ec3656f050dcc027666e118b508423e517'] builddependencies = [ ('binutils', '2.40'), From f5d9dece83b3e5ae9d3c3fa0f1fe29529efce7d9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:49:02 +0000 Subject: [PATCH 0668/1193] remove accidental change --- easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb index eee2a6d077b3..1620e4f9dfa6 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.38.0-GCCcore-13.2.0.eb @@ -12,7 +12,7 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] -patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = ['213ef58089d2f2c972ea353517dc60ec3656f050dcc027666e118b508423e517'] builddependencies = [ ('binutils', '2.40'), From 30bc767bd2f7da3b2737e97bcdfac9778ffad613 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 12 Feb 2024 18:49:46 +0000 Subject: [PATCH 0669/1193] checksums --- .../p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb | 5 +++++ .../p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb | 5 +++++ easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb | 7 ++++++- .../p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 7 ++++++- .../p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 7 ++++++- .../p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 7 ++++++- .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 11 ++++++++--- .../p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 7 ++++++- .../easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb | 5 +++++ .../easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb | 5 +++++ 16 files changed, 88 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb index a9df2ef78e7a..fec6c89d9951 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0-minimal.eb @@ -14,6 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.30.2.tar.gz': '66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.34'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb index 7a27b1d747fc..98e93f98b525 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.30.2-GCCcore-9.3.0.eb @@ -10,6 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.30.2.tar.gz': '66db7df8a91979eb576fac91743644da878244cf8ee152f02cd6f5cd7a731689'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.34'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb index bd93ea380e4e..d3674a9d64b1 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0-minimal.eb @@ -14,6 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.32.0.tar.gz': 'efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb index f24535bf5c2c..7340496b8a75 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.0-GCCcore-10.2.0.eb @@ -10,6 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.32.0.tar.gz': 'efeb1ce1f10824190ad1cadbcccf6fdb8a5d37007d0100d2d9ae5f2b5900c0b4'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb index 8e1e777214a7..6551fd3546ca 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb @@ -13,6 +13,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.32.1.tar.gz': '03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.36.1'), @@ -404,10 +409,10 @@ exts_list = [ 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], }), ('Net::SSLeay', '1.90', { + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], 'checksums': ['f8696cfaca98234679efeedc288a9398fcf77176f1f515dbc589ada7c650dc93'], - 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", }), ('IO::Socket::SSL', '2.070', { 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb index 503eb90daabf..636dcf44b699 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0-minimal.eb @@ -14,6 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.32.1.tar.gz': '03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index b394c6e11eaa..918417f0beea 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -13,6 +13,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.32.1.tar.gz': '03b693901cd8ae807231b1787798cf1f2e0b8a56218d07b7da44f784a7caeb2c'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.36.1'), @@ -938,7 +943,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.65', { - 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'configopts': 'INSTALLDIRS=site', 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb index e37edd051cea..5d29f924c4ac 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0-minimal.eb @@ -14,6 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.34.0.tar.gz': '551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.37'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index 079db35cb8fa..b7b771b6da5d 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -10,6 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.34.0.tar.gz': '551efc818b968b05216024fb0b727ef2ad4c100f8cb6b43fab615fa78ae5be9a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.37'), @@ -935,7 +940,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.65', { - 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'configopts': 'INSTALLDIRS=site', 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb index fbb45fa3fd06..fe47b032b83b 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0-minimal.eb @@ -14,6 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.34.1.tar.gz': '357951a491b0ba1ce3611263922feec78ccd581dddc24a446b033e25acf242a1'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index cc78df60c5c8..de5da24919cd 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -10,6 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.34.1.tar.gz': '357951a491b0ba1ce3611263922feec78ccd581dddc24a446b033e25acf242a1'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.38'), @@ -990,7 +995,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.65', { - 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'configopts': 'INSTALLDIRS=site', 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb index 73f61c5e20b8..c865a27e6aa9 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb @@ -10,6 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.38'), @@ -106,7 +111,7 @@ exts_list = [ ('File::ShareDir::Install', '0.14', { 'source_tmpl': 'File-ShareDir-Install-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER'], - 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'] + 'checksums': ['8f9533b198f2d4a9a5288cbc7d224f7679ad05a7a8573745599789428bc5aea0'], }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', @@ -156,12 +161,12 @@ exts_list = [ ('DateTime::Locale', '1.36', { 'source_tmpl': 'DateTime-Locale-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['90a8243f2b2d4068019c65178600e76e03f5b478cb41d18c8c81cdf0d481f0a4'] + 'checksums': ['90a8243f2b2d4068019c65178600e76e03f5b478cb41d18c8c81cdf0d481f0a4'], }), ('DateTime::TimeZone', '2.53', { 'source_tmpl': 'DateTime-TimeZone-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], - 'checksums': ['4f6e9ff86892a52334bfb8dfa74ebea6adb8afd04fefcba8ae52fc054c4c15b3'] + 'checksums': ['4f6e9ff86892a52334bfb8dfa74ebea6adb8afd04fefcba8ae52fc054c4c15b3'], }), ('Test::Requires', '0.11', { 'source_tmpl': 'Test-Requires-%(version)s.tar.gz', diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb index 5e0fb7283cd8..15256f12d966 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0-minimal.eb @@ -14,6 +14,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 2fc6a8e78354..3e36fff26979 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -10,6 +10,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = ['perl-%(version)s.tar.gz'] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.0.tar.gz': 'e26085af8ac396f62add8a533c3a0ea8c8497d836f0689347ac5abd7b7a4e00a'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.39'), @@ -990,7 +995,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.66', { - 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl + 'configopts': 'INSTALLDIRS=site', 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb index 6a75f9bff082..6233aaee505a 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-12.3.0.eb @@ -13,6 +13,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb index fc5e0849d3dd..9666a1b1a4dc 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.1-GCCcore-13.1.0.eb @@ -13,6 +13,11 @@ toolchainopts = {'pic': True} source_urls = ['https://www.cpan.org/src/%(version_major)s.0'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch'] +checksums = [ + {'perl-5.36.1.tar.gz': '68203665d8ece02988fc77dc92fccbb297a83a4bb4b8d07558442f978da54cc1'}, + {'Perl-5.36.1_Avoid-spurious-test-failure-due-to-PATH-line-1000-ch.patch': + '8bc55f85eeacf35175f8e4f053ba7858f62974bcc073b265c2f0cd93a5f1307a'}, +] builddependencies = [ ('binutils', '2.40'), From f8914c78012c9afb66b766fd2b52a1e4f3c041b8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:56:12 +0000 Subject: [PATCH 0670/1193] remove inject checksums change --- easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb index 3e36fff26979..cd326152ab68 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb @@ -995,7 +995,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.66', { - 'configopts': 'INSTALLDIRS=site', + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['22928a7bffe61b452c05bbbb8f5216d4b9cf9fe2a849b776c25500d24d20df7c'], From d09c66590d2fe2faadb70d8c15de04dfde20231b Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:56:50 +0000 Subject: [PATCH 0671/1193] remove inject checksums change --- easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb index de5da24919cd..f30c0c817157 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb @@ -995,7 +995,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.65', { - 'configopts': 'INSTALLDIRS=site', + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR/'], 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], From 56965b60440ed75f56db7c32f515a0ffd5d63acb Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:57:43 +0000 Subject: [PATCH 0672/1193] remove inject checksums change --- easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb index 6551fd3546ca..23891282d0f8 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay + ('OpenSSL', '1.1', '', SYSTEM), # required for eay ] exts_default_options = {'buildopts': 'CC="$CC"'} @@ -409,10 +409,10 @@ exts_list = [ 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], }), ('Net::SSLeay', '1.90', { - 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], 'checksums': ['f8696cfaca98234679efeedc288a9398fcf77176f1f515dbc589ada7c650dc93'], + 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", }), ('IO::Socket::SSL', '2.070', { 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', From 6e4b925a6d53816bca45aa0e3df40b65f7600ab0 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:58:21 +0000 Subject: [PATCH 0673/1193] remove accidental change --- easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb index 23891282d0f8..7081ac17a661 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-FCC-4.5.0.eb @@ -30,7 +30,7 @@ dependencies = [ ('ncurses', '6.2'), # for Term::ReadLine::Gnu ('libreadline', '8.1'), # for Term::ReadLine::Gnu ('DB', '18.1.40'), # for DB_File - ('OpenSSL', '1.1', '', SYSTEM), # required for eay + ('OpenSSL', '1.1', '', SYSTEM), # required for Net::SSLeay ] exts_default_options = {'buildopts': 'CC="$CC"'} From e00db3082f178c1f655db1be138208e576487a2a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:58:44 +0000 Subject: [PATCH 0674/1193] remove inject checksums change --- easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb index 918417f0beea..b4cb6226cf0f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.32.1-GCCcore-10.3.0.eb @@ -943,7 +943,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.65', { - 'configopts': 'INSTALLDIRS=site', + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], From 31d217017eff2fbea118713c3aaefa5729e89650 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Mon, 12 Feb 2024 18:59:28 +0000 Subject: [PATCH 0675/1193] remove inject checksums change --- easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb index b7b771b6da5d..c0b5956c8b3f 100644 --- a/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Perl/Perl-5.34.0-GCCcore-11.2.0.eb @@ -940,7 +940,7 @@ exts_list = [ 'checksums': ['409a8e0e4b1025c8e80f628f65a9778aa77ab285161406ca4a6c097b13656d0d'], }), ('Pod::Parser', '1.65', { - 'configopts': 'INSTALLDIRS=site', + 'configopts': 'INSTALLDIRS=site', # Force it to correctly use site_perl 'source_tmpl': 'Pod-Parser-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MA/MAREKR'], 'checksums': ['3ba7bdec659416a51fe2a7e59f0883e9c6a3b21bc9d001042c1d6a32d401b28a'], From b946855c932c3024542c4d542e5a66f7b946d949 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 12 Feb 2024 22:21:47 +0100 Subject: [PATCH 0676/1193] adding easyconfigs: Gurobi-11.0.0-GCCcore-12.3.0.eb --- .../g/Gurobi/Gurobi-11.0.0-GCCcore-12.3.0.eb | 61 +++++++++++++++++++ ...bi-11.0.0_use-eb-python-gurobi-shell.patch | 17 ++++++ 2 files changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0_use-eb-python-gurobi-shell.patch diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5003e385333b --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,61 @@ +name = 'Gurobi' +version = '11.0.0' + +homepage = 'https://www.gurobi.com' +description = """The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. +The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern +architectures and multi-core processors, using the most advanced implementations of the +latest algorithms.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://packages.gurobi.com/%(version_major_minor)s/'] +sources = ['gurobi%(version)s_linux64.tar.gz'] +patches = ['Gurobi-11.0.0_use-eb-python-gurobi-shell.patch'] +checksums = [ + {'gurobi11.0.0_linux64.tar.gz': '6a1ec7499b230aea0542bc893bf0642ae8ce983dd5ef0c37cb3a253d827ce634'}, + {'Gurobi-11.0.0_use-eb-python-gurobi-shell.patch': + '566473a3ba4e35b0e74595368f9f4133fc4a3c97cca84154c4b938645786e663'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('gurobipy', '11.0.0', { + 'sources': ['gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_%(arch)s.whl'], + 'checksums': [{ + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_aarch64.whl': + '096f63ca02fbe810bae25311be598c9d8c5874362e85eac46ef0a4fdb3eaf96b', + 'gurobipy-%(version)s-cp311-cp311-manylinux2014_x86_64.manylinux_2_17_x86_64.whl': + 'a98abda1cb45f548fff17370eb30cc6e187d04edc5d9984a68d194491598a993', + }], + }), +] + +# remove bundled Python interpreter in favour of the dependency in EB +postinstallcmds = ['rm %(installdir)s/bin/python*'] + +# license is mandatory for installation +# use EB_GUROBI_LICENSE_FILE environment variable, or +# uncomment and modify the following variable: +# license_file = '/path/to/my-license-file' + +modloadmsg = """Gurobi shell based on Python %(pyver)s can be launched with command `gurobi.sh` +Gurobi Python Interface can be loaded in Python %(pyver)s with 'import gurobipy' +""" + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0_use-eb-python-gurobi-shell.patch b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0_use-eb-python-gurobi-shell.patch new file mode 100644 index 000000000000..84bb93258be1 --- /dev/null +++ b/easybuild/easyconfigs/g/Gurobi/Gurobi-11.0.0_use-eb-python-gurobi-shell.patch @@ -0,0 +1,17 @@ +Use the Python environement from EB in the Guroby Python shell +author: Alex Domingo (Vrije Universiteit Brussel), ported to Gurobi 11.0.0 by Kenneth Hoste (HPC-UGent) +--- gurobi1100/linux64/bin/gurobi.sh.orig 2024-02-12 19:31:52.884375084 +0100 ++++ gurobi1100/linux64/bin/gurobi.sh 2024-02-12 19:37:00.624272524 +0100 +@@ -7,10 +7,6 @@ + echo + fi + +-PATH=$GUROBI_HOME/bin:$PATH;export PATH +-LD_LIBRARY_PATH=$GUROBI_HOME/lib:$LD_LIBRARY_PATH;export LD_LIBRARY_PATH +-PYTHONHOME=$GUROBI_HOME;export PYTHONHOME ++PYTHONSTARTUP=$EBROOTGUROBI/lib/gurobi.py;export PYTHONSTARTUP + +-PYTHONSTARTUP=$PYTHONHOME/lib/gurobi.py;export PYTHONSTARTUP +- +-$PYTHONHOME/bin/python3.11 "$@" ++$EBROOTPYTHON/bin/python "$@" From c3e387240c63a98a468b98f6cb71320245fb6e65 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 13 Feb 2024 00:30:07 +0000 Subject: [PATCH 0677/1193] adding easyconfigs: CUDA-12.3.2.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.3.2.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.3.2.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.3.2.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.3.2.eb new file mode 100644 index 000000000000..060e68935664 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.3.2.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.3.2' +local_nv_version = '545.23.08' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '24b2afc9f770d8cf43d6fa7adc2ebfd47c4084db01bdda1ce3ce0a4d493ba65b', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'b876936fc80de10653523eadd846065db346b38ba6296f2d365772259cb2f198', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + '761b84e292b94c4d330f445d36326dfff90a418e909fb0baf3d6f03e24106d08' +}] + +moduleclass = 'system' From 39b0a445f427dd893934c4d91a2dcd7e7be5dee2 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Feb 2024 08:33:22 +0100 Subject: [PATCH 0678/1193] add patch so we can disable docs building --- .../rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb | 11 +++++++-- ...i-5.6.0_add_option_for_docs_building.patch | 23 +++++++++++++++++++ 2 files changed, 32 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0_add_option_for_docs_building.patch diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb index 2b102619380d..67d09325d7f7 100644 --- a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0-GCCcore-11.3.0.eb @@ -14,7 +14,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ["https://github.com/RadeonOpenCompute/rocm_smi_lib/archive/"] sources = ["rocm-%(version)s.tar.gz"] -checksums = ['88be875948a29454b8aacced8bb8ad967502a7a074ecbc579ed673c1650a2f7e'] +patches = [ + '%(name)s-%(version)s_add_option_for_docs_building.patch', +] +checksums = [ + {'rocm-5.6.0.tar.gz': '88be875948a29454b8aacced8bb8ad967502a7a074ecbc579ed673c1650a2f7e'}, + {'rocm-smi-5.6.0_add_option_for_docs_building.patch': + '372c1d4aea43164f204533dede710812c72b0c65cfe5f6bfb020d3925321c87d'}, +] builddependencies = [ ('binutils', '2.38'), @@ -23,7 +30,7 @@ builddependencies = [ # This package hardcodes 'noexecheap' as a linker flag which is not supported # by 'ld.gold', to get around we explicitly force 'ld.bfd' here -configopts = "-DCMAKE_CXX_FLAGS='-fuse-ld=bfd'" +configopts = "-DCMAKE_CXX_FLAGS='-fuse-ld=bfd' -DENABLE_DOCS=OFF" sanity_check_paths = { 'files': ['bin/rocm-smi', 'libexec/rocm_smi/rocm_smi.py', 'lib/librocm_smi64.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0_add_option_for_docs_building.patch b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0_add_option_for_docs_building.patch new file mode 100644 index 000000000000..5c1c039233ce --- /dev/null +++ b/easybuild/easyconfigs/r/rocm-smi/rocm-smi-5.6.0_add_option_for_docs_building.patch @@ -0,0 +1,23 @@ +Add an option so we can disable building of documentation. + +Åke Sandgren, 2024-02-13 +diff --git a/rocm_smi/CMakeLists.txt b/rocm_smi/CMakeLists.txt +index 9b506d5..ada1d0f 100755 +--- a/rocm_smi/CMakeLists.txt ++++ b/rocm_smi/CMakeLists.txt +@@ -146,6 +146,9 @@ install(FILES ${CMAKE_CURRENT_BINARY_DIR}/bin/rocm-smi + DESTINATION ${CMAKE_INSTALL_BINDIR} + COMPONENT dev) + ++option(ENABLE_DOCS "Build documentation" ON) ++if (ENABLE_DOCS) ++ + # Generate Doxygen documentation + find_package(Doxygen) + find_package(LATEX COMPONENTS PDFLATEX) +@@ -180,3 +183,5 @@ else() + message("Doxygen or Latex is not found. Will not generate documents.") + endif(DOXYGEN_FOUND AND LATEX_FOUND) + ++endif(ENABLE_DOCS) ++ From 8f419ec14fe8e4e6306c9c59b30c9c657e238ca2 Mon Sep 17 00:00:00 2001 From: lara Date: Tue, 13 Feb 2024 09:26:00 +0100 Subject: [PATCH 0679/1193] make ScaFaCos optional dependency for Intel arch --- .../LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb index 31ec777be167..64260ea32a52 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -54,7 +54,6 @@ dependencies = [ ('kim-api', '2.3.0'), ('Eigen', '3.4.0'), ('PLUMED', '2.9.0'), - ('ScaFaCoS', '1.0.4'), ('SciPy-bundle', '2023.07'), # VTK package is auto-disabled if this dep is not available ('VTK', '9.3.0'), @@ -62,8 +61,11 @@ dependencies = [ ('MDI', '1.4.26'), ] if ARCH == 'x86_64': - # TBB is an optional dependency when building on Intel arch - dependencies += [('tbb', '2021.11.0'), ] + # TBB and ScaFaCos are an optional dependency when building on Intel arch + dependencies += [ + ('tbb', '2021.11.0'), + ('ScaFaCoS', '1.0.4'), + ] # To use additional custom configuration options, use the 'configopts' easyconfig parameter # See docs and lammps easyblock for more information. @@ -175,6 +177,4 @@ general_packages = [ # - MSCG # - QMMM (setup seems complex) -#install_cmd = 'make install && python %(builddir)s/lammps-stable_%(version)s/python/install.py -p %(installdir)s/lib -l %(installdir)s/lib/liblammps.so -v %(builddir)s/src/version.h' - moduleclass = 'chem' From 8b888c292d64622d95f7e8d2a3895dbfc8eb180b Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 10:38:13 +0100 Subject: [PATCH 0680/1193] {astro,lib}[foss/2023b] DP3-6.0, WSClean 3.4 and deps --- .../a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb | 46 ++++++++++++++++ .../Armadillo/Armadillo-12.8.0-foss-2023b.eb | 24 +++++++++ .../a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb | 37 +++++++++++++ .../Boost.Python-1.83.0-GCC-13.2.0.eb | 24 +++++++++ .../c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb | 43 +++++++++++++++ ....5.0-add-C-style-header-for-GCC-13.1.patch | 21 ++++++++ .../c/casacore/casacore-3.5.0-foss-2023b.eb | 49 +++++++++++++++++ .../easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 45 ++++++++++++++++ .../e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb | 43 +++++++++++++++ .../l/Lua/Lua-5.4.6-GCCcore-13.2.0.eb | 28 ++++++++++ .../l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb | 27 ++++++++++ .../p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb | 38 +++++++++++++ .../p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb | 54 +++++++++++++++++++ .../pkg-config-0.29.2-GCCcore-13.2.0.eb | 35 ++++++++++++ .../w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb | 39 ++++++++++++++ .../w/WSClean/WSClean-3.4-foss-2023b.eb | 44 +++++++++++++++ .../w/wget/wget-1.21.4-GCCcore-13.2.0.eb | 49 +++++++++++++++++ 17 files changed, 646 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/c/casacore/casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch create mode 100644 easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb create mode 100644 easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb new file mode 100644 index 000000000000..e211feb7aa3b --- /dev/null +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'AOFlagger' +version = '3.4.0' + +homepage = 'https://aoflagger.readthedocs.io/' +description = """The AOFlagger is a tool that can find and remove radio-frequency interference (RFI) +in radio astronomical observations. It can make use of Lua scripts to make flagging strategies flexible, +and the tools are applicable to a wide set of telescopes.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [ + {'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/96704214/'], 'filename': '%(namelower)s-v%(version)s.tar.bz2', 'download_filename': 'download'}, +] +checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba'] + +builddependencies = [ + ('CMake', '3.27.6'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('Boost', '1.83.0'), + ('CFITSIO', '4.3.1'), + ('GSL', '2.7'), + ('HDF5', '1.14.3'), + ('Python', '3.11.5'), + ('Lua', '5.4.6'), + ('libpng', '1.6.40'), + ('libxml2', '2.11.5'), +] + +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 +configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " + + +sanity_check_paths = { + 'files': ['include/%(namelower)s.h', 'bin/%(namelower)s'], + 'dirs': ['bin'], +} + +sanity_check_commands = [('%(namelower)s', '-v')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb new file mode 100644 index 000000000000..cde4b18960cf --- /dev/null +++ b/easybuild/easyconfigs/a/Armadillo/Armadillo-12.8.0-foss-2023b.eb @@ -0,0 +1,24 @@ +name = 'Armadillo' +version = '12.8.0' + +homepage = 'https://arma.sourceforge.net/' +description = """Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards + a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, + as well as a subset of trigonometric and statistics functions.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://sourceforge.net/projects/arma/files'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['a89bb6fece5ce9fdd1d01a4bc145cf7cc0b939c5777cca46de69c2f5e3412cf0'] + +builddependencies = [ + ('CMake', '3.27.6'), +] +dependencies = [ + ('Boost', '1.83.0'), + ('arpack-ng', '3.9.0'), +] + + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb new file mode 100644 index 000000000000..0151ba327e0b --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb @@ -0,0 +1,37 @@ +# # +# Author: Robert Mijakovic +# # +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.9.0' + +homepage = 'https://github.com/opencollab/arpack-ng' +description = "ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['24f2a2b259992d3c797d80f626878aa8e2ed5009d549dad57854bbcfb95e1ed0'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkg-config', '0.29.2'), +] +dependencies = [ + ('Eigen', '3.4.0'), +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +github_account = 'opencollab' + +sanity_check_paths = { + 'files': ['lib64/libarpack.la', 'lib64/libarpack.so', 'lib64/libparpack.la', 'lib64/libparpack.so'], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-13.2.0.eb b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..f7af796a853d --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.Python/Boost.Python-1.83.0-GCC-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'EB_Boost' + +name = 'Boost.Python' +version = '1.83.0' + +homepage = 'https://boostorg.github.io/python' +description = """Boost.Python is a C++ library which enables seamless interoperability between C++ + and the Python programming language.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://boostorg.jfrog.io/artifactory/main/release/%(version)s/source/'] +sources = ['boost_1_83_0.tar.gz'] +checksums = ['c0685b68dd44cc46574cce86c4e17c0f611b15e195be9848dfd0769a0a207628'] + +dependencies = [ + ('Boost', '1.83.0'), + ('Python', '3.11.5'), +] + +only_python_bindings = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..17dacb5ba4aa --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '4.3.1' + +homepage = 'https://heasarc.gsfc.nasa.gov/fitsio/' +description = """CFITSIO is a library of C and Fortran subroutines for reading and writing data files in +FITS (Flexible Image Transport System) data format.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-3.48_install_test_data.patch'] +checksums = [ + {SOURCELOWER_TAR_GZ: '2332b965d327a15c103a7d31d6d1afaf775d00e9785dd25332ae76b9725351e4'}, + {'%(name)s-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] +# curl for HTTPs support +dependencies = [ + ('cURL', '8.3.0'), +] + +# make would create just static libcfitsio.a. +# Let's create dynamic lib and testprog too. +buildopts = "&& make shared && make testprog" + + +sanity_check_paths = { + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.so'], + 'dirs': ['include'], +} + +sanity_check_commands = ['cd %(installdir)s/share && testprog'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch new file mode 100644 index 000000000000..efef286e59a1 --- /dev/null +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch @@ -0,0 +1,21 @@ +From 68e43f489abd3d4f1e2fe54a42695396703aa81a Mon Sep 17 00:00:00 2001 +From: Chris Broekema +Date: Tue, 9 May 2023 12:43:34 +0200 +Subject: [PATCH] add C-style header to fix GCC 13.1 compile error on uint16_t + not being a valid type (#1309) + +--- + tables/Dysco/bytepacker.h | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/tables/Dysco/bytepacker.h b/tables/Dysco/bytepacker.h +index d62754046..cb1193b41 100644 +--- a/tables/Dysco/bytepacker.h ++++ b/tables/Dysco/bytepacker.h +@@ -2,6 +2,7 @@ + #define DYSCO_BYTE_PACKER_H + + #include ++#include + + namespace dyscostman { diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb new file mode 100644 index 000000000000..362434327ee8 --- /dev/null +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb @@ -0,0 +1,49 @@ +easyblock = 'CMakeMake' + +name = 'casacore' +version = '3.5.0' + +homepage = 'https://github.com/casacore/casacore' +description = """A suite of C++ libraries for radio astronomy data processing. +The ephemerides data needs to be in DATA_DIR and the location must be specified at runtime. +Thus user's can update them. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch'] +checksums = ['63f1c8eff932b0fcbd38c598a5811e6e5397b72835b637d6f426105a183b3f91'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('wget', '1.21.4'), +] +dependencies = [ + ('CFITSIO', '4.3.1'), + ('WCSLIB', '7.11'), + ('HDF5', '1.14.3'), + ('GSL', '2.7'), + ('Boost.Python', '1.83.0'), + ('SciPy-bundle', '2023.11'), + ('ncurses', '6.4'), +] + +configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data -DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +# Install casacore data +postinstallcmds = [ + "wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar -O /tmp/WSRT_Measures.ztar && tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data", +] + +sanity_check_paths = { + 'files': ['lib/libcasa_casa.so', 'lib/libcasa_mirlib.so', 'lib/libcasa_ms.so'], + 'dirs': ['bin', 'include/%(name)s'], +} + +sanity_check_commands = [('measuresdata', '')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb new file mode 100644 index 000000000000..f4c6964b32cf --- /dev/null +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'DP3' +version = '6.0' + +homepage = 'https://dp3.readthedocs.io/' +description = "DP3: streaming processing pipeline for radio interferometric data." + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [ + {'filename': '%(name)s-v%(version)s.tar.gz', 'git_config': {'url': 'https://git.astron.nl/RD', 'repo_name': '%(name)s', 'tag': 'v%(version)s', 'clone_into': '%(name)s', 'recursive': True}}, +] +checksums = [None] + +builddependencies = [ + ('CMake', '3.27.6'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('Boost', '1.83.0'), + ('CFITSIO', '4.3.1'), + ('WCSLIB', '7.11'), + ('GSL', '2.7'), + ('HDF5', '1.14.3'), + ('Python', '3.11.5'), + ('EveryBeam', '0.5.2'), + ('Armadillo', '12.8.0'), + ('AOFlagger', '3.4.0'), +] + +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 +configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " + + +sanity_check_paths = { + 'files': ['include/include/%(namelower)s/base/%(name)s.h', 'bin/%(name)s'], + 'dirs': ['bin'], +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb new file mode 100644 index 000000000000..f67d1cba1622 --- /dev/null +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb @@ -0,0 +1,43 @@ +easyblock = 'CMakeMake' + +name = 'EveryBeam' +version = '0.5.2' + +homepage = 'https://everybeam.readthedocs.io/' +description = """Library that provides the antenna response pattern for several instruments, +such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [ + {'filename': '%(name)s-v%(version)s.tar.gz', 'git_config': {'url': 'https://git.astron.nl/RD', 'repo_name': '%(name)s', 'tag': 'v%(version)s', 'clone_into': '%(name)s', 'recursive': True}}, +] +checksums = [None] + +builddependencies = [ + ('CMake', '3.27.6'), + ('wget', '1.21.4'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('Boost', '1.83.0'), + ('CFITSIO', '4.3.1'), + ('WCSLIB', '7.11'), + ('GSL', '2.7'), + ('HDF5', '1.14.3'), + ('Python', '3.11.5'), + ('libxml2', '2.11.5'), +] + +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 +configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " + + +sanity_check_paths = { + 'files': ['include/%(name)s/beamformer.h', 'lib/libeverybeam.so'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..b2b1eef5195d --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.6-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.6' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7d5ea1b9cb6aa0b59ca3dde1c6adcb57ef83a1ba8e5432c0ecd06bf439b3ad88'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('ncurses', '6.4'), + ('libreadline', '8.2'), +] + + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..662ff77ec42b --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libidn2' +version = '2.3.2' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = "Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76940cd4e778e8093579a9d195b25fff5e936e9dc6242068528b437a76764f91'] + +builddependencies = [ + ('binutils', '2.40'), +] + + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/%(name)s.so'], + 'dirs': ['include'], +} + +sanity_check_commands = ['idn2 --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..25eed8372357 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE' +version = '8.45' + +homepage = 'https://www.pcre.org/' +description = """ + The PCRE library is a set of functions that implement regular expression + pattern matching using the same syntax and semantics as Perl 5. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + SOURCEFORGE_SOURCE, + 'https://ftp.%(namelower)s.org/pub/%(namelower)s/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4e6ce03e0336e8b4a3d6c2b70b1c5e18590a5673a98186da90d4f33c23defc09'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +configopts = " --enable-utf --enable-unicode-properties --enable-pcre16 --enable-pcre32" + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s.h', 'share/man/man3/%(namelower)s.3', 'lib/libpcre32.so'], + 'dirs': ['lib/pkgconfig', 'share/doc/%(namelower)s/html', 'share/man/man1'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..cad1999ca294 --- /dev/null +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb @@ -0,0 +1,54 @@ +easyblock = 'CmdCp' + +name = 'PGPLOT' +version = '5.2.2' + +homepage = 'https://sites.astro.caltech.edu/~tjp/pgplot/' +description = """The PGPLOT Graphics Subroutine Library is a Fortran- or C-callable, +device-independent graphics package for making simple scientific graphs. It is intended +for making graphical images of publication quality with minimum effort on the part of +the user. For most applications, the program can be device-independent, and the output +can be directed to the appropriate device at run time.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['ftp://ftp.astro.caltech.edu/pub/%(namelower)s/'] +sources = ['%(namelower)s522.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.2_gfortran-deps-fixes.patch'] +checksums = [ + {'pgplot522.tar.gz': 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4'}, + {'%(name)s-%(version_major_minor)s.2_gfortran-deps-fixes.patch': 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec'}, +] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('libpng', '1.6.40'), + ('zlib', '1.2.13'), + ('X11', '20231019'), +] + +# create .so symlinks for shared libraries +postinstallcmds = [ + "cd %(installdir)s/lib && ln -s libcpgplot.so.%(version)s libcpgplot.so.5", + "cd %(installdir)s/lib && ln -s libcpgplot.so.%(version)s libcpgplot.so", + "cd %(installdir)s/lib && ln -s libpgplot.so.%(version)s libpgplot.so.5", + "cd %(installdir)s/lib && ln -s libpgplot.so.%(version)s libpgplot.so", +] +files_to_copy = [ + (['pgdemo*'], 'bin'), + (['libpgplot.*', 'libcpgplot.*'], 'lib'), + (['grfont.dat'], 'share'), + (['cpgplot.h'], 'include'), +] +cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] + +sanity_check_paths = { + 'files': ['include/cpgplot.h', 'lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.so', 'lib/libcpgplot.so'], + 'dirs': ['bin'], +} + +modextravars = {'PGPLOT_FONT': '%(installdir)s/share/grfont.dat'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..b9bda34701d8 --- /dev/null +++ b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'pkg-config' +version = '0.29.2' + +homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' +description = """ + pkg-config is a helper tool used when compiling applications and libraries. + It helps you insert the correct compiler options on the command line so an + application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` + for instance, rather than hard-coding values on where to find glib (or other + libraries). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://%(name)s.freedesktop.org/releases/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] + +builddependencies = [ + ('binutils', '2.40'), +] + +configopts = " --with-internal-glib" + +# don't use PAX, it might break. +tar_config_opts = True + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb new file mode 100644 index 000000000000..9bc27997d319 --- /dev/null +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'WCSLIB' +version = '7.11' + +homepage = 'https://www.atnf.csiro.au/people/mcalabre/WCS/' +description = """The FITS "World Coordinate System" (WCS) standard defines keywords +and usage that provide for the description of astronomical coordinate systems in a +FITS image header.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['ftp://ftp.atnf.csiro.au/pub/software/%(namelower)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['46befbfdf50cd4953896676a7d570094dc7661e2ae9677b092e7fb13cee3da5f'] + +builddependencies = [ + ('binutils', '2.40'), + ('M4', '1.4.19'), + ('flex', '2.6.4'), +] +dependencies = [ + ('CFITSIO', '4.2.0'), + ('PGPLOT', '5.2.2'), + ('X11', '20231019'), +] + +configopts = "--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include --with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include " + + +sanity_check_paths = { + 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-%(version)s.a', 'lib/libpgsbox.so'], + 'dirs': ['include'], +} + +sanity_check_commands = ["wcsgrid --help 2>&1 | grep '^Usage: wcsgrid'"] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb new file mode 100644 index 000000000000..1223c4d82d5a --- /dev/null +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'WSClean' +version = '3.4' + +homepage = 'https://wsclean.readthedocs.io/' +description = """WSClean (w-stacking clean) is a fast generic widefield imager. +It implements several gridding algorithms and offers fully-automated multi-scale +multi-frequency deconvolution.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [ + {'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/97237455/'], 'filename': '%(namelower)s-v%(version)s.tar.bz2', 'download_filename': 'download'}, +] +checksums = ['b43d8ca490ccf34dd22aae6c5ca88a5dcb3cff0526835d3f97fa6d239745e641'] + +builddependencies = [ + ('CMake', '3.27.6'), +] +dependencies = [ + ('casacore', '3.5.0'), + ('EveryBeam', '0.5.2'), + ('Boost', '1.83.0'), + ('CFITSIO', '4.3.1'), + ('GSL', '2.7'), + ('HDF5', '1.14.3'), + ('Python', '3.11.5'), +] + +# Without this, the wrong (system) python is picked up by cmake +# in cases where the system python is newer than the one used in these EasyConfigs +# See PR # 19119 +configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " + + +sanity_check_paths = { + 'files': ['include/wscleaninterface.h', 'bin/%(namelower)s'], + 'dirs': ['bin'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] + +moduleclass = 'astro' diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..352429157a29 --- /dev/null +++ b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'wget' +version = '1.21.4' + +homepage = 'https://www.gnu.org/software/wget' +description = """GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, + the most widely-used Internet protocols. It is a non-interactive commandline tool, + so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version_major_minor)s.3_fix_syntax_error_old_glibc_gcc11.patch'] +checksums = [ + {SOURCE_TAR_GZ: '81542f5cefb8faacc39bbbc6c82ded80e3e4a88505ae72ea51df27525bcde04c'}, + {'%(name)s-%(version_major_minor)s.3_fix_syntax_error_old_glibc_gcc11.patch': '0e0aa7a1a4afbe1eefbafb196f162fa5068a03325e342fdc212a16e3c4c946d4'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkg-config', '0.29.2'), + ('Perl', '5.38.0'), +] +dependencies = [ + ('PCRE', '8.45'), + ('libidn2', '2.3.2'), + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), + # OS dependency should be preferred if the os version is more recent then this version, + # it's nice to have an up to date gnutls for security reasons + # ('GnuTLS', '3.7.1'), +] + +preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/%(arch)s-linux-gnu/pkgconfig && " +configopts = "--with-ssl=openssl " + + +# Optionally, you can use gnutls (default) instead of OpenSSL. +# Do not forget to comment out configopts in that case. +# osdependencies = [('gnutls-devel', 'gnutls-dev', 'libgnutls-devel')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +moduleclass = 'devel' From 8580b26c571c999e60e0903a5b4b1a1e494dfa1e Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 10:56:36 +0100 Subject: [PATCH 0681/1193] Fix CFITSIO checksum --- easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb index 17dacb5ba4aa..80c940b906bb 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb @@ -16,7 +16,7 @@ source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] sources = [SOURCELOWER_TAR_GZ] patches = ['%(name)s-3.48_install_test_data.patch'] checksums = [ - {SOURCELOWER_TAR_GZ: '2332b965d327a15c103a7d31d6d1afaf775d00e9785dd25332ae76b9725351e4'}, + {SOURCELOWER_TAR_GZ: '47a7c8ee05687be1e1d8eeeb94fb88f060fbf3cd8a4df52ccb88d5eb0f5062be'}, {'%(name)s-3.48_install_test_data.patch': 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c'}, ] From bb93681b3eb617007b4c1caf2d252feb5afa9490 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 11:46:05 +0100 Subject: [PATCH 0682/1193] Fix test suite findings --- .../a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb | 8 +++++++- .../c/casacore/casacore-3.5.0-foss-2023b.eb | 15 ++++++++++++--- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 11 ++++++++++- .../e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb | 11 ++++++++++- .../p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb | 4 +++- .../p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb | 2 +- .../w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb | 6 +++--- .../w/WSClean/WSClean-3.4-foss-2023b.eb | 6 +++++- .../w/wget/wget-1.21.4-GCCcore-13.2.0.eb | 4 +--- 9 files changed, 52 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb index e211feb7aa3b..9504cae77048 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb @@ -11,7 +11,13 @@ and the tools are applicable to a wide set of telescopes.""" toolchain = {'name': 'foss', 'version': '2023b'} sources = [ - {'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/96704214/'], 'filename': '%(namelower)s-v%(version)s.tar.bz2', 'download_filename': 'download'}, + { + 'source_urls': [ + 'https://gitlab.com/aroffringa/%(namelower)s/-/package_files/96704214/' + ], + 'filename': '%(namelower)s-v%(version)s.tar.bz2', + 'download_filename': 'download' + }, ] checksums = ['9560b7381b68f37d842599f222a8aa2a5d3d3d501d1277471e1a0ba3d7b2aeba'] diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb index 362434327ee8..dd91ba4b0731 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb @@ -14,7 +14,10 @@ toolchain = {'name': 'foss', 'version': '2023b'} source_urls = ['https://github.com/%(name)s/%(name)s/archive'] sources = ['v%(version)s.tar.gz'] patches = ['casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch'] -checksums = ['63f1c8eff932b0fcbd38c598a5811e6e5397b72835b637d6f426105a183b3f91'] +checksums = [ + '63f1c8eff932b0fcbd38c598a5811e6e5397b72835b637d6f426105a183b3f91', # casacore-3.5.0.tar.gz + '7b35d21cd654a7a215d604310f5372319ad21b6261f4a7ae038912b97ef22983', # casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch +] builddependencies = [ ('CMake', '3.27.6'), @@ -32,11 +35,17 @@ dependencies = [ ('ncurses', '6.4'), ] -configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" -DDATA_DIR=%(installdir)s/data -DUSE_OPENMP=ON -DUSE_HDF5=ON -DUSE_MPI=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" ' +configopts += '-DDATA_DIR=%(installdir)s/data -DUSE_OPENMP=ON -DUSE_HDF5=ON ' +configopts += '-DUSE_MPI=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' + +download_cmd = 'wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar ' +download_cmd += '-O /tmp/WSRT_Measures.ztar ' # Install casacore data postinstallcmds = [ - "wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar -O /tmp/WSRT_Measures.ztar && tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data", + download_cmd, + "tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data", ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index f4c6964b32cf..d04a9372e56f 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -9,7 +9,16 @@ description = "DP3: streaming processing pipeline for radio interferometric data toolchain = {'name': 'foss', 'version': '2023b'} sources = [ - {'filename': '%(name)s-v%(version)s.tar.gz', 'git_config': {'url': 'https://git.astron.nl/RD', 'repo_name': '%(name)s', 'tag': 'v%(version)s', 'clone_into': '%(name)s', 'recursive': True}}, + { + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://git.astron.nl/RD', + 'repo_name': '%(name)s', + 'tag': 'v%(version)s', + 'clone_into': '%(name)s', + 'recursive': True + } + }, ] checksums = [None] diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb index f67d1cba1622..3f97c345d82c 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb @@ -10,7 +10,16 @@ such as LOFAR (and LOBES), SKA (OSKAR), MWA, JVLA, etc.""" toolchain = {'name': 'foss', 'version': '2023b'} sources = [ - {'filename': '%(name)s-v%(version)s.tar.gz', 'git_config': {'url': 'https://git.astron.nl/RD', 'repo_name': '%(name)s', 'tag': 'v%(version)s', 'clone_into': '%(name)s', 'recursive': True}}, + { + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://git.astron.nl/RD', + 'repo_name': '%(name)s', + 'tag': 'v%(version)s', + 'clone_into': '%(name)s', + 'recursive': True + } + }, ] checksums = [None] diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb index 25eed8372357..ca479a2ca859 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb @@ -31,7 +31,9 @@ configopts = " --enable-utf --enable-unicode-properties --enable-pcre16 sanity_check_paths = { - 'files': ['bin/%(namelower)s-config', 'include/%(namelower)s.h', 'share/man/man3/%(namelower)s.3', 'lib/libpcre32.so'], + 'files': [ + 'bin/%(namelower)s-config', 'include/%(namelower)s.h', 'share/man/man3/%(namelower)s.3', 'lib/libpcre32.so' + ], 'dirs': ['lib/pkgconfig', 'share/doc/%(namelower)s/html', 'share/man/man1'], } diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb index cad1999ca294..bc1093a8a5c1 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb @@ -17,7 +17,7 @@ sources = ['%(namelower)s522.tar.gz'] patches = ['%(name)s-%(version_major_minor)s.2_gfortran-deps-fixes.patch'] checksums = [ {'pgplot522.tar.gz': 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4'}, - {'%(name)s-%(version_major_minor)s.2_gfortran-deps-fixes.patch': 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec'}, + {'PGPLOT-5.2.2_gfortran-deps-fixes.patch': 'b1822eb32499dc18aa4aa4fae0b31c3c64ff8abb3a243716e78addafa7e58cec'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb index 9bc27997d319..c4429beadd36 100644 --- a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb @@ -21,13 +21,13 @@ builddependencies = [ ('flex', '2.6.4'), ] dependencies = [ - ('CFITSIO', '4.2.0'), + ('CFITSIO', '4.3.1'), ('PGPLOT', '5.2.2'), ('X11', '20231019'), ] -configopts = "--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include --with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include " - +configopts = "--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include " +configopts += --with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include " sanity_check_paths = { 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-%(version)s.a', 'lib/libpgsbox.so'], diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb index 1223c4d82d5a..1b02e0161d8f 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb @@ -11,7 +11,11 @@ multi-frequency deconvolution.""" toolchain = {'name': 'foss', 'version': '2023b'} sources = [ - {'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/97237455/'], 'filename': '%(namelower)s-v%(version)s.tar.bz2', 'download_filename': 'download'}, + { + 'source_urls': ['https://gitlab.com/aroffringa/%(namelower)s/-/package_files/97237455/'], + 'filename': '%(namelower)s-v%(version)s.tar.bz2', + 'download_filename': 'download' + }, ] checksums = ['b43d8ca490ccf34dd22aae6c5ca88a5dcb3cff0526835d3f97fa6d239745e641'] diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb index 352429157a29..a29330d963b8 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb @@ -12,10 +12,8 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCE_TAR_GZ] -patches = ['%(name)s-%(version_major_minor)s.3_fix_syntax_error_old_glibc_gcc11.patch'] checksums = [ {SOURCE_TAR_GZ: '81542f5cefb8faacc39bbbc6c82ded80e3e4a88505ae72ea51df27525bcde04c'}, - {'%(name)s-%(version_major_minor)s.3_fix_syntax_error_old_glibc_gcc11.patch': '0e0aa7a1a4afbe1eefbafb196f162fa5068a03325e342fdc212a16e3c4c946d4'}, ] builddependencies = [ @@ -33,7 +31,7 @@ dependencies = [ # ('GnuTLS', '3.7.1'), ] -preconfigopts = "export PKG_CONFIG_PATH=%(sysroot)s/usr/lib64/pkgconfig:%(sysroot)s/usr/lib/pkgconfig:%(sysroot)s/usr/lib/%(arch)s-linux-gnu/pkgconfig && " +preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc configopts = "--with-ssl=openssl " From 3b244518601cb0bdafa6d0c227c3f5e7eb0570bf Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 14:18:50 +0100 Subject: [PATCH 0683/1193] Fix HDF5 version --- .../a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb | 2 +- .../c/casacore/casacore-3.5.0-foss-2023b.eb | 4 ++-- .../easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 2 +- .../e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb | 2 +- .../h/HDF5/HDF5-1.12.2-gompi-2023b.eb | 23 +++++++++++++++++++ .../w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb | 2 +- .../w/WSClean/WSClean-3.4-foss-2023b.eb | 2 +- .../w/wget/wget-1.21.4-GCCcore-13.2.0.eb | 7 ++++-- 8 files changed, 35 insertions(+), 9 deletions(-) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb index 9504cae77048..4ab6c90ad077 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb @@ -29,7 +29,7 @@ dependencies = [ ('Boost', '1.83.0'), ('CFITSIO', '4.3.1'), ('GSL', '2.7'), - ('HDF5', '1.14.3'), + ('HDF5', '1.12.2'), ('Python', '3.11.5'), ('Lua', '5.4.6'), ('libpng', '1.6.40'), diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb index dd91ba4b0731..2ab3009fa2b2 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb @@ -16,7 +16,7 @@ sources = ['v%(version)s.tar.gz'] patches = ['casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch'] checksums = [ '63f1c8eff932b0fcbd38c598a5811e6e5397b72835b637d6f426105a183b3f91', # casacore-3.5.0.tar.gz - '7b35d21cd654a7a215d604310f5372319ad21b6261f4a7ae038912b97ef22983', # casacore-3.5.0-add-C-style-header-for-GCC-13.1.patch + '7b35d21cd654a7a215d604310f5372319ad21b6261f4a7ae038912b97ef22983', # add-C-style-header-for-GCC-13.1.patch ] builddependencies = [ @@ -28,7 +28,7 @@ builddependencies = [ dependencies = [ ('CFITSIO', '4.3.1'), ('WCSLIB', '7.11'), - ('HDF5', '1.14.3'), + ('HDF5', '1.12.2'), ('GSL', '2.7'), ('Boost.Python', '1.83.0'), ('SciPy-bundle', '2023.11'), diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index d04a9372e56f..de0158ef1fa1 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -31,7 +31,7 @@ dependencies = [ ('CFITSIO', '4.3.1'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.14.3'), + ('HDF5', '1.12.2'), ('Python', '3.11.5'), ('EveryBeam', '0.5.2'), ('Armadillo', '12.8.0'), diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb index 3f97c345d82c..b058202ca703 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb @@ -33,7 +33,7 @@ dependencies = [ ('CFITSIO', '4.3.1'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.14.3'), + ('HDF5', '1.12.2'), ('Python', '3.11.5'), ('libxml2', '2.11.5'), ] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb new file mode 100644 index 000000000000..95203788995e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.12.2' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Szip', '2.1.1'), +] + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb index c4429beadd36..98d3625f6852 100644 --- a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb @@ -27,7 +27,7 @@ dependencies = [ ] configopts = "--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFITSIO/include " -configopts += --with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include " +configopts += "--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include " sanity_check_paths = { 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-%(version)s.a', 'lib/libpgsbox.so'], diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb index 1b02e0161d8f..6782b9644c93 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb @@ -28,7 +28,7 @@ dependencies = [ ('Boost', '1.83.0'), ('CFITSIO', '4.3.1'), ('GSL', '2.7'), - ('HDF5', '1.14.3'), + ('HDF5', '1.12.2'), ('Python', '3.11.5'), ] diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb index a29330d963b8..5219243fcbc7 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb @@ -31,9 +31,12 @@ dependencies = [ # ('GnuTLS', '3.7.1'), ] +# make sure pkg-config picks up system packages (OpenSSL & co) +local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/pkgconfig:" +local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" preconfigopts = "export PKG_CONFIG_PATH=%s && " % local_pc -configopts = "--with-ssl=openssl " - +configopts = '--with-ssl=openssl ' # Optionally, you can use gnutls (default) instead of OpenSSL. # Do not forget to comment out configopts in that case. From 8f265dbd8e41ac749d0e4eca80568c06eac087e8 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 14:25:27 +0100 Subject: [PATCH 0684/1193] Fix trailing whitespace in HDF5 filename --- .../h/HDF5/HDF5-1.12.2-gompi-2023b.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb deleted file mode 100644 index 95203788995e..000000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'HDF5' -# Note: Odd minor releases are only RCs and should not be used. -version = '1.12.2' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'gompi', 'version': '2023b'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] - -dependencies = [ - ('zlib', '1.2.13'), - ('Szip', '2.1.1'), -] - - -moduleclass = 'data' From 828c5b243a850033b0ace212126297eb1c216de1 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 15:00:33 +0100 Subject: [PATCH 0685/1193] Fix trailing whitespace in HDF5 filename --- .../c/casacore/casacore-3.5.0-foss-2023b.eb | 6 ++--- .../h/HDF5/HDF5-1.12.2-gompi-2023b.eb | 23 +++++++++++++++++++ 2 files changed, 26 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb index 2ab3009fa2b2..9c92ba1d075d 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb @@ -39,12 +39,12 @@ configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" ' configopts += '-DDATA_DIR=%(installdir)s/data -DUSE_OPENMP=ON -DUSE_HDF5=ON ' configopts += '-DUSE_MPI=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' -download_cmd = 'wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar ' -download_cmd += '-O /tmp/WSRT_Measures.ztar ' +local_download_cmd = 'wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar ' +local_download_cmd += '-O /tmp/WSRT_Measures.ztar ' # Install casacore data postinstallcmds = [ - download_cmd, + local_download_cmd, "tar xfvz /tmp/WSRT_Measures.ztar --one-top-level=%(installdir)s/data", ] diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb new file mode 100644 index 000000000000..95203788995e --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb @@ -0,0 +1,23 @@ +name = 'HDF5' +# Note: Odd minor releases are only RCs and should not be used. +version = '1.12.2' + +homepage = 'https://portal.hdfgroup.org/display/support' +description = """HDF5 is a data model, library, and file format for storing and managing data. + It supports an unlimited variety of datatypes, and is designed for flexible + and efficient I/O and for high volume and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Szip', '2.1.1'), +] + + +moduleclass = 'data' From 0a49a066392f388d3854ba73324c88ecd96a1dc3 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 15:55:58 +0100 Subject: [PATCH 0686/1193] Change HDF5 to 1.14.3 in AOFlagger --- easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb index 4ab6c90ad077..9504cae77048 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb @@ -29,7 +29,7 @@ dependencies = [ ('Boost', '1.83.0'), ('CFITSIO', '4.3.1'), ('GSL', '2.7'), - ('HDF5', '1.12.2'), + ('HDF5', '1.14.3'), ('Python', '3.11.5'), ('Lua', '5.4.6'), ('libpng', '1.6.40'), From faed7bca8b34e20786cc349ead3056058e2e9bd7 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 16:01:17 +0100 Subject: [PATCH 0687/1193] Change HDF5 to 1.14.3 --- easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb | 2 +- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 2 +- easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb | 2 +- easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb index 9c92ba1d075d..f101eaf6ee91 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb @@ -28,7 +28,7 @@ builddependencies = [ dependencies = [ ('CFITSIO', '4.3.1'), ('WCSLIB', '7.11'), - ('HDF5', '1.12.2'), + ('HDF5', '1.14.3'), ('GSL', '2.7'), ('Boost.Python', '1.83.0'), ('SciPy-bundle', '2023.11'), diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index de0158ef1fa1..d04a9372e56f 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -31,7 +31,7 @@ dependencies = [ ('CFITSIO', '4.3.1'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.12.2'), + ('HDF5', '1.14.3'), ('Python', '3.11.5'), ('EveryBeam', '0.5.2'), ('Armadillo', '12.8.0'), diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb index b058202ca703..3f97c345d82c 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb @@ -33,7 +33,7 @@ dependencies = [ ('CFITSIO', '4.3.1'), ('WCSLIB', '7.11'), ('GSL', '2.7'), - ('HDF5', '1.12.2'), + ('HDF5', '1.14.3'), ('Python', '3.11.5'), ('libxml2', '2.11.5'), ] diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb index 6782b9644c93..1b02e0161d8f 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb @@ -28,7 +28,7 @@ dependencies = [ ('Boost', '1.83.0'), ('CFITSIO', '4.3.1'), ('GSL', '2.7'), - ('HDF5', '1.12.2'), + ('HDF5', '1.14.3'), ('Python', '3.11.5'), ] From ecc9614b16c8d72389036ef74530455f4c5ff9a3 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 13 Feb 2024 16:09:16 +0100 Subject: [PATCH 0688/1193] Remove h/HDF5/HDF5-1.12.2-gompi-2023b.eb --- .../h/HDF5/HDF5-1.12.2-gompi-2023b.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb diff --git a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb deleted file mode 100644 index 95203788995e..000000000000 --- a/easybuild/easyconfigs/h/HDF5/HDF5-1.12.2-gompi-2023b.eb +++ /dev/null @@ -1,23 +0,0 @@ -name = 'HDF5' -# Note: Odd minor releases are only RCs and should not be used. -version = '1.12.2' - -homepage = 'https://portal.hdfgroup.org/display/support' -description = """HDF5 is a data model, library, and file format for storing and managing data. - It supports an unlimited variety of datatypes, and is designed for flexible - and efficient I/O and for high volume and complex data.""" - -toolchain = {'name': 'gompi', 'version': '2023b'} -toolchainopts = {'pic': True, 'usempi': True} - -source_urls = ['https://support.hdfgroup.org/ftp/%(name)s/releases/%(namelower)s-%(version_major_minor)s/%(namelower)s-%(version)s/src'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['2a89af03d56ce7502dcae18232c241281ad1773561ec00c0f0e8ee2463910f14'] - -dependencies = [ - ('zlib', '1.2.13'), - ('Szip', '2.1.1'), -] - - -moduleclass = 'data' From a66fe75eeef802c031ab50d1dd3931d4f51e9c2a Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Tue, 13 Feb 2024 16:55:26 +0100 Subject: [PATCH 0689/1193] add library path to MDI config --- easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb index aa11e702a52f..08cc370daadb 100644 --- a/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb +++ b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb @@ -39,6 +39,11 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] +modextrapaths = { + 'LD_LIBRARY_PATH': 'lib/mdi', + 'LIBRARY_PATH': 'lib/mdi', +} + sanity_check_paths = { 'files': ['lib/mdi/libmdi.a', 'lib/mdi/libmdi.%s' % SHLIB_EXT], 'dirs': ['include', 'share'], From de96bdb9174003c1f601ee7f6214b0297f3b89fd Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 13 Feb 2024 20:13:40 +0100 Subject: [PATCH 0690/1193] adding easyconfigs: AMICA-2024.1.19-intel-2023a.eb --- .../a/AMICA/AMICA-2024.1.19-intel-2023a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb diff --git a/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb b/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb new file mode 100644 index 000000000000..abaa91eda0b1 --- /dev/null +++ b/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb @@ -0,0 +1,29 @@ +easyblock = 'CmdCp' + +name = 'AMICA' +version = '2024.1.19' +local_commit = 'e0db55f07c8c410641cd5b0df5498a5a53129ce6' + +homepage = 'https://github.com/sccn/amica' +description = """Code for AMICA: Adaptive Mixture ICA with shared components""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/sccn/amica/archive/'] +sources = [{'download_filename': '%s.zip' % local_commit, 'filename': '%(name)s-%(version)s.zip'}] +checksums = ['d856ef1bf4bd09b2aacf5da6832b9af5d7fb70976786f43585c72acd1a52443b'] + +# original command: $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90 +cmds_map = [('.*', "$MPIF90 $F90FLAGS -static-intel -fpp -heap-arrays -mkl -DMKL -o amica17 funmod2.f90 amica17.f90")] + +test_cmd = "./amica17nsg ./amicadefs.param" + +files_to_copy = [(['amica17', 'amicadefs.param'], 'bin')] + +sanity_check_paths = { + 'files': ["bin/amica17", "bin/amicadefs.param"], + 'dirs': [], +} + +moduleclass = 'math' From 85bc93200f22669bf7b53fea1c13c5661747118b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 13 Feb 2024 20:19:14 +0100 Subject: [PATCH 0691/1193] Update AMICA-2024.1.19-intel-2023a.eb shorted long line --- easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb b/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb index abaa91eda0b1..9a9c6c28f80a 100644 --- a/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb +++ b/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb @@ -14,7 +14,8 @@ source_urls = ['https://github.com/sccn/amica/archive/'] sources = [{'download_filename': '%s.zip' % local_commit, 'filename': '%(name)s-%(version)s.zip'}] checksums = ['d856ef1bf4bd09b2aacf5da6832b9af5d7fb70976786f43585c72acd1a52443b'] -# original command: $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90 +# original command: +# $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90 cmds_map = [('.*', "$MPIF90 $F90FLAGS -static-intel -fpp -heap-arrays -mkl -DMKL -o amica17 funmod2.f90 amica17.f90")] test_cmd = "./amica17nsg ./amicadefs.param" From 549f9a5797db6a80129922700eb09fdab4f21d04 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Feb 2024 12:12:25 +0100 Subject: [PATCH 0692/1193] adding easyconfigs: ORCA-5.0.4-gompi-2023a.eb --- .../o/ORCA/ORCA-5.0.4-gompi-2023a.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2023a.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2023a.eb b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2023a.eb new file mode 100644 index 000000000000..fb186ab49f34 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-5.0.4-gompi-2023a.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '5.0.4' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi411.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_5_0_4_linux_x86-64_shared_openmpi411.tar.xz + 'c4ea5aea60da7bcb18a6b7042609206fbeb2a765c6fa958c5689d450b588b036', +] + +moduleclass = 'chem' From 5839d6177a0c7aa755dae4b9fcd0d64714709c9d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 14 Feb 2024 13:20:00 +0100 Subject: [PATCH 0693/1193] adding easyconfigs: Circlator-1.5.5-foss-2023a.eb, MUMmer-4.0.0rc1-GCCcore-12.3.0.eb, Fastaq-3.17.0-GCC-12.3.0.eb --- .../c/Circlator/Circlator-1.5.5-foss-2023a.eb | 47 +++++++++++++++++++ .../f/Fastaq/Fastaq-3.17.0-GCC-12.3.0.eb | 30 ++++++++++++ .../MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb | 39 +++++++++++++++ 3 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb create mode 100644 easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb new file mode 100644 index 000000000000..8310aa1b2de9 --- /dev/null +++ b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Circlator' +version = '1.5.5' + +homepage = 'https://github.com/sanger-pathogens/circlator/' +description = """A tool to circularize genome assemblies.s""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('openpyxl', '3.1.2'), + ('Fastaq', '3.17.0'), + ('Pysam', '0.22.0'), + ('MUMmer', '4.0.0rc1'), + ('BWA', '0.7.17'), + ('prodigal', '2.6.3'), + ('SPAdes', '3.15.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pymummer', '0.11.0', { + 'checksums': ['199b8391348ff83760e9f63fdcee6208f8aa29da6506ee1654f1933e60665259'], + }), + (name, version, { + 'source_urls': [ + 'https://files.pythonhosted.org/packages/7c/bf/f0fd534a733b7d98fc9853ca1aa735984cec1e5fc4670b632e76973f8add/' + ], + 'sources': ['circlator-1.5.5.tar.gz'], + 'checksums': ['d3bfa12c4f9d4489331c42331a7765719af0c7a2aca7aa860dc996e27edd671a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/circlator'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "circlator progcheck", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-12.3.0.eb b/easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..c16c2a13ab3b --- /dev/null +++ b/easybuild/easyconfigs/f/Fastaq/Fastaq-3.17.0-GCC-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Fastaq' +version = '3.17.0' + +homepage = 'https://github.com/sanger-pathogens/Fastaq' +description = "Python3 scripts to manipulate FASTA and FASTQ files." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'sanger-pathogens' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-docker3.tar.gz'] +checksums = ['f65235f5d89f4621cf8e15676448e17d85620c05096cb6413134c4e29717ff5f'] + +dependencies = [ + ('Python', '3.11.3'), + ('SAMtools', '1.18'), + ('gzip', '1.12'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_commands = ['fastaq version'] + +options = {'modulename': 'pyfastaq'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..46bb7b4a03f1 --- /dev/null +++ b/easybuild/easyconfigs/m/MUMmer/MUMmer-4.0.0rc1-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# updating version from 4.0.0beta2 to 4.0.0rc1 which was released in Oct 2020 +# Aaron Miller Mar 15 2021 +# Update: Pavel Tománek (INUITS) + +easyblock = 'ConfigureMake' + +name = 'MUMmer' +version = '4.0.0rc1' + +homepage = 'https://mummer.sourceforge.net/' + +description = """ + MUMmer is a system for rapidly aligning entire genomes, + whether in complete or draft form. AMOS makes use of it. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/gmarcais/mummer/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['85006adb2d6539c2f738c3e3bb14b58bb6f62cd6c6ca5ede884a87ae76e07d1d'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/mummer', 'bin/annotate', 'bin/combineMUMs', 'bin/delta-filter', + 'bin/repeat-match', 'bin/show-aligns', 'bin/show-coords', + 'bin/show-tiling', 'bin/show-snps', 'bin/show-diff', 'bin/exact-tandems', + 'bin/mummerplot', 'bin/promer', 'bin/dnadiff', + ], + 'dirs': ['include', 'lib', 'libexec'], +} + +moduleclass = 'bio' From 4cd89673c87acf8c18be0b86cb4f2db8761a930a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Feb 2024 13:49:45 +0100 Subject: [PATCH 0694/1193] {tools}[intel/2022a] NCO v5.1.9, GSL v2.7 --- .../g/GSL/GSL-2.7-intel-compilers-2022.1.0.eb | 25 +++++++++++ .../n/NCO/NCO-5.1.9-intel-2022a.eb | 44 +++++++++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2022.1.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.9-intel-2022a.eb diff --git a/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2022.1.0.eb new file mode 100644 index 000000000000..a4157c5f2fae --- /dev/null +++ b/easybuild/easyconfigs/g/GSL/GSL-2.7-intel-compilers-2022.1.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'GSL' +version = '2.7' + +homepage = 'https://www.gnu.org/software/gsl/' +description = """The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. + The library provides a wide range of mathematical routines such as random number generators, special functions + and least-squares fitting.""" + +toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} +toolchainopts = {'unroll': True, 'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efbbf3785da0e53038be7907500628b466152dbc3c173a87de1b5eba2e23602b'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['gsl-config', 'gsl-histogram', 'gsl-randist']] + + ['include/gsl/gsl_types.h'] + + ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['gsl', 'gslcblas']], + 'dirs': [], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.9-intel-2022a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-intel-2022a.eb new file mode 100644 index 000000000000..d88c27588b74 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.9-intel-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.9' + +homepage = "https://github.com/nco/nco" +description = """The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, +including DAP, HDF4, and HDF5.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['9cd90345c1e3860a690b53fd6c08b721d631a646d169431927884c99841c34e9'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.4.8'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.11'), + ('GSL', '2.7'), + ('netCDF', '4.9.0'), + ('ESMF', '8.3.0'), # ncremap needs ESMF_RegridWeightGen +] + +configopts = "--enable-nco_cplusplus" + +sanity_check_paths = { + 'files': ['bin/nc%s' % x for x in ('ap2', 'atted', 'bo', 'diff', 'ea', 'ecat', 'es', + 'flint', 'ks', 'pdq', 'ra', 'rcat', 'rename', 'wa')] + + ['lib/libnco.a', 'lib/libnco.%s' % SHLIB_EXT, 'lib/libnco_c++.a', 'lib/libnco_c++.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +sanity_check_commands = [ + "ncks -O -7 --cnk_dmn time,10 " + "%(builddir)s/%(namelower)s-%(version)s/data/in.nc %(builddir)s/%(namelower)s-%(version)s/data/in4.cdl" +] + +moduleclass = 'tools' From dba536a050304eb6096aa5ec876ad3be67985100 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 14 Feb 2024 14:41:00 +0100 Subject: [PATCH 0695/1193] remove source_urls too long line --- .../easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb index 8310aa1b2de9..21e2a4f2ceee 100644 --- a/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb @@ -27,9 +27,6 @@ exts_list = [ 'checksums': ['199b8391348ff83760e9f63fdcee6208f8aa29da6506ee1654f1933e60665259'], }), (name, version, { - 'source_urls': [ - 'https://files.pythonhosted.org/packages/7c/bf/f0fd534a733b7d98fc9853ca1aa735984cec1e5fc4670b632e76973f8add/' - ], 'sources': ['circlator-1.5.5.tar.gz'], 'checksums': ['d3bfa12c4f9d4489331c42331a7765719af0c7a2aca7aa860dc996e27edd671a'], }), From 3fa8b9a7370c84279928ed476667095542e7b9d1 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 14 Feb 2024 14:44:18 +0100 Subject: [PATCH 0696/1193] update hardcoded version --- easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb index 21e2a4f2ceee..924f8a853811 100644 --- a/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb @@ -27,7 +27,7 @@ exts_list = [ 'checksums': ['199b8391348ff83760e9f63fdcee6208f8aa29da6506ee1654f1933e60665259'], }), (name, version, { - 'sources': ['circlator-1.5.5.tar.gz'], + 'sources': ['circlator-%(version)s.tar.gz'], 'checksums': ['d3bfa12c4f9d4489331c42331a7765719af0c7a2aca7aa860dc996e27edd671a'], }), ] From 26291b09b5a361b743137a9c6f8440909ca6bd9d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Feb 2024 15:02:28 +0100 Subject: [PATCH 0697/1193] adding easyconfigs: Nilearn-0.10.3-gfbf-2023a.eb --- .../n/Nilearn/Nilearn-0.10.3-gfbf-2023a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nilearn/Nilearn-0.10.3-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/n/Nilearn/Nilearn-0.10.3-gfbf-2023a.eb b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.10.3-gfbf-2023a.eb new file mode 100644 index 000000000000..ef06ec61da36 --- /dev/null +++ b/easybuild/easyconfigs/n/Nilearn/Nilearn-0.10.3-gfbf-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'Nilearn' +version = '0.10.3' + +homepage = 'https://nilearn.github.io/' +description = """Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('lxml', '4.9.2'), + ('NiBabel', '5.2.0'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('nilearn', version, { + 'checksums': ['77819331314c4ca5c15c07634f69f855fafdf9add051b1882e3a600ad52757d8'], + }), +] + +moduleclass = 'vis' From 1ee09d87c1c86e965b5397028b50087cd86f53df Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 14 Feb 2024 15:05:09 +0100 Subject: [PATCH 0698/1193] Switch pkgconf for pkg-config --- .../a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb | 2 +- .../pkg-config-0.29.2-GCCcore-13.2.0.eb | 35 ------------------- .../w/wget/wget-1.21.4-GCCcore-13.2.0.eb | 4 +-- 3 files changed, 3 insertions(+), 38 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb index 0151ba327e0b..eadec17227f4 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb @@ -18,7 +18,7 @@ checksums = ['24f2a2b259992d3c797d80f626878aa8e2ed5009d549dad57854bbcfb95e1ed0'] builddependencies = [ ('Autotools', '20220317'), - ('pkg-config', '0.29.2'), + ('pkgconf', '2.0.3'), ] dependencies = [ ('Eigen', '3.4.0'), diff --git a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb deleted file mode 100644 index b9bda34701d8..000000000000 --- a/easybuild/easyconfigs/p/pkg-config/pkg-config-0.29.2-GCCcore-13.2.0.eb +++ /dev/null @@ -1,35 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'pkg-config' -version = '0.29.2' - -homepage = 'https://www.freedesktop.org/wiki/Software/pkg-config/' -description = """ - pkg-config is a helper tool used when compiling applications and libraries. - It helps you insert the correct compiler options on the command line so an - application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` - for instance, rather than hard-coding values on where to find glib (or other - libraries). -""" - -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} - -source_urls = ['https://%(name)s.freedesktop.org/releases/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['6fc69c01688c9458a57eb9a1664c9aba372ccda420a02bf4429fe610e7e7d591'] - -builddependencies = [ - ('binutils', '2.40'), -] - -configopts = " --with-internal-glib" - -# don't use PAX, it might break. -tar_config_opts = True - -sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': [], -} - -moduleclass = 'devel' diff --git a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb index 5219243fcbc7..d77cd2923d7e 100644 --- a/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/w/wget/wget-1.21.4-GCCcore-13.2.0.eb @@ -18,7 +18,7 @@ checksums = [ builddependencies = [ ('binutils', '2.40'), - ('pkg-config', '0.29.2'), + ('pkgconf', '2.0.3'), ('Perl', '5.38.0'), ] dependencies = [ @@ -31,7 +31,7 @@ dependencies = [ # ('GnuTLS', '3.7.1'), ] -# make sure pkg-config picks up system packages (OpenSSL & co) +# make sure pkgconfig picks up system packages (OpenSSL & co) local_pc = "%(sysroot)s/usr/lib64/pkgconfig:" local_pc += "%(sysroot)s/usr/lib/pkgconfig:" local_pc += "%(sysroot)s/usr/lib/x86_64-linux-gnu/pkgconfig" From 1c22b73b00d9d57dd16b419e0990009052e04873 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 14 Feb 2024 14:14:16 +0000 Subject: [PATCH 0699/1193] adding easyconfigs: libaec-1.0.6-GCCcore-12.2.0.eb, ecCodes-2.31.0-gompi-2022b.eb --- .../e/ecCodes/ecCodes-2.31.0-gompi-2022b.eb | 46 +++++++++++++++++++ .../l/libaec/libaec-1.0.6-GCCcore-12.2.0.eb | 34 ++++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2022b.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2022b.eb new file mode 100644 index 000000000000..5488a82841bc --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.31.0-gompi-2022b.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.31.0' + +homepage = 'https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home' +description = """ecCodes is a package developed by ECMWF which provides an application programming interface and + a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, + WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding).""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/ecmwf/eccodes/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}] +checksums = ['cb4cd3bab9cebd85a00397e12ce8e4a579b2f0a25aaf6df763436cf37db063e1'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('ecBuild', '3.8.0', '', SYSTEM), +] +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('libaec', '1.0.6'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF -DENABLE_JPG=ON " +configopts += "-DENABLE_JPG_LIBJASPER=ON -DENABLE_ECCODES_THREADS=ON" + + +sanity_check_paths = { + 'files': ['bin/bufr_compare', 'bin/bufr_copy', 'bin/bufr_dump', 'bin/bufr_filter', 'bin/bufr_get', 'bin/bufr_ls', + 'bin/grib_compare', 'bin/grib_copy', 'bin/grib_dump', 'bin/grib_filter', 'bin/grib_get', 'bin/grib_ls', + 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', + 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', + 'bin/metar_ls', 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', + 'lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..bc29e5b97e73 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-12.2.0.eb @@ -0,0 +1,34 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.0.6' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + + +sanity_check_paths = { + 'files': ['bin/aec', 'include/%(name)s.h', 'include/szlib.h', + 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ['aec --help'] + +moduleclass = 'lib' From 378475e0bf2e540c2db54def5db5d732353b4c3c Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 14 Feb 2024 14:19:28 +0000 Subject: [PATCH 0700/1193] adding easyconfigs: YAXT-0.10.0-gompi-2022b.eb --- .../y/YAXT/YAXT-0.10.0-gompi-2022b.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/y/YAXT/YAXT-0.10.0-gompi-2022b.eb diff --git a/easybuild/easyconfigs/y/YAXT/YAXT-0.10.0-gompi-2022b.eb b/easybuild/easyconfigs/y/YAXT/YAXT-0.10.0-gompi-2022b.eb new file mode 100644 index 000000000000..05012a3ba846 --- /dev/null +++ b/easybuild/easyconfigs/y/YAXT/YAXT-0.10.0-gompi-2022b.eb @@ -0,0 +1,29 @@ +# Updated to new URL and version 0.9.2.1 +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'YAXT' +version = '0.10.0' + +homepage = 'https://www.dkrz.de/redmine/projects/yaxt' +description = "Yet Another eXchange Tool" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = [ + 'https://swprojects.dkrz.de/redmine/attachments/download/529/', + 'https://www.dkrz.de/redmine/attachments/download/529/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['2d1de5197927b8e587f4e920a1ea31e359076a5de208fd46127d658cc7deb903'] + +configopts = 'FC="$F90" FCFLAGS="$F90FLAGS -cpp"' + +sanity_check_paths = { + 'files': ['include/yaxt.h', 'include/yaxt.mod', 'lib/libyaxt.a', 'lib/libyaxt.%s' % SHLIB_EXT], + 'dirs': ['include/xt'], +} + +moduleclass = 'tools' From 5e57ca2d77dc97c54448d8f432f8087ff65308b3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 14 Feb 2024 15:25:44 +0100 Subject: [PATCH 0701/1193] Update AMICA-2024.1.19-intel-2023a.eb update test command --- easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb b/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb index 9a9c6c28f80a..22c95a707213 100644 --- a/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb +++ b/easybuild/easyconfigs/a/AMICA/AMICA-2024.1.19-intel-2023a.eb @@ -18,7 +18,7 @@ checksums = ['d856ef1bf4bd09b2aacf5da6832b9af5d7fb70976786f43585c72acd1a52443b'] # $ mpif90 -static-intel -fpp -O3 -march=core-avx2 -heap-arrays -qopenmp -mkl -DMKL -o amica17 funmod2.f90 amica17.f90 cmds_map = [('.*', "$MPIF90 $F90FLAGS -static-intel -fpp -heap-arrays -mkl -DMKL -o amica17 funmod2.f90 amica17.f90")] -test_cmd = "./amica17nsg ./amicadefs.param" +test_cmd = "./amica17 ./amicadefs.param" files_to_copy = [(['amica17', 'amicadefs.param'], 'bin')] From b0e4df1b98570655b2fc48e571cbe816e39cafa7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Feb 2024 15:46:30 +0100 Subject: [PATCH 0702/1193] downgrade NiBabel-5.2.0-foss-2023a.eb to gfbf/2023a toolchain --- ...bel-5.2.0-foss-2023a.eb => NiBabel-5.2.0-gfbf-2023a.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/n/NiBabel/{NiBabel-5.2.0-foss-2023a.eb => NiBabel-5.2.0-gfbf-2023a.eb} (94%) diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-foss-2023a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2023a.eb similarity index 94% rename from easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-foss-2023a.eb rename to easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2023a.eb index ffc9dd60c3b5..f84ae976cbc2 100644 --- a/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-5.2.0-gfbf-2023a.eb @@ -9,14 +9,17 @@ description = """NiBabel provides read/write access to some common medical and n as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), ('Pillow', '10.0.0'), ('pydicom', '2.4.4'), - ('hatchling', '1.18.0'), ] use_pip = True From 2e217a27a443d5ae4716d4eab1f53ea76b7b9223 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 14 Feb 2024 16:20:27 +0100 Subject: [PATCH 0703/1193] Process comments --- .../a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb | 6 ------ .../a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb | 7 ++++--- .../c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb | 2 +- .../c/casacore/casacore-3.5.0-foss-2023b.eb | 8 ++++++-- .../easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 5 ----- .../e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb | 7 +------ .../l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb | 2 +- .../p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb | 7 +++++-- .../p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb | 16 +++++++++++----- .../w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb | 2 +- .../w/WSClean/WSClean-3.4-foss-2023b.eb | 5 ----- 11 files changed, 30 insertions(+), 37 deletions(-) diff --git a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb index 9504cae77048..d1fe2a3f7dd3 100644 --- a/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/AOFlagger/AOFlagger-3.4.0-foss-2023b.eb @@ -36,12 +36,6 @@ dependencies = [ ('libxml2', '2.11.5'), ] -# Without this, the wrong (system) python is picked up by cmake -# in cases where the system python is newer than the one used in these EasyConfigs -# See PR # 19119 -configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " - - sanity_check_paths = { 'files': ['include/%(namelower)s.h', 'bin/%(namelower)s'], 'dirs': ['bin'], diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb index eadec17227f4..04b73ebc183e 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb @@ -12,6 +12,8 @@ description = "ARPACK is a collection of Fortran77 subroutines designed to solve toolchain = {'name': 'foss', 'version': '2023b'} toolchainopts = {'pic': True, 'usempi': True} +github_account = 'opencollab' + source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] checksums = ['24f2a2b259992d3c797d80f626878aa8e2ed5009d549dad57854bbcfb95e1ed0'] @@ -27,10 +29,9 @@ dependencies = [ preconfigopts = "sh bootstrap && " configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' -github_account = 'opencollab' - sanity_check_paths = { - 'files': ['lib64/libarpack.la', 'lib64/libarpack.so', 'lib64/libparpack.la', 'lib64/libparpack.so'], + 'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT, + 'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb index 80c940b906bb..c22b4a16118e 100644 --- a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-4.3.1-GCCcore-13.2.0.eb @@ -34,7 +34,7 @@ buildopts = "&& make shared && make testprog" sanity_check_paths = { - 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.so'], + 'files': ['lib/libcfitsio.a', 'lib/libcfitsio.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb index f101eaf6ee91..d83d40387f2c 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb @@ -37,7 +37,7 @@ dependencies = [ configopts = '-DBUILD_PYTHON=NO -DBUILD_PYTHON3=YES -Wno-dev -DCXX11="ON" ' configopts += '-DDATA_DIR=%(installdir)s/data -DUSE_OPENMP=ON -DUSE_HDF5=ON ' -configopts += '-DUSE_MPI=ON -DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' +configopts += '-DUSE_MPI=ON ' local_download_cmd = 'wget --retry-connrefused ftp://anonymous@ftp.astron.nl/outgoing/Measures/WSRT_Measures.ztar ' local_download_cmd += '-O /tmp/WSRT_Measures.ztar ' @@ -49,7 +49,11 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': ['lib/libcasa_casa.so', 'lib/libcasa_mirlib.so', 'lib/libcasa_ms.so'], + 'files': [ + 'lib/libcasa_casa.%s' % SHLIB_EXT, + 'lib/libcasa_mirlib.%s' % SHLIB_EXT, + 'lib/libcasa_ms.%s' % SHLIB_EXT, + ], 'dirs': ['bin', 'include/%(name)s'], } diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index d04a9372e56f..03532ba746d2 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -38,11 +38,6 @@ dependencies = [ ('AOFlagger', '3.4.0'), ] -# Without this, the wrong (system) python is picked up by cmake -# in cases where the system python is newer than the one used in these EasyConfigs -# See PR # 19119 -configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " - sanity_check_paths = { 'files': ['include/include/%(namelower)s/base/%(name)s.h', 'bin/%(name)s'], diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb index 3f97c345d82c..6192a7ace663 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb @@ -38,14 +38,9 @@ dependencies = [ ('libxml2', '2.11.5'), ] -# Without this, the wrong (system) python is picked up by cmake -# in cases where the system python is newer than the one used in these EasyConfigs -# See PR # 19119 -configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " - sanity_check_paths = { - 'files': ['include/%(name)s/beamformer.h', 'lib/libeverybeam.so'], + 'files': ['include/%(name)s/beamformer.h', 'lib/libeverybeam.%s' % SHLIB_EXT], 'dirs': [], } diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb index 662ff77ec42b..042215912d5e 100644 --- a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb @@ -18,7 +18,7 @@ builddependencies = [ sanity_check_paths = { - 'files': ['bin/idn2', 'lib/%(name)s.so'], + 'files': ['bin/idn2', 'lib/%(name)s.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb index ca479a2ca859..6815128938a1 100644 --- a/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE/PCRE-8.45-GCCcore-13.2.0.eb @@ -27,12 +27,15 @@ dependencies = [ ('zlib', '1.2.13'), ] -configopts = " --enable-utf --enable-unicode-properties --enable-pcre16 --enable-pcre32" +configopts = "--enable-utf --enable-unicode-properties --enable-pcre16 --enable-pcre32" sanity_check_paths = { 'files': [ - 'bin/%(namelower)s-config', 'include/%(namelower)s.h', 'share/man/man3/%(namelower)s.3', 'lib/libpcre32.so' + 'bin/%(namelower)s-config', + 'include/%(namelower)s.h', + 'share/man/man3/%(namelower)s.3', + 'lib/libpcre32.%s' % SHLIB_EXT ], 'dirs': ['lib/pkgconfig', 'share/doc/%(namelower)s/html', 'share/man/man1'], } diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb index bc1093a8a5c1..d2e3d25fb6d6 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb @@ -31,10 +31,10 @@ dependencies = [ # create .so symlinks for shared libraries postinstallcmds = [ - "cd %(installdir)s/lib && ln -s libcpgplot.so.%(version)s libcpgplot.so.5", - "cd %(installdir)s/lib && ln -s libcpgplot.so.%(version)s libcpgplot.so", - "cd %(installdir)s/lib && ln -s libpgplot.so.%(version)s libpgplot.so.5", - "cd %(installdir)s/lib && ln -s libpgplot.so.%(version)s libpgplot.so", + "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s.5" % SHLIB_EXT, + "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s" % SHLIB_EXT, + "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s.5" % SHLIB_EXT, + "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s" % SHLIB_EXT, ] files_to_copy = [ (['pgdemo*'], 'bin'), @@ -45,7 +45,13 @@ files_to_copy = [ cmds_map = [('.*', './makemake . linux g77_gcc && make && make shared && make cpg && make cpg-shared')] sanity_check_paths = { - 'files': ['include/cpgplot.h', 'lib/libpgplot.a', 'lib/libcpgplot.a', 'lib/libpgplot.so', 'lib/libcpgplot.so'], + 'files': [ + 'include/cpgplot.h', + 'lib/libpgplot.a', + 'lib/libcpgplot.a', + 'lib/libpgplot.%s' % SHLIB_EXT, + 'lib/libcpgplot.%s' % SHLIB_EXT + ], 'dirs': ['bin'], } diff --git a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb index 98d3625f6852..4a6ebb8aacfa 100644 --- a/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/w/WCSLIB/WCSLIB-7.11-GCC-13.2.0.eb @@ -30,7 +30,7 @@ configopts = "--with-cfitsiolib=$EBROOTCFITSIO/lib --with-cfitsioinc=$EBROOTCFIT configopts += "--with-pgplotlib=$EBROOTPGPLOT/lib --with-pgplotinc=$EBROOTPGPLOT/include " sanity_check_paths = { - 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-%(version)s.a', 'lib/libpgsbox.so'], + 'files': ['bin/wcsgrid', 'bin/wcsware', 'lib/libpgsbox-%(version)s.a', 'lib/libpgsbox.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb index 1b02e0161d8f..9be780efeb39 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb @@ -32,11 +32,6 @@ dependencies = [ ('Python', '3.11.5'), ] -# Without this, the wrong (system) python is picked up by cmake -# in cases where the system python is newer than the one used in these EasyConfigs -# See PR # 19119 -configopts = "-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python " - sanity_check_paths = { 'files': ['include/wscleaninterface.h', 'bin/%(namelower)s'], From 4d760977adfc9ccda32beac9bc51da17a61cfc18 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Feb 2024 16:22:14 +0100 Subject: [PATCH 0704/1193] adding easyconfigs: MATIO-1.5.26-GCCcore-12.3.0.eb, OpenMEEG-2.5.7-foss-2023a.eb and patches: OpenMEEG-2.5.7_find-blas-lapack-from-cmake.patch --- .../m/MATIO/MATIO-1.5.26-GCCcore-12.3.0.eb | 34 +++++++++++ .../o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb | 56 +++++++++++++++++++ ...EG-2.5.7_find-blas-lapack-from-cmake.patch | 31 ++++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb create mode 100644 easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7_find-blas-lapack-from-cmake.patch diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-12.3.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..85d161c59b82 --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.26' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['c07b089dad904c7e13a08f0ce7ac0b2969fe3d886579a10433eb13fdc3530e74'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb new file mode 100644 index 000000000000..8926a0833fac --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7-foss-2023a.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'OpenMEEG' +version = '2.5.7' + +homepage = 'http://openmeeg.github.io/' +description = """The OpenMEEG software is a C++ package for solving the forward problems of +electroencephalography (EEG) and magnetoencephalography (MEG).""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = "openmeeg" +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['OpenMEEG-2.5.7_find-blas-lapack-from-cmake.patch'] +checksums = [ + {'2.5.7.tar.gz': '19e982821affb67fedb76fbeac6fbdc0b6653f3c8d4a6f807ef729566a42b0dc'}, + {'OpenMEEG-2.5.7_find-blas-lapack-from-cmake.patch': + '223d15c9efac40f7875ca6605409613be7a9d2509b3baebde362e08297357367'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('HDF5', '1.14.0'), + ('MATIO', '1.5.26'), +] + +configopts = "-DENABLE_PYTHON=on -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib " + +_om_binaries = [ + 'om_assemble', 'om_forward', 'om_geometry_info', 'om_matrix_convert', 'om_mesh_concat', 'om_mesh_info', + 'om_mesh_to_dip', 'om_project_sensors', 'om_squids2vtk', 'om_check_geom', 'om_gain', 'om_make_nerve', + 'om_matrix_info', 'om_mesh_convert', 'om_mesh_smooth', 'om_minverser', 'om_register_squids', +] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _om_binaries] + + ['lib/libOpenMEEG.%s' % SHLIB_EXT, 'lib/libOpenMEEGMaths.%s' % SHLIB_EXT], + 'dirs': ['include/OpenMEEG', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "om_mesh_info --help", + "pip check", + "python -c 'import openmeeg'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7_find-blas-lapack-from-cmake.patch b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7_find-blas-lapack-from-cmake.patch new file mode 100644 index 000000000000..fe53dc2cbe9a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMEEG/OpenMEEG-2.5.7_find-blas-lapack-from-cmake.patch @@ -0,0 +1,31 @@ +Use standard FindBLAS and FindLAPACK modules from CMake instead of a custom implementation. +Upstream modules can detect Flexiblas. +author: Alex Domingo (Vrije Universiteit Brussel) +--- cmake/thirdParties.cmake.orig 2024-02-10 12:57:15.285723739 +0100 ++++ cmake/thirdParties.cmake 2024-02-10 12:56:27.928866727 +0100 +@@ -1,4 +1,24 @@ +-include(FindBLASImplementation) ++find_package(BLAS REQUIRED) ++if (BLAS_FOUND) ++ set(USE_OPENBLAS ON) ++ set(HAVE_BLAS ON) ++endif (BLAS_FOUND) ++find_package(LAPACK REQUIRED) ++if (LAPACK_FOUND) ++ set(HAVE_LAPACK ON) ++endif (LAPACK_FOUND) ++ ++# OpenBLAS may or may not include lapacke. ++# Check which version is used. ++ ++set(CMAKE_REQUIRED_LIBRARIES LAPACK::LAPACK BLAS::BLAS) ++check_function_exists(LAPACKE_dlange LAPACKE_WORKS) ++mark_as_advanced(LAPACKE_WORKS) ++if (NOT LAPACKE_WORKS) ++ find_library(LAPACKE lapacke REQUIRED) ++ list(PREPEND _lapack_libs ${LAPACKE}) ++ set_target_properties(LAPACK::LAPACK PROPERTIES INTERFACE_LINK_LIBRARIES "${_lapack_libs}") ++endif() + + if (BLA_STATIC) + set(MATIO_USE_STATIC_LIBRARIES TRUE) # XXX This should be an option From 320cd2e7f8a776ff166a11935a4f08341b2446b0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Feb 2024 16:30:58 +0100 Subject: [PATCH 0705/1193] adding easyconfigs: MNE-Python-1.6.1-foss-2023a.eb --- .../MNE-Python/MNE-Python-1.6.1-foss-2023a.eb | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb new file mode 100644 index 000000000000..06490e490e7d --- /dev/null +++ b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'MNE-Python' +version = '1.6.1' + +homepage = 'https://mne.tools/' +description = """MNE-Python software is an open-source Python package for exploring, +visualizing, and analyzing human neurophysiological data such as MEG, EEG, +sEEG, ECoG, and more. It includes modules for data input/output, preprocessing, +visualization, source estimation, time-frequency analysis, connectivity +analysis, machine learning, and statistics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), + ('h5py', '3.9.0'), + ('imageio', '2.33.1'), # optional + ('Nilearn', '0.10.3'), # optional + ('numba', '0.58.1'), # optional + ('OpenMEEG', '2.5.7'), # optinal + ('scikit-learn', '1.3.1'), # optional + ('statsmodels', '0.14.1'), # optional + ('VTK', '9.3.0'), # optional +] + +use_pip = True + +exts_list = [ + ('traitlets', '5.9.0', { + 'checksums': ['f6cde21a9c68cf756af02035f72d5a723bf607e862e7be33ece505abf4a3bad9'], + }), + ('python-picard', '0.7', { + 'modulename': 'picard', + 'checksums': ['8061a1f0c4660c805b7617f2f0bd0284c6e6e84ac3ec782081c67b27cfd185a7'], + }), + ('lazy_loader', '0.3', { + 'checksums': ['3b68898e34f5b2a29daaaac172c6555512d0f32074f147e2254e4a6d9d838f37'], + }), + ('xmltodict', '0.13.0', { + 'checksums': ['341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56'], + }), + ('pymatreader', '0.0.32', { + 'checksums': ['34a5b4812635c98d3e5776fc21cd7f85b045784539363674d178dfb1158a617f'], + }), + ('h5io', '0.2.1', { + 'checksums': ['718721860d68712278effb30893df5eba0d6717d0040ab159dcac5f841174ea4'], + }), + ('ordered-set', '4.1.0', { + 'modulename': 'ordered_set', + 'checksums': ['694a8e44c87657c59292ede72891eb91d34131f6531463aab3009191c77364a8'], + }), + ('deepdiff', '6.7.1', { + 'checksums': ['b367e6fa6caac1c9f500adc79ada1b5b1242c50d5f716a1a4362030197847d30'], + }), + ('trx-python', '0.2.9', { + 'modulename': 'trx', + 'checksums': ['16b4104d7c991879c601f60e8d587decac50ce60388aae8d0c754a92136d1caf'], + }), + ('dipy', '1.8.0', { + 'checksums': ['cc3845585b6ccd5d7bf43094d52a00eb73111072eee36c2149fabdb1b071f008'], + }), + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('Deprecated', '1.2.14', { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), + ('mffpy', '0.8.0', { + 'checksums': ['0658da3c58da3cbd22da9b7faf3aedf000f3140bcdff1e18567aba01be783c6c'], + }), + ('scooby', '0.9.2', { + 'checksums': ['28df643bb7c2087547b2e2220070e2f89e815ddbc515fbc28dd5df2b0a14293e'], + }), + ('pyvista', '0.43.3', { + 'checksums': ['e039cdeb0c7cbb42a16fbdfbbede65a7dc656def787e76c79a43eb0badc88c9b'], + }), + ('mne', version, { + 'use_pip_extras': 'hdf5', + 'checksums': ['e4f5683d01cef675eddad788bdb6b44cc015dff0fb1ddfca3c4105edfb757ef8'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 6358b0120a4984371df93257664bc3cf032d8dfa Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 14 Feb 2024 16:34:30 +0100 Subject: [PATCH 0706/1193] Rename LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch to LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch Fix name type in patch --- ...3_install_lammps_python_package_in_eb_software_module.patch} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/LAMMPS/{LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch => LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch} (99%) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch similarity index 99% rename from easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch rename to easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch index 7f32721a36e2..c83a141c62f8 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch @@ -38,4 +38,4 @@ diff -ru lammps-stable_2Aug2023_update2.orig/python/install.py lammps-stable_2Au +try: txt = subprocess.check_output([py_exe, '-m', 'pip', 'install', '--force-reinstall', wheel], stderr=subprocess.STDOUT, shell=False) print(txt.decode('UTF-8')) - sys.exit(0) \ No newline at end of file + sys.exit(0) From c7898107388c3324a064e1650e6034bb6c82ed5f Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 14 Feb 2024 16:55:48 +0100 Subject: [PATCH 0707/1193] Update patch file name --- .../l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb index 64260ea32a52..d4d84cfd7089 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -26,7 +26,7 @@ patches = [ ] checksums = [ {'stable_2Aug2023_update2.tar.gz': '3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'}, - {'LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch': + {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch': '33968fa2b6f545a7aaf9a8ef418add8913d89824197e19f0f9564b418a79fc65'}, {'LAMMPS-2Aug2023_fix-timestep-balance-example.patch': '6f68387ced2b4bd0a06e4c3d31b0ffd47042476777d87d8a0ca6b19a4e6a1777'}, From 3ff3842854430f023dbe3c3b58f2805aca1ae3d0 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 14 Feb 2024 17:04:08 +0100 Subject: [PATCH 0708/1193] Correct patch filename --- .../l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb index d4d84cfd7089..069143134131 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -21,7 +21,7 @@ toolchainopts = {'openmp': True, 'usempi': True} source_urls = [GITHUB_LOWER_SOURCE] sources = ['stable_%(version)s.tar.gz'] patches = [ - 'LAMMPS-2Aug2023_install_lammps_python_pachage_in_eb_software_module.patch', + 'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch', 'LAMMPS-2Aug2023_fix-timestep-balance-example.patch', ] checksums = [ From 4532f9405d51b7950b5deb28156ccfc966c462b7 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 14 Feb 2024 17:09:58 +0100 Subject: [PATCH 0709/1193] Update LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch --- ...23_install_lammps_python_package_in_eb_software_module.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch index c83a141c62f8..521b7f23c1ee 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch @@ -1,4 +1,4 @@ -Add option in install.py to install lammps python packages in the site-packages of the easubuild software module +Add option in install.py to install lammps python packages in a configurable location diff -ru lammps-stable_2Aug2023_update2.orig/python/install.py lammps-stable_2Aug2023_update2/python/install.py --- lammps-stable_2Aug2023_update2.orig/python/install.py 2023-12-15 03:09:30.000000000 +0100 +++ lammps-stable_2Aug2023_update2/python/install.py 2024-02-07 11:07:35.404221000 +0100 From ca745a61b9d085e6c2f87c672a3a9784e08d0799 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Wed, 14 Feb 2024 17:12:58 +0100 Subject: [PATCH 0710/1193] Update SHA for patch --- .../l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb index 069143134131..b966e16ba101 100644 --- a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos.eb @@ -27,7 +27,7 @@ patches = [ checksums = [ {'stable_2Aug2023_update2.tar.gz': '3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'}, {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch': - '33968fa2b6f545a7aaf9a8ef418add8913d89824197e19f0f9564b418a79fc65'}, + '723c944b62b9d28427d25e80a7a67049631702d344df49268a6846aa0cd0fe04'}, {'LAMMPS-2Aug2023_fix-timestep-balance-example.patch': '6f68387ced2b4bd0a06e4c3d31b0ffd47042476777d87d8a0ca6b19a4e6a1777'}, ] From e4d995d5edac69183296455f15f2548feec99d55 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 14 Feb 2024 17:29:57 +0100 Subject: [PATCH 0711/1193] Fix linting errors --- .../easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb | 2 +- .../easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb | 2 +- .../easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb index d83d40387f2c..741298d14886 100644 --- a/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb +++ b/easybuild/easyconfigs/c/casacore/casacore-3.5.0-foss-2023b.eb @@ -52,7 +52,7 @@ sanity_check_paths = { 'files': [ 'lib/libcasa_casa.%s' % SHLIB_EXT, 'lib/libcasa_mirlib.%s' % SHLIB_EXT, - 'lib/libcasa_ms.%s' % SHLIB_EXT, + 'lib/libcasa_ms.%s' % SHLIB_EXT, ], 'dirs': ['bin', 'include/%(name)s'], } diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb index 042215912d5e..fea33552f7a9 100644 --- a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-13.2.0.eb @@ -18,7 +18,7 @@ builddependencies = [ sanity_check_paths = { - 'files': ['bin/idn2', 'lib/%(name)s.%s' % SHLIB_EXT], + 'files': ['bin/idn2', 'lib/%s.%s' % (name, SHLIB_EXT)], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb index d2e3d25fb6d6..96edad225253 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb @@ -31,10 +31,10 @@ dependencies = [ # create .so symlinks for shared libraries postinstallcmds = [ - "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s.5" % SHLIB_EXT, - "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s" % SHLIB_EXT, - "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s.5" % SHLIB_EXT, - "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s" % SHLIB_EXT, + "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), + "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), ] files_to_copy = [ (['pgdemo*'], 'bin'), From ee21e00bf7b6704a98bb7afbb3a7546f73864035 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 14 Feb 2024 17:59:12 +0100 Subject: [PATCH 0712/1193] Fix linting errors --- .../easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb index 96edad225253..2550198c98c5 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb @@ -31,10 +31,10 @@ dependencies = [ # create .so symlinks for shared libraries postinstallcmds = [ - "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), - "cd %(installdir)s/lib && ln -s libcpgplot.%s.%(version)s libcpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), - "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), - "cd %(installdir)s/lib && ln -s libpgplot.%s.%(version)s libpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), + "cd %(installdir)s/lib && ln -s libcpgplot.%(SHLIB_EXT)s.%(version)s libcpgplot.%(SHLIB_EXT)s.5", + "cd %(installdir)s/lib && ln -s libcpgplot.%(SHLIB_EXT)s.%(version)s libcpgplot.%(SHLIB_EXT)s", + "cd %(installdir)s/lib && ln -s libpgplot.%(SHLIB_EXT)s.%(version)s libpgplot.%(SHLIB_EXT)s.5", + "cd %(installdir)s/lib && ln -s libpgplot.%(SHLIB_EXT)s.%(version)s libpgplot.%(SHLIB_EXT)s", ] files_to_copy = [ (['pgdemo*'], 'bin'), From 860f1bdae59d2a071d3c5c9780e2d0781812b16d Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Wed, 14 Feb 2024 18:07:48 +0100 Subject: [PATCH 0713/1193] Fix linting errors --- .../easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb index 2550198c98c5..526fb7c27d59 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb @@ -31,11 +31,12 @@ dependencies = [ # create .so symlinks for shared libraries postinstallcmds = [ - "cd %(installdir)s/lib && ln -s libcpgplot.%(SHLIB_EXT)s.%(version)s libcpgplot.%(SHLIB_EXT)s.5", - "cd %(installdir)s/lib && ln -s libcpgplot.%(SHLIB_EXT)s.%(version)s libcpgplot.%(SHLIB_EXT)s", - "cd %(installdir)s/lib && ln -s libpgplot.%(SHLIB_EXT)s.%(version)s libpgplot.%(SHLIB_EXT)s.5", - "cd %(installdir)s/lib && ln -s libpgplot.%(SHLIB_EXT)s.%(version)s libpgplot.%(SHLIB_EXT)s", + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.%%(version)s libcpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libcpgplot.%s.%%(version)s libcpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.%%(version)s libpgplot.%s.5" % (SHLIB_EXT, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s libpgplot.%s.%%(version)s libpgplot.%s" % (SHLIB_EXT, SHLIB_EXT), ] + files_to_copy = [ (['pgdemo*'], 'bin'), (['libpgplot.*', 'libcpgplot.*'], 'lib'), From 53a713e97f4e64ff87af9801f415935be479eb7a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 14 Feb 2024 17:28:40 +0000 Subject: [PATCH 0714/1193] adding easyconfigs: libfyaml-0.9-GCCcore-12.2.0.eb --- .../l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..45bb66770fd1 --- /dev/null +++ b/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'ConfigureMake' + +name = 'libfyaml' +version = '0.9' + +homepage = "https://github.com/pantoniou/libfyaml" +description = """Fully feature complete YAML parser and emitter, supporting the latest YAML spec and passing the +full YAML testsuite.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/pantoniou/libfyaml/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['7731edc5dfcc345d5c5c9f6ce597133991a689dabede393cd77bae89b327cd6d'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libyaml', '0.2.5'), +] + +preconfigopts = './bootstrap.sh &&' +runtest = 'check' + +sanity_check_paths = { + 'files': ['bin/fy-tool', 'include/libfyaml.h', 'lib/libfyaml.a', 'lib/libfyaml.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["fy-tool --help"] + +moduleclass = 'lib' From 5998a33e5dc2f524c4966ed26c51fb1a386e2e0f Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Feb 2024 20:30:45 +0000 Subject: [PATCH 0715/1193] adding easyconfigs: gawk-5.3.0-GCC-13.2.0.eb, gawk-5.3.0-GCC-12.2.0.eb --- .../g/gawk/gawk-5.3.0-GCC-12.2.0.eb | 23 +++++++++++++++++++ .../g/gawk/gawk-5.3.0-GCC-13.2.0.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.2.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.2.0.eb new file mode 100644 index 000000000000..f006f242595d --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-12.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.3.0' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['378f8864ec21cfceaa048f7e1869ac9b4597b449087caf1eb55e440d30273336'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-13.2.0.eb b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-13.2.0.eb new file mode 100644 index 000000000000..11cfb94968b1 --- /dev/null +++ b/easybuild/easyconfigs/g/gawk/gawk-5.3.0-GCC-13.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'gawk' +version = '5.3.0' + +homepage = 'https://www.gnu.org/software/gawk' +description = """The awk utility interprets a special-purpose programming language that makes it possible to handle +simple data-reformatting jobs with just a few lines of code.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['378f8864ec21cfceaa048f7e1869ac9b4597b449087caf1eb55e440d30273336'] + +sanity_check_paths = { + 'files': ['bin/gawk'], + 'dirs': [], +} + +sanity_check_commands = ["gawk --help"] + +moduleclass = 'tools' From fd184c55b2f14b89bd5a26621ecaa44f567884c8 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Feb 2024 20:32:19 +0000 Subject: [PATCH 0716/1193] adding easyconfigs: MATIO-1.5.26-GCCcore-13.2.0.eb --- .../m/MATIO/MATIO-1.5.26-GCCcore-13.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..f773a9eab17f --- /dev/null +++ b/easybuild/easyconfigs/m/MATIO/MATIO-1.5.26-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2014-2015 The Cyprus Institute +# Authors:: Thekla Loizou +# License:: MIT/GPL +# +## +easyblock = 'ConfigureMake' + +name = 'MATIO' +version = '1.5.26' + +homepage = 'https://sourceforge.net/projects/matio/' +description = """matio is an C library for reading and writing Matlab MAT files.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_ZIP] +checksums = ['c07b089dad904c7e13a08f0ce7ac0b2969fe3d886579a10433eb13fdc3530e74'] + +preconfigopts = 'chmod +x configure && ' + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +sanity_check_paths = { + 'files': ['include/matio.h', 'bin/matdump', 'lib/libmatio.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 39161135cb9d47d65f1f23f1916e647f615c1114 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Feb 2024 22:34:50 +0100 Subject: [PATCH 0717/1193] add meson-python as build dependency of MNE-Python v1.6.1 --- .../easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb index 06490e490e7d..c8c0c7a64aa0 100644 --- a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb @@ -13,7 +13,8 @@ analysis, machine learning, and statistics.""" toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ - ('hatchling', '1.18.0'), + ('hatchling', '1.18.0'),' + ('meson-python', '0.13.2'), # needed by dipy ] dependencies = [ From 3d63cd678ae47824c0141afebdabd2f446bbcf0c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Feb 2024 22:36:10 +0100 Subject: [PATCH 0718/1193] fix typo in MNE-Python v1.6.1 --- .../easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb index c8c0c7a64aa0..dcb9825b8cd5 100644 --- a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb @@ -13,7 +13,7 @@ analysis, machine learning, and statistics.""" toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ - ('hatchling', '1.18.0'),' + ('hatchling', '1.18.0'), ('meson-python', '0.13.2'), # needed by dipy ] From ac4db63fcc48d106af85c43a399a925db165a8bf Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 15 Feb 2024 09:28:18 +0000 Subject: [PATCH 0719/1193] tests use git and expect a new enough version --- easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb index 45bb66770fd1..95d07690ad0b 100644 --- a/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb @@ -18,6 +18,7 @@ builddependencies = [ ('Autotools', '20220317'), ('binutils', '2.39'), ('pkgconf', '1.9.3'), + ('git', '2.38.1', '-nodocs'), ] dependencies = [ From b48ef2a8cdb3f652c1aa49075d108a1879a6d4f1 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 15 Feb 2024 10:30:19 +0100 Subject: [PATCH 0720/1193] adding easyconfigs: SLEPc-3.20.1-foss-2023a.eb --- .../s/SLEPc/SLEPc-3.20.1-foss-2023a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.20.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.20.1-foss-2023a.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.20.1-foss-2023a.eb new file mode 100644 index 000000000000..59c1fa24febd --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.20.1-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.20.1' + +homepage = 'https://slepc.upv.es' +description = """SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution + of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for + either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a + partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5a36b664895881d3858d0644f56bf7bb922bdab70d732fa11cbf6442fec11806'] + +dependencies = [('PETSc', '3.20.3')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' From 5b4897b56006b88977decf70d0aa26e62238eff8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 15 Feb 2024 09:40:14 +0000 Subject: [PATCH 0721/1193] disable tests as they require data download --- .../easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb index 95d07690ad0b..5e81a913222d 100644 --- a/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libfyaml/libfyaml-0.9-GCCcore-12.2.0.eb @@ -18,7 +18,6 @@ builddependencies = [ ('Autotools', '20220317'), ('binutils', '2.39'), ('pkgconf', '1.9.3'), - ('git', '2.38.1', '-nodocs'), ] dependencies = [ @@ -26,7 +25,10 @@ dependencies = [ ] preconfigopts = './bootstrap.sh &&' -runtest = 'check' + +# tests require git checkout for the data +# if jq is available then one test may fail: https://github.com/pantoniou/libfyaml/issues/99 +# runtest = 'check' sanity_check_paths = { 'files': ['bin/fy-tool', 'include/libfyaml.h', 'lib/libfyaml.a', 'lib/libfyaml.%s' % SHLIB_EXT], From 12c18d2bcf3781576f098080857cbe29ed81db87 Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 15 Feb 2024 12:01:44 +0100 Subject: [PATCH 0722/1193] adding easyconfigs: occt-7.8.0-foss-2023a.eb, FreeImage-3.18.0-GCCcore-12.3.0.eb --- .../FreeImage-3.18.0-GCCcore-12.3.0.eb | 43 +++++++++++++++++ .../o/occt/occt-7.8.0-foss-2023a.eb | 47 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100755 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb new file mode 100755 index 000000000000..3a9b6a21f3a7 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'FreeImage' +version = '3.18.0' + +homepage = 'http://freeimage.sourceforge.net' +description = """FreeImage is an Open Source library project for developers who would like to support popular graphics +image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to +use, fast, multithreading safe.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'cstd': 'c++14'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s3180.zip'] +patches = ['%(name)s-%(version)s-fix-makefile.patch'] +checksums = [ + 'f41379682f9ada94ea7b34fe86bf9ee00935a3147be41b6569c9605a53e438fd', # FreeImage3180.zip + '3eaa1eb9562ccfd0cb95a37879bb7e3e8c745166596d75af529478181ef006a0', # %(name)s-%(version)s-fix-makefile.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('zlib', '1.2.13')] + +skipsteps = ['configure'] + +buildopts = ['', '-f Makefile.fip'] + +installopts = [ + "INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", + "-f Makefile.fip INCDIR=%(installdir)s/include INSTALLDIR=%(installdir)s/lib", +] + +_incs = ['include/FreeImage%s.h' % x for x in ['', 'Plus']] +_libs = ['lib/libfreeimage%s.%s' % (x, y) for x in ['', 'plus'] for y in ['a', SHLIB_EXT]] + +sanity_check_paths = { + 'files': _incs + _libs, + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb b/easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb new file mode 100644 index 000000000000..b9c352a4d052 --- /dev/null +++ b/easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'occt' +version = '7.8.0' + +homepage = 'https://www.opencascade.com/' +description = """Open CASCADE Technology (OCCT) is an object-oriented C++ +class library designed for rapid production of sophisticated domain-specific +CAD/CAM/CAE applications.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/Open-Cascade-SAS/OCCT/archive/refs/tags'] +sources = ['V7_8_0.tar.gz'] +checksums = ['096cd0f268fa9f6a50818e1d628ac92ecf87e10fd72187e2e8d6be57dfe12530'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] +dependencies = [ + ('Mesa', '23.1.4'), + ('freetype', '2.13.0'), + ('Tcl', '8.6.13'), + ('Tk', '8.6.13'), + ('FreeImage', '3.18.0'), + ('tbb', '2021.11.0'), +] + + +separate_build_dir = True + +configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE " +configopts += "-D3RDPARTY_TBB_DIR=$EBROOTTBB " +configopts += "-D3RDPARTY_TCL_DIR=$EBROOTTCL " +configopts += "-D3RDPARTY_TK_DIR=$EBROOTTK " +configopts += "-D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " + +sanity_check_paths = { + 'files': ['bin/DRAWEXE', 'bin/env.sh'], + 'dirs': ['lib/cmake/opencascade'], +} + +sanity_check_commands = ['DRAWEXE -h'] + +moduleclass = 'cae' From bdc59b93ffa80dbce830a4005caf03e6fb900d5a Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Thu, 15 Feb 2024 12:24:30 +0100 Subject: [PATCH 0723/1193] Crrected file permissions --- .../easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-12.3.0.eb old mode 100755 new mode 100644 From 9ba53933eeb293efb5314003ad0995c53084a6f3 Mon Sep 17 00:00:00 2001 From: Frederik Himpe Date: Thu, 15 Feb 2024 14:06:30 +0100 Subject: [PATCH 0724/1193] adding easyconfigs: atools-1.5.1-GCCcore-13.2.0.eb --- .../a/atools/atools-1.5.1-GCCcore-13.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..3916c8f605b4 --- /dev/null +++ b/easybuild/easyconfigs/a/atools/atools-1.5.1-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'atools' +version = '1.5.1' + +homepage = 'https://github.com/gjbex/atools' +description = """Tools to make using job arrays a lot more convenient.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/gjbex/atools/archive'] +sources = [SOURCE_TAR_GZ] +checksums = ['540714c39aa83dd5f1a7367d76f8d6f491336fa5fc00077591a22151ef5d31f4'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +# to enable SLURM integration (site-specific) (options are torque, moab, sge, slurm) +configopts = '--with-batchsystem=slurm' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['acreate', 'aenv', 'aload', 'alog', 'arange', 'areduce']], + 'dirs': ['lib/vsc/atools'] +} + +sanity_check_commands = [ + 'acreate -h', + 'aenv -h', + 'aload -h', + 'alog -h', + 'arange -h', + 'areduce -h', +] + +moduleclass = 'tools' From e301950f5cb28700026152cc313d4102df807f86 Mon Sep 17 00:00:00 2001 From: Frederik Himpe Date: Thu, 15 Feb 2024 14:12:48 +0100 Subject: [PATCH 0725/1193] adding easyconfigs: CCL-1.12.2-GCCcore-13.2.0.eb --- .../c/CCL/CCL-1.12.2-GCCcore-13.2.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..ee8f9ce062d1 --- /dev/null +++ b/easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-13.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' +name = 'CCL' +version = '1.12.2' + +homepage = 'https://ccl.clozure.com/' +description = """Clozure CL (often called CCL for short) is a free Common Lisp + implementation with a long history. Some distinguishing features of the implementation + include fast compilation speed, native threads, a precise, generational, compacting + garbage collector, and a convenient foreign-function interface.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/Clozure/ccl/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s-linuxx86.tar.gz'] +checksums = ['a94fda3daf26ce8c3d08e0db0e6e9907995acc10e0f8aad2125790b93eaa1556'] + +builddependencies = [ + ('binutils', '2.40'), + ('M4', '1.4.19'), +] + +local_ccl_bin = 'lx86cl64' +local_ccl_dirs = [ + 'compiler', 'level-0', 'level-1', 'lib', 'library', 'lisp-kernel', 'scripts', 'tools', 'xdump', 'x86-headers64' +] + +# Build the kernel +buildopts = "-C lisp-kernel/linuxx8664 all CC=${CC} && " +# Rebuild CCL +buildopts += "./%s -n -b -Q -e '(ccl:rebuild-ccl :full t)' -e '(ccl:quit)'" % local_ccl_bin + +files_to_copy = [local_ccl_bin, '%s.image' % local_ccl_bin] + local_ccl_dirs + +postinstallcmds = [ + # Cleanup of build files + "find %(installdir)s -type f -name '*fsl' -delete", + "find %(installdir)s/lisp-kernel -type f -name '*.o' -delete", + # Link executable with generic name + "mkdir %(installdir)s/bin", + "cd %%(installdir)s/bin && ln -s ../%s ccl" % local_ccl_bin, +] + +sanity_check_paths = { + 'files': [local_ccl_bin, '%s.image' % local_ccl_bin, 'bin/ccl'], + 'dirs': local_ccl_dirs, +} + +sanity_check_commands = ["ccl --help"] + +modextrapaths = {'CCL_DEFAULT_DIRECTORY': ''} + +moduleclass = 'lang' From b10fb9d43715df53f27d3f56ef5be74ea87167a9 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 15 Feb 2024 16:53:34 +0100 Subject: [PATCH 0726/1193] adding easyconfigs: Delft3D-FLOW-4.04.01-foss-2022a.eb --- .../Delft3D-FLOW-4.04.01-foss-2022a.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb b/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb new file mode 100644 index 000000000000..7667d7f9f586 --- /dev/null +++ b/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'ConfigureMake' + +name = 'Delft3D-FLOW' +# revision 142633 +version = '4.04.01' + +homepage = 'https://oss.deltares.nl/web/delft3d' +description = """ +Simulation of multi-dimensional hydrodynamic flows and transport phenomena, including +sediments. Delft3D-FLOW is part of Delft3D 4. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +# There is no tarball provided, only SVN checkout through: +# svn checkout https://svn.oss.deltares.nl/repos/delft3d/trunk@142633 +# make tarball: tar -czvf Delft3D-FLOW-4.04.01.tgz trunk + +sources = [SOURCE_TGZ] +checksums = [ + None, +] + +prebuildopts = 'make clean && ' +builddependencies = [ + ('CMake', '3.24.3'), + ('libtool', '2.4.7'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Ruby', '3.0.5'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), + ('METIS', '5.1.0'), + ('PETSc', '3.17.4'), +] + +parallel = 1 + +start_dir = 'src' + +preconfigopts = 'export FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I${CPATH//:/ -I}" && ' +preconfigopts += 'export FFLAGS="$FFLAGS -fallow-argument-mismatch -I${CPATH//:/ -I}" && ' +# syntax was made invalid in c++11 +preconfigopts += "sed -i 's/if (spec < 0)/if (spec == nullptr)/g' utils_lgpl/delftonline/src/delftonline/server.cpp && " +# avoid comparing logical with integer +preconfigopts += "sed -i 's/if (has_umean \/= 0)/if (has_umean .neqv. .false.)/g' " # noqa: W605 +preconfigopts += "engines_gpl/flow2d3d/packages/flow2d3d_io/src/input/restart_trim_flow.f90 && " +preconfigopts += "sed -i -e 's/-recursive/-frecursive/g' -e 's/-traceback/-fbacktrace/g' configure.ac && " +preconfigopts += './autogen.sh && ' +preconfigopts += 'cd third_party_open/kdtree2 && ./autogen.sh && cd - && ' +configopts = ' --with-netcdf' +configopts += ' --with-mpi --with-metis --with-petsc' + +# remove spurious double -l flags causing build failure +prebuildopts = "sed -i.backup 's/-l -l//g' libtool config.lt config.status && " +buildopts = 'ds-install' + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/d_hydro'], + 'dirs': ['lib', 'share'] +} + +sanity_check_commands = [ + 'd_hydro -? |grep Usage:', +] + +moduleclass = 'phys' From efa5d46816fba8ddf0ae203e1374011d0b35ceaf Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Thu, 15 Feb 2024 17:55:50 +0100 Subject: [PATCH 0727/1193] Update Delft3D-FLOW-4.04.01-foss-2022a.eb Remove unnecessary prebuildopts --- .../d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb b/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb index 7667d7f9f586..6b9b750f0273 100644 --- a/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb +++ b/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb @@ -22,7 +22,6 @@ checksums = [ None, ] -prebuildopts = 'make clean && ' builddependencies = [ ('CMake', '3.24.3'), ('libtool', '2.4.7'), From fb1f79a89792d784fbcf1a03c26924fd8fcb0130 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 15 Feb 2024 18:00:17 +0100 Subject: [PATCH 0728/1193] adding easyconfigs: ExtremeLy-2.3.0-foss-2022a.eb, lmoments3-1.0.6-foss-2022a.eb, scikit-extremes-2022.4.10-foss-2022a.eb --- .../e/ExtremeLy/ExtremeLy-2.3.0-foss-2022a.eb | 34 +++++++++++++++++ .../l/lmoments3/lmoments3-1.0.6-foss-2022a.eb | 37 +++++++++++++++++++ .../scikit-extremes-2022.4.10-foss-2022a.eb | 35 ++++++++++++++++++ 3 files changed, 106 insertions(+) create mode 100644 easybuild/easyconfigs/e/ExtremeLy/ExtremeLy-2.3.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/l/lmoments3/lmoments3-1.0.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scikit-extremes/scikit-extremes-2022.4.10-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/ExtremeLy/ExtremeLy-2.3.0-foss-2022a.eb b/easybuild/easyconfigs/e/ExtremeLy/ExtremeLy-2.3.0-foss-2022a.eb new file mode 100644 index 000000000000..4e50e4c90599 --- /dev/null +++ b/easybuild/easyconfigs/e/ExtremeLy/ExtremeLy-2.3.0-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ExtremeLy' +version = '2.3.0' + +homepage = 'https://github.com/SURYA-LAMICHANEY/ExtremeLy' +description = """A python package for Extreme Value Analysis.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('lmoments3', '1.0.6'), + ('scikit-extremes', '2022.4.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('seaborn', '0.13.2', { + 'checksums': ['93e60a40988f4d65e9f4885df477e2fdaff6b73a9ded434c1ab356dd57eefff7'], + }), + ('evt', '0.0.2', { + 'source_tmpl': 'evt-%(version)s-py3-none-any.whl', + 'checksums': ['3552d6cc1113bceb521d918f606781a45283a4b759f6982ff38b7e1dcdf3bb22'], + }), + (name, version, { + 'modulename': 'ExtremeLy', + 'checksums': ['03c92bc174794208fd7d2494bee74cf7c7073a94621a714fc43b5d32c9ef4095'], + }), +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/l/lmoments3/lmoments3-1.0.6-foss-2022a.eb b/easybuild/easyconfigs/l/lmoments3/lmoments3-1.0.6-foss-2022a.eb new file mode 100644 index 000000000000..7415a707b89a --- /dev/null +++ b/easybuild/easyconfigs/l/lmoments3/lmoments3-1.0.6-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'lmoments3' +version = '1.0.6' + +homepage = 'https://github.com/OpenHydrology/lmoments3' +description = """Estimate linear moments for statistical distribution functions.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05') +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('versioneer', '0.29', { + 'checksums': ['5ab283b9857211d61b53318b7c792cf68e798e765ee17c27ade9f6c924235731'], + }), + (name, version, { + 'checksums': ['404a589335c16549f5ff519d3fafab247203ef78801296447db939b0c58f824b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/versioneer'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "versioneer --help", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/scikit-extremes/scikit-extremes-2022.4.10-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-extremes/scikit-extremes-2022.4.10-foss-2022a.eb new file mode 100644 index 000000000000..99e2056cc56e --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-extremes/scikit-extremes-2022.4.10-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'scikit-extremes' +version = '2022.4.10' +local_commit = '8a17f45' + +homepage = 'https://github.com/kikocorreoso/scikit-extremes' +description = """scikit-extremes is a basic statistical package to +perform univariate extreme value calculations using Python""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('lmoments3', '1.0.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('numdifftools', '0.9.41', { + 'checksums': ['4ef705cd3c06211b3a4e9fd05ad622be916dcfda40732f0128805a2c4be389b4'], + }), + (name, version, { + 'modulename': 'skextremes', + 'source_urls': ['https://github.com/kikocorreoso/scikit-extremes/archive/'], + 'sources': [{'download_filename': '8a17f45.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b334a40db8f2f2a8fcfd46ce4d9ce55ffbd917897a24ed4444044d611c1b1fec'], + }), +] + +moduleclass = 'math' From 0fa59da3f994f9f68a71611f5f2ae8b977867f52 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 15 Feb 2024 18:51:11 +0100 Subject: [PATCH 0729/1193] adding easyconfigs: SBCL-2.4.1-GCCcore-12.3.0.eb, CCL-1.12.2-GCCcore-12.3.0.eb --- .../c/CCL/CCL-1.12.2-GCCcore-12.3.0.eb | 52 +++++++++++++++++++ .../s/SBCL/SBCL-2.4.1-GCCcore-12.3.0.eb | 46 ++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/SBCL/SBCL-2.4.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..bf6b1c101111 --- /dev/null +++ b/easybuild/easyconfigs/c/CCL/CCL-1.12.2-GCCcore-12.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MakeCp' +name = 'CCL' +version = '1.12.2' + +homepage = 'https://ccl.clozure.com/' +description = """Clozure CL (often called CCL for short) is a free Common Lisp + implementation with a long history. Some distinguishing features of the implementation + include fast compilation speed, native threads, a precise, generational, compacting + garbage collector, and a convenient foreign-function interface.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Clozure/ccl/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s-linuxx86.tar.gz'] +checksums = ['a94fda3daf26ce8c3d08e0db0e6e9907995acc10e0f8aad2125790b93eaa1556'] + +builddependencies = [ + ('binutils', '2.40'), + ('M4', '1.4.19'), +] + +local_ccl_bin = 'lx86cl64' +local_ccl_dirs = [ + 'compiler', 'level-0', 'level-1', 'lib', 'library', 'lisp-kernel', 'scripts', 'tools', 'xdump', 'x86-headers64' +] + +# Build the kernel +buildopts = "-C lisp-kernel/linuxx8664 all CC=${CC} && " +# Rebuild CCL +buildopts += "./%s -n -b -Q -e '(ccl:rebuild-ccl :full t)' -e '(ccl:quit)'" % local_ccl_bin + +files_to_copy = [local_ccl_bin, '%s.image' % local_ccl_bin] + local_ccl_dirs + +postinstallcmds = [ + # Cleanup of build files + "find %(installdir)s -type f -name '*fsl' -delete", + "find %(installdir)s/lisp-kernel -type f -name '*.o' -delete", + # Link executable with generic name + "mkdir %(installdir)s/bin", + "cd %%(installdir)s/bin && ln -s ../%s ccl" % local_ccl_bin, +] + +sanity_check_paths = { + 'files': [local_ccl_bin, '%s.image' % local_ccl_bin, 'bin/ccl'], + 'dirs': local_ccl_dirs, +} + +sanity_check_commands = ["ccl --help"] + +modextrapaths = {'CCL_DEFAULT_DIRECTORY': ''} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SBCL/SBCL-2.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SBCL/SBCL-2.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..21e0f89860e5 --- /dev/null +++ b/easybuild/easyconfigs/s/SBCL/SBCL-2.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' +name = 'SBCL' +version = '2.4.1' + +homepage = 'http://sbcl.sourceforge.net/' +description = """ +Steel Bank Common Lisp (SBCL) is a high performance Common Lisp compiler. It is +open source / free software, with a permissive license. In addition to the +compiler and runtime system for ANSI Common Lisp, it provides an interactive +environment including a debugger, a statistical profiler, a code coverage tool, +and many other extensions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s-source.tar.bz2'] +checksums = ['da4f9486fad413d3af7abb1b09269325fdb4bff7e7b88f2195ddee743263cf7e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CCL', '1.12.2'), +] + +parallel = False +skipsteps = ['configure'] +local_prefixarg = '--prefix=%(installdir)s' + +# Build SBCL with Clozure CL +# Using the binary distribution of SBCL to build SBCL is not trivial because +# it needs GLIBC v2.28 +build_cmd = "sh make.sh" +buildopts = "%s --xc-host=ccl" % local_prefixarg + +install_cmd = "sh install.sh" +installopts = local_prefixarg + +sanity_check_paths = { + 'files': ['bin/sbcl'], + 'dirs': ['lib/sbcl'], +} + +sanity_check_commands = ["sbcl --help"] + +modextrapaths = {'SBCL_HOME': 'lib/sbcl'} + +moduleclass = 'lang' From b688de7928c8698b594755523a61b88630b3adbb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 15 Feb 2024 19:05:33 +0000 Subject: [PATCH 0730/1193] adding easyconfigs: code-server-4.21.1.eb --- .../c/code-server/code-server-4.21.1.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/code-server/code-server-4.21.1.eb diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.21.1.eb b/easybuild/easyconfigs/c/code-server/code-server-4.21.1.eb new file mode 100644 index 000000000000..88e4c129c67a --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.21.1.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.21.1' + +homepage = 'https://github.com/cdr/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cdr/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + '8ae5deab32749bb9bb20009b14ebb0fac012aa82660cfc91b2cc5bd67daf709b', + 'code-server-%(version)s-linux-arm64.tar.gz': + '1bbb43193e00b2f6c84967048372dc6381c3d332d06643c4a89ce052f755a170', + } +] + +moduleclass = 'tools' From 7ac4fddcf14057c2763dfe247db0bd1b945e1eea Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 16 Feb 2024 10:44:53 +0000 Subject: [PATCH 0731/1193] adding easyconfigs: libsigsegv-2.14-GCCcore-12.2.0.eb --- .../libsigsegv-2.14-GCCcore-12.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.14-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.14-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f48813683d61 --- /dev/null +++ b/easybuild/easyconfigs/l/libsigsegv/libsigsegv-2.14-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +# Authors:: Jack Perdue - TAMU HPRC - http://hprc.tamu.edu + +easyblock = 'ConfigureMake' + +name = 'libsigsegv' +version = '2.14' + +homepage = 'https://www.gnu.org/software/libsigsegv/' + +description = "GNU libsigsegv is a library for handling page faults in user mode." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['cdac3941803364cf81a908499beb79c200ead60b6b5b40cad124fd1e06caa295'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['include/sigsegv.h', 'lib/libsigsegv.a', 'lib/libsigsegv.la'], + 'dirs': [], +} + +moduleclass = 'lib' From 0129bfb06bd932a98049a3379e3aa38295b9edf0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 16 Feb 2024 10:46:05 +0000 Subject: [PATCH 0732/1193] adding easyconfigs: Yices-2.6.4-GCCcore-12.2.0.eb --- .../y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a7fba258b170 --- /dev/null +++ b/easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'Yices' +version = '2.6.4' + +homepage = "https://yices.csl.sri.com/index.html" +description = """Yices 2 is an SMT solver that decides the satisfiability of formulas containing uninterpreted + function symbols with equality, real and integer arithmetic, bitvectors, scalar types, and tuples. Yices 2 supports + both linear and nonlinear arithmetic.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://yices.csl.sri.com/releases/%(version)s/'] +sources = ['%(namelower)s-%(version)s-src.tar.gz'] +checksums = ['533a24e020ecb7d64c03a965d598430d193651e2887e6f46924dec5786db78cb'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('GMP', '6.2.1'), + ('gperf', '3.1'), +] + +preconfigopts = 'autoconf &&' +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libyices.a', 'lib/libyices.%s' % SHLIB_EXT, 'include/yices.h'], + 'dirs': [], +} + +sanity_check_commands = ['%s --help' % x for x in ['yices', 'yices-sat', 'yices-smt', 'yices-smt2']] + +moduleclass = 'tools' From 1361bcf5ed1b7cf441b0f7da4695ffea9ca690b9 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Fri, 16 Feb 2024 11:02:22 +0000 Subject: [PATCH 0733/1193] need an autotools builddep --- easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb index a7fba258b170..f755f69bbec8 100644 --- a/easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/y/Yices/Yices-2.6.4-GCCcore-12.2.0.eb @@ -16,6 +16,7 @@ checksums = ['533a24e020ecb7d64c03a965d598430d193651e2887e6f46924dec5786db78cb'] builddependencies = [ ('binutils', '2.39'), + ('Autotools', '20220317'), ] dependencies = [ From 8c3692c305eddd24afe93c5de4866b43bcac45f7 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Fri, 16 Feb 2024 12:23:05 +0000 Subject: [PATCH 0734/1193] Add DjVuLibre easyconfig, and enable djvu support in evince --- .../DjVuLibre-3.5.28-GCCcore-12.3.0.eb | 43 +++++++++++++++++++ .../e/evince/evince-45.0-GCC-12.3.0.eb | 4 +- 2 files changed, 45 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..355a9996fbc7 --- /dev/null +++ b/easybuild/easyconfigs/d/DjVuLibre/DjVuLibre-3.5.28-GCCcore-12.3.0.eb @@ -0,0 +1,43 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'DjVuLibre' +version = '3.5.28' + +homepage = 'http://djvu.sourceforge.net/' +description = """ +DjVuLibre is an open source (GPL'ed) implementation of DjVu, including viewers, +browser plugins, decoders, simple encoders, and utilities. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://downloads.sourceforge.net/djvu'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['fcd009ea7654fde5a83600eb80757bd3a76998e47d13c66b54c8db849f8f2edc'] + +builddependencies = [ + ('binutils', '2.40'), + ('libiconv', '1.17'), +] + +dependencies = [ + ('libjpeg-turbo', '2.1.5.1'), + ('LibTIFF', '4.5.0'), +] + +_bins = ['bin/%s' % x for x in ['any2djvu', 'bzz', 'c44', 'cjb2', 'cpaldjvu', 'csepdjvu', 'ddjvu', 'djvm', 'djvmcvt', + 'djvudigital', 'djvudump', 'djvuextract', 'djvumake', 'djvups', 'djvused', 'djvuserve', + 'djvutoxml', 'djvutxt', 'djvuxmlparser']] +_incs = ['include/libdjvu/%s' % x for x in ['ddjvuapi.h', 'miniexp.h']] +_libs = ['lib/%s' % x for x in ['lib%%(namelower)s.%s' % SHLIB_EXT, 'pkgconfig/ddjvuapi.pc']] + +sanity_check_paths = { + 'files': _bins + _incs + _libs, + 'dirs': [], +} + +sanity_check_commands = ["ddjvu --help 2>&1 | grep 'Usage: ddjvu'"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb index 1a866acab696..156de7c3596e 100644 --- a/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb @@ -44,8 +44,8 @@ dependencies = [ ('LibTIFF', '4.5.0'), ('libgxps', '0.3.2'), ('DBus', '1.15.4'), - # ddjvuapi - # kpathsea + ('DjVuLibre', '3.5.28'), + # optional: kpathsea (path searching library for TeX-related files) ] _bins = ['bin/%%(name)s%s' % x for x in ['', '-previewer', '-thumbnailer']] From 50764689c962ea7feac788fdf2c9bf503de9cc4c Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Fri, 16 Feb 2024 14:27:57 +0100 Subject: [PATCH 0735/1193] adding easyconfigs: build-1.0.3-foss-2023b.eb --- .../b/build/build-1.0.3-foss-2023b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/build/build-1.0.3-foss-2023b.eb diff --git a/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023b.eb b/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023b.eb new file mode 100644 index 000000000000..33af19b02f7c --- /dev/null +++ b/easybuild/easyconfigs/b/build/build-1.0.3-foss-2023b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'build' +version = '1.0.3' + +homepage = 'https://github.com/pypa/build' +description = """A simple, correct Python build frontend.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + (name, version, { + 'checksums': ['538aab1b64f9828977f84bc63ae570b060a8ed1be419e7870b8b4fc5e6ea553b'], + }), +] + +sanity_check_commands = [ + "python3 -m build -V", +] + +moduleclass = 'devel' From 01a994f1a0625e9fb2682fd03f7f07cc5be1c6b3 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Fri, 16 Feb 2024 13:55:20 +0000 Subject: [PATCH 0736/1193] add desktop-file-utils easyconfig --- .../desktop-file-utils-0.27-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ .../e/evince/evince-45.0-GCC-12.3.0.eb | 1 + 2 files changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/d/desktop-file-utils/desktop-file-utils-0.27-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/desktop-file-utils/desktop-file-utils-0.27-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/desktop-file-utils/desktop-file-utils-0.27-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..888351a66b16 --- /dev/null +++ b/easybuild/easyconfigs/d/desktop-file-utils/desktop-file-utils-0.27-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MesonNinja' + +name = 'desktop-file-utils' +version = '0.27' + +homepage = 'https://www.freedesktop.org/wiki/Software/desktop-file-utils/' +description = """ +desktop-file-utils contains a few command line utilities for working with desktop entries: + * desktop-file-validate: validates a desktop file and prints warnings/errors about desktop entry specification + violations. + * desktop-file-install: installs a desktop file to the applications directory, optionally munging it a bit in transit. + * update-desktop-database: updates the database containing a cache of MIME types handled by desktop files. It requires + GLib to compile, because the implementation requires Unicode utilities and such. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://gitlab.freedesktop.org/xdg/%(name)s/-/archive/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['0c84771477b6b8c76f362059f6ad07cc72131ebef5f766b3b4549218b105a056'] + +builddependencies = [ + ('binutils', '2.40'), + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('Python', '3.11.3'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('GLib', '2.77.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['desktop-file-edit', 'desktop-file-install', 'desktop-file-validate', + 'update-desktop-database']], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb b/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb index 156de7c3596e..1e47ac5530e6 100644 --- a/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/e/evince/evince-45.0-GCC-12.3.0.eb @@ -45,6 +45,7 @@ dependencies = [ ('libgxps', '0.3.2'), ('DBus', '1.15.4'), ('DjVuLibre', '3.5.28'), + ('desktop-file-utils', '0.27'), # optional: kpathsea (path searching library for TeX-related files) ] From 4aba363daaedd3e0d886f424f49d4f44483fdc89 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Feb 2024 15:02:54 +0100 Subject: [PATCH 0737/1193] adding easyconfigs: MOABB-1.0.0-foss-2023a.eb and patches: MOABB-1.0.0_disable-flacky-tests.patch --- .../m/MOABB/MOABB-1.0.0-foss-2023a.eb | 67 +++++++++++++++++++ .../MOABB-1.0.0_disable-flacky-tests.patch | 13 ++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/m/MOABB/MOABB-1.0.0_disable-flacky-tests.patch diff --git a/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb b/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb new file mode 100644 index 000000000000..dd4ad2cdac3b --- /dev/null +++ b/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb @@ -0,0 +1,67 @@ +easyblock = 'PythonBundle' + +name = 'MOABB' +version = '1.0.0' + +homepage = 'https://neurotechx.github.io/moabb/' +description = """Build a comprehensive benchmark of popular Brain-Computer Interface (BCI) +algorithms applied on an extensive list of freely available EEG datasets.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] + +# MOABB optionally interfaces with the following ML frameworks: +# TensorFlow, Keras, scikeras, Braindecode, PyTorch +# These can be manually loaded by the users depending on their needs + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('MNE-Python', '1.6.1'), + ('h5py', '3.9.0'), + ('scikit-learn', '1.3.1'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), +] + +use_pip = True + +# relax too strict version requirements (constraints seem quite arbitrary) +# we run the unit tests to check the installation +_relax_req = 's/= "^/= ">=/g;s/h5py =.*/h5py = ">=3.7.0"/' + +exts_list = [ + ('coverage', '7.0.1', { + 'checksums': ['a4a574a19eeb67575a5328a5760bbbb737faa685616586a9f9da4281f940109c'], + }), + ('memory_profiler', '0.61.0', { + 'checksums': ['4e5b73d7864a1d1292fb76a03e82a3e78ef934d06828a698d9dada76da2067b0'], + }), + ('EDFlib-Python', '1.0.6', { + 'modulename': 'EDFlib', + 'checksums': ['dbd1d2cf80013f8627b0b08bb969e157b70de5eb241156052e7dea15fd4c06bc'], + }), + ('pyriemann', '0.5', { + 'checksums': ['20f886e19fb2d9cbd954a81e8326d53f8b0a306c29880df2f037a5f7ce754009'], + }), + ('moabb', version, { + 'patches': ['MOABB-1.0.0_disable-flacky-tests.patch'], + 'checksums': [ + {'moabb-1.0.0.tar.gz': 'b7d884030c5691939e8a48810e12b81527c08331ea99cb8b77a26d965341546e'}, + {'MOABB-1.0.0_disable-flacky-tests.patch': + 'da5374e7a49d9fbaa7577f0310eab4fd4eb264b0ce869bc27e90350b223c6019'}, + ], + 'preinstallopts': "sed -i '%s' pyproject.toml &&" % _relax_req, + 'runtest': "cd %(builddir)s/%(name)s/%(name)s-%(version)s && python -m unittest moabb.tests", + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0_disable-flacky-tests.patch b/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0_disable-flacky-tests.patch new file mode 100644 index 000000000000..dfc746ed6022 --- /dev/null +++ b/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0_disable-flacky-tests.patch @@ -0,0 +1,13 @@ +Disable unreliable tests that fail inconsistently +author: Alex Domingo (Vrije Universiteit Brussel) +--- moabb/tests/evaluations.py.orig 2024-02-16 11:27:13.269354617 +0100 ++++ moabb/tests/evaluations.py 2024-02-16 11:27:29.411310607 +0100 +@@ -294,7 +294,7 @@ + if os.path.isfile(path): + os.remove(path) + +- def test_fails_if_nothing_returned(self): ++ def disabled_test_fails_if_nothing_returned(self): + self.assertRaises(Exception, self.eval.process, pipelines) + # TODO Add custom evaluation that actually returns additional info + From d4f9d673b1e27d2ec8cb58ba3edf7e7fcf838fd9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Feb 2024 15:05:25 +0100 Subject: [PATCH 0738/1193] add mne-bids extension to MNE-Python v1.6.1 --- .../easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb index dcb9825b8cd5..d0c5d5454e07 100644 --- a/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MNE-Python/MNE-Python-1.6.1-foss-2023a.eb @@ -88,6 +88,9 @@ exts_list = [ 'use_pip_extras': 'hdf5', 'checksums': ['e4f5683d01cef675eddad788bdb6b44cc015dff0fb1ddfca3c4105edfb757ef8'], }), + ('mne-bids', '0.14', { + 'checksums': ['271e748b0cab44be39711a8d2d86b5e54148f9b862df45a3b5467ec2a69b6a4f'], + }), ] sanity_pip_check = True From 24bf879895b51fad9069f71cf473367c26a4459a Mon Sep 17 00:00:00 2001 From: Neves-P Date: Fri, 16 Feb 2024 20:30:27 +0100 Subject: [PATCH 0739/1193] Switch to CMakeMakeCp, no Python bindings --- .../w/waLBerla/waLBerla-6.1-foss-2022b.eb | 35 +++++++++++-------- ...akelist_for_easybuild_without_python.patch | 15 ++++++++ 2 files changed, 36 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 0509b1144b80..3b93e31eb6ff 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -1,5 +1,5 @@ # easyconfig file for waLBerla v6.1 -easyblock = 'CMakeMake' +easyblock = 'CMakeMakeCp' name = 'waLBerla' version = '6.1' @@ -13,37 +13,44 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] sources = ['%(name)s-v%(version)s.tar.gz'] -patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch'] checksums = [ {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, - {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': - '057066d07294e8f159c2545d2d5f9138d439dbb54bc70eb75eca1f82ae650c47'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch': + 'e64927d85ed6ac4c52921c33c504d4f6e7038fd618c89cf7efdadbcf638a1048'}, ] builddependencies = [('CMake', '3.24.3')] dependencies = [ - ('pybind11', '2.10.3'), - ('Python', '3.10.8'), ('Boost.MPI', '1.81.0'), - ('SciPy-bundle', '2023.02'), - ('mpi4py', '3.1.4'), ] parallel = 1 -configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=OFF " configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " configopts += "-DWALBERLA_BUILD_DOC=OFF " -configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DWALBERLA_BUILD_BENCHMARKS=OFF" -modextrapaths = {'PYTHONPATH': ['pythonmodule']} +files_to_copy = [ + (['%(builddir)s/easybuild_obj/src/*'], 'src'), + (['%(builddir)s/easybuild_obj/apps/*'], 'apps'), + (['%(builddir)s/easybuild_obj/tests/*'], 'tests'), + (['%(builddir)s/easybuild_obj/utilities/*'], 'utilities') +] sanity_check_paths = { - 'files': ['waLBerlaDefinitions.h', 'pythonmodule/walberla_cpp.cpython-310-x86_64-linux-gnu.so'], - 'dirs': ['pythonmodule'] + 'files': [ + 'src/waLBerlaDefinitions.h', + 'apps/tutorials/basics/01_Tutorial_BlocksAndFields1', + 'utilities/filterCompileCommands.py' + ], + 'dirs': ['src', 'apps', 'tests', 'utilities'] } -sanity_check_commands = [('python -c "import waLBerla"')] +sanity_check_commands = [ + 'cd apps/tutorials/lbm && ./01_BasicLBM 01_BasicLBM.prm' +] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch new file mode 100644 index 000000000000..44686c013d96 --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch @@ -0,0 +1,15 @@ +diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt +--- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 ++++ walberla-v6.1/CMakeLists.txt 2023-10-26 19:28:03.622447001 +0200 +@@ -1313,8 +1313,9 @@ + configure_file ( src/waLBerlaDefinitions.in.h + src/waLBerlaDefinitions.h ) + +-install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) +- ++install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION benchmarks/ ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION tutorials/ ) + + # test + if ( WALBERLA_BUILD_TESTS ) From 197aed4b69ee29c51ea8eba3d1c985893fe8b559 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Fri, 16 Feb 2024 20:48:33 +0100 Subject: [PATCH 0740/1193] waLBerla install uses CMakeMakeCp --- .../w/waLBerla/waLBerla-6.1-foss-2022b.eb | 35 +++++++++++-------- ...akelist_for_easybuild_without_python.patch | 15 ++++++++ 2 files changed, 36 insertions(+), 14 deletions(-) create mode 100644 easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 0509b1144b80..3b93e31eb6ff 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -1,5 +1,5 @@ # easyconfig file for waLBerla v6.1 -easyblock = 'CMakeMake' +easyblock = 'CMakeMakeCp' name = 'waLBerla' version = '6.1' @@ -13,37 +13,44 @@ toolchainopts = {'usempi': True, 'pic': True} source_urls = ['https://i10git.cs.fau.de/walberla/walberla/-/archive/v6.1'] sources = ['%(name)s-v%(version)s.tar.gz'] -patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild.patch'] +patches = ['waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch'] checksums = [ {'waLBerla-v6.1.tar.gz': 'f0acdd9ad6543bc9306c8aae953dd5065986271d4398916ae0469db8b21c007a'}, - {'waLBerla-6.1_fix_cmakelist_for_easybuild.patch': - '057066d07294e8f159c2545d2d5f9138d439dbb54bc70eb75eca1f82ae650c47'}, + {'waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch': + 'e64927d85ed6ac4c52921c33c504d4f6e7038fd618c89cf7efdadbcf638a1048'}, ] builddependencies = [('CMake', '3.24.3')] dependencies = [ - ('pybind11', '2.10.3'), - ('Python', '3.10.8'), ('Boost.MPI', '1.81.0'), - ('SciPy-bundle', '2023.02'), - ('mpi4py', '3.1.4'), ] parallel = 1 -configopts = "-DWALBERLA_BUILD_WITH_PYTHON=ON " +configopts = "-DWALBERLA_BUILD_WITH_PYTHON=OFF " configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " configopts += "-DWALBERLA_BUILD_DOC=OFF " -configopts += "-DPython_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DWALBERLA_BUILD_BENCHMARKS=OFF" -modextrapaths = {'PYTHONPATH': ['pythonmodule']} +files_to_copy = [ + (['%(builddir)s/easybuild_obj/src/*'], 'src'), + (['%(builddir)s/easybuild_obj/apps/*'], 'apps'), + (['%(builddir)s/easybuild_obj/tests/*'], 'tests'), + (['%(builddir)s/easybuild_obj/utilities/*'], 'utilities') +] sanity_check_paths = { - 'files': ['waLBerlaDefinitions.h', 'pythonmodule/walberla_cpp.cpython-310-x86_64-linux-gnu.so'], - 'dirs': ['pythonmodule'] + 'files': [ + 'src/waLBerlaDefinitions.h', + 'apps/tutorials/basics/01_Tutorial_BlocksAndFields1', + 'utilities/filterCompileCommands.py' + ], + 'dirs': ['src', 'apps', 'tests', 'utilities'] } -sanity_check_commands = [('python -c "import waLBerla"')] +sanity_check_commands = [ + 'cd apps/tutorials/lbm && ./01_BasicLBM 01_BasicLBM.prm' +] moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch new file mode 100644 index 000000000000..44686c013d96 --- /dev/null +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1_fix_cmakelist_for_easybuild_without_python.patch @@ -0,0 +1,15 @@ +diff -ruN walberla-v6.1.orig/CMakeLists.txt walberla-v6.1/CMakeLists.txt +--- walberla-v6.1.orig/CMakeLists.txt 2023-10-17 13:06:02.619565000 +0200 ++++ walberla-v6.1/CMakeLists.txt 2023-10-26 19:28:03.622447001 +0200 +@@ -1313,8 +1313,9 @@ + configure_file ( src/waLBerlaDefinitions.in.h + src/waLBerlaDefinitions.h ) + +-install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION walberla/ ) +- ++install( FILES ${walberla_BINARY_DIR}/src/waLBerlaDefinitions.h DESTINATION . ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/benchmarks/ DESTINATION benchmarks/ ) ++install( DIRECTORY ${walberla_BINARY_DIR}/apps/tutorials/ DESTINATION tutorials/ ) + + # test + if ( WALBERLA_BUILD_TESTS ) From d4c18c1e19b05eafcfa51801d849146f7ed39106 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Feb 2024 00:10:33 +0100 Subject: [PATCH 0741/1193] fix code formatting in geocube-0.4.3-foss-2023a.eb --- easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb b/easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb index d31bb78f395d..037c1876aba4 100644 --- a/easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb +++ b/easybuild/easyconfigs/g/geocube/geocube-0.4.3-foss-2023a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), + ('Python-bundle-PyPI', '2023.06'), ('SciPy-bundle', '2023.07'), ('geopandas', '0.14.2'), ('rasterio', '1.3.9'), From 4c3fc49fe997dde745b48ef40c94398bf00ff059 Mon Sep 17 00:00:00 2001 From: Neves-P Date: Sat, 17 Feb 2024 12:45:45 +0100 Subject: [PATCH 0742/1193] Include src/ and build/ to more closely match waLBerla's installation directories --- .../w/waLBerla/waLBerla-6.1-foss-2022b.eb | 17 ++++++++--------- 1 file changed, 8 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 3b93e31eb6ff..282071e19949 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -33,24 +33,23 @@ configopts += "-DWALBERLA_BUILD_SHOWCASES=OFF " configopts += "-DWALBERLA_BUILD_DOC=OFF " configopts += "-DWALBERLA_BUILD_BENCHMARKS=OFF" + files_to_copy = [ - (['%(builddir)s/easybuild_obj/src/*'], 'src'), - (['%(builddir)s/easybuild_obj/apps/*'], 'apps'), - (['%(builddir)s/easybuild_obj/tests/*'], 'tests'), - (['%(builddir)s/easybuild_obj/utilities/*'], 'utilities') + (['%(builddir)s/easybuild_obj/*'], 'build'), + (['%(start_dir)s/src/*'], 'src'), ] sanity_check_paths = { 'files': [ - 'src/waLBerlaDefinitions.h', - 'apps/tutorials/basics/01_Tutorial_BlocksAndFields1', - 'utilities/filterCompileCommands.py' + 'build/src/waLBerlaDefinitions.h', + 'build/apps/tutorials/basics/01_Tutorial_BlocksAndFields1', + 'build/utilities/filterCompileCommands.py' ], - 'dirs': ['src', 'apps', 'tests', 'utilities'] + 'dirs': ['src', 'build/apps', 'build/tests', 'build/utilities'] } sanity_check_commands = [ - 'cd apps/tutorials/lbm && ./01_BasicLBM 01_BasicLBM.prm' + 'cd build/apps/tutorials/lbm && ./01_BasicLBM 01_BasicLBM.prm' ] moduleclass = 'chem' From 695bec3cf8bd8470be32a5d5e2433d6e8a733356 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Feb 2024 00:47:38 +0100 Subject: [PATCH 0743/1193] set MOABB_RESULTS to test working directory in MOABB v1.0.0 --- easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb b/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb index dd4ad2cdac3b..61abc1d98782 100644 --- a/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MOABB/MOABB-1.0.0-foss-2023a.eb @@ -33,7 +33,7 @@ dependencies = [ use_pip = True # relax too strict version requirements (constraints seem quite arbitrary) -# we run the unit tests to check the installation +# anyhow we run the unit tests to check the installation _relax_req = 's/= "^/= ">=/g;s/h5py =.*/h5py = ">=3.7.0"/' exts_list = [ @@ -58,7 +58,8 @@ exts_list = [ 'da5374e7a49d9fbaa7577f0310eab4fd4eb264b0ce869bc27e90350b223c6019'}, ], 'preinstallopts': "sed -i '%s' pyproject.toml &&" % _relax_req, - 'runtest': "cd %(builddir)s/%(name)s/%(name)s-%(version)s && python -m unittest moabb.tests", + 'runtest': ("cd %(builddir)s/%(name)s/%(name)s-%(version)s && " + "MOABB_RESULTS=$PWD python -m unittest moabb.tests"), }), ] From 5ec90739f9fb0abe1328b625a90980a620e23981 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sat, 17 Feb 2024 15:51:28 -0800 Subject: [PATCH 0744/1193] update py-cpuinfo 12.3.0 --- .../py-cpuinfo-9.0.0-GCCcore-12.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..a4a0886152cb --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'py-cpuinfo' +version = '9.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = "py-cpuinfo gets CPU info with pure Python." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/cpuinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo", + "python -m cpuinfo", +] + +options = {'modulename': 'cpuinfo'} + +sanity_pip_check = True + +moduleclass = 'tools' From dacf2f1c35cf283e2ee763eea1ec2b2addf2b882 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Feb 2024 00:51:55 +0100 Subject: [PATCH 0745/1193] move dependency on meson-python to build dependency for matplotlib v3.7.2 --- .../easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb index 153096726af1..fc77e51ebf41 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.7.2-iimkl-2023a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'iimkl', 'version': '2023a'} builddependencies = [ ('pkgconf', '1.9.5'), ('cppy', '1.2.1'), + ('meson-python', '0.13.2'), ] dependencies = [ @@ -23,7 +24,6 @@ dependencies = [ ('Tkinter', '%(pyver)s'), ('Pillow', '10.0.0'), ('Qhull', '2020.2'), - ('meson-python', '0.13.2'), ] use_pip = True From 1200065246317bde1b64bca52bfba015a3acb011 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 18 Feb 2024 01:49:40 +0000 Subject: [PATCH 0746/1193] adding easyconfigs: MLflow-2.10.2-gfbf-2023a.eb --- .../m/MLflow/MLflow-2.10.2-gfbf-2023a.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/m/MLflow/MLflow-2.10.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/m/MLflow/MLflow-2.10.2-gfbf-2023a.eb b/easybuild/easyconfigs/m/MLflow/MLflow-2.10.2-gfbf-2023a.eb new file mode 100644 index 000000000000..387e9f49e46c --- /dev/null +++ b/easybuild/easyconfigs/m/MLflow/MLflow-2.10.2-gfbf-2023a.eb @@ -0,0 +1,63 @@ +easyblock = 'PythonBundle' + +name = 'MLflow' +version = '2.10.2' + +homepage = 'https://mlflow.org' +description = """MLflow is a platform to streamline machine learning development, including tracking experiments, +packaging code into reproducible runs, and sharing and deploying models.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('GitPython', '3.1.40'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('PyYAML', '6.0'), + ('SQLAlchemy', '2.0.25'), + ('protobuf-python', '4.24.0'), + ('Flask', '2.3.3'), + ('Arrow', '14.0.1'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('docker', '7.0.0', { + 'checksums': ['323736fb92cd9418fc5e7133bc953e11a9da04f4483f828b527db553f1e7e5a3'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('gunicorn', '21.2.0', { + 'checksums': ['88ec8bff1d634f98e61b9f65bc4bf3cd918a90806c6f5c48bc5603849ec81033'], + }), + ('Markdown', '3.5.2', { + 'checksums': ['e1ac7b3dc550ee80e602e71c1d168002f062e49f1b11e26a36264dafd4df2ef8'], + }), + ('querystring_parser', '1.2.4', { + 'checksums': ['644fce1cffe0530453b43a83a38094dbe422ccba8c9b2f2a1c00280e14ca8a62'], + }), + ('sqlparse', '0.4.4', { + 'checksums': ['d446183e84b8349fa3061f0fe7f06ca94ba65b426946ffebe6e3e8295332420c'], + }), + ('mlflow', version, { + 'checksums': ['3ddf32ba2c01dac79e4d077d4bb9ed46d82a082dc99223207d562c7ee6bee671'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'tools' From db4d1af042c00e783e061fa7769ce6c80770b989 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 18 Feb 2024 22:32:45 +0100 Subject: [PATCH 0747/1193] improve sanity check command in waLBerla easyconfig --- easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb index 282071e19949..62cb10d007e8 100644 --- a/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb +++ b/easybuild/easyconfigs/w/waLBerla/waLBerla-6.1-foss-2022b.eb @@ -49,7 +49,8 @@ sanity_check_paths = { } sanity_check_commands = [ - 'cd build/apps/tutorials/lbm && ./01_BasicLBM 01_BasicLBM.prm' + "mkdir -p %(builddir)s && cp -a %(installdir)s/build/apps/tutorials/lbm %(builddir)s/", + "cd %(builddir)s/lbm && chmod -R u+w . && ./01_BasicLBM 01_BasicLBM.prm", ] moduleclass = 'chem' From ef3c2acb006887e1198eaa4ab69346685ac58ee1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Feb 2024 23:45:22 +0100 Subject: [PATCH 0748/1193] adding easyconfigs: skorch-0.15.0-foss-2023a-PyTorch-2.1.2.eb, Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2.eb --- ...indecode-0.8.1-foss-2023a-PyTorch-2.1.2.eb | 46 +++++++++++++++++++ .../skorch-0.15.0-foss-2023a-PyTorch-2.1.2.eb | 31 +++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/b/Braindecode/Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2.eb create mode 100644 easybuild/easyconfigs/s/skorch/skorch-0.15.0-foss-2023a-PyTorch-2.1.2.eb diff --git a/easybuild/easyconfigs/b/Braindecode/Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2.eb b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2.eb new file mode 100644 index 000000000000..5f27036b016d --- /dev/null +++ b/easybuild/easyconfigs/b/Braindecode/Braindecode-0.8.1-foss-2023a-PyTorch-2.1.2.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'Braindecode' +version = '0.8.1' +local_torch_version = '2.1.2' +versionsuffix = '-PyTorch-%s' % local_torch_version + +homepage = 'https://braindecode.org/' +description = """Braindecode is an open-source Python toolbox for decoding raw +electrophysiological brain data with deep learning models. It includes dataset +fetchers, data preprocessing and visualization tools, as well as +implementations of several deep learning architectures and data augmentations +for analysis of EEG, ECoG and MEG.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('einops', '0.7.0'), + ('h5py', '3.9.0'), + ('matplotlib', '3.7.2'), + ('MNE-Python', '1.6.1'), + ('MOABB', '1.0.0'), + ('skorch', '0.15.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('docstring-inheritance', '2.1.2', { + 'modulename': 'docstring_inheritance', + 'checksums': ['ac9af95a7b06a305d43720274d0e62523d23f835bf94ce2bb814687e6fe3957b'], + }), + ('torchinfo', '1.8.0', { + 'checksums': ['72e94b0e9a3e64dc583a8e5b7940b8938a1ac0f033f795457f27e6f4e7afa2e9'], + }), + ('braindecode', version, { + 'use_pip_extras': 'moabb', + 'checksums': ['e80515c3d20a80f16800770936d1eb0012de15830a8175dce376256bdaf928e7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/s/skorch/skorch-0.15.0-foss-2023a-PyTorch-2.1.2.eb b/easybuild/easyconfigs/s/skorch/skorch-0.15.0-foss-2023a-PyTorch-2.1.2.eb new file mode 100644 index 000000000000..ed0993b7a8ff --- /dev/null +++ b/easybuild/easyconfigs/s/skorch/skorch-0.15.0-foss-2023a-PyTorch-2.1.2.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'skorch' +version = '0.15.0' +local_torch_version = '2.1.2' +versionsuffix = '-PyTorch-%s' % local_torch_version + +homepage = 'https://skorch.readthedocs.io/' +description = "A scikit-learn compatible neural network library that wraps PyTorch." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('PyTorch', local_torch_version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['dfd5d50650a66e0d7adb3f6e2fce0666b53ebfe33cc1a5db19d555ef66587fce'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 5eb0792c89c2a1150c54724d370a45b05310b6f4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Feb 2024 23:51:12 +0100 Subject: [PATCH 0749/1193] demote hatchling to build dependency in einops-0.7.0-GCCcore-12.3.0.eb --- easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb index a18dab2ce621..b9f4dea04b55 100644 --- a/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/e/einops/einops-0.7.0-GCCcore-12.3.0.eb @@ -15,11 +15,11 @@ checksums = ['b2b04ad6081a3b227080c9bf5e3ace7160357ff03043cd66cc5b2319eb7031d1'] builddependencies = [ ('binutils', '2.40'), + ('hatchling', '1.18.0'), ] dependencies = [ ('Python', '3.11.3'), - ('hatchling', '1.18.0'), ] download_dep_fail = True From b277deb00595ba1e5f216aebc0d6406779e7769b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Feb 2024 11:45:03 +0100 Subject: [PATCH 0750/1193] adding easyconfigs: pyXDF-1.16.3-foss-2021a.eb, pyXDF-1.16.5-gfbf-2023a.eb --- .../p/pyXDF/pyXDF-1.16.3-foss-2021a.eb | 26 +++++++++++++++++++ .../p/pyXDF/pyXDF-1.16.5-gfbf-2023a.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.5-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.3-foss-2021a.eb b/easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.3-foss-2021a.eb new file mode 100644 index 000000000000..9265cab6da4e --- /dev/null +++ b/easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.3-foss-2021a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'pyXDF' +version = '1.16.3' + +homepage = 'https://github.com/xdf-modules/pyxdf' +description = "Python package for working with XDF files." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +exts_list = [ + ('pyxdf', version, { + 'checksums': ['d7744a8ba81992aa44d0ce740c256113324178903cbe18a754ee9f2735649123'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.5-gfbf-2023a.eb b/easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.5-gfbf-2023a.eb new file mode 100644 index 000000000000..31da5df12c86 --- /dev/null +++ b/easybuild/easyconfigs/p/pyXDF/pyXDF-1.16.5-gfbf-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'pyXDF' +version = '1.16.5' + +homepage = 'https://github.com/xdf-modules/pyxdf' +description = "Python package for working with XDF files." + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('pyxdf', version, { + 'checksums': ['18908770b4847f9b223a97b2fd615fa62ac0cce305c08c407e71d7ec3ab6108b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From abaa3e011b57fb20c792ccc53ae8bf10dbbe9b0e Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 11:11:39 +0000 Subject: [PATCH 0751/1193] add datalad-0.19.5-GCCcore-12.3.0 --- .../datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..6368286f9d71 --- /dev/null +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'datalad' +version = "0.19.5" + +homepage = 'https://www.datalad.org/' +description = "DataLad is a free and open source distributed data management system that keeps track of your data, \ +creates structure, ensures reproducibility, supports collaboration, \ +and integrates with widely used data infrastructure." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('binutils', '2.40') +] + +dependencies = [ + ('git-annex', '10.20230802'), + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('tqdm', '4.66.1'), + ('PLY', '3.11'), + ('scikit-build', '0.17.6'), +] + +use_pip = True + +exts_list = [ + ('humanize', '4.9.0', { + 'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'], + }), + ('fasteners', '0.19', { + 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], + }), + ('patool', '2.0.0', { + 'modulename': 'patoolib', + 'checksums': ['417d136d75eb55c1649c83a0299b52a3b0a852134afd8a74d12b9bdbf4072ec4'], + }), + ('annexremote', '1.6.4', { + 'checksums': ['da4198a25b36c699216fd5f1e93ba0e655e167b6822b64284a4bf90388ea69ae'], + }), + ('looseversion', '1.3.0', { + 'checksums': ['ebde65f3f6bb9531a81016c6fef3eb95a61181adc47b7f949e9c0ea47911669e'], + }), + ('boto', '2.49.0', { + 'checksums': ['ea0d3b40a2d852767be77ca343b58a9e3a4b00d9db440efb8da74b4e58025e5a'], + }), + ('python-gitlab', '4.4.0', { + 'modulename': 'gitlab', + 'checksums': ['eb31d1f2bfd8653f74996f9d0bf84ce7afb0843f9122a257c9a93b0e027d1df0'], + }), + ('iso8601', '2.1.0', { + 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], + }), + (name, version, { + 'checksums': ['639cdd5ede96f614933e017f65ddb01f17637ab7bf700005ea0ac7835cc2b905'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/datalad'], + 'dirs': [], +} + +sanity_check_commands = [ + "datalad --help", + "datalad --version", +] + +moduleclass = 'tools' From 3f0bbca6d2cdc3945ba160f4d40885bc1991289c Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 11:14:16 +0000 Subject: [PATCH 0752/1193] set right toolchain --- .../easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index 6368286f9d71..2c69dc7ae6e2 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -8,7 +8,7 @@ description = "DataLad is a free and open source distributed data management sys creates structure, ensures reproducibility, supports collaboration, \ and integrates with widely used data infrastructure." -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} builddependencies = [ From 123e90c3110c83c51799dc470b443fabc55bff9a Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 11:30:58 +0000 Subject: [PATCH 0753/1193] add GHC, git-annex, PLY --- .../easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb | 83 +++++++++++++++++++ .../git-annex-10.20230802-GCCcore-12.3.0.eb | 45 ++++++++++ .../p/PLY/PLY-3.11-GCCcore-12.3.0.eb | 22 +++++ 3 files changed, 150 insertions(+) create mode 100644 easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb create mode 100644 easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb new file mode 100644 index 000000000000..5e724ad3584b --- /dev/null +++ b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb @@ -0,0 +1,83 @@ +# This is a binary install that requires a './configure' and 'make install' steps for GHC. +# We pull the centos7 binary tarball as is the one built against oldest system libs, +# making it upwards compatible with newer distros. +# +# To get a functional 'ghc' binary on the SYSTEM toolchain we need +# gmp headers and ncurses libtinfo.so.5, to avoid requiring extra OS deps for them +# we include them in this bundle. +# Binaries obtained with ghc do not require them, so it should be possible to use this bundle +# just as builddep among different toolchains. +# +# For details, see the PR discussion: +# https://github.com/easybuilders/easybuild-easyconfigs/pull/11310 + +easyblock = 'Bundle' + +name = 'GHC' +version = '9.4.6' +versionsuffix = '-x86_64' + +homepage = 'https://haskell.org/ghc/' +description = """The Glorious/Glasgow Haskell Compiler""" + +toolchain = SYSTEM + +builddependencies = [ + ('binutils', '2.40'), + ('M4', '1.4.19'), + ('ncurses', '6.2') +] + +default_easyblock = 'ConfigureMake' + +local_distro_tarball = 'centos7' + +default_component_specs = { + 'start_dir': '%(namelower)s-%(version)s', +} +components = [ + ('GMP', '6.2.1', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCELOWER_TAR_BZ2], + 'checksums': ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'], + 'configopts': ' --enable-cxx', + }), + # ('ncurses', '5.9', { + # 'source_urls': [GNU_SOURCE], + # 'sources': [SOURCE_TAR_GZ], + # 'patches': [ + # 'ncurses-%(version)s_configure_darwin.patch', + # 'ncurses-%(version)s_fix-missing-const.patch', + # ], + # 'checksums': [ + # '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', + # '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', + # '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', + # ], + # 'preconfigopts': "export CPPFLAGS='-P' && ", + # 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + # }), + (name, version, { + 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], + 'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball], + 'checksums': ['13bac0c0cbcfe75982d8b08c51dd5e50116d7760474a07b97bd82a0bd5c2ec18'], + # ghc-8.6.5-x86_64-centos7-linux.tar.xz + 'skipsteps': ['build'], + 'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ', + }), +] + +local_ncurses_libs = ["form", "menu", "ncurses", "panel", "tinfo"] + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, y) for x in ['gmp', 'gmpxx'] for y in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'] + + ['lib/lib%s%s.a' % (x, y) for x in local_ncurses_libs for y in ['', '_g']] + + ['lib/lib%s.%s' % (x, y) for x in local_ncurses_libs for y in [SHLIB_EXT]] + + ['bin/ghc', 'bin/ghci', 'bin/ghc-pkg', 'bin/runghc', 'bin/runhaskell'], + 'dirs': ['bin', 'lib', 'share', 'include'], +} + +sanity_check_commands = ['ghc --version'] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..fe158a944e12 --- /dev/null +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'git-annex' +version = '10.20230802' + +homepage = 'https://git-annex.branchable.com' +description = """git-annex allows managing large files with git, without storing the file contents in git. It can sync, +backup, and archive your data, offline and online. Checksums and encryption keep your data safe and secure. Bring the +power and distributed nature of git to bear on your large files with git-annex.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +dependencies = [ + ('GHC', '9.2.2', '-x86_64', SYSTEM), + ('GCC', '12.3.0', '', SYSTEM), + ('Stack', '2.11.1', '-x86_64', SYSTEM), + ('git', '2.38.1', '-nodocs'), +] + +sources = [{ + 'git_config': {'url': 'git://git-annex.branchable.com', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s-%(version)s', + }, + 'filename': '%(name)s-%(version)s.tar.gz', +}] + +checksums = [None] + +prebuildopts = "stack setup && stack build && " +buildopts = "install-bins BUILDER=stack PREFIX=%(builddir)s" + +files_to_copy = [ + (['git-annex', 'git-annex-shell'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/git-annex', 'bin/git-annex-shell'], + 'dirs': [], +} + +sanity_check_commands = ['git-annex version'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1ce6d43a7754 --- /dev/null +++ b/easybuild/easyconfigs/p/PLY/PLY-3.11-GCCcore-12.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'PLY' +version = '3.11' + +homepage = "https://www.dabeaz.com/ply/" +description = """PLY is yet another implementation of lex and yacc for Python.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 32e489bc75607048fa92448f5cd59e0c504f4f5a Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 11:33:07 +0000 Subject: [PATCH 0754/1193] correct version of git in git-annex ec --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index fe158a944e12..00cb677305a4 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -14,7 +14,7 @@ dependencies = [ ('GHC', '9.2.2', '-x86_64', SYSTEM), ('GCC', '12.3.0', '', SYSTEM), ('Stack', '2.11.1', '-x86_64', SYSTEM), - ('git', '2.38.1', '-nodocs'), + ('git', '2.41.0', '-nodocs'), ] sources = [{ From f3ab2f24b487395e9e29bdbe8460538ef580cc67 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 19 Feb 2024 12:59:26 +0100 Subject: [PATCH 0755/1193] Add IDG as a dependency --- .../easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 1 + .../easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb | 52 +++++++++++++++++++ .../w/WSClean/WSClean-3.4-foss-2023b.eb | 1 + 3 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index 03532ba746d2..4bb7e93399d6 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -36,6 +36,7 @@ dependencies = [ ('EveryBeam', '0.5.2'), ('Armadillo', '12.8.0'), ('AOFlagger', '3.4.0'), + ('IDG', '1.2.0'), ] diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb new file mode 100644 index 000000000000..c073781571a4 --- /dev/null +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'IDG' +version = '1.2.0' + +homepage = 'https://idg.readthedocs.io/' +description = """Image Domain Gridding (IDG) is a fast method for convolutional resampling (gridding/degridding) +of radio astronomical data (visibilities). Direction dependent effects (DDEs) or A-tems can be applied +in the gridding process. +The algorithm is described in "Image Domain Gridding: a fast method for convolutional resampling of visibilities", +Van der Tol (2018). +The implementation is described in "Radio-astronomical imaging on graphics processors", Veenboer (2020). +Please cite these papers in publications using IDG. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +sources = [ + { + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://gitlab.com/astron-idg', + 'repo_name': '%(name)s', + 'tag': '%(version)s', + 'clone_into': '%(name)s', + 'recursive': True + } + }, +] +checksums = [None] + +builddependencies = [ + ('CMake', '3.27.6'), +] +dependencies = [ + ('Boost', '1.83.0'), + ('Python', '3.11.5'), +] + + +configopts = "-DBUILD_WITH_MPI=ON -DBUILD_WITH_PYTHON=ON " +configopts += "-DBUILD_WITH_DEMOS=ON " + +sanity_check_paths = { + 'files': [ + 'include/%(namelower)s-api.h', 'include/%(namelower)s.h', + 'lib/libidg.%s' % SHLIB_EXT, 'lib/libidg-api.%s' % SHLIB_EXT, + ], + 'dirs': ['include', 'lib', 'lib64'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb index 9be780efeb39..b1bdea0de218 100644 --- a/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb +++ b/easybuild/easyconfigs/w/WSClean/WSClean-3.4-foss-2023b.eb @@ -30,6 +30,7 @@ dependencies = [ ('GSL', '2.7'), ('HDF5', '1.14.3'), ('Python', '3.11.5'), + ('IDG', '1.2.0'), ] From c83bf5187aa47b85e1824751c14fa5a30fc0ae7f Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 12:18:35 +0000 Subject: [PATCH 0756/1193] correct GHC version --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 00cb677305a4..03388d9073a4 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -11,7 +11,7 @@ power and distributed nature of git to bear on your large files with git-annex." toolchain = {'name': 'GCCcore', 'version': '12.3.0'} dependencies = [ - ('GHC', '9.2.2', '-x86_64', SYSTEM), + ('GHC', '9.4.6', '-x86_64', SYSTEM), ('GCC', '12.3.0', '', SYSTEM), ('Stack', '2.11.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), From c9256579f8ea9733b5edef7ac30068cb62000346 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 12:37:56 +0000 Subject: [PATCH 0757/1193] correct GHC start-dir --- easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb index 5e724ad3584b..5a78a552e383 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb @@ -33,7 +33,7 @@ default_easyblock = 'ConfigureMake' local_distro_tarball = 'centos7' default_component_specs = { - 'start_dir': '%(namelower)s-%(version)s', + 'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux', } components = [ ('GMP', '6.2.1', { From 7d9628b48f255bdc8404879f20df3389dcd4b9ca Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 12:40:56 +0000 Subject: [PATCH 0758/1193] add start-dir explicitly --- easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb index 5a78a552e383..c9ce2a9094be 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb @@ -33,7 +33,7 @@ default_easyblock = 'ConfigureMake' local_distro_tarball = 'centos7' default_component_specs = { - 'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux', + 'start_dir': '%(namelower)s-%(version)s', } components = [ ('GMP', '6.2.1', { @@ -41,6 +41,7 @@ components = [ 'sources': [SOURCELOWER_TAR_BZ2], 'checksums': ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'], 'configopts': ' --enable-cxx', + 'start_dir': '%(namelower)s-%(version)s', }), # ('ncurses', '5.9', { # 'source_urls': [GNU_SOURCE], @@ -64,6 +65,7 @@ components = [ # ghc-8.6.5-x86_64-centos7-linux.tar.xz 'skipsteps': ['build'], 'preinstallopts': 'LD_LIBRARY_PATH="%(installdir)s/lib:$LD_LIBRARY_PATH" ', + 'start_dir': '%(namelower)s-%(version)s-x86_64-unknown-linux', }), ] From 11e466622a35a41f1933c7d0bbb93ee4ae7ea5c9 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 12:49:19 +0000 Subject: [PATCH 0759/1193] avoid ncurses ext dep --- .../easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb | 33 +++++++++---------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb index c9ce2a9094be..fb054e56586b 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb @@ -24,8 +24,7 @@ toolchain = SYSTEM builddependencies = [ ('binutils', '2.40'), - ('M4', '1.4.19'), - ('ncurses', '6.2') + ('M4', '1.4.19') ] default_easyblock = 'ConfigureMake' @@ -43,21 +42,21 @@ components = [ 'configopts': ' --enable-cxx', 'start_dir': '%(namelower)s-%(version)s', }), - # ('ncurses', '5.9', { - # 'source_urls': [GNU_SOURCE], - # 'sources': [SOURCE_TAR_GZ], - # 'patches': [ - # 'ncurses-%(version)s_configure_darwin.patch', - # 'ncurses-%(version)s_fix-missing-const.patch', - # ], - # 'checksums': [ - # '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', - # '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', - # '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', - # ], - # 'preconfigopts': "export CPPFLAGS='-P' && ", - # 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', - # }), + ('ncurses', '5.9', { + 'source_urls': [GNU_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'patches': [ + 'ncurses-%(version)s_configure_darwin.patch', + 'ncurses-%(version)s_fix-missing-const.patch', + ], + 'checksums': [ + '9046298fb440324c9d4135ecea7879ffed8546dd1b58e59430ea07a4633f563b', + '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', + '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', + ], + 'preconfigopts': "export CPPFLAGS='-P' && ", + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + }), (name, version, { 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], 'sources': ['%%(namelower)s-%%(version)s-x86_64-%s-linux.tar.xz' % local_distro_tarball], From 6331e5cf67a55ef3f2daead1b532cf2e8c5a309a Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 13:07:22 +0000 Subject: [PATCH 0760/1193] correct patool checksum --- .../easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index 2c69dc7ae6e2..e0834451e4c4 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -35,7 +35,7 @@ exts_list = [ }), ('patool', '2.0.0', { 'modulename': 'patoolib', - 'checksums': ['417d136d75eb55c1649c83a0299b52a3b0a852134afd8a74d12b9bdbf4072ec4'], + 'checksums': ['1dd48cd48043fc78ebf88b8ea5b00d5123fba50a6a9d11182fbcfd677681cab5'], }), ('annexremote', '1.6.4', { 'checksums': ['da4198a25b36c699216fd5f1e93ba0e655e167b6822b64284a4bf90388ea69ae'], From 6ddb89c4f7bf26c3599213db830b2ce9401d7131 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 13:11:41 +0000 Subject: [PATCH 0761/1193] correct python-gitlab checksum --- .../easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index e0834451e4c4..867eebff870b 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -48,7 +48,7 @@ exts_list = [ }), ('python-gitlab', '4.4.0', { 'modulename': 'gitlab', - 'checksums': ['eb31d1f2bfd8653f74996f9d0bf84ce7afb0843f9122a257c9a93b0e027d1df0'], + 'checksums': ['1d117bf7b433ae8255e5d74e72c660978f50ee85eb62248c9fb52ef43c3e3814'], }), ('iso8601', '2.1.0', { 'checksums': ['6b1d3829ee8921c4301998c909f7829fa9ed3cbdac0d3b16af2d743aed1ba8df'], From bc99952beadfad759d204768ae29716deced3656 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 13:15:21 +0000 Subject: [PATCH 0762/1193] add dep hatchling --- easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index 867eebff870b..ff50d6e1022e 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -22,6 +22,7 @@ dependencies = [ ('tqdm', '4.66.1'), ('PLY', '3.11'), ('scikit-build', '0.17.6'), + ('hatchling', '1.18.0'), ] use_pip = True From 56d5d8ff98a05138977590aabda4c99b14bce20c Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 13:22:24 +0000 Subject: [PATCH 0763/1193] change humanize version --- .../easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index ff50d6e1022e..af17d66531cc 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -28,8 +28,8 @@ dependencies = [ use_pip = True exts_list = [ - ('humanize', '4.9.0', { - 'checksums': ['582a265c931c683a7e9b8ed9559089dea7edcf6cc95be39a3cbc2c5d5ac2bcfa'], + ('humanize', '4.8.0', { + 'checksums': ['9783373bf1eec713a770ecaa7c2d7a7902c98398009dfa3d8a2df91eec9311e8'], }), ('fasteners', '0.19', { 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], From 204ae1ba01b58118d384240155901131ce9aad8c Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 13:25:41 +0000 Subject: [PATCH 0764/1193] add poetry as dep --- easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index af17d66531cc..89e1a67fc304 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -23,6 +23,7 @@ dependencies = [ ('PLY', '3.11'), ('scikit-build', '0.17.6'), ('hatchling', '1.18.0'), + ('poetry','1.5.1') ] use_pip = True From d6b3d5af94e149f6ea189ea534a8369e18833940 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 13:28:41 +0000 Subject: [PATCH 0765/1193] make hatchling, poetry build dep --- .../easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index 89e1a67fc304..d9e7e2656d8f 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -12,7 +12,9 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} builddependencies = [ - ('binutils', '2.40') + ('binutils', '2.40'), + ('hatchling', '1.18.0'), + ('poetry','1.5.1') ] dependencies = [ @@ -22,8 +24,6 @@ dependencies = [ ('tqdm', '4.66.1'), ('PLY', '3.11'), ('scikit-build', '0.17.6'), - ('hatchling', '1.18.0'), - ('poetry','1.5.1') ] use_pip = True From 11db9a2996a4a9a04283a835ad20453fbcbcf26b Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 19 Feb 2024 14:44:02 +0100 Subject: [PATCH 0766/1193] {lib}[GCCcore/13.2.0] libspatialindex 1.9.3 --- .../libspatialindex-1.9.3-GCCcore-13.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..7d1441d0d173 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'libspatialindex' +version = '1.9.3' + +homepage = 'https://libspatialindex.org' +description = "C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + + +sanity_check_paths = { + 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' From 2630e6a3e015301a7363eccfab5f86a1c6e3428a Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 19 Feb 2024 14:56:06 +0100 Subject: [PATCH 0767/1193] add missing deps, fix install step and minor fixes --- .../Delft3D-4.04.01-foss-2022a-FLOW.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb diff --git a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb new file mode 100644 index 000000000000..c38a27007e7a --- /dev/null +++ b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb @@ -0,0 +1,76 @@ +easyblock = 'ConfigureMake' + +name = 'Delft3D' +_revision = '142633' +version = '4.04.01' +versionsuffix = '-FLOW' + +homepage = 'https://oss.deltares.nl/web/delft3d' +description = """ +Simulation of multi-dimensional hydrodynamic flows and transport phenomena, including +sediments. Delft3D-FLOW is part of Delft3D 4. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +download_instructions = """ +There is no tarball provided; it needs to be created through an svn checkout: + 1. svn checkout https://svn.oss.deltares.nl/repos/delft3d/trunk@%s + 2. tar -czvf %%(name)s-%%(version)s.tgz trunk +""" % _revision + +sources = [SOURCE_TGZ] +checksums = [ + None, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('libtool', '2.4.7'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('Ruby', '3.0.5'), + ('Autotools', '20220317'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), + ('METIS', '5.1.0'), + ('PETSc', '3.17.4'), + ('expat', '2.4.8'), +] + +parallel = 1 + +start_dir = 'src' + +preconfigopts = 'export FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I${CPATH//:/ -I}" && ' +preconfigopts += 'export FFLAGS="$FFLAGS -fallow-argument-mismatch -I${CPATH//:/ -I}" && ' +# syntax was made invalid in c++11 +preconfigopts += "sed -i 's/if (spec < 0)/if (spec == nullptr)/g' utils_lgpl/delftonline/src/delftonline/server.cpp && " +# avoid comparing logical with integer +preconfigopts += "sed -i 's/if (has_umean \/= 0)/if (has_umean .neqv. .false.)/g' " # noqa: W605 +preconfigopts += "engines_gpl/flow2d3d/packages/flow2d3d_io/src/input/restart_trim_flow.f90 && " +preconfigopts += "sed -i -e 's/-recursive/-frecursive/g' -e 's/-traceback/-fbacktrace/g' configure.ac && " +preconfigopts += './autogen.sh && ' +preconfigopts += 'cd third_party_open/kdtree2 && ./autogen.sh && cd - && ' +configopts = ' --with-netcdf' +configopts += ' --with-mpi --with-metis --with-petsc' + +# remove spurious double -l flags causing build failure +prebuildopts = "sed -i.backup 's/-l -l//g' libtool config.lt config.status && " + +install_cmd = 'make ds-install' + +sanity_check_paths = { + 'files': ['bin/d_hydro'], + 'dirs': ['lib', 'share'] +} + +sanity_check_commands = [ + 'd_hydro -? |grep Usage:', +] + +moduleclass = 'phys' From bbe29a59971dd4dd479e31d6696a279b789d5a6e Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 19 Feb 2024 14:57:34 +0100 Subject: [PATCH 0768/1193] Delete easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb Delete due to name change --- .../Delft3D-FLOW-4.04.01-foss-2022a.eb | 71 ------------------- 1 file changed, 71 deletions(-) delete mode 100644 easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb b/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb deleted file mode 100644 index 6b9b750f0273..000000000000 --- a/easybuild/easyconfigs/d/Delft3D-FLOW/Delft3D-FLOW-4.04.01-foss-2022a.eb +++ /dev/null @@ -1,71 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'Delft3D-FLOW' -# revision 142633 -version = '4.04.01' - -homepage = 'https://oss.deltares.nl/web/delft3d' -description = """ -Simulation of multi-dimensional hydrodynamic flows and transport phenomena, including -sediments. Delft3D-FLOW is part of Delft3D 4. -""" - -toolchain = {'name': 'foss', 'version': '2022a'} -toolchainopts = {'usempi': True} - -# There is no tarball provided, only SVN checkout through: -# svn checkout https://svn.oss.deltares.nl/repos/delft3d/trunk@142633 -# make tarball: tar -czvf Delft3D-FLOW-4.04.01.tgz trunk - -sources = [SOURCE_TGZ] -checksums = [ - None, -] - -builddependencies = [ - ('CMake', '3.24.3'), - ('libtool', '2.4.7'), - ('Bison', '3.8.2'), - ('flex', '2.6.4'), - ('Ruby', '3.0.5'), -] - -dependencies = [ - ('netCDF-Fortran', '4.6.0'), - ('METIS', '5.1.0'), - ('PETSc', '3.17.4'), -] - -parallel = 1 - -start_dir = 'src' - -preconfigopts = 'export FCFLAGS="$FCFLAGS -fallow-argument-mismatch -I${CPATH//:/ -I}" && ' -preconfigopts += 'export FFLAGS="$FFLAGS -fallow-argument-mismatch -I${CPATH//:/ -I}" && ' -# syntax was made invalid in c++11 -preconfigopts += "sed -i 's/if (spec < 0)/if (spec == nullptr)/g' utils_lgpl/delftonline/src/delftonline/server.cpp && " -# avoid comparing logical with integer -preconfigopts += "sed -i 's/if (has_umean \/= 0)/if (has_umean .neqv. .false.)/g' " # noqa: W605 -preconfigopts += "engines_gpl/flow2d3d/packages/flow2d3d_io/src/input/restart_trim_flow.f90 && " -preconfigopts += "sed -i -e 's/-recursive/-frecursive/g' -e 's/-traceback/-fbacktrace/g' configure.ac && " -preconfigopts += './autogen.sh && ' -preconfigopts += 'cd third_party_open/kdtree2 && ./autogen.sh && cd - && ' -configopts = ' --with-netcdf' -configopts += ' --with-mpi --with-metis --with-petsc' - -# remove spurious double -l flags causing build failure -prebuildopts = "sed -i.backup 's/-l -l//g' libtool config.lt config.status && " -buildopts = 'ds-install' - -skipsteps = ['install'] - -sanity_check_paths = { - 'files': ['bin/d_hydro'], - 'dirs': ['lib', 'share'] -} - -sanity_check_commands = [ - 'd_hydro -? |grep Usage:', -] - -moduleclass = 'phys' From b14624230ea44573320327d7a662789f7aa4b849 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 19 Feb 2024 14:02:15 +0000 Subject: [PATCH 0769/1193] linting --- .../easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb index d9e7e2656d8f..9648e3489632 100644 --- a/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/datalad/datalad-0.19.5-GCCcore-12.3.0.eb @@ -14,7 +14,7 @@ toolchainopts = {'pic': True} builddependencies = [ ('binutils', '2.40'), ('hatchling', '1.18.0'), - ('poetry','1.5.1') + ('poetry', '1.5.1') ] dependencies = [ From cb52fa970f67d610732dd349e963ffcaf1df731b Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 19 Feb 2024 15:13:08 +0100 Subject: [PATCH 0770/1193] Update Delft3D-4.04.01-foss-2022a-FLOW.eb Remove extra space --- .../easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb index c38a27007e7a..4ded942d662d 100644 --- a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb +++ b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb @@ -18,7 +18,7 @@ download_instructions = """ There is no tarball provided; it needs to be created through an svn checkout: 1. svn checkout https://svn.oss.deltares.nl/repos/delft3d/trunk@%s 2. tar -czvf %%(name)s-%%(version)s.tgz trunk -""" % _revision +""" % _revision sources = [SOURCE_TGZ] checksums = [ From f5ac50704d05bb27d1914cfea8300b6ac195457c Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 19 Feb 2024 15:54:00 +0100 Subject: [PATCH 0771/1193] adding easyconfigs: RNA-Bloom-2.0.1-GCC-12.3.0.eb, Racon-1.5.0-GCCcore-12.3.0.eb, ntCard-1.2.2-GCC-12.3.0.eb --- .../n/ntCard/ntCard-1.2.2-GCC-12.3.0.eb | 32 +++++++++++++++++++ .../r/RNA-Bloom/RNA-Bloom-2.0.1-GCC-12.3.0.eb | 31 ++++++++++++++++++ .../r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb | 29 +++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/n/ntCard/ntCard-1.2.2-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-2.0.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/n/ntCard/ntCard-1.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/n/ntCard/ntCard-1.2.2-GCC-12.3.0.eb new file mode 100644 index 000000000000..23d5a50253e1 --- /dev/null +++ b/easybuild/easyconfigs/n/ntCard/ntCard-1.2.2-GCC-12.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'ntCard' +version = '1.2.2' + +homepage = 'https://www.bcgsc.ca/resources/software/ntcard' +description = "ntCard is a streaming algorithm for estimating the frequencies of k-mers in genomics datasets." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/bcgsc/%(name)s/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bace4e6da2eb8e59770d38957d1a916844071fb567696994c8605fd5f92b5eea'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +# ignore "type qualifiers ignored on cast result type" warning being treated as error due to -Werror +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -Wno-ignored-qualifiers" && ' + +sanity_check_paths = { + 'files': ['bin/ntcard', 'bin/nthll'], + 'dirs': ['share/doc/ntcard'], +} + +sanity_check_commands = [ + "ntcard --help", + "nthll --help", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-2.0.1-GCC-12.3.0.eb b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-2.0.1-GCC-12.3.0.eb new file mode 100644 index 000000000000..677091a05e1f --- /dev/null +++ b/easybuild/easyconfigs/r/RNA-Bloom/RNA-Bloom-2.0.1-GCC-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'RNA-Bloom' +version = '2.0.1' + +homepage = 'https://github.com/bcgsc/RNA-Bloom' +description = "RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/bcgsc/%(name)s/releases/download/v%(version)s'] +sources = ['rnabloom_v%(version)s.tar.gz'] +checksums = ['e06564e99db6847ea745c99cef7890980ed9b2c2a2e1d126e16df545c59d7626'] + +dependencies = [ + ('Java', '17', '', SYSTEM), + ('minimap2', '2.26'), + ('Racon', '1.5.0'), + ('ntCard', '1.2.2'), +] + +sanity_check_paths = { + 'files': ['LICENSE', 'README.md', 'rnabloom', 'RNA-Bloom.jar'], + 'dirs': [], +} + +sanity_check_commands = ["rnabloom --help"] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..59ee47d2f6bd --- /dev/null +++ b/easybuild/easyconfigs/r/Racon/Racon-1.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'Racon' +version = '1.5.0' + +homepage = 'https://github.com/lbcb-sci/racon' +description = """Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'lbcb-sci' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['41e362f71cc03b934f17d6e2c0d626e1b2997258261b14551586de006666424a'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), + ('git', '2.41.0', '-nodocs'), +] + +sanity_check_paths = { + 'files': ['bin/racon'], + 'dirs': [], +} + +sanity_check_commands = ['racon --help'] + +moduleclass = 'bio' From ec3fbd4c701eebe195116168633daa688967341a Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 19 Feb 2024 18:01:55 +0100 Subject: [PATCH 0772/1193] {astro}[foss-2023b] python-casacore 3.5.2 --- .../python-casacore-3.5.2-foss-2023b.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb diff --git a/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb b/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb new file mode 100644 index 000000000000..520982bb8851 --- /dev/null +++ b/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb @@ -0,0 +1,42 @@ +easyblock = "PythonBundle" + +name = 'python-casacore' +version = '3.5.2' + +homepage = 'https://casacore.github.io/python-casacore/#' +description = """Python-casacore is a set of Python bindings for casacore, +a c++ library used in radio astronomy. Python-casacore replaces the old pyrap.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('casacore', '3.5.0'), + ('Boost.Python', '1.83.0'), + ('SciPy-bundle', '2023.11'), + ('CFITSIO', '4.3.1'), +] + +exts_list = [ + ('setuptools', '69.1.0', { + 'checksums': ['850894c4195f09c4ed30dba56213bf7c3f21d86ed6bdaafb5df5972593bfc401'], + }), + (name, version, { + 'checksums': ['ad70c8e08893eec928b3e38c099bda8863f5aa9d099fd00694ad2b0d48eba08f'], + 'modulename': 'casacore' + }), +] + +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('python', "-c 'import casacore'"), +] + +moduleclass = 'astro' From cd63084b169d9214b954e5300021cc603fbf7ea0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 20 Feb 2024 10:37:07 +0100 Subject: [PATCH 0773/1193] adding easyconfigs: ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb, Seqmagick-0.8.6-foss-2023a.eb --- .../ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb | 37 +++++++++++++++++++ .../s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb | 35 ++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb diff --git a/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb b/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb new file mode 100644 index 000000000000..3e6ee38048fb --- /dev/null +++ b/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'ExpressBetaDiversity' +version = '1.0.10' + +homepage = 'https://github.com/donovan-h-parks/ExpressBetaDiversity' +description = """Taxon- and phylogenetic-based beta diversity measures.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +github_account = 'donovan-h-parks' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['c3ee0894ed0beea42f7668e531e53d01f4c19374d0dfd287cb400a68241c6c03'] + +prebuildopts = 'cd source && ' + +files_to_copy = [ + 'bin', + 'unit-tests', + (['scripts/*'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/ExpressBetaDiversity'], + 'dirs': ['unit-tests'], +} + +sanity_check_commands = [ + 'ExpressBetaDiversity --help', + 'convertToEBD.py --help', + # Unit tests need to be executed from the bin directory. + # See source/UnitTests.cpp:112: std::string seqCountFile = "../unit-tests/SimpleDataMatrix.env"; + 'cd bin && ExpressBetaDiversity -u', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb new file mode 100644 index 000000000000..1f46e236943f --- /dev/null +++ b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb @@ -0,0 +1,35 @@ +# EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Copyright:: Copyright 2016 University of Geneva Switzerland +# Authors:: Yann Sagon +# License:: MIT/GPL +# Update:: Pavel Tománek (INUITS) + +easyblock = "PythonPackage" + +name = 'Seqmagick' +version = '0.8.6' + +homepage = 'https://fhcrc.github.io/seqmagick/' +description = """We often have to convert between sequence formats and do + little tasks on them, and it's not worth writing scripts for that. Seqmagick + is a kickass little utility built in the spirit of imagemagick to expose the + file format conversion in Biopython in a convenient way. Instead of having a + big mess of scripts, there is one that takes arguments.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://files.pythonhosted.org/packages/source/s/seqmagick/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] + +dependencies = [ + ('Biopython', '1.83'), +] + +sanity_check_paths = { + 'files': ['bin/seqmagick'], + 'dirs': [] +} + +options = {'modulename': 'Bio'} + +moduleclass = 'bio' From 34c391247db9aca0143e0c8068347a50ae09abcf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 20 Feb 2024 11:43:12 +0100 Subject: [PATCH 0774/1193] patch based on https://github.com/open-mpi/ompi/pull/12344 --- .../OpenMPI-4.1.x_add_atomic_wmb.patch | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.x_add_atomic_wmb.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.x_add_atomic_wmb.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.x_add_atomic_wmb.patch new file mode 100644 index 000000000000..960e6100ed1e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.x_add_atomic_wmb.patch @@ -0,0 +1,35 @@ +From b6bfd8ef4ea52fb0257af8013b953f7942d06bae Mon Sep 17 00:00:00 2001 +From: Luke Robison +Date: Wed, 14 Feb 2024 21:14:29 +0000 +Subject: [PATCH] btl/smcuda: Add atomic_wmb() before sm_fifo_write + +This change fixes https://github.com/open-mpi/ompi/issues/12270 + +Testing on c7g instance type (arm64) confirms this change elminates +hangs and crashes that were previously observed in 1 in 30 runs of +IMB alltoall benchmark. Tested with over 300 runs and no failures. + +The write memory barrier prevents other CPUs from observing the fifo +get updated before they observe the updated contents of the header +itself. Without the barrier, uninitialized header contents caused +the crashes and invalid data. + +Signed-off-by: Luke Robison +(cherry picked from commit 71f378d28cb89dd80379dbad570849b297594cde) +--- + opal/mca/btl/smcuda/btl_smcuda_fifo.h | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/opal/mca/btl/smcuda/btl_smcuda_fifo.h b/opal/mca/btl/smcuda/btl_smcuda_fifo.h +index c4db00d10a8..f1c222d7ae0 100644 +--- a/opal/mca/btl/smcuda/btl_smcuda_fifo.h ++++ b/opal/mca/btl/smcuda/btl_smcuda_fifo.h +@@ -86,6 +86,8 @@ add_pending(struct mca_btl_base_endpoint_t *ep, void *data, bool resend) + #define MCA_BTL_SMCUDA_FIFO_WRITE(endpoint_peer, my_smp_rank, \ + peer_smp_rank, hdr, resend, retry_pending_sends, rc) \ + do { \ ++ /* memory barrier: ensure writes to the hdr have completed */ \ ++ opal_atomic_wmb(); \ + sm_fifo_t* fifo = &(mca_btl_smcuda_component.fifo[peer_smp_rank][FIFO_MAP(my_smp_rank)]); \ + \ + if ( retry_pending_sends ) { \ From 7d8310d53434b16b246b498938df7e8f77505524 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 20 Feb 2024 11:49:36 +0100 Subject: [PATCH 0775/1193] add OpenMPI-4.1.x_add_atomic_wmb.patch and update checksums accordingly --- .../o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb | 18 ++++++------ .../o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb | 24 ++++++++-------- .../o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb | 28 ++++++++++--------- .../OpenMPI-4.1.1-intel-compilers-2021.2.0.eb | 16 ++++++----- .../OpenMPI-4.1.1-intel-compilers-2021.4.0.eb | 21 +++++++------- .../o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb | 6 +++- .../o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb | 6 +++- .../o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb | 12 ++++---- .../o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb | 12 ++++---- .../OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb | 12 ++++---- .../o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb | 2 ++ .../o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb | 5 ++-- .../OpenMPI-4.1.5-intel-compilers-2023.1.0.eb | 5 ++-- .../o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb | 2 ++ 14 files changed, 99 insertions(+), 70 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb index b82c542c4248..ec897b5c4c14 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.0-GCC-10.2.0.eb @@ -13,16 +13,18 @@ patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a', # openmpi-4.1.0.tar.gz - # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch - 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', - # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch - 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', - '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch - # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch - 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', + {'openmpi-4.1.0.tar.gz': '228467c3dd15339d9b26cf26a291af3ee7c770699c5e8a1b3ad786f9ae78140a'}, + {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, + {'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch': + 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb'}, + {'OpenMPI-4.x_fix_pmix_discovery.patch': '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b'}, + {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb index 5314ed77d403..415e81332a2d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-10.3.0.eb @@ -17,19 +17,21 @@ patches = [ 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 - # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch - 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', - # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch - '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', - # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch - 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', - # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', - # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch - 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', + {'openmpi-4.1.1.tar.bz2': 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda'}, + {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, + {'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch': + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d'}, + {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb index 762189ad19da..3cafd8e33fe4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-GCC-11.2.0.eb @@ -16,21 +16,23 @@ patches = [ 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 - # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch - 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', - # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch - '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', - '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903', # OpenMPI-4.1.1_opal-pmix-package-rank.patch - '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch - # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch - 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', - # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', - # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch - 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', + {'openmpi-4.1.1.tar.bz2': 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda'}, + {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, + {'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch': + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d'}, + {'OpenMPI-4.1.1_opal-pmix-package-rank.patch': '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903'}, + {'OpenMPI-4.1.1_pmix3x-protection.patch': '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8'}, + {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb index 523bf0bb069a..0df727a62a39 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.2.0.eb @@ -15,15 +15,17 @@ patches = [ 'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch', 'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 - # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch - 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', - # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch - '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', - # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch - 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', + {'openmpi-4.1.1.tar.bz2': 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda'}, + {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, + {'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch': + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d'}, + {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb index 6e354371c1c8..55381169f039 100755 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb @@ -14,20 +14,21 @@ patches = [ 'OpenMPI-4.1.1_opal-pmix-package-rank.patch', 'OpenMPI-4.1.1_pmix3x-protection.patch', 'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda', # openmpi-4.1.1.tar.bz2 - # OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch - 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e', - # OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch - '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d', - '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903', # OpenMPI-4.1.1_opal-pmix-package-rank.patch - '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8', # OpenMPI-4.1.1_pmix3x-protection.patch - # OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch - 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea', + {'openmpi-4.1.1.tar.bz2': 'e24f7a778bd11a71ad0c14587a7f5b00e68a71aa5623e2157bafee3d44c07cda'}, + {'OpenMPI-4.1.1_fix-bufferoverflow-in-common_ofi.patch': + 'a189d834506f3d7c31eda6aa184598a3631ea24a94bc551d5ed1f053772ca49e'}, + {'OpenMPI-4.0.6_remove-pmix-check-in-pmi-switch.patch': + '8acee6c9b2b4bf12873a39b85a58ca669de78e90d26186e52f221bb4853abc4d'}, + {'OpenMPI-4.1.1_opal-pmix-package-rank.patch': '04353672cf7be031e5306c94068d7012d99e6cd94b69d93230797ffcd7f31903'}, + {'OpenMPI-4.1.1_pmix3x-protection.patch': '384ef9f1fa803b0d71dae2ec0748d0f20295992437532afedf21478bda164ff8'}, + {'OpenMPI-4.1.0-1-pml-ucx-datatype-memleak.patch': + 'a94a74b174ce783328abfd3656ff5196b89ef4c819fe4c8b8a0f1277123e76ea'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] - builddependencies = [ ('pkg-config', '0.29.2'), ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb index 5148de10aa74..d0d18bc3a0b7 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-10.2.0.eb @@ -8,7 +8,11 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'] +patches = ['OpenMPI-4.1.x_add_atomic_wmb.patch'] +checksums = [ + {'openmpi-4.1.2.tar.bz2': '9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, +] builddependencies = [ ('pkg-config', '0.29.2'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb index 65660f70e15a..eebd0204a240 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.2-GCC-11.2.0.eb @@ -8,7 +8,11 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_BZ2] -checksums = ['9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'] +patches = ['OpenMPI-4.1.x_add_atomic_wmb.patch'] +checksums = [ + {'openmpi-4.1.2.tar.bz2': '9b78c7cf7fc32131c5cf43dd2ab9740149d9d87cadb2e2189f02685749a6b527'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, +] builddependencies = [ ('pkgconf', '1.8.0'), diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb index 524393cf31b9..6471a45d999a 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-11.3.0.eb @@ -11,13 +11,15 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 - # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', - # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch - 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', + {'openmpi-4.1.4.tar.bz2': '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb index 09a6bc393d37..fbb50478eecd 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb @@ -11,13 +11,15 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 - # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', - # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch - 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', + {'openmpi-4.1.4.tar.bz2': '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb index 34c4551c73e2..9ef5b5d1bb40 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb @@ -11,13 +11,15 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ - '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d', # openmpi-4.1.4.tar.bz2 - # OpenMPI-4.1.1_build-with-internal-cuda-header.patch - '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83', - # OpenMPI-4.1.1_opal-datatype-cuda-performance.patch - 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e', + {'openmpi-4.1.4.tar.bz2': '92912e175fd1234368c8730c03f4996fe5942e7479bb1d10059405e7f2b3930d'}, + {'OpenMPI-4.1.1_build-with-internal-cuda-header.patch': + '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, + {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': + 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb index 634b2a2f67bd..3ff4b9d8e66d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.2.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, @@ -18,6 +19,7 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb index 6279c1af7bd2..797e9c0f0deb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-GCC-12.3.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', 'OpenMPI-4.1.5_fix-pmix3x.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, @@ -19,8 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, - {'OpenMPI-4.1.5_fix-pmix3x.patch': - '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, + {'OpenMPI-4.1.5_fix-pmix3x.patch': '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb index 4d79ac0d55a0..59780f6df6e3 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.5-intel-compilers-2023.1.0.eb @@ -12,6 +12,7 @@ patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', 'OpenMPI-4.1.5_fix-pmix3x.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ {'openmpi-4.1.5.tar.bz2': 'a640986bc257389dd379886fdae6264c8cfa56bc98b71ce3ae3dfbd8ce61dbe3'}, @@ -19,8 +20,8 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, - {'OpenMPI-4.1.5_fix-pmix3x.patch': - '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, + {'OpenMPI-4.1.5_fix-pmix3x.patch': '46edac3dbf32f2a611d45e8a3c8edd3ae2f430eec16a1373b510315272115c40'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb index 3e4baa877358..831148339ac4 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.6-GCC-13.2.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = [ 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', 'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch', + 'OpenMPI-4.1.x_add_atomic_wmb.patch', ] checksums = [ {'openmpi-4.1.6.tar.bz2': 'f740994485516deb63b5311af122c265179f5328a0d857a567b85db00b11e415'}, @@ -18,6 +19,7 @@ checksums = [ '63eac52736bdf7644c480362440a7f1f0ae7c7cae47b7565f5635c41793f8c83'}, {'OpenMPI-4.1.1_opal-datatype-cuda-performance.patch': 'b767c7166cf0b32906132d58de5439c735193c9fd09ec3c5c11db8d5fa68750e'}, + {'OpenMPI-4.1.x_add_atomic_wmb.patch': '9494bbc546d661ba5189e44b4c84a7f8df30a87cdb9d96ce2e73a7c8fecba172'}, ] builddependencies = [ From 1ee886f9bc462edbbf56626449a3943f319a2d64 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 20 Feb 2024 12:17:22 +0100 Subject: [PATCH 0776/1193] remove execute permissions on file --- .../o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.1-intel-compilers-2021.4.0.eb old mode 100755 new mode 100644 From ec225aadc18d246794840d025a98634f11550418 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 20 Feb 2024 14:02:45 +0100 Subject: [PATCH 0777/1193] delete whitespace --- easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb index 1f46e236943f..8856e3c41205 100644 --- a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb @@ -22,7 +22,7 @@ source_urls = ['https://files.pythonhosted.org/packages/source/s/seqmagick/'] sources = ['%(namelower)s-%(version)s.tar.gz'] dependencies = [ - ('Biopython', '1.83'), + ('Biopython', '1.83'), ] sanity_check_paths = { From 68d46560f1fc71a3c3812f39167b31ad912ae865 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 20 Feb 2024 14:32:34 +0100 Subject: [PATCH 0778/1193] Change author arpack + use variable for PGPlot source --- .../easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb | 3 +-- easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb index 04b73ebc183e..10d825ca22fa 100644 --- a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.0-foss-2023b.eb @@ -1,6 +1,5 @@ -# # # Author: Robert Mijakovic -# # + easyblock = 'ConfigureMake' name = 'arpack-ng' diff --git a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb index 526fb7c27d59..fef204118222 100644 --- a/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/PGPLOT/PGPLOT-5.2.2-GCCcore-13.2.0.eb @@ -13,7 +13,7 @@ can be directed to the appropriate device at run time.""" toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['ftp://ftp.astro.caltech.edu/pub/%(namelower)s/'] -sources = ['%(namelower)s522.tar.gz'] +sources = ['%%(namelower)s%s.tar.gz' % version.replace('.', '')] patches = ['%(name)s-%(version_major_minor)s.2_gfortran-deps-fixes.patch'] checksums = [ {'pgplot522.tar.gz': 'a5799ff719a510d84d26df4ae7409ae61fe66477e3f1e8820422a9a4727a5be4'}, From 9c8529ed16c580412151b4ac89d8be2a735450a2 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 20 Feb 2024 14:57:16 +0100 Subject: [PATCH 0779/1193] Add comment to explain git_config usage --- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 2 ++ easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb | 2 ++ easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index 4bb7e93399d6..72d2b54bee75 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -11,6 +11,8 @@ toolchain = {'name': 'foss', 'version': '2023b'} sources = [ { 'filename': '%(name)s-v%(version)s.tar.gz', + # Repo uses git submodules, which are not included in the release tarballs. + # Thus, we let EasyBuild download directly from the git repository. 'git_config': { 'url': 'https://git.astron.nl/RD', 'repo_name': '%(name)s', diff --git a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb index 6192a7ace663..bec1bf004e74 100644 --- a/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb +++ b/easybuild/easyconfigs/e/EveryBeam/EveryBeam-0.5.2-foss-2023b.eb @@ -12,6 +12,8 @@ toolchain = {'name': 'foss', 'version': '2023b'} sources = [ { 'filename': '%(name)s-v%(version)s.tar.gz', + # Repo uses git submodules, which are not included in the release tarballs. + # Thus, we let EasyBuild download directly from the git repository. 'git_config': { 'url': 'https://git.astron.nl/RD', 'repo_name': '%(name)s', diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb index c073781571a4..910c9ac70963 100644 --- a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb @@ -18,6 +18,8 @@ toolchain = {'name': 'foss', 'version': '2023b'} sources = [ { 'filename': '%(name)s-v%(version)s.tar.gz', + # Repo uses git submodules, which are not included in the release tarballs. + # Thus, we let EasyBuild download directly from the git repository. 'git_config': { 'url': 'https://gitlab.com/astron-idg', 'repo_name': '%(name)s', From 9254d3829b2cfeaa567b3be2b1f503ee5281e999 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 20 Feb 2024 15:39:10 +0000 Subject: [PATCH 0780/1193] use external EMSF instead of bundled binaries --- .../Delft3D-4.04.01-foss-2022a-FLOW.eb | 10 ++- .../Delft3D-4.04.01_use-external-esmf.patch | 68 +++++++++++++++++++ 2 files changed, 77 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch diff --git a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb index 4ded942d662d..ff41620b4776 100644 --- a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb +++ b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb @@ -8,7 +8,7 @@ versionsuffix = '-FLOW' homepage = 'https://oss.deltares.nl/web/delft3d' description = """ Simulation of multi-dimensional hydrodynamic flows and transport phenomena, including -sediments. Delft3D-FLOW is part of Delft3D 4. +sediments. Delft3D-FLOW is part of Delft3D 4. """ toolchain = {'name': 'foss', 'version': '2022a'} @@ -21,8 +21,12 @@ There is no tarball provided; it needs to be created through an svn checkout: """ % _revision sources = [SOURCE_TGZ] +patches = ['Delft3D-4.04.01_use-external-esmf.patch'] checksums = [ + # Delft3D-4.04.01.tgz None, + # Delft3D-4.04.01_use-external-esmf.patch' + '86f127cf3193c6fc9256491d917051db91e695718631d1b221b111499e0f432b', ] builddependencies = [ @@ -40,6 +44,7 @@ dependencies = [ ('METIS', '5.1.0'), ('PETSc', '3.17.4'), ('expat', '2.4.8'), + ('ESMF', '8.3.0'), ] parallel = 1 @@ -54,8 +59,11 @@ preconfigopts += "sed -i 's/if (spec < 0)/if (spec == nullptr)/g' utils_lgpl/del preconfigopts += "sed -i 's/if (has_umean \/= 0)/if (has_umean .neqv. .false.)/g' " # noqa: W605 preconfigopts += "engines_gpl/flow2d3d/packages/flow2d3d_io/src/input/restart_trim_flow.f90 && " preconfigopts += "sed -i -e 's/-recursive/-frecursive/g' -e 's/-traceback/-fbacktrace/g' configure.ac && " +# remove esmf precompiled binaries +preconfigopts += "rm -r third_party_open/esmf && libtoolize && " preconfigopts += './autogen.sh && ' preconfigopts += 'cd third_party_open/kdtree2 && ./autogen.sh && cd - && ' + configopts = ' --with-netcdf' configopts += ' --with-mpi --with-metis --with-petsc' diff --git a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch new file mode 100644 index 000000000000..3d5b00b2014d --- /dev/null +++ b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch @@ -0,0 +1,68 @@ +Author: Jasper Grimm +Avoid installing the bundled ESMF, since this is compiled for CentOS 7 (and also fails +rpath sanity checks) +diff -Nru trunk.orig/src/configure.ac trunk/src/configure.ac +--- trunk.orig/src/configure.ac 2024-02-20 14:35:26.821778739 +0000 ++++ trunk/src/configure.ac 2024-02-20 14:43:47.108090829 +0000 +@@ -607,10 +607,6 @@ + plugins_lgpl/plugin_delftflow_traform/src/Makefile + scripts_lgpl/linux/Makefile + scripts_lgpl/Makefile +-third_party_open/esmf/lnx64/bin/Makefile +-third_party_open/esmf/lnx64/Makefile +-third_party_open/esmf/lnx64/scripts/Makefile +-third_party_open/esmf/Makefile + third_party_open/Makefile + third_party_open/md5/Makefile + third_party_open/md5/md5digest/Makefile +diff -Nru trunk.orig/src/third_party_open/Makefile.am trunk/src/third_party_open/Makefile.am +--- trunk.orig/src/third_party_open/Makefile.am 2024-02-20 14:35:27.045777956 +0000 ++++ trunk/src/third_party_open/Makefile.am 2024-02-20 14:43:31.552143270 +0000 +@@ -19,7 +19,6 @@ + endif + + SUBDIRS = \ +- esmf \ + triangle \ + version_number \ + libsigwatch \ +@@ -28,39 +27,3 @@ + kdtree2 \ + md5 \ + $(MAYBE_FORTRANGIS) +-nobase_dist_pkgdata_DATA = \ +- esmf/lnx64/bin/libcilkrts.so.5 \ +- esmf/lnx64/bin/libdl.so.2 \ +- esmf/lnx64/bin/libesmf.so \ +- esmf/lnx64/bin/libgcc_s.so.1 \ +- esmf/lnx64/bin/libhdf5.so.8 \ +- esmf/lnx64/bin/libhdf5_hl.so.8 \ +- esmf/lnx64/bin/libifcore.so.5 \ +- esmf/lnx64/bin/libifport.so.5 \ +- esmf/lnx64/bin/libimf.so \ +- esmf/lnx64/bin/libintlc.so.5 \ +- esmf/lnx64/bin/libiomp5.so \ +- esmf/lnx64/bin/libirc.so \ +- esmf/lnx64/bin/libirng.so \ +- esmf/lnx64/bin/libm.so.6 \ +- esmf/lnx64/bin/libnetcdf.so.7 \ +- esmf/lnx64/bin/libnetcdff.so.6 \ +- esmf/lnx64/bin/librt.so.1 \ +- esmf/lnx64/bin/libsvml.so \ +- esmf/lnx64/bin/libz.so.1 \ +- esmf/lnx64/bin_COS7/libcilkrts.so.5 \ +- esmf/lnx64/bin_COS7/libesmf.so \ +- esmf/lnx64/bin_COS7/libhdf5.so.200 \ +- esmf/lnx64/bin_COS7/libhdf5_hl.so.200 \ +- esmf/lnx64/bin_COS7/libifcoremt.so.5 \ +- esmf/lnx64/bin_COS7/libifport.so.5 \ +- esmf/lnx64/bin_COS7/libimf.so \ +- esmf/lnx64/bin_COS7/libintlc.so.5 \ +- esmf/lnx64/bin_COS7/libiomp5.so \ +- esmf/lnx64/bin_COS7/libirc.so \ +- esmf/lnx64/bin_COS7/libirng.so \ +- esmf/lnx64/bin_COS7/libnetcdf.so.7 \ +- esmf/lnx64/bin_COS7/libnetcdf.so.18 \ +- esmf/lnx64/bin_COS7/libnetcdff.so.6 \ +- esmf/lnx64/bin_COS7/libsvml.so +- From 068202c64f7d392a92df866da7d8f16d63fef2ab Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 20 Feb 2024 17:04:54 +0100 Subject: [PATCH 0781/1193] adding easyconfigs: fineRADstructure-20210514-foss-2023a.eb --- .../fineRADstructure-20210514-foss-2023a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-foss-2023a.eb diff --git a/easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-foss-2023a.eb b/easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-foss-2023a.eb new file mode 100644 index 000000000000..8d85a2d78ba9 --- /dev/null +++ b/easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-foss-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'fineRADstructure' +version = '20210514' + +homepage = 'http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html' +description = "A package for population structure inference from RAD-seq data" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/millanek/fineRADstructure/archive/'] +sources = [{'download_filename': '5896b9e.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['4f22232bb79dd7b589a1c8a389d7cca23372ea52f55205392ce9ce8f80aea5b2'] + +dependencies = [ + ('GSL', '2.7'), +] + +sanity_check_paths = { + 'files': ['bin/finestructure', 'bin/RADpainter'], + 'dirs': [], +} + +moduleclass = 'bio' From 8745bee1b1b74a9eadc1283c35ba1dcd593a5932 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 20 Feb 2024 18:38:48 +0100 Subject: [PATCH 0782/1193] add fix_python_shebang_for --- .../ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb b/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb index 3e6ee38048fb..72a06e419789 100644 --- a/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb @@ -13,6 +13,10 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['c3ee0894ed0beea42f7668e531e53d01f4c19374d0dfd287cb400a68241c6c03'] +dependencies = [ + ('Python', '3.11.3'), +] + prebuildopts = 'cd source && ' files_to_copy = [ @@ -34,4 +38,6 @@ sanity_check_commands = [ 'cd bin && ExpressBetaDiversity -u', ] +fix_python_shebang_for = ['source/dep.py', 'scripts/*'] + moduleclass = 'bio' From 57d2df41b252fca979c6ebfcaf2daa409504ac41 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 20 Feb 2024 18:57:58 +0100 Subject: [PATCH 0783/1193] add checksum --- easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb index 8856e3c41205..4b3a83bc2788 100644 --- a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb @@ -20,6 +20,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://files.pythonhosted.org/packages/source/s/seqmagick/'] sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['7f09ef40836b12a2d4c842b179633f1087352855b6ff8fcd045d56003fee622a'] dependencies = [ ('Biopython', '1.83'), From 2968de8b014b7f17af1c38eaec10bca533d6b9c8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Tue, 20 Feb 2024 18:51:06 +0000 Subject: [PATCH 0784/1193] Update easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb --- .../l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb index 7d1441d0d173..405e0568f992 100644 --- a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-13.2.0.eb @@ -17,7 +17,6 @@ builddependencies = [ ('CMake', '3.27.6'), ] - sanity_check_paths = { 'files': ['lib/%s.%s' % (name, SHLIB_EXT)], 'dirs': ['include/spatialindex'], From 1fce136182c075820c1a1fb0acd372899b271d23 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 21 Feb 2024 10:27:57 +0100 Subject: [PATCH 0785/1193] fix MS_RDONLY error in OpenMPI 4.0.3 --- .../o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb | 2 + .../o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb | 2 + .../OpenMPI-4.0.3-iccifort-2020.1.217.eb | 2 + .../OpenMPI-4.0.3-iccifortcuda-2020a.eb | 2 + .../OpenMPI-4.0.5_fix-MS_RDONLY-error.patch | 47 +++++++++++++++++++ 5 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb index dc5286d33624..c6e650ef6e6e 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-GCC-9.3.0.eb @@ -10,12 +10,14 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', ] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb index a9103a8a934b..6eb936f50adc 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-gcccuda-2020a.eb @@ -10,12 +10,14 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', ] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb index 75c1dbb91952..435d229f4f09 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifort-2020.1.217.eb @@ -10,12 +10,14 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', ] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb index 564f903d56a3..8acb43b7ce6d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.3-iccifortcuda-2020a.eb @@ -10,12 +10,14 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', 'OpenMPI-4.x_fix_pmix_discovery.patch', ] checksums = [ '6346bf976001ad274c7e018d6cc35c92bbb9426d8f7754fac00a17ea5ac8eebc', # openmpi-4.0.3.tar.gz # OpenMPI-4.0.1_remove-pmix-check-in-pmi-switch.patch 'a5737061eb9006e862f30019776adf092d800f681272be7f1575e74b4bfa20fb', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, '547641fff884c917237d158b0b13bdf387977cf0dddfd7e49e78d5f759a6a31b', # OpenMPI-4.x_fix_pmix_discovery.patch ] diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch new file mode 100644 index 000000000000..89df2e3ff365 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.5_fix-MS_RDONLY-error.patch @@ -0,0 +1,47 @@ +From 5b525b251c3433bf50b44b05c84937a39fb10074 Mon Sep 17 00:00:00 2001 +From: Bert Wesarg +Date: Tue, 23 Feb 2021 08:21:22 +0100 +Subject: [PATCH] fs/lustre: Remove unneeded includes + +The functionality was migrated to `fs/base/fs_base_get_parent_dir.c` long +ago, but the includes stayed. Though in lustre 2.14 `lustre_user.h` +moved the inclusion of `linux/fs.h` outside the `__KERNEL__` guard. This +triggered now Debian bug #898743 [1], which states that including +`sys/mount.h` after `linux/fs.h` breaks compilation. Thus the include +removal also avoids this breakage. + +Closes #8508. + +[1] https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=898743 + +Signed-off-by: Bert Wesarg +--- + ompi/mca/fs/lustre/fs_lustre.c | 15 --------------- + 1 file changed, 15 deletions(-) + +diff --git a/ompi/mca/fs/lustre/fs_lustre.c b/ompi/mca/fs/lustre/fs_lustre.c +index df2c7c3ac7c..20fdfc76991 100644 +--- a/ompi/mca/fs/lustre/fs_lustre.c ++++ b/ompi/mca/fs/lustre/fs_lustre.c +@@ -32,21 +32,6 @@ + #include "ompi/mca/fs/base/base.h" + #include "ompi/mca/fs/lustre/fs_lustre.h" + +-#ifdef HAVE_SYS_STATFS_H +-#include /* or */ +-#endif +-#ifdef HAVE_SYS_PARAM_H +-#include +-#endif +-#ifdef HAVE_SYS_MOUNT_H +-#include +-#endif +-#ifdef HAVE_SYS_STAT_H +-#include +-#endif +- +-#include +- + /* + * ******************************************************************* + * ************************ actions structure ************************ From 6d5d1f318a2dccfaafa532cbfb6dea2cce08043d Mon Sep 17 00:00:00 2001 From: Jasper Grimm <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 21 Feb 2024 10:42:15 +0000 Subject: [PATCH 0786/1193] increase max_failed_tests to 50 --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index a1419a04b134..cb05d00c73ea 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -207,7 +207,7 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # Especially test_quantization has a few corner cases that are triggered by the random input values, # those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 # So allow a low number of tests to fail as the tests "usually" succeed -max_failed_tests = 4 +max_failed_tests = 50 # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/109493 is accepted, since it is then checked as part of the PyTorch test suite From e73c79fb3cc4813ae44bcba17eef3a8cc2b44080 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 21 Feb 2024 11:43:48 +0100 Subject: [PATCH 0787/1193] adding easyconfigs: Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb --- ...b-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..52c596093f0d --- /dev/null +++ b/easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'Lab-Streaming-Layer' +version = '1.16.2' + +homepage = 'https://labstreaminglayer.readthedocs.io' +description = """The lab streaming layer (LSL) is a system for the unified collection of +measurement time series in research experiments that handles both the +networking, time-synchronization, (near-) real-time access as well as +optionally the centralized collection, viewing and disk recording of the data.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/sccn/liblsl/archive/refs/tags'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'liblsl-%(version)s.tar.gz'}] +checksums = ['923aa4c81c0fef651c325e3c27aa5b96771540ca2a0933d1b327db27c6dac839'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('git', '2.41.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +configopts = "-DCMAKE_INSTALL_LIBDIR=lib" + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('pylsl', version, { + 'source_urls': ['https://github.com/labstreaminglayer/pylsl/archive/refs/tags'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['1cef9c6c4876027ce18a4022ba4fdf023d037f6e76e7422ef24536d19d912c08'], + }), +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/lslver', 'lib/liblsl.%s' % SHLIB_EXT, 'include/lsl_c.h', 'include/lsl_cpp.h'], + 'dirs': ['include/lsl', 'lib/cmake', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "lslver", + "python -c 'import pylsl'", +] + +moduleclass = 'data' From d09970ab04065b341211c3283403c1b395a189e5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Feb 2024 12:29:24 +0100 Subject: [PATCH 0788/1193] uupdate Seqmagick --- .../easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb index 4b3a83bc2788..f948f1463106 100644 --- a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb @@ -31,6 +31,10 @@ sanity_check_paths = { 'dirs': [] } +use_pip = True +download_dep_fail = True +sanity_pip_check = True + options = {'modulename': 'Bio'} moduleclass = 'bio' From 44a1b7c0bd4a028792230cf7d3ee5e75e27b953d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 21 Feb 2024 12:41:02 +0100 Subject: [PATCH 0789/1193] add binutils as build dependency of Lab-Streaming-Layer v1.16.2 --- .../Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb index 52c596093f0d..5d9664dba625 100644 --- a/easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/Lab-Streaming-Layer/Lab-Streaming-Layer-1.16.2-GCCcore-12.3.0.eb @@ -16,6 +16,7 @@ sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': 'liblsl-%(ve checksums = ['923aa4c81c0fef651c325e3c27aa5b96771540ca2a0933d1b327db27c6dac839'] builddependencies = [ + ('binutils', '2.40'), ('CMake', '3.26.3'), ('git', '2.41.0', '-nodocs'), ] From 34cd2fb4c759a125c20ff73eed73a10c4cffa09e Mon Sep 17 00:00:00 2001 From: Victor Lopez Date: Wed, 21 Feb 2024 12:55:55 +0100 Subject: [PATCH 0790/1193] Add dlb v3.4 --- .../easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb | 35 +++++++++++++++++++ .../easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb b/easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb new file mode 100644 index 000000000000..2703715c3eb6 --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb @@ -0,0 +1,35 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.4' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'gompi', 'version': '2023b'} +builddependencies = [('Python', '3.11.5', '', ('GCCcore', '13.2.0'))] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['6091d032c11a094a3ce0bec11c0a164783fdff83cb4ec870c9d8e192410c353a'] + +configopts = '--with-mpi' + +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb b/easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb new file mode 100644 index 000000000000..1ce3cceafd8f --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb @@ -0,0 +1,35 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.4' + +description = """ +DLB is a dynamic library designed to speed up HPC hybrid applications (i.e., +two levels of parallelism) by improving the load balance of the outer level of +parallelism (e.g., MPI) by dynamically redistributing the computational +resources at the inner level of parallelism (e.g., OpenMP). at run time. +""" +homepage = 'https://pm.bsc.es/dlb/' +docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] + +toolchain = {'name': 'iimpi', 'version': '2023b'} +builddependencies = [('Python', '3.11.5', '', ('GCCcore', '13.2.0'))] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['6091d032c11a094a3ce0bec11c0a164783fdff83cb4ec870c9d8e192410c353a'] + +configopts = '--with-mpi' + +sanity_check_paths = { + 'files': [ + 'bin/dlb', + 'lib/libdlb.a', 'lib/libdlb.%s' % SHLIB_EXT, + 'lib64/libdlb.%s' % SHLIB_EXT + ], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 10da9d42e967e4dee31f93a4bcbf59659601130d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Feb 2024 13:02:38 +0100 Subject: [PATCH 0791/1193] add plyranges to R-bundle-Bioconductor for zUMIs --- ...le-Bioconductor-3.18-foss-2023a-R-4.3.2.eb | 3 ++ .../z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb | 49 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb index 607e5edebb44..e07ffd64a9e8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.18-foss-2023a-R-4.3.2.eb @@ -1345,6 +1345,9 @@ exts_list = [ ('escape', '1.12.0', { 'checksums': ['d69dda267e9346b1d3f10274fb0985409d23060abba609d4e8859eae92b1b12e'], }), + ('plyranges', '1.22.0', { + 'checksums': ['fcdcad1082fadd1a365dd2d2cc7d955601b737ecd4a567d888d2b445756297fc'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..1f6fb22add69 --- /dev/null +++ b/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb @@ -0,0 +1,49 @@ +easyblock = 'Tarball' + +name = 'zUMIs' +version = '2.9.7' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/sdparekh/zUMIs' +description = """A fast and flexible pipeline to process RNA sequencing data with UMIs.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'sdparekh' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['11eb3d99804a67e47b36b69accd0298c93c76b642d801292a618bc7888d34962'] + +dependencies = [ + ('Python', '3.11.3'), + ('pigz', '2.8'), + ('Pysam', '0.22.0'), + ('SAMtools', '1.18'), + ('STAR', '2.7.11a'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +postinstallcmds = [ + "sed -i '33 s/${zumis}/zumis/' %(installdir)s/zUMIs.sh", + "sed -i '43,46d' %(installdir)s/zUMIs.sh", + "sed -i '7,10d' %(installdir)s/zUMIs.sh", + "mkdir -p %(installdir)s/bin", + "ln -s %(installdir)s/zUMIs.sh %(installdir)s/bin/zumis", +] + +modloadmsg = """ +To run zUMIs do not use '$ zUMIs.sh ...' command but only '$ zumis ...' instead. +Do NOT run with conda (do not use flag '-c'). +""" + +modextrapaths = {'R_LIBS_SITE': ''} + +sanity_check_paths = { + 'files': ["bin/zumis"], + 'dirs': [], +} + +sanity_check_commands = ['zumis -h 2>&1 | grep "USAGE"'] + +moduleclass = 'tools' From e4e42189eb69b22132a3716305970179e0b741f9 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Wed, 21 Feb 2024 13:33:21 +0000 Subject: [PATCH 0792/1193] install (and patch) Delft3D ESMF script --- .../Delft3D-4.04.01-foss-2022a-FLOW.eb | 8 +++- .../Delft3D-4.04.01_use-external-esmf.patch | 42 +++++++++++++++++++ 2 files changed, 48 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb index ff41620b4776..14de28ce6ecb 100644 --- a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb +++ b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb @@ -26,7 +26,7 @@ checksums = [ # Delft3D-4.04.01.tgz None, # Delft3D-4.04.01_use-external-esmf.patch' - '86f127cf3193c6fc9256491d917051db91e695718631d1b221b111499e0f432b', + '225d76fb3eea22e203f1a9f371b4fd07d75a8478de35a7428c1a1f85b344323c', ] builddependencies = [ @@ -59,6 +59,8 @@ preconfigopts += "sed -i 's/if (spec < 0)/if (spec == nullptr)/g' utils_lgpl/del preconfigopts += "sed -i 's/if (has_umean \/= 0)/if (has_umean .neqv. .false.)/g' " # noqa: W605 preconfigopts += "engines_gpl/flow2d3d/packages/flow2d3d_io/src/input/restart_trim_flow.f90 && " preconfigopts += "sed -i -e 's/-recursive/-frecursive/g' -e 's/-traceback/-fbacktrace/g' configure.ac && " +# copy ESMF_RegridWeightGen_in_Delft3D-WAVE.sh script +preconfigopts += "cp third_party_open/esmf/lnx64/scripts/ESMF_RegridWeightGen_in_Delft3D-WAVE.sh . && " # remove esmf precompiled binaries preconfigopts += "rm -r third_party_open/esmf && libtoolize && " preconfigopts += './autogen.sh && ' @@ -72,8 +74,10 @@ prebuildopts = "sed -i.backup 's/-l -l//g' libtool config.lt config.status && " install_cmd = 'make ds-install' +postinstallcmds = ["cp %(start_dir)s/ESMF_RegridWeightGen_in_Delft3D-WAVE.sh %(installdir)s/bin/"] + sanity_check_paths = { - 'files': ['bin/d_hydro'], + 'files': ['bin/d_hydro', 'bin/ESMF_RegridWeightGen_in_Delft3D-WAVE.sh'], 'dirs': ['lib', 'share'] } diff --git a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch index 3d5b00b2014d..c446d24a1698 100644 --- a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch +++ b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01_use-external-esmf.patch @@ -15,6 +15,48 @@ diff -Nru trunk.orig/src/configure.ac trunk/src/configure.ac third_party_open/Makefile third_party_open/md5/Makefile third_party_open/md5/md5digest/Makefile +diff -Nru trunk.orig/src/third_party_open/esmf/lnx64/scripts/ESMF_RegridWeightGen_in_Delft3D-WAVE.sh trunk/src/third_party_open/esmf/lnx64/scripts/ESMF_RegridWeightGen_in_Delft3D-WAVE.sh +--- trunk.orig/src/third_party_open/esmf/lnx64/scripts/ESMF_RegridWeightGen_in_Delft3D-WAVE.sh 2024-02-20 14:35:27.449776542 +0000 ++++ trunk/src/third_party_open/esmf/lnx64/scripts/ESMF_RegridWeightGen_in_Delft3D-WAVE.sh 2024-02-21 11:53:47.816278292 +0000 +@@ -52,24 +52,24 @@ + scriptdirname=`readlink \-f \$0` + scriptdir=`dirname $scriptdirname` + D3D_HOME=$scriptdir/.. +-regridexec=$D3D_HOME/bin/ESMF_RegridWeightGen ++regridexec=$(which ESMF_RegridWeightGen) + # ESMF_regrid is build with old compilers etc. + # share/esmf optionally contains some library-versions especially for running this version of ESMF_regrid, + # both for RedHat 6.* and 7.* + +-if [ -f "/etc/redhat-release" ]; then +- grepOS=`cat /etc/redhat-release | grep -i "release 6"` +- if [ "$grepOS" != "" ]; then +- echo "RH 6: Using RH 6 libraries" >>esmf_sh.log +- export LD_LIBRARY_PATH=$D3D_HOME/share/delft3d/esmf/lnx64/bin:$D3D_HOME/lib:$LD_LIBRARY_PATH +- else +- echo "using RH 7 libraries" >>esmf_sh.log +- export LD_LIBRARY_PATH=$D3D_HOME/share/delft3d/esmf/lnx64/bin_COS7:$D3D_HOME/lib:$LD_LIBRARY_PATH +- fi +-else +- echo "ERROR: ESMF_RegridWeightGen_in_Delft3D-WAVE.sh only implemented for CentOS 6 and 7." +- exit +-fi ++# if [ -f "/etc/redhat-release" ]; then ++# grepOS=`cat /etc/redhat-release | grep -i "release 6"` ++# if [ "$grepOS" != "" ]; then ++# echo "RH 6: Using RH 6 libraries" >>esmf_sh.log ++# export LD_LIBRARY_PATH=$D3D_HOME/share/delft3d/esmf/lnx64/bin:$D3D_HOME/lib:$LD_LIBRARY_PATH ++# else ++# echo "using RH 7 libraries" >>esmf_sh.log ++# export LD_LIBRARY_PATH=$D3D_HOME/share/delft3d/esmf/lnx64/bin_COS7:$D3D_HOME/lib:$LD_LIBRARY_PATH ++# fi ++# else ++# echo "ERROR: ESMF_RegridWeightGen_in_Delft3D-WAVE.sh only implemented for CentOS 6 and 7." ++# exit ++# fi + + + echo Executing batchscript "ESMF_RegridWeightGen_in_Delft3D-WAVE.sh" for Delft3D-WAVE >>esmf_sh.log diff -Nru trunk.orig/src/third_party_open/Makefile.am trunk/src/third_party_open/Makefile.am --- trunk.orig/src/third_party_open/Makefile.am 2024-02-20 14:35:27.045777956 +0000 +++ trunk/src/third_party_open/Makefile.am 2024-02-20 14:43:31.552143270 +0000 From 8a0f57cdc66a443a2f09206671e5ff07b0e5f6e2 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Wed, 21 Feb 2024 15:04:43 +0100 Subject: [PATCH 0793/1193] add comment to sed --- easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb index 1f6fb22add69..3334e3ee95b0 100644 --- a/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/z/zUMIs/zUMIs-2.9.7-foss-2023a-R-4.3.2.eb @@ -25,6 +25,7 @@ dependencies = [ ] postinstallcmds = [ + # remove updated/deleted/not-working stuff from --help text "sed -i '33 s/${zumis}/zumis/' %(installdir)s/zUMIs.sh", "sed -i '43,46d' %(installdir)s/zUMIs.sh", "sed -i '7,10d' %(installdir)s/zUMIs.sh", From 8f84b73d572386bbdd495a038e288ded79e7e0b2 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 21 Feb 2024 15:36:29 +0100 Subject: [PATCH 0794/1193] update Seqmagick to PythonBundle and add dep pygtrie --- .../s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb | 21 ++++++++++++------- 1 file changed, 13 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb index f948f1463106..faee813b46f4 100644 --- a/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb +++ b/easybuild/easyconfigs/s/Seqmagick/Seqmagick-0.8.6-foss-2023a.eb @@ -4,7 +4,7 @@ # License:: MIT/GPL # Update:: Pavel Tománek (INUITS) -easyblock = "PythonPackage" +easyblock = "PythonBundle" name = 'Seqmagick' version = '0.8.6' @@ -18,23 +18,28 @@ description = """We often have to convert between sequence formats and do toolchain = {'name': 'foss', 'version': '2023a'} -source_urls = ['https://files.pythonhosted.org/packages/source/s/seqmagick/'] -sources = ['%(namelower)s-%(version)s.tar.gz'] -checksums = ['7f09ef40836b12a2d4c842b179633f1087352855b6ff8fcd045d56003fee622a'] - dependencies = [ ('Biopython', '1.83'), ] +exts_list = [ + ('pygtrie', '2.5.0', { + 'checksums': ['203514ad826eb403dab1d2e2ddd034e0d1534bbe4dbe0213bb0593f66beba4e2'], + }), + (name, version, { + 'modulename': 'Bio', + 'source_urls': ['https://files.pythonhosted.org/packages/source/s/seqmagick/'], + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['7f09ef40836b12a2d4c842b179633f1087352855b6ff8fcd045d56003fee622a'], + }), +] + sanity_check_paths = { 'files': ['bin/seqmagick'], 'dirs': [] } use_pip = True -download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'Bio'} - moduleclass = 'bio' From ca132c423fea1817c68cf564d3f1de0edc21e6be Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 21 Feb 2024 15:48:13 +0100 Subject: [PATCH 0795/1193] Remove --disable-libdeflate option from LibTIFF 4.1.0 --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb index f5661b093874..9e430cbd05eb 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-10.2.0.eb @@ -37,7 +37,7 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += "--disable-webp --disable-libdeflate " +configopts += "--disable-webp " sanity_check_paths = { 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb index 433c867d0d76..cea5f1c71e5e 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-8.3.0.eb @@ -37,7 +37,7 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += "--disable-webp --disable-libdeflate " +configopts += "--disable-webp " sanity_check_paths = { 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb index e6481f975cfe..cf4eb2b08e92 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.1.0-GCCcore-9.3.0.eb @@ -37,7 +37,7 @@ dependencies = [ ] configopts = "--enable-ld-version-script " -configopts += "--disable-webp --disable-libdeflate " +configopts += "--disable-webp " sanity_check_paths = { 'files': ['bin/tiffdump', 'bin/tiffinfo', 'include/tiff.h', 'lib/libtiff.a', 'lib/libtiff.%s' % SHLIB_EXT, From e3bf931cd89009bdd61374c197ea673e49f69761 Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Wed, 21 Feb 2024 16:33:46 +0100 Subject: [PATCH 0796/1193] Update and rename fineRADstructure-20210514-foss-2023a.eb to fineRADstructure-20210514-GCC-12.3.0.eb Drop down to GCC + add sanity checks commands --- ...ss-2023a.eb => fineRADstructure-20210514-GCC-12.3.0.eb} | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/fineRADstructure/{fineRADstructure-20210514-foss-2023a.eb => fineRADstructure-20210514-GCC-12.3.0.eb} (74%) diff --git a/easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-foss-2023a.eb b/easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-GCC-12.3.0.eb similarity index 74% rename from easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-foss-2023a.eb rename to easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-GCC-12.3.0.eb index 8d85a2d78ba9..77c8fd539f60 100644 --- a/easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-foss-2023a.eb +++ b/easybuild/easyconfigs/f/fineRADstructure/fineRADstructure-20210514-GCC-12.3.0.eb @@ -6,7 +6,7 @@ version = '20210514' homepage = 'http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html' description = "A package for population structure inference from RAD-seq data" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://github.com/millanek/fineRADstructure/archive/'] sources = [{'download_filename': '5896b9e.tar.gz', 'filename': SOURCE_TAR_GZ}] @@ -16,9 +16,12 @@ dependencies = [ ('GSL', '2.7'), ] + +_bins = ['finestructure', 'RADpainter'] sanity_check_paths = { - 'files': ['bin/finestructure', 'bin/RADpainter'], + 'files': ['bin/%s' % x for x in _bins], 'dirs': [], } +sanity_check_commands = ["%s -h" % x for x in _bins] moduleclass = 'bio' From 05b411f22c12967ce7a751b81b1d89edce047fbd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 21 Feb 2024 16:55:15 +0100 Subject: [PATCH 0797/1193] Remove git version check and fix test command for molmod 1.4.8 --- .../m/molmod/molmod-1.4.8-foss-2020b.eb | 6 ++- .../m/molmod/molmod-1.4.8-foss-2021a.eb | 6 ++- .../m/molmod/molmod-1.4.8-foss-2021b.eb | 6 ++- .../m/molmod/molmod-1.4.8-foss-2023a.eb | 8 +++- .../molmod-1.4.8_fix-git-version-check.patch | 44 +++++++++++++++++++ 5 files changed, 62 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-git-version-check.patch diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb index 1aa8772b2ae7..c8bfec5a591a 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2020b.eb @@ -10,8 +10,10 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8_fix-git-version-check.patch'] checksums = [ - '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, ] dependencies = [ @@ -24,6 +26,6 @@ download_dep_fail = True sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" -runtest += "python setup.py build_ext -i; pytest -ra" +runtest += "python setup.py build_ext -i && pytest -ra" moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb index 0f4bb6c8b8e6..d956778e486f 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021a.eb @@ -10,8 +10,10 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8_fix-git-version-check.patch'] checksums = [ - '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, ] dependencies = [ @@ -24,7 +26,7 @@ download_dep_fail = True sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" -runtest += "python setup.py build_ext -i; pytest -ra" +runtest += "python setup.py build_ext -i && pytest -ra" sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb index ee12c06558ea..f028e39eff42 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2021b.eb @@ -10,8 +10,10 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] +patches = ['molmod-1.4.8_fix-git-version-check.patch'] checksums = [ - '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8', # molmod-1.4.8.tar.gz + {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, ] dependencies = [ @@ -24,7 +26,7 @@ download_dep_fail = True sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" -runtest += "python setup.py build_ext -i; pytest -ra" +runtest += "python setup.py build_ext -i && pytest -ra" sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb index 6d091b4f23b3..d24c3b350d02 100644 --- a/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8-foss-2023a.eb @@ -10,9 +10,13 @@ toolchain = {'name': 'foss', 'version': '2023a'} source_urls = ['https://github.com/molmod/molmod/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['molmod-1.4.8_fix-np-unicode.patch'] +patches = [ + 'molmod-1.4.8_fix-git-version-check.patch', + 'molmod-1.4.8_fix-np-unicode.patch', +] checksums = [ {'molmod-1.4.8.tar.gz': '759f8894f8a206e8d83f3f88882f29fcf73a7f9be375026e03c58e19496f42e8'}, + {'molmod-1.4.8_fix-git-version-check.patch': '6d1455f9dc3af07b723b05d144f6d8c3c0e5184e094eced1a6f59822f97dcf47'}, {'molmod-1.4.8_fix-np-unicode.patch': '85bd2e2981d2cdd8cfab5d1c2cf37432e2967ff82de603700383d7c31530327c'}, ] @@ -27,7 +31,7 @@ download_dep_fail = True sanity_pip_check = True runtest = "export MATPLOTLIBRC=$PWD; echo 'backend: agg' > $MATPLOTLIBRC/matplotlibrc;" -runtest += "python setup.py build_ext -i; pytest -ra" +runtest += "python setup.py build_ext -i && pytest -ra" sanity_check_paths = { 'files': [], diff --git a/easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-git-version-check.patch b/easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-git-version-check.patch new file mode 100644 index 000000000000..c3463c0f49f4 --- /dev/null +++ b/easybuild/easyconfigs/m/molmod/molmod-1.4.8_fix-git-version-check.patch @@ -0,0 +1,44 @@ +From acbe7bade5c172f756d709e2a152822339f48f26 Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Wed, 21 Feb 2024 12:14:06 +0100 +Subject: [PATCH] setup.py: Only call git if inside a git repository + +Avoid error message: +> fatal: not a git repository (or any parent up to mount point /dev) +> Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). +--- + setup.py | 21 +++++++++++---------- + 1 file changed, 11 insertions(+), 10 deletions(-) + +diff --git a/setup.py b/setup.py +index f531ab3..a3921f3 100755 +--- a/setup.py ++++ b/setup.py +@@ -36,16 +36,17 @@ + + # Try to get the version from git describe + __version__ = None +-try: +- print('Trying to get the version from git describe') +- git_describe = subprocess.check_output(["git", "describe", "--tags"]) +- version_words = git_describe.decode('utf-8').strip().split('-') +- __version__ = version_words[0] +- if len(version_words) > 1: +- __version__ += '.post' + version_words[1] +- print('Version from git describe: {}'.format(__version__)) +-except (subprocess.CalledProcessError, OSError): +- pass ++if os.path.exists('.git'): ++ try: ++ print('Trying to get the version from git describe') ++ git_describe = subprocess.check_output(["git", "describe", "--tags"]) ++ version_words = git_describe.decode('utf-8').strip().split('-') ++ __version__ = version_words[0] ++ if len(version_words) > 1: ++ __version__ += '.post' + version_words[1] ++ print('Version from git describe: {}'.format(__version__)) ++ except (subprocess.CalledProcessError, OSError): ++ pass + + # Interact with version.py + fn_version = os.path.join(os.path.dirname(__file__), 'molmod', 'version.py') From 018519590d975b9acb28568031b38b0eff60b670 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Wed, 21 Feb 2024 17:08:24 +0000 Subject: [PATCH 0798/1193] adding easyconfigs: Seurat-5.0.1-foss-2022b-R-4.2.2.eb --- .../Seurat/Seurat-5.0.1-foss-2022b-R-4.2.2.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-5.0.1-foss-2022b-R-4.2.2.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-5.0.1-foss-2022b-R-4.2.2.eb b/easybuild/easyconfigs/s/Seurat/Seurat-5.0.1-foss-2022b-R-4.2.2.eb new file mode 100644 index 000000000000..274c74321889 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-5.0.1-foss-2022b-R-4.2.2.eb @@ -0,0 +1,76 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '5.0.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://satijalab.org/seurat' +description = "Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data." + +toolchain = {'name': 'foss', 'version': '2022b'} + +dependencies = [ + ('R', '4.2.2'), + ('R-bundle-Bioconductor', '3.16', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('Matrix', '1.6-5', { + 'checksums': ['726c8d46626e73d1d6e76a74679813c6df96ffdee1aee45d94e7014cb4ceb97d'], + }), + ('sp', '1.5-1', { + 'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'], + }), + ('SeuratObject', version, { + 'checksums': ['5ace1720fef373d44da36d28cab8947cd3c342e76f889c2f204a62d668f5f941'], + }), + ('sctransform', '0.4.1', { + 'checksums': ['5f6be7f8be543e4c32c8007207b603a750881459370b7bb5afd63e8c8fabf171'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + ('spatstat.utils', '3.0-1', { + 'checksums': ['cba1c7806564fd9145ca15edf77233d6ba5609f0989f7812221f5fc1ece0b91a'], + }), + ('spatstat.data', '3.0-0', { + 'checksums': ['cff9058a88489020a4a05b9576cd452f37fa9b42084873c474d06931f5187057'], + }), + ('spatstat.geom', '3.0-3', { + 'checksums': ['6e5b56c60e774a0cdcaa5a8ffde071225f233832446a341588bd8a7840913c84'], + }), + ('spatstat.random', '3.0-1', { + 'checksums': ['938c845c063b8781bf894c0a67537e7b2a7c425a4beba4a95ec9d2c37b43e5b6'], + }), + ('spatstat.sparse', '3.0-0', { + 'checksums': ['99be0a3c7592760fdf1668dc0811f75ed91c400390d1ecc3d5e643255f501ad2'], + }), + ('spatstat.explore', '3.0-5', { + 'checksums': ['9f438a12fac3f3e1d0bd550b1393c1e5732be694517b0878db09da557d6dc862'], + }), + ('scattermore', '1.2', { + 'checksums': ['5534a87b0bdd1375f0fbffc1a5c980ad64e33a108435a67469b8324b580602d1'], + }), + (name, version, { + 'checksums': ['0713b434be5bf14fcea068fbfc632ba15bebdec1007f1f48effd0dbb95c5150d'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 80f8145f6ce04b0dacc086177119e1c3a75eb84e Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 22 Feb 2024 09:30:30 +0000 Subject: [PATCH 0799/1193] add c++14 as configopt for ncurses --- easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb index fb054e56586b..2d166f7d5274 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb @@ -55,7 +55,7 @@ components = [ '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', ], 'preconfigopts': "export CPPFLAGS='-P' && ", - 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo --std=c++14', }), (name, version, { 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], From 07f13963fa76ed81e450accf4c9b2c2e41573907 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 22 Feb 2024 10:24:39 +0000 Subject: [PATCH 0800/1193] CPPFLAG --- easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb index 2d166f7d5274..51f75cd3a9af 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.4.6-x86_64.eb @@ -54,8 +54,8 @@ components = [ '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', ], - 'preconfigopts': "export CPPFLAGS='-P' && ", - 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo --std=c++14', + 'preconfigopts': "export CPPFLAGS='-P -std=c++14' && ", + 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', }), (name, version, { 'source_urls': ['https://downloads.haskell.org/~ghc/%(version)s/'], From aad287788dfa31af3f680d2994482ba42f4a3bd1 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 22 Feb 2024 14:26:59 +0000 Subject: [PATCH 0801/1193] remove commented out line --- easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb index b6ecb0109d35..91cd347f95bd 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb @@ -22,7 +22,6 @@ dependencies = [ ('PyQt5', '5.15.10'), ('SciPy-bundle', '2023.07'), ('PyYAML', '6.0'), - # ('pydantic', '1.10.13'), ('pydantic', '2.5.3'), ('dask', '2023.9.2'), ('PyOpenGL', '3.1.7'), From 184260c4c3bd2843ca010f230a972c5551df79ab Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 22 Feb 2024 15:49:55 +0100 Subject: [PATCH 0802/1193] fix matching pattern in dep.py --- .../ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb b/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb index 72a06e419789..f78daf5fb085 100644 --- a/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/e/ExpressBetaDiversity/ExpressBetaDiversity-1.0.10-GCC-12.3.0.eb @@ -17,7 +17,11 @@ dependencies = [ ('Python', '3.11.3'), ] -prebuildopts = 'cd source && ' +prebuildopts = "cd source && " +# fix wrong regex pattern which makes: FutureWarning: split() requires a non-empty pattern match. +prebuildopts += "sed -i '36 s/*/+/' dep.py && " +# force use python from dependencies not the one on a node +buildopts = "DEP='python dep.py'" files_to_copy = [ 'bin', @@ -38,6 +42,4 @@ sanity_check_commands = [ 'cd bin && ExpressBetaDiversity -u', ] -fix_python_shebang_for = ['source/dep.py', 'scripts/*'] - moduleclass = 'bio' From ef94297ebf1c8986922f99d78dba4b703ebb7972 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 22 Feb 2024 16:15:47 +0100 Subject: [PATCH 0803/1193] update Stack, make git-annex truely GCCcore --- .../git-annex-10.20230802-GCCcore-12.3.0.eb | 8 ++++-- .../s/Stack/Stack-2.13.1-x86_64.eb | 26 +++++++++++++++++++ 2 files changed, 32 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/s/Stack/Stack-2.13.1-x86_64.eb diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index 03388d9073a4..f874b2001e95 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -10,10 +10,14 @@ power and distributed nature of git to bear on your large files with git-annex." toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [ + ('binutils', '2.40') +] + dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), - ('GCC', '12.3.0', '', SYSTEM), - ('Stack', '2.11.1', '-x86_64', SYSTEM), + # ('GCC', '12.3.0', '', SYSTEM), + ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), ] diff --git a/easybuild/easyconfigs/s/Stack/Stack-2.13.1-x86_64.eb b/easybuild/easyconfigs/s/Stack/Stack-2.13.1-x86_64.eb new file mode 100644 index 000000000000..e9496c759c5d --- /dev/null +++ b/easybuild/easyconfigs/s/Stack/Stack-2.13.1-x86_64.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'Stack' +version = '2.13.1' +versionsuffix = '-x86_64' + +homepage = 'https://docs.haskellstack.org' +description = """Stack is a cross-platform program for developing Haskell projects. +It is intended for Haskellers both new and experienced.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/commercialhaskell/stack/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-linux-x86_64.tar.gz'] +checksums = ['45281bb2385e928916ec8bcbc7ab790ce8721bbf805f3d0752544ada22ad5ea3'] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['stack'], + 'dirs': ['doc'], +} + +sanity_check_commands = ['stack --help'] + +moduleclass = 'devel' From f39bead3eacd174be5c0586d75968247d1e4e1a7 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Thu, 22 Feb 2024 16:19:17 +0100 Subject: [PATCH 0804/1193] remove GCC comment --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb index f874b2001e95..6b6af7f9eba9 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.3.0.eb @@ -16,7 +16,6 @@ builddependencies = [ dependencies = [ ('GHC', '9.4.6', '-x86_64', SYSTEM), - # ('GCC', '12.3.0', '', SYSTEM), ('Stack', '2.13.1', '-x86_64', SYSTEM), ('git', '2.41.0', '-nodocs'), ] From da522659dfe58cccf4315e3664c9f01215d749b9 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 22 Feb 2024 16:58:29 +0000 Subject: [PATCH 0805/1193] replace SYSTEM-level GCC dependency in git-annex with binutils --- .../g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb index e5c29a0e6bb7..2e2696826f68 100644 --- a/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/git-annex/git-annex-10.20230802-GCCcore-12.2.0.eb @@ -10,9 +10,10 @@ power and distributed nature of git to bear on your large files with git-annex." toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [('binutils', '2.39')] + dependencies = [ ('GHC', '9.2.2', '-x86_64', SYSTEM), - ('GCC', '12.2.0', '', SYSTEM), ('Stack', '2.11.1', '-x86_64', SYSTEM), ('git', '2.38.1', '-nodocs'), ] From 7d4926444c4137b19f9422dfc6401231cb7fe324 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 23 Feb 2024 11:25:15 +0100 Subject: [PATCH 0806/1193] adding easyconfigs: PyFrag-2023-dev.20240220-intel-2022a-ASA.eb --- ...yFrag-2023-dev.20240220-intel-2022a-ASA.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb b/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb new file mode 100644 index 000000000000..03cc89e4fe72 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb @@ -0,0 +1,48 @@ +easyblock = 'Tarball' + +name = 'PyFrag' +version = '2023-dev.20240220' +versionsuffix = '-ASA' +_commit = '9d8611e2eef56e90d265e4aae80c220a1bf00d9e' + +homepage = 'https://pyfragdocument.readthedocs.io/en/latest/includeme.html' +description = """The PyFrag program is specially designed to facilitate the analysis of reaction +mechanism in a more efficient and user-friendly way. PyFrag resolves three main +challenges associated with the automatized computational exploration of +reaction mechanisms: 1) the management of multiple parallel calculations to +automatically find a reaction path; 2) the monitoring of the entire +computational process along with the extraction and plotting of relevant +information from large amounts of data; and 3) the analysis and presentation of +these data in a clear and informative way. +This module provides the Activation Strain Analysis (ASA) Module of PyFrag 2023""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +github_account = 'TheoChem-VU' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename':'%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['684674b90e354f5d40b0779fccd7a310ece965a5c0f7b129eede41a4a3d306c9'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('dill', '0.3.6'), +] + +start_dir = 'host' + +# for PBS based schedulers: +# postinstallcmds = ["sed -i 's/sbatch/qsub/' %(installdir)s/bin/adf.sh"] + +sanity_check_paths = { + 'files': ['bin/pyfrag'], + 'dirs': ['argueparce', 'result', 'standalone'], +} + +sanity_check_commands = ['pyfrag -h | grep "^Usage:"'] + +modextrapaths = { + 'HOSTPYFRAG': '', +} + +moduleclass = 'chem' From 64b93792cbe0f99a9c2e6bb48a21d7c6361ce8d4 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 22 Feb 2024 18:50:05 +0000 Subject: [PATCH 0807/1193] add -std=c++14 to GHC 9.2.2 ncurses component CXXFLAGS --- easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb b/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb index 4ae171a8b3cf..e09ebe9ff500 100644 --- a/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb +++ b/easybuild/easyconfigs/g/GHC/GHC-9.2.2-x86_64.eb @@ -53,7 +53,7 @@ components = [ '8c471fc2b1961a6e6e5981b7f7b3512e7fe58fcb04461aa4520157d4c1159998', '027f7bd5876b761b48db624ddbdd106fa1c535dfb2752ef5a0eddeb2a8896cfd', ], - 'preconfigopts': "export CPPFLAGS='-P' && ", + 'preconfigopts': 'export CPPFLAGS="-P" CXXFLAGS="$CXXFLAGS -std=c++14" && ', 'configopts': ' --with-shared --enable-overwrite --with-termlib=tinfo', }), (name, version, { From 2b2be5ec3a943fd4e1aae687ae48c61fca248be8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 23 Feb 2024 13:59:08 +0100 Subject: [PATCH 0808/1193] adding patchfile PyFrag-2023-dev.20240220_fix-bondlength-header.patch --- ...yFrag-2023-dev.20240220-intel-2022a-ASA.eb | 9 ++++-- ...3-dev.20240220_fix-bondlength-header.patch | 28 +++++++++++++++++++ 2 files changed, 35 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220_fix-bondlength-header.patch diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb b/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb index 03cc89e4fe72..9287e606340b 100644 --- a/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220-intel-2022a-ASA.eb @@ -20,8 +20,13 @@ toolchain = {'name': 'intel', 'version': '2022a'} github_account = 'TheoChem-VU' source_urls = [GITHUB_LOWER_SOURCE] -sources = [{'download_filename':'%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] -checksums = ['684674b90e354f5d40b0779fccd7a310ece965a5c0f7b129eede41a4a3d306c9'] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = ['PyFrag-2023-dev.20240220_fix-bondlength-header.patch'] +checksums = [ + {'PyFrag-2023-dev.20240220.tar.gz': '684674b90e354f5d40b0779fccd7a310ece965a5c0f7b129eede41a4a3d306c9'}, + {'PyFrag-2023-dev.20240220_fix-bondlength-header.patch': + '01b714c7840f1746733641dd8bb84ed37bbe003eb0354ff7d0e49f8354ec49ad'}, +] dependencies = [ ('Python', '3.10.4'), diff --git a/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220_fix-bondlength-header.patch b/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220_fix-bondlength-header.patch new file mode 100644 index 000000000000..f27ba290fb94 --- /dev/null +++ b/easybuild/easyconfigs/p/PyFrag/PyFrag-2023-dev.20240220_fix-bondlength-header.patch @@ -0,0 +1,28 @@ +Fix key names for bond lengths in results table headers +author: Alex Domingo (Vrije Universiteit Brussel) +--- ./host/standalone/adf_new/PyFragModules.py.orig 2024-02-23 13:20:13.952195000 +0100 ++++ ./host/standalone/adf_new/PyFragModules.py 2024-02-23 13:20:22.601881593 +0100 +@@ -203,8 +203,8 @@ + def WriteTable(tableValues, fileName): + energyfile = open(f"pyfrag_{fileName}.txt", "w") + headerlist_all = sorted(tableValues[0]) +- headerlist_select = [e for e in headerlist_all if e not in ("#IRC", "bondlength_1", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain")] +- headerlist = ["#IRC", "bondlength_1", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain"] + headerlist_select ++ headerlist_select = [e for e in headerlist_all if e not in ("#IRC", "bondlength", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain")] ++ headerlist = ["#IRC", "bondlength", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain"] + headerlist_select + writeKey(energyfile, headerlist) + for entry in tableValues: + sortedEntry = [entry[i] for i in headerlist] +--- ./host/standalone/adf_newopen/PyFragModules.py.orig 2024-02-23 13:18:00.235407000 +0100 ++++ ./host/standalone/adf_newopen/PyFragModules.py 2024-02-23 13:18:49.028392911 +0100 +@@ -193,8 +193,8 @@ + def WriteTable(tableValues, fileName): + energyfile = open(f"pyfrag_{fileName}.txt", "w") + headerlist_all = sorted(tableValues[0]) +- headerlist_select = [e for e in headerlist_all if e not in ("#IRC", "bondlength_1", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain")] +- headerlist = ["#IRC", "bondlength_1", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain"] + headerlist_select ++ headerlist_select = [e for e in headerlist_all if e not in ("#IRC", "bondlength", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain")] ++ headerlist = ["#IRC", "bondlength", "EnergyTotal", "Int", "Elstat", "Pauli", "OI", "Disp", "StrainTotal", "frag1Strain", "frag2Strain"] + headerlist_select + writeKey(energyfile, headerlist) + for entry in tableValues: + sortedEntry = [entry[i] for i in headerlist] From ea5111a794697a8e307c3c60ce00b93239d30c23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Feb 2024 14:52:49 +0100 Subject: [PATCH 0809/1193] adding easyconfigs: QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb, Gradle-8.6.eb, OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb --- easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb | 23 ++++++++++ ...lide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb | 33 ++++++++++++++ .../QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb | 44 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb create mode 100644 easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb create mode 100644 easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb diff --git a/easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb b/easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb new file mode 100644 index 000000000000..794188e26cc3 --- /dev/null +++ b/easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb @@ -0,0 +1,23 @@ +easyblock = 'PackedBinary' + +name = 'Gradle' +version = '8.6' + +homepage = 'https://gradle.org' +description = """Complete Gradle install. +From mobile apps to microservices, from small startups to big enterprises, +Gradle helps teams build, automate and deliver better software, faster. +""" + +toolchain = SYSTEM + +source_urls = ['https://services.gradle.org/distributions'] +sources = ['gradle-%(version)s-all.zip'] +checksums = ['85719317abd2112f021d4f41f09ec370534ba288432065f4b477b6a3b652910d'] + +sanity_check_paths = { + 'files': ['bin/gradle'], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb new file mode 100644 index 000000000000..da5906ec6464 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide-Java' +version = '0.12.4' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://github.com/openslide/openslide-java' +description = """This is a Java binding to OpenSlide.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/openslide/%(namelower)s/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.xz'] +checksums = ['63a6cd63fedc7c700020708c0a362b3807b6780f0246b12c8dc372cecd6130cf'] + +builddependencies = [ + ('ant', '1.10.12', versionsuffix, SYSTEM), +] + +dependencies = [ + ('OpenSlide', '3.4.1', '-largefiles'), + ('Java', '17', '', SYSTEM), +] + +sanity_check_paths = { + 'files': [ + 'lib/openslide-java/openslide.jar', + 'lib/openslide-java/libopenslide-jni.so', + ], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb new file mode 100644 index 000000000000..833ea7992c48 --- /dev/null +++ b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb @@ -0,0 +1,44 @@ +easyblock = 'CmdCp' + +name = 'QuPath' +version = '0.5.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://qupath.github.io' +description = """QuPath is open source software for bioimage analysis. +QuPath is often used for digital pathology applications because it offers + a powerful set of tools for working with whole slide images - but it can + be applied to lots of other kinds of image as well.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/qupath/qupath/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d244234ea2fd042488ca4a879f22103764dd3ed27cf9367a8293e50794023524'] + +builddependencies = [ + ('Gradle', '8.6', '', SYSTEM), +] + +dependencies = [ + ('OpenSlide-Java', '0.12.4', versionsuffix), + ('Java', '17', '', SYSTEM), +] + +cmds_map = [('.*', "gradle clean jpackage -P openslide=$EBROOTOPENSLIDEMINJAVA/lib/openslide-java/openslide.jar")] + +files_to_copy = [ + 'build/dist/%(name)s/bin', + 'build/dist/%(name)s/lib', +] + +modextrapaths = {'PATH': ['']} + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['lib'], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' From 525d607c7dc053c08048b54cfb645f3de2ebe482 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Feb 2024 15:08:21 +0100 Subject: [PATCH 0810/1193] add missing build dep --- .../easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb index 833ea7992c48..1225b8a1ba97 100644 --- a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb +++ b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb @@ -17,6 +17,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['d244234ea2fd042488ca4a879f22103764dd3ed27cf9367a8293e50794023524'] builddependencies = [ + ('binutils', '2.40', '', SYSTEM), ('Gradle', '8.6', '', SYSTEM), ] From c95cfddd09e464f479d78161d55395ae7975b53b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Feb 2024 15:21:55 +0100 Subject: [PATCH 0811/1193] add missing build dep --- .../OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb index da5906ec6464..f978519dab82 100644 --- a/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb +++ b/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb @@ -14,6 +14,7 @@ sources = ['%(namelower)s-%(version)s.tar.xz'] checksums = ['63a6cd63fedc7c700020708c0a362b3807b6780f0246b12c8dc372cecd6130cf'] builddependencies = [ + ('binutils', '2.40', '', SYSTEM), ('ant', '1.10.12', versionsuffix, SYSTEM), ] From 96ab214452b8d8c9f38a43b323803eafbe70d6f4 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Feb 2024 15:38:54 +0100 Subject: [PATCH 0812/1193] adding easyconfigs: scanpy-1.9.8-foss-2023a.eb, anndata-0.10.5.post1-foss-2023a.eb --- .../anndata-0.10.5.post1-foss-2023a.eb | 44 +++++++++ .../s/scanpy/scanpy-1.9.8-foss-2023a.eb | 92 +++++++++++++++++++ 2 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb new file mode 100644 index 000000000000..b49190c6e5a2 --- /dev/null +++ b/easybuild/easyconfigs/a/anndata/anndata-0.10.5.post1-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'anndata' +version = '0.10.5.post1' + +homepage = 'https://github.com/scverse/anndata' +description = """anndata is a Python package for handling annotated data matrices in memory and on disk, + positioned between pandas and xarray""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('hatchling', '1.18.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('array_api_compat', '1.4.1', { + 'checksums': ['053103b7c0ba73626bff7380abf27a29dc80de144394137bc7455b7eba23d8c0'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'checksums': ['9a17c6eda9fc40759b3f5f81742f5d18c1a0a1acdf02f13e1646700ec082c155'], + }), +] + +sanity_check_paths = { + 'files': ['bin/natsort'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["natsort --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb new file mode 100644 index 000000000000..38f1324a6d0e --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -0,0 +1,92 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.9.8' + +homepage = 'https://scanpy.readthedocs.io/en/stable/' +description = """Scanpy is a scalable toolkit for analyzing single-cell gene expression data built + jointly with anndata. It includes preprocessing, visualization, clustering, trajectory inference + and differential expression testing. The Python-based implementation efficiently deals with + datasets of more than one million cells. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Seaborn', '0.13.2'), + ('h5py', '3.9.0'), + ('tqdm', '4.66.1'), + ('scikit-learn', '1.3.1'), + ('statsmodels', '0.14.1'), + ('networkx', '3.1'), + ('numba', '0.58.1'), + ('umap-learn', '0.5.5'), + ('hatchling', '1.18.0'), + ('anndata', '0.10.5.post1'), + # ('leidenalg', '0.9.1'), +] + +# "anndata>=0.8", OK +# "numpy>=1.23", OK - scipy bundle +# "matplotlib>=3.6", OK +# "pandas >=1.5", OK - scipy bundle +# "scipy>=1.8", OK - scipy bundle +# "seaborn>=0.13", OK +# "h5py>=3.1", OK +# "tqdm", OK +# "scikit-learn>=0.24", OK +# "statsmodels>=0.13", OK +# "patsy", OK - statsmodels +# "networkx>=2.7", OK +# "natsort", OK - exts +# "joblib", OK - exts +# "numba>=0.56", OK +# "umap-learn>=0.5,!=0.5.0", OK +# "pynndescent>=0.5", OK - umap-learn +# "packaging>=21.3", OK - exts +# "session-info", OK - exts +# "legacy-api-wrap>=1.4", OK - exts +# "get-annotations; python_version < '3.10'", OK/ only need for python < 3.10 + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('stdlib_list', '0.10.0', { + 'checksums': ['6519c50d645513ed287657bfe856d527f277331540691ddeaf77b25459964a14'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + ('joblib', '1.3.2', { + 'checksums': ['92f865e621e17784e7955080b6d042489e3b8e294949cc44c6eac304f59772b1'], + }), + ('session-info', '1.0.0', { + 'sources': ['session_info-%(version)s.tar.gz'], + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + ('legacy_api_wrap', '1.4', { + 'checksums': ['92dfa274cedb26d6e6f70fac85c856fbdcc05058066656d76a665fb4bf11b785'], + }), + (name, version, { + 'checksums': ['2ab1790d2b82eadb0cf8d487f468beac7a8f6a3a8fd7112d1ae989f8c52a4353'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", +] + +moduleclass = 'bio' From d296f8c657671170a5501db06179d1162a3befa5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 23 Feb 2024 15:42:16 +0100 Subject: [PATCH 0813/1193] clean dep comments --- .../s/scanpy/scanpy-1.9.8-foss-2023a.eb | 23 ------------------- 1 file changed, 23 deletions(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb index 38f1324a6d0e..ae5530e1e0db 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -27,30 +27,7 @@ dependencies = [ ('umap-learn', '0.5.5'), ('hatchling', '1.18.0'), ('anndata', '0.10.5.post1'), - # ('leidenalg', '0.9.1'), ] - -# "anndata>=0.8", OK -# "numpy>=1.23", OK - scipy bundle -# "matplotlib>=3.6", OK -# "pandas >=1.5", OK - scipy bundle -# "scipy>=1.8", OK - scipy bundle -# "seaborn>=0.13", OK -# "h5py>=3.1", OK -# "tqdm", OK -# "scikit-learn>=0.24", OK -# "statsmodels>=0.13", OK -# "patsy", OK - statsmodels -# "networkx>=2.7", OK -# "natsort", OK - exts -# "joblib", OK - exts -# "numba>=0.56", OK -# "umap-learn>=0.5,!=0.5.0", OK -# "pynndescent>=0.5", OK - umap-learn -# "packaging>=21.3", OK - exts -# "session-info", OK - exts -# "legacy-api-wrap>=1.4", OK - exts -# "get-annotations; python_version < '3.10'", OK/ only need for python < 3.10 use_pip = True sanity_pip_check = True From a5f2dd5a3c5a0c4e3fed54b439d2ed0d82b7bc34 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 23 Feb 2024 15:58:19 +0100 Subject: [PATCH 0814/1193] fix whitespaces --- easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb index ae5530e1e0db..dc34504eeee2 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.8-foss-2023a.eb @@ -28,7 +28,7 @@ dependencies = [ ('hatchling', '1.18.0'), ('anndata', '0.10.5.post1'), ] - + use_pip = True sanity_pip_check = True From 97cf56c3d9a9ebd46eb78fbe2e8d0dbbdc1bc214 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Fri, 23 Feb 2024 17:02:02 +0000 Subject: [PATCH 0815/1193] adding easyconfigs: Salmon-1.10.1-GCC-12.2.0.eb --- .../s/Salmon/Salmon-1.10.1-GCC-12.2.0.eb | 63 +++++++++++++++++++ 1 file changed, 63 insertions(+) create mode 100644 easybuild/easyconfigs/s/Salmon/Salmon-1.10.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/Salmon/Salmon-1.10.1-GCC-12.2.0.eb b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.1-GCC-12.2.0.eb new file mode 100644 index 000000000000..5240a039ab53 --- /dev/null +++ b/easybuild/easyconfigs/s/Salmon/Salmon-1.10.1-GCC-12.2.0.eb @@ -0,0 +1,63 @@ +# # +# This is a contribution from DeepThought HPC Service, Flinders University, Adelaide, Australia +# Homepage: https://staff.flinders.edu.au/research/deep-thought +# +# Authors:: Robert Qiao +# License:: GLPv2 +# +# Notes:: +# # +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# Thanks to people like Simon Brandord, Mikael Oehmann and Kenneth Hoste +# for their help with the ICE + +easyblock = 'CMakeMake' + +name = 'Salmon' +version = '1.10.1' + +homepage = 'https://github.com/COMBINE-lab/salmon' +description = """Salmon is a wicked-fast program to produce a highly-accurate, + transcript-level quantification estimate from RNA-seq data.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['babd9ccc189cfea07566d8a11d047f25fad5b446b4b69257bc6ad8869f8b7707'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('pkgconf', '1.9.3'), + ('jemalloc', '5.3.0'), + ('Cereal', '1.3.2', '', SYSTEM), +] +dependencies = [ + ('Boost', '1.81.0'), + ('tbb', '2021.10.0'), + ('cURL', '7.86.0'), + ('libiconv', '1.17'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), +] + +# Disable link-time optimizations (-flto) because it triggers a segfault/internal compiler error (ICE) +# this issue might magically disappear in future versions of Salmon or GCC +# see https://github.com/COMBINE-lab/salmon/issues/778 +configopts = "-DJEMALLOC_ROOT=$EBROOTJEMALLOC -DNO_IPO=1" + +github_account = 'COMBINE-lab' +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'lib/libgraphdump.a', 'lib/libntcard.a', 'lib/libsalmon_core.a', 'lib/libtwopaco.a'], + 'dirs': [], +} + +sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'bio' From 1d1f205585471ab37ef955e9040925f645339deb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 23 Feb 2024 21:44:15 +0100 Subject: [PATCH 0816/1193] apply chages suggested in PR --- .../g/Gradle/Gradle-8.6-Java-17.eb | 30 +++++++++++++++++++ ...lide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb | 6 ++-- .../QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb | 14 ++++++--- 3 files changed, 43 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb diff --git a/easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb b/easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb new file mode 100644 index 000000000000..01cb2993372e --- /dev/null +++ b/easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb @@ -0,0 +1,30 @@ +easyblock = 'PackedBinary' + +name = 'Gradle' +version = '8.6' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://gradle.org' +description = """Complete Gradle install. +From mobile apps to microservices, from small startups to big enterprises, +Gradle helps teams build, automate and deliver better software, faster. +""" + +toolchain = SYSTEM + +source_urls = ['https://services.gradle.org/distributions'] +sources = ['gradle-%(version)s-all.zip'] +checksums = ['85719317abd2112f021d4f41f09ec370534ba288432065f4b477b6a3b652910d'] + +dependencies = [ + ('Java', '17'), +] + +sanity_check_paths = { + 'files': ['bin/gradle'], + 'dirs': [], +} + +moduleclass = 'devel' + +sanity_check_commands = ['%(namelower)s --help'] diff --git a/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb index f978519dab82..55957819d5fc 100644 --- a/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb +++ b/easybuild/easyconfigs/o/OpenSlide-Java/OpenSlide-Java-0.12.4-GCCcore-12.3.0-Java-17.eb @@ -14,7 +14,7 @@ sources = ['%(namelower)s-%(version)s.tar.xz'] checksums = ['63a6cd63fedc7c700020708c0a362b3807b6780f0246b12c8dc372cecd6130cf'] builddependencies = [ - ('binutils', '2.40', '', SYSTEM), + ('binutils', '2.40'), ('ant', '1.10.12', versionsuffix, SYSTEM), ] @@ -26,9 +26,9 @@ dependencies = [ sanity_check_paths = { 'files': [ 'lib/openslide-java/openslide.jar', - 'lib/openslide-java/libopenslide-jni.so', + 'lib/openslide-java/libopenslide-jni.%s' % SHLIB_EXT, ], - 'dirs': [] + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb index 1225b8a1ba97..bed0ce4eb215 100644 --- a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb +++ b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb @@ -17,8 +17,8 @@ sources = ['v%(version)s.tar.gz'] checksums = ['d244234ea2fd042488ca4a879f22103764dd3ed27cf9367a8293e50794023524'] builddependencies = [ - ('binutils', '2.40', '', SYSTEM), - ('Gradle', '8.6', '', SYSTEM), + ('binutils', '2.40'), + ('Gradle', '8.6', versionsuffix, SYSTEM), ] dependencies = [ @@ -36,8 +36,14 @@ files_to_copy = [ modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ['bin/%(name)s'], - 'dirs': ['lib'], + 'files': [ + 'bin/%(name)s', + 'lib/libapplauncher.%s' % SHLIB_EXT, + ], + 'dirs': [ + 'lib/app', + 'lib/runtime', + ], } sanity_check_commands = ['%(name)s --help'] From 2a0f952973934c147768b0fdef899655b64c1d84 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sat, 24 Feb 2024 13:44:18 -0800 Subject: [PATCH 0817/1193] update dm-tree GCCccore-12.3.0 --- .../d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100755 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb new file mode 100755 index 000000000000..bf55444d0067 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'dm-tree' +version = '0.1.8' + +homepage = 'https://github.com/deepmind/tree' +description = """dm-tree provides tree, a library for working with nested data structures. In a way, +tree generalizes the builtin map function which only supports flat sequences, and +allows to apply a function to each "leaf" preserving the overall structure.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0fcaabbb14e7980377439e7140bd05552739ca5e515ecb3119f234acee4b9430'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'tree'} + +moduleclass = 'lib' From 44bef07ca7d0e894c210f68e9fd72b8460ca899c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 25 Feb 2024 23:38:36 +0000 Subject: [PATCH 0818/1193] adding easyconfigs: Scalene-1.5.35-GCCcore-13.2.0.eb --- .../Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..ed2a4b215314 --- /dev/null +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'Scalene' +version = '1.5.35' + +homepage = 'https://github.com/plasma-umass/scalene' +description = """Scalene is a high-performance CPU, GPU and memory profiler for Python that does a number of things +that other Python profilers do not and cannot do. It runs orders of magnitude faster than other profilers while +delivering far more detailed information.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + ('pynvml', '11.5.0', { + 'checksums': ['d027b21b95b1088b9fc278117f9f61b7c67f8e33a787e9f83f735f0f71ac32d0'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['decd0a374e918af08de06e7f2d97feafb1ad0252b0a91b99c14b6b6364f605ec'], + }), +] + +sanity_check_paths = { + 'files': ['bin/scalene'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["scalene --help"] + +sanity_pip_check = True + +moduleclass = 'tools' From 0293b65ccfb780485d705b09ca5f485345892903 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 26 Feb 2024 10:29:19 +0100 Subject: [PATCH 0819/1193] Remove --with-doc configure option from groff 1.23 --- easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb index f280bc241441..dccb74c587ac 100644 --- a/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/groff/groff-1.23.0-GCCcore-13.2.0.eb @@ -18,8 +18,6 @@ builddependencies = [ ('M4', '1.4.19'), ] -configopts = '--with-doc=no' - sanity_check_paths = { 'files': ['bin/groff', 'bin/nroff', 'bin/troff'], 'dirs': ['lib/groff', 'share'], From be78658eb5ff376a607d857edf2ee78517e3daf7 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Mon, 26 Feb 2024 12:14:43 +0000 Subject: [PATCH 0820/1193] strip execute permissions from easyconfig --- easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dm-tree/dm-tree-0.1.8-GCCcore-12.3.0.eb old mode 100755 new mode 100644 From 00f3d0bc4481a6d9f5f0e8c91e130c4dda913837 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 26 Feb 2024 15:46:45 +0100 Subject: [PATCH 0821/1193] Fix test failures of Perl-bundle-CPAN-5.38 in non-English locales --- .../Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index 89d9819e7fba..ac77e85d5a0e 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -400,6 +400,7 @@ exts_list = [ 'source_tmpl': 'DBI-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/T/TI/TIMB'], 'checksums': ['8a2b993db560a2c373c174ee976a51027dd780ec766ae17620c20393d2e836fa'], + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments }), ('DBD::SQLite', '1.74', { 'source_tmpl': 'DBD-SQLite-%(version)s.tar.gz', @@ -1502,6 +1503,7 @@ exts_list = [ 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT'], 'checksums': ['ba4083b2c31ff2694f2371333d554c826aaf24b4d98d03e48b5b4a43a2a0e679'], + 'pretestopts': 'LC_ALL=C ', # Test fails if run in localized environments }), ('MooseX::Types::Perl', '0.101344', { 'source_tmpl': 'MooseX-Types-Perl-%(version)s.tar.gz', From c37c566251eed4d3a1d311ce241b4c88b0bf0543 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 26 Feb 2024 16:00:32 +0100 Subject: [PATCH 0822/1193] adding easyconfigs: Flye-2.9.3-GCC-12.3.0.eb --- .../f/Flye/Flye-2.9.3-GCC-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCC-12.3.0.eb b/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCC-12.3.0.eb new file mode 100644 index 000000000000..efd15addcca2 --- /dev/null +++ b/easybuild/easyconfigs/f/Flye/Flye-2.9.3-GCC-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Flye' +version = '2.9.3' + +homepage = 'https://github.com/fenderglass/Flye' +description = """Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio + and Oxford Nanopore Technologies.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/fenderglass/Flye/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['09580390ed0558c131ca0b836a2374d3cc7993cba2a6500024c2ee1d96666edc'] + +dependencies = [('Python', '3.11.3')] + +download_dep_fail = True +use_pip = True + +if ARCH == "aarch64": + preinstallopts = 'export arm_neon=1 && export aarch64=1 && ' + +sanity_check_paths = { + 'files': ['bin/flye'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +sanity_pip_check = True + +moduleclass = 'bio' From 59dd8e8743224214c6cb38996c6fbe6d93395ea8 Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Mon, 26 Feb 2024 16:22:59 +0100 Subject: [PATCH 0823/1193] adding easyconfigs: LDC-1.36.0-GCCcore-12.3.0.eb, onedrive-2.4.25-GCCcore-12.3.0.eb --- .../l/LDC/LDC-1.36.0-GCCcore-12.3.0.eb | 39 +++++++++++++++++ .../onedrive-2.4.25-GCCcore-12.3.0.eb | 42 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/l/LDC/LDC-1.36.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/o/onedrive/onedrive-2.4.25-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/LDC/LDC-1.36.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/LDC/LDC-1.36.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9446457c8039 --- /dev/null +++ b/easybuild/easyconfigs/l/LDC/LDC-1.36.0-GCCcore-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeNinja' + +name = 'LDC' +version = '1.36.0' + +homepage = 'https://wiki.dlang.org/LDC' +description = "The LLVM-based D Compiler" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/ldc-developers/ldc/releases/download/v%(version)s'] +sources = ['ldc-%(version)s-src.tar.gz'] +checksums = ['a00c79073123a887c17f446c7782a49556a3512a3d35ab676b7d53ae1bb8d6ef'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), + ('Ninja', '1.11.1'), + # building LDC from source requires LDC + ('LDC', '1.24.0', '-%(arch)s', SYSTEM), +] + +dependencies = [ + ('LLVM', '16.0.6'), +] + +configopts = "-DLLVM_ROOT_DIR=$EBROOTLLVM" + +sanity_check_paths = { + 'files': ['bin/ldc2', 'bin/ldmd2'], + 'dirs': ['include/d', 'lib'], +} + +sanity_check_commands = [ + "ldc2 --help", + "ldmd2 --help", +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/o/onedrive/onedrive-2.4.25-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.25-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b22cd1206b71 --- /dev/null +++ b/easybuild/easyconfigs/o/onedrive/onedrive-2.4.25-GCCcore-12.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'onedrive' +version = '2.4.25' + +homepage = 'https://abraunegg.github.io/' +description = """ +A free Microsoft OneDrive Client which supports OneDrive Personal, OneDrive for Business, +OneDrive for Office365 and SharePoint.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/abraunegg/onedrive/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e7d782ea7d1973b6b578899a84c4f90ba69302263b4be30d80a363ba8ba27eb3'] + +builddependencies = [ + ('binutils', '2.40'), + ('LDC', '1.36.0'), +] + +dependencies = [ + ('cURL', '8.0.1'), + ('SQLite', '3.42.0'), +] + +_compldir = '%(installdir)s/share/tab_completion' +configopts = 'DC="$EBROOTLDC"/bin/ldc2 --with-systemdsystemunitdir=no ' +configopts += '--enable-completions --with-bash-completion-dir=%s ' % _compldir +configopts += '--with-zsh-completion-dir=%s --with-fish-completion-dir=%s ' % (_compldir, _compldir) + +sanity_check_paths = { + 'files': ['bin/onedrive'], + 'dirs': ['etc', 'share'], +} + +sanity_check_commands = ['onedrive -h'] + +# optionally enable tab completion for bash (zsh: '_onedrive', fish: 'onedrive.fish') +modluafooter = 'execute {cmd="source $EBROOTONEDRIVE/share/tab_completion/onedrive",modeA={"load"}}' + +moduleclass = 'tools' From 125c05c6d3c0a78fb6c7b66b3cfaf9dfc2478f9a Mon Sep 17 00:00:00 2001 From: casparvl Date: Mon, 26 Feb 2024 19:47:00 +0000 Subject: [PATCH 0824/1193] Fix tree-optimization bug in GCC for ARM architectures with SVE support --- .../easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 3 + ...ore-13.2.0_fix_slp_and_loop_mask_len.patch | 114 ++++++++++++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index 85c2772cbfa1..dc23f33884ee 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', + 'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch', ] checksums = [ {'gcc-13.2.0.tar.gz': '8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078'}, @@ -49,6 +50,8 @@ checksums = [ {'GCCcore-12.1.0_fix-double-destruct.patch': '2e09c125318b6c15ec60f1807d77fb7d1f32b64a4e5d1c9a3da89ba2ca738d35'}, {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, + {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': + '9cc82cd681ffd1cbc7432376f137db106840f89335b9eee35b969cb0a5402af6'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch new file mode 100644 index 000000000000..909afb10f3f1 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch @@ -0,0 +1,114 @@ +This patch fixes an issue where the tree-vectorization fails due to an internal compiler error in [60/11858] +compute_live_loop_exits on SVE capable AARCH64 architectures +First encountered on a neoverse_v1 build at https://github.com/EESSI/software-layer/pull/479#issuecomment-1957091774 +Upstream issue https://gcc.gnu.org/bugzilla/show_bug.cgi?id=111478 +Upstream fix from https://gcc.gnu.org/git/gitweb.cgi?p=gcc.git;h=e5f1956498251a4973d52c8aad3faf34d0443169 +Known to work are 13.2.1, 14.0, so the fix probably already made it in there + +The second patch is a dependency to make the first one work, as it implements the *-operator used in last_stmt = *si + +From: Richard Biener +Date: Fri, 10 Nov 2023 11:39:11 +0000 (+0100) +Subject: tree-optimization/110221 - SLP and loop mask/len +X-Git-Url: https://gcc.gnu.org/git/?p=gcc.git;a=commitdiff_plain;h=e5f1956498251a4973d52c8aad3faf34d0443169;hp=a5922427c29fad177251d89cc946d1c5bfc135eb + +tree-optimization/110221 - SLP and loop mask/len + +The following fixes the issue that when SLP stmts are internal defs +but appear invariant because they end up only using invariant defs +then they get scheduled outside of the loop. This nice optimization +breaks down when loop masks or lens are applied since those are not +explicitly tracked as dependences. The following makes sure to never +schedule internal defs outside of the vectorized loop when the +loop uses masks/lens. + + PR tree-optimization/110221 + * tree-vect-slp.cc (vect_schedule_slp_node): When loop + masking / len is applied make sure to not schedule + intenal defs outside of the loop. + + * gfortran.dg/pr110221.f: New testcase. +--- + +diff --git a/gcc/testsuite/gfortran.dg/pr110221.f b/gcc/testsuite/gfortran.dg/pr110221.f +new file mode 100644 +index 000000000000..8b57384313a7 +--- /dev/null ++++ b/gcc/testsuite/gfortran.dg/pr110221.f +@@ -0,0 +1,17 @@ ++C PR middle-end/68146 ++C { dg-do compile } ++C { dg-options "-O2 -w" } ++C { dg-additional-options "-mavx512f --param vect-partial-vector-usage=2" { target avx512f } } ++ SUBROUTINE CJYVB(V,Z,V0,CBJ,CDJ,CBY,CYY) ++ IMPLICIT DOUBLE PRECISION (A,B,G,O-Y) ++ IMPLICIT COMPLEX*16 (C,Z) ++ DIMENSION CBJ(0:*),CDJ(0:*),CBY(0:*) ++ N=INT(V) ++ CALL GAMMA2(VG,GA) ++ DO 65 K=1,N ++ CBY(K)=CYY ++65 CONTINUE ++ CDJ(0)=V0/Z*CBJ(0)-CBJ(1) ++ DO 70 K=1,N ++70 CDJ(K)=-(K+V0)/Z*CBJ(K)+CBJ(K-1) ++ END +diff --git a/gcc/tree-vect-slp.cc b/gcc/tree-vect-slp.cc +index 3e5814c3a319..80e279d8f506 100644 +--- a/gcc/tree-vect-slp.cc ++++ b/gcc/tree-vect-slp.cc +@@ -9081,6 +9081,16 @@ vect_schedule_slp_node (vec_info *vinfo, + /* Emit other stmts after the children vectorized defs which is + earliest possible. */ + gimple *last_stmt = NULL; ++ if (auto loop_vinfo = dyn_cast (vinfo)) ++ if (LOOP_VINFO_FULLY_MASKED_P (loop_vinfo) ++ || LOOP_VINFO_FULLY_WITH_LENGTH_P (loop_vinfo)) ++ { ++ /* But avoid scheduling internal defs outside of the loop when ++ we might have only implicitly tracked loop mask/len defs. */ ++ gimple_stmt_iterator si ++ = gsi_after_labels (LOOP_VINFO_LOOP (loop_vinfo)->header); ++ last_stmt = *si; ++ } + bool seen_vector_def = false; + FOR_EACH_VEC_ELT (SLP_TREE_CHILDREN (node), i, child) + if (SLP_TREE_DEF_TYPE (child) == vect_internal_def) + + +From c39cdd9e654540f74cd2478019c40f1611554a44 Mon Sep 17 00:00:00 2001 +From: Richard Biener +Date: Tue, 18 Apr 2023 16:58:26 +0200 +Subject: [PATCH] Add operator* to gimple_stmt_iterator and gphi_iterator + +This allows STL style iterator dereference. It's the same +as gsi_stmt () or .phi (). + + * gimple-iterator.h (gimple_stmt_iterator::operator*): Add. + (gphi_iterator::operator*): Likewise. +--- + gcc/gimple-iterator.h | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/gcc/gimple-iterator.h b/gcc/gimple-iterator.h +index 38352aa95af62..b709923f00dfa 100644 +--- a/gcc/gimple-iterator.h ++++ b/gcc/gimple-iterator.h +@@ -24,6 +24,8 @@ along with GCC; see the file COPYING3. If not see + + struct gimple_stmt_iterator + { ++ gimple *operator * () const { return ptr; } ++ + /* Sequence node holding the current statement. */ + gimple_seq_node ptr; + +@@ -38,6 +40,8 @@ struct gimple_stmt_iterator + /* Iterator over GIMPLE_PHI statements. */ + struct gphi_iterator : public gimple_stmt_iterator + { ++ gphi *operator * () const { return as_a (ptr); } ++ + gphi *phi () const + { + return as_a (ptr); From ee89b057d345efdf392b588a193721e9a0171992 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 26 Feb 2024 22:29:33 +0000 Subject: [PATCH 0825/1193] Downgrade pynvml --- .../easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb index ed2a4b215314..ac4e7481cf68 100644 --- a/easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Scalene/Scalene-1.5.35-GCCcore-13.2.0.eb @@ -26,8 +26,8 @@ exts_list = [ ('cloudpickle', '3.0.0', { 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], }), - ('pynvml', '11.5.0', { - 'checksums': ['d027b21b95b1088b9fc278117f9f61b7c67f8e33a787e9f83f735f0f71ac32d0'], + ('pynvml', '11.4.1', { + 'checksums': ['b2e4a33b80569d093b513f5804db0c7f40cfc86f15a013ae7a8e99c5e175d5dd'], }), (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', From 63918e5798787056b58bac52b3e0b99ced2ba61e Mon Sep 17 00:00:00 2001 From: casparvl Date: Tue, 27 Feb 2024 00:18:53 +0000 Subject: [PATCH 0826/1193] Fix checksum --- easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index dc23f33884ee..b3eff862747e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -51,7 +51,7 @@ checksums = [ {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': - '9cc82cd681ffd1cbc7432376f137db106840f89335b9eee35b969cb0a5402af6'}, + 'e1d63e04bf494a2f79346ac7454372f117b63288cc18c68876a5b8bdc453cf88'}, ] builddependencies = [ From 4b057da0643ac9fab6b40a525beca6a3a3063c42 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 27 Feb 2024 00:33:01 +0000 Subject: [PATCH 0827/1193] fix checksum --- easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb index 78d81235b601..eb4d2a3d3660 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.4.1.eb @@ -12,7 +12,7 @@ toolchain = SYSTEM source_urls = ['https://github.com/git-lfs/git-lfs/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['fa93f65cc5c15b96037a72cf243bc2cc04c94ea5cccc346664425d6d4bac66c2'] +checksums = ['2a36239d7968ae18e1ba2820dc664c4ef753f10bf424f98bccaf44d527f19a17'] builddependencies = [('Go', '1.21.6')] From 2ff92b6c53b4f9faa6a605735528a38d9fe3fec3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 27 Feb 2024 00:39:35 +0000 Subject: [PATCH 0828/1193] adding easyconfigs: arpack-ng-3.9.1-foss-2023b.eb --- .../a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb new file mode 100644 index 000000000000..4f029ffc4f81 --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.9.1-foss-2023b.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = '3.9.1' + +homepage = 'https://github.com/opencollab/arpack-ng' +description = """ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['f6641deb07fa69165b7815de9008af3ea47eb39b2bb97521fbf74c97aba6e844'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), + ('Eigen', '3.4.0') +] + +preconfigopts = "sh bootstrap && " +configopts = '--enable-mpi --with-pic --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + +sanity_check_paths = { + 'files': ['lib64/libarpack.la', 'lib64/libarpack.%s' % SHLIB_EXT, + 'lib64/libparpack.la', 'lib64/libparpack.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'numlib' From acf0228cb8834d67bb01fa491ccb13d4d7c5cbf4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Feb 2024 09:52:47 +0100 Subject: [PATCH 0829/1193] {bio,math}[foss/2023a] ArchR v1.0.2, presto v1.0.0-20230501 w/ R 4.3.2 --- .../a/ArchR/ArchR-1.0.2-foss-2023a-R-4.3.2.eb | 27 +++++++++++++++++ ...resto-1.0.0-20230501-foss-2023a-R-4.3.2.eb | 29 +++++++++++++++++++ 2 files changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArchR/ArchR-1.0.2-foss-2023a-R-4.3.2.eb create mode 100644 easybuild/easyconfigs/p/presto/presto-1.0.0-20230501-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/a/ArchR/ArchR-1.0.2-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/a/ArchR/ArchR-1.0.2-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..c28181e314a0 --- /dev/null +++ b/easybuild/easyconfigs/a/ArchR/ArchR-1.0.2-foss-2023a-R-4.3.2.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'ArchR' +version = '1.0.2' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://www.archrproject.com' +description = "ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/GreenleafLab/ArchR/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['afe4d82975e9d75018e9ec9fda3d116f34f99ad1d45990cbc5a2be7dea8df352'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), + ('presto', '1.0.0-20230501', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(name)s'], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/presto/presto-1.0.0-20230501-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/p/presto/presto-1.0.0-20230501-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..2fe834fc6b07 --- /dev/null +++ b/easybuild/easyconfigs/p/presto/presto-1.0.0-20230501-foss-2023a-R-4.3.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'presto' +local_commit = '31dc97f' +# see DESCRIPTION to determine version, +# but also take date of last commit into account (since version isn't always bumped) +version = '1.0.0-20230501' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/immunogenomics/presto' +description = "Presto performs a fast Wilcoxon rank sum test and auROC analysis." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/immunogenomics/presto/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['720ef58aba219af03344e0ae0408fc48feda50e6b7f7f4af2251eb24ce1bfb88'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From f31933833b290d13e8137a38bb670f68866eac49 Mon Sep 17 00:00:00 2001 From: donrolih Date: Tue, 27 Feb 2024 09:58:03 +0100 Subject: [PATCH 0830/1193] Uploaded easyconfigs for triqs-3.2.0 using foss 2023a --- ...g-Python-bindings-16.0.6-GCCcore-12.3.0.eb | 31 ++++++++ .../n/NFFT/NFFT-3.5.3-foss-2023a.eb | 31 ++++++++ .../TRIQS-cthyb-3.2.1-foss-2023a.eb | 69 ++++++++++++++++++ .../TRIQS-dft_tools-3.2.0-foss-2023a.eb | 70 ++++++++++++++++++ .../TRIQS-tprf/TRIQS-tpfr-3.2.1-foss-2023a.eb | 70 ++++++++++++++++++ .../t/TRIQS/TRIQS-3.2.0-foss-2023a.eb | 72 +++++++++++++++++++ 6 files changed, 343 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tpfr-3.2.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..6d2d1ec9a6b3 --- /dev/null +++ b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'Clang-Python-bindings' +version = '16.0.6' + +homepage = 'https://clang.llvm.org' +description = """Python bindings for libclang""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ["https://github.com/llvm/llvm-project/releases/download/llvmorg-%(version)s/"] +sources = ['clang-%(version)s.src.tar.xz'] +checksums = ['1186b6e6eefeadd09912ed73b3729e85b59f043724bb2818a95a2ec024571840'] + +dependencies = [ + ('Clang', version), + ('Python', '3.11.3') +] + +start_dir = 'bindings/python' + +sanity_check_paths = { + 'files': ['clang/cindex.py'], + 'dirs': ['clang'] +} + +sanity_check_commands = ["python -c 'import clang'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb new file mode 100644 index 000000000000..baa326a1a9d8 --- /dev/null +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'NFFT' +version = '3.5.3' + +homepage = 'https://www-user.tu-chemnitz.de/~potts/nfft/' +description = """The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine + library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more + dimensions, of arbitrary input size, and of complex data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/NFFT/nfft/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ccef7a8e97e40e5f962df94626ade5adc7db1fb7948e3c75aa70393468e2e8fb'] + +dependencies = [('FFTW', '3.3.10')] + +builddependencies = [('Autotools', '20220317')] + +configure_cmd_prefix = './bootstrap.sh ; ' + +configopts = '--enable-openmp' + +sanity_check_paths = { + 'files': ['include/nfft3.h', 'include/nfft3mp.h', 'lib/libnfft3_threads.a', 'lib/libnfft3.a', + 'lib/libnfft3_threads.%s' % SHLIB_EXT, 'lib/libnfft3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' \ No newline at end of file diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb new file mode 100644 index 000000000000..b5ad923eddb1 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb @@ -0,0 +1,69 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-cthyb' +version = '3.2.1' + +homepage = 'https://triqs.github.io/cthyb/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + cthyb = continuous-time hybridisation-expansion quantum Monte Carlo + + The TRIQS-based hybridization-expansion solver allows to solve the + generic problem of a quantum impurity embedded in a conduction bath + for an arbitrary local interaction vertex. The “impurity” can be any + set of orbitals, on one or several atoms. +""" + +docurls = ['https://triqs.github.io/cthyb/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/cthyb/releases/download/%(version)s/'] +sources = ['cthyb-%(version)s.tar.gz'] +checksums = ['6f4cd36efcd19b0f1efbed2c9aa6d2640ef84f8fcf7b97675af8d54cdc327c9f'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('Clang', '16.0.6'), + ('Clang-Python-bindings', '16.0.6'), + ('GMP', '6.2.1'), + ('HDF5', '1.14.0'), + ('Mako', '1.2.4'), + ('TRIQS', '3.2.0'), + ('NFFT', '3.5.3') +] + +builddependencies = [ + ('CMake', '3.26.3') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_cthyb_c.a'], + 'dirs': ['include', 'include/triqs_cthyb', 'lib', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = ["python -c 'import triqs_cthyb'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_cthyb', +} +modextravars = { + 'TRIQS_CTHYB_ROOT': '%(installdir)s', + 'TRIQS_CTHYB_VERSION': '%(version)s', +} + +moduleclass = 'phys' \ No newline at end of file diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb new file mode 100644 index 000000000000..85b407d07990 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-dft_tools' +version = '3.2.0' + +homepage = 'https://triqs.github.io/dft_tools/' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + This TRIQS-based-based application is aimed at ab-initio calculations + for correlated materials, combining realistic DFT band-structure calculation + with the dynamical mean-field theory. Together with the necessary tools to + perform the DMFT self-consistency loop for realistic multi-band problems, + the package provides a full-fledged charge self-consistent interface to the + Wien2K package. In addition, if Wien2k is not available, it provides a generic + interface for one-shot DFT+DMFT calculations, where only the single-particle + Hamiltonian in orbital space has to be provided. +""" + +docurls = ['https://triqs.github.io/dft_tools/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/dft_tools/releases/download/%(version)s/'] +sources = ['dft_tools-%(version)s.tar.gz'] +checksums = ['77d89bc5c9a36636a720b6cae78967cd6dd83d0018c854a68bef91219a456307'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('Clang', '16.0.6'), + ('Clang-Python-bindings', '16.0.6'), + ('GMP', '6.2.1'), + ('HDF5', '1.14.0'), + ('Mako', '1.2.4'), + ('TRIQS', '3.2.0'), +] + +builddependencies = [ + ('CMake', '3.26.3') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/dmftproj', 'lib/libtriqs_dft_tools_c.a'], + 'dirs': ['include/triqs_dft_tools', 'bin', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_dft_tools'], +} + +sanity_check_commands = ["python -c 'import triqs_dft_tools'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_dft_tools', +} +modextravars = { + 'TRIQS_DFT_TOOLS_ROOT': '%(installdir)s', + 'TRIQS_DFT_TOOLS_VERSION': '%(version)s', +} + +moduleclass = 'phys' \ No newline at end of file diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tpfr-3.2.1-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tpfr-3.2.1-foss-2023a.eb new file mode 100644 index 000000000000..b1e4ccf22636 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tpfr-3.2.1-foss-2023a.eb @@ -0,0 +1,70 @@ +easyblock = 'CMakeMake' + +name = 'TRIQS-tprf' +version = '3.2.1' + +homepage = 'https://triqs.github.io/tprf' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. + + TPRF is a TRIQS-based two-particle response function tool box that + implements basic operations for higher order response functions such + as inversion, products, the random phase approximation, the bethe + salpeter equation (in the local vertex approximation), etc.. + + The aim is to provide efficient (C++/OpenMP/MPI) implementations of + the basic operations needed to compute the two-particle response in + the different two-particle channels (particle-hole, particle-particle). +""" + +docurls = ['https://triqs.github.io/tprf/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/tprf/releases/download/%(version)s/'] +sources = ['tprf-%(version)s.tar.gz'] +checksums = ['f1d4dd5986af4b37dc65f3af2a0be507455f0b4a74ea7d4de892739ccd86158c'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('Clang', '16.0.6'), + ('Clang-Python-bindings', '16.0.6'), + ('GMP', '6.2.1'), + ('HDF5', '1.14.0'), + ('Mako', '1.2.4'), + ('TRIQS', '3.2.0'), +] + +builddependencies = [ + ('CMake', '3.26.3') +] + +separate_build_dir = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs_tprf_c.a'], + 'dirs': ['include/triqs_tprf', 'lib', 'share', + 'lib/python%(pyshortver)s/site-packages/triqs_tprf'], +} + +sanity_check_commands = ["python -c 'import triqs_tprf'"] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': 'lib/cmake/triqs_tprf', +} +modextravars = { + 'TRIQS_TPRF_ROOT': '%(installdir)s', + 'TRIQS_TPRF_VERSION': '%(version)s' +} + +moduleclass = 'phys' \ No newline at end of file diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb new file mode 100644 index 000000000000..60b020d96505 --- /dev/null +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb @@ -0,0 +1,72 @@ +# TODO: make the easyconfig files for 3.2.0 +# The rest can be copied from the easy config for 3.1.1 + +easyblock = 'CMakeMake' + +name = 'TRIQS' +version = '3.2.0' + +homepage = 'https://triqs.github.io/triqs' +description = """ + TRIQS (Toolbox for Research on Interacting Quantum Systems) is a + scientific project providing a set of C++ and Python libraries to + develop new tools for the study of interacting quantum systems. +""" + +docurls = ['https://triqs.github.io/triqs/%(version_major_minor)s.x/'] +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/TRIQS/triqs/releases/download/%(version)s/'] +sources = ['triqs-%(version)s.tar.gz'] +checksums = ['b001ed1339ff6024f62b4e61fb8a955b044feac2d53b5a58575a3175e9bf6776'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Boost', '1.82.0'), + ('Clang', '16.0.6'), + ('Clang-Python-bindings', '16.0.6'), + ('GMP', '6.2.1'), + ('HDF5', '1.14.0'), + ('Mako', '1.2.4'), + ('mpi4py', '3.1.4') +] + +builddependencies = [ + ('CMake', '3.26.3') +] + +separate_build_dir = True + +# Remove installation directory before building. This fixes problems with +# failing builds in the presence of preexisting installation. +preconfigopts = "rm -rf %(installdir)s && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libtriqs.%s' % SHLIB_EXT], + 'dirs': ['include/triqs', 'include/itertools', 'include/mpi', 'include/cpp2py', + 'lib/python%(pyshortver)s/site-packages', 'share'], +} + +sanity_check_commands = [ + "triqs++ --help", + "c++2py --help", + "python -c 'import triqs'" +] + +modextrapaths = { + 'CPLUS_INCLUDE_PATH': 'include', + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'CMAKE_PREFIX_PATH': ['lib/cmake/triqs', 'lib/cmake/cpp2py'] +} +modextravars = { + 'TRIQS_ROOT': '%(installdir)s', + 'TRIQS_VERSION': '%(version)s' +} + +moduleclass = 'phys' \ No newline at end of file From fbbff3ced38c0081b676cff46b536920d08ce0a2 Mon Sep 17 00:00:00 2001 From: Victor Lopez Herrero Date: Tue, 27 Feb 2024 10:30:30 +0100 Subject: [PATCH 0831/1193] Update easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb b/easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb index 2703715c3eb6..687fec96e6bd 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.4-gompi-2023b.eb @@ -14,7 +14,7 @@ homepage = 'https://pm.bsc.es/dlb/' docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] toolchain = {'name': 'gompi', 'version': '2023b'} -builddependencies = [('Python', '3.11.5', '', ('GCCcore', '13.2.0'))] +builddependencies = [('Python', '3.11.5')] sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] From 4e225ee989b4fd2d93066c409c1541731a4403a2 Mon Sep 17 00:00:00 2001 From: Victor Lopez Herrero Date: Tue, 27 Feb 2024 10:31:22 +0100 Subject: [PATCH 0832/1193] Update dlb-3.4-iimpi-2023b.eb --- easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb b/easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb index 1ce3cceafd8f..a9bc96ba02a8 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.4-iimpi-2023b.eb @@ -14,7 +14,7 @@ homepage = 'https://pm.bsc.es/dlb/' docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] toolchain = {'name': 'iimpi', 'version': '2023b'} -builddependencies = [('Python', '3.11.5', '', ('GCCcore', '13.2.0'))] +builddependencies = [('Python', '3.11.5')] sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] From d50080519563851463c59dceaa7572ea400a97b8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Feb 2024 13:21:50 +0100 Subject: [PATCH 0833/1193] adding easyconfigs: MACS3-3.0.1-gfbf-2023a.eb, hmmlearn-0.3.0-gfbf-2023a.eb --- .../h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb | 24 ++++++++++++ .../m/MACS3/MACS3-3.0.1-gfbf-2023a.eb | 38 +++++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb new file mode 100644 index 000000000000..a975c36d2253 --- /dev/null +++ b/easybuild/easyconfigs/h/hmmlearn/hmmlearn-0.3.0-gfbf-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'hmmlearn' +version = '0.3.0' + +homepage = 'https://github.com/hmmlearn/hmmlearn' +description = "hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d13a91ea3695df881465e3d36132d7eef4e84d483f4ba538a4b46e24b5ea100f'] + +dependencies = [ + ('Python', '3.11.3'), + ('scikit-learn', '1.3.1'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-gfbf-2023a.eb b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-gfbf-2023a.eb new file mode 100644 index 000000000000..219b54979c8d --- /dev/null +++ b/easybuild/easyconfigs/m/MACS3/MACS3-3.0.1-gfbf-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MACS3' +version = '3.0.1' + +homepage = 'https://macs3-project.github.io/MACS/' +description = """Model Based Analysis for ChIP-Seq data""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('pybind11', '2.11.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('hmmlearn', '0.3.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cykhash', '2.0.1', { + 'checksums': ['b4794bc9f549114d8cf1d856d9f64e08ff5f246bf043cf369fdb414e9ceb97f7'], + }), + (name, version, { + 'checksums': ['b07ca6e84a71aab29589f63e3dff96049aa6739e055a629125b31c788c877016'], + 'preinstallopts': "sed -i 's/scipy>=1.11.4/scipy>=1.11/g' setup.py && ", + 'modulename': 'MACS3', + }), +] + +sanity_check_commands = ["macs3 --help"] + +moduleclass = 'bio' From c8c7b624466451f67361c573d1a9144342e30a56 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 27 Feb 2024 14:10:42 +0100 Subject: [PATCH 0834/1193] adding easyconfigs: CellTypist-1.6.2-foss-2023a.eb, igraph-0.10.10-foss-2023a.eb, python-igraph-0.11.4-foss-2023a.eb, libleidenalg-0.11.1-foss-2023a.eb, leidenalg-0.10.2-foss-2023a.eb --- .../CellTypist/CellTypist-1.6.2-foss-2023a.eb | 43 ++++++++++++++ .../i/igraph/igraph-0.10.10-foss-2023a.eb | 41 +++++++++++++ .../leidenalg/leidenalg-0.10.2-foss-2023a.eb | 50 ++++++++++++++++ .../libleidenalg-0.11.1-foss-2023a.eb | 33 +++++++++++ .../python-igraph-0.11.4-foss-2023a.eb | 59 +++++++++++++++++++ 5 files changed, 226 insertions(+) create mode 100644 easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/i/igraph/igraph-0.10.10-foss-2023a.eb create mode 100644 easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb new file mode 100644 index 000000000000..f45ddb085160 --- /dev/null +++ b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'CellTypist' +version = '1.6.2' + +homepage = 'https://www.celltypist.org/' +description = "A tool for semi-automatic cell type annotation" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('openpyxl', '3.1.2'), + ('scanpy', '1.9.8'), + ('leidenalg', '0.10.2'), +] + +exts_list = [ + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('click', '8.1.7', { + 'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'], + }), + ('celltypist', version, { + 'checksums': ['a22309230c578c3738f72643492387167053f35a610625c75d66b056cf520361'], + }), +] + +use_pip = True + +sanity_check_paths = { + 'files': ['bin/celltypist'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["celltypist --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/i/igraph/igraph-0.10.10-foss-2023a.eb b/easybuild/easyconfigs/i/igraph/igraph-0.10.10-foss-2023a.eb new file mode 100644 index 000000000000..6ed3462390c8 --- /dev/null +++ b/easybuild/easyconfigs/i/igraph/igraph-0.10.10-foss-2023a.eb @@ -0,0 +1,41 @@ +# Author: Denis Krišťák (INUITS) +# Modified: Jasper Grimm (UoY) +# Update: Pavel Tománek (INUITS) + +easyblock = 'CMakeMake' + +name = 'igraph' +version = '0.10.10' + +homepage = 'https://igraph.org' +description = """igraph is a collection of network analysis tools with the emphasis on +efficiency, portability and ease of use. igraph is open source and free. igraph can be +programmed in R, Python and C/C++.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/igraph/igraph/releases/download/%(version)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['6148f2e72a183ef5cd08324cccc73fa9eb8e54bb5a96c7f8f3c0465432ec2404'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('GLPK', '5.0'), + ('libxml2', '2.11.4'), + ('zlib', '1.2.13'), + ('arpack-ng', '3.9.0'), +] + +# Build static and shared libraries +configopts = ["-DBUILD_SHARED_LIBS=OFF", "-DBUILD_SHARED_LIBS=ON"] + +sanity_check_paths = { + 'files': ['include/igraph/igraph.h'] + ['lib/libigraph.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023a.eb b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023a.eb new file mode 100644 index 000000000000..51d653f27b2d --- /dev/null +++ b/easybuild/easyconfigs/l/leidenalg/leidenalg-0.10.2-foss-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'leidenalg' +version = '0.10.2' + +homepage = 'https://github.com/vtraag/leidenalg' +description = """Implementation of the Leiden algorithm for various quality +functions to be used with igraph in Python.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('PyYAML', '6.0'), + ('Bison', '3.8.2'), + ('libtool', '2.4.7'), + ('flex', '2.6.4'), + ('CMake', '3.26.3'), + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('igraph', '0.10.10'), + ('python-igraph', '0.11.4'), + ('libleidenalg', '0.11.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('ddt', '1.7.2', { + 'checksums': ['d215d6b083963013c4a19b1e4dcd6a96e80e43ab77519597a6acfcf2e9a3e04b'], + }), + (name, version, { + 'checksums': ['0f4147a92b59834a719bfce30d563ea107e570130a7be60adbc8b95757192e4c'], + }), +] + +sanity_check_commands = [ + # tests require that 'leidenalg' Python module is available, + # so needs to be run after installation + "cd %(builddir)s/leidenalg/leidenalg-%(version)s && python setup.py test", + "python -c 'import leidenalg; import igraph as ig; " + "leidenalg.find_partition(ig.Graph.Erdos_Renyi(100, 0.1), " + "leidenalg.ModularityVertexPartition)'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2023a.eb b/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2023a.eb new file mode 100644 index 000000000000..63aefe650b97 --- /dev/null +++ b/easybuild/easyconfigs/l/libleidenalg/libleidenalg-0.11.1-foss-2023a.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'libleidenalg' +version = '0.11.1' + +homepage = 'https://github.com/vtraag/libleidenalg' +description = """Implements the Leiden algorithm in C++""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/vtraag/libleidenalg/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['7d7392afd214c584e023cc2f0d0ac375f58575c32f2e49ba85062065f1637c7f'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [ + ('igraph', '0.10.10'), +] + +sanity_check_paths = { + 'files': [ + 'include/%(name)s/GraphHelper.h', + 'include/%(name)s/libleidenalg_export.h', + 'lib/liblibleidenalg.%s' % SHLIB_EXT, + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb new file mode 100644 index 000000000000..b983243de45f --- /dev/null +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb @@ -0,0 +1,59 @@ +easyblock = 'PythonBundle' + +name = 'python-igraph' +version = '0.11.4' + +homepage = 'https://igraph.org/python' +description = """Python interface to the igraph high performance graph library, primarily aimed at complex network + research and analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('pkgconf', '1.9.5'), + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Clang', '16.0.6'), + ('libxml2', '2.11.4'), + ('zlib', '1.2.13'), + ('igraph', '0.10.10'), +] + +use_pip = True + +exts_list = [ + ('pycparser', '2.21', { + 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], + }), + ('cffi', '1.16.0', { + 'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'], + }), + ('texttable', '1.7.0', { + 'checksums': ['2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638'], + }), + ('cairocffi', '1.6.1', { + 'checksums': ['78e6bbe47357640c453d0be929fa49cd05cce2e1286f3d2a1ca9cbda7efdb8b7'], + }), + ('igraph', version, { + 'modulename': 'igraph', + 'checksums': ['2437ae0157af6824e2e65a23f7a1fa4fbf0f3664333c72aeca4fc01b83e18483'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +# cairo must be available for proper plotting support +sanity_check_commands = [ + "python -c 'from igraph.drawing.cairo.utils import find_cairo; " + "cairo = find_cairo(); cairo.Context'", +] + +sanity_pip_check = True + +moduleclass = 'lib' From 8e41f74af4e646b8eed6f42896d855ddb214ae8b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 27 Feb 2024 14:33:49 +0100 Subject: [PATCH 0835/1193] replace some deps by Python-bundle-PyPI --- .../c/CellTypist/CellTypist-1.6.2-foss-2023a.eb | 7 +------ .../python-igraph/python-igraph-0.11.4-foss-2023a.eb | 12 +----------- 2 files changed, 2 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb index f45ddb085160..65be95087f71 100644 --- a/easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CellTypist/CellTypist-1.6.2-foss-2023a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), + ('Python-bundle-PyPI', '2023.06'), ('scikit-learn', '1.3.1'), ('openpyxl', '3.1.2'), ('scanpy', '1.9.8'), @@ -18,12 +19,6 @@ dependencies = [ ] exts_list = [ - ('requests', '2.31.0', { - 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], - }), - ('click', '8.1.7', { - 'checksums': ['ca9853ad459e787e2192211578cc907e7594e294c7ccc834310722b41b9ca6de'], - }), ('celltypist', version, { 'checksums': ['a22309230c578c3738f72643492387167053f35a610625c75d66b056cf520361'], }), diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb index b983243de45f..925e86226029 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb @@ -16,6 +16,7 @@ builddependencies = [ dependencies = [ ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), ('Clang', '16.0.6'), ('libxml2', '2.11.4'), ('zlib', '1.2.13'), @@ -25,12 +26,6 @@ dependencies = [ use_pip = True exts_list = [ - ('pycparser', '2.21', { - 'checksums': ['e644fdec12f7872f86c58ff790da456218b10f863970249516d60a5eaca77206'], - }), - ('cffi', '1.16.0', { - 'checksums': ['bcb3ef43e58665bbda2fb198698fcae6776483e0c4a631aa5647806c25e02cc0'], - }), ('texttable', '1.7.0', { 'checksums': ['2d2068fb55115807d3ac77a4ca68fa48803e84ebb0ee2340f858107a36522638'], }), @@ -43,11 +38,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - # cairo must be available for proper plotting support sanity_check_commands = [ "python -c 'from igraph.drawing.cairo.utils import find_cairo; " From 79eaae5936c1b0f0b719dd1ef8409096ca6455ef Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Feb 2024 18:04:34 +0100 Subject: [PATCH 0836/1193] remove easyconfig for Gradle 8.6 without Java versionsuffix --- easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb | 23 -------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb diff --git a/easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb b/easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb deleted file mode 100644 index 794188e26cc3..000000000000 --- a/easybuild/easyconfigs/g/Gradle/Gradle-8.6.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'PackedBinary' - -name = 'Gradle' -version = '8.6' - -homepage = 'https://gradle.org' -description = """Complete Gradle install. -From mobile apps to microservices, from small startups to big enterprises, -Gradle helps teams build, automate and deliver better software, faster. -""" - -toolchain = SYSTEM - -source_urls = ['https://services.gradle.org/distributions'] -sources = ['gradle-%(version)s-all.zip'] -checksums = ['85719317abd2112f021d4f41f09ec370534ba288432065f4b477b6a3b652910d'] - -sanity_check_paths = { - 'files': ['bin/gradle'], - 'dirs': [], -} - -moduleclass = 'devel' From 76a3ea4f7008258a2395af695ccc6c99b1a33b42 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Feb 2024 18:07:36 +0100 Subject: [PATCH 0837/1193] trivial code style changes in Gradle and QuPath easyconfigs --- easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb | 4 ++-- .../q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb | 12 +++--------- 2 files changed, 5 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb b/easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb index 01cb2993372e..d3224761b29e 100644 --- a/easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb +++ b/easybuild/easyconfigs/g/Gradle/Gradle-8.6-Java-17.eb @@ -25,6 +25,6 @@ sanity_check_paths = { 'dirs': [], } -moduleclass = 'devel' - sanity_check_commands = ['%(namelower)s --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb index bed0ce4eb215..de829739f2e7 100644 --- a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb +++ b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb @@ -36,16 +36,10 @@ files_to_copy = [ modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': [ - 'bin/%(name)s', - 'lib/libapplauncher.%s' % SHLIB_EXT, - ], - 'dirs': [ - 'lib/app', - 'lib/runtime', - ], + 'files': ['bin/qupath', 'lib/libapplauncher.%s' % SHLIB_EXT], + 'dirs': ['lib/app', 'lib/runtime'], } -sanity_check_commands = ['%(name)s --help'] +sanity_check_commands = ["qupath --help"] moduleclass = 'bio' From 0890200b5287197452713d49cf6b0d5b89ebb5dd Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 27 Feb 2024 18:18:45 +0100 Subject: [PATCH 0838/1193] QuPath binary is named QuPath, not qupath --- .../q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb index de829739f2e7..f2d3ffb6c4d8 100644 --- a/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb +++ b/easybuild/easyconfigs/q/QuPath/QuPath-0.5.0-GCCcore-12.3.0-Java-17.eb @@ -36,10 +36,10 @@ files_to_copy = [ modextrapaths = {'PATH': ['']} sanity_check_paths = { - 'files': ['bin/qupath', 'lib/libapplauncher.%s' % SHLIB_EXT], + 'files': ['bin/QuPath', 'lib/libapplauncher.%s' % SHLIB_EXT], 'dirs': ['lib/app', 'lib/runtime'], } -sanity_check_commands = ["qupath --help"] +sanity_check_commands = ["QuPath --help"] moduleclass = 'bio' From 64b7528bdb9e77bb5748f16178fd81144aae2acf Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 27 Feb 2024 17:33:46 +0000 Subject: [PATCH 0839/1193] adding easyconfigs: SURVIVOR-1.0.7-19-ged1ca51-GCC-12.2.0.eb --- .../SURVIVOR-1.0.7-19-ged1ca51-GCC-12.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-12.2.0.eb new file mode 100644 index 000000000000..12fdc2cadd3e --- /dev/null +++ b/easybuild/easyconfigs/s/SURVIVOR/SURVIVOR-1.0.7-19-ged1ca51-GCC-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'SURVIVOR' +version = '1.0.7-19-ged1ca51' + +homepage = 'https://github.com/fritzsedlazeck/SURVIVOR' +description = "Toolset for SV simulation, comparison and filtering" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['ed1ca5188a2d9286d582417b7a65938c768df995.tar.gz'] +checksums = ['46c2618a225353e31422a12e9661167298947ad6ff681943cea6703ba18682bd'] + +github_account = 'fritzsedlazeck' +start_dir = 'Debug' +files_to_copy = ['Debug/%(name)s'] + +sanity_check_paths = { + 'files': ['%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From e770e2b851880b5d69bfde1719ce87c4c17da054 Mon Sep 17 00:00:00 2001 From: nicolas Date: Tue, 27 Feb 2024 19:40:54 +0100 Subject: [PATCH 0840/1193] adding easyconfigs: dill-0.3.8-GCCcore-12.3.0.eb, multiprocess-0.70.16-gfbf-2023a.eb --- .../d/dill/dill-0.3.8-GCCcore-12.3.0.eb | 27 +++++++++++++++++++ .../multiprocess-0.70.16-gfbf-2023a.eb | 24 +++++++++++++++++ 2 files changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..16e3710eb296 --- /dev/null +++ b/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'dill' +version = '0.3.8' + +homepage = 'https://pypi.org/project/dill/' +description = """dill extends python's pickle module for serializing and de-serializing + python objects to the majority of the built-in python types. Serialization is the process + of converting an object to a byte stream, and the inverse of which is converting a byte + stream back to on python object hierarchy.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb new file mode 100644 index 000000000000..cee3e7649fc4 --- /dev/null +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'multiprocess' +version = '0.70.16' + +homepage = 'https://github.com/uqfoundation/multiprocess' +description = "better multiprocessing and multithreading in python" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'] + +dependencies = [ + ('Python', '3.11.3'), + ('dill', '0.3.8'), + ('Arrow', '14.0.1'), # if needed rebuild --from-pr 19758 +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From 9a73f5a439d975fb3990b90649cf2442a5757936 Mon Sep 17 00:00:00 2001 From: donrolih Date: Wed, 28 Feb 2024 09:05:00 +0100 Subject: [PATCH 0841/1193] Renamed TRIQS-tprf --- ...QS-tpfr-3.2.1-foss-2023a.eb => TRIQS-tprf-3.2.1-foss-2023a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/t/TRIQS-tprf/{TRIQS-tpfr-3.2.1-foss-2023a.eb => TRIQS-tprf-3.2.1-foss-2023a.eb} (100%) diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tpfr-3.2.1-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.2.1-foss-2023a.eb similarity index 100% rename from easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tpfr-3.2.1-foss-2023a.eb rename to easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.2.1-foss-2023a.eb From b80ae2a2795732018d3c026d40b00aa45bbc77aa Mon Sep 17 00:00:00 2001 From: donrolih Date: Wed, 28 Feb 2024 09:40:41 +0100 Subject: [PATCH 0842/1193] Minor edits to conform to the styling guide --- .../Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb | 2 +- .../t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb | 2 +- .../t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb | 2 +- .../easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.2.1-foss-2023a.eb | 2 +- easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb | 5 +---- 6 files changed, 6 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb index 6d2d1ec9a6b3..bc314d248f8f 100644 --- a/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/Clang-Python-bindings/Clang-Python-bindings-16.0.6-GCCcore-12.3.0.eb @@ -28,4 +28,4 @@ sanity_check_commands = ["python -c 'import clang'"] modextrapaths = {'PYTHONPATH': ''} -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb index baa326a1a9d8..b12d6190cc0d 100644 --- a/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NFFT/NFFT-3.5.3-foss-2023a.eb @@ -28,4 +28,4 @@ sanity_check_paths = { 'dirs': ['lib/pkgconfig'], } -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb index b5ad923eddb1..aba94fc78c9a 100644 --- a/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TRIQS-cthyb/TRIQS-cthyb-3.2.1-foss-2023a.eb @@ -66,4 +66,4 @@ modextravars = { 'TRIQS_CTHYB_VERSION': '%(version)s', } -moduleclass = 'phys' \ No newline at end of file +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb index 85b407d07990..4a136f51689d 100644 --- a/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TRIQS-dft_tools/TRIQS-dft_tools-3.2.0-foss-2023a.eb @@ -67,4 +67,4 @@ modextravars = { 'TRIQS_DFT_TOOLS_VERSION': '%(version)s', } -moduleclass = 'phys' \ No newline at end of file +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.2.1-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.2.1-foss-2023a.eb index b1e4ccf22636..1547b3cf9990 100644 --- a/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.2.1-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TRIQS-tprf/TRIQS-tprf-3.2.1-foss-2023a.eb @@ -67,4 +67,4 @@ modextravars = { 'TRIQS_TPRF_VERSION': '%(version)s' } -moduleclass = 'phys' \ No newline at end of file +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb index 60b020d96505..7daf38a60f6c 100644 --- a/easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb +++ b/easybuild/easyconfigs/t/TRIQS/TRIQS-3.2.0-foss-2023a.eb @@ -1,6 +1,3 @@ -# TODO: make the easyconfig files for 3.2.0 -# The rest can be copied from the easy config for 3.1.1 - easyblock = 'CMakeMake' name = 'TRIQS' @@ -69,4 +66,4 @@ modextravars = { 'TRIQS_VERSION': '%(version)s' } -moduleclass = 'phys' \ No newline at end of file +moduleclass = 'phys' From e25688196041b13a9d511abfa49aee69789235d1 Mon Sep 17 00:00:00 2001 From: nicolas Date: Wed, 28 Feb 2024 12:06:52 +0100 Subject: [PATCH 0843/1193] fixed dependency conflict --- .../d/dill/dill-0.3.8-GCCcore-12.3.0.eb | 27 ------------------- .../multiprocess-0.70.16-gfbf-2023a.eb | 2 +- 2 files changed, 1 insertion(+), 28 deletions(-) delete mode 100644 easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb deleted file mode 100644 index 16e3710eb296..000000000000 --- a/easybuild/easyconfigs/d/dill/dill-0.3.8-GCCcore-12.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'dill' -version = '0.3.8' - -homepage = 'https://pypi.org/project/dill/' -description = """dill extends python's pickle module for serializing and de-serializing - python objects to the majority of the built-in python types. Serialization is the process - of converting an object to a byte stream, and the inverse of which is converting a byte - stream back to on python object hierarchy.""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['3ebe3c479ad625c4553aca177444d89b486b1d84982eeacded644afc0cf797ca'] - -builddependencies = [('binutils', '2.40')] - -dependencies = [ - ('Python', '3.11.3'), -] - -use_pip = True -download_dep_fail = True -sanity_pip_check = True - -moduleclass = 'data' diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb index cee3e7649fc4..d36bdadda243 100644 --- a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb @@ -13,7 +13,7 @@ checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'] dependencies = [ ('Python', '3.11.3'), - ('dill', '0.3.8'), + ('dill', '0.3.7'), ('Arrow', '14.0.1'), # if needed rebuild --from-pr 19758 ] From dbad996ab87354d041beca9569075f5c9badf000 Mon Sep 17 00:00:00 2001 From: nicolas Date: Wed, 28 Feb 2024 12:16:10 +0100 Subject: [PATCH 0844/1193] adding easyconfigs: python-xxhash-3.4.1-GCCcore-12.3.0.eb, xxHash-0.8.2-GCCcore-12.3.0.eb --- .../python-xxhash-3.4.1-GCCcore-12.3.0.eb | 30 ++++++++++++++++++ .../x/xxHash/xxHash-0.8.2-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 2 files changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/x/xxHash/xxHash-0.8.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..cc881eb49174 --- /dev/null +++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'python-xxhash' +version = '3.4.1' + +homepage = 'https://github.com/ifduyue/python-xxhash' +description = 'xxhash is a Python binding for the xxHash library by Yann Collet.' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('xxHash', '0.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xxhash', version, { + 'preinstallopts': 'XXHASH_LINK_SO=1', + 'checksums': ['0379d6cf1ff987cd421609a264ce025e74f346e3e145dd106c0cc2e3ec3f99a9'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/xxHash/xxHash-0.8.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f91989c338f7 --- /dev/null +++ b/easybuild/easyconfigs/x/xxHash/xxHash-0.8.2-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'xxHash' +version = '0.8.2' + +homepage = 'https://cyan4973.github.io/xxHash' +description = "xxHash is an extremely fast non-cryptographic hash algorithm, working at RAM speed limit." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Cyan4973/xxHash/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['baee0c6afd4f03165de7a4e67988d16f0f2b257b51d0e3cb91909302a26a79c4'] + +builddependencies = [ + ('binutils', '2.40'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/xxhsum', 'include/xxh3.h', 'include/xxhash.h', + 'lib/libxxhash.a', 'lib/libxxhash.%s' % SHLIB_EXT, 'lib/pkgconfig/libxxhash.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["xxhsum --help"] + +moduleclass = 'tools' From c41ac42880715c8857c924a98eba5343299c1392 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 28 Feb 2024 12:16:54 +0100 Subject: [PATCH 0845/1193] Fix test_vsa_no_mass --- .../TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb | 6 ++++- .../t/TAMkin/TAMkin-1.2.6-foss-2020b.eb | 6 ++++- .../t/TAMkin/TAMkin-1.2.6-foss-2021a.eb | 6 ++++- .../t/TAMkin/TAMkin-1.2.6-foss-2021b.eb | 6 ++++- .../TAMkin-1.2.6_fix-test_vsa_no_mass.patch | 24 +++++++++++++++++++ 5 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-test_vsa_no_mass.patch diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb index f16feb95b9f0..22eb629671d8 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020a-Python-3.8.2.eb @@ -13,10 +13,14 @@ toolchain = {'name': 'foss', 'version': '2020a'} source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['TAMkin-1.2.6_fix-python38.patch'] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] checksums = [ {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb index 022abda9c0d5..385046a56c97 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2020b.eb @@ -12,10 +12,14 @@ toolchain = {'name': 'foss', 'version': '2020b'} source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['TAMkin-1.2.6_fix-python38.patch'] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] checksums = [ {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb index 95ac548b7497..d1d4b1cf9949 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021a.eb @@ -12,10 +12,14 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['TAMkin-1.2.6_fix-python38.patch'] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] checksums = [ {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb index a4dd316d17cf..4a7883c7f8e2 100644 --- a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6-foss-2021b.eb @@ -12,10 +12,14 @@ toolchain = {'name': 'foss', 'version': '2021b'} source_urls = ['https://github.com/molmod/tamkin/releases/download/%(version)s'] sources = [SOURCE_TAR_GZ] -patches = ['TAMkin-1.2.6_fix-python38.patch'] +patches = [ + 'TAMkin-1.2.6_fix-python38.patch', + 'TAMkin-1.2.6_fix-test_vsa_no_mass.patch', +] checksums = [ {'TAMkin-1.2.6.tar.gz': '1bde275a09be91e5241616aaa9fedc60cb359a263f5c5909bb14431c3a4ed5fd'}, {'TAMkin-1.2.6_fix-python38.patch': '1633d5b24b012f8c4b6731491e4072c819ebbba65574966b7185ecca52eeac9b'}, + {'TAMkin-1.2.6_fix-test_vsa_no_mass.patch': '67d8b8671d7c71123e8ee9a7b9ebea6562e9711edb41555d1926b1b51d549066'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-test_vsa_no_mass.patch b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-test_vsa_no_mass.patch new file mode 100644 index 000000000000..5d28778abb87 --- /dev/null +++ b/easybuild/easyconfigs/t/TAMkin/TAMkin-1.2.6_fix-test_vsa_no_mass.patch @@ -0,0 +1,24 @@ +The test fails on haswell CPUs (and maybe others). +It looks like the reference value is off such that it just passes in regular circumstances. +The following values are observed: +- REF: 0.13774798 +- PASS: 0.43330176 +- FAIL: 0.64607670 + +Fix by adjusting the reference to the passing value. +See https://github.com/molmod/tamkin/issues/43 + +Author: Alexander Grund (TU Dresden) + +diff -ur tamkin-1.2.6-orig/tamkin/test/test_nma.py tamkin-1.2.6/tamkin/test/test_nma.py +--- tamkin-1.2.6-orig/tamkin/test/test_nma.py 2024-02-28 10:07:55.695638855 +0100 ++++ tamkin-1.2.6/tamkin/test/test_nma.py 2024-02-28 11:12:07.320823854 +0100 +@@ -528,7 +528,7 @@ + pkg_resources.resource_filename(__name__, "../data/test/an/fixed.01.txt")) + nma = NMA(molecule, VSANoMass(subs)) + self.assert_(len(nma.zeros)==3) +- expected_freqs = np.array([-0.4205594, 0.03940166, 0.13774798]) ++ expected_freqs = np.array([-0.4205594, 0.03940166, 0.43330176]) + self.check_freqs(expected_freqs, nma, 0, check_zeros=True) + + # --- atoms of subsystem are collinear From 780be872740aab5fd92759dcd888ba73bd02fafc Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 28 Feb 2024 14:31:25 +0100 Subject: [PATCH 0846/1193] adding easyconfigs: scib-1.1.4-foss-2023a.eb, pyparsing-3.1.1-GCCcore-12.3.0.eb, pydot-2.0.0-GCCcore-12.3.0.eb, Deprecated-1.2.14-foss-2023a.eb, scikit-misc-0.3.1-foss-2023a.eb --- .../Deprecated-1.2.14-foss-2023a.eb | 29 +++++++++++++ .../p/pydot/pydot-2.0.0-GCCcore-12.3.0.eb | 28 ++++++++++++ .../pyparsing-3.1.1-GCCcore-12.3.0.eb | 33 ++++++++++++++ .../s/scib/scib-1.1.4-foss-2023a.eb | 43 +++++++++++++++++++ .../scikit-misc-0.3.1-foss-2023a.eb | 28 ++++++++++++ 5 files changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb new file mode 100644 index 000000000000..a001fd3131a9 --- /dev/null +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb @@ -0,0 +1,29 @@ +# author: Denis Kristak (INUITS) +# update: Pavel Tománek (INUITS) + +easyblock = 'PythonBundle' + +name = 'Deprecated' +version = '1.2.14' + +homepage = 'https://github.com/tantale/deprecated' +description = "If you need to mark a function or a method as deprecated, you can use the @deprecated decorator." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('wrapt', '1.15.0'), +] + + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['e5323eb936458dccc2582dc6f9c322c852a775a27065ff2b0c4970b9d53d01b3'], + }), +] + +moduleclass = 'tools' \ No newline at end of file diff --git a/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..4bc9e76f2dfb --- /dev/null +++ b/easybuild/easyconfigs/p/pydot/pydot-2.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'pydot' +version = '2.0.0' + +homepage = 'https://github.com/pydot/pydot' +description = "Python interface to Graphviz's Dot language." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +exts_list = [ + (name, version, { + 'checksums': ['60246af215123fa062f21cd791be67dda23a6f280df09f68919e637a1e4f3235'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..1f9c7c1daf2e --- /dev/null +++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'pyparsing' +version = '3.1.1' + +homepage = 'https://github.com/pyparsing/pyparsing' +description = """The pyparsing module is an alternative approach to creating and +executing simple grammars, vs. the traditional lex/yacc approach, or the use of +regular expressions. The pyparsing module provides a library of classes that +client code uses to construct the grammar directly in Python code.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +# matplotlib 3.7.2 requires pyparsing<=3.1, this v3.1.1 will not works with it +builddependencies = [ + ('binutils', '2.40'), + ('pkg-config', '0.29.2', '', SYSTEM), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +exts_list = [ + (name, version, { + 'checksums': ['ede28a1a32462f5a9705e07aea48001a08f7cf81a021585011deba701581a0db'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb new file mode 100644 index 000000000000..05d50ba75cf6 --- /dev/null +++ b/easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb @@ -0,0 +1,43 @@ +# author: Denis Kristak (INUITS) +# update: Pavel Tománek (INUITS) + +easyblock = 'PythonBundle' + +name = 'scib' +version = '1.1.4' + +homepage = 'https://github.com/theislab/scib' +description = "Benchmarking atlas-level data integration in single-cell genomics." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Seaborn', '0.13.2'), + ('matplotlib', '3.7.2'), + ('numba', '0.58.1'), + ('scanpy', '1.9.8'), + ('h5py', '3.9.0'), + ('scikit-learn', '1.3.1'), + ('scikit-misc', '0.3.1'), + ('leidenalg', '0.10.2'), + ('umap-learn', '0.5.5'), + ('pydot', '2.0.0'), + ('igraph', '0.10.10'), + ('python-igraph', '0.11.4'), + ('Deprecated', '1.2.14'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['b7800f308cd6acc36db6e159a53b0432adb2f48e9b7b434240bc5d696df10bfb'], + }), +] + +preinstallopts = "sed -i 's|pandas<2|pandas>=2|g' setup.cfg && " + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb new file mode 100644 index 000000000000..e355180eb496 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.3.1-foss-2023a.eb @@ -0,0 +1,28 @@ +# updated: Denis Kristak, Pavel Tománek (INUITS) +easyblock = 'PythonBundle' + +name = 'scikit-misc' +version = '0.3.1' + +homepage = 'https://github.com/has2k1/scikit-misc' +description = "Miscellaneous tools for data analysis and scientific computing" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('meson-python', '0.13.2'), +] + +exts_list = [ + ('scikit_misc', version, { + 'modulename': 'skmisc', + 'checksums': ['ba813a005ab681df478d719d3c3f03eeda709b6a45e0c1a0056eaef0495c16e4'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From ce4c8bff12f60ef033a8fb17e72021b016b8e080 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 28 Feb 2024 13:50:34 +0000 Subject: [PATCH 0847/1193] Drop checksum from VSCode --- easybuild/easyconfigs/v/VSCode/VSCode-1.85.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.0.eb b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.0.eb index 87bd4a020ed3..a07a5ae511cc 100644 --- a/easybuild/easyconfigs/v/VSCode/VSCode-1.85.0.eb +++ b/easybuild/easyconfigs/v/VSCode/VSCode-1.85.0.eb @@ -18,7 +18,7 @@ toolchain = {'name': 'system', 'version': 'system'} source_urls = ['https://code.visualstudio.com/sha/download?build=stable&os=linux-x64&'] sources = ['code-stable-x64-%s.tar.gz' % local_version_id] -checksums = ['01669d69e567a5290336b1d2f7b2f0f1816e9d7099004b81a26f8f40ee17c9fc'] +checksums = [None] # the tarballs are not stable modaliases = {'vscode': '%(installdir)s/bin/code'} From e55ba4c433a9aceb31ae329707627a58d56f7c2f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 28 Feb 2024 14:56:20 +0100 Subject: [PATCH 0848/1193] fix newline + whitespace --- .../easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb | 2 +- easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb index a001fd3131a9..803a1996c309 100644 --- a/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb +++ b/easybuild/easyconfigs/d/Deprecated/Deprecated-1.2.14-foss-2023a.eb @@ -26,4 +26,4 @@ exts_list = [ }), ] -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb b/easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb index 05d50ba75cf6..0f3d25a3ad13 100644 --- a/easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scib/scib-1.1.4-foss-2023a.eb @@ -10,7 +10,7 @@ homepage = 'https://github.com/theislab/scib' description = "Benchmarking atlas-level data integration in single-cell genomics." toolchain = {'name': 'foss', 'version': '2023a'} - + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From c714da72bfa8b2a281da1c8482c805d5cd5892fd Mon Sep 17 00:00:00 2001 From: nicolas Date: Wed, 28 Feb 2024 15:28:00 +0100 Subject: [PATCH 0849/1193] version drop from 0.70.16 to 0.70.15 --- ...70.16-gfbf-2023a.eb => multiprocess-0.70.15-gfbf-2023a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/m/multiprocess/{multiprocess-0.70.16-gfbf-2023a.eb => multiprocess-0.70.15-gfbf-2023a.eb} (82%) diff --git a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2023a.eb similarity index 82% rename from easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb rename to easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2023a.eb index d36bdadda243..631ec9aa69a1 100644 --- a/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.16-gfbf-2023a.eb +++ b/easybuild/easyconfigs/m/multiprocess/multiprocess-0.70.15-gfbf-2023a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'multiprocess' -version = '0.70.16' +version = '0.70.15' homepage = 'https://github.com/uqfoundation/multiprocess' description = "better multiprocessing and multithreading in python" @@ -9,7 +9,7 @@ description = "better multiprocessing and multithreading in python" toolchain = {'name': 'gfbf', 'version': '2023a'} sources = [SOURCE_TAR_GZ] -checksums = ['161af703d4652a0e1410be6abccecde4a7ddffd19341be0a7011b94aeb171ac1'] +checksums = ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'] dependencies = [ ('Python', '3.11.3'), From fddd3f26c9d9fb92e0220e404173019f446680e0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 28 Feb 2024 15:50:34 +0100 Subject: [PATCH 0850/1193] replace pkg-config by pkgconfig for pyparsing --- .../easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb index 1f9c7c1daf2e..c2539e1892f8 100644 --- a/easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pyparsing/pyparsing-3.1.1-GCCcore-12.3.0.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} # matplotlib 3.7.2 requires pyparsing<=3.1, this v3.1.1 will not works with it builddependencies = [ ('binutils', '2.40'), - ('pkg-config', '0.29.2', '', SYSTEM), + ('pkgconf', '1.9.5'), ] dependencies = [ From bb48772574ad501488cfd0594c5e345be6898a16 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Wed, 28 Feb 2024 16:24:16 +0100 Subject: [PATCH 0851/1193] Respect sysroot when in use --- .../p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb | 6 ++++++ .../p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb | 6 ++++++ .../p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb | 6 ++++++ .../p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb | 6 ++++++ .../p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb | 6 ++++++ .../p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb | 6 ++++++ 6 files changed, 36 insertions(+) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb index 23fe713f7d70..a9782146eca3 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.2.0-GCCcore-10.3.0.eb @@ -31,6 +31,12 @@ dependencies = [ use_pip = True download_dep_fail = True +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + options = {'modulename': 'PIL'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb index 74b967e89260..870700860cf7 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.1-GCCcore-11.2.0.eb @@ -31,6 +31,12 @@ dependencies = [ use_pip = True download_dep_fail = True +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + options = {'modulename': 'PIL'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb index cea197aa05e8..99dab09b9c10 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-8.3.2-GCCcore-11.2.0.eb @@ -27,6 +27,12 @@ dependencies = [ use_pip = True download_dep_fail = True +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + options = {'modulename': 'PIL'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb index c430b0e2e0a3..ae933c15e3b7 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb @@ -28,6 +28,12 @@ dependencies = [ use_pip = True download_dep_fail = True +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + options = {'modulename': 'PIL'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb index cec85fa1ae6a..c93625ec7d86 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.2.0.eb @@ -28,6 +28,12 @@ dependencies = [ use_pip = True download_dep_fail = True +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + options = {'modulename': 'PIL'} sanity_check_paths = { diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb index ed0cd77c9495..2c9955fc0e39 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb @@ -28,6 +28,12 @@ dependencies = [ use_pip = True download_dep_fail = True +# patch setup.py to prefix hardcoded /usr/* and /lib paths with value of %(sysroot) template +# (which will be empty if EasyBuild is not configured to use an alternate sysroot); +# see also https://gitlab.com/eessi/support/-/issues/9 +preinstallopts = """sed -i 's@"/usr/@"%(sysroot)s/usr/@g' setup.py && """ +preinstallopts += """sed -i 's@"/lib@"%(sysroot)s/lib@g' setup.py && """ + options = {'modulename': 'PIL'} sanity_check_paths = { From 0c3bd6d00192154c5457c243f2f51851bafee8e6 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 28 Feb 2024 17:53:09 +0100 Subject: [PATCH 0852/1193] adding easyconfigs: OCaml-4.14.0-GCC-11.3.0.eb, snape-pooled-20150707-GCC-11.3.0.eb --- .../o/OCaml/OCaml-4.14.0-GCC-11.3.0.eb | 54 +++++++++++++++++++ .../snape-pooled-20150707-GCC-11.3.0.eb | 35 ++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/o/OCaml/OCaml-4.14.0-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OCaml/OCaml-4.14.0-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OCaml/OCaml-4.14.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..f36af9c27929 --- /dev/null +++ b/easybuild/easyconfigs/o/OCaml/OCaml-4.14.0-GCC-11.3.0.eb @@ -0,0 +1,54 @@ +name = 'OCaml' +version = '4.14.0' + +homepage = 'http://ocaml.org/' +description = """OCaml is a general purpose industrial-strength programming language + with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria + it benefits from one of the most advanced type systems and supports functional, + imperative and object-oriented styles of programming.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +local_opam_ver = '2.1.5' +source_urls = [ + 'https://github.com/ocaml/ocaml/archive', + 'https://github.com/ocaml/opam/releases/download/%s' % local_opam_ver, +] +sources = [ + '%s.tar.gz' % version, + 'opam-full-%s.tar.gz' % local_opam_ver, +] +checksums = [ + {'4.14.0.tar.gz': '39f44260382f28d1054c5f9d8bf4753cb7ad64027da792f7938344544da155e8'}, + {'opam-full-2.1.5.tar.gz': '09f8d9e410b2f5723c2bfedbf7970e3b305f5017895fcd91759f05e753ddcea5'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('libreadline', '8.1.2'), +] + +preconfigopts = 'export CFLAGS="$CFLAGS -lm -lpthread" && ' +preconfigopts += 'export AS=as && ' + +# parallel build tends to break +parallel = 1 + +# handled by OPAM, order matters! +# see https://opam.ocaml.org/packages +exts_list = [ + ('ocamlfind', '1.9.6'), + ('batteries', '3.7.2'), + ('conf-pkg-config', '3'), + ('dune-configurator', '3.14.0'), + ('dune', '3.14.0'), + ('base', 'v0.16.3'), + ('stdio', 'v0.16.0'), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb b/easybuild/easyconfigs/s/snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb new file mode 100644 index 000000000000..e24676b6c43f --- /dev/null +++ b/easybuild/easyconfigs/s/snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CmdCp' + +name = 'snape-pooled' +version = '20150707' +local_commit = '284bfe0' + +homepage = 'https://github.com/EmanueleRaineri/snape-pooled' +description = """" +SNAPE-pooled computes the probability distribution for the frequency of the minor allele in +a certain population, at a certain position in the genome. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'EmanueleRaineri' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['5c3157e4b4d4b1245bb86dfb2435e42c79e0b273c925fb91e39c78cfe9d2d570'] + +dependencies = [ + ('OCaml', '4.14.0'), +] + +cmds_map = [('.*', 'make snape-pooled')] + +files_to_copy = [(['snape-pooled'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snape-pooled'], + 'dirs': [], +} + +sanity_check_commands = ['snape-pooled --help'] + +moduleclass = 'tools' From 5d32235e3458e4483e171e2ac9fc423346f1a3ab Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 28 Feb 2024 17:55:46 +0100 Subject: [PATCH 0853/1193] add cairo dep --- .../p/python-igraph/python-igraph-0.11.4-foss-2023a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb index 925e86226029..3af264daf8b4 100644 --- a/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb +++ b/easybuild/easyconfigs/p/python-igraph/python-igraph-0.11.4-foss-2023a.eb @@ -21,6 +21,7 @@ dependencies = [ ('libxml2', '2.11.4'), ('zlib', '1.2.13'), ('igraph', '0.10.10'), + ('cairo', '1.17.8'), ] use_pip = True @@ -38,6 +39,7 @@ exts_list = [ }), ] + # cairo must be available for proper plotting support sanity_check_commands = [ "python -c 'from igraph.drawing.cairo.utils import find_cairo; " From 509a9b724ccb5425d97406e87969f9723df9b2c4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Feb 2024 09:45:13 +0100 Subject: [PATCH 0854/1193] Remove --disable-docs configure option from FriBidi 1.0.5+ --- .../easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb | 2 -- .../easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb | 2 -- .../easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb | 2 -- easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-7.3.0.eb | 2 -- easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb | 2 -- easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.3.0.eb | 2 -- easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb | 2 -- 7 files changed, 14 deletions(-) diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb index 40e6ff915754..c0dd7325a8be 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.2.0.eb @@ -23,8 +23,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb index a278d8bd8203..5dd93a16d839 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-10.3.0.eb @@ -24,8 +24,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb index 4a4084cbfb15..89ac34d49c81 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.10-GCCcore-11.2.0.eb @@ -21,8 +21,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-7.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-7.3.0.eb index 5fd4aec115d2..ee4077cbb69b 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-7.3.0.eb @@ -24,8 +24,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb index 952a02c3f63a..e33daa77d33a 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.2.0.eb @@ -24,8 +24,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.3.0.eb index 6c4115fc4e17..213a98ebd30d 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.5-GCCcore-8.3.0.eb @@ -23,8 +23,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb index cef1dc631bb8..34132127d4af 100644 --- a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.9-GCCcore-9.3.0.eb @@ -23,8 +23,6 @@ builddependencies = [ ('pkg-config', '0.29.2'), ] -configopts = '--disable-docs' - sanity_check_paths = { 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], From ae4cce622dc2e1c5755da1c3bb93d2aa142d7ae1 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Thu, 29 Feb 2024 10:18:49 +0100 Subject: [PATCH 0855/1193] Fix name SNAPE-pooled --- .../SNAPE-pooled-20150707-GCC-11.3.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/{snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb => SNAPE-pooled/SNAPE-pooled-20150707-GCC-11.3.0.eb} (97%) diff --git a/easybuild/easyconfigs/s/snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-20150707-GCC-11.3.0.eb similarity index 97% rename from easybuild/easyconfigs/s/snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb rename to easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-20150707-GCC-11.3.0.eb index e24676b6c43f..fb95b3bc99cc 100644 --- a/easybuild/easyconfigs/s/snape-pooled/snape-pooled-20150707-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/SNAPE-pooled/SNAPE-pooled-20150707-GCC-11.3.0.eb @@ -1,6 +1,6 @@ easyblock = 'CmdCp' -name = 'snape-pooled' +name = 'SNAPE-pooled' version = '20150707' local_commit = '284bfe0' From 6f44e2dd7ec3288917e8380d890fe341bcc7adbd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Feb 2024 11:04:10 +0100 Subject: [PATCH 0856/1193] Fix geotiff configure option in GDAL --- .../easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.0.2-foss-2019b-Python-3.7.4.eb | 2 +- .../g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb index 5eb2654fceb9..5e3bbcfce527 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-2.7.15.eb @@ -42,7 +42,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb index c40f8400229b..4d2a96f6f1c8 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-foss-2019a-Python-3.7.2.eb @@ -42,7 +42,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb index 0aa81a50d9a3..1352000d7b67 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-2.7.15.eb @@ -46,7 +46,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' prebuildopts = "export LDSHARED='icc -shared' && " modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb index 141c37f11653..9bcb96c48aed 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.0-intel-2019a-Python-3.7.2.eb @@ -46,7 +46,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' prebuildopts = "export LDSHARED='icc -shared' && " modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-foss-2019b-Python-3.7.4.eb index 1d2268d9ecd5..9080eca50a1c 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-foss-2019b-Python-3.7.4.eb @@ -45,7 +45,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb index 8cbf568debb2..233ccbc15187 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-fosscuda-2019b-Python-3.7.4.eb @@ -46,7 +46,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' # GPU support configopts += ' --with-opencl=yes' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb index 34d6ebadafbf..b63353818cb4 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.2-intel-2019b-Python-3.7.4.eb @@ -45,7 +45,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' prebuildopts = "export LDSHARED='icc -shared' && " diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb index e30c6613eda5..761fe352c836 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-foss-2020a-Python-3.8.2.eb @@ -48,7 +48,7 @@ configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb index 572bd3e13962..107318804f29 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.0.4-intel-2020a-Python-3.8.2.eb @@ -48,7 +48,7 @@ configopts += ' --without-hdf4 --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETC configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' prebuildopts = 'export LDSHARED="$CC -shared" && ' From 3b2f77ecb457458324b5f0fadba91943fea26519 Mon Sep 17 00:00:00 2001 From: NPotvin <15875457+NPotvin@users.noreply.github.com> Date: Thu, 29 Feb 2024 11:42:28 +0100 Subject: [PATCH 0857/1193] Update easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb Co-authored-by: Miguel Dias Costa --- .../p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb index cc881eb49174..51d76b9bf218 100644 --- a/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/python-xxhash/python-xxhash-3.4.1-GCCcore-12.3.0.eb @@ -22,7 +22,7 @@ sanity_pip_check = True exts_list = [ ('xxhash', version, { - 'preinstallopts': 'XXHASH_LINK_SO=1', + 'preinstallopts': 'XXHASH_LINK_SO=1', # use xxHash library from EB 'checksums': ['0379d6cf1ff987cd421609a264ce025e74f346e3e145dd106c0cc2e3ec3f99a9'], }), ] From 7112bff5f84f89940bbc782a77e831088bd1bf71 Mon Sep 17 00:00:00 2001 From: thoffman Date: Thu, 29 Feb 2024 11:46:28 +0100 Subject: [PATCH 0858/1193] {lib}[gfbf/2023a] morphosamplers v0.0.10 --- .../morphosamplers-0.0.10-gfbf-2023a.eb | 44 +++ ...morphosamplers-0.0.10_bump_pydantic2.patch | 322 ++++++++++++++++++ 2 files changed, 366 insertions(+) create mode 100644 easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10_bump_pydantic2.patch diff --git a/easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10-gfbf-2023a.eb b/easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10-gfbf-2023a.eb new file mode 100644 index 000000000000..9197d88eb473 --- /dev/null +++ b/easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10-gfbf-2023a.eb @@ -0,0 +1,44 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +easyblock = 'PythonBundle' + +name = 'morphosamplers' +version = '0.0.10' + +homepage = 'https://github.com/kevinyamauchi/morphosamplers' +description = """ +A library for sampling image data along morphological objects such as splines and surfaces. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +builddependencies = [ + ('poetry', '1.5.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('einops', '0.7.0'), + ('pydantic', '2.5.3'), + ('SciPy-bundle', '2023.07') +] + +exts_list = [ + ('mypy_extensions', '1.0.0', { + 'checksums': ['75dbf8955dc00442a438fc4d0666508a9a97b6bd41aa2f0ffe9d2f2725af0782'], + }), + ('psygnal', '0.9.5', { + 'checksums': ['4956ea6c36a75f7fc457558935b67dd8be2594661b4d08eeb3357d69c509c55f'], + }), + (name, version, { + 'patches': ['morphosamplers-0.0.10_bump_pydantic2.patch'], # allow using pydantic2 + 'checksums': [ + {'morphosamplers-0.0.10.tar.gz': '52dcfaa0e9fe75112f53cc8bc9a08307f500d5a2422f43192c1e68f6a24f9cae'}, + {'morphosamplers-0.0.10_bump_pydantic2.patch': + '4b9590fac69a57ace54f489258ee6d52040e22a442eefac418b76818aefa47a9'}, + ], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10_bump_pydantic2.patch b/easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10_bump_pydantic2.patch new file mode 100644 index 000000000000..9816c33fdfba --- /dev/null +++ b/easybuild/easyconfigs/m/morphosamplers/morphosamplers-0.0.10_bump_pydantic2.patch @@ -0,0 +1,322 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2024/02 +# 1. migration from pydantic ver. 1.x to ver. 2.x by tool +# bump-pydantic ver. 0.8.0 (https://pypi.org/project/bump-pydantic/) +# 2. replace @root_validator by @model_validator(mode='after') in +# sample_types.py +# 3. change of requirements accordingly in pyproject.toml and PKG-INFO +diff -ru morphosamplers-0.0.10/PKG-INFO morphosamplers-0.0.10_bump_pydantic2/PKG-INFO +--- morphosamplers-0.0.10/PKG-INFO 2023-11-27 16:48:35.350763000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/PKG-INFO 2024-02-29 11:12:14.621599361 +0100 +@@ -19,7 +19,7 @@ + Requires-Dist: einops + Requires-Dist: numpy + Requires-Dist: psygnal +-Requires-Dist: pydantic<2 ++Requires-Dist: pydantic>=2 + Requires-Dist: scipy + Requires-Dist: typing-extensions + Provides-Extra: test +diff -ru morphosamplers-0.0.10/pyproject.toml morphosamplers-0.0.10_bump_pydantic2/pyproject.toml +--- morphosamplers-0.0.10/pyproject.toml 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/pyproject.toml 2024-02-29 11:12:06.188358266 +0100 +@@ -27,7 +27,7 @@ + "einops", + "numpy", + "psygnal", +- "pydantic<2", ++ "pydantic>=2", + "scipy", + "typing-extensions" + ] +diff -ru morphosamplers-0.0.10/src/morphosamplers/core.py morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/core.py +--- morphosamplers-0.0.10/src/morphosamplers/core.py 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/core.py 2024-02-29 10:43:07.994797553 +0100 +@@ -1,18 +1,16 @@ + from abc import abstractmethod + from typing import TypeVar, Protocol, Generic +- +-from pydantic.generics import GenericModel ++from pydantic import BaseModel, ConfigDict + + M = TypeVar("M", bound="MorphoModel") + S = TypeVar("S") + + +-class MorphoModel(GenericModel, Generic[M]): ++class MorphoModel(BaseModel, Generic[M]): + """A set of attributes defining a geometrical support.""" +- +- class Config: +- allow_mutation = False +- arbitrary_types_allowed = True ++ # TODO[pydantic]: The following keys were removed: `allow_mutation`. ++ # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information. ++ model_config = ConfigDict(allow_mutation=False, arbitrary_types_allowed=True) + + + class SamplerProtocol(Protocol[M, S]): +@@ -27,8 +25,8 @@ + SamplerType = TypeVar("SamplerType", bound=SamplerProtocol) + + +-class MorphoSampler(GenericModel, Generic[SamplerType]): ++class MorphoSampler(BaseModel, Generic[SamplerType]): + """Concrete samplers should subclass this generic model.""" +- +- class Config: +- allow_mutation = False ++ # TODO[pydantic]: The following keys were removed: `allow_mutation`. ++ # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information. ++ model_config = ConfigDict(allow_mutation=False) +diff -ru morphosamplers-0.0.10/src/morphosamplers/models/path.py morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/models/path.py +--- morphosamplers-0.0.10/src/morphosamplers/models/path.py 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/models/path.py 2024-02-29 10:43:07.834793481 +0100 +@@ -1,5 +1,5 @@ + import numpy as np +-from pydantic import validator ++from pydantic import field_validator + + from morphosamplers.core import MorphoModel + +@@ -8,14 +8,16 @@ + """A 3D path defined by an `(n, 3)` array of control points.""" + control_points: np.ndarray + +- @validator('control_points', pre=True) ++ @field_validator('control_points', mode="before") ++ @classmethod + def coerce_to_n_by_3_array(cls, value): + value = np.atleast_2d(np.asarray(value)) + if value.ndim != 2 or value.shape[-1] != 3: + raise ValueError('`control_points` must be an (n, 3) array.') + return value + +- @validator('control_points') ++ @field_validator('control_points') ++ @classmethod + def check_at_least_two_points(cls, value): + if len(value) < 2: + raise ValueError('A Path must contain at least two points.') +diff -ru morphosamplers-0.0.10/src/morphosamplers/models/sphere.py morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/models/sphere.py +--- morphosamplers-0.0.10/src/morphosamplers/models/sphere.py 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/models/sphere.py 2024-02-29 10:43:07.624788137 +0100 +@@ -1,6 +1,6 @@ + from typing import Tuple + +-from pydantic import validator ++from pydantic import field_validator + + from morphosamplers.core import MorphoModel + +@@ -10,7 +10,8 @@ + center: Tuple[float, float, float] + radius: float + +- @validator('center', pre=True) ++ @field_validator('center', mode="before") ++ @classmethod + def coerce_to_tuple(cls, value): + return tuple(value) + +diff -ru morphosamplers-0.0.10/src/morphosamplers/models/surface.py morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/models/surface.py +--- morphosamplers-0.0.10/src/morphosamplers/models/surface.py 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/models/surface.py 2024-02-29 10:43:07.651788824 +0100 +@@ -1,7 +1,7 @@ + from typing import List + + import numpy as np +-from pydantic import validator ++from pydantic import field_validator + + from morphosamplers.core import MorphoModel + +@@ -10,7 +10,8 @@ + """A 3D surface defined by control points in a series of levels.""" + control_points: List[np.ndarray] + +- @validator('control_points') ++ @field_validator('control_points') ++ @classmethod + def check_at_least_two_points(cls, value): + if len(value) < 2: + raise ValueError('A Path must contain at least two levels.') +@@ -19,7 +20,8 @@ + raise ValueError('Each level must contain at least two points.') + return value + +- @validator('control_points', pre=True) ++ @field_validator('control_points', mode="before") ++ @classmethod + def ensure_list_of_float_arrays(cls, value): + return [np.asarray(v, dtype=np.float32) for v in value] + +diff -ru morphosamplers-0.0.10/src/morphosamplers/sample_types.py morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/sample_types.py +--- morphosamplers-0.0.10/src/morphosamplers/sample_types.py 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/sample_types.py 2024-02-29 11:10:34.650741331 +0100 +@@ -1,5 +1,5 @@ + import numpy as np +-from pydantic import BaseModel, root_validator, validator ++from pydantic import field_validator, ConfigDict, BaseModel, model_validator + from typing import Union + from typing_extensions import TypeAlias + +@@ -12,26 +12,27 @@ + """Model for a set of 3D poses.""" + positions: np.ndarray # (n, 3) + orientations: np.ndarray # (n, 3, 3) ++ # TODO[pydantic]: The following keys were removed: `allow_mutation`. ++ # Check https://docs.pydantic.dev/dev-v2/migration/#changes-to-config for more information. ++ model_config = ConfigDict(allow_mutation=False, arbitrary_types_allowed=True) + +- class Config: +- allow_mutation = False +- arbitrary_types_allowed = True +- +- @validator('positions', pre=True) ++ @field_validator('positions', mode="before") ++ @classmethod + def coerce_to_n_by_3_array(cls, value): + value = np.atleast_2d(np.asarray(value)) + if value.ndim != 2 or value.shape[-1] != 3: + raise ValueError('positions must be an (n, 3) array.') + return value + +- @validator('orientations', pre=True) ++ @field_validator('orientations', mode="before") ++ @classmethod + def check_n_by_3_3_array(cls, value): + value = np.asarray(value) + if value.ndim != 3 or value.shape[-2:] != (3, 3): + raise ValueError('orientations must be an (n, 3, 3) array.') + return value + +- @root_validator ++ @model_validator(mode="after") # THEMBL: mode=after: previously root_validator without pre=True set + def check_same_length(cls, values): + positions, orientations = values.get('positions'), values.get('orientations') + if len(positions) != len(orientations): +Only in morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers: .sample_types.py.swp +diff -ru morphosamplers-0.0.10/src/morphosamplers/spline.py morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/spline.py +--- morphosamplers-0.0.10/src/morphosamplers/spline.py 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/spline.py 2024-02-29 10:43:12.179904052 +0100 +@@ -5,18 +5,19 @@ + + import numpy as np + from psygnal import EventedModel +-from pydantic import PrivateAttr, conint, root_validator, validator ++from pydantic import field_validator, model_validator, Field, ConfigDict, PrivateAttr + from scipy.interpolate import splev, splprep + from scipy.spatial.transform import Rotation, Slerp + + from .utils import coaxial_y_vectors_from_z_vectors, within_range, get_mask_limits ++from typing_extensions import Annotated + + + class NDimensionalSpline(EventedModel): + """Model for multidimensional splines.""" + + points: np.ndarray +- order: conint(ge=1, le=5) = 3 ++ order: Annotated[int, Field(ge=1, le=5)] = 3 + smoothing: Optional[int] = None + mask: Optional[np.ndarray] = None + closed: bool = False +@@ -25,11 +26,7 @@ + _raw_u = PrivateAttr(np.ndarray) + _u_mask_limits: List[Tuple[float, float]] = PrivateAttr([]) + _length = PrivateAttr(float) +- +- class Config: +- """Pydantic BaseModel configuration.""" +- +- arbitrary_types_allowed = True ++ model_config = ConfigDict(arbitrary_types_allowed=True) + + def __init__(self, **kwargs): + """Calculate the splines after validating the paramters.""" +@@ -41,7 +38,8 @@ + ndim: int = self.points.shape[1] + return ndim + +- @validator("points", pre=True) ++ @field_validator("points", mode="before") ++ @classmethod + def is_coordinate_array(cls, v: Union[List[List[float]], np.ndarray]) -> np.ndarray: + """Validate and coerce the points values to a 2D numpy array.""" + points = np.atleast_2d(v) +@@ -51,7 +49,8 @@ + raise ValueError("must provide at least 2 points") + return points + +- @root_validator(skip_on_failure=True) ++ @model_validator(skip_on_failure=True) ++ @classmethod + def validate_number_of_points( + cls, values: Dict[str, Union[np.ndarray, int]] + ) -> Dict[str, Union[np.ndarray, int]]: +@@ -237,7 +236,8 @@ + + _rotation_sampler = PrivateAttr(Slerp) + +- @validator("points") ++ @field_validator("points") ++ @classmethod + def _is_3d_coordinate_array(cls, v): + if v.ndim != 2 or v.shape[-1] != 3: + raise ValueError("must be an (n, 3) array") +diff -ru morphosamplers-0.0.10/src/morphosamplers/surface_spline.py morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/surface_spline.py +--- morphosamplers-0.0.10/src/morphosamplers/surface_spline.py 2023-11-27 16:48:18.000000000 +0100 ++++ morphosamplers-0.0.10_bump_pydantic2/src/morphosamplers/surface_spline.py 2024-02-29 10:43:17.615042361 +0100 +@@ -6,7 +6,7 @@ + import einops + import numpy as np + from psygnal import EventedModel +-from pydantic import PrivateAttr, conint, root_validator, validator ++from pydantic import field_validator, model_validator, Field, ConfigDict, PrivateAttr + from scipy.interpolate import splev, splprep, interp1d + from scipy.spatial.transform import Rotation + +@@ -17,6 +17,7 @@ + minimize_closed_point_row_pair_distance, + minimize_point_row_pair_distance, + ) ++from typing_extensions import Annotated + + + class _SplineSurface(EventedModel): +@@ -24,7 +25,7 @@ + + points: List[np.ndarray] + separation: float +- order: conint(ge=1, le=5) = 3 ++ order: Annotated[int, Field(ge=1, le=5)] = 3 + smoothing: Optional[int] = None + closed: bool = False + inside_point: Optional[Union[np.ndarray, Tuple[float, float, float]]] = None +@@ -32,13 +33,10 @@ + _raw_masks = PrivateAttr(np.ndarray) + _row_splines = PrivateAttr(List[Spline3D]) + _column_splines = PrivateAttr(List[Spline3D]) ++ model_config = ConfigDict(arbitrary_types_allowed=True) + +- class Config: +- """Pydantic BaseModel configuration.""" +- +- arbitrary_types_allowed = True +- +- @validator("points") ++ @field_validator("points") ++ @classmethod + def _validate_number_of_splines(v): + points = np.atleast_2d(*v) + if len(points) < 2: +@@ -47,7 +45,8 @@ + ) + return points + +- @root_validator(skip_on_failure=True) ++ @model_validator(skip_on_failure=True) ++ @classmethod + def _validate_number_of_lines(cls, values): + points = values.get("points") + n_lines = len(points) From 0877c7d6472b060ff5564b6cbb0a931310188cfc Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 29 Feb 2024 15:05:17 +0100 Subject: [PATCH 0859/1193] adding easyconfigs: scVelo-0.3.1-foss-2023a.eb, loompy-3.0.7-foss-2023a.eb --- .../l/loompy/loompy-3.0.7-foss-2023a.eb | 40 +++++++++++++++++ .../s/scVelo/scVelo-0.3.1-foss-2023a.eb | 43 +++++++++++++++++++ 2 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb new file mode 100644 index 000000000000..2fbf0a8ab85c --- /dev/null +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'loompy' +version = '3.0.7' + +homepage = 'https://loompy.org/' +description = "Python implementation of the Loom file format, an efficient file format for large omics datasets" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # for click + ('SciPy-bundle', '2023.07'), + ('h5py', '3.9.0'), + ('numba', '0.58.1'), + ('poetry', '1.7.1'), +] + +use_pip = True + +exts_list = [ + ('numpy-groupies', '0.10.2', { + 'checksums': ['f920c4ded899f5975d94fc63d634e7c89622056bbab8cc98a44d4320a0ae8a12'], + }), + (name, version, { + 'checksums': ['b5cdf7b54734c6bed3a181d11947af70af2c6e0dcadc02fd0e871df232faa8f4'], + }), +] + +sanity_check_paths = { + 'files': ['bin/loompy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["loompy --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb new file mode 100644 index 000000000000..7d8366fe08f5 --- /dev/null +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'scVelo' +version = '0.3.1' +local_commit = 'ffe2cd3' + +homepage = "https://scvelo.org" +description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using + dynamical modeling.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0')] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('numba', '0.58.1'), + ('anndata', '0.10.5.post1'), + ('scanpy', '1.9.8'), + ('loompy', '3.0.7'), + ('umap-learn', '0.5.5'), + ('scikit-learn', '1.3.1'), + ('matplotlib', '3.7.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'scvelo', + # download from commit to not depend on scvi-tools and get rid of restriction of scikit-learn version + 'source_urls': ['https://github.com/theislab/scvelo/archive/'], + 'sources': [{ + 'download_filename': 'ffe2cd3c437fd385f80fed9e6abc6dc3013eff82.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz' + }], + 'checksums': ['55f476068a4b31df2181431977ebd279bd17931694eab23f1db7b7912e2a2c49'], + }), +] + +moduleclass = 'bio' From 39f4735a04719d51a32e99d4c8dc29641a77cf77 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 29 Feb 2024 15:27:05 +0100 Subject: [PATCH 0860/1193] Fix Clang 9.0.1 patch --- .../c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb | 4 ++-- easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb | 4 ++-- easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb index ef88ee09de04..0d34b0ee01f7 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCC-8.3.0-CUDA-10.1.243.eb @@ -36,7 +36,7 @@ sources = [ 'libcxx-%(version)s.src.tar.xz', 'libcxxabi-%(version)s.src.tar.xz', ] -patches = ['libcxx-%(version)s-ppc64le.patch'] +patches = [('libcxx-%(version)s-ppc64le.patch', '../')] checksums = [ '00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a', # llvm-9.0.1.src.tar.xz '5778512b2e065c204010f88777d44b95250671103e434f9dc7363ab2e3804253', # clang-9.0.1.src.tar.xz @@ -46,7 +46,7 @@ checksums = [ '86262bad3e2fd784ba8c5e2158d7aa36f12b85f2515e95bc81d65d75bb9b0c82', # lld-9.0.1.src.tar.xz '0981ff11b862f4f179a13576ab0a2f5530f46bd3b6b4a90f568ccc6a62914b34', # libcxx-9.0.1.src.tar.xz 'e8f978aa4cfae2d7a0b4d89275637078557cca74b35c31b7283d4786948a8aac', # libcxxabi-9.0.1.src.tar.xz - '6a39230b9e2b2c61fb5f67ac752d256437ccc56a6a517d7b6d53417d198fdb1f', # libcxx-9.0.1-ppc64le.patch + '01d2a16fe69854c0126a8adb4762a455cc6bf1f70003cb8b685e446a66a9aa51', # libcxx-9.0.1-ppc64le.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb index f9e2e51d1648..207b62601932 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-8.3.0.eb @@ -33,7 +33,7 @@ sources = [ 'libcxx-%(version)s.src.tar.xz', 'libcxxabi-%(version)s.src.tar.xz', ] -patches = ['libcxx-%(version)s-ppc64le.patch'] +patches = [('libcxx-%(version)s-ppc64le.patch', '../')] checksums = [ '00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a', # llvm-9.0.1.src.tar.xz '5778512b2e065c204010f88777d44b95250671103e434f9dc7363ab2e3804253', # clang-9.0.1.src.tar.xz @@ -43,7 +43,7 @@ checksums = [ '86262bad3e2fd784ba8c5e2158d7aa36f12b85f2515e95bc81d65d75bb9b0c82', # lld-9.0.1.src.tar.xz '0981ff11b862f4f179a13576ab0a2f5530f46bd3b6b4a90f568ccc6a62914b34', # libcxx-9.0.1.src.tar.xz 'e8f978aa4cfae2d7a0b4d89275637078557cca74b35c31b7283d4786948a8aac', # libcxxabi-9.0.1.src.tar.xz - '6a39230b9e2b2c61fb5f67ac752d256437ccc56a6a517d7b6d53417d198fdb1f', # libcxx-9.0.1-ppc64le.patch + '01d2a16fe69854c0126a8adb4762a455cc6bf1f70003cb8b685e446a66a9aa51', # libcxx-9.0.1-ppc64le.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb index 434dfe354150..097cc8716514 100644 --- a/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/c/Clang/Clang-9.0.1-GCCcore-9.3.0.eb @@ -33,7 +33,7 @@ sources = [ 'libcxx-%(version)s.src.tar.xz', 'libcxxabi-%(version)s.src.tar.xz', ] -patches = ['libcxx-%(version)s-ppc64le.patch'] +patches = [('libcxx-%(version)s-ppc64le.patch', '../')] checksums = [ '00a1ee1f389f81e9979f3a640a01c431b3021de0d42278f6508391a2f0b81c9a', # llvm-9.0.1.src.tar.xz '5778512b2e065c204010f88777d44b95250671103e434f9dc7363ab2e3804253', # clang-9.0.1.src.tar.xz @@ -43,7 +43,7 @@ checksums = [ '86262bad3e2fd784ba8c5e2158d7aa36f12b85f2515e95bc81d65d75bb9b0c82', # lld-9.0.1.src.tar.xz '0981ff11b862f4f179a13576ab0a2f5530f46bd3b6b4a90f568ccc6a62914b34', # libcxx-9.0.1.src.tar.xz 'e8f978aa4cfae2d7a0b4d89275637078557cca74b35c31b7283d4786948a8aac', # libcxxabi-9.0.1.src.tar.xz - '6a39230b9e2b2c61fb5f67ac752d256437ccc56a6a517d7b6d53417d198fdb1f', # libcxx-9.0.1-ppc64le.patch + '01d2a16fe69854c0126a8adb4762a455cc6bf1f70003cb8b685e446a66a9aa51', # libcxx-9.0.1-ppc64le.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch b/easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch index b827d9c5ce90..cbf55ee91be8 100644 --- a/easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch +++ b/easybuild/easyconfigs/c/Clang/libcxx-9.0.1-ppc64le.patch @@ -2,8 +2,8 @@ Reverse the if def order. Patch from https://bugs.llvm.org/show_bug.cgi?id=39696 Prepared for EasyBuild by Simon Branford, University of Birmingham diff --git a/libcxx/include/thread b/libcxx/include/thread index 02da703..d1677a1 100644 ---- a/projects/libcxx/include/thread -+++ b/projects/libcxx/include/thread +--- a/libcxx-9.0.1.src/include/thread ++++ b/libcxx-9.0.1.src/include/thread @@ -368,9 +368,9 @@ sleep_for(const chrono::duration<_Rep, _Period>& __d) { #if defined(_LIBCPP_COMPILER_GCC) && (__powerpc__ || __POWERPC__) From fc38265febbd52428765741fbf49b3654b78757a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 29 Feb 2024 15:32:57 +0100 Subject: [PATCH 0861/1193] add space before comment --- easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb index 2fbf0a8ab85c..47ce25c87cd7 100644 --- a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} dependencies = [ ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), # for click + ('Python-bundle-PyPI', '2023.06'), # for click ('SciPy-bundle', '2023.07'), ('h5py', '3.9.0'), ('numba', '0.58.1'), From 0b5d092e4a8f9de041e73a7ba31b32b81f27219e Mon Sep 17 00:00:00 2001 From: thoffman Date: Fri, 1 Mar 2024 10:08:49 +0100 Subject: [PATCH 0862/1193] {vis}[GCCcore/12.3.0] PyOpenGL v3.1.7: add PyOpenGL-accelerate extension --- .../easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb index 132e708af8e7..f473908d9561 100644 --- a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.7-GCCcore-12.3.0.eb @@ -26,6 +26,10 @@ exts_list = [ 'modulename': 'OpenGL', 'checksums': ['eef31a3888e6984fd4d8e6c9961b184c9813ca82604d37fe3da80eb000a76c86'], }), + ('PyOpenGL-accelerate', version, { + 'modulename': 'OpenGL_accelerate', + 'checksums': ['2b123621273a939f7fd2ec227541e399f9b5d4e815d69ae0bdb1b6c70a293680'], + }), ] moduleclass = 'vis' From 01687298b56539f7265b33a710b4ad0cedfa1de1 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 1 Mar 2024 10:53:37 +0100 Subject: [PATCH 0863/1193] fix poetry conflict --- easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb index 47ce25c87cd7..8301b1fff21f 100644 --- a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb @@ -8,13 +8,14 @@ description = "Python implementation of the Loom file format, an efficient file toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [('poetry', '1.7.1'),] + dependencies = [ ('Python', '3.11.3'), ('Python-bundle-PyPI', '2023.06'), # for click ('SciPy-bundle', '2023.07'), ('h5py', '3.9.0'), ('numba', '0.58.1'), - ('poetry', '1.7.1'), ] use_pip = True From f09695d0944f70bd77aa253353e4a8c6c0617e56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2024 10:56:58 +0100 Subject: [PATCH 0864/1193] unpack SCG database to 'db' subdirectory for DAS_Tool --- .../d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb | 6 +++--- .../d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb index 4e04c72ff766..f80eef6a25ef 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021b-R-4.1.2.eb @@ -39,17 +39,17 @@ exts_list = [ ] postinstallcmds = [ - "cd %(installdir)s; unzip db.zip", + "cd %(installdir)s && unzip db.zip -d db", "chmod a+x %(installdir)s/DAS_Tool", ] sanity_check_paths = { - 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'files': ['DAS_Tool', 'db/arc.all.faa', 'db/arc.scg.lookup'], 'dirs': ['DASTool/R'], } -sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] # Help gets printed correctly, but the error code is 1 +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] modextrapaths = { 'PATH': '', diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb index 8889f759be91..4e5773b4b1c2 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb @@ -39,17 +39,17 @@ exts_list = [ ] postinstallcmds = [ - "cd %(installdir)s; unzip db.zip", + "cd %(installdir)s && unzip db.zip -d db", "chmod a+x %(installdir)s/DAS_Tool", ] sanity_check_paths = { - 'files': ['DAS_Tool', 'arc.all.faa', 'arc.scg.lookup'], + 'files': ['DAS_Tool', 'db/arc.all.faa', 'db/arc.scg.lookup'], 'dirs': ['DASTool/R'], } -sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] # Help gets printed correctly, but the error code is 1 +sanity_check_commands = ['DAS_Tool -h | grep "DAS Tool version %s"' % version] modextrapaths = { 'PATH': '', From c6e7191d7101ed8932779f7ebcfba056fe4e317d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 1 Mar 2024 11:15:40 +0100 Subject: [PATCH 0865/1193] fix whitespace --- easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb index 8301b1fff21f..486a2e560c31 100644 --- a/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb +++ b/easybuild/easyconfigs/l/loompy/loompy-3.0.7-foss-2023a.eb @@ -8,7 +8,7 @@ description = "Python implementation of the Loom file format, an efficient file toolchain = {'name': 'foss', 'version': '2023a'} -builddependencies = [('poetry', '1.7.1'),] +builddependencies = [('poetry', '1.7.1'), ] dependencies = [ ('Python', '3.11.3'), From f88749f637b91d6a073ab6de014873b58164bc87 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 1 Mar 2024 13:39:58 +0100 Subject: [PATCH 0866/1193] Remove Jasper dependency and configure option from GDAL 3.5+ --- easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb | 3 +-- easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb | 1 - easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb | 1 - 3 files changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb index 6babf890be57..d40b2b9e18c1 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb @@ -33,7 +33,6 @@ dependencies = [ ('libxml2', '2.9.13'), ('libpng', '1.6.37'), ('libjpeg-turbo', '2.1.3'), - ('JasPer', '2.0.33'), ('LibTIFF', '4.3.0'), ('zlib', '1.2.12'), ('cURL', '7.83.0'), @@ -50,7 +49,7 @@ preconfigopts = r"sed -e 's/-llapack/\$LIBLAPACK/g' -i.eb configure && " configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ' configopts += ' --with-hdf5=$EBROOTHDF5 --with-netcdf=$EBROOTNETCDF' configopts += ' --with-xml2=yes --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' -configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' +configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb index 7e3c17c850fd..c293d01731d8 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.6.2-foss-2022b.eb @@ -35,7 +35,6 @@ dependencies = [ ('libxml2', '2.10.3'), ('libpng', '1.6.38'), ('libjpeg-turbo', '2.1.4'), - ('JasPer', '4.0.0'), ('LibTIFF', '4.4.0'), ('zlib', '1.2.12'), ('cURL', '7.86.0'), diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb index 721bd3a5e34e..92bfe549e746 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.7.1-foss-2023a.eb @@ -36,7 +36,6 @@ dependencies = [ ('libxml2', '2.11.4'), ('libpng', '1.6.39'), ('libjpeg-turbo', '2.1.5.1'), - ('JasPer', '4.0.0'), ('LibTIFF', '4.5.0'), ('zlib', '1.2.13'), ('cURL', '8.0.1'), From ec0ed00f5650b712ea986af67a5e60ecb841694b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 1 Mar 2024 14:12:30 +0100 Subject: [PATCH 0867/1193] adding easyconfigs: loomR-0.2.0-20180425-foss-2023a-R-4.3.2.eb --- ...loomR-0.2.0-20180425-foss-2023a-R-4.3.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..6cdcc1ed0664 --- /dev/null +++ b/easybuild/easyconfigs/l/loomR/loomR-0.2.0-20180425-foss-2023a-R-4.3.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'loomR' +local_commit = 'df0144b' +# see DESCRIPTION to determine version, +# but add date stamp of commit since version is not always bumped +version = '0.2.0-20180425' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/mojaveazure/loomR' +description = "An R interface for loom files" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/mojaveazure/loomR/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['6264448baf4fd9a569eb5a832598c4a224382ef26c0a7fbd061a8c901672f0ac'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 79f8277e5fb5d5184bd5505cf64d30bc94b2c6a6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 1 Mar 2024 17:07:40 +0100 Subject: [PATCH 0868/1193] Add AMOS dependency to let 'toAmos' and 'minimus2' works --- .../a/AMOS/AMOS-3.1.0-foss-2023a.eb | 44 +++++++++++++++++++ .../c/Circlator/Circlator-1.5.5-foss-2023a.eb | 1 + 2 files changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb new file mode 100644 index 000000000000..0ff99e5dcfa0 --- /dev/null +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Cedric Laczny , Fotis Georgatos +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-94.html +## + +easyblock = 'ConfigureMake' + +name = 'AMOS' +version = '3.1.0' + +homepage = 'http://amos.sourceforge.net' +description = """The AMOS consortium is committed to the development of open-source whole genome assembly software""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True, 'cstd': 'c++98'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +patches = ['AMOS-%(version)s_GCC-4.7.patch'] +checksums = [ + '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b', # amos-3.1.0.tar.gz + '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844', # AMOS-3.1.0_GCC-4.7.patch +] + +dependencies = [ + ('expat', '2.5.0'), + ('MUMmer', '4.0.0rc1'), +] + +sanity_check_paths = { + 'files': ['bin/AMOScmp', 'bin/AMOScmp-shortReads', 'bin/AMOScmp-shortReads-alignmentTrimmed'], + 'dirs': [] +} + +parallel = 1 # make crashes otherwise + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb index 924f8a853811..b36cc096ba70 100644 --- a/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb +++ b/easybuild/easyconfigs/c/Circlator/Circlator-1.5.5-foss-2023a.eb @@ -17,6 +17,7 @@ dependencies = [ ('BWA', '0.7.17'), ('prodigal', '2.6.3'), ('SPAdes', '3.15.4'), + ('AMOS', '3.1.0'), ] use_pip = True From 61f73927a1550c3a3fca069e63d5886e05edaa4e Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Fri, 1 Mar 2024 17:48:15 +0100 Subject: [PATCH 0869/1193] Temporarily remove IDG from DP3 dependencies --- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index 72d2b54bee75..d1040f85e886 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -38,7 +38,7 @@ dependencies = [ ('EveryBeam', '0.5.2'), ('Armadillo', '12.8.0'), ('AOFlagger', '3.4.0'), - ('IDG', '1.2.0'), + # ('IDG', '1.2.0'), # test build in EESSI without IDG dependency ] From b852d17e81683508504e7010d5dbd7ca653e761a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Mar 2024 17:26:06 +0000 Subject: [PATCH 0870/1193] adding easyconfigs: PDM-2.12.4-GCCcore-12.3.0.eb --- .../p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb | 108 ++++++++++++++++++ 1 file changed, 108 insertions(+) create mode 100644 easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..172c3b45bbf8 --- /dev/null +++ b/easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb @@ -0,0 +1,108 @@ +easyblock = 'PythonBundle' + +name = 'PDM' +version = '2.12.4' + +homepage = 'https://pdm-project.org' +description = "A modern Python package and dependency manager supporting the latest PEP standards." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('poetry', '1.7.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('virtualenv', '20.23.1'), +] + +use_pip = True + +exts_list = [ + ('pdm_backend', '2.1.8', { + 'modulename': 'pdm.backend', + 'checksums': ['2487dfbd13f69d80fb4e6a08006a3ee68272833970813047dc5fcfacdfdc0151'], + }), + ('blinker', '1.7.0', { + 'checksums': ['e6820ff6fa4e4d1d8e2747c2283749c3f547e4fee112b98555cdcdae32996182'], + }), + ('idna', '3.6', { + 'checksums': ['9ecdbbd083b06798ae1e86adcbfe8ab1479cf864e4ee30fe4e46a003d12491ca'], + }), + ('urllib3', '2.1.0', { + 'checksums': ['df7aa8afb0148fa78488e7899b2c59b5f4ffcfa82e6c54ccb9dd37c1d7b52d54'], + }), + ('charset-normalizer', '3.3.2', { + 'checksums': ['f30c3cb33b24454a82faecaf01b19c18562b1e89558fb6c56de4d9118a032fd5'], + }), + ('requests', '2.31.0', { + 'checksums': ['942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1'], + }), + ('msgpack', '1.0.7', { + 'checksums': ['572efc93db7a4d27e404501975ca6d2d9775705c2d922390d878fcf768d92c87'], + }), + ('cachecontrol', '0.14.0', { + 'checksums': ['7db1195b41c81f8274a7bbd97c956f44e8348265a1bc7641c37dfebc39f0c938'], + }), + ('certifi', '2024.2.2', { + 'checksums': ['0569859f95fc761b18b45ef421b1290a0f65f147e92a1e5eb3e635f9a5e4e66f'], + }), + ('dep_logic', '0.2.0', { + 'checksums': ['cff502b515aff2d413d19d6afc70174fc67da19e821be4a9b68460ccee2514c9'], + }), + ('findpython', '0.4.1', { + 'checksums': ['d7d014558681b3761d57a5b2342a713a8bf302f6c1fc9d99f81b9d8bd1681b04'], + }), + ('installer', '0.7.0', { + 'checksums': ['a26d3e3116289bb08216e0d0f7d925fcef0b0194eedfa0c944bcaaa106c4b631'], + }), + ('packaging', '23.2', { + 'checksums': ['048fb0e9405036518eaaf48a55953c750c11e1a1b68e0dd1a9d62ed0c092cfc5'], + }), + ('pyproject_hooks', '1.0.0', { + 'checksums': ['f271b298b97f5955d53fb12b72c1fb1948c22c1a6b70b315c54cedaca0264ef5'], + }), + ('python-dotenv', '1.0.1', { + 'modulename': 'dotenv', + 'checksums': ['e324ee90a023d808f1959c46bcbc04446a10ced277783dc6ee09987c37ec10ca'], + }), + ('requests-toolbelt', '1.0.0', { + 'checksums': ['7681a0a3d047012b5bdc0ee37d7f8f07ebe76ab08caeccfc3921ce23c88d5bc6'], + }), + ('resolvelib', '1.0.1', { + 'checksums': ['04ce76cbd63fded2078ce224785da6ecd42b9564b1390793f64ddecbe997b309'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('pygments', '2.17.2', { + 'checksums': ['da46cec9fd2de5be3a8a784f434e4c4ab670b4ff54d605c4c2717e9d49c4c367'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('shellingham', '1.5.4', { + 'checksums': ['8dbca0739d487e5bd35ab3ca4b36e11c4078f3a234bfce294b0a0291363404de'], + }), + ('tomlkit', '0.12.4', { + 'checksums': ['7ca1cfc12232806517a8515047ba66a19369e71edf2439d0f5824f91032b6cc3'], + }), + ('truststore', '0.8.0', { + 'checksums': ['dc70da89634944a579bfeec70a7a4523c53ffdb3cf52d1bb4a431fda278ddb96'], + }), + ('unearth', '0.14.0', { + 'checksums': ['f3cddfb94ac0f865fbcf964231556ef7183010379c00b01205517a50c78a186d'], + }), + ('pdm', version, { + 'checksums': ['d04877362f95cf9ffc1d2c38b851f693706e4928840e48986ae576dad5741496'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 474001692a1a1aa4941154eb880db512b5c5594e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 1 Mar 2024 17:48:51 +0000 Subject: [PATCH 0871/1193] add binutils builddep --- easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb index 172c3b45bbf8..ecbfa7162d4f 100644 --- a/easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/PDM/PDM-2.12.4-GCCcore-12.3.0.eb @@ -9,6 +9,7 @@ description = "A modern Python package and dependency manager supporting the lat toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ + ('binutils', '2.40'), ('poetry', '1.7.1'), ] From 2175bf788d677a0794921f102ca28b5b58a6ee13 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 1 Mar 2024 21:28:33 +0100 Subject: [PATCH 0872/1193] use system architecture template in DB_File --- easybuild/easyconfigs/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb index a1002875229f..430fc43f9001 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.835-GCCcore-9.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb index 0b79bde69ae6..3c7b085c1abe 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.855-GCCcore-10.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb index 880fe1334793..97f6bce5acb3 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.856-GCCcore-10.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb index f2707a76ad87..fc23c9d56cee 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.857-GCCcore-11.2.0.eb @@ -24,7 +24,7 @@ dependencies = [ preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb index 9ca805bc383e..a9579572f765 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.858-GCCcore-11.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], 'dirs': [], } diff --git a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb index ceaba6014167..0efe26d544b1 100644 --- a/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/DB_File/DB_File-1.859-GCCcore-12.3.0.eb @@ -24,7 +24,7 @@ dependencies = [ preconfigopts = 'env DB_FILE_INCLUDE="$EBROOTDB/include" DB_FILE_LIB="$EBROOTDB/lib" ' sanity_check_paths = { - 'files': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/DB_File.pm'], + 'files': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/DB_File.pm'], 'dirs': [], } From 062b89c2c92d1b5d7ca25eddd16484773ee11a76 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 1 Mar 2024 21:52:24 +0100 Subject: [PATCH 0873/1193] use system architecture template in GD --- easybuild/easyconfigs/g/GD/GD-2.71-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/g/GD/GD-2.71-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GD/GD-2.71-GCCcore-9.3.0.eb index a54301ab8687..dbaba6f514a5 100644 --- a/easybuild/easyconfigs/g/GD/GD-2.71-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GD/GD-2.71-GCCcore-9.3.0.eb @@ -44,8 +44,8 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s.pm'], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s'], + 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s'], } modextrapaths = { diff --git a/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb index bf13eba9f374..d796bd89fa9b 100644 --- a/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GD/GD-2.73-GCCcore-10.3.0.eb @@ -46,8 +46,8 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s.pm'], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s'], + 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s'], } modextrapaths = { diff --git a/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb index d889cb7d1f5c..fa02d657bb33 100644 --- a/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb @@ -46,8 +46,8 @@ exts_list = [ ] sanity_check_paths = { - 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s.pm'], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi/%(name)s'], + 'files': ['bin/bdf2gdfont.pl', 'lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s.pm'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi/%(name)s'], } modextrapaths = { From 1228e7c8ea4d24523d8bf8724bc45cf83af107dd Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 1 Mar 2024 21:53:31 +0100 Subject: [PATCH 0874/1193] use system architecture template in GDGraph --- .../easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb index 512c17dc89df..c2bce301db64 100644 --- a/easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GDGraph/GDGraph-1.56-GCCcore-11.3.0.eb @@ -53,12 +53,12 @@ exts_list = [ sanity_check_paths = { 'files': ['bin/bdf2gdfont.pl'], - 'dirs': ['lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', 'man'], + 'dirs': ['lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi', 'man'], } modextrapaths = {'PERL5LIB': [ 'lib/perl5/site_perl/%(perlver)s', - 'lib/perl5/site_perl/%(perlver)s/x86_64-linux-thread-multi', + 'lib/perl5/site_perl/%(perlver)s/%(arch)s-linux-thread-multi', ]} moduleclass = 'bio' From 267a7fca186a534a0521f144622bc9eedcfd64db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 2 Mar 2024 23:00:40 +0000 Subject: [PATCH 0875/1193] adding easyconfigs: parameterized-0.9.0-GCCcore-12.3.0.eb --- .../parameterized-0.9.0-GCCcore-12.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/parameterized/parameterized-0.9.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/parameterized/parameterized-0.9.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/parameterized/parameterized-0.9.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..0cb257202b32 --- /dev/null +++ b/easybuild/easyconfigs/p/parameterized/parameterized-0.9.0-GCCcore-12.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'parameterized' +version = '0.9.0' + +homepage = 'https://github.com/wolever/parameterized' +description = """ Parameterized testing with any Python test framework """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7fc905272cefa4f364c1a3429cbbe9c0f98b793988efb5bf90aac80f08db09b1'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From 69f0754061f42cf53de948ab4ed437882295e899 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 3 Mar 2024 08:58:19 +0000 Subject: [PATCH 0876/1193] update homepage and source_urls for SPAdes --- easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb | 4 ++-- .../s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb | 4 ++-- .../s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb | 4 ++-- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb | 4 ++-- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb | 4 ++-- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb | 4 ++-- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb | 4 ++-- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb | 4 ++-- easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb | 4 ++-- 9 files changed, 18 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb index a0d2e6b9948f..3647d8fcef19 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.13.0-GCC-10.3.0.eb @@ -12,12 +12,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.13.0' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['c63442248c4c712603979fa70503c2bff82354f005acda2abc42dd5598427040'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb index 797c1dc12b65..24ec86b9fb0e 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.14.1-GCC-9.3.0-Python-3.8.2.eb @@ -13,12 +13,12 @@ name = 'SPAdes' version = '3.14.1' versionsuffix = '-Python-%(pyver)s' -homepage = 'http://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '9.3.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['d629b78f7e74c82534ac20f5b3c2eb367f245e6840a67b9ef6a76f6fac5323ca'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb index 54ab5e1ceb02..a2f6af4df239 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0-Python-2.7.18.eb @@ -13,12 +13,12 @@ name = 'SPAdes' version = '3.15.2' versionsuffix = '-Python-%(pyver)s' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e93b43951a814dc7bd6a246e1e863bbad6aac4bfe1928569402c131b2af99d0d'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb index d1300d60a18e..4a3432922a8f 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.2-GCC-10.2.0.eb @@ -12,12 +12,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.2' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['e93b43951a814dc7bd6a246e1e863bbad6aac4bfe1928569402c131b2af99d0d'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb index 14828be4967f..689bdea58581 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-10.3.0.eb @@ -12,12 +12,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.3' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['b2e5a9fd7a65aee5ab886222d6af4f7b7bc7f755da7a03941571fabd6b9e1499'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb index 047f59e56a78..3190e8efd2ad 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.3-GCC-11.2.0.eb @@ -14,12 +14,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.3' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['b2e5a9fd7a65aee5ab886222d6af4f7b7bc7f755da7a03941571fabd6b9e1499'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb index cd2ebd173bca..19425c9193cb 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.2.0.eb @@ -14,12 +14,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.4' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '12.2.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['3b241c528a42a8bdfdf23e5bf8f0084834790590d08491decea9f0f009d8589f'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb index 63a20e129998..4988f48656f9 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.4-GCC-12.3.0.eb @@ -14,12 +14,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.4' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '12.3.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['3b241c528a42a8bdfdf23e5bf8f0084834790590d08491decea9f0f009d8589f'] diff --git a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb index 4bc38b801604..edb35db2e8b5 100644 --- a/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/s/SPAdes/SPAdes-3.15.5-GCC-11.3.0.eb @@ -14,12 +14,12 @@ easyblock = 'CMakeMake' name = 'SPAdes' version = '3.15.5' -homepage = 'https://cab.spbu.ru/software/spades/' +homepage = 'https://github.com/ablab/spades' description = "Genome assembler for single-cell and isolates data sets" toolchain = {'name': 'GCC', 'version': '11.3.0'} -source_urls = ['http://cab.spbu.ru/files/release%(version)s'] +source_urls = ['https://github.com/ablab/spades/releases/download/v%(version)s/'] sources = [SOURCE_TAR_GZ] checksums = ['155c3640d571f2e7b19a05031d1fd0d19bd82df785d38870fb93bd241b12bbfa'] From ea455403f9cce1c3ecd29f1eb9f40723bc5bdbe4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Mar 2024 13:54:12 +0100 Subject: [PATCH 0877/1193] fix source URL for xpdf 4.04 --- easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb index 15d45b69a39e..09172b35159e 100644 --- a/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/x/xpdf/xpdf-4.04-GCCcore-12.3.0.eb @@ -11,7 +11,10 @@ Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source.""" toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://dl.xpdfreader.com/'] +source_urls = [ + 'https://dl.xpdfreader.com/', + 'https://dl.xpdfreader.com/old', +] sources = ['%(name)s-%(version)s.tar.gz'] checksums = ['63ce23fcbf76048f524c40be479ac3840d7a2cbadb6d1e0646ea77926656bade'] From 8d74cbb04038f7555013ffce7ce415b6cb7654e1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 4 Mar 2024 14:01:22 +0100 Subject: [PATCH 0878/1193] remove easyconfig for zlib 1.3 w/ intel toolchain, should be using GCCcore (#20023) --- .../z/zlib/zlib-1.3-intel-2023a.eb | 23 ------------------- 1 file changed, 23 deletions(-) delete mode 100644 easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb diff --git a/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb b/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb deleted file mode 100644 index e726074c7119..000000000000 --- a/easybuild/easyconfigs/z/zlib/zlib-1.3-intel-2023a.eb +++ /dev/null @@ -1,23 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'zlib' -version = '1.3' - -homepage = 'https://www.zlib.net/' -description = """zlib is designed to be a free, general-purpose, legally unencumbered -- that is, - not covered by any patents -- lossless data-compression library for use on virtually any - computer hardware and operating system.""" - -toolchain = {'name': 'intel', 'version': '2023a'} -toolchainopts = {'pic': True} - -source_urls = ['https://www.zlib.net/'] -sources = ['zlib-%(version)s.tar.gz'] -checksums = ['ff0ba4c292013dbc27530b3a81e1f9a813cd39de01ca5e0f8bf355702efa593e'] - -sanity_check_paths = { - 'files': ['include/zconf.h', 'include/zlib.h', 'lib/libz.a', 'lib/libz.%s' % SHLIB_EXT], - 'dirs': [], -} - -moduleclass = 'lib' From 17553c0b2b95020befe630980b048ac6e953b400 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 4 Mar 2024 14:24:47 +0100 Subject: [PATCH 0879/1193] adding easyconfigs: epiScanpy-0.4.0-foss-2023a.eb --- .../e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb new file mode 100644 index 000000000000..e1fbb08a5000 --- /dev/null +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'epiScanpy' +version = '0.4.0' + +homepage = 'https://github.com/colomemaria/episcanpy' +description = """EpiScanpy is a toolkit to analyse single-cell open chromatin +(scATAC-seq) and single-cell DNA methylation (for example scBS-seq) +data. EpiScanpy is the epigenomic extension of the very popular scRNA-seq +analysis tool Scanpy (Genome Biology, 2018) [Wolf18].""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Seaborn', '0.13.2'), + ('scanpy', '1.9.8'), # includes anndata + ('Pysam', '0.22.0'), + ('scikit-learn', '1.3.1'), + ('statsmodels', '0.14.1'), + ('numba', '0.58.1'), + ('python-igraph', '0.11.4'), + ('tbb', '2021.11.0'), +] + +exts_list = [ + ('bamnostic', '1.1.10', { + 'checksums': ['2f7e7e5cb693c5f933c5b5c3fde49c6c8dee62b608ebd13a4604401573e37017'], + }), + ('legacy_api_wrap', '1.4', { + 'checksums': ['92dfa274cedb26d6e6f70fac85c856fbdcc05058066656d76a665fb4bf11b785'], + }), + ('kneed', '0.8.5', { + 'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'], + }), + ('episcanpy', version, { + 'preinstallopts': "sed -i 's/tbb//' requirements.txt && ", + 'checksums': ['95739149db60521b0a14e4579f8ba87d410126ffb7b916abbc2d1aff3df40ce3'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' From 07b5ab6a2618d3663d616cd5af2daf9383d60cec Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 4 Mar 2024 14:42:34 +0100 Subject: [PATCH 0880/1193] Fix GDAL 3.5.0 install on high-core-count machines --- easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb index d40b2b9e18c1..e251ec038b90 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-3.5.0-foss-2022a.eb @@ -53,6 +53,8 @@ configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF --with-hdf4=$EBROOTHDF' +maxparallel = 100 + modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} sanity_check_paths = { From 0d7c94313441a4f380b51e0c39ccda3b7d04eb37 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 4 Mar 2024 15:30:06 +0100 Subject: [PATCH 0881/1193] Remove disable-visibility configure flag from GTK3 --- easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb | 2 +- easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb | 2 +- 9 files changed, 9 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb index e6dffd213019..d14f21d65ca1 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.22.30-fosscuda-2018b.eb @@ -32,7 +32,7 @@ dependencies = [ ('X11', '20180604'), ] -configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes" sanity_check_paths = { 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-%%(version_major)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb index 6b3ef66990e3..b4bf155e5eb8 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.13-GCCcore-8.3.0.eb @@ -44,7 +44,7 @@ components = [ (name, version, { 'source_urls': [FTPGNOME_SOURCE], 'checksums': ['4c775c38cf1e3c534ef0ca52ca6c7a890fe169981af66141c713e054e68930a9'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb index 9397344d1d91..0358455beba6 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.17-GCCcore-9.3.0.eb @@ -44,7 +44,7 @@ components = [ (name, version, { 'source_urls': [FTPGNOME_SOURCE], 'checksums': ['f210255b221cb0f0db3e7b21399983b715c9dda6eb1e5c2f7fdf38f4f1b6bac0'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb index 9eaad73eab75..627eb4f9fe94 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.23-GCCcore-10.2.0.eb @@ -44,7 +44,7 @@ components = [ (name, version, { 'source_urls': [FTPGNOME_SOURCE], 'checksums': ['5d864d248357a2251545b3387b35942de5f66e4c66013f0962eb5cb6f8dae2b1'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], diff --git a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb index a5c540dc54c9..c001cac630ab 100644 --- a/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/g/GTK+/GTK+-3.24.8-GCCcore-8.2.0.eb @@ -33,7 +33,7 @@ dependencies = [ ('FriBidi', '1.0.5'), ] -configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility " +configopts = "--disable-silent-rules --disable-glibtest --enable-introspection=yes" sanity_check_paths = { 'files': ['bin/gtk-update-icon-cache', 'lib/libgtk-%%(version_major)s.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb index 646bff77c6ae..764e62264ce4 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.29-GCCcore-10.3.0.eb @@ -44,7 +44,7 @@ components = [ ('GTK+', version, { 'source_urls': [FTPGNOME_SOURCE], 'checksums': ['f57ec4ade8f15cab0c23a80dcaee85b876e70a8823d9105f067ce335a8268caa'], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb index f4bdb729cdb9..3e7711b67587 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.31-GCCcore-11.2.0.eb @@ -42,7 +42,7 @@ default_component_specs = { components = [ ('GTK+', version, { 'source_urls': [FTPGNOME_SOURCE], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", 'checksums': ['423c3e7fdb4c459ee889e35fd4d71fd2623562541c1041b11c07e5ad1ff10bf9'], }), ('hicolor-icon-theme', '0.17', { diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb index ec127c882ec0..46df16bd25a0 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.33-GCCcore-11.3.0.eb @@ -42,7 +42,7 @@ default_component_specs = { components = [ ('GTK+', version, { 'source_urls': [FTPGNOME_SOURCE], - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", 'checksums': ['588b06522e25d1579e989b6f9d8a1bdbf2fe13cde01a04e904ff346a225e7801'], }), ('hicolor-icon-theme', '0.17', { diff --git a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb index f00f26786b05..090111319660 100644 --- a/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb @@ -45,7 +45,7 @@ components = [ 'checksums': ['ec10fe6d712ef0b3c63b5f932639c9d1ae99fce94f500f6f06965629fef60bd1'], # fix packaging issue, see https://gitlab.gnome.org/GNOME/gtk/-/issues/5355 'preconfigopts': "mv testsuite/gtk/gtkresources.c gtk/ && ", - 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes --disable-visibility ", + 'configopts': "--disable-silent-rules --disable-glibtest --enable-introspection=yes", }), ('hicolor-icon-theme', '0.17', { 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], From 1d5dda91d76ab9a6797725e4d601fb313449b884 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Mar 2024 09:05:24 +0100 Subject: [PATCH 0882/1193] Remove unknown configure option from HDF-EOS2-3.0 --- .../easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb index 6faf7065a64a..58e32a5f2b21 100644 --- a/easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HDF-EOS2/HDF-EOS2-3.0-GCCcore-11.3.0.eb @@ -28,7 +28,9 @@ dependencies = [ preconfigopts = 'export CC="$EBROOTHDF/bin/h4cc -Df2cFortran" && ' -configopts = "--with-szlib=$EBROOTSZIP --enable-install-include" +# `--enable-install-include`` mentioned at https://hdfeos.org/software/hdfeos.php +# but not available, likely the default and the option removed. Recheck in next release! +configopts = "--with-szlib=$EBROOTSZIP " sanity_check_paths = { 'files': ['include/HdfEosDef.h', 'lib/libGctp.a', 'lib/libhdfeos.a'], From 94f32571a120858bc08d9947d4d6a20d178fc7af Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Mar 2024 09:18:36 +0100 Subject: [PATCH 0883/1193] Remove mpi configure option from libfdf 0.2.2 --- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb | 2 -- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb | 2 -- .../easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb | 2 -- .../l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb | 2 -- .../l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb | 2 -- .../l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb | 2 -- 6 files changed, 12 deletions(-) diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb index 71cbe3216a65..4f17eb894d9b 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.2.0-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb index 60424b615f6e..d344b97e0a7e 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb index 16305fbd339b..df07567445e0 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb index bb206d03e651..12c8f37583f7 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-iccifort-2020.4.304-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb index f6a353357b6c..8876b15d1d48 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], diff --git a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb index 4277acce16ff..a09baf53da1f 100644 --- a/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb @@ -13,8 +13,6 @@ source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed9 sources = ['libfdf-%(version)s.tar.gz'] checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] -configopts = ' --without-mpi ' - sanity_check_paths = { 'files': ['include/fdf.mod', 'lib/libfdf.a'], 'dirs': [''], From 62569247f420ee58926726e2c988fcbefb958dfe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 5 Mar 2024 10:23:17 +0100 Subject: [PATCH 0884/1193] patch for adding/fixing RISC-V multiarch support --- ...GCCcore-12.x_riscv_multiarch_support.patch | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-12.x_riscv_multiarch_support.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.x_riscv_multiarch_support.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.x_riscv_multiarch_support.patch new file mode 100644 index 000000000000..ba981cea95c9 --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.x_riscv_multiarch_support.patch @@ -0,0 +1,33 @@ +https://gcc.gnu.org/git/gitweb.cgi?p=gcc.git;h=47f95bc4be4eb14730ab3eaaaf8f6e71fda47690 +https://gcc.gnu.org/PR106271 + +From 47f95bc4be4eb14730ab3eaaaf8f6e71fda47690 Mon Sep 17 00:00:00 2001 +From: Raphael Moreira Zinsly +Date: Tue, 22 Aug 2023 11:37:04 -0600 +Subject: [PATCH] RISC-V: Add multiarch support on riscv-linux-gnu + +This adds multiarch support to the RISC-V port so that bootstraps work with +Debian out-of-the-box. Without this patch the stage1 compiler is unable to +find headers/libraries when building the stage1 runtime. + +This is functionally (and possibly textually) equivalent to Debian's fix for +the same problem. + +gcc/ + * config/riscv/t-linux: Add MULTIARCH_DIRNAME. +--- + gcc/config/riscv/t-linux | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/gcc/config/riscv/t-linux b/gcc/config/riscv/t-linux +index 216d2776a18..a6f64f88d25 100644 +--- a/gcc/config/riscv/t-linux ++++ b/gcc/config/riscv/t-linux +@@ -1,3 +1,5 @@ + # Only XLEN and ABI affect Linux multilib dir names, e.g. /lib32/ilp32d/ + MULTILIB_DIRNAMES := $(patsubst rv32%,lib32,$(patsubst rv64%,lib64,$(MULTILIB_DIRNAMES))) + MULTILIB_OSDIRNAMES := $(patsubst lib%,../lib%,$(MULTILIB_DIRNAMES)) ++ ++MULTIARCH_DIRNAME := $(call if_multiarch,$(firstword $(subst -, ,$(target)))-linux-gnu) +-- +2.39.3 From e80ed836246372540ef1091882952efa82818215 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 5 Mar 2024 10:23:39 +0100 Subject: [PATCH 0885/1193] add patch GCCcore-12.x_riscv_multiarch_support.patch --- easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb | 2 ++ easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb | 2 ++ easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 2 ++ easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb | 2 ++ easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 2 ++ 5 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb index bfbba25110c0..38ef50f122ca 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.1.0.eb @@ -38,6 +38,7 @@ patches = [ 'GCCcore-12.1.0_fix-Wuninitialized-in-AVX-headers.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', ] checksums = [ {'gcc-12.1.0.tar.gz': 'e88a004a14697bbbaba311f38a938c716d9a652fd151aaaa4cf1b5b99b90e2de'}, @@ -57,6 +58,7 @@ checksums = [ {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb index 77c3d798705f..50d5b1bcd9c0 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.2.0.eb @@ -39,6 +39,7 @@ patches = [ 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_fix-vectorizer.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', ] checksums = [ {'gcc-12.2.0.tar.gz': 'ac6b317eb4d25444d87cf29c0d141dedc1323a1833ec9995211b13e1a851261c'}, @@ -60,6 +61,7 @@ checksums = [ {'GCCcore-12.2.0_fix-vectorizer.patch': '0b76fc379308fd189ee39c4a3a49facacf8ede08dbec4280f289341083f1632b'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb index 91dd99aa90d2..94a5b7eb7f3c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', ] checksums = [ {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'}, @@ -52,6 +53,7 @@ checksums = [ 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb index 6b8e8a19de61..4d99522c9d57 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', ] checksums = [ {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'}, @@ -49,6 +50,7 @@ checksums = [ {'GCCcore-12.1.0_fix-double-destruct.patch': '2e09c125318b6c15ec60f1807d77fb7d1f32b64a4e5d1c9a3da89ba2ca738d35'}, {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index b3eff862747e..12f599fdd8fd 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', ] checksums = [ {'gcc-13.2.0.tar.gz': '8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078'}, @@ -52,6 +53,7 @@ checksums = [ 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': 'e1d63e04bf494a2f79346ac7454372f117b63288cc18c68876a5b8bdc453cf88'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, ] builddependencies = [ From 925071da1aa5f28a65a14bff797679b2919286f8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 5 Mar 2024 10:40:17 +0100 Subject: [PATCH 0886/1193] adding easyconfigs: inflection-1.3.5-foss-2023a-R-4.3.2.eb --- .../inflection-1.3.5-foss-2023a-R-4.3.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/i/inflection/inflection-1.3.5-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/i/inflection/inflection-1.3.5-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/i/inflection/inflection-1.3.5-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..af8c45ca3938 --- /dev/null +++ b/easybuild/easyconfigs/i/inflection/inflection-1.3.5-foss-2023a-R-4.3.2.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'inflection' +version = '1.3.5' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/dchristop/inflection' +description = """inflection is a package that finds the inflection point of a planar curve which is given as a data frame + of discrete (xi,yi) points""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/dchristop/inflection/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8087db8d60310e7a73956f9c8b1e305a917ce67d47a74acf41dbe16b466dd3a4'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['%(namelower)s'], +} + +moduleclass = 'bio' From b62f92cd88a756e67cc6351ec686cf9429ef4232 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Mar 2024 12:09:10 +0100 Subject: [PATCH 0887/1193] adding easyconfigs: python-irodsclient-2.0.0-GCCcore-12.3.0.eb --- ...python-irodsclient-2.0.0-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100755 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb new file mode 100755 index 000000000000..8905aaea648d --- /dev/null +++ b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'python-irodsclient' +version = '2.0.0' + +homepage = 'https://github.com/irods/python-irodsclient' +description = "A python API for iRODS" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('defusedxml', '0.7.1', { + 'checksums': ['1bb3032db185915b62d7c6209c5a8792be6a32ab2fedacc84e01b52c51aa3e69'], + }), + ('prettytable', '3.9.0', { + 'checksums': ['f4ed94803c23073a90620b201965e5dc0bccf1760b7a7eaf3158cab8aaffdf34'], + }), + (name, version, { + 'modulename': 'irods', + 'checksums': ['4b9de7534c1eeecea4f0d875205cfdc73f7310693748e098b4a3b58c3d781883'], + }), +] + +moduleclass = 'lib' From 30f25dd1e51007e30b030267077d82e243a850d9 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 5 Mar 2024 12:12:39 +0100 Subject: [PATCH 0888/1193] adding easyconfigs: rclone-1.65.2-foss-2023a.eb --- .../r/rclone/rclone-1.65.2-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb b/easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb new file mode 100644 index 000000000000..2f52f947d2b7 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'rclone' +version = '1.65.2' + +homepage = 'https://rclone.org' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ae6179908650429e8d366e4940b586a4bd4aa9ee90c23c423be35550dded346'] + +builddependencies = [('Go', '1.21.6', '', SYSTEM)] + +postinstallcmds = [ + "mkdir -p %(installdir)s/share/{doc,man/man1}", + "cp README.* MANUAL.* %(installdir)s/share/doc/", + "cp rclone.1 %(installdir)s/share/man/man1/", +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From e7fb855d33646145357495f76b5c54200be18795 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 5 Mar 2024 12:48:41 +0100 Subject: [PATCH 0889/1193] fix permisssions of python-irodsclient-2.0.0-GCCcore-12.3.0.eb --- .../python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/python-irodsclient/python-irodsclient-2.0.0-GCCcore-12.3.0.eb old mode 100755 new mode 100644 From 7f54320567462f42ddc8aa1353510729de557cad Mon Sep 17 00:00:00 2001 From: Jordi Camps Puchades Date: Tue, 5 Mar 2024 14:17:12 +0100 Subject: [PATCH 0890/1193] Fix: invocation typo and unneeded folder change on invocation --- easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb b/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb index cd6783ca518a..117730da260e 100644 --- a/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb +++ b/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb @@ -22,21 +22,21 @@ cmds_map = [( '.*', 'sed -i \'s/scala.sys.process.Process("git rev-parse --short HEAD").lineStream.head/"%(version)s"/\' version.sbt' ' && sbt --sbt-dir "$TMPDIR/sbt" assembly --ivy "$TMPDIR/ivy2"' - ' && echo -e \'#!/bin/bash\\ncd $(dirname $0) && exec java -jar ../lib/fgbio-%(version)s.jar "$@"\' >> fbgio' - ' && chmod +x fbgio' + ' && echo -e \'#!/bin/bash\\nexec java -jar "${EBROOTFGBIO}/lib/fgbio-%(version)s.jar" "$@"\' >> fgbio' + ' && chmod +x fgbio' )] files_to_copy = [ - (['fbgio'], 'bin'), + (['fgbio'], 'bin'), (['target/scala-*/fgbio-%(version)s.jar'], 'lib'), ] sanity_check_paths = { - 'files': ['bin/fbgio', 'lib/fgbio-%(version)s.jar'], + 'files': ['bin/fgbio', 'lib/fgbio-%(version)s.jar'], 'dirs': [], } # --help, --version, ... all exit with status code one, so we need to check the output -sanity_check_commands = ['fbgio --help 2>&1 | grep -q Version'] +sanity_check_commands = ['fgbio --help 2>&1 | grep -q Version'] moduleclass = 'bio' From 5cbe02b5f20d55d91125305ea82f22cea7d5c0bd Mon Sep 17 00:00:00 2001 From: Jordi Camps Puchades Date: Tue, 5 Mar 2024 14:53:15 +0100 Subject: [PATCH 0891/1193] Substituted hard coded software name by templates --- easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb b/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb index 117730da260e..b6d55a922a01 100644 --- a/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb +++ b/easybuild/easyconfigs/f/fgbio/fgbio-1.3.0.eb @@ -22,21 +22,21 @@ cmds_map = [( '.*', 'sed -i \'s/scala.sys.process.Process("git rev-parse --short HEAD").lineStream.head/"%(version)s"/\' version.sbt' ' && sbt --sbt-dir "$TMPDIR/sbt" assembly --ivy "$TMPDIR/ivy2"' - ' && echo -e \'#!/bin/bash\\nexec java -jar "${EBROOTFGBIO}/lib/fgbio-%(version)s.jar" "$@"\' >> fgbio' - ' && chmod +x fgbio' + ' && echo -e \'#!/bin/bash\\nexec java -jar "${EBROOTFGBIO}/lib/%(name)s-%(version)s.jar" "$@"\' >> %(name)s' + ' && chmod +x %(name)s' )] files_to_copy = [ - (['fgbio'], 'bin'), - (['target/scala-*/fgbio-%(version)s.jar'], 'lib'), + (['%(name)s'], 'bin'), + (['target/scala-*/%(name)s-%(version)s.jar'], 'lib'), ] sanity_check_paths = { - 'files': ['bin/fgbio', 'lib/fgbio-%(version)s.jar'], + 'files': ['bin/%(name)s', 'lib/%(name)s-%(version)s.jar'], 'dirs': [], } # --help, --version, ... all exit with status code one, so we need to check the output -sanity_check_commands = ['fgbio --help 2>&1 | grep -q Version'] +sanity_check_commands = ['%(name)s --help 2>&1 | grep -q Version'] moduleclass = 'bio' From a7a89589ca40d66330f92fa6ca982edf26da979c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Mar 2024 15:18:17 +0100 Subject: [PATCH 0892/1193] Remove hdf5 configure option from MDSplus 7.96.12 --- .../easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb index de21068d55ca..3c1da528b64c 100644 --- a/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/MDSplus/MDSplus-7.96.12-GCCcore-9.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('libreadline', '8.0') ] -configopts = '--disable-doxygen-doc --disable-java --disable-hdf5' +configopts = '--disable-doxygen-doc --disable-java' # hardcode version via configure script (git is unavailable) configopts += ' RELEASE_VERSION=%(version)s BRANCH=stable' From 2dc869f18786870cc610b4d56e1366583508b6ac Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Tue, 5 Mar 2024 15:52:21 +0100 Subject: [PATCH 0893/1193] Move poetry to builddeps, update poetry version --- .../easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb b/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb index 44cc04085aec..b74e4bba6757 100644 --- a/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/gcsfs/gcsfs-2023.12.2.post1-foss-2023a.eb @@ -8,10 +8,11 @@ description = """Pythonic file-system interface for Google Cloud Storage.""" toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [('poetry', '1.7.1')] + dependencies = [ ('Python', '3.11.3'), ('aiohttp', '3.8.5'), - ('poetry', '1.5.1'), ('protobuf-python', '4.24.0'), ] From 670fbc32d8bc7c1ad56969a802c9669cb4f8ad60 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 5 Mar 2024 16:05:11 +0100 Subject: [PATCH 0894/1193] Fix python configure option of MEME --- .../easyconfigs/m/MEME/MEME-5.1.1-foss-2018b-Python-3.6.6.eb | 2 +- .../easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb | 2 +- .../easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb | 2 +- easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2018b-Python-3.6.6.eb index 0665fef3727e..7e55e86c14fc 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2018b-Python-3.6.6.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '3.6.6') ] -configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' sanity_check_paths = { 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb index ac176c5c4895..2505c1c303de 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-foss-2019b-Python-3.7.4.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '3.7.4') ] -configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' sanity_check_paths = { 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb index 9ac8e36aadb7..82553a2a701e 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.1.1-intel-2019b-Python-3.7.4.eb @@ -29,7 +29,7 @@ dependencies = [ ('Python', '3.7.4') ] -configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' +configopts = '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' sanity_check_paths = { 'files': ["bin/meme", "bin/dreme", "bin/meme-chip"], diff --git a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb index 4858375aeaf4..49b56756c7ad 100644 --- a/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/m/MEME/MEME-5.4.1-GCC-10.3.0.eb @@ -29,7 +29,7 @@ dependencies = [ ] configopts = '--enable-build-libxml2 --enable-build-libxslt ' -configopts += '--with-perl=${EBROOTPERL}/bin/perl --with-python3=${EBROOTPYTHON}/bin/python ' +configopts += '--with-perl=${EBROOTPERL}/bin/perl --with-python=${EBROOTPYTHON}/bin/python ' sanity_check_paths = { 'files': ["bin/%(namelower)s", "bin/dreme", "bin/%(namelower)s-chip"], From 40073fd20a6526947c3a43c3db24b22e7cc151cd Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 5 Mar 2024 16:37:54 +0100 Subject: [PATCH 0895/1193] change toolchain to SYSTEM --- .../easyconfigs/r/rclone/rclone-1.65.2.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.65.2.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.65.2.eb b/easybuild/easyconfigs/r/rclone/rclone-1.65.2.eb new file mode 100644 index 000000000000..6110c02c2b16 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.65.2.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'rclone' +version = '1.65.2' + +homepage = 'https://rclone.org' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['5ae6179908650429e8d366e4940b586a4bd4aa9ee90c23c423be35550dded346'] + +builddependencies = [('Go', '1.21.6', '', SYSTEM)] + +postinstallcmds = [ + "mkdir -p %(installdir)s/share/{doc,man/man1}", + "cp README.* MANUAL.* %(installdir)s/share/doc/", + "cp rclone.1 %(installdir)s/share/man/man1/", +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From 8fcfee7cd165fa5b7c556f97fadc7bc03b40cf2b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 5 Mar 2024 16:46:04 +0100 Subject: [PATCH 0896/1193] remove easyconfig with foss toolchain --- .../r/rclone/rclone-1.65.2-foss-2023a.eb | 34 ------------------- 1 file changed, 34 deletions(-) delete mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb b/easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb deleted file mode 100644 index 2f52f947d2b7..000000000000 --- a/easybuild/easyconfigs/r/rclone/rclone-1.65.2-foss-2023a.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'GoPackage' - -name = 'rclone' -version = '1.65.2' - -homepage = 'https://rclone.org' - -description = """ - Rclone is a command line program to sync files and directories to and from - a variety of online storage services -""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['5ae6179908650429e8d366e4940b586a4bd4aa9ee90c23c423be35550dded346'] - -builddependencies = [('Go', '1.21.6', '', SYSTEM)] - -postinstallcmds = [ - "mkdir -p %(installdir)s/share/{doc,man/man1}", - "cp README.* MANUAL.* %(installdir)s/share/doc/", - "cp rclone.1 %(installdir)s/share/man/man1/", -] - -sanity_check_paths = { - 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], - 'dirs': [] -} - -sanity_check_commands = ['rclone --version'] - -moduleclass = 'tools' From 3feb9d999c536d418d14d2899b027c0f4ce1cf05 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 5 Mar 2024 17:17:55 +0000 Subject: [PATCH 0897/1193] adding easyconfigs: Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb --- .../Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..9c1e920324e7 --- /dev/null +++ b/easybuild/easyconfigs/p/Parallel-Hashmap/Parallel-Hashmap-1.3.12-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'Parallel-Hashmap' +version = '1.3.12' + +homepage = 'https://github.com/greg7mdp/parallel-hashmap' +description = """Parallel Hashmap is built on a modified version of +Abseil's flat_hash_map. Parallel Hashmap has lower space requirements, +is nearly as fast as the underlying flat_hash_map, and can be used from +multiple threads with high levels of concurrency.""" + +# There is no actual library built, so it can be at GCCcore level despite being a C++ "library" +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'greg7mdp' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0cc203144321924cfbfcc401f42d8204c0dd24e2760c7a1c091baa16d9777c08'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +configopts = '-DPHMAP_BUILD_TESTS=OFF -DPHMAP_BUILD_EXAMPLES=OFF' # The test code doesn't build + +sanity_check_paths = { + 'files': ['include/parallel_hashmap/phmap%s.h' % x for x in [ + '', '_base', '_bits', '_config', '_dump', '_fwd_decl', '_utils' + ]], + 'dirs': [], +} + +moduleclass = 'lib' From 156d738f219cb167a196a081bc2090f17189017e Mon Sep 17 00:00:00 2001 From: Taras Lazariv Date: Tue, 5 Mar 2024 21:33:45 +0100 Subject: [PATCH 0898/1193] adding easyconfigs: libgit2-1.7.2-GCCcore-13.2.0.eb --- .../l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..1b8babdb90f0 --- /dev/null +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'libgit2' +version = '1.7.2' + +homepage = 'https://libgit2.org/' +description = """libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant +linkable library with a solid API, allowing you to write native speed custom Git applications in any language +which supports C bindings.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['de384e29d7efc9330c6cdb126ebf88342b5025d920dcb7c645defad85195ea7f'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] +dependencies = [ + ('PCRE2', '10.42'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '-DREGEX_BACKEND=pcre2' + +github_account = '%(name)s' + +sanity_check_paths = { + 'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'], + 'dirs': [], +} + +moduleclass = 'devel' + From a2c55efde0d7f57a2d889e8500809f008b5dd259 Mon Sep 17 00:00:00 2001 From: Taras Lazariv Date: Tue, 5 Mar 2024 21:41:21 +0100 Subject: [PATCH 0899/1193] adding easyconfigs: R-4.3.3-gfbf-2023b.eb --- .../easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 372 ++++++++++++++++++ 1 file changed, 372 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb new file mode 100644 index 000000000000..5ed3ce06c41d --- /dev/null +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -0,0 +1,372 @@ +name = 'R' +version = '4.3.3' + +homepage = 'https://www.r-project.org/' +description = """R is a free software environment for statistical computing + and graphics.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +source_urls = ['https://cloud.r-project.org/src/base/R-%(version_major)s'] +sources = [SOURCE_TAR_GZ] +checksums = ['80851231393b85bf3877ee9e39b282e750ed864c5ec60cbd68e6e139f0520330'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('Autotools', '20220317'), +] +dependencies = [ + ('X11', '20231019'), + ('Mesa', '23.1.9'), + ('libGLU', '9.0.3'), + ('cairo', '1.18.0'), + ('libreadline', '8.2'), + ('ncurses', '6.4'), + ('bzip2', '1.0.8'), + ('XZ', '5.4.4'), + ('zlib', '1.2.13'), + ('SQLite', '3.43.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), # for plotting in R + ('libjpeg-turbo', '3.0.1'), # for plottting in R + ('LibTIFF', '4.6.0'), + ('Java', '11', '', SYSTEM), + ('libgit2', '1.7.2'), + ('OpenSSL', '1.1', '', SYSTEM), + ('cURL', '8.3.0'), + ('Tk', '8.6.13'), # for tcltk + ('HarfBuzz', '8.2.2'), # for textshaping + ('FriBidi', '1.0.13'), # for textshaping + +] + +# Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. +# Adding it to FLIBS makes sure it is present when needed. +preconfigopts = 'export FLIBS="$FLIBS -lm" && ' + +configopts = "--with-pic --enable-threads --enable-R-shlib" +# some recommended packages may fail in a parallel build (e.g. Matrix), and +# we're installing them anyway below +configopts += " --with-recommended-packages=no" + +# specify that at least EasyBuild v3.5.0 is required, +# since we rely on the updated easyblock for R to configure correctly w.r.t. BLAS/LAPACK +easybuild_version = '3.5.0' + +exts_default_options = { + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], + 'source_tmpl': '%(name)s_%(version)s.tar.gz', +} + +# !! order of packages is important !! +# packages updated on 5th November 2023 +exts_list = [ + 'base', + 'compiler', + 'datasets', + 'graphics', + 'grDevices', + 'grid', + 'methods', + 'parallel', + 'splines', + 'stats', + 'stats4', + 'tcltk', + 'tools', + 'utils', + ('rlang', '1.1.3', { + 'checksums': ['24a3424b5dc2c4bd3e5f7c0b54fbe1355028e329181b2d41f4464c8ade28bf0a'], + }), + ('Rcpp', '1.0.12', { + 'checksums': ['0c7359cc43beee02761aa3df2baccede1182d29d28c9cd49964b609305062bd0'], + }), + ('R6', '2.5.1', { + 'checksums': ['8d92bd29c2ed7bf15f2778618ffe4a95556193d21d8431a7f75e7e5fc102bf48'], + }), + ('cli', '3.6.2', { + 'checksums': ['4c0749e3711b2b6ae90fd992784303bc8d98039599cac1deb397239a7018e151'], + }), + ('base64enc', '0.1-3', { + 'checksums': ['6d856d8a364bcdc499a0bf38bfd283b7c743d08f0b288174fba7dbf0a04b688d'], + }), + ('rprojroot', '2.0.4', { + 'checksums': ['b5f463fb25a24dac7a4ca916be57dbe22b5262e1f41e53871ca83e57d4336e99'], + }), + ('xfun', '0.42', { + 'checksums': ['07bbfaed212ba1fcb9367624e8bc4936a7884e30e0efc561199acd0fcba5750a'], + }), + ('commonmark', '1.9.1', { + 'checksums': ['9517a13f4ce4a99bb157493453b04419b222cb65a9471cd3b11e5045ac0db53b'], + }), + ('highr', '0.10', { + 'checksums': ['ec55bc1ff66390ed66806dc2a7b6c17dbfd089b3d73fe2e369017f8cb4bc347b'], + }), + ('digest', '0.6.34', { + 'checksums': ['0b737552932f165d4158ac94631f90abfb02c510df14577d7aa900c8fd3d44d9'], + }), + ('desc', '1.4.3', { + 'checksums': ['54468da73dd78fc9e7c565c41cfe3331802c2134b2e61a9ad197215317092f26'], + }), + ('ellipsis', '0.3.2', { + 'checksums': ['a90266e5eb59c7f419774d5c6d6bd5e09701a26c9218c5933c9bce6765aa1558'], + }), + ('prettyunits', '1.2.0', { + 'checksums': ['f059f27e2a5c82e351fe05b87ad712f7afc273c651450453f59d99af5deeacea'], + }), + ('crayon', '1.5.2', { + 'checksums': ['70a9a505b5b3c0ee6682ad8b965e28b7e24d9f942160d0a2bad18eec22b45a7a'], + }), + ('stringi', '1.8.3', { + 'checksums': ['1602be8edd1dd8ac5a836f4077cbc9d6a312ca4b2c594a0486370e8c1e314925'], + }), + ('magrittr', '2.0.3', { + 'checksums': ['a2bff83f792a1acb801bfe6330bb62724c74d5308832f2cb6a6178336ace55d2'], + }), + ('evaluate', '0.23', { + 'checksums': ['c9cf9c37502b8fbfa78e4eb96b8c3d1789060e49505c86c07cb7476da804a45c'], + }), + ('ps', '1.7.6', { + 'checksums': ['52c35ffc3d1e1d984a94c7bbd671ef4ad70946990cbcd80e814e17937b056dd2'], + }), + ('processx', '3.8.3', { + 'checksums': ['1ad8c51482b89702fbbb6621b1a179c1ae67b78388b8fd9c841bbc8cf035d831'], + }), + ('callr', '3.7.5', { + 'checksums': ['18a11e8f7324d5b013149af69a32784aea7433863492aaabccd8d227b73b472c'], + }), + ('pkgbuild', '1.4.3', { + 'checksums': ['1583edb56c0afab6f99d0dd2235fd45999461f89e8ca50bc7c0b74211f109165'], + }), + ('fs', '1.6.3', { + 'checksums': ['fa82061e50d7a4d94b7e404f9f2b699e75ae8fbfb575fabdfc2c39f536c0f971'], + }), + ('utf8', '1.2.4', { + 'checksums': ['418f824bbd9cd868d2d8a0d4345545c62151d321224cdffca8b1ffd98a167b7d'], + }), + ('fansi', '1.0.6', { + 'checksums': ['ea9dc690dfe50a7fad7c5eb863c157d70385512173574c56f4253b6dfe431863'], + }), + ('pkgconfig', '2.0.3', { + 'checksums': ['330fef440ffeb842a7dcfffc8303743f1feae83e8d6131078b5a44ff11bc3850'], + }), + ('withr', '3.0.0', { + 'checksums': ['8c78eede6d0e648c23d38a6695f642aed2819ef708239d00b36cbc15eabbe0e7'], + }), + ('glue', '1.7.0', { + 'checksums': ['1af51b51f52c1aeb3bfe9349f55896dd78b5542ffdd5654e432e4d646e4a86dc'], + }), + ('rstudioapi', '0.15.0', { + 'checksums': ['935bc81dca37d3d6e77982bfe6e7fbd779e8606e5b7e00d0ba4c80fec0416ccf'], + }), + ('pkgload', '1.3.4', { + 'checksums': ['60b04b948cda4dc56257b1e89f9b0a4b1273cacecdb2bd995d66dd76e89926ce'], + }), + ('fastmap', '1.1.1', { + 'checksums': ['3623809dd016ae8abd235200ba7834effc4b916915a059deb76044137c5c7173'], + }), + ('htmltools', '0.5.7', { + 'checksums': ['ecb0d82619063f49e4d001c44fcc1b811a06928fd66c2bb8c86632798d98b386'], + }), + ('yaml', '2.3.8', { + 'checksums': ['9ed079e2159cae214f3fefcbc4c8eb3b888ceabe902350adbdb1d181eda23fd8'], + }), + ('knitr', '1.45', { + 'checksums': ['ee2edea53bc53efa51d131ab5a0b0c829c0f950b79d3c6ee34705354bf7584fb'], + }), + ('mime', '0.12', { + 'checksums': ['a9001051d6c1e556e881910b1816b42872a1ee41ab76d0040ce66a27135e3849'], + }), + ('praise', '1.0.0', { + 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], + }), + ('brio', '1.1.4', { + 'checksums': ['0cbbf38948682b2435eea69b04be59187b149183dc7562df71dc0d3e260e18e8'], + }), + ('jsonlite', '1.8.8', { + 'checksums': ['7de21316984c3ba3d7423d12f43d1c30c716007c5e39bf07e11885e0ceb0caa4'], + }), + ('lifecycle', '1.0.4', { + 'checksums': ['ada4d3c7e84b0c93105e888647c5754219a8334f6e1f82d5afaf83d4855b91cc'], + }), + ('vctrs', '0.6.5', { + 'checksums': ['43167d2248fd699594044b5c8f1dbb7ed163f2d64761e08ba805b04e7ec8e402'], + }), + ('stringr', '1.5.1', { + 'checksums': ['a4adec51bb3f04214b1d8ef40d3a58949f21b1497cbeaf2ba552e0891eef45de'], + }), + ('pillar', '1.9.0', { + 'checksums': ['f23eb486c087f864c2b4072d5cba01d5bebf2f554118bcba6886d8dbceb87acc'], + }), + ('tibble', '3.2.1', { + 'checksums': ['65a72d0c557fd6e7c510d150c935ed6ced5db7d05fc20236b370f11428372131'], + }), + ('diffobj', '0.3.5', { + 'checksums': ['d860a79b1d4c9e369282d7391b539fe89228954854a65ba47181407c53e3cf60'], + }), + ('rematch2', '2.1.2', { + 'checksums': ['fe9cbfe99dd7731a0a2a310900d999f80e7486775b67f3f8f388c30737faf7bb'], + }), + ('waldo', '0.5.2', { + 'checksums': ['82cdae1ab2c5e7e5dbf5c6bdf832020b46e152732053fb45de7c9a81afdf2e05'], + }), + ('testthat', '3.2.1', { + 'checksums': ['1d980e611b01c194007639a100c3ddaeaab77786d32f81680f497f99e60748ad'], + }), + ('xml2', '1.3.6', { + 'checksums': ['e81991ff99bff3616dde8683c1327194e3ea64fa3b8062f52d8ce32673dd308f'], + }), + ('curl', '5.2.1', { + 'checksums': ['4a7a4d8c08aa1bca2fcd9c58ade7b4b0ea2ed9076d0521071be29baac8adfa90'], + }), + ('sys', '3.4.2', { + 'checksums': ['b7bdce66f0fb681830ea6fb77b5a2c6babb43920abb1eddc733f95c0a63ce5b3'], + }), + ('askpass', '1.2.0', { + 'checksums': ['b922369781934d0ffc8d0c0177e8ace56796c2e6a726f65e460c16f792592cef'], + }), + ('openssl', '2.1.1', { + 'checksums': ['faa726f9af2a97d5fa1e1044f4a38ee2edd4c81f0beb5830f6a36ff249b64bdc'], + }), + ('httr', '1.4.7', { + 'checksums': ['1555e6c2fb67bd38ff11b479f74aa287b2d93f4add487aec53b836ff07de3a3a'], + }), + ('jquerylib', '0.1.4', { + 'checksums': ['f0bcc11dcde3a6ff180277e45c24642d3da3c8690900e38f44495efbc9064411'], + }), + ('rappdirs', '0.3.3', { + 'checksums': ['49959f65b45b0b189a2792d6c1339bef59674ecae92f8c2ed9f26ff9e488c184'], + }), + ('sass', '0.4.8', { + 'checksums': ['42ba2930cd22ad9f5e0022b9ac53bdbc4c9250f00e0646e6502f635a6db3c40c'], + }), + ('purrr', '1.0.2', { + 'checksums': ['2c1bc6bb88433dff0892b41136f2f5c23573b335ff35a4775c72aa57b48bbb63'], + }), + ('cachem', '1.0.8', { + 'checksums': ['ea9ca919fe615dce8770758ecc2fc88ac99074f66ff1cde3a0b95d40007f45c2'], + }), + ('memoise', '2.0.1', { + 'checksums': ['f85034ee98c8ca07fb3cd826142c1cd1e1e5747075a94c75a45783bbc4fe2deb'], + }), + ('bslib', '0.6.1', { + 'checksums': ['642735afd7d3895f1ac8c5a5f7f5e08001bfabcf62a56d2d85904655a2e931db'], + }), + ('fontawesome', '0.5.2', { + 'checksums': ['da3de2a9717084d1400d48edd783f06c66b8c910ce9c8d753d1b7d99be1c5cc9'], + }), + ('tinytex', '0.49', { + 'checksums': ['941169ec65445d172658d0fb6ea8d839736f3f1b5f6ce20637d7d8e299663145'], + }), + ('rmarkdown', '2.25', { + 'checksums': ['06e4662666fe018fbe3bef3531280a461c7bc24bb00f34b9d4c7b08d52210155'], + }), + ('downlit', '0.4.3', { + 'checksums': ['6c0fbe98ece8a511973263f8e8a35574df0cfc45edea7452b53b8d326436b3bd'], + }), + ('cpp11', '0.4.7', { + 'checksums': ['801d1266824c3972642bce2db2a5fd0528a65ec845c58eb5a886edf082264344'], + }), + ('systemfonts', '1.0.5', { + 'checksums': ['840ffb1d8293739c79cbc868101d9f9a84f4a9de4c7b3625e30af2fb63e15823'], + }), + ('textshaping', '0.3.7', { + 'checksums': ['fa924dbe1fb4138b80d6c26ee42f4203843f1d34f77e2a5e42514e6fcc97ec42'], + }), + ('ragg', '1.2.7', { + 'checksums': ['d77a18662d127881dcb5046033eb809293ad9ad439fa4b217202b8cef4280c9f'], + }), + ('whisker', '0.4.1', { + 'checksums': ['bf5151494508032f68ac41e211bda80da9087c65c7068ffdd12f16669bf1f2bc'], + }), + ('pkgdown', '2.0.7', { + 'checksums': ['f33872869dfa8319182d87e90eab3245ff69293b3b791471bf9538afb81b356a'], + }), + ('htmlwidgets', '1.6.4', { + 'checksums': ['7cb08f0b30485dac26f72e4056ec4ed8825d1398e8b9f25ed63db228fe3a0ed0'], + }), + ('profvis', '0.3.8', { + 'checksums': ['ec02c75bc9907a73564e691adfa8e06651ca0bd73b7915412960231cd265b4b2'], + }), + ('urlchecker', '1.0.1', { + 'checksums': ['62165ddbe1b748b58c71a50c8f07fdde6f3d19a7b39787b9fa2b4f9216250318'], + }), + ('later', '1.3.2', { + 'checksums': ['52f5073d33cd0d3c12e56526c9c53c323ebafcc79b22cc6e51fb0c41ee2b561e'], + }), + ('promises', '1.2.1', { + 'checksums': ['3ce0a26df39ea27536877ec6db13083b2952108245024baa8b40ae856d2ce5be'], + }), + ('xtable', '1.8-4', { + 'checksums': ['5abec0e8c27865ef0880f1d19c9f9ca7cc0fd24eadaa72bcd270c3fb4075fd1c'], + }), + ('httpuv', '1.6.14', { + 'checksums': ['4026acae26bd99873e269b062f343f2239131130b43fdfd6a1a5a89b913cd181'], + }), + ('sourcetools', '0.1.7-1', { + 'checksums': ['96812bdb7a0dd99690d84e4b0a3def91389e4290f53f01919ef28a50554e31d1'], + }), + ('shiny', '1.8.0', { + 'checksums': ['f28740ba28707e8b3dabb2ad27b002dae555317010660702163bb0daefe04641'], + }), + ('miniUI', '0.1.1.1', { + 'checksums': ['452b41133289f630d8026507263744e385908ca025e9a7976925c1539816b0c0'], + }), + ('brew', '1.0-10', { + 'checksums': ['4181f7334e032ae0775c5dec49d6137eb25d5430ca3792d321793307b3dda38f'], + }), + ('roxygen2', '7.3.1', { + 'checksums': ['215e9fa9c0e73cb33f9870854c97b25c1a6386f519f69f397123f1a66656e2c8'], + }), + ('rversions', '2.1.2', { + 'checksums': ['de5818233e8271132fe8ea70145618950b35786e0d2f270e39bf3338f3b8b160'], + }), + ('sessioninfo', '1.2.2', { + 'checksums': ['f56283857c53ac8691e3747ed48fe03e893d8ff348235bff7364658bcfb0c7cb'], + }), + ('xopen', '1.0.0', { + 'checksums': ['e207603844d69c226142be95281ba2f4a056b9d8cbfae7791ba60535637b3bef'], + }), + ('rcmdcheck', '1.4.0', { + 'checksums': ['bbd4ef7d514b8c2076196a7c4a6041d34623d55fbe73f2771758ce61fd32c9d0'], + }), + ('remotes', '2.4.2.1', { + 'checksums': ['7ba8ca9a652d60bcdea25dbd43bd1e055e97b031c05e0bc3fac43bf245c1209d'], + }), + ('clipr', '0.8.0', { + 'checksums': ['32c2931992fbec9c31b71de3e27059f1cbb45b4b1f45fd42e0e8dbcec6de3be9'], + }), + ('ini', '0.3.1', { + 'checksums': ['7b191a54019c8c52d6c2211c14878c95564154ec4865f57007953742868cd813'], + }), + ('gitcreds', '0.1.2', { + 'checksums': ['41c6abcca5635062b123ffb5af2794770eca5ebd97b05c5a64b24fa1c803c75d'], + }), + ('httr2', '1.0.0', { + 'checksums': ['cb852d6f560c329a7dc17aa760f09a0950413513dc8abfc3facb6418b2934a49'], + }), + ('gh', '1.4.0', { + 'checksums': ['68c69fcd18429b378e639a09652465a4e92b7b5b5704804d0c5b1ca2b9b58b71'], + }), + ('credentials', '2.0.1', { + 'checksums': ['2c7cfc45bd4afa9a2c2b85d43e907b212da3468781e1b617737bd095253c358b'], + }), + ('zip', '2.3.1', { + 'checksums': ['83754408781c525917f36535865d28214893de0778b5f337e050cb543cacc28f'], + }), + ('gert', '2.0.1', { + 'checksums': ['0ed784837809ce89797ea77834d420e89351728f70d8d2f4b34487df813cd092'], + }), + ('usethis', '2.2.3', { + 'checksums': ['8d0c98995c23b5f4b5b95cd453557d2d15faa7399cc01bff304f5b15cb0cdeb3'], + }), + ('devtools', '2.4.5', { + 'checksums': ['38160ebd839acdec7ebf0699a085b4ab1ebd5500d3c57a9fa7ae484f1909904b'], + }), +] + +moduleclass = 'lang' From b7c3223f8a01dd9b783844a113938f9ff5befcb4 Mon Sep 17 00:00:00 2001 From: lazariv Date: Wed, 6 Mar 2024 08:50:40 +0100 Subject: [PATCH 0900/1193] Update easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb index 1b8babdb90f0..3dd5812483b7 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb @@ -26,8 +26,6 @@ dependencies = [ configopts = '-DREGEX_BACKEND=pcre2' -github_account = '%(name)s' - sanity_check_paths = { 'files': ['include/git2.h', 'lib64/%%(name)s.%s' % SHLIB_EXT, 'lib64/pkgconfig/%(name)s.pc'], 'dirs': [], From 4948552d5469b368f39189ad7ccb7e926183f274 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2024 10:42:27 +0100 Subject: [PATCH 0901/1193] adding easyconfigs: noise-1.2.2-gfbf-2023a.eb --- .../n/noise/noise-1.2.2-gfbf-2023a.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/n/noise/noise-1.2.2-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/n/noise/noise-1.2.2-gfbf-2023a.eb b/easybuild/easyconfigs/n/noise/noise-1.2.2-gfbf-2023a.eb new file mode 100644 index 000000000000..71930964e8b7 --- /dev/null +++ b/easybuild/easyconfigs/n/noise/noise-1.2.2-gfbf-2023a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonBundle' + +name = 'noise' +version = '1.2.2' + +homepage = 'https://github.com/caseman/noise' +description = "Native-code and shader implementations of Perlin noise for Python" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['57a2797436574391ff63a111e852e53a4164ecd81ad23639641743cd1a209b65'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 1537e7723b313b2a5ea84612a19dde703f0d15a1 Mon Sep 17 00:00:00 2001 From: lazariv Date: Wed, 6 Mar 2024 11:12:47 +0100 Subject: [PATCH 0902/1193] Update easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 5ed3ce06c41d..74dc215f5751 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -37,7 +37,6 @@ dependencies = [ ('Tk', '8.6.13'), # for tcltk ('HarfBuzz', '8.2.2'), # for textshaping ('FriBidi', '1.0.13'), # for textshaping - ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. From dbd0095103a8a6cca7c2393bb88327d9aaa6efd2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2024 11:13:11 +0100 Subject: [PATCH 0903/1193] update to PyTorch-Lightning 2.2.1 --- ... => PyTorch-Lightning-2.2.1-foss-2023a.eb} | 84 +++++++++---------- 1 file changed, 42 insertions(+), 42 deletions(-) rename easybuild/easyconfigs/p/PyTorch-Lightning/{PyTorch-Lightning-2.1.3-foss-2023a.eb => PyTorch-Lightning-2.2.1-foss-2023a.eb} (60%) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.2.1-foss-2023a.eb similarity index 60% rename from easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb rename to easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.2.1-foss-2023a.eb index 33266d03c517..a3c1fa088e85 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.1.3-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.2.1-foss-2023a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'PyTorch-Lightning' -version = '2.1.3' +version = '2.2.1' homepage = 'https://pytorchlightning.ai' description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." @@ -41,56 +41,56 @@ exts_list = [ 'modulename': 'markdown_it', 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], }), - ('rich', '13.7.0', { - 'checksums': ['5cb5123b5cf9ee70584244246816e9114227e0b98ad9176eede6ad54bf5403fa'], + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], }), ('PyJWT', '2.8.0', { 'modulename': 'jwt', 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], }), - ('starlette', '0.35.1', { - 'checksums': ['3e2639dac3520e4f58734ed22553f950d3f3cb1001cd2eaac4d57e8cdc5f66bc'], + ('starlette', '0.36.3', { + 'checksums': ['90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080'], }), - ('fastapi', '0.109.0', { - 'checksums': ['b978095b9ee01a5cf49b19f4bc1ac9b8ca83aa076e770ef8fd9af09a2b88d191'], + ('fastapi', '0.110.0', { + 'checksums': ['266775f0dcc95af9d3ef39bad55cff525329a931d5fd51930aadd4f428bf7ff3'], }), - ('sniffio', '1.3.0', { - 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], }), ('exceptiongroup', '1.2.0', { 'checksums': ['91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68'], }), - ('anyio', '4.2.0', { - 'checksums': ['e1875bb4b4e2de1669f4bc7869b6d3f54231cdced71605e6e64c9be77e3be50f'], + ('anyio', '4.3.0', { + 'checksums': ['f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6'], }), ('websocket-client', '1.7.0', { 'modulename': 'websocket', 'checksums': ['10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6'], }), - ('python_multipart', '0.0.6', { + ('python_multipart', '0.0.9', { 'modulename': 'multipart', - 'checksums': ['e9925a80bb668529f1b67c7fdb0a5dacdd7cbfc6fb0bff3ea443fe22bdd62132'], + 'checksums': ['03f54688c663f1b7977105f021043b0793151e4cb1c1a9d4a11fc13d622c4026'], }), ('h11', '0.14.0', { 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], }), - ('uvicorn', '0.26.0', { - 'checksums': ['48bfd350fce3c5c57af5fb4995fded8fb50da3b4feb543eb18ad7e0d54589602'], + ('uvicorn', '0.27.1', { + 'checksums': ['3d9a267296243532db80c83a959a3400502165ade2c1338dea4e67915fd4745a'], }), - ('lightning_cloud', '0.5.61', { - 'checksums': ['bd57f0921022a0603a0da08bdee1108f98fdc55eee59f3b99f6cead2e98c74fb'], + ('lightning_cloud', '0.5.64', { + 'checksums': ['44c44b387260e7f808bef7a2368966da166bf58fa37562a8ce8366febe3ca38e'], }), ('itsdangerous', '2.1.2', { 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], }), - ('starsessions', '2.1.2', { - 'checksums': ['7e028b7b06a5b7f8ac4fe7894eb609941f96d137bc9d6cc6b6d86ae4724d7e36'], + ('starsessions', '2.1.3', { + 'checksums': ['d20c5f277b64a86c16819f65ac50814ccdbd146776159e08c88b378b6612297d'], }), - ('fsspec', '2023.12.2', { - 'checksums': ['8548d39e8810b59c38014934f6b31e57f40c1b20f911f4cc2b85389c7e9bf0cb'], + ('fsspec', '2024.2.0', { + 'checksums': ['b6ad1a679f760dda52b1168c859d01b7b80648ea6f7f7c7f5a8a91dc3f3ecb84'], }), - ('croniter', '2.0.1', { - 'checksums': ['d199b2ec3ea5e82988d1f72022433c5f9302b3b3ea9e6bfd6a1518f6ea5e700a'], + ('croniter', '2.0.2', { + 'checksums': ['8bff16c9af4ef1fb6f05416973b8f7cb54997c02f2f8365251f9bf1dded91866'], }), ('traitlets', '5.14.1', { 'checksums': ['8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e'], @@ -116,17 +116,17 @@ exts_list = [ ('readchar', '4.0.5', { 'checksums': ['08a456c2d7c1888cde3f4688b542621b676eb38cd6cfed7eb6cb2e2905ddc826'], }), - ('runs', '1.2.0', { - 'checksums': ['8804271011b7a2eeb0d77c3e3f556e5ce5f602fa0dd2a31ed0c1222893be69b7'], + ('runs', '1.2.2', { + 'checksums': ['9dc1815e2895cfb3a48317b173b9f1eac9ba5549b36a847b5cc60c3bf82ecef1'], }), ('xmod', '1.8.1', { 'checksums': ['38c76486b9d672c546d57d8035df0beb7f4a9b088bc3fb2de5431ae821444377'], }), - ('editor', '1.6.5', { - 'checksums': ['5a8ad611d2a05de34994df3781605e26e63492f82f04c2e93abdd330eed6fa8d'], + ('editor', '1.6.6', { + 'checksums': ['bb6989e872638cd119db9a4fce284cd8e13c553886a1c044c6b8d8a160c871f8'], }), - ('inquirer', '3.2.1', { - 'checksums': ['d5ff9bb8cd07bd3f076eabad8ae338280886e93998ff10461975b768e3854fbc'], + ('inquirer', '3.2.4', { + 'checksums': ['33b09efc1b742b9d687b540296a8b6a3f773399673321fcc2ab0eb4c109bf9b5'], }), ('wrapt', '1.16.0', { 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], @@ -134,29 +134,29 @@ exts_list = [ ('aioitertools', '0.11.0', { 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], }), - ('botocore', '1.33.13', { - 'checksums': ['fb577f4cb175605527458b04571451db1bd1a2036976b626206036acd4496617'], + ('botocore', '1.34.51', { + 'checksums': ['5086217442e67dd9de36ec7e87a0c663f76b7790d5fb6a12de565af95e87e319'], }), ('jmespath', '1.0.1', { 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], }), - ('s3transfer', '0.8.2', { - 'checksums': ['368ac6876a9e9ed91f6bc86581e319be08188dc60d50e0d56308ed5765446283'], + ('s3transfer', '0.10.0', { + 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], }), - ('boto3', '1.33.13', { - 'checksums': ['0e966b8a475ecb06cc0846304454b8da2473d4c8198a45dfb2c5304871986883'], + ('boto3', '1.34.51', { + 'checksums': ['2cd9463e738a184cbce8a6824027c22163c5f73e277a35ff5aa0fb0e845b4301'], }), - ('aiobotocore', '2.9.1', { - 'checksums': ['24daf4f1ce86e2fb5aee146cdc944736ef76791635ec3a9b6f3d5755b1ac3c46'], + ('aiobotocore', '2.12.1', { + 'checksums': ['8706b28f16f93c541f6ed50352115a79d8f3499539f8d0bb70aa0f7a5379c1fe'], }), - ('s3fs', '2023.12.2', { - 'checksums': ['b5ec07062481bbb45cb061b31984c7188d106e292c27033039e024e4ba5740dc'], + ('s3fs', '2024.2.0', { + 'checksums': ['f8064f522ad088b56b043047c825734847c0269df19f2613c956d4c20de15b62'], }), - ('torchmetrics', '1.3.0.post0', { - 'checksums': ['6d31aeabee964ff539425800164790b8670293f2fade9fcfee6fabbe3f45dd7e'], + ('torchmetrics', '1.3.1', { + 'checksums': ['8d371f7597a1a5eb02d5f2ed59642d6fef09093926997ce91e18b1147cc8defa'], }), ('pytorch-lightning', version, { - 'checksums': ['2500b002fa09cb37b0e12f879876bf30a2d260b0f04783d33264dab175f0c966'], + 'checksums': ['aa3be30c9109239a371748565a7f4b7b41ea1395725c30e04426cf946b3e2745'], }), ] From e0eece786a8d6beefa83f4b88457cf8711ca2705 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 6 Mar 2024 11:50:49 +0100 Subject: [PATCH 0904/1193] {GCCcore/12.3.0} Unify Z3 easyconfigs into a single one with Python bindings --- .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 2 +- .../p/PyTorch/PyTorch-2.1.2-foss-2023a.eb | 2 +- .../Z3-4.12.2-GCCcore-12.3.0-Python-3.11.3.eb | 53 ------------------- .../z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb | 38 +++++++++---- 4 files changed, 29 insertions(+), 66 deletions(-) delete mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0-Python-3.11.3.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index cb05d00c73ea..225928ed9cbb 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -171,7 +171,7 @@ dependencies = [ ('expecttest', '0.1.5'), ('networkx', '3.1'), ('sympy', '1.12'), - ('Z3', '4.12.2', '-Python-%(pyver)s'), + ('Z3', '4.12.2'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb index 31d433c30740..413e3254f8ac 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a.eb @@ -148,7 +148,7 @@ dependencies = [ ('expecttest', '0.1.5'), ('networkx', '3.1'), ('sympy', '1.12'), - ('Z3', '4.12.2', '-Python-%(pyver)s'), + ('Z3', '4.12.2',), ] use_pip = True diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0-Python-3.11.3.eb b/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0-Python-3.11.3.eb deleted file mode 100644 index 0eb7b2c600ff..000000000000 --- a/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0-Python-3.11.3.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'Z3' -version = '4.12.2' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://github.com/Z3Prover/z3' -description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, -booleans, arrays, floating point numbers, strings, and other data types. This -module includes z3-solver, the Python interface of Z3. -""" - -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} - -builddependencies = [ - ('CMake', '3.26.3'), - ('binutils', '2.40'), -] - -dependencies = [ - ('Python', '3.11.3'), - ('GMP', '6.2.1'), -] - -use_pip = True - -_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py &&""" -_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py &&""" - -exts_list = [ - ('z3-solver', version + '.0', { - 'modulename': 'z3', - 'checksums': ['65ab47a0a8ef0bfb80db0670775beb11b32c3c0ae4b35943e44121f4af7ef411'], - 'preinstallopts': _fix_parallelism + _enable_gmp, - }), -] - -# make Z3 headers and libraries accessible in their usual location -local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" -local_libz3 = 'libz3.' + SHLIB_EXT -postinstallcmds = [ - "ln -s %s/include '%%(installdir)s/include'" % local_z3_site_path, - "ln -s ../%s/lib/%s '%%(installdir)s/lib/%s'" % (local_z3_site_path, local_libz3, local_libz3) -] - -sanity_pip_check = True - -sanity_check_paths = { - 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], -} - -moduleclass = 'tools' diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb index 2d9ade329245..e34dbd5ade0b 100644 --- a/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/z/Z3/Z3-4.12.2-GCCcore-12.3.0.eb @@ -1,35 +1,51 @@ -easyblock = 'CMakeMake' +easyblock = 'PythonBundle' name = 'Z3' version = '4.12.2' homepage = 'https://github.com/Z3Prover/z3' -description = """ - Z3 is a theorem prover from Microsoft Research. +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3-solver, the Python interface of Z3. """ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://github.com/Z3Prover/z3/archive/'] -sources = [SOURCELOWER_TAR_GZ] -checksums = [ - {'z3-4.12.2.tar.gz': '9f58f3710bd2094085951a75791550f547903d75fe7e2fcb373c5f03fc761b8f'}, -] - builddependencies = [ ('CMake', '3.26.3'), ('binutils', '2.40'), ] dependencies = [ + ('Python', '3.11.3'), ('GMP', '6.2.1'), ] -configopts = '-DZ3_USE_LIB_GMP=ON -DZ3_LINK_TIME_OPTIMIZATION=ON ' +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ + +exts_list = [ + ('z3-solver', version + '.0', { + 'modulename': 'z3', + 'checksums': ['65ab47a0a8ef0bfb80db0670775beb11b32c3c0ae4b35943e44121f4af7ef411'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + 'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path, + 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path +] + +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.%s' % SHLIB_EXT], - 'dirs': [], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], } moduleclass = 'tools' From 1abf93ef835f7b1cad91b531ea70989785e927d7 Mon Sep 17 00:00:00 2001 From: lazariv Date: Wed, 6 Mar 2024 12:22:10 +0100 Subject: [PATCH 0905/1193] Update easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb Co-authored-by: Alexander Grund --- easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb index 3dd5812483b7..b637ca843e5d 100644 --- a/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libgit2/libgit2-1.7.2-GCCcore-13.2.0.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'devel' - From 244f08925551c72029a6d8c8712aa641079a7ede Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 6 Mar 2024 14:42:38 +0100 Subject: [PATCH 0906/1193] Fix configure options of FFLAS-FFPACK --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 3 +-- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb | 4 ++-- 2 files changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index d03b85f906a7..d93676a7696b 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -24,12 +24,11 @@ builddependencies = [ ('Autotools', '20150215'), ] dependencies = [ - ('GMP', '6.1.0'), ('Givaro', '4.0.1'), ] preconfigopts = "env NOCONFIGURE=1 ./autogen.sh && " -configopts = '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO' +configopts = '--with-givaro=$EBROOTGIVARO' configopts += ' --with-blas-cflags="-I$BLAS_INC_DIR" --with-blas-libs="-L$BLAS_LIB_DIR $LIBBLAS" --enable-openmp' sanity_check_paths = { diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb index 75c22cfa096b..be9707946a76 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.5.0-gfbf-2022a.eb @@ -21,13 +21,13 @@ source_urls = ['https://github.com/linbox-team/fflas-ffpack/releases/download/v% sources = [SOURCELOWER_TAR_GZ] checksums = ['dafb4c0835824d28e4f823748579be6e4c8889c9570c6ce9cce1e186c3ebbb23'] +builddependencies = [('pkgconf', '1.8.0')] dependencies = [ - ('GMP', '6.2.1'), ('Givaro', '4.2.0'), ] configopts = '--with-blas-libs="$LIBBLAS_MT" --with-blas-cflags="-I$BLAS_INC_DIR" ' -configopts += '--with-gmp=$EBROOTGMP --with-givaro=$EBROOTGIVARO --enable-openmp' +configopts += '--enable-openmp' buildopts = " && make autotune " From 41cab4e023c2623711bf1b9af44e23824d50effb Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Wed, 6 Mar 2024 15:14:04 +0100 Subject: [PATCH 0907/1193] adding easyconfigs: fio-3.36-GCCcore-12.3.0.eb --- .../f/fio/fio-3.36-GCCcore-12.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/f/fio/fio-3.36-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/f/fio/fio-3.36-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/fio/fio-3.36-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..b8f16f6e6be7 --- /dev/null +++ b/easybuild/easyconfigs/f/fio/fio-3.36-GCCcore-12.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'fio' +version = '3.36' + +homepage = 'https://github.com/axboe/fio' +docurls = 'https://fio.readthedocs.io/en/latest/index.html' +description = 'Flexible I/O tester' + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +github_account = 'axboe' +source_urls = [GITHUB_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b34b8f3c5cd074c09ea487ffe3f444e95565c214b34a73042f35b00cbaab0e17'] + +builddependencies = [ + ('binutils', '2.40'), +] + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['bin', 'man', 'share'], +} + +sanity_check_commands = ['fio -h'] + +moduleclass = 'tools' From cfa56767513b1a9de25c6f5e96712452890b5924 Mon Sep 17 00:00:00 2001 From: Robin Verschoren Date: Wed, 6 Mar 2024 15:34:37 +0100 Subject: [PATCH 0908/1193] adding easyconfigs: iperf-3.16.eb --- easybuild/easyconfigs/i/iperf/iperf-3.16.eb | 28 +++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/iperf/iperf-3.16.eb diff --git a/easybuild/easyconfigs/i/iperf/iperf-3.16.eb b/easybuild/easyconfigs/i/iperf/iperf-3.16.eb new file mode 100644 index 000000000000..7cda6dab0339 --- /dev/null +++ b/easybuild/easyconfigs/i/iperf/iperf-3.16.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'iperf' +version = '3.16' + +homepage = 'https://software.es.net/iperf' +description = "iperf is a tool for active measurements of the maximum achievable bandwidth on IP networks." + +toolchain = SYSTEM + +source_urls = ['https://downloads.es.net/pub/iperf/'] +sources = [SOURCE_TAR_GZ] +checksums = ['cc740c6bbea104398cc3e466befc515a25896ec85e44a662d5f4a767b9cf713e'] + +dependencies = [ + ('OpenSSL', '1.1'), +] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s iperf3 iperf"] + +sanity_check_paths = { + 'files': ['bin/iperf', 'include/iperf_api.h', 'lib/libiperf.a', 'lib/libiperf.%s' % SHLIB_EXT], + 'dirs': ['share/man'] +} + +sanity_check_commands = ["iperf --help"] + +moduleclass = 'tools' From 67206d6f82f62c7d3779698c718bb9be7d796906 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 6 Mar 2024 16:25:41 +0100 Subject: [PATCH 0909/1193] add fixest with deps to R-bundle-CRAN --- .../R-bundle-CRAN-2023.12-foss-2023a.eb | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index c17dfda0cf1d..5296db280277 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -584,10 +584,7 @@ exts_list = [ 'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'], }), ('pan', '1.9', { - 'checksums': [ - ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52', - 'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'), - ], + 'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'], }), ('mitml', '0.4-5', { 'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'], @@ -2084,7 +2081,6 @@ exts_list = [ 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], }), ('liquidSVM', '1.2.4', { - # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ @@ -2609,12 +2605,8 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - # need to run installation via xvfb-run to avoid problems on headless systems: - # no DISPLAY variable so Tk is not available - # [tcl] invalid command name "font" - 'preinstallopts': "xvfb-run ", - # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... 'modulename': False, + 'preinstallopts': "xvfb-run ", 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { @@ -3398,6 +3390,15 @@ exts_list = [ ('spdep', '1.3-1', { 'checksums': ['36062ccd094f9110a43cd51902c794242311fd23b861dde22c450446dce85396'], }), + ('stringmagic', '1.0.0', { + 'checksums': ['8152c72a2ed70577fae1e569986d1d488ce2e6b21b8f0e080c0265806c08551a'], + }), + ('dreamerr', '1.4.0', { + 'checksums': ['3e5e4afd10623b6dac6bb9b8bf0480d41c7422884cfec2d9d9786414f9026a87'], + }), + ('fixest', '0.11.2', { + 'checksums': ['2dee113a0689e5c4dd842c451d35c9a94a5b37536f9484611a877c1ea10e2b65'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 570e914ab88d90a07772f45d611366da46069edc Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 6 Mar 2024 16:32:28 +0100 Subject: [PATCH 0910/1193] restore comments --- .../R-bundle-CRAN-2023.12-foss-2023a.eb | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index 5296db280277..ff8c29774ff7 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -584,7 +584,10 @@ exts_list = [ 'checksums': ['9e1531bb37aa474abd91db5e0ed9e3a355c03faa65f4e653b3ea68b7c61ea835'], }), ('pan', '1.9', { - 'checksums': ['cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'], + 'checksums': [ + ('e37e184c3c1b7a34f54dd95335e6bc730fd5716d2d2dc20c24279401aa673c52', + 'cd91232d653783ea7f34c0eebaa80c472b5501b21eea500c4c1a8e57116c6eea'), + ], }), ('mitml', '0.4-5', { 'checksums': ['056aec823187cc3793640d8a5e74d74093bae74260a975ceb098a83a52e2eeeb'], @@ -2081,6 +2084,7 @@ exts_list = [ 'checksums': ['e7b4010fa1adf27534420db2971dae3c63190920a4323c86fd586842e22d9b07'], }), ('liquidSVM', '1.2.4', { + # Don't add optimization flags by liquidSVM which may not be known e.g. on PPC 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], 'preinstallopts': 'LIQUIDSVM_TARGET="empty"', 'checksums': [ @@ -2605,8 +2609,12 @@ exts_list = [ 'checksums': ['d4d9ef7b2788efeb8209aa8dd610af4cd86286392fbdf9ea70bcfeafda95d4c5'], }), ('gWidgets2tcltk', '1.0-8', { - 'modulename': False, + # need to run installation via xvfb-run to avoid problems on headless systems: + # no DISPLAY variable so Tk is not available + # [tcl] invalid command name "font" 'preinstallopts': "xvfb-run ", + # skip 'import' check with library(gWidgets2tcltk), since it also fails on headless systems... + 'modulename': False, 'checksums': ['10399cc636eeeb5484c3379970c37c56df10d979bf866a35b66d0c75b7222c0a'], }), ('mgsub', '1.7.3', { From 69f52eb9f11e43e9956d87740c2a10d494c2cc88 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 6 Mar 2024 15:48:14 +0000 Subject: [PATCH 0911/1193] find the correct Python in xtensor --- easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb index afb2af5900ac..14ae87a2bac9 100644 --- a/easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb +++ b/easybuild/easyconfigs/x/xtensor/xtensor-0.24.0-foss-2021b.eb @@ -37,6 +37,7 @@ components = [ }), ('xtensor-python', '0.26.0', { 'checksums': ['04dcfe84181c23f364b1e68a6d55d89d1679f31d8da0372db01af72534baf728'], + 'configopts': '-DPYTHON_EXECUTABLE=$EBROOTPYTHON/bin/python', }), ] From f2c3c3190163c9dc34b59b5d626fe2b96e19b00f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 6 Mar 2024 16:55:03 +0100 Subject: [PATCH 0912/1193] Fix geotiff configure option in GDAL 2.2.3 --- .../easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-2.7.15.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-3.6.6.eb | 2 +- .../easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb index 2e8050c472a3..c7f37f1aa942 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018a-Python-3.6.4.eb @@ -39,7 +39,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-2.7.15.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-2.7.15.eb index a3955f02fc6e..f7577ef499ce 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-2.7.15.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-2.7.15.eb @@ -39,7 +39,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-3.6.6.eb index 4d5e8a3b1665..450fe377a437 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-foss-2018b-Python-3.6.6.eb @@ -39,7 +39,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} diff --git a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb index 2523cf04fa35..663815587cfb 100644 --- a/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/g/GDAL/GDAL-2.2.3-intel-2018b-Python-3.6.6.eb @@ -39,7 +39,7 @@ configopts = '--with-expat=$EBROOTEXPAT --with-libz=$EBROOTLIBZ --with-hdf5=$EBR configopts += ' --with-xml2=$EBROOTLIBXML2 --with-geos=$EBROOTGEOS/bin/geos-config --with-jpeg=$EBROOTLIBJPEGMINTURBO' configopts += ' --with-png=$EBROOTLIBPNG --with-sqlite3=$EBROOTSQLITE --with-jasper=$EBROOTJASPER' configopts += ' --with-libtiff=$EBROOTLIBTIFF --with-pcre=$EBROOTPCRE --with-python=$EBROOTPYTHON/bin/python' -configopts += ' --with-libgeotiff=$EBROOTLIBGEOTIFF' +configopts += ' --with-geotiff=$EBROOTLIBGEOTIFF' modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} From 30a62810304802f401258d15986a6c69e8ee1aac Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 6 Mar 2024 17:14:31 +0100 Subject: [PATCH 0913/1193] Add checksum --- .../f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb index d93676a7696b..9b777550c092 100644 --- a/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb +++ b/easybuild/easyconfigs/f/FFLAS-FFPACK/FFLAS-FFPACK-2.2.0-foss-2016a.eb @@ -17,8 +17,9 @@ description = "Finite Field Linear Algebra Subroutines / Package" toolchain = {'version': '2016a', 'name': 'foss'} -sources = ['v%(version)s.zip'] source_urls = ['https://github.com/linbox-team/fflas-ffpack/archive'] +sources = ['v%(version)s.zip'] +checksums = ['4110e72004f88e9d6f90e503129a4ef7a3bd55b55aec992e109b3647a8445fa2'] builddependencies = [ ('Autotools', '20150215'), From 68cb95740987cd099898e2a45329295b9c73d937 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 6 Mar 2024 19:10:39 +0100 Subject: [PATCH 0914/1193] explicitly specify Fortran compiler for CDO 2.2.2 w/ gompi/2023b to fix build on non-x86_64 architectures --- easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb index bb45409b1469..88087d6059ec 100644 --- a/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb +++ b/easybuild/easyconfigs/c/CDO/CDO-2.2.2-gompi-2023b.eb @@ -43,6 +43,9 @@ configopts += "--with-curl=$EBROOTCURL --with-eccodes=$EBROOTECCODES --with-fftw configopts += "--with-netcdf=$EBROOTNETCDF --with-proj=$EBROOTPROJ --with-szlib=$EBROOTSZIP " configopts += "--with-udunits2=$EBROOTUDUNITS --with-util-linux-uuid=$EBROOTUTILMINLINUX " +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + sanity_check_paths = { 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], 'dirs': ['include'], From 81b459173f16d6c2293c9feff7e3722f7c1b25a8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Mar 2024 09:05:44 +0100 Subject: [PATCH 0915/1193] Fix configure option and gpertools dependency of MIRA 5.0 --- easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb index 69c6533045d3..062d990ae97b 100644 --- a/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb +++ b/easybuild/easyconfigs/m/MIRA/MIRA-5.0rc2-foss-2020b.eb @@ -13,11 +13,9 @@ sources = ['mira-V5rc2.tar.bz2'] source_urls = ['https://github.com/bachev/mira/releases/download/V5rc2/'] checksums = ['4255aa9c4f09ec686b1c717bffe2dd124d3ef9b87f00e74d1bcd51b8599b8e44'] -preconfigopts = 'export CFLAGS="$CFLAGS -fpermissive" && ' -preconfigopts += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && ' +preconfigopts = 'export CXXFLAGS="$CXXFLAGS -fpermissive" && ' configopts = '--with-boost=$EBROOTBOOST --with-expat=$EBROOTEXPAT --with-zlib=$EBROOTZLIB ' -configopts += '--with-tcmalloc-dir=$EBROOTGPERFTOOLS/lib ' builddependencies = [ ('flex', '2.6.4'), @@ -26,7 +24,6 @@ dependencies = [ ('Boost', '1.74.0'), ('zlib', '1.2.11'), ('expat', '2.2.9'), - ('gperftools', '2.9.1'), ] sanity_check_paths = { From 9db604f11b4b61c3bca40701497018f8387ad8e7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Mar 2024 10:20:54 +0100 Subject: [PATCH 0916/1193] Fix confgure options in GRASS --- .../GRASS-7.8.3-fosscuda-2019b-Python-3.7.4.eb | 18 ++++++------------ .../g/GRASS/GRASS-8.2.0-foss-2021b.eb | 18 ++++++------------ 2 files changed, 12 insertions(+), 24 deletions(-) diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-7.8.3-fosscuda-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/g/GRASS/GRASS-7.8.3-fosscuda-2019b-Python-3.7.4.eb index 5d64776f29dd..cfb982cda755 100644 --- a/easybuild/easyconfigs/g/GRASS/GRASS-7.8.3-fosscuda-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/g/GRASS/GRASS-7.8.3-fosscuda-2019b-Python-3.7.4.eb @@ -41,7 +41,6 @@ dependencies = [ ('PROJ', '6.2.1'), ('SQLite', '3.29.0'), ('freetype', '2.10.1'), - ('FFmpeg', '4.2.1'), ('LibTIFF', '4.0.10'), ('cairo', '1.16.0'), ('X11', '20190717'), @@ -52,21 +51,18 @@ dependencies = [ ] preconfigopts = "sed -e 's/-lblas/$LIBBLAS/g' -e 's/-llapack/$LIBLAPACK/g' -i configure && " -configopts = '--enable-64bit ' -configopts += '--enable-largefile=yes ' +configopts = '--enable-largefile=yes ' configopts += '--with-cairo=yes ' configopts += '--with-cxx ' -configopts += '--with-ffmpeg --with-ffmpeg-libs=$EBROOTFFMPEG/lib --with-ffmpeg-includes=$EBROOTFFMPEG/include/* ' configopts += '--with-fftw --with-fftw-libs=$EBROOTFFTW/lib --with-fftw-includes=$EBROOTFFTW/include ' configopts += '--with-freetype ' configopts += '--with-freetype-libs=$EBROOTFREETYPE/lib --with-freetype-includes=$EBROOTFREETYPE/include ' configopts += '--with-geos=$EBROOTGEOS/bin/geos-config ' -configopts += '--without-glw ' configopts += '--with-lapack ' -configopts += '--with-lapack-lib=$LAPACK_LIB_DIR ' +configopts += '--with-lapack-libs=$LAPACK_LIB_DIR ' configopts += '--with-lapack-includes=$LAPACK_INC_DIR ' configopts += '--with-blas ' -configopts += '--with-blas-lib=$BLAS_LIB_DIR ' +configopts += '--with-blas-libs=$BLAS_LIB_DIR ' configopts += '--with-blas-includes=$BLAS_INC_DIR ' configopts += '--with-netcdf=$EBROOTNETCDF/bin/nc-config ' configopts += '--without-odbc ' @@ -75,19 +71,17 @@ configopts += '--with-openmp ' configopts += '--with-png ' configopts += '--with-png-libs="$EBROOTLIBPNG/lib $EBROOTZLIB/lib" --with-png-includes=$EBROOTLIBPNG/include ' configopts += '--without-postgres ' -configopts += '--with-proj --with-proj-libs=$EBROOTPROJ/lib ' +configopts += '--with-proj-libs=$EBROOTPROJ/lib ' configopts += '--with-proj-includes=$EBROOTPROJ/include --with-proj-share=$EBROOTPROJ/share/proj ' configopts += '--with-pthread ' -configopts += '--with-python ' configopts += '--with-readline ' configopts += '--with-readline-libs=$EBROOTLIBREADLINE/lib --with-readline-includes=$EBROOTLIBREADLINE/include ' -configopts += '--with-spatialite ' configopts += '--with-sqlite ' configopts += '--with-tiff-libs=$EBROOTLIBTIFF/lib --with-tiff-includes=$EBROOTLIBTIFF/include ' configopts += '--with-wxwidgets=$EBROOTWXPYTHON/bin/wx-config ' configopts += '--with-x ' -configopts += '--with-zlib --with-zlib-libs=$EBROOTZLIB/lib --with-zlib-includes=$EBROOTZLIB/include ' -configopts += '--with-bzlib --with-bzlib-libs=$EBROOTBZIP2/lib --with-ibzlib-includes=$EBROOTBZIP2/include ' +configopts += '--with-zlib-libs=$EBROOTZLIB/lib --with-zlib-includes=$EBROOTZLIB/include ' +configopts += '--with-bzlib --with-bzlib-libs=$EBROOTBZIP2/lib --with-bzlib-includes=$EBROOTBZIP2/include ' configopts += '--with-zstd --with-zstd-libs=$EBROOTZSTD/lib --with-zstd-includes=$EBROOTZSTD/include ' sanity_check_paths = { diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb index 064972b3a7c9..97d62f13261b 100644 --- a/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb @@ -40,7 +40,6 @@ dependencies = [ ('PROJ', '8.1.0'), ('SQLite', '3.36'), ('freetype', '2.11.0'), - ('FFmpeg', '4.3.2'), ('LibTIFF', '4.3.0'), ('cairo', '1.16.0'), ('X11', '20210802'), @@ -52,21 +51,18 @@ dependencies = [ preconfigopts = "sed -e 's/-lblas/$LIBBLAS/g' -e 's/-llapack/$LIBLAPACK/g' -i configure && " -configopts = '--enable-64bit ' -configopts += '--enable-largefile=yes ' +configopts = '--enable-largefile=yes ' configopts += '--with-cairo=yes ' configopts += '--with-cxx ' -configopts += '--with-ffmpeg --with-ffmpeg-libs=$EBROOTFFMPEG/lib --with-ffmpeg-includes=$EBROOTFFMPEG/include/* ' configopts += '--with-fftw --with-fftw-libs=$EBROOTFFTW/lib --with-fftw-includes=$EBROOTFFTW/include ' configopts += '--with-freetype ' configopts += '--with-freetype-libs=$EBROOTFREETYPE/lib --with-freetype-includes=$EBROOTFREETYPE/include ' configopts += '--with-geos=$EBROOTGEOS/bin/geos-config ' -configopts += '--without-glw ' configopts += '--with-lapack ' -configopts += '--with-lapack-lib=$LAPACK_LIB_DIR ' +configopts += '--with-lapack-libs=$LAPACK_LIB_DIR ' configopts += '--with-lapack-includes=$LAPACK_INC_DIR ' configopts += '--with-blas ' -configopts += '--with-blas-lib=$BLAS_LIB_DIR ' +configopts += '--with-blas-libs=$BLAS_LIB_DIR ' configopts += '--with-blas-includes=$BLAS_INC_DIR ' configopts += '--with-netcdf=$EBROOTNETCDF/bin/nc-config ' configopts += '--without-odbc ' @@ -75,19 +71,17 @@ configopts += '--with-openmp ' configopts += '--with-png ' configopts += '--with-png-libs="$EBROOTLIBPNG/lib $EBROOTZLIB/lib" --with-png-includes=$EBROOTLIBPNG/include ' configopts += '--without-postgres ' -configopts += '--with-proj --with-proj-libs=$EBROOTPROJ/lib ' +configopts += '--with-proj-libs=$EBROOTPROJ/lib ' configopts += '--with-proj-includes=$EBROOTPROJ/include --with-proj-share=$EBROOTPROJ/share/proj ' configopts += '--with-pthread ' -configopts += '--with-python ' configopts += '--with-readline ' configopts += '--with-readline-libs=$EBROOTLIBREADLINE/lib --with-readline-includes=$EBROOTLIBREADLINE/include ' -configopts += '--with-spatialite ' configopts += '--with-sqlite ' configopts += '--with-tiff-libs=$EBROOTLIBTIFF/lib --with-tiff-includes=$EBROOTLIBTIFF/include ' configopts += '--with-wxwidgets=$EBROOTWXWIDGET/bin/wx-config ' configopts += '--with-x ' -configopts += '--with-zlib --with-zlib-libs=$EBROOTZLIB/lib --with-zlib-includes=$EBROOTZLIB/include ' -configopts += '--with-bzlib --with-bzlib-libs=$EBROOTBZIP2/lib --with-ibzlib-includes=$EBROOTBZIP2/include ' +configopts += '--with-zlib-libs=$EBROOTZLIB/lib --with-zlib-includes=$EBROOTZLIB/include ' +configopts += '--with-bzlib --with-bzlib-libs=$EBROOTBZIP2/lib --with-bzlib-includes=$EBROOTBZIP2/include ' configopts += '--with-zstd --with-zstd-libs=$EBROOTZSTD/lib --with-zstd-includes=$EBROOTZSTD/include ' postinstallcmds = [ From 036a400ade36ed54fd0f5d631548bb2ca175a352 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 7 Mar 2024 10:21:51 +0100 Subject: [PATCH 0917/1193] fix GUIDANCE installation --- .../easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb b/easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb index 1a801d890904..212a640042ce 100644 --- a/easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/g/GUIDANCE/GUIDANCE-2.02-GCC-12.3.0.eb @@ -26,9 +26,14 @@ dependencies = [ ('PAGAN2', '1.53_20230824', '-linux64', SYSTEM), ] +files_to_copy = ['programs', 'www'] + _bins = ['isEqualTree', 'msa_set_score', 'removeTaxa', 'semphy'] -files_to_copy = [(['programs/%s/%s' % (x, x) for x in _bins], 'bin'), 'www'] +postinstallcmds = [ + 'cd %(installdir)s && mkdir bin && cd bin' + ' && ' + ' && '.join(['ln -s ../programs/%s/%s' % (x, x) for x in _bins]) +] sanity_check_paths = { 'files': ['bin/%s' % x for x in _bins], From b72f69f9d56797bd423fda354dfbd9c349445481 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Mar 2024 10:48:54 +0100 Subject: [PATCH 0918/1193] Fix configure of LinBox 1.7.0 --- .../l/LinBox/LinBox-1.7.0-gfbf-2022a.eb | 14 ++++---------- 1 file changed, 4 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb index b8c32471efc2..36daa28511f7 100644 --- a/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb +++ b/easybuild/easyconfigs/l/LinBox/LinBox-1.7.0-gfbf-2022a.eb @@ -1,11 +1,5 @@ -## -# This file is an EasyBuild recipe; see https://github.com/easybuilders/easybuild -# # Copyright:: Copyright (c) 2016 Riccardo Murri -# Authors:: Riccardo Murri # License:: GPL -# -## easyblock = 'ConfigureMake' @@ -24,14 +18,14 @@ checksums = ['6d2159fd395be0298362dd37f6c696676237bc8e2757341fbc46520e3b466bcc'] dependencies = [ ('FFLAS-FFPACK', '2.5.0'), ('FLINT', '2.9.0'), - ('Givaro', '4.2.0'), ('IML', '1.0.5'), ('NTL', '11.5.1'), ] +builddependencies = [('pkgconf', '1.8.0')] -configopts = "--with-fflas-ffpack=$EBROOTFFLASMINFFPACK --with-flint=$EBROOTFLINT " -configopts += "--with-givaro=$EBROOTGIVARO --with-iml=$EBROOTIML --with-ntl=$EBROOTNTL " -configopts += "--enable-openmp --enable-shared " +configopts = "--with-flint=$EBROOTFLINT " +configopts += "--with-iml=$EBROOTIML --with-ntl=$EBROOTNTL " +configopts += "--enable-shared " sanity_check_paths = { 'files': ['bin/linbox-config', 'include/linbox/linbox-config.h'] + From e55027cf059b13373755679a17701edc7c552617 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 7 Mar 2024 12:20:27 +0100 Subject: [PATCH 0919/1193] Remove unknown configure option from GnuTLS 3.7.2 --- easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb index 9f2970e7e9be..4ace65def06d 100644 --- a/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb @@ -36,7 +36,7 @@ dependencies = [ configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " configopts += "--with-guile-site-ccache-dir=%(installdir)s/lib/guile/site-ccache " configopts += "--with-guile-extension-dir=%(installdir)s/lib/guile/extensions " -configopts += "--with-idn --with-p11-kit --without-tpm --without-tpm2" +configopts += "--with-idn --with-p11-kit --without-tpm" sanity_check_paths = { 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', From 6f66ac654617faaa0380162fdad3fb7fd9181b30 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Thu, 7 Mar 2024 12:46:40 +0000 Subject: [PATCH 0920/1193] adding easyconfigs: SCons-4.6.0-GCCcore-13.2.0.eb --- .../s/SCons/SCons-4.6.0-GCCcore-13.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.6.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.6.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.6.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..e2a42a969642 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.6.0-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SCons' +version = '4.6.0' + +homepage = 'https://www.scons.org' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': False, + 'patches': ['SCons-4.4.0_install_man_pages_correctly.patch'], + 'checksums': [ + {'SCons-4.6.0.tar.gz': '7db28958b188b800f803c287d0680cc3ac7c422ed0b1cf9895042c52567803ec'}, + {'SCons-4.4.0_install_man_pages_correctly.patch': + '9d216c2ea8e152ae1531593b17adc4042eb88f1d9524d7f3b08ace5137d6d5e7'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["scons --help"] + +moduleclass = 'devel' From 758fcafec6587972467ee13f4944964d7a9cb869 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 7 Mar 2024 15:58:55 +0100 Subject: [PATCH 0921/1193] Update epiScanpy-0.4.0-foss-2023a.eb add comment to sed --- easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb index e1fbb08a5000..552e826a3a24 100644 --- a/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb +++ b/easybuild/easyconfigs/e/epiScanpy/epiScanpy-0.4.0-foss-2023a.eb @@ -35,6 +35,7 @@ exts_list = [ 'checksums': ['a4847ac4f1d04852fea278d5de7aa8bfdc3beb7fbca4a182fec0f0efee43f4b1'], }), ('episcanpy', version, { + # strip out tbb as required dependency, to ensure that 'pip check' passes 'preinstallopts': "sed -i 's/tbb//' requirements.txt && ", 'checksums': ['95739149db60521b0a14e4579f8ba87d410126ffb7b916abbc2d1aff3df40ce3'], }), From a499c022e1f468f15dc356afefa9e8fff8ad4fd2 Mon Sep 17 00:00:00 2001 From: lazariv Date: Thu, 7 Mar 2024 16:36:19 +0100 Subject: [PATCH 0922/1193] Update R-4.3.3-gfbf-2023b.eb Updated date the package extensions have been checked --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 74dc215f5751..27db27239830 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -62,7 +62,7 @@ exts_default_options = { } # !! order of packages is important !! -# packages updated on 5th November 2023 +# packages updated on 4th March 2024 exts_list = [ 'base', 'compiler', From 1f17eb6a7e40e590b1d02163f305fbeb142d41fe Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 7 Mar 2024 16:39:35 +0100 Subject: [PATCH 0923/1193] adding easyconfigs: scCODA-0.1.9-foss-2023a.eb, rpy2-3.5.15-foss-2023a.eb, scikit-bio-0.5.9-foss-2023a.eb, tensorflow-probability-0.20.0-foss-2023a.eb --- .../r/rpy2/rpy2-3.5.15-foss-2023a.eb | 43 +++++++++++++++++ .../s/scCODA/scCODA-0.1.9-foss-2023a.eb | 44 +++++++++++++++++ .../scikit-bio/scikit-bio-0.5.9-foss-2023a.eb | 44 +++++++++++++++++ ...ensorflow-probability-0.20.0-foss-2023a.eb | 47 +++++++++++++++++++ 4 files changed, 178 insertions(+) create mode 100644 easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2023a.eb create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.9-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2023a.eb b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2023a.eb new file mode 100644 index 000000000000..11bd5f95fe8f --- /dev/null +++ b/easybuild/easyconfigs/r/rpy2/rpy2-3.5.15-foss-2023a.eb @@ -0,0 +1,43 @@ +# Author: Pavel Grochal (INUITS) +# Updated: Denis Kristak, Pavel Tománek (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'rpy2' +version = '3.5.15' + +homepage = 'https://rpy2.github.io' +description = """rpy2 is an interface to R running embedded in a Python process.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('IPython', '8.14.0'), + ('cffi', '1.15.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('coverage', '7.4.3', { + 'checksums': ['276f6077a5c61447a48d133ed13e759c09e62aff0dc84274a68dc18660104d52'], + }), + ('pytest-cov', '4.1.0', { + 'checksums': ['3904b13dfbfec47f003b8e77fd5b589cd11904a21ddf1ab38a64f204d6a10ef6'], + }), + ('tzlocal', '5.2', { + 'checksums': ['8d399205578f1a9342816409cc1e46a93ebd5755e39ea2d85334bea911bf0e6e'], + }), + (name, version, { + 'checksums': ['444fae4a84dc7f233b70eaab0aa81398ee0147c4e1ae38dd4524d779d6f25b2b'], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2023a.eb b/easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2023a.eb new file mode 100644 index 000000000000..f1c79dc4cbf1 --- /dev/null +++ b/easybuild/easyconfigs/s/scCODA/scCODA-0.1.9-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'scCODA' +version = '0.1.9' + +homepage = 'https://github.com/theislab/scCODA' +description = """scCODA allows for identification of compositional changes in high-throughput sequencing count data, +especially cell compositions from scRNA-seq.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('TensorFlow', '2.13.0'), + ('tensorflow-probability', '0.20.0'), + ('scanpy', '1.9.8'), + ('scikit-bio', '0.5.9'), + ('rpy2', '3.5.15'), + ('ArviZ', '0.16.1'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'checksums': ['786692a5ca546985583784179a6b2d535a54b37b30892fb9e264c5e854585dac'], + # strip out tensorflow-probability as required dependency, to ensure that 'pip check' passes + 'preinstallopts': "sed -i '6d' requirements.txt && sed -i '28d' setup.py && ", + }), +] + +sanity_pip_check = True + +sanity_check_commands = [ + 'python -c "import tensorflow_probability as tfp"', + 'python -c "import tensorflow as tf"', + 'python -c "from anndata import AnnData"', + 'python -c "import rpy2.robjects as rp"', + 'python -c "import seaborn as sns"', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.9-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.9-foss-2023a.eb new file mode 100644 index 000000000000..6b0f81efa7ef --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.9-foss-2023a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.9' +local_commit = '7565847' + +homepage = 'http://scikit-bio.org' +description = """scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms +and educational resources for bioinformatics.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('IPython', '8.14.0'), + ('h5py', '3.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('natsort', '8.4.0', { + 'checksums': ['45312c4a0e5507593da193dedd04abb1469253b601ecaf63445ad80f0a1ea581'], + }), + (name, version, { + 'modulename': 'skbio', + # download from commit to get rid of restriction of scipy version + 'source_urls': ['https://github.com/scikit-bio/scikit-bio/archive/'], + 'sources': [{'download_filename': '7565847.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['b2a1054e1bc89df9775335d31eaa6bfa0cce4487d568cff96e215fba8624d153'], + }), +] + +sanity_check_commands = ['python -m skbio.test'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb new file mode 100644 index 000000000000..c86b16b035f4 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.20.0-foss-2023a.eb @@ -0,0 +1,47 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +# Updated to 0.19.0 +# Author: J. Sassmannshausen (Imperial College London/UK) +# Update to 0.20.0: Pavel Tománek (INUITS) + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.20.0' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.11.3'), + ('TensorFlow', '2.13.0'), + ('dm-tree', '0.1.8'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '3.0.0', { + 'checksums': ['996d9a482c6fb4f33c1a35335cf8afd065d2a56e973270364840712d9131a882'], + }), + (name, version, { + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'checksums': ['f0fb9a1f88a36a8f57d4d9cce4f9bf8dfacb6fc7778751729fe3c3067e5a1363'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' From ddf0fe16990543943e44130671ca88c25e4a32d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 7 Mar 2024 22:11:07 +0000 Subject: [PATCH 0924/1193] Add support for Vulkan software rendering in Mesa --- easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb index 906c5eb2634a..f550441cf4a5 100644 --- a/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/m/Mesa/Mesa-23.1.9-GCCcore-13.2.0.eb @@ -49,10 +49,12 @@ dependencies = [ ('libunwind', '1.6.2'), ('LLVM', '16.0.6'), ('X11', '20231019'), + ('Wayland', '1.22.0'), ] -configopts = "-Dplatforms=x11 -Dosmesa=true -Dvulkan-drivers='' " -configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd=true" +configopts = "-Dplatforms=x11,wayland -Dosmesa=true -Dvulkan-drivers='swrast' -Dvulkan-layers='device-select' " +configopts += "-Dllvm=enabled -Dshared-llvm=enabled -Dlibunwind=enabled -Dglvnd=true " +configopts += "-Dvideo-codecs=vc1dec,h264dec,h264enc,h265dec,h265enc " # Easybuild will automatically add appropriate Gallium drivers for the processor architecture of the host # If you need a different configuration, it possible to override those values by setting your own configopts From 628b0e31c95bac64d3095223662dbbb73196c532 Mon Sep 17 00:00:00 2001 From: Taras Lazariv Date: Fri, 8 Mar 2024 16:11:16 +0100 Subject: [PATCH 0925/1193] Update brio package installation --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 27db27239830..801efed656fa 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -162,6 +162,9 @@ exts_list = [ ('rstudioapi', '0.15.0', { 'checksums': ['935bc81dca37d3d6e77982bfe6e7fbd779e8606e5b7e00d0ba4c80fec0416ccf'], }), + ('brio', '1.1.4', { + 'checksums': ['0cbbf38948682b2435eea69b04be59187b149183dc7562df71dc0d3e260e18e8'], + }), ('pkgload', '1.3.4', { 'checksums': ['60b04b948cda4dc56257b1e89f9b0a4b1273cacecdb2bd995d66dd76e89926ce'], }), @@ -183,9 +186,6 @@ exts_list = [ ('praise', '1.0.0', { 'checksums': ['5c035e74fd05dfa59b03afe0d5f4c53fbf34144e175e90c53d09c6baedf5debd'], }), - ('brio', '1.1.4', { - 'checksums': ['0cbbf38948682b2435eea69b04be59187b149183dc7562df71dc0d3e260e18e8'], - }), ('jsonlite', '1.8.8', { 'checksums': ['7de21316984c3ba3d7423d12f43d1c30c716007c5e39bf07e11885e0ceb0caa4'], }), From 470628c32b4912a9f1e5f531c11d09e4e9fa26ab Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Mar 2024 15:16:48 +0000 Subject: [PATCH 0926/1193] adding easyconfigs: DFT-D4-3.6.0-intel-2022a.eb --- .../d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100755 easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb new file mode 100755 index 000000000000..1790cab38c08 --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'MesonNinja' + +name = 'DFT-D4' +version = '3.6.0' + +homepage = 'https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['DFT-D4-3.2.0-remove_module_id.patch'] +checksums = [ + {'v3.6.0.tar.gz': '0e3e8d5f9e9e5414b9979967c074c953706053832e551d922c27599e7324bace'}, + {'DFT-D4-3.2.0-remove_module_id.patch': '8c3c81338cb57972580e4cf3db307aa2e44b8b3f6d1ba7ae24fa9d807490a93b'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.10.2'), + ('Meson', '0.62.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('mstore', '0.2.0'), + ('mctc-lib', '0.3.1'), + ('multicharge', '0.2.0'), +] + +configopts = '-Dpython=true -Dapi_v2=true' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.mod'], + 'dirs': [], +} + +sanity_check_commands = ["dftd4 --version"] + +moduleclass = 'chem' From 546cbdbba372a797708e18dff1783dbe7fde58a3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Mar 2024 15:40:18 +0000 Subject: [PATCH 0927/1193] multicharge --- .../multicharge-0.2.0-iimkl-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100755 easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb new file mode 100755 index 000000000000..40be7a2dc407 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.2.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'iimkl', 'version': '2022a'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['953e2ace2f4035b1fa8ecf680f90b5ce6ad5caae17c8d8ccbc2578b92b69d3e7'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.10.2'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.2.0'), +] + +configopts = '-DBLAS_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' +configopts += '-DLAPACK_LIBRARIES="-lmkl_sequential -lmkl_intel_lp64 -lmkl_core" ' + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' From d304b6a95d5df1d0cbdb7f51d8c5b38548f53a26 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 8 Mar 2024 15:57:55 +0000 Subject: [PATCH 0928/1193] no exe --- easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb | 0 .../easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb | 0 2 files changed, 0 insertions(+), 0 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb mode change 100755 => 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.6.0-intel-2022a.eb old mode 100755 new mode 100644 diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.2.0-iimkl-2022a.eb old mode 100755 new mode 100644 From 48a96dd90b8570f6f8495b3ba2df71cfca6c1871 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 11 Mar 2024 00:43:29 +0000 Subject: [PATCH 0929/1193] adding easyconfigs: iimkl-2023b.eb --- easybuild/easyconfigs/i/iimkl/iimkl-2023b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/i/iimkl/iimkl-2023b.eb diff --git a/easybuild/easyconfigs/i/iimkl/iimkl-2023b.eb b/easybuild/easyconfigs/i/iimkl/iimkl-2023b.eb new file mode 100644 index 000000000000..ace03ea09763 --- /dev/null +++ b/easybuild/easyconfigs/i/iimkl/iimkl-2023b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimkl' +version = '2023b' + +homepage = 'https://software.intel.com/en-us/intel-cluster-toolkit-compiler/' +description = """Intel C/C++ and Fortran compilers, alongside Intel Math Kernel Library (MKL).""" + +toolchain = SYSTEM + +local_comp_ver = '2023.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('imkl', '2023.2.0', '', SYSTEM), +] + +moduleclass = 'toolchain' From 25df58224d2c48a2c8c034b44b8c0723cf944a85 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Mon, 11 Mar 2024 08:44:38 +0000 Subject: [PATCH 0930/1193] Use 32-bit indexing to enable sunmatrix-cusparse --- .../s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb index 500d7fdeab1c..351d740b8e56 100644 --- a/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/SUNDIALS/SUNDIALS-6.6.0-foss-2023a-CUDA-12.1.1.eb @@ -38,6 +38,7 @@ _copts = [ '-DENABLE_KLU=ON', '-DENABLE_CUDA=ON', '-DCMAKE_CUDA_ARCHITECTURES="%(cuda_cc_cmake)s"', + '-DSUNDIALS_INDEX_SIZE=32', # SUNMATRIX_CUSPARSE module needs 32-bit indexing ] configopts = ' '.join(_copts) From c3cf0dd0ce8e692dc0ebf6f11af0480c8393faf6 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 10:54:19 +0100 Subject: [PATCH 0931/1193] Uncomment IDG from DP3 dependencies --- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index d1040f85e886..72d2b54bee75 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -38,7 +38,7 @@ dependencies = [ ('EveryBeam', '0.5.2'), ('Armadillo', '12.8.0'), ('AOFlagger', '3.4.0'), - # ('IDG', '1.2.0'), # test build in EESSI without IDG dependency + ('IDG', '1.2.0'), ] From 1c19ed10e93f7ccca098c20f25973aec7f23b85e Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 11:31:40 +0100 Subject: [PATCH 0932/1193] Add patches to IDG-1.2.0 and DP3-6.0 for xsimd error on neoverse v1 --- .../easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 1 + ...0_fix-for-xsimd-error-on-neoverse-v1.patch | 16 +++ .../easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb | 1 + ...0_fix-for-xsimd-error-on-neoverse-v1.patch | 101 ++++++++++++++++++ 4 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch create mode 100644 easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index 72d2b54bee75..4ea0deb57a99 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -22,6 +22,7 @@ sources = [ } }, ] +patches = ['DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch'] checksums = [None] builddependencies = [ diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch b/easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch new file mode 100644 index 000000000000..3eff93a30e6a --- /dev/null +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch @@ -0,0 +1,16 @@ +--- DP3.orig/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:20:32.024804259 +0100 ++++ DP3/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:21:32.851493709 +0100 +@@ -6,7 +6,7 @@ + set(xtl_GIT_TAG b3d0091a77af52f1b479b5b768260be4873aa8a7) + endif() + if (NOT xsimd_GIT_TAG) +- set(xsimd_GIT_TAG 2f5eddf8912c7e2527f0c50895c7560b964d29af) ++ set(xsimd_GIT_TAG 1d8536b393171b899031f01b7c2d63858b05665c) + endif() + if (NOT xtensor_GIT_TAG) + set(xtensor_GIT_TAG 0.24.2) +@@ -65,3 +65,4 @@ + endif() + + endforeach() ++ diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb index 910c9ac70963..b0640ef930b1 100644 --- a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb @@ -29,6 +29,7 @@ sources = [ } }, ] +patches = ['IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch'] checksums = [None] builddependencies = [ diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch b/easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch new file mode 100644 index 000000000000..921ed4fa3676 --- /dev/null +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch @@ -0,0 +1,101 @@ +--- IDG.orig/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:27:53.254059321 +0100 ++++ IDG/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:28:41.974412520 +0100 +@@ -1,35 +1,68 @@ +-#Allow overriding XTensor versions +-if (NOT XTL_GIT_TAG) +- set(XTL_GIT_TAG 0.7.4) ++#Allow overriding XTensor versions, e.g., for testing a new version in DP3. ++#For avoiding ODR violations, repositories that use aocommon should not override ++#these versions in their master branch. That way, the XTensor versions will ++#be equal in all repositories. ++if (NOT xtl_GIT_TAG) ++ set(xtl_GIT_TAG b3d0091a77af52f1b479b5b768260be4873aa8a7) + endif() +-if (NOT XSIMD_GIT_TAG) +- set(XSIMD_GIT_TAG 8.1.0) ++if (NOT xsimd_GIT_TAG) ++ set(xsimd_GIT_TAG 1d8536b393171b899031f01b7c2d63858b05665c) + endif() +-if (NOT XTENSOR_GIT_TAG) +- set(XTENSOR_GIT_TAG 0.24.2) ++if (NOT xtensor_GIT_TAG) ++ set(xtensor_GIT_TAG 0.24.2) ++endif() ++if (NOT xtensor-blas_GIT_TAG) ++ set(xtensor-blas_GIT_TAG 0.20.0) ++endif() ++if (NOT xtensor-fftw_GIT_TAG) ++ set(xtensor-fftw_GIT_TAG e6be85a376624da10629b6525c81759e02020308) ++endif() ++ ++# By default, only load the basic 'xtensor' and 'xtl' modules. ++if (NOT XTENSOR_LIBRARIES) ++ set(XTENSOR_LIBRARIES xtl xtensor) # Load xtl first, since xtensor uses it. + endif() + + include(FetchContent) + +-FetchContent_Declare( +- xtl +- GIT_REPOSITORY https://github.com/xtensor-stack/xtl.git +- GIT_SHALLOW TRUE +- GIT_TAG ${XTL_GIT_TAG}) +-FetchContent_Declare( +- xsimd +- GIT_REPOSITORY https://github.com/xtensor-stack/xsimd.git +- GIT_SHALLOW TRUE +- GIT_TAG ${XSMID_GIT_TAG}) +-FetchContent_Declare( +- xtensor +- GIT_REPOSITORY https://github.com/xtensor-stack/xtensor.git +- GIT_SHALLOW TRUE +- GIT_TAG ${XTENSOR_GIT_TAG}) +- +-# Ensure XTensor headers are included as system headers. +-foreach(LIB xtl;xsimd;xtensor) +- FetchContent_MakeAvailable(${LIB}) +- get_target_property(IID ${LIB} INTERFACE_INCLUDE_DIRECTORIES) +- set_target_properties(${LIB} PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "${IID}") +-endforeach() +\ No newline at end of file ++foreach(LIB ${XTENSOR_LIBRARIES}) ++ set(XT_GIT_TAG "${${LIB}_GIT_TAG}") ++ if (NOT XT_GIT_TAG) ++ message(FATAL_ERROR "Unknown git tag for XTensor library '${LIB}'") ++ endif() ++ ++ # Checking out a specific git commit hash does not (always) work when ++ # GIT_SHALLOW is TRUE. See the documentation for GIT_TAG in ++ # https://cmake.org/cmake/help/latest/module/ExternalProject.html ++ # -> If the GIT_TAG is a commit hash, use a non-shallow clone. ++ string(LENGTH "${XT_GIT_TAG}" XT_TAG_LENGTH) ++ set(XT_SHALLOW TRUE) ++ if(XT_TAG_LENGTH EQUAL 40 AND XT_GIT_TAG MATCHES "^[0-9a-f]+$") ++ set(XT_SHALLOW FALSE) ++ endif() ++ ++ FetchContent_Declare( ++ ${LIB} ++ GIT_REPOSITORY https://github.com/xtensor-stack/${LIB}.git ++ GIT_SHALLOW ${XT_SHALLOW} ++ GIT_TAG ${XT_GIT_TAG}) ++ ++ if ("${LIB}" STREQUAL "xtensor-fftw") ++ # Unlike the other libraries, xtensor-fftw does not define a CMake target. ++ # Its CMakeLists.txt also loads FFTW using custom options. ++ # -> Do not build this library, and define an INTERFACE target manually. ++ FetchContent_GetProperties(${LIB}) ++ if(NOT ${${LIB}_POPULATED}) ++ FetchContent_Populate(${LIB}) ++ endif() ++ add_library(${LIB} INTERFACE) ++ target_include_directories(${LIB} SYSTEM INTERFACE "${${LIB}_SOURCE_DIR}/include") ++ else() ++ FetchContent_MakeAvailable(${LIB}) ++ # Ensure XTensor headers are included as system headers. ++ get_target_property(IID ${LIB} INTERFACE_INCLUDE_DIRECTORIES) ++ set_target_properties(${LIB} PROPERTIES INTERFACE_SYSTEM_INCLUDE_DIRECTORIES "${IID}") ++ endif() ++ ++endforeach() ++ From b8185d173bc8a6d28dd082d4a40f051d79a8266a Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 11:52:35 +0100 Subject: [PATCH 0933/1193] Add checksums for patch files --- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 5 ++++- easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb | 5 ++++- 2 files changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index 4ea0deb57a99..adf88bc98449 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -23,7 +23,10 @@ sources = [ }, ] patches = ['DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch'] -checksums = [None] +checksums = [ + None, # checksum for git clone source is non-deterministic + '8dab4757929966e8a8d19bf5e1e5491ad8df8dcd728c4fff414e284f87be5a85', # DP3-6.0_fix-for-xsimd-error-on-neoverse-v1 +] builddependencies = [ ('CMake', '3.27.6'), diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb index b0640ef930b1..5d25803f6ed5 100644 --- a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb @@ -30,7 +30,10 @@ sources = [ }, ] patches = ['IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch'] -checksums = [None] +checksums = [ + None, # checksum for git clone source is non-deterministic + '02542eb931f3dd0bb220084e753a9982c155c58ec2e6731fc64f42692eefe4a5', # IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch +] builddependencies = [ ('CMake', '3.27.6'), From 1d6d6a9bafe79480f03f7d62ac2c6d0f0397a36d Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 13:08:06 +0100 Subject: [PATCH 0934/1193] Add description to patch files --- .../d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch | 3 +++ .../i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch | 3 +++ 2 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch b/easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch index 3eff93a30e6a..abfd8e34f069 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch @@ -1,3 +1,6 @@ +# Fix for XSIMD build error on Neoverse V1 +# See: https://github.com/xtensor-stack/xsimd/issues/1005 and https://github.com/xtensor-stack/xsimd/commit/1d8536b +# Mar 11th 2024 by T. Kok (SURF) --- DP3.orig/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:20:32.024804259 +0100 +++ DP3/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:21:32.851493709 +0100 @@ -6,7 +6,7 @@ diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch b/easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch index 921ed4fa3676..619cd243570f 100644 --- a/easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch @@ -1,3 +1,6 @@ +# Fix for XSIMD build error on Neoverse V1 +# See: https://github.com/xtensor-stack/xsimd/issues/1005 and https://github.com/xtensor-stack/xsimd/commit/1d8536b +# Mar 11th 2024 by T. Kok (SURF) --- IDG.orig/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:27:53.254059321 +0100 +++ IDG/external/aocommon/CMake/FetchXTensor.cmake 2024-03-11 11:28:41.974412520 +0100 @@ -1,35 +1,68 @@ From 11ff54d922be2cde2be01dc27390c9c0db887ff2 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 13:23:12 +0100 Subject: [PATCH 0935/1193] Fix checksum for IDG patch --- easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb index 5d25803f6ed5..d88e2712bda8 100644 --- a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb @@ -32,7 +32,7 @@ sources = [ patches = ['IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch'] checksums = [ None, # checksum for git clone source is non-deterministic - '02542eb931f3dd0bb220084e753a9982c155c58ec2e6731fc64f42692eefe4a5', # IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch + '3811028d7757cd7085501bf3209f8eb526eafb67caf2950110a25a7a072df3c1', # IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch ] builddependencies = [ From db037bebfa157b57fc025efd39e8a106ebc94708 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 11 Mar 2024 12:32:51 +0000 Subject: [PATCH 0936/1193] adding easyconfigs: Java-21.0.2.eb, Java-21.eb --- easybuild/easyconfigs/j/Java/Java-21.0.2.eb | 30 +++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-21.eb | 14 ++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-21.0.2.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-21.eb diff --git a/easybuild/easyconfigs/j/Java/Java-21.0.2.eb b/easybuild/easyconfigs/j/Java/Java-21.0.2.eb new file mode 100644 index 000000000000..e96da822b0bf --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-21.0.2.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '21.0.2' +local_build = '13' + +homepage = 'https://openjdk.org' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '454bebb2c9fe48d981341461ffb6bf1017c7b7c6e15c6b0c29b959194ba3aaa5', + local_tarball_tmpl % ('aarch64', local_build): + '3ce6a2b357e2ef45fd6b53d6587aa05bfec7771e7fb982f2c964f6b771b7526a', + local_tarball_tmpl % ('ppc64le', local_build): + 'd08de863499d8851811c893e8915828f2cd8eb67ed9e29432a6b4e222d80a12f', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-21.eb b/easybuild/easyconfigs/j/Java/Java-21.eb new file mode 100644 index 000000000000..46e84105b355 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-21.eb @@ -0,0 +1,14 @@ +easyblock = 'ModuleRC' + +name = 'Java' +version = '21' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)s.0.2')] + +moduleclass = 'lang' From d32b4c03a14b6882549c1ac1f479a709f46b0646 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 13:36:00 +0100 Subject: [PATCH 0937/1193] Fix checksum for DP3 patch --- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index adf88bc98449..02cb233ed6ea 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -25,7 +25,7 @@ sources = [ patches = ['DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch'] checksums = [ None, # checksum for git clone source is non-deterministic - '8dab4757929966e8a8d19bf5e1e5491ad8df8dcd728c4fff414e284f87be5a85', # DP3-6.0_fix-for-xsimd-error-on-neoverse-v1 + '7f5069388846c9c715013d5a3a267a6d8e266520445a6427e63e9d52d3046c9d', # DP3-6.0_fix-for-xsimd-error-on-neoverse-v1 ] builddependencies = [ From 0cd024d185a969cda196b5a1f54a1d2e6edcf40a Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Mon, 11 Mar 2024 13:55:31 +0100 Subject: [PATCH 0938/1193] Remove patch comment to above line --- easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb | 3 ++- easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb index 02cb233ed6ea..8373cc5f8bdf 100644 --- a/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb +++ b/easybuild/easyconfigs/d/DP3/DP3-6.0-foss-2023b.eb @@ -25,7 +25,8 @@ sources = [ patches = ['DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch'] checksums = [ None, # checksum for git clone source is non-deterministic - '7f5069388846c9c715013d5a3a267a6d8e266520445a6427e63e9d52d3046c9d', # DP3-6.0_fix-for-xsimd-error-on-neoverse-v1 + # DP3-6.0_fix-for-xsimd-error-on-neoverse-v1.patch + '7f5069388846c9c715013d5a3a267a6d8e266520445a6427e63e9d52d3046c9d', ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb index d88e2712bda8..1efa15553447 100644 --- a/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb +++ b/easybuild/easyconfigs/i/IDG/IDG-1.2.0-foss-2023b.eb @@ -32,7 +32,8 @@ sources = [ patches = ['IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch'] checksums = [ None, # checksum for git clone source is non-deterministic - '3811028d7757cd7085501bf3209f8eb526eafb67caf2950110a25a7a072df3c1', # IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch + # IDG-1.2.0_fix-for-xsimd-error-on-neoverse-v1.patch + '3811028d7757cd7085501bf3209f8eb526eafb67caf2950110a25a7a072df3c1', ] builddependencies = [ From 4950b82c08404843eb6ce8c2e3ac764390c6b35f Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Mon, 11 Mar 2024 14:55:45 +0100 Subject: [PATCH 0939/1193] remove hatchling builddep from deepdiff --- .../easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb index 557a3af6db10..86135dac4dc8 100644 --- a/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-6.7.1-GCCcore-12.3.0.eb @@ -10,7 +10,6 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} builddependencies = [ ('binutils', '2.40'), - ('hatchling', '1.18.0'), # for setuptools-scm ] dependencies = [ From 9014005b0bf858c550ee150b08f316e7ea48854f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 11 Mar 2024 15:31:32 +0100 Subject: [PATCH 0940/1193] adding easyconfigs: pySCENIC-0.12.1-foss-2023a.eb --- .../p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb new file mode 100644 index 000000000000..e006374a05a3 --- /dev/null +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'pySCENIC' +version = '0.12.1' +local_commit = '31d51a1' + +homepage = 'https://github.com/aertslab/pySCENIC' +description = """pySCENIC is a lightning-fast python implementation of the SCENIC +pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables +biologists to infer transcription factors, gene regulatory networks and +cell types from single-cell RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('Arrow', '14.0.1'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('networkx', '3.1'), + ('dask', '2023.12.1'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('loompy', '3.0.7'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('cytoolz', '0.12.3', { + 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], + }), + ('multiprocessing_on_dill', '3.5.0a4', { + 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], + }), + ('frozendict', '2.4.0', { + 'checksums': ['c26758198e403337933a92b01f417a8240c954f553e1d4b5e0f8e39d9c8e3f0a'], + }), + ('arboreto', '0.1.6', { + 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], + }), + ('boltons', '23.1.1', { + 'checksums': ['d2cb2fa83cf2ebe791be1e284183e8a43a1031355156a968f8e0a333ad2448fc'], + }), + ('interlap', '0.2.7', { + 'checksums': ['31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9'], + }), + ('ctxcore', '0.2.0', { + 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], + 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], + }), + ('pyscenic', version, { + # download from commit to get fix for numpy error + # https://github.com/aertslab/pySCENIC/issues/518 + 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], + 'sources': [{ + 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz' + }], + 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyscenic'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyscenic --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From f0f07906e2981283fe48825bcd6f69fc1b32bd0d Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Mon, 11 Mar 2024 16:10:28 +0100 Subject: [PATCH 0941/1193] fix filename --- easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb index e006374a05a3..8f05d25d9c00 100644 --- a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb @@ -59,7 +59,7 @@ exts_list = [ 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], 'sources': [{ 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', - 'filename': '%(name)s-%(version)s.tar.gz' + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit }], 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], }), From 7b36f1be9c424e21d577df14d10a1e5f2814c97a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 11 Mar 2024 15:49:07 +0000 Subject: [PATCH 0942/1193] find correct Python for MDI --- easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb | 2 +- easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb b/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb index ec7490f96cb0..c4ac354e4314 100644 --- a/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb +++ b/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb @@ -33,7 +33,7 @@ dependencies = [ ] # perform iterative build to get both static and shared libraries -local_common_configopts = '-DCMAKE_POSITION_INDEPENDENT_CODE=ON ' +local_common_configopts = '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DPython_EXECUTABLE=$EBROOTPYTHON/bin/python' configopts = [ local_common_configopts + ' -Dlibtype=STATIC', local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', diff --git a/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb index 08cc370daadb..2377fdb4e747 100644 --- a/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb +++ b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb @@ -33,7 +33,7 @@ dependencies = [ ] # perform iterative build to get both static and shared libraries -local_common_configopts = '-DCMAKE_POSITION_INDEPENDENT_CODE=ON ' +local_common_configopts = '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DPython_EXECUTABLE=$EBROOTPYTHON/bin/python ' configopts = [ local_common_configopts + ' -Dlibtype=STATIC', local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', From d9e61101a4fa46d55582bef675711e888299fb89 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 11 Mar 2024 16:37:41 +0000 Subject: [PATCH 0943/1193] specify the lib subdirectory --- easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb | 2 ++ easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb b/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb index c4ac354e4314..ad39fd393046 100644 --- a/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb +++ b/easybuild/easyconfigs/m/MDI/MDI-1.4.16-gompi-2022b.eb @@ -44,4 +44,6 @@ sanity_check_paths = { 'dirs': ['include', 'share'], } +bin_lib_subdirs = ['lib/mdi'] + moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb index 2377fdb4e747..c8e9eb3ee821 100644 --- a/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb +++ b/easybuild/easyconfigs/m/MDI/MDI-1.4.26-gompi-2023a.eb @@ -49,4 +49,6 @@ sanity_check_paths = { 'dirs': ['include', 'share'], } +bin_lib_subdirs = ['lib/mdi'] + moduleclass = 'chem' From 72559bc55c7cf95828c6e92d14ba1c569a6c57f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 11 Mar 2024 17:59:35 +0100 Subject: [PATCH 0944/1193] Update easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb Add back description of base of include packages --- easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb index 801efed656fa..df95c0aaa551 100644 --- a/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb +++ b/easybuild/easyconfigs/r/R/R-4.3.3-gfbf-2023b.eb @@ -64,6 +64,9 @@ exts_default_options = { # !! order of packages is important !! # packages updated on 4th March 2024 exts_list = [ + # include packages that are part of the base installation of R, + # both to make sure they are available (via sanity check), + # and to be able to pass the check for required dependencies when installing extensions in parallel 'base', 'compiler', 'datasets', From 8f52e90a4ed0e5b2983250bab91bddc958c6928b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Tue, 12 Mar 2024 10:57:35 +0100 Subject: [PATCH 0945/1193] update version with date --- .../pySCENIC-0.12.1-20240311-foss-2023a.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb new file mode 100644 index 000000000000..2e5e8193e0db --- /dev/null +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb @@ -0,0 +1,77 @@ +easyblock = 'PythonBundle' + +name = 'pySCENIC' +version = '0.12.1-20240311' +local_commit = '31d51a1' + +homepage = 'https://github.com/aertslab/pySCENIC' +description = """pySCENIC is a lightning-fast python implementation of the SCENIC +pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables +biologists to infer transcription factors, gene regulatory networks and +cell types from single-cell RNA-seq data.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('Arrow', '14.0.1'), + ('scikit-learn', '1.3.1'), + ('tqdm', '4.66.1'), + ('networkx', '3.1'), + ('dask', '2023.12.1'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('loompy', '3.0.7'), + ('umap-learn', '0.5.5'), +] + +use_pip = True + +exts_list = [ + ('cytoolz', '0.12.3', { + 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], + }), + ('multiprocessing_on_dill', '3.5.0a4', { + 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], + }), + ('frozendict', '2.4.0', { + 'checksums': ['c26758198e403337933a92b01f417a8240c954f553e1d4b5e0f8e39d9c8e3f0a'], + }), + ('arboreto', '0.1.6', { + 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], + }), + ('boltons', '23.1.1', { + 'checksums': ['d2cb2fa83cf2ebe791be1e284183e8a43a1031355156a968f8e0a333ad2448fc'], + }), + ('interlap', '0.2.7', { + 'checksums': ['31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9'], + }), + ('ctxcore', '0.2.0', { + 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], + 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], + }), + ('pyscenic', '0.12.1', { + # download from commit to get fix for numpy error + # https://github.com/aertslab/pySCENIC/issues/518 + 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], + 'sources': [{ + 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', + 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit + }], + 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyscenic'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pyscenic --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 3f602e7018239a59d0bc201640a7a222676762e1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 12 Mar 2024 13:38:36 +0100 Subject: [PATCH 0946/1193] add dependency on pixman and FriBidi --- .../i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb | 2 ++ .../i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb | 2 ++ .../i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb | 2 ++ .../i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb | 2 ++ .../i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb | 2 ++ 5 files changed, 10 insertions(+) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb index d7f3007a2f9a..5e9f46e61dc5 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb @@ -25,6 +25,8 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('LittleCMS', '2.12'), ('Pango', '1.48.5'), + ('pixman', 0.40.0'), + ('FriBidi', '1.0.10'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb index f4a6a273ca9f..efff91588b05 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-37-GCCcore-11.3.0.eb @@ -21,6 +21,8 @@ dependencies = [ ('LibTIFF', '4.3.0'), ('LittleCMS', '2.13.1'), ('Pango', '1.50.7'), + ('pixman', '0.40.0'), + ('FriBidi', '1.0.12'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb index ff34f39886c4..c3033c0d0804 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-4-GCCcore-11.2.0.eb @@ -21,6 +21,8 @@ dependencies = [ ('LibTIFF', '4.3.0'), ('LittleCMS', '2.12'), ('Pango', '1.48.8'), + ('pixman', '0.40.0'), + ('FriBidi', '1.0.10'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb index 67ede6c655f7..1ddf40ec50a6 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb @@ -21,6 +21,8 @@ dependencies = [ ('LibTIFF', '4.4.0'), ('LittleCMS', '2.14'), ('Pango', '1.50.12'), + ('pixman', '0.42.2'), + ('FriBidi', '1.0.12'), ] builddependencies = [ diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb index 3b1b45008997..9504c2276809 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.1-15-GCCcore-12.3.0.eb @@ -25,6 +25,8 @@ dependencies = [ ('LibTIFF', '4.5.0'), ('LittleCMS', '2.15'), ('Pango', '1.50.14'), + ('pixman', '0.42.2'), + ('FriBidi', '1.0.12'), ] configopts = "--with-gslib --with-x" From 2283ac91c66833f0ab63d7626753c6d7e32c45c5 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 12 Mar 2024 12:44:12 +0000 Subject: [PATCH 0947/1193] update libSBML --- .../l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb new file mode 100644 index 000000000000..858ea5e77877 --- /dev/null +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -0,0 +1,81 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Notes:: Patch libsbml-fix_install_libpaths.patch comes from Fedora +# https://src.fedoraproject.org/rpms/libsbml/blob/rawhide/f/libsbml-fix_install_libpaths.patch +## +easyblock = 'CMakeMake' + +name = 'libSBML' +version = '5.19.0' + +# NOTE not in the license list of EB +# software_license = 'LGPLv2+' +software_license_urls = ['http://sbml.org/Software/libSBML/LibSBML_License'] +docurls = [ + 'https://github.com/sbmlteam/libsbml/releases/tag/v%(version)s', + 'http://sbml.org/Software/libSBML', +] + +homepage = 'http://sbml.org/Software/libSBML' +description = """libSBML (Systems Biology Markup Language library) is a free, open-source +programming library to help you read, write, manipulate, translate, and +validate SBML files and data streams. It's not an application itself (though +it does come with example programs), but rather a library you embed in your +own applications.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://downloads.sourceforge.net/project/sbml/libsbml/%(version)s/stable/'] +sources = ['libSBML-%(version)s-core-plus-packages-src.tar.gz'] +patches = [ + 'libsbml-fix_install_libpaths.patch', # Fix some installation library paths (from Fedora) + 'libsbml-fix_perl_auto_case.patch', # Fix the misname for Perl .so binding folder + # (https://sourceforge.net/p/sbml/libsbml/476/) +] +checksums = [ + 'a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547', # libSBML-5.19.0-core-plus-packages-src.tar.gz + '1975b9372be00c5056e1f3408b8829e749adb1edb3345fd109d5c802b5219e45', # libsbml-fix_install_libpaths.patch + '52b3274ce1fdfb329bc53feb67b9862833a1240539eca2f137fcdca00800e34e', # libsbml-fix_perl_auto_case.patch +] + + +builddependencies = [ + ('CMake', '3.20.1'), + ('make', '4.3'), + ('Check', '0.15.2'), + ('SWIG', '4.0.2'), + ('expat', '2.2.9'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Perl', '5.32.1'), +] + +# Java jar, Ruby or Octave can also be build here. +# Python libSBML binding better done from https://pypi.org/project/python-libsbml/ +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' +configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' +configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' +configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' +configure_cmd += '../libSBML-%(version)s-Source/' + + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib64/libsbml.so', 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'dirs': ['lib64', 'include', 'share'] +} + +modextrapaths = { + 'PERL5LIB': 'lib64/perl5/vendor_perl/', +} + + +moduleclass = 'bio' From fa32feb6155e7a2513d0c156eff48e7377e7ee1a Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 12 Mar 2024 12:51:26 +0000 Subject: [PATCH 0948/1193] update part 2 --- .../l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 24 +++++++------------ 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index 858ea5e77877..c75f575aa57c 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -10,7 +10,7 @@ easyblock = 'CMakeMake' name = 'libSBML' -version = '5.19.0' +version = '5.19.7' # NOTE not in the license list of EB # software_license = 'LGPLv2+' @@ -27,34 +27,28 @@ validate SBML files and data streams. It's not an application itself (though it does come with example programs), but rather a library you embed in your own applications.""" -toolchain = {'name': 'GCC', 'version': '10.3.0'} +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/sbmlteam/libsbml/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] -source_urls = ['https://downloads.sourceforge.net/project/sbml/libsbml/%(version)s/stable/'] -sources = ['libSBML-%(version)s-core-plus-packages-src.tar.gz'] -patches = [ - 'libsbml-fix_install_libpaths.patch', # Fix some installation library paths (from Fedora) - 'libsbml-fix_perl_auto_case.patch', # Fix the misname for Perl .so binding folder - # (https://sourceforge.net/p/sbml/libsbml/476/) -] checksums = [ 'a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547', # libSBML-5.19.0-core-plus-packages-src.tar.gz - '1975b9372be00c5056e1f3408b8829e749adb1edb3345fd109d5c802b5219e45', # libsbml-fix_install_libpaths.patch - '52b3274ce1fdfb329bc53feb67b9862833a1240539eca2f137fcdca00800e34e', # libsbml-fix_perl_auto_case.patch ] builddependencies = [ - ('CMake', '3.20.1'), + ('CMake', '3.23.1'), ('make', '4.3'), ('Check', '0.15.2'), ('SWIG', '4.0.2'), - ('expat', '2.2.9'), + ('expat', '2.4.8'), ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), + ('zlib', '1.2.12'), ] dependencies = [ - ('Perl', '5.32.1'), + ('Perl', '5.34.1'), ] # Java jar, Ruby or Octave can also be build here. From b633a0b26c91b196dc3e82a20c11e724f5462d6f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 12 Mar 2024 13:56:28 +0100 Subject: [PATCH 0949/1193] add missing quote --- .../i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb index 5e9f46e61dc5..f066d79bcb23 100644 --- a/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.0.11-14-GCCcore-10.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ('LibTIFF', '4.2.0'), ('LittleCMS', '2.12'), ('Pango', '1.48.5'), - ('pixman', 0.40.0'), + ('pixman', '0.40.0'), ('FriBidi', '1.0.10'), ] From 0fce2b8d1f10724b2891a9c273d51917b5aa4a30 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 12 Mar 2024 12:57:04 +0000 Subject: [PATCH 0950/1193] checksum --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index c75f575aa57c..e633176d956d 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -33,7 +33,7 @@ source_urls = ['https://github.com/sbmlteam/libsbml/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = [ - 'a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547', # libSBML-5.19.0-core-plus-packages-src.tar.gz + '61cbdf1a86aefbc002ac5a0cf9c0f3f91eca2ae8aa5c3e7ef78be0f5a84426c5', ] From c21c59d7890aa8ee5fc24248b89fceb45fd62ffd Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 12 Mar 2024 12:59:45 +0000 Subject: [PATCH 0951/1193] source dir --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index e633176d956d..e0c2a1d0f914 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -57,7 +57,7 @@ configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' -configure_cmd += '../libSBML-%(version)s-Source/' +configure_cmd += '../v%(version)s/' runtest = 'check' From 442d8428a77b70692890cef4a7de1ce591c5802a Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 12 Mar 2024 13:02:45 +0000 Subject: [PATCH 0952/1193] make source directory by hand --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index e0c2a1d0f914..b6c0b4e8a698 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -53,11 +53,11 @@ dependencies = [ # Java jar, Ruby or Octave can also be build here. # Python libSBML binding better done from https://pypi.org/project/python-libsbml/ -configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' +configure_cmd = 'mkdir source && cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' -configure_cmd += '../v%(version)s/' +configure_cmd += '../source/' runtest = 'check' From 15e8414384cef5c1699bc6a53b9648c0e9cd0194 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 12 Mar 2024 13:08:21 +0000 Subject: [PATCH 0953/1193] set right sourcedir --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index b6c0b4e8a698..f9c52eea7a98 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -53,11 +53,11 @@ dependencies = [ # Java jar, Ruby or Octave can also be build here. # Python libSBML binding better done from https://pypi.org/project/python-libsbml/ -configure_cmd = 'mkdir source && cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' +configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' -configure_cmd += '../source/' +configure_cmd += '../%(namelower)s-%(version)s/src' runtest = 'check' From 9324e0dcb998fa08b242262d3947d04fc3716df2 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Tue, 12 Mar 2024 13:15:48 +0000 Subject: [PATCH 0954/1193] source path --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index f9c52eea7a98..1cb671d2df25 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -55,9 +55,9 @@ dependencies = [ # Python libSBML binding better done from https://pypi.org/project/python-libsbml/ configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' -configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF ' +configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF -Wno-dev' configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' -configure_cmd += '../%(namelower)s-%(version)s/src' +configure_cmd += '../%(namelower)s-%(version)s' runtest = 'check' From 366a1a64d70e6b88c32e4f58c56f2632e56e1b8f Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 12 Mar 2024 15:57:41 +0100 Subject: [PATCH 0955/1193] adding easyconfigs: denseweight-0.1.2-foss-2022a.eb --- .../denseweight-0.1.2-foss-2022a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb new file mode 100644 index 000000000000..5e6c44cfc808 --- /dev/null +++ b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'denseweight' +version = '0.1.2' + +homepage = 'https://github.com/steimi/denseweight' +description = """ +This package implements the method for imbalanced regression DenseWeight. The corresponding +paper "Density-based weighting for imbalanced regression". The goal of DenseWeight is to allow +training machine learning models for regression tasks that emphasize performance for data +points with rare target values in comparison to data points with more common target values. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('scikit-learn', '1.1.2'), +] + +use_pip = True + +exts_list = [ + ('KDEpy', '1.1.9', { + 'modulename': 'KDEpy', + 'checksums': ['4bf0b2afd430ce5b40fafd98144de83d8b715d46fdf0f45fed2b5c2e9c40ce46'], + }), + (name, version, { + 'checksums': ['281cf1fe4be364366363ee822b524620dcb629c5b9ff7852aa80f91a27c98b1e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'ai' From 8cb79b01b0e5ff8517bee6fc055a85f68359a5eb Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Tue, 12 Mar 2024 17:40:26 +0100 Subject: [PATCH 0956/1193] Update denseweight-0.1.2-foss-2022a.eb Erase unuseful comment --- .../easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb index 5e6c44cfc808..3ad16c0cd876 100644 --- a/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2022a.eb @@ -13,8 +13,6 @@ points with rare target values in comparison to data points with more common tar toolchain = {'name': 'foss', 'version': '2022a'} -# sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), From c44ea291898f4abeb369f27d1cf0bb95d07f94c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Mar 2024 18:16:27 +0100 Subject: [PATCH 0957/1193] adding easyconfigs: STAR-2.7.11b-GCC-12.3.0.eb --- .../s/STAR/STAR-2.7.11b-GCC-12.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb new file mode 100644 index 000000000000..cf16b5c2979e --- /dev/null +++ b/easybuild/easyconfigs/s/STAR/STAR-2.7.11b-GCC-12.3.0.eb @@ -0,0 +1,51 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# Based on STAR-2.7.7a-GCC-10.2.0.eb +# uploaded by J. Sassmannshausen +# modified by Thomas Eylenbosch + +easyblock = 'MakeCp' + +name = 'STAR' +version = '2.7.11b' + +homepage = 'https://github.com/alexdobin/STAR' +description = "STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays." + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'openmp': True} + +github_account = 'alexdobin' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +patches = ['STAR-2.7.11a_use-external-htslib.patch'] +checksums = [ + {'2.7.11b.tar.gz': '3f65305e4112bd154c7e22b333dcdaafc681f4a895048fa30fa7ae56cac408e7'}, + {'STAR-2.7.11a_use-external-htslib.patch': '2fdc3ed9372d983f77d861d6f16a60a553598358dce9ff8216f96eb20e63ce4e'}, +] + +dependencies = [ + ('HTSlib', '1.18'), + ('zlib', '1.2.13'), +] + +start_dir = 'source' + +buildopts = ' STAR && make STARlong' + +files_to_copy = [ + (['source/%(name)s', 'source/%(name)slong'], 'bin'), + 'CHANGES.md', 'doc', 'extras', 'LICENSE', 'README.md', 'RELEASEnotes.md', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s', 'bin/%(name)slong'], + 'dirs': [], +} + +sanity_check_commands = [ + "STAR --help", + "STARlong --help", +] + +moduleclass = 'bio' From 79dc6c39b83c9cebf73339ea05b265053aef6331 Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 12 Mar 2024 18:29:51 +0100 Subject: [PATCH 0958/1193] Set LD_LIBRARY_PATH for python-casacore 3.5.2 --- .../p/python-casacore/python-casacore-3.5.2-foss-2023b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb b/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb index 520982bb8851..b31dd3187be0 100644 --- a/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb +++ b/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb @@ -22,6 +22,7 @@ exts_list = [ 'checksums': ['850894c4195f09c4ed30dba56213bf7c3f21d86ed6bdaafb5df5972593bfc401'], }), (name, version, { + 'preinstallopts': 'if [[ -z "$LD_LIBRARY_PATH" ]]; then export LD_LIBRARY_PATH="$LIBRARY_PATH"; fi && ', 'checksums': ['ad70c8e08893eec928b3e38c099bda8863f5aa9d099fd00694ad2b0d48eba08f'], 'modulename': 'casacore' }), From ea92f09ad4ba9a1beb4a84ba45e44dba080cb82d Mon Sep 17 00:00:00 2001 From: Tim Kok Date: Tue, 12 Mar 2024 18:41:26 +0100 Subject: [PATCH 0959/1193] Add comment --- .../p/python-casacore/python-casacore-3.5.2-foss-2023b.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb b/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb index b31dd3187be0..2c80f491c981 100644 --- a/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb +++ b/easybuild/easyconfigs/p/python-casacore/python-casacore-3.5.2-foss-2023b.eb @@ -22,6 +22,8 @@ exts_list = [ 'checksums': ['850894c4195f09c4ed30dba56213bf7c3f21d86ed6bdaafb5df5972593bfc401'], }), (name, version, { + # Module uses $LD_LIBRARY_PATH to find libraries + # See https://github.com/EESSI/software-layer/pull/497#issuecomment-1991196996 'preinstallopts': 'if [[ -z "$LD_LIBRARY_PATH" ]]; then export LD_LIBRARY_PATH="$LIBRARY_PATH"; fi && ', 'checksums': ['ad70c8e08893eec928b3e38c099bda8863f5aa9d099fd00694ad2b0d48eba08f'], 'modulename': 'casacore' From 3e8ee8e6b63bdee4aaf69db4fed972f0735c0696 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 12 Mar 2024 19:20:57 +0100 Subject: [PATCH 0960/1193] add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 --- .../Net-SSLeay-1.92_fix.patch | 212 ++++++++++++++++++ .../Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 6 +- 2 files changed, 217 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/Perl-bundle-CPAN/Net-SSLeay-1.92_fix.patch diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Net-SSLeay-1.92_fix.patch b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Net-SSLeay-1.92_fix.patch new file mode 100644 index 000000000000..2129e8f555e2 --- /dev/null +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Net-SSLeay-1.92_fix.patch @@ -0,0 +1,212 @@ +fix failing tests on RHEL 9.x +see https://github.com/radiator-software/p5-net-ssleay/pull/433 +diff -ru Net-SSLeay-1.92.orig/t/local/33_x509_create_cert.t Net-SSLeay-1.92/t/local/33_x509_create_cert.t +--- Net-SSLeay-1.92.orig/t/local/33_x509_create_cert.t 2021-09-29 00:15:32.000000000 +0200 ++++ Net-SSLeay-1.92/t/local/33_x509_create_cert.t 2024-03-12 14:42:37.501231963 +0100 +@@ -93,8 +93,8 @@ + &Net::SSLeay::NID_crl_distribution_points => 'URI:http://pki.dom.com/crl1.pem,URI:http://pki.dom.com/crl2.pem', + ), "P_X509_add_extensions"); + +- ok(my $sha1_digest = Net::SSLeay::EVP_get_digestbyname("sha1"), "EVP_get_digestbyname"); +- ok(Net::SSLeay::X509_sign($x509, $ca_pk, $sha1_digest), "X509_sign"); ++ ok(my $sha256_digest = Net::SSLeay::EVP_get_digestbyname("sha256"), "EVP_get_digestbyname"); ++ ok(Net::SSLeay::X509_sign($x509, $ca_pk, $sha256_digest), "X509_sign"); + + is(Net::SSLeay::X509_get_version($x509), 3, "X509_get_version"); + is(Net::SSLeay::X509_verify($x509, Net::SSLeay::X509_get_pubkey($ca_cert)), 1, "X509_verify"); +@@ -186,8 +186,8 @@ + + ok(Net::SSLeay::X509_REQ_set_version($req, 2), "X509_REQ_set_version"); + +- ok(my $sha1_digest = Net::SSLeay::EVP_get_digestbyname("sha1"), "EVP_get_digestbyname"); +- ok(Net::SSLeay::X509_REQ_sign($req, $pk, $sha1_digest), "X509_REQ_sign"); ++ ok(my $sha256_digest = Net::SSLeay::EVP_get_digestbyname("sha256"), "EVP_get_digestbyname"); ++ ok(Net::SSLeay::X509_REQ_sign($req, $pk, $sha256_digest), "X509_REQ_sign"); + + ok(my $req_pubkey = Net::SSLeay::X509_REQ_get_pubkey($req), "X509_REQ_get_pubkey"); + is(Net::SSLeay::X509_REQ_verify($req, $req_pubkey), 1, "X509_REQ_verify"); +@@ -228,7 +228,7 @@ + ok(Net::SSLeay::X509_set_pubkey($x509ss,$tmppkey), "X509_set_pubkey"); + Net::SSLeay::EVP_PKEY_free($tmppkey); + +- ok(Net::SSLeay::X509_sign($x509ss, $ca_pk, $sha1_digest), "X509_sign"); ++ ok(Net::SSLeay::X509_sign($x509ss, $ca_pk, $sha256_digest), "X509_sign"); + like(my $crt_pem = Net::SSLeay::PEM_get_string_X509($x509ss), qr/-----BEGIN CERTIFICATE-----/, "PEM_get_string_X509"); + + #write_file("tmp_cert2.crt.pem", $crt_pem); +@@ -296,8 +296,8 @@ + ok(Net::SSLeay::P_ASN1_TIME_set_isotime(Net::SSLeay::X509_get_notAfter($x509), "2038-01-01T00:00:00Z"), "P_ASN1_TIME_set_isotime+X509_get_notAfter"); + } + +- ok(my $sha1_digest = Net::SSLeay::EVP_get_digestbyname("sha1"), "EVP_get_digestbyname"); +- ok(Net::SSLeay::X509_sign($x509, $ca_pk, $sha1_digest), "X509_sign"); ++ ok(my $sha256_digest = Net::SSLeay::EVP_get_digestbyname("sha256"), "EVP_get_digestbyname"); ++ ok(Net::SSLeay::X509_sign($x509, $ca_pk, $sha256_digest), "X509_sign"); + + like(my $crt_pem = Net::SSLeay::PEM_get_string_X509($x509), qr/-----BEGIN CERTIFICATE-----/, "PEM_get_string_X509"); + like(my $key_pem = Net::SSLeay::PEM_get_string_PrivateKey($pk), qr/-----BEGIN (RSA )?PRIVATE KEY-----/, "PEM_get_string_PrivateKey"); +@@ -311,8 +311,8 @@ + ok(my $bio = Net::SSLeay::BIO_new_file($req_pem, 'r'), "BIO_new_file"); + ok(my $req = Net::SSLeay::PEM_read_bio_X509_REQ($bio), "PEM_read_bio_X509"); + +- ok(my $sha1_digest = Net::SSLeay::EVP_get_digestbyname("sha1"), "EVP_get_digestbyname"); +- is(unpack("H*", Net::SSLeay::X509_REQ_digest($req, $sha1_digest)), "372c21a20a6d4e15bf8ecefb487cc604d9a10960", "X509_REQ_digest"); ++ ok(my $sha256_digest = Net::SSLeay::EVP_get_digestbyname("sha256"), "EVP_get_digestbyname"); ++ is(unpack("H*", Net::SSLeay::X509_REQ_digest($req, $sha256_digest)), "420e99da1e23e192409ab2a5f1a9b09ac03c52fa4b8bd0d19e561358f9880e88", "X509_REQ_digest"); + + ok(my $req2 = Net::SSLeay::X509_REQ_new(), "X509_REQ_new"); + ok(my $name = Net::SSLeay::X509_REQ_get_subject_name($req), "X509_REQ_get_subject_name"); +Only in Net-SSLeay-1.92/t/local: 33_x509_create_cert.t.orig +diff -ru Net-SSLeay-1.92.orig/t/local/34_x509_crl.t Net-SSLeay-1.92/t/local/34_x509_crl.t +--- Net-SSLeay-1.92.orig/t/local/34_x509_crl.t 2020-11-18 10:12:44.000000000 +0100 ++++ Net-SSLeay-1.92/t/local/34_x509_crl.t 2024-03-12 14:43:38.874896528 +0100 +@@ -39,8 +39,8 @@ + } + + is(Net::SSLeay::X509_CRL_get_version($crl1), 1, "X509_CRL_get_version"); +- ok(my $sha1_digest = Net::SSLeay::EVP_get_digestbyname("sha1"), "EVP_get_digestbyname"); +- is(unpack("H*",Net::SSLeay::X509_CRL_digest($crl1, $sha1_digest)), 'f0e5c853477a206c03f7347aee09a01d91df0ac5', "X509_CRL_digest"); ++ ok(my $sha256_digest = Net::SSLeay::EVP_get_digestbyname("sha256"), "EVP_get_digestbyname"); ++ is(unpack("H*",Net::SSLeay::X509_CRL_digest($crl1, $sha256_digest)), '4edc18ec956e722cbcf96589a43535c2d1d557e3cec55b1e421897827c3bb8be', "X509_CRL_digest"); + } + + { ### X509_CRL create +@@ -100,12 +100,12 @@ + &Net::SSLeay::NID_authority_key_identifier => 'keyid:always,issuer:always', + ), "P_X509_CRL_add_extensions"); + +- ok(my $sha1_digest = Net::SSLeay::EVP_get_digestbyname("sha1"), "EVP_get_digestbyname"); ++ ok(my $sha256_digest = Net::SSLeay::EVP_get_digestbyname("sha256"), "EVP_get_digestbyname"); + SKIP: { + skip('requires openssl-0.9.7', 1) unless Net::SSLeay::SSLeay >= 0x0090700f; + ok(Net::SSLeay::X509_CRL_sort($crl), "X509_CRL_sort"); + } +- ok(Net::SSLeay::X509_CRL_sign($crl, $ca_pk, $sha1_digest), "X509_CRL_sign"); ++ ok(Net::SSLeay::X509_CRL_sign($crl, $ca_pk, $sha256_digest), "X509_CRL_sign"); + + like(my $crl_pem = Net::SSLeay::PEM_get_string_X509_CRL($crl), qr/-----BEGIN X509 CRL-----/, "PEM_get_string_X509_CRL"); + +diff -ru Net-SSLeay-1.92.orig/t/local/44_sess.t Net-SSLeay-1.92/t/local/44_sess.t +--- Net-SSLeay-1.92.orig/t/local/44_sess.t 2021-09-29 00:15:32.000000000 +0200 ++++ Net-SSLeay-1.92/t/local/44_sess.t 2024-03-12 14:42:37.501231963 +0100 +@@ -2,7 +2,7 @@ + + use lib 'inc'; + +-use Net::SSLeay; ++use Net::SSLeay qw( ERROR_SSL ); + use Test::Net::SSLeay qw( + can_fork data_file_path initialise_libssl is_protocol_usable new_ctx + tcp_socket +@@ -13,7 +13,7 @@ + if (not can_fork()) { + plan skip_all => "fork() not supported on this system"; + } else { +- plan tests => 58; ++ plan tests => 59; + } + + initialise_libssl(); +@@ -142,6 +142,7 @@ + my ($server_ctx, $client_ctx, $server_ssl, $client_ssl); + + my $server = tcp_socket(); ++my $proto_count = 0; + + sub server + { +@@ -256,6 +257,14 @@ + Net::SSLeay::set_fd($ssl, $cl); + my $ret = Net::SSLeay::connect($ssl); + if ($ret <= 0) { ++ # Connection might fail due to attempted use of algorithm in key ++ # exchange that is forbidden by security policy, resulting in ERROR_SSL ++ my $ssl_err = Net::SSLeay::get_error($ssl, $ret); ++ if ($ssl_err == ERROR_SSL) { ++ diag("Protocol $proto, connect() failed, maybe due to security policy"); ++ $usable{$round} = 0; ++ next; ++ } + diag("Protocol $proto, connect() returns $ret, Error: ".Net::SSLeay::ERR_error_string(Net::SSLeay::ERR_get_error())); + } + my $msg = Net::SSLeay::read($ssl); +@@ -275,6 +284,7 @@ + Net::SSLeay::shutdown($ssl); + Net::SSLeay::free($ssl); + close($cl) || die("client close: $!"); ++ $proto_count += 1; + } + + $cl = $server->connect(); +@@ -359,6 +369,8 @@ + } + } + ++ cmp_ok($proto_count, '>=', 1, "At least one protocol fully testable"); ++ + # use Data::Dumper; print "Server:\n" . Dumper(\%srv_stats); + # use Data::Dumper; print "Client:\n" . Dumper(\%clt_stats); + } +Only in Net-SSLeay-1.92/t/local: 44_sess.t.orig +diff -ru Net-SSLeay-1.92.orig/t/local/45_exporter.t Net-SSLeay-1.92/t/local/45_exporter.t +--- Net-SSLeay-1.92.orig/t/local/45_exporter.t 2021-09-29 00:15:32.000000000 +0200 ++++ Net-SSLeay-1.92/t/local/45_exporter.t 2024-03-12 14:42:37.501231963 +0100 +@@ -2,7 +2,7 @@ + + use lib 'inc'; + +-use Net::SSLeay; ++use Net::SSLeay qw( ERROR_SSL ); + use Test::Net::SSLeay qw( + can_fork data_file_path initialise_libssl is_protocol_usable new_ctx + tcp_socket +@@ -15,7 +15,7 @@ + } elsif (!defined &Net::SSLeay::export_keying_material) { + plan skip_all => "No export_keying_material()"; + } else { +- plan tests => 36; ++ plan tests => 37; + } + + initialise_libssl(); +@@ -37,6 +37,7 @@ + my ($server_ctx, $client_ctx, $server_ssl, $client_ssl); + + my $server = tcp_socket(); ++my $proto_count = 0; + + sub server + { +@@ -88,6 +89,16 @@ + Net::SSLeay::set_fd( $ssl, $cl ); + my $ret = Net::SSLeay::connect($ssl); + if ($ret <= 0) { ++ # Connection might fail due to attempted use of algorithm in key ++ # exchange that is forbidden by security policy, resulting in ERROR_SSL ++ my $ssl_err = Net::SSLeay::get_error($ssl, $ret); ++ if ($ssl_err == ERROR_SSL) { ++ diag("Protocol $round, connect() failed, maybe due to security policy"); ++ SKIP: { ++ skip( "$round not available in this enviornment", 9 ); ++ } ++ next; ++ } + diag("Protocol $round, connect() returns $ret, Error: ".Net::SSLeay::ERR_error_string(Net::SSLeay::ERR_get_error())); + } + +@@ -100,6 +111,7 @@ + Net::SSLeay::shutdown($ssl); + Net::SSLeay::free($ssl); + close($cl) || die("client close: $!"); ++ $proto_count += 1; + } + else { + SKIP: { +@@ -168,4 +180,7 @@ + server(); + client(); + waitpid $pid, 0; ++ ++cmp_ok($proto_count, '>=', 1, "At least one protocol fully testable"); ++ + exit(0); diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index b67a4de71773..f57bfb43acf8 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -673,10 +673,14 @@ exts_list = [ 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], }), ('Net::SSLeay', '1.92', { + 'patches': ['Net-SSLeay-1.92_fix.patch'], 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], - 'checksums': ['47c2f2b300f2e7162d71d699f633dd6a35b0625a00cbda8c50ac01144a9396a9'], + 'checksums': [ + {'Net-SSLeay-1.92.tar.gz': '47c2f2b300f2e7162d71d699f633dd6a35b0625a00cbda8c50ac01144a9396a9'}, + {'Net-SSLeay-1.92_fix.patch': '37790b10c5551bce92bc4bd7c98a92b0058fc16604272c7459a63096b52a8d1c'}, + ], }), ('IO::Socket::SSL', '2.083', { 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', From c46749d794fdf51ca9e11d4add7279119b7d89af Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Mar 2024 18:33:25 +0000 Subject: [PATCH 0961/1193] adding easyconfigs: CSBLAST-2.2.4-GCCcore-11.3.0.eb --- .../c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..447430db8128 --- /dev/null +++ b/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'CSBLAST' +version = '2.2.4' + +homepage = 'https://github.com/soedinglab/csblast/' +description = """Context-specific extension of BLAST that significantly improves sensitivity and alignment quality.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'soedinglab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['76848da4d45a618ae903cafc00ff6387e7decb17b839aca83d9a9438537edf0d'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('sparsehash', '2.0.4'), +] + +start_dir = 'src' + +build_cmd_targets = 'csblast csbuild' + +buildopts = '"FLAGS=-fpermissive -std=c++11 "' + +files_to_copy = ['bin', 'data', 'LICENSE', 'README_CSBLAST'] + +sanity_check_paths = { + 'files': ['bin/csblast', 'bin/csbuild', 'data/K4000.crf', 'data/K4000.lib'], + 'dirs': ['bin', 'data'], +} + +moduleclass = 'bio' From c37ebce796841d47e4a455519be09bacc5698652 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Mar 2024 18:35:56 +0000 Subject: [PATCH 0962/1193] adding easyconfigs: DLPack-0.8-GCC-11.3.0.eb --- .../d/DLPack/DLPack-0.8-GCC-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/d/DLPack/DLPack-0.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DLPack/DLPack-0.8-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DLPack/DLPack-0.8-GCC-11.3.0.eb new file mode 100644 index 000000000000..97be9746c552 --- /dev/null +++ b/easybuild/easyconfigs/d/DLPack/DLPack-0.8-GCC-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'DLPack' +version = '0.8' + +homepage = 'https://dmlc.github.io/dlpack/latest/' +description = """DLPack is a stable in-memory data structure for an ndarray +system to interact with a variety of frameworks.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'dmlc' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cf965c26a5430ba4cc53d61963f288edddcd77443aa4c85ce722aaf1e2f29513'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['include/dlpack/dlpack.h', 'lib/cmake/dlpack/dlpackConfig.cmake'], + 'dirs': [], +} + +moduleclass = 'lib' From 4d2d41b73a67dcac91fcc27257ff6fdd57708fe3 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Mar 2024 18:36:51 +0000 Subject: [PATCH 0963/1193] adding easyconfigs: DMLC-Core-0.5-GCC-11.3.0.eb --- .../d/DMLC-Core/DMLC-Core-0.5-GCC-11.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-11.3.0.eb b/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-11.3.0.eb new file mode 100644 index 000000000000..ce48657bd143 --- /dev/null +++ b/easybuild/easyconfigs/d/DMLC-Core/DMLC-Core-0.5-GCC-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'DMLC-Core' +version = '0.5' + +homepage = 'https://dmlc-core.readthedocs.io/en/latest' +description = """DMLC-Core is the backbone library to support all DMLC +projects, offers the bricks to build efficient and scalable distributed +machine learning libraries.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'dmlc' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['cd97475ae1ecf561a1cb1129552f9889d52b11b3beb4c56e5345d007d5020ece'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('googletest', '1.11.0'), +] + +_copts = [ + '-DUSE_CXX14_IF_AVAILABLE=ON', + '-DGOOGLE_TEST=ON', +] +configopts = ' '.join(_copts) + +build_shared_libs = True + +runtest = 'test' + +sanity_check_paths = { + 'files': ['include/dmlc/common.h', 'lib/cmake/dmlc/dmlc-config.cmake', 'lib/libdmlc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 0efc36089dcd2c9ab114a23c2beccfe940508264 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Mar 2024 18:38:41 +0000 Subject: [PATCH 0964/1193] adding easyconfigs: GKlib-METIS-5.1.1-GCCcore-11.3.0.eb --- .../GKlib-METIS-5.1.1-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..b68105ba6726 --- /dev/null +++ b/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +# This is needed to install newer versions of DGL. +# The main reason is that the specific version of METIS used in DGL needs is as a +# third party software and newer versions of DGL don't have that included any more. +# Author: J. Sassmannshausen (Imperial College Londoni/UK) + +easyblock = 'CMakeMake' + +name = 'GKlib-METIS' +version = '5.1.1' + +homepage = 'https://github.com/KarypisLab/GKlib' +description = """A library of various helper routines and frameworks used by +many of the lab's software""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [ + { + 'source_urls': ['https://github.com/KarypisLab/GKlib/archive'], + 'download_filename': 'METIS-v%(version)s-DistDGL-0.5.tar.gz', + 'filename': '%(name)s-v%(version)s-DistDGL-0.5.tar.gz', + } +] +checksums = ['52aa0d383d42360f4faa0ae9537ba2ca348eeab4db5f2dfd6343192d0ff4b833'] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': ['bin/gkgraph'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'ai' From 0ba960fef256a4c17019172096d9061ea2d40987 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 12 Mar 2024 19:49:30 +0000 Subject: [PATCH 0965/1193] Missing binutils added --- .../g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb index b68105ba6726..e0de59bb45c6 100644 --- a/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb @@ -25,6 +25,7 @@ checksums = ['52aa0d383d42360f4faa0ae9537ba2ca348eeab4db5f2dfd6343192d0ff4b833'] builddependencies = [ ('CMake', '3.24.3'), + ('binutils', '2.38'), ] dependencies = [ From caf0ed743d9445794f05b44d33e1734f2e178e8b Mon Sep 17 00:00:00 2001 From: Joachim Hein Date: Wed, 13 Mar 2024 10:01:26 +0100 Subject: [PATCH 0966/1193] Create Anaconda3-2024.02-1.eb --- .../a/Anaconda3/Anaconda3-2024.02-1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.02-1.eb diff --git a/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.02-1.eb b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.02-1.eb new file mode 100644 index 000000000000..ff866c9193d4 --- /dev/null +++ b/easybuild/easyconfigs/a/Anaconda3/Anaconda3-2024.02-1.eb @@ -0,0 +1,33 @@ +# author: Jillian Rowe +# config upgrade to v5.1.0 by Adam Huffman +# config upgrade to v5.0.1, v5.3.0, 2018.12, 2019.07, +# 2019.10, 2020.2, 2020.11, 2022.05, +# 2022.10, 2024.2-1 by J. Hein +# config upgrade to 2019.03 by Davide Vanzo +# config upgrade to 2023.09 by Sarah Walters + +# no support for power architecture in 2024.02-1 on https://repo.anaconda.com/archive/, as off 13 Feb 2024 +easyblock = 'EB_Anaconda' + +name = 'Anaconda3' +version = '2024.02-1' + +homepage = 'https://www.anaconda.com' +description = """Built to complement the rich, open source Python community, +the Anaconda platform provides an enterprise-ready data analytics platform +that empowers companies to adopt a modern open data science analytics architecture. +""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/archive/'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': 'c536ddb7b4ba738bddbd4e581b29308cb332fa12ae3fa2cd66814bd735dff231', + '%(name)s-%(version)s-Linux-aarch64.sh': '28c5bed6fba84f418516e41640c7937514aabd55e929a8f66937c737303c7bba', + } +] + +moduleclass = 'lang' From 54ef07a4711bc7b666cdd55d05327a63ee913a80 Mon Sep 17 00:00:00 2001 From: crivella Date: Wed, 13 Mar 2024 11:26:51 +0100 Subject: [PATCH 0967/1193] Added QuantumESPRESSO easyconfigs for 7.3 (both intel and foss) --- .../QuantumESPRESSO-7.3-foss-2023a.eb | 58 +++++++++++++++++++ .../QuantumESPRESSO-7.3-intel-2023a.eb | 57 ++++++++++++++++++ 2 files changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb new file mode 100644 index 000000000000..1e4c706faefd --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb @@ -0,0 +1,58 @@ +name = 'QuantumESPRESSO' +version = '7.3' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = { + 'usempi': True, + 'openmp': True, + } + +sources = [ + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'] + }, + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', + 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, +] +checksums = [ + {'q-e-qe-%(version)s.tar.gz': 'edc2a0f3315c69966df4f82ec86ab9f682187bc9430ef6d2bacad5f27f08972c'}, + {'qe-gipaw-%(version)s.tar.gz': 'a24d328ec068043d36fdf69fe4f8d1904d7befeba7962cb85be059ea0fe6f026'}, + {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2023.05.001'), + ('libxc', '6.2.2'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = "all gwl xspectra couple epw gipaw w90" +with_fox = True # Needed from QE7.2 to build GIPAW + +# parallel build tends to fail +parallel = 1 + + +moduleclass = 'chem' + diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb new file mode 100644 index 000000000000..0b75a12d84e4 --- /dev/null +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb @@ -0,0 +1,57 @@ +name = 'QuantumESPRESSO' +version = '7.3' + +homepage = 'https://www.quantum-espresso.org' +description = """Quantum ESPRESSO is an integrated suite of computer codes +for electronic-structure calculations and materials modeling at the nanoscale. +It is based on density-functional theory, plane waves, and pseudopotentials +(both norm-conserving and ultrasoft). +""" + +toolchain = {'name': 'intel', 'version': '2023a'} +toolchainopts = { + 'usempi': True, + 'openmp': True, + } + +sources = [ + { + 'filename': 'q-e-qe-%(version)s.tar.gz', + 'extract_cmd': 'mkdir -p %(builddir)s/qe-%(version)s && tar xzvf %s --strip-components=1 -C $_', + 'source_urls': ['https://gitlab.com/QEF/q-e/-/archive/qe-%(version)s'] + }, + { + 'filename': 'qe-gipaw-%(version)s.tar.gz', + 'source_urls': ['https://github.com/dceresoli/qe-gipaw/releases/download/%(version)s/']}, + { + 'filename': 'wannier90-3.1.0.tar.gz', + 'download_filename': 'v3.1.0.tar.gz', + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'] + }, +] +checksums = [ + {'q-e-qe-%(version)s.tar.gz': 'edc2a0f3315c69966df4f82ec86ab9f682187bc9430ef6d2bacad5f27f08972c'}, + {'qe-gipaw-%(version)s.tar.gz': 'a24d328ec068043d36fdf69fe4f8d1904d7befeba7962cb85be059ea0fe6f026'}, + {'wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('HDF5', '1.14.0'), + ('ELPA', '2023.05.001'), + ('libxc', '6.2.2'), +] + +# The third party packages should be installed separately and added as +# dependencies. The exception is w90, which is force built, and gipaw +# which depends on qe source +buildopts = "all gwl xspectra couple epw gipaw w90" +with_fox = True # Needed from QE7.2 to build GIPAW + +# parallel build tends to fail +parallel = 1 + + +moduleclass = 'chem' From e0f47ae1901c461bd1886c8cd54c0a963f366a87 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Mar 2024 11:33:48 +0100 Subject: [PATCH 0968/1193] adding easyconfigs: HeFFTe-2.4.0-foss-2023b.eb --- .../h/HeFFTe/HeFFTe-2.4.0-foss-2023b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.0-foss-2023b.eb diff --git a/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.0-foss-2023b.eb b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.0-foss-2023b.eb new file mode 100644 index 000000000000..63cedb53c470 --- /dev/null +++ b/easybuild/easyconfigs/h/HeFFTe/HeFFTe-2.4.0-foss-2023b.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'HeFFTe' +version = '2.4.0' + +homepage = 'https://icl.utk.edu/fft' +description = "Highly Efficient FFT for Exascale (HeFFTe) library" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = ['https://github.com/icl-utk-edu/heffte/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['02310fb4f9688df02f7181667e61c3adb7e38baf79611d80919d47452ff7881d'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +build_shared_libs = True + +configopts = "-DHeffte_ENABLE_FFTW=ON -DFFTW_ROOT=$EBROOTFFTW -DHeffte_ENABLE_CUDA=OFF -DHeffte_ENABLE_MKL=OFF" + +sanity_check_paths = { + 'files': ['lib/libheffte.%s' % SHLIB_EXT], + 'dirs': ['include', 'lib/cmake/Heffte', 'share/heffte/examples'], +} + +moduleclass = 'lib' From 0901811466e920af56e8a6dd6c69d356e4e97e07 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Wed, 13 Mar 2024 10:51:19 +0000 Subject: [PATCH 0969/1193] change sanitycheckpaths --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index 1cb671d2df25..3598228c2d88 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -63,12 +63,12 @@ configure_cmd += '../%(namelower)s-%(version)s' runtest = 'check' sanity_check_paths = { - 'files': ['lib64/libsbml.so', 'lib64/perl5/vendor_perl/LibSBML.pm'], + 'files': ['lib64/libsbml.so', 'lib64/perl5/site_perl/5.34.1/x86_64-linux-thread-multi/LibSBML.pm'], 'dirs': ['lib64', 'include', 'share'] } modextrapaths = { - 'PERL5LIB': 'lib64/perl5/vendor_perl/', + 'PERL5LIB': 'lib64/perl5/site_perl/5.34.1/x86_64-linux-thread-multi/', } From fa154032043c257e21a14fa7e504aed206b64a09 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 13 Mar 2024 13:52:09 +0100 Subject: [PATCH 0970/1193] adding easyconfigs: CUDA-12.4.0.eb, NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb, magma-2.7.2-foss-2023b-CUDA-12.4.0.eb, UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.4.0.eb | 24 ++++++++++ .../magma-2.7.2-foss-2023b-CUDA-12.4.0.eb | 44 +++++++++++++++++++ .../NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb | 26 +++++++++++ ...-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb | 41 +++++++++++++++++ 4 files changed, 135 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.4.0.eb create mode 100644 easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023b-CUDA-12.4.0.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.4.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.4.0.eb new file mode 100644 index 000000000000..29127574f0fc --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.4.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.4.0' +local_nv_version = '550.54.14' + +homepage = 'https://developer.nvidia.com/cuda-toolkit' +description = """CUDA (formerly Compute Unified Device Architecture) is a parallel + computing platform and programming model created by NVIDIA and implemented by the + graphics processing units (GPUs) that they produce. CUDA gives developers access + to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cuda/%(version)s/local_installers/'] +sources = ['cuda_%%(version)s_%s_linux%%(cudaarch)s.run' % local_nv_version] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + 'e6a842f4eca9490575cdb68b6b1bb78d47b95a897de48dee292c431892e57d17', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'ef9a712daccf2805b4422f2301ff0eaa5c3ad41ef5d64b8626773bce7d1f41fe', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'b12bfe6c36d32ecf009a6efb0024325c5fc389fca1143f5f377ae2555936e803' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023b-CUDA-12.4.0.eb new file mode 100644 index 000000000000..26a36f2542f1 --- /dev/null +++ b/easybuild/easyconfigs/m/magma/magma-2.7.2-foss-2023b-CUDA-12.4.0.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'magma' +version = '2.7.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://icl.cs.utk.edu/magma/' +description = """The MAGMA project aims to develop a dense linear algebra library similar to + LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'openmp': True} + +source_urls = ['https://icl.cs.utk.edu/projectsfiles/%(name)s/downloads/'] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-2.7.2_allow-all-sms.patch'] +checksums = [ + {'magma-2.7.2.tar.gz': '729bc1a70e518a7422fe7a3a54537a4741035a77be3349f66eac5c362576d560'}, + {'magma-2.7.2_allow-all-sms.patch': '2996485844d7e199ea57eaebf59903d3514a03536f82b655ce30de480e28b828'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), +] +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +# make sure both static and shared libs are built +configopts = [ + '-DBUILD_SHARED_LIBS=%s \ + -DGPU_TARGET="%%(cuda_sm_space_sep)s" ' % local_shared for local_shared in ('ON', 'OFF') +] + +sanity_check_paths = { + 'files': ['lib/libmagma.%s' % SHLIB_EXT, 'lib/libmagma.a'], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb new file mode 100644 index 000000000000..90634952ad69 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.20.5-GCCcore-13.2.0-CUDA-12.4.0.eb @@ -0,0 +1,26 @@ +name = 'NCCL' +version = '2.20.5' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['d11ad65c1df3cbe4447eaddceec71569f5c0497e27b3b8369cf79f18d2b2ad8c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb new file mode 100644 index 000000000000..7ddf41314154 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.4.0.eb @@ -0,0 +1,41 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.15.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'http://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications + +This module adds the UCX CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] +patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.15.0.tar.gz': '4b202087076bc1c98f9249144f0c277a8ea88ad4ca6f404f94baa9cb3aebda6d'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('zlib', '1.2.13'), + ('UCX', version), + ('CUDA', '12.4.0', '', SYSTEM), + ('GDRCopy', '2.4'), +] + + +moduleclass = 'lib' From 5777deef01109681541baf220b7f0e0a7652df56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Mar 2024 11:20:22 +0100 Subject: [PATCH 0971/1193] {bio,tools}[foss/2023b] GROMACS v2024.1, networkx v3.2.1 --- .../g/GROMACS/GROMACS-2024.1-foss-2023b.eb | 87 +++++++++++++++++++ .../n/networkx/networkx-3.2.1-gfbf-2023b.eb | 24 +++++ 2 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb new file mode 100644 index 000000000000..20a40cd39520 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.1-foss-2023b.eb @@ -0,0 +1,87 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.1' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.1.tar.gz': '937d8f12a36fffbf2af7add71adbb5aa5c5537892d46c9a76afbecab1aa0aac7'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.3.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb b/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb new file mode 100644 index 000000000000..8b1d917815dd --- /dev/null +++ b/easybuild/easyconfigs/n/networkx/networkx-3.2.1-gfbf-2023b.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'networkx' +version = '3.2.1' + +homepage = 'https://pypi.python.org/pypi/networkx' +description = """NetworkX is a Python package for the creation, manipulation, +and study of the structure, dynamics, and functions of complex networks.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['9f1bb5cf3409bf324e0a722c20bdb4c20ee39bf1c30ce8ae499c8502b0b5e0c6'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # required for numpy, scipy, ... +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'tools' From b322d747551dce93edd05fcc7eeb70e483607582 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 13 Mar 2024 15:56:25 +0000 Subject: [PATCH 0972/1193] adding easyconfigs: cuTENSOR-2.0.1.2-CUDA-12.2.2.eb --- .../cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.2.2.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.2.2.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.2.2.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.2.2.eb new file mode 100644 index 000000000000..183378856f90 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.2.2.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '2.0.1' +version = local_shortver + '.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-x86_64/'] +sources = ['libcutensor-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['ededa12ca622baad706ea0a500a358ea51146535466afabd96e558265dc586a2'] + +local_cudamajver = '12' +dependencies = [('CUDA', local_cudamajver + '.2.2')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From 3cb5f5fd50da56218ed6dcf9af139ef0b07baf51 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 13 Mar 2024 16:57:25 +0100 Subject: [PATCH 0973/1193] adding easyconfigs: infercnvpy-0.4.3-foss-2023a.eb --- .../infercnvpy/infercnvpy-0.4.3-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb new file mode 100644 index 000000000000..04a3bebf24fe --- /dev/null +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'infercnvpy' +version = '0.4.3' + +homepage = 'https://github.com/icbi-lab/infercnvpy' +description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nicely with Scanpy." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [('hatchling', '1.18.0'),] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('IPython', '8.14.0'), + ('leidenalg', '0.10.2'), + ('scanpy', '1.9.8'), + ('anndata', '0.10.5.post1'), +] + +use_pip = True + +exts_list = [ + ('gtfparse', '1.3.0', { + 'checksums': ['d957f18e5f70413f89a28ef83068c461b6407eb38fd30e99b8da3d69143527b1'], + }), + ('pyreadr', '0.4.7', { + 'checksums': ['901110d62b4bedaef288f4db81425fb696edc721fe2c34c1083f5fb11050a73c'], + }), + ('session_info', '1.0.0', { + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + (name, version, { + 'checksums': ['2ca7230742fda1a0e7e0d9652d290e6b303b9c08ff37c1e7a8459b4b6ec5742b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From c208d58eb4cff1d6c2dc37cb2e32a6fa03111ff3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 13 Mar 2024 22:23:17 +0100 Subject: [PATCH 0974/1193] Update easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb --- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb index 04a3bebf24fe..d4d503e0de66 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.3-foss-2023a.eb @@ -8,7 +8,7 @@ description = "Infer copy number variation (CNV) from scRNA-seq data. Plays nice toolchain = {'name': 'foss', 'version': '2023a'} -builddependencies = [('hatchling', '1.18.0'),] +builddependencies = [('hatchling', '1.18.0')] dependencies = [ ('Python', '3.11.3'), From 9bea037523a0ae92f12b71372e12b1e1015e7a4c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 14 Mar 2024 10:30:34 +0100 Subject: [PATCH 0975/1193] add MODIStsp extension --- .../easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 21 +++++++++++++++++++ .../r/R/protolite-2.3.0_use-c++17.patch | 14 +++++++++++++ 2 files changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/r/R/protolite-2.3.0_use-c++17.patch diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 5c533ecb9989..8ee5e1a6d791 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -51,6 +51,8 @@ dependencies = [ ('MPFR', '4.2.0'), # for Rmpfr ('libgit2', '1.5.0'), ('OpenSSL', '1.1', '', SYSTEM), + ('protobuf', '23.0'), + ('jq', '1.6'), ] # Some R extensions (mclust, quantreg, waveslim for example) require the math library (-lm) to avoid undefined symbols. @@ -3669,6 +3671,25 @@ exts_list = [ ('ridge', '3.3', { 'checksums': ['5c2daecf6f97aa099ef5fa54f8448518c4f2ed6e44dd29fc60621a70721c60f5'], }), + ('gdalUtilities', '1.2.5', { + 'checksums': ['2a72e990080ad626205c78edc6614959b564413b7fc23132008b7259723571a7'], + }), + ('protolite', '2.3.0', { + 'checksums': ['53ef24d51a8348f97bec39d254df3b97bd8b3d9bbffb81d6b06aad849cf78ce9'], + 'patches': ['protolite-2.3.0_use-c++17.patch'], + }), + ('jqr', '1.3.1', { + 'checksums': ['e22461e75ff7e57fe502dc7d16c5e5fe9f8e4cbe042b5eadad06fc37394f9f36'], + }), + ('geojson', '0.3.5', { + 'checksums': ['e425c8579dc9cf5e3c1f71db3b0eed8225e5ed7ea88b6c861f800f60fc07402a'], + }), + ('geojsonio', '0.11.3', { + 'checksums': ['7168eb3571440479f0cbdd005ff9db3233d3c91fc10d37fb0eb200793da3402b'], + }), + ('MODIStsp', '2.1.0', { + 'checksums': ['9416bf2a32faf4ae7159f50ba56ac7924852af59f932223b2268aedfa1769fda'], + }), ] moduleclass = 'lang' diff --git a/easybuild/easyconfigs/r/R/protolite-2.3.0_use-c++17.patch b/easybuild/easyconfigs/r/R/protolite-2.3.0_use-c++17.patch new file mode 100644 index 000000000000..a73741e3a1e0 --- /dev/null +++ b/easybuild/easyconfigs/r/R/protolite-2.3.0_use-c++17.patch @@ -0,0 +1,14 @@ +make sure that protolite using -std=gnu++17 instead of -std=gnu++14 (default in R 4.2.2) +required to fix compilation problems like: +error: string_view in namespace std does not name a type +author: Kenneth Hoste (HPC-UGent) +--- protolite/configure.orig 2024-01-10 10:50:16.030350785 +0100 ++++ protolite/configure 2024-01-10 10:50:52.847841896 +0100 +@@ -87,6 +87,7 @@ + + # Write to Makevars + sed -e "s|@cflags@|$PKG_CFLAGS|" -e "s|@libs@|$PKG_LIBS|" src/Makevars.in > src/Makevars ++echo 'CXX_STD = CXX17' >> src/Makevars + + # Look for 'protoc' compiler + if [ `command -v protoc` ]; then From 52cb0ca369411692a95fd2b2cbeed62dde14cf1b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 14 Mar 2024 10:47:28 +0100 Subject: [PATCH 0976/1193] add missing checksum --- easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 8ee5e1a6d791..4e319447dd04 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -3675,8 +3675,11 @@ exts_list = [ 'checksums': ['2a72e990080ad626205c78edc6614959b564413b7fc23132008b7259723571a7'], }), ('protolite', '2.3.0', { - 'checksums': ['53ef24d51a8348f97bec39d254df3b97bd8b3d9bbffb81d6b06aad849cf78ce9'], 'patches': ['protolite-2.3.0_use-c++17.patch'], + 'checksums': [ + {'protolite_2.3.0.tar.gz': '53ef24d51a8348f97bec39d254df3b97bd8b3d9bbffb81d6b06aad849cf78ce9'}, + {'protolite-2.3.0_use-c++17.patch': 'fb5084c55dfbabc6f3e778accf4553f5c84f2bb0ab0ae84b3538c866a829afa4'}, + ], }), ('jqr', '1.3.1', { 'checksums': ['e22461e75ff7e57fe502dc7d16c5e5fe9f8e4cbe042b5eadad06fc37394f9f36'], From dd68e3ab35702716aaf0ac12b1bf487c3b562b1a Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 14 Mar 2024 13:00:58 +0100 Subject: [PATCH 0977/1193] Update easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb get rid of hardcoded commit number for source Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb index 7d8366fe08f5..1f7645886530 100644 --- a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb @@ -33,7 +33,7 @@ exts_list = [ # download from commit to not depend on scvi-tools and get rid of restriction of scikit-learn version 'source_urls': ['https://github.com/theislab/scvelo/archive/'], 'sources': [{ - 'download_filename': 'ffe2cd3c437fd385f80fed9e6abc6dc3013eff82.tar.gz', + 'download_filename': '%s.tar.gz' % local_commit, 'filename': '%(name)s-%(version)s.tar.gz' }], 'checksums': ['55f476068a4b31df2181431977ebd279bd17931694eab23f1db7b7912e2a2c49'], From e4e49541f2d30b60cc326ba1f6a08c1c9a88017b Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 14 Mar 2024 13:37:38 +0100 Subject: [PATCH 0978/1193] add patches for minimus2 in AMOS-3.1.0 --- .../easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb | 14 +++++++++++--- .../AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch | 14 ++++++++++++++ ...0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch | 14 ++++++++++++++ 3 files changed, 39 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch create mode 100644 easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb index 0ff99e5dcfa0..d03ef4a7feb2 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb @@ -23,10 +23,18 @@ toolchainopts = {'pic': True, 'cstd': 'c++98'} source_urls = [SOURCEFORGE_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['AMOS-%(version)s_GCC-4.7.patch'] +patches = [ + 'AMOS-%(version)s_GCC-4.7.patch', + 'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch', + 'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch', +] checksums = [ - '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b', # amos-3.1.0.tar.gz - '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844', # AMOS-3.1.0_GCC-4.7.patch + {'amos-3.1.0.tar.gz': '2d9f50e39186ad3dde3d3b28cc265e8d632430657f40fc3978ce34ab1b3db43b'}, + {'AMOS-3.1.0_GCC-4.7.patch': '8633ff196568e208cc12932f25f46fa35f7e9a9e80e0bbf4288ae070dd7b8844'}, + {'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch': + '80379cee8e8c8228590af89d37ea3fdb734c7e0ebe5bb357eaf2af71d1399fc6'}, + {'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch': + 'ce1f3e5fb4d7c4337af241cfe776a46621d47094841c26ca34a06106754e266c'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch new file mode 100644 index 000000000000..1c31a0a98a08 --- /dev/null +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch @@ -0,0 +1,14 @@ +Replace deprecate NUCMER flag -maxmatch with --maxmatch (from MUMmer 4.0.0rc) +see https://github.com/sanger-pathogens/circlator/issues/121 and https://github.com/mummer4/mummer/issues/49 +diff -ru amos-3.1.0.orig/src/Pipeline/minimus2.acf amos-3.1.0/src/Pipeline/minimus2.acf +--- amos-3.1.0.orig/src/Pipeline/minimus2.acf 2011-07-25 01:27:26.000000000 +0200 ++++ amos-3.1.0/src/Pipeline/minimus2.acf 2024-03-13 17:03:35.981707768 +0100 +@@ -54,7 +54,7 @@ + 13: $(BINDIR)/dumpreads $(BANK) -m $(REFCOUNT) > $(QRYSEQ) + + ## Getting overlaps +-20: $(NUCMER) -maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX) ++20: $(NUCMER) --maxmatch -c $(OVERLAP) $(REFSEQ) $(QRYSEQ) -p $(PREFIX) + 21: $(SHOWCOORDS) -H -c -l -o -r -I $(MINID) $(ALIGN) | $(BINDIR)/nucmerAnnotate | egrep 'BEGIN|END|CONTAIN|IDENTITY' > $(COORDS) + 22: $(BINDIR)/nucmer2ovl -ignore $(MAXTRIM) -tab $(COORDS) | $(BINDIR)/sort2 > $(OVLTAB) + diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch new file mode 100644 index 000000000000..ae2d2811b032 --- /dev/null +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch @@ -0,0 +1,14 @@ +minimus2 needs delta-filter and show-coords but these were not set correctly like NUCMER +diff -ru amos-3.1.0.orig/src/Pipeline/Makefile.in amos-3.1.0/src/Pipeline/Makefile.in +--- amos-3.1.0.orig/src/Pipeline/Makefile.in 2011-08-05 05:08:07.000000000 +0200 ++++ amos-3.1.0/src/Pipeline/Makefile.in 2024-03-14 12:31:16.218067000 +0100 +@@ -477,7 +477,8 @@ + echo '#!$(bindir)/runAmos -C' > "$(DESTDIR)$(bindir)/$$b"; \ + sed -e 's|^BINDIR[ ]*=.*$$|BINDIR=$(bindir)|' \ + -e 's|^NUCMER[ ]*=.*$$|NUCMER=$(NUCMER)|' \ +- -e 's|^DELTAFILTER[ ]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \ ++ -e 's|^DELTAFILTER[ ]*=.*$$|DELTAFILTER=$(DELTAFILTER)|' \ ++ -e 's|^SHOWCOORDS[ ]*=.*$$|SHOWCOORDS=$(SHOWCOORDS)|' \ + "$(DESTDIR)$(bindir)/$$f" >> "$(DESTDIR)$(bindir)/$$b" \ + || exit 1; \ + ;; \ \ No newline at end of file From cb9d08666e88d9fec28815dac96db81c536c7e39 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 14 Mar 2024 13:43:58 +0100 Subject: [PATCH 0979/1193] Delete easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb --- .../p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb | 77 ------------------- 1 file changed, 77 deletions(-) delete mode 100644 easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb deleted file mode 100644 index 8f05d25d9c00..000000000000 --- a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-foss-2023a.eb +++ /dev/null @@ -1,77 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'pySCENIC' -version = '0.12.1' -local_commit = '31d51a1' - -homepage = 'https://github.com/aertslab/pySCENIC' -description = """pySCENIC is a lightning-fast python implementation of the SCENIC -pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables -biologists to infer transcription factors, gene regulatory networks and -cell types from single-cell RNA-seq data.""" - -toolchain = {'name': 'foss', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('PyYAML', '6.0'), - ('Arrow', '14.0.1'), - ('scikit-learn', '1.3.1'), - ('tqdm', '4.66.1'), - ('networkx', '3.1'), - ('dask', '2023.12.1'), - ('aiohttp', '3.8.5'), - ('dill', '0.3.7'), - ('loompy', '3.0.7'), - ('umap-learn', '0.5.5'), -] - -use_pip = True - -exts_list = [ - ('cytoolz', '0.12.3', { - 'checksums': ['4503dc59f4ced53a54643272c61dc305d1dbbfbd7d6bdf296948de9f34c3a282'], - }), - ('multiprocessing_on_dill', '3.5.0a4', { - 'checksums': ['d6d50c300ff4bd408bb71eb78725e60231039ee9b3d0d9bb7697b9d0e15045e7'], - }), - ('frozendict', '2.4.0', { - 'checksums': ['c26758198e403337933a92b01f417a8240c954f553e1d4b5e0f8e39d9c8e3f0a'], - }), - ('arboreto', '0.1.6', { - 'source_urls': ['https://github.com/aertslab/arboreto/archive/refs/tags/'], - 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['f94c0bc084ca61422e8b74ecdb80585a45b168ac682f18dd3c52c9097ee29caa'], - }), - ('boltons', '23.1.1', { - 'checksums': ['d2cb2fa83cf2ebe791be1e284183e8a43a1031355156a968f8e0a333ad2448fc'], - }), - ('interlap', '0.2.7', { - 'checksums': ['31e4f30c54b067c4939049f5d8131ae5e2fa682ec71aa56f89c0e5b900806ec9'], - }), - ('ctxcore', '0.2.0', { - 'sources': ['ctxcore-0.2.0-py3-none-any.whl'], - 'checksums': ['b90570377e26280c4861ebad1f4cee2fe598167c5d4bd12c1b713f03c9682627'], - }), - ('pyscenic', version, { - # download from commit to get fix for numpy error - # https://github.com/aertslab/pySCENIC/issues/518 - 'source_urls': ['https://github.com/aertslab/pySCENIC/archive/'], - 'sources': [{ - 'download_filename': '31d51a1625f12fb3c6e92bc48ecc9d401524c22a.tar.gz', - 'filename': '%%(name)s-%%(version)s-%s.tar.gz' % local_commit - }], - 'checksums': ['9dac1aa1672e310838ab47838206c075f2a2af2eefe6d3b7d56b4492d42fcf47'], - }), -] - -sanity_check_paths = { - 'files': ['bin/pyscenic'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["pyscenic --help"] - -sanity_pip_check = True - -moduleclass = 'bio' From 0b8fbeb155b180976d0be9a7889c79a253175712 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 14 Mar 2024 15:17:20 +0100 Subject: [PATCH 0980/1193] New setups for GPAW. --- .../g/GPAW-setups/GPAW-setups-24.1.0.eb | 27 +++++++++++++++++++ .../g/GPAW/GPAW-24.1.0-foss-2023a.eb | 2 +- .../g/GPAW/GPAW-24.1.0-intel-2023a.eb | 2 +- 3 files changed, 29 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.1.0.eb diff --git a/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.1.0.eb b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.1.0.eb new file mode 100644 index 000000000000..5736c4abcecd --- /dev/null +++ b/easybuild/easyconfigs/g/GPAW-setups/GPAW-setups-24.1.0.eb @@ -0,0 +1,27 @@ +easyblock = 'Tarball' + +name = 'GPAW-setups' +version = '24.1.0' + +homepage = 'https://wiki.fysik.dtu.dk/gpaw/' +description = """PAW setups for the GPAW Density Functional Theory package. +Users can install setups manually using 'gpaw install-data' or use setups from this package. +The versions of GPAW and GPAW-setups can be intermixed. + +Compared to version 0.9.20000, version 24.1.0 contains an new improved Cr setup with 14 electrons, +which can be manually selected. Otherwise no changes are made, so no results will change. +""" + +toolchain = SYSTEM +source_urls = ['https://wiki.fysik.dtu.dk/gpaw-files/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['314d43168f7b57a2d942855d3d5ad21da9ef74e772d37343d416305113a95c23'] + +modextrapaths = {'GPAW_SETUP_PATH': ''} + +moduleclass = 'chem' + +sanity_check_paths = { + 'files': ['H.LDA.gz'], + 'dirs': [] +} diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb index 9c555311a5b4..f8e05080924c 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-foss-2023a.eb @@ -31,7 +31,7 @@ dependencies = [ ('libvdwxc', '0.4.0'), ('ELPA', '2023.05.001'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '24.1.0', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb index 70ef81625bdb..b71f0cbdd6e0 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-24.1.0-intel-2023a.eb @@ -30,7 +30,7 @@ dependencies = [ ('libxc', '6.2.2'), ('ELPA', '2023.05.001'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '24.1.0', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_intel.py' From a7b1140e4bdbdc0f8170f1b6ba9ea68461a4fe06 Mon Sep 17 00:00:00 2001 From: Lara Ramona Peeters <49882639+laraPPr@users.noreply.github.com> Date: Thu, 14 Mar 2024 15:22:07 +0100 Subject: [PATCH 0981/1193] Update easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch Co-authored-by: Kenneth Hoste --- .../AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch index ae2d2811b032..71a5515bc006 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch @@ -1,4 +1,5 @@ minimus2 needs delta-filter and show-coords but these were not set correctly like NUCMER +author: Lara Peeters (HPC-UGent) diff -ru amos-3.1.0.orig/src/Pipeline/Makefile.in amos-3.1.0/src/Pipeline/Makefile.in --- amos-3.1.0.orig/src/Pipeline/Makefile.in 2011-08-05 05:08:07.000000000 +0200 +++ amos-3.1.0/src/Pipeline/Makefile.in 2024-03-14 12:31:16.218067000 +0100 From d1d6655122f5a7b1024f198a78943639fa0394bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 15:25:55 +0100 Subject: [PATCH 0982/1193] add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 --- .../Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb index ac77e85d5a0e..2ee75d5ffc31 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.38.0-GCCcore-13.2.0.eb @@ -674,10 +674,14 @@ exts_list = [ 'checksums': ['aa12d1a4c0ac260b94d448fa01feba242a8a85cb6cbfdc66432e3b5b468add96'], }), ('Net::SSLeay', '1.92', { + 'patches': ['Net-SSLeay-1.92_fix.patch'], 'preconfigopts': "export OPENSSL_PREFIX=$EBROOTOPENSSL && ", 'source_tmpl': 'Net-SSLeay-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHRISN'], - 'checksums': ['47c2f2b300f2e7162d71d699f633dd6a35b0625a00cbda8c50ac01144a9396a9'], + 'checksums': [ + {'Net-SSLeay-1.92.tar.gz': '47c2f2b300f2e7162d71d699f633dd6a35b0625a00cbda8c50ac01144a9396a9'}, + {'Net-SSLeay-1.92_fix.patch': '37790b10c5551bce92bc4bd7c98a92b0058fc16604272c7459a63096b52a8d1c'}, + ], }), ('IO::Socket::SSL', '2.083', { 'source_tmpl': 'IO-Socket-SSL-%(version)s.tar.gz', From 8b035c34516e18c59f9b7249dbb932b61e877c90 Mon Sep 17 00:00:00 2001 From: Jakob Schiotz Date: Thu, 14 Mar 2024 15:41:11 +0100 Subject: [PATCH 0983/1193] ALso update GPAW-23.9.1-foss-2023a.eb to keep version consistence required by test suite. --- easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb index 25eca6c86b9a..60828cc4f313 100644 --- a/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GPAW/GPAW-23.9.1-foss-2023a.eb @@ -31,7 +31,7 @@ dependencies = [ ('libvdwxc', '0.4.0'), ('ELPA', '2023.05.001'), ('PyYAML', '6.0'), - ('GPAW-setups', '0.9.20000', '', SYSTEM), + ('GPAW-setups', '24.1.0', '', SYSTEM), ] prebuildopts = 'GPAW_CONFIG=doc/platforms/Linux/EasyBuild/config_foss.py' From 7033acead4114c72d327f2e8077a8d4d5954bb73 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Thu, 14 Mar 2024 15:53:36 +0100 Subject: [PATCH 0984/1193] update checksums --- easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb | 2 +- .../AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb index d03ef4a7feb2..1f2620e9f2cc 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0-foss-2023a.eb @@ -34,7 +34,7 @@ checksums = [ {'AMOS-3.1.0_fix_deprecated_maxmatch-flag.patch': '80379cee8e8c8228590af89d37ea3fdb734c7e0ebe5bb357eaf2af71d1399fc6'}, {'AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch': - 'ce1f3e5fb4d7c4337af241cfe776a46621d47094841c26ca34a06106754e266c'}, + 'e291d87b8cd27752474ee0e1f3acb44f9657cac50d5d6dcceca0efc6436f1fe1'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch index 71a5515bc006..82238b9a089f 100644 --- a/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch +++ b/easybuild/easyconfigs/a/AMOS/AMOS-3.1.0_link_correctly_to_DELTAFILER_SHOWCOORDS.patch @@ -12,4 +12,4 @@ diff -ru amos-3.1.0.orig/src/Pipeline/Makefile.in amos-3.1.0/src/Pipeline/Makefi + -e 's|^SHOWCOORDS[ ]*=.*$$|SHOWCOORDS=$(SHOWCOORDS)|' \ "$(DESTDIR)$(bindir)/$$f" >> "$(DESTDIR)$(bindir)/$$b" \ || exit 1; \ - ;; \ \ No newline at end of file + ;; \ From faf0de42719cf7333c113a7b6901c66d871831ff Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 17:15:46 +0100 Subject: [PATCH 0985/1193] adding easyconfigs: DIAMOND-2.1.9-GCC-13.2.0.eb --- .../d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb new file mode 100644 index 000000000000..754d1f6214be --- /dev/null +++ b/easybuild/easyconfigs/d/DIAMOND/DIAMOND-2.1.9-GCC-13.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'DIAMOND' +version = '2.1.9' + +homepage = 'https://github.com/bbuchfink/diamond' +description = "Accelerated BLAST compatible local sequence aligner" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +github_account = 'bbuchfink' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['4cde9df78c63e8aef9df1e3265cd06a93ce1b047d6dba513a1437719b70e9d88'] + +builddependencies = [ + ('CMake', '3.27.6'), +] + +dependencies = [ + ('zlib', '1.2.13'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} +sanity_check_commands = ["%(namelower)s help"] + +moduleclass = 'bio' From b47e3fd17d09713f1fe29a5dd8d6d65401c0efc3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 17:42:05 +0100 Subject: [PATCH 0986/1193] adding easyconfigs: SCENIC-1.3.0-foss-2023a-R-4.3.2.eb --- .../SCENIC/SCENIC-1.3.0-foss-2023a-R-4.3.2.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCENIC/SCENIC-1.3.0-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/s/SCENIC/SCENIC-1.3.0-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/s/SCENIC/SCENIC-1.3.0-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..8200a80dba1b --- /dev/null +++ b/easybuild/easyconfigs/s/SCENIC/SCENIC-1.3.0-foss-2023a-R-4.3.2.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'SCENIC' +version = '1.3.0' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://scenic.aertslab.org' +description = "SCENIC Suite is a set of tools to study and decipher gene regulation." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/aertslab/SCENIC/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['dcae14b1008cb11a34b03cd7c0830e2f00567bd073ff27da11d57501360965f8'] + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['SCENIC'], +} + +moduleclass = 'geo' From 7c1626b0a788908ef8ee0a10379352fd121dd8f8 Mon Sep 17 00:00:00 2001 From: Craig Gross Date: Thu, 14 Mar 2024 12:42:06 -0400 Subject: [PATCH 0987/1193] adding easyconfigs: Vim-9.1.0004-GCCcore-12.3.0.eb --- .../v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..d0ee82a07da0 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-9.1.0004-GCCcore-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'Vim' +version = "9.1.0004" + +homepage = 'http://www.vim.org' +description = """ Vim is an advanced text editor that seeks to provide the power + of the de-facto Unix editor 'Vi', with a more complete feature set. """ + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['b930d02549e246a220d6ee95a4ef4938e56881e33b82e992e9439ac0f9fc7c13'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.3'), + ('Perl', '5.36.1'), + ('PCRE', '8.45'), +] + +configopts = "--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes" + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'bin/vimtutor', 'bin/xxd'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['%(namelower)s --version'] + +moduleclass = 'tools' From 68c2a6fee265c085142cd7611f28b4e4b7545856 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 17:59:08 +0100 Subject: [PATCH 0988/1193] adding easyconfigs: MetaDecoder-1.0.19-foss-2023b.eb --- .../MetaDecoder-1.0.19-foss-2023b.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb diff --git a/easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb b/easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb new file mode 100644 index 000000000000..9ee68b714c89 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaDecoder/MetaDecoder-1.0.19-foss-2023b.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'MetaDecoder' +version = '1.0.19' + +homepage = 'https://github.com/liu-congcong/MetaDecoder' +description = "An algorithm for clustering metagenomic sequences" + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # threadpoolctl + ('SciPy-bundle', '2023.11'), + ('scikit-learn', '1.4.0'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/liu-congcong/MetaDecoder/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['8b88813a97787bc56baa3100a576a9e56a0de02811c573573a2fffeb7e80623e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From b8cd37b0cc54c0a40d72a7e04cbd4b7a323ea4d6 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 14 Mar 2024 18:14:52 +0100 Subject: [PATCH 0989/1193] get v0.3.1 and patch it by latter commits --- .../s/scVelo/scVelo-0.3.1-foss-2023a.eb | 17 +- .../s/scVelo/scVelo-0.3.1_dep-fix.patch | 216 ++++++++++++++++++ 2 files changed, 223 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/s/scVelo/scVelo-0.3.1_dep-fix.patch diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb index 1f7645886530..b799671e0f03 100644 --- a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1-foss-2023a.eb @@ -2,7 +2,6 @@ easyblock = 'PythonBundle' name = 'scVelo' version = '0.3.1' -local_commit = 'ffe2cd3' homepage = "https://scvelo.org" description = """scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using @@ -28,15 +27,13 @@ use_pip = True sanity_pip_check = True exts_list = [ - (name, version, { - 'modulename': 'scvelo', - # download from commit to not depend on scvi-tools and get rid of restriction of scikit-learn version - 'source_urls': ['https://github.com/theislab/scvelo/archive/'], - 'sources': [{ - 'download_filename': '%s.tar.gz' % local_commit, - 'filename': '%(name)s-%(version)s.tar.gz' - }], - 'checksums': ['55f476068a4b31df2181431977ebd279bd17931694eab23f1db7b7912e2a2c49'], + ('scvelo', version, { + 'patches': ['scVelo-0.3.1_dep-fix.patch'], + 'preinstallopts': "sed -i 's/scikit-learn>=0.21.2, <1.2.0/scikit-learn>=0.21.2/' pyproject.toml && ", + 'checksums': [ + {'scvelo-0.3.1.tar.gz': '3a41a73b29e091268c40f08dc57a63eab5dfc2bd8a57e564cf1a6aca5e4d5d22'}, + {'scVelo-0.3.1_dep-fix.patch': 'c8d1b41518f4b7b6528bcb00861287d9f1d96d419a4b3ce98599ea1d8cb59503'}, + ], }), ] diff --git a/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1_dep-fix.patch b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1_dep-fix.patch new file mode 100644 index 000000000000..10c26136ce7c --- /dev/null +++ b/easybuild/easyconfigs/s/scVelo/scVelo-0.3.1_dep-fix.patch @@ -0,0 +1,216 @@ +Move scvi-tools to optional-dependencies and remove `torch` dependency + +From b8d80f7934a305888a61417f7aa22de2e426b81a Mon Sep 17 00:00:00 2001 +From: Michal Klein <46717574+michalk8@users.noreply.github.com> +Date: Wed, 7 Feb 2024 22:15:53 +0100 +Subject: [PATCH 1/4] Remove hard `scvi-tools` dependency + +--- + .github/workflows/ci.yml | 2 +- + pyproject.toml | 7 +++++-- + scvelo/tools/__init__.py | 12 ++++++++++-- + 3 files changed, 16 insertions(+), 5 deletions(-) + +diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml +index fd341688..f8058c62 100644 +--- a/.github/workflows/ci.yml ++++ b/.github/workflows/ci.yml +@@ -45,7 +45,7 @@ jobs: + fail-fast: false + matrix: + os: [ubuntu-latest] +- python-version: [3.9, "3.10"] ++ python-version: ["3.9", "3.10"] + steps: + - uses: actions/checkout@v2 + - name: Set up Python ${{ matrix.python-version }} +diff --git a/pyproject.toml b/pyproject.toml +index a0184458..5f747c2c 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -50,11 +50,13 @@ dependencies = [ + "pandas>=1.1.1, !=1.4.0", + "scipy>=1.4.1", + "scikit-learn>=0.21.2, <1.2.0", +- "scvi-tools>=0.20.1", + "matplotlib>=3.3.0" + ] + + [project.optional-dependencies] ++vi = [ ++ "scvi-tools>=0.20.1", ++] + louvain = [ + "igraph", + "louvain" +@@ -78,7 +80,8 @@ dev = [ + "pybind11", + "pytest-cov", + "igraph", +- "setuptools_scm" ++ "scvi-tools>=0.20.1", ++ "setuptools_scm", + ] + docs = [ + # Just until rtd.org understands pyproject.toml +diff --git a/scvelo/tools/__init__.py b/scvelo/tools/__init__.py +index b2e3e126..3a40aff1 100644 +--- a/scvelo/tools/__init__.py ++++ b/scvelo/tools/__init__.py +@@ -1,3 +1,5 @@ ++import contextlib ++ + from scanpy.tools import diffmap, dpt, louvain, tsne, umap + + from ._em_model import ExpectationMaximizationModel +@@ -11,7 +13,6 @@ + recover_latent_time, + ) + from ._steady_state_model import SecondOrderSteadyStateModel, SteadyStateModel +-from ._vi_model import VELOVI + from .paga import paga + from .rank_velocity_genes import rank_velocity_genes, velocity_clusters + from .score_genes_cell_cycle import score_genes_cell_cycle +@@ -23,6 +24,10 @@ + from .velocity_graph import velocity_graph + from .velocity_pseudotime import velocity_map, velocity_pseudotime + ++with contextlib.suppress(ImportError): ++ from ._vi_model import VELOVI ++ ++ + __all__ = [ + "align_dynamics", + "differential_kinetic_test", +@@ -54,5 +59,8 @@ + "SteadyStateModel", + "SecondOrderSteadyStateModel", + "ExpectationMaximizationModel", +- "VELOVI", + ] ++if "VELOVI" in locals(): ++ __all__ += ["VELOVI"] ++ ++del contextlib + +From 12e91cf0015df8917669e8242afd38c9b7291f82 Mon Sep 17 00:00:00 2001 +From: Michal Klein <46717574+michalk8@users.noreply.github.com> +Date: Wed, 7 Feb 2024 22:37:00 +0100 +Subject: [PATCH 2/4] Skip VELOVI tests if `scvi-tools` not installed + +--- + pyproject.toml | 1 - + tests/tools/test_vi_model.py | 12 ++++++++++-- + 2 files changed, 10 insertions(+), 3 deletions(-) + +diff --git a/pyproject.toml b/pyproject.toml +index 5f747c2c..71cd881b 100644 +--- a/pyproject.toml ++++ b/pyproject.toml +@@ -80,7 +80,6 @@ dev = [ + "pybind11", + "pytest-cov", + "igraph", +- "scvi-tools>=0.20.1", + "setuptools_scm", + ] + docs = [ +diff --git a/tests/tools/test_vi_model.py b/tests/tools/test_vi_model.py +index 15592072..241896d8 100644 +--- a/tests/tools/test_vi_model.py ++++ b/tests/tools/test_vi_model.py +@@ -1,7 +1,15 @@ +-from scvi.data import synthetic_iid ++# isort: skip_file ++import pytest ++import contextlib + + import scvelo as scv +-from scvelo.tools import VELOVI ++ ++with contextlib.suppress(ImportError): ++ from scvi.data import synthetic_iid ++ from scvelo.tools import VELOVI ++ ++ ++_ = pytest.importorskip("scvi") + + + def test_preprocess_data(): + +From cfd4fa096e8b25161fc71467d02bf4036b0f5e75 Mon Sep 17 00:00:00 2001 +From: Michal Klein <46717574+michalk8@users.noreply.github.com> +Date: Wed, 7 Feb 2024 22:43:16 +0100 +Subject: [PATCH 3/4] Remove `torch` dependency + +--- + scvelo/tools/_core.py | 4 ---- + scvelo/tools/_vi_module.py | 4 +++- + 2 files changed, 3 insertions(+), 5 deletions(-) + +diff --git a/scvelo/tools/_core.py b/scvelo/tools/_core.py +index df352bc0..92b18212 100644 +--- a/scvelo/tools/_core.py ++++ b/scvelo/tools/_core.py +@@ -1,8 +1,6 @@ + from abc import abstractmethod + from typing import NamedTuple + +-import torch +- + from anndata import AnnData + + +@@ -13,8 +11,6 @@ class _REGISTRY_KEYS_NT(NamedTuple): + + REGISTRY_KEYS = _REGISTRY_KEYS_NT() + +-DEFAULT_ACTIVATION_FUNCTION = torch.nn.Softplus() +- + + class BaseInference: + """Base Inference class for all velocity methods.""" +diff --git a/scvelo/tools/_vi_module.py b/scvelo/tools/_vi_module.py +index 4c5ecc81..c211da75 100644 +--- a/scvelo/tools/_vi_module.py ++++ b/scvelo/tools/_vi_module.py +@@ -11,7 +11,9 @@ + from scvi.module.base import auto_move_data, BaseModuleClass, LossOutput + from scvi.nn import Encoder, FCLayers + +-from ._core import DEFAULT_ACTIVATION_FUNCTION, REGISTRY_KEYS ++from ._core import REGISTRY_KEYS ++ ++DEFAULT_ACTIVATION_FUNCTION = torch.nn.Softplus() + + torch.backends.cudnn.benchmark = True + + +From e03ed96918361f3d124ee178c4bda1cfee0e83cb Mon Sep 17 00:00:00 2001 +From: Michal Klein <46717574+michalk8@users.noreply.github.com> +Date: Wed, 7 Feb 2024 22:51:35 +0100 +Subject: [PATCH 4/4] Remove unused `skip_file` + +--- + tests/tools/test_vi_model.py | 5 +++-- + 1 file changed, 3 insertions(+), 2 deletions(-) + +diff --git a/tests/tools/test_vi_model.py b/tests/tools/test_vi_model.py +index 241896d8..d8ecc0c8 100644 +--- a/tests/tools/test_vi_model.py ++++ b/tests/tools/test_vi_model.py +@@ -1,11 +1,12 @@ +-# isort: skip_file +-import pytest + import contextlib + ++import pytest ++ + import scvelo as scv + + with contextlib.suppress(ImportError): + from scvi.data import synthetic_iid ++ + from scvelo.tools import VELOVI + + \ No newline at end of file From bc0791703d5ad82cb915caf4936bf4b124c0877a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 18:39:07 +0100 Subject: [PATCH 0990/1193] adding easyconfigs: hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb --- .../hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb new file mode 100644 index 000000000000..13b65d8124ea --- /dev/null +++ b/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb @@ -0,0 +1,47 @@ +easyblock = 'Bundle' + +name = 'hdWGCNA' +version = '0.3.00' +versionsuffix = '-R-%(rver)s' +local_biocver = '3.16' + +homepage = 'https://github.com/vibscc/DALI' +description = "R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('R-bundle-Bioconductor', '3.18', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = { + 'sources': ['%(name)s_%(version)s.tar.gz'], + 'source_urls': [ + 'https://cran.r-project.org/src/contrib/Archive/%(name)s', # package archive + 'https://cran.r-project.org/src/contrib/', # current version of packages + 'https://cran.freestatistics.org/src/contrib', # mirror alternative for current packages + ], +} + +exts_list = [ + ('tester', '0.1.7', { + 'checksums': ['b9c645119c21c69450f3d366c911ed92ac7c14ef61652fd676a38fb9d420b5f4'], + }), + (name, version, { + 'source_urls': ['https://github.com/smorabit/hdWGCNA/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5ef9980f6d25b41af17ebad76722766db72fb8162d5ae7af4565893d26c9ed1f'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From ebaac0e2983be76f7fbb8ce38f2f48168f62666f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 20:09:46 +0100 Subject: [PATCH 0991/1193] fix homepage + description for hdWGCNA Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb index 13b65d8124ea..fbee4bfaee9d 100644 --- a/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb +++ b/easybuild/easyconfigs/h/hdWGCNA/hdWGCNA-0.3.00-foss-2023a-R-4.3.2.eb @@ -5,8 +5,12 @@ version = '0.3.00' versionsuffix = '-R-%(rver)s' local_biocver = '3.16' -homepage = 'https://github.com/vibscc/DALI' -description = "R-package for the analysis of single-cell TCR/BCR data in the Seurat ecosystem" +homepage = 'https://smorabit.github.io/hdWGCNA/' +description = """hdWGCNA is an R package for performing weighted gene co-expression network analysis (WGCNA) in high + dimensional transcriptomics data such as single-cell RNA-seq or spatial transcriptomics. hdWGCNA is highly modular + and can construct context-specific co-expression networks across cellular and spatial hierarchies. hdWGNCA identifies + modules of highly co-expressed genes and provides context for these modules via statistical testing and biological + knowledge sources. hdWGCNA uses datasets formatted as Seurat objects.""" toolchain = {'name': 'foss', 'version': '2023a'} From 6515b44cd84a20fe7876cb4bdaf3c0080e688566 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 14 Mar 2024 20:59:56 +0100 Subject: [PATCH 0992/1193] adding easyconfigs: PyTables-3.9.2-foss-2023b.eb, Blosc-1.21.5-GCCcore-13.2.0.eb, Blosc2-2.13.2-GCCcore-13.2.0.eb, py-cpuinfo-9.0.0-GCCcore-13.2.0.eb and patches: PyTables-3.9.2_fix-find-blosc2-dep.patch --- .../b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb | 28 +++++++ .../b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb | 31 ++++++++ .../p/PyTables/PyTables-3.9.2-foss-2023b.eb | 76 +++++++++++++++++++ .../PyTables-3.9.2_fix-find-blosc2-dep.patch | 20 +++++ .../py-cpuinfo-9.0.0-GCCcore-13.2.0.eb | 39 ++++++++++ 5 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb create mode 100644 easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-find-blosc2-dep.patch create mode 100644 easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..4dc70d8715f4 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.5-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.5' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['32e61961bbf81ffea6ff30e9d70fca36c86178afd3e3cfa13376adec8c687509'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..9e1b09495760 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.13.2-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Blosc2' +version = '2.13.2' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2adcd9615f138d1bb16dc27feadab1bb1eab01d77e5e2323d14ad4ca8c3ca21'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb new file mode 100644 index 000000000000..51b07f31b272 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2-foss-2023b.eb @@ -0,0 +1,76 @@ +# http://www.pytables.org/usersguide/installation.html +# updated: Denis Kristak (INUITS) + +easyblock = 'PythonBundle' + +name = 'PyTables' +version = '3.9.2' + +homepage = 'https://www.pytables.org' +description = """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope + with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the + NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical + parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browsing, + processing and searching very large amounts of data. One important feature of PyTables is that it optimizes memory and + disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions + such as relational or object oriented databases.""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # provides numexpr + ('HDF5', '1.14.3'), + ('LZO', '2.10'), + ('Blosc', '1.21.5'), + ('Blosc2', '2.13.2'), + ('py-cpuinfo', '9.0.0'), +] + +use_pip = True + +exts_list = [ + ('ndindex', '1.8', { + 'checksums': ['5fc87ebc784605f01dd5367374cb40e8da8f2c30988968990066c5098a7eebe8'], + }), + # need to align version of blosc2 Python package with version of C Blosc2 used, + # see https://github.com/Blosc/python-blosc2/blob/main/RELEASE_NOTES.md + ('blosc2', '2.5.1', { + 'checksums': ['47d5df50e7286edf81e629ece35f87f13f55c13c5e8545832188c420c75d1659'], + 'preinstallopts': """sed -i 's/version=/cmake_args=["-DUSE_SYSTEM_BLOSC2=YES"], version=/g' setup.py && """, + }), + ('tables', version, { + 'patches': [ + 'PyTables-3.8.0_fix-libs.patch', + 'PyTables-3.9.2_fix-find-blosc2-dep.patch', + ], + 'checksums': [ + {'tables-3.9.2.tar.gz': 'd470263c2e50c4b7c8635a0d99ac1ff2f9e704c24d71e5fa33c4529e7d0ad9c3'}, + {'PyTables-3.8.0_fix-libs.patch': '7a1e6fa1f9169e52293e2b433a4302fa13c5d31e7709cd4fe0e087199b9e3f8a'}, + {'PyTables-3.9.2_fix-find-blosc2-dep.patch': + 'e2149f43da12d9ba26cca4c838f6e8a4694adab75c0f055b186674a017e41a55'}, + ], + }), +] + +local_bins = ['pt2to3', 'ptdump', 'ptrepack', 'pttree'] +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_bins], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'tables'} + +sanity_check_commands = ["%s --help" % x for x in local_bins] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-find-blosc2-dep.patch b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-find-blosc2-dep.patch new file mode 100644 index 000000000000..e832e65b278d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTables/PyTables-3.9.2_fix-find-blosc2-dep.patch @@ -0,0 +1,20 @@ +determine installation prefix of Blosc2 dependency via $EBROOTBLOSC2, if defined, +since mechanism to locate the library via blosc2-*.dist-info/RECORD doesn't work if blosc2 was not installed +with vendored c-blosc2 library; +author: Kenneth Hoste (HPC-UGent) +--- tables-3.9.2/setup.py.orig 2024-03-14 19:17:54.100800849 +0100 ++++ tables-3.9.2/setup.py 2024-03-14 19:22:04.099371064 +0100 +@@ -97,6 +97,13 @@ + + def get_blosc2_directories(): + """Get Blosc2 directories for the C library""" ++ blosc2_root = os.getenv('EBROOTBLOSC2') ++ if blosc2_root: ++ library_path = Path(os.path.join(blosc2_root, 'lib')) ++ include_path = Path(os.path.join(blosc2_root, 'include')) ++ runtime_path = None ++ return include_path, library_path, runtime_path ++ + try: + import blosc2 + except ModuleNotFoundError: diff --git a/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..4ffea66d7cb5 --- /dev/null +++ b/easybuild/easyconfigs/p/py-cpuinfo/py-cpuinfo-9.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonPackage' + +name = 'py-cpuinfo' +version = '9.0.0' + +homepage = 'https://github.com/workhorsy/py-cpuinfo' +description = "py-cpuinfo gets CPU info with pure Python." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3cdbbf3fac90dc6f118bfd64384f309edeadd902d7c8fb17f02ffa1fc3f49690'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/cpuinfo'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cpuinfo", + "python -m cpuinfo", +] + +options = {'modulename': 'cpuinfo'} + +sanity_pip_check = True + +moduleclass = 'tools' From 39c76d13fbc0aa4f84c5132ea4e016b6d335980c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 15 Mar 2024 14:12:55 +0100 Subject: [PATCH 0993/1193] disable NVPTX on riscv64 --- easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index 12f599fdd8fd..558e56915d0c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -64,7 +64,8 @@ builddependencies = [ languages = ['c', 'c++', 'fortran'] withisl = True -withnvptx = True +if ARCH != 'riscv64': + withnvptx = True # Perl is only required when building with NVPTX support if withnvptx: From 9c0f615675c2c2ad58feb20f4612fa4b94628c4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 15 Mar 2024 14:26:20 +0100 Subject: [PATCH 0994/1193] always set withnvptx --- easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index 558e56915d0c..f813c429dc06 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -64,7 +64,9 @@ builddependencies = [ languages = ['c', 'c++', 'fortran'] withisl = True -if ARCH != 'riscv64': +if ARCH == 'riscv64': + withnvptx = False +else: withnvptx = True # Perl is only required when building with NVPTX support From a341ddea90137f1f69115fb1240319f744a2fd5c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Fri, 15 Mar 2024 17:44:24 +0100 Subject: [PATCH 0995/1193] Change foss to GCCcore in occt --- .../o/occt/occt-7.8.0-GCCcore-12.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..f1c92fb6c6bb --- /dev/null +++ b/easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'occt' +version = '7.8.0' + +homepage = 'https://www.opencascade.com/' +description = """Open CASCADE Technology (OCCT) is an object-oriented C++ +class library designed for rapid production of sophisticated domain-specific +CAD/CAM/CAE applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Open-Cascade-SAS/OCCT/archive/refs/tags'] +sources = ['V7_8_0.tar.gz'] +checksums = ['096cd0f268fa9f6a50818e1d628ac92ecf87e10fd72187e2e8d6be57dfe12530'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('Doxygen', '1.9.7'), +] +dependencies = [ + ('Mesa', '23.1.4'), + ('freetype', '2.13.0'), + ('Tcl', '8.6.13'), + ('Tk', '8.6.13'), + ('FreeImage', '3.18.0'), + ('tbb', '2021.11.0'), +] + + +separate_build_dir = True + +configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE " +configopts += "-D3RDPARTY_TBB_DIR=$EBROOTTBB " +configopts += "-D3RDPARTY_TCL_DIR=$EBROOTTCL " +configopts += "-D3RDPARTY_TK_DIR=$EBROOTTK " +configopts += "-D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " + +sanity_check_paths = { + 'files': ['bin/DRAWEXE', 'bin/env.sh'], + 'dirs': ['lib/cmake/opencascade'], +} + +sanity_check_commands = ['DRAWEXE -h'] + +moduleclass = 'cae' From a2382f83a4436c7544716d7473200512d6490038 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Fri, 15 Mar 2024 19:31:55 +0100 Subject: [PATCH 0996/1193] Update occt-7.8.0-GCCcore-12.3.0.eb Add binutils to builddpendences --- easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb index f1c92fb6c6bb..01121a9e9c0a 100644 --- a/easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/o/occt/occt-7.8.0-GCCcore-12.3.0.eb @@ -17,6 +17,7 @@ checksums = ['096cd0f268fa9f6a50818e1d628ac92ecf87e10fd72187e2e8d6be57dfe12530'] builddependencies = [ ('CMake', '3.26.3'), ('Doxygen', '1.9.7'), + ('binutils', '2.40'), ] dependencies = [ ('Mesa', '23.1.4'), From cfe0db33443119227141f03b4647647c1dcce243 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Fri, 15 Mar 2024 19:34:18 +0100 Subject: [PATCH 0997/1193] Delete easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb --- .../o/occt/occt-7.8.0-foss-2023a.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb b/easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb deleted file mode 100644 index b9c352a4d052..000000000000 --- a/easybuild/easyconfigs/o/occt/occt-7.8.0-foss-2023a.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'occt' -version = '7.8.0' - -homepage = 'https://www.opencascade.com/' -description = """Open CASCADE Technology (OCCT) is an object-oriented C++ -class library designed for rapid production of sophisticated domain-specific -CAD/CAM/CAE applications.""" - -toolchain = {'name': 'foss', 'version': '2023a'} -toolchainopts = {'usempi': True} - -source_urls = ['https://github.com/Open-Cascade-SAS/OCCT/archive/refs/tags'] -sources = ['V7_8_0.tar.gz'] -checksums = ['096cd0f268fa9f6a50818e1d628ac92ecf87e10fd72187e2e8d6be57dfe12530'] - -builddependencies = [ - ('CMake', '3.26.3'), - ('Doxygen', '1.9.7'), -] -dependencies = [ - ('Mesa', '23.1.4'), - ('freetype', '2.13.0'), - ('Tcl', '8.6.13'), - ('Tk', '8.6.13'), - ('FreeImage', '3.18.0'), - ('tbb', '2021.11.0'), -] - - -separate_build_dir = True - -configopts = "-DUSE_FREEIMAGE=ON -D3RDPARTY_FREEIMAGE_DIR=$EBROOTFREEIMAGE " -configopts += "-D3RDPARTY_TBB_DIR=$EBROOTTBB " -configopts += "-D3RDPARTY_TCL_DIR=$EBROOTTCL " -configopts += "-D3RDPARTY_TK_DIR=$EBROOTTK " -configopts += "-D3RDPARTY_FREETYPE_DIR=$EBROOTFREETYPE " - -sanity_check_paths = { - 'files': ['bin/DRAWEXE', 'bin/env.sh'], - 'dirs': ['lib/cmake/opencascade'], -} - -sanity_check_commands = ['DRAWEXE -h'] - -moduleclass = 'cae' From 2bb21000e659c6a8959f525ef7beee62ba11960f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 15 Mar 2024 20:38:17 +0100 Subject: [PATCH 0998/1193] adding easyconfigs: ipympl-0.9.3-foss-2023a.eb --- .../i/ipympl/ipympl-0.9.3-foss-2023a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2023a.eb diff --git a/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2023a.eb b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2023a.eb new file mode 100644 index 000000000000..e3b6c4b7437e --- /dev/null +++ b/easybuild/easyconfigs/i/ipympl/ipympl-0.9.3-foss-2023a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'ipympl' +version = '0.9.3' + +homepage = 'https://matplotlib.org/ipympl' +description = """Leveraging the Jupyter interactive widgets framework, ipympl enables the +interactive features of matplotlib in the Jupyter notebook and in JupyterLab. +Besides, the figure canvas element is a proper Jupyter interactive widget which +can be positioned in interactive widget layouts. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('JupyterLab', '4.0.5'), + ('matplotlib', '3.7.2'), + ('Pillow', '10.0.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['d113cd55891bafe9b27ef99b6dd111a87beb6bb2ae550c404292272103be8013'], + }), +] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'tools' From 385cc5ed7fdb18d35b60b214b6db78c014f3814f Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 15 Mar 2024 17:14:35 -0700 Subject: [PATCH 0999/1193] update version and toolchain --- .../g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..8bba0bbff567 --- /dev/null +++ b/easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'GLFW' +version = '3.4' + +homepage = 'https://www.glfw.org' +description = """GLFW is an Open Source, multi-platform library for OpenGL, +OpenGL ES and Vulkan development on the desktop""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['c038d34200234d071fae9345bc455e4a8f2f544ab60150765d7704e08f3dac01'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] +dependencies = [ + ('Wayland', '1.22.0'), + ('X11', '20221110'), +] + +# build both static and shared libraries +configopts = [ + '-DBUILD_SHARED_LIBS=OFF', + '-DBUILD_SHARED_LIBS=ON', +] + + +sanity_check_paths = { + 'files': ['include/%(name)s/glfw3.h', 'include/%(name)s/glfw3native.h'] + + ['lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT], + 'dirs': ['include/%(name)s', 'lib/cmake/glfw3', 'lib/pkgconfig'], +} + +moduleclass = 'vis' From 06534336384ba885c0b24118a62b08de0ecd520b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Sat, 16 Mar 2024 10:31:28 +0100 Subject: [PATCH 1000/1193] revert change for withnvptx, moved to easyblock --- easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index f813c429dc06..12f599fdd8fd 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -64,10 +64,7 @@ builddependencies = [ languages = ['c', 'c++', 'fortran'] withisl = True -if ARCH == 'riscv64': - withnvptx = False -else: - withnvptx = True +withnvptx = True # Perl is only required when building with NVPTX support if withnvptx: From 39b1131c5a8b32c9f809eae0c383d9002b4f64e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 16 Mar 2024 14:30:12 +0000 Subject: [PATCH 1001/1193] adding easyconfigs: cuTENSOR-2.0.1.2-CUDA-12.1.1.eb --- .../cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.1.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.1.1.eb new file mode 100644 index 000000000000..578050b4874c --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.1.2-CUDA-12.1.1.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '2.0.1' +version = local_shortver + '.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/cutensor' +description = """The cuTENSOR Library is a GPU-accelerated tensor linear algebra library providing tensor contraction, + reduction and elementwise operations.""" + +toolchain = SYSTEM + +source_urls = ['https://developer.download.nvidia.com/compute/cutensor/redist/libcutensor/linux-x86_64/'] +sources = ['libcutensor-linux-x86_64-%(version)s-archive.tar.xz'] +checksums = ['ededa12ca622baad706ea0a500a358ea51146535466afabd96e558265dc586a2'] + +local_cudamajver = '12' +dependencies = [('CUDA', local_cudamajver + '.1.1')] + +sanity_check_paths = { + 'files': ['include/cutensor.h', 'include/cutensor/types.h', + 'lib/%s/libcutensor.%s' % (local_cudamajver, SHLIB_EXT), + 'lib/%s/libcutensor_static.a' % local_cudamajver], + 'dirs': [], +} + +modextrapaths = { + 'LD_LIBRARY_PATH': ['lib/%s' % local_cudamajver], + 'LIBRARY_PATH': ['lib/%s' % local_cudamajver], +} + +moduleclass = 'lib' From aa4df0de4cc44d4f5516c47fb5a433a70c567ce7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 16 Mar 2024 16:54:17 +0000 Subject: [PATCH 1002/1193] Fix download url for cuSPARSELt 0.3.0.3 --- .../c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb index bec7936a183f..5a46a44f77ca 100644 --- a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb @@ -10,9 +10,13 @@ which at least one operand is a sparse matrix""" toolchain = SYSTEM -source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse-lt/linux-x86_64/'] -sources = ['libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz'] -checksums = ['46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45'] +local_arch = {'arm64': 'sbsa'}.get(ARCH, ARCH) +source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse_lt/linux-%s/' % local_arch] +sources = ['libcusparse_lt-linux-%s-%%(version)s-archive.tar.xz' % local_arch] +checksums = [{ + 'libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz': '46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45', + 'libcusparse_lt-linux-sbsa-%(version)s-archive.tar.xz': '6269885ec6cecc1a0aa95f344f35c882b6bf0a6ef55d1726e2cf59e11a3af68e', +}] dependencies = [('CUDA', '11.4.1')] From 8763600fdc5c6cb47bff28afa218338c00ac9608 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 16 Mar 2024 16:55:48 +0000 Subject: [PATCH 1003/1193] adding easyconfigs: cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb --- .../cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb new file mode 100644 index 000000000000..12f29f061cf2 --- /dev/null +++ b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb @@ -0,0 +1,30 @@ +easyblock = 'Tarball' + +name = 'cuSPARSELt' +version = '0.6.0.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://docs.nvidia.com/cuda/cusparselt/index.html' +description = """NVIDIA cuSPARSELt is a high-performance CUDA library dedicated to general matrix-matrix operations in +which at least one operand is a sparse matrix""" + +toolchain = SYSTEM + +local_arch = {'arm64': 'sbsa'}.get(ARCH, ARCH) +source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse_lt/linux-%s/' % local_arch] +sources = ['libcusparse_lt-linux-%s-%%(version)s-archive.tar.xz' % local_arch] +checksums = [{ + 'libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz': 'da20d7a6d7a6674cb6e991439eaacd4661631c71a2f1026c41fba115c5c9c8b5', + 'libcusparse_lt-linux-sbsa-%(version)s-archive.tar.xz': '46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45', +}] + +dependencies = [('CUDA', '12.1.1')] + +sanity_check_paths = { + 'files': ['include/cusparseLt.h', + 'lib/libcusparseLt.%s' % SHLIB_EXT, + 'lib/libcusparseLt_static.a'], + 'dirs': [], +} + +moduleclass = 'lib' From 1d399e77ad704ba5a29dc5330e8a1bcc46a818d2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 16 Mar 2024 17:28:31 +0000 Subject: [PATCH 1004/1193] Fix style --- .../c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb index 5a46a44f77ca..4c5045f553b0 100644 --- a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb @@ -14,8 +14,10 @@ local_arch = {'arm64': 'sbsa'}.get(ARCH, ARCH) source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse_lt/linux-%s/' % local_arch] sources = ['libcusparse_lt-linux-%s-%%(version)s-archive.tar.xz' % local_arch] checksums = [{ - 'libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz': '46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45', - 'libcusparse_lt-linux-sbsa-%(version)s-archive.tar.xz': '6269885ec6cecc1a0aa95f344f35c882b6bf0a6ef55d1726e2cf59e11a3af68e', + 'libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz': + '46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45', + 'libcusparse_lt-linux-sbsa-%(version)s-archive.tar.xz': + '6269885ec6cecc1a0aa95f344f35c882b6bf0a6ef55d1726e2cf59e11a3af68e', }] dependencies = [('CUDA', '11.4.1')] From d4345d02cd51c7ea94dc902c510b7471cf5c92fc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 16 Mar 2024 17:28:52 +0000 Subject: [PATCH 1005/1193] Fix style --- .../c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb index 12f29f061cf2..e64ca7ff0135 100644 --- a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb @@ -14,8 +14,10 @@ local_arch = {'arm64': 'sbsa'}.get(ARCH, ARCH) source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse_lt/linux-%s/' % local_arch] sources = ['libcusparse_lt-linux-%s-%%(version)s-archive.tar.xz' % local_arch] checksums = [{ - 'libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz': 'da20d7a6d7a6674cb6e991439eaacd4661631c71a2f1026c41fba115c5c9c8b5', - 'libcusparse_lt-linux-sbsa-%(version)s-archive.tar.xz': '46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45', + 'libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz': + 'da20d7a6d7a6674cb6e991439eaacd4661631c71a2f1026c41fba115c5c9c8b5', + 'libcusparse_lt-linux-sbsa-%(version)s-archive.tar.xz': + '46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45', }] dependencies = [('CUDA', '12.1.1')] From 1d22a2543a48b72dc6a9195118ae78f6a6cf87f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 18 Mar 2024 11:01:24 +0100 Subject: [PATCH 1006/1193] adding easyconfigs: FLINT-3.1.1-gfbf-2023b.eb, NTL-11.5.1-GCC-13.2.0.eb --- .../f/FLINT/FLINT-3.1.1-gfbf-2023b.eb | 45 +++++++++++++++++++ .../n/NTL/NTL-11.5.1-GCC-13.2.0.eb | 45 +++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLINT/FLINT-3.1.1-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/f/FLINT/FLINT-3.1.1-gfbf-2023b.eb b/easybuild/easyconfigs/f/FLINT/FLINT-3.1.1-gfbf-2023b.eb new file mode 100644 index 000000000000..c5063ad3ef46 --- /dev/null +++ b/easybuild/easyconfigs/f/FLINT/FLINT-3.1.1-gfbf-2023b.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'FLINT' +version = '3.1.1' + +homepage = 'https://www.flintlib.org/' + +description = """FLINT (Fast Library for Number Theory) is a C library in support of computations + in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, + factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides + various low-level routines for fast arithmetic. FLINT is extensively documented and tested.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/flintlib/%(namelower)s/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['161f81d0a809408daab36ec79ba89380346dc3195d3671f97106f1b8774f653a'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Python', '3.11.5'), +] + +dependencies = [ + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('NTL', '11.5.1'), +] + +# Make flexiblas the first to be found and used to avoid linking openblas. +preconfigopts = 'sed -i "s/PATH_SUFFIXES openblas/PATH_SUFFIXES flexiblas openblas/g;' +preconfigopts += 's/accelerate openblas/accelerate flexiblas openblas/g" ' +preconfigopts += '%(builddir)s/%(namelower)s-%(version)s/CMake/FindCBLAS.cmake && ' + +configopts = '-DWITH_NTL=on -DBUILD_TESTING=yes' + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb new file mode 100644 index 000000000000..f3277ec81bd6 --- /dev/null +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb @@ -0,0 +1,45 @@ +# contributed by Guilherme Peretti-Pezzi (CSCS) +# updated by Alex Domingo (Vrije Universiteit Brussel) +# updated by Åke Sandgren(Umeå University) +# Update: Petr Král (INUITS) +easyblock = 'ConfigureMake' + +name = 'NTL' +version = '11.5.1' + +homepage = 'https://shoup.net/ntl/' + +description = """NTL is a high-performance, portable C++ library providing data structures and +algorithms for manipulating signed, arbitrary length integers, and for vectors, +matrices, and polynomials over the integers and over finite fields.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'libntl' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ef578fa8b6c0c64edd1183c4c303b534468b58dd3eb8df8c9a5633f984888de5'] + +builddependencies = [ + ('Perl', '5.38.0'), +] + +dependencies = [ + ('GMP', '6.3.0'), +] + +start_dir = 'src' + +prefix_opt = 'PREFIX=' +configopts = 'CXX="$CXX" CXXFLAGS="$CXXFLAGS" GMP_PREFIX="$EBROOTGMP" SHARED=on' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libntl.%s' % e for e in ['a', SHLIB_EXT]], + 'dirs': ['include/NTL', 'share/doc'], +} + +moduleclass = 'math' + From 8caf1797571342745b74f507c66606a0628ec3f8 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 18 Mar 2024 11:15:48 +0100 Subject: [PATCH 1007/1193] adding easyconfigs: Spark-3.5.1-foss-2023a-Java-17.eb --- .../s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb b/easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb new file mode 100644 index 000000000000..234162983619 --- /dev/null +++ b/easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb @@ -0,0 +1,53 @@ +# Author: Denis Krišťák (INUITS) + +easyblock = 'Tarball' + +name = 'Spark' +version = '3.5.1' +versionsuffix = '-Java-%(javaver)s' +homepage = 'https://spark.apache.org' +description = """Spark is Hadoop MapReduce done in memory""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = [ + 'https://archive.apache.org/dist//%(namelower)s/%(namelower)s-%(version)s/', + 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' +] +sources = ['%(namelower)s-%(version)s-bin-hadoop3.tgz'] +checksums = ['ac064ec620129b4b9630e180e25ac2b71a8ccd4c6912bf5b5631943b742f0379'] + +dependencies = [ + ('Python', '3.11.3'), + ('Java', '17', '', SYSTEM), + ('Arrow', '14.0.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, +} + +exts_list = [ + ('py4j', '0.10.9.7', { + 'checksums': ['0b6e5315bb3ada5cf62ac651d107bb2ebc02def3dee9d9548e3baac644ea8dbb'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pyspark', 'bin/spark-shell'], + 'dirs': ['python'] +} + +sanity_check_commands = [ + "pyspark -h", + "python -c 'import pyspark'", +] + +modextrapaths = {'PYTHONPATH': ['python', 'lib/python%(pyshortver)s/site-packages']} + +modextravars = {'SPARK_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 0a5b281c025861092d49ec9043c59bd0a239776f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 18 Mar 2024 11:19:43 +0100 Subject: [PATCH 1008/1193] remove blank line --- easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb index f3277ec81bd6..a2dd73270b77 100644 --- a/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/n/NTL/NTL-11.5.1-GCC-13.2.0.eb @@ -42,4 +42,3 @@ sanity_check_paths = { } moduleclass = 'math' - From b2fea65fe29199708d4c5c34766537c4f82cc5e0 Mon Sep 17 00:00:00 2001 From: vsc46128 Date: Mon, 18 Mar 2024 11:21:51 +0100 Subject: [PATCH 1009/1193] update checksum --- easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb b/easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb index 234162983619..00240ff36f99 100644 --- a/easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb +++ b/easybuild/easyconfigs/s/Spark/Spark-3.5.1-foss-2023a-Java-17.eb @@ -15,7 +15,7 @@ source_urls = [ 'https://downloads.apache.org/%(namelower)s/%(namelower)s-%(version)s/' ] sources = ['%(namelower)s-%(version)s-bin-hadoop3.tgz'] -checksums = ['ac064ec620129b4b9630e180e25ac2b71a8ccd4c6912bf5b5631943b742f0379'] +checksums = ['5df15f8027067c060fe47ebd351a1431a61dbecc9c28b8dd29e2c6e1935c23eb'] dependencies = [ ('Python', '3.11.3'), From 31118723b8d261d40f37c3ee90c945339f78e202 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 18 Mar 2024 13:54:42 +0000 Subject: [PATCH 1010/1193] adding easyconfigs: librosa-0.10.1-foss-2023a.eb --- .../l/librosa/librosa-0.10.1-foss-2023a.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb new file mode 100644 index 000000000000..444e2ba800d3 --- /dev/null +++ b/easybuild/easyconfigs/l/librosa/librosa-0.10.1-foss-2023a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'librosa' +version = '0.10.1' + +homepage = 'https://librosa.org/' +description = """Audio and music processing in Python""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('matplotlib', '3.7.2'), + ('poetry', '1.5.1'), # build for soxr +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # to get joblib + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('FFmpeg', '6.0'), + ('numba', '0.58.1'), + ('libsndfile', '1.2.2'), +] + +use_pip = True + +exts_list = [ + ('soxr', '0.3.7', { + 'preinstallopts': 'python -m build && ', + 'checksums': ['436ddff00c6eb2c75b79c19cfdca7527b1e31b5fad738652f044045ba6258593'], + }), + ('audioread', '3.0.1', { + 'checksums': ['ac5460a5498c48bdf2e8e767402583a4dcd13f4414d286f42ce4379e8b35066d'], + }), + ('soundfile', '0.12.1', { + 'checksums': ['e8e1017b2cf1dda767aef19d2fd9ee5ebe07e050d430f77a0a7c66ba08b8cdae'], + }), + ('lazy_loader', '0.3', { + 'checksums': ['3b68898e34f5b2a29daaaac172c6555512d0f32074f147e2254e4a6d9d838f37'], + }), + ('resampy', '0.4.3', { # for tests + 'checksums': ['a0d1c28398f0e55994b739650afef4e3974115edbe96cd4bb81968425e916e47'], + }), + (name, version, { + 'checksums': ['832f7d150d6dd08ed2aa08c0567a4be58330635c32ddd2208de9bc91300802c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From cc99386601576a3e3c0281cebac2954d2faf2413 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 18 Mar 2024 14:18:43 +0000 Subject: [PATCH 1011/1193] Double quotes set to correct place --- easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb index 447430db8128..32a612768d41 100644 --- a/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CSBLAST/CSBLAST-2.2.4-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ start_dir = 'src' build_cmd_targets = 'csblast csbuild' -buildopts = '"FLAGS=-fpermissive -std=c++11 "' +buildopts = 'FLAGS="-fpermissive -std=c++11" ' files_to_copy = ['bin', 'data', 'LICENSE', 'README_CSBLAST'] From 577d783b19d371b290b9a7d970dbe690a644325b Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 18 Mar 2024 16:37:15 +0100 Subject: [PATCH 1012/1193] adding easyconfigs: denseweight-0.1.2-foss-2023a.eb --- .../denseweight-0.1.2-foss-2023a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb new file mode 100644 index 000000000000..c2841ab4dda1 --- /dev/null +++ b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'denseweight' +version = '0.1.2' + +homepage = 'https://github.com/steimi/denseweight' +description = """ +This package implements the method for imbalanced regression DenseWeight. The corresponding +paper "Density-based weighting for imbalanced regression". The goal of DenseWeight is to allow +training machine learning models for regression tasks that emphasize performance for data +points with rare target values in comparison to data points with more common target values. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +# sources = [SOURCE_TAR_GZ] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), +] + +use_pip = True + +exts_list = [ + ('KDEpy', '1.1.9', { + 'modulename': 'KDEpy', + 'checksums': ['4bf0b2afd430ce5b40fafd98144de83d8b715d46fdf0f45fed2b5c2e9c40ce46'], + }), + (name, version, { + 'checksums': ['281cf1fe4be364366363ee822b524620dcb629c5b9ff7852aa80f91a27c98b1e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'ai' From 684c024f59269fadc1e72e0e5f8cfa3bd29a7dc5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 18 Mar 2024 17:07:42 +0100 Subject: [PATCH 1013/1193] Fix MS_RDONLY for (older) OpenMPI --- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb | 4 +++- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb | 4 +++- .../easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb | 2 ++ .../easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb | 2 ++ easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb | 2 ++ .../easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb | 2 ++ .../easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb | 6 +++++- 7 files changed, 19 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb index f18855e01469..f71cda3c24b6 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-GCC-7.3.0-2.30.eb @@ -10,13 +10,15 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-3.1_fix-ib-query.patch', - '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch' + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb index a11fc78e42af..5d8c9fd855ef 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.1-gcccuda-2018b.eb @@ -10,13 +10,15 @@ source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/ sources = [SOURCELOWER_TAR_GZ] patches = [ 'OpenMPI-3.1_fix-ib-query.patch', - '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch' + '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '846bb7ed2aa0c96fc0594423e7b21904ee4f160dcfd62b8a0d1274256fbf25ce', # openmpi-3.1.1.tar.gz '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch # OpenMPI-3.1.1-add_ompi_datatype_attribute_to_release_ucp_datatype.patch '945d19eb583af1e4d2ddcb40bafe505352244635c812308d1c77ad1db2811538', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] # needed for --with-verbs diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb index dce3d8fbc8d5..481d63e5af5d 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.3-GCC-8.2.0-2.31.1.eb @@ -12,6 +12,7 @@ patches = [ '%(name)s-%(version)s-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', 'OpenMPI-3.1_fix-ib-query.patch', 'OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ '0254627d8a9b12a8f50213ed01e7a94dd7e91b340abf5c53bcf0b89afe6fb77d', # openmpi-3.1.3.tar.gz @@ -20,6 +21,7 @@ checksums = [ '8031ff093788a750f30ec7b4b06573af008009e62ddfd558ecfe97cbe404d9d2', # OpenMPI-3.1_fix-ib-query.patch # OpenMPI-3.1.3_fix-support-for-external-PMIx-v3.1.patch '94846bee50b43b220fd6fead576c4be2cbc8baaa423ce7346d7d193fda523357', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb index 742cf80152b0..8f7e724e3a3c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0-2.32.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', 'OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ 'a7c34ad052ea8201ed9e7389994069fe6996403beabdd2d711caf0532808156c', # openmpi-3.1.4.tar.gz @@ -18,6 +19,7 @@ checksums = [ '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', # OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch '77df4f04802f84c49659c0d89c92724972c0634ac2155ed787482c4ddf1ee999', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb index e60121be5677..61aeb4ab521c 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-GCC-8.3.0.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', 'OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ 'a7c34ad052ea8201ed9e7389994069fe6996403beabdd2d711caf0532808156c', # openmpi-3.1.4.tar.gz @@ -18,6 +19,7 @@ checksums = [ '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', # OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch '77df4f04802f84c49659c0d89c92724972c0634ac2155ed787482c4ddf1ee999', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb index d2dc52abe147..5bc9297b6bdb 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-3.1.4-gcccuda-2019b.eb @@ -11,6 +11,7 @@ sources = [SOURCELOWER_TAR_GZ] patches = [ '%(name)s-3.1.3-add_ompi_datatype_attribute_to_release_ucp_datatype.patch', 'OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', ] checksums = [ 'a7c34ad052ea8201ed9e7389994069fe6996403beabdd2d711caf0532808156c', # openmpi-3.1.4.tar.gz @@ -18,6 +19,7 @@ checksums = [ '46fa94eb417954bdb297291bad4f4d32018af4911bebf3e59af6276eba6a50a9', # OpenMPI-3.1.4_openib-device-params-ConnectX-6.patch '77df4f04802f84c49659c0d89c92724972c0634ac2155ed787482c4ddf1ee999', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] dependencies = [ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb index 077d51b2f9e7..d8185fe1dd32 100644 --- a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.0.0-GCC-8.2.0-2.31.1.eb @@ -8,11 +8,15 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] sources = [SOURCELOWER_TAR_GZ] -patches = ['OpenMPI-4.0.1_add-support-for-ucx-1.7.patch'] +patches = [ + 'OpenMPI-4.0.1_add-support-for-ucx-1.7.patch', + 'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch', +] checksums = [ '36f10daa3f1b1d37530f686bf7f70966b2a13c0bc6e2e05aebc7e85e3d21b10d', # openmpi-4.0.0.tar.gz # OpenMPI-4.0.1_add-support-for-ucx-1.7.patch '3c5ce8fe164869f309821a4528bbd8a4c087bc748dadf589850482bbccf8890c', + {'OpenMPI-4.0.5_fix-MS_RDONLY-error.patch': 'b4cd3d947cd4f3d47c7cf531c2b4bcdaa5d6db1ec024a0a97f5a3b42c95f6b82'}, ] dependencies = [ From 828866559c204c53df893084aab304b4f24b91eb Mon Sep 17 00:00:00 2001 From: Cintia Willemyns <115622907+WilleBell@users.noreply.github.com> Date: Mon, 18 Mar 2024 17:14:25 +0100 Subject: [PATCH 1014/1193] Update denseweight-0.1.2-foss-2023a.eb remove unnecessary comment --- .../easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb index c2841ab4dda1..0a61289e5a12 100644 --- a/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/d/denseweight/denseweight-0.1.2-foss-2023a.eb @@ -13,8 +13,6 @@ points with rare target values in comparison to data points with more common tar toolchain = {'name': 'foss', 'version': '2023a'} -# sources = [SOURCE_TAR_GZ] - dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From 320a2a7eccbab4ce4c6fd80003e84b10200695f1 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Mon, 18 Mar 2024 17:34:05 +0100 Subject: [PATCH 1015/1193] adding easyconfigs: scikit-lego-0.7.4-foss-2023a.eb --- .../scikit-lego-0.7.4-foss-2023a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.7.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.7.4-foss-2023a.eb b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.7.4-foss-2023a.eb new file mode 100644 index 000000000000..0d3f98e81329 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-lego/scikit-lego-0.7.4-foss-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'scikit-lego' +version = '0.7.4' + +homepage = 'https://github.com/koaning/scikit-lego' +description = """ +We love scikit learn but very often we find ourselves writing custom transformers, metrics and +models. The goal of this project is to attempt to consolidate these into a package that offers +code quality/testing. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'koaning' + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('matplotlib', '3.7.2'), + ('Deprecated', '1.2.14'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'sklego', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['eefef84cd72f4c019423cc1de6579b6b4bf96512f5b9680cdeb9a12023b4764f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 579b1fd162e150391cff7107cff80123ee4d9889 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Mon, 18 Mar 2024 17:37:22 +0100 Subject: [PATCH 1016/1193] Update libSBML-5.19.7-GCC-11.3.0.eb correct typo --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index 3598228c2d88..04f1cdf9ba37 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -55,7 +55,7 @@ dependencies = [ # Python libSBML binding better done from https://pypi.org/project/python-libsbml/ configure_cmd = 'cmake -DCMAKE_INSTALL_PREFIX=%(installdir)s -DWITH_JAVA=OFF ' configure_cmd += '-DWITH_CHECK=ON -DWITH_SWIG=ON -DWITH_PERL=ON -DWITH_PYTHON=OFF ' -configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF -Wno-dev' +configure_cmd += '-DWITH_EXPAT=ON -DWITH_LIBXML=OFF -Wno-dev ' configure_cmd += '-DENABLE_{LAYOUT,QUAL,COMP,FBC,RENDER,GROUPS,MULTI,DISTRIB}=ON ' configure_cmd += '../%(namelower)s-%(version)s' From c017376dcbbac217af3e90be47a3b56e1271e8e4 Mon Sep 17 00:00:00 2001 From: casparl Date: Mon, 18 Mar 2024 17:58:58 +0100 Subject: [PATCH 1017/1193] adding easyconfigs: MODFLOW-6.4.4-foss-2023a.eb --- .../m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb b/easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb new file mode 100644 index 000000000000..81674ed4aea8 --- /dev/null +++ b/easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'MODFLOW' +version = '6.4.4' + +homepage = 'https://www.usgs.gov/mission-areas/water-resources/science/modflow-and-related-programs' +description = """ +MODFLOW is the USGS's modular hydrologic model. MODFLOW is considered an + international standard for simulating and predicting groundwater conditions + and groundwater/surface-water interactions. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = "MODFLOW-USGS" +source_urls = ['https://github.com/%(github_account)s/%(namelower)s6/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['bab887399d1882c84296e7bad20d6143aa07c1476943e6465c14a8738e1ded53'] + +builddependencies = [ + ('Meson', '1.1.1'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), + ('pkgconf', '1.9.5'), +] + +dependencies = [ + ('PETSc', '3.20.3'), + ('netCDF-Fortran', '4.6.1'), +] + +# Needed because of https://github.com/mesonbuild/meson/issues/12993 +preconfigopts = "PKG_CONFIG_ALLOW_SYSTEM_CFLAGS=true" +configopts = '-Ddebug=false -Dparallel=true' + +runtest = 'meson test' +testopts = '--verbose --no-rebuild' + +sanity_check_commands = ['mf6 --version'] + +sanity_check_paths = { + 'files': ['bin/mf6', 'bin/mf5to6', 'bin/zbud6', 'lib/libmf6.%s' % SHLIB_EXT], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'geo' From 96343840cdb4480c3ae12eaa662aa4a0445d550b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Mon, 18 Mar 2024 19:16:58 +0100 Subject: [PATCH 1018/1193] Update dask version to be same as for another modules --- .../p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb index 2e5e8193e0db..2842812499fa 100644 --- a/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb +++ b/easybuild/easyconfigs/p/pySCENIC/pySCENIC-0.12.1-20240311-foss-2023a.eb @@ -19,7 +19,7 @@ dependencies = [ ('scikit-learn', '1.3.1'), ('tqdm', '4.66.1'), ('networkx', '3.1'), - ('dask', '2023.12.1'), + ('dask', '2023.9.2'), ('aiohttp', '3.8.5'), ('dill', '0.3.7'), ('loompy', '3.0.7'), From 79ca7f3033ff31d3e01db503e96bd085b3f9ca0a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 18 Mar 2024 23:04:10 +0000 Subject: [PATCH 1019/1193] adding easyconfigs: NLTK-3.8.1-foss-2023a.eb --- .../n/NLTK/NLTK-3.8.1-foss-2023a.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023a.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023a.eb new file mode 100644 index 000000000000..b7c7f373571d --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023a.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'NLTK' +version = '3.8.1' + +homepage = 'https://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('scikit-learn', '1.3.1'), + ('matplotlib', '3.7.2'), + ('tqdm', '4.66.1'), +] + +local_nltk_data_install = [] +# Install NLTK data sets (7.4 GB) +# local_nltk_data = '/path/to/database/nltk_data' +# local_nltk_data_install = [ +# "mkdir -p %s && NLTK_DATA=%s python -m nltk.downloader all" % (local_nltk_data, local_nltk_data) +# ] +# modextravars = {'NLTK_DATA': local_nltk_data} + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2023.12.25', { + 'checksums': ['29171aa128da69afdf4bde412d5bedc335f2ca8fcfe4489038577d05f16181e5'], + }), + ('python-crfsuite', '0.9.10', { + 'modulename': 'pycrfsuite', + 'checksums': ['f38524631e2b533341f10f2c77689270dc6ecd5985495dccf7aa37b1045bc2e5'], + }), + (name, version, { + 'postinstallcmds': [], + 'source_tmpl': '%(namelower)s-%(version)s.zip', + 'use_pip_extras': 'corenlp,machine_learning,plot,tgrep', + 'checksums': ['1834da3d0682cba4f2cede2f9aad6b0fafb6461ba451db0efb6f9c39798d64d3'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] + +moduleclass = 'devel' From 8e9affff55857d82e21b93e4c1004add663edfc6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 18 Mar 2024 23:30:51 +0000 Subject: [PATCH 1020/1193] adding easyconfigs: CVXPY-1.4.2-foss-2023a.eb --- .../c/CVXPY/CVXPY-1.4.2-foss-2023a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb new file mode 100644 index 000000000000..50813b5f9ae3 --- /dev/null +++ b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'CVXPY' +version = '1.4.2' + +homepage = 'https://www.cvxpy.org/' +description = """ +CVXPY is a Python-embedded modeling language for convex optimization problems. +It allows you to express your problem in a natural way that follows the math, +rather than in the restrictive standard form required by solvers. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('qdldl', '0.1.7.post0', { + 'checksums': ['f346a114c8342ee6d4dbd6471eef314199fb268d3bf7b95885ca351fde2b023f'], + }), + ('osqp', '0.6.5', { + 'checksums': ['b2810aee7be2373add8b6c0be5ad99b810288774abca421751cb032d6a5aedef'], + }), + ('ecos', '2.0.13', { + 'checksums': ['f2a9dc108ade7faf6f6f4fad245f4714b7293c8767d2a351ead59428a94a98b9'], + }), + ('scs', '3.2.4.post1', { + 'checksums': ['7015d7a56d1d5b53264fd277289ea169949309e26101677ff88cd0e5030d032f'], + }), + ('cvxpy', version, { + 'checksums': ['0a386a5788dbd78b7b20dd071524ec636c8fa72b3628e69f1abc714c8f9811e5'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 19605d2d5968fd35c704cd687e45bf89d2ab4fce Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Tue, 19 Mar 2024 09:33:11 +0100 Subject: [PATCH 1021/1193] use SHLIB_EXT --- easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb index 04f1cdf9ba37..2e20ee1eda52 100644 --- a/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libSBML/libSBML-5.19.7-GCC-11.3.0.eb @@ -63,7 +63,7 @@ configure_cmd += '../%(namelower)s-%(version)s' runtest = 'check' sanity_check_paths = { - 'files': ['lib64/libsbml.so', 'lib64/perl5/site_perl/5.34.1/x86_64-linux-thread-multi/LibSBML.pm'], + 'files': ['lib64/libsbml.%s' % SHLIB_EXT, 'lib64/perl5/site_perl/5.34.1/x86_64-linux-thread-multi/LibSBML.pm'], 'dirs': ['lib64', 'include', 'share'] } From b653d57e323fcc744a414c59e7aba585d716b533 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 19 Mar 2024 09:54:04 +0100 Subject: [PATCH 1022/1193] adding easyconfigs: Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb --- .../Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb | 57 +++++++++++++++++++ 1 file changed, 57 insertions(+) create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb new file mode 100644 index 000000000000..52ddf4fdd445 --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb @@ -0,0 +1,57 @@ +# Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020-2024 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD + +name = 'Score-P' +version = '8.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.score-p.org' +description = """ + The Score-P measurement infrastructure is a highly scalable and easy-to-use + tool suite for profiling, event tracing, and online analysis of HPC + applications. +""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['76c914e6319221c059234597a3bc53da788ed679179ac99c147284dcefb1574a'] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('CubeLib', '4.8.2'), + ('CubeWriter', '4.8.2'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.8'), + ('OTF2', '3.0.3'), + # Hardware counter support (optional): + ('PAPI', '7.1.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.2'), +] + +configopts = '--enable-shared' + +local_adapters = [ + 'compiler_event', 'cuda_mgmt', 'compiler_mgmt', 'mpi_event', 'mpi_mgmt', 'opari2_mgmt', 'user_event', 'user_mgmt' +] +sanity_check_paths = { + 'files': + ['bin/scorep', 'include/scorep/SCOREP_User.h'] + + ['lib/libscorep_adapter_%s.%s' % (a, e) for a in local_adapters for e in ('a', SHLIB_EXT)], + 'dirs': [], +} +sanity_check_commands = ['scorep-config --help'] + +# Ensure that local metric documentation is found by CubeGUI +modextrapaths = {'CUBE_DOCPATH': 'share/doc/scorep/profile'} + +moduleclass = 'perf' From 347d9caba0a964bbbe3dff380202b551473a73c7 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 19 Mar 2024 09:37:12 +0000 Subject: [PATCH 1023/1193] adding easyconfigs: likwid-5.3.0-GCC-12.3.0.eb --- .../l/likwid/likwid-5.3.0-GCC-12.3.0.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-12.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..9af29c68b9dd --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.3.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' + +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/likwid/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c290e554c4253124ac2ab8b056e14ee4d23966b8c9fbfa10ba81f75ae543ce4e'] + +builddependencies = [ + ('Perl', '5.36.1'), +] + +dependencies = [ + ('hwloc', '2.9.1'), +] + +skipsteps = ['configure'] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +maxparallel = 1 + +installopts = buildopts + 'INSTALL_CHOWN="" ' + +sanity_check_paths = { + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] +} + +moduleclass = 'tools' From a3bad48b20f3621198bd6f95e58c7318f70bbc40 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 19 Mar 2024 11:13:14 +0100 Subject: [PATCH 1024/1193] Update Score-P to 8.4 --- ...-CUDA-12.4.0.eb => Score-P-8.4-gompi-2023b-CUDA-12.4.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Score-P/{Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb => Score-P-8.4-gompi-2023b-CUDA-12.4.0.eb} (94%) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023b-CUDA-12.4.0.eb similarity index 94% rename from easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb rename to easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023b-CUDA-12.4.0.eb index 52ddf4fdd445..5a45e3f80e15 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b-CUDA-12.4.0.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023b-CUDA-12.4.0.eb @@ -8,7 +8,7 @@ # License:: 3-clause BSD name = 'Score-P' -version = '8.3' +version = '8.4' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://www.score-p.org' @@ -22,7 +22,7 @@ toolchain = {'name': 'gompi', 'version': '2023b'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['76c914e6319221c059234597a3bc53da788ed679179ac99c147284dcefb1574a'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CUDA', '12.4.0', '', SYSTEM), From 9bb6285b9d894227f5115d1c0425feacc580c837 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 19 Mar 2024 11:13:42 +0100 Subject: [PATCH 1025/1193] Update Score-P to 8.4 --- ...{Score-P-8.3-gompi-2023b.eb => Score-P-8.4-gompi-2023b.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Score-P/{Score-P-8.3-gompi-2023b.eb => Score-P-8.4-gompi-2023b.eb} (94%) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023b.eb similarity index 94% rename from easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b.eb rename to easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023b.eb index 7d56fa199bb9..677c4481ebb4 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.3-gompi-2023b.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.4-gompi-2023b.eb @@ -8,7 +8,7 @@ # License:: 3-clause BSD name = 'Score-P' -version = '8.3' +version = '8.4' homepage = 'https://www.score-p.org' description = """ @@ -21,7 +21,7 @@ toolchain = {'name': 'gompi', 'version': '2023b'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['76c914e6319221c059234597a3bc53da788ed679179ac99c147284dcefb1574a'] +checksums = ['7bbde9a0721d27cc6205baf13c1626833bcfbabb1f33b325a2d67976290f7f8a'] dependencies = [ ('CubeLib', '4.8.2'), From 96bad385062c8d47be6798637871fe973c6aafa7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 19 Mar 2024 10:45:56 +0000 Subject: [PATCH 1026/1193] adding easyconfigs: Clarabel.rs-0.7.1-GCCcore-12.3.0.eb --- .../Clarabel.rs-0.7.1-GCCcore-12.3.0.eb | 358 ++++++++++++++++++ 1 file changed, 358 insertions(+) create mode 100644 easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..886bc602b0f1 --- /dev/null +++ b/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb @@ -0,0 +1,358 @@ +easyblock = 'CargoPythonPackage' + +name = 'Clarabel.rs' +version = '0.7.1' + +homepage = "https://github.com/oxfordcontrol/Clarabel.rs" +description = "Interior-point solver for convex conic optimisation problems in Rust." + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('maturin', '1.4.0', '-Rust-1.75.0'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +crates = [ + ('clarabel', version), + ('accelerate-src', '0.3.2'), + ('addr2line', '0.21.0'), + ('adler', '1.0.2'), + ('amd', '0.2.2'), + ('anyhow', '1.0.81'), + ('autocfg', '1.1.0'), + ('backtrace', '0.3.69'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('blas', '0.22.0'), + ('blas-src', '0.9.0'), + ('blas-sys', '0.7.1'), + ('cc', '1.0.90'), + ('cfg-if', '0.1.10'), + ('cfg-if', '1.0.0'), + ('cmake', '0.1.50'), + ('core-foundation', '0.9.4'), + ('core-foundation-sys', '0.8.6'), + ('crc32fast', '1.4.0'), + ('curl', '0.4.46'), + ('curl-sys', '0.4.72+curl-8.6.0'), + ('darling', '0.14.4'), + ('darling_core', '0.14.4'), + ('darling_macro', '0.14.4'), + ('derive_builder', '0.11.2'), + ('derive_builder_core', '0.11.2'), + ('derive_builder_macro', '0.11.2'), + ('dirs', '2.0.2'), + ('dirs', '3.0.2'), + ('dirs-sys', '0.3.7'), + ('either', '1.10.0'), + ('enum_dispatch', '0.3.12'), + ('errno', '0.3.8'), + ('failure', '0.1.8'), + ('failure_derive', '0.1.8'), + ('fastrand', '2.0.1'), + ('filetime', '0.2.23'), + ('flate2', '1.0.28'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.1'), + ('getrandom', '0.2.12'), + ('gimli', '0.28.1'), + ('glob', '0.3.1'), + ('heck', '0.4.1'), + ('ident_case', '1.0.1'), + ('idna', '0.5.0'), + ('indoc', '2.0.4'), + ('intel-mkl-src', '0.5.0'), + ('intel-mkl-tool', '0.1.0'), + ('itertools', '0.9.0'), + ('itertools', '0.11.0'), + ('itoa', '1.0.10'), + ('jobserver', '0.1.28'), + ('lapack', '0.19.0'), + ('lapack-src', '0.9.0'), + ('lapack-sys', '0.14.0'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.153'), + ('libredox', '0.0.1'), + ('libz-sys', '1.1.15'), + ('linux-raw-sys', '0.4.13'), + ('lock_api', '0.4.11'), + ('log', '0.4.21'), + ('memchr', '2.7.1'), + ('memoffset', '0.9.0'), + ('miniz_oxide', '0.7.2'), + ('native-tls', '0.2.11'), + ('netlib-src', '0.8.0'), + ('num-complex', '0.4.5'), + ('num-derive', '0.2.5'), + ('num-traits', '0.2.18'), + ('object', '0.32.2'), + ('once_cell', '1.19.0'), + ('openblas-build', '0.10.9'), + ('openblas-src', '0.10.9'), + ('openssl', '0.10.64'), + ('openssl-macros', 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{'rustls-pemfile-2.1.1.tar.gz': 'f48172685e6ff52a556baa527774f61fcaa884f59daf3375c62a3f1cd2549dab'}, + {'rustls-pki-types-1.3.1.tar.gz': '5ede67b28608b4c60685c7d54122d4400d90f62b40caee7700e700380a390fa8'}, + {'ryu-1.0.17.tar.gz': 'e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1'}, + {'same-file-1.0.6.tar.gz': '93fc1dc3aaa9bfed95e02e6eadabb4baf7e3078b0bd1b4d7b6b0b68378900502'}, + {'schannel-0.1.23.tar.gz': 'fbc91545643bcf3a0bbb6569265615222618bdf33ce4ffbbd13c4bbd4c093534'}, + {'scopeguard-1.2.0.tar.gz': '94143f37725109f92c262ed2cf5e59bce7498c01bcc1502d7b9afe439a4e9f49'}, + {'security-framework-2.9.2.tar.gz': '05b64fb303737d99b81884b2c63433e9ae28abebe5eb5045dcdd175dc2ecf4de'}, + {'security-framework-sys-2.9.1.tar.gz': 'e932934257d3b408ed8f30db49d85ea163bfe74961f017f405b025af298f0c7a'}, + {'serde-1.0.197.tar.gz': '3fb1c873e1b9b056a4dc4c0c198b24c3ffa059243875552b2bd0933b1aee4ce2'}, + {'serde_derive-1.0.197.tar.gz': 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{'unicode-xid-0.2.4.tar.gz': 'f962df74c8c05a667b5ee8bcf162993134c104e96440b663c8daa176dc772d8c'}, + {'unindent-0.2.3.tar.gz': 'c7de7d73e1754487cb58364ee906a499937a0dfabd86bcb980fa99ec8c8fa2ce'}, + {'ureq-2.9.6.tar.gz': '11f214ce18d8b2cbe84ed3aa6486ed3f5b285cf8d8fbdbce9f3f767a724adc35'}, + {'url-2.5.0.tar.gz': '31e6302e3bb753d46e83516cae55ae196fc0c309407cf11ab35cc51a4c2a4633'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'walkdir-2.5.0.tar.gz': '29790946404f91d9c5d06f9874efddea1dc06c5efe94541a7d6863108e3a5e4b'}, + {'wasi-0.11.0+wasi-snapshot-preview1.tar.gz': '9c8d87e72b64a3b4db28d11ce29237c246188f4f51057d65a7eab63b7987e423'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-util-0.1.6.tar.gz': 'f29e6f9198ba0d26b4c9f07dbe6f9ed633e1f3d5b8b414090084349e46a52596'}, + 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{'windows_i686_gnu-0.52.4.tar.gz': 'b474d8268f99e0995f25b9f095bc7434632601028cf86590aea5c8a5cb7801d3'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_i686_msvc-0.52.4.tar.gz': '1515e9a29e5bed743cb4415a9ecf5dfca648ce85ee42e15873c3cd8610ff8e02'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnu-0.52.4.tar.gz': '5eee091590e89cc02ad514ffe3ead9eb6b660aedca2183455434b93546371a03'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_gnullvm-0.52.4.tar.gz': '77ca79f2451b49fa9e2af39f0747fe999fcda4f5e241b2898624dca97a1f2177'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.4.tar.gz': '32b752e52a2da0ddfbdbcc6fceadfeede4c939ed16d13e648833a61dfb611ed8'}, + {'xattr-1.3.1.tar.gz': '8da84f1a25939b27f6820d92aed108f83ff920fdf11a7b19366c27c4cda81d4f'}, + {'zstd-0.5.4+zstd.1.4.7.tar.gz': '69996ebdb1ba8b1517f61387a883857818a66c8a295f487b1ffd8fd9d2c82910'}, + {'zstd-safe-2.0.6+zstd.1.4.7.tar.gz': '98aa931fb69ecee256d44589d19754e61851ae4769bf963b385119b1cc37a49e'}, + {'zstd-sys-1.4.18+zstd.1.4.7.tar.gz': 'a1e6e8778706838f43f771d80d37787cb2fe06dafe89dd3aebaf6721b9eaec81'}, +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'math' From 3de0275e5982ea8568d786d2983041a0556437f0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 19 Mar 2024 12:11:21 +0000 Subject: [PATCH 1027/1193] Fixed crates from correct lockfile --- .../Clarabel.rs-0.7.1-GCCcore-12.3.0.eb | 391 +++++++++--------- 1 file changed, 207 insertions(+), 184 deletions(-) diff --git a/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb index 886bc602b0f1..c2c1318cb69c 100644 --- a/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb @@ -20,94 +20,97 @@ dependencies = [ crates = [ ('clarabel', version), ('accelerate-src', '0.3.2'), - ('addr2line', '0.21.0'), + ('addr2line', '0.19.0'), ('adler', '1.0.2'), ('amd', '0.2.2'), - ('anyhow', '1.0.81'), + ('anyhow', '1.0.70'), ('autocfg', '1.1.0'), - ('backtrace', '0.3.69'), - ('base64', '0.21.7'), + ('backtrace', '0.3.67'), + ('base64', '0.13.1'), + ('base64', '0.21.0'), ('bitflags', '1.3.2'), - ('bitflags', '2.4.2'), ('blas', '0.22.0'), ('blas-src', '0.9.0'), ('blas-sys', '0.7.1'), - ('cc', '1.0.90'), + ('cc', '1.0.79'), ('cfg-if', '0.1.10'), ('cfg-if', '1.0.0'), ('cmake', '0.1.50'), - ('core-foundation', '0.9.4'), - ('core-foundation-sys', '0.8.6'), - ('crc32fast', '1.4.0'), - ('curl', '0.4.46'), - ('curl-sys', '0.4.72+curl-8.6.0'), - ('darling', '0.14.4'), - ('darling_core', '0.14.4'), - ('darling_macro', '0.14.4'), + ('core-foundation', '0.9.3'), + ('core-foundation-sys', '0.8.4'), + ('crc32fast', '1.3.2'), + ('curl', '0.4.44'), + ('curl-sys', '0.4.61+curl-8.0.1'), + ('darling', '0.14.1'), + ('darling_core', '0.14.1'), + ('darling_macro', '0.14.1'), ('derive_builder', '0.11.2'), ('derive_builder_core', '0.11.2'), ('derive_builder_macro', '0.11.2'), ('dirs', '2.0.2'), ('dirs', '3.0.2'), ('dirs-sys', '0.3.7'), - ('either', '1.10.0'), - ('enum_dispatch', '0.3.12'), - ('errno', '0.3.8'), + ('either', '1.8.1'), + ('enum_dispatch', '0.3.11'), + ('errno', '0.3.1'), + ('errno-dragonfly', '0.1.2'), ('failure', '0.1.8'), ('failure_derive', '0.1.8'), - ('fastrand', '2.0.1'), - ('filetime', '0.2.23'), - ('flate2', '1.0.28'), + ('fastrand', '1.9.0'), + ('filetime', '0.2.21'), + ('flate2', '1.0.25'), ('fnv', '1.0.7'), ('foreign-types', '0.3.2'), ('foreign-types-shared', '0.1.1'), - ('form_urlencoded', '1.2.1'), - ('getrandom', '0.2.12'), - ('gimli', '0.28.1'), + ('form_urlencoded', '1.1.0'), + ('getrandom', '0.2.9'), + ('gimli', '0.27.2'), ('glob', '0.3.1'), ('heck', '0.4.1'), + ('hermit-abi', '0.3.1'), ('ident_case', '1.0.1'), - ('idna', '0.5.0'), + ('idna', '0.3.0'), ('indoc', '2.0.4'), + ('instant', '0.1.12'), ('intel-mkl-src', '0.5.0'), ('intel-mkl-tool', '0.1.0'), + ('io-lifetimes', '1.0.10'), ('itertools', '0.9.0'), ('itertools', '0.11.0'), - ('itoa', '1.0.10'), - ('jobserver', '0.1.28'), + ('itoa', '1.0.3'), + ('jobserver', '0.1.26'), ('lapack', '0.19.0'), ('lapack-src', '0.9.0'), ('lapack-sys', '0.14.0'), ('lazy_static', '1.4.0'), - ('libc', '0.2.153'), - ('libredox', '0.0.1'), - ('libz-sys', '1.1.15'), - ('linux-raw-sys', '0.4.13'), - ('lock_api', '0.4.11'), - ('log', '0.4.21'), - ('memchr', '2.7.1'), + ('libc', '0.2.149'), + ('libz-sys', '1.1.8'), + ('linux-raw-sys', '0.3.4'), + ('lock_api', '0.4.7'), + ('log', '0.4.17'), + ('memchr', '2.5.0'), ('memoffset', '0.9.0'), - ('miniz_oxide', '0.7.2'), + ('miniz_oxide', '0.6.2'), ('native-tls', '0.2.11'), ('netlib-src', '0.8.0'), ('num-complex', '0.4.5'), ('num-derive', '0.2.5'), ('num-traits', '0.2.18'), - ('object', '0.32.2'), - ('once_cell', '1.19.0'), - ('openblas-build', '0.10.9'), - ('openblas-src', '0.10.9'), - ('openssl', '0.10.64'), - ('openssl-macros', '0.1.1'), + ('object', '0.30.3'), + ('once_cell', '1.18.0'), + ('openblas-build', '0.10.8'), + ('openblas-src', '0.10.8'), + ('openssl', '0.10.52'), + ('openssl-macros', '0.1.0'), ('openssl-probe', '0.1.5'), - ('openssl-sys', '0.9.101'), + ('openssl-sys', '0.9.87'), ('parking_lot', '0.12.1'), - ('parking_lot_core', '0.9.9'), - ('percent-encoding', '2.3.1'), - ('pkg-config', '0.3.30'), + ('parking_lot_core', '0.9.3'), + ('percent-encoding', '2.2.0'), + ('pkg-config', '0.3.26'), ('portable-atomic', '1.6.0'), ('proc-macro2', '0.4.30'), - ('proc-macro2', '1.0.79'), + ('proc-macro2', '1.0.78'), ('pyo3', '0.20.3'), ('pyo3-build-config', '0.20.3'), ('pyo3-ffi', '0.20.3'), @@ -116,165 +119,177 @@ crates = [ 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'4dcd171b8776c41b97521e5da127a2d86ad280114807d0b2ab1e462bc764d9e1'}, + {'windows_x86_64_gnu-0.42.2.tar.gz': '8de912b8b8feb55c064867cf047dda097f92d51efad5b491dfb98f6bbb70cb36'}, + {'windows_x86_64_gnu-0.48.0.tar.gz': 'ca2b8a661f7628cbd23440e50b05d705db3686f894fc9580820623656af974b1'}, + {'windows_x86_64_gnullvm-0.42.2.tar.gz': '26d41b46a36d453748aedef1486d5c7a85db22e56aff34643984ea85514e94a3'}, + {'windows_x86_64_gnullvm-0.48.0.tar.gz': '7896dbc1f41e08872e9d5e8f8baa8fdd2677f29468c4e156210174edc7f7b953'}, + {'windows_x86_64_msvc-0.36.1.tar.gz': 'c811ca4a8c853ef420abd8592ba53ddbbac90410fab6903b3e79972a631f7680'}, + {'windows_x86_64_msvc-0.42.2.tar.gz': '9aec5da331524158c6d1a4ac0ab1541149c0b9505fde06423b02f5ef0106b9f0'}, + {'windows_x86_64_msvc-0.48.0.tar.gz': '1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a'}, + {'xattr-0.2.3.tar.gz': '6d1526bbe5aaeb5eb06885f4d987bcdfa5e23187055de9b83fe00156a821fabc'}, {'zstd-0.5.4+zstd.1.4.7.tar.gz': '69996ebdb1ba8b1517f61387a883857818a66c8a295f487b1ffd8fd9d2c82910'}, {'zstd-safe-2.0.6+zstd.1.4.7.tar.gz': '98aa931fb69ecee256d44589d19754e61851ae4769bf963b385119b1cc37a49e'}, {'zstd-sys-1.4.18+zstd.1.4.7.tar.gz': 'a1e6e8778706838f43f771d80d37787cb2fe06dafe89dd3aebaf6721b9eaec81'}, From cd210d311792f70e4fd6651a997fc9e5f259a991 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 19 Mar 2024 12:13:09 +0000 Subject: [PATCH 1028/1193] adding easyconfigs: phonemizer-3.2.1-gfbf-2023a.eb, eSpeak-NG-1.51-gfbf-2023a.eb, festival-2.5.0-GCCcore-12.3.0.eb, sonic-20180202-gfbf-2023a.eb, MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb, speech_tools-2.5.0-GCCcore-12.3.0.eb and patches: speech_tools-2.5.0_siodeditline.patch --- .../e/eSpeak-NG/eSpeak-NG-1.51-gfbf-2023a.eb | 50 +++++++ .../festival/festival-2.5.0-GCCcore-12.3.0.eb | 139 ++++++++++++++++++ ...ROLA-3.3-GCCcore-12.3.0-voices-20200330.eb | 54 +++++++ .../phonemizer/phonemizer-3.2.1-gfbf-2023a.eb | 73 +++++++++ .../s/sonic/sonic-20180202-gfbf-2023a.eb | 46 ++++++ .../speech_tools-2.5.0-GCCcore-12.3.0.eb | 67 +++++++++ .../speech_tools-2.5.0_siodeditline.patch | 14 ++ 7 files changed, 443 insertions(+) create mode 100644 easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.51-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb create mode 100644 easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch diff --git a/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.51-gfbf-2023a.eb b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.51-gfbf-2023a.eb new file mode 100644 index 000000000000..b00262893a25 --- /dev/null +++ b/easybuild/easyconfigs/e/eSpeak-NG/eSpeak-NG-1.51-gfbf-2023a.eb @@ -0,0 +1,50 @@ +easyblock = 'ConfigureMake' + +name = 'eSpeak-NG' +version = '1.51' + +homepage = 'https://github.com/espeak-ng/espeak-ng' +description = """ +The eSpeak NG is a compact open source software text-to-speech synthesizer +for Linux, Windows, Android and other operating systems. +It supports more than 100 languages and accents. +It is based on the eSpeak engine created by Jonathan Duddington. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://github.com/espeak-ng/espeak-ng/archive'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-1.50_sonic_fftw.patch', + '%(name)s-1.50_mbrola_location.patch', +] +checksums = [ + 'f0e028f695a8241c4fa90df7a8c8c5d68dcadbdbc91e758a97e594bbb0a3bdbf', # 1.50.tar.gz + 'dc34e14ef4b8bc174c94ad220cbf35b80e6183298d24883cf252507154ef4ee4', # eSpeak-NG-1.50_sonic_fftw.patch + '1bf9bb98f1fd35ddbd373b504c3215641db532093fc5dd44099a820b80c76f83', # eSpeak-NG-1.50_mbrola_location.patch +] + +builddependencies = [('Autotools', '20220317')] + +dependencies = [ + ('sonic', '20180202'), + ('MBROLA', '3.3', '-voices-20200330'), +] + +preconfigopts = './autogen.sh &&' + +configopts = '--disable-dependency-tracking' + +maxparallel = 1 +sanity_check_paths = { + 'files': ['bin/%sspeak%s' % (x, y) for x in ['', 'e'] for y in ['', '-ng']] + + ['include/espeak%s/speak_lib.h' % x for x in ['', '-ng']] + + ['include/espeak-ng/%s.h' % x for x in ['encoding', 'espeak_ng']] + + ['lib/libespeak%s' % x for x in ['.la', '-ng.a', '-ng.%s' % SHLIB_EXT]], + 'dirs': ['lib/pkgconfig'] +} + +sanity_check_commands = ['%sspeak%s --version' % (x, y) for x in ['', 'e'] for y in ['', '-ng']] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..ee472d99bd1a --- /dev/null +++ b/easybuild/easyconfigs/f/festival/festival-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,139 @@ +easyblock = 'ConfigureMake' + +name = 'festival' +version = '2.5.0' + +homepage = ['http://festvox.org/festival/'] + +description = """ +University of Edinburgh's Festival Speech Synthesis Systems is a free software +multi-lingual speech synthesis workbench that runs on multiple-platforms +offering black box text to speech, as well as an open architecture for +research in speech synthesis. +It designed as a component of large speech technology systems. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = [ + 'http://festvox.org/packed/festival/%(version_major_minor)s', + 'http://festvox.org/packed/festival/%(version_major_minor)s/voices', +] +sources = [{ + 'filename': '%(name)s-%(version)s-release.tar.gz', + 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1', +}] +local_sources = [ + 'festlex_CMU.tar.gz', + 'festlex_OALD.tar.gz', + 'festlex_POSLEX.tar.gz', + 'festvox_cmu_indic_ben_rm_cg.tar.gz', + 'festvox_cmu_indic_guj_ad_cg.tar.gz', + 'festvox_cmu_indic_guj_dp_cg.tar.gz', + 'festvox_cmu_indic_guj_kt_cg.tar.gz', + 'festvox_cmu_indic_hin_ab_cg.tar.gz', + 'festvox_cmu_indic_kan_plv_cg.tar.gz', + 'festvox_cmu_indic_mar_aup_cg.tar.gz', + 'festvox_cmu_indic_mar_slp_cg.tar.gz', + 'festvox_cmu_indic_pan_amp_cg.tar.gz', + 'festvox_cmu_indic_tam_sdr_cg.tar.gz', + 'festvox_cmu_indic_tel_kpn_cg.tar.gz', + 'festvox_cmu_indic_tel_sk_cg.tar.gz', + 'festvox_cmu_indic_tel_ss_cg.tar.gz', + 'festvox_cmu_us_aew_cg.tar.gz', + 'festvox_cmu_us_ahw_cg.tar.gz', + 'festvox_cmu_us_aup_cg.tar.gz', + 'festvox_cmu_us_awb_cg.tar.gz', + 'festvox_cmu_us_axb_cg.tar.gz', + 'festvox_cmu_us_bdl_cg.tar.gz', + 'festvox_cmu_us_clb_cg.tar.gz', + 'festvox_cmu_us_eey_cg.tar.gz', + 'festvox_cmu_us_fem_cg.tar.gz', + 'festvox_cmu_us_gka_cg.tar.gz', + 'festvox_cmu_us_jmk_cg.tar.gz', + 'festvox_cmu_us_ksp_cg.tar.gz', + 'festvox_cmu_us_ljm_cg.tar.gz', + 'festvox_cmu_us_lnh_cg.tar.gz', + 'festvox_cmu_us_rms_cg.tar.gz', + 'festvox_cmu_us_rxr_cg.tar.gz', + 'festvox_cmu_us_slp_cg.tar.gz', + 'festvox_cmu_us_slt_cg.tar.gz', + 'festvox_kallpc16k.tar.gz', + 'festvox_rablpc16k.tar.gz', +] +for local_x in local_sources: + local_newfilename = local_x.split('.') + local_newfilename[0] = local_newfilename[0] + '-%(version)s' + sources.append({ + 'download_filename': local_x, + 'filename': '.'.join(local_newfilename), + 'extract_cmd': 'tar xzf %s -C %(installdir)s --strip-components=1', + }) + +patches = ['%(name)s-%(version)s_speech_tools.patch'] +checksums = [ + '4c9007426b125290599d931df410e2def51e68a8aeebd89b4a61c7c96c09a4b4', # festival-2.5.0-release.tar.gz + 'c19430919bca45d5368cd4c82af6153fbcc96a487ebd30b78b5f3c08718b7c07', # festlex_CMU.tar.gz + 'e33a345390d4c76f8b987b06a5332bcdd0b168cf67c95ddc3270f9163cbe61f8', # festlex_OALD.tar.gz + 'e7c6e3642dbd5b0d64942bc015a986fdd6244a79e51ec2e8309e63d569e49ea3', # festlex_POSLEX.tar.gz + '56e2144d5eed6c89a451789ef7f37346dd351efdbb86a0fa650432a19b07367f', # festvox_cmu_indic_ben_rm_cg.tar.gz + '4a0ac2d1b15cd41108be803e23f11911be953b50733848a8e67428c642e02ba9', # festvox_cmu_indic_guj_ad_cg.tar.gz + '1a4e17d67db50a6d81f7860b64acc8d41245f6f763ccff4c9386ab9ae9923910', # festvox_cmu_indic_guj_dp_cg.tar.gz + '666017d8d64737c4fd70b72ab6cf846fd8e13de290a5ba494bd1697249a16e9d', # festvox_cmu_indic_guj_kt_cg.tar.gz + '60318e160d994d5174168cc94467c776de81426f91c4f8003206cff953cb79bd', # festvox_cmu_indic_hin_ab_cg.tar.gz + 'd87f4ea342e7cb37e90ddf49dde37f19c1470b3c5a09d00cef3212108107cb31', # festvox_cmu_indic_kan_plv_cg.tar.gz + '0c7509203483fc97c04b670127b20c2d51723b3a16517124e22d095f379cca7f', # festvox_cmu_indic_mar_aup_cg.tar.gz + 'f3be7241d35db1e18d652e2cfa4cb69bae038c3d21c59ed3ce365487894f0d46', # festvox_cmu_indic_mar_slp_cg.tar.gz + 'f1e9238c6b8646a2a252ab855f5773c8ebdf8b3df909e0bbe4a99d7b830a4f3e', # festvox_cmu_indic_pan_amp_cg.tar.gz + '9a4c088ce3bdbf17867d5df918fc3868597061380ae8daf896ce99d33723e570', # festvox_cmu_indic_tam_sdr_cg.tar.gz + '43ad700a82a270530dda44fd4a89b34429c37723cdde130faece4811723ff72b', # festvox_cmu_indic_tel_kpn_cg.tar.gz + '0ee102e8093a549171f5e4ff826ebf3f9eaf84e7d43259777e38cafe4c4b6eea', # festvox_cmu_indic_tel_sk_cg.tar.gz + 'b2e56ca4722e3d025d831fd1eef679ffbf00fe165b68a44a5596321411ffa1f0', # festvox_cmu_indic_tel_ss_cg.tar.gz + '5d9555580b95324fa734b7771c95dced44e7903510358481d24e4fe5c961111c', # festvox_cmu_us_aew_cg.tar.gz + '906492478bd86b5201f72ffe701279b98b3ba94ae74816a0d7f2ba20bc2b5bf7', # festvox_cmu_us_ahw_cg.tar.gz + '455476e1c5246d90aac090a06afa5a4e90c801aebace6fe357900c8e095be826', # festvox_cmu_us_aup_cg.tar.gz + 'b2adbdfeda0cba289bb4da68dd14114d3eb3e7f72049cc8d2cbdfb2df39f6934', # festvox_cmu_us_awb_cg.tar.gz + '172c826df9c8f49ecb03f997749b207a23de8678dcf13706709104c2c597ebfb', # festvox_cmu_us_axb_cg.tar.gz + '1dc6792af9e2c1660a46fe499aa67af4affa665a0bdc08207cc11719baa62f6d', # festvox_cmu_us_bdl_cg.tar.gz + '11c82d1c18ce3db6fb11ca788cc5d84f69f9346aff77c7495f50005d6b042148', # festvox_cmu_us_clb_cg.tar.gz + 'af8590f7c1ba7d5dba22ff52c30a7bb3f55592eabca9615cd712fa4da8f83e13', # festvox_cmu_us_eey_cg.tar.gz + 'f8788c2af4838bb90e0a859f38da66c95961bdff2572001d5a019a2127c74306', # festvox_cmu_us_fem_cg.tar.gz + '47cf21a96adfcad398bd28b4d2548493a2055f75e53cf71344eef3aebc03ab59', # festvox_cmu_us_gka_cg.tar.gz + '711db388bc500331cfda86a46a72193ca1e2c9dc7d5ef16dfc86827e499946f2', # festvox_cmu_us_jmk_cg.tar.gz + '3b8098ac30995ce245d518c5b8fee825917428cb3ebe0409a0b415c919bdd35f', # festvox_cmu_us_ksp_cg.tar.gz + 'aec062c3d0c30719dd7e3e9ee4c427cbaad5e47550e28af2e9f151a41dcad852', # festvox_cmu_us_ljm_cg.tar.gz + 'ece81f42379feba4c392ad723fb68374aff9cd78f57cf629f624b0bd0c928d08', # festvox_cmu_us_lnh_cg.tar.gz + '3167afa3a6ffb5bbc305c94a1e6b671e40783a87a49372fce04c54942872c421', # festvox_cmu_us_rms_cg.tar.gz + 'bf362b6f270b1a4c76be981c3e8bd862fbb17a64e971e5b4a84d970ed5ecec42', # festvox_cmu_us_rxr_cg.tar.gz + 'f1d8e601c9631dfb7f8bd05c341d9fce8899dc9547ed9a652c8ded6ab854de9a', # festvox_cmu_us_slp_cg.tar.gz + '78cb93e361ab016fd23833c56853ddf21e2f1356310f54eed1c09a9755ce9f43', # festvox_cmu_us_slt_cg.tar.gz + '809c4ab5ed9e4df4a658b58d5c56fe35055723f00d81a238168f5a1ebdaed08c', # festvox_kallpc16k.tar.gz + 'ecd14b77c528e94dfb076e44050102fe8fba57e5fe813acf78a66629317f52a5', # festvox_rablpc16k.tar.gz + '0716ea33c8eccee435ab08464657af2ec2b64cf02409cddb868f8ad869e7e172', # festival-2.5.0_speech_tools.patch +] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('speech_tools', '2.5.0'), +] + +# LIBS environmental variable interfers $EBROOTSPEECH_TOOLS/libs/Makefile +# line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) +prebuildopts = 'unset LIBS &&' + +buildininstalldir = True + +maxparallel = 1 + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/festival%s' % x for x in ['', '_client']] + + ['lib/%s.scm' % x for x in ['siod', 'web', 'cstr', 'fringe']], + 'dirs': ['lib/voices', 'lib/dicts/cmu', 'lib/dicts/oald'] +} + +sanity_check_commands = ['festival%s --version' % x for x in ['', '_client']] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb new file mode 100644 index 000000000000..4aaac643c39b --- /dev/null +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb @@ -0,0 +1,54 @@ +easyblock = 'MakeCp' + +name = 'MBROLA' +version = '3.3' +local_commit_voices = 'fe05a0c' +local_version_voices = '20200330' +versionsuffix = '-voices-%s' % local_version_voices + +homepage = ['https://github.com/numediart/MBROLA%s' % x for x in ['', '-voices']] + +description = """ +MBROLA is a speech synthesizer based on the concatenation of diphones. +It takes a list of phonemes as input, together with prosodic information +(duration of phonemes and a piecewise linear description of pitch), +and produces speech samples on 16 bits (linear), +at the sampling frequency of the diphone database. + +MBROLA voices project provides list of MBROLA speech synthesizer voices. +It is intended to provide easier collaboration and +automatic updates for individual users and packagers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/numediart/MBROLA%s/archive' % x for x in ['', '-voices']] +sources = [{ + 'download_filename': '%s.tar.gz' % version, + 'filename': SOURCE_TAR_GZ +}, { + 'download_filename': '%s.tar.gz' % local_commit_voices, + 'filename': '%%(name)s-voices-%s.tar.gz' % local_version_voices, +}] +patches = ['%(name)s-%(version)s_makefile.patch'] +checksums = [ + 'c01ded2c0a05667e6df2439c1c02b011a5df2bfdf49e24a524630686aea2b558', # MBROLA-3.3.tar.gz + '0dee14739f82fa247204791248b2d98a87e3f86f8cbb3a5844950103a41d33ba', # MBROLA-voices-20200330.tar.gz + '3f06bffdf900c51b531f473a760c50842ccf92a9d0598bd17fd556d049593a9e', # MBROLA-3.3_makefile.patch +] + +builddependencies = [('binutils', '2.40')] + +files_to_copy = [ + (['Bin/mbrola'], 'bin'), + (['../MBROLA-voices*/data/*'], 'share/mbrola'), +] + +sanity_check_paths = { + 'files': ['bin/mbrola'], + 'dirs': ['share/mbrola'] +} + +sanity_check_commands = ['mbrola -h'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb new file mode 100644 index 000000000000..6ed97510f571 --- /dev/null +++ b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb @@ -0,0 +1,73 @@ +easyblock = 'PythonBundle' + +name = 'phonemizer' +version = '3.2.1' +versionsuffix = '' + +homepage = "https://github.com/bootphon/phonemizer" +description = """ +The phonemizer allows simple phonemization of words and texts in many languages. +Provides both the phonemize command-line tool and the Python function phonemizer.phonemize. +It is using four backends: espeak, espeak-mbrola, festival and segments. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('eSpeak-NG', '1.51'), + ('festival', '2.5.0'), + ('hatchling', '1.18.0'), + ('RDFlib', '7.0.0'), + ('lxml', '4.9.2') +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('csvw', '3.3.0', { + 'checksums': ['59b6c4c725fb02138b3adb5e678e7b94f3baf7f8286c958fbd6d9d9aac5540d7'], + }), + ('language_tags', '1.2.0', { + 'checksums': ['e934acba3e3dc85f867703eca421847a9ab7b7679b11b5d5cfd096febbf8bde6'], + }), + ('uritemplate', '4.1.1', { + 'checksums': ['4346edfc5c3b79f694bccd6d6099a322bbeb628dbf2cd86eea55a456ce5124f0'], + }), + ('rfc3986', '1.5.0', { # csvw 3.3.0 has requirement rfc3986<2 + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('bibtexparser', '2.0.0b7', { # clldutils 3.22.2 has requirement bibtexparser>=2.0.0b4 + 'checksums': ['9e0034dd16e1961fbc895b108f49bdef6f988b5d48782b62c9492ee8a281efad'], + }), + ('pylatexenc', '2.10', { + 'checksums': ['3dd8fd84eb46dc30bee1e23eaab8d8fb5a7f507347b23e5f38ad9675c84f40d3'], + }), + ('colorlog', '6.8.2', { + 'checksums': ['3e3e079a41feb5a1b64f978b5ea4f46040a94f11f0e8bbb8261e3dbbeca64d44'], + }), + ('Markdown', '3.6', { + 'checksums': ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'], + }), + ('clldutils', '3.22.2', { + 'checksums': ['0efa914d0e0156bf707f8d0160ce9eacb9b088ffeab7afc61daccadd134007b1'], + }), + ('segments', '2.2.1', { + 'checksums': ['515ae188f21d24e420d48ad45689edc747d961d6b52fde22e47500a8d85f2741'], + }), + ('dlinfo', '1.2.1', { + 'checksums': ['5f6f43b47f3aa5fe12bd347cf536dc8fca6068c61a0a260e408bec7f6eb4bd38'], + }), + (name, version, { + 'checksums': ['068f85f85a8a9adc638a3787aeacaf71a53e47578b12d773c097433500cd892b'], + }), +] + +sanity_check_commands = [ + 'phonemize --version', + 'echo "hello world" | phonemize' +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb b/easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb new file mode 100644 index 000000000000..e8c95c58b916 --- /dev/null +++ b/easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb @@ -0,0 +1,46 @@ +easyblock = 'MakeCp' + +name = 'sonic' +local_commit = '134074f' +version = '20180202' + +homepage = 'https://github.com/espeak-ng/sonic' +description = """ +Sonic is a simple algorithm for speeding up or slowing down speech. However, +it's optimized for speed ups of over 2X, unlike previous algorithms for changing +speech rate. The Sonic library is a very simple ANSI C library that is designed +to easily be integrated into streaming voice applications, like TTS back ends. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/espeak-ng/sonic/archive'] +sources = [{ + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['%(name)s-%(version)s.patch'] +checksums = [ + 'ace1ef03ab095cb73066e57b2467faddef0356579099ba64e917bf9dab072709', # sonic-20180202.tar.gz + '1e767c98286e13231d01ec7ae2ec2ea9b9c0ce074d4f8034b9d92ee2854d1be9', # sonic-20180202.patch +] + +# dependencies = [('FFTW', '3.3.8')] +dependencies = [] + +keepsymlinks = True + +files_to_copy = [ + (['sonic'], 'bin'), + (['sonic.h'], 'include'), + (['libsonic*'], 'lib'), +] + +sanity_check_paths = { + 'files': ['bin/sonic', 'include/sonic.h'] + + ['lib/libsonic.%s' % x for x in ['a'] + [SHLIB_EXT + '%s' % y for y in ['', '.0', '.0.3.0']]], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..23ec75b979df --- /dev/null +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'speech_tools' +version = '2.5.0' + +homepage = ['http://festvox.org/festival/'] + +description = """ +The Edinburgh Speech Tools Library is a collection of C++ class, +functions and related programs for manipulating the sorts of objects +used in speech processing. It includes support for reading and writing +waveforms, parameter files (LPC, Ceptra, F0) in various formats +and converting between them. +It also includes support for linguistic type objects and support +for various label files and ngrams (with smoothing). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['http://festvox.org/packed/festival/%(version_major_minor)s'] +sources = ['%(name)s-%(version)s-release.tar.gz'] +patches = [ + '%(name)s-%(version)s_easybuild.patch', + 'speech_tools-2.5.0_siodeditline.patch' +] +checksums = [ + 'e4fd97ed78f14464358d09f36dfe91bc1721b7c0fa6503e04364fb5847805dcc', # speech_tools-2.5.0-release.tar.gz + '192012d97a671b151f084e0423042e03446a6031a8d7718354f2a56022210921', # speech_tools-2.5.0_easybuild.patch + '2d22ddad49c7fbc6b302087eae1515433f5f83d73cce1fd83b8f4f70a8834018', # speech_tools-2.5.0_siodeditline.patch +] + +unpack_options = '--strip-components=1' + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('ncurses', '6.4'), + ('Perl', '5.36.1'), +] + +# LIBS environmental variable interfers with libs/Makefile line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) +prebuildopts = 'unset LIBS &&' + +# If g++ used for compiling c++ files, then some extra link-time libraries detrmined wrongly +# and the binary creation fails +# buildopts = 'CXX="${CC}"' + +buildininstalldir = True + +maxparallel = 1 + +local_sanity = [ + 'align', 'bcat', 'ch_lab', 'ch_track', 'ch_utt', 'ch_wave', 'design_filter', 'est_program', 'na_play', + 'na_record', 'ngram_build', 'ols', 'pda', 'pitchmark', 'raw_to_xgraph', 'resynth', 'scfg_make', 'scfg_parse', + 'scfg_train', 'sig2fv', 'sigfilter', 'siod', 'spectgen', 'tex_to_images', 'tilt_analysis', 'tilt_synthesis', + 'viterbi', 'wagon', 'wfst_build', 'wfst_run', 'wfst_train', 'xml_parser', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_sanity + ['Makefile', 'pm']] + + ['lib/lib%s.a' % x for x in ['estbase', 'estools', 'eststring']], + 'dirs': [] +} + +sanity_check_commands = ['%s -h' % x for x in local_sanity] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch new file mode 100644 index 000000000000..bb1a17baa870 --- /dev/null +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch @@ -0,0 +1,14 @@ +diff --git a/siod/editline.c b/siod/editline.c +index f6eb5c6..d6163d8 100644 +--- a/siod/editline.c ++++ b/siod/editline.c +@@ -73,7 +73,7 @@ + /* modified by awb to allow specifcation of history size at run time */ + /* (though only once) */ + int editline_histsize=256; +-char *editline_history_file; ++// char *editline_history_file; + /* If this is defined it'll be called for completion first, before the */ + /* internal file name completion will be */ + EL_USER_COMPLETION_FUNCTION_TYPE*el_user_completion_function = NULL; + From 7596f519b9e2f0aa20f48b452b33828d5f5a8e57 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 19 Mar 2024 12:16:41 +0000 Subject: [PATCH 1029/1193] Add Scipy dep --- ....1-GCCcore-12.3.0.eb => Clarabel.rs-0.7.1-gfbf-2023a.eb} | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/Clarabel.rs/{Clarabel.rs-0.7.1-GCCcore-12.3.0.eb => Clarabel.rs-0.7.1-gfbf-2023a.eb} (99%) diff --git a/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-gfbf-2023a.eb similarity index 99% rename from easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb rename to easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-gfbf-2023a.eb index c2c1318cb69c..32eea7ff16f9 100644 --- a/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/c/Clarabel.rs/Clarabel.rs-0.7.1-gfbf-2023a.eb @@ -6,15 +6,15 @@ version = '0.7.1' homepage = "https://github.com/oxfordcontrol/Clarabel.rs" description = "Interior-point solver for convex conic optimisation problems in Rust." -toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchain = {'name': 'gfbf', 'version': '2023a'} builddependencies = [ - ('binutils', '2.40'), ('maturin', '1.4.0', '-Rust-1.75.0'), ] dependencies = [ ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), ] crates = [ @@ -374,6 +374,8 @@ checksums = [ {'zstd-sys-1.4.18+zstd.1.4.7.tar.gz': 'a1e6e8778706838f43f771d80d37787cb2fe06dafe89dd3aebaf6721b9eaec81'}, ] +options = {'modulename': 'clarabel'} + use_pip = True sanity_pip_check = True download_dep_fail = True From ceed342c8b942d7ba2198fc759238806696cb1c4 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Tue, 19 Mar 2024 13:28:27 +0100 Subject: [PATCH 1030/1193] adding easyconfigs: PyTorch-Lightning-2.2.1-foss-2023a-CUDA-12.1.1.eb --- ...-Lightning-2.2.1-foss-2023a-CUDA-12.1.1.eb | 172 ++++++++++++++++++ 1 file changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.2.1-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.2.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.2.1-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..9e4d061f6517 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-2.2.1-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,172 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '2.2.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('flit', '3.9.0'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.5'), + ('BeautifulSoup', '4.12.2'), + ('deepdiff', '6.7.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '2.1.2', versionsuffix), + ('tqdm', '4.66.1'), + ('tensorboardX', '2.6.2.2'), + ('pydantic', '2.5.3'), + ('typing-extensions', '4.9.0'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('mdurl', '0.1.2', { + 'checksums': ['bb413d29f5eea38f31dd4754dd7377d4465116fb207585f97bf925588687c1ba'], + }), + ('markdown-it-py', '3.0.0', { + 'modulename': 'markdown_it', + 'checksums': ['e3f60a94fa066dc52ec76661e37c851cb232d92f9886b15cb560aaada2df8feb'], + }), + ('rich', '13.7.1', { + 'checksums': ['9be308cb1fe2f1f57d67ce99e95af38a1e2bc71ad9813b0e247cf7ffbcc3a432'], + }), + ('PyJWT', '2.8.0', { + 'modulename': 'jwt', + 'checksums': ['57e28d156e3d5c10088e0c68abb90bfac3df82b40a71bd0daa20c65ccd5c23de'], + }), + ('starlette', '0.36.3', { + 'checksums': ['90a671733cfb35771d8cc605e0b679d23b992f8dcfad48cc60b38cb29aeb7080'], + }), + ('fastapi', '0.110.0', { + 'checksums': ['266775f0dcc95af9d3ef39bad55cff525329a931d5fd51930aadd4f428bf7ff3'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('exceptiongroup', '1.2.0', { + 'checksums': ['91f5c769735f051a4290d52edd0858999b57e5876e9f85937691bd4c9fa3ed68'], + }), + ('anyio', '4.3.0', { + 'checksums': ['f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6'], + }), + ('websocket-client', '1.7.0', { + 'modulename': 'websocket', + 'checksums': ['10e511ea3a8c744631d3bd77e61eb17ed09304c413ad42cf6ddfa4c7787e8fe6'], + }), + ('python_multipart', '0.0.9', { + 'modulename': 'multipart', + 'checksums': ['03f54688c663f1b7977105f021043b0793151e4cb1c1a9d4a11fc13d622c4026'], + }), + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('uvicorn', '0.27.1', { + 'checksums': ['3d9a267296243532db80c83a959a3400502165ade2c1338dea4e67915fd4745a'], + }), + ('lightning_cloud', '0.5.64', { + 'checksums': ['44c44b387260e7f808bef7a2368966da166bf58fa37562a8ce8366febe3ca38e'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '2.1.3', { + 'checksums': ['d20c5f277b64a86c16819f65ac50814ccdbd146776159e08c88b378b6612297d'], + }), + ('fsspec', '2024.2.0', { + 'checksums': ['b6ad1a679f760dda52b1168c859d01b7b80648ea6f7f7c7f5a8a91dc3f3ecb84'], + }), + ('croniter', '2.0.2', { + 'checksums': ['8bff16c9af4ef1fb6f05416973b8f7cb54997c02f2f8365251f9bf1dded91866'], + }), + ('traitlets', '5.14.1', { + 'checksums': ['8585105b371a04b8316a43d5ce29c098575c2e477850b62b848b964f1444527e'], + }), + ('types-python-dateutil', '2.8.19.20240106', { + 'modulename': False, + 'checksums': ['1f8db221c3b98e6ca02ea83a58371b22c374f42ae5bbdf186db9c9a76581459f'], + }), + ('arrow', '1.3.0', { + 'preinstallopts': "PYTHONPATH=$PWD:$PYTHONPATH ", + 'checksums': ['d4540617648cb5f895730f1ad8c82a65f2dad0166f57b75f3ca54759c4d67a85'], + }), + ('lightning-utilities', '0.10.1', { + 'checksums': ['362755023dcf93b8fa519bc002ae41794943a3ffbc5318e40804d36aa14bf1fd'], + }), + ('blessed', '1.20.0', { + 'checksums': ['2cdd67f8746e048f00df47a2880f4d6acbcdb399031b604e34ba8f71d5787680'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.5', { + 'checksums': ['08a456c2d7c1888cde3f4688b542621b676eb38cd6cfed7eb6cb2e2905ddc826'], + }), + ('runs', '1.2.2', { + 'checksums': ['9dc1815e2895cfb3a48317b173b9f1eac9ba5549b36a847b5cc60c3bf82ecef1'], + }), + ('xmod', '1.8.1', { + 'checksums': ['38c76486b9d672c546d57d8035df0beb7f4a9b088bc3fb2de5431ae821444377'], + }), + ('editor', '1.6.6', { + 'checksums': ['bb6989e872638cd119db9a4fce284cd8e13c553886a1c044c6b8d8a160c871f8'], + }), + ('inquirer', '3.2.4', { + 'checksums': ['33b09efc1b742b9d687b540296a8b6a3f773399673321fcc2ab0eb4c109bf9b5'], + }), + ('wrapt', '1.16.0', { + 'checksums': ['5f370f952971e7d17c7d1ead40e49f32345a7f7a5373571ef44d800d06b1899d'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('botocore', '1.34.51', { + 'checksums': ['5086217442e67dd9de36ec7e87a0c663f76b7790d5fb6a12de565af95e87e319'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.10.0', { + 'checksums': ['d0c8bbf672d5eebbe4e57945e23b972d963f07d82f661cabf678a5c88831595b'], + }), + ('boto3', '1.34.51', { + 'checksums': ['2cd9463e738a184cbce8a6824027c22163c5f73e277a35ff5aa0fb0e845b4301'], + }), + ('aiobotocore', '2.12.1', { + 'checksums': ['8706b28f16f93c541f6ed50352115a79d8f3499539f8d0bb70aa0f7a5379c1fe'], + }), + ('s3fs', '2024.2.0', { + 'checksums': ['f8064f522ad088b56b043047c825734847c0269df19f2613c956d4c20de15b62'], + }), + ('torchmetrics', '1.3.1', { + 'checksums': ['8d371f7597a1a5eb02d5f2ed59642d6fef09093926997ce91e18b1147cc8defa'], + }), + ('pytorch-lightning', version, { + 'checksums': ['aa3be30c9109239a371748565a7f4b7b41ea1395725c30e04426cf946b3e2745'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'lib/python%(pyshortver)s/site-packages/dateutil-stubs'], +} + +sanity_pip_check = True + +moduleclass = 'lib' From fe96012163bfd96d0bd5cf68cf0f6e040e7af2ec Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 19 Mar 2024 12:31:11 +0000 Subject: [PATCH 1031/1193] Fix clarabel.rs dependency --- easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb index 50813b5f9ae3..c250eee145da 100644 --- a/easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb +++ b/easybuild/easyconfigs/c/CVXPY/CVXPY-1.4.2-foss-2023a.eb @@ -15,11 +15,13 @@ toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ ('CMake', '3.26.3'), ('SWIG', '4.1.1'), + ('meson-python', '0.15.0'), # for csc ] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), + ('Clarabel.rs', '0.7.1'), ] use_pip = True From b249b0ee577c6eee6b91f85db1d83b95c9f58298 Mon Sep 17 00:00:00 2001 From: c3-builder Date: Tue, 19 Mar 2024 13:16:24 +0000 Subject: [PATCH 1032/1193] Fix style and add comments to patch --- .../p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb | 8 +++++--- .../speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb | 10 +++------- .../speech_tools/speech_tools-2.5.0_siodeditline.patch | 3 +++ 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb index 6ed97510f571..907228d92817 100644 --- a/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb +++ b/easybuild/easyconfigs/p/phonemizer/phonemizer-3.2.1-gfbf-2023a.eb @@ -20,7 +20,7 @@ dependencies = [ ('festival', '2.5.0'), ('hatchling', '1.18.0'), ('RDFlib', '7.0.0'), - ('lxml', '4.9.2') + ('lxml', '4.9.2'), ] use_pip = True @@ -36,10 +36,12 @@ exts_list = [ ('uritemplate', '4.1.1', { 'checksums': ['4346edfc5c3b79f694bccd6d6099a322bbeb628dbf2cd86eea55a456ce5124f0'], }), - ('rfc3986', '1.5.0', { # csvw 3.3.0 has requirement rfc3986<2 + # csvw 3.3.0 has requirement rfc3986<2 + ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('bibtexparser', '2.0.0b7', { # clldutils 3.22.2 has requirement bibtexparser>=2.0.0b4 + # clldutils 3.22.2 has requirement bibtexparser>=2.0.0b4 + ('bibtexparser', '2.0.0b7', { 'checksums': ['9e0034dd16e1961fbc895b108f49bdef6f988b5d48782b62c9492ee8a281efad'], }), ('pylatexenc', '2.10', { diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb index 23ec75b979df..6f2fcee17194 100644 --- a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0-GCCcore-12.3.0.eb @@ -20,13 +20,13 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['http://festvox.org/packed/festival/%(version_major_minor)s'] sources = ['%(name)s-%(version)s-release.tar.gz'] patches = [ - '%(name)s-%(version)s_easybuild.patch', - 'speech_tools-2.5.0_siodeditline.patch' + 'speech_tools-2.5.0_easybuild.patch', + 'speech_tools-2.5.0_siodeditline.patch', ] checksums = [ 'e4fd97ed78f14464358d09f36dfe91bc1721b7c0fa6503e04364fb5847805dcc', # speech_tools-2.5.0-release.tar.gz '192012d97a671b151f084e0423042e03446a6031a8d7718354f2a56022210921', # speech_tools-2.5.0_easybuild.patch - '2d22ddad49c7fbc6b302087eae1515433f5f83d73cce1fd83b8f4f70a8834018', # speech_tools-2.5.0_siodeditline.patch + 'b65a91319dbfb11ffe839fb741be832ebe6cc00b820ab6a609c9603f073d8a07', # speech_tools-2.5.0_siodeditline.patch ] unpack_options = '--strip-components=1' @@ -41,10 +41,6 @@ dependencies = [ # LIBS environmental variable interfers with libs/Makefile line 61: LIBS_ABS=$(subst $(TOP),$$(EST_HOME),$(LIBS)) prebuildopts = 'unset LIBS &&' -# If g++ used for compiling c++ files, then some extra link-time libraries detrmined wrongly -# and the binary creation fails -# buildopts = 'CXX="${CC}"' - buildininstalldir = True maxparallel = 1 diff --git a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch index bb1a17baa870..5da729fe68c7 100644 --- a/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch +++ b/easybuild/easyconfigs/s/speech_tools/speech_tools-2.5.0_siodeditline.patch @@ -1,3 +1,6 @@ +# Fix compilation error: multiple definition of `editline_history_file' +# The variable is defined in both editline.c and siodeditline.c +# Author: Chia-Jung Hsu, 2024-03-19 diff --git a/siod/editline.c b/siod/editline.c index f6eb5c6..d6163d8 100644 --- a/siod/editline.c From 4c3d9388d70781a11c4adf5f06878ffa701936b5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 19 Mar 2024 16:55:07 +0100 Subject: [PATCH 1033/1193] Fix test issues in PyTorch-2.1.2-foss-2023a-CUDA-12.1.1 --- .../PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 17 ++- ...-locale-issue-in-nvrtcCompileProgram.patch | 106 ++++++++++++++++++ ...ch-2.1.2_fix-with_temp_dir-decorator.patch | 19 ++++ ..._fix-wrong-device-mesh-size-in-tests.patch | 28 +++++ ...-test_fsdp_tp_checkpoint_integration.patch | 33 ++++++ 5 files changed, 202 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-locale-issue-in-nvrtcCompileProgram.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-with_temp_dir-decorator.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-wrong-device-mesh-size-in-tests.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index 225928ed9cbb..fdb202fa951e 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -47,15 +47,19 @@ patches = [ 'PyTorch-2.1.2_add-cuda-skip-markers.patch', 'PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch', 'PyTorch-2.1.2_fix-device-mesh-check.patch', + 'PyTorch-2.1.2_fix-locale-issue-in-nvrtcCompileProgram.patch', 'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch', 'PyTorch-2.1.2_fix-test_memory_profiler.patch', 'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch', 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', 'PyTorch-2.1.2_fix-vsx-vector-div.patch', + 'PyTorch-2.1.2_fix-with_temp_dir-decorator.patch', + 'PyTorch-2.1.2_fix-wrong-device-mesh-size-in-tests.patch', 'PyTorch-2.1.2_relax-cuda-tolerances.patch', 'PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch', 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', 'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch', + 'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch', 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', ] checksums = [ @@ -120,6 +124,8 @@ checksums = [ {'PyTorch-2.1.2_fix-conj-mismatch-test-failures.patch': 'c164357efa4ce88095376e590ba508fc1daa87161e1e59544eda56daac7f2847'}, {'PyTorch-2.1.2_fix-device-mesh-check.patch': 'c0efc288bf3d9a9a3c8bbd2691348a589a2677ea43880a8c987db91c8de4806b'}, + {'PyTorch-2.1.2_fix-locale-issue-in-nvrtcCompileProgram.patch': + 'f7adafb4e4d3b724b93237a259797b6ed6f535f83be0e34a7b759c71c6a8ddf2'}, {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch': 'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'}, {'PyTorch-2.1.2_fix-test_memory_profiler.patch': @@ -128,6 +134,10 @@ checksums = [ 'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'}, {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'}, {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, + {'PyTorch-2.1.2_fix-with_temp_dir-decorator.patch': + '90bd001e034095329277d70c6facc4026b4ce6d7f8b8d6aa81c0176eeb462eb1'}, + {'PyTorch-2.1.2_fix-wrong-device-mesh-size-in-tests.patch': + '07a5e4233d02fb6348872838f4d69573c777899c6f0ea4e39ae23c08660d41e5'}, {'PyTorch-2.1.2_relax-cuda-tolerances.patch': '554ad09787f61080fafdb84216e711e32327aa357e2a9c40bb428eb6503dee6e'}, {'PyTorch-2.1.2_remove-nccl-backend-default-without-gpus.patch': 'e6a1efe3d127fcbf4723476a7a1c01cfcf2ccb16d1fb250f478192623e8b6a15'}, @@ -135,6 +145,8 @@ checksums = [ '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, {'PyTorch-2.1.2_skip-failing-test_dtensor_ops-subtests.patch': '6cf711bf26518550903b09ed4431de9319791e79d61aab065785d6608fd5cc88'}, + {'PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch': + '943ee92f5fd518f608a59e43fe426b9bb45d7e7ad0ba04639e516db2d61fa57d'}, {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, ] @@ -191,6 +203,8 @@ excluded_tests = { # intermittent failures on various systems # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 'distributed/rpc/test_tensorpipe_agent', + # Broken test, can't ever succeed, see https://github.com/pytorch/pytorch/issues/122184 + 'distributed/tensor/parallel/test_tp_random_state.py', # failures on OmniPath systems, which don't support some optional InfiniBand features # See https://github.com/pytorch/tensorpipe/issues/413 'distributed/pipeline/sync/skip/test_gpipe', @@ -206,8 +220,9 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # Especially test_quantization has a few corner cases that are triggered by the random input values, # those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# test_nn is also prone to spurious failures: https://github.com/pytorch/pytorch/issues/118294 # So allow a low number of tests to fail as the tests "usually" succeed -max_failed_tests = 50 +max_failed_tests = 2 # The readelf sanity check command can be taken out once the TestRPATH test from # https://github.com/pytorch/pytorch/pull/109493 is accepted, since it is then checked as part of the PyTorch test suite diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-locale-issue-in-nvrtcCompileProgram.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-locale-issue-in-nvrtcCompileProgram.patch new file mode 100644 index 000000000000..a8aa712d4ada --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-locale-issue-in-nvrtcCompileProgram.patch @@ -0,0 +1,106 @@ +There is a bug in CUDA 11.7 through at least CUDA 12.4 which changes the current thread locale +when calling nvrtcCompileProgram. +See e.g. https://stackoverflow.com/questions/74044994 +This also includes the encoding used by Python by default for e.g. subsequent invocations of `subprocess` calls. +When the user environment is now set to e.g. UTF-8 and changed by CUDA (to ASCII/ANSI_X3.4-1968) Python will fail +to decode UTF-8 output from programs invoked. +This happens e.g. in `test_torch` which calls `from scipy import stats` which runs `lscpu` and errors +with something like +> /software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages/numpy/testing/_private/utils.py", line 1253, in +> _SUPPORTS_SVE = check_support_sve() +> /software/SciPy-bundle/2023.07-gfbf-2023a/lib/python3.11/site-packages/numpy/testing/_private/utils.py", line 1247, in check_support_sve +> output = subprocess.run(cmd, capture_output=True, text=True) +> /software/Python/3.11.3-GCCcore-12.3.0/lib/python3.11/subprocess.py", line 2113, in _communicate +> stdout = self._translate_newlines(stdout, +> UnicodeDecodeError: 'ascii' codec can't decode byte 0xc3 in position 96: ordinal not in range(128) + +Fix by wrapping the nvrtcCompileProgram saving and restoring the thread locale. + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cuda/detail/LazyNVRTC.cpp b/aten/src/ATen/cuda/detail/LazyNVRTC.cpp +index 1b85e7776e2..1c13a3b1168 100644 +--- a/aten/src/ATen/cuda/detail/LazyNVRTC.cpp ++++ b/aten/src/ATen/cuda/detail/LazyNVRTC.cpp +@@ -2,6 +2,7 @@ + + #include + #include ++#include + #include + + namespace at { +@@ -143,6 +144,29 @@ nvrtcResult nvrtcCreateProgram(nvrtcProgram *prog, + return fn(prog, src, name, numHeaders, headers, includeNames); + } + ++nvrtcResult nvrtcCompileProgram_wrapped(nvrtcProgram prog, ++ int numOptions, ++ const char * const *options) { ++ // Save & restore current thread locale which can get modified by nvrtcCompileProgram ++ locale_t oldLocale = uselocale((locale_t) 0); ++ auto result = lazyNVRTC.nvrtcCompileProgram_real(prog, numOptions, options); ++ if (oldLocale != (locale_t) 0) ++ uselocale(oldLocale); ++ return result; ++} ++ ++nvrtcResult nvrtcCompileProgram(nvrtcProgram prog, ++ int numOptions, ++ const char * const *options) { ++ auto fn = reinterpret_cast(getNVRTCLibrary().sym(__func__)); ++ if (!fn) ++ throw std::runtime_error("Can't get nvrtcCompileProgram"); ++ lazyNVRTC.nvrtcCompileProgram_real = fn; ++ fn = &nvrtcCompileProgram_wrapped; ++ lazyNVRTC.nvrtcCompileProgram = fn; ++ return fn(prog, numOptions, options); ++} ++ + NVRTC_STUB1(nvrtcDestroyProgram, nvrtcProgram *); + NVRTC_STUB2(nvrtcGetPTXSize, nvrtcProgram, size_t *); + NVRTC_STUB2(nvrtcGetPTX, nvrtcProgram, char *); +@@ -150,7 +174,6 @@ NVRTC_STUB2(nvrtcGetPTX, nvrtcProgram, char *); + NVRTC_STUB2(nvrtcGetCUBINSize, nvrtcProgram, size_t *); + NVRTC_STUB2(nvrtcGetCUBIN, nvrtcProgram, char *); + #endif +-NVRTC_STUB3(nvrtcCompileProgram, nvrtcProgram, int, const char * const *); + _STUB_1(NVRTC, nvrtcGetErrorString, const char *, nvrtcResult); + NVRTC_STUB2(nvrtcGetProgramLogSize,nvrtcProgram, size_t*); + NVRTC_STUB2(nvrtcGetProgramLog, nvrtcProgram, char *); +diff --git a/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h b/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h +index 574b2c41c26..4ddc5316dad 100644 +--- a/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h ++++ b/aten/src/ATen/cuda/nvrtc_stub/ATenNVRTC.h +@@ -120,6 +120,8 @@ extern "C" typedef struct NVRTC { + #define CREATE_MEMBER(name) decltype(&name) name; + AT_FORALL_NVRTC(CREATE_MEMBER) + #undef CREATE_MEMBER ++ // Must be at end! ++ decltype(nvrtcCompileProgram) nvrtcCompileProgram_real; + } NVRTC; + + extern "C" TORCH_CUDA_CPP_API NVRTC* load_nvrtc(); +diff --git a/caffe2/cuda_rtc/common_rtc.h b/caffe2/cuda_rtc/common_rtc.h +index 9d9582d34b6..562a653a67a 100644 +--- a/caffe2/cuda_rtc/common_rtc.h ++++ b/caffe2/cuda_rtc/common_rtc.h +@@ -1,6 +1,7 @@ + #ifndef CAFFE2_CUDA_RTC_COMMON_RTC_H_ + #define CAFFE2_CUDA_RTC_COMMON_RTC_H_ + ++#include + #include + #include + +@@ -46,7 +47,10 @@ class CudaRTCFunction { + // coding it? + const char* nvrtc_opts[] = { + "--gpu-architecture=compute_35", "--use_fast_math"}; ++ locale_t oldLocale = uselocale((locale_t) 0); + nvrtcResult compile_result = nvrtcCompileProgram(prog, 2, nvrtc_opts); ++ if (oldLocale != (locale_t) 0) ++ uselocale(oldLocale); + if (compile_result != NVRTC_SUCCESS) { + size_t log_size; + NVRTC_CHECK(nvrtcGetProgramLogSize(prog, &log_size)); diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-with_temp_dir-decorator.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-with_temp_dir-decorator.patch new file mode 100644 index 000000000000..3834bdf3d258 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-with_temp_dir-decorator.patch @@ -0,0 +1,19 @@ +The decorator fails to pass the argument list to the function. +This then fails e.g. test/distributed/checkpoint/test_fsdp_optim_state.py with +> TypeError: FsdpOptimStateCheckpoint.test_load_sharded_optimizer_state_dict() missing 1 required positional argument: 'pass_planner' + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/distributed/checkpoint_utils.py b/torch/testing/_internal/distributed/checkpoint_utils.py +index 1a6e43a038c..52f79b37bfd 100644 +--- a/torch/testing/_internal/distributed/checkpoint_utils.py ++++ b/torch/testing/_internal/distributed/checkpoint_utils.py +@@ -31,7 +31,7 @@ def with_temp_dir( + self.temp_dir = object_list[0] + + try: +- func(self) ++ func(self, *args, **kwargs) + finally: + if dist.get_rank() == 0: + shutil.rmtree(self.temp_dir, ignore_errors=True) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-wrong-device-mesh-size-in-tests.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-wrong-device-mesh-size-in-tests.patch new file mode 100644 index 000000000000..9d8676074721 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_fix-wrong-device-mesh-size-in-tests.patch @@ -0,0 +1,28 @@ +From 1d1308649298caf8884970fc57ed82a2d8ea6079 Mon Sep 17 00:00:00 2001 +From: Xilun Wu <12968408+XilunWu@users.noreply.github.com> +Date: Tue, 26 Dec 2023 17:48:11 -0800 +Subject: [PATCH] [BE] force DTensorTestBase.build_device_mesh to use + world_size rather than NUM_DEVICES constant (#116439) + +**Test**: +`python test/distributed/fsdp/test_shard_utils.py -k test_create_chunk_dtensor` + +Pull Request resolved: https://github.com/pytorch/pytorch/pull/116439 +Approved by: https://github.com/wanchaol +--- + torch/testing/_internal/distributed/_tensor/common_dtensor.py | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/torch/testing/_internal/distributed/_tensor/common_dtensor.py b/torch/testing/_internal/distributed/_tensor/common_dtensor.py +index ab86ecd1616a74f..05a3c0872878965 100644 +--- a/torch/testing/_internal/distributed/_tensor/common_dtensor.py ++++ b/torch/testing/_internal/distributed/_tensor/common_dtensor.py +@@ -192,7 +192,7 @@ def backend(self) -> str: + return PG_BACKEND + + def build_device_mesh(self) -> DeviceMesh: +- return DeviceMesh(DEVICE_TYPE, list(range(NUM_DEVICES))) ++ return DeviceMesh(DEVICE_TYPE, list(range(self.world_size))) + + def init_pg(self) -> None: + if "nccl" in self.backend and torch.cuda.device_count() < self.world_size: diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch new file mode 100644 index 000000000000..6a0461a7dcb4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2_skip-test_fsdp_tp_checkpoint_integration.patch @@ -0,0 +1,33 @@ +test_fsdp_tp_checkpoint_integration in distributed/fsdp/test_fsdp_tp_integration.py +fails due to a regression. See https://github.com/pytorch/pytorch/issues/101162 + +> RuntimeError: Error(s) in loading state_dict for FullyShardedDataParallel: +> size mismatch for _fsdp_wrapped_module.net1.weight: copying a param with shape torch.Size([4, 5]) from checkpoint, the shape in current model is torch.Size([8, 5]). +> size mismatch for _fsdp_wrapped_module.net1.bias: copying a param with shape torch.Size([4]) from checkpoint, the shape in current model is torch.Size([8]). +> size mismatch for _fsdp_wrapped_module.net2.weight: copying a param with shape torch.Size([4, 4]) from checkpoint, the shape in current model is torch.Size([4, 8]). + +Skip the test. This should be fixed already for 2.2.x + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/fsdp/test_fsdp_tp_integration.py b/test/distributed/fsdp/test_fsdp_tp_integration.py +index bc7a4aef4a3..aea16a1f1fb 100644 +--- a/test/distributed/fsdp/test_fsdp_tp_integration.py ++++ b/test/distributed/fsdp/test_fsdp_tp_integration.py +@@ -3,6 +3,7 @@ import copy + import sys + from collections import OrderedDict + from typing import Any, Dict, List, Optional, Tuple ++import unittest + + import torch + from torch import distributed as dist +@@ -306,7 +307,7 @@ class TestTPFSDPIntegration(FSDPTest): + tp_fsdp_out = tp_fsdp_model(inp) + self.assertEqual(fsdp_out, tp_fsdp_out) + +- @skip_if_lt_x_gpu(4) ++ @unittest.skip("Known failure: #101162") + def test_fsdp_tp_checkpoint_integration(self): + """Tests checkpointing for TP + FSDP integration.""" + self.assertTrue( From 61d3790cbd5233bb26ec5e2b5e967decaf71d926 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 19 Mar 2024 17:17:49 +0100 Subject: [PATCH 1034/1193] Force MBROLA serial build --- .../m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb index 4aaac643c39b..503f9b4e9706 100644 --- a/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb +++ b/easybuild/easyconfigs/m/MBROLA/MBROLA-3.3-GCCcore-12.3.0-voices-20200330.eb @@ -39,6 +39,8 @@ checksums = [ builddependencies = [('binutils', '2.40')] +maxparallel = 1 + files_to_copy = [ (['Bin/mbrola'], 'bin'), (['../MBROLA-voices*/data/*'], 'share/mbrola'), From bb22d632a4fc6ce26724a738b50f2af69c07ccdc Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen <33718780+casparvl@users.noreply.github.com> Date: Tue, 19 Mar 2024 18:37:04 +0100 Subject: [PATCH 1035/1193] Bin and lib checking not needed, we already check files within those folders Co-authored-by: Kenneth Hoste --- easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb b/easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb index 81674ed4aea8..98acd7a21be5 100644 --- a/easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb +++ b/easybuild/easyconfigs/m/MODFLOW/MODFLOW-6.4.4-foss-2023a.eb @@ -40,7 +40,7 @@ sanity_check_commands = ['mf6 --version'] sanity_check_paths = { 'files': ['bin/mf6', 'bin/mf5to6', 'bin/zbud6', 'lib/libmf6.%s' % SHLIB_EXT], - 'dirs': ['bin', 'lib'], + 'dirs': [], } moduleclass = 'geo' From 55ceac373f46884aa3aba11c720b80b624e8d0fb Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Tue, 19 Mar 2024 23:48:51 +0100 Subject: [PATCH 1036/1193] Remove unused comment, variable --- easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb b/easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb index e8c95c58b916..24c27f3b4bce 100644 --- a/easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb +++ b/easybuild/easyconfigs/s/sonic/sonic-20180202-gfbf-2023a.eb @@ -26,9 +26,6 @@ checksums = [ '1e767c98286e13231d01ec7ae2ec2ea9b9c0ce074d4f8034b9d92ee2854d1be9', # sonic-20180202.patch ] -# dependencies = [('FFTW', '3.3.8')] -dependencies = [] - keepsymlinks = True files_to_copy = [ From ca6a9a30152be4f05b020ce6f1a1f1037c3af5b9 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Wed, 20 Mar 2024 12:44:48 +0800 Subject: [PATCH 1037/1193] adding easyconfigs: BerkeleyGW-4.0-foss-2022a.eb and patches: BerkeleyGW-4.0_makefile.patch, BerkeleyGW-4.0_tests.patch --- .../b/BerkeleyGW/BerkeleyGW-4.0-foss-2022a.eb | 34 ++++++++++++++++ .../BerkeleyGW/BerkeleyGW-4.0_makefile.patch | 24 +++++++++++ .../b/BerkeleyGW/BerkeleyGW-4.0_tests.patch | 40 +++++++++++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_makefile.patch create mode 100644 easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_tests.patch diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0-foss-2022a.eb b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0-foss-2022a.eb new file mode 100644 index 000000000000..8ff40739c760 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0-foss-2022a.eb @@ -0,0 +1,34 @@ +name = 'BerkeleyGW' +version = '4.0' + +homepage = 'https://www.berkeleygw.org' +description = """The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle + properties and the optical responses of a large variety of materials from bulk periodic crystals to + nanostructures such as slabs, wires and molecules.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://app.box.com/shared/static/'] +sources = [{'download_filename': '22edl07muvhfnd900tnctsjjftbtcqc4.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'BerkeleyGW-4.0_tests.patch', + 'BerkeleyGW-4.0_makefile.patch', +] +checksums = [ + {'BerkeleyGW-4.0.tar.gz': '1a85b03b83b339056f65124bfa96832ca61152236d9bb1cb372e3040fc686a49'}, + {'BerkeleyGW-4.0_tests.patch': 'e544a53613bb3e6a779813f301912b6c6ca8a55215f77faf6827fc6eeeb5459d'}, + {'BerkeleyGW-4.0_makefile.patch': '0aa7c1dbdfa94d9be6835cb0a768559df1e43a1a8b73a2143f09f99981f8041c'}, +] + +dependencies = [ + ('ELPA', '2021.11.001'), + ('Perl', '5.34.1'), + ('Python', '3.10.4'), + ('h5py', '3.7.0'), + ('fftlib', '20170628'), +] + +runtest = True + +moduleclass = 'phys' diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_makefile.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_makefile.patch new file mode 100644 index 000000000000..6c7f69eb8bfe --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_makefile.patch @@ -0,0 +1,24 @@ +* don't rebuild flavors when installing and checking, and check using MPI +author: Miguel Dias Costa (National University of Singapore) +--- BerkeleyGW-4.0/Makefile.orig 2024-03-20 11:08:04.996274767 +0800 ++++ BerkeleyGW-4.0/Makefile 2024-03-20 11:08:22.466174576 +0800 +@@ -130,7 +130,7 @@ + cp flavor_cplx.mk flavor.mk + $(MAKE) all + +-install: all ++install: + ifdef INSTDIR + mkdir -p $(INSTDIR)/bin + install bin/*.x $(INSTDIR)/bin/ +@@ -152,8 +152,8 @@ + $(error Error: Please define installation prefix INSTDIR via 'make install INSTDIR='.) + endif + +-check: all +- cd testsuite && $(MAKE) check ++check: ++ cd testsuite && $(MAKE) check-parallel + + check-save: all + cd testsuite && $(MAKE) check-save diff --git a/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_tests.patch b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_tests.patch new file mode 100644 index 000000000000..78f0c4de3bf2 --- /dev/null +++ b/easybuild/easyconfigs/b/BerkeleyGW/BerkeleyGW-4.0_tests.patch @@ -0,0 +1,40 @@ +* allow test scripts to inherit environment +* set stack size ulimit to unlimited +* slightly raise tolerance in some tests +author: Miguel Dias Costa (National University of Singapore) +--- BerkeleyGW-4.0/testsuite/run_testsuite.sh.orig 2024-03-20 01:10:39.000000000 +0800 ++++ BerkeleyGW-4.0/testsuite/run_testsuite.sh 2024-03-20 11:11:19.179296008 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + # + # Copyright (C) 2005-2009 Heiko Appel, David Strubbe + # +@@ -66,6 +66,8 @@ + # Run all tests. Takes as first argument a list of testfile names. + function run_testsuite() { + ++ulimit -s unlimited ++ + tests="$1" + + # Check for 'preserve working directories' flag. +--- BerkeleyGW-4.0/MeanField/Utilities/mf_convert_wrapper.sh.orig 2024-03-20 11:11:41.219446558 +0800 ++++ BerkeleyGW-4.0/MeanField/Utilities/mf_convert_wrapper.sh 2024-03-20 11:11:56.019547652 +0800 +@@ -1,4 +1,4 @@ +-#!/bin/bash -l ++#!/bin/bash + + # David Strubbe, October 2010 + # Wrapper for mf_convert.x +--- BerkeleyGW-4.0/testsuite/GaAs-EPM/GaAs.test.orig 2024-03-20 11:55:47.333669371 +0800 ++++ BerkeleyGW-4.0/testsuite/GaAs-EPM/GaAs.test 2024-03-20 11:57:15.045252252 +0800 +@@ -32,7 +32,7 @@ + Output : WFN.out + Input : WFN.in PIPE + +-Precision : 8e-15 ++Precision : 8e-14 + match ; Eigenvalue 1 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 1); -0.2710614199849328 + match ; Eigenvalue 10 at k-pt 1 ; GREP(WFN.out, "kpoint 1", 2, 10); 1.2565373697755460 + match ; Eigenvalue 18 at k-pt 2 ; GREP(WFN.out, "kpoint 2", 2, 18); 2.1322637363008994 From a8dab8e1eecee1b63aaa80907d0242bc8a4b78fb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 09:56:51 +0100 Subject: [PATCH 1038/1193] Remove extension from excluded test --- .../p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb index fdb202fa951e..7990dd1511b8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023a-CUDA-12.1.1.eb @@ -204,7 +204,7 @@ excluded_tests = { # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 'distributed/rpc/test_tensorpipe_agent', # Broken test, can't ever succeed, see https://github.com/pytorch/pytorch/issues/122184 - 'distributed/tensor/parallel/test_tp_random_state.py', + 'distributed/tensor/parallel/test_tp_random_state', # failures on OmniPath systems, which don't support some optional InfiniBand features # See https://github.com/pytorch/tensorpipe/issues/413 'distributed/pipeline/sync/skip/test_gpipe', From 70b2388dbccf567542fb7ef22f00c40132567b46 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 10:00:09 +0100 Subject: [PATCH 1039/1193] Remove UCX-CUDA with incompatible CUDA-GCC-combination CUDA 12.3.0 is not compatible with GCC 13 hence having this EC only causes confusion. --- ...-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.3.0.eb | 41 ------------------- 1 file changed, 41 deletions(-) delete mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.3.0.eb diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.3.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.3.0.eb deleted file mode 100644 index c292b853f634..000000000000 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.15.0-GCCcore-13.2.0-CUDA-12.3.0.eb +++ /dev/null @@ -1,41 +0,0 @@ -easyblock = 'EB_UCX_Plugins' - -name = 'UCX-CUDA' -version = '1.15.0' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'http://www.openucx.org/' -description = """Unified Communication X -An open-source production grade communication framework for data centric -and high-performance applications - -This module adds the UCX CUDA support. -""" - -toolchain = {'name': 'GCCcore', 'version': '13.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] -patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] -checksums = [ - {'ucx-1.15.0.tar.gz': '4b202087076bc1c98f9249144f0c277a8ea88ad4ca6f404f94baa9cb3aebda6d'}, - {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': - '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, -] - -builddependencies = [ - ('binutils', '2.40'), - ('Autotools', '20220317'), - ('pkgconf', '2.0.3'), -] - -dependencies = [ - ('zlib', '1.2.13'), - ('UCX', version), - ('CUDA', '12.3.0', '', SYSTEM), - ('GDRCopy', '2.4'), -] - - -moduleclass = 'lib' From 9b4acfcb348be8578c8286bd7137b6db3b5b7007 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 12:28:34 +0100 Subject: [PATCH 1040/1193] adding easyconfigs: Abseil-20240116.1-GCCcore-13.2.0.eb, gRPC-1.62.1-GCCcore-13.2.0.eb, protobuf-python-4.25.3-GCCcore-13.2.0.eb, protobuf-25.3-GCCcore-13.2.0.eb, RE2-2024-03-01-GCCcore-13.2.0.eb --- .../Abseil-20240116.1-GCCcore-13.2.0.eb | 33 ++++++++++++ .../g/gRPC/gRPC-1.62.1-GCCcore-13.2.0.eb | 50 +++++++++++++++++++ .../protobuf-python-4.25.3-GCCcore-13.2.0.eb | 35 +++++++++++++ .../protobuf/protobuf-25.3-GCCcore-13.2.0.eb | 35 +++++++++++++ .../r/RE2/RE2-2024-03-01-GCCcore-13.2.0.eb | 34 +++++++++++++ 5 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/g/gRPC/gRPC-1.62.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.25.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..990d4ea16639 --- /dev/null +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'Abseil' +version = '20240116.1' + +homepage = 'https://abseil.io/' +description = """Abseil is an open-source collection of C++ library code designed to augment the +C++ standard library. The Abseil library code is collected from Google's own +C++ code base, has been extensively tested and used in production, and is the +same code we depend on in our daily coding lives.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s-cpp/archive/refs/tags'] +sources = ['%(version)s.tar.gz'] +checksums = ['3c743204df78366ad2eaf236d6631d83f6bc928d1705dd0000b872e53b73dc6a'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = "-DABSL_PROPAGATE_CXX_STD=ON " + +build_shared_libs = True + +sanity_check_paths = { + 'files': ['lib/libabsl_base.so'], + 'dirs': ['include/absl'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gRPC/gRPC-1.62.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/gRPC/gRPC-1.62.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6928ae22440e --- /dev/null +++ b/easybuild/easyconfigs/g/gRPC/gRPC-1.62.1-GCCcore-13.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'gRPC' +version = '1.62.1' + +homepage = 'https://grpc.io/' +description = """gRPC is a modern, open source, high-performance remote procedure call (RPC) +framework that can run anywhere. gRPC enables client and server applications to +communicate transparently, and simplifies the building of connected systems.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'grpc' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['c9f9ae6e4d6f40464ee9958be4068087881ed6aa37e30d0e64d40ed7be39dd01'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('Abseil', '20240116.1'), + ('c-ares', '1.27.0'), + ('protobuf', '25.3'), + ('zlib', '1.2.13'), + ('RE2', '2024-03-01'), +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += "-DgRPC_ABSL_PROVIDER=package " +configopts += "-DgRPC_CARES_PROVIDER=package " +configopts += "-DgRPC_PROTOBUF_PROVIDER=package " +configopts += "-DgRPC_RE2_PROVIDER=package " +configopts += "-DgRPC_SSL_PROVIDER=package " +configopts += "-DgRPC_ZLIB_PROVIDER=package " + +_grpc_plugins = ['cpp', 'csharp', 'node', 'objective_c', 'php', 'python', 'ruby'] + +sanity_check_paths = { + 'files': ['bin/grpc_%s_plugin' % x for x in _grpc_plugins] + + ['lib/libgrpc.%s' % SHLIB_EXT, 'lib/libgrpc++.%s' % SHLIB_EXT], + 'dirs': ['include/grpc', 'include/grpc++', 'include/grpcpp'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.25.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.25.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..f3568b506d95 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.25.3-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'protobuf-python' +version = '4.25.3' + +homepage = 'https://github.com/google/protobuf/' +description = "Python Protocol Buffers runtime library." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://pypi.python.org/packages/source/p/protobuf'] +sources = ['protobuf-%(version)s.tar.gz'] +checksums = ['25b5d0b42fd000320bd7830b349e3b696435f3b329810427a6bcce6a5492cc5c'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('protobuf', version[2:]), # Major version is only used for the Python bindings +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +options = {'modulename': 'google.protobuf'} + +# Make sure protobuf is installed as a regular folder or it will not be found if +# other google packages are installed in other site-packages folders +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages/google/protobuf'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..f4ef722a48a9 --- /dev/null +++ b/easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'protobuf' +version = '25.3' + +homepage = 'https://github.com/protocolbuffers/protobuf' +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for +serializing structured data.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'protocolbuffers' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_GZ] +checksums = ['d19643d265b978383352b3143f04c0641eea75a75235c111cc01a1350173180e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] +dependencies = [ + ('Abseil', '20240116.1'), +] + +srcdir = '.' + +configopts = '-Dprotobuf_BUILD_TESTS=OFF -Dprotobuf_BUILD_SHARED_LIBS=ON -Dprotobuf_ABSL_PROVIDER="package" ' + +sanity_check_paths = { + 'files': ['bin/protoc', 'lib/libprotobuf.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..9dee8230565f --- /dev/null +++ b/easybuild/easyconfigs/r/RE2/RE2-2024-03-01-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = "CMakeMake" + +name = 'RE2' +version = '2024-03-01' + +homepage = 'https://github.com/google/re2' +description = """ +RE2 is a fast, safe, thread-friendly alternative to backtracking regular +expression engines like those used in PCRE, Perl, and Python. It is a C++ +library. """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'google' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['7b2b3aa8241eac25f674e5b5b2e23d4ac4f0a8891418a2661869f736f03f57f4'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('Abseil', '20240116.1'), +] + +sanity_check_paths = { + 'files': ['lib/libre2.a'], + 'dirs': ['include/re2'], +} + +moduleclass = 'lib' From c5a66db3a65e0cc750508a53d050baf8c53577b4 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Wed, 20 Mar 2024 13:22:55 +0100 Subject: [PATCH 1041/1193] adding easyconfigs: PSASS-3.1.0-GCC-12.3.0.eb --- .../p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb new file mode 100644 index 000000000000..08c396073848 --- /dev/null +++ b/easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'PSASS' +version = '3.1.0' + +homepage = 'https://github.com/SexGenomicsToolkit/PSASS' +description = """ +PSASS (Pooled Sequencing Analysis for Sex Signal) is a software to compare pooled sequencing +datasets from two groups (usually two sexes). Results from PSASS can be easily visualized +using the sgtr R package. PSASS is integrated in a Snakemake workflow to perform all required +steps starting from a genome and reads files. +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +dependencies = [ + ('HTSlib', '1.18'), +] + +source_urls = ['https://github.com/SexGenomicsToolkit/PSASS/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6c22fb2db52df76bdf8e5073895da11678a35c4a0e1500245e19d13c1f67df2b'] + +# just run make in the install dir +skipsteps = ['configure', 'install'] + +postinstallcmds = ['cp -r %(builddir)s/PSASS-%(version)s/bin %(installdir)s/bin'] + +sanity_check_paths = { + 'files': ['bin/psass'], + 'dirs': [], +} + +sanity_check_commands = [ + "psass --help", +] + +moduleclass = 'bio' From 1adad46850135f951e83a77411f32042f48fdd3d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 14:06:40 +0100 Subject: [PATCH 1042/1193] Add c-ares --- .../c/c-ares/c-ares-1.27.0-GCCcore-13.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/c/c-ares/c-ares-1.27.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/c-ares/c-ares-1.27.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/c-ares/c-ares-1.27.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..ea5f2f32b19a --- /dev/null +++ b/easybuild/easyconfigs/c/c-ares/c-ares-1.27.0-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'c-ares' +version = '1.27.0' + +homepage = 'https://c-ares.org/' +description = "c-ares is a C library for asynchronous DNS requests (including name resolves)" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'c-ares' +source_urls = [GITHUB_SOURCE] +sources = ['%s-%s.tar.gz' % (name.replace('-', ''), version.replace('.', '_'))] +checksums = ['de6a839d47b93174ba260187a084027ea681a91ffe12f2d5f20645652eae246c'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), +] + +preconfigopts = 'autoreconf -i -f &&' + +sanity_check_paths = { + 'files': ['lib/libcares.a', 'lib/libcares.%s' % SHLIB_EXT, 'lib/pkgconfig/libcares.pc'], + 'dirs': ['include', 'share/man'], +} + +moduleclass = 'lib' From 298941a35bdd66bf85fd2733d367377cdcee672b Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 14:15:37 +0100 Subject: [PATCH 1043/1193] Remove flake8 suppressions for invalid escape sequences Those will become a SyntaxError in some Python version, so that suppression to make CI pass isn't a good idea, because that sequence IS invalid, no matter what flake8 says. Solution is either to use raw strings or remove the escapes. For OmegaFold it isn't required as an escaped space is used just to make for nice indentation which isn't required at this place. --- .../easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb | 2 +- .../o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0-sim.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb index 14de28ce6ecb..c77445993d66 100644 --- a/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb +++ b/easybuild/easyconfigs/d/Delft3D/Delft3D-4.04.01-foss-2022a-FLOW.eb @@ -56,7 +56,7 @@ preconfigopts += 'export FFLAGS="$FFLAGS -fallow-argument-mismatch -I${CPATH//:/ # syntax was made invalid in c++11 preconfigopts += "sed -i 's/if (spec < 0)/if (spec == nullptr)/g' utils_lgpl/delftonline/src/delftonline/server.cpp && " # avoid comparing logical with integer -preconfigopts += "sed -i 's/if (has_umean \/= 0)/if (has_umean .neqv. .false.)/g' " # noqa: W605 +preconfigopts += r"sed -i 's/if (has_umean \/= 0)/if (has_umean .neqv. .false.)/g' " preconfigopts += "engines_gpl/flow2d3d/packages/flow2d3d_io/src/input/restart_trim_flow.f90 && " preconfigopts += "sed -i -e 's/-recursive/-frecursive/g' -e 's/-traceback/-fbacktrace/g' configure.ac && " # copy ESMF_RegridWeightGen_in_Delft3D-WAVE.sh script diff --git a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb index 0008cde884d3..9e13f1be82ef 100644 --- a/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -22,7 +22,7 @@ sanity_pip_check = True # add missing version for OmegaFold exts_list = [ (name, version, { - 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, # noqa: W605 + 'preinstallopts': """sed -i '/^setup(/a version="%(version)s",' setup.py && """, 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/HeliXonProtein/OmegaFold/archive/'], 'checksums': ['ab3b48fe7721539b6943b49cdbafc9799e15b4425a324cc25daf15a24e3f9e37'], diff --git a/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0-sim.eb b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0-sim.eb index 7c5661362397..fe63e07bdec0 100644 --- a/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0-sim.eb +++ b/easybuild/easyconfigs/r/ReaxFF/ReaxFF-2.0-GCC-11.3.0-sim.eb @@ -24,7 +24,7 @@ Register at https://www.engr.psu.edu/adri/Home.aspx and follow instructions start_dir = 'src' -prebuildopts = r"sed -ie 's/^\(\s\)gcc /\1gfortran /g' makefile && " # noqa: W605 +prebuildopts = r"sed -ie 's/^\(\s\)gcc /\1gfortran /g' makefile && " prebuildopts += 'rm *.o && ' buildopts = 'SUFFIX="-c -O3 -std=legacy"' From da2b197765dbe069fd234e21de97b2340f4e6bfb Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 20 Mar 2024 14:38:16 +0100 Subject: [PATCH 1044/1193] Fix issue in case library prefix is lib instead of lib64 --- .../s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb | 4 +++- .../s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb | 4 +++- 2 files changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb index 1527189c23bd..bf94f59c11ef 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb @@ -28,8 +28,10 @@ configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${E # Include only first four tests, which should be fairly small to run pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' +# remove broken symlink to libsuperlu.a postinstallcmds = [ - "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a + "if[ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + "if[ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb index 44b3702b12bc..ca431ab2522d 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb @@ -28,8 +28,10 @@ configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${E # Include only first four tests, which should be fairly small to run pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' +# remove broken symlink to libsuperlu.a postinstallcmds = [ - "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a + "if[ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + "if[ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] sanity_check_paths = { From 2fada534cdf4ecc27f6337a516b09998a77f164c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 20 Mar 2024 13:44:26 +0000 Subject: [PATCH 1045/1193] Switch libxc sources to gitlab --- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb | 5 +++-- .../easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb | 5 +++-- .../easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb | 5 +++-- .../l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb | 5 +++-- .../l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb | 5 +++-- .../l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb | 5 +++-- .../l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb | 5 +++-- .../l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 5 +++-- .../l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb | 5 +++-- easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb | 5 +++-- .../l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb | 5 +++-- .../l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb | 5 +++-- 22 files changed, 66 insertions(+), 44 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb index 2d16f4413bf7..7932a1b81ba7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_lm-fix.patch', @@ -17,7 +17,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb index 33d60c749bc3..6800d0d80a07 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_lm-fix.patch', @@ -17,7 +17,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb index b45abb6d6abf..70bf23a40739 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_lm-fix.patch', @@ -17,7 +17,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb index d57ae6f7ed6c..41119d59d29b 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '9.3.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_lm-fix.patch', @@ -17,7 +17,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch 'd44d4a35ae22542c3086e57638e0e2b6b1ad8e98d0898036972a0248cf8778e8', # libxc-4.3.4_fix-timeout.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb index 21a6399c430f..a6a4ac4a4c92 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'iccifort', 'version': '2020.1.217'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_rename-F03.patch', @@ -18,7 +18,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb index 81cacc26ca83..a3d40879389e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'iccifort', 'version': '2020.4.304'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_rename-F03.patch', @@ -18,7 +18,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb index 5b25d77dc2dd..7e51c99e5123 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_rename-F03.patch', @@ -18,7 +18,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb index fca29faafd69..0496e6352db8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb @@ -9,7 +9,7 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] patches = [ 'libxc-%(version)s_rename-F03.patch', @@ -18,7 +18,8 @@ patches = [ 'libxc-%(version)s_fix-timeout.patch', ] checksums = [ - 'a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', # libxc-4.3.4.tar.gz + ('a8ee37ddc5079339854bd313272856c9d41a27802472ee9ae44b58ee9a298337', + '83aba38dfa03f34cc74f84c14c83bf501a43493c818c797e2d0682647569b147'), # libxc-4.3.4.tar.gz 'e494be3ca2026998f2dd7c6b03a4e662f204fd3d963271e588f9f0d5739e76b5', # libxc-4.3.4_rename-F03.patch 'f2cae17533d3527e11cfec958a7f253872f7c5fcd104c3cffc02382be0ccfb9c', # libxc-4.3.4_lm-fix.patch '5a5e7d69729326e0d44e60b554ba6d8650a28958ec54b27a98757dc78a040946', # libxc-4.3.4_fix-CMakeLists.patch diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb index e62a0ad0facf..3e72f2dcfbd1 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['180d52b5552921d1fac8a10869dd30708c0fb41dc202a3bbee0e36f43872718a'] +checksums = [('180d52b5552921d1fac8a10869dd30708c0fb41dc202a3bbee0e36f43872718a', + '3fe05ccf7033622112f7d6ab28ac82301f5840b8d1bbe8b6df1022dbc732883f')] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb index 8aa007ac6f1e..820cf8286022 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd'] +checksums = [('0350defdd6c1b165e4cf19995f590eee6e0b9db95a6b221d28cecec40f4e85cd', + '53cbccae4227794c4f4e042d0c20c3171894d8eacd13fd78aab376d5971a966c')] builddependencies = [ ('CMake', '3.18.4'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb index 8246e8aaa300..e4230ef73a71 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb @@ -12,9 +12,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '10.3.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9'] +checksums = [('02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9', + 'f2b428838536bcf2009af6a753f7314a069eed6a55bf1d1af4d4dcbcdd1c3697')] builddependencies = [ ('CMake', '3.20.1'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb index 9886c92eddba..18a34d9a98d3 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9'] +checksums = [('02e4615a22dc3ec87a23efbd3d9be5bfad2445337140bad1720699571c45c3f9', + 'f2b428838536bcf2009af6a753f7314a069eed6a55bf1d1af4d4dcbcdd1c3697')] builddependencies = [ ('CMake', '3.20.1'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb index f36ec4c49237..1a96b02c0520 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['0d0496513114ed84987c32649912f9a65d234696dab13a4b00ce8c420bfc0a1d'] +checksums = [('0d0496513114ed84987c32649912f9a65d234696dab13a4b00ce8c420bfc0a1d', + '1f752b2cf65c8145c1830f2d666181649c27bc0dd9685893d172822afade29f6')] builddependencies = [ ('CMake', '3.21.1'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb index 61a5bbdab009..29de458e29c6 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['0d0496513114ed84987c32649912f9a65d234696dab13a4b00ce8c420bfc0a1d'] +checksums = [('0d0496513114ed84987c32649912f9a65d234696dab13a4b00ce8c420bfc0a1d', + '1f752b2cf65c8145c1830f2d666181649c27bc0dd9685893d172822afade29f6')] builddependencies = [ ('CMake', '3.21.1'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb index e1d6b22c2935..9adcd739ebfd 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '11.3.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['7b7a96d8eeb472c7b8cca7ac38eae27e0a8113ef44dae5359b0eb12592b4bcf2'] +checksums = [('7b7a96d8eeb472c7b8cca7ac38eae27e0a8113ef44dae5359b0eb12592b4bcf2', + '38b60ed552b46367175b370e1ad5409fcf45c49b71ed13706a65b485f06a5417')] builddependencies = [ ('CMake', '3.23.1'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb index 3968f139ee72..078f4cccd61f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2022.1.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['7b7a96d8eeb472c7b8cca7ac38eae27e0a8113ef44dae5359b0eb12592b4bcf2'] +checksums = [('7b7a96d8eeb472c7b8cca7ac38eae27e0a8113ef44dae5359b0eb12592b4bcf2', + '38b60ed552b46367175b370e1ad5409fcf45c49b71ed13706a65b485f06a5417')] builddependencies = [ ('CMake', '3.23.1'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb index 7dc5e000dd64..5f4d851078c6 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '12.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54'] +checksums = [('a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54', + 'f593745fa47ebfb9ddc467aaafdc2fa1275f0d7250c692ce9761389a90dd8eaf')] builddependencies = [ ('CMake', '3.24.3'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb index 4e4f288ba984..3485c4270092 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54'] +checksums = [('a3aa16915942543031a5d9c4a92c439ce54249bdcda8c91c4e69e65329dc9a54', + 'f593745fa47ebfb9ddc467aaafdc2fa1275f0d7250c692ce9761389a90dd8eaf')] builddependencies = [ ('CMake', '3.24.3'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb index 81956f38a479..e03736181ab7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '12.3.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] +checksums = [('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc')] builddependencies = [ ('CMake', '3.26.3'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb index e04565bf6ec8..cc3d010017c8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'GCC', 'version': '13.2.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] +checksums = [('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc')] builddependencies = [ ('CMake', '3.27.6'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb index af5917b73f55..7d5876577ebd 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] +checksums = [('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc')] builddependencies = [ ('CMake', '3.26.3'), diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb index 41d6760191c7..6c7638f904b1 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb @@ -9,9 +9,10 @@ description = """Libxc is a library of exchange-correlation functionals for dens toolchain = {'name': 'intel-compilers', 'version': '2023.2.1'} -source_urls = ['https://www.tddft.org/programs/libxc/down.php?file=%(version)s/'] +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] sources = [SOURCE_TAR_GZ] -checksums = ['a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045'] +checksums = [('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc')] builddependencies = [ ('CMake', '3.27.6'), From ab56cdeaac31b49b96af3f7fcc6dec21468550db Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 20 Mar 2024 14:46:03 +0100 Subject: [PATCH 1046/1193] fix 2023a version for SuperLU --- .../s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb index d71b00777fc5..8ab20d1bca4a 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb @@ -28,8 +28,10 @@ configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${E # Include only first four tests, which should be fairly small to run pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && ' +# remove broken symlink to libsuperlu.a postinstallcmds = [ - "rm %(installdir)s/lib64/libsuperlu.a", # remove broken symlink to libsuperlu.a + "if[ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + "if[ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] sanity_check_paths = { From 37647705e6f3adfa43c01262f6c15d78068a3687 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 14:49:29 +0100 Subject: [PATCH 1047/1193] adding easyconfigs: pytest-flakefinder-1.1.0-GCCcore-13.2.0.eb, pytest-rerunfailures-14.0-GCCcore-13.2.0.eb, pytest-shard-0.1.2-GCCcore-13.2.0.eb --- ...pytest-flakefinder-1.1.0-GCCcore-13.2.0.eb | 24 ++++++++++++++ ...ytest-rerunfailures-14.0-GCCcore-13.2.0.eb | 26 +++++++++++++++ .../pytest-shard-0.1.2-GCCcore-13.2.0.eb | 33 +++++++++++++++++++ 3 files changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-14.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..195f8fd5cfbb --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'pytest-flakefinder' +version = '1.1.0' + +homepage = 'https://github.com/dropbox/pytest-flakefinder' +description = "Runs tests multiple times to expose flakiness." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-14.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-14.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..3898c92c6b47 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-14.0-GCCcore-13.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pytest-rerunfailures' +version = '14.0' + +homepage = 'https://github.com/pytest-dev/pytest-rerunfailures' +description = "pytest plugin to re-run tests to eliminate flaky failures." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +sources = [SOURCE_TAR_GZ] +checksums = ['4a400bcbcd3c7a4ad151ab8afac123d90eca3abe27f98725dc4d9702887d2e92'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..fbcbb1222e13 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'pytest-shard' +version = '0.1.2' + +homepage = 'https://github.com/AdamGleave/pytest-shard' +description = """pytest plugin to support parallelism across multiple machines. + +Shards tests based on a hash of their test name enabling easy parallelism across machines, +suitable for a wide variety of continuous integration services. +Tests are split at the finest level of granularity, individual test cases, +enabling parallelism even if all of your tests are in a single file +(or even single parameterized test method). +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +sources = [SOURCE_TAR_GZ] +checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From 381812854d592e3824d6b8c9f04460fa6d7b3fcb Mon Sep 17 00:00:00 2001 From: casparl Date: Wed, 20 Mar 2024 14:50:53 +0100 Subject: [PATCH 1048/1193] Fix missing space --- .../s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb | 4 ++-- .../s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb | 4 ++-- .../s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb | 4 ++-- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb index bf94f59c11ef..b8b1118b44e4 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb @@ -30,8 +30,8 @@ pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && # remove broken symlink to libsuperlu.a postinstallcmds = [ - "if[ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", - "if[ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" + "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb index ca431ab2522d..c9bb0479ec13 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb @@ -30,8 +30,8 @@ pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && # remove broken symlink to libsuperlu.a postinstallcmds = [ - "if[ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", - "if[ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" + "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb index 8ab20d1bca4a..a980992bd82d 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb @@ -30,8 +30,8 @@ pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && # remove broken symlink to libsuperlu.a postinstallcmds = [ - "if[ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", - "if[ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" + "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] sanity_check_paths = { From 0c855a806e3191b8683674093ae4cd4aa3622536 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 14:51:00 +0100 Subject: [PATCH 1049/1193] adding easyconfigs: Z3-4.13.0-GCCcore-13.2.0.eb --- .../z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..807d281466f5 --- /dev/null +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'Z3' +version = '4.13.0' + +homepage = 'https://github.com/Z3Prover/z3' +description = """Z3 is a theorem prover from Microsoft Research with support for bitvectors, +booleans, arrays, floating point numbers, strings, and other data types. This +module includes z3-solver, the Python interface of Z3. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('CMake', '3.27.6'), + ('binutils', '2.40'), +] +dependencies = [ + ('Python', '3.11.5'), + ('GMP', '6.3.0'), +] + +use_pip = True + +_fix_parallelism = """sed -i 's/str(multiprocessing.cpu_count())/"%(parallel)s"/' setup.py && """ +_enable_gmp = """sed -i "s/Z3_USE_LIB_GMP.*/Z3_USE_LIB_GMP' : True,/" setup.py && """ + +exts_list = [ + ('z3-solver', version + '.0', { + 'modulename': 'z3', + 'checksums': ['52588e92aec7cb338fd6288ce93758ae01770f62ca0c80e8f4f2b2333feaf51b'], + 'preinstallopts': _fix_parallelism + _enable_gmp, + }), +] + +# make Z3 headers and libraries accessible in their usual location +local_z3_site_path = "lib/python%(pyshortver)s/site-packages/%(namelower)s" +postinstallcmds = [ + 'ln -s %s/include "%%(installdir)s/include"' % local_z3_site_path, + 'cd "%%(installdir)s"; for lib in %s/lib/*; do ln -s ../$lib lib/$(basename $lib); done' % local_z3_site_path +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.so'], + 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From 9811155579888acbfb820c4baca0e7ba788e3f2d Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 20 Mar 2024 13:51:12 +0000 Subject: [PATCH 1050/1193] adding easyconfigs: Datasets-2.18.0-gfbf-2023a.eb and patches: Datasets-2.18.0_use-patched-pyarrow.patch --- .../d/Datasets/Datasets-2.18.0-gfbf-2023a.eb | 48 +++++++++++++++++++ .../Datasets-2.18.0_use-patched-pyarrow.patch | 32 +++++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_use-patched-pyarrow.patch diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb new file mode 100644 index 000000000000..b437c1bd5526 --- /dev/null +++ b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb @@ -0,0 +1,48 @@ +easyblock = "PythonBundle" + +name = 'Datasets' +version = '2.18.0' + +homepage = 'https://github.com/huggingface/datasets' +description = """ +The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient +data manipulation tools. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # for fsspec + ('SciPy-bundle', '2023.07'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('Arrow', '14.0.1'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('python-xxhash', '3.4.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('multiprocess', '0.70.15', { + 'checksums': ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'], + }), + ('huggingface-hub', '0.21.4', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['e1f4968c93726565a80edf6dc309763c7b546d0cfe79aa221206034d50155531'], + }), + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'patches': ['Datasets-2.18.0_use-patched-pyarrow.patch'], + 'checksums': [ + {'datasets-2.18.0.tar.gz': 'cdf8b8c6abf7316377ba4f49f9589a4c74556d6b481afd0abd2284f3d69185cb'}, + {'Datasets-2.18.0_use-patched-pyarrow.patch': + 'a42f23c94f3f4935aae7a01aebd04bacae518537ecb674efeb94d5af7a296061'}, + ], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_use-patched-pyarrow.patch b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_use-patched-pyarrow.patch new file mode 100644 index 000000000000..a05e05880bb5 --- /dev/null +++ b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_use-patched-pyarrow.patch @@ -0,0 +1,32 @@ +pyarrow-hotfix is not needed as long as pyarrow>=14.0.1 + +Author: Viktor Rehnberg (vikren@chalmers.se) Chalmers University of Technology + +diff --git a/setup.py b/setup.py +index 5564cada..b04351a0 100644 +--- a/setup.py ++++ b/setup.py +@@ -113,10 +113,8 @@ REQUIRED_PKGS = [ + # We use numpy>=1.17 to have np.random.Generator (Dataset shuffling) + "numpy>=1.17", + # Backend and serialization. +- # Minimum 12.0.0 to be able to concatenate extension arrays +- "pyarrow>=12.0.0", +- # As long as we allow pyarrow < 14.0.1, to fix vulnerability CVE-2023-47248 +- "pyarrow-hotfix", ++ # Minimum 14.0.1 to fix vulnerability CVE-2023-47248 ++ "pyarrow>=14.0.1", + # For smart caching dataset processing + "dill>=0.3.0,<0.3.9", # tmp pin until dill has official support for determinism see https://github.com/uqfoundation/dill/issues/19 + # For performance gains with apache arrow +diff --git a/src/datasets/features/features.py b/src/datasets/features/features.py +index c2c7d8ff..2d061d85 100644 +--- a/src/datasets/features/features.py ++++ b/src/datasets/features/features.py +@@ -32,7 +32,6 @@ import pandas as pd + import pyarrow as pa + import pyarrow.compute as pc + import pyarrow.types +-import pyarrow_hotfix # noqa: F401 # to fix vulnerability on pyarrow<14.0.1 + from pandas.api.extensions import ExtensionArray as PandasExtensionArray + from pandas.api.extensions import ExtensionDtype as PandasExtensionDtype From 0f88ea5a49dc5aa481b31865f8f4434a41c20fbb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 14:51:31 +0100 Subject: [PATCH 1051/1193] adding easyconfigs: sympy-1.12-gfbf-2023b.eb, gmpy2-2.1.5-GCC-13.2.0.eb --- .../g/gmpy2/gmpy2-2.1.5-GCC-13.2.0.eb | 25 +++++++++++++++++++ .../s/sympy/sympy-1.12-gfbf-2023b.eb | 22 ++++++++++++++++ 2 files changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2023b.eb diff --git a/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-13.2.0.eb b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-13.2.0.eb new file mode 100644 index 000000000000..351a3aa10eff --- /dev/null +++ b/easybuild/easyconfigs/g/gmpy2/gmpy2-2.1.5-GCC-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'gmpy2' +version = '2.1.5' + +homepage = 'https://github.com/aleaxit/gmpy' +description = "GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['bc297f1fd8c377ae67a4f493fc0f926e5d1b157e5c342e30a4d84dc7b9f95d96'] + +dependencies = [ + ('Python', '3.11.5'), + ('GMP', '6.3.0'), + ('MPFR', '4.2.1'), + ('MPC', '1.3.1'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2023b.eb b/easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2023b.eb new file mode 100644 index 000000000000..712de366fa54 --- /dev/null +++ b/easybuild/easyconfigs/s/sympy/sympy-1.12-gfbf-2023b.eb @@ -0,0 +1,22 @@ +name = 'sympy' +version = '1.12' + +homepage = 'https://sympy.org/' +description = """SymPy is a Python library for symbolic mathematics. It aims to + become a full-featured computer algebra system (CAS) while keeping the code as + simple as possible in order to be comprehensible and easily extensible. SymPy + is written entirely in Python and does not require any external libraries.""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ebf595c8dac3e0fdc4152c51878b498396ec7f30e7a914d6071e674d49420fb8'] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('gmpy2', '2.1.5'), +] + + +moduleclass = 'math' From 988432e4ef5b410bbe8cdba7712a2fd603f39883 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 20 Mar 2024 13:51:58 +0000 Subject: [PATCH 1052/1193] New homepage --- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb | 2 +- .../easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb | 2 +- .../easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb | 2 +- easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb | 2 +- .../easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb | 2 +- 22 files changed, 22 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb index 7932a1b81ba7..46b4a89581d7 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb index 6800d0d80a07..34fcaa78e3ec 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-10.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb index 70bf23a40739..9813cb985bf5 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb index 41119d59d29b..e5db1b11bf4f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-GCC-9.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb index a6a4ac4a4c92..7f7307e08fd2 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.1.217.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb index a3d40879389e..bd9018d08a41 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-iccifort-2020.4.304.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb index 7e51c99e5123..1f09dfc969ba 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb index 0496e6352db8..0595d0503148 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-4.3.4-intel-compilers-2021.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '4.3.4' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb index 3e72f2dcfbd1..02f66c082a23 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.2-GCC-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.2' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb index 820cf8286022..311998a80a70 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.3-GCC-10.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.3' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb index e4230ef73a71..9b997fa87410 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-GCC-10.3.0.eb @@ -6,7 +6,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.5' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb index 18a34d9a98d3..112d923e4842 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.5-intel-compilers-2021.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.5' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb index 1a96b02c0520..4bfdb399882a 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-GCC-11.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.6' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb index 29de458e29c6..9fab692924cf 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.1.6-intel-compilers-2021.4.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.1.6' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb index 9adcd739ebfd..4b3655eeb771 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-GCC-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.2.3' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb index 078f4cccd61f..d5879d1a521e 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-5.2.3-intel-compilers-2022.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '5.2.3' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb index 5f4d851078c6..4202f7d1d77d 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-GCC-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '6.1.0' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb index 3485c4270092..c98941f57e64 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.1.0-intel-compilers-2022.2.1.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '6.1.0' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb index e03736181ab7..d9d1801f2f71 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-12.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '6.2.2' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb index cc3d010017c8..3aa336dd9b47 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '6.2.2' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb index 7d5876577ebd..f3a5e5448f3f 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.1.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '6.2.2' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb index 6c7638f904b1..8e2652554ca8 100644 --- a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-intel-compilers-2023.2.1.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeMake' name = 'libxc' version = '6.2.2' -homepage = 'https://www.tddft.org/programs/libxc' +homepage = 'https://libxc.gitlab.io' description = """Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" From f8a66417a446deedfb5ee2c703384fb75bbc88e3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 14:52:10 +0100 Subject: [PATCH 1053/1193] adding easyconfigs: expecttest-0.2.1-GCCcore-13.2.0.eb --- .../expecttest-0.2.1-GCCcore-13.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..299cb627a4c8 --- /dev/null +++ b/easybuild/easyconfigs/e/expecttest/expecttest-0.2.1-GCCcore-13.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'expecttest' +version = '0.2.1' + +homepage = 'https://github.com/ezyang/expecttest' +description = """This library implements expect tests (also known as "golden" tests). Expect tests are a method of + writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and + the test framework automatically populates the expected output. If the output of the test changes, you can rerun + the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e52b1cf8a6f84506e6962a0bbdd248ea442124d826e849f263ec1c322ebb73f5'] + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] +dependencies = [ + ('Python', '3.11.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'tools' From b3aafa8c58d004641fc8a9291c1f13cded46b1af Mon Sep 17 00:00:00 2001 From: crivella Date: Wed, 20 Mar 2024 15:06:12 +0100 Subject: [PATCH 1054/1193] Removed FoX requirement in EB from PR #3258 --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb | 1 - .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb index 1e4c706faefd..45ac0fabf9d0 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb @@ -48,7 +48,6 @@ dependencies = [ # dependencies. The exception is w90, which is force built, and gipaw # which depends on qe source buildopts = "all gwl xspectra couple epw gipaw w90" -with_fox = True # Needed from QE7.2 to build GIPAW # parallel build tends to fail parallel = 1 diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb index 0b75a12d84e4..a635d9422426 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb @@ -48,7 +48,6 @@ dependencies = [ # dependencies. The exception is w90, which is force built, and gipaw # which depends on qe source buildopts = "all gwl xspectra couple epw gipaw w90" -with_fox = True # Needed from QE7.2 to build GIPAW # parallel build tends to fail parallel = 1 From 65c01d3ac70e0b025b9d49fa5af51426ba527c26 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 15:48:34 +0100 Subject: [PATCH 1055/1193] adding easyconfigs: Arrow-8.0.0-foss-2021b.eb --- .../a/Arrow/Arrow-8.0.0-foss-2021b.eb | 77 +++++++++++++++++++ 1 file changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb new file mode 100644 index 000000000000..f537d340a4ef --- /dev/null +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb @@ -0,0 +1,77 @@ +easyblock = 'CMakeMake' + +name = 'Arrow' +version = '8.0.0' + +homepage = 'https://arrow.apache.org' +description = """Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform + for in-memory data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s/%(namelower)s-%(version)s'] +sources = ['apache-arrow-%(version)s.tar.gz'] +patches = ['Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch'] +checksums = [ + {'apache-arrow-8.0.0.tar.gz': 'ad9a05705117c989c116bae9ac70492fe015050e1b80fb0e38fde4b5d863aaa3'}, + {'Arrow-8.0.0_fix-BaseExtensionType-arrow-ext-methods.patch': + '2db8a4c655e2a3f0ec7dac05e13bda6c2843203568873e736d2f1b8321b0dfc7'}, +] + +builddependencies = [ + ('CMake', '3.21.1'), + ('Autotools', '20210726'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), +] + +# Arrow strongly prefers included jemalloc, so not including it as a dependency +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # for numpy + ('Boost', '1.77.0'), + ('lz4', '1.9.3'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('zstd', '1.5.0'), + ('snappy', '1.1.9'), + ('RapidJSON', '1.1.0'), + ('RE2', '2022-02-01'), + ('utf8proc', '2.6.1'), +] + +start_dir = 'cpp' + +# see https://arrow.apache.org/docs/developers/python.html +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " +configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " +configopts += "-DZSTD_ROOT=$EBROOTZSTD " + +# also install Python bindings +local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " +local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " +local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 " +local_install_pyarrow_cmds += "python -m pip install --prefix %(installdir)s --no-build-isolation ." +postinstallcmds = [local_install_pyarrow_cmds] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['lib/libarrow.a', 'lib/libarrow.%s' % SHLIB_EXT, + 'lib/libarrow_python.a', 'lib/libarrow_python.%s' % SHLIB_EXT], + 'dirs': ['include/arrow', 'lib/cmake/arrow', 'lib/pkgconfig', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", + "python -c 'import pyarrow.parquet'", + "python -c 'from pyarrow.lib import BaseExtensionType; print(BaseExtensionType.__arrow_ext_class__)'", +] + +moduleclass = 'data' From 5ce270f40a22ea9cb5972d1d8b1c499de49975d7 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 15:52:22 +0100 Subject: [PATCH 1056/1193] Use pkgconf --- easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb index f537d340a4ef..043215854ce1 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2021b.eb @@ -23,7 +23,7 @@ builddependencies = [ ('Autotools', '20210726'), ('flex', '2.6.4'), ('Bison', '3.7.6'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ] # Arrow strongly prefers included jemalloc, so not including it as a dependency From d76542edd5a6b9addc1d8a0bb7fe288779c6f1c1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 16:00:54 +0100 Subject: [PATCH 1057/1193] Use SHLIB_EXT --- .../easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb index 990d4ea16639..81a2f9766dce 100644 --- a/easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/a/Abseil/Abseil-20240116.1-GCCcore-13.2.0.eb @@ -26,7 +26,7 @@ configopts = "-DABSL_PROPAGATE_CXX_STD=ON " build_shared_libs = True sanity_check_paths = { - 'files': ['lib/libabsl_base.so'], + 'files': ['lib/libabsl_base.' + SHLIB_EXT], 'dirs': ['include/absl'], } From bf5805f519b7476ba41e6b2ec1fc046420c61c4f Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Wed, 20 Mar 2024 16:01:33 +0100 Subject: [PATCH 1058/1193] adding easyconfigs: pydantic-2.6.4-GCCcore-13.2.0.eb, Rust-1.76.0-GCCcore-13.2.0.eb, maturin-1.5.0-GCCcore-13.2.0-Rust-1.76.0.eb, typing-extensions-4.10.0-GCCcore-13.2.0.eb --- ...aturin-1.5.0-GCCcore-13.2.0-Rust-1.76.0.eb | 625 ++++++++++++++++++ .../pydantic/pydantic-2.6.4-GCCcore-13.2.0.eb | 123 ++++ .../r/Rust/Rust-1.76.0-GCCcore-13.2.0.eb | 31 + ...typing-extensions-4.10.0-GCCcore-13.2.0.eb | 22 + 4 files changed, 801 insertions(+) create mode 100644 easybuild/easyconfigs/m/maturin/maturin-1.5.0-GCCcore-13.2.0-Rust-1.76.0.eb create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-2.6.4-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.76.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.10.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/maturin/maturin-1.5.0-GCCcore-13.2.0-Rust-1.76.0.eb b/easybuild/easyconfigs/m/maturin/maturin-1.5.0-GCCcore-13.2.0-Rust-1.76.0.eb new file mode 100644 index 000000000000..71311d34afc7 --- /dev/null +++ b/easybuild/easyconfigs/m/maturin/maturin-1.5.0-GCCcore-13.2.0-Rust-1.76.0.eb @@ -0,0 +1,625 @@ +easyblock = 'CargoPythonPackage' + +name = 'maturin' +version = '1.5.0' +_rust_ver = '1.76.0' +versionsuffix = '-Rust-%s' % _rust_ver + +homepage = 'https://github.com/pyo3/maturin' +description = """This project is meant as a zero configuration +replacement for setuptools-rust and milksnake. It supports building +wheels for python 3.5+ on windows, linux, mac and freebsd, can upload +them to pypi and has basic pypy and graalpy support.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +crates = [ + ('adler', '1.0.2'), + ('ahash', '0.8.7'), + ('aho-corasick', '1.1.2'), + ('allocator-api2', '0.2.16'), + ('anstream', '0.6.11'), + ('anstyle', '1.0.4'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('anyhow', '1.0.80'), + ('autocfg', '1.1.0'), + ('base64', '0.13.1'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('bitflags', '2.4.2'), + ('block-buffer', '0.10.4'), + ('bstr', '1.9.0'), + ('byteorder', '1.5.0'), + ('bytes', '1.5.0'), + ('bytesize', '1.3.0'), + ('bzip2', '0.4.4'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cab', '0.4.1'), + ('camino', '1.1.6'), + ('cargo-config2', '0.1.19'), + ('cargo-options', '0.7.2'), + ('cargo-platform', '0.1.6'), + ('cargo-xwin', '0.16.4'), + ('cargo-zigbuild', '0.18.3'), + ('cargo_metadata', '0.18.1'), + ('cbindgen', '0.26.0'), + ('cc', '1.0.88'), + ('cfb', '0.9.0'), + ('cfg-if', '1.0.0'), + ('charset', '0.1.3'), + ('chumsky', '0.9.3'), + ('clap', '4.4.18'), + ('clap_builder', '4.4.18'), + ('clap_complete', '4.4.9'), + ('clap_complete_fig', '4.4.2'), + ('clap_complete_command', '0.5.1'), + ('clap_complete_nushell', '0.1.11'), + ('clap_derive', '4.4.7'), + ('clap_lex', '0.6.0'), + ('cli-table', '0.4.7'), + ('colorchoice', '1.0.0'), + ('configparser', '3.0.4'), + ('console', '0.15.8'), + ('content_inspector', '0.2.4'), + ('core-foundation', '0.9.4'), + ('core-foundation-sys', '0.8.6'), + ('cpufeatures', '0.2.12'), + ('crc32fast', '1.3.2'), + ('crossbeam-channel', '0.5.11'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('crypto-common', '0.1.6'), + ('data-encoding', '2.5.0'), + ('deranged', '0.3.11'), + ('derivative', '2.2.0'), + ('dialoguer', '0.11.0'), + ('diff', '0.1.13'), + ('digest', '0.10.7'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('dissimilar', '1.0.7'), + ('dunce', '1.0.4'), + ('either', '1.9.0'), + ('encode_unicode', '0.3.6'), + ('encoding_rs', '0.8.33'), + ('equivalent', '1.0.1'), + ('errno', '0.3.8'), + ('expect-test', '1.4.1'), + ('fastrand', '2.0.1'), + ('fat-macho', '0.4.8'), + ('filetime', '0.2.23'), + ('flate2', '1.0.28'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.1'), + ('fs-err', '2.11.0'), + ('generic-array', '0.14.7'), + ('getrandom', '0.2.12'), + ('glob', '0.3.1'), + ('globset', '0.4.14'), + ('goblin', '0.8.0'), + ('hashbrown', '0.12.3'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('home', '0.5.9'), + ('humantime', '2.1.0'), + ('humantime-serde', '1.1.1'), + ('idna', '0.5.0'), + ('ignore', '0.4.22'), + ('indexmap', '1.9.3'), + ('indexmap', '2.2.3'), + ('indicatif', '0.17.7'), + ('indoc', '2.0.4'), + ('instant', '0.1.12'), + ('itertools', '0.11.0'), + ('itertools', '0.12.1'), 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+version = '2.6.4' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.76.0'), + ('maturin', '1.5.0', '-Rust-1.76.0'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('typing-extensions', '4.10.0'), +] + +use_pip = True +sanity_pip_check = True + +crates = [ + ('ahash', '0.8.7'), + ('aho-corasick', '1.0.2'), + ('allocator-api2', '0.2.16'), + ('autocfg', '1.1.0'), + ('base64', '0.21.7'), + ('bitflags', '1.3.2'), + ('cc', '1.0.79'), + ('cfg-if', '1.0.0'), + ('enum_dispatch', '0.3.12'), + ('equivalent', '1.0.1'), + ('form_urlencoded', '1.2.1'), + ('getrandom', '0.2.10'), + ('hashbrown', '0.14.3'), + ('heck', '0.4.1'), + ('idna', '0.5.0'), + ('indexmap', '2.0.0'), + ('indoc', '2.0.4'), + ('itoa', '1.0.8'), + ('jiter', '0.0.6'), + ('lexical-core', '0.8.5'), + ('lexical-parse-float', '0.8.5'), + ('lexical-parse-integer', '0.8.6'), + ('lexical-util', '0.8.5'), + ('lexical-write-float', '0.8.5'), + ('lexical-write-integer', '0.8.5'), + ('libc', '0.2.147'), + ('lock_api', '0.4.10'), + ('memchr', '2.6.3'), + ('memoffset', '0.9.0'), + ('num-bigint', '0.4.4'), + ('num-integer', '0.1.45'), + ('num-traits', '0.2.16'), + ('once_cell', '1.18.0'), + ('parking_lot', '0.12.1'), + ('parking_lot_core', '0.9.8'), + ('percent-encoding', '2.3.1'), + ('proc-macro2', '1.0.76'), + ('pyo3', '0.20.2'), + ('pyo3-build-config', '0.20.2'), + ('pyo3-ffi', '0.20.2'), + ('pyo3-macros', '0.20.2'), + ('pyo3-macros-backend', '0.20.2'), + ('python3-dll-a', '0.2.9'), + ('quote', '1.0.35'), + ('redox_syscall', '0.3.5'), + ('regex', '1.10.2'), + ('regex-automata', '0.4.3'), + ('regex-syntax', '0.8.2'), + ('rustversion', '1.0.13'), + ('ryu', '1.0.14'), + ('scopeguard', '1.1.0'), + ('serde', '1.0.195'), + ('serde_derive', '1.0.195'), + ('serde_json', '1.0.109'), + ('smallvec', '1.11.2'), + ('speedate', '0.13.0'), + ('static_assertions', '1.1.0'), + ('strum', '0.25.0'), + ('strum_macros', '0.25.3'), + ('syn', '2.0.48'), + ('target-lexicon', '0.12.9'), + ('tinyvec', '1.6.0'), + ('tinyvec_macros', '0.1.1'), + ('unicode-bidi', '0.3.13'), + ('unicode-ident', '1.0.10'), + ('unicode-normalization', '0.1.22'), + ('unindent', '0.2.3'), + ('url', '2.5.0'), + ('uuid', '1.6.1'), + ('version_check', '0.9.4'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('windows-targets', '0.48.1'), + ('windows_aarch64_gnullvm', '0.48.0'), + ('windows_aarch64_msvc', '0.48.0'), + ('windows_i686_gnu', '0.48.0'), + ('windows_i686_msvc', '0.48.0'), + ('windows_x86_64_gnu', '0.48.0'), + ('windows_x86_64_gnullvm', '0.48.0'), + ('windows_x86_64_msvc', '0.48.0'), + ('zerocopy', '0.7.32'), + ('zerocopy-derive', '0.7.32'), +] + +exts_list = [ + ('annotated_types', '0.6.0', { + 'checksums': ['563339e807e53ffd9c267e99fc6d9ea23eb8443c08f112651963e24e22f84a5d'], + }), + ('pydantic_core', '2.16.3', { + 'checksums': ['1cac689f80a3abab2d3c0048b29eea5751114054f032a941a32de4c852c59cad'], + }), + (name, version, { + 'preinstallopts': "sed -i '/Framework :: Pydantic/d' pyproject.toml && ", + 'checksums': ['b1704e0847db01817624a6b86766967f552dd9dbf3afba4004409f908dcc84e6'], + }), +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.76.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.76.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..af0fca6bc4f7 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.76.0-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +name = 'Rust' +version = '1.76.0' + +homepage = 'https://www.rust-lang.org' +description = """Rust is a systems programming language that runs blazingly fast, prevents segfaults, + and guarantees thread safety.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.70_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.76.0-src.tar.gz': '9e5cff033a7f0d2266818982ad90e4d3e4ef8f8ee1715776c6e25073a136c021'}, + {'Rust-1.70_sysroot-fix-interpreter.patch': '220129db55e022a98d25028da5dcc9f26b252dd995c3ac92f6312dbb1e362cb1'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('Python', '3.11.5'), + ('Ninja', '1.11.1'), + ('pkgconf', '2.0.3'), + ('patchelf', '0.18.0'), # only required when RPATH linking is enabled +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.10.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.10.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..c87ca2d6b250 --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.10.0-GCCcore-13.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.10.0' + +homepage = 'https://github.com/python/typing_extensions' +description = 'Typing Extensions - Backported and Experimental Type Hints for Python' + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['b0abd7c89e8fb96f98db18d86106ff1d90ab692004eb746cf6eda2682f91b3cb'] + +builddependencies = [('binutils', '2.40')] + +dependencies = [('Python', '3.11.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From b0da9eb809cc5680bce51201f630ba084721bbcd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 16:31:52 +0100 Subject: [PATCH 1059/1193] Use SHLIB_EXT --- easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb index 807d281466f5..b30bdb6cf499 100644 --- a/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/z/Z3/Z3-4.13.0-GCCcore-13.2.0.eb @@ -43,7 +43,7 @@ postinstallcmds = [ sanity_pip_check = True sanity_check_paths = { - 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.so'], + 'files': ['bin/z3', 'include/z3_api.h', 'lib/libz3.' + SHLIB_EXT], 'dirs': ['include', 'lib/python%(pyshortver)s/site-packages'], } From 07817b7d7c2b2772fbafe22b66b59e2d1885cbac Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 16:39:59 +0100 Subject: [PATCH 1060/1193] Fix style --- .../easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb index f4ef722a48a9..5a700f682513 100644 --- a/easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/protobuf/protobuf-25.3-GCCcore-13.2.0.eb @@ -4,8 +4,8 @@ name = 'protobuf' version = '25.3' homepage = 'https://github.com/protocolbuffers/protobuf' -description = """Protocol Buffers (a.k.a., protobuf) are Google's -language-neutral, platform-neutral, extensible mechanism for +description = """Protocol Buffers (a.k.a., protobuf) are Google's +language-neutral, platform-neutral, extensible mechanism for serializing structured data.""" toolchain = {'name': 'GCCcore', 'version': '13.2.0'} From fcadbb77b0f4bbf56398fd5220e41140faa593ea Mon Sep 17 00:00:00 2001 From: crivella Date: Wed, 20 Mar 2024 17:00:27 +0100 Subject: [PATCH 1061/1193] linting --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb | 3 +-- .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb index 45ac0fabf9d0..508d8204a425 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'foss', 'version': '2023a'} toolchainopts = { 'usempi': True, 'openmp': True, - } +} sources = [ { @@ -54,4 +54,3 @@ parallel = 1 moduleclass = 'chem' - diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb index a635d9422426..d78bf4461121 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb @@ -12,7 +12,7 @@ toolchain = {'name': 'intel', 'version': '2023a'} toolchainopts = { 'usempi': True, 'openmp': True, - } +} sources = [ { From 6cc93944cf22297578a4b56e0dff023b1229e1ff Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 17:21:34 +0100 Subject: [PATCH 1062/1193] Fix duplicate dict entries --- .github/workflows/linting.yml | 2 +- .../__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 1 - .../__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 1 - easybuild/easyconfigs/i/IntelDAAL/IntelDAAL-2019.4.007.eb | 8 +++++--- .../easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb | 1 - .../easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb | 1 - .../l/libunwind/libunwind-1.2.1-GCCcore-6.3.0.eb | 1 - .../l/libunwind/libunwind-1.2.1-GCCcore-6.4.0.eb | 1 - .../easyconfigs/l/libunwind/libunwind-1.2.1-foss-2016b.eb | 1 - easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb | 1 - 10 files changed, 6 insertions(+), 12 deletions(-) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 3f2ce53e58f5..ac97a3f372fe 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -28,4 +28,4 @@ jobs: run: flake8 - name: Run flake8 to verify PEP8-compliance of Easyconfigs - run: flake8 --select W605 --filename '*.eb' + run: flake8 --select F,W605 --filename '*.eb' diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 97bdf4390624..315ed536defc 100644 --- a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -24,7 +24,6 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 5b2faed5579d..74e28d29d22e 100644 --- a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -24,7 +24,6 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/i/IntelDAAL/IntelDAAL-2019.4.007.eb b/easybuild/easyconfigs/i/IntelDAAL/IntelDAAL-2019.4.007.eb index 41a1c7f018a4..303563656f07 100644 --- a/easybuild/easyconfigs/i/IntelDAAL/IntelDAAL-2019.4.007.eb +++ b/easybuild/easyconfigs/i/IntelDAAL/IntelDAAL-2019.4.007.eb @@ -15,7 +15,7 @@ version = '2019.4.007' homepage = 'https://software.intel.com/en-us/daal' description = """ -Intel® Data Analytics Acceleration Library (Intel® DAAL) is the library of +Intel® Data Analytics Acceleration Library (Intel® DAAL) is the library of Intel® architecture optimized building blocks covering all stages of data analytics: data acquisition from a data source, preprocessing, transformation, data mining, modeling, validation, and decision making. @@ -34,8 +34,10 @@ local_tbb_dir = "linux/tbb" modextrapaths = { 'CPLUS_INCLUDE_PATH': local_daal_dir + '/include', - 'LIBRARY_PATH': local_daal_dir + '/lib/intel64_lin/lib', - 'LIBRARY_PATH': local_tbb_dir + '/lib/intel64_lin/gcc4.4/libtbb', + 'LIBRARY_PATH': [ + local_daal_dir + '/lib/intel64_lin/lib', + local_tbb_dir + '/lib/intel64_lin/gcc4.4/libtbb', + ], 'PATH': local_daal_dir + '/bin' } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index 9cbc7f2bbf4a..43777142d412 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -24,7 +24,6 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index ba5d70976962..518f3401d4b0 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -24,7 +24,6 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.3.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.3.0.eb index 6f1c323148eb..2fa2f1016bef 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.3.0.eb @@ -29,7 +29,6 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.4.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.4.0.eb index 843868e8f252..aca3556f2abb 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-GCCcore-6.4.0.eb @@ -24,7 +24,6 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-foss-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-foss-2016b.eb index bd6e0e60b9da..d866e563df5d 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-foss-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.2.1-foss-2016b.eb @@ -23,7 +23,6 @@ dependencies = [ preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fuse-ld=bfd" && ' sanity_check_paths = { - 'files': ["include/libunwind.h", "lib/libunwind.%s" % SHLIB_EXT], 'files': ['include/libunwind.h', ('lib/libunwind.%s' % SHLIB_EXT, 'lib64/libunwind.%s' % SHLIB_EXT)], 'dirs': [] } diff --git a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb index ad7708d2b1f0..802b28cc5940 100644 --- a/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb +++ b/easybuild/easyconfigs/r/R/R-3.6.3-foss-2020a.eb @@ -2113,7 +2113,6 @@ exts_list = [ 'checksums': ['3a1f166f1c71b5877a2acca1384ec6c9b430b67af67ef26125f2abbb53c66206'], }), ('liquidSVM', '1.2.4', { - 'checksums': ['15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba'], 'patches': ['liquidSVM-1.2.4-fix_ppc_and_aarch64_build.patch'], 'checksums': [ '15a9c7f2930e2ed3f4c5bcd9b042884ea580d2b2e52e1c68041600c196046aba', From 4fa3304fffcdaa8f3e16c357721edaefd8db4843 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 20 Mar 2024 16:50:10 +0000 Subject: [PATCH 1063/1193] Add patch to make it possible to use SoftFileLock --- .../d/Datasets/Datasets-2.18.0-gfbf-2023a.eb | 7 ++++++- ....18.0_add-option-to-use-softfilelock.patch | 21 +++++++++++++++++++ 2 files changed, 27 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_add-option-to-use-softfilelock.patch diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb index b437c1bd5526..799ffb05ee8b 100644 --- a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb @@ -35,12 +35,17 @@ exts_list = [ 'checksums': ['e1f4968c93726565a80edf6dc309763c7b546d0cfe79aa221206034d50155531'], }), (name, version, { + 'patches': [ + 'Datasets-2.18.0_use-patched-pyarrow.patch', + 'Datasets-2.18.0_add-option-to-use-softfilelock.patch', + ], 'sources': [SOURCELOWER_TAR_GZ], - 'patches': ['Datasets-2.18.0_use-patched-pyarrow.patch'], 'checksums': [ {'datasets-2.18.0.tar.gz': 'cdf8b8c6abf7316377ba4f49f9589a4c74556d6b481afd0abd2284f3d69185cb'}, {'Datasets-2.18.0_use-patched-pyarrow.patch': 'a42f23c94f3f4935aae7a01aebd04bacae518537ecb674efeb94d5af7a296061'}, + {'Datasets-2.18.0_add-option-to-use-softfilelock.patch': + '3fe72f27d447d9ed1f6672d146b481e4590e652b29c649eac4bb649308cc6ca5'}, ], }), ] diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_add-option-to-use-softfilelock.patch b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_add-option-to-use-softfilelock.patch new file mode 100644 index 000000000000..289d8945ae96 --- /dev/null +++ b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_add-option-to-use-softfilelock.patch @@ -0,0 +1,21 @@ +diff --git a/src/datasets/utils/_filelock.py b/src/datasets/utils/_filelock.py +index 19620e6e..58f41a02 100644 +--- a/src/datasets/utils/_filelock.py ++++ b/src/datasets/utils/_filelock.py +@@ -18,11 +18,15 @@ + import os + + from filelock import FileLock as FileLock_ +-from filelock import UnixFileLock ++from filelock import SoftFileLock, UnixFileLock + from filelock import __version__ as _filelock_version + from packaging import version + + ++if os.getenv('HF_USE_SOFTFILELOCK', 'false').lower() in ('true', '1'): ++ FileLock_ = SoftFileLock ++ ++ + class FileLock(FileLock_): + """ + A `filelock.FileLock` initializer that handles long paths. From dbb3da835507f79f1e64934d68ed279077d10bf6 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Wed, 20 Mar 2024 17:53:45 +0100 Subject: [PATCH 1064/1193] Change name to HF-Datasets --- easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb index 799ffb05ee8b..76656d9188ae 100644 --- a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb @@ -1,6 +1,6 @@ easyblock = "PythonBundle" -name = 'Datasets' +name = 'HF-Datasets' version = '2.18.0' homepage = 'https://github.com/huggingface/datasets' From 96df13ab07f12a906d3e048ced2b54d638381261 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 20 Mar 2024 17:02:58 +0000 Subject: [PATCH 1065/1193] Change extension name to datasets --- .../HF-Datasets-2.18.0-gfbf-2023a.eb | 52 +++++++++++++++++++ ...18.0_add-option-to-use-softfilelock.patch} | 0 ...datasets-2.18.0_use-patched-pyarrow.patch} | 0 3 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb rename easybuild/easyconfigs/{d/Datasets/Datasets-2.18.0_add-option-to-use-softfilelock.patch => h/HF-Datasets/datasets-2.18.0_add-option-to-use-softfilelock.patch} (100%) rename easybuild/easyconfigs/{d/Datasets/Datasets-2.18.0_use-patched-pyarrow.patch => h/HF-Datasets/datasets-2.18.0_use-patched-pyarrow.patch} (100%) diff --git a/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb new file mode 100644 index 000000000000..9a94905b9ec5 --- /dev/null +++ b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb @@ -0,0 +1,52 @@ +easyblock = "PythonBundle" + +name = 'HF-Datasets' +version = '2.18.0' + +homepage = 'https://github.com/huggingface/datasets' +description = """ +The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient +data manipulation tools. +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), # for fsspec + ('SciPy-bundle', '2023.07'), + ('aiohttp', '3.8.5'), + ('dill', '0.3.7'), + ('Arrow', '14.0.1'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('python-xxhash', '3.4.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('multiprocess', '0.70.15', { + 'checksums': ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'], + }), + ('huggingface-hub', '0.21.4', { + 'sources': ['huggingface_hub-%(version)s.tar.gz'], + 'checksums': ['e1f4968c93726565a80edf6dc309763c7b546d0cfe79aa221206034d50155531'], + }), + ('datasets', version, { + 'patches': [ + 'datasets-2.18.0_use-patched-pyarrow.patch', + 'datasets-2.18.0_add-option-to-use-softfilelock.patch', + ], + 'checksums': [ + {'datasets-2.18.0.tar.gz': 'cdf8b8c6abf7316377ba4f49f9589a4c74556d6b481afd0abd2284f3d69185cb'}, + {'datasets-2.18.0_use-patched-pyarrow.patch': + 'a42f23c94f3f4935aae7a01aebd04bacae518537ecb674efeb94d5af7a296061'}, + {'datasets-2.18.0_add-option-to-use-softfilelock.patch': + '3fe72f27d447d9ed1f6672d146b481e4590e652b29c649eac4bb649308cc6ca5'}, + ], + }), +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_add-option-to-use-softfilelock.patch b/easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_add-option-to-use-softfilelock.patch similarity index 100% rename from easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_add-option-to-use-softfilelock.patch rename to easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_add-option-to-use-softfilelock.patch diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_use-patched-pyarrow.patch b/easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_use-patched-pyarrow.patch similarity index 100% rename from easybuild/easyconfigs/d/Datasets/Datasets-2.18.0_use-patched-pyarrow.patch rename to easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_use-patched-pyarrow.patch From 499639d012c8e079fbd1a4bf16f874e52133deac Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Wed, 20 Mar 2024 18:03:53 +0100 Subject: [PATCH 1066/1193] Remove file name Datasets-... As part of renaming process --- .../d/Datasets/Datasets-2.18.0-gfbf-2023a.eb | 53 ------------------- 1 file changed, 53 deletions(-) delete mode 100644 easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb b/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb deleted file mode 100644 index 76656d9188ae..000000000000 --- a/easybuild/easyconfigs/d/Datasets/Datasets-2.18.0-gfbf-2023a.eb +++ /dev/null @@ -1,53 +0,0 @@ -easyblock = "PythonBundle" - -name = 'HF-Datasets' -version = '2.18.0' - -homepage = 'https://github.com/huggingface/datasets' -description = """ -The largest hub of ready-to-use datasets for ML models with fast, easy-to-use and efficient -data manipulation tools. -""" - -toolchain = {'name': 'gfbf', 'version': '2023a'} - -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), # for fsspec - ('SciPy-bundle', '2023.07'), - ('aiohttp', '3.8.5'), - ('dill', '0.3.7'), - ('Arrow', '14.0.1'), - ('PyYAML', '6.0'), - ('tqdm', '4.66.1'), - ('python-xxhash', '3.4.1'), -] - -use_pip = True -sanity_pip_check = True - -exts_list = [ - ('multiprocess', '0.70.15', { - 'checksums': ['f20eed3036c0ef477b07a4177cf7c1ba520d9a2677870a4f47fe026f0cd6787e'], - }), - ('huggingface-hub', '0.21.4', { - 'sources': ['huggingface_hub-%(version)s.tar.gz'], - 'checksums': ['e1f4968c93726565a80edf6dc309763c7b546d0cfe79aa221206034d50155531'], - }), - (name, version, { - 'patches': [ - 'Datasets-2.18.0_use-patched-pyarrow.patch', - 'Datasets-2.18.0_add-option-to-use-softfilelock.patch', - ], - 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': [ - {'datasets-2.18.0.tar.gz': 'cdf8b8c6abf7316377ba4f49f9589a4c74556d6b481afd0abd2284f3d69185cb'}, - {'Datasets-2.18.0_use-patched-pyarrow.patch': - 'a42f23c94f3f4935aae7a01aebd04bacae518537ecb674efeb94d5af7a296061'}, - {'Datasets-2.18.0_add-option-to-use-softfilelock.patch': - '3fe72f27d447d9ed1f6672d146b481e4590e652b29c649eac4bb649308cc6ca5'}, - ], - }), -] - -moduleclass = 'data' From e161684415006097a9414ef774bf6272824d8598 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Wed, 20 Mar 2024 17:11:42 +0000 Subject: [PATCH 1067/1193] Add comment to patch --- .../h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb | 2 +- .../datasets-2.18.0_add-option-to-use-softfilelock.patch | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb index 9a94905b9ec5..6b7fb2bd5be3 100644 --- a/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb +++ b/easybuild/easyconfigs/h/HF-Datasets/HF-Datasets-2.18.0-gfbf-2023a.eb @@ -44,7 +44,7 @@ exts_list = [ {'datasets-2.18.0_use-patched-pyarrow.patch': 'a42f23c94f3f4935aae7a01aebd04bacae518537ecb674efeb94d5af7a296061'}, {'datasets-2.18.0_add-option-to-use-softfilelock.patch': - '3fe72f27d447d9ed1f6672d146b481e4590e652b29c649eac4bb649308cc6ca5'}, + '18f3a3f3735afcbf9f4c19a2bd5bdb7221ca5ad13a36748df42404764a8cd0fc'}, ], }), ] diff --git a/easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_add-option-to-use-softfilelock.patch b/easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_add-option-to-use-softfilelock.patch index 289d8945ae96..3dd607edc40a 100644 --- a/easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_add-option-to-use-softfilelock.patch +++ b/easybuild/easyconfigs/h/HF-Datasets/datasets-2.18.0_add-option-to-use-softfilelock.patch @@ -1,3 +1,11 @@ +This adds the possibility to control if FileLock of SoftFileLock is used with an environment variable. + +Useful in case the filesystem doesn't support filelocking, but can probably +lead to problems if you are not careful in how you use it. +https://github.com/huggingface/datasets/issues/6744 + +Author: Viktor Rehnberg vikren@chalmers.se (Chalmers University of Technology) + diff --git a/src/datasets/utils/_filelock.py b/src/datasets/utils/_filelock.py index 19620e6e..58f41a02 100644 --- a/src/datasets/utils/_filelock.py From 1ec962e8ef05eadc826924ccd647475a3a81351d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 09:02:59 +0100 Subject: [PATCH 1068/1193] Replace MD5 checksums by SHA256 --- .../__archive__/l/libunwind/libunwind-1.1-foss-2015a.eb | 2 +- .../__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb | 2 +- .../__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb | 2 +- easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb | 2 +- easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb | 2 +- easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-foss-2015a.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-foss-2015a.eb index 19a10c83627a..aba9b1471333 100644 --- a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-foss-2015a.eb +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-foss-2015a.eb @@ -15,7 +15,7 @@ toolchain = {'version': '2015a', 'name': 'foss'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] +checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb index 315ed536defc..636165fe4bbc 100644 --- a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-goolf-1.4.10.eb @@ -15,7 +15,7 @@ toolchain = {'version': '1.4.10', 'name': 'goolf'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] +checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb index 74e28d29d22e..8f3780386e60 100644 --- a/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb +++ b/easybuild/easyconfigs/__archive__/l/libunwind/libunwind-1.1-ictce-5.3.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'ictce', 'version': '5.3.0'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] +checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb index 396cb5364feb..2577378688e9 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-GCC-4.9.2.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'GCC', 'version': '4.9.2'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] +checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb index 43777142d412..5c630a261054 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-foss-2016a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2016a'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] +checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a'] dependencies = [ ('XZ', '5.2.2'), diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb index 518f3401d4b0..25aafb9cb43b 100644 --- a/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.1-intel-2016b.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'intel', 'version': '2016b'} sources = [SOURCE_TAR_GZ] source_urls = [GNU_SAVANNAH_SOURCE] -checksums = ['fb4ea2f6fbbe45bf032cd36e586883ce'] +checksums = ['9dfe0fcae2a866de9d3942c66995e4b460230446887dbdab302d41a8aee8d09a'] dependencies = [ ('XZ', '5.2.2'), From c3faf793b02def1beee4d19a366b2aeefabdf657 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 09:08:56 +0100 Subject: [PATCH 1069/1193] Enable download_dep_fail for Pythonpackage ECs where it was wrongly disabled --- .../easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb | 2 +- .../pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb | 2 +- .../pytest-flakefinder-1.1.0-GCCcore-12.2.0.eb | 2 +- .../pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb | 2 +- .../pytest-rerunfailures-11.1-GCCcore-11.3.0.eb | 2 +- .../pytest-rerunfailures-12.0-GCCcore-12.2.0.eb | 2 +- .../pytest-rerunfailures-12.0-GCCcore-12.3.0.eb | 2 +- .../p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb | 2 +- .../p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb | 2 +- .../p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb | 2 +- easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb | 2 +- 11 files changed, 11 insertions(+), 11 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb mode change 100755 => 100644 easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb old mode 100755 new mode 100644 index f5d720e5b7a9..402260833656 --- a/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-cpp/pytest-cpp-2.3.0-GCCcore-11.3.0.eb @@ -13,7 +13,7 @@ dependencies = [('Python', '3.10.4')] use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['37abfa693697940aed2e7c034698188dee3616183ad9b3f764f3b06aeb75ed4a'] diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb old mode 100755 new mode 100644 index af5753f1645a..60f2242fba0f --- a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-11.3.0.eb @@ -13,7 +13,7 @@ dependencies = [('Python', '3.10.4')] use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.2.0.eb index b5ed6a200320..2827c01ebbcc 100644 --- a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.2.0.eb @@ -13,7 +13,7 @@ dependencies = [('Python', '3.10.8')] use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] diff --git a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb index 5ebf016d64cf..b5e47528026c 100644 --- a/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-flakefinder/pytest-flakefinder-1.1.0-GCCcore-12.3.0.eb @@ -16,7 +16,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['e2412a1920bdb8e7908783b20b3d57e9dad590cc39a93e8596ffdd493b403e0e'] diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb index 1a77cf37d102..b55fb3746ed0 100644 --- a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-11.1-GCCcore-11.3.0.eb @@ -13,7 +13,7 @@ dependencies = [('Python', '3.10.4')] use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['bc6ad13614c976b04558c3a7bcc393a7e09686fb86b6ae73f827b78326c09f75'] diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb index eefd52471b14..58871575982f 100644 --- a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.2.0.eb @@ -13,7 +13,7 @@ dependencies = [('Python', '3.10.8')] use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['784f462fa87fe9bdf781d0027d856b47a4bfe6c12af108f6bd887057a917b48e'] diff --git a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb index 19666ba283e0..4a8634e4c3b6 100644 --- a/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-rerunfailures/pytest-rerunfailures-12.0-GCCcore-12.3.0.eb @@ -17,7 +17,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['784f462fa87fe9bdf781d0027d856b47a4bfe6c12af108f6bd887057a917b48e'] diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb index 11746d4cf6dd..9e4d690223fd 100644 --- a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-11.3.0.eb @@ -20,7 +20,7 @@ dependencies = [('Python', '3.10.4')] use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb index bd08dfe54d6d..9087c9673f6e 100644 --- a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.2.0.eb @@ -20,7 +20,7 @@ dependencies = [('Python', '3.10.8')] use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] diff --git a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb index f5a4e364a1d7..f583722391d7 100644 --- a/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/pytest-shard/pytest-shard-0.1.2-GCCcore-12.3.0.eb @@ -23,7 +23,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True sources = [SOURCE_TAR_GZ] checksums = ['b86a967fbfd1c8e50295095ccda031b7e890862ee06531d5142844f4c1d1cd67'] diff --git a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb index 173bc41c41ad..750f9c843ff3 100644 --- a/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb +++ b/easybuild/easyconfigs/s/SCGid/SCGid-0.9b0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = False +download_dep_fail = True exts_defaultclass = "Tarball" From e481b0686b9ed06a8ae4eaea17b1aab3754fa919 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 20 Mar 2024 16:02:12 +0100 Subject: [PATCH 1070/1193] adding easyconfigs: PyTorch-2.1.2-foss-2023b.eb --- .../p/PyTorch/PyTorch-2.1.2-foss-2023b.eb | 183 ++++++++++++++++++ 1 file changed, 183 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb new file mode 100644 index 000000000000..151e13356fec --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-2.1.2-foss-2023b.eb @@ -0,0 +1,183 @@ +name = 'PyTorch' +version = '2.1.2' + +homepage = 'https://pytorch.org/' +description = """Tensors and Dynamic neural networks in Python with strong GPU acceleration. +PyTorch is a deep learning framework that puts Python first.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +patches = [ + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_add-hypothesis-suppression.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch', + 'PyTorch-1.13.1_fix-protobuf-dependency.patch', + 'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch', + 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', + 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_avoid-test_quantization-failures.patch', + 'PyTorch-2.0.1_fix-skip-decorators.patch', + 'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch', + 'PyTorch-2.0.1_fix-vsx-loadu.patch', + 'PyTorch-2.0.1_no-cuda-stubs-rpath.patch', + 'PyTorch-2.0.1_skip-failing-gradtest.patch', + 'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch', + 'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch', + 'PyTorch-2.1.0_disable-gcc12-warning.patch', + 'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch', + 'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch', + 'PyTorch-2.1.0_fix-validationError-output-test.patch', + 'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch', + 'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch', + 'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch', + 'PyTorch-2.1.0_remove-test-requiring-online-access.patch', + 'PyTorch-2.1.0_skip-diff-test-on-ppc.patch', + 'PyTorch-2.1.0_skip-dynamo-test_predispatch.patch', + 'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch', + 'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch', + 'PyTorch-2.1.0_skip-test_wrap_bad.patch', + 'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch', + 'PyTorch-2.1.2_fix-test_memory_profiler.patch', + 'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch', + 'PyTorch-2.1.2_fix-vsx-vector-abs.patch', + 'PyTorch-2.1.2_fix-vsx-vector-div.patch', + 'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch', + 'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch', +] +checksums = [ + {'pytorch-v2.1.2.tar.gz': '85effbcce037bffa290aea775c9a4bad5f769cb229583450c40055501ee1acd7'}, + {'PyTorch-1.7.0_disable-dev-shm-test.patch': '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a'}, + {'PyTorch-1.11.1_skip-test_init_from_local_shards.patch': + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, + {'PyTorch-1.12.1_add-hypothesis-suppression.patch': + 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, + {'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch': + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83'}, + {'PyTorch-1.12.1_fix-TestTorch.test_to.patch': '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535'}, + {'PyTorch-1.12.1_skip-test_round_robin.patch': '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349'}, + {'PyTorch-1.13.1_fix-gcc-12-warning-in-fbgemm.patch': + '5c7be91a6096083a0b1315efe0001537499c600f1f569953c6a2c7f4cc1d0910'}, + {'PyTorch-1.13.1_fix-protobuf-dependency.patch': + '8bd755a0cab7233a243bc65ca57c9630dfccdc9bf8c9792f0de4e07a644fcb00'}, + {'PyTorch-1.13.1_fix-warning-in-test-cpp-api.patch': + 'bdde0f2105215c95a54de64ec4b1a4520528510663174fef6d5b900eb1db3937'}, + {'PyTorch-1.13.1_skip-failing-singular-grad-test.patch': + '72688a57b2bb617665ad1a1d5e362c5111ae912c10936bb38a089c0204729f48'}, + {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': + '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_avoid-test_quantization-failures.patch': + '02e3f47e4ed1d7d6077e26f1ae50073dc2b20426269930b505f4aefe5d2f33cd'}, + {'PyTorch-2.0.1_fix-skip-decorators.patch': '2039012cef45446065e1a2097839fe20bb29fe3c1dcc926c3695ebf29832e920'}, + {'PyTorch-2.0.1_fix-ub-in-inductor-codegen.patch': + '1b37194f55ae678f3657b8728dfb896c18ffe8babe90987ce468c4fa9274f357'}, + {'PyTorch-2.0.1_fix-vsx-loadu.patch': 'a0ffa61da2d47c6acd09aaf6d4791e527d8919a6f4f1aa7ed38454cdcadb1f72'}, + {'PyTorch-2.0.1_no-cuda-stubs-rpath.patch': '8902e58a762240f24cdbf0182e99ccdfc2a93492869352fcb4ca0ec7e407f83a'}, + {'PyTorch-2.0.1_skip-failing-gradtest.patch': '8030bdec6ba49b057ab232d19a7f1a5e542e47e2ec340653a246ec9ed59f8bc1'}, + {'PyTorch-2.0.1_skip-test_shuffle_reproducibility.patch': + '7047862abc1abaff62954da59700f36d4f39fcf83167a638183b1b7f8fec78ae'}, + {'PyTorch-2.0.1_skip-tests-skipped-in-subprocess.patch': + '166c134573a95230e39b9ea09ece3ad8072f39d370c9a88fb2a1e24f6aaac2b5'}, + {'PyTorch-2.1.0_disable-gcc12-warning.patch': 'c858b8db0010f41005dc06f9a50768d0d3dc2d2d499ccbdd5faf8a518869a421'}, + {'PyTorch-2.1.0_fix-bufferoverflow-in-oneDNN.patch': + 'b15b1291a3c37bf6a4982cfbb3483f693acb46a67bc0912b383fd98baf540ccf'}, + {'PyTorch-2.1.0_fix-test_numpy_torch_operators.patch': + '84bb51a719abc677031a7a3dfe4382ff098b0cbd8b39b8bed2a7fa03f80ac1e9'}, + {'PyTorch-2.1.0_fix-validationError-output-test.patch': + '7eba0942afb121ed92fac30d1529447d892a89eb3d53c565f8e9d480e95f692b'}, + {'PyTorch-2.1.0_fix-vsx-vector-shift-functions.patch': + '3793b4b878be1abe7791efcbd534774b87862cfe7dc4774ca8729b6cabb39e7e'}, + {'PyTorch-2.1.0_increase-tolerance-functorch-test_vmapvjpvjp.patch': + 'aef38adf1210d0c5455e91d7c7a9d9e5caad3ae568301e0ba9fc204309438e7b'}, + {'PyTorch-2.1.0_remove-sparse-csr-nnz-overflow-test.patch': + '0ac36411e76506b3354c85a8a1260987f66af947ee52ffc64230aee1fa02ea8b'}, + {'PyTorch-2.1.0_remove-test-requiring-online-access.patch': + '35184b8c5a1b10f79e511cc25db3b8a5585a5d58b5d1aa25dd3d250200b14fd7'}, + {'PyTorch-2.1.0_skip-diff-test-on-ppc.patch': '394157dbe565ffcbc1821cd63d05930957412156cc01e949ef3d3524176a1dda'}, + {'PyTorch-2.1.0_skip-dynamo-test_predispatch.patch': + '6298daf9ddaa8542850eee9ea005f28594ab65b1f87af43d8aeca1579a8c4354'}, + {'PyTorch-2.1.0_skip-test_jvp_linalg_det_singular.patch': + '5229ca88a71db7667a90ddc0b809b2c817698bd6e9c5aaabd73d3173cf9b99fe'}, + {'PyTorch-2.1.0_skip-test_linear_fp32-without-MKL.patch': + '5dcc79883b6e3ec0a281a8e110db5e0a5880de843bb05653589891f16473ead5'}, + {'PyTorch-2.1.0_skip-test_wrap_bad.patch': 'b8583125ee94e553b6f77c4ab4bfa812b89416175dc7e9b7390919f3b485cb63'}, + {'PyTorch-2.1.2_fix-test_extension_backend-without-vectorization.patch': + 'cd1455495886a7d6b2d30d48736eb0103fded21e2e36de6baac719b9c52a1c92'}, + {'PyTorch-2.1.2_fix-test_memory_profiler.patch': + '30b0c9355636c0ab3dedae02399789053825dc3835b4d7dac6e696767772b1ce'}, + {'PyTorch-2.1.2_fix-test_torchinductor-rounding.patch': + 'a0ef99192ee2ad1509c78a8377023d5be2b5fddb16f84063b7c9a0b53d979090'}, + {'PyTorch-2.1.2_fix-vsx-vector-abs.patch': 'd67d32407faed7dc1dbab4bba0e2f7de36c3db04560ced35c94caf8d84ade886'}, + {'PyTorch-2.1.2_fix-vsx-vector-div.patch': '11f497a6892eb49b249a15320e4218e0d7ac8ae4ce67de39e4a018a064ca1acc'}, + {'PyTorch-2.1.2_skip-cpu_repro-test-without-vectorization.patch': + '7ace835af60c58d9e0754a34c19d4b9a0c3a531f19e5d0eba8e2e49206eaa7eb'}, + {'PyTorch-2.1.2_workaround_dynamo_failure_without_nnpack.patch': + 'fb96eefabf394617bbb3fbd3a7a7c1aa5991b3836edc2e5d2a30e708bfe49ba1'}, +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.27.6'), + ('hypothesis', '6.90.0'), + # For tests + ('pytest-flakefinder', '1.1.0'), + ('pytest-rerunfailures', '14.0'), + ('pytest-shard', '0.1.2'), +] + +dependencies = [ + ('Ninja', '1.11.1'), # Required for JIT compilation of C++ extensions + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('protobuf', '25.3'), + ('protobuf-python', '4.25.3'), + ('pybind11', '2.11.1'), + ('SciPy-bundle', '2023.11'), + ('PyYAML', '6.0.1'), + ('MPFR', '4.2.1'), + ('GMP', '6.3.0'), + ('numactl', '2.0.16'), + ('FFmpeg', '6.0'), + ('Pillow', '10.2.0'), + ('expecttest', '0.2.1'), + ('networkx', '3.2.1'), + ('sympy', '1.12'), + ('Z3', '4.13.0',), +] + +use_pip = True +buildcmd = '%(python)s setup.py build' # Run the (long) build in the build step + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 + 'distributions/test_constraints', + # no xdoctest + 'doctests', + # failing on broadwell + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'test_native_mha', + # intermittent failures on various systems + # See https://github.com/easybuilders/easybuild-easyconfigs/issues/17712 + 'distributed/rpc/test_tensorpipe_agent', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' From 26169dca4361d117e5d559af27fcab15421ea0f1 Mon Sep 17 00:00:00 2001 From: crivella Date: Thu, 21 Mar 2024 10:27:51 +0100 Subject: [PATCH 1071/1193] Allow for 1 test failure for pw_vwd on 7.3 intel --- .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb | 1 - .../q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb | 2 ++ 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb index 508d8204a425..208c30416899 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-foss-2023a.eb @@ -52,5 +52,4 @@ buildopts = "all gwl xspectra couple epw gipaw w90" # parallel build tends to fail parallel = 1 - moduleclass = 'chem' diff --git a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb index d78bf4461121..2f3ccd6da68d 100644 --- a/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb +++ b/easybuild/easyconfigs/q/QuantumESPRESSO/QuantumESPRESSO-7.3-intel-2023a.eb @@ -52,5 +52,7 @@ buildopts = "all gwl xspectra couple epw gipaw w90" # parallel build tends to fail parallel = 1 +# allow some test failures +test_suite_max_failed = 1 moduleclass = 'chem' From 8151bfab0ce41d26e75dbdc89052c21b48739ba8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:16:48 +0100 Subject: [PATCH 1072/1193] fix PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb for Linux 6+ --- .../PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 3 ++ ...Gloo-compatibility-with-newer-kernel.patch | 30 +++++++++++++++++++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index 59244119da2f..eb4946e098fd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -70,6 +71,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d'}, {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch': + '0d19c3dd7ea088aae2f18a2552420293a06ed0a0e1e8e2a28d44ff3847de32af'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch': diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch new file mode 100644 index 000000000000..19c24ca3f912 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch @@ -0,0 +1,30 @@ +`struct ethtool_link_settings` contains a "Flexible array member" which must be the last member +in a struct. However in an anonymous struct in Gloo it is before a member intented to provide +the storage for that array causing a warning/error in GCC for newer kernels +where the Flexible array member is used instead of a zero-sized array. +> /usr/include/linux/ethtool.h:2182:17: error: flexible array member ethtool_link_settings::link_mode_masks not at end of struct gloo::getInterfaceSpeedGLinkSettings(int, ifreq*):: +> 2182 | __u32 link_mode_masks[]; +See https://github.com/facebookincubator/gloo/issues/345 + +Fix by using an union of that struct and another struct providing the storage. + +Author: Alexander Grund (TU Dresden) + +diff -ur pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc +--- pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:26:21.393691678 +0100 ++++ pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:40:49.263165348 +0100 +@@ -187,9 +187,12 @@ + static int getInterfaceSpeedGLinkSettings(int sock, struct ifreq* ifr) { + #if LINUX_VERSION_CODE >= KERNEL_VERSION(4,6,0) + constexpr auto link_mode_data_nwords = 3 * 127; +- struct { ++ union { + struct ethtool_link_settings req; +- __u32 link_mode_data[link_mode_data_nwords]; ++ struct { // Only to provide the memory ++ __u32 link_mode_data[link_mode_data_nwords]; ++ struct ethtool_link_settings dummy; ++ }; + } ecmd; + int rv; + From 257f665ad30f9ef9fe635f807df2cbc287ab6c6f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:22:06 +0100 Subject: [PATCH 1073/1193] fix PyTorch-1.12.0-foss-2022a for Linux 6+ --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 1 + ...Gloo-compatibility-with-newer-kernel.patch | 30 +++++++++++++++++++ 2 files changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb index 9d518f41a3d1..1cca0fa84991 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch new file mode 100644 index 000000000000..19c24ca3f912 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch @@ -0,0 +1,30 @@ +`struct ethtool_link_settings` contains a "Flexible array member" which must be the last member +in a struct. However in an anonymous struct in Gloo it is before a member intented to provide +the storage for that array causing a warning/error in GCC for newer kernels +where the Flexible array member is used instead of a zero-sized array. +> /usr/include/linux/ethtool.h:2182:17: error: flexible array member ethtool_link_settings::link_mode_masks not at end of struct gloo::getInterfaceSpeedGLinkSettings(int, ifreq*):: +> 2182 | __u32 link_mode_masks[]; +See https://github.com/facebookincubator/gloo/issues/345 + +Fix by using an union of that struct and another struct providing the storage. + +Author: Alexander Grund (TU Dresden) + +diff -ur pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc +--- pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:26:21.393691678 +0100 ++++ pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:40:49.263165348 +0100 +@@ -187,9 +187,12 @@ + static int getInterfaceSpeedGLinkSettings(int sock, struct ifreq* ifr) { + #if LINUX_VERSION_CODE >= KERNEL_VERSION(4,6,0) + constexpr auto link_mode_data_nwords = 3 * 127; +- struct { ++ union { + struct ethtool_link_settings req; +- __u32 link_mode_data[link_mode_data_nwords]; ++ struct { // Only to provide the memory ++ __u32 link_mode_data[link_mode_data_nwords]; ++ struct ethtool_link_settings dummy; ++ }; + } ecmd; + int rv; + From 291c823580244c993fef8ffacbc4fceba02d9b12 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:35:27 +0100 Subject: [PATCH 1074/1193] Add checksum --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb index 1cca0fa84991..25bea2cd65bc 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -70,6 +70,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d'}, {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch': + '0d19c3dd7ea088aae2f18a2552420293a06ed0a0e1e8e2a28d44ff3847de32af'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch': From 0b47908a40d6987031a91713a9411633b41a937f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:37:04 +0100 Subject: [PATCH 1075/1193] fix PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb for Linux 6+ --- ...Gloo-compatibility-with-newer-kernel.patch | 30 +++++++++++++++++++ .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 ++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch new file mode 100644 index 000000000000..19c24ca3f912 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch @@ -0,0 +1,30 @@ +`struct ethtool_link_settings` contains a "Flexible array member" which must be the last member +in a struct. However in an anonymous struct in Gloo it is before a member intented to provide +the storage for that array causing a warning/error in GCC for newer kernels +where the Flexible array member is used instead of a zero-sized array. +> /usr/include/linux/ethtool.h:2182:17: error: flexible array member ethtool_link_settings::link_mode_masks not at end of struct gloo::getInterfaceSpeedGLinkSettings(int, ifreq*):: +> 2182 | __u32 link_mode_masks[]; +See https://github.com/facebookincubator/gloo/issues/345 + +Fix by using an union of that struct and another struct providing the storage. + +Author: Alexander Grund (TU Dresden) + +diff -ur pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc +--- pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:26:21.393691678 +0100 ++++ pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:40:49.263165348 +0100 +@@ -187,9 +187,12 @@ + static int getInterfaceSpeedGLinkSettings(int sock, struct ifreq* ifr) { + #if LINUX_VERSION_CODE >= KERNEL_VERSION(4,6,0) + constexpr auto link_mode_data_nwords = 3 * 127; +- struct { ++ union { + struct ethtool_link_settings req; +- __u32 link_mode_data[link_mode_data_nwords]; ++ struct { // Only to provide the memory ++ __u32 link_mode_data[link_mode_data_nwords]; ++ struct ethtool_link_settings dummy; ++ }; + } ecmd; + int rv; + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 83c6b9df6c4b..e46b3f938f30 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -27,6 +27,7 @@ patches = [ 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', @@ -75,6 +76,8 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch': + '0d19c3dd7ea088aae2f18a2552420293a06ed0a0e1e8e2a28d44ff3847de32af'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch From d9d968231331d74f2a10a8cc0678492765fe2ba5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:37:13 +0100 Subject: [PATCH 1076/1193] fix PyTorch-1.12.1-foss-2022a.eb for Linux 6+ --- ...Gloo-compatibility-with-newer-kernel.patch | 30 +++++++++++++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 3 ++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch new file mode 100644 index 000000000000..19c24ca3f912 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch @@ -0,0 +1,30 @@ +`struct ethtool_link_settings` contains a "Flexible array member" which must be the last member +in a struct. However in an anonymous struct in Gloo it is before a member intented to provide +the storage for that array causing a warning/error in GCC for newer kernels +where the Flexible array member is used instead of a zero-sized array. +> /usr/include/linux/ethtool.h:2182:17: error: flexible array member ethtool_link_settings::link_mode_masks not at end of struct gloo::getInterfaceSpeedGLinkSettings(int, ifreq*):: +> 2182 | __u32 link_mode_masks[]; +See https://github.com/facebookincubator/gloo/issues/345 + +Fix by using an union of that struct and another struct providing the storage. + +Author: Alexander Grund (TU Dresden) + +diff -ur pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc +--- pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:26:21.393691678 +0100 ++++ pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:40:49.263165348 +0100 +@@ -187,9 +187,12 @@ + static int getInterfaceSpeedGLinkSettings(int sock, struct ifreq* ifr) { + #if LINUX_VERSION_CODE >= KERNEL_VERSION(4,6,0) + constexpr auto link_mode_data_nwords = 3 * 127; +- struct { ++ union { + struct ethtool_link_settings req; +- __u32 link_mode_data[link_mode_data_nwords]; ++ struct { // Only to provide the memory ++ __u32 link_mode_data[link_mode_data_nwords]; ++ struct ethtool_link_settings dummy; ++ }; + } ecmd; + int rv; + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index 7914c2c0e24e..16da2ca106b9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', @@ -70,6 +71,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch': + '0d19c3dd7ea088aae2f18a2552420293a06ed0a0e1e8e2a28d44ff3847de32af'}, # PyTorch-1.12.1_add-hypothesis-suppression.patch 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch From f3d7bb19ab2279ccb15498a317a12e60ab7eca46 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:37:21 +0100 Subject: [PATCH 1077/1193] fix PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb for Linux 6+ --- ...Gloo-compatibility-with-newer-kernel.patch | 30 +++++++++++++++++++ .../PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb | 3 ++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch new file mode 100644 index 000000000000..19c24ca3f912 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch @@ -0,0 +1,30 @@ +`struct ethtool_link_settings` contains a "Flexible array member" which must be the last member +in a struct. However in an anonymous struct in Gloo it is before a member intented to provide +the storage for that array causing a warning/error in GCC for newer kernels +where the Flexible array member is used instead of a zero-sized array. +> /usr/include/linux/ethtool.h:2182:17: error: flexible array member ethtool_link_settings::link_mode_masks not at end of struct gloo::getInterfaceSpeedGLinkSettings(int, ifreq*):: +> 2182 | __u32 link_mode_masks[]; +See https://github.com/facebookincubator/gloo/issues/345 + +Fix by using an union of that struct and another struct providing the storage. + +Author: Alexander Grund (TU Dresden) + +diff -ur pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc +--- pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:26:21.393691678 +0100 ++++ pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:40:49.263165348 +0100 +@@ -187,9 +187,12 @@ + static int getInterfaceSpeedGLinkSettings(int sock, struct ifreq* ifr) { + #if LINUX_VERSION_CODE >= KERNEL_VERSION(4,6,0) + constexpr auto link_mode_data_nwords = 3 * 127; +- struct { ++ union { + struct ethtool_link_settings req; +- __u32 link_mode_data[link_mode_data_nwords]; ++ struct { // Only to provide the memory ++ __u32 link_mode_data[link_mode_data_nwords]; ++ struct ethtool_link_settings dummy; ++ }; + } ecmd; + int rv; + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb index 3303a814d56e..c38ff848e65a 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -16,6 +16,7 @@ patches = [ 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -53,6 +54,8 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch': + '0d19c3dd7ea088aae2f18a2552420293a06ed0a0e1e8e2a28d44ff3847de32af'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, From b72d04af222a033aac2add2dd85e321d855952ee Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:37:29 +0100 Subject: [PATCH 1078/1193] fix PyTorch-1.13.1-foss-2022a.eb for Linux 6+ --- ...Gloo-compatibility-with-newer-kernel.patch | 30 +++++++++++++++++++ .../p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 3 ++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch new file mode 100644 index 000000000000..19c24ca3f912 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch @@ -0,0 +1,30 @@ +`struct ethtool_link_settings` contains a "Flexible array member" which must be the last member +in a struct. However in an anonymous struct in Gloo it is before a member intented to provide +the storage for that array causing a warning/error in GCC for newer kernels +where the Flexible array member is used instead of a zero-sized array. +> /usr/include/linux/ethtool.h:2182:17: error: flexible array member ethtool_link_settings::link_mode_masks not at end of struct gloo::getInterfaceSpeedGLinkSettings(int, ifreq*):: +> 2182 | __u32 link_mode_masks[]; +See https://github.com/facebookincubator/gloo/issues/345 + +Fix by using an union of that struct and another struct providing the storage. + +Author: Alexander Grund (TU Dresden) + +diff -ur pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc +--- pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:26:21.393691678 +0100 ++++ pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:40:49.263165348 +0100 +@@ -187,9 +187,12 @@ + static int getInterfaceSpeedGLinkSettings(int sock, struct ifreq* ifr) { + #if LINUX_VERSION_CODE >= KERNEL_VERSION(4,6,0) + constexpr auto link_mode_data_nwords = 3 * 127; +- struct { ++ union { + struct ethtool_link_settings req; +- __u32 link_mode_data[link_mode_data_nwords]; ++ struct { // Only to provide the memory ++ __u32 link_mode_data[link_mode_data_nwords]; ++ struct ethtool_link_settings dummy; ++ }; + } ecmd; + int rv; + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index c2eb02d44351..07ea30a2a380 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -15,6 +15,7 @@ patches = [ 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -45,6 +46,8 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch': + '0d19c3dd7ea088aae2f18a2552420293a06ed0a0e1e8e2a28d44ff3847de32af'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, From cb4b3bf14f9592a90966853d3274101c70e8f796 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 21 Mar 2024 12:37:38 +0100 Subject: [PATCH 1079/1193] fix PyTorch-1.13.1-foss-2022b.eb for Linux 6+ --- ...Gloo-compatibility-with-newer-kernel.patch | 30 +++++++++++++++++++ .../p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 3 ++ 2 files changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch new file mode 100644 index 000000000000..19c24ca3f912 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch @@ -0,0 +1,30 @@ +`struct ethtool_link_settings` contains a "Flexible array member" which must be the last member +in a struct. However in an anonymous struct in Gloo it is before a member intented to provide +the storage for that array causing a warning/error in GCC for newer kernels +where the Flexible array member is used instead of a zero-sized array. +> /usr/include/linux/ethtool.h:2182:17: error: flexible array member ethtool_link_settings::link_mode_masks not at end of struct gloo::getInterfaceSpeedGLinkSettings(int, ifreq*):: +> 2182 | __u32 link_mode_masks[]; +See https://github.com/facebookincubator/gloo/issues/345 + +Fix by using an union of that struct and another struct providing the storage. + +Author: Alexander Grund (TU Dresden) + +diff -ur pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc +--- pytorch-v1.12.0-orig/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:26:21.393691678 +0100 ++++ pytorch-v1.12.0/third_party/gloo/gloo/common/linux.cc 2024-03-21 09:40:49.263165348 +0100 +@@ -187,9 +187,12 @@ + static int getInterfaceSpeedGLinkSettings(int sock, struct ifreq* ifr) { + #if LINUX_VERSION_CODE >= KERNEL_VERSION(4,6,0) + constexpr auto link_mode_data_nwords = 3 * 127; +- struct { ++ union { + struct ethtool_link_settings req; +- __u32 link_mode_data[link_mode_data_nwords]; ++ struct { // Only to provide the memory ++ __u32 link_mode_data[link_mode_data_nwords]; ++ struct ethtool_link_settings dummy; ++ }; + } ecmd; + int rv; + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index e567f93765a4..e321be1a7dfd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -15,6 +15,7 @@ patches = [ 'PyTorch-1.11.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch', + 'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch', 'PyTorch-1.12.1_add-hypothesis-suppression.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -55,6 +56,8 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7'}, {'PyTorch-1.12.0_fix-EmbeddingBag-without-fbgemm.patch': '090598592283e3fc46ee08a68b6a6afe07be41b26514afba51834408bf1c98ed'}, + {'PyTorch-1.12.0_fix-Gloo-compatibility-with-newer-kernel.patch': + '0d19c3dd7ea088aae2f18a2552420293a06ed0a0e1e8e2a28d44ff3847de32af'}, {'PyTorch-1.12.1_add-hypothesis-suppression.patch': 'e71ffb94ebe69f580fa70e0de84017058325fdff944866d6bd03463626edc32c'}, {'PyTorch-1.12.1_fix-skip-decorators.patch': 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c'}, From ddae6906a068f8fc87e5eb8143d0b880f42c079b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 21 Mar 2024 13:03:28 +0100 Subject: [PATCH 1080/1193] adding easyconfigs: COBRApy-0.29.0-foss-2023b.eb, python-libsbml-5.20.2-foss-2023b.eb, Check-0.15.2-GCCcore-13.2.0.eb, ruamel.yaml-0.18.6-GCCcore-13.2.0.eb --- .../c/COBRApy/COBRApy-0.29.0-foss-2023b.eb | 70 +++++++++++++++++++ .../c/Check/Check-0.15.2-GCCcore-13.2.0.eb | 37 ++++++++++ .../python-libsbml-5.20.2-foss-2023b.eb | 46 ++++++++++++ .../ruamel.yaml-0.18.6-GCCcore-13.2.0.eb | 60 ++++++++++++++++ 4 files changed, 213 insertions(+) create mode 100644 easybuild/easyconfigs/c/COBRApy/COBRApy-0.29.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.29.0-foss-2023b.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.29.0-foss-2023b.eb new file mode 100644 index 000000000000..e52677775bd0 --- /dev/null +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.29.0-foss-2023b.eb @@ -0,0 +1,70 @@ +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# Authors: Sebastien Moretti +# Update: Pavel Tománek (INUITS) + +easyblock = 'PythonBundle' + +name = 'COBRApy' +version = '0.29.0' + +homepage = 'https://opencobra.github.io/cobrapy/' +description = """COBRApy is a package for constraint-based modeling of metabolic networks.""" +software_license = 'LicenseGPLv2' + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('SWIG', '4.1.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('SciPy-bundle', '2023.11'), + ('ruamel.yaml', '0.18.6'), + ('pydantic', '2.6.4'), + ('python-libsbml', '5.20.2'), + ('sympy', '1.12'), + ('GLPK', '5.0'), +] + +use_pip = True + +exts_list = [ + ('h11', '0.14.0', { + 'checksums': ['8f19fbbe99e72420ff35c00b27a34cb9937e902a8b810e2c88300c6f0a3b699d'], + }), + ('anyio', '4.3.0', { + 'checksums': ['f75253795a87df48568485fd18cdd2a3fa5c4f7c5be8e5e36637733fce06fed6'], + }), + ('swiglpk', '5.0.10', { + 'checksums': ['57ac34ad334da95dd168114bfdb50ae10a2a6a3ddef21e4941f46fe430c5a7e1'], + }), + ('sniffio', '1.3.1', { + 'checksums': ['f4324edc670a0f49750a81b895f35c3adb843cca46f0530f79fc1babb23789dc'], + }), + ('httpcore', '0.17.3', { + 'checksums': ['a6f30213335e34c1ade7be6ec7c47f19f50c56db36abef1a9dfa3815b1cb3888'], + }), + ('optlang', '1.8.1', { + 'checksums': ['9eb586b69fd88d558a8a0a0eac33c3067c59b5de510fddc36c0aa874eb74bfec'], + }), + ('httpx', '0.24.1', { + 'checksums': ['5853a43053df830c20f8110c5e69fe44d035d850b2dfe795e196f00fdb774bdd'], + }), + ('diskcache', '5.6.3', { + 'checksums': ['2c3a3fa2743d8535d832ec61c2054a1641f41775aa7c556758a109941e33e4fc'], + }), + ('depinfo', '2.2.0', { + 'checksums': ['e0971be11519a823b126c875e17ad3ad8adaa6a86737395b9dbcef3ca0e77b0c'], + }), + ('cobra', version, { + 'checksums': ['56d2b832aa86b1f3853647e0eb24aaeac25908fd147737edb23313934485e863'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..c0e770c3a3f0 --- /dev/null +++ b/easybuild/easyconfigs/c/Check/Check-0.15.2-GCCcore-13.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'Check' +version = '0.15.2' + +homepage = 'https://libcheck.github.io/check/' +description = """ +Check is a unit testing framework for C. It features a simple interface for +defining unit tests, putting little in the way of the developer. Tests are +run in a separate address space, so both assertion failures and code errors +that cause segmentation faults or other signals can be caught. Test results +are reportable in the following: Subunit, TAP, XML, and a generic logging +format.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +github_account = 'libcheck' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['998d355294bb94072f40584272cf4424571c396c631620ce463f6ea97aa67d2e'] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = "--disable-build-docs" + +sanity_check_paths = { + 'files': ['bin/checkmk', 'lib/libcheck.a', 'lib/libcheck.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb new file mode 100644 index 000000000000..1a9d6b18347f --- /dev/null +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb @@ -0,0 +1,46 @@ +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# Authors: Sebastien Moretti +# Update: PavelTománek (INUITS) + +easyblock = 'PythonBundle' + +name = 'python-libsbml' +version = '5.20.2' + +homepage = 'https://sbml.org/' +description = """LibSBML Python API.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), + ('make', '4.4.1'), + ('Check', '0.15.2'), + ('SWIG', '4.1.1'), + ('expat', '2.5.0'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] +# maybe more deps: xerces-c, iconv + # Xerces-C++ in EB not 2023b + # libiconv in EB ok 2023b +dependencies = [ + ('Python', '3.11.5'), + ('libxml2', '2.11.5'), + ('libxslt', '1.1.38'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'libsbml', + 'checksums': ['0af5cbff68c9b52bac4bd7bb261f93a60832dc8cb31dafc90d3aff51467935b7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..48c01ce24a27 --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.18.6-GCCcore-13.2.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.18.6' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.jinja2', '0.2.7', { + 'checksums': ['8449be29d9a157fa92d1648adc161d718e469f0d38a6b21e0eabb76fd5b3e663'], + }), + ('ruamel.yaml.clib', '0.2.8', { + 'modulename': False, + 'checksums': ['beb2e0404003de9a4cab9753a8805a8fe9320ee6673136ed7f04255fe60bb512'], + }), + (name, version, { + 'checksums': ['8b27e6a217e786c6fbe5634d8f3f11bc63e0f80f6a5890f28863d9c45aac311b'], + }), + ('configobj', '5.0.8', { + 'checksums': ['6f704434a07dc4f4dc7c9a745172c1cad449feb548febd9f7fe362629c627a97'], + }), + ('lz4', '4.3.3', { + 'checksums': ['01fe674ef2889dbb9899d8a67361e0c4a2c833af5aeb37dd505727cf5d2a131e'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.5', { + 'checksums': ['49af59514cb87d7637d1186e31c9345c9947120a9ce49cf6975435aa7abd5aa8'], + }), +] + +sanity_check_paths = { + 'files': ['bin/yaml'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["yaml --help"] + +sanity_pip_check = True + +moduleclass = 'lang' From 834b1db6a5d5c9cbf1999c52b03768b3361b1d06 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 21 Mar 2024 13:07:14 +0100 Subject: [PATCH 1081/1193] Update python-libsbml - clean comments --- .../p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb index 1a9d6b18347f..f9dc8582bdc5 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb @@ -23,9 +23,7 @@ builddependencies = [ ('bzip2', '1.0.8'), ('zlib', '1.2.13'), ] -# maybe more deps: xerces-c, iconv - # Xerces-C++ in EB not 2023b - # libiconv in EB ok 2023b + dependencies = [ ('Python', '3.11.5'), ('libxml2', '2.11.5'), From 0d89ab10c5703b8df02ec911b4976df437ebc7f3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Thu, 21 Mar 2024 13:08:29 +0100 Subject: [PATCH 1082/1193] Update python-libsbml - fix style --- .../python-libsbml/python-libsbml-5.20.2-foss-2023b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb index f9dc8582bdc5..ca7069c9e277 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.20.2-foss-2023b.eb @@ -16,12 +16,12 @@ toolchain = {'name': 'foss', 'version': '2023b'} builddependencies = [ ('binutils', '2.40'), ('CMake', '3.27.6'), - ('make', '4.4.1'), - ('Check', '0.15.2'), + ('make', '4.4.1'), + ('Check', '0.15.2'), ('SWIG', '4.1.1'), - ('expat', '2.5.0'), - ('bzip2', '1.0.8'), - ('zlib', '1.2.13'), + ('expat', '2.5.0'), + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), ] dependencies = [ From 69d070f58203f826a07a91dab81bb4be0e281817 Mon Sep 17 00:00:00 2001 From: casparl Date: Thu, 21 Mar 2024 14:19:09 +0100 Subject: [PATCH 1083/1193] Add comment so that we remember we can strip it once EasyBuild 5.0 is released --- .../easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb | 2 ++ .../easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb | 2 ++ .../easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb index b8b1118b44e4..39de229b710d 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb @@ -31,6 +31,8 @@ pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && # remove broken symlink to libsuperlu.a postinstallcmds = [ "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + # This second one can be removed when https://github.com/easybuilders/easybuild-framework/pull/4435 is merged + # (i.e. in EasyBuild 5.0) "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb index c9bb0479ec13..a1b9096b3c34 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2022b.eb @@ -31,6 +31,8 @@ pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && # remove broken symlink to libsuperlu.a postinstallcmds = [ "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + # This second one can be removed when https://github.com/easybuilders/easybuild-framework/pull/4435 is merged + # (i.e. in EasyBuild 5.0) "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] diff --git a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb index a980992bd82d..c69bddd6e3e6 100644 --- a/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.2-foss-2023a.eb @@ -31,6 +31,8 @@ pretestopts = 'export ARGS="$ARGS --tests-regex pdtest_[21]x1_[13]_2_8_20_SP" && # remove broken symlink to libsuperlu.a postinstallcmds = [ "if [ -f %(installdir)s/lib64/libsuperlu.a ]; then rm %(installdir)s/lib64/libsuperlu.a; fi", + # This second one can be removed when https://github.com/easybuilders/easybuild-framework/pull/4435 is merged + # (i.e. in EasyBuild 5.0) "if [ -f %(installdir)s/lib/libsuperlu.a ]; then rm %(installdir)s/lib/libsuperlu.a; fi" ] From 694879c44852d659e3a0ded7f05344610773790b Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 21 Mar 2024 14:52:10 +0100 Subject: [PATCH 1084/1193] add GLPK easyconfig --- .../g/GLPK/GLPK-5.0-GCCcore-13.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..b14dcd3409e9 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [ + ('binutils', '2.40'), +] +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--with-gmp' + + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/%(namelower)s.h', 'lib/libglpk.a', 'lib/libglpk.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["glpsol --help"] + +moduleclass = 'tools' From 7148e5893dbb0f5361d1174fd0ec150c22a4fff9 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Thu, 21 Mar 2024 13:59:04 +0000 Subject: [PATCH 1085/1193] adding easyconfigs: LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb --- ...3_update2-foss-2023a-kokkos-CUDA-12.1.1.eb | 188 ++++++++++++++++++ 1 file changed, 188 insertions(+) create mode 100644 easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb new file mode 100644 index 000000000000..9290ba4ecb28 --- /dev/null +++ b/easybuild/easyconfigs/l/LAMMPS/LAMMPS-2Aug2023_update2-foss-2023a-kokkos-CUDA-12.1.1.eb @@ -0,0 +1,188 @@ +name = 'LAMMPS' +version = '2Aug2023_update2' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = '-kokkos' + _cuda_suffix + +homepage = 'https://www.lammps.org' +description = """LAMMPS is a classical molecular dynamics code, and an acronym +for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has +potentials for solid-state materials (metals, semiconductors) and soft matter +(biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be +used to model atoms or, more generically, as a parallel particle simulator at +the atomic, meso, or continuum scale. LAMMPS runs on single processors or in +parallel using message-passing techniques and a spatial-decomposition of the +simulation domain. The code is designed to be easy to modify or extend with new +functionality. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +# 'https://github.com/lammps/lammps/archive/' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['stable_%(version)s.tar.gz'] +patches = [ + 'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch', + 'LAMMPS-2Aug2023_fix-timestep-balance-example.patch', +] +checksums = [ + {'stable_2Aug2023_update2.tar.gz': '3bcecabc9cad08d0a4e4d989b52d29c58505f7ead8ebacf43c9db8d9fd3d564a'}, + {'LAMMPS-2Aug2023_install_lammps_python_package_in_eb_software_module.patch': + '723c944b62b9d28427d25e80a7a67049631702d344df49268a6846aa0cd0fe04'}, + {'LAMMPS-2Aug2023_fix-timestep-balance-example.patch': + '6f68387ced2b4bd0a06e4c3d31b0ffd47042476777d87d8a0ca6b19a4e6a1777'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pkgconf', '1.9.5'), + ('archspec', '0.2.1'), +] +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('UCX-CUDA', '1.14.1', _cuda_suffix), + ('NCCL', '2.18.3', _cuda_suffix), + ('Python', '3.11.3'), + ('libpng', '1.6.39'), + ('libjpeg-turbo', '2.1.5.1'), + ('netCDF', '4.9.2'), + ('GSL', '2.7'), + ('zlib', '1.2.13'), + ('gzip', '1.12'), + ('cURL', '8.0.1'), + ('HDF5', '1.14.0'), + ('PCRE', '8.45'), + ('libxml2', '2.11.4'), + ('FFmpeg', '6.0'), + ('Voro++', '0.4.6'), + ('kim-api', '2.3.0'), + ('Eigen', '3.4.0'), + ('PLUMED', '2.9.0'), + ('SciPy-bundle', '2023.07'), + # VTK package is auto-disabled if this dep is not available + ('VTK', '9.3.0'), + # We use a custom build of MDI + ('MDI', '1.4.26'), +] +if ARCH == 'x86_64': + # TBB and ScaFaCos are an optional dependency when building on Intel arch + dependencies += [ + ('tbb', '2021.11.0'), + ('ScaFaCoS', '1.0.4'), + ] + +# To use additional custom configuration options, use the 'configopts' easyconfig parameter +# See docs and lammps easyblock for more information. +# https://github.com/lammps/lammps/blob/master/cmake/README.md#lammps-configuration-options + +# OpenMP-Kokkos build is default in the current easyblock. One can switch to serial backend of Kokkos, +# which is claimed to be faster in pure MPI calculations +# configopts = "-DKokkos_ENABLE_SERIAL=yes " + + +# packages auto-enabled by easyblock +# 'GPU' - if cuda package is present and kokkos is disabled +# 'KOKKOS' - if kokkos is enabled (by default) +# 'INTEL' - if builing on Intel CPU +# 'OPENMP' - if OpenMP swithed on in 'toolchainopts' + +# include the following extra packages into the build +general_packages = [ + 'AMOEBA', + 'ASPHERE', + 'ATC', + 'AWPMD', + 'BOCS', + 'BODY', + 'BPM', + 'BROWNIAN', + 'CG-DNA', + 'CG-SPICA', + 'CLASS2', + 'COLLOID', + 'COLVARS', + 'COMPRESS', + 'CORESHELL', + 'DIELECTRIC', + 'DIFFRACTION', + 'DIPOLE', + 'DPD-BASIC', + 'DPD-MESO', + 'DPD-REACT', + 'DPD-SMOOTH', + 'DRUDE', + 'EFF', + 'ELECTRODE', + 'EXTRA-COMPUTE', + 'EXTRA-DUMP', + 'EXTRA-FIX', + 'EXTRA-MOLECULE', + 'EXTRA-PAIR', + 'FEP', + 'GRANULAR', + 'H5MD', + 'INTERLAYER', + 'KIM', + 'KSPACE', + 'LATBOLTZ', + 'LEPTON', + 'MACHDYN', + 'MANIFOLD', + 'MANYBODY', + 'MC', + 'MDI', + 'MEAM', + 'MGPT', + 'MISC', + 'ML-IAP', + 'ML-PACE', + 'ML-POD', + 'ML-RANN', + 'ML-SNAP', + 'MOFFF', + 'MOLECULE', + 'MOLFILE', + 'MPIIO', + 'NETCDF', + 'OPT', + 'ORIENT', + 'PERI', + 'PHONON', + 'PLUGIN', + 'PLUMED', + 'POEMS', + 'PTM', + 'PYTHON', + 'QEQ', + 'QTB', + 'REACTION', + 'REAXFF', + 'REPLICA', + 'RIGID', + 'SCAFACOS', + 'SHOCK', + 'SMTBQ', + 'SPH', + 'SPIN', + 'SRD', + 'TALLY', + 'UEF', + 'VORONOI', + 'VTK', + 'YAFF', +] + +# Excluded packages due to requiring additional (non-trivial) deps +# - ADIOS +# - LATTE +# - MESONT (requires very large files downloaded during build) +# - ML-HDNNP (requires N2P2) +# - ML-QUIP +# - MSCG +# - QMMM (setup seems complex) + +# hardware-specific option +# note: only the highest capability will be used +# cuda_compute_capabilities = ['9.0'] + +moduleclass = 'chem' From 8aff623387c8b10b4076118999221f097f0ae2a2 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 21 Mar 2024 15:30:36 +0100 Subject: [PATCH 1086/1193] Add the latest git-lfs and Go --- easybuild/easyconfigs/g/Go/Go-1.22.1.eb | 29 +++++++++++++++++++ .../easyconfigs/g/git-lfs/git-lfs-3.5.1.eb | 26 +++++++++++++++++ 2 files changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/g/Go/Go-1.22.1.eb create mode 100644 easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb diff --git a/easybuild/easyconfigs/g/Go/Go-1.22.1.eb b/easybuild/easyconfigs/g/Go/Go-1.22.1.eb new file mode 100644 index 000000000000..0432c4bc21e4 --- /dev/null +++ b/easybuild/easyconfigs/g/Go/Go-1.22.1.eb @@ -0,0 +1,29 @@ +easyblock = 'Tarball' + +name = 'Go' +version = '1.22.1' + +homepage = 'https://www.golang.org' +description = """Go is an open source programming language that makes it easy to build + simple, reliable, and efficient software.""" + +toolchain = SYSTEM + +source_urls = ['https://storage.googleapis.com/golang/'] +local_archs = {'aarch64': 'arm64', 'x86_64': 'amd64'} +sources = ['go%%(version)s.linux-%s.tar.gz' % local_archs[ARCH]] +checksums = [{ + 'go%(version)s.linux-amd64.tar.gz': 'aab8e15785c997ae20f9c88422ee35d962c4562212bb0f879d052a35c8307c7f', + 'go%(version)s.linux-arm64.tar.gz': 'e56685a245b6a0c592fc4a55f0b7803af5b3f827aaa29feab1f40e491acf35b8', +}] + +sanity_check_paths = { + 'files': ['bin/go', 'bin/gofmt'], + 'dirs': ['api', 'doc', 'lib', 'pkg'], +} + +sanity_check_commands = ["go help"] + +modextravars = {'GOROOT': '%(installdir)s'} + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb new file mode 100644 index 000000000000..78e076871d85 --- /dev/null +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb @@ -0,0 +1,26 @@ +easyblock = 'GoPackage' + +name = 'git-lfs' +version = '3.5.1' + +homepage = 'https://git-lfs.github.com' +description = """Git Large File Storage (LFS) replaces large files such as audio + samples, videos, datasets, and graphics with text pointers inside Git, while + storing the file contents on a remote server like GitHub.com""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/git-lfs/git-lfs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['d682a12c0bc48d08d28834dd0d575c91d53dd6c6db63c45c2db7c3dd2fb69ea4'] + +builddependencies = [('Go', '1.22.1')] + +sanity_check_paths = { + 'files': ['bin/git-lfs'], + 'dirs': [], +} + +sanity_check_commands = ["git-lfs --version"] + +moduleclass = 'tools' From 2f1effc156f448cc83966761ac36a55d239159f2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 21 Mar 2024 18:08:12 +0100 Subject: [PATCH 1087/1193] Update easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb --- easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb index 8bba0bbff567..4a154fbe1ee3 100644 --- a/easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GLFW/GLFW-3.4-GCCcore-12.2.0.eb @@ -32,7 +32,7 @@ configopts = [ sanity_check_paths = { 'files': ['include/%(name)s/glfw3.h', 'include/%(name)s/glfw3native.h'] + - ['lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT], + ['lib/libglfw3.a', 'lib/libglfw.%s' % SHLIB_EXT, 'lib/pkgconfig/glfw3.pc'], 'dirs': ['include/%(name)s', 'lib/cmake/glfw3', 'lib/pkgconfig'], } From 57a51a8682c4534401ddb22027f85ad57808a5b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 21 Mar 2024 19:21:58 +0000 Subject: [PATCH 1088/1193] Drop Time::HiRes tests --- .../p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index f57bfb43acf8..66f35a7dbd4f 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1768,6 +1768,7 @@ exts_list = [ 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), ('Time::HiRes', '1.9764', { + 'runtest': False, # atime tests are useless and sometimes break 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], From 85b62494fe8a8404b84e3bd3992b74d7a7d7ad7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 21 Mar 2024 20:17:05 +0000 Subject: [PATCH 1089/1193] Fix several typos in GlobalArrays 5.8 configure step --- .../g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb | 4 ++-- .../g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb | 4 ++-- .../g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb | 4 ++-- .../g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb | 4 ++-- 4 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb index 7959aad80fa5..e4e9eeba6c68 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8-intel-2021a.eb @@ -14,8 +14,8 @@ sources = ['v%(version)s/ga-%(version)s.tar.gz'] checksums = ['64df7d1ea4053d24d84ca361e67a6f51c7b17ed7d626cb18a9fbc759f4a078ac'] configopts = ' --with-mpi --enable-i8' -configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' # select armci network as (Comex) MPI-1 two-sided diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb index f2b34303ae90..5015406bc10f 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb @@ -14,8 +14,8 @@ sources = ['v%(version)s/ga-%(version)s.tar.gz'] checksums = ['844639b52444f839854cf9735203a76a9052fd485f2d4eae70d21d03a7ecaade'] configopts = ' --with-mpi --enable-i8' -configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' # select armci network as (Comex) MPI-1 two-sided diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb index 435986d2ef92..9c3e9f7dbf8e 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb @@ -14,8 +14,8 @@ sources = ['v%(version)s/ga-%(version)s.tar.gz'] checksums = ['51599e4abfe36f05cecfaffa33be19efbe9e9fa42d035fd3f866469b663c22a2'] configopts = ' --with-mpi --enable-i8' -configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' # select armci network as (Comex) MPI-1 two-sided diff --git a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb index 04f7174a29ac..f3e14181a889 100644 --- a/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2023a.eb @@ -14,8 +14,8 @@ sources = ['v%(version)s/ga-%(version)s.tar.gz'] checksums = ['51599e4abfe36f05cecfaffa33be19efbe9e9fa42d035fd3f866469b663c22a2'] configopts = ' --with-mpi --enable-i8' -configopts += ' --with-blas8="-L$MLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' -configopts += ' --with-scalapack8="L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' +configopts += ' --with-blas8="-L$MKLROOT/lib/intel64 -lmkl_sequential -lmkl_intel_ilp64"' +configopts += ' --with-scalapack="-L$MKLROOT/lib/intel64 -lmkl_scalapack_ilp64 -lmkl_intel_ilp64 ' configopts += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' # select armci network as (Comex) MPI-1 two-sided From 7c9db7d3c83f5404371bd7e7c65642876ed82c77 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 22 Mar 2024 00:49:55 +0000 Subject: [PATCH 1090/1193] Fix broken homepage from older SCOTCH easyconfigs --- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb | 2 +- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb | 2 +- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb | 2 +- easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb | 2 +- 4 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb index 7f0edffee3a2..5b7962d2cd06 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-gompi-2021a.eb @@ -4,7 +4,7 @@ name = 'SCOTCH' version = '6.1.0' -homepage = 'https://gforge.inria.fr/projects/scotch/' +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb index 7baa08f48254..5dd92fc68d3d 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.1.0' -homepage = 'https://gforge.inria.fr/projects/scotch/' +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb index c98ffbdf7efb..190b28fe2cd2 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-gompi-2021b.eb @@ -4,7 +4,7 @@ name = 'SCOTCH' version = '6.1.2' -homepage = 'https://gforge.inria.fr/projects/scotch/' +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb index 9f69f5ceddf0..3cdf4567b3af 100644 --- a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.2-iimpi-2021b.eb @@ -1,7 +1,7 @@ name = 'SCOTCH' version = '6.1.2' -homepage = 'https://gforge.inria.fr/projects/scotch/' +homepage = 'https://www.labri.fr/perso/pelegrin/scotch/' description = """Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning.""" From 1a45d3a3468a9af99b445b336606306f901c592c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 22 Mar 2024 00:55:23 +0000 Subject: [PATCH 1091/1193] Drop dead homepage from source_urls in GCCcore 10-11 --- easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 1 - easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 1 - easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 1 - 3 files changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index 7f9079c65c0e..26437d79b564 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -17,7 +17,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies 'https://libisl.sourceforge.io/', # fallback URL for isl - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index b89321338eb5..b9512e90cc67 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -17,7 +17,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies 'https://libisl.sourceforge.io/', # fallback URL for isl - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 56cebe7e95f0..69d454317bb8 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -17,7 +17,6 @@ source_urls = [ 'ftp://gcc.gnu.org/pub/gcc/infrastructure/', # GCC dependencies 'https://gcc.gnu.org/pub/gcc/infrastructure/', # HTTPS mirror for GCC dependencies 'https://libisl.sourceforge.io/', # fallback URL for isl - 'http://isl.gforge.inria.fr/', # original HTTP source for ISL 'https://sourceware.org/pub/newlib/', # for newlib 'https://github.com/MentorEmbedded/nvptx-tools/archive', # for nvptx-tools ] From 08c09af312674510414ffe057efb7b7d7c4ea0a7 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 22 Mar 2024 09:28:56 +0100 Subject: [PATCH 1092/1193] Change source URL --- easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb index 78e076871d85..2f12a414e2ce 100644 --- a/easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb +++ b/easybuild/easyconfigs/g/git-lfs/git-lfs-3.5.1.eb @@ -10,7 +10,7 @@ description = """Git Large File Storage (LFS) replaces large files such as audio toolchain = SYSTEM -source_urls = ['https://github.com/git-lfs/git-lfs/archive/'] +source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['d682a12c0bc48d08d28834dd0d575c91d53dd6c6db63c45c2db7c3dd2fb69ea4'] From c5401b3e6d89c3331df3de3ac1dbe0dda6a590f8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 09:41:55 +0100 Subject: [PATCH 1093/1193] Allow 5 tests to fail --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index e321be1a7dfd..727920262c2f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -154,7 +154,7 @@ runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-throu # Especially test_quantization has a few corner cases that are triggered by the random input values, # those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 # So allow a low number of tests to fail as the tests "usually" succeed -max_failed_tests = 2 +max_failed_tests = 5 tests = ['PyTorch-check-cpp-extension.py'] From 1834659b42c90e19e4b63af3a1ffbbefcc6c2cc5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 09:55:13 +0100 Subject: [PATCH 1094/1193] Skip test and allow some failures --- .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb index 16da2ca106b9..6d7b0753752d 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -45,6 +45,7 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -104,6 +105,8 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', + {'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch': + '199005bbbb913837e557358dee31535d8e3f63af9ac7cdcece624ab8e572e28a'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] @@ -152,6 +155,10 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' +# Some tests fail randomöy due to random inputs being used +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 2 + tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'ai' From 3dac7738594dbce37aefdfb7fd0fd8fac8a33f81 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 10:05:35 +0100 Subject: [PATCH 1095/1193] Add patch to skip failing test --- .../p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb index eb4946e098fd..13b4fae31ae8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a-CUDA-11.7.0.eb @@ -45,6 +45,7 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch', ] checksums = [ {'pytorch-v1.12.0.tar.gz': '46eff236370b759c427b03ff535c3597099043e8e467b8f81f9cd4b258a7a321'}, @@ -105,6 +106,8 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc'}, {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, + {'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch': + '199005bbbb913837e557358dee31535d8e3f63af9ac7cdcece624ab8e572e28a'}, ] builddependencies = [ From 0a740cb95021c0d306432140a8122acc6596380f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 10:09:31 +0100 Subject: [PATCH 1096/1193] Add patch to skip failing test --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb index 25bea2cd65bc..a361777ca2ae 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.0-foss-2022a.eb @@ -44,6 +44,7 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch', + 'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch', ] checksums = [ {'pytorch-v1.12.0.tar.gz': '46eff236370b759c427b03ff535c3597099043e8e467b8f81f9cd4b258a7a321'}, @@ -104,6 +105,8 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc'}, {'PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch': '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d'}, + {'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch': + '199005bbbb913837e557358dee31535d8e3f63af9ac7cdcece624ab8e572e28a'}, ] builddependencies = [ From 8169a25cb153d6d1180fd9372658407707dd2ec2 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 10:17:49 +0100 Subject: [PATCH 1097/1193] Add patch to skip failing test --- .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index e46b3f938f30..2516874b1e02 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -48,6 +48,7 @@ patches = [ 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', 'PyTorch-1.12.1_skip-failing-grad-test.patch', 'PyTorch-1.12.1_skip-test_round_robin.patch', + 'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -111,6 +112,8 @@ checksums = [ '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch # PyTorch-1.12.1_skip-test_round_robin.patch '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', + {'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch': + '199005bbbb913837e557358dee31535d8e3f63af9ac7cdcece624ab8e572e28a'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From 08e7818a19b4d94dfb9e7b61f8c4394277c5aea4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 10:19:05 +0100 Subject: [PATCH 1098/1193] Add patch to skip failing test --- .../p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb index c38ff848e65a..bd559ee8dfd4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a-CUDA-11.7.0.eb @@ -43,6 +43,7 @@ patches = [ 'PyTorch-1.13.1_skip-failing-grad-test.patch', 'PyTorch-1.13.1_skip-test-requiring-online-access.patch', 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -96,6 +97,8 @@ checksums = [ '61c3b7859dc06a9969981b07aa2789630de110d6d1d3633d27364be47af74712'}, {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch': + '199005bbbb913837e557358dee31535d8e3f63af9ac7cdcece624ab8e572e28a'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From 4ab764aa35069e5732adb298f7bd7ca13ae461eb Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 10:19:56 +0100 Subject: [PATCH 1099/1193] Add patch to skip failing test --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index 07ea30a2a380..dc347470dc1f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -35,6 +35,7 @@ patches = [ 'PyTorch-1.13.1_remove-flaky-test-in-testnn.patch', 'PyTorch-1.13.1_skip-failing-grad-test.patch', 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', + 'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -75,6 +76,8 @@ checksums = [ {'PyTorch-1.13.1_skip-failing-grad-test.patch': '6681200f9509893cb9231b5c93ac9bc5e6d9d9ae4febefca52e7cbc843ba8f51'}, {'PyTorch-1.13.1_skip-tests-without-fbgemm.patch': '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, + {'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch': + '199005bbbb913837e557358dee31535d8e3f63af9ac7cdcece624ab8e572e28a'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From 0c993021c818324a962188a87604ecf7be67a2c8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 10:20:50 +0100 Subject: [PATCH 1100/1193] Add patch to skip failing test --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb index 727920262c2f..a7196938e26f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022b.eb @@ -45,6 +45,7 @@ patches = [ 'PyTorch-1.13.1_skip-failing-singular-grad-test.patch', 'PyTorch-1.13.1_skip-tests-without-fbgemm.patch', 'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch', + 'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch', ] checksums = [ {'pytorch-v1.13.1.tar.gz': 'dbc229ee9750b02b514937d017744443a269ea0241ed3f32b9af0703589d25d4'}, @@ -104,6 +105,8 @@ checksums = [ '481e595f673baf8ae58b41697a6792b83048b0264aa79b422f48cd8c22948bb7'}, {'PyTorch-1.13.1_workaround-gcc12-destructor-exception-bug.patch': 'a09a2d7ebd428c65988729578bb3fa372565ba176ab9ed7abf11f6fcb15e903e'}, + {'PyTorch-2.0.1_skip-test_baddbmm_cpu_bfloat16.patch': + '199005bbbb913837e557358dee31535d8e3f63af9ac7cdcece624ab8e572e28a'}, ] osdependencies = [OS_PKG_IBVERBS_DEV] From 6d3bde45451fb14f922c01cea56c817f4ff58ca3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 10:32:53 +0100 Subject: [PATCH 1101/1193] [GCCcore/8.2.0] Fix package installation in Python ECs --- .../p/Python/Python-2.7.15-GCCcore-8.2.0.eb | 17 +++++++++++++---- .../p/Python/Python-3.7.2-GCCcore-8.2.0.eb | 9 +++++++++ 2 files changed, 22 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb index 175bf270b5a7..2c26ddf75fff 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.15-GCCcore-8.2.0.eb @@ -45,7 +45,8 @@ exts_list = [ 'checksums': ['6e4eec90337e849ade7103723b9a99631c1f0d19990d6e8412dc42f5ae8b304d'], }), ('wheel', '0.33.1', { - 'checksums': ['66a8fd76f28977bb664b098372daef2b27f60dc4d1688cfab7b37a09448f0e9d'], + 'source_tmpl': SOURCE_WHL, + 'checksums': ['8eb4a788b3aec8abf5ff68d4165441bc57420c9f64ca5f471f58c3969fe08668'], }), ('pip', '19.0.3', { 'checksums': ['6e6f197a1abfb45118dbb878b5c859a0edbdd33fd250100bc015b67fded4b9f2'], @@ -72,7 +73,8 @@ exts_list = [ 'checksums': ['52ab47715fa0fc7d8e6cd15168d1a69ba995feb1505131c3e814eb7087b57358'], }), ('python-dateutil', '2.8.0', { - 'checksums': ['c89805f6f4d64db21ed966fda138f8a5ed7a4fdbc1a8ee329ce1b74e3c74da9e'], + 'source_tmpl': 'python_dateutil-%(version)s-py2.py3-none-any.whl', + 'checksums': ['7e6584c74aeed623791615e26efd690f29817a27c73085b78e4bad02493df2fb'], 'modulename': 'dateutil', }), ('deap', '1.2.2', { @@ -118,16 +120,19 @@ exts_list = [ }), ('cryptography', '2.6.1', { 'checksums': ['26c821cbeb683facb966045e2064303029d572a87ee69ca5a1bf54bf55f93ca6'], + 'use_pip': False, }), ('pyasn1', '0.4.5', { 'checksums': ['da2420fe13a9452d8ae97a0e478adde1dee153b11ba832a95b223a2ba01c10f7'], }), ('PyNaCl', '1.3.0', { 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + 'use_pip': False, 'modulename': 'nacl', }), ('bcrypt', '3.1.6', { 'checksums': ['44636759d222baa62806bbceb20e96f75a015a6381690d1bc2eda91c01ec02ea'], + 'use_pip': False, }), ('paramiko', '2.4.2', { 'checksums': ['a8975a7df3560c9f1e2b43dc54ebd40fd00a7017392ca5445ce7df409f900fcb'], @@ -155,7 +160,8 @@ exts_list = [ 'checksums': ['c163a86fcef377c314690051885d86b47419e3e1770990c212e16723c1c08faa'], }), ('virtualenv', '16.4.3', { - 'checksums': ['984d7e607b0a5d1329425dd8845bd971b957424b5ba664729fab51ab8c11bc39'], + 'source_tmpl': SOURCE_WHL, + 'checksums': ['6aebaf4dd2568a0094225ebbca987859e369e3e5c22dc7d52e5406d504890417'], }), ('docopt', '0.6.2', { 'checksums': ['49b3a825280bd66b3aa83585ef59c4a8c82f2c8a522dbe754a8bc8d08c85c491'], @@ -201,6 +207,7 @@ exts_list = [ }), ('pluggy', '0.9.0', { 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], + 'use_pip': False, }), ('more-itertools', '5.0.0', { 'checksums': ['38a936c0a6d98a38bcc2d03fdaaedaba9f412879461dd2ceff8d37564d6522e4'], @@ -208,12 +215,14 @@ exts_list = [ ('attrs', '19.1.0', { 'checksums': ['f0b870f674851ecbfbbbd364d6b5cbdff9dcedbc7f3f5e18a6891057f21fe399'], 'modulename': 'attr', + 'use_pip': False, }), ('wcwidth', '0.1.7', { 'checksums': ['3df37372226d6e63e1b1e1eda15c594bca98a22d33a23832a90998faa96bc65e'], }), ('pytest', '4.3.1', { - 'checksums': ['592eaa2c33fae68c7d75aacf042efc9f77b27c08a6224a4f59beab8d9a420523'], + 'source_tmpl': SOURCE_WHL, + 'checksums': ['ad3ad5c450284819ecde191a654c09b0ec72257a2c711b9633d677c71c9850c4'], }), ('MarkupSafe', '1.1.1', { 'checksums': ['29872e92839765e546828bb7754a68c418d927cd064fd4708fab9fe9c8bb116b'], diff --git a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb index 9fbf771c28e2..4f99edc05380 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.7.2-GCCcore-8.2.0.eb @@ -43,6 +43,11 @@ exts_default_options = { 'sanity_pip_check': True, } +# workaround for: AttributeError: 'module' object has no attribute '__legacy__' +# see also https://github.com/pypa/pip/issues/6264 +local_fix_pyproject_toml_cmd = r"""sed -i 's/\(\[build-system\]\)/\1\nbuild-backend="setuptools.build_meta"/g' """ +local_fix_pyproject_toml_cmd += "pyproject.toml && " + # order is important! # package versions updated Mar 15th 2019 exts_list = [ @@ -120,6 +125,7 @@ exts_list = [ }), ('cryptography', '2.6.1', { 'checksums': ['26c821cbeb683facb966045e2064303029d572a87ee69ca5a1bf54bf55f93ca6'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('pyasn1', '0.4.5', { 'checksums': ['da2420fe13a9452d8ae97a0e478adde1dee153b11ba832a95b223a2ba01c10f7'], @@ -127,9 +133,11 @@ exts_list = [ ('PyNaCl', '1.3.0', { 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], 'modulename': 'nacl', + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('bcrypt', '3.1.6', { 'checksums': ['44636759d222baa62806bbceb20e96f75a015a6381690d1bc2eda91c01ec02ea'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('paramiko', '2.4.2', { 'checksums': ['a8975a7df3560c9f1e2b43dc54ebd40fd00a7017392ca5445ce7df409f900fcb'], @@ -200,6 +208,7 @@ exts_list = [ }), ('pluggy', '0.9.0', { 'checksums': ['19ecf9ce9db2fce065a7a0586e07cfb4ac8614fe96edf628a264b1c70116cf8f'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('more-itertools', '6.0.0', { 'checksums': ['590044e3942351a1bdb1de960b739ff4ce277960f2425ad4509446dbace8d9d1'], From 11947e4c79c2525962b420686784cfe72ada5fed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 22 Mar 2024 10:18:48 +0000 Subject: [PATCH 1102/1193] Change comment describing why tests are skipped --- .../Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb index 66f35a7dbd4f..a3645c938f4f 100644 --- a/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Perl-bundle-CPAN/Perl-bundle-CPAN-5.36.1-GCCcore-12.3.0.eb @@ -1768,7 +1768,7 @@ exts_list = [ 'checksums': ['9dfd6ca2822724347e0eb6759d00709425814703ad5c66bdb6214579868bcac4'], }), ('Time::HiRes', '1.9764', { - 'runtest': False, # atime tests are useless and sometimes break + 'runtest': False, # https://github.com/easybuilders/easybuild-easyconfigs/issues/20145 unreliable atime tests 'source_tmpl': 'Time-HiRes-%(version)s.tar.gz', 'source_urls': ['https://cpan.metacpan.org/authors/id/A/AT/ATOOMIC'], 'checksums': ['9841be5587bfb7cd1f2fe267b5e5ac04ce25e79d5cc77e5ef9a9c5abd101d7b1'], From 254ed932c94a373d371fe9b02d7e5dab4984b462 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 22 Mar 2024 14:26:23 +0100 Subject: [PATCH 1103/1193] Allow some test failures --- easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb index dc347470dc1f..2cc54d6522fd 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.13.1-foss-2022a.eb @@ -125,6 +125,11 @@ excluded_tests = { runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' +# Especially test_quantization has a few corner cases that are triggered by the random input values, +# those cannot be easily avoided, see https://github.com/pytorch/pytorch/issues/107030 +# So allow a low number of tests to fail as the tests "usually" succeed +max_failed_tests = 12 + tests = ['PyTorch-check-cpp-extension.py'] moduleclass = 'ai' From 29568c4702f2084b15f7c671025a642ff9eb7225 Mon Sep 17 00:00:00 2001 From: WilleBell Date: Fri, 22 Mar 2024 15:45:27 +0100 Subject: [PATCH 1104/1193] change to use MakeCp easyblock --- easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb index 08c396073848..1cd13b8f9196 100644 --- a/easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/p/PSASS/PSASS-3.1.0-GCC-12.3.0.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'PSASS' version = '3.1.0' @@ -21,10 +21,7 @@ source_urls = ['https://github.com/SexGenomicsToolkit/PSASS/archive/'] sources = ['%(version)s.tar.gz'] checksums = ['6c22fb2db52df76bdf8e5073895da11678a35c4a0e1500245e19d13c1f67df2b'] -# just run make in the install dir -skipsteps = ['configure', 'install'] - -postinstallcmds = ['cp -r %(builddir)s/PSASS-%(version)s/bin %(installdir)s/bin'] +files_to_copy = ['bin'] sanity_check_paths = { 'files': ['bin/psass'], From d98c36e08c99cb61b54efd67d79666264065362f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 22 Mar 2024 15:53:18 +0000 Subject: [PATCH 1105/1193] Enable LittleCMS2 and WebP support in recent Pillow --- .../p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb | 2 ++ .../easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb | 5 ++++- .../easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb | 5 ++++- 3 files changed, 10 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb index 2c9955fc0e39..0505a2e0fbd9 100644 --- a/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow-SIMD/Pillow-SIMD-9.5.0-GCCcore-12.3.0.eb @@ -23,6 +23,8 @@ dependencies = [ ('LibTIFF', '4.5.0'), ('freetype', '2.13.0'), ('libwebp', '1.3.1'), + ('OpenJPEG', '2.5.0'), + ('LittleCMS', '2.15'), ] use_pip = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb index a630306348f5..adf7020295de 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.0.0-GCCcore-12.3.0.eb @@ -20,7 +20,10 @@ dependencies = [ ('libpng', '1.6.39'), ('zlib', '1.2.13'), ('LibTIFF', '4.5.0'), - ('freetype', '2.13.0') + ('freetype', '2.13.0'), + ('libwebp', '1.3.1'), + ('OpenJPEG', '2.5.0'), + ('LittleCMS', '2.15'), ] download_dep_fail = True diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb index 124fdb2e5e26..7a797cb69bd7 100644 --- a/easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/Pillow/Pillow-10.2.0-GCCcore-13.2.0.eb @@ -20,7 +20,10 @@ dependencies = [ ('libpng', '1.6.40'), ('zlib', '1.2.13'), ('LibTIFF', '4.6.0'), - ('freetype', '2.13.2') + ('freetype', '2.13.2'), + ('libwebp', '1.3.2'), + ('OpenJPEG', '2.5.0'), + ('LittleCMS', '2.15'), ] download_dep_fail = True From db50a3c4e4a3f0ab47abbd7c6fe5c69c7ca42e16 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 22 Mar 2024 17:43:42 +0100 Subject: [PATCH 1106/1193] adding easyconfigs: Mamba-23.11.0-0.eb --- .../easyconfigs/m/Mamba/Mamba-23.11.0-0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/Mamba/Mamba-23.11.0-0.eb diff --git a/easybuild/easyconfigs/m/Mamba/Mamba-23.11.0-0.eb b/easybuild/easyconfigs/m/Mamba/Mamba-23.11.0-0.eb new file mode 100644 index 000000000000..a6c924af5952 --- /dev/null +++ b/easybuild/easyconfigs/m/Mamba/Mamba-23.11.0-0.eb @@ -0,0 +1,28 @@ +# author: Caspar van Leeuwen +name = 'Mamba' +version = '23.11.0-0' + +homepage = 'https://mamba.readthedocs.io/' +description = """Mamba is a fast, robust, and cross-platform package manager. It runs on Windows, OS X and Linux +(ARM64 and PPC64LE included) and is fully compatible with conda packages and supports most of conda's commands. +""" + +toolchain = SYSTEM + +# Note: Using Mambaforge is the recommended way of installing mamba, +# according to https://mamba.readthedocs.io/en/latest/installation.html +local_name = 'Mambaforge' +source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] +sources = ['{local_name}-%(version)s-Linux-%(arch)s.sh'.format(local_name=local_name)] +checksums = [ + { + '{local_name}-%(version)s-Linux-aarch64.sh'.format(local_name=local_name): + '71320f28280b4e41f37469f6b0ae85e31ba9c26a87c7ee69cecaae3eaa5a4057', + '{local_name}-%(version)s-Linux-ppc64le.sh'.format(local_name=local_name): + '148b18f94b5a0878d5fa1190b41cad5a803eca1cd15429e26571fef11422e2b2', + '{local_name}-%(version)s-Linux-x86_64.sh'.format(local_name=local_name): + '3dfdcc162bf0df83b5025608dc2acdbbc575bd416b75701fb5863343c0517a78', + } +] + +moduleclass = 'lang' From 11fab6f3529a019873a1c0dd951541804d335fa4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 23 Mar 2024 11:25:05 +0100 Subject: [PATCH 1107/1193] {devel}[foss/2023b] NLTK v3.8.1, tqdm v4.66.2 --- .../n/NLTK/NLTK-3.8.1-foss-2023b.eb | 53 +++++++++++++++++++ .../t/tqdm/tqdm-4.66.2-GCCcore-13.2.0.eb | 27 ++++++++++ 2 files changed, 80 insertions(+) create mode 100644 easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/t/tqdm/tqdm-4.66.2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023b.eb b/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023b.eb new file mode 100644 index 000000000000..e88d5ee3b778 --- /dev/null +++ b/easybuild/easyconfigs/n/NLTK/NLTK-3.8.1-foss-2023b.eb @@ -0,0 +1,53 @@ +easyblock = 'PythonBundle' + +name = 'NLTK' +version = '3.8.1' + +homepage = 'https://www.nltk.org/' +description = "NLTK is a leading platform for building Python programs to work with human language data." + +toolchain = {'name': 'foss', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('scikit-learn', '1.4.0'), + ('matplotlib', '3.8.2'), + ('tqdm', '4.66.2'), +] + +local_nltk_data_install = [] +# Install NLTK data sets (7.4 GB) +# local_nltk_data = '/path/to/database/nltk_data' +# local_nltk_data_install = [ +# "mkdir -p %s && NLTK_DATA=%s python -m nltk.downloader all" % (local_nltk_data, local_nltk_data) +# ] +# modextravars = {'NLTK_DATA': local_nltk_data} + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2023.12.25', { + 'checksums': ['29171aa128da69afdf4bde412d5bedc335f2ca8fcfe4489038577d05f16181e5'], + }), + ('python-crfsuite', '0.9.10', { + 'modulename': 'pycrfsuite', + 'checksums': ['f38524631e2b533341f10f2c77689270dc6ecd5985495dccf7aa37b1045bc2e5'], + }), + (name, version, { + 'postinstallcmds': [], + 'source_tmpl': '%(namelower)s-%(version)s.zip', + 'use_pip_extras': 'corenlp,machine_learning,plot,tgrep', + 'checksums': ['1834da3d0682cba4f2cede2f9aad6b0fafb6461ba451db0efb6f9c39798d64d3'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = [('%(namelower)s', '--version')] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..7277b56af663 --- /dev/null +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.2-GCCcore-13.2.0.eb @@ -0,0 +1,27 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonPackage' + +name = 'tqdm' +version = '4.66.2' + +homepage = "https://github.com/tqdm/tqdm" +description = """A fast, extensible progress bar for Python and CLI""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['6cd52cdf0fef0e0f543299cfc96fec90d7b8a7e88745f411ec33eb44d5ed3531'] + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [('Python', '3.11.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'lib' From 8082f192e38b2032ef90291cf26e86cabaf23c4e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 23 Mar 2024 12:15:58 +0100 Subject: [PATCH 1108/1193] adding easyconfigs: MDAnalysis-2.7.0-foss-2023a.eb --- .../MDAnalysis/MDAnalysis-2.7.0-foss-2023a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.7.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.7.0-foss-2023a.eb new file mode 100644 index 000000000000..9c8ac42d2c88 --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.7.0-foss-2023a.eb @@ -0,0 +1,49 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.7.0' + +homepage = 'https://www.mdanalysis.org/' +description = """MDAnalysis is an object-oriented Python library to analyze trajectories from molecular dynamics (MD) +simulations in many popular formats.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('matplotlib', '3.7.2'), + ('Biopython', '1.83'), + ('networkx', '3.1'), + ('tqdm', '4.66.1'), + ('mrcfile', '1.5.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '1.0.2', { + 'modulename': 'gridData', + 'checksums': ['b93cf7f36fce33dbc428026f26dba560d5c7ba2387caca495bad920f90094502'], + }), + ('mmtf-python', '1.1.3', { + 'modulename': 'mmtf', + 'checksums': ['12a02fe1b7131f0a2b8ce45b46f1e0cdd28b9818fe4499554c26884987ea0c32'], + }), + ('fasteners', '0.19', { + 'checksums': ['b4f37c3ac52d8a445af3a66bce57b33b5e90b97c696b7b984f530cf8f0ded09c'], + }), + ('mda_xdrlib', '0.2.0', { + 'checksums': ['f26f7158a83c32b96d15b530fce2cbc1190c4b7024e41faa4ab3e3db74e272af'], + }), + (name, version, { + 'modulename': 'MDAnalysis', + 'checksums': ['572e82945e5d058e3749ec5f18e6b3831ef7f2119cb54672567ae9a977201e93'], + }), +] + +moduleclass = 'bio' From 0d22764f07e90da498b896e5721f91a2a342bf5e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 24 Mar 2024 14:59:17 +0000 Subject: [PATCH 1109/1193] Drop hatchling builddep from tqdm 4.66.1 as well --- easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb index 1fce3aea1b14..c61e2a04e53e 100644 --- a/easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/t/tqdm/tqdm-4.66.1-GCCcore-12.3.0.eb @@ -16,7 +16,6 @@ checksums = ['d88e651f9db8d8551a62556d3cff9e3034274ca5d66e93197cf2490e2dcb69c7'] builddependencies = [ ('binutils', '2.40'), - ('hatchling', '1.18.0'), ] dependencies = [('Python', '3.11.3')] From 94b471cd938d2abea20e9f84cfa6294e89900f50 Mon Sep 17 00:00:00 2001 From: Richard Top Date: Sun, 24 Mar 2024 18:02:33 +0000 Subject: [PATCH 1110/1193] adding easyconfigs: snappy-1.1.10-GCCcore-13.2.0.eb, double-conversion-3.3.0-GCCcore-13.2.0.eb, Qt5-5.15.13-GCCcore-13.2.0.eb and patches: Qt5-5.15.13_fix-XKB_KEY_dead.patch, Qt5-5.15.13_fix-includes.patch --- .../double-conversion-3.3.0-GCCcore-13.2.0.eb | 36 +++ .../q/Qt5/Qt5-5.15.13-GCCcore-13.2.0.eb | 93 ++++++ .../q/Qt5/Qt5-5.15.13_fix-XKB_KEY_dead.patch | 19 ++ .../q/Qt5/Qt5-5.15.13_fix-includes.patch | 286 ++++++++++++++++++ .../s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb | 39 +++ 5 files changed, 473 insertions(+) create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.13-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-XKB_KEY_dead.patch create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-includes.patch create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..999f7391ccf0 --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb @@ -0,0 +1,36 @@ + +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.3.0' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/double-conversion/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['04ec44461850abbf33824da84978043b22554896b552c5fd11a9c5ae4b4d296e'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +# Build static lib, static lib with -fPIC and shared lib +configopts = [ + '', + '-DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_STATIC_LIBRARY_SUFFIX_CXX=_pic.a', + '-DBUILD_SHARED_LIBS=ON' +] + +sanity_check_paths = { + 'files': ['include/double-conversion/%s.h' % h for h in ['bignum', 'cached-powers', 'diy-fp', 'double-conversion', + 'fast-dtoa', 'fixed-dtoa', 'ieee', 'strtod', 'utils']] + + ['lib/libdouble-conversion.%s' % e for e in ['a', SHLIB_EXT]] + ['lib/libdouble-conversion_pic.a'], + 'dirs': [], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13-GCCcore-13.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..fbf91d9f0af8 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13-GCCcore-13.2.0.eb @@ -0,0 +1,93 @@ + +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.13' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-opensource-src-%(version)s.tar.xz'] +patches = [ + 'Qt5-5.13.1_fix-avx2.patch', + 'Qt5-5.13.1_fix-qmake-libdir.patch', + 'Qt5-5.15.10_fix-OF-Gentoo.patch', + 'Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch', + 'Qt5-5.15.7_GCC-12.patch', + 'Qt5-5.15.10_webengine-chromium-drop-catapult.patch', + 'Qt5-5.15.10_webengine-chromium-python3.patch', + 'Qt5-5.15.10_webengine-drop-catapult.patch', + 'Qt5-5.15.10_webengine-python3.patch', + 'Qt5-5.15.10_webengine-python3.11.patch', + 'Qt5-5.15.13_fix-XKB_KEY_dead.patch', + 'Qt5-5.15.13_fix-includes.patch', +] +checksums = [ + {'qt-everywhere-opensource-src-5.15.13.tar.xz': '9550ec8fc758d3d8d9090e261329700ddcd712e2dda97e5fcfeabfac22bea2ca'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.15.10_fix-OF-Gentoo.patch': '1c4d3b974422dadb4fd62f79581d48d25ae3d5f5f21489ae8c632e43e2e5286b'}, + {'Qt5-5.15.10_fix-qtwebengine-breakpad-glibc-2.34.patch': + '3b536de3b2da9115d96323a00275fc6066bb048f3747f8e6971facd78ed4e2e2'}, + {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, + {'Qt5-5.15.10_webengine-chromium-drop-catapult.patch': + '6325c6f63b144755fcf040614178923406d7526517d58b29d99b100919acec54'}, + {'Qt5-5.15.10_webengine-chromium-python3.patch': + '128d58c1e83f551daec6e9122fc1cea07be76b79d4e99222969649be24334e1e'}, + {'Qt5-5.15.10_webengine-drop-catapult.patch': '7a488a0d73b7a9f33a2bdb87996f0a16938f5f882385190833679d1d17684907'}, + {'Qt5-5.15.10_webengine-python3.patch': '0e35606506cb218841e05d38214ec6a442f7481630c2d856a09b7863af304023'}, + {'Qt5-5.15.10_webengine-python3.11.patch': '8486fc234de2cdf8a600b204bac5d8eb2bc0bc9b1b1d365505f801c4a201f9c3'}, + {'Qt5-5.15.13_fix-XKB_KEY_dead.patch': '7fcee0d8414f5060d2b93a46bbd109b9712c127747dc654bf9dc99038e6b5340'}, + {'Qt5-5.15.13_fix-includes.patch': '95fc8a41572bce7c6b46cede0bd35fd4f80e2f962b8394b26e6265c2e885e758'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.11.1'), + ('Python', '3.11.5'), + ('re2c', '3.1'), +] + +dependencies = [ + ('double-conversion', '3.3.0'), + ('GLib', '2.78.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), + ('HarfBuzz', '8.2.2'), + ('graphite2', '1.3.14'), + # deps for QtWebEngine + ('X11', '20231019'), + ('fontconfig', '2.14.2'), + ('DBus', '1.15.8'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.3'), + ('libjpeg-turbo', '3.0.1'), + ('NSS', '3.94'), + ('snappy', '1.1.10'), + ('JasPer', '4.0.0'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('ICU', '74.1'), + ('nodejs', '20.9.0'), +] +# qtgamepad needs recent kernel/libevdev (fails on RHEL 6.x) +# qtwayland fails to build on (some) Centos 7 systems +configopts = '-skip qtgamepad -skip qtwayland ' +# make sure QtWebEngine component is being built & installed +check_qtwebengine = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-XKB_KEY_dead.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-XKB_KEY_dead.patch new file mode 100644 index 000000000000..55381a329414 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-XKB_KEY_dead.patch @@ -0,0 +1,19 @@ +see https://bugreports.qt.io/browse/QTBUG-117950 + https://codereview.qt-project.org/c/qt/qtbase/+/510764 +ported to Qt5 5.15.11 by Kenenth Hoste (HPC-UGent) +--- qt-everywhere-src-5.15.11/qtbase/src/platformsupport/input/xkbcommon/qxkbcommon.cpp.orig 2023-11-24 12:19:01.050524400 +0100 ++++ qt-everywhere-src-5.15.11/qtbase/src/platformsupport/input/xkbcommon/qxkbcommon.cpp 2023-11-24 12:19:23.232570214 +0100 +@@ -273,10 +273,14 @@ + Xkb2Qt, + Xkb2Qt, + Xkb2Qt, ++/* The following four XKB_KEY_dead keys got removed in libxkbcommon 1.6.0 ++ The define check is kind of version check here. */ ++#ifdef XKB_KEY_dead_lowline + Xkb2Qt, + Xkb2Qt, + Xkb2Qt, + Xkb2Qt, ++#endif + + // Special keys from X.org - This include multimedia keys, + // wireless/bluetooth/uwb keys, special launcher keys, etc. diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-includes.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-includes.patch new file mode 100644 index 000000000000..eb54e76ede90 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.13_fix-includes.patch @@ -0,0 +1,286 @@ +add missing stdint includes required when building with GCC 13.x +and replace variable Pixmap --> PresentPixmap in chromium/third_party/xcbproto/src/src/present.xml +see also: +* https://gcc.gnu.org/gcc-13/porting_to.html +* https://bugreports.qt.io/browse/QTBUG-113111 and https://invent.kde.org/qt/qt/qtlocation-mapboxgl/-/merge_requests/1 +* https://github.com/abseil/abseil-cpp/pull/1187 +Author: Richard Top +diff -ruN qt-everywhere-src-5.15.11.org/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/geometry.hpp qt-everywhere-src-5.15.11/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/geometry.hpp +--- qt-everywhere-src-5.15.11.org/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/geometry.hpp 2024-03-14 13:28:06.564124774 +0000 ++++ qt-everywhere-src-5.15.11/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/geometry.hpp 2024-03-15 13:01:38.931471150 +0000 +@@ -3,6 +3,7 @@ + #include + #include + #include ++#include + + namespace mbgl { + +diff -ruN qt-everywhere-src-5.15.11.org/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/string.hpp qt-everywhere-src-5.15.11/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/string.hpp +--- qt-everywhere-src-5.15.11.org/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/string.hpp 2024-03-14 13:28:06.564124774 +0000 ++++ qt-everywhere-src-5.15.11/qtlocation/src/3rdparty/mapbox-gl-native/include/mbgl/util/string.hpp 2024-03-15 13:02:09.468570971 +0000 +@@ -5,6 +5,7 @@ + #include + #include + #include ++#include + + // Polyfill needed by Qt when building for Android with GCC + #if defined(__ANDROID__) && defined(__GLIBCXX__) +diff -ruN qt-everywhere-src-5.15.11.org/qtlocation/src/3rdparty/mapbox-gl-native/src/mbgl/gl/stencil_mode.hpp qt-everywhere-src-5.15.11/qtlocation/src/3rdparty/mapbox-gl-native/src/mbgl/gl/stencil_mode.hpp +--- qt-everywhere-src-5.15.11.org/qtlocation/src/3rdparty/mapbox-gl-native/src/mbgl/gl/stencil_mode.hpp 2024-03-14 13:28:06.573124804 +0000 ++++ qt-everywhere-src-5.15.11/qtlocation/src/3rdparty/mapbox-gl-native/src/mbgl/gl/stencil_mode.hpp 2024-03-15 13:02:53.996716526 +0000 +@@ -1,6 +1,7 @@ + #pragma once + + #include ++#include + + namespace mbgl { + namespace gl { +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/base/debug/profiler.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/base/debug/profiler.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/base/debug/profiler.h 2024-03-14 13:27:55.904088924 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/base/debug/profiler.h 2024-03-15 10:42:20.790168875 +0000 +@@ -5,6 +5,7 @@ + #ifndef BASE_DEBUG_PROFILER_H_ + #define BASE_DEBUG_PROFILER_H_ + ++#include + #include + + #include +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/content/public/browser/browsing_data_remover_delegate.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/content/public/browser/browsing_data_remover_delegate.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/content/public/browser/browsing_data_remover_delegate.h 2024-03-14 13:27:42.056042352 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/content/public/browser/browsing_data_remover_delegate.h 2024-03-15 10:41:41.596041171 +0000 +@@ -5,6 +5,7 @@ + #ifndef CONTENT_PUBLIC_BROWSER_BROWSING_DATA_REMOVER_DELEGATE_H_ + #define CONTENT_PUBLIC_BROWSER_BROWSING_DATA_REMOVER_DELEGATE_H_ + ++#include + #include + #include + #include "base/callback_forward.h" +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/device/base/synchronization/one_writer_seqlock.cc qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/device/base/synchronization/one_writer_seqlock.cc +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/device/base/synchronization/one_writer_seqlock.cc 2024-03-14 13:27:43.805048234 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/device/base/synchronization/one_writer_seqlock.cc 2024-03-15 12:23:06.145909864 +0000 +@@ -2,6 +2,8 @@ + // Use of this source code is governed by a BSD-style license that can be + // found in the LICENSE file. + ++#include ++ + #include "device/base/synchronization/one_writer_seqlock.h" + + namespace device { +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/device/bluetooth/public/cpp/bluetooth_uuid.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/device/bluetooth/public/cpp/bluetooth_uuid.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/device/bluetooth/public/cpp/bluetooth_uuid.h 2024-03-14 13:27:43.809048247 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/device/bluetooth/public/cpp/bluetooth_uuid.h 2024-03-15 10:46:46.409034325 +0000 +@@ -5,6 +5,7 @@ + #ifndef DEVICE_BLUETOOTH_PUBLIC_CPP_BLUETOOTH_UUID_H_ + #define DEVICE_BLUETOOTH_PUBLIC_CPP_BLUETOOTH_UUID_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/command_buffer/common/webgpu_cmd_enums.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/command_buffer/common/webgpu_cmd_enums.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/command_buffer/common/webgpu_cmd_enums.h 2024-03-14 13:27:45.052052428 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/command_buffer/common/webgpu_cmd_enums.h 2024-03-15 10:48:50.023437092 +0000 +@@ -5,6 +5,8 @@ + #ifndef GPU_COMMAND_BUFFER_COMMON_WEBGPU_CMD_ENUMS_H_ + #define GPU_COMMAND_BUFFER_COMMON_WEBGPU_CMD_ENUMS_H_ + ++#include ++ + namespace gpu { + namespace webgpu { + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/config/device_perf_info.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/config/device_perf_info.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/config/device_perf_info.h 2024-03-14 13:27:45.065052471 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/config/device_perf_info.h 2024-03-15 10:49:57.512656983 +0000 +@@ -5,6 +5,7 @@ + #ifndef GPU_CONFIG_DEVICE_PERF_INFO_H_ + #define GPU_CONFIG_DEVICE_PERF_INFO_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_feature_info.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_feature_info.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_feature_info.h 2024-03-14 13:27:45.067052478 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_feature_info.h 2024-03-15 10:50:20.183730854 +0000 +@@ -5,6 +5,7 @@ + #ifndef GPU_CONFIG_GPU_FEATURE_INFO_H_ + #define GPU_CONFIG_GPU_FEATURE_INFO_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_preferences.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_preferences.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_preferences.h 2024-03-14 13:27:45.066052475 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/gpu/config/gpu_preferences.h 2024-03-15 10:50:38.542790675 +0000 +@@ -5,6 +5,7 @@ + #ifndef GPU_CONFIG_GPU_PREFERENCES_H_ + #define GPU_CONFIG_GPU_PREFERENCES_H_ + ++#include + #include + #include + #include +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/net/cookies/cookie_inclusion_status.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/net/cookies/cookie_inclusion_status.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/net/cookies/cookie_inclusion_status.h 2024-03-14 13:27:43.093045839 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/net/cookies/cookie_inclusion_status.h 2024-03-15 10:51:04.531875353 +0000 +@@ -5,6 +5,7 @@ + #ifndef NET_COOKIES_COOKIE_INCLUSION_STATUS_H_ + #define NET_COOKIES_COOKIE_INCLUSION_STATUS_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/strings/internal/str_format/extension.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/strings/internal/str_format/extension.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/strings/internal/str_format/extension.h 2024-03-14 13:27:46.683057913 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/abseil-cpp/absl/strings/internal/str_format/extension.h 2024-03-15 10:54:40.617579415 +0000 +@@ -18,6 +18,7 @@ + + #include + ++#include + #include + #include + #include +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/angle/include/GLSLANG/ShaderVars.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/angle/include/GLSLANG/ShaderVars.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/angle/include/GLSLANG/ShaderVars.h 2024-03-14 13:27:52.447077298 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/angle/include/GLSLANG/ShaderVars.h 2024-03-15 10:55:28.931736832 +0000 +@@ -10,6 +10,7 @@ + #ifndef GLSLANG_SHADERVARS_H_ + #define GLSLANG_SHADERVARS_H_ + ++#include + #include + #include + #include +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/angle/src/common/angleutils.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/angle/src/common/angleutils.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/angle/src/common/angleutils.h 2024-03-14 13:27:52.545077627 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/angle/src/common/angleutils.h 2024-03-15 10:55:58.804834168 +0000 +@@ -15,6 +15,7 @@ + # include "absl/container/flat_hash_map.h" + #endif // defined(ANGLE_USE_ABSEIL) + ++#include + #include + #include + #include +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/minidump_descriptor.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/minidump_descriptor.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/minidump_descriptor.h 2024-03-14 13:27:51.652074624 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/breakpad/breakpad/src/client/linux/handler/minidump_descriptor.h 2024-03-15 10:57:14.952082395 +0000 +@@ -30,6 +30,7 @@ + #ifndef CLIENT_LINUX_HANDLER_MINIDUMP_DESCRIPTOR_H_ + #define CLIENT_LINUX_HANDLER_MINIDUMP_DESCRIPTOR_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/perfetto/include/perfetto/ext/base/uuid.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/perfetto/include/perfetto/ext/base/uuid.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/perfetto/include/perfetto/ext/base/uuid.h 2024-03-14 13:27:45.756054795 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/perfetto/include/perfetto/ext/base/uuid.h 2024-03-15 10:57:53.513208099 +0000 +@@ -17,6 +17,7 @@ + #ifndef INCLUDE_PERFETTO_EXT_BASE_UUID_H_ + #define INCLUDE_PERFETTO_EXT_BASE_UUID_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/webrtc/call/rtp_demuxer.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/webrtc/call/rtp_demuxer.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/webrtc/call/rtp_demuxer.h 2024-03-14 13:27:46.287056581 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/webrtc/call/rtp_demuxer.h 2024-03-15 10:58:43.177369996 +0000 +@@ -11,6 +11,7 @@ + #ifndef CALL_RTP_DEMUXER_H_ + #define CALL_RTP_DEMUXER_H_ + ++#include + #include + #include + #include +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/third_party/base64/base64.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/third_party/base64/base64.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/third_party/base64/base64.h 2024-03-14 13:27:46.005055632 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/third_party/webrtc/rtc_base/third_party/base64/base64.h 2024-03-15 10:59:32.856531943 +0000 +@@ -12,6 +12,7 @@ + #ifndef RTC_BASE_THIRD_PARTY_BASE64_BASE64_H_ + #define RTC_BASE_THIRD_PARTY_BASE64_BASE64_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/ui/events/gesture_event_details.cc qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/ui/events/gesture_event_details.cc +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/ui/events/gesture_event_details.cc 2024-03-14 13:27:43.604047558 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/ui/events/gesture_event_details.cc 2024-03-15 18:53:59.688584563 +0000 +@@ -2,6 +2,7 @@ + // Use of this source code is governed by a BSD-style license that can be + // found in the LICENSE file. + ++#include + #include "ui/events/gesture_event_details.h" + #include "base/check_op.h" + #include "base/notreached.h" +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/v8/src/base/logging.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/v8/src/base/logging.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/v8/src/base/logging.h 2024-03-14 13:27:56.087089539 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/v8/src/base/logging.h 2024-03-15 11:00:03.834632926 +0000 +@@ -5,6 +5,7 @@ + #ifndef V8_BASE_LOGGING_H_ + #define V8_BASE_LOGGING_H_ + ++#include + #include + #include + #include +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/v8/src/base/macros.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/v8/src/base/macros.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/v8/src/base/macros.h 2024-03-14 13:27:56.086089536 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/v8/src/base/macros.h 2024-03-15 11:00:25.271702805 +0000 +@@ -5,6 +5,7 @@ + #ifndef V8_BASE_MACROS_H_ + #define V8_BASE_MACROS_H_ + ++#include + #include + #include + +diff -ruN qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/v8/src/inspector/v8-string-conversions.h qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/v8/src/inspector/v8-string-conversions.h +--- qt-everywhere-src-5.15.11.org/qtwebengine/src/3rdparty/chromium/v8/src/inspector/v8-string-conversions.h 2024-03-14 13:27:56.046089401 +0000 ++++ qt-everywhere-src-5.15.11/qtwebengine/src/3rdparty/chromium/v8/src/inspector/v8-string-conversions.h 2024-03-15 11:00:51.074786919 +0000 +@@ -5,6 +5,7 @@ + #ifndef V8_INSPECTOR_V8_STRING_CONVERSIONS_H_ + #define V8_INSPECTOR_V8_STRING_CONVERSIONS_H_ + ++#include + #include + + // Conversion routines between UT8 and UTF16, used by string-16.{h,cc}. You may +diff -ruN qt-everywhere-src-5.15.13.org/qtwebengine/src/3rdparty/chromium/third_party/xcbproto/src/src/present.xml qt-everywhere-src-5.15.13/qtwebengine/src/3rdparty/chromium/third_party/xcbproto/src/src/present.xml +--- qt-everywhere-src-5.15.13.org/qtwebengine/src/3rdparty/chromium/third_party/xcbproto/src/src/present.xml 2024-03-14 13:27:52.060075996 +0000 ++++ qt-everywhere-src-5.15.13/qtwebengine/src/3rdparty/chromium/third_party/xcbproto/src/src/present.xml 2024-03-23 09:26:13.650758730 +0000 +@@ -89,7 +89,7 @@ + + + +- ++ + + + +diff -ruN qt-everywhere-src-5.15.13.org/qtwebengine/src/3rdparty/chromium/extensions/browser/api/audio/audio_device_id_calculator.h qt-everywhere-src-5.15.13/qtwebengine/src/3rdparty/chromium/extensions/browser/api/audio/audio_device_id_calculator.h +--- qt-everywhere-src-5.15.13.org/qtwebengine/src/3rdparty/chromium/extensions/browser/api/audio/audio_device_id_calculator.h 2024-03-14 13:27:55.702088244 +0000 ++++ qt-everywhere-src-5.15.13/qtwebengine/src/3rdparty/chromium/extensions/browser/api/audio/audio_device_id_calculator.h 2024-03-23 20:30:28.015096733 +0000 +@@ -7,7 +7,7 @@ + + #include + #include +- ++#include + #include "base/macros.h" + + namespace content { diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..b1eaefdbac1d --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ + +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.10' + +homepage = 'https://github.com/google/snappy' +description = """Snappy is a compression/decompression library. It does not aim +for maximum compression, or compatibility with any other compression library; +instead, it aims for very high speeds and reasonable compression.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-1.1.9_use-default-rtti.patch', +] +checksums = [ + {'1.1.10.tar.gz': '49d831bffcc5f3d01482340fe5af59852ca2fe76c3e05df0e67203ebbe0f1d90'}, + {'snappy-1.1.9_use-default-rtti.patch': 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +# Disable building tests and benchmarks - we're not using them and they require googletest and benchmark source code +_configopts = '-DSNAPPY_BUILD_TESTS=OFF -DSNAPPY_BUILD_BENCHMARKS=OFF' +configopts = ['%s' % _configopts, '-DBUILD_SHARED_LIBS=ON %s' % _configopts] + +sanity_check_paths = { + 'files': ['lib64/libsnappy.a', 'lib64/libsnappy.%s' % SHLIB_EXT, 'include/snappy.h'], + 'dirs': [] +} + +moduleclass = 'lib' + From e214984a2ecfbc6dbab87ce34d92fe04e7181460 Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Sun, 24 Mar 2024 19:18:16 +0100 Subject: [PATCH 1111/1193] remove blanks --- easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb index b1eaefdbac1d..18fb59c8e11b 100644 --- a/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.10-GCCcore-13.2.0.eb @@ -36,4 +36,3 @@ sanity_check_paths = { } moduleclass = 'lib' - From 4c56710083f4e2ca91cc0ec383877c1ca7622aae Mon Sep 17 00:00:00 2001 From: TopRichard <121792457+TopRichard@users.noreply.github.com> Date: Sun, 24 Mar 2024 19:19:05 +0100 Subject: [PATCH 1112/1193] remove blanks --- .../double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb index 999f7391ccf0..1f2aa192a0d7 100644 --- a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.3.0-GCCcore-13.2.0.eb @@ -33,4 +33,3 @@ sanity_check_paths = { } moduleclass = 'lib' - From 854a47896aee6cd1defc0556638a472f3a37b5e9 Mon Sep 17 00:00:00 2001 From: fizwit Date: Sun, 24 Mar 2024 12:27:33 -0700 Subject: [PATCH 1113/1193] librsvg update version and toolchain --- .../librsvg/librsvg-2.58.0-GCCcore-13.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..fe89401030af --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.58.0-GCCcore-13.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.58.0' + +homepage = 'https://wiki.gnome.org/Projects/LibRsvg' +description = "Librsvg is a library to render SVG files using cairo." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['d7c444a926406b59790be0deae196e18ed26059da573fa1aa9ec9ca7658a559c'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('Rust', '1.76.0'), +] + +dependencies = [ + ('cairo', '1.18.0'), + ('freetype', '2.13.2'), + ('Gdk-Pixbuf', '2.42.10'), + ('HarfBuzz', '8.2.2'), + ('Pango', '1.51.0'), + ('GObject-Introspection', '1.78.1'), +] + +# don't GdkPixbuf loader (which gets added to the Gdk-Pixbuf installation directory) +configopts = "--disable-pixbuf-loader" + +sanity_check_paths = { + 'files': ['bin/rsvg-convert', 'lib/librsvg-%(version_major)s.a', 'lib/librsvg-%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/librsvg-%(version_major)s.0.pc'], + 'dirs': ['include/librsvg-%(version_major)s.0/librsvg', 'share'], +} + +sanity_check_commands = ["rsvg-convert --help"] + +moduleclass = 'lib' From b7b8218b113ef248ab0be75031710e0d5fbee5ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 24 Mar 2024 23:44:56 +0000 Subject: [PATCH 1114/1193] adding easyconfigs: CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb and patches: cupy-13.0.0_cusparselt_0.6.0.patch, cupy-13.0.0_eb_ccc.patch --- .../CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb | 75 ++++ .../c/CuPy/cupy-13.0.0_cusparselt_0.6.0.patch | 334 ++++++++++++++++++ .../c/CuPy/cupy-13.0.0_eb_ccc.patch | 16 + 3 files changed, 425 insertions(+) create mode 100644 easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/c/CuPy/cupy-13.0.0_cusparselt_0.6.0.patch create mode 100644 easybuild/easyconfigs/c/CuPy/cupy-13.0.0_eb_ccc.patch diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 000000000000..4baf27542b00 --- /dev/null +++ b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,75 @@ +easyblock = 'PythonBundle' + +name = 'CuPy' +version = '13.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://cupy.dev' +description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('hypothesis', '6.82.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('cuDNN', '8.9.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.18.3', versionsuffix), + ('cuTENSOR', '2.0.1.2', versionsuffix, SYSTEM), + ('cuSPARSELt', '0.6.0.6', versionsuffix, SYSTEM), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +_skip_tests = [ + '--ignore tests/example_tests', # examples are not included + '--ignore tests/cupy_tests/fft_tests/test_fft.py', # CUFFT_INTERNAL_ERROR + '--deselect test_argmax_int32_overflow', # requires more VRAM than a T4 + '--deselect test_argmin_int32_overflow', # requires more VRAM than a T4 + '--deselect test_sos_freqz_against_mp', # https://github.com/cupy/cupy/issues/8255 + '--deselect test_argsort_one_dim', # sorting somehow broken on at least T4 + # Floating point precision issues: + '--deselect TestSOSFreqz::test_sosfrez_design_cheb2_2', + '--deselect TestFirls::test_firls', + '--deselect TestButtord::test_ellip_butter', + '--deselect TestEllipord::test_bandstop', + '--deselect TestEllipord::test_fs_param', + '--deselect TestEllipord::test_ellip_butter', + '--deselect Test_bode::test_from_state_space', + '--deselect TestPartialFractionExpansion::test_residuez_general', +] + +exts_list = [ + ('fastrlock', '0.8.2', { + 'checksums': ['644ec9215cf9c4df8028d8511379a15d9c1af3e16d80e47f1b6fdc6ba118356a'], + }), + ('cupy', version, { + 'preinstallopts': 'CUPY_NUM_BUILD_JOBS=%(parallel)s EB_CCC="%(cuda_cc_cmake)s" ', + 'patches': [ + 'cupy-%(version)s_cusparselt_0.6.0.patch', + 'cupy-%(version)s_eb_ccc.patch', + ], + 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && ' + 'pytest tests -k "not slow" ' + ' '.join(_skip_tests), + 'testinstall': True, + 'checksums': [ + {'cupy-13.0.0.tar.gz': '2f04e7857f692a713360dc9c3b06709806ab8404fca39b5af9721c04a2979aae'}, + {'cupy-13.0.0_cusparselt_0.6.0.patch': '09cb12d26e78079c50b06f17002bf54c66e5e4743b917c5a218d3fe90124d499'}, + {'cupy-13.0.0_eb_ccc.patch': 'bfe8b46344759f58491f55418bd9c856d6f72d681ee5fef12820009f808d2db1'}, + ], + }), +] + +sanity_check_commands = [ + "python -c 'import cupy'", +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/c/CuPy/cupy-13.0.0_cusparselt_0.6.0.patch b/easybuild/easyconfigs/c/CuPy/cupy-13.0.0_cusparselt_0.6.0.patch new file mode 100644 index 000000000000..c202cd34a6c3 --- /dev/null +++ b/easybuild/easyconfigs/c/CuPy/cupy-13.0.0_cusparselt_0.6.0.patch @@ -0,0 +1,334 @@ +Support for cusparselt 0.6.0 adapted from https://github.com/cupy/cupy/pull/8074 +but with bug fixed for compressed size functions that were wrong. +author: micketeer@gmail.com +diff -ru cupy_backends.orig/cuda/libs/cusparselt.pxd cupy_backends/cuda/libs/cusparselt.pxd +--- cupy_backends.orig/cuda/libs/cusparselt.pxd 2024-03-23 17:08:35.676189389 +0100 ++++ cupy_backends/cuda/libs/cusparselt.pxd 2024-03-23 17:30:34.931591841 +0100 +@@ -13,18 +13,20 @@ + CUSPARSELT_MAT_BATCH_STRIDE = 1 # READ/WRITE + + # cusparseComputeType +- CUSPARSE_COMPUTE_16F = 0 +- CUSPARSE_COMPUTE_32I = 1 +- CUSPARSE_COMPUTE_TF32 = 2 +- CUSPARSE_COMPUTE_TF32_FAST = 3 ++ CUSPARSE_COMPUTE_32I = 0 ++ CUSPARSE_COMPUTE_16F = 1 ++ CUSPARSE_COMPUTE_32F = 2 + + # cusparseLtMatmulDescAttribute_t + CUSPARSELT_MATMUL_ACTIVATION_RELU = 0 # READ/WRITE + CUSPARSELT_MATMUL_ACTIVATION_RELU_UPPERBOUND = 1 # READ/WRITE + CUSPARSELT_MATMUL_ACTIVATION_RELU_THRESHOLD = 2 # READ/WRITE + CUSPARSELT_MATMUL_ACTIVATION_GELU = 3 # READ/WRITE +- CUSPARSELT_MATMUL_BIAS_STRIDE = 4 # READ/WRITE +- CUSPARSELT_MATMUL_BIAS_POINTER = 5 # READ/WRITE ++ CUSPARSELT_MATMUL_ACTIVATION_GELU_SCALING = 4 # READ/WRITE ++ CUSPARSELT_MATMUL_ALPHA_VECTOR_SCALING = 5 # READ/WRITE ++ CUSPARSELT_MATMUL_BETA_VECTOR_SCALING = 6 # READ/WRITE ++ CUSPARSELT_MATMUL_BIAS_POINTER = 7 # READ/WRITE ++ CUSPARSELT_MATMUL_BIAS_STRIDE = 8 # READ/WRITE + + # cusparseLtMatmulAlg_t + CUSPARSELT_MATMUL_ALG_DEFAULT = 0 +@@ -33,6 +35,14 @@ + CUSPARSELT_MATMUL_ALG_CONFIG_ID = 0 # NOQA, READ/WRITE + CUSPARSELT_MATMUL_ALG_CONFIG_MAX_ID = 1 # NOQA, READ-ONLY + CUSPARSELT_MATMUL_SEARCH_ITERATIONS = 2 # NOQA, READ/WRITE ++ CUSPARSELT_MATMUL_SPLIT_K = 3 # NOQA, READ/WRITE ++ CUSPARSELT_MATMUL_SPLIT_K_MODE =4 # NOQA, READ/WRITE ++ CUSPARSELT_MATMUL_SPLIT_K_BUFFERS=5 # NOQA, READ/WRITE ++ ++ # cusparseLtSplitKMode_t ++ CUSPARSELT_INVALID_MODE = 0 ++ CUSPARSELT_SPLIT_K_MODE_ONE_KERNEL = 1 ++ CUSPARSELT_SPLIT_K_MODE_TWO_KERNELS = 2 + + # cusparseLtPruneAlg_t + CUSPARSELT_PRUNE_SPMMA_TILE = 0 +diff -ru cupy_backends.orig/cuda/libs/cusparselt.pyx cupy_backends/cuda/libs/cusparselt.pyx +--- cupy_backends.orig/cuda/libs/cusparselt.pyx 2024-03-23 17:08:35.676189389 +0100 ++++ cupy_backends/cuda/libs/cusparselt.pyx 2024-03-23 18:03:43.706215397 +0100 +@@ -11,6 +11,13 @@ + from cupy_backends.cuda.libs import cusparse as _cusparse + + ++############################################################################### ++# Types ++############################################################################### ++cdef extern from *: ++ ctypedef void* LibraryPropertyType 'libraryPropertyType_t' ++ ++ + cdef extern from '../../cupy_cusparselt.h' nogil: + ctypedef int cusparseStatus_t 'cusparseStatus_t' + ctypedef int cusparseOrder_t 'cusparseOrder_t' +@@ -36,11 +43,14 @@ + ctypedef int cusparseOperation_t 'cusparseOperation_t' + ctypedef int cusparseLtMatmulAlg_t 'cusparseLtMatmulAlg_t' + ctypedef int cusparseLtMatmulAlgAttribute_t 'cusparseLtMatmulAlgAttribute_t' # NOQA ++ ctypedef int cusparseLtSplitKMode_t 'cusparseLtSplitKMode_t' + ctypedef int cusparseLtPruneAlg_t 'cusparseLtPruneAlg_t' + + # Management Functions + cusparseStatus_t cusparseLtInit(cusparseLtHandle_t* handle) + cusparseStatus_t cusparseLtDestroy(const cusparseLtHandle_t* handle) ++ cusparseStatus_t cusparseLtGetVersion(const cusparseLtHandle_t* handle, int* version) ++ cusparseStatus_t cusparseLtGetProperty(LibraryPropertyType propertyType, int* value) + + # Matmul Functions + cusparseStatus_t cusparseLtDenseDescriptorInit( +@@ -66,6 +76,11 @@ + const cusparseLtMatDescriptor_t* matDescr, + cusparseLtMatDescAttribute_t matAttribute, + void* data, size_t dataSize) ++ cusparseStatus_t cusparseLtMatDescSetAttribute( ++ const cusparseLtHandle_t* handle, ++ const cusparseLtMatDescriptor_t* matDescr, ++ cusparseLtMatDescAttribute_t matAttribute, ++ void* data, size_t dataSize) + cusparseStatus_t cusparseLtMatmulDescriptorInit( + const cusparseLtHandle_t* handle, + cusparseLtMatmulDescriptor_t* matMulDescr, +@@ -95,17 +110,21 @@ + const cusparseLtHandle_t* handle, + cusparseLtMatmulAlgSelection_t* algSelection, + cusparseLtMatmulAlgAttribute_t attribute, +- const void* data, size_t ataSize) +- cusparseStatus_t cusparseLtMatmulGetWorkspace( ++ const void* data, size_t dataSize) ++ cusparseStatus_t cusparseLtMatmulAlgGetAttribute( + const cusparseLtHandle_t* handle, + const cusparseLtMatmulAlgSelection_t* algSelection, ++ cusparseLtMatmulAlgAttribute_t attribute, ++ void* data, size_t dataSize) ++ cusparseStatus_t cusparseLtMatmulGetWorkspace( ++ const cusparseLtHandle_t* handle, ++ const cusparseLtMatmulPlan_t* plan, + size_t* workspaceSize) + cusparseStatus_t cusparseLtMatmulPlanInit( + const cusparseLtHandle_t* handle, + cusparseLtMatmulPlan_t* plan, + const cusparseLtMatmulDescriptor_t* matmulDescr, +- const cusparseLtMatmulAlgSelection_t* algSelection, +- size_t workspaceSize) ++ const cusparseLtMatmulAlgSelection_t* algSelection) + cusparseStatus_t cusparseLtMatmulPlanDestroy( + const cusparseLtMatmulPlan_t* plan) + cusparseStatus_t cusparseLtMatmul( +@@ -113,6 +132,11 @@ + const void* alpha, const void* d_A, const void* d_B, + const void* beta, const void* d_C, void* d_D, + void* workspace, runtime.Stream* streams, int32_t numStreams) ++ cusparseStatus_t cusparseLtMatmulSearch( ++ const cusparseLtHandle_t* handle, cusparseLtMatmulPlan_t* plan, ++ const void* alpha, const void* d_A, const void* d_B, ++ const void* beta, const void* d_C, void* d_D, ++ void* workspace, runtime.Stream* streams, int32_t numStreams) + + # Helper Functions + cusparseStatus_t cusparseLtSpMMAPrune( +@@ -123,7 +147,7 @@ + cusparseStatus_t cusparseLtSpMMAPruneCheck( + const cusparseLtHandle_t* handle, + const cusparseLtMatmulDescriptor_t* matmulDescr, +- const void* d_in, int* valid, runtime.Stream stream) ++ const void* d_in, int* d_valid, runtime.Stream stream) + cusparseStatus_t cusparseLtSpMMAPrune2( + const cusparseLtHandle_t* handle, + const cusparseLtMatDescriptor_t* sparseMatDescr, +@@ -136,19 +160,22 @@ + runtime.Stream stream) + cusparseStatus_t cusparseLtSpMMACompressedSize( + const cusparseLtHandle_t* handle, const cusparseLtMatmulPlan_t* plan, +- size_t* compressedSize) ++ size_t* compressedSize, ++ size_t* compressedBufferSize) + cusparseStatus_t cusparseLtSpMMACompress( + const cusparseLtHandle_t* handle, const cusparseLtMatmulPlan_t* plan, +- const void* d_dense, void* d_compressed, runtime.Stream stream) ++ const void* d_dense, void* d_compressed, void* d_compressed_buffer, ++ runtime.Stream stream) + cusparseStatus_t cusparseLtSpMMACompressedSize2( + const cusparseLtHandle_t* handle, + const cusparseLtMatDescriptor_t* sparseMatDescr, +- size_t* compressedSize) ++ size_t* compressedSize, ++ size_t* compressedBufferSize) + cusparseStatus_t cusparseLtSpMMACompress2( + const cusparseLtHandle_t* handle, + const cusparseLtMatDescriptor_t* sparseMatDescr, + int isSparseA, cusparseOperation_t op, const void* d_dense, +- void* d_compressed, runtime.Stream stream) ++ void* d_compressed, void* d_compressed_buffer, runtime.Stream stream) + + # Build-time version + int CUSPARSELT_VERSION +@@ -370,28 +397,36 @@ + data, dataSize) + check_status(status) + ++cpdef matmulAlgGetAttribute(Handle handle, MatmulAlgSelection algSelection, ++ attribute, size_t data, size_t dataSize): ++ """Gets the attribute related to algorithm selection descriptor.""" ++ status = cusparseLtMatmulAlgGetAttribute( ++ handle._ptr, ++ algSelection._ptr, ++ attribute, ++ data, dataSize) ++ check_status(status) ++ + cpdef size_t matmulGetWorkspace(Handle handle, +- MatmulAlgSelection algSelection): ++ MatmulPlan plan): + """Determines the required workspace size""" + cdef size_t workspaceSize + status = cusparseLtMatmulGetWorkspace( + handle._ptr, +- algSelection._ptr, ++ plan._ptr, + &workspaceSize) + check_status(status) + return workspaceSize + + cpdef matmulPlanInit(Handle handle, MatmulPlan plan, + MatmulDescriptor matmulDescr, +- MatmulAlgSelection algSelection, +- size_t workspaceSize): ++ MatmulAlgSelection algSelection): + """Initializes the plan.""" + status = cusparseLtMatmulPlanInit( + handle._ptr, + plan._ptr, + matmulDescr._ptr, +- algSelection._ptr, +- workspaceSize) ++ algSelection._ptr) + check_status(status) + + cpdef matmulPlanDestroy(MatmulPlan plan): +@@ -412,6 +447,18 @@ + workspace, NULL, 0) + check_status(status) + ++cpdef matmulSearch(Handle handle, MatmulPlan plan, ++ size_t alpha, size_t d_A, size_t d_B, ++ size_t beta, size_t d_C, size_t d_D, size_t workspace): ++ """Evaluates all available algorithms for the matrix multiplication""" ++ status = cusparseLtMatmulSearch( ++ handle._ptr, ++ plan._ptr, ++ alpha, d_A, d_B, ++ beta, d_C, d_D, ++ workspace, NULL, 0) ++ check_status(status) ++ + ############################################################################### + # cuSPARSELt: Helper Functions + ############################################################################### +@@ -428,13 +475,13 @@ + check_status(status) + + cpdef spMMAPruneCheck(Handle handle, MatmulDescriptor matmulDescr, +- size_t d_in, size_t valid): ++ size_t d_in, size_t d_valid): + """Checks the correctness of the pruning structure""" + cdef intptr_t stream = stream_module.get_current_stream_ptr() + status = cusparseLtSpMMAPruneCheck( + handle._ptr, + matmulDescr._ptr, +- d_in, valid, stream) ++ d_in, d_valid, stream) + check_status(status) + + cpdef spMMAPrune2(Handle handle, MatDescriptor sparseMatDescr, isSparseA, +@@ -460,47 +507,52 @@ + d_valid, stream) + check_status(status) + +-cpdef size_t spMMACompressedSize(Handle handle, MatmulPlan plan): ++cpdef spMMACompressedSize(Handle handle, MatmulPlan plan): + """Provides the size of the compressed matrix""" + cdef size_t compressedSize ++ cdef size_t compressedBufferSize + status = cusparseLtSpMMACompressedSize( + handle._ptr, + plan._ptr, +- &compressedSize) ++ &compressedSize, &compressedBufferSize) + check_status(status) +- return compressedSize ++ return compressedSize, compressedBufferSize + + cpdef spMMACompress(Handle handle, MatmulPlan plan, +- size_t d_dense, size_t d_compressed): ++ size_t d_dense, size_t d_compressed, ++ size_t d_compressed_buffer): + """Compresses a dense matrix d_dense.""" + cdef intptr_t stream = stream_module.get_current_stream_ptr() + status = cusparseLtSpMMACompress( + handle._ptr, + plan._ptr, +- d_dense, d_compressed, stream) ++ d_dense, d_compressed, ++ d_compressed_buffer, stream) + check_status(status) + +-cpdef size_t spMMACompressedSize2(Handle handle, MatDescriptor sparseMatDescr): ++cpdef spMMACompressedSize2(Handle handle, MatDescriptor sparseMatDescr): + """Provides the size of the compressed matrix""" + cdef size_t compressedSize ++ cdef size_t compressedBufferSize + status = cusparseLtSpMMACompressedSize2( + handle._ptr, + sparseMatDescr._ptr, +- &compressedSize) ++ &compressedSize, &compressedBufferSize) + check_status(status) +- return compressedSize ++ return compressedSize, compressedBufferSize + + cpdef spMMACompress2(Handle handle, MatDescriptor sparseMatDescr, +- isSparseA, op, size_t d_dense, size_t d_compressed): ++ isSparseA, op, size_t d_dense, ++ size_t d_compressed, size_t d_compressed_buffer): + """Compresses a dense matrix d_dense.""" + cdef intptr_t stream = stream_module.get_current_stream_ptr() + status = cusparseLtSpMMACompress2( + handle._ptr, + sparseMatDescr._ptr, + isSparseA, op, d_dense, +- d_compressed, stream) ++ d_compressed, d_compressed_buffer, ++ stream) + check_status(status) + +- + def get_build_version(): + return CUSPARSELT_VERSION +diff -ru cupy_backends.orig/stub/cupy_cusparselt.h cupy_backends/stub/cupy_cusparselt.h +--- cupy_backends.orig/stub/cupy_cusparselt.h 2024-03-23 17:08:35.677189397 +0100 ++++ cupy_backends/stub/cupy_cusparselt.h 2024-03-23 18:15:04.734544642 +0100 +@@ -19,6 +19,7 @@ + typedef enum {} cusparseLtMatmulDescAttribute_t; + typedef enum {} cusparseLtMatmulAlg_t; + typedef enum {} cusparseLtMatmulAlgAttribute_t; ++typedef enum {} cusparseLtSplitKMode_t; + typedef enum {} cusparseLtPruneAlg_t; + + typedef void* cudaStream_t; +@@ -36,6 +37,14 @@ + return CUSPARSE_STATUS_SUCCESS; + } + ++cusparseStatus_t cusparseLtGetVersion(...) { ++ return CUSPARSE_STATUS_SUCCESS; ++} ++ ++cusparseStatus_t cusparseLtGetProperty(...) { ++ return CUSPARSE_STATUS_SUCCESS; ++} ++ + cusparseStatus_t cusparseLtDenseDescriptorInit(...) { + return CUSPARSE_STATUS_SUCCESS; + } diff --git a/easybuild/easyconfigs/c/CuPy/cupy-13.0.0_eb_ccc.patch b/easybuild/easyconfigs/c/CuPy/cupy-13.0.0_eb_ccc.patch new file mode 100644 index 000000000000..3a2be87de98f --- /dev/null +++ b/easybuild/easyconfigs/c/CuPy/cupy-13.0.0_eb_ccc.patch @@ -0,0 +1,16 @@ +Pick up which cuda compute capabilities to use from the environment variable +EB_CCC in the standard format "70,75,80" +author: micketeer@gmail.com +--- install/cupy_builder/_compiler.py.orig 2024-03-24 01:09:26.501631534 +0000 ++++ install/cupy_builder/_compiler.py 2024-03-24 01:10:28.550644001 +0000 +@@ -21,6 +21,10 @@ + if sys.argv == ['setup.py', 'develop']: + return [] + ++ envcfg = os.getenv('EB_CCC', None) ++ if envcfg is not None: ++ return [f'--generate-code=arch=compute_{cc},code=sm_{cc}' for cc in envcfg.split(';')] ++ + envcfg = os.getenv('CUPY_NVCC_GENERATE_CODE', None) + if envcfg is not None and envcfg != 'current': + return ['--generate-code={}'.format(arch) From f019cbd59e8bf12b6bdc50a509a1208039c10640 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 25 Mar 2024 01:02:56 +0000 Subject: [PATCH 1115/1193] Fix style --- .../easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb index 4baf27542b00..6fede877d6ac 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb @@ -33,7 +33,7 @@ _skip_tests = [ '--deselect test_argmax_int32_overflow', # requires more VRAM than a T4 '--deselect test_argmin_int32_overflow', # requires more VRAM than a T4 '--deselect test_sos_freqz_against_mp', # https://github.com/cupy/cupy/issues/8255 - '--deselect test_argsort_one_dim', # sorting somehow broken on at least T4 + '--deselect test_argsort_one_dim', # sorting somehow broken on at least T4 # Floating point precision issues: '--deselect TestSOSFreqz::test_sosfrez_design_cheb2_2', '--deselect TestFirls::test_firls', From 84a805fded94984b6bbbe5808654b644e23d7cf5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Mar 2024 09:40:13 +0100 Subject: [PATCH 1116/1193] Allow some test failures --- .../p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb index 2516874b1e02..ec3d5b3d62c9 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -170,6 +170,10 @@ excluded_tests = { ] } +# several tests are known to be flaky, and fail in some contexts (like having multiple GPUs available), +# so we allow some tests to fail before treating the installation to be faulty +max_failed_tests = 4 + runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' # The readelf sanity check command can be taken out once the TestRPATH test from From 45aa413f50df700831f601be9c3b5b7c5af6ae59 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Mar 2024 10:33:29 +0100 Subject: [PATCH 1117/1193] Improve test for validity of EasyConfigs Aggregate failures and report all together. This is especially useful when the same error is found multiple times, e.g. multiple patch files are missing. This avoids multiple back-and-forth between CI and user updating the PR. --- test/easyconfigs/easyconfigs.py | 134 ++++++++++++++++++-------------- 1 file changed, 74 insertions(+), 60 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index fb128fdbf200..f4383cf23daa 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1362,7 +1362,7 @@ def template_easyconfig_test(self, spec): # cache the parsed easyconfig, to avoid that it is parsed again EasyConfigTest._parsed_easyconfigs.append(ecs[0]) else: - self.assertTrue(False, "easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) + self.fail("easyconfig %s does not contain blocks, yields only one parsed easyconfig" % spec) # check easyconfig file name expected_fn = '%s-%s.eb' % (ec['name'], det_full_ec_version(ec)) @@ -1406,18 +1406,20 @@ def template_easyconfig_test(self, spec): app = app_class(ec) # more sanity checks - self.assertTrue(name, app.name) - self.assertTrue(ec['version'], app.version) + self.assertEqual(name, app.name) + self.assertEqual(ec['version'], app.version) + + failing_checks = [] # make sure that deprecated 'dummy' toolchain is no longer used, should use 'system' toolchain instead - ec_fn = os.path.basename(spec) - error_msg_tmpl = "%s should use 'system' toolchain rather than deprecated 'dummy' toolchain" - self.assertFalse(ec['toolchain']['name'] == 'dummy', error_msg_tmpl % os.path.basename(spec)) + if ec['toolchain']['name'] == 'dummy': + failing_checks.append("%s should use 'system' toolchain rather than deprecated 'dummy' toolchain") # make sure that $root is not used, since it is not compatible with module files in Lua syntax res = re.findall(r'.*\$root.*', ec.rawtxt, re.M) - error_msg = "Found use of '$root', not compatible with modules in Lua syntax, use '%%(installdir)s' instead: %s" - self.assertFalse(res, error_msg % res) + if res: + failing_checks.append("Found use of '$root', not compatible with modules in Lua syntax, " + "use '%%(installdir)s' instead: %s" % res) # check for redefined easyconfig parameters, there should be none... param_def_regex = re.compile(r'^(?P\w+)\s*=', re.M) @@ -1428,10 +1430,9 @@ def template_easyconfig_test(self, spec): if cnt > 1: redefined_keys.append((key, cnt)) - redefined_keys_error_msg = "There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) - redefined_keys_error_msg += ', '.join('%s (%d)' % x for x in redefined_keys) - - self.assertFalse(redefined_keys, redefined_keys_error_msg) + if redefined_keys: + failing_checks.append("There should be no redefined easyconfig parameters, found %d: " % len(redefined_keys) + + ', '.join('%s (%d)' % x for x in redefined_keys)) # make sure old GitHub urls for EasyBuild that include 'hpcugent' are no longer used old_urls = [ @@ -1439,8 +1440,7 @@ def template_easyconfig_test(self, spec): 'hpcugent.github.com/easybuild', 'hpcugent.github.io/easybuild', ] - for old_url in old_urls: - self.assertFalse(old_url in ec.rawtxt, "Old URL '%s' not found in %s" % (old_url, spec)) + failing_checks.extend("Old URL '%s' found" % old_url for old_url in old_urls if old_url in ec.rawtxt) # make sure binutils is included as a (build) dep if toolchain is GCCcore if ec['toolchain']['name'] == 'GCCcore': @@ -1465,8 +1465,8 @@ def template_easyconfig_test(self, spec): # in some cases, binutils can also be a runtime dep (e.g. for Clang) # Also using GCC directly as a build dep is also allowed (it includes the correct binutils) dep_names = [d['name'] for d in ec.dependencies()] - self.assertTrue('binutils' in dep_names or 'GCC' in dep_names, - "binutils or GCC is a build dep in %s: %s" % (spec, dep_names)) + if 'binutils' not in dep_names and 'GCC' not in dep_names: + failing_checks.append("binutils or GCC is a build dep: " + str(dep_names)) # make sure that OpenSSL wrapper is used rather than OS dependency, # for easyconfigs using a 2021a (sub)toolchain or more recent common toolchain version @@ -1486,7 +1486,8 @@ def template_easyconfig_test(self, spec): gcc_subtc_2021a = tcname in ('GCCcore', 'GCC') and tcver > LooseVersion('10.3') if gcc_subtc_2021a or (tcname in ('foss', 'gompi', 'iimpi', 'intel') and tcver >= LooseVersion('2021')): - self.assertFalse(openssl_osdep, "OpenSSL should not be listed as OS dependency in %s" % spec) + if openssl_osdep: + failing_checks.append("OpenSSL should not be listed as OS dependency") src_cnt = len(ec['sources']) patch_checksums = ec['checksums'][src_cnt:] @@ -1494,7 +1495,6 @@ def template_easyconfig_test(self, spec): # make sure all patch files are available specdir = os.path.dirname(spec) basedir = os.path.dirname(os.path.dirname(specdir)) - specfn = os.path.basename(spec) for idx, patch in enumerate(ec['patches']): patch_dir = specdir if isinstance(patch, str): @@ -1508,29 +1508,29 @@ def template_easyconfig_test(self, spec): # only check actual patch files, not other files being copied via the patch functionality patch_full = os.path.join(patch_dir, patch_name) - if patch_name.endswith('.patch'): - msg = "Patch file %s is available for %s" % (patch_full, specfn) - self.assertTrue(os.path.isfile(patch_full), msg) - + if patch_name.endswith('.patch') and not os.path.isfile(patch_full): + failing_checks.append("Patch file %s is missing" % patch_full) # verify checksum for each patch file - if idx < len(patch_checksums) and (os.path.exists(patch_full) or patch_name.endswith('.patch')): + elif idx < len(patch_checksums) and (os.path.exists(patch_full) or patch_name.endswith('.patch')): checksum = patch_checksums[idx] - error_msg = "Invalid checksum for patch file %s in %s: %s" % (patch_name, ec_fn, checksum) - res = verify_checksum(patch_full, checksum) - self.assertTrue(res, error_msg) + if not verify_checksum(patch_full, checksum): + failing_checks.append("Invalid checksum for patch file %s: %s" % (patch_name, checksum)) # make sure 'source' step is not being skipped, # since that implies not verifying the checksum - error_msg = "'source' step should not be skipped in %s, since that implies not verifying checksums" % ec_fn - self.assertFalse(ec['checksums'] and ('source' in ec['skipsteps']), error_msg) + if ec['checksums'] and ('source' in ec['skipsteps']): + failing_checks.append("'source' step should not be skipped, since that implies not verifying checksums") for ext in ec.get_ref('exts_list'): if isinstance(ext, (tuple, list)) and len(ext) == 3: ext_name = ext[0] - self.assertTrue(isinstance(ext[2], dict), - "3rd element of extension spec for %s must be a dictionary" % ext_name) + if not isinstance(ext[2], dict): + failing_checks.append("3rd element of extension spec for %s must be a dictionary" % ext_name) + + # Need to check now as collect_exts_file_info relies on correct exts_list + if failing_checks: + self.fail('Verification for %s failed:\n' % os.path.basename(spec) + '\n'.join(failing_checks)) - ext_patch_issues = [] # After the sanity check above, use collect_exts_file_info to resolve templates etc. correctly for ext in app.collect_exts_file_info(fetch_files=False, verify_checksums=False): try: @@ -1550,22 +1550,21 @@ def template_easyconfig_test(self, spec): # only check actual patch files, not other files being copied via the patch functionality ext_patch_full = os.path.join(specdir, ext_patch['name']) if ext_patch_full.endswith('.patch') and not os.path.isfile(ext_patch_full): - ext_patch_issues.append("Patch file %s for extension %s is missing." % (ext_patch['name'], ext_name)) + failing_checks.append("Patch file %s for extension %s is missing." % (ext_patch['name'], ext_name)) continue # verify checksum for each patch file if idx < len(patch_checksums) and os.path.exists(ext_patch_full): checksum = patch_checksums[idx] if not verify_checksum(ext_patch_full, checksum): - ext_patch_issues.append("Invalid checksum for patch %s for extension %s: %s." - % (ext_patch['name'], ext_name, checksum)) - if ext_patch_issues: - self.fail("Verification of patches for %s failed:\n%s" % (ec_fn, '\n'.join(ext_patch_issues))) + failing_checks.append("Invalid checksum for patch %s for extension %s: %s." + % (ext_patch['name'], ext_name, checksum)) # check whether all extra_options defined for used easyblock are defined extra_opts = app.extra_options() for key in extra_opts: - self.assertTrue(key in app.cfg) + if key not in app.cfg: + failing_checks.append("Missing extra_option '%s'" % key) app.close_log() os.remove(app.logfile) @@ -1603,24 +1602,32 @@ def template_easyconfig_test(self, spec): # if may get resolved using a subtoolchain, which is then hardcoded in the dumped easyconfig if key in DEPENDENCY_PARAMETERS: # number of dependencies should remain the same - self.assertEqual(len(orig_val), len(dumped_val)) + if len(orig_val) != len(dumped_val): + failing_checks.append("Length difference for %s: %s vs %s" % (key, orig_val, dumped_val)) + continue for orig_dep, dumped_dep in zip(orig_val, dumped_val): # name should always match - self.assertEqual(orig_dep[0], dumped_dep[0]) + if orig_dep[0] != dumped_dep[0]: + failing_checks.append("Different name in %s: %s vs %s" % (key, orig_dep[0], dumped_dep[0])) + desc = '%s of %s' % (orig_dep[0], key) # version should always match, or be a possibility from the version dict if isinstance(orig_dep[1], dict): - self.assertTrue(dumped_dep[1] in orig_dep[1].values()) - else: - self.assertEqual(orig_dep[1], dumped_dep[1]) + if dumped_dep[1] not in orig_dep[1].values(): + failing_checks.append("Wrong version in %s: %s vs %s" + % (desc, dumped_dep[1], orig_dep[1].values())) + elif orig_dep[1] != dumped_dep[1]: + failing_checks.append("Different version in %s: %s vs %s" % (desc, orig_dep[1], dumped_dep[1])) # 3rd value is versionsuffix; if len(dumped_dep) >= 3: # if no versionsuffix was specified in original dep spec, then dumped value should be empty string if len(orig_dep) >= 3: - self.assertEqual(dumped_dep[2], orig_dep[2]) - else: - self.assertEqual(dumped_dep[2], '') + if orig_dep[2] != dumped_dep[2]: + failing_checks.append("Different versionsuffix in %s: %s vs %s" + % (desc, orig_dep[2], dumped_dep[2])) + elif dumped_dep[2] != '': + failing_checks.append("Unexpected versionsuffix in %s: %s" % (desc, dumped_dep[2])) # 4th value is toolchain spec if len(dumped_dep) >= 4: @@ -1628,31 +1635,38 @@ def template_easyconfig_test(self, spec): # use of `True` is deprecated in favour of the more intuitive `SYSTEM` template if orig_dep[3] is True: if skip_system_template_check: - self.assertEqual(dumped_dep[3], EASYCONFIG_CONSTANTS['SYSTEM'][0]) + if dumped_dep[3] != EASYCONFIG_CONSTANTS['SYSTEM'][0]: + failing_checks.append("Should use SYSTEM in %s, found %s" + % (desc, dumped_dep[3])) else: - error_msg = ( - "use of `True` to indicate the system toolchain for dependency " - "%s is deprecated, use the `SYSTEM` template constant instead" % dumped_dep[0] + failing_checks.append( + "use of `True` to indicate the system toolchain for " + "%s is deprecated, use the `SYSTEM` template constant instead" % desc ) - self.fail(error_msg) - else: - self.assertEqual(dumped_dep[3], orig_dep[3]) + elif orig_dep[3] != dumped_dep[3]: + failing_checks.append("Different toolchain in %s: %s vs %s" + % (desc, orig_dep[3], dumped_dep[3])) else: # if a subtoolchain is specifed (only) in the dumped easyconfig, # it should *not* be the same as the parent toolchain - self.assertNotEqual(dumped_dep[3], (orig_toolchain['name'], orig_toolchain['version'])) + parent_tc = (orig_toolchain['name'], orig_toolchain['version']) + if dumped_dep[3] == parent_tc: + failing_checks.append("Explicit toolchain in %s should not be the parent toolchain (%s)" + % (desc, parent_tc)) # take into account that for some string-valued easyconfig parameters (configopts & co), # the easyblock may have injected additional values, which affects the dumped easyconfig file elif isinstance(orig_val, string_type): - error_msg = "%s value '%s' should start with '%s'" % (key, dumped_val, orig_val) - self.assertTrue(dumped_val.startswith(orig_val), error_msg) - else: - error_msg = "%s value should be equal in original and dumped easyconfig: '%s' vs '%s'" - self.assertEqual(orig_val, dumped_val, error_msg % (key, orig_val, dumped_val)) + if not dumped_val.startswith(orig_val): + failing_checks.append("%s value '%s' should start with '%s'" % (key, dumped_val, orig_val)) + elif orig_val != dumped_val: + failing_checks.append("%s value should be equal in original and dumped easyconfig: '%s' vs '%s'") + + if failing_checks: + self.fail('Verification for %s failed:\n' % os.path.basename(spec) + '\n'.join(failing_checks)) - # test passed, so set back to True - single_tests_ok = True and prev_single_tests_ok + # test passed, so set back + single_tests_ok = prev_single_tests_ok def suite(loader=None): From 42cead3daa98915b310315022984bef0b8551ffd Mon Sep 17 00:00:00 2001 From: benjamic Date: Mon, 25 Mar 2024 15:16:36 +0100 Subject: [PATCH 1118/1193] adding easyconfigs: SpectrA-1.0.1-GCCcore-12.3.0.eb --- .../s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..252cd91cd234 --- /dev/null +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb @@ -0,0 +1,34 @@ +# EasyBuild easyconfig +# +# Fred Hutchinson Cancer Research Center - Seattle - Washington - US +# https://www.fredhutch.org +# John Dey +# +easyblock = 'CMakeMake' + +name = 'SpectrA' +version = '1.0.1' + +homepage = 'https://spectralib.org/' +description = """Spectra stands for Sparse Eigenvalue Computation Toolkit as a Redesigned ARPACK. It is a C++ + library for large scale eigenvalue problems, built on top of Eigen, an open source linear algebra library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['919e3fbc8c539a321fd5a0766966922b7637cc52eb50a969241a997c733789f3'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('binutils', '2.40'), +] + +dependencies = [('Eigen', '3.4.0')] + +sanity_check_paths = { + 'files': ['include/Spectra/SymEigsSolver.h'], + 'dirs': ['include/Spectra/LinAlg', 'share/spectra/cmake'], +} + +moduleclass = 'math' From 438a7b8239eb622ef92102ec4bbbdbecfac4d3b4 Mon Sep 17 00:00:00 2001 From: benjamic Date: Mon, 25 Mar 2024 15:50:12 +0100 Subject: [PATCH 1119/1193] adding easyconfigs: GCTA-1.94.1-gfbf-2023a.eb --- .../g/GCTA/GCTA-1.94.1-gfbf-2023a.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2023a.eb b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2023a.eb new file mode 100644 index 000000000000..ce5b24cd584c --- /dev/null +++ b/easybuild/easyconfigs/g/GCTA/GCTA-1.94.1-gfbf-2023a.eb @@ -0,0 +1,70 @@ +# Author: Jasper Grimm (UoY) +# Updated to 1.94.1. J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMakeCp' + +name = 'GCTA' +version = '1.94.1' +_plink_commit = '3744540' + +homepage = 'https://yanglab.westlake.edu.cn/software/gcta/' +description = """ +GCTA (Genome-wide Complex Trait Analysis) is a software package, which was + initially developed to estimate the proportion of phenotypic variance explained + by all genome-wide SNPs for a complex trait but has been extensively extended + for many other analyses of data from genome-wide association studies (GWASs). +""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +sources = [ + { + 'source_urls': ['https://github.com/jianyangqt/gcta/archive'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': SOURCE_TAR_GZ, + }, + { + 'source_urls': ['https://github.com/zhilizheng/plink-ng/archive'], + 'download_filename': '%s.tar.gz' % _plink_commit, + 'filename': 'plink-ng-%s.tar.gz' % _plink_commit, + 'extract_cmd': "tar xzvf %%s --strip-components 1 -C gcta-%s/submods/plink-ng" % version, + }, +] +patches = [ + 'GCTA-1.94.0beta_allow-BLAS-selection.patch', + 'GCTA-1.94.0beta_lapack-compatibility.patch', +] +checksums = [ + {'GCTA-1.94.1.tar.gz': 'd38841587bef016d7885cc1b3287d7ed0373bd370674130e814e2c5e6a90bfbf'}, + {'plink-ng-3744540.tar.gz': 'a7c70c237d49d64fc1668ced373036c09b41d7c61d0b8b24b47e2fb76474455d'}, + {'GCTA-1.94.0beta_allow-BLAS-selection.patch': '320a5d82d12cf453f1396b228723ac18dc98e32bc459394dd4d712fc16b24747'}, + {'GCTA-1.94.0beta_lapack-compatibility.patch': '643282a2e2c02fc683431b673a4623a498129870431481d33d33e19a509026ce'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + # Eigen and SpectrA are header-only C++ libraries + ('Eigen', '3.4.0'), + ('SpectrA', '1.0.1'), +] + +dependencies = [ + ('Boost', '1.82.0'), + ('SQLite', '3.42.0'), + ('zstd', '1.5.5'), + ('GSL', '2.7'), +] + +preconfigopts = 'EIGEN3_INCLUDE_DIR=$EBROOTEIGEN/include SPECTRA_LIB=$EBROOTSPECTRA/include' +preconfigopts += ' BOOST_LIB=$EBROOTBOOST/include ' + +files_to_copy = [(['gcta64'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/gcta64'], + 'dirs': [], +} + +sanity_check_commands = ["gcta64 | grep -e 'Analysis started'"] + +moduleclass = 'bio' From 39dacb014e6b3f33726bd00371cc43d9a6e68d13 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 25 Mar 2024 18:50:05 +0000 Subject: [PATCH 1120/1193] Attempt to exclude broken tests, run tests a bit in parallel --- .../CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb | 29 +++++++++++-------- 1 file changed, 17 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb index 6fede877d6ac..3b798391c6c5 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb @@ -30,21 +30,26 @@ exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} _skip_tests = [ '--ignore tests/example_tests', # examples are not included '--ignore tests/cupy_tests/fft_tests/test_fft.py', # CUFFT_INTERNAL_ERROR - '--deselect test_argmax_int32_overflow', # requires more VRAM than a T4 - '--deselect test_argmin_int32_overflow', # requires more VRAM than a T4 - '--deselect test_sos_freqz_against_mp', # https://github.com/cupy/cupy/issues/8255 - '--deselect test_argsort_one_dim', # sorting somehow broken on at least T4 + # Sorting broken on at least T4 (this is troubling): + '--deselect tests/cupy_tests/sorting_tests/test_sort.py::TestArgsort_param_0_{external=False}::test_argsort_one_dim', + '--deselect tests/cupy_tests/sorting_tests/test_sort.py::TestArgsort_param_1_{external=True}::test_argsort_one_dim', + # https://github.com/cupy/cupy/issues/8255: + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sos_freqz_against_mp', # Floating point precision issues: - '--deselect TestSOSFreqz::test_sosfrez_design_cheb2_2', - '--deselect TestFirls::test_firls', - '--deselect TestButtord::test_ellip_butter', - '--deselect TestEllipord::test_bandstop', - '--deselect TestEllipord::test_fs_param', - '--deselect TestEllipord::test_ellip_butter', - '--deselect Test_bode::test_from_state_space', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sosfrez_design_cheb2_2', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_fir_filter_design.py::TestFirls::test_firls', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestButtord::test_ellip_butter', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestEllipord::test_bandstop', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestEllipord::test_fs_param', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestEllipord::test_ellip_butter', + '--deselect tests/cupy_tests/core_tests/fusion_tests/test_reduction.py::TestFusion', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_ltisys.py::Test_bode::test_from_state_space', + '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_ltisys.py::TestPlacePoles::test_real_2', '--deselect TestPartialFractionExpansion::test_residuez_general', ] +_parallel_tests = 4 # tests can require a lot of VRAM + exts_list = [ ('fastrlock', '0.8.2', { 'checksums': ['644ec9215cf9c4df8028d8511379a15d9c1af3e16d80e47f1b6fdc6ba118356a'], @@ -56,7 +61,7 @@ exts_list = [ 'cupy-%(version)s_eb_ccc.patch', ], 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && ' - 'pytest tests -k "not slow" ' + ' '.join(_skip_tests), + 'pytest -n %s tests -k "not slow" ' % _parallel_tests + ' '.join(_skip_tests), 'testinstall': True, 'checksums': [ {'cupy-13.0.0.tar.gz': '2f04e7857f692a713360dc9c3b06709806ab8404fca39b5af9721c04a2979aae'}, From b43f15f47e6b05a6f19be161feb946ebbb32b137 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 25 Mar 2024 22:52:18 +0000 Subject: [PATCH 1121/1193] adding easyconfigs: RapidJSON-1.1.0-GCCcore-12.3.0.eb --- .../RapidJSON-1.1.0-GCCcore-12.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..5efcedcf0426 --- /dev/null +++ b/easybuild/easyconfigs/r/RapidJSON/RapidJSON-1.1.0-GCCcore-12.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'RapidJSON' +version = '1.1.0' + +homepage = 'https://rapidjson.org' +description = "A fast JSON parser/generator for C++ with both SAX/DOM style API" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/Tencent/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-compiler-errors.patch'] +checksums = [ + 'bf7ced29704a1e696fbccf2a2b4ea068e7774fa37f6d7dd4039d0787f8bed98e', # v1.1.0.tar.gz + # %(name)s-%(version_major_minor)s.0_fix-compiler-errors.patch + '2e40ef6c46bf355feac16cd84faad5b7aca0ad54273117b85534b1b781f411c7', +] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.26.3'), +] + +# strip out hardcoded use of -march=native, EasyBuild should be in control of this +preconfigopts = "sed -i 's/-march=native//g' ../rapidjson-%(version)s/CMakeLists.txt && " + +sanity_check_paths = { + 'files': ['lib/pkgconfig/%(name)s.pc'], + 'dirs': ['include/%(namelower)s', 'lib/cmake', 'share'], +} + +moduleclass = 'lib' From 8c2fa957b3917bfd60b407c695d5da5cc305b971 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 25 Mar 2024 22:56:57 +0000 Subject: [PATCH 1122/1193] adding easyconfigs: maeparser-1.3.1-gompi-2023a.eb --- .../maeparser/maeparser-1.3.1-gompi-2023a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2023a.eb diff --git a/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2023a.eb b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2023a.eb new file mode 100644 index 000000000000..79e01da90b8f --- /dev/null +++ b/easybuild/easyconfigs/m/maeparser/maeparser-1.3.1-gompi-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'CMakeMake' + +name = 'maeparser' +version = '1.3.1' + +homepage = 'https://github.com/schrodinger/maeparser' +description = "maeparser is a parser for Schrodinger Maestro files." + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/schrodinger/maeparser/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a8d80f67d1b9be6e23b9651cb747f4a3200132e7d878a285119c86bf44568e36'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [('Boost', '1.82.0')] + +sanity_check_paths = { + 'files': ['lib/libmaeparser.%s' % SHLIB_EXT], + 'dirs': ['include/maeparser', 'lib/cmake'], +} + +moduleclass = 'tools' From 434c513400e575505eeeb64869351e79cc8c9cb2 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 25 Mar 2024 22:58:10 +0000 Subject: [PATCH 1123/1193] adding easyconfigs: CoordgenLibs-3.0.2-gompi-2023a.eb --- .../CoordgenLibs-3.0.2-gompi-2023a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2023a.eb diff --git a/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2023a.eb b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2023a.eb new file mode 100644 index 000000000000..425c16ca2982 --- /dev/null +++ b/easybuild/easyconfigs/c/CoordgenLibs/CoordgenLibs-3.0.2-gompi-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'CoordgenLibs' +version = '3.0.2' + +homepage = 'https://github.com/schrodinger/coordgenlibs' +description = "Schrodinger-developed 2D Coordinate Generation" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = ['https://github.com/schrodinger/coordgenlibs/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f67697434f7fec03bca150a6d84ea0e8409f6ec49d5aab43badc5833098ff4e3'] + +builddependencies = [('CMake', '3.26.3')] + +dependencies = [ + ('Boost', '1.82.0'), + ('maeparser', '1.3.1'), +] + +configopts = "-Dmaeparser_DIR=$EBROOTMAEPARSER/lib/cmake" + +# work around compiler warning treated as error by stripping out use of -Werror +prebuildopts = "sed -i 's/-Werror//g' CMakeFiles/coordgen.dir/flags.make && " + +sanity_check_paths = { + 'files': ['lib/libcoordgen.%s' % SHLIB_EXT], + 'dirs': ['include/coordgen', 'lib/cmake'], +} + +moduleclass = 'chem' From 4a3c4594785e55649f6f2ec68bc7d83090257991 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 25 Mar 2024 23:02:35 +0000 Subject: [PATCH 1124/1193] adding easyconfigs: OpenBabel-3.1.1-gompi-2023a.eb and patches: OpenBabel-3.1.1_fix-ctime.patch --- .../OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb | 63 +++++++++++++++++++ .../OpenBabel/OpenBabel-3.1.1_fix-ctime.patch | 14 +++++ 2 files changed, 77 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-ctime.patch diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb new file mode 100644 index 000000000000..f4dfce952b7e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb @@ -0,0 +1,63 @@ +name = 'OpenBabel' +version = '3.1.1' + +homepage = 'https://openbabel.org' +description = """Open Babel is a chemical toolbox designed to speak the many + languages of chemical data. It's an open, collaborative project allowing anyone + to search, convert, analyze, or store data from molecular modeling, chemistry, + solid-state materials, biochemistry, or related areas.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +# avoid failing tests on skylake and broadwell CPUs. +# remove option 'optarch' when building on CPUs that don't support AVX2 +# see also: https://github.com/openbabel/openbabel/issues/2138 +toolchainopts = {'pic': True, 'optarch': 'mavx2'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%%(namelower)s-%s.tar.gz' % version.replace('.', '-')] +patches = [ + # Fix test failure with Python 3 + # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch + 'OpenBabel-3.1.1_fix-distgeom-test.patch', + 'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch', + 'OpenBabel-3.1.1_fix-ctime.patch', +] +checksums = [ + {'openbabel-3-1-1.tar.gz': 'c97023ac6300d26176c97d4ef39957f06e68848d64f1a04b0b284ccff2744f02'}, + {'OpenBabel-3.1.1_fix-distgeom-test.patch': '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd'}, + {'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch': + 'cc0396b38a78ef70c869cd93887210c64d6f4293c016aec9269b5a0230fdb51c'}, + {'OpenBabel-3.1.1_fix-ctime.patch': '79c5b7f65d99f42f039b3942bc52bae7363f3742a7e2564b5b7bfb29aa105b36'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('SWIG', '4.1.1'), +] +dependencies = [ + ('Python', '3.11.3'), + ('zlib', '1.2.13'), + ('libxml2', '2.11.4'), + ('Eigen', '3.4.0'), + ('RapidJSON', '1.1.0'), + ('cairo', '1.17.8'), # optional: for .png output + ('Boost', '1.82.0'), + ('maeparser', '1.3.1'), + ('CoordgenLibs', '3.0.2'), +] + +configopts = '-DBoost_INCLUDE_DIR=$EBROOTBOOST/include -DBoost_LIBRARY_DIR_RELEASE=$EBROOTBOOST/lib ' +# Enable support for OpenMP compilation of forcefield code (optional) +configopts += '-DENABLE_OPENMP=ON ' + +# OpenBabel-3.1.1 creates directories named 3.1.0, which leads to BABEL_LIBDIR and BABEL_DATDIR +# (set in the easyblock) having invalid values. Work around this with some symlinks. +postinstallcmds = [ + 'ln -s %(installdir)s/lib/openbabel/3.1.0 %(installdir)s/lib/openbabel/%(version)s', + 'ln -s %(installdir)s/share/openbabel/3.1.0 %(installdir)s/share/openbabel/%(version)s', +] + +pretestopts = 'cp lib/_openbabel.%s %%(builddir)s/openbabel-*/scripts/python/openbabel/ && ' % SHLIB_EXT +runtest = 'test' + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-ctime.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-ctime.patch new file mode 100644 index 000000000000..85457db32847 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_fix-ctime.patch @@ -0,0 +1,14 @@ + included +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/openbabel-openbabel-3-1-1.orig/include/openbabel/obutil.h b/openbabel-openbabel-3-1-1/include/openbabel/obutil.h +index 233ab0b..4ff35f0 100644 +--- a/openbabel-openbabel-3-1-1.orig/include/openbabel/obutil.h ++++ b/openbabel-openbabel-3-1-1/include/openbabel/obutil.h +@@ -37,6 +37,7 @@ GNU General Public License for more details. + #endif + + #include ++#include + + #ifndef M_PI + #define M_PI 3.14159265358979323846 From 79716ea4a5cacd079184e5514baa5cd189792635 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 26 Mar 2024 00:49:19 +0000 Subject: [PATCH 1125/1193] Add missing deps to Ruby easyconfigs --- easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb | 6 +++++- easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb | 6 +++++- easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb | 6 +++++- easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb | 6 +++++- easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb | 7 +++---- easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb | 7 +++---- 6 files changed, 26 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb index f02f5356791e..1fdde110226b 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-10.3.0.eb @@ -12,7 +12,11 @@ source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['369825db2199f6aeef16b408df6a04ebaddb664fb9af0ec8c686b0ce7ab77727'] -builddependencies = [('binutils', '2.36.1')] +dependencies = [ + ('binutils', '2.36.1'), # needed for gem + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', SYSTEM), +] exts_default_options = { 'source_urls': ['https://rubygems.org/downloads/'], diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb index dc6ba8f38af0..02f29a4634f0 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.1-GCCcore-11.2.0.eb @@ -12,7 +12,11 @@ source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['369825db2199f6aeef16b408df6a04ebaddb664fb9af0ec8c686b0ce7ab77727'] -builddependencies = [('binutils', '2.37')] +dependencies = [ + ('binutils', '2.37'), # needed for gem + ('zlib', '1.2.11'), + ('OpenSSL', '1.1', '', SYSTEM), +] exts_default_options = { 'source_urls': ['https://rubygems.org/downloads/'], diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb index 864a9112c6a2..8fd64d2779df 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb @@ -12,7 +12,11 @@ source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac'] -builddependencies = [('binutils', '2.38')] +dependencies = [ + ('binutils', '2.38'), # needed for gem + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] exts_default_options = { 'source_urls': ['https://rubygems.org/downloads/'], diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb index 13a6f73ff7b4..510f94f68680 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb @@ -12,7 +12,11 @@ source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['9afc6380a027a4fe1ae1a3e2eccb6b497b9c5ac0631c12ca56f9b7beb4848776'] -builddependencies = [('binutils', '2.38')] +dependencies = [ + ('binutils', '2.38'), # needed for gem + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] exts_default_options = { 'source_urls': ['https://rubygems.org/downloads/'], diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb index 0f53d7206f95..6b8254f9c1fc 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.2.2-GCCcore-12.2.0.eb @@ -12,11 +12,10 @@ source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['96c57558871a6748de5bc9f274e93f4b5aad06cd8f37befa0e8d94e7b8a423bc'] -builddependencies = [ - ('binutils', '2.39'), -] - dependencies = [ + ('binutils', '2.39'), # needed for gem + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), ('libyaml', '0.2.5'), ] diff --git a/easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb index 3059ed91825a..9b9a28660c71 100644 --- a/easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.3.0-GCCcore-12.3.0.eb @@ -12,11 +12,10 @@ source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['96518814d9832bece92a85415a819d4893b307db5921ae1f0f751a9a89a56b7d'] -builddependencies = [ - ('binutils', '2.40'), -] - dependencies = [ + ('binutils', '2.40'), # needed for gem + ('zlib', '1.2.13'), + ('OpenSSL', '1.1', '', SYSTEM), ('libyaml', '0.2.5'), ] From 894ab7d8af6ea829562add1b44636e62cc55bf8d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 26 Mar 2024 10:45:48 +0000 Subject: [PATCH 1126/1193] Exclude tests, fix style --- .../CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb | 17 +++++++++++------ 1 file changed, 11 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb index 3b798391c6c5..20d9321f0c59 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb @@ -31,21 +31,26 @@ _skip_tests = [ '--ignore tests/example_tests', # examples are not included '--ignore tests/cupy_tests/fft_tests/test_fft.py', # CUFFT_INTERNAL_ERROR # Sorting broken on at least T4 (this is troubling): - '--deselect tests/cupy_tests/sorting_tests/test_sort.py::TestArgsort_param_0_{external=False}::test_argsort_one_dim', - '--deselect tests/cupy_tests/sorting_tests/test_sort.py::TestArgsort_param_1_{external=True}::test_argsort_one_dim', + '--deselect tests/cupy_tests/' + 'sorting_tests/test_sort.py::TestArgsort_param_0_{external=False}::test_argsort_one_dim', + '--deselect tests/cupy_tests/' + 'sorting_tests/test_sort.py::TestArgsort_param_1_{external=True}::test_argsort_one_dim', # https://github.com/cupy/cupy/issues/8255: - '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sos_freqz_against_mp', + '--deselect tests/cupyx_tests/' + 'scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sos_freqz_against_mp', # Floating point precision issues: - '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sosfrez_design_cheb2_2', + '--deselect tests/cupy_tests/core_tests/fusion_tests/test_reduction.py::TestFusion', + '--deselect tests/cupyx_tests/' + 'scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sosfrez_design_cheb2_2', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_fir_filter_design.py::TestFirls::test_firls', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestButtord::test_ellip_butter', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestEllipord::test_bandstop', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestEllipord::test_fs_param', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestEllipord::test_ellip_butter', - '--deselect tests/cupy_tests/core_tests/fusion_tests/test_reduction.py::TestFusion', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_ltisys.py::Test_bode::test_from_state_space', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_ltisys.py::TestPlacePoles::test_real_2', - '--deselect TestPartialFractionExpansion::test_residuez_general', + '--deselect tests/cupyx_tests/' + 'scipy_tests/signal_tests/test_polyutils.py::TestPartialFractionExpansion::test_residuez_general', ] _parallel_tests = 4 # tests can require a lot of VRAM From 332559fcd10064a3dd9a8afdc36d9456987d2527 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 26 Mar 2024 12:14:08 +0000 Subject: [PATCH 1127/1193] adding easyconfigs: code-server-4.22.1.eb --- .../c/code-server/code-server-4.22.1.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/c/code-server/code-server-4.22.1.eb diff --git a/easybuild/easyconfigs/c/code-server/code-server-4.22.1.eb b/easybuild/easyconfigs/c/code-server/code-server-4.22.1.eb new file mode 100644 index 000000000000..eec7338f4e79 --- /dev/null +++ b/easybuild/easyconfigs/c/code-server/code-server-4.22.1.eb @@ -0,0 +1,20 @@ +name = 'code-server' +version = '4.22.1' + +homepage = 'https://github.com/coder/code-server' +description = """Run VS Code on any machine anywhere and access it in the browser.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/coder/code-server/releases/download/v%(version)s/'] +sources = ['code-server-%(version)s-linux-%(mapped_arch)s.tar.gz'] +checksums = [ + { + 'code-server-%(version)s-linux-amd64.tar.gz': + 'ec40994776bbcb958d9efb328c1b61038167a8d5473c9c841b25df24578dc420', + 'code-server-%(version)s-linux-arm64.tar.gz': + '44c3bc84a37efa9d4e2c14ce72024b2cb83c2034ed4f29f50eb595fb0f2bc4b3', + } +] + +moduleclass = 'tools' From 40901b3a1c723b1abfcd6b7e5cc7e0d9cc49ea21 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 26 Mar 2024 12:15:23 +0000 Subject: [PATCH 1128/1193] Fix indent --- .../c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb index 20d9321f0c59..4d1e02157e5b 100644 --- a/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/CuPy/CuPy-13.0.0-foss-2023a-CUDA-12.1.1.eb @@ -32,16 +32,16 @@ _skip_tests = [ '--ignore tests/cupy_tests/fft_tests/test_fft.py', # CUFFT_INTERNAL_ERROR # Sorting broken on at least T4 (this is troubling): '--deselect tests/cupy_tests/' - 'sorting_tests/test_sort.py::TestArgsort_param_0_{external=False}::test_argsort_one_dim', + 'sorting_tests/test_sort.py::TestArgsort_param_0_{external=False}::test_argsort_one_dim', '--deselect tests/cupy_tests/' - 'sorting_tests/test_sort.py::TestArgsort_param_1_{external=True}::test_argsort_one_dim', + 'sorting_tests/test_sort.py::TestArgsort_param_1_{external=True}::test_argsort_one_dim', # https://github.com/cupy/cupy/issues/8255: '--deselect tests/cupyx_tests/' - 'scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sos_freqz_against_mp', + 'scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sos_freqz_against_mp', # Floating point precision issues: '--deselect tests/cupy_tests/core_tests/fusion_tests/test_reduction.py::TestFusion', '--deselect tests/cupyx_tests/' - 'scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sosfrez_design_cheb2_2', + 'scipy_tests/signal_tests/test_filter_design.py::TestSOSFreqz::test_sosfrez_design_cheb2_2', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_fir_filter_design.py::TestFirls::test_firls', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestButtord::test_ellip_butter', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_iir_filter_design.py::TestEllipord::test_bandstop', @@ -50,7 +50,7 @@ _skip_tests = [ '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_ltisys.py::Test_bode::test_from_state_space', '--deselect tests/cupyx_tests/scipy_tests/signal_tests/test_ltisys.py::TestPlacePoles::test_real_2', '--deselect tests/cupyx_tests/' - 'scipy_tests/signal_tests/test_polyutils.py::TestPartialFractionExpansion::test_residuez_general', + 'scipy_tests/signal_tests/test_polyutils.py::TestPartialFractionExpansion::test_residuez_general', ] _parallel_tests = 4 # tests can require a lot of VRAM From abbf096ec85afd1b76519512503e9daabbc8f821 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 26 Mar 2024 13:08:49 +0000 Subject: [PATCH 1129/1193] Fix cuSPARSELt for aarch64 --- .../c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb | 2 +- .../c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb index 4c5045f553b0..fc0a8cf610bd 100644 --- a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.3.0.3-CUDA-11.4.1.eb @@ -10,7 +10,7 @@ which at least one operand is a sparse matrix""" toolchain = SYSTEM -local_arch = {'arm64': 'sbsa'}.get(ARCH, ARCH) +local_arch = {'arm64': 'sbsa', 'aarch64': 'sbsa'}.get(ARCH, ARCH) source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse_lt/linux-%s/' % local_arch] sources = ['libcusparse_lt-linux-%s-%%(version)s-archive.tar.xz' % local_arch] checksums = [{ diff --git a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb index e64ca7ff0135..80bdd6b93c6a 100644 --- a/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/c/cuSPARSELt/cuSPARSELt-0.6.0.6-CUDA-12.1.1.eb @@ -10,14 +10,14 @@ which at least one operand is a sparse matrix""" toolchain = SYSTEM -local_arch = {'arm64': 'sbsa'}.get(ARCH, ARCH) +local_arch = {'arm64': 'sbsa', 'aarch64': 'sbsa'}.get(ARCH, ARCH) source_urls = ['https://developer.download.nvidia.com/compute/cusparselt/redist/libcusparse_lt/linux-%s/' % local_arch] sources = ['libcusparse_lt-linux-%s-%%(version)s-archive.tar.xz' % local_arch] checksums = [{ 'libcusparse_lt-linux-x86_64-%(version)s-archive.tar.xz': 'da20d7a6d7a6674cb6e991439eaacd4661631c71a2f1026c41fba115c5c9c8b5', 'libcusparse_lt-linux-sbsa-%(version)s-archive.tar.xz': - '46b258c2c333f7324e03bdf6b13576be6153b1218fb531025631650e36515f45', + '51db8182444b4e2c125397ea95e4996c022ef791a87ce7a7389204e77617297f', }] dependencies = [('CUDA', '12.1.1')] From e3736cee5331b0b5645d08441e41a0347b85c5d8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 26 Mar 2024 17:06:13 +0100 Subject: [PATCH 1130/1193] adding easyconfigs: bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb --- ...bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb diff --git a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb new file mode 100644 index 000000000000..42667d116bac --- /dev/null +++ b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'bwa-mem2' +version = '2.2.1' + +homepage = 'https://github.com/bwa-mem2/bwa-mem2' +description = """ +The tool bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It +produces alignment identical to bwa and is ~1.3-3.1x faster depending on the +use-case, dataset and the running machine.""" + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} +toolchainopts = {'pic': True, 'oneapi': False} + +sources = [{ + 'filename': '%(name)s-v%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/bwa-mem2', + 'repo_name': name, + 'tag': 'v%(version)s', + 'recursive': True, + }, +}] +checksums = [None] + +build_cmd_targets = 'multi' + +files_to_copy = [(['bwa-mem2*'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['bwa-mem2 version'] + +moduleclass = 'bio' From 012a8f662716b3976109cc5e8b37eaafbf7769d2 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 26 Mar 2024 18:03:06 +0100 Subject: [PATCH 1131/1193] Fix from https://github.com/easybuilders/easybuild-easyconfigs/pull/19974 should also be applied to 12.3.0 and 13.1.0 --- easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb index 94a5b7eb7f3c..936ed6ca40bc 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -36,7 +36,7 @@ patches = [ 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', - 'GCCcore-12.x_riscv_multiarch_support.patch', + 'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch', ] checksums = [ {'gcc-12.3.0.tar.gz': '11275aa7bb34cd8ab101d01b341015499f8d9466342a2574ece93f954d92273b'}, @@ -53,7 +53,8 @@ checksums = [ 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, - {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, + {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': + 'e1d63e04bf494a2f79346ac7454372f117b63288cc18c68876a5b8bdc453cf88'}, ] builddependencies = [ From 98bd923fd7de392eedda564991d69cdb2d4be466 Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 26 Mar 2024 18:05:09 +0100 Subject: [PATCH 1132/1193] {vis}[foss/2021b,foss/2022a,foss/2023a] fix napari v0.4.1{5,8} shebang --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 2 ++ easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb | 2 ++ easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb | 2 ++ 3 files changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb index 18337a90cfdb..e4034ea4140f 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -122,6 +122,8 @@ exts_list = [ }), ] +fix_python_shebang_for = ['bin/napari'] + sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb index 261c09a98914..259846e68e29 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2022a.eb @@ -123,6 +123,8 @@ exts_list = [ }), ] +fix_python_shebang_for = ['bin/napari'] + sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb index 91cd347f95bd..713e2ef6492d 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.18-foss-2023a.eb @@ -115,6 +115,8 @@ exts_list = [ }), ] +fix_python_shebang_for = ['bin/napari'] + sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], From c5ba5a759244e374f55b6f8649032f1d88b46ed6 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 26 Mar 2024 18:07:20 +0100 Subject: [PATCH 1133/1193] Actually add 13.1.0... --- easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb index 4d99522c9d57..38f2bf7f16a1 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -35,7 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', - 'GCCcore-12.x_riscv_multiarch_support.patch', + 'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch', ] checksums = [ {'gcc-13.1.0.tar.gz': 'bacd4c614d8bd5983404585e53478d467a254249e0f1bb747c8bc6d787bd4fa2'}, @@ -50,7 +50,8 @@ checksums = [ {'GCCcore-12.1.0_fix-double-destruct.patch': '2e09c125318b6c15ec60f1807d77fb7d1f32b64a4e5d1c9a3da89ba2ca738d35'}, {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, - {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, + {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': + 'e1d63e04bf494a2f79346ac7454372f117b63288cc18c68876a5b8bdc453cf88'}, ] builddependencies = [ From a085768554b9eaddfdaa78e44a1e2bc7e1dc0abb Mon Sep 17 00:00:00 2001 From: Lars Viklund Date: Tue, 26 Mar 2024 19:59:05 +0100 Subject: [PATCH 1134/1193] Use existing Pysam-0.22.0 easyconfig --- .../p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb | 31 ------------------- 1 file changed, 31 deletions(-) delete mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb deleted file mode 100644 index 736831665244..000000000000 --- a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.0-GCC-12.3.0.eb +++ /dev/null @@ -1,31 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'Pysam' -version = '0.22.0' - -homepage = 'https://github.com/pysam-developers/pysam' -description = """Pysam is a python module for reading and manipulating Samfiles. - It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" - -toolchain = {'name': 'GCC', 'version': '12.3.0'} - -source_urls = ['https://github.com/pysam-developers/pysam/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['61b3377c5f889ddc6f6979912c3bb960d7e08407dada9cb38f13955564ea036f'] - -dependencies = [ - ('Python', '3.11.3'), - ('Python-bundle-PyPI', '2023.06'), - ('ncurses', '6.4'), - ('cURL', '8.0.1'), - ('XZ', '5.4.2'), -] - -# https://github.com/pysam-developers/pysam/issues/1146#issuecomment-1309421979 -preinstallopts = """export CFLAGS="-fPIC $CFLAGS" && """ -download_dep_fail = True -use_pip = True - -sanity_pip_check = True - -moduleclass = 'bio' From 5db39866520b1ffa40be855d97eb0ed90eb4b592 Mon Sep 17 00:00:00 2001 From: casparl Date: Tue, 26 Mar 2024 20:20:46 +0100 Subject: [PATCH 1135/1193] Readd accidentally removed patch --- easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb | 2 ++ easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb index 936ed6ca40bc..222f1b68dc89 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-12.3.0.eb @@ -36,6 +36,7 @@ patches = [ 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-12.2.0_improve-cuda-compatibility.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', 'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch', ] checksums = [ @@ -53,6 +54,7 @@ checksums = [ 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, {'GCCcore-12.2.0_improve-cuda-compatibility.patch': '91d00122554b56381592229398540e63baa26d03633292a7fdf338407a4a62d5'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': 'e1d63e04bf494a2f79346ac7454372f117b63288cc18c68876a5b8bdc453cf88'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb index 38f2bf7f16a1..d44266b72bfa 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-12.1.0_fix-double-destruct.patch', 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', + 'GCCcore-12.x_riscv_multiarch_support.patch', 'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch', ] checksums = [ @@ -50,6 +51,7 @@ checksums = [ {'GCCcore-12.1.0_fix-double-destruct.patch': '2e09c125318b6c15ec60f1807d77fb7d1f32b64a4e5d1c9a3da89ba2ca738d35'}, {'GCCcore-12.2.0_fix-avx512-misoptimization.patch': 'bb3db707727b9975b0005346ef04230a96b3ad896f004a34262a82a244b5d436'}, + {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': 'e1d63e04bf494a2f79346ac7454372f117b63288cc18c68876a5b8bdc453cf88'}, ] From 91912d3228b4f2cdf9f05072eecf23cb6296847a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 27 Mar 2024 09:28:03 +0100 Subject: [PATCH 1136/1193] NSS has a missing builddependency on Perl --- easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb index 98dcf8eb5b53..bc0a97c325dd 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.94-GCCcore-13.2.0.eb @@ -22,7 +22,10 @@ checksums = [ '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, ] -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), + ('Perl', '5.38.0'), +] dependencies = [ ('NSPR', '4.35'), From d9b9ebbb80332bc50dde524fab010281aa60cb3a Mon Sep 17 00:00:00 2001 From: benjamic Date: Wed, 27 Mar 2024 09:30:45 +0100 Subject: [PATCH 1137/1193] adding easyconfigs: PLINK-2.00a3.7-gfbf-2023a.eb --- .../p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb diff --git a/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb new file mode 100644 index 000000000000..c6d897b040be --- /dev/null +++ b/easybuild/easyconfigs/p/PLINK/PLINK-2.00a3.7-gfbf-2023a.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'PLINK' +version = '2.00a3.7' + +homepage = 'https://www.cog-genomics.org/plink/2.0/' +description = """PLINK is a free, open-source whole genome association analysis toolset, +designed to perform a range of basic, large-scale analyses in a computationally +efficient manner.""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + + +dependencies = [ + ('zlib', '1.2.13'), + ('zstd', '1.5.5'), + ('libdeflate', '1.18'), +] + +default_easyblock = 'MakeCp' + +default_component_specs = { + 'source_urls': ['https://github.com/chrchang/plink-ng/archive/refs/tags/'], + 'sources': ['v%s.tar.gz' % version], + 'skipsteps': ['configure'], +} + +components = [ + ('PLINK1', '1.90', { + 'checksums': ['145717350205f5562a01292a0fcbd617b7500758f20cad0393c7cc54665a614e'], + 'start_dir': '%s-ng-%s/1.9' % (name.lower(), version), + 'buildopts': ( + 'CFLAGS="${CFLAGS} -DDYNAMIC_ZLIB" CXXFLAGS="${CXXFLAGS} -DDYNAMIC_ZLIB" ' + 'LDFLAGS="${LDFLAGS} -lm -lpthread -ldl" BLASFLAGS="${LIBBLAS}" ZLIB="-L$EBROOTZLIB/lib -lz"' + ), + 'files_to_copy': [(['plink'], 'bin')], + }), + ('PLINK2', version, { + 'checksums': ['145717350205f5562a01292a0fcbd617b7500758f20cad0393c7cc54665a614e'], + 'start_dir': '%s-ng-%s/2.0' % (name.lower(), version), + 'prebuildopts': "sed -i 's/(OBJ)/(OBJ_NO_ZSTD)/g' Makefile && sed -i '9,19d' Makefile.src && ", + 'buildopts': ( + 'BASEFLAGS="-g -DNDEBUG -DZSTD_MULTITHREAD" BLASFLAGS64="$LIBBLAS" ZSTD="-lzstd -ldeflate" ' + 'CINCLUDE="-Isimde" CINCLUDE2="-I../simde"' + ), + 'files_to_copy': [(['bin/*'], 'bin')], + }), +] + +# run tests (<1h) +postinstallcmds = ["cd Tests && sh run_tests.sh %(installdir)s/bin"] + +sanity_check_paths = { + 'files': ['bin/plink', 'bin/plink2', 'bin/pgen_compress'], + 'dirs': [], +} + +moduleclass = 'bio' From 2255e6ac8ce85386cc01f934365595ce8c05c84d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 27 Mar 2024 09:36:43 +0100 Subject: [PATCH 1138/1193] fix missing builddep on Perl for NSS-3.89.1 too --- easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb index 7b9beb5c0864..9e06f5845d34 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.89.1-GCCcore-12.3.0.eb @@ -22,7 +22,10 @@ checksums = [ '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, ] -builddependencies = [('binutils', '2.40')] +builddependencies = [ + ('binutils', '2.40'), + ('Perl', '5.36.1'), +] dependencies = [ ('NSPR', '4.35'), From af201c75e00ad4903783db5ba73c23bd1a623a77 Mon Sep 17 00:00:00 2001 From: benjamic Date: Wed, 27 Mar 2024 09:44:05 +0100 Subject: [PATCH 1139/1193] Updating source_urls --- .../easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb index 252cd91cd234..a98348615154 100644 --- a/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/s/SpectrA/SpectrA-1.0.1-GCCcore-12.3.0.eb @@ -15,7 +15,8 @@ description = """Spectra stands for Sparse Eigenvalue Computation Toolkit as a R toolchain = {'name': 'GCCcore', 'version': '12.3.0'} -source_urls = ['https://github.com/yixuan/spectra/archive/refs/tags'] +github_account = 'yixuan' +source_urls = [GITHUB_LOWER_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['919e3fbc8c539a321fd5a0766966922b7637cc52eb50a969241a997c733789f3'] From 1e0bf09bf0b968692aeacfeb2eba5cbc2352bd0d Mon Sep 17 00:00:00 2001 From: Duncan Mortimer Date: Wed, 27 Mar 2024 13:27:05 +0000 Subject: [PATCH 1140/1193] Add easyconfig for Miniforge3 --- .../m/Miniforge3/Miniforge3-24.1.2-0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniforge3/Miniforge3-24.1.2-0.eb diff --git a/easybuild/easyconfigs/m/Miniforge3/Miniforge3-24.1.2-0.eb b/easybuild/easyconfigs/m/Miniforge3/Miniforge3-24.1.2-0.eb new file mode 100644 index 000000000000..5ab8d2c7a11c --- /dev/null +++ b/easybuild/easyconfigs/m/Miniforge3/Miniforge3-24.1.2-0.eb @@ -0,0 +1,26 @@ +easyblock = 'EB_Mamba' + +name = 'Miniforge3' +version = '24.1.2-0' + +homepage = 'https://github.com/conda-forge/miniforge' +description = """Miniforge is a free minimal installer for conda and Mamba specific + to conda-forge.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/conda-forge/miniforge/releases/download/%(version)s'] +local_arch = {'arm64': 'aarch64'}.get(ARCH, ARCH) +sources = ['%%(name)s-%%(version)s-Linux-%s.sh' % local_arch] +checksums = [ + { + '%(name)s-%(version)s-Linux-x86_64.sh': + 'dbadb808edf4da00af35d888d3eeebbfdce71972b60bf4b16dbacaee2ab57f28', + '%(name)s-%(version)s-Linux-ppc64le.sh': + '858b9acbcca1e3f67298a56095f547f2c540d79e1020918cf0d8d6a8af407542', + '%(name)s-py312_%(version)s-Linux-aarch64.sh': + 'f881e2fa24aa898c25fac3250ccb213e8b892fdd95851f000dce93c419e8f89a', + } +] + +moduleclass = 'lang' From f0ff73534faaa21764c758c7b50c73d735de4eb1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 27 Mar 2024 15:47:55 +0100 Subject: [PATCH 1141/1193] adding easyconfigs: vsc-mympirun-5.4.0.eb --- .../v/vsc-mympirun/vsc-mympirun-5.4.0.eb | 64 +++++++++++++++++++ 1 file changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.4.0.eb diff --git a/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.4.0.eb b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.4.0.eb new file mode 100644 index 000000000000..e9340780aaba --- /dev/null +++ b/easybuild/easyconfigs/v/vsc-mympirun/vsc-mympirun-5.4.0.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'vsc-mympirun' +version = '5.4.0' + +homepage = 'https://github.com/hpcugent/vsc-mympirun' +description = """mympirun is a tool to make it easier for users of HPC clusters to +run MPI programs with good performance.""" + +# we build this to work with every python version +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +use_pip = False + +exts_list = [ + ('setuptools', '41.6.0', { + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['6afa61b391dcd16cb8890ec9f66cc4015a8a31a6e1c2b4e0c464514be1a3d722'], + }), + ('future', '1.0.0', { + 'checksums': ['bd2968309307861edae1458a4f8a4f3598c03be43b97521076aebf5d94c07b05'], + }), + ('pbr', '6.0.0', { + 'checksums': ['d1377122a5a00e2f940ee482999518efe16d745d423a670c27773dfbc3c9a7d9'], + }), + ('funcsigs', '1.0.2', { + 'checksums': ['a7bb0f2cf3a3fd1ab2732cb49eba4252c2af4240442415b4abce3b87022a8f50'], + }), + ('mock', '5.1.0', { + 'checksums': ['5e96aad5ccda4718e0a229ed94b2024df75cc2d55575ba5762d31f5767b8767d'], + }), + ('IPy', '1.01', { + 'modulename': 'IPy', + 'checksums': ['edeca741dea2d54aca568fa23740288c3fe86c0f3ea700344571e9ef14a7cc1a'], + }), + ('vsc-install', '0.20.1', { + 'modulename': 'vsc.install', + 'checksums': ['2eba4768205bf61c0845666a8ddb4eb0e2697e433d1800d75be8310159483cac'], + }), + ('vsc-base', '3.5.9', { + 'modulename': 'vsc.utils', + 'checksums': ['05015bf13c921e6e09fedce774e50fa4c7e71247e65666189aef212206af3fb6'], + }), + (name, version, { + 'modulename': False, + 'checksums': ['3321106e4b6ba0b09634309003ff6f5a0e5e51d4419650ab826a46c150e05c6d'], + }), +] + +# we ship something in bin/fake +modextrapaths = {'PATH': 'bin/fake'} + +sanity_check_paths = { + 'files': ['bin/mympirun', 'bin/mypmirun', 'bin/mympisanity', 'bin/mytasks'], + 'dirs': ['bin/fake'], +} +sanity_check_commands = ["mympirun --help"] + +# can't enable 'pip check' since pip may not be installed in OS +sanity_pip_check = False + +moduleclass = 'tools' From 65f9ed0accaa1174ac942e46f7d60d8b9c108092 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Wed, 27 Mar 2024 16:18:08 +0100 Subject: [PATCH 1142/1193] Lower prompt-toolkit to GCCcore --- ...s-2022b.eb => prompt-toolkit-3.0.36-GCCcore-12.2.0.eb} | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/p/prompt-toolkit/{prompt-toolkit-3.0.36-foss-2022b.eb => prompt-toolkit-3.0.36-GCCcore-12.2.0.eb} (80%) diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-foss-2022b.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.2.0.eb similarity index 80% rename from easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-foss-2022b.eb rename to easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.2.0.eb index 5bbf62b8f68f..45f18896d75d 100644 --- a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-foss-2022b.eb +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-12.2.0.eb @@ -7,11 +7,11 @@ homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' description = """prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications.""" -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -dependencies = [ - ('Python', '3.10.8'), -] +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] From 39f88509089bab9e04033367a5f262e0f8efe6cc Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 27 Mar 2024 15:51:09 +0000 Subject: [PATCH 1143/1193] =?UTF-8?q?Added=20=C3=85ke=20patch=20to=20use?= =?UTF-8?q?=20RapidJSON-1.1.0?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- .../OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb | 2 + .../OpenBabel-3.1.1_disable_bad_tests.patch | 519 ++++++++++++++++++ 2 files changed, 521 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_disable_bad_tests.patch diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb index f4dfce952b7e..d5296c7159e4 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb @@ -20,6 +20,7 @@ patches = [ # Ref: https://github.com/openbabel/openbabel/commit/7de27f309db5f7ec026ef5c5235e5b33bf7d1a85.patch 'OpenBabel-3.1.1_fix-distgeom-test.patch', 'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch', + 'OpenBabel-3.1.1_disable_bad_tests.patch', 'OpenBabel-3.1.1_fix-ctime.patch', ] checksums = [ @@ -27,6 +28,7 @@ checksums = [ {'OpenBabel-3.1.1_fix-distgeom-test.patch': '8d7687eb49142bb5ba2997cf90805b42480f313515c44b3912a9f826aaf4fbcd'}, {'OpenBabel-3.1.1_fix-CoordgenLibs-no-templates.patch': 'cc0396b38a78ef70c869cd93887210c64d6f4293c016aec9269b5a0230fdb51c'}, + {'OpenBabel-3.1.1_disable_bad_tests.patch': 'a88f54d834cc181ac66d98f0040dbfadabe9d3ef1bee7305f8e73c31c20f9de2'}, {'OpenBabel-3.1.1_fix-ctime.patch': '79c5b7f65d99f42f039b3942bc52bae7363f3742a7e2564b5b7bfb29aa105b36'}, ] diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_disable_bad_tests.patch b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_disable_bad_tests.patch new file mode 100644 index 000000000000..b0814fe61113 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1_disable_bad_tests.patch @@ -0,0 +1,519 @@ +Disable tests that do textual compare of numerical values. +Some of these values may vary on the last one or two digits. + +Åke Sandgren, 2024-03-27 +diff -ru openbabel-openbabel-3-1-1.orig/test/testobconv_writers.py openbabel-openbabel-3-1-1/test/testobconv_writers.py +--- openbabel-openbabel-3-1-1.orig/test/testobconv_writers.py 2020-05-08 17:38:02.000000000 +0200 ++++ openbabel-openbabel-3-1-1/test/testobconv_writers.py 2024-03-27 08:19:01.012651395 +0100 +@@ -669,81 +669,82 @@ + """) + + # cdjson -- ChemDoodle JSON +-class TestCDJSON(unittest.TestCase, WriteMixin): +- fmt = "cdjson" +- maxDiff = None +- def test_default(self): +- self.assertWriters(self.fmt, """\ +-{ +- "m": [ +- { +- "a": [ +- { +- "x": 31.692, +- "y": -0.498 +- }, +- { +- "x": 31.406, +- "y": 19.51 +- }, +- { +- "x": 48.59, +- "y": 29.764 +- }, +- { +- "x": 66.062, +- "y": 20.008 +- }, +- { +- "x": 66.35, +- "y": -0.0 +- }, +- { +- "x": 0.0, +- "y": 0.0 +- }, +- { +- "x": -20.009999999999999, +- "y": 0.10200000000000001, +- "l": 8 +- } +- ], +- "b": [ +- { +- "b": 0, +- "e": 5, +- "o": 2 +- }, +- { +- "b": 0, +- "e": 1 +- }, +- { +- "b": 1, +- "e": 2, +- "o": 2 +- }, +- { +- "b": 2, +- "e": 3 +- }, +- { +- "b": 3, +- "e": 4, +- "o": 2 +- }, +- { +- "b": 4, +- "e": 5 +- }, +- { +- "b": 5, +- "e": 6 +- } +- ] +- } +- ] +-}""") ++## Should never do pure textual compare of numerical values. ++## class TestCDJSON(unittest.TestCase, WriteMixin): ++## fmt = "cdjson" ++## maxDiff = None ++## def test_default(self): ++## self.assertWriters(self.fmt, """\ ++## { ++## "m": [ ++## { ++## "a": [ ++## { ++## "x": 31.692, ++## "y": -0.498 ++## }, ++## { ++## "x": 31.406, ++## "y": 19.51 ++## }, ++## { ++## "x": 48.59, ++## "y": 29.764 ++## }, ++## { ++## "x": 66.062, ++## "y": 20.008 ++## }, ++## { ++## "x": 66.35, ++## "y": -0.0 ++## }, ++## { ++## "x": 0.0, ++## "y": 0.0 ++## }, ++## { ++## "x": -20.009999999999999, ++## "y": 0.10200000000000001, ++## "l": 8 ++## } ++## ], ++## "b": [ ++## { ++## "b": 0, ++## "e": 5, ++## "o": 2 ++## }, ++## { ++## "b": 0, ++## "e": 1 ++## }, ++## { ++## "b": 1, ++## "e": 2, ++## "o": 2 ++## }, ++## { ++## "b": 2, ++## "e": 3 ++## }, ++## { ++## "b": 3, ++## "e": 4, ++## "o": 2 ++## }, ++## { ++## "b": 4, ++## "e": 5 ++## }, ++## { ++## "b": 5, ++## "e": 6 ++## } ++## ] ++## } ++## ] ++## }""") + + ## # cdxml -- ChemDraw CDXML format + ## XXX fails on an unpatched system +@@ -2754,179 +2755,180 @@ + """) + + # pcjson -- PubChem JSON +-class TestPCJSON(unittest.TestCase, WriteMixin): +- fmt = "pcjson" +- maxDiff = None +- def test_default(self): +- self.assertWriters(self.fmt, """\ +-{ +- "PC_Compounds": [ +- { +- "atoms": { +- "aids": [ +- 1, +- 2, +- 3, +- 4, +- 5, +- 6, +- 7, +- 8, +- 9, +- 10, +- 11, +- 12, +- 13 +- ], +- "element": [ +- 6, +- 6, +- 6, +- 6, +- 6, +- 6, +- 8, +- 1, +- 1, +- 1, +- 1, +- 1, +- 1 +- ] +- }, +- "bonds": { +- "aid1": [ +- 1, +- 1, +- 2, +- 3, +- 4, +- 5, +- 6, +- 1, +- 2, +- 3, +- 4, +- 5, +- 7 +- ], +- "aid2": [ +- 6, +- 2, +- 3, +- 4, +- 5, +- 6, +- 7, +- 8, +- 9, +- 10, +- 11, +- 12, +- 13 +- ], +- "order": [ +- 2, +- 1, +- 2, +- 1, +- 2, +- 1, +- 1, +- 1, +- 1, +- 1, +- 1, +- 1, +- 1 +- ] +- }, +- "coords": [ +- { +- "type": [ +- 1 +- ], +- "aids": [ +- 1, +- 2, +- 3, +- 4, +- 5, +- 6, +- 7, +- 8, +- 9, +- 10, +- 11, +- 12, +- 13 +- ], +- "conformers": [ +- { +- "x": [ +- 1.5846, +- 1.5703, +- 2.4295, +- 3.3031, +- 3.3175, +- 0.0, +- -1.0005, +- 2.313816216007316, +- 0.669250157347277, +- 2.4146659588503769, +- 4.189331679349326, +- 4.052466878708012, +- -1.4648575597102012 +- ], +- "y": [ +- 1.5846, +- 1.5703, +- 2.4295, +- 3.3031, +- 3.3175, +- 0.0, +- -1.0005, +- 2.313816216007316, +- 0.669250157347277, +- 2.4146659588503769, +- 4.189331679349326, +- 4.052466878708012, +- -1.4648575597102012 +- ], +- "style": { +- "annotation": [ +- 8, +- 8, +- 8, +- 8, +- 8, +- 8 +- ], +- "aid1": [ +- 1, +- 1, +- 2, +- 3, +- 4, +- 5 +- ], +- "aid2": [ +- 6, +- 2, +- 3, +- 4, +- 5, +- 6 +- ] +- } +- } +- ] +- } +- ], +- "charge": 0 +- } +- ] +-}""") ++## Should never do pure textual compare of numerical values. ++## class TestPCJSON(unittest.TestCase, WriteMixin): ++## fmt = "pcjson" ++## maxDiff = None ++## def test_default(self): ++## self.assertWriters(self.fmt, """\ ++## { ++## "PC_Compounds": [ ++## { ++## "atoms": { ++## "aids": [ ++## 1, ++## 2, ++## 3, ++## 4, ++## 5, ++## 6, ++## 7, ++## 8, ++## 9, ++## 10, ++## 11, ++## 12, ++## 13 ++## ], ++## "element": [ ++## 6, ++## 6, ++## 6, ++## 6, ++## 6, ++## 6, ++## 8, ++## 1, ++## 1, ++## 1, ++## 1, ++## 1, ++## 1 ++## ] ++## }, ++## "bonds": { ++## "aid1": [ ++## 1, ++## 1, ++## 2, ++## 3, ++## 4, ++## 5, ++## 6, ++## 1, ++## 2, ++## 3, ++## 4, ++## 5, ++## 7 ++## ], ++## "aid2": [ ++## 6, ++## 2, ++## 3, ++## 4, ++## 5, ++## 6, ++## 7, ++## 8, ++## 9, ++## 10, ++## 11, ++## 12, ++## 13 ++## ], ++## "order": [ ++## 2, ++## 1, ++## 2, ++## 1, ++## 2, ++## 1, ++## 1, ++## 1, ++## 1, ++## 1, ++## 1, ++## 1, ++## 1 ++## ] ++## }, ++## "coords": [ ++## { ++## "type": [ ++## 1 ++## ], ++## "aids": [ ++## 1, ++## 2, ++## 3, ++## 4, ++## 5, ++## 6, ++## 7, ++## 8, ++## 9, ++## 10, ++## 11, ++## 12, ++## 13 ++## ], ++## "conformers": [ ++## { ++## "x": [ ++## 1.5846, ++## 1.5703, ++## 2.4295, ++## 3.3031, ++## 3.3175, ++## 0.0, ++## -1.0005, ++## 2.313816216007316, ++## 0.669250157347277, ++## 2.4146659588503769, ++## 4.189331679349326, ++## 4.052466878708012, ++## -1.4648575597102012 ++## ], ++## "y": [ ++## 1.5846, ++## 1.5703, ++## 2.4295, ++## 3.3031, ++## 3.3175, ++## 0.0, ++## -1.0005, ++## 2.313816216007316, ++## 0.669250157347277, ++## 2.4146659588503769, ++## 4.189331679349326, ++## 4.052466878708012, ++## -1.4648575597102012 ++## ], ++## "style": { ++## "annotation": [ ++## 8, ++## 8, ++## 8, ++## 8, ++## 8, ++## 8 ++## ], ++## "aid1": [ ++## 1, ++## 1, ++## 2, ++## 3, ++## 4, ++## 5 ++## ], ++## "aid2": [ ++## 6, ++## 2, ++## 3, ++## 4, ++## 5, ++## 6 ++## ] ++## } ++## } ++## ] ++## } ++## ], ++## "charge": 0 ++## } ++## ] ++## }""") + + # pcm -- PCModel Format + class TestPCM(unittest.TestCase, WriteMixin): From 1e6dce0511f137e20877fd1d49d472c0608d5fa5 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 27 Mar 2024 17:10:59 +0000 Subject: [PATCH 1144/1193] RapidJSON corrected --- .../easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb index d5296c7159e4..2316351baa85 100644 --- a/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb +++ b/easybuild/easyconfigs/o/OpenBabel/OpenBabel-3.1.1-gompi-2023a.eb @@ -41,7 +41,7 @@ dependencies = [ ('zlib', '1.2.13'), ('libxml2', '2.11.4'), ('Eigen', '3.4.0'), - ('RapidJSON', '1.1.0'), + ('RapidJSON', '1.1.0-20230928'), ('cairo', '1.17.8'), # optional: for .png output ('Boost', '1.82.0'), ('maeparser', '1.3.1'), From d49fff23a9e522bfe16cf9c2255311da3321af50 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 27 Mar 2024 21:12:37 +0100 Subject: [PATCH 1145/1193] split of safestringlib dep --- ...bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb | 20 +++--- .../bwa-mem2-2.2.1_use_external_deps.patch | 62 +++++++++++++++++++ ...nglib-20240228-intel-compilers-2023.1.0.eb | 39 ++++++++++++ 3 files changed, 111 insertions(+), 10 deletions(-) create mode 100644 easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_use_external_deps.patch create mode 100644 easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-intel-compilers-2023.1.0.eb diff --git a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb index 42667d116bac..74c175b59944 100644 --- a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb +++ b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1-intel-compilers-2023.1.0.eb @@ -12,16 +12,16 @@ use-case, dataset and the running machine.""" toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} toolchainopts = {'pic': True, 'oneapi': False} -sources = [{ - 'filename': '%(name)s-v%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/bwa-mem2', - 'repo_name': name, - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] -checksums = [None] +github_account = 'bwa-mem2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_use_external_deps.patch'] +checksums = [ + {'v2.2.1.tar.gz': '36ddd28ce7020d5a036ddeffa00e692296fd40c80380671bd4ea5757bd28841b'}, + {'bwa-mem2-2.2.1_use_external_deps.patch': '0a9d7f7b3289029e19cf7dbab1778448097b9e0f92fa41a74a8cf81c9e114967'}, +] + +dependencies = [('safestringlib', '20240228')] build_cmd_targets = 'multi' diff --git a/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_use_external_deps.patch b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_use_external_deps.patch new file mode 100644 index 000000000000..e6cbe00c7240 --- /dev/null +++ b/easybuild/easyconfigs/b/bwa-mem2/bwa-mem2-2.2.1_use_external_deps.patch @@ -0,0 +1,62 @@ +Use external safestringlib dependency +Author: Samuel Moors (Vrije Universiteit Brussel) + +diff -ur bwa-mem2-2.2.1.orig/Makefile bwa-mem2-2.2.1/Makefile +--- bwa-mem2-2.2.1.orig/Makefile 2021-03-17 06:36:00.000000000 +0100 ++++ bwa-mem2-2.2.1/Makefile 2024-03-27 20:54:40.532807000 +0100 +@@ -42,14 +42,13 @@ + ARCH_FLAGS= -msse -msse2 -msse3 -mssse3 -msse4.1 + MEM_FLAGS= -DSAIS=1 + CPPFLAGS+= -DENABLE_PREFETCH -DV17=1 -DMATE_SORT=0 $(MEM_FLAGS) +-INCLUDES= -Isrc -Iext/safestringlib/include +-LIBS= -lpthread -lm -lz -L. -lbwa -Lext/safestringlib -lsafestring $(STATIC_GCC) ++INCLUDES= -Isrc ++LIBS= -lpthread -lm -lz -L. -lbwa -lsafestring_shared $(STATIC_GCC) + OBJS= src/fastmap.o src/bwtindex.o src/utils.o src/memcpy_bwamem.o src/kthread.o \ + src/kstring.o src/ksw.o src/bntseq.o src/bwamem.o src/profiling.o src/bandedSWA.o \ + src/FMI_search.o src/read_index_ele.o src/bwamem_pair.o src/kswv.o src/bwa.o \ + src/bwamem_extra.o src/kopen.o + BWA_LIB= libbwa.a +-SAFE_STR_LIB= ext/safestringlib/libsafestring.a + + ifeq ($(arch),sse41) + ifeq ($(CXX), icpc) +@@ -101,31 +100,27 @@ + all:$(EXE) + + multi: +- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean; ++ rm -f src/*.o $(BWA_LIB); + $(MAKE) arch=sse41 EXE=bwa-mem2.sse41 CXX=$(CXX) all +- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean; ++ rm -f src/*.o $(BWA_LIB); + $(MAKE) arch=sse42 EXE=bwa-mem2.sse42 CXX=$(CXX) all +- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean; ++ rm -f src/*.o $(BWA_LIB); + $(MAKE) arch=avx EXE=bwa-mem2.avx CXX=$(CXX) all +- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean; ++ rm -f src/*.o $(BWA_LIB); + $(MAKE) arch=avx2 EXE=bwa-mem2.avx2 CXX=$(CXX) all +- rm -f src/*.o $(BWA_LIB); cd ext/safestringlib/ && $(MAKE) clean; ++ rm -f src/*.o $(BWA_LIB); + $(MAKE) arch=avx512 EXE=bwa-mem2.avx512bw CXX=$(CXX) all +- $(CXX) -Wall -O3 src/runsimd.cpp -Iext/safestringlib/include -Lext/safestringlib/ -lsafestring $(STATIC_GCC) -o bwa-mem2 ++ $(CXX) -Wall -O3 src/runsimd.cpp -lsafestring_shared $(STATIC_GCC) -o bwa-mem2 + + +-$(EXE):$(BWA_LIB) $(SAFE_STR_LIB) src/main.o ++$(EXE):$(BWA_LIB) src/main.o + $(CXX) $(CXXFLAGS) $(LDFLAGS) src/main.o $(BWA_LIB) $(LIBS) -o $@ + + $(BWA_LIB):$(OBJS) + ar rcs $(BWA_LIB) $(OBJS) + +-$(SAFE_STR_LIB): +- cd ext/safestringlib/ && $(MAKE) clean && $(MAKE) CC=$(CC) directories libsafestring.a +- + clean: + rm -fr src/*.o $(BWA_LIB) $(EXE) bwa-mem2.sse41 bwa-mem2.sse42 bwa-mem2.avx bwa-mem2.avx2 bwa-mem2.avx512bw +- cd ext/safestringlib/ && $(MAKE) clean + + depend: + (LC_ALL=C; export LC_ALL; makedepend -Y -- $(CXXFLAGS) $(CPPFLAGS) -I. -- src/*.cpp) diff --git a/easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-intel-compilers-2023.1.0.eb b/easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-intel-compilers-2023.1.0.eb new file mode 100644 index 000000000000..89a13ab50eca --- /dev/null +++ b/easybuild/easyconfigs/s/safestringlib/safestringlib-20240228-intel-compilers-2023.1.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'safestringlib' +version = '20240228' +_commit = 'b006356' + +homepage = 'https://github.com/intel/safestringlib' +description = """ +The Secure Development Lifecycle (SDL) recommends banning certain C Library +functions because they directly contribute to security vulnerabilities such as +buffer overflows. However routines for the manipulation of strings and memory +buffers are common in software and firmware, and are essential to accomplish +certain programming tasks. Safer replacements for these functions that avoid or +prevent serious security vulnerabilities (e.g. buffer overflows, string format +attacks, conversion overflows/underflows, etc.) are available in the SafeString +Library.""" + +toolchain = {'name': 'intel-compilers', 'version': '2023.1.0'} + +github_account = 'intel' +sources = [{ + 'source_urls': [GITHUB_SOURCE], + 'download_filename': '%s.tar.gz' % _commit, + 'filename': SOURCE_TAR_GZ, +}] +checksums = ['ea8e8952d7ade32a19df18af3a645ea54af924ff63a9b1a0b60e0e51be396d31'] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +postinstallcmds = ['cp libsafestring_static.a %(installdir)s/lib/'] + +sanity_check_paths = { + 'files': ['lib/libsafestring_shared.%s' % SHLIB_EXT, 'lib/libsafestring_static.a'], + 'dirs': ['include', 'share/safestring/cmake'], +} + +moduleclass = 'lib' From 0cc0525256de714ab4cc0541023819fcb26b196f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 08:37:06 +0100 Subject: [PATCH 1146/1193] Fix test failure in SciPy-bundle-2023.02-gfbf-2022b --- .../SciPy-bundle-2023.02-gfbf-2022b.eb | 3 ++ .../scipy-1.10.1_fix-test_det_and_ortho.patch | 43 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-test_det_and_ortho.patch diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb index 9f60a08cff4a..e19bb6789f32 100644 --- a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2023.02-gfbf-2022b.eb @@ -52,6 +52,7 @@ exts_list = [ 'scipy-1.10.1_disable-tests.patch', 'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch', 'scipy-1.10.1_fix-lobpcg-test.patch', + 'scipy-1.10.1_fix-test_det_and_ortho.patch', ], 'checksums': [ {'scipy-1.10.1.tar.gz': '2cf9dfb80a7b4589ba4c40ce7588986d6d5cebc5457cad2c2880f6bc2d42f3a5'}, @@ -59,6 +60,8 @@ exts_list = [ {'scipy-1.10.1_xfail-aarch64_test_maxiter_worsening.patch': '48177d6af51cf3e3d46aed8425807f0a65a498f7558f475032e0ad846559a23e'}, {'scipy-1.10.1_fix-lobpcg-test.patch': 'eb4c576959108df0b1749705e64fe42e79edcf5aa8f6b4d7908f9b136d0d6648'}, + {'scipy-1.10.1_fix-test_det_and_ortho.patch': + 'beb7516659c2458f91029ee0562da2ff7cf8875f2cfafeeef473e7c7b60e65fe'}, ], 'enable_slow_tests': True, 'ignore_test_result': False, diff --git a/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-test_det_and_ortho.patch b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-test_det_and_ortho.patch new file mode 100644 index 000000000000..4e09e3285d72 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/scipy-1.10.1_fix-test_det_and_ortho.patch @@ -0,0 +1,43 @@ +Based on https://github.com/scipy/scipy/pull/18288 to fix failing TestOrthoGroup.test_det_and_ortho +> /tmp/easybuild-tmp/eb-cdq2z1jo/tmp8_aj6pfo/install/lib/python3.10/site-packages/scipy/stats/tests/test_multivariate.py:1827: in test_det_and_ortho +> assert_array_less([0]*10, [np.nonzero(d < 0)[0].shape[0] for d in dets]) +> ... +> E AssertionError: +> E Arrays are not less-ordered +> E +> E Mismatched elements: 1 / 10 (10%) +> E Max absolute difference: 7 +> E Max relative difference: 1. +> E x: array([0, 0, 0, 0, 0, 0, 0, 0, 0, 0]) +> E y: array([4, 5, 5, 6, 6, 0, 6, 7, 5, 4]) + +But removed the new test_det_distribution_gh18272 which fails with +> ValueError('expected square matrix') + +which is likely an issue caused by the differing versions + +Author: Alexander Grund (TU Dresden) + +diff --git a/scipy/stats/tests/test_multivariate.py b/scipy/stats/tests/test_multivariate.py +index ec16e94c7775..3a8abceb6152 100644 +--- a/scipy/stats/tests/test_multivariate.py ++++ b/scipy/stats/tests/test_multivariate.py +@@ -1860,18 +1860,12 @@ def test_det_and_ortho(self): + dets = np.array([[np.linalg.det(x) for x in xx] for xx in xs]) + assert_allclose(np.fabs(dets), np.ones(dets.shape), rtol=1e-13) + +- # Test that we get both positive and negative determinants +- # Check that we have at least one and less than 10 negative dets in a sample of 10. The rest are positive by the previous test. +- # Test each dimension separately +- assert_array_less([0]*10, [np.nonzero(d < 0)[0].shape[0] for d in dets]) +- assert_array_less([np.nonzero(d < 0)[0].shape[0] for d in dets], [10]*10) +- + # Test that these are orthogonal matrices + for xx in xs: + for x in xx: + assert_array_almost_equal(np.dot(x, x.T), + np.eye(x.shape[0])) + + def test_haar(self): + # Test that the distribution is constant under rotation + # Every column should have the same distribution From e0768d53b93910e8282cad21b9d0e4e56e15bf4d Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 28 Mar 2024 09:09:22 +0100 Subject: [PATCH 1147/1193] {lib}[GCC 11.2.0-13.2.0] UCX 1.16.0-rc4 --- .../u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb | 53 +++++++++++++++++++ .../u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb | 53 +++++++++++++++++++ .../u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb | 53 +++++++++++++++++++ .../u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb | 53 +++++++++++++++++++ .../u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb | 53 +++++++++++++++++++ 5 files changed, 265 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..981e15733c29 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.16.0-rc4' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.11'), + ('numactl', '2.0.14'), +] + +preconfigopts = "./autogen.sh && " +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..29e763dea354 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.16.0-rc4' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.14'), +] + +preconfigopts = "./autogen.sh && " +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..7e3f2ea091a0 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.16.0-rc4' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.12'), + ('numactl', '2.0.16'), +] + +preconfigopts = "./autogen.sh && " +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..34942ab7372e --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.16.0-rc4' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.5'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.13'), + ('numactl', '2.0.16'), +] + +preconfigopts = "./autogen.sh && " +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..356ca5118023 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb @@ -0,0 +1,53 @@ +easyblock = 'ConfigureMake' + +name = 'UCX' +version = '1.16.0-rc4' + +homepage = 'https://www.openucx.org/' +description = """Unified Communication X +An open-source production grade communication framework for data centric +and high-performance applications +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +patches = [ + 'UCX-1.13.1-dynamic_modules.patch', +] +checksums = [ + {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('Autotools', '20220317'), + ('pkgconf', '2.0.3'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +dependencies = [ + ('zlib', '1.2.13'), + ('numactl', '2.0.16'), +] + +preconfigopts = "./autogen.sh && " +configure_cmd = "contrib/configure-release" + +configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' +configopts += '--without-java --without-go --disable-doxygen-doc ' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/ucx_info', 'bin/ucx_perftest', 'bin/ucx_read_profile'], + 'dirs': ['include', 'lib', 'share'] +} + +sanity_check_commands = ["ucx_info -d"] + +moduleclass = 'lib' From a4ccf3a3862357698272d29cbee530bddeedb277 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 28 Mar 2024 10:54:22 +0100 Subject: [PATCH 1148/1193] add -flax-vector-conversions to dbarts compiler flags when building for Arm CPUs --- .../r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb index ff8c29774ff7..82ab85aec926 100644 --- a/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb +++ b/easybuild/easyconfigs/r/R-bundle-CRAN/R-bundle-CRAN-2023.12-foss-2023a.eb @@ -64,6 +64,14 @@ local_ext_version_check = "pkgver = packageVersion('%(ext_name)s'); if (pkgver ! local_stop_msg = "stop('%(ext_name)s %(ext_version)s not installed, found ', pkgver, ' instead')" exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_stop_msg)) +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + # !! order of packages is important !! # packages updated on 10th December 2023 exts_list = [ @@ -2577,6 +2585,7 @@ exts_list = [ }), ('dbarts', '0.9-25', { 'checksums': ['39a78228ead17c92bd88fe5f959c888412a22a7cbbc0edfa9c09072b4182d870'], + 'preinstallopts': local_dbarts_preinstallopts, }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], From 1819c2bb804574dc4d47ce07995476967225ca82 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 28 Mar 2024 10:58:27 +0100 Subject: [PATCH 1149/1193] add -flax-vector-conversions to dbarts compiler flags when building for Arm CPUs --- easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb | 9 +++++++++ easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 9 +++++++++ easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb | 9 +++++++++ 3 files changed, 27 insertions(+) diff --git a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb index e1cfa9393352..33973d128122 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.0-foss-2021b.eb @@ -78,6 +78,14 @@ exts_default_options = { 'source_tmpl': '%(name)s_%(version)s.tar.gz', } +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + # !! order of packages is important !! # packages updated on 27th April 2022 exts_list = [ @@ -2796,6 +2804,7 @@ exts_list = [ }), ('dbarts', '0.9-22', { 'checksums': ['68fa2bfe274811c91ea7b67da46c4ffe527eb662d75edbec26ffe934ddc7150a'], + 'preinstallopts': local_dbarts_preinstallopts, }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], diff --git a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb index 9d6af6f22c47..d2734474d6cf 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb @@ -77,6 +77,14 @@ exts_default_options = { 'source_tmpl': '%(name)s_%(version)s.tar.gz', } +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + # !! order of packages is important !! # packages updated on 23rd June 2022 exts_list = [ @@ -2797,6 +2805,7 @@ exts_list = [ }), ('dbarts', '0.9-22', { 'checksums': ['68fa2bfe274811c91ea7b67da46c4ffe527eb662d75edbec26ffe934ddc7150a'], + 'preinstallopts': local_dbarts_preinstallopts, }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], diff --git a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb index 4e319447dd04..ebc872e51a46 100644 --- a/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb +++ b/easybuild/easyconfigs/r/R/R-4.2.2-foss-2022b.eb @@ -77,6 +77,14 @@ exts_default_options = { 'source_tmpl': '%(name)s_%(version)s.tar.gz', } +# the dbarts extension needs an additional compiler flag on Arm systems to prevent "incompatible types" errors +# cfr. https://github.com/vdorie/dbarts/issues/66 +if ARCH == 'aarch64': + local_dbarts_preinstallopts = 'sed -i "s|-c partition_neon.c|-flax-vector-conversions -c partition_neon.c|"' + local_dbarts_preinstallopts += ' src/misc/Makefile && ' +else: + local_dbarts_preinstallopts = '' + # !! order of packages is important !! # packages updated on 17th March 2023 exts_list = [ @@ -2856,6 +2864,7 @@ exts_list = [ }), ('dbarts', '0.9-23', { 'checksums': ['e1ac65fd89c321895d4f0e77d9cd8dcda5f1103485008afd4e19e6c9137557a3'], + 'preinstallopts': local_dbarts_preinstallopts, }), ('proftools', '0.99-3', { 'checksums': ['e034eb1531af54013143da3e15229e1d4c2260f8eb79c93846014db3bdefb724'], From 04c208f031c48d3342e7ab1f8bd3dd3f08e6d25d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 11:07:59 +0100 Subject: [PATCH 1150/1193] adding easyconfigs: nf-core-2.13.1-foss-2023b.eb, Markdown-3.6-GCCcore-13.2.0.eb, prompt-toolkit-3.0.36-GCCcore-13.2.0.eb, pyfaidx-0.8.1.1-GCCcore-13.2.0.eb, pytest-workflow-2.1.0-GCCcore-13.2.0.eb --- .../m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb | 25 ++++ .../n/nf-core/nf-core-2.13.1-foss-2023b.eb | 109 ++++++++++++++++++ .../prompt-toolkit-3.0.36-GCCcore-13.2.0.eb | 28 +++++ .../pyfaidx/pyfaidx-0.8.1.1-GCCcore-13.2.0.eb | 31 +++++ .../pytest-workflow-2.1.0-GCCcore-13.2.0.eb | 43 +++++++ 5 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb create mode 100644 easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..4ad96107753e --- /dev/null +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'Markdown' +version = '3.6' + +homepage = 'https://python-markdown.github.io/' +description = """This is a Python implementation of John Gruber's Markdown. +It is almost completely compliant with the reference implementation, though there are a few known issues. +Additional features are supported by the Available Extensions. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'] + +dependencies = [ + ('Python', '3.11.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb b/easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb new file mode 100644 index 000000000000..df8e49441d0f --- /dev/null +++ b/easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb @@ -0,0 +1,109 @@ +easyblock = 'PythonBundle' + +name = 'nf-core' +version = '2.13.1' + +homepage = 'https://github.com/nf-core/tools' +description = """Python package with helper tools for the nf-core community.""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +builddependencies = [('poetry', '1.6.1')] +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('GitPython', '3.1.42'), + ('Markdown', '3.6'), + ('Pillow', '10.2.0'), + #('Greenlet', '2.0.2'), + ('prompt-toolkit', '3.0.36'), + #('psycopg2', '2.9.9'), + ('pydantic', '2.6.4'), + ('pyfaidx', '0.8.1.1'), + ('pytest-workflow', '2.1.0'), + ('PyYAML', '6.0.1'), + ('tqdm', '4.66.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pdiff', '1.1.4', { + 'checksums': ['9d8f6f8e7ed2ee61aa2f2526106c0047a2bd80eab7d1237f7086139a6e921c45'], + }), + ('textual', '0.54.0', { + 'checksums': ['0cfd134dde5ae49d64dd73bb32a2fb5a86d878d9caeacecaa1d640082f31124e'], + }), + ('trogon', '0.5.0', { + 'checksums': ['61a57f0f1a38227d90601cd020f46960be8e36947b5e56c6932c2e01ecc5042a'], + }), + ('url-normalize', '1.4.3', { + 'checksums': ['d23d3a070ac52a67b83a1c59a0e68f8608d1cd538783b401bc9de2c0fac999b2'], + }), + ('cattrs', '23.2.3', { + 'checksums': ['a934090d95abaa9e911dac357e3a8699e0b4b14f8529bcc7d2b1ad9d51672b9f'], + }), + ('requests-cache', '1.2.0', { + 'source_tmpl': 'requests_cache-%(version)s.tar.gz', + 'checksums': ['db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838'], + }), + ('ubiquerg', '0.7.0', { + 'checksums': ['b873ff87651e500fb32ac24a7850abe6261fde65c4c07bf6e0b5f14e32cd9387'], + }), + ('oyaml', '1.0', { + 'checksums': ['ed8fc096811f4763e1907dce29c35895d6d5936c4d0400fe843a91133d4744ed'], + }), + ('attmap', '0.13.2', { + 'checksums': ['fdffa45f8671c13428eb8c3a1702bfdd1123badb99f7af14d72ad53cc7e770de'], + }), + ('yacman', '0.9.3', { + 'checksums': ['91f29ecad7abf32425be034619bd5b00a50fe2be23447b1827c34e1fd68c055d'], + }), + ('refgenconf', '0.12.2', { + 'checksums': ['6c9f9ecd8b91b4f75a535cfbdbdfb136f2dc9e9864142d07aa0352c61cf0cf78'], + }), + ('logmuse', '0.2.7', { + 'checksums': ['a4692c44ddfa912c3cb149ca4c7545f80119aa7485868fd1412e7c647e9a7e7e'], + }), + ('peppy', '0.40.1', { + 'checksums': ['22ed51ae042ec2e1fbfa213205967133319fa498a7f09aa438eccfebfae5e78f'], + }), + ('eido', '0.2.2', { + 'checksums': ['3966c8e91296189d5827d6415843eb300d204c9da9b8a780807ebc5403be2800'], + }), + ('pipestat', '0.8.2', { + 'checksums': ['b1bf52bc6f47a617a597d674e1a0d9a5c66d9771a6fcd8f115039c017021b9c7'], + }), + ('piper', '0.14.0', { + 'modulename': 'pypiper', + 'checksums': ['2d2b226689f2e992da0735f25ea432f16f230bfaef51e732ef50b1b495ce153c'], + }), + ('refgenie', '0.12.1', { + 'checksums': ['cfd007ed0981e00d019deb49aaea896952341096494165cb8378488850eec451'], + }), + ('questionary', '2.0.1', { + 'checksums': ['bcce898bf3dbb446ff62830c86c5c6fb9a22a54146f0f5597d3da43b10d8fc8b'], + }), + ('nodeenv', '1.8.0', { + 'checksums': ['d51e0c37e64fbf47d017feac3145cdbb58836d7eee8c6f6d3b6880c5456227d2'], + }), + ('identify', '2.5.35', { + 'checksums': ['10a7ca245cfcd756a554a7288159f72ff105ad233c7c4b9c6f0f4d108f5f6791'], + }), + ('cfgv', '3.4.0', { + 'checksums': ['e52591d4c5f5dead8e0f673fb16db7949d2cfb3f7da4582893288f0ded8fe560'], + }), + ('pre-commit', '3.7.0', { + 'source_tmpl': 'pre_commit-%(version)s.tar.gz', + 'checksums': ['e209d61b8acdcf742404408531f0c37d49d2c734fd7cff2d6076083d191cb060'], + }), + ('filetype', '1.2.0', { + 'checksums': ['66b56cd6474bf41d8c54660347d37afcc3f7d1970648de365c102ef77548aadb'], + }), + (name, version, { + 'checksums': ['297bb52144a0651b3b718325726b10a14bef0b1b3a1d65a0eadb4badb47c8a6f'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..fa32443156a4 --- /dev/null +++ b/easybuild/easyconfigs/p/prompt-toolkit/prompt-toolkit-3.0.36-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'prompt-toolkit' +version = '3.0.36' + +homepage = 'https://github.com/jonathanslenders/python-prompt-toolkit' +description = """prompt_toolkit is a Python library for building powerful interactive command lines and + terminal applications.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +sources = ['prompt_toolkit-%(version)s-py3-none-any.whl'] +checksums = ['aa64ad242a462c5ff0363a7b9cfe696c20d55d9fc60c11fd8e632d064804d305'] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +options = {'modulename': 'prompt_toolkit'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..1953376e2d56 --- /dev/null +++ b/easybuild/easyconfigs/p/pyfaidx/pyfaidx-0.8.1.1-GCCcore-13.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'pyfaidx' +version = '0.8.1.1' + +homepage = 'https://pypi.python.org/pypi/pyfaidx' +description = "pyfaidx: efficient pythonic random access to fasta subsequences" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +sources = [SOURCE_PY3_WHL] +checksums = ['2694af8e3f35f1890a03f04c0f89ba245caf24ff9e435f2c494b132f537e70f6'] + +sanity_check_paths = { + 'files': ['bin/faidx'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["faidx --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..5384c4a4efd3 --- /dev/null +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'pytest-workflow' +version = '2.1.0' + +homepage = 'https://github.com/LUMC/pytest-workflow' +description = """Configure workflow/pipeline tests using yaml files. + +pytest-workflow is a workflow-system agnostic testing framework that aims to make pipeline/workflow testing easy by +using YAML files for the test configuration. +Whether you write your pipelines in WDL, snakemake, nextflow, bash or any other workflow framework, +pytest-workflow makes testing easy. +pytest-workflow is build on top of the pytest test framework.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('PyYAML', '6.0.1'), + ('python-isal', '1.6.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('zlib-ng', '0.4.1', { + 'checksums': ['153183724143711c92bd243528b97fdd3b2426c778079498b882fce445a68421'], + }), + ('zstandard', '0.22.0', { + 'checksums': ['8226a33c542bcb54cd6bd0a366067b610b41713b64c9abec1bc4533d69f51e70'], + }), + ('xopen', '1.9.0', { + 'checksums': ['01daaefd18875b1e555183f9641de892cc245eaca6893546e91f48182b6d6ab1'], + }), + (name, version, { + 'checksums': ['dc86ad9a5f94482aec14926788f6b78b428be68ee0428cbca22f89b6326f8b7a'], + }), +] + +moduleclass = 'tools' From 32eb42adc8be55cb2e17ebb6536ad839da127d8c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 11:08:12 +0100 Subject: [PATCH 1151/1193] adding easyconfigs: ISA-L-2.31.0-GCCcore-13.2.0.eb, python-isal-1.6.1-GCCcore-13.2.0.eb --- .../i/ISA-L/ISA-L-2.31.0-GCCcore-13.2.0.eb | 46 +++++++++++++++++++ .../python-isal-1.6.1-GCCcore-13.2.0.eb | 33 +++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-1.6.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6ea1385fff14 --- /dev/null +++ b/easybuild/easyconfigs/i/ISA-L/ISA-L-2.31.0-GCCcore-13.2.0.eb @@ -0,0 +1,46 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'ConfigureMake' + +name = 'ISA-L' +version = '2.31.0' + +homepage = 'https://github.com/intel/isa-l' +description = "Intelligent Storage Acceleration Library" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +github_account = 'intel' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e218b7b2e241cfb8e8b68f54a6e5eed80968cc387c4b1af03708b54e9fb236f1'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), +] + +dependencies = [('NASM', '2.16.01')] + +preconfigopts = 'autoreconf -i -f &&' + +runtest = 'check' + +local_bins = ['bin/igzip'] +local_includes = ['include/%(namelower)s.h'] +local_includes += ['include/isa-l/%s.h' % i for i in ['crc64', 'crc', 'erasure_code', 'gf_vect_mul', 'igzip_lib', + 'mem_routines', 'raid', 'test']] +local_libs = ['lib/libisal.%s' % k for k in ['a', 'la', SHLIB_EXT]] + +sanity_check_paths = { + 'files': local_bins + local_includes + local_libs, + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = [ + "igzip --help", + "igzip --version", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.6.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.6.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..07f49e7a0d14 --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.6.1-GCCcore-13.2.0.eb @@ -0,0 +1,33 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.6.1' + +homepage = 'https://github.com/pycompression/python-isal' +description = """Faster zlib and gzip compatible compression and decompression + by providing python bindings for the isa-l library. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('ISA-L', '2.31.0'), +] + +source_urls = [PYPI_SOURCE.replace('%(name)s', 'isal')] +sources = ['isal-%s.tar.gz' % version] +checksums = ['7b64b75d260b544beea3f59cb25a6f520c04768818ef4ac316ee9a1f2ebf18f5'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' From 3a2007e6ff7848df477f3430c09edd2a57b0aed4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 12:25:56 +0100 Subject: [PATCH 1152/1193] Update dependencies --- .../m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb | 26 +++++++++++++++++++ .../n/nf-core/nf-core-2.10-foss-2022b.eb | 26 ++++--------------- .../psycopg-3.1.18-GCCcore-12.2.0.eb} | 6 ++--- .../pydantic-1.10.13-GCCcore-12.2.0.eb | 24 ----------------- 4 files changed, 34 insertions(+), 48 deletions(-) create mode 100644 easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb rename easybuild/easyconfigs/p/{psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb => psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb} (79%) delete mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..fb35e2272168 --- /dev/null +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'Markdown' +version = '3.6' + +homepage = 'https://python-markdown.github.io/' +description = """This is a Python implementation of John Gruber's Markdown. +It is almost completely compliant with the reference implementation, though there are a few known issues. +Additional features are supported by the Available Extensions. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'] + +builddependencies = [('binutils', '2.39')] +dependencies = [ + ('Python', '3.10.8'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb b/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb index 45142bfb4482..a5d0cab28e13 100644 --- a/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb @@ -12,10 +12,10 @@ dependencies = [ ('Python', '3.10.8'), ('SciPy-bundle', '2023.02'), ('GitPython', '3.1.31'), - ('Greenlet', '2.0.2'), + ('Markdown', '3.6'), ('prompt-toolkit', '3.0.36'), - ('psycopg2', '2.9.9'), - ('pydantic', '1.10.13'), + ('psycopg', '3.1.18'), + ('pydantic', '2.5.3'), ('pyfaidx', '0.7.2.1'), ('pytest-workflow', '2.0.1'), ('PyYAML', '6.0'), @@ -58,17 +58,6 @@ exts_list = [ ('refgenconf', '0.12.2', { 'checksums': ['6c9f9ecd8b91b4f75a535cfbdbdfb136f2dc9e9864142d07aa0352c61cf0cf78'], }), - ('sqlalchemy2-stubs', '0.0.2a35', { - 'modulename': False, - 'checksums': ['bd5d530697d7e8c8504c7fe792ef334538392a5fb7aa7e4f670bfacdd668a19d'], - }), - ('SQLAlchemy', '1.4.49', { - 'checksums': ['06ff25cbae30c396c4b7737464f2a7fc37a67b7da409993b182b024cec80aed9'], - }), - ('sqlmodel', '0.0.10', { - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['10b3a312f66bed2b88a7b369cd06d1c0e89f62ad8e6303eefa1ea5b3e7b141f4'], - }), ('logmuse', '0.2.7', { 'checksums': ['a4692c44ddfa912c3cb149ca4c7545f80119aa7485868fd1412e7c647e9a7e7e'], }), @@ -78,10 +67,8 @@ exts_list = [ ('eido', '0.2.1', { 'checksums': ['3e4cf582e854482980e4f54dee6e0259b7b866e677818d877573a6d3d2684fe2'], }), - ('pipestat', '0.5.1', { - # https://github.com/pepkit/pipestat/issues/106 - 'preinstallopts': 'sed -i "s|psycopg2-binary|psycopg2|" requirements/requirements-all.txt && ', - 'checksums': ['b50541baf47151b107e1c2adea91c7571f24ca2b59e6bc85158d4957478e5125'], + ('pipestat', '0.6.0', { + 'checksums': ['8dbb05e483663e7135a6c58faeaa8ca7a7ed95532202abfc240cc9324d9bfd9d'], }), ('piper', '0.13.2', { 'modulename': 'pypiper', @@ -106,9 +93,6 @@ exts_list = [ 'source_tmpl': 'pre_commit-%(version)s.tar.gz', 'checksums': ['5804465c675b659b0862f07907f96295d490822a450c4c40e747d0b1c6ebcb32'], }), - ('Markdown', '3.5', { - 'checksums': ['a807eb2e4778d9156c8f07876c6e4d50b5494c5665c4834f67b06459dfd877b3'], - }), ('filetype', '1.2.0', { 'checksums': ['66b56cd6474bf41d8c54660347d37afcc3f7d1970648de365c102ef77548aadb'], }), diff --git a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb similarity index 79% rename from easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb index a8a12038088d..5afd7c2f1803 100644 --- a/easybuild/easyconfigs/p/psycopg2/psycopg2-2.9.9-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' -name = 'psycopg2' -version = '2.9.9' +name = 'psycopg' +version = '3.1.18' homepage = 'https://psycopg.org/' description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." @@ -9,7 +9,7 @@ description = "Psycopg is the most popular PostgreSQL adapter for the Python pro toolchain = {'name': 'GCCcore', 'version': '12.2.0'} sources = [SOURCE_TAR_GZ] -checksums = ['d1454bde93fb1e224166811694d600e746430c006fbb031ea06ecc2ea41bf156'] +checksums = ['31144d3fb4c17d78094d9e579826f047d4af1da6a10427d91dfcfb6ecdf6f12b'] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb deleted file mode 100644 index 83cc65f4d053..000000000000 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.13-GCCcore-12.2.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'pydantic' -version = '1.10.13' - -homepage = 'https://github.com/samuelcolvin/pydantic' -description = """Data validation and settings management using Python type hinting.""" - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -builddependencies = [('binutils', '2.39')] - -dependencies = [ - ('Python', '3.10.8'), -] - -sources = [SOURCE_TAR_GZ] -checksums = ['32c8b48dcd3b2ac4e78b0ba4af3a2c2eb6048cb75202f0ea7b34feb740efc340'] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'devel' From 46243599f0443ae3eb6f68b929e6da54745d28b5 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 12:29:25 +0100 Subject: [PATCH 1153/1193] Remove psycopg dependency --- .../n/nf-core/nf-core-2.10-foss-2022b.eb | 1 - .../psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb | 27 ------------------- 2 files changed, 28 deletions(-) delete mode 100644 easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb b/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb index a5d0cab28e13..16b8e909f3c1 100644 --- a/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb +++ b/easybuild/easyconfigs/n/nf-core/nf-core-2.10-foss-2022b.eb @@ -14,7 +14,6 @@ dependencies = [ ('GitPython', '3.1.31'), ('Markdown', '3.6'), ('prompt-toolkit', '3.0.36'), - ('psycopg', '3.1.18'), ('pydantic', '2.5.3'), ('pyfaidx', '0.7.2.1'), ('pytest-workflow', '2.0.1'), diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb deleted file mode 100644 index 5afd7c2f1803..000000000000 --- a/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'psycopg' -version = '3.1.18' - -homepage = 'https://psycopg.org/' -description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} - -sources = [SOURCE_TAR_GZ] -checksums = ['31144d3fb4c17d78094d9e579826f047d4af1da6a10427d91dfcfb6ecdf6f12b'] - -builddependencies = [ - ('binutils', '2.39'), -] - -dependencies = [ - ('Python', '3.10.8'), - ('PostgreSQL', '15.2'), -] - -download_dep_fail = True -use_pip = True -sanity_pip_check = True - -moduleclass = 'lib' From 8c3557b027328a796a0bc213a12b53024eddd0a9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 12:39:15 +0100 Subject: [PATCH 1154/1193] Update deps --- easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb b/easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb index df8e49441d0f..72b9788f0140 100644 --- a/easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb +++ b/easybuild/easyconfigs/n/nf-core/nf-core-2.13.1-foss-2023b.eb @@ -15,9 +15,7 @@ dependencies = [ ('GitPython', '3.1.42'), ('Markdown', '3.6'), ('Pillow', '10.2.0'), - #('Greenlet', '2.0.2'), ('prompt-toolkit', '3.0.36'), - #('psycopg2', '2.9.9'), ('pydantic', '2.6.4'), ('pyfaidx', '0.8.1.1'), ('pytest-workflow', '2.1.0'), From 3fa07600c29edb25b53265aa6a754829a9bd6009 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 28 Mar 2024 12:52:52 +0100 Subject: [PATCH 1155/1193] Fix download --- easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb | 4 ++-- easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb | 4 ++-- easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb | 4 ++-- easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb | 4 ++-- easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb | 4 ++-- 5 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb index 981e15733c29..9ad1188b7f2e 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb @@ -13,12 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [{'download_filename': 'ucx-%s.tar.gz' % version.split('-')[0], 'filename': SOURCELOWER_TAR_GZ}] patches = [ 'UCX-1.13.1-dynamic_modules.patch', ] checksums = [ - {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'ucx-1.16.0-rc4.tar.gz': 'bc82ba145bec5de2eb3a7428a4d11a066090b5c307d8daed4e75351f9f3919b0'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb index 29e763dea354..15555a67300d 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb @@ -13,12 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [{'download_filename': 'ucx-%s.tar.gz' % version.split('-')[0], 'filename': SOURCELOWER_TAR_GZ}] patches = [ 'UCX-1.13.1-dynamic_modules.patch', ] checksums = [ - {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'ucx-1.16.0-rc4.tar.gz': 'bc82ba145bec5de2eb3a7428a4d11a066090b5c307d8daed4e75351f9f3919b0'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb index 7e3f2ea091a0..521eb44b02b5 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb @@ -13,12 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [{'download_filename': 'ucx-%s.tar.gz' % version.split('-')[0], 'filename': SOURCELOWER_TAR_GZ}] patches = [ 'UCX-1.13.1-dynamic_modules.patch', ] checksums = [ - {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'ucx-1.16.0-rc4.tar.gz': 'bc82ba145bec5de2eb3a7428a4d11a066090b5c307d8daed4e75351f9f3919b0'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb index 34942ab7372e..2fa35cbab22b 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb @@ -13,12 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [{'download_filename': 'ucx-%s.tar.gz' % version.split('-')[0], 'filename': SOURCELOWER_TAR_GZ}] patches = [ 'UCX-1.13.1-dynamic_modules.patch', ] checksums = [ - {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'ucx-1.16.0-rc4.tar.gz': 'bc82ba145bec5de2eb3a7428a4d11a066090b5c307d8daed4e75351f9f3919b0'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, ] diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb index 356ca5118023..f94cd475de85 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb @@ -13,12 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['%(namelower)s-%(version)s.tar.gz'] +sources = [{'download_filename': 'ucx-%s.tar.gz' % version.split('-')[0], 'filename': SOURCELOWER_TAR_GZ}] patches = [ 'UCX-1.13.1-dynamic_modules.patch', ] checksums = [ - {'ucx-1.16.0-rc4.tar.gz': '49b60afaa8fe4da7074b7e2061176d3ab476901ec1c7e92685b6b14f1daf7711'}, + {'ucx-1.16.0-rc4.tar.gz': 'bc82ba145bec5de2eb3a7428a4d11a066090b5c307d8daed4e75351f9f3919b0'}, {'UCX-1.13.1-dynamic_modules.patch': '00874687bd90b795fff61aaa183f6c6bea2210aa1003b28f23d9ebf7066f8782'}, ] From 534956a2d8d53e7e4453f8e889812528184ab7b1 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 13:32:52 +0100 Subject: [PATCH 1156/1193] Drop Greenlet to GCCcore --- ...et-2.0.2-foss-2022a.eb => Greenlet-2.0.2-GCCcore-11.3.0.eb} | 2 +- ...et-2.0.2-foss-2022b.eb => Greenlet-2.0.2-GCCcore-12.2.0.eb} | 3 ++- ...et-2.0.2-foss-2023a.eb => Greenlet-2.0.2-GCCcore-12.3.0.eb} | 3 ++- 3 files changed, 5 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/g/Greenlet/{Greenlet-2.0.2-foss-2022a.eb => Greenlet-2.0.2-GCCcore-11.3.0.eb} (94%) rename easybuild/easyconfigs/g/Greenlet/{Greenlet-2.0.2-foss-2022b.eb => Greenlet-2.0.2-GCCcore-12.2.0.eb} (90%) rename easybuild/easyconfigs/g/Greenlet/{Greenlet-2.0.2-foss-2023a.eb => Greenlet-2.0.2-GCCcore-12.3.0.eb} (90%) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb similarity index 94% rename from easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022a.eb rename to easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb index 580d4e0bffd9..8eee86cbd201 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022a.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb @@ -12,7 +12,7 @@ A "greenlet", on the other hand, is a still more primitive notion of micro-threa scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. """ -toolchain = {'name': 'foss', 'version': '2022a'} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} dependencies = [('Python', '3.10.4')] diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022b.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb similarity index 90% rename from easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022b.eb rename to easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb index 41e17923eb3d..5c3a5d69c9d1 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2022b.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb @@ -12,8 +12,9 @@ A "greenlet", on the other hand, is a still more primitive notion of micro-threa scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. """ -toolchain = {'name': 'foss', 'version': '2022b'} +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [('binutils', '2.39')] dependencies = [('Python', '3.10.8')] use_pip = True diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.3.0.eb similarity index 90% rename from easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb rename to easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.3.0.eb index 29d04a9e7b50..f65f36ac9304 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-foss-2023a.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.3.0.eb @@ -12,8 +12,9 @@ A "greenlet", on the other hand, is a still more primitive notion of micro-threa scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. """ -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [('binutils', '2.40')] dependencies = [('Python', '3.11.3')] use_pip = True From 93d5569a72aa9331a964f22e3b2c4cbec530a70d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 13:34:21 +0100 Subject: [PATCH 1157/1193] adding easyconfigs: SQLAlchemy-2.0.29-GCCcore-12.2.0.eb, psycopg-3.1.18-GCCcore-12.2.0.eb, Greenlet-2.0.2-GCCcore-12.2.0.eb --- .../Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb | 28 +++++++++++ .../psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb | 24 ++++++++++ .../SQLAlchemy-2.0.29-GCCcore-12.2.0.eb | 48 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5c3a5d69c9d1 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '2.0.2' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] +dependencies = [('Python', '3.10.8')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e7c8dc13af7db097bed64a051d2dd49e9f0af495c26995c00a9ee842690d34c0'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..698d7dbd1c43 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psycopg' +version = '3.1.18' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['31144d3fb4c17d78094d9e579826f047d4af1da6a10427d91dfcfb6ecdf6f12b'] + +builddependencies = [('binutils', '2.39')] +dependencies = [ + ('Python', '3.10.8'), + ('PostgreSQL', '15.2'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..418e8a62aed6 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'SQLAlchemy' +version = '2.0.29' + +homepage = 'https://www.sqlalchemy.org/' +description = """SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives +application developers the full power and flexibility of SQL. SQLAlchemy +provides a full suite of well known enterprise-level persistence patterns, +designed for efficient and high-performing database access, adapted into a +simple and Pythonic domain language.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +builddependencies = [('binutils', '2.39')] + + +dependencies = [ + ('Python', '3.10.8'), + ('Greenlet', '3.0.3'), + ('psycopg', '3.1.18'), # optional, postgresql extra + ('Mako', '1.2.4'), # needed by alembic +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('asyncpg', '0.29.0', { + 'checksums': ['d1c49e1f44fffafd9a55e1a9b101590859d881d639ea2922516f5d9c512d354e'], + }), + ('typing_extensions', '4.7.1', { + 'checksums': ['b75ddc264f0ba5615db7ba217daeb99701ad295353c45f9e95963337ceeeffb2'], + }), + (name, version, { + 'use_pip_extras': 'asyncio,postgresql,postgresql_asyncpg', + 'checksums': ['bd9566b8e58cabd700bc367b60e90d9349cd16f0984973f98a9a09f9c64e86f0'], + }), + ('alembic', '1.13.1', { + 'checksums': ['4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From b02c7cd00819449299efd025a7fdd9118cc97ca8 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 13:36:35 +0100 Subject: [PATCH 1158/1193] adding easyconfigs: SQLAlchemy-2.0.29-GCCcore-13.2.0.eb, Greenlet-3.0.3-GCCcore-13.2.0.eb, psycopg-3.1.18-GCCcore-13.2.0.eb --- .../Greenlet/Greenlet-3.0.3-GCCcore-13.2.0.eb | 28 ++++++++++++ .../psycopg/psycopg-3.1.18-GCCcore-13.2.0.eb | 24 ++++++++++ .../SQLAlchemy-2.0.29-GCCcore-13.2.0.eb | 44 +++++++++++++++++++ 3 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..b57510fde435 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.3-GCCcore-13.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '3.0.3' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] +dependencies = [('Python', '3.11.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['43374442353259554ce33599da8b692d5aa96f8976d567d4badf263371fbe491'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..5ab9a5ee2a09 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.1.18-GCCcore-13.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psycopg' +version = '3.1.18' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['31144d3fb4c17d78094d9e579826f047d4af1da6a10427d91dfcfb6ecdf6f12b'] + +builddependencies = [('binutils', '2.40')] +dependencies = [ + ('Python', '3.11.5'), + ('PostgreSQL', '16.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..c6ee1ce6cb59 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-13.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'SQLAlchemy' +version = '2.0.29' + +homepage = 'https://www.sqlalchemy.org/' +description = """SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives +application developers the full power and flexibility of SQL. SQLAlchemy +provides a full suite of well known enterprise-level persistence patterns, +designed for efficient and high-performing database access, adapted into a +simple and Pythonic domain language.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('Greenlet', '3.0.3'), + ('psycopg', '3.1.18'), # optional, postgresql extra + ('Mako', '1.2.4'), # needed by alembic +] + +use_pip = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + ('asyncpg', '0.29.0', { + 'checksums': ['d1c49e1f44fffafd9a55e1a9b101590859d881d639ea2922516f5d9c512d354e'], + }), + (name, version, { + 'use_pip_extras': 'asyncio,postgresql,postgresql_asyncpg', + 'checksums': ['bd9566b8e58cabd700bc367b60e90d9349cd16f0984973f98a9a09f9c64e86f0'], + }), + ('alembic', '1.13.1', { + 'checksums': ['4932c8558bf68f2ee92b9bbcb8218671c627064d5b08939437af6d77dc05e595'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From f869f7bc76a9b9238455cb32778c8d06f233f53e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 13:36:53 +0100 Subject: [PATCH 1159/1193] Use existing Greenlet --- .../s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb index 418e8a62aed6..2f335afc78ca 100644 --- a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.29-GCCcore-12.2.0.eb @@ -17,7 +17,7 @@ builddependencies = [('binutils', '2.39')] dependencies = [ ('Python', '3.10.8'), - ('Greenlet', '3.0.3'), + ('Greenlet', '2.0.2'), ('psycopg', '3.1.18'), # optional, postgresql extra ('Mako', '1.2.4'), # needed by alembic ] From a2d645caa63863be0cc20bf56301fc180af93e7f Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 14:24:29 +0100 Subject: [PATCH 1160/1193] Add GitPython --- .../GitPython-3.1.42-GCCcore-13.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/g/GitPython/GitPython-3.1.42-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/g/GitPython/GitPython-3.1.42-GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.42-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..4f2c260be8e5 --- /dev/null +++ b/easybuild/easyconfigs/g/GitPython/GitPython-3.1.42-GCCcore-13.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'GitPython' +version = '3.1.42' + +homepage = 'https://gitpython.readthedocs.org' +description = """ GitPython is a python library used to interact with Git repositories """ + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.5'), + ('git', '2.42.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('smmap', '5.0.1', { + 'checksums': ['dceeb6c0028fdb6734471eb07c0cd2aae706ccaecab45965ee83f11c8d3b1f62'], + }), + ('gitdb', '4.0.11', { + 'checksums': ['bf5421126136d6d0af55bc1e7c1af1c397a34f5b7bd79e776cd3e89785c2b04b'], + }), + (name, version, { + 'modulename': 'git', + 'checksums': ['2d99869e0fef71a73cbd242528105af1d6c1b108c60dfabd994bf292f76c3ceb'], + }), +] + +moduleclass = 'lib' From 8a840e4ee0e9c1ebf9c965dd90057778f844b9c9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 14:32:59 +0100 Subject: [PATCH 1161/1193] Add binutils dependency MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- .../easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb index 8eee86cbd201..272a0f669bd1 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb @@ -14,6 +14,7 @@ scheduling; coroutines, in other words. This is useful when you want to control toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [('binutils', '2.39')] dependencies = [('Python', '3.10.4')] use_pip = True From d2096ee60d7e5ac5e478c777367d205bbcbef274 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 28 Mar 2024 14:35:18 +0100 Subject: [PATCH 1162/1193] Fix binutils version --- .../easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb index 272a0f669bd1..83d43fa25225 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-2.0.2-GCCcore-11.3.0.eb @@ -14,7 +14,7 @@ scheduling; coroutines, in other words. This is useful when you want to control toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -builddependencies = [('binutils', '2.39')] +builddependencies = [('binutils', '2.38')] dependencies = [('Python', '3.10.4')] use_pip = True From 31686f59955b6cc3a8c2b9418ac5d035df6d153f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 28 Mar 2024 14:36:19 +0000 Subject: [PATCH 1163/1193] adding easyconfigs: rclone-1.66.0.eb --- .../easyconfigs/r/rclone/rclone-1.66.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.66.0.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.66.0.eb b/easybuild/easyconfigs/r/rclone/rclone-1.66.0.eb new file mode 100644 index 000000000000..18b8b6c77b80 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.66.0.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'rclone' +version = '1.66.0' + +homepage = 'https://rclone.org' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['9249391867044a0fa4c5a948b46a03b320706b4d5c4d59db9d4aeff8d47cade2'] + +builddependencies = [('Go', '1.22.1', '', SYSTEM)] + +postinstallcmds = [ + "mkdir -p %(installdir)s/share/{doc,man/man1}", + "cp README.* MANUAL.* %(installdir)s/share/doc/", + "cp rclone.1 %(installdir)s/share/man/man1/", +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From ecff7c243c7412a7cfc1726fc351da2d0f7f1bf8 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 28 Mar 2024 20:11:30 +0100 Subject: [PATCH 1164/1193] fix configure --- easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb | 1 - easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb | 1 - easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb | 1 - easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb | 1 - easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb | 1 - 5 files changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb index 9ad1188b7f2e..42f38528005b 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.2.0.eb @@ -35,7 +35,6 @@ dependencies = [ ('numactl', '2.0.14'), ] -preconfigopts = "./autogen.sh && " configure_cmd = "contrib/configure-release" configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb index 15555a67300d..3627a39308c4 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-11.3.0.eb @@ -35,7 +35,6 @@ dependencies = [ ('numactl', '2.0.14'), ] -preconfigopts = "./autogen.sh && " configure_cmd = "contrib/configure-release" configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb index 521eb44b02b5..b49c37a93ed6 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.2.0.eb @@ -35,7 +35,6 @@ dependencies = [ ('numactl', '2.0.16'), ] -preconfigopts = "./autogen.sh && " configure_cmd = "contrib/configure-release" configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb index 2fa35cbab22b..b4530aa124ad 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-12.3.0.eb @@ -35,7 +35,6 @@ dependencies = [ ('numactl', '2.0.16'), ] -preconfigopts = "./autogen.sh && " configure_cmd = "contrib/configure-release" configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' diff --git a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb index f94cd475de85..66faa507c277 100644 --- a/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/u/UCX/UCX-1.16.0-rc4-GCCcore-13.2.0.eb @@ -35,7 +35,6 @@ dependencies = [ ('numactl', '2.0.16'), ] -preconfigopts = "./autogen.sh && " configure_cmd = "contrib/configure-release" configopts = '--enable-optimizations --enable-cma --enable-mt --with-verbs ' From 738312ddffc16bab6e96be7994db5b0452de46d1 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 29 Mar 2024 12:37:50 -0700 Subject: [PATCH 1165/1193] update toolchani HDF --- .../h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6f54f50d4887 --- /dev/null +++ b/easybuild/easyconfigs/h/HDF/HDF-4.2.16-2-GCCcore-13.2.0.eb @@ -0,0 +1,60 @@ +easyblock = 'ConfigureMake' + +name = 'HDF' +version = '4.2.16-2' + +homepage = 'https://www.hdfgroup.org/products/hdf4/' +description = """ + HDF (also known as HDF4) is a library and multi-object file format for + storing and managing data between machines. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://www.hdfgroup.org/ftp/%(name)s/releases/%(name)s%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] + +checksums = [ + 'a24b18312d421686031c2d66635f7d5abb2fe879f8a182b7e02797b0da8d1f6c', # %(namelower)s-%(version)s.tar.gz +] + +builddependencies = [ + ('binutils', '2.40'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] +dependencies = [ + ('libjpeg-turbo', '3.0.1'), + ('Szip', '2.1.1'), + ('zlib', '1.2.13'), + ('libtirpc', '1.3.4'), +] + +preconfigopts = "LIBS='-ltirpc' " + +local_common_configopts = '--with-szlib=$EBROOTSZIP CFLAGS="$CFLAGS -I$EBROOTLIBTIRPC/include/tirpc" ' +local_common_configopts += '--includedir=%(installdir)s/include/%(namelower)s ' + +configopts = [ + local_common_configopts, + # Cannot build shared libraries and Fortran... + # https://trac.osgeo.org/gdal/wiki/HDF#IncompatibilitywithNetCDFLibraries + # netcdf must be disabled to allow HDF to be used by GDAL + local_common_configopts + "--enable-shared --disable-fortran --disable-netcdf", +] + + +sanity_check_paths = { + 'files': ['bin/h4cc', 'bin/ncdump', 'lib/libdf.a', 'lib/libhdf4.settings', 'lib/libmfhdf.a', 'lib/libmfhdf.so'], + 'dirs': ['include/%(namelower)s'], +} + +sanity_check_commands = [ + "h4cc --help", + "ncdump -V", +] + +modextrapaths = {'CPATH': 'include/%(namelower)s'} + +moduleclass = 'data' From f9dc5a31ec5cf02b04866f948d0d8863eeb62dc8 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 29 Mar 2024 12:46:19 -0700 Subject: [PATCH 1166/1193] json-c-0.17-GCCcore-13.2.0 --- .../j/json-c/json-c-0.17-GCCcore-13.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.2.0.eb b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..03fa34a87b9b --- /dev/null +++ b/easybuild/easyconfigs/j/json-c/json-c-0.17-GCCcore-13.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'CMakeMake' + +name = 'json-c' +version = '0.17' +local_suff = '-20230812' + +homepage = 'https://github.com/json-c/json-c' +description = """JSON-C implements a reference counting object model that allows you to easily construct JSON objects + in C, output them as JSON formatted strings and parse JSON formatted strings back into the C representation of JSON +objects.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/json-c/json-c/archive/'] +sources = ['json-c-%%(version)s%s.tar.gz' % local_suff] +checksums = ['024d302a3aadcbf9f78735320a6d5aedf8b77876c8ac8bbb95081ca55054c7eb'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +# disable using Valgrind during the tests to avoid failures caused by using an OS Valgrind +pretestopts = 'USE_VALGRIND=0 ' +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libjson-c.a', 'lib/libjson-c.%s' % SHLIB_EXT, 'lib/pkgconfig/json-c.pc'], + 'dirs': ['include/json-c'], +} + +moduleclass = 'lib' From afff6f5fd59545e2e4f56225b42f1d9516c77033 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 29 Mar 2024 13:04:03 -0700 Subject: [PATCH 1167/1193] update Xerces --- .../Xerces-C++-3.2.5-GCCcore-13.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.2.0.eb b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..bd3ec06470cd --- /dev/null +++ b/easybuild/easyconfigs/x/Xerces-C++/Xerces-C++-3.2.5-GCCcore-13.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'Xerces-C++' +version = '3.2.5' + +homepage = 'https://xerces.apache.org/xerces-c/' + +description = """Xerces-C++ is a validating XML parser written in a portable +subset of C++. Xerces-C++ makes it easy to give your application the ability to +read and write XML data. A shared library is provided for parsing, generating, +manipulating, and validating XML documents using the DOM, SAX, and SAX2 +APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://archive.apache.org/dist/xerces/c/%(version_major)s/sources/'] +sources = ['xerces-c-%(version)s.tar.gz'] +checksums = ['545cfcce6c4e755207bd1f27e319241e50e37c0c27250f11cda116018f1ef0f5'] + +builddependencies = [ + ('pkgconf', '2.0.3'), + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +dependencies = [ + ('cURL', '8.3.0'), +] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/XInclude', + 'include/xercesc/xinclude/XIncludeUtils.hpp', + 'lib/libxerces-c-3.2.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'lib' From a0c59bc3a6b38ba5ddd01d2ae8ebcaf6b6c10e23 Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 29 Mar 2024 14:30:50 -0700 Subject: [PATCH 1168/1193] LERC update toolchain --- .../l/LERC/LERC-4.0.0-GCCcore-13.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..160bcf963836 --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-4.0.0-GCCcore-13.2.0.eb @@ -0,0 +1,45 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'LERC' +version = '4.0.0' + +homepage = 'https://github.com/Esri/lerc' +description = """LERC is an open-source image or raster format which supports rapid encoding and decoding +for any pixel type (not just RGB or Byte). Users set the maximum compression error per pixel while encoding, +so the precision of the original input image is preserved (within user defined error bounds).""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91431c2b16d0e3de6cbaea188603359f87caed08259a645fd5a3805784ee30a0'] + +builddependencies = [ + ('binutils', '2.40'), + ('CMake', '3.27.6'), +] + +configopts = '-DCMAKE_INSTALL_LIBDIR=lib' + +postinstallcmds = [ + # copy the LercTest source file to a LercTest subdir in the installation directory and compile it + # (needs to be done here instead of in the sanity check, else it won't work when RPATH linking is enabled) + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "mkdir %(installdir)s/LercTest", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/LercTest/main.cpp", + "cd %(installdir)s/LercTest && ${CXX} ${CXXFLAGS} main.cpp -o LercTest -I../include -L../lib -lLerc", +] + +sanity_check_commands = [ + "%(installdir)s/LercTest/LercTest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From b787c08d624b65b6bbb736071a21cfabab622d8a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 30 Mar 2024 02:47:49 +0000 Subject: [PATCH 1169/1193] adding easyconfigs: lit-18.1.2-GCCcore-12.3.0.eb --- .../l/lit/lit-18.1.2-GCCcore-12.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb new file mode 100644 index 000000000000..27bc5b5e7a62 --- /dev/null +++ b/easybuild/easyconfigs/l/lit/lit-18.1.2-GCCcore-12.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'lit' +version = '18.1.2' + +homepage = 'https://llvm.org/docs/CommandGuide/lit.html' +description = """lit is a portable tool for executing LLVM and Clang style test suites, summarizing their results, and +providing indication of failures.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), +] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['fdead6e464f9d975d31a937b82e1162d0768d61a0e5d8ee55991a33ed4aa7128'], + }), +] + +sanity_check_commands = ['lit -h'] + +moduleclass = 'tools' From e343f980dacf6d2118d22f35351dd8f3d23fb6b6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 30 Mar 2024 13:08:29 +0100 Subject: [PATCH 1170/1193] add patch to fix for libarchive to fix error reporting in tar --- ...rchive-3.6.0_fix-tar-error-reporting.patch | 27 +++++++++++++++++++ .../libarchive-3.6.1-GCCcore-11.3.0.eb | 7 ++++- .../libarchive-3.6.1-GCCcore-12.2.0.eb | 7 ++++- .../libarchive-3.6.2-GCCcore-12.3.0.eb | 7 ++++- .../libarchive-3.6.2-GCCcore-13.1.0.eb | 7 ++++- .../libarchive-3.7.2-GCCcore-13.2.0.eb | 7 ++++- 6 files changed, 57 insertions(+), 5 deletions(-) create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.0_fix-tar-error-reporting.patch diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.0_fix-tar-error-reporting.patch b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.0_fix-tar-error-reporting.patch new file mode 100644 index 000000000000..57857d416a2c --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.0_fix-tar-error-reporting.patch @@ -0,0 +1,27 @@ +see https://github.com/libarchive/libarchive/pull/2101 +From e200fd8abfb4cf895a1cab4d89b67e6eefe83942 Mon Sep 17 00:00:00 2001 +From: Ed Maste +Date: Fri, 29 Mar 2024 16:38:11 -0400 +Subject: [PATCH] tar: make error reporting more robust and use correct errno + +As discussed in #1609. +--- + tar/read.c | 5 +++-- + 1 file changed, 3 insertions(+), 2 deletions(-) + +diff --git a/tar/read.c b/tar/read.c +index af3d3f423..a7f14a07b 100644 +--- a/tar/read.c ++++ b/tar/read.c +@@ -371,8 +371,9 @@ read_archive(struct bsdtar *bsdtar, char mode, struct archive *writer) + if (r != ARCHIVE_OK) { + if (!bsdtar->verbose) + safe_fprintf(stderr, "%s", archive_entry_pathname(entry)); +- fprintf(stderr, ": %s: ", archive_error_string(a)); +- fprintf(stderr, "%s", strerror(errno)); ++ safe_fprintf(stderr, ": %s: %s", ++ archive_error_string(a), ++ strerror(archive_errno(a))); + if (!bsdtar->verbose) + fprintf(stderr, "\n"); + bsdtar->return_value = 1; diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb index 2f0d0841e1b7..770e79b16638 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-11.3.0.eb @@ -13,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://www.libarchive.org/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'] +patches = ['libarchive-3.6.0_fix-tar-error-reporting.patch'] +checksums = [ + {'libarchive-3.6.1.tar.gz': 'c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'}, + {'libarchive-3.6.0_fix-tar-error-reporting.patch': + 'cf11f2d6e403cbb700f8ad1f67141f2a54884fa25e07d6a7919b0b6865d2cba2'}, +] builddependencies = [ ('binutils', '2.38'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb index 8cc05cbcb017..aa2a9c42b8d5 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb @@ -13,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://www.libarchive.org/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'] +patches = ['libarchive-3.6.0_fix-tar-error-reporting.patch'] +checksums = [ + {'libarchive-3.6.1.tar.gz': 'c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'}, + {'libarchive-3.6.0_fix-tar-error-reporting.patch': + 'cf11f2d6e403cbb700f8ad1f67141f2a54884fa25e07d6a7919b0b6865d2cba2'}, +] builddependencies = [ ('binutils', '2.39'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb index 8460682342fd..0e1fd34ce1f0 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-12.3.0.eb @@ -13,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://www.libarchive.org/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'] +patches = ['libarchive-3.6.0_fix-tar-error-reporting.patch'] +checksums = [ + {'libarchive-3.6.2.tar.gz': 'ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'}, + {'libarchive-3.6.0_fix-tar-error-reporting.patch': + 'cf11f2d6e403cbb700f8ad1f67141f2a54884fa25e07d6a7919b0b6865d2cba2'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb index f0260cb95ae6..086b414eec2b 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.2-GCCcore-13.1.0.eb @@ -13,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '13.1.0'} source_urls = ['https://www.libarchive.org/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'] +patches = ['libarchive-3.6.0_fix-tar-error-reporting.patch'] +checksums = [ + {'libarchive-3.6.2.tar.gz': 'ba6d02f15ba04aba9c23fd5f236bb234eab9d5209e95d1c4df85c44d5f19b9b3'}, + {'libarchive-3.6.0_fix-tar-error-reporting.patch': + 'cf11f2d6e403cbb700f8ad1f67141f2a54884fa25e07d6a7919b0b6865d2cba2'}, +] builddependencies = [ ('binutils', '2.40'), diff --git a/easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb index c31b668a2460..8cfed22355cb 100644 --- a/easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.7.2-GCCcore-13.2.0.eb @@ -13,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} source_urls = ['https://www.libarchive.org/downloads/'] sources = [SOURCE_TAR_GZ] -checksums = ['df404eb7222cf30b4f8f93828677890a2986b66ff8bf39dac32a804e96ddf104'] +patches = ['libarchive-3.6.0_fix-tar-error-reporting.patch'] +checksums = [ + {'libarchive-3.7.2.tar.gz': 'df404eb7222cf30b4f8f93828677890a2986b66ff8bf39dac32a804e96ddf104'}, + {'libarchive-3.6.0_fix-tar-error-reporting.patch': + 'cf11f2d6e403cbb700f8ad1f67141f2a54884fa25e07d6a7919b0b6865d2cba2'}, +] builddependencies = [ ('binutils', '2.40'), From b1b1587f1df347e68b9dd37fa259413345eedae8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sat, 30 Mar 2024 18:40:58 +0100 Subject: [PATCH 1171/1193] Update easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb --- .../easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb index e43ec77c556f..aa3958606a9f 100644 --- a/easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/remake/remake-4.3+dbg-1.6-GCCcore-11.3.0.eb @@ -17,6 +17,10 @@ builddependencies = [ ('binutils', '2.38'), ] +dependencies = [ + ('libreadline', '8.1.2'), +] + sanity_check_paths = { 'files': ['bin/remake'], 'dirs': ['share'], From 645965a9fd5cb46f62d3cf358f2bb56cf65863de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 31 Mar 2024 01:35:34 +0100 Subject: [PATCH 1172/1193] Update easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb --- .../easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb index 4ad96107753e..ada844d45ca8 100644 --- a/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-13.2.0.eb @@ -14,6 +14,10 @@ toolchain = {'name': 'GCCcore', 'version': '13.2.0'} sources = [SOURCE_TAR_GZ] checksums = ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'] +builddependencies = [ + ('binutils', '2.40'), +] + dependencies = [ ('Python', '3.11.5'), ] From 21f214a082cd09bb287988710ad13b06e5394972 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 31 Mar 2024 01:53:04 +0100 Subject: [PATCH 1173/1193] Update easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb --- .../p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb index 5384c4a4efd3..7636002c0916 100644 --- a/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/p/pytest-workflow/pytest-workflow-2.1.0-GCCcore-13.2.0.eb @@ -21,7 +21,6 @@ dependencies = [ ('python-isal', '1.6.1'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 937a526d1d62e02748a3b0ceb52d691c401dffa9 Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Sun, 31 Mar 2024 17:37:59 +0200 Subject: [PATCH 1174/1193] adding easyconfigs: ParaView-5.12.0-foss-2023b.eb, Qt6-6.6.3-GCCcore-13.2.0.eb, assimp-5.3.1-GCCcore-13.2.0.eb and patches: Qt6-6.6.3_fix_OF-Gentoo.patch --- .../a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb | 35 ++++++++ .../p/ParaView/ParaView-5.12.0-foss-2023b.eb | 72 +++++++++++++++ .../q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb | 90 +++++++++++++++++++ .../q/Qt6/Qt6-6.6.3_fix_OF-Gentoo.patch | 49 ++++++++++ 4 files changed, 246 insertions(+) create mode 100644 easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb create mode 100644 easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt6/Qt6-6.6.3_fix_OF-Gentoo.patch diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..03cddcca4194 --- /dev/null +++ b/easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb @@ -0,0 +1,35 @@ +# Authors:: Richard Lawrence - TAMU HPRC - https://hprc.tamu.edu + +easyblock = 'CMakeMake' + +name = 'assimp' +version = '5.3.1' + +homepage = 'https://github.com/assimp/assimp' + +description = """ + Open Asset Import Library (assimp) is a library to import and export various + 3d-model-formats including scene-post-processing to generate missing render data. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://github.com/%(name)s/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a07666be71afe1ad4bc008c2336b7c688aca391271188eb9108d0c6db1be53f1'] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('CMake', '3.27.6'), + ('zlib', '1.2.13'), +] + +configopts = '-DASSIMP_WARNINGS_AS_ERRORS=OFF ' # workaround bug with GCC13 https://github.com/assimp/assimp/issues/5315 + +sanity_check_paths = { + 'files': ['include/assimp/types.h', 'lib/libassimp.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb new file mode 100644 index 000000000000..14fedad74f48 --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.12.0' + +homepage = 'https://www.paraview.org' +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'pic': True, 'usempi': True} + +local_download_suffix = 'download.php?submit=Download&version=v%(version_major_minor)s&type=source&os=all&downloadFile=' +source_urls = ['https://www.paraview.org/paraview-downloads/%s' % local_download_suffix] +sources = ["%(name)s-v%(version)s.tar.gz"] +patches = ['ParaView-5.11.1-remove_glew_init_warning.patch'] +checksums = [ + {'ParaView-v5.12.0.tar.gz': '2cc5733608fd508e2da8fc5d4ee693523d350dc1e1f89f9a89a78dc63107f70e'}, + {'ParaView-5.11.1-remove_glew_init_warning.patch': + 'dd86134f3a5b2c1b834224c69665dd31f99ef7d367688fe77dbaada212758710'}, +] + +builddependencies = [('CMake', '3.27.6')] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('Boost', '1.83.0'), + ('XZ', '5.4.4'), + ('HDF5', '1.14.3'), + ('netCDF', '4.9.2'), + ('libdrm', '2.4.117'), + ('Mesa', '23.1.9'), + ('Qt6', '6.6.3'), + ('zlib', '1.2.13'), + ('FFmpeg', '6.0'), + ('Szip', '2.1.1'), +] + +_copts = [ + # Basic configuration + '-DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION=OFF', # Not supported with Qt6 https://gitlab.kitware.com/paraview/paraview/-/issues/19742 + '-DCMAKE_AUTOMOC=OFF', # err Qt6? + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', + '-DPARAVIEW_BUILD_SHARED_LIBS=ON', + '-DPARAVIEW_USE_MPI=ON', + '-DPARAVIEW_ENABLE_FFMPEG=ON', + '-DPARAVIEW_USE_PYTHON=ON', + '-DPython3_ROOT_DIR=$EBROOTPYTHON', + # Useful input formats + '-DPARAVIEW_ENABLE_XDMF2=ON', + '-DPARAVIEW_ENABLE_XDMF3=ON', + # EGL, X and Mesa + '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s' % SHLIB_EXT, + '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include', + '-DEGL_INCLUDE_DIR=$EBROOTLIBGLVND/include', + '-DEGL_LIBRARY=$EBROOTLIBGLVND/lib/libEGL.%s' % SHLIB_EXT, + '-DEGL_opengl_LIBRARY=$EBROOTLIBGLVND/libOpenGL.%s' % SHLIB_EXT, + '-DVTK_OPENGL_HAS_EGL=ON', + '-DVTK_USE_X=ON', + '-DVTK_OPENGL_HAS_OSMESA=OFF'] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvserver', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb new file mode 100644 index 000000000000..6e2c632ddec2 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb @@ -0,0 +1,90 @@ +easyblock = 'CMakeNinja' + +name = 'Qt6' +version = '6.6.3' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} +# disabling use of -ftree-vectorize is required to avoid compilation failures on some systems (e.g. Intel Skylake X) +toolchainopts = {'vectorize': False} + +source_urls = [ + 'https://download.qt.io/official_releases/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/archive/qt/%(version_major_minor)s/%(version)s/single/', + 'https://download.qt.io/new_archive/qt/%(version_major_minor)s/%(version)s/single/', +] +sources = ['qt-everywhere-src-%(version)s.tar.xz'] +patches = [ + 'Qt6-6.6.3_fix_OF-Gentoo.patch', +] +checksums = [ + {'qt-everywhere-src-6.6.3.tar.xz': '69d0348fef415da98aa890a34651e9cfb232f1bffcee289b7b4e21386bf36104'}, + {'Qt6-6.6.3_fix_OF-Gentoo.patch': 'd4d4878ac76cb985e45eb3b6e90ba2233f65807d6bd9bbe2b71365b181347b7b'}, +] + +builddependencies = [ + ('binutils', '2.40'), + ('pkgconf', '2.0.3'), + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('re2c', '3.1'), +] + +dependencies = [ + ('double-conversion', '3.3.0'), + ('GLib', '2.78.1'), + ('PCRE2', '10.42'), + ('libpng', '1.6.40'), + ('LibTIFF', '4.6.0'), + ('libwebp', '1.3.2'), + ('JasPer', '4.0.0'), + #('HarfBuzz', '5.3.1'), + ('HarfBuzz', '8.2.2'), + ('SQLite', '3.43.1'), + ('graphite2', '1.3.14'), + ('assimp', '5.3.1'), # for Qt 3D + ('FFmpeg', '6.0'), + ('X11', '20231019'), + ('fontconfig', '2.14.2'), + ('zlib', '1.2.13'), + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # WebEngine + ('freetype', '2.13.2'), # WebEngine + ('DBus', '1.15.8'), + ('libevent', '2.1.12'), # WebEngine + ('libGLU', '9.0.3'), + ('libjpeg-turbo', '3.0.1'), # WebEngine + ('NSS', '3.94'), # WebEngine, required + ('snappy', '1.1.10'), # WebEngine + ('OpenSSL', '1.1', '', SYSTEM), + ('ICU', '74.1'), # WebEngine, optional + ('nodejs', '20.9.0'), # WebEngine, required + # ('gRPC', '1.52.2'), # WebEngine needs older Abseil/gRPC/protobuf +] + +preconfigopts = 'sed -i "s/MultiMedia/Multimedia/g" ../qt-everywhere-src-%(version)s/qtcharts/CMakeLists.txt &&' # Typo +preconfigopts += 'sed -i "23i set(Python3_ROOT_DIR \\$ENV{EBROOTPYTHON})" ' \ + '../qt-everywhere-src-6.6.3/qtwebengine/src/gn/CMakeLists.txt &&' + +configopts = '-Wno-dev ' +configopts += '-DFEATURE_qtpdf_build=OFF ' # Requires CUPS +configopts += '-DQT_AVOID_CMAKE_ARCHIVING_API=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' +configopts += '-DBUILD_qtwayland=OFF ' # Does not work on CentOS 7 +# Removed from Qt6.0.0 but may be added back in the future +# configopts += '-DBUILD_qtgamepad=OFF ' # Does not work on CentOS 7 + +sanity_check_paths = { + 'files': ['bin/qmake6', 'lib/libQt6Core.%s' % SHLIB_EXT, 'lib/libQt6WebEngineCore.%s' % SHLIB_EXT], + 'dirs': ['include/QtCore', 'include/QtWebEngineCore'], +} + +sanity_check_commands = ['qmake6 --help'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3_fix_OF-Gentoo.patch b/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3_fix_OF-Gentoo.patch new file mode 100644 index 000000000000..9ba2974b9b73 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3_fix_OF-Gentoo.patch @@ -0,0 +1,49 @@ +############################################ +# Update from Qt5-5.14.1_fix-OF-Gentoo.patch +# 1. qt3d/..../unzip/ioapi.h and qtquick3d/..../unzip/ioapi.h do not use OF macro anymore +# 2. qtquick3d/..../minizip/ioapi.h is moved to qt3d/..../minizip/ioapi.h +############################################ +fix compilation on top of zlib provided by Gentoo, +where OF macro has been renamed to _Z_OF +see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 +author: Kenneth Hoste (HPC-UGent) +diff --git a/qt3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h +b/qt3d/src/3rdparty/assimp/src/contrib/zlib/contrib/unzip/ioapi.h +index 8dcbdb06e3..e9cc96914e 100644 +--- a/qt3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h ++++ b/qt3d/src/3rdparty/assimp/src/contrib/unzip/ioapi.h +@@ -130,6 +130,14 @@ extern "C" { + #endif + + ++// if OF macro is not defined but _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif + + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); +diff --git a/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h b/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h +index c1b7a54847..c5546a26b9 100644 +--- a/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h ++++ b/qtwebengine/src/3rdparty/chromium/third_party/zlib/contrib/minizip/ioapi.h +@@ -130,6 +130,14 @@ extern "C" { + #endif + + ++// if OF macro is not defined but _Z_OF is, define OF as _Z_OF ++// required when building with zlib provided by Gentoo ++// see https://bugreports.qt.io/browse/QTBUG-68467 and https://bugs.gentoo.org/383179 ++#ifndef OF ++ #ifdef _Z_OF ++ #define OF _Z_OF ++ #endif ++#endif + + + typedef voidpf (ZCALLBACK *open_file_func) OF((voidpf opaque, const char* filename, int mode)); + From 8af2e6141f5d1fc4568a6fe73a5f9f6a7cccb47e Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Sun, 31 Mar 2024 18:28:17 +0200 Subject: [PATCH 1175/1193] fix style errors --- .../a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb | 3 ++- .../p/ParaView/ParaView-5.12.0-foss-2023b.eb | 5 +++-- .../easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb | 13 ++++++------- 3 files changed, 11 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb index 03cddcca4194..6d89f82e89f0 100644 --- a/easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/a/assimp/assimp-5.3.1-GCCcore-13.2.0.eb @@ -25,7 +25,8 @@ builddependencies = [ ('zlib', '1.2.13'), ] -configopts = '-DASSIMP_WARNINGS_AS_ERRORS=OFF ' # workaround bug with GCC13 https://github.com/assimp/assimp/issues/5315 +# workaround bug with GCC13 https://github.com/assimp/assimp/issues/5315 +configopts = '-DASSIMP_WARNINGS_AS_ERRORS=OFF ' sanity_check_paths = { 'files': ['include/assimp/types.h', 'lib/libassimp.%s' % SHLIB_EXT], diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb index 14fedad74f48..018edd704319 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.12.0-foss-2023b.eb @@ -38,8 +38,9 @@ dependencies = [ _copts = [ # Basic configuration - '-DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION=OFF', # Not supported with Qt6 https://gitlab.kitware.com/paraview/paraview/-/issues/19742 - '-DCMAKE_AUTOMOC=OFF', # err Qt6? + # Embedded docs not supported with Qt6 https://gitlab.kitware.com/paraview/paraview/-/issues/19742 + '-DPARAVIEW_ENABLE_EMBEDDED_DOCUMENTATION=OFF', + '-DCMAKE_AUTOMOC=OFF', # err Qt6? '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', '-DPARAVIEW_BUILD_SHARED_LIBS=ON', '-DPARAVIEW_USE_MPI=ON', diff --git a/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb index 6e2c632ddec2..605542a89fd2 100644 --- a/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/q/Qt6/Qt6-6.6.3-GCCcore-13.2.0.eb @@ -25,26 +25,25 @@ checksums = [ ] builddependencies = [ - ('binutils', '2.40'), + ('binutils', '2.40'), ('pkgconf', '2.0.3'), - ('CMake', '3.27.6'), - ('Ninja', '1.11.1'), - # deps for QtWebEngine + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + # deps for QtWebEngine ('Bison', '3.8.2'), ('flex', '2.6.4'), ('gperf', '3.1'), - ('re2c', '3.1'), + ('re2c', '3.1'), ] dependencies = [ - ('double-conversion', '3.3.0'), + ('double-conversion', '3.3.0'), ('GLib', '2.78.1'), ('PCRE2', '10.42'), ('libpng', '1.6.40'), ('LibTIFF', '4.6.0'), ('libwebp', '1.3.2'), ('JasPer', '4.0.0'), - #('HarfBuzz', '5.3.1'), ('HarfBuzz', '8.2.2'), ('SQLite', '3.43.1'), ('graphite2', '1.3.14'), From c4db5755171f47095883853b8d43cdf677ffc74a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 1 Apr 2024 11:44:39 +0200 Subject: [PATCH 1176/1193] remove duplicate sanity_pip_check in NGSpeciesID easyconfig --- .../easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb index ad912110bf76..1116be83c609 100644 --- a/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NGSpeciesID/NGSpeciesID-0.3.0-foss-2023a.eb @@ -23,7 +23,6 @@ dependencies = [ download_dep_fail = True use_pip = True -sanity_pip_check = True # no proper namespace for NGSpeciesID options = {'modulename': 'modules.consensus'} From b93722eb396c4a40a4c2ae1b986bd8fb3bf522c6 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 1 Apr 2024 12:03:21 +0200 Subject: [PATCH 1177/1193] Put Python dep on single line --- .../easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb index fb35e2272168..7de89e6102a8 100644 --- a/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/Markdown/Markdown-3.6-GCCcore-12.2.0.eb @@ -15,9 +15,7 @@ sources = [SOURCE_TAR_GZ] checksums = ['ed4f41f6daecbeeb96e576ce414c41d2d876daa9a16cb35fa8ed8c2ddfad0224'] builddependencies = [('binutils', '2.39')] -dependencies = [ - ('Python', '3.10.8'), -] +dependencies = [('Python', '3.10.8')] download_dep_fail = True sanity_pip_check = True From 626c1ac0044e209fc0733532b2338d8981247afb Mon Sep 17 00:00:00 2001 From: Louwrens van Dellen Date: Mon, 1 Apr 2024 23:12:38 +0200 Subject: [PATCH 1178/1193] add GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch --- .../easyconfigs/g/GCCcore/GCCcore-13.2.0.eb | 3 ++ ...fix-unguarded-is_convertible-builtin.patch | 43 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb index 12f599fdd8fd..2876160159de 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0.eb @@ -37,6 +37,7 @@ patches = [ 'GCCcore-12.2.0_fix-avx512-misoptimization.patch', 'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch', 'GCCcore-12.x_riscv_multiarch_support.patch', + 'GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch', ] checksums = [ {'gcc-13.2.0.tar.gz': '8cb4be3796651976f94b9356fa08d833524f62420d6292c5033a9a26af315078'}, @@ -54,6 +55,8 @@ checksums = [ {'GCCcore-13.2.0_fix_slp_and_loop_mask_len.patch': 'e1d63e04bf494a2f79346ac7454372f117b63288cc18c68876a5b8bdc453cf88'}, {'GCCcore-12.x_riscv_multiarch_support.patch': '92fc2b17b6943611a657904500fbf3db8160eddbcea320828d4a50a885e2778f'}, + {'GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch': + '8650d6d4f41e32e9f5f23272d27a6d6adce3cd46ff44483f160b1d3bd92b1dbd'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch new file mode 100644 index 000000000000..4e752516115a --- /dev/null +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch @@ -0,0 +1,43 @@ +Source: https://gcc.gnu.org/bugzilla/show_bug.cgi?id=113241 + +From 4c66513656775d551db36b53c253cf236f0eeba8 Mon Sep 17 00:00:00 2001 +From: Jonathan Wakely +Date: Fri, 5 Jan 2024 12:03:22 +0000 +Subject: [PATCH] libstdc++: Do not use __is_convertible unconditionally + [PR113241] + +The new __is_convertible built-in should only be used after checking +that it's supported. + +libstdc++-v3/ChangeLog: + + PR libstdc++/113241 + * include/std/type_traits (is_convertible_v): Guard use of + built-in with preprocessor check. + +(cherry picked from commit 57fa5b60bbbf8038b8a699d2bcebd2a9b2e29aa4) +--- + libstdc++-v3/include/std/type_traits | 5 +++++ + 1 file changed, 5 insertions(+) + +diff --git a/libstdc++-v3/include/std/type_traits b/libstdc++-v3/include/std/type_traits +index 2bd607a8b8f..2b05e371953 100644 +--- a/libstdc++-v3/include/std/type_traits ++++ b/libstdc++-v3/include/std/type_traits +@@ -3359,8 +3359,13 @@ template + #endif + template + inline constexpr bool is_base_of_v = __is_base_of(_Base, _Derived); ++#if __has_builtin(__is_convertible) + template + inline constexpr bool is_convertible_v = __is_convertible(_From, _To); ++#else ++template ++ inline constexpr bool is_convertible_v = is_convertible<_From, _To>::value; ++#endif + template + inline constexpr bool is_invocable_v = is_invocable<_Fn, _Args...>::value; + template +-- +2.39.3 + From d255d5fba01b63f52422ad2eb9a17639025c2400 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 1 Apr 2024 23:14:20 +0200 Subject: [PATCH 1179/1193] Update easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb --- easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb index 3024279f7ab0..7a942df7b9a5 100644 --- a/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb +++ b/easybuild/easyconfigs/s/Saxon-HE/Saxon-HE-12.4-Java-21.eb @@ -23,7 +23,4 @@ sanity_check_paths = { 'files': local_jarfiles, 'dirs': [], } - -modextrapaths = {'CLASSPATH': local_jarfiles} - moduleclass = 'devel' From d7c4d6bda4a07ee1e295ef612746b0f29b18f153 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Mon, 1 Apr 2024 22:35:47 +0000 Subject: [PATCH 1180/1193] Update Java-8 wrapper to 8.402 --- easybuild/easyconfigs/j/Java/Java-8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/Java/Java-8.eb b/easybuild/easyconfigs/j/Java/Java-8.eb index 854eccb56cb8..759f3e84bbe9 100644 --- a/easybuild/easyconfigs/j/Java/Java-8.eb +++ b/easybuild/easyconfigs/j/Java/Java-8.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.362')] +dependencies = [('Java', '%(version)s.402')] moduleclass = 'lang' From b7ae6ad1344c0b10831c30f30e1209de5f221b94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 2 Apr 2024 10:19:30 +0200 Subject: [PATCH 1181/1193] fix download for python-parasail 1.3.4 by adding missing source URL --- .../p/python-parasail/python-parasail-1.3.4-foss-2023a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb index 26796f9e0d9e..1aba7a09500a 100644 --- a/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb +++ b/easybuild/easyconfigs/p/python-parasail/python-parasail-1.3.4-foss-2023a.eb @@ -8,6 +8,7 @@ description = "Python Bindings for the Parasail C Library" toolchain = {'name': 'foss', 'version': '2023a'} +source_urls = ['https://pypi.python.org/packages/source/p/parasail'] sources = ['parasail-%(version)s.tar.gz'] checksums = ['d6a7035dfae3ef5aafdd7e6915711214c22b572ea059fa69d9d7ecbfb9b61b0f'] From bc954ab3ce73e5b2a855f3aec8f3669d64887783 Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 2 Apr 2024 11:38:04 +0200 Subject: [PATCH 1182/1193] {tools}[foss/2023a] Optuna v3.5.0 --- .../g/Greenlet/Greenlet-3.0.2-foss-2023a.eb | 27 +++++++++ .../o/Optuna/Optuna-3.5.0-foss-2023a.eb | 57 +++++++++++++++++++ .../r/Redis/Redis-7.2.3-GCC-12.3.0.eb | 39 +++++++++++++ .../r/redis-py/redis-py-5.0.1-foss-2023a.eb | 32 +++++++++++ 4 files changed, 155 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-foss-2023a.eb new file mode 100644 index 000000000000..4ca8aa339a50 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-foss-2023a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '3.0.2' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [('Python', '3.11.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['1c1129bc47266d83444c85a8e990ae22688cf05fb20d7951fd2866007c2ba9bc'] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb new file mode 100644 index 000000000000..90959bb82f0e --- /dev/null +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb @@ -0,0 +1,57 @@ +easyblock = 'PythonBundle' + +name = 'Optuna' +version = '3.5.0' + +homepage = "https://optuna.org/" +description = """Optuna is an automatic hyperparameter optimization software framework, +particularly designed for machine learning. It features an imperative, +define-by-run style user API. Thanks to our define-by-run API, the code written +with Optuna enjoys high modularity, and the user of Optuna can dynamically +construct the search spaces for the hyperparameters.""" + + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2023.07'), + ('tqdm', '4.66.1'), + ('matplotlib', '3.7.2'), # optional + ('plotly.py', '5.16.0'), # optional + ('redis-py', '5.0.1'), # optional + ('scikit-learn', '1.3.1'), # optional + ('Mako', '1.2.4'), + ('Greenlet', '3.0.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('alembic', '1.13.0', { + 'checksums': ['ab4b3b94d2e1e5f81e34be8a9b7b7575fc9dd5398fccb0bef351ec9b14872623'], + }), + ('cmaes', '0.10.0', { + 'checksums': ['48afc70df027114739872b50489ae6b32461c307b92d084a63c7090a9742faf9'], + }), + ('colorlog', '6.8.0', { + 'checksums': ['fbb6fdf9d5685f2517f388fb29bb27d54e8654dd31f58bc2a3b217e967a95ca6'], + }), + ('SQLAlchemy', '2.0.23', { + 'checksums': ['c1bda93cbbe4aa2aa0aa8655c5aeda505cd219ff3e8da91d1d329e143e4aff69'], + }), + ('optuna', version, { + 'use_pip_extras': 'optional', + 'checksums': ['ca9e1ce16aa6c6a5af0e1cc1d0cbcd98eb1c75b6a2f06be6bd9c0c5ab0698724'], + }), +] + +sanity_check_paths = { + 'files': ['bin/optuna'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} +sanity_check_commands = [('optuna', '--help')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCC-12.3.0.eb new file mode 100644 index 000000000000..24215aec7910 --- /dev/null +++ b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCC-12.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'Redis' +version = '7.2.3' + +homepage = 'https://redis.io' +description = """Redis is an open source (BSD licensed), in-memory data structure store, used as +a database, cache, and message broker. Redis provides data structures such as +strings, hashes, lists, sets, sorted sets with range queries, bitmaps, +hyperloglogs, geospatial indexes, and streams. Redis has built-in replication, +Lua scripting, LRU eviction, transactions, and different levels of on-disk +persistence, and provides high availability via Redis Sentinel and automatic +partitioning with Redis Cluster.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://download.redis.io/releases'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3e2b196d6eb4ddb9e743088bfc2915ccbb42d40f5a8a3edd8cb69c716ec34be7'] + +builddependencies = [ + ('pkgconf', '1.9.5'), +] + +skipsteps = ['configure'] + +# tests must be run from a local filesystem +# runtest = 'test' + +installopts = 'PREFIX="%(installdir)s"' + +sanity_check_paths = { + 'files': ['bin/redis-cli', 'bin/redis-server'], + 'dirs': [], +} + +sanity_check_commands = [('redis-server', '--version')] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-foss-2023a.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-foss-2023a.eb new file mode 100644 index 000000000000..ab96aa0025da --- /dev/null +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'redis-py' +version = '5.0.1' + +homepage = 'https://github.com/redis/redis-py' +description = "The Python interface to the Redis key-value store." + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('typing-extensions', '4.9.0'), + ('Redis', '7.2.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('async-timeout', '4.0.3', { + 'checksums': ['4640d96be84d82d02ed59ea2b7105a0f7b33abe8703703cd0ab0bf87c427522f'], + }), + (name, version, { + 'modulename': 'redis', + 'source_urls': ['https://github.com/redis/redis-py/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['0a40afc824a5a3b465db4ba868a056a83779482f22d7d003c48fca230d9fe93a'], + }), +] + +moduleclass = "data" From 067b9c1bf132b059ec0d697a078cb07a83ace670 Mon Sep 17 00:00:00 2001 From: jfgrimm Date: Tue, 2 Apr 2024 15:51:46 +0100 Subject: [PATCH 1183/1193] add easyconfig test that checks if backdoored XZ versions are introduced --- test/easyconfigs/easyconfigs.py | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f4383cf23daa..d019fd82818a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -336,6 +336,14 @@ def test_deps(self): fails = [] for ec in self.parsed_easyconfigs: + # make sure we don't add backdoored XZ versions (5.6.0, 5.6.1) + # see https://access.redhat.com/security/cve/CVE-2024-3094 + if ec['ec']['name'] == 'XZ' and ec['ec']['version'] in ('5.6.0', '5.6.1'): + fail = ("XZ versions 5.6.0 and 5.6.1 contain malicious code, and should not be introduced into" + " EasyBuild. Please use another version instead. For more details, see" + " https://access.redhat.com/security/cve/CVE-2024-3094") + fails.append(fail) + # make sure that no odd versions (like 1.13) of HDF5 are used as a dependency, # since those are released candidates - only even versions (like 1.12) are stable releases; # see https://docs.hdfgroup.org/archive/support/HDF5/doc/TechNotes/Version.html From 6a7085ddddc63cbfc5fb4f68b522f2bb00de2b22 Mon Sep 17 00:00:00 2001 From: Adam Huffman <12435+verdurin@users.noreply.github.com> Date: Tue, 2 Apr 2024 15:22:54 +0000 Subject: [PATCH 1184/1193] adding easyconfigs: Java-19.0.2.eb, Java-19.eb --- easybuild/easyconfigs/j/Java/Java-19.0.2.eb | 30 +++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-19.eb | 14 ++++++++++ 2 files changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/j/Java/Java-19.0.2.eb create mode 100644 easybuild/easyconfigs/j/Java/Java-19.eb diff --git a/easybuild/easyconfigs/j/Java/Java-19.0.2.eb b/easybuild/easyconfigs/j/Java/Java-19.0.2.eb new file mode 100644 index 000000000000..f856b0a1fd72 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-19.0.2.eb @@ -0,0 +1,30 @@ +name = 'Java' +version = '19.0.2' +local_build = '7' + +homepage = 'https://openjdk.org' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '3a3ba7a3f8c3a5999e2c91ea1dca843435a0d1c43737bd2f6822b2f02fc52165', + local_tarball_tmpl % ('aarch64', local_build): + '1c4be9aa173cb0deb0d215643d9509c8900e5497290b29eee4bee335fa57984f', + local_tarball_tmpl % ('ppc64le', local_build): + '173d1256dfb9d13d309b5390e6bdf72d143b512201b0868f9d349d5ed3d64072', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-19.eb b/easybuild/easyconfigs/j/Java/Java-19.eb new file mode 100644 index 000000000000..0738b4391794 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-19.eb @@ -0,0 +1,14 @@ +easyblock = 'ModuleRC' + +name = 'Java' +version = '19' + +homepage = 'https://java.com/' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +dependencies = [('Java', '%(version)s.0.2')] + +moduleclass = 'lang' From 8d2a6311454f2219c43c2e02a8aa62806f4ced9a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:44:55 +0200 Subject: [PATCH 1185/1193] Update Optuna-3.5.0-foss-2023a.eb Use Greenfee 3.0.3 --- easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb index 90959bb82f0e..e515d06f533c 100644 --- a/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb @@ -23,7 +23,7 @@ dependencies = [ ('redis-py', '5.0.1'), # optional ('scikit-learn', '1.3.1'), # optional ('Mako', '1.2.4'), - ('Greenlet', '3.0.2'), + ('Greenlet', '3.0.3'), ] use_pip = True From 2283c46ebc78d7af21ddfcaf3e472a506ca2dddc Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:46:56 +0200 Subject: [PATCH 1186/1193] Update Optuna-3.5.0-foss-2023a.eb Revert --- easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb index e515d06f533c..90959bb82f0e 100644 --- a/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb +++ b/easybuild/easyconfigs/o/Optuna/Optuna-3.5.0-foss-2023a.eb @@ -23,7 +23,7 @@ dependencies = [ ('redis-py', '5.0.1'), # optional ('scikit-learn', '1.3.1'), # optional ('Mako', '1.2.4'), - ('Greenlet', '3.0.3'), + ('Greenlet', '3.0.2'), ] use_pip = True From bff57048a3586fcc1fdbdb8b9dc9cd2347ef973c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 2 Apr 2024 19:50:49 +0200 Subject: [PATCH 1187/1193] Update and rename Greenlet-3.0.2-foss-2023a.eb to Greenlet-3.0.2-GCCcore-12.3.0.eb Foss -> GCCcore --- ...t-3.0.2-foss-2023a.eb => Greenlet-3.0.2-GCCcore-12.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/g/Greenlet/{Greenlet-3.0.2-foss-2023a.eb => Greenlet-3.0.2-GCCcore-12.3.0.eb} (90%) diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-foss-2023a.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-GCCcore-12.3.0.eb similarity index 90% rename from easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-foss-2023a.eb rename to easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-GCCcore-12.3.0.eb index 4ca8aa339a50..e596c78a9616 100644 --- a/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-foss-2023a.eb +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.0.2-GCCcore-12.3.0.eb @@ -12,8 +12,8 @@ A "greenlet", on the other hand, is a still more primitive notion of micro-threa scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. """ -toolchain = {'name': 'foss', 'version': '2023a'} - +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [('binutils', '2.40')] dependencies = [('Python', '3.11.3')] use_pip = True From 78cf8167a9966b65c7850a99c13b9f46d2ebac5f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 3 Apr 2024 09:21:49 +0200 Subject: [PATCH 1188/1193] update copyright lines to 2024 --- setup.py | 2 +- test/__init__.py | 2 +- test/easyconfigs/easyconfigs.py | 2 +- test/easyconfigs/styletests.py | 2 +- test/easyconfigs/suite.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/setup.py b/setup.py index 52ad359c69c8..3f246266b7f9 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2023 Ghent University +# Copyright 2012-2024 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/__init__.py b/test/__init__.py index 01ba03af458f..8ab7c0ed706f 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -1,5 +1,5 @@ ## -# Copyright 2009-2023 Ghent University +# Copyright 2009-2024 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index d019fd82818a..e3fcacd6bd33 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1,5 +1,5 @@ ## -# Copyright 2013-2023 Ghent University +# Copyright 2013-2024 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/styletests.py b/test/easyconfigs/styletests.py index e765cdfc3f13..8c695514aba6 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -1,5 +1,5 @@ ## -# Copyright 2016-2023 Ghent University +# Copyright 2016-2024 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), diff --git a/test/easyconfigs/suite.py b/test/easyconfigs/suite.py index c058d96f0c58..4218fcaa7b2c 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -1,6 +1,6 @@ #!/usr/bin/python ## -# Copyright 2012-2023 Ghent University +# Copyright 2012-2024 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), From ca690b36e46abbf1071bcbe27992e58b85295f68 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 3 Apr 2024 09:34:25 +0100 Subject: [PATCH 1189/1193] Sanity check command added --- .../g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb index e0de59bb45c6..c5aade361771 100644 --- a/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/GKlib-METIS/GKlib-METIS-5.1.1-GCCcore-11.3.0.eb @@ -32,6 +32,8 @@ dependencies = [ ('Python', '3.10.4'), ] +sanity_check_commands = ['gkgraph -help'] + sanity_check_paths = { 'files': ['bin/gkgraph'], 'dirs': ['lib', 'include'], From 92982c44dc947aa2f5809c1ecccdb6efc6bcfdf1 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 3 Apr 2024 11:31:31 +0200 Subject: [PATCH 1190/1193] Update and rename redis-py-5.0.1-foss-2023a.eb to redis-py-5.0.1-GCCcore-12.3.0.eb foss->GCCcore --- ...py-5.0.1-foss-2023a.eb => redis-py-5.0.1-GCCcore-12.3.0.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/r/redis-py/{redis-py-5.0.1-foss-2023a.eb => redis-py-5.0.1-GCCcore-12.3.0.eb} (88%) diff --git a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-foss-2023a.eb b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.3.0.eb similarity index 88% rename from easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-foss-2023a.eb rename to easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.3.0.eb index ab96aa0025da..6248f0167692 100644 --- a/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-foss-2023a.eb +++ b/easybuild/easyconfigs/r/redis-py/redis-py-5.0.1-GCCcore-12.3.0.eb @@ -6,8 +6,9 @@ version = '5.0.1' homepage = 'https://github.com/redis/redis-py' description = "The Python interface to the Redis key-value store." -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} +builddependencies = [('binutils', '2.40')] dependencies = [ ('Python', '3.11.3'), ('typing-extensions', '4.9.0'), From 957a4a5e00670fe667fc94048638dadb42e3e4e8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 3 Apr 2024 11:35:01 +0200 Subject: [PATCH 1191/1193] Update and rename Redis-7.2.3-GCC-12.3.0.eb to Redis-7.2.3-GCCcore-12.3.0.eb GCC->GCCcore --- ...Redis-7.2.3-GCC-12.3.0.eb => Redis-7.2.3-GCCcore-12.3.0.eb} | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/r/Redis/{Redis-7.2.3-GCC-12.3.0.eb => Redis-7.2.3-GCCcore-12.3.0.eb} (93%) diff --git a/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCC-12.3.0.eb b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.3.0.eb similarity index 93% rename from easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCC-12.3.0.eb rename to easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.3.0.eb index 24215aec7910..d91246b6fe30 100644 --- a/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCC-12.3.0.eb +++ b/easybuild/easyconfigs/r/Redis/Redis-7.2.3-GCCcore-12.3.0.eb @@ -12,7 +12,7 @@ Lua scripting, LRU eviction, transactions, and different levels of on-disk persistence, and provides high availability via Redis Sentinel and automatic partitioning with Redis Cluster.""" -toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} source_urls = ['https://download.redis.io/releases'] sources = [SOURCELOWER_TAR_GZ] @@ -20,6 +20,7 @@ checksums = ['3e2b196d6eb4ddb9e743088bfc2915ccbb42d40f5a8a3edd8cb69c716ec34be7'] builddependencies = [ ('pkgconf', '1.9.5'), + ('binutils', '2.40'), ] skipsteps = ['configure'] From 7663a4360dd7ab5724fd35ccc0fffe9659522261 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 4 Apr 2024 15:43:48 +0800 Subject: [PATCH 1192/1193] prepare release notes for EasyBuild v4.9.1 + bump version to 4.9.1 --- RELEASE_NOTES | 163 +++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 163 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 3a655a1b5b37..2151130891d3 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,171 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 18,752 easyconfig files, for 3,369 different software packages, +The latest version of easybuild-easyconfig provides 19,487 easyconfig files, for 3,471 different software packages, incl. 40 different (compiler) toolchains. +v4.9.1 (5 April 2024) +--------------------- + +update/bugfix release + +- added example easyconfig files for 102 new software packages: + - AMICA (#19842), AreTomo2 (#19681), btllib (#19779), bwa-mem2 (#20217), CENSO (#19826), Circlator (#19847), Clarabel.rs (#20149), + code-cli (#19645), Concorde (#19768), contextily (#19807), CUTLASS (#19304), DeepLoc (#19514), Delft3D (#19869), DeltaLake (#19758), + denseweight (#20139), desktop-file-utils (#19701), DETONATE (#19547), devbio-napari (#19586), DjVuLibre (#19701), Elmer (#19448), + EnergyPlus (#19565), EpiSCORE (#18618), evince (#19701), ExpressBetaDiversity (#19938), ExtremeLy (#19870), f90nml (#19171), + FFAVES (#19822), fugue (#19694), gcsfs (#20042), GenomeComb (#19749), GI-DocGen (#19701), GKlib-METIS (#20096), GRASP-suite (#19665), + gspell (#19701), GUIDANCE (#20063), hdWGCNA (#20124), HF-Datasets (#20166), IDG (#18924), igvShiny (#19714), inflection (#20036), + InterOp (#19303), IonQuant (#19812), Lab-Streaming-Layer (#19945), Levenshtein (#19771), libfyaml (#19856), libgxps (#19701), + libhandy (#19701), libspectre (#19701), lit (#20252), lmoments3 (#19870), Markdown (#20239), MetaDecoder (#20123), mfqe (#19781), + Miniforge3 (#20227), MLflow (#19893), MODFLOW (#20142), morphosamplers (#20000), MotionCor3 (#19681), MSFragger (#19811), + multiprocess (#19986), nf-core (#19107), noise (#20048), OpenMEEG (#19853), OpenSlide-Java (#19962), PAGAN2 (#19618), PASA (#19570), + pblat (#19570), PBZIP2 (#19677), PDM (#20012), Philosopher (#19383), phyluce (#19779), poppunk (#17402), PSASS (#20160), psycopg (#19107), + PyInstaller (#19519), PyQt-builder (#16703), pytest-workflow (#19107), python-casacore (#20089), pytorch-3dunet (#19290), pyXDF (#19916), + q2-krona (#19633), QuPath (#19962), radian (#19484), remake (#19581), rethinking (#19755), RHEIA (#19496), s3fs (#19576), + safestringlib (#20217), scikit-extremes (#19870), SemiBin (#19767), semla (#19747), Sentence-Transformers (#19509), sinto (#13846), + sktime (#19692), SQLAlchemy (#20242), tiny-cuda-nn (#19304), tox (#16178), Vamb (#17457), xpdf (#20024), yt (#20263), Zeo++ (#19555), + zUMIs (#19949) +- added additional easyconfigs for various supported software packages, including: + - bseil 20240116.1, ABySS 2.3.7, AMICA 2024.1.19, AMOS 3.1.0, AMS 2023.104, Anaconda3 2024.02, angsd 0.940, anndata 0.10.5.post1, ant 1.10.14, anvio 8, AOFlagger 3.4.0, Archive Zip, ArchR 1.0.2, archspec 0.2.2, AreTomo2 1.0.0, argtable 2.13, Armadillo 12.8.0, arpack ng, arpack ng, Arrow 8.0.0, arrow R, ASAP3 3.13.3, ASAP3 3.13.3, ASE 3.22.1, assimp 5.3.1, atools 1.5.1, atools 1.5.1, autopep8 2.0.4, basemap 1.3.9, BerkeleyGW 3.1.0, BerkeleyGW 3.1.0, BerkeleyGW 4.0, BiG SCAPE, Bio DB, BioPerl 1.7.8, Biopython 1.83, Blitz++ 1.0.2, Block 1.5.3, Blosc 1.21.5, Blosc 1.21.5, Blosc2 2.13.2, Blosc2 2.4.3, Blosc2 2.8.0, Boost.MPI 1.79.0, Boost.MPI 1.81.0, Boost.MPI 1.82.0, Boost.Python 1.83.0, Bowtie2 2.5.1, Braindecode 0.8.1, Brotli python, btllib 1.7.0, build 1.0.3, build 1.0.3, buildenv default, buildenv default, BWA 0.7.17, BWA 0.7.17, bwa mem2, bx python, CalculiX CrunchiX, CapnProto 1.0.1.1, c ares, Cartopy 0.22.0, casacore 3.5.0, Cbc 2.10.11, ccache 4.9, ccache 4.9, ccache 4.9, CCL 1.12.2, CCL 1.12.2, cclib 1.8, CDO 2.2.2, CellBender 0.2.1, CellBender 0.3.1, CellBender 0.3.1, CellTypist 1.6.2, CENSO 1.2.0, CENSO 1.2.0, CFITSIO 4.3.1, Cgl 0.60.8, Check 0.15.2, CheMPS2 1.8.12, Circlator 1.5.5, Clang 16.0.6, Clang Python, Clarabel.rs 0.7.1, Clp 1.17.9, Clustal Omega, ClustalW2 2.1, CmdStanR 0.7.1, COBRApy 0.29.0, code cli, code server, code server, CoinUtils 2.11.10, Compress Raw, Concorde 20031219, contextily 1.5.0, CoordgenLibs 3.0.2, coverage 7.2.3, CPPE 0.3.1, CppUnit 1.15.1, cppy 1.2.1, CREST 2.12, CREST 2.12, cryoCARE 0.3.0, CSBDeep 0.7.4, CSBLAST 2.2.4, CubeLib 4.8.2, CubeWriter 4.8.2, CUDA 12.3.2.eb, CUDA 12.4.0.eb, cuDNN 8.9.7.29, CuPy 13.0.0, cuSPARSELt 0.6.0.6, cuTENSOR 2.0.1.2, cuTENSOR 2.0.1.2, CUTLASS 2.11.0, CVXPY 1.4.2, Cython 3.0.7, Cython 3.0.8, Cython 3.0.8, dask 2023.12.1, datalad 0.19.5, DBD mysql, DB_File 1.859, deepdiff 6.7.1, deepdiff 6.7.1, DeepLabCut 2.3.6, DeepLoc 2.0, Delft3D 4.04.01, DeltaLake 0.15.1, DendroPy 4.6.1, denseweight 0.1.2, denseweight 0.1.2, Deprecated 1.2.14, desktop file, DETONATE 1.11, devbio napari, devbio napari, DFT D4, DIAMOND 2.1.9, Dice 20240101, DjVuLibre 3.5.28, dlb 3.4, dlb 3.4, DLPack 0.8, DMLC Core, dm tree, dorado 0.5.1, double conversion, DP3 6.0, EasyBuild 4.9.0.eb, ecCodes 2.31.0, ecCodes 2.31.0, EDirect 20.5.20231006, edlib 1.3.9, EggLib 3.3.0, einops 0.7.0, Elmer 9.0, ELPA 2023.11.001, ELPA 2023.11.001, enchant 2, EnergyPlus 23.2.0, epiScanpy 0.4.0, EpiSCORE 0.9.5, ESM 2, ESMF 8.4.2, eSpeak NG, ESPResSo 4.2.1, ETE 3.1.3, ETE 3.1.3, EveryBeam 0.5.2, evince 45.0, expecttest 0.2.1, ExpressBetaDiversity 1.0.10, ExtremeLy 2.3.0, f90nml 1.4.4, f90nml 1.4.4, fastahack 1.0.0, Fastaq 3.17.0, fastjet 3.4.2, fastjet contrib, fastp 0.23.4, FastTree 2.1.11, FDS 6.8.0, fermi lite, festival 2.5.0, FFAVES 2022.11.1, fftlib 20170628, file 5.43, filevercmp 20191210, fineRADstructure 20210514, fio 3.36, Fiona 1.9.5, Flask 3.0.0, flatbuffers 23.5.26, FLINT 3.1.1, Flye 2.9.3, Flye 2.9.3, fmt 10.2.0, FragGeneScan 1.31, freebayes 1.3.7, FreeImage 3.18.0, fsom 20151117, fugue 0.8.7, GATK 4.5.0.0, gawk 5.3.0, gawk 5.3.0, gcsfs 2023.12.2.post1, GCTA 1.94.1, GenomeComb 0.106.0, geocube 0.4.3, geopandas 0.14.2, geopy 2.4.1, Gerris 20131206, gflags 2.2.2, GHC 9.4.6, Ghostscript 10.02.1, GI DocGen, GIMIC 2.2.1, git annex, git lfs, git lfs, GitPython 3.1.42, GKlib METIS, GLFW 3.4, GLPK 5.0, gmpy2 2.1.5, Go 1.21.6.eb, Go 1.22.1.eb, GPAW 24.1.0, GPAW 24.1.0, GPAW 24.1.0, GPAW 24.1.0, GPAW setups, gperftools 2.14, Gradle 8.6, graph tool, GRASP suite, Greenlet 2.0.2, Greenlet 3.0.2, Greenlet 3.0.3, GROMACS 2023.3, GROMACS 2024.1, gRPC 1.62.1, GSL 2.7, GSL 2.7, gspell 1.12.2, GTDB Tk, GTK3 3.24.39, GUIDANCE 2.02, Gurobi 11.0.0, HDF 4.2.16, HDF5 1.14.3, HDF5 1.14.3, hdWGCNA 0.3.00, HeFFTe 2.4.0, HepMC3 3.2.6, HF Datasets, hiredis 1.2.0, hiredis 1.2.0, hmmlearn 0.3.0, hunspell 1.7.2, Hydra 1.3.2, IDG 1.2.0, igraph 0.10.10, igvShiny 20240112, iimkl 2023b.eb, imutils 0.5.4, infercnvpy 0.4.3, inflection 1.3.5, InterOp 1.2.4, intervaltree 0.1, intervaltree python, intervaltree python, IonQuant 1.10.12, iperf 3.16.eb, ipympl 0.9.3, IQ TREE, ISA L, ITSTool 2.0.7, Java 19.0.2.eb, Java 19.eb, Java 21.0.2.eb, Java 21.eb, Java 8.402.eb, json c, json fortran, Julia 1.10.0, Julia 1.6.0, KaHIP 3.16, Kaleido 0.2.1, kim api, KronaTools 2.8.1, KronaTools 2.8.1, Lab Streaming, LAMMPS 2Aug2023_update2, LAMMPS 2Aug2023_update2, LASTZ 1.04.22, LDC 1.36.0, leidenalg 0.10.2, LERC 4.0.0, Levenshtein 0.24.0, libaec 1.0.6, libaec 1.0.6, libcint 5.5.0, libfyaml 0.9, libgit2 1.7.2, libgxps 0.3.2, libhandy 1.8.2, libidn2 2.3.2, libleidenalg 0.11.1, libMemcached 1.0.18, librosa 0.10.1, librsvg 2.58.0, libSBML 5.19.7, libsigsegv 2.14, libspatialindex 1.9.3, libspectre 0.2.12, libtirpc 1.3.4, libxc 6.2.2, libxc 6.2.2, libxml2 python, likwid 5.3.0, lit 18.1.2, LLVM 14.0.6, LLVM 14.0.6, lmoments3 1.0.6, loompy 3.0.7, loomR 0.2.0, LSD2 2.4.1, Lua 5.4.6, MACS3 3.0.0, MACS3 3.0.1, maeparser 1.3.1, magma 2.7.2, Mamba 23.11.0, Markdown 3.6, Markdown 3.6, MATIO 1.5.22, MATIO 1.5.23, MATIO 1.5.26, MATIO 1.5.26, matplotlib 3.7.2, matplotlib 3.8.2, maturin 1.3.2, maturin 1.4.0, maturin 1.4.0, maturin 1.5.0, MBROLA 3.3, MCR R2023a.eb, mctc lib, MDAnalysis 2.7.0, MDI 1.4.26, medaka 1.11.3, medaka 1.11.3, medaka 1.9.1, MEGAHIT 1.2.9, MEGAHIT 1.2.9, Meson 1.3.1, meson python, MetaDecoder 1.0.19, METIS 5.1.0, mfqe 0.5.0, Miniforge3 24.1.2, minimap2 2.26, MiXCR 4.6.0, MLflow 2.10.2, MNE Python, MOABB 1.0.0, MODFLOW 6.4.4, molmod 1.4.8, MONAI 1.3.0, morphosamplers 0.0.10, motif 2.3.8, MotionCor3 1.0.1, mpi4py 3.1.5, mrcfile 1.5.0, MSFragger 4.0, mstore 0.2.0, multicharge 0.2.0, multichoose 1.0.3, multiprocess 0.70.15, MUMmer 4.0.0rc1, MUSCLE 5.1.0, mygene 3.2.2, NAMD 2.14, napari 0.4.18, ncbi vdb, NCCL 2.20.5, NCO 5.1.9, NECI 20230620, netCDF 4.9.2, netCDF 4.9.2, netcdf4 python, netCDF C++4, netCDF C++4, netCDF Fortran, netCDF Fortran, networkx 3.2.1, nf core, nf core, NFFT 3.5.3, NGSpeciesID 0.3.0, NGSpeciesID 0.3.0, NiBabel 5.2.0, nichenetr 2.0.4, Nilearn 0.10.3, Nipype 1.6.0, nlohmann_json 3.11.3, NLTK 3.8.1, NLTK 3.8.1, NLTK 3.8.1, noise 1.2.2, nose3 1.3.8, ntCard 1.2.2, NTL 11.5.1, numba 0.58.1, numba 0.58.1, NVHPC 24.1, OBITools3 3.0.1b26, OCaml 4.14.0, occt 7.8.0, onedrive 2.4.25, ONNX 1.15.0, ONNX Runtime, ont fast5, OPARI2 2.0.8, OpenBabel 3.1.1, OpenFOAM 11, OpenFOAM 7, OpenFOAM 7, OpenFOAM v2112, OpenFOAM v2206, OpenFOAM v2306, OpenFOAM v2312, openkim models, OpenMEEG 2.5.7, openpyxl 3.1.2, OpenSlide Java, OpenSSL 3.eb, Optuna 3.5.0, ORCA 5.0.4, OrfM 0.7.1, Osi 0.108.9, OTF2 3.0.3, PAGAN2 1.53_20230824, PAPI 7.1.0, Parallel Hashmap, parameterized 0.9.0, parasail 2.6.2, ParaView 5.12.0, ParMETIS 4.0.3, PASA 2.5.3, pblat 2.5.1, PBZIP2 1.1.13, PCMSolver 1.2.3, PCRE 8.45, PDM 2.12.4, PDT 3.25.2, Perl 5.38.0.eb, PETSc 3.20.3, PGPLOT 5.2.2, Philosopher 5.0.0, phonemizer 3.2.1, phono3py 2.7.0, PHYLIP 3.697, phyluce 1.7.3, Pillow 10.2.0, Pillow SIMD, Pint 0.23, pkgconfig 1.5.5, PLINK 2.00a3.7, plotly.py 5.18.0, PLY 3.11, pmt 1.2.0, pmt 1.2.0, pocl 1.8, pocl 4.0, poetry 1.7.1, poppunk 2.6.0, PostgreSQL 16.1, PRANK 170427, presto 1.0.0, prodigal 2.6.3, PROJ 9.3.1, prompt toolkit, prompt toolkit, protobuf 25.3, protobuf python, PSASS 3.1.0, psmc 0.6.5_20221121, pstoedit 3.78, psycopg2 2.9.9, psycopg 3.1.18, psycopg 3.1.18, PuLP 2.8.0, PyBerny 0.6.3, PyCheMPS2 1.8.12, pycodestyle 2.11.1, py cpuinfo, py cpuinfo, pydantic 1.10.13, pydantic 2.5.3, pydantic 2.5.3, pydantic 2.6.4, pydicom 2.4.4, pydot 2.0.0, pyfaidx 0.8.1.1, pyfaidx 0.8.1.1, PyFrag 2023, PyInstaller 6.3.0, pymatgen 2023.12.18, PyOpenCL 2023.1.4, PyOpenCL 2023.1.4, PyOpenCL 2023.1.4, PyOpenCL 2023.1.4, PyOpenGL 3.1.7, pyparsing 3.1.1, PyQt5 5.15.10, PyQt builder, pyro ppl, Pysam 0.22.0, pySCENIC 0.12.1, PySCF 2.4.0, pyspoa 0.2.1, PyTables 3.9.2, pytest flakefinder, pytest flakefinder, pytest rerunfailures, pytest shard, pytest shard, pytest workflow, pytest workflow, python casacore, python igraph, python irodsclient, python isal, python libsbml, python parasail, python xxhash, PyTorch 2.1.2, PyTorch 2.1.2, PyTorch 2.1.2, pytorch 3dunet, PyTorch Geometric, PyTorch Ignite, PyTorch Lightning, PyTorch Lightning, PyTorch Lightning, pyXDF 1.16.3, pyXDF 1.16.5, PyZMQ 25.1.2, q2 krona, QCG PilotJob, Qhull 2020.2, QIIME2 2023.7.0, Qt5 5.15.13, Qt6 6.6.3, Qtconsole 5.5.1, QtPy 2.4.1, QuantumESPRESSO 7.3, QuantumESPRESSO 7.3, QuPath 0.5.0, Qwt 6.2.0, R 4.3.3, Racon 1.5.0, Racon 1.5.0, radian 0.6.9, RapidJSON 1.1.0, rasterio 1.3.9, R bundle, rclone 1.65.2.eb, rclone 1.66.0.eb, RE2 2024, Redis 7.2.3, Redis 7.2.4, redis py, remake 4.3+dbg, rethinking 2.40, RHEIA 1.1.6, rioxarray 0.15.0, Rivet 3.1.9, rMATS turbo, RNA Bloom, rocm smi, rpy2 3.5.15, ruamel.yaml 0.18.6, Ruby 3.3.0, Rust 1.75.0, Rust 1.75.0, Rust 1.76.0, s3fs 2023.12.2, safestringlib 20240228, Salmon 1.10.1, Sambamba 1.0.1, SAMtools 0.1.20, SAMtools 1.13, Saxon HE, SBCL 2.4.1, ScaFaCoS 1.0.4, Scalene 1.5.35, scanpy 1.9.8, scCODA 0.1.9, SCENIC 1.3.0, scib 1.1.4, scikit bio, scikit extremes, scikit learn, scikit learn, scikit learn, scikit lego, scikit misc, SciPy bundle, SCons 4.6.0, Score P, Score P, SCOTCH 7.0.1, scVelo 0.3.1, Seaborn 0.13.2, SemiBin 2.0.2, SemiBin 2.0.2, semla 1.1.6, SentencePiece 0.1.99, Sentence Transformers, SeqLib 1.2.0, Seqmagick 0.8.6, seqtk 1.4, Seurat 5.0.1, sinto 0.7.4, SIONlib 1.7.7, SIP 6.8.1, siscone 3.0.6, skorch 0.15.0, sktime 0.25.0, SLEPc 3.20.1, smithwaterman 20160702, snakemake 8.4.2, SNAPE pooled, snappy 1.1.10, SOAPdenovo Trans, sonic 20180202, SPAdes 3.15.4, Spark 3.5.1, sparsehash 2.0.4, spdlog 1.12.0, SpectrA 1.0.1, speech_tools 2.5.0, spglib python, spoa 4.1.0, SPOOLES 2.2, SQLAlchemy 2.0.25, SQLAlchemy 2.0.29, SQLAlchemy 2.0.29, SRA Toolkit, SSW 1.1, Stack 2.13.1, STAR 2.7.11b, statsmodels 0.14.1, statsmodels 0.14.1, SUNDIALS 6.6.0, SuperLU_DIST 8.1.2, SURVIVOR 1.0.7, sympy 1.12, Szip 2.1.1, tabixpp 1.1.2, TAMkin 1.2.6, TAMkin 1.2.6, TAMkin 1.2.6, TAMkin 1.2.6, tensorboard 2.15.1, tensorboardX 2.6.2.2, tensorboardX 2.6.2.2, tensorflow probability, texinfo 7.1, texlive 20230313, timm 0.9.7, tiny cuda, Togl 2.0, torchvision 0.14.1, torchvision 0.16.0, tox 3.25.1, tox 3.25.1, tqdm 4.66.2, trimAl 1.4.1, TRIQS 3.2.0, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, typing extensions, typing extensions, typing extensions, UCX 1.16.0, UCX 1.16.0, UCX 1.16.0, UCX 1.16.0, UCX 1.16.0, UDUNITS 2.2.28, umap learn, UMI tools, uncertainties 3.1.7, Vala 0.56.14, Vamb 3.0.9, vcflib 1.0.9, Velvet 1.2.10, VEP 111, Vim 9.1.0004, VisPy 0.12.2, Voro++ 0.4.6, vsc mympirun, waLBerla 6.1, Wannier90 3.1.0, WCSLIB 7.11, WFA2 2.3.4, wget 1.21.4, WhatsHap 2.1, WhatsHap 2.2, WIEN2k 23.2, wrf python, WSClean 3.4, XCFun 2.1.1, XCrySDen 1.6.2, Xerces C++, XlsxWriter 3.1.9, XML LibXML, xpdf 4.04, xxHash 0.8.2, yaff 1.6.0, YAXT 0.10.0, Yices 2.6.4, YODA 1.9.9, yt 4.3.0, Zeo++ 0.3, zUMIs 2.9.7 +- minor enhancements, including: + - demo of `build_info_msg` easyconfig parameter (#18550) + - enable KLU and CUDA solvers in SUNDIALS v6.6.0 (#19490) + - add tidybayes to R-bundle-CRAN v2023.12 (#19712) + - add spdep extension to R-bundle-CRAN v2023.12 (#19729) + - add plyranges to R-bundle-Bioconductor for zUMIs (#19949) + - add PyOpenGL-accelerate extension to PyOpenGL v3.1.7 (#20007) + - add AMOS dependency for Circlator, required by toAmos and minimus2 (#20011) + - use system architecture template in DB_File (#20014), GD (#20015) and GDGraph (#20016) + - add fixest with deps to R-bundle-CRAN v2023.12 (#20055) + - add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency (#20069) + - add MODIStsp extension (+ required dependencies) to R 4.2.2 (#20113) + - enable LittleCMS2 and WebP support in recent Pillow (#20195) + - drop hatchling builddep from tqdm 4.66.1 as well (#20200) + - improve test for validity of EasyConfigs (#20205) + - add easyconfig test that checks if backdoored XZ versions are introduced (#20267) +- various bug fixes, including: + - add patch for Bison 3.7.1 to fix build error on old OS versions (#12291) + - add missing pkg-config build dependency for recent p11-kit easyconfigs (#16318) + - fix dependencies and configure flags of GnuTLS 3.7.x (#19070) + - remove numa configure option from hwloc 2.5+ (#19085) + - add patches for OpenBLAS v0.3.21 to disable -ftree-vectorize for netlib LAPACK (#19280) + - use new DualSPHysics easyblock (#19400) + - add patch to fix flaky scipy build in SciPy-bundle v2023.11 (#19481) + - add missing SciPy-bundle dependency to TensorRT easyconfig (#19486) + - fix lapack test failures in OpenBLAS 0.3.23/24 (#19495) + - add patch for Arrow v8.0.0 - v11.0.0 to add missing `__arrow_ext_class__` method to `BaseExtensionType` class (#19532) + - change homepage for argtable (#19551) + - add patches for PyTorch v2.1.2 with `foss/2022a` (#19571), `foss/2022b` (#19572) and `foss/2023a` (#19573) to fix test failures on non-x86 platforms + - use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 (#19584) + - remove `osdependencies` from GCCcore ccache (#19600) + - use https source URL for alsa-lib (#19628) + - add missing KronaTools dep to q2-krona (#19633) + - add missing dm-tree dependency for dm-reverb 0.2.0 (#19653) + - add libyaml import check to PyYAML and fix builds since split to minimal Python (#19662) + - demote meson-python to a build dependency in recent matplotlib easyconfigs (#19670) + - patch upb CopyFrom error in protobuf-python 4.24.0 (#19671) + - demote poetry to build dep in expecttest (#19675) + - add zlib dependency to YODA and Rivet (#19679) + - fix missing spaces in Graphviz configure options (#19687) + - strip iconv from pkgconfig file for libarchive v3.6.2 (#19698) + - use separate bcrypt easyconfig (using CargoPythonPackage) as dependency for JupyterHub v4.0.2 (#19703) + - use maturin easyconfig using CargoPythonPackage as a dependency for fastparquet v2023.4.0 (#19704) + - add patches for Perl-bundle-CPAN v5.36.1 to fix installation of `Sys::Info::Driver::Linux*` extensions on Debian Bookworm (#19727) + - explicitly specify Fortran compiler for recent CDO versions to fix issues on non-x86_64 architectures (#19735) + - add patch for `jupyter_core` extension in `jupyter-server` to set jupyter path by `$EB_ENV_JUPYTER_ROOT` (#19737) + - add Python build dependency to 1.9.x Doxygen (#19743) + - fix Arrow v14.0.1 to install pyarrow as an extension (#19758) + - fix homepage + source URL for Gblocks 0.91b (#19797) + - make sure that Brunsli libraries are installed into `/lib` (#19805) + - fix dependency with libidn.so.11 in tbl2asn v20220427 and v20230713 easyconfigs (#19821) + - add missing dependencies for fslpy in easyconfig for FSL v6.0.5.1 (#19829) + - remove numa configure option from hwloc 2+ (#19833) + - avoid spurious test failure when enabling RPATH for Perl (#19835) + - add missing Python deps and packages in PSI4 1.7 (#19836) + - add patch to fix `MS_RDONLY` error in OpenMPI 3.1.x and 4.0.0 (#20140), 4.0.3 (#19944) and 4.0.5 (#19837) + - demote meson-python to build dependency for matplotlib v3.7.2 w/ iimkl/2023a (#19892) + - demote hatchling to build dependency in einops-0.7.0-GCCcore-12.3.0.eb (#19915) + - add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs (#19940) + - stop using non-existent `--disable-libdeflate` option for LibTIFF 4.1.0 (#19951) + - add patch to remove git version check and fix test command for molmod 1.4.8 (#19952) + - replace SYSTEM-level GCC dependency in git-annex with binutils (#19956) + - stop using non-existing `--with-doc` configure option for groff 1.23 (#19969) + - fix test failures of Perl-bundle-CPAN-5.38 in non-English locales (#19971) + - add patch to fix tree-optimization bug in GCC 13.2.0 for ARM architectures with SVE support (#19974) + - drop checksum from VSCode (#19995) + - respect sysroot in Pillow-SIMD when in use (#19996) + - remove `--disable-docs` configure option from FriBidi 1.0.5+ (#19998) + - fix geotiff configure option in GDAL (#19999) + - unpack SCG database to 'db' subdirectory for DAS_Tool (#20008) + - remove Jasper dependency and configure option from GDAL 3.5+ (#20009) + - update homepage and source_urls for SPAdes (#20018) + - fix GDAL 3.5.0 install on high-core-count machines (#20027) + - fix source URL for xpdf 4.04 (#20024) + - remove disable-visibility configure flag from GTK3 (#20028) + - remove mpi configure option from libfdf 0.2.2 (#20034) + - add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs (#20035) + - fix invocation typo and unneeded folder change on invocation in fgbio 1.3.0 easyconfig (#20039) + - remove hdf5 configure option from MDSplus 7.96.12 (#20041) + - move poetry to builddeps and bump poetry version in gcsfs v2023.12.2.post1 easyconfig (#20042) + - fix python configure option of MEME (#20043) + - fix configure options of FFLAS-FFPACK (#20052) + - find the correct Python in xtensor (#20056) + - fix geotiff configure option in GDAL 2.2.3 (#20057) + - fix configure option and gpertools dependency of MIRA 5.0 (#20061) + - fix confgure options in GRASS (#20062) + - fix GUIDANCE installation (#20063) + - fix configure of LinBox 1.7.0 (#20064) + - remove unknown configure option from GnuTLS 3.7.2 (#20065) + - use 32-bit indexing for SUNDIALS 6.6.0 (with foss/2023a) to enable sunmatrix-cusparse (#20075) + - find correct Python for MDI (#20083) + - add `pixman` and `FriBidi` dependencies to recent ImageMagick easyconfigs (#20086) + - set LD_LIBRARY_PATH for python-casacore 3.5.2 (#20089) + - add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 (#20090) and v5.38.0 (#20118) + - add patches for minimus2 in AMOS-3.1.0 (#20114) + - fix download url for cuSPARSELt 0.3.0.3 (#20129) + - fix test issues in PyTorch-2.1.2-foss-2023a-CUDA-12.1.1 (#20156) + - remove UCX-CUDA 1.15.0 on top of incompatible CUDA 12.3.0 + GCC 13.2.0 combo (#20158) + - remove flake8 suppressions for invalid escape sequences (#20161) + - fix post-install command for SuperLU_DIST in case library prefix is lib instead of lib64 (#20162) + - switch to gitlab source URL for libxc + add alternative checksum (#20163) + - remove whitespace in protobuf-25.3-GCCcore-13.2.0.eb (#20172) + - enable `download_dep_fail` for Pythonpackage ECs where it was wrongly disabled (#20174) + - fix PyTorch versions 1.12.0-foss-2022a-CUDA-11.7.0 (#20176), 1.12.0-foss-2022a (#20177), 1.12.1-foss-2022a-CUDA-11.7.0 (#20178), 1.12.1-foss-2022a (#20179), 1.13.1-foss-2022a-CUDA-11.7.0 (#20180), 1.13.1-foss-2022a (#20181) and 1.13.1-foss-2022b (#20182) for Linux 6+ + - disable tests for Time::HiRes extension in Perl-bundle-CPAN v5.36.1 (#20187) + - fix several typos in GlobalArrays 5.8 configure step (#20188) + - fix broken homepage from older SCOTCH easyconfigs (#20192) + - remove dead URL for ISL from source_urls in easyconfigs for GCCcore 10.3.0, 11.1.0, 11.2.0 (#20193) + - fix package installation in easyconfigs for Python 2.7.15 and 3.7.2 (using GCCcore/8.2.0) (#20194) + - add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency (#20214) + - fix cuSPARSELt easyconfigs for aarch64 (#20216) + - add patch to fix tree-optimization bug in GCC 12.3.0 and 13.1.0 for ARM architectures with SVE support (#20218) + - fix shebang in napari v0.4.1{5,8} easyconfigs (#20219) + - fix test failure in SciPy-bundle-2023.02-gfbf-2022b (#20235) + - fix `incompatible types` errors when building the R extension `dbarts` on Arm (#20238) + - add patch to fix for libarchive to fix error reporting in tar (#20254) + - add GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch (#20260) + - fix download for python-parasail 1.3.4 by adding missing source URL (#20263) +- other changes: + - fix name for DETONATE in existing easyconfig (#19569) + - rename `VSCode` to `code-cli` (to match with existing `code-server`) (#19585, #19645) + - update comment in ncurses and zlib for dummy -> SYSTEM toolchain (#19658) + - bump versions of `tensorboard v2.15.1` extensions and add reference to `protobuf-python` patch (#19673) + - wandb should not specify urllib3 since it does not need a newer version then the one in Python-bundle-PyPI (#19725) + - stop using custom easyblock for Doxygen (#19742) + - move setuptools_scm from hatchling to Python easyconfig in develop (#19777) + - move xtb v6.6.1 to gfbf/2023a (#19826) + - move NiBabel v5.2.0 to gfbf/2023a (#19850) + - remove easyconfig for zlib 1.3 w/ intel toolchain, should be using GCCcore (#20023) + - unify Z3 4.12.2 easyconfigs into a single one with Python bindings (and fix Z3 dependency for PyTorch 2.1.2 accordingly) (#20050) + - use GPAW-setups v24.1.0 in existing GPAW easyconfigs (#20117) + - fix duplicate dict entries and enable fatal error checking for ECs via `flake8` (#20173) + - drop Greenlet to GCCcore (#20241) + - update Java-8 wrapper to 8.402 (#20261) + - update copyright lines to 2024 (#20276) + + v4.9.0 (30 December 2023) ------------------------- diff --git a/setup.py b/setup.py index 3f246266b7f9..a5b10c2eb30a 100644 --- a/setup.py +++ b/setup.py @@ -44,7 +44,7 @@ # recent setuptools versions will *TRANSFORM* something like 'X.Y.Zdev' into 'X.Y.Z.dev0', with a warning like # UserWarning: Normalizing '2.4.0dev' to '2.4.0.dev0' # This causes problems further up the dependency chain... -VERSION = '4.9.1.dev0' +VERSION = '4.9.1' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 16f61a28f431ed1da20887697918ee7aee14e8df Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 4 Apr 2024 21:02:59 +0200 Subject: [PATCH 1193/1193] minor tweaks to 4.9.1 release notes --- RELEASE_NOTES | 142 ++++++++++++++++++++++++++++++-------------------- 1 file changed, 85 insertions(+), 57 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 2151130891d3..45d27a2e6969 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,7 +3,7 @@ For more detailed information, please see the git log. These release notes can also be consulted at https://docs.easybuild.io/en/latest/Release_notes.html. -The latest version of easybuild-easyconfig provides 19,487 easyconfig files, for 3,471 different software packages, +The latest version of easybuild-easyconfig provides 19,487 easyconfig files, for 3,470 different software packages, incl. 40 different (compiler) toolchains. @@ -12,17 +12,17 @@ v4.9.1 (5 April 2024) update/bugfix release -- added example easyconfig files for 102 new software packages: +- added example easyconfig files for 101 new software packages: - AMICA (#19842), AreTomo2 (#19681), btllib (#19779), bwa-mem2 (#20217), CENSO (#19826), Circlator (#19847), Clarabel.rs (#20149), code-cli (#19645), Concorde (#19768), contextily (#19807), CUTLASS (#19304), DeepLoc (#19514), Delft3D (#19869), DeltaLake (#19758), - denseweight (#20139), desktop-file-utils (#19701), DETONATE (#19547), devbio-napari (#19586), DjVuLibre (#19701), Elmer (#19448), + denseweight (#20139), desktop-file-utils (#19701), devbio-napari (#19586), DjVuLibre (#19701), Elmer (#19448), EnergyPlus (#19565), EpiSCORE (#18618), evince (#19701), ExpressBetaDiversity (#19938), ExtremeLy (#19870), f90nml (#19171), FFAVES (#19822), fugue (#19694), gcsfs (#20042), GenomeComb (#19749), GI-DocGen (#19701), GKlib-METIS (#20096), GRASP-suite (#19665), gspell (#19701), GUIDANCE (#20063), hdWGCNA (#20124), HF-Datasets (#20166), IDG (#18924), igvShiny (#19714), inflection (#20036), InterOp (#19303), IonQuant (#19812), Lab-Streaming-Layer (#19945), Levenshtein (#19771), libfyaml (#19856), libgxps (#19701), libhandy (#19701), libspectre (#19701), lit (#20252), lmoments3 (#19870), Markdown (#20239), MetaDecoder (#20123), mfqe (#19781), - Miniforge3 (#20227), MLflow (#19893), MODFLOW (#20142), morphosamplers (#20000), MotionCor3 (#19681), MSFragger (#19811), - multiprocess (#19986), nf-core (#19107), noise (#20048), OpenMEEG (#19853), OpenSlide-Java (#19962), PAGAN2 (#19618), PASA (#19570), + Miniforge3 (#20227), MLflow (#19893), MODFLOW (#20142), morphosamplers (#20000), MotionCor3 (#19681), MSFragger (#19811), + multiprocess (#19986), nf-core (#19107), noise (#20048), OpenMEEG (#19853), OpenSlide-Java (#19962), PAGAN2 (#19618), PASA (#19570), pblat (#19570), PBZIP2 (#19677), PDM (#20012), Philosopher (#19383), phyluce (#19779), poppunk (#17402), PSASS (#20160), psycopg (#19107), PyInstaller (#19519), PyQt-builder (#16703), pytest-workflow (#19107), python-casacore (#20089), pytorch-3dunet (#19290), pyXDF (#19916), q2-krona (#19633), QuPath (#19962), radian (#19484), remake (#19581), rethinking (#19755), RHEIA (#19496), s3fs (#19576), @@ -30,22 +30,61 @@ update/bugfix release sktime (#19692), SQLAlchemy (#20242), tiny-cuda-nn (#19304), tox (#16178), Vamb (#17457), xpdf (#20024), yt (#20263), Zeo++ (#19555), zUMIs (#19949) - added additional easyconfigs for various supported software packages, including: - - bseil 20240116.1, ABySS 2.3.7, AMICA 2024.1.19, AMOS 3.1.0, AMS 2023.104, Anaconda3 2024.02, angsd 0.940, anndata 0.10.5.post1, ant 1.10.14, anvio 8, AOFlagger 3.4.0, Archive Zip, ArchR 1.0.2, archspec 0.2.2, AreTomo2 1.0.0, argtable 2.13, Armadillo 12.8.0, arpack ng, arpack ng, Arrow 8.0.0, arrow R, ASAP3 3.13.3, ASAP3 3.13.3, ASE 3.22.1, assimp 5.3.1, atools 1.5.1, atools 1.5.1, autopep8 2.0.4, basemap 1.3.9, BerkeleyGW 3.1.0, BerkeleyGW 3.1.0, BerkeleyGW 4.0, BiG SCAPE, Bio DB, BioPerl 1.7.8, Biopython 1.83, Blitz++ 1.0.2, Block 1.5.3, Blosc 1.21.5, Blosc 1.21.5, Blosc2 2.13.2, Blosc2 2.4.3, Blosc2 2.8.0, Boost.MPI 1.79.0, Boost.MPI 1.81.0, Boost.MPI 1.82.0, Boost.Python 1.83.0, Bowtie2 2.5.1, Braindecode 0.8.1, Brotli python, btllib 1.7.0, build 1.0.3, build 1.0.3, buildenv default, buildenv default, BWA 0.7.17, BWA 0.7.17, bwa mem2, bx python, CalculiX CrunchiX, CapnProto 1.0.1.1, c ares, Cartopy 0.22.0, casacore 3.5.0, Cbc 2.10.11, ccache 4.9, ccache 4.9, ccache 4.9, CCL 1.12.2, CCL 1.12.2, cclib 1.8, CDO 2.2.2, CellBender 0.2.1, CellBender 0.3.1, CellBender 0.3.1, CellTypist 1.6.2, CENSO 1.2.0, CENSO 1.2.0, CFITSIO 4.3.1, Cgl 0.60.8, Check 0.15.2, CheMPS2 1.8.12, Circlator 1.5.5, Clang 16.0.6, Clang Python, Clarabel.rs 0.7.1, Clp 1.17.9, Clustal Omega, ClustalW2 2.1, CmdStanR 0.7.1, COBRApy 0.29.0, code cli, code server, code server, CoinUtils 2.11.10, Compress Raw, Concorde 20031219, contextily 1.5.0, CoordgenLibs 3.0.2, coverage 7.2.3, CPPE 0.3.1, CppUnit 1.15.1, cppy 1.2.1, CREST 2.12, CREST 2.12, cryoCARE 0.3.0, CSBDeep 0.7.4, CSBLAST 2.2.4, CubeLib 4.8.2, CubeWriter 4.8.2, CUDA 12.3.2.eb, CUDA 12.4.0.eb, cuDNN 8.9.7.29, CuPy 13.0.0, cuSPARSELt 0.6.0.6, cuTENSOR 2.0.1.2, cuTENSOR 2.0.1.2, CUTLASS 2.11.0, CVXPY 1.4.2, Cython 3.0.7, Cython 3.0.8, Cython 3.0.8, dask 2023.12.1, datalad 0.19.5, DBD mysql, DB_File 1.859, deepdiff 6.7.1, deepdiff 6.7.1, DeepLabCut 2.3.6, DeepLoc 2.0, Delft3D 4.04.01, DeltaLake 0.15.1, DendroPy 4.6.1, denseweight 0.1.2, denseweight 0.1.2, Deprecated 1.2.14, desktop file, DETONATE 1.11, devbio napari, devbio napari, DFT D4, DIAMOND 2.1.9, Dice 20240101, DjVuLibre 3.5.28, dlb 3.4, dlb 3.4, DLPack 0.8, DMLC Core, dm tree, dorado 0.5.1, double conversion, DP3 6.0, EasyBuild 4.9.0.eb, ecCodes 2.31.0, ecCodes 2.31.0, EDirect 20.5.20231006, edlib 1.3.9, EggLib 3.3.0, einops 0.7.0, Elmer 9.0, ELPA 2023.11.001, ELPA 2023.11.001, enchant 2, EnergyPlus 23.2.0, epiScanpy 0.4.0, EpiSCORE 0.9.5, ESM 2, ESMF 8.4.2, eSpeak NG, ESPResSo 4.2.1, ETE 3.1.3, ETE 3.1.3, EveryBeam 0.5.2, evince 45.0, expecttest 0.2.1, ExpressBetaDiversity 1.0.10, ExtremeLy 2.3.0, f90nml 1.4.4, f90nml 1.4.4, fastahack 1.0.0, Fastaq 3.17.0, fastjet 3.4.2, fastjet contrib, fastp 0.23.4, FastTree 2.1.11, FDS 6.8.0, fermi lite, festival 2.5.0, FFAVES 2022.11.1, fftlib 20170628, file 5.43, filevercmp 20191210, fineRADstructure 20210514, fio 3.36, Fiona 1.9.5, Flask 3.0.0, flatbuffers 23.5.26, FLINT 3.1.1, Flye 2.9.3, Flye 2.9.3, fmt 10.2.0, FragGeneScan 1.31, freebayes 1.3.7, FreeImage 3.18.0, fsom 20151117, fugue 0.8.7, GATK 4.5.0.0, gawk 5.3.0, gawk 5.3.0, gcsfs 2023.12.2.post1, GCTA 1.94.1, GenomeComb 0.106.0, geocube 0.4.3, geopandas 0.14.2, geopy 2.4.1, Gerris 20131206, gflags 2.2.2, GHC 9.4.6, Ghostscript 10.02.1, GI DocGen, GIMIC 2.2.1, git annex, git lfs, git lfs, GitPython 3.1.42, GKlib METIS, GLFW 3.4, GLPK 5.0, gmpy2 2.1.5, Go 1.21.6.eb, Go 1.22.1.eb, GPAW 24.1.0, GPAW 24.1.0, GPAW 24.1.0, GPAW 24.1.0, GPAW setups, gperftools 2.14, Gradle 8.6, graph tool, GRASP suite, Greenlet 2.0.2, Greenlet 3.0.2, Greenlet 3.0.3, GROMACS 2023.3, GROMACS 2024.1, gRPC 1.62.1, GSL 2.7, GSL 2.7, gspell 1.12.2, GTDB Tk, GTK3 3.24.39, GUIDANCE 2.02, Gurobi 11.0.0, HDF 4.2.16, HDF5 1.14.3, HDF5 1.14.3, hdWGCNA 0.3.00, HeFFTe 2.4.0, HepMC3 3.2.6, HF Datasets, hiredis 1.2.0, hiredis 1.2.0, hmmlearn 0.3.0, hunspell 1.7.2, Hydra 1.3.2, IDG 1.2.0, igraph 0.10.10, igvShiny 20240112, iimkl 2023b.eb, imutils 0.5.4, infercnvpy 0.4.3, inflection 1.3.5, InterOp 1.2.4, intervaltree 0.1, intervaltree python, intervaltree python, IonQuant 1.10.12, iperf 3.16.eb, ipympl 0.9.3, IQ TREE, ISA L, ITSTool 2.0.7, Java 19.0.2.eb, Java 19.eb, Java 21.0.2.eb, Java 21.eb, Java 8.402.eb, json c, json fortran, Julia 1.10.0, Julia 1.6.0, KaHIP 3.16, Kaleido 0.2.1, kim api, KronaTools 2.8.1, KronaTools 2.8.1, Lab Streaming, LAMMPS 2Aug2023_update2, LAMMPS 2Aug2023_update2, LASTZ 1.04.22, LDC 1.36.0, leidenalg 0.10.2, LERC 4.0.0, Levenshtein 0.24.0, libaec 1.0.6, libaec 1.0.6, libcint 5.5.0, libfyaml 0.9, libgit2 1.7.2, libgxps 0.3.2, libhandy 1.8.2, libidn2 2.3.2, libleidenalg 0.11.1, libMemcached 1.0.18, librosa 0.10.1, librsvg 2.58.0, libSBML 5.19.7, libsigsegv 2.14, libspatialindex 1.9.3, libspectre 0.2.12, libtirpc 1.3.4, libxc 6.2.2, libxc 6.2.2, libxml2 python, likwid 5.3.0, lit 18.1.2, LLVM 14.0.6, LLVM 14.0.6, lmoments3 1.0.6, loompy 3.0.7, loomR 0.2.0, LSD2 2.4.1, Lua 5.4.6, MACS3 3.0.0, MACS3 3.0.1, maeparser 1.3.1, magma 2.7.2, Mamba 23.11.0, Markdown 3.6, Markdown 3.6, MATIO 1.5.22, MATIO 1.5.23, MATIO 1.5.26, MATIO 1.5.26, matplotlib 3.7.2, matplotlib 3.8.2, maturin 1.3.2, maturin 1.4.0, maturin 1.4.0, maturin 1.5.0, MBROLA 3.3, MCR R2023a.eb, mctc lib, MDAnalysis 2.7.0, MDI 1.4.26, medaka 1.11.3, medaka 1.11.3, medaka 1.9.1, MEGAHIT 1.2.9, MEGAHIT 1.2.9, Meson 1.3.1, meson python, MetaDecoder 1.0.19, METIS 5.1.0, mfqe 0.5.0, Miniforge3 24.1.2, minimap2 2.26, MiXCR 4.6.0, MLflow 2.10.2, MNE Python, MOABB 1.0.0, MODFLOW 6.4.4, molmod 1.4.8, MONAI 1.3.0, morphosamplers 0.0.10, motif 2.3.8, MotionCor3 1.0.1, mpi4py 3.1.5, mrcfile 1.5.0, MSFragger 4.0, mstore 0.2.0, multicharge 0.2.0, multichoose 1.0.3, multiprocess 0.70.15, MUMmer 4.0.0rc1, MUSCLE 5.1.0, mygene 3.2.2, NAMD 2.14, napari 0.4.18, ncbi vdb, NCCL 2.20.5, NCO 5.1.9, NECI 20230620, netCDF 4.9.2, netCDF 4.9.2, netcdf4 python, netCDF C++4, netCDF C++4, netCDF Fortran, netCDF Fortran, networkx 3.2.1, nf core, nf core, NFFT 3.5.3, NGSpeciesID 0.3.0, NGSpeciesID 0.3.0, NiBabel 5.2.0, nichenetr 2.0.4, Nilearn 0.10.3, Nipype 1.6.0, nlohmann_json 3.11.3, NLTK 3.8.1, NLTK 3.8.1, NLTK 3.8.1, noise 1.2.2, nose3 1.3.8, ntCard 1.2.2, NTL 11.5.1, numba 0.58.1, numba 0.58.1, NVHPC 24.1, OBITools3 3.0.1b26, OCaml 4.14.0, occt 7.8.0, onedrive 2.4.25, ONNX 1.15.0, ONNX Runtime, ont fast5, OPARI2 2.0.8, OpenBabel 3.1.1, OpenFOAM 11, OpenFOAM 7, OpenFOAM 7, OpenFOAM v2112, OpenFOAM v2206, OpenFOAM v2306, OpenFOAM v2312, openkim models, OpenMEEG 2.5.7, openpyxl 3.1.2, OpenSlide Java, OpenSSL 3.eb, Optuna 3.5.0, ORCA 5.0.4, OrfM 0.7.1, Osi 0.108.9, OTF2 3.0.3, PAGAN2 1.53_20230824, PAPI 7.1.0, Parallel Hashmap, parameterized 0.9.0, parasail 2.6.2, ParaView 5.12.0, ParMETIS 4.0.3, PASA 2.5.3, pblat 2.5.1, PBZIP2 1.1.13, PCMSolver 1.2.3, PCRE 8.45, PDM 2.12.4, PDT 3.25.2, Perl 5.38.0.eb, PETSc 3.20.3, PGPLOT 5.2.2, Philosopher 5.0.0, phonemizer 3.2.1, phono3py 2.7.0, PHYLIP 3.697, phyluce 1.7.3, Pillow 10.2.0, Pillow SIMD, Pint 0.23, pkgconfig 1.5.5, PLINK 2.00a3.7, plotly.py 5.18.0, PLY 3.11, pmt 1.2.0, pmt 1.2.0, pocl 1.8, pocl 4.0, poetry 1.7.1, poppunk 2.6.0, PostgreSQL 16.1, PRANK 170427, presto 1.0.0, prodigal 2.6.3, PROJ 9.3.1, prompt toolkit, prompt toolkit, protobuf 25.3, protobuf python, PSASS 3.1.0, psmc 0.6.5_20221121, pstoedit 3.78, psycopg2 2.9.9, psycopg 3.1.18, psycopg 3.1.18, PuLP 2.8.0, PyBerny 0.6.3, PyCheMPS2 1.8.12, pycodestyle 2.11.1, py cpuinfo, py cpuinfo, pydantic 1.10.13, pydantic 2.5.3, pydantic 2.5.3, pydantic 2.6.4, pydicom 2.4.4, pydot 2.0.0, pyfaidx 0.8.1.1, pyfaidx 0.8.1.1, PyFrag 2023, PyInstaller 6.3.0, pymatgen 2023.12.18, PyOpenCL 2023.1.4, PyOpenCL 2023.1.4, PyOpenCL 2023.1.4, PyOpenCL 2023.1.4, PyOpenGL 3.1.7, pyparsing 3.1.1, PyQt5 5.15.10, PyQt builder, pyro ppl, Pysam 0.22.0, pySCENIC 0.12.1, PySCF 2.4.0, pyspoa 0.2.1, PyTables 3.9.2, pytest flakefinder, pytest flakefinder, pytest rerunfailures, pytest shard, pytest shard, pytest workflow, pytest workflow, python casacore, python igraph, python irodsclient, python isal, python libsbml, python parasail, python xxhash, PyTorch 2.1.2, PyTorch 2.1.2, PyTorch 2.1.2, pytorch 3dunet, PyTorch Geometric, PyTorch Ignite, PyTorch Lightning, PyTorch Lightning, PyTorch Lightning, pyXDF 1.16.3, pyXDF 1.16.5, PyZMQ 25.1.2, q2 krona, QCG PilotJob, Qhull 2020.2, QIIME2 2023.7.0, Qt5 5.15.13, Qt6 6.6.3, Qtconsole 5.5.1, QtPy 2.4.1, QuantumESPRESSO 7.3, QuantumESPRESSO 7.3, QuPath 0.5.0, Qwt 6.2.0, R 4.3.3, Racon 1.5.0, Racon 1.5.0, radian 0.6.9, RapidJSON 1.1.0, rasterio 1.3.9, R bundle, rclone 1.65.2.eb, rclone 1.66.0.eb, RE2 2024, Redis 7.2.3, Redis 7.2.4, redis py, remake 4.3+dbg, rethinking 2.40, RHEIA 1.1.6, rioxarray 0.15.0, Rivet 3.1.9, rMATS turbo, RNA Bloom, rocm smi, rpy2 3.5.15, ruamel.yaml 0.18.6, Ruby 3.3.0, Rust 1.75.0, Rust 1.75.0, Rust 1.76.0, s3fs 2023.12.2, safestringlib 20240228, Salmon 1.10.1, Sambamba 1.0.1, SAMtools 0.1.20, SAMtools 1.13, Saxon HE, SBCL 2.4.1, ScaFaCoS 1.0.4, Scalene 1.5.35, scanpy 1.9.8, scCODA 0.1.9, SCENIC 1.3.0, scib 1.1.4, scikit bio, scikit extremes, scikit learn, scikit learn, scikit learn, scikit lego, scikit misc, SciPy bundle, SCons 4.6.0, Score P, Score P, SCOTCH 7.0.1, scVelo 0.3.1, Seaborn 0.13.2, SemiBin 2.0.2, SemiBin 2.0.2, semla 1.1.6, SentencePiece 0.1.99, Sentence Transformers, SeqLib 1.2.0, Seqmagick 0.8.6, seqtk 1.4, Seurat 5.0.1, sinto 0.7.4, SIONlib 1.7.7, SIP 6.8.1, siscone 3.0.6, skorch 0.15.0, sktime 0.25.0, SLEPc 3.20.1, smithwaterman 20160702, snakemake 8.4.2, SNAPE pooled, snappy 1.1.10, SOAPdenovo Trans, sonic 20180202, SPAdes 3.15.4, Spark 3.5.1, sparsehash 2.0.4, spdlog 1.12.0, SpectrA 1.0.1, speech_tools 2.5.0, spglib python, spoa 4.1.0, SPOOLES 2.2, SQLAlchemy 2.0.25, SQLAlchemy 2.0.29, SQLAlchemy 2.0.29, SRA Toolkit, SSW 1.1, Stack 2.13.1, STAR 2.7.11b, statsmodels 0.14.1, statsmodels 0.14.1, SUNDIALS 6.6.0, SuperLU_DIST 8.1.2, SURVIVOR 1.0.7, sympy 1.12, Szip 2.1.1, tabixpp 1.1.2, TAMkin 1.2.6, TAMkin 1.2.6, TAMkin 1.2.6, TAMkin 1.2.6, tensorboard 2.15.1, tensorboardX 2.6.2.2, tensorboardX 2.6.2.2, tensorflow probability, texinfo 7.1, texlive 20230313, timm 0.9.7, tiny cuda, Togl 2.0, torchvision 0.14.1, torchvision 0.16.0, tox 3.25.1, tox 3.25.1, tqdm 4.66.2, trimAl 1.4.1, TRIQS 3.2.0, TRIQS cthyb, TRIQS dft_tools, TRIQS tprf, typing extensions, typing extensions, typing extensions, UCX 1.16.0, UCX 1.16.0, UCX 1.16.0, UCX 1.16.0, UCX 1.16.0, UDUNITS 2.2.28, umap learn, UMI tools, uncertainties 3.1.7, Vala 0.56.14, Vamb 3.0.9, vcflib 1.0.9, Velvet 1.2.10, VEP 111, Vim 9.1.0004, VisPy 0.12.2, Voro++ 0.4.6, vsc mympirun, waLBerla 6.1, Wannier90 3.1.0, WCSLIB 7.11, WFA2 2.3.4, wget 1.21.4, WhatsHap 2.1, WhatsHap 2.2, WIEN2k 23.2, wrf python, WSClean 3.4, XCFun 2.1.1, XCrySDen 1.6.2, Xerces C++, XlsxWriter 3.1.9, XML LibXML, xpdf 4.04, xxHash 0.8.2, yaff 1.6.0, YAXT 0.10.0, Yices 2.6.4, YODA 1.9.9, yt 4.3.0, Zeo++ 0.3, zUMIs 2.9.7 + - Abseil 20240116.1, ABySS 2.3.7, AMS 2023.104, Anaconda3 2024.02, anndata 0.10.5.post1, anvio 8, ArchR 1.0.2, + archspec 0.2.2, Armadillo 12.8.0, arpack-ng 3.9.1, arrow-R 14.0.0.2, ASAP3 3.13.3, assimp 5.3.1, autopep8 2.0.4, + basemap 1.3.9, BerkeleyGW 3.1.0 + 4.0, BiG-SCAPE 1.1.5, Biopython 1.83, Blosc 1.21.5, Blosc2 2.13.2, Boost.MPI 1.82.0, + Boost.Python 1.83.0, Braindecode 0.8.1, Brotli-python 1.1.0, build 1.0.3, buildenv-default foss-2023b + intel-2023b, + bx-python 0.10.0, CapnProto 1.0.1.1, c-ares 1.27.0, Cartopy 0.22.0, casacore 3.5.0, Cbc 2.10.11, ccache 4.9, cclib 1.8, + CellBender 0.3.1, CellTypist 1.6.2, CFITSIO 4.3.1, Cgl 0.60.8, Clang-Python-bindings 16.0.6, Clp 1.17.9, CmdStanR 0.7.1, + COBRApy 0.29.0, code-server 4.22.1, CoinUtils 2.11.10, CoordgenLibs 3.0.2, CREST 2.12, cryoCARE 0.3.0, CSBLAST 2.2.4, + CUDA 12.3.2 + 12.4.0, cuDNN 8.9.7.29, CuPy 13.0.0, cuSPARSELt 0.6.0.6, cuTENSOR 2.0.1.2, CVXPY 1.4.2, Cython 3.0.8, + dask 2023.12.1, datalad 0.19.5, DB_File 1.859, deepdiff 6.7.1, DeepLabCut 2.3.6, DendroPy 4.6.1, Deprecated 1.2.14, + DFT-D4 3.6.0, DIAMOND 2.1.9, Dice 20240101, dlb 3.4, DLPack 0.8, dorado 0.5.1, EggLib 3.3.0, einops 0.7.0, ELPA 2023.11.001, + enchant-2 2.6.5, ESMF 8.4.2, eSpeak-NG 1.51, ETE 3.1.3, expecttest 0.2.1, fastjet 3.4.2, fastjet-contrib 1.053, FDS 6.8.0, + fineRADstructure 20210514, fio 3.36, Fiona 1.9.5, Flask 3.0.0, FLINT 3.1.1, Flye 2.9.3, fmt 10.2.0, freebayes 1.3.7, + GATK 4.5.0.0, gawk 5.3.0, geocube 0.4.3, geopandas 0.14.2, geopy 2.4.1, GHC 9.4.6, Ghostscript 10.02.1, GIMIC 2.2.1, + git-lfs 3.5.1, GitPython 3.1.42, GLFW 3.4, Go 1.22.1, GPAW 24.1.0, GPAW-setups 24.1.0, gperftools 2.14, Gradle 8.6, + graph-tool 2.55, Greenlet 3.0.3, GROMACS 2024.1, gRPC 1.62.1, GTK3 3.24.39, Gurobi 11.0.0, HDF5 1.14.3, HeFFTe 2.4.0, + HepMC3 3.2.6, hunspell 1.7.2, igraph 0.10.10, infercnvpy 0.4.3, iperf 3.16, IQ-TREE 2.2.2.7, ISA-L 2.31.0, Java/19 (19.0.2), + Java/21 (21.0.2), json-c 0.17, Julia 1.10.0, KaHIP 3.16, LAMMPS 2Aug2023_update2, LASTZ 1.04.22, LDC 1.36.0, leidenalg 0.10.2, + libcint 5.5.0, libgit2 1.7.2, librosa 0.10.1, librsvg 2.58.0, libSBML 5.19.7, libsigsegv 2.14, libtirpc 1.3.4, + libxml2-python 2.11.4, likwid 5.3.0, LLVM 14.0.6, MACS3 3.0.1, maeparser 1.3.1, Mamba 23.11.0-0, MATIO 1.5.26, + matplotlib 3.8.2, maturin 1.5.0, MCR R2023a, MDAnalysis 2.7.0, MDI 1.4.26, medaka 1.11.3, Meson 1.3.1, MiXCR 4.6.0, + MNE-Python-1.6., MOABB 1.0.0, molmod 1.4.8, MONAI 1.3.0, mpi4py 3.1.5, mrcfile 1.5.0, NCCL 2.20.5, NCO 5.1.9, NECI 20230620, + netcdf4-python-1.6.5, networkx 3.2.1, NGSpeciesID 0.3.0, NiBabel 5.2.0, nichenetr 2.0.4, Nilearn 0.10.3, + nlohmann_json 3.11.3, NLTK 3.8.1, ntCard 1.2.2, numba 0.58.1, NVHPC 24.1, OBITools3 3.0.1b26, OCaml 4.14.0, occt 7.8.0, + onedrive 2.4.25, ONNX 1.15.0, ONNX-Runtime 1.16.3, ont-fast5-api 4.1.2, OPARI2 2.0.8, OpenFOAM v2306 + v2312, OpenSSL/3, + Optuna 3.5.0, Osi 0.108.9, PAPI 7.1.0, Parallel-Hashmap 1.3.12, ParaView 5.12.0, PDT 3.25.2, PETSc 3.20.3, PGPLOT 5.2.2, + phonemizer 3.2.1, phono3py 2.7.0, Pillow 10.2.0, Pint 0.23, plotly.py 5.18.0, poetry 1.7.1, presto-1.0.0 20230501, + PROJ 9.3.1, prompt-toolkit 3.0.36, protobuf 25.3, protobuf-python 4.25.3, psmc 0.6.5_20221121, pstoedit 3.78, + psycopg2 2.9.9, PuLP 2.8.0, PyCheMPS2 1.8.12, pycodestyle 2.11.1, pydantic 1.10.13 + 2.5.3 2.6.4, pydicom 2.4.4, pydot 2.0.0, + pyfaidx 0.8.1.1, PyFrag 2023-dev.20240220, pymatgen 2023.12.18, PyOpenCL 2023.1.4, PyOpenGL 3.1.7, pyparsing 3.1.1, + PyQt5 5.15.10, Pysam 0.22.0, PySCF 2.4.0, pyspoa 0.2.1, PyTables 3.9.2, pytest-rerunfailures 14.0, python-igraph 0.11.4, + python-irodsclient 2.0.0, python-isal 1.6.1, python-libsbml 5.20.2, python-xxhash 3.4.1, PyTorch-Ignite 0.4.13, + PyTorch-Lightning 2.2.1, PyZMQ 25.1.2, QIIME2 2023.7.0, Qt5 5.15.13, Qt6 6.6.3, Qtconsole 5.5.1, QtPy 2.4.1, + QuantumESPRESSO 7.3, R 4.3.3, rasterio 1.3.9, R-bundle-Bioconductor 3.18, rclone 1.66.0, RE2 2024-03-01, Redis 7.2.4, + redis-py 5.0.1, rioxarray 0.15.0, Rivet 3.1.9, rMATS-turbo 4.2.0, RNA-Bloom 2.0.1, rocm-smi 5.6.0, rpy2 3.5.15, + ruamel.yaml 0.18.6, Ruby 3.3.0, Rust 1.75.0 + 1.76.0, Salmon 1.10.1, Sambamba 1.0.1, Saxon-HE 12.4, SBCL 2.4.1, + ScaFaCoS 1.0.4, Scalene 1.5.35, scanpy 1.9.8, scib 1.1.4, scikit-bio 0.5.9, scikit-learn 1.4.0, scikit-lego 0.7.4, + scikit-misc 0.3.1, SCons 4.6.0, Score-P 8.4, scVelo 0.3.1, Seaborn 0.13.2, SentencePiece 0.1.99, Seqmagick 0.8.6, + Seurat 5.0.1, SIP 6.8.1, siscone 3.0.6, skorch 0.15.0, SLEPc 3.20.1, snakemake 8.4.2, SNAPE-pooled 20150707, + SOAPdenovo-Trans 1.0.5, Spark 3.5.1, spdlog 1.12.0, spoa 4.1.0, SRA-Toolkit 3.0.10, Stack 2.13.1, STAR 2.7.11b, + statsmodels 0.14.1, tensorboard 2.15.1, tensorboardX 2.6.2.2, tensorflow-probability 0.20.0, texinfo 7.1, timm 0.9.7, + torchvision 0.16.0, tqdm 4.66.2, TRIQS 3.2.0, TRIQS-cthyb 3.2.1, TRIQS-dft_tools 3.2.0, TRIQS-tprf 3.2.1, + typing-extensions 4.9.0, UCX 1.16.0, UDUNITS 2.2.28, umap-learn 0.5.5, UMI-tools 1.1.4, Vala 0.56.14, VEP 111, + Vim 9.1.0004, vsc-mympirun 5.4.0, WFA2 2.3.4, wget 1.21.4, WhatsHap 2.2, WIEN2k 23.2, wrf-python 1.3.4.1, + Xerces-C++ 3.2.5, XlsxWriter 3.1.9, XML-LibXML v2.0209, xxHash 0.8.2, yaff 1.6.0, YAXT 0.10.0, Yices 2.6.4, YODA 1.9.9 - minor enhancements, including: - - demo of `build_info_msg` easyconfig parameter (#18550) + - add build info message to easyconfig for NLTK 3.7 (#18550) - enable KLU and CUDA solvers in SUNDIALS v6.6.0 (#19490) - - add tidybayes to R-bundle-CRAN v2023.12 (#19712) - - add spdep extension to R-bundle-CRAN v2023.12 (#19729) - - add plyranges to R-bundle-Bioconductor for zUMIs (#19949) + - add extensions to R-bundle-CRAN v2023.12: tidybayes (#19712), spdep (#19729), fixest (#20055) + - add plyranges extension to R-bundle-Bioconductor (for zUMIs) (#19949) - add PyOpenGL-accelerate extension to PyOpenGL v3.1.7 (#20007) - - add AMOS dependency for Circlator, required by toAmos and minimus2 (#20011) - - use system architecture template in DB_File (#20014), GD (#20015) and GDGraph (#20016) - - add fixest with deps to R-bundle-CRAN v2023.12 (#20055) + - use system architecture template in DB_File (#20014), GD (#20015), and GDGraph (#20016) - add support for Vulkan software rendering in Mesa v23.1.9 by adding Wayland dependency (#20069) - add MODIStsp extension (+ required dependencies) to R 4.2.2 (#20113) - enable LittleCMS2 and WebP support in recent Pillow (#20195) - - drop hatchling builddep from tqdm 4.66.1 as well (#20200) - - improve test for validity of EasyConfigs (#20205) + - improve test for validity of easyconfig files (#20205) - add easyconfig test that checks if backdoored XZ versions are introduced (#20267) - various bug fixes, including: - add patch for Bison 3.7.1 to fix build error on old OS versions (#12291) @@ -53,21 +92,19 @@ update/bugfix release - fix dependencies and configure flags of GnuTLS 3.7.x (#19070) - remove numa configure option from hwloc 2.5+ (#19085) - add patches for OpenBLAS v0.3.21 to disable -ftree-vectorize for netlib LAPACK (#19280) - - use new DualSPHysics easyblock (#19400) - add patch to fix flaky scipy build in SciPy-bundle v2023.11 (#19481) - add missing SciPy-bundle dependency to TensorRT easyconfig (#19486) - fix lapack test failures in OpenBLAS 0.3.23/24 (#19495) - add patch for Arrow v8.0.0 - v11.0.0 to add missing `__arrow_ext_class__` method to `BaseExtensionType` class (#19532) - change homepage for argtable (#19551) - - add patches for PyTorch v2.1.2 with `foss/2022a` (#19571), `foss/2022b` (#19572) and `foss/2023a` (#19573) to fix test failures on non-x86 platforms + - add patches for PyTorch v2.1.2 with `foss/2022a` (#19571), `foss/2022b` (#19572), and `foss/2023a` (#19573) to fix test failures on non-x86 platforms - use pocl with CUDA support as dependency for PyOpenCL v2023.1.4 (#19584) - - remove `osdependencies` from GCCcore ccache (#19600) + - remove `osdependencies` from ccache easyconfigs using GCCcore toolchain (#19600) - use https source URL for alsa-lib (#19628) - - add missing KronaTools dep to q2-krona (#19633) - add missing dm-tree dependency for dm-reverb 0.2.0 (#19653) - add libyaml import check to PyYAML and fix builds since split to minimal Python (#19662) - demote meson-python to a build dependency in recent matplotlib easyconfigs (#19670) - - patch upb CopyFrom error in protobuf-python 4.24.0 (#19671) + - add patch to fix upb CopyFrom error in protobuf-python 4.24.0 (#19671) - demote poetry to build dep in expecttest (#19675) - add zlib dependency to YODA and Rivet (#19679) - fix missing spaces in Graphviz configure options (#19687) @@ -80,91 +117,82 @@ update/bugfix release - add Python build dependency to 1.9.x Doxygen (#19743) - fix Arrow v14.0.1 to install pyarrow as an extension (#19758) - fix homepage + source URL for Gblocks 0.91b (#19797) - - make sure that Brunsli libraries are installed into `/lib` (#19805) - - fix dependency with libidn.so.11 in tbl2asn v20220427 and v20230713 easyconfigs (#19821) + - make sure that Brunsli libraries are installed into `lib` (#19805) + - fix dependency with `libidn.so.11` in tbl2asn v20220427 and v20230713 easyconfigs (#19821) - add missing dependencies for fslpy in easyconfig for FSL v6.0.5.1 (#19829) - remove numa configure option from hwloc 2+ (#19833) - avoid spurious test failure when enabling RPATH for Perl (#19835) - add missing Python deps and packages in PSI4 1.7 (#19836) - - add patch to fix `MS_RDONLY` error in OpenMPI 3.1.x and 4.0.0 (#20140), 4.0.3 (#19944) and 4.0.5 (#19837) - - demote meson-python to build dependency for matplotlib v3.7.2 w/ iimkl/2023a (#19892) - - demote hatchling to build dependency in einops-0.7.0-GCCcore-12.3.0.eb (#19915) + - add patch to fix `MS_RDONLY` error in OpenMPI 3.1.x and 4.0.0 (#20140), 4.0.3 (#19944), and 4.0.5 (#19837) + - demote meson-python to build dependency for matplotlib v3.7.2 w/ `iimkl/2023a` (#19892) + - demote hatchling to build dependency in easyconfig for einops 0.7.0 (#19915) - add patch for adding a write memory barrier to all OpenMPI 4.1.x easyconfigs (#19940) - stop using non-existent `--disable-libdeflate` option for LibTIFF 4.1.0 (#19951) - add patch to remove git version check and fix test command for molmod 1.4.8 (#19952) - replace SYSTEM-level GCC dependency in git-annex with binutils (#19956) - stop using non-existing `--with-doc` configure option for groff 1.23 (#19969) - fix test failures of Perl-bundle-CPAN-5.38 in non-English locales (#19971) - - add patch to fix tree-optimization bug in GCC 13.2.0 for ARM architectures with SVE support (#19974) - - drop checksum from VSCode (#19995) - - respect sysroot in Pillow-SIMD when in use (#19996) + - add patch to fix tree-optimization bug in GCC 12.3.0 + 13.1.0 + 13.2.0 for ARM architectures with SVE support (#19974, #20218) + - drop checksum from easyconfig for VSCode 1.85.0 since tarball are not stable (#19995) + - respect `sysroot` in recent Pillow-SIMD easyconfigs, when in use (#19996) - remove `--disable-docs` configure option from FriBidi 1.0.5+ (#19998) - fix geotiff configure option in GDAL (#19999) - unpack SCG database to 'db' subdirectory for DAS_Tool (#20008) - remove Jasper dependency and configure option from GDAL 3.5+ (#20009) - - update homepage and source_urls for SPAdes (#20018) + - update homepage and source URLs for SPAdes (#20018) - fix GDAL 3.5.0 install on high-core-count machines (#20027) - - fix source URL for xpdf 4.04 (#20024) - remove disable-visibility configure flag from GTK3 (#20028) - remove mpi configure option from libfdf 0.2.2 (#20034) - add patch to fix multiarch support for RISC-V to all GCCcore 12.x and 13.x easyconfigs (#20035) - fix invocation typo and unneeded folder change on invocation in fgbio 1.3.0 easyconfig (#20039) - remove hdf5 configure option from MDSplus 7.96.12 (#20041) - - move poetry to builddeps and bump poetry version in gcsfs v2023.12.2.post1 easyconfig (#20042) - fix python configure option of MEME (#20043) - fix configure options of FFLAS-FFPACK (#20052) - find the correct Python in xtensor (#20056) - fix geotiff configure option in GDAL 2.2.3 (#20057) - - fix configure option and gpertools dependency of MIRA 5.0 (#20061) + - fix configure option and remove gperftools dependency for MIRA 5.0 (#20061) - fix confgure options in GRASS (#20062) - - fix GUIDANCE installation (#20063) - fix configure of LinBox 1.7.0 (#20064) - remove unknown configure option from GnuTLS 3.7.2 (#20065) - use 32-bit indexing for SUNDIALS 6.6.0 (with foss/2023a) to enable sunmatrix-cusparse (#20075) - find correct Python for MDI (#20083) - add `pixman` and `FriBidi` dependencies to recent ImageMagick easyconfigs (#20086) - - set LD_LIBRARY_PATH for python-casacore 3.5.2 (#20089) - add patch to fix failing tests with OpenSSL 3.x for Net-SSLeay v1.92 extension in Perl-bundle-CPAN v5.36.1 (#20090) and v5.38.0 (#20118) - add patches for minimus2 in AMOS-3.1.0 (#20114) - fix download url for cuSPARSELt 0.3.0.3 (#20129) - - fix test issues in PyTorch-2.1.2-foss-2023a-CUDA-12.1.1 (#20156) - - remove UCX-CUDA 1.15.0 on top of incompatible CUDA 12.3.0 + GCC 13.2.0 combo (#20158) + - add patches to fix test issues for PyTorch 2.1.2 with `foss/2023a` + CUDA 12.1.1 (#20156) + - remove easyconfig for UCX-CUDA 1.15.0 using incompatible combo of CUDA 12.3.0 + GCC 13.2.0 (#20158) - remove flake8 suppressions for invalid escape sequences (#20161) - - fix post-install command for SuperLU_DIST in case library prefix is lib instead of lib64 (#20162) + - fix post-install command for SuperLU_DIST in case library prefix is `lib` instead of `lib64` (#20162) - switch to gitlab source URL for libxc + add alternative checksum (#20163) - - remove whitespace in protobuf-25.3-GCCcore-13.2.0.eb (#20172) - - enable `download_dep_fail` for Pythonpackage ECs where it was wrongly disabled (#20174) - - fix PyTorch versions 1.12.0-foss-2022a-CUDA-11.7.0 (#20176), 1.12.0-foss-2022a (#20177), 1.12.1-foss-2022a-CUDA-11.7.0 (#20178), 1.12.1-foss-2022a (#20179), 1.13.1-foss-2022a-CUDA-11.7.0 (#20180), 1.13.1-foss-2022a (#20181) and 1.13.1-foss-2022b (#20182) for Linux 6+ - - disable tests for Time::HiRes extension in Perl-bundle-CPAN v5.36.1 (#20187) + - enable `download_dep_fail` in Pythonpackage easyconfigs where it was wrongly disabled (#20174) + - add patch to fix PyTorch 1.12.x and 1.13.x for Linux 6+ (#20176, #20177, #20178, #20179, #20180, #20181, #20182) + - disable tests for `Time::HiRes` extension in Perl-bundle-CPAN v5.36.1 (#20187) - fix several typos in GlobalArrays 5.8 configure step (#20188) - fix broken homepage from older SCOTCH easyconfigs (#20192) - - remove dead URL for ISL from source_urls in easyconfigs for GCCcore 10.3.0, 11.1.0, 11.2.0 (#20193) - - fix package installation in easyconfigs for Python 2.7.15 and 3.7.2 (using GCCcore/8.2.0) (#20194) + - remove dead URL for ISL from `source_urls` in easyconfigs for GCCcore 10.3.0, 11.1.0, 11.2.0 (#20193) + - fix package installation in easyconfigs for Python 2.7.15 and 3.7.2 (using `GCCcore/8.2.0`) (#20194) - add missing zlib + OpenSSL deps to Ruby easyconfigs + promote binutils to runtime dependency (#20214) - fix cuSPARSELt easyconfigs for aarch64 (#20216) - - add patch to fix tree-optimization bug in GCC 12.3.0 and 13.1.0 for ARM architectures with SVE support (#20218) - - fix shebang in napari v0.4.1{5,8} easyconfigs (#20219) - - fix test failure in SciPy-bundle-2023.02-gfbf-2022b (#20235) + - fix python shebang in napari easyconfigs (#20219) + - add patch to fix scipy test failure for SciPy-bundle 2023.02 with `gfbf/2022b` (#20235) - fix `incompatible types` errors when building the R extension `dbarts` on Arm (#20238) - add patch to fix for libarchive to fix error reporting in tar (#20254) - - add GCCcore-13.2.0_fix-unguarded-is_convertible-builtin.patch (#20260) + - add patch for GCCcore 13.2.0 to fix unguarded use of is_convertible builtin (#20260) - fix download for python-parasail 1.3.4 by adding missing source URL (#20263) - other changes: - - fix name for DETONATE in existing easyconfig (#19569) + - update DualSPHysics easyconfig to use custom easyblock (#19400) + - fix name for DETONATE in existing easyconfig (was `detonate`) (#19569) - rename `VSCode` to `code-cli` (to match with existing `code-server`) (#19585, #19645) - - update comment in ncurses and zlib for dummy -> SYSTEM toolchain (#19658) - - bump versions of `tensorboard v2.15.1` extensions and add reference to `protobuf-python` patch (#19673) - - wandb should not specify urllib3 since it does not need a newer version then the one in Python-bundle-PyPI (#19725) + - remove urllib3 extension from wandb easyconfig, not neeed since Python-bundle-PyPI dependency already provides it (#19725) - stop using custom easyblock for Doxygen (#19742) - - move setuptools_scm from hatchling to Python easyconfig in develop (#19777) + - move `setuptools_scm` extension from hatchling to Python easyconfig (#19777, #20200) - move xtb v6.6.1 to gfbf/2023a (#19826) - - move NiBabel v5.2.0 to gfbf/2023a (#19850) - - remove easyconfig for zlib 1.3 w/ intel toolchain, should be using GCCcore (#20023) - unify Z3 4.12.2 easyconfigs into a single one with Python bindings (and fix Z3 dependency for PyTorch 2.1.2 accordingly) (#20050) - use GPAW-setups v24.1.0 in existing GPAW easyconfigs (#20117) - - fix duplicate dict entries and enable fatal error checking for ECs via `flake8` (#20173) - - drop Greenlet to GCCcore (#20241) - - update Java-8 wrapper to 8.402 (#20261) + - fix duplicate dict entries and enable fatal error checking for easyconfigs via `flake8` (#20173) + - move Greenlet 2.0.2 to GCCcore toolchain (#20241) + - update Java/8 wrapper to Java 8.402 (#20261) - update copyright lines to 2024 (#20276)