From 776e29481f0f4db09cd9dcb4a5497a465789e027 Mon Sep 17 00:00:00 2001 From: sassy Date: Sat, 13 Jun 2020 23:20:35 +0000 Subject: [PATCH 001/939] New EC for version 1.9.1 and download URL changed for both versions --- .../FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ .../FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 46 +++++++++++++++++++ .../f/FLANN/cmake-flann-1.8.4.patch | 23 ++++++++++ .../f/FLANN/cmake-flann-1.9.1.patch | 21 +++++++++ 4 files changed, 136 insertions(+) create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb create mode 100644 easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch create mode 100644 easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb new file mode 100644 index 000000000000..bf9a0af1ea83 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.8.4' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/mariusmuja/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mariusmuja/flann/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = [ + 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz + '491b1ead0bd4167d1d3e59cecb188cc54cb1ee854179b9571a68ab02f934bcb6', # cmake-flann-1.8.4.patch' +] + +builddependencies = [('CMake', '3.16.4')] +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), +] + +separate_build_dir = True + +patches = ['cmake-flann-1.8.4.patch'] + +preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb new file mode 100644 index 000000000000..4f8590bfeb0e --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -0,0 +1,46 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen + +easyblock = 'CMakeMake' + +name = 'FLANN' +version = '1.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://github.com/mariusmuja/flann/' +description = "FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces." + +toolchain = {'name': 'foss', 'version': '2020a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://github.com/mariusmuja/flann/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = [ + 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz + '14218e775a8de5197bad1afa470e66e53a8a850b5a7ae2c0d2e840727030a7a2', # cmake-flann-1.9.1.patch +] + +builddependencies = [('CMake', '3.16.4')] +dependencies = [ + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), +] + +separate_build_dir = True + +patches = ['cmake-flann-1.9.1.patch'] + +preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' +configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" + +modextrapaths = {'PYTHONPATH': ['share/flann/python']} + +sanity_check_paths = { + 'files': ['lib/libflann_cpp_s.a', 'lib/libflann_s.a', + 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], + 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], +} +sanity_check_commands = [('python', '-c "import pyflann"')] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch new file mode 100644 index 000000000000..e06e7f70eedc --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch @@ -0,0 +1,23 @@ +diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists.txt +--- flann-1.8.4.orig/src/cpp/CMakeLists.txt 2013-01-24 17:54:36.000000000 +0000 ++++ flann-1.8.4/src/cpp/CMakeLists.txt 2020-06-12 22:23:14.032194077 +0000 +@@ -29,7 +29,7 @@ + endif() + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann_cpp SHARED "") ++ add_library(flann_cpp SHARED empty.cpp) + set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) + +@@ -83,7 +83,7 @@ + set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann SHARED "") ++ add_library(flann SHARED empty.cpp) + set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) + else() + + diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch new file mode 100644 index 000000000000..ae411342b6e7 --- /dev/null +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch @@ -0,0 +1,21 @@ +diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists.txt +--- flann-1.9.1.orig/src/cpp/CMakeLists.txt 2016-08-04 23:20:50.000000000 +0000 ++++ flann-1.9.1/src/cpp/CMakeLists.txt 2020-06-13 20:56:59.634970091 +0000 +@@ -29,7 +29,7 @@ + endif() + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann_cpp SHARED "") ++ add_library(flann_cpp SHARED empty.cpp) + set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) + +@@ -83,7 +83,7 @@ + set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) + + if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) +- add_library(flann SHARED "") ++ add_library(flann SHARED empty.cpp) + set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) + target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) + else() From 9b7629fce074a1b5e9a8b2be781fe521e31b8b31 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 14 Jun 2020 13:38:05 +0000 Subject: [PATCH 002/939] Style corrected --- .../f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 4f8590bfeb0e..952488f148ea 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -23,8 +23,8 @@ checksums = [ builddependencies = [('CMake', '3.16.4')] dependencies = [ - ('Python', '3.8.2'), - ('SciPy-bundle', '2020.03', '-Python-3.8.2'), + ('Python', '3.8.2'), + ('SciPy-bundle', '2020.03', '-Python-3.8.2'), ] separate_build_dir = True From e14d534992fe3b8a63b462b1a5f252a1b6428626 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Jul 2020 21:09:19 +0000 Subject: [PATCH 003/939] Patch files updated --- .../FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 3 +-- .../FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 3 +-- .../f/FLANN/cmake-flann-1.8.4.patch | 18 +++++++++++------- .../f/FLANN/cmake-flann-1.9.1.patch | 16 +++++++++++----- 4 files changed, 24 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index bf9a0af1ea83..ff188f432914 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '491b1ead0bd4167d1d3e59cecb188cc54cb1ee854179b9571a68ab02f934bcb6', # cmake-flann-1.8.4.patch' + '662e5972487a6616cbca36ac9459bcc3ca773ed781564ed2532d9792d97c2897', # cmake-flann-1.8.4.patch' ] builddependencies = [('CMake', '3.16.4')] @@ -31,7 +31,6 @@ separate_build_dir = True patches = ['cmake-flann-1.8.4.patch'] -preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 952488f148ea..1dad550d3d02 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -18,7 +18,7 @@ source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '14218e775a8de5197bad1afa470e66e53a8a850b5a7ae2c0d2e840727030a7a2', # cmake-flann-1.9.1.patch + '479068a9f1c745780a7fbf55e6ba02011d5a6ca0a917ce0d4e11367c14a8cf78', # cmake-flann-1.9.1.patch ] builddependencies = [('CMake', '3.16.4')] @@ -31,7 +31,6 @@ separate_build_dir = True patches = ['cmake-flann-1.9.1.patch'] -preconfigopts = 'touch %(builddir)s/flann-%(version)s/src/cpp/empty.cpp && ' configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch index e06e7f70eedc..db8f515db340 100644 --- a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch @@ -1,7 +1,10 @@ -diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists.txt ---- flann-1.8.4.orig/src/cpp/CMakeLists.txt 2013-01-24 17:54:36.000000000 +0000 -+++ flann-1.8.4/src/cpp/CMakeLists.txt 2020-06-12 22:23:14.032194077 +0000 -@@ -29,7 +29,7 @@ +# Flann fails to build with newer versions of CMake, see: +# https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails +diff --git a/flann-1.8.4.orig/src/cpp/CMakeLists.txt b/flann-1.8.4/src/cpp/CMakeLists.txt +index 78a204a..d9b5777 100644 +--- a/flann-1.8.4.orig/src/cpp/CMakeLists.txt ++++ b/flann-1.8.4/src/cpp/CMakeLists.txt +@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) endif() if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -10,7 +13,7 @@ diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) -@@ -83,7 +83,7 @@ +@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS) set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -19,5 +22,6 @@ diff -Nru flann-1.8.4.orig/src/cpp/CMakeLists.txt flann-1.8.4/src/cpp/CMakeLists set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() - - +diff --git a/flann-1.8.4/src/cpp/empty.cpp b/flann-1.8.4/src/cpp/empty.cpp +new file mode 100644 +index 0000000..e69de29 diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch index ae411342b6e7..4f3c2fd45f96 100644 --- a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch +++ b/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch @@ -1,7 +1,10 @@ -diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists.txt ---- flann-1.9.1.orig/src/cpp/CMakeLists.txt 2016-08-04 23:20:50.000000000 +0000 -+++ flann-1.9.1/src/cpp/CMakeLists.txt 2020-06-13 20:56:59.634970091 +0000 -@@ -29,7 +29,7 @@ +# Flann fails to build with newer versions of CMake, see: +# https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails +diff --git a/flann-1.9.1.orig/src/cpp/CMakeLists.txt b/flann-1.9.1/src/cpp/CMakeLists.txt +index 49c53f0..0976e41 100644 +--- a/flann-1.9.1.orig/src/cpp/CMakeLists.txt ++++ b/flann-1.9.1/src/cpp/CMakeLists.txt +@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) endif() if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -10,7 +13,7 @@ diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) -@@ -83,7 +83,7 @@ +@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS) set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) @@ -19,3 +22,6 @@ diff -Nru flann-1.9.1.orig/src/cpp/CMakeLists.txt flann-1.9.1/src/cpp/CMakeLists set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() +diff --git a/flann-1.9.1/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp +new file mode 100644 +index 0000000..e69de29 From 8e87416d80f9e095c14718940a04b98d173fba26 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 6 Jul 2020 21:29:37 +0000 Subject: [PATCH 004/939] Patch files name updated --- .../easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 2 +- .../{cmake-flann-1.8.4.patch => FLANN-1.8.4_fix-cmake.patch} | 0 .../easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 2 +- .../{cmake-flann-1.9.1.patch => FLANN-1.9.1_fix-cmake.patch} | 0 4 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/f/FLANN/{cmake-flann-1.8.4.patch => FLANN-1.8.4_fix-cmake.patch} (100%) rename easybuild/easyconfigs/f/FLANN/{cmake-flann-1.9.1.patch => FLANN-1.9.1_fix-cmake.patch} (100%) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index ff188f432914..438121d4c3d0 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -29,7 +29,7 @@ dependencies = [ separate_build_dir = True -patches = ['cmake-flann-1.8.4.patch'] +patches = ['%(name)s-%(version)s_fix-cmake.patch'] configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch similarity index 100% rename from easybuild/easyconfigs/f/FLANN/cmake-flann-1.8.4.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 1dad550d3d02..aaef2f96e6a5 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -29,7 +29,7 @@ dependencies = [ separate_build_dir = True -patches = ['cmake-flann-1.9.1.patch'] +patches = ['%(name)s-%(version)s_fix-cmake.patch'] configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" diff --git a/easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch similarity index 100% rename from easybuild/easyconfigs/f/FLANN/cmake-flann-1.9.1.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch From f36c897b397fcc3f3139e9ffe0e6f114677adc58 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 18:53:31 +0000 Subject: [PATCH 005/939] Addressed the suggested changes, merged 2 patch file into one --- .../FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 6 ++--- .../f/FLANN/FLANN-1.8.4_fix-cmake.patch | 27 ------------------- .../FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 5 ++-- ..._fix-cmake.patch => FLANN-fix-cmake.patch} | 11 +++++--- 4 files changed, 13 insertions(+), 36 deletions(-) delete mode 100644 easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch rename easybuild/easyconfigs/f/FLANN/{FLANN-1.9.1_fix-cmake.patch => FLANN-fix-cmake.patch} (74%) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index 438121d4c3d0..38bb91aac900 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -16,9 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-fix-cmake.patch'] + checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '662e5972487a6616cbca36ac9459bcc3ca773ed781564ed2532d9792d97c2897', # cmake-flann-1.8.4.patch' + '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] @@ -29,8 +31,6 @@ dependencies = [ separate_build_dir = True -patches = ['%(name)s-%(version)s_fix-cmake.patch'] - configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch deleted file mode 100644 index db8f515db340..000000000000 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch +++ /dev/null @@ -1,27 +0,0 @@ -# Flann fails to build with newer versions of CMake, see: -# https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails -diff --git a/flann-1.8.4.orig/src/cpp/CMakeLists.txt b/flann-1.8.4/src/cpp/CMakeLists.txt -index 78a204a..d9b5777 100644 ---- a/flann-1.8.4.orig/src/cpp/CMakeLists.txt -+++ b/flann-1.8.4/src/cpp/CMakeLists.txt -@@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) - endif() - - if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) -- add_library(flann_cpp SHARED "") -+ add_library(flann_cpp SHARED empty.cpp) - set_target_properties(flann_cpp PROPERTIES LINKER_LANGUAGE CXX) - target_link_libraries(flann_cpp -Wl,-whole-archive flann_cpp_s -Wl,-no-whole-archive) - -@@ -83,7 +83,7 @@ if (BUILD_C_BINDINGS) - set_property(TARGET flann_s PROPERTY COMPILE_DEFINITIONS FLANN_STATIC) - - if(CMAKE_SYSTEM_NAME STREQUAL "Linux" AND CMAKE_COMPILER_IS_GNUCC) -- add_library(flann SHARED "") -+ add_library(flann SHARED empty.cpp) - set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) - target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) - else() -diff --git a/flann-1.8.4/src/cpp/empty.cpp b/flann-1.8.4/src/cpp/empty.cpp -new file mode 100644 -index 0000000..e69de29 diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index aaef2f96e6a5..b1d818c4301c 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -16,9 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] +patches = ['%(name)s-fix-cmake.patch'] + checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '479068a9f1c745780a7fbf55e6ba02011d5a6ca0a917ce0d4e11367c14a8cf78', # cmake-flann-1.9.1.patch + '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] @@ -29,7 +31,6 @@ dependencies = [ separate_build_dir = True -patches = ['%(name)s-%(version)s_fix-cmake.patch'] configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch similarity index 74% rename from easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch index 4f3c2fd45f96..78ff18ab0655 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1_fix-cmake.patch +++ b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch @@ -1,9 +1,12 @@ # Flann fails to build with newer versions of CMake, see: # https://stackoverflow.com/questions/50763621/building-flann-with-cmake-fails -diff --git a/flann-1.9.1.orig/src/cpp/CMakeLists.txt b/flann-1.9.1/src/cpp/CMakeLists.txt +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt index 49c53f0..0976e41 100644 ---- a/flann-1.9.1.orig/src/cpp/CMakeLists.txt -+++ b/flann-1.9.1/src/cpp/CMakeLists.txt +--- a/src/cpp/CMakeLists.txt ++++ b/src/cpp/CMakeLists.txt @@ -29,7 +29,7 @@ if (BUILD_CUDA_LIB) endif() @@ -22,6 +25,6 @@ index 49c53f0..0976e41 100644 set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() -diff --git a/flann-1.9.1/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp +diff --git a/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp new file mode 100644 index 0000000..e69de29 From ad95d3bd6cc9330aa7878b1c8711dac6f7541651 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 18:56:50 +0000 Subject: [PATCH 006/939] Corrected patch-file --- easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch index 78ff18ab0655..a1932dfb5737 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch +++ b/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch @@ -25,6 +25,6 @@ index 49c53f0..0976e41 100644 set_target_properties(flann PROPERTIES LINKER_LANGUAGE CXX) target_link_libraries(flann -Wl,-whole-archive flann_s -Wl,-no-whole-archive) else() -diff --git a/src/cpp/empty.cpp b/flann-1.9.1/src/cpp/empty.cpp +diff --git a/src/cpp/empty.cpp b/src/cpp/empty.cpp new file mode 100644 index 0000000..e69de29 From 21ea1b000045f21575d9cf599ed0133456783856 Mon Sep 17 00:00:00 2001 From: Sassy Date: Thu, 11 Mar 2021 23:12:35 +0000 Subject: [PATCH 007/939] Checksum updated in EC files --- .../easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 2 +- .../easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index 38bb91aac900..e13b4bfa6cc4 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ patches = ['%(name)s-fix-cmake.patch'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index b1d818c4301c..35ecc7037055 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -20,7 +20,7 @@ patches = ['%(name)s-fix-cmake.patch'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '0ab2575d78c27f7b4f42b69261a181a4d92f09baf391d6f386fc4b7f2380c33b', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] From e49abd1841c7f113b88efb6d61c256d19ed7778f Mon Sep 17 00:00:00 2001 From: Sassy Date: Mon, 22 Mar 2021 21:03:59 +0000 Subject: [PATCH 008/939] Name of patchfile changed as requested --- .../f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 4 ++-- .../{FLANN-fix-cmake.patch => FLANN-1.8.4_fix-cmake.patch} | 0 .../f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 4 ++-- 3 files changed, 4 insertions(+), 4 deletions(-) rename easybuild/easyconfigs/f/FLANN/{FLANN-fix-cmake.patch => FLANN-1.8.4_fix-cmake.patch} (100%) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index e13b4bfa6cc4..6bae64530232 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -16,11 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-fix-cmake.patch'] +patches = ['%(name)s-%(version)s_fix-cmake.patch'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz - '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch similarity index 100% rename from easybuild/easyconfigs/f/FLANN/FLANN-fix-cmake.patch rename to easybuild/easyconfigs/f/FLANN/FLANN-1.8.4_fix-cmake.patch diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index 35ecc7037055..a8e0f8d3ec09 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -16,11 +16,11 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-fix-cmake.patch'] +patches = ['%(name)s-1.8.4_fix-cmake.patch'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz - '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-fix-cmake.patch + '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch ] builddependencies = [('CMake', '3.16.4')] From 1c65c097bd413e0f57c0f816fa0f647c8870956e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 25 Aug 2021 13:46:40 +0200 Subject: [PATCH 009/939] adding easyconfigs: MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb --- ...OOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb new file mode 100644 index 000000000000..16f3bf08a8c4 --- /dev/null +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -0,0 +1,66 @@ +easyblock = 'Binary' + +name = 'MOOSE' +# corresponds to commit f5fa9f0 +version = '2021-05-18' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://mooseframework.inl.gov' +description = """The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a finite-element, multiphysics +framework primarily developed by Idaho National Laboratory""" + +toolchain = {'name': 'foss', 'version': '2019b'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.7.4'), + ('libpng', '1.6.37'), + ('PETSc', '3.12.4', versionsuffix), + ('SLEPc', '3.12.2', versionsuffix), + ('VTK', '8.2.0', versionsuffix), + ('sympy', '1.5.1', versionsuffix), + ('ParMETIS', '4.0.3'), +] + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/idaholab', + 'repo_name': 'moose', + 'tag': version, + 'recursive': True, + 'keep_git_dir': True, + }, +}] +checksums = [None] + +extract_sources = True + +buildininstalldir = True + +# see https://mooseframework.inl.gov/getting_started/installation/hpc_install_moose.html +# enable building libmesh with -march=native +local_libmesg_configopts = "--disable-warnings --enable-march --with-mpi=$EBROOTMPI" +install_cmd = "sed 's/--disable-warnings/%s/g' scripts/update_and_rebuild_libmesh.sh && " % local_libmesg_configopts +# build vendored copy of libmesh +install_cmd += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && export MOOSE_JOBS="%(parallel)s V=1" && ' +install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update && " +# build MOOSE itself +install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " +# run tests +install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " +# run tests, but tolerate failures +install_cmd += "(python run_tests -j %(parallel)s || echo 'Some tests are failing!' >&2 ) " + +sanity_check_paths = { + 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, + 'moose/moosetools/contrib/hit/hit.%s' % SHLIB_EXT, + 'moose/moosetools/contrib/hit/libhit-opt.%s' % SHLIB_EXT], + 'dirs': ['moose/libmesh', 'moose/python', 'moose/scripts'], +} + +modextrapaths = {'PYTHONPATH': ['moose/python', 'moose/moosetools/contrib/hit']} + +modextravars = {'MOOSE_DIR': '%(installdir)s/moose'} + +moduleclass = 'phys' From bf2486e7b750dfd8b20fece4966125bd9781df53 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 09:50:19 +0200 Subject: [PATCH 010/939] adding easyconfigs: Chemaxon_Marvin-21.14.eb --- .../Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 69 +++++++++++++++++++ 1 file changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb new file mode 100644 index 000000000000..b54cae19c1b6 --- /dev/null +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -0,0 +1,69 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +## + +# rpm file extension does not look to be known yet: Unknown file type for file *.rpm (at easybuild/tools/filetools.py) +# easyblock = 'Rpm' +easyblock = 'Binary' + +name = 'Chemaxon_Marvin' +version = '21.14' + +homepage = 'https://chemaxon.com/products/marvin' +description = """Marvin suite is a chemically intelligent desktop toolkit built +to help you draw, edit, publish, render, import and export your chemical structures +and as well as allowing you to convert between various chemical and graphical file +formats. It is free for individual, academic and non-commercial use.""" + +# NOTE not in the license list of EB +# software_license = 'Proprietary: Personal, Commercial or Academic' +software_license_urls = ['https://www.chemaxon.com/marvin/license.html'] +docurls = [ + 'https://docs.chemaxon.com/display/docs/marvinsketch-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/marvinview-user-s-guide.md', + 'https://docs.chemaxon.com/display/docs/file-formats.md', +] + +toolchain = SYSTEM + +sources = ['marvin_linux_%(version)s.rpm'] +checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] + + +osdependencies = [('rpm', 'cpio')] # for extracting rpm-files + +dependencies = [ + ('Java', '11'), +] + +extract_sources = False + +install_cmd = 'rpm2cpio ' + sources[0] + ' | cpio -idmv && ' +install_cmd += 'cd opt/chemaxon/marvinsuite/ && ' +install_cmd += 'chmod -x bin/*.bat && ' +install_cmd += 'cp -ar . %(installdir)s/' + +# plugins directory is empty +sanity_check_paths = { + 'files': ["bin/cxcalc", "bin/cxtrain", "bin/evaluate", "bin/molconvert", + "bin/msketch", "bin/mview", "EULA.html", "README"], + 'dirs': ['lib'] +} + +sanity_check_commands = ["molconvert"] + +# You need a key/license file to fully activate Chemaxon Marvin +# +# COMMERCIAL +# For commercial use please contact sales@chemaxon.com +# NON-COMMERCIAL +# For personal use get a key to be renewed every 2 months at https://chemaxon.com/products/marvin/download +# For academic use get a key for research or educational purposes at https://chemaxon.com/academic-license +# +# The license file "license.cxl" has to be placed in $HOME/.chemaxon/ + +moduleclass = 'chem' From 323c0b438e12959c6f965d294a75269d2772b64e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 10 Sep 2021 10:37:55 +0200 Subject: [PATCH 011/939] Clarify where to get download files and license + Clarify why *easyblock = "Rpm"* cannot be used --- .../easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb index b54cae19c1b6..d7523baf6be1 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -6,8 +6,8 @@ # ## -# rpm file extension does not look to be known yet: Unknown file type for file *.rpm (at easybuild/tools/filetools.py) -# easyblock = 'Rpm' +# Cannot use *easyblock = 'Rpm'* because the RPM misses some fields: +# Summary and License fields must be present in package: (main package) easyblock = 'Binary' name = 'Chemaxon_Marvin' @@ -30,10 +30,10 @@ docurls = [ toolchain = SYSTEM +# Download and license at https://chemaxon.com/products/marvin sources = ['marvin_linux_%(version)s.rpm'] checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] - osdependencies = [('rpm', 'cpio')] # for extracting rpm-files dependencies = [ From 99cc4d8ab6cef6e35a1b06d7e997ef7d791e353e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 12:23:14 +0200 Subject: [PATCH 012/939] add -DLIBMESH_HAVE_XDR to $CXXFLAGS for LibMesh in MOOSE easyconfig Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 16f3bf08a8c4..99576611ef9a 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -43,7 +43,7 @@ buildininstalldir = True local_libmesg_configopts = "--disable-warnings --enable-march --with-mpi=$EBROOTMPI" install_cmd = "sed 's/--disable-warnings/%s/g' scripts/update_and_rebuild_libmesh.sh && " % local_libmesg_configopts # build vendored copy of libmesh -install_cmd += 'export CXXFLAGS="$CXXFLAGS -fpermissive" && export MOOSE_JOBS="%(parallel)s V=1" && ' +install_cmd += 'export CXXFLAGS="$CXXFLAGS -fpermissive -DLIBMESH_HAVE_XDR" && export MOOSE_JOBS="%(parallel)s V=1" && ' install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update && " # build MOOSE itself install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " From 89690026f8d3b213f331f4aaebe26b25cf02854e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 12:23:32 +0200 Subject: [PATCH 013/939] add libtirpc dependency in MOOSE easyconfig Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 99576611ef9a..29000d825e42 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -15,6 +15,7 @@ toolchainopts = {'usempi': True} dependencies = [ ('Python', '3.7.4'), ('libpng', '1.6.37'), + ('libtirpc', '1.2.6'), ('PETSc', '3.12.4', versionsuffix), ('SLEPc', '3.12.2', versionsuffix), ('VTK', '8.2.0', versionsuffix), From 61acc42159f74c91d01f554256ded80f4345ece1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 14 Sep 2021 21:09:39 +0200 Subject: [PATCH 014/939] run MOOSE tests with --max-fails 10000 Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 29000d825e42..a75bf142bb7a 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -51,7 +51,7 @@ install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s h # run tests install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " # run tests, but tolerate failures -install_cmd += "(python run_tests -j %(parallel)s || echo 'Some tests are failing!' >&2 ) " +install_cmd += "(python run_tests -j %(parallel)s --max-fails 10000 || echo 'Some tests are failing!' >&2 ) " sanity_check_paths = { 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, From 57d80ed0298fcd9cd0c13ee0dd378f64c88da4ba Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 17 Jan 2022 17:13:15 +0100 Subject: [PATCH 015/939] adding easyconfigs: NAMD-2.14-foss-2021a-CUDA-11.3.1.eb --- .../NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..ba107970cf12 --- /dev/null +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,37 @@ +name = 'NAMD' +version = '2.14' +versionsuffix = '-CUDA-%(cudaver)s' + +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': '2021a'} +toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} + +source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] +sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +patches = [ + "%(name)s-%(version)s_Linux-POWER-cuda.patch", + "%(name)s-%(version)s-use_system_mremap_decl.patch" +] +checksums = [ + '34044d85d9b4ae61650ccdba5cda4794088c3a9075932392dd0752ef8c049235', # NAMD_2.14_Source.tar.gz + 'db4aeb482dfa805c859ea18940026395763169e0257401ee5341ca550029031c', # NAMD-2.14_Linux-POWER-cuda.patch + 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch +] + +# support for GCC 8+ on POWER +dependencies = [ + ('Tcl', '8.6.11'), + ('CUDA', '11.3.1', '', True), +] + +builddependencies = [ + ('tcsh', '6.22.04'), +] + +charm_arch = "multicore-linux-%(arch)s" +charm_extra_cxxflags = '-fpermissive' + +moduleclass = 'chem' From d5ef6355affca756b7e6aef53a51df68a90907fa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 24 Jan 2022 15:49:00 +0100 Subject: [PATCH 016/939] adding easyconfigs: NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb --- .../NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 67 +++++++++++++++++++ 1 file changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb new file mode 100644 index 000000000000..c25db2388cfa --- /dev/null +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -0,0 +1,67 @@ +easyblock = 'ConfigureMake' + +name = 'NVSHMEM' +version = '2.4.1' +versionsuffix = '-CUDA-%(cudaver)s' + +local_cuda_version = '11.4.1' + +homepage = 'https://developer.nvidia.com/nvshmem' +description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides +efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a +global address space for data that spans the memory of multiple GPUs and can be +accessed with fine-grained GPU-initiated operations, CPU-initiated operations, +and operations on CUDA streams. +""" + +toolchain = {'name': 'gompi', 'version': '2021b'} + +# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +sources = ['%(namelower)s_src_%(version)s-3.txz'] +checksums = ['8b6c0eab321b6352911e470f9e81a777a49e58148ec3728453b9522446dba178'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('CUDA', local_cuda_version, '', True), + ('UCX-CUDA', '1.11.2', versionsuffix), + ('NCCL', '2.10.3', f'-CUDA-{local_cuda_version}'), +] + +skipsteps = ['configure'] + +prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' +prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' + +prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' +prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' +prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' + +prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' +prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' + +prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' +prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' +prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' + +prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' +prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' +prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' +prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' +prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' + +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +modextravars = {'NVSHMEM_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 1c9f72d7d5b9b61fca330fd031cfa59540609e9b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 24 Jan 2022 16:03:34 +0100 Subject: [PATCH 017/939] update easyconfigs: NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb --- .../n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb index c25db2388cfa..908356d7fdae 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -4,8 +4,6 @@ name = 'NVSHMEM' version = '2.4.1' versionsuffix = '-CUDA-%(cudaver)s' -local_cuda_version = '11.4.1' - homepage = 'https://developer.nvidia.com/nvshmem' description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a @@ -26,9 +24,9 @@ builddependencies = [ ] dependencies = [ - ('CUDA', local_cuda_version, '', True), + ('CUDA', '11.4.1', '', True), ('UCX-CUDA', '1.11.2', versionsuffix), - ('NCCL', '2.10.3', f'-CUDA-{local_cuda_version}'), + ('NCCL', '2.10.3', versionsuffix), ] skipsteps = ['configure'] From 4052e4c93a11a298c79a6db79148c792aa966aaf Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sat, 5 Feb 2022 13:36:17 +0000 Subject: [PATCH 018/939] adding easyconfigs: MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb, MONAI-0.8.0-foss-2021a.eb --- .../MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 46 +++++++++++++++++++ .../m/MONAI/MONAI-0.8.0-foss-2021a.eb | 45 ++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..2e4087428913 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonPackage' + +name = 'MONAI' +version = '0.8.0' +versionsuffix = '-CUDA-%(cudaver)s' + +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': '2021a'} + +github_account = 'Project-MONAI' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), + ('ITK', '5.2.1'), + ('NiBabel', '3.2.1'), + ('scikit-image', '0.18.3'), + ('tensorboard', '2.8.0'), + ('torchvision', '0.11.1', versionsuffix), + ('tqdm', '4.61.2'), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'BUILD_MONAI=1' + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb new file mode 100644 index 000000000000..7a2477f2af65 --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonPackage' + +name = 'MONAI' +version = '0.8.0' + +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': '2021a'} + +github_account = 'Project-MONAI' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), + ('ITK', '5.2.1'), + ('NiBabel', '3.2.1'), + ('scikit-image', '0.18.3'), + ('tensorboard', '2.8.0'), + ('torchvision', '0.11.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'BUILD_MONAI=1' + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'dirs': [''], +} + +moduleclass = 'vis' From 9ccf8a84163d3c742b4ac69569b868f615f35aad Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Sun, 20 Feb 2022 18:13:43 +0000 Subject: [PATCH 019/939] Added checksum --- .../easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 3 ++- easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb index 2e4087428913..1315a7276424 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -15,7 +15,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'Project-MONAI' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] +checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479', + 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ ('CUDA', '11.3.1', '', True), diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb index 7a2477f2af65..0d9e772ecb6e 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -14,7 +14,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'Project-MONAI' source_urls = [GITHUB_SOURCE] sources = ['%(version)s.tar.gz'] -checksums = ['b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479'] +checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479', + 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ ('CUDA', '11.3.1', '', True), From 4f7df0034e369e25fde8ee4d44713d21c95d33a2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 9 Mar 2022 17:02:53 +0200 Subject: [PATCH 020/939] adding easyconfigs: dm-reverb-0.7.0-foss-2021b.eb and patches: dm-reverb-0.7.0_eb-build-environment.patch --- .../d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb | 41 ++ ...dm-reverb-0.7.0_eb-build-environment.patch | 687 ++++++++++++++++++ 2 files changed, 728 insertions(+) create mode 100644 easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb new file mode 100644 index 000000000000..52279474a017 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0-foss-2021b.eb @@ -0,0 +1,41 @@ +name = 'dm-reverb' +version = '0.7.0' + +homepage = 'https://github.com/deepmind/reverb' +description = """ +Reverb is an efficient and easy-to-use data storage and transport system +designed for machine learning research. Reverb is primarily used as an +experience replay system for distributed reinforcement learning algorithms but +the system also supports multiple data structure representations such as FIFO, +LIFO, and priority queues.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/deepmind/reverb/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = ['dm-reverb-0.7.0_eb-build-environment.patch'] +checksums = [ + '11fd16db4dab60cc3e827fe8311921797c8e0371e55a2e0f2798ae7d9aabe47c', # v0.7.0.tar.gz + 'eb75e3ec778a1cafafd93d5dbd0d7530ea785c0378e0ee1ef2321ce7599aa7f0', # dm-reverb-0.7.0_eb-build-environment.patch +] + +builddependencies = [ + ('Bazel', '3.7.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('TensorFlow', '2.7.1'), + ('Abseil', '20210324.2'), + ('dm-tree', '0.1.6'), + ('gRPC', '1.44.0'), + ('protobuf', '3.17.3'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), +] + +sanity_pip_check = True + +options = {'modulename': 'reverb'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch new file mode 100644 index 000000000000..a1d6297a79c2 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-reverb/dm-reverb-0.7.0_eb-build-environment.patch @@ -0,0 +1,687 @@ +Refactor the build environment to use dependencies from EasyBuild +* fix detection of Python installation +* disable toolchain definitions with gcc-7 +* use C++11 ABI as it is used in protobuf from EB +* define a single local repo using files from EB for the following dependencies: + * local com_google_protobuf replaces protobuf_archive, protobuf_protoc and + external com_google_protobuf + * local zlib replaces zlib_includes and external zlib + * local snappy replaces snappy_includes + * local pybind11 replaces http archive source + * local com_github_grpc_grpc replaces http archive source + * local com_google_absl replaces http archive source +author: Alex Domingo (Vrije Universiteit Brussel) +diff --git a/WORKSPACE.orig b/WORKSPACE +index 5d47f95..6d587ab 100644 +--- a/WORKSPACE.orig ++++ b/WORKSPACE +@@ -13,8 +13,15 @@ workspace(name = "reverb") + # + # *WARNING* If using the REVERB_PROTOC_VERSION environment variable, sha256 + # checking is disabled. Use at your own risk. +-PROTOC_VERSION = "3.9.0" +-PROTOC_SHA256 = "15e395b648a1a6dda8fd66868824a396e9d3e89bc2c8648e3b9ab9801bea5d55" ++#PROTOC_VERSION = "3.9.0" ++#PROTOC_SHA256 = "15e395b648a1a6dda8fd66868824a396e9d3e89bc2c8648e3b9ab9801bea5d55" ++ ++load( ++ "//reverb/cc/platform/default:repo.bzl", ++ "cc_tf_configure", ++) ++ ++cc_tf_configure() + + load("@bazel_tools//tools/build_defs/repo:http.bzl", "http_archive") + +@@ -28,72 +35,6 @@ http_archive( + ], + ) + +-http_archive( +- name = "com_google_absl", +- sha256 = "35f22ef5cb286f09954b7cc4c85b5a3f6221c9d4df6b8c4a1e9d399555b366ee", # SHARED_ABSL_SHA +- strip_prefix = "abseil-cpp-997aaf3a28308eba1b9156aa35ab7bca9688e9f6", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-cpp/archive/997aaf3a28308eba1b9156aa35ab7bca9688e9f6.tar.gz", +- "https://github.com/abseil/abseil-cpp/archive/997aaf3a28308eba1b9156aa35ab7bca9688e9f6.tar.gz", +- ], +-) +- + # Note that the Python dependencies are not tracked by bazel here, but + # in setup.py. + +-## Begin GRPC related deps +-http_archive( +- name = "com_github_grpc_grpc", +- patch_cmds = [ +- """sed -i.bak 's/"python",/"python3",/g' third_party/py/python_configure.bzl""", +- """sed -i.bak 's/PYTHONHASHSEED=0/PYTHONHASHSEED=0 python3/g' bazel/cython_library.bzl""", +- ], +- sha256 = "39bad059a712c6415b168cb3d922cb0e8c16701b475f047426c81b46577d844b", +- strip_prefix = "grpc-reverb_fix", +- urls = [ +- # Patched version of GRPC / boringSSL to make it compile with old TF GCC compiler +- "https://github.com/qstanczyk/grpc/archive/reverb_fix.tar.gz", +- ], +-) +- +- +-load("@com_github_grpc_grpc//bazel:grpc_deps.bzl", "grpc_deps") +- +-grpc_deps() +- +-load("@com_github_grpc_grpc//bazel:grpc_extra_deps.bzl", "grpc_extra_deps") +- +-grpc_extra_deps() +- +- +-load("@upb//bazel:workspace_deps.bzl", "upb_deps") +- +-upb_deps() +- +-load( +- "@build_bazel_rules_apple//apple:repositories.bzl", +- "apple_rules_dependencies", +-) +- +-apple_rules_dependencies() +- +-load( +- "@build_bazel_apple_support//lib:repositories.bzl", +- "apple_support_dependencies", +-) +- +-apple_support_dependencies() +-## End GRPC related deps +- +-load( +- "//reverb/cc/platform/default:repo.bzl", +- "cc_tf_configure", +- "reverb_protoc_deps", +- "reverb_python_deps", +-) +- +-cc_tf_configure() +- +-reverb_python_deps() +- +-reverb_protoc_deps(version = PROTOC_VERSION, sha256 = PROTOC_SHA256) +diff --git a/reverb/cc/platform/default/BUILD.orig b/reverb/cc/platform/default/BUILD +index 372653e..897c346 100644 +--- a/reverb/cc/platform/default/BUILD.orig ++++ b/reverb/cc/platform/default/BUILD +@@ -18,7 +18,7 @@ reverb_cc_library( + srcs = ["snappy.cc"], + deps = [ + "//reverb/cc/platform:snappy_hdr", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ] + reverb_tf_deps(), + alwayslink = 1, + ) +@@ -30,7 +30,7 @@ reverb_cc_library( + "//reverb/cc/checkpointing:interface", + "//reverb/cc/platform:checkpointing_hdr", + "//reverb/cc/platform:tfrecord_checkpointer", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ], + alwayslink = 1, + ) +@@ -48,7 +48,7 @@ reverb_cc_library( + "//reverb/cc/platform:status_macros", + "//reverb/cc/platform:tfrecord_checkpointer", + "//reverb/cc/support:periodic_closure", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ] + reverb_grpc_deps(), + alwayslink = 1, + ) +@@ -60,7 +60,7 @@ reverb_cc_library( + "status_matchers.h", + ], + deps = [ +- "@com_google_absl//absl/status", ++ "@com_google_absl//:absl", + ], + ) + +@@ -68,7 +68,7 @@ reverb_cc_library( + name = "status_matchers", + hdrs = ["status_matchers.h"], + deps = [ +- "@com_google_absl//absl/status", ++ "@com_google_absl//:absl", + ], + ) + +@@ -77,8 +77,7 @@ reverb_cc_library( + srcs = ["thread.cc"], + deps = [ + "//reverb/cc/platform:thread_hdr", +- "@com_google_absl//absl/memory", +- "@com_google_absl//absl/strings", ++ "@com_google_absl//:absl", + ], + alwayslink = 1, + ) +@@ -101,7 +100,7 @@ reverb_cc_library( + hdrs = ["hash_map.h"], + deps = [ + ":hash", +- "@com_google_absl//absl/container:flat_hash_map", ++ "@com_google_absl//:absl", + ], + ) + +@@ -110,7 +109,7 @@ reverb_cc_library( + hdrs = ["hash_set.h"], + deps = [ + ":hash", +- "@com_google_absl//absl/container:flat_hash_set", ++ "@com_google_absl//:absl", + ], + ) + +diff --git a/reverb/cc/platform/default/repo.bzl.orig b/reverb/cc/platform/default/repo.bzl +index 1daac52..f6d55e3 100644 +--- a/reverb/cc/platform/default/repo.bzl.orig ++++ b/reverb/cc/platform/default/repo.bzl +@@ -91,13 +91,13 @@ def _find_python_solib_path(repo_ctx): + version = exec_result.stdout.splitlines()[-1] + basename = "lib{}.so".format(version) + exec_result = repo_ctx.execute( +- ["{}-config".format(version), "--configdir"], ++ ["{}-config".format(version), "--prefix"], + quiet = True, + ) + if exec_result.return_code != 0: + fail("Could not locate python shared library path:\n{}" + .format(exec_result.stderr)) +- solib_dir = exec_result.stdout.splitlines()[-1] ++ solib_dir = "{}/{}".format(exec_result.stdout.splitlines()[-1], "lib") + full_path = repo_ctx.path("{}/{}".format(solib_dir, basename)) + if not full_path.exists: + fail("Unable to find python shared library file:\n{}/{}" +@@ -125,64 +125,121 @@ cc_library( + ) + + def _nsync_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink(tf_include_path + "/external", "nsync_includes") ++ nsync_root = repo_ctx.os.environ.get("EBROOTNSYNC") ++ repo_ctx.symlink(nsync_root, "nsync") + repo_ctx.file( + "BUILD", + content = """ + cc_library( + name = "includes", +- hdrs = glob(["nsync_includes/nsync/public/*.h"]), +- includes = ["nsync_includes"], ++ hdrs = glob(["nsync/**/*.h"]), ++ includes = ["nsync/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _zlib_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink( +- tf_include_path + "/external/zlib", +- "zlib", +- ) ++def _zlib_repo_impl(repo_ctx): ++ zlib_root = repo_ctx.os.environ.get("EBROOTZLIB") ++ repo_ctx.symlink(zlib_root, "zlib") + repo_ctx.file( + "BUILD", + content = """ + cc_library( ++ name = "libz", ++ srcs = ["zlib/lib/libz.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( + name = "includes", + hdrs = glob(["zlib/**/*.h"]), +- includes = ["zlib"], ++ includes = ["zlib/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _snappy_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink( +- tf_include_path + "/external/snappy", +- "snappy", +- ) ++def _snappy_repo_impl(repo_ctx): ++ snappy_root = repo_ctx.os.environ.get("EBROOTSNAPPY") ++ repo_ctx.symlink(snappy_root, "snappy") + repo_ctx.file( + "BUILD", + content = """ + cc_library( ++ name = "libsnappy", ++ srcs = ["snappy/lib/libsnappy.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( + name = "includes", +- hdrs = glob(["snappy/*.h"]), +- includes = ["snappy"], ++ hdrs = glob(["snappy/**/*.h"]), ++ includes = ["snappy/include"], + visibility = ["//visibility:public"], + ) + """, + executable = False, + ) + +-def _protobuf_includes_repo_impl(repo_ctx): +- tf_include_path = _find_tf_include_path(repo_ctx) +- repo_ctx.symlink(tf_include_path, "tf_includes") ++def _pybind11_includes_repo_impl(repo_ctx): ++ pybind_root = repo_ctx.os.environ.get("EBROOTPYBIND11") ++ repo_ctx.symlink("{}/include".format(pybind_root), "include") ++ repo_ctx.symlink(Label("//third_party:pybind11.BUILD"), "BUILD") ++ ++def _protobuf_repo_impl(repo_ctx): ++ protobuf_root = repo_ctx.os.environ.get("EBROOTPROTOBUF") ++ repo_ctx.symlink(protobuf_root, "protobuf") + repo_ctx.symlink(Label("//third_party:protobuf.BUILD"), "BUILD") + ++def _absl_repo_impl(repo_ctx): ++ absl_root = repo_ctx.os.environ.get("EBROOTABSEIL") ++ repo_ctx.symlink(absl_root, "absl") ++ repo_ctx.file( ++ "BUILD", ++ content = """ ++cc_library( ++ name = "absl", ++ hdrs = glob(["absl/**/*.h", "absl/**/*.inc"]), ++ srcs = glob(["absl/lib/*.so"]), ++ includes = ["absl/include"], ++ visibility = ["//visibility:public"], ++) ++""", ++ executable = False, ++ ) ++ ++def _grpc_repo_impl(repo_ctx): ++ grpc_root = repo_ctx.os.environ.get("EBROOTGRPC") ++ repo_ctx.symlink(grpc_root, "grpc") ++ repo_ctx.file( ++ "BUILD", ++ content = """ ++cc_library( ++ name = "grpc++", ++ hdrs = glob(["grpc/**/*.h"]), ++ srcs = glob(["grpc/lib/*.so"]), ++ includes = ["grpc/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "grpc++_codegen_proto", ++ hdrs = glob([ ++ "grpc/include/*/impl/codegen/*.h", ++ "grpc/include/*/impl/codegen/security/*.h", ++ ]), ++ includes = ["grpc/include"], ++ visibility = ["//visibility:public"], ++) ++filegroup( ++ name = "grpc_cpp_plugin", ++ srcs = ["grpc/bin/grpc_cpp_plugin"], ++ visibility = ["//visibility:public"], ++) ++""", ++ executable = False, ++ ) ++ + def _tensorflow_includes_repo_impl(repo_ctx): + tf_include_path = _find_tf_include_path(repo_ctx) + repo_ctx.symlink(tf_include_path, "tensorflow_includes") +@@ -200,11 +257,11 @@ cc_library( + ), + includes = ["tensorflow_includes"], + deps = [ +- "@com_google_absl//absl/container:flat_hash_map", ++ "@com_google_absl//:absl", + "@eigen_archive//:includes", +- "@protobuf_archive//:includes", +- "@zlib_includes//:includes", +- "@snappy_includes//:includes", ++ "@com_google_protobuf//:includes", ++ "@zlib//:includes", ++ "@snappy//:includes", + ], + visibility = ["//visibility:public"], + ) +@@ -226,7 +283,12 @@ def _tensorflow_solib_repo_impl(repo_ctx): + cc_library( + name = "framework_lib", + srcs = ["tensorflow_solib/libtensorflow_framework.so.2"], +- deps = ["@python_includes", "@python_includes//:numpy_includes"], ++ deps = [ ++ "@python_includes", ++ "@python_includes//:numpy_includes", ++ "@zlib//:libz", ++ "@snappy//:libsnappy", ++ ], + visibility = ["//visibility:public"], + ) + """, +@@ -275,17 +337,29 @@ def cc_tf_configure(): + ) + make_nsync_repo(name = "nsync_includes") + make_zlib_repo = repository_rule( +- implementation = _zlib_includes_repo_impl, ++ implementation = _zlib_repo_impl, + ) +- make_zlib_repo(name = "zlib_includes") ++ make_zlib_repo(name = "zlib") + make_snappy_repo = repository_rule( +- implementation = _snappy_includes_repo_impl, ++ implementation = _snappy_repo_impl, + ) +- make_snappy_repo(name = "snappy_includes") ++ make_snappy_repo(name = "snappy") ++ make_pybind11_repo = repository_rule( ++ implementation = _pybind11_includes_repo_impl, ++ ) ++ make_pybind11_repo(name = "pybind11") + make_protobuf_repo = repository_rule( +- implementation = _protobuf_includes_repo_impl, ++ implementation = _protobuf_repo_impl, ++ ) ++ make_protobuf_repo(name = "com_google_protobuf") ++ make_absl_repo = repository_rule( ++ implementation = _absl_repo_impl, + ) +- make_protobuf_repo(name = "protobuf_archive") ++ make_absl_repo(name = "com_google_absl") ++ make_grpc_repo = repository_rule( ++ implementation = _grpc_repo_impl, ++ ) ++ make_grpc_repo(name = "com_github_grpc_grpc") + make_tfinc_repo = repository_rule( + implementation = _tensorflow_includes_repo_impl, + ) +@@ -298,65 +372,3 @@ def cc_tf_configure(): + implementation = _python_includes_repo_impl, + ) + make_python_inc_repo(name = "python_includes") +- +-def reverb_python_deps(): +- http_archive( +- name = "pybind11", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/pybind/pybind11/archive/v2.4.3.tar.gz", +- "https://github.com/pybind/pybind11/archive/v2.4.3.tar.gz", +- ], +- sha256 = "1eed57bc6863190e35637290f97a20c81cfe4d9090ac0a24f3bbf08f265eb71d", +- strip_prefix = "pybind11-2.4.3", +- build_file = clean_dep("//third_party:pybind11.BUILD"), +- ) +- +- http_archive( +- name = "absl_py", +- sha256 = "603febc9b95a8f2979a7bdb77d2f5e4d9b30d4e0d59579f88eba67d4e4cc5462", +- strip_prefix = "abseil-py-pypi-v0.9.0", +- urls = [ +- "https://storage.googleapis.com/mirror.tensorflow.org/github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", +- "https://github.com/abseil/abseil-py/archive/pypi-v0.9.0.tar.gz", +- ], +- ) +- +-def _reverb_protoc_archive(ctx): +- version = ctx.attr.version +- sha256 = ctx.attr.sha256 +- +- override_version = ctx.os.environ.get("REVERB_PROTOC_VERSION") +- if override_version: +- sha256 = "" +- version = override_version +- +- urls = [ +- "https://github.com/protocolbuffers/protobuf/releases/download/v%s/protoc-%s-linux-x86_64.zip" % (version, version), +- ] +- ctx.download_and_extract( +- url = urls, +- sha256 = sha256, +- ) +- +- ctx.file( +- "BUILD", +- content = """ +-filegroup( +- name = "protoc_bin", +- srcs = ["bin/protoc"], +- visibility = ["//visibility:public"], +-) +-""", +- executable = False, +- ) +- +-reverb_protoc_archive = repository_rule( +- implementation = _reverb_protoc_archive, +- attrs = { +- "version": attr.string(mandatory = True), +- "sha256": attr.string(mandatory = True), +- }, +-) +- +-def reverb_protoc_deps(version, sha256): +- reverb_protoc_archive(name = "protobuf_protoc", version = version, sha256 = sha256) +diff --git a/reverb/cc/platform/default/build_rules.bzl.orig b/reverb/cc/platform/default/build_rules.bzl +index fa8560f..6bf3694 100644 +--- a/reverb/cc/platform/default/build_rules.bzl.orig ++++ b/reverb/cc/platform/default/build_rules.bzl +@@ -90,12 +90,12 @@ def reverb_cc_proto_library(name, srcs = [], deps = [], **kwargs): + srcs = srcs, + outs = gen_srcs + gen_hdrs, + tools = dep_srcs + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -E -e 's#reverb(/.*|$$)##') +- $(location @protobuf_protoc//:protoc_bin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --cpp_out=$$OUTDIR {}""".format( +@@ -165,12 +165,12 @@ def reverb_py_proto_library(name, srcs = [], deps = [], **kwargs): + srcs = srcs, + outs = gen_srcs, + tools = proto_deps + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -E -e 's#reverb(/.*|$$)##') +- $(location @protobuf_protoc//:protoc_bin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --python_out=$$OUTDIR {}""".format( +@@ -227,14 +227,14 @@ def reverb_cc_grpc_library( + srcs = srcs, + outs = gen_srcs + gen_hdrs + gen_mocks, + tools = proto_src_deps + [ +- "@protobuf_protoc//:protoc_bin", ++ "@com_google_protobuf//:protoc_bin", + "@tensorflow_includes//:protos", +- "@com_github_grpc_grpc//src/compiler:grpc_cpp_plugin", ++ "@com_github_grpc_grpc//:grpc_cpp_plugin", + ], + cmd = """ + OUTDIR=$$(echo $(RULEDIR) | sed -e 's#reverb/.*##') +- $(location @protobuf_protoc//:protoc_bin) \ +- --plugin=protoc-gen-grpc=$(location @com_github_grpc_grpc//src/compiler:grpc_cpp_plugin) \ ++ $(location @com_google_protobuf//:protoc_bin) \ ++ --plugin=protoc-gen-grpc=$(location @com_github_grpc_grpc//:grpc_cpp_plugin) \ + --proto_path=external/tensorflow_includes/tensorflow_includes/ \ + --proto_path=. \ + --grpc_out={} {}""".format( +@@ -544,6 +544,8 @@ def reverb_tf_ops_visibility(): + + def reverb_tf_deps(): + return [ ++ "@zlib//:libz", ++ "@snappy//:libsnappy", + "@tensorflow_includes//:includes", + "@tensorflow_solib//:framework_lib", + ] +@@ -552,24 +554,4 @@ def reverb_grpc_deps(): + return ["@com_github_grpc_grpc//:grpc++"] + + def reverb_absl_deps(): +- return [ +- # We purposefully don't include absl::flat_hash_{map,set} so that users +- # are forced to use platform:hash_{map,set}, which uses a safer hasher. +- "@com_google_absl//absl/base", +- "@com_google_absl//absl/base:core_headers", +- "@com_google_absl//absl/functional:bind_front", +- "@com_google_absl//absl/memory", +- "@com_google_absl//absl/numeric:int128", +- "@com_google_absl//absl/random", +- "@com_google_absl//absl/random:distributions", +- "@com_google_absl//absl/status", +- "@com_google_absl//absl/status:statusor", +- "@com_google_absl//absl/strings", +- "@com_google_absl//absl/strings:cord", +- "@com_google_absl//absl/strings:str_format", +- "@com_google_absl//absl/synchronization", +- "@com_google_absl//absl/time", +- "@com_google_absl//absl/types:optional", +- "@com_google_absl//absl/types:span", +- "@com_google_absl//absl/flags:flag", +- ] ++ return ["@com_google_absl//:absl"] +diff --git a/third_party/protobuf.BUILD.orig b/third_party/protobuf.BUILD +index b8e9496..7d601a5 100644 +--- a/third_party/protobuf.BUILD.orig ++++ b/third_party/protobuf.BUILD +@@ -1,10 +1,10 @@ + _CHECK_VERSION = """ +-PROTOC_VERSION=$$($(location @protobuf_protoc//:protoc_bin) --version \ ++PROTOC_VERSION=$$($(location protobuf/bin/protoc) --version \ + | cut -d' ' -f2 | sed -e 's/\\./ /g') + PROTOC_VERSION=$$(printf '%d%03d%03d' $${PROTOC_VERSION}) + TF_PROTO_VERSION=$$(grep '#define PROTOBUF_MIN_PROTOC_VERSION' \ +- $(location tf_includes/google/protobuf/port_def.inc) | cut -d' ' -f3) +-if [ "$${PROTOC_VERSION}" -ne "$${TF_PROTO_VERSION}" ]; then ++ $(location protobuf/include/google/protobuf/port_def.inc) | cut -d' ' -f3) ++if [ "$${PROTOC_VERSION}" -lt "$${TF_PROTO_VERSION}" ]; then + echo !!!!!!!!!!!!!!!!!!!!!!!!!!!!! 1>&2 + echo Your protoc version does not match the tensorflow proto header \ + required version: "$${PROTOC_VERSION}" vs. "$${TF_PROTO_VERSION}" 1>&2 +@@ -20,9 +20,9 @@ genrule( + name = "compare_protobuf_version", + outs = ["versions_compared"], + srcs = [ +- "tf_includes/google/protobuf/port_def.inc", ++ "protobuf/include/google/protobuf/port_def.inc", + ], +- tools = ["@protobuf_protoc//:protoc_bin"], ++ tools = ["protobuf/bin/protoc"], + cmd = _CHECK_VERSION, + ) + +@@ -30,11 +30,45 @@ cc_library( + name = "includes", + data = [":versions_compared"], + hdrs = glob([ +- "tf_includes/google/protobuf/*.h", +- "tf_includes/google/protobuf/*.inc", +- "tf_includes/google/protobuf/**/*.h", +- "tf_includes/google/protobuf/**/*.inc", ++ "protobuf/include/google/protobuf/*.h", ++ "protobuf/include/google/protobuf/*.inc", ++ "protobuf/include/google/protobuf/**/*.h", ++ "protobuf/include/google/protobuf/**/*.inc", + ]), +- includes = ["tf_includes"], ++ includes = ["protobuf/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf_headers", ++ data = [":versions_compared"], ++ hdrs = glob([ ++ "protobuf/include/google/protobuf/*.h", ++ "protobuf/include/google/protobuf/*.inc", ++ "protobuf/include/google/protobuf/**/*.h", ++ "protobuf/include/google/protobuf/**/*.inc", ++ ]), ++ includes = ["protobuf/include"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf_lite", ++ srcs = ["protobuf/lib/libprotobuf-lite.so"], ++ visibility = ["//visibility:public"], ++) ++cc_library( ++ name = "protobuf", ++ srcs = ["protobuf/lib/libprotobuf.so"], ++ visibility = ["//visibility:public"], ++ deps = [":protobuf_lite"], ++) ++cc_library( ++ name = "protoc_lib", ++ srcs = ["protobuf/lib/libprotoc.so"], ++ visibility = ["//visibility:public"], ++ deps = [":protobuf"], ++) ++filegroup( ++ name = "protoc_bin", ++ srcs = ["protobuf/bin/protoc"], + visibility = ["//visibility:public"], + ) +diff --git a/reverb/cc/opensource/opensource_only.files.orig b/reverb/cc/opensource/opensource_only.files +index 375df63..d74bec1 100644 +--- a/reverb/cc/opensource/opensource_only.files.orig ++++ b/reverb/cc/opensource/opensource_only.files +@@ -1,8 +1,5 @@ + reverb/third_party/BUILD.oss + reverb/third_party/protobuf.BUILD.oss + reverb/third_party/pybind11.BUILD.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/BUILD.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/cc_toolchain_config.bzl.oss +-reverb/third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/dummy_toolchain.bzl.oss + reverb/platform/default/BUILD.oss + reverb/pip_package/BUILD.oss +diff --git a/third_party/opensource_only.files.orig b/third_party/opensource_only.files +index e1f9e12..f3e999c 100644 +--- a/third_party/opensource_only.files.orig ++++ b/third_party/opensource_only.files +@@ -6,6 +6,3 @@ reverb/pip_package/setup.py: + third_party/BUILD: + third_party/protobuf.BUILD: + third_party/pybind11.BUILD: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/BUILD: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/cc_toolchain_config.bzl: +-third_party/toolchains/preconfig/ubuntu16.04/gcc7_manylinux2010/dummy_toolchain.bzl: +diff --git a/.bazelrc.orig b/.bazelrc +index f4b08d3..89f82dd 100644 +--- a/.bazelrc.orig ++++ b/.bazelrc +@@ -13,7 +13,7 @@ build:manylinux2010 --crosstool_top=//third_party/toolchains/preconfig/ubuntu16. + + build -c opt + build --cxxopt="-std=c++14" +-build --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=0" ++build --cxxopt="-D_GLIBCXX_USE_CXX11_ABI=1" + build --auto_output_filter=subpackages + build --copt="-Wall" --copt="-Wno-sign-compare" + build --linkopt="-lrt -lm" From 99c487735e62ceec71b088f80fcbd4ec8fcedcc6 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 12:51:21 +0100 Subject: [PATCH 021/939] adding easyconfigs: Scoary-1.6.16-foss-2021a.eb, ETE-3.1.2-foss-2021a.eb --- .../easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb | 34 +++++++++++++++++ .../s/Scoary/Scoary-1.6.16-foss-2021a.eb | 38 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb new file mode 100644 index 000000000000..05d4d90ee50a --- /dev/null +++ b/easybuild/easyconfigs/e/ETE/ETE-3.1.2-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ETE' +version = '3.1.2' + +homepage = 'http://etetoolkit.org' +description = """A Python framework for the analysis and visualization of trees""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/e/ete3'] +sources = ['ete3-%(version)s.tar.gz'] +checksums = ['4fc987b8c529889d6608fab1101f1455cb5cbd42722788de6aea9c7d0a8e59e9'] + +dependencies = [ + ('lxml', '4.6.3'), + ('Python', '3.9.5'), + ('PyQt5', '5.15.4'), + ('SciPy-bundle', '2021.05'), +] + +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/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb new file mode 100644 index 000000000000..412551c4fc97 --- /dev/null +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Scoary' +version = '1.6.16' + +homepage = 'https://github.com/AdmiralenOla/Scoary' +description = "Microbial pan-GWAS using the output from Roary" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Tkinter', '%(pyver)s'), + ('ETE', '3.1.2'), +] + +exts_list = [ + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + (name, version, { + 'source_tmpl': 'scoary-%(version)s.tar.gz', + 'checksums': ['f433343422c5805a70a20f7fe83851490ae3cdf07745c65680de5feea40a6dca'], + 'modulename': False, + }), +] + + +sanity_check_paths = { + 'files': ['bin/scoary', 'bin/scoary_GUI', 'bin/vcf2scoary'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 57a9e0110a0becccbcb0eb7f5541a39f1307b450 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:10:54 +0100 Subject: [PATCH 022/939] Add missing sanity_pip_check --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 412551c4fc97..d3a039e96017 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -29,10 +29,11 @@ exts_list = [ }), ] - sanity_check_paths = { 'files': ['bin/scoary', 'bin/scoary_GUI', 'bin/vcf2scoary'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'bio' From 7759425f0ef22774b4967c87825dd87a3bbff6ad Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:32:06 +0100 Subject: [PATCH 023/939] Add other missing pip boilerplate --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index d3a039e96017..58b681985362 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -18,6 +18,9 @@ dependencies = [ ('ETE', '3.1.2'), ] +download_dep_fail = True +use_pip = True + exts_list = [ ('argparse', '1.4.0', { 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], From 2741fae7c06171aeba482a3cbd2419f679d3bd53 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 25 Apr 2022 15:57:46 +0100 Subject: [PATCH 024/939] download_dep_fail not required... --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 58b681985362..6e3329bd511d 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -18,7 +18,6 @@ dependencies = [ ('ETE', '3.1.2'), ] -download_dep_fail = True use_pip = True exts_list = [ From 5983128b51f152c2195e2f23e3c69688f97f7ae9 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 6 May 2022 22:45:38 +0100 Subject: [PATCH 025/939] adding easyconfigs: Octave-7.1.0-foss-2021b.eb --- .../o/Octave/Octave-7.1.0-foss-2021b.eb | 78 +++++++++++++++++++ 1 file changed, 78 insertions(+) create mode 100644 easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb new file mode 100644 index 000000000000..03d83437388f --- /dev/null +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -0,0 +1,78 @@ +name = 'Octave' +version = '7.1.0' + +homepage = 'https://www.gnu.org/software/octave/' +description = """GNU Octave is a high-level interpreted language, primarily intended for numerical computations.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d4a9d81f3f67b4a6e07cb7a80dcb10ad5e9176fcc30762c70a81580a64b8b0b6'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('Autotools', '20210726'), + ('gperf', '3.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20210802'), + ('PCRE', '8.45'), + ('ncurses', '6.2'), + ('libreadline', '8.1'), + ('arpack-ng', '3.8.0'), + ('cURL', '7.78.0'), + ('FLTK', '1.3.7'), + ('fontconfig', '2.13.94'), + ('freetype', '2.11.0'), + ('GLPK', '5.0'), + ('GL2PS', '1.4.2'), + ('gnuplot', '5.4.2'), + ('Java', '17', '', True), + ('zlib', '1.2.11'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('Qhull', '2020.2'), + ('Qt5', '5.15.2'), + ('HDF5', '1.12.1'), + ('qrupdate', '1.1.2'), + ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), + ('texinfo', '6.8'), + ('libsndfile', '1.0.31'), + ('GraphicsMagick', '1.3.36'), +] + +configopts = '--disable-docs ' +# correct for both GCC and Intel compilers +configopts += '--enable-fortran-calling-convention=gfortran' + +local_pkg_url = 'https://downloads.sourceforge.net/' +local_pkg_url += 'project/octave/Octave%20Forge%20Packages/Individual%20Package%20Releases/' +exts_default_options = {'source_urls': [local_pkg_url]} + +exts_list = [ + ('control', '3.4.0', { + 'checksums': ['6ec6a06e13ad288afad8631cc41f7247e47096fa1e8d04240d4ed01efbe4a77a'], + }), + ('general', '2.1.2', { + 'checksums': ['a30cd1a79743c62528dae46ebd4a83f848ae46a1c1dac3eaabc36662d42294cf'], + }), + ('io', '2.6.4', { + 'checksums': ['a74a400bbd19227f6c07c585892de879cd7ae52d820da1f69f1a3e3e89452f5a'], + }), + ('signal', '1.4.2', { + 'checksums': ['62a4e06117dcc43c36169905f8255d015481ca982aeae9013b0d9df3e48e7062'], + }), + ('statistics', '1.4.3', { + 'checksums': ['9801b8b4feb26c58407c136a9379aba1e6a10713829701bb3959d9473a67fa05'], + }), + ('struct', '1.0.17', { + 'checksums': ['0137bbb5df650f29104f6243502f3a2302aaaa5e42ea9f02d8a3943aaf668433'], + }), +] + +moduleclass = 'math' From e0f709a58f277382dc5884ad44e64c84d7c23d9d Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 6 May 2022 22:49:14 +0100 Subject: [PATCH 026/939] adding easyconfigs: texinfo-6.8-GCCcore-11.2.0.eb --- .../t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..c5b14ad74b1a --- /dev/null +++ b/easybuild/easyconfigs/t/texinfo/texinfo-6.8-GCCcore-11.2.0.eb @@ -0,0 +1,40 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'texinfo' +version = '6.8' + +homepage = 'https://www.gnu.org/software/texinfo/' +description = """Texinfo is the official documentation format of the GNU project.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['8eb753ed28bca21f8f56c1a180362aed789229bd62fff58bf8368e9beb59fec4'] + +builddependencies = [('binutils', '2.37')] + +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 b8d87bcc7e8438b2235acf4573fe08bad65b4415 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 24 May 2022 17:00:00 +0200 Subject: [PATCH 027/939] {cae}[intel/2021a] OpenFOAM v9, ParaView v5.9.1, CGAL v4.14.3, SCOTCH v6.1.0 --- .../c/CGAL/CGAL-4.14.3-iimpi-2021a.eb | 37 ++++++++++++ .../o/OpenFOAM/OpenFOAM-9-intel-2021a.eb | 37 ++++++++++++ .../ParaView-5.9.1-intel-2021a-mpi.eb | 60 +++++++++++++++++++ .../s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb | 19 ++++++ 4 files changed, 153 insertions(+) create mode 100644 easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb create mode 100644 easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb diff --git a/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb new file mode 100644 index 000000000000..5c3fd5e85772 --- /dev/null +++ b/easybuild/easyconfigs/c/CGAL/CGAL-4.14.3-iimpi-2021a.eb @@ -0,0 +1,37 @@ +name = 'CGAL' +version = '4.14.3' + +homepage = 'https://www.cgal.org/' +description = """The goal of the CGAL Open Source Project is to provide easy access to efficient + and reliable geometric algorithms in the form of a C++ library.""" + +toolchain = {'name': 'iimpi', 'version': '2021a'} +toolchainopts = {'strict': True} + +source_urls = ['https://github.com/CGAL/cgal/releases/download/releases%2FCGAL-%(version)s'] +sources = [SOURCE_TAR_XZ] +checksums = ['5bafe7abe8435beca17a1082062d363368ec1e3f0d6581bb0da8b010fb389fe4'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Eigen', '3.3.9'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('Python', '3.9.5'), + ('Boost', '1.76.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('Mesa', '21.1.1'), + ('libGLU', '9.0.1'), + ('Qt5', '5.15.2'), +] + +configopts = "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include\;$EBROOTLIBGLU/include " +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DWITH_ZLIB=ON -DWITH_MPFR=ON -DWITH_OpenGL=ON -DWITH_Eigen3=ON " +configopts += "-DWITH_GMPXX=ON -DWITH_LAPACK=ON -DWITH_BLAS=ON " + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb new file mode 100644 index 000000000000..bcf1776f9808 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-9-intel-2021a.eb @@ -0,0 +1,37 @@ +name = 'OpenFOAM' +version = '9' + +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': 'intel', 'version': '2021a'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-cleanup.patch'] +checksums = [ + '0c48fb56e2fbb4dd534112811364d3b2dc12106e670a6486b361e4f864b435ee', # version-9.tar.gz + '4b638891f32badde1a5b1b364bc3bd5e0eda180b9d9a8afdf797d5818b8b494e', # OpenFOAM-9-cleanup.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('CMake', '3.20.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('libreadline', '8.1'), + ('ncurses', '6.2'), + # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) + ('METIS', '5.1.0'), + ('SCOTCH', '6.1.0'), + ('CGAL', '4.14.3'), + ('ParaView', '5.9.1', '-mpi'), + ('gnuplot', '5.4.2'), +] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb new file mode 100644 index 000000000000..acf68e2e8cee --- /dev/null +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.9.1-intel-2021a-mpi.eb @@ -0,0 +1,60 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'CMakeMake' + +name = 'ParaView' +version = '5.9.1' +versionsuffix = '-mpi' + +homepage = "https://www.paraview.org" +description = "ParaView is a scientific parallel visualizer." + +toolchain = {'name': 'intel', 'version': '2021a'} +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"] +checksums = ['efbcba00ba38c23d0ada1bde7144a8745caa308d9e1f94a4a71d8af63732266f'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('XZ', '5.2.5'), + ('HDF5', '1.10.7'), + ('netCDF', '4.8.0'), + ('libGLU', '9.0.1'), + ('X11', '20210518'), + ('Mesa', '21.1.1'), + ('Qt5', '5.15.2'), + ('zlib', '1.2.11'), + ('FFmpeg', '4.3.2'), + ('Szip', '2.1.1'), +] + +builddependencies = [('CMake', '3.20.1')] + +separate_build_dir = True + +# Paraview +configopts = '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON -DPARAVIEW_BUILD_SHARED_LIBS=ON ' +configopts += '-DPARAVIEW_USE_MPI=ON ' +configopts += '-DPARAVIEW_ENABLE_FFMPEG=ON ' +configopts += '-DPARAVIEW_USE_PYTHON=ON ' +configopts += '-DPython3_ROOT_DIR=$EBROOTPYTHON ' + +# OpenGL & Mesa +configopts += '-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s ' % SHLIB_EXT +configopts += '-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include ' + +sanity_check_paths = { + 'files': ['bin/paraview', 'bin/pvpython'], + 'dirs': ['include/paraview-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['python -c "import paraview"'] + +modextrapaths = {'PYTHONPATH': ['lib64/python%(pyshortver)s/site-packages', 'lib/python%(pyshortver)s/site-packages']} + +moduleclass = 'vis' 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 new file mode 100644 index 000000000000..7baa08f48254 --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-6.1.0-iimpi-2021a.eb @@ -0,0 +1,19 @@ +name = 'SCOTCH' +version = '6.1.0' + +homepage = 'https://gforge.inria.fr/projects/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': 'iimpi', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['4fe537f608f0fe39ec78807f90203f9cca1181deb16bfa93b7d4cd440e01bbd1'] + +dependencies = [ + ('zlib', '1.2.11'), +] + +moduleclass = 'math' From 1e99ae552d5767f214ff9f96d87db5f006380c4a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 20:56:19 +0200 Subject: [PATCH 028/939] adding easyconfigs: tokenizers-0.12.1-GCCcore-10.3.0.eb --- .../tokenizers-0.12.1-GCCcore-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..ea5fce7f67ca --- /dev/null +++ b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.12.1-GCCcore-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'tokenizers' +version = '0.12.1' + +homepage = 'https://github.com/huggingface/tokenizers' +description = "Fast State-of-the-Art Tokenizers optimized for Research and Production" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['070746f86efa6c873db341e55cf17bb5e7bdd5450330ca8eca542f5c3dab2c66'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Rust', '1.60.0'), +] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From dcaf15510d7ee82f3c88ca50ae669cb88a1a1be1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 1 Jun 2022 21:01:56 +0200 Subject: [PATCH 029/939] {lib}[foss/2021a] flair-NLP v0.11.3, gensim v4.2.0, Hyperopt v0.2.7, SentencePiece v0.1.96 w/ Python 3.9.5 --- .../flair-NLP/flair-NLP-0.11.3-foss-2021a.eb | 95 +++++++++++++++++++ .../g/gensim/gensim-4.2.0-foss-2021a.eb | 30 ++++++ .../h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb | 35 +++++++ .../SentencePiece-0.1.96-GCC-10.3.0.eb | 65 +++++++++++++ 4 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb new file mode 100644 index 000000000000..dd85efe2e48f --- /dev/null +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a.eb @@ -0,0 +1,95 @@ +easyblock = 'PythonBundle' + +name = 'flair-NLP' +version = '0.11.3' + +homepage = 'https://github.com/flairNLP/flair' +description = "A very simple framework for state-of-the-art NLP" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('lxml', '4.6.3'), + ('gensim', '4.2.0'), + ('Hyperopt', '0.2.7'), + ('BeautifulSoup', '4.10.0'), + ('SentencePiece', '0.1.96'), + ('tokenizers', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('bpemb', '0.3.3', { + 'checksums': ['ad86ba9b1623ecc3be6fcc5ba4408e23a30e118b7e1d683d292f4be788798ffe'], + }), + ('conllu', '4.4.2', { + 'checksums': ['d5ba2f9ebf5c9af86d560e11681a172f6cd8a934967baa6839ba9a0648919c10'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + ('gdown', '4.4.0', { + 'checksums': ['18fc3a4da4a2273deb7aa29c7486be4df3919d904158ad6a6a3e25c8115470d7'], + }), + ('huggingface_hub', '0.7.0', { + 'checksums': ['8154dc2fad84b32a4bca18372a647d9381ed8550a80b11050758357b8fcea639'], + }), + ('Janome', '0.4.2', { + 'checksums': ['14c31bbfc11724da299b4b71a06bccb3af9a105e7c912bc38a22132d8991ec97'], + }), + ('overrides', '3.1.0', { + 'checksums': ['30f761124579e59884b018758c4d7794914ef02a6c038621123fec49ea7599c6'], + }), + ('importlib_metadata', '3.10.1', { + 'checksums': ['c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1'], + }), + ('konoha', '4.6.5', { + 'checksums': ['c83023e3bda68aa910bfc115c6ab72d10b2b9478093253b4e17a20b0acf6bb7f'], + }), + ('langdetect', '1.0.9', { + 'checksums': ['cbc1fef89f8d062739774bd51eda3da3274006b3661d199c2655f6b3f6d605a0'], + }), + ('mpld3', '0.5.8', { + 'checksums': ['1a167dbef836dd7c66d8aa71c06a32d50bffa18725f304d93cb74fdb3545043b'], + }), + ('pptree', '3.1', { + 'checksums': ['4dd0ba2f58000cbd29d68a5b64bac29bcb5a663642f79404877c0059668a69f6'], + }), + ('segtok', '1.5.11', { + 'checksums': ['8ab2dd44245bcbfec25b575dc4618473bbdf2af8c2649698cd5a370f42f3db23'], + }), + ('sqlitedict', '2.0.0', { + 'checksums': ['23a370416f4e1e962daa293382f3a8dbc4127e6a0abc06a5d4e58e6902f05d17'], + }), + ('transformers', '4.19.2', { + 'checksums': ['e19a4ff07458eda143c738e5259caf48449fcf078a63d6b1bd1aa806543440a3'], + }), + ('Wikipedia-API', '0.5.4', { + 'checksums': ['5173d4db641cdb78d96f2b052df2232bcdc00cf32a424c43402958a40f783992'], + 'modulename': 'wikipediaapi', + }), + ('flair', version, { + # can't use PyPI source tarball, because requirements.txt is missing; + # see also https://github.com/flairNLP/flair/issues/2759 + 'source_urls': ['https://github.com/flairNLP/flair/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c780320d6d85075e25638a7157a16409f46bc9496db31fbbaa92aeac448f1cf9'], + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb b/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb new file mode 100644 index 000000000000..2270b2977d2c --- /dev/null +++ b/easybuild/easyconfigs/g/gensim/gensim-4.2.0-foss-2021a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'gensim' +version = '4.2.0' + +homepage = 'https://radimrehurek.com/gensim' +description = """Gensim is a Python library for topic modelling, document indexing and similarity retrieval with + large corpora.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, pandas +] + +use_pip = True + +exts_list = [ + ('smart_open', '6.0.0', { + 'checksums': ['d60106b96f0bcaedf5f1cd46ff5524a1c3d02d5653425618bb0fa66e158d22b0'], + }), + (name, version, { + 'checksums': ['995ebd2970a31d47c100aaac10212f47e2bf12e2b06536d38883c951ff34eef1'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb new file mode 100644 index 000000000000..9cc986b48f52 --- /dev/null +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.7-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Hyperopt' +version = '0.2.7' + +homepage = 'http://hyperopt.github.io/hyperopt/' +description = """hyperopt is a Python library for optimizing over awkward search spaces with real-valued, + discrete, and conditional dimensions.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.0.0', { + 'checksums': ['5cd02f3b417a783ba84a4ec3e290ff7929009fe51f6405423cfccfadd43ba4a4'], + }), + ('py4j', '0.10.9.5', { + 'checksums': ['276a4a3c5a2154df1860ef3303a927460e02e97b047dc0a47c1c3fb8cce34db6'], + }), + ('hyperopt', version, { + 'checksums': ['1bf89ae58050bbd32c7307199046117feee245c2fd9ab6255c7308522b7ca149'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb new file mode 100644 index 000000000000..c4db4aa9a4d8 --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.96-GCC-10.3.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.96' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('gperftools', '2.9.1'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5198f31c3bb25e685e9e68355a3bf67a1db23c9e8bdccc33dc015f496a44df7a'], +} + +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 a8ba288f3cbe8f590458ff691db99e9a7de97f1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 3 Jun 2022 20:38:17 +0200 Subject: [PATCH 030/939] {lib}[foss/2021a] flair-NLP v0.11.3 w/ Python 3.9.5 + CUDA 11.3.1 --- ...flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..1ad8d95623ed --- /dev/null +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'flair-NLP' +version = '0.11.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/flairNLP/flair' +description = "A very simple framework for state-of-the-art NLP" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('Python', '3.9.5'), + ('PyTorch', '1.10.0', versionsuffix), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('scikit-learn', '0.24.2'), + ('lxml', '4.6.3'), + ('gensim', '4.2.0'), + ('Hyperopt', '0.2.7'), + ('BeautifulSoup', '4.10.0'), + ('SentencePiece', '0.1.96'), + ('tokenizers', '0.12.1'), +] + +use_pip = True + +exts_list = [ + ('bpemb', '0.3.3', { + 'checksums': ['ad86ba9b1623ecc3be6fcc5ba4408e23a30e118b7e1d683d292f4be788798ffe'], + }), + ('conllu', '4.4.2', { + 'checksums': ['d5ba2f9ebf5c9af86d560e11681a172f6cd8a934967baa6839ba9a0648919c10'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('Deprecated', '1.2.13', { + 'checksums': ['43ac5335da90c31c24ba028af536a91d41d53f9e6901ddb021bcc572ce44e38d'], + }), + ('ftfy', '6.1.1', { + 'checksums': ['bfc2019f84fcd851419152320a6375604a0f1459c281b5b199b2cd0d2e727f8f'], + }), + ('gdown', '4.4.0', { + 'checksums': ['18fc3a4da4a2273deb7aa29c7486be4df3919d904158ad6a6a3e25c8115470d7'], + }), + ('huggingface_hub', '0.7.0', { + 'checksums': ['8154dc2fad84b32a4bca18372a647d9381ed8550a80b11050758357b8fcea639'], + }), + ('Janome', '0.4.2', { + 'checksums': ['14c31bbfc11724da299b4b71a06bccb3af9a105e7c912bc38a22132d8991ec97'], + }), + ('overrides', '3.1.0', { + 'checksums': ['30f761124579e59884b018758c4d7794914ef02a6c038621123fec49ea7599c6'], + }), + ('importlib_metadata', '3.10.1', { + 'checksums': ['c9356b657de65c53744046fa8f7358afe0714a1af7d570c00c3835c2d724a7c1'], + }), + ('konoha', '4.6.5', { + 'checksums': ['c83023e3bda68aa910bfc115c6ab72d10b2b9478093253b4e17a20b0acf6bb7f'], + }), + ('langdetect', '1.0.9', { + 'checksums': ['cbc1fef89f8d062739774bd51eda3da3274006b3661d199c2655f6b3f6d605a0'], + }), + ('mpld3', '0.5.8', { + 'checksums': ['1a167dbef836dd7c66d8aa71c06a32d50bffa18725f304d93cb74fdb3545043b'], + }), + ('pptree', '3.1', { + 'checksums': ['4dd0ba2f58000cbd29d68a5b64bac29bcb5a663642f79404877c0059668a69f6'], + }), + ('segtok', '1.5.11', { + 'checksums': ['8ab2dd44245bcbfec25b575dc4618473bbdf2af8c2649698cd5a370f42f3db23'], + }), + ('sqlitedict', '2.0.0', { + 'checksums': ['23a370416f4e1e962daa293382f3a8dbc4127e6a0abc06a5d4e58e6902f05d17'], + }), + ('transformers', '4.19.2', { + 'checksums': ['e19a4ff07458eda143c738e5259caf48449fcf078a63d6b1bd1aa806543440a3'], + }), + ('Wikipedia-API', '0.5.4', { + 'checksums': ['5173d4db641cdb78d96f2b052df2232bcdc00cf32a424c43402958a40f783992'], + 'modulename': 'wikipediaapi', + }), + ('flair', version, { + # can't use PyPI source tarball, because requirements.txt is missing; + # see also https://github.com/flairNLP/flair/issues/2759 + 'source_urls': ['https://github.com/flairNLP/flair/archive/refs/tags'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['c780320d6d85075e25638a7157a16409f46bc9496db31fbbaa92aeac448f1cf9'], + 'preinstallopts': "sed -i 's/==/>=/g' requirements.txt && ", + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 75b46a40a55ff45d3b4561bfcfb8e8f25f20b006 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Jun 2022 17:49:13 +0200 Subject: [PATCH 031/939] adding easyconfigs: MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb new file mode 100644 index 000000000000..0e578acd269b --- /dev/null +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -0,0 +1,31 @@ +easyblock = 'Tarball' + +name = 'MultilevelEstimators' +version = '0.1.0' +local_julia_ver = '1.7.2' +versionsuffix = "-Julia-%s" % local_julia_ver + +homepage = 'https://github.com/PieterjanRobbe/MultilevelEstimators.jl' +description = "The Julia module for Multilevel Monte Carlo methods" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), + ('Julia', local_julia_ver, '-linux-%s' % ARCH, True), +] + +postinstallcmds = [ + "cd %(installdir)s && mkdir pkgs", + """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && + julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["pkgs"] +} + +modextrapaths = {'JULIA_DEPOT_PATH': 'pkgs'} + +moduleclass = 'lib' From fd21fd2caa58f12bfebb710a88f5d2118ad8c158 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 7 Jun 2022 20:40:03 +0200 Subject: [PATCH 032/939] Removed trailing whitespace --- .../MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index 0e578acd269b..ca021785912f 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -17,7 +17,7 @@ dependencies = [ postinstallcmds = [ "cd %(installdir)s && mkdir pkgs", - """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && + """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage ] From e01ed4a02f35733e18af7988cbec30a09b3f0399 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 22 Jun 2022 13:14:17 +0200 Subject: [PATCH 033/939] adding easyconfigs: Trinity-2.9.1-foss-2020b-Python-3.8.6.eb --- .../Trinity-2.9.1-foss-2020b-Python-3.8.6.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb new file mode 100644 index 000000000000..0375526f35fb --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb @@ -0,0 +1,50 @@ +## +# 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:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.9.1' +versionsuffix = '-Python-%(pyver)s' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +checksums = ['98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455'] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Bowtie2', '2.4.2'), + ('HTSlib', '1.12'), + ('Jellyfish', '2.3.0'), + ('kallisto', '0.46.2'), + ('ncurses', '6.2'), + ('Salmon', '1.4.0'), + ('SAMtools', '1.11'), + ('zlib', '1.2.11'), +] + +withsampledata = True + +moduleclass = 'bio' From 3f8147af708fd71a3ab954af95bbd2052715e8c9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 23 Jun 2022 14:15:11 +0200 Subject: [PATCH 034/939] adding easyconfigs: imbalanced-learn-0.9.0-foss-2021b.eb --- .../imbalanced-learn-0.9.0-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb new file mode 100644 index 000000000000..ba39fe52cf23 --- /dev/null +++ b/easybuild/easyconfigs/i/imbalanced-learn/imbalanced-learn-0.9.0-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'imbalanced-learn' +version = '0.9.0' + +homepage = 'https://github.com/scikit-learn-contrib/imbalanced-learn' +description = """imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in + datasets showing strong between-class imbalance.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('scikit-learn', '1.0.1'), +] + +exts_list = [ + (name, version, { + 'modulename': 'imblearn', + 'checksums': ['836a4c137cc3c10310d4f6cd5ec34600ff488d7f8c243a997c3f9b551c91d0b2'], + }), +] + +use_pip = True + +sanity_pip_check = True + +moduleclass = 'tools' From 891504d787ece5b15caf2824a5ee850bbdde0da8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 24 Jun 2022 10:35:48 +0200 Subject: [PATCH 035/939] Add a link where to find download files once logged in --- .../easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb index d7523baf6be1..adadbfe31a00 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb @@ -31,6 +31,8 @@ docurls = [ toolchain = SYSTEM # Download and license at https://chemaxon.com/products/marvin +# Once logged in download files can be found here: +# https://chemaxon.com/products/marvin/download#download sources = ['marvin_linux_%(version)s.rpm'] checksums = ['3102f30479a365758fd14ca5efcdacfe0624db80a35b146ba9a5d07e948bd8dc'] From fd4b8c78a2dbc42649ab7d1f14e4bbdcc9e4dd89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:14:22 +0200 Subject: [PATCH 036/939] adding easyconfigs: Boost.MPI-1.77.0-gompi-2021b.eb --- .../Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb new file mode 100644 index 000000000000..f0d6e24166d7 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.77.0-gompi-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'EB_Boost' + +name = 'Boost.MPI' +version = '1.77.0' + +homepage = 'https://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +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 = ['5347464af5b14ac54bb945dc68f1dd7c56f0dad7262816b956138fc53bcc0131'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('ICU', '69.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From 4264534fa65657d9a60c7fd9f183ea328194fed6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 11:20:38 +0200 Subject: [PATCH 037/939] adding easyconfigs: SISSO++-1.1-foss-2021b.eb --- .../s/SISSO++/SISSO++-1.1-foss-2021b.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb new file mode 100644 index 000000000000..53ebb6d4cada --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1-foss-2021b.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'SISSO++' +version = '1.1' + +homepage = 'https://gitlab.com/sissopp_developers/sissopp' +description = "C++ implementation of SISSO with built in Python bindings for an efficient python interface" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/sissopp_developers/sissopp/-/archive/v%(version)s/'] +sources = [{ + 'git_config': { + 'url': 'https://gitlab.com/sissopp_developers/', + 'repo_name': 'sissopp', + 'recursive': True, + 'commit': 'v%(version)s', + }, + 'filename': SOURCE_TAR_GZ, +}] +patches = ['SISSO++-1.1_cmake-mpi-fix.patch'] +checksums = [ + None, # SISSO++-1.1.tar.gz + '614f13ef34dc1d1b2fe0e9868cdcf576a0dacb336759f5295115131d15e9c35a', +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Doxygen', '1.9.1'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Boost.Python', '1.77.0'), + ('Boost.MPI', '1.77.0'), + ('Clp', '1.17.7'), + ('NLopt', '2.7.0'), + ('pybind11', '2.7.1'), + ('fmt', '7.1.1'), + ('googletest', '1.11.0'), +] + +preconfigopts = "export BOOST_ROOT=$EBROOTBOOSTMPI && " +configopts = "-DEXTERNAL_BOOST=ON -DBUILD_PYTHON=ON -DPYTHON_INSTDIR=%(installdir)s" + +sanity_check_paths = { + 'files': ['bin/sisso++', 'lib/libsisso.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["python -c 'import sissopp'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'math' From 72c10836b64162fb32399acb6c42ee32c4ae7c28 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 24 Jun 2022 12:24:04 +0200 Subject: [PATCH 038/939] add patch file for SISSO++ --- .../s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch diff --git a/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch new file mode 100644 index 000000000000..d91c3e3fe6d9 --- /dev/null +++ b/easybuild/easyconfigs/s/SISSO++/SISSO++-1.1_cmake-mpi-fix.patch @@ -0,0 +1,19 @@ +workaround for $MPI_CXX_LIBRARIES being empty and CMake tripping over that with: +CMake Error at CMakeLists.txt:252 (list): + list GET given empty list +author: Kenneth Hoste (HPC-UGent) +--- sissopp/CMakeLists.txt.orig 2022-06-23 17:17:12.083398990 +0200 ++++ sissopp/CMakeLists.txt 2022-06-23 17:17:26.326311818 +0200 +@@ -248,9 +248,9 @@ + # Check MPI + find_package(MPI REQUIRED) + include_directories(${MPI_CXX_INCLUDE_DIRS}) +-set(MPI_LIBRARIES, ${MPI_CXX_LIBRARIES}) +-list(GET MPI_CXX_LIBRARIES 0 MPI_LIBRARY) +-get_filename_component(MPI_DIR ${MPI_LIBRARY} DIRECTORY) ++#set(MPI_LIBRARIES, ${MPI_CXX_LIBRARIES}) ++#list(GET MPI_CXX_LIBRARIES 0 MPI_LIBRARY) ++#get_filename_component(MPI_DIR ${MPI_LIBRARY} DIRECTORY) + + # Build libnlopt + if(BUILD_PARAMS) From 762e7f67cae60ed4d08bad02a721bf7f61bcf6a4 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 13:49:54 +0200 Subject: [PATCH 039/939] remove python version suffix --- .../t/Trinity/Trinity-2.9.1-foss-2020b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb new file mode 100644 index 000000000000..25ad6257c8aa --- /dev/null +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -0,0 +1,49 @@ +## +# 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:: Custom +# +# Notes:: +## + +name = 'Trinity' +version = '2.9.1' + +homepage = 'https://trinityrnaseq.github.io' +description = """Trinity represents a novel method for the efficient and robust de novo reconstruction + of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, + Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" + +toolchain = {'name': 'foss', 'version': '2020b'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v%(version)s'] +sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] +checksums = ['98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455'] + +builddependencies = [ + ('Autotools', '20200321'), + ('CMake', '3.18.4'), +] + +dependencies = [ + ('Java', '11', '', True), + ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Perl', '5.32.0'), + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Bowtie2', '2.4.2'), + ('HTSlib', '1.12'), + ('Jellyfish', '2.3.0'), + ('kallisto', '0.46.2'), + ('ncurses', '6.2'), + ('Salmon', '1.4.0'), + ('SAMtools', '1.11'), + ('zlib', '1.2.11'), +] + +withsampledata = True + +moduleclass = 'bio' From 8b796db089bc68c281c228674d0f535844959cd0 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 14:08:16 +0200 Subject: [PATCH 040/939] use version without suffix --- .../Trinity-2.9.1-foss-2020b-Python-3.8.6.eb | 50 ------------------- 1 file changed, 50 deletions(-) delete mode 100644 easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb deleted file mode 100644 index 0375526f35fb..000000000000 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b-Python-3.8.6.eb +++ /dev/null @@ -1,50 +0,0 @@ -## -# 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:: Custom -# -# Notes:: -## - -name = 'Trinity' -version = '2.9.1' -versionsuffix = '-Python-%(pyver)s' - -homepage = 'https://trinityrnaseq.github.io' -description = """Trinity represents a novel method for the efficient and robust de novo reconstruction - of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, - Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.""" - -toolchain = {'name': 'foss', 'version': '2020b'} -toolchainopts = {'optarch': True} - -source_urls = ['https://github.com/trinityrnaseq/trinityrnaseq/releases/download/v%(version)s'] -sources = ['trinityrnaseq-v%(version)s.FULL.tar.gz'] -checksums = ['98d98bc21cd5dd32b408ed52586d01a15873b49b96de3264d42616bdcfc9d455'] - -builddependencies = [ - ('Autotools', '20200321'), - ('CMake', '3.18.4'), -] - -dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), - ('Perl', '5.32.0'), - ('Python', '3.8.6'), - ('SciPy-bundle', '2020.11'), - ('Bowtie2', '2.4.2'), - ('HTSlib', '1.12'), - ('Jellyfish', '2.3.0'), - ('kallisto', '0.46.2'), - ('ncurses', '6.2'), - ('Salmon', '1.4.0'), - ('SAMtools', '1.11'), - ('zlib', '1.2.11'), -] - -withsampledata = True - -moduleclass = 'bio' From 8d47e77a817b86c084028c1bc0503bce6d8f43dc Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Fri, 24 Jun 2022 14:58:51 +0200 Subject: [PATCH 041/939] stay with HTSlib 1.11 for foss/2020b --- easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb index 25ad6257c8aa..f2e75d38711c 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -35,7 +35,7 @@ dependencies = [ ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), ('Bowtie2', '2.4.2'), - ('HTSlib', '1.12'), + ('HTSlib', '1.11'), ('Jellyfish', '2.3.0'), ('kallisto', '0.46.2'), ('ncurses', '6.2'), From 72ab1ca18f2e461b9468ef42928315b12e00ebf5 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 27 Jun 2022 14:38:22 +0100 Subject: [PATCH 042/939] set JUPYTER_PATH in modextrapaths for IRkernel 1.x --- .../IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb | 7 ++++--- .../IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb | 7 ++++--- .../IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb | 7 ++++--- .../IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb | 7 ++++--- .../i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb | 7 ++++--- 5 files changed, 20 insertions(+), 15 deletions(-) diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb index fe42a2e870a7..515926174ff5 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2019b-R-3.6.2-Python-3.7.4.eb @@ -44,7 +44,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel local_kerneldir = '%(installdir)s/IRkernel' @@ -53,8 +56,6 @@ postinstallcmds = [ 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir) ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb index db893db1a39c..68c33b16ff99 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-foss-2020a-R-3.6.3-Python-3.8.2.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb index 32f9762476cd..c9b0e435d6c0 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.1-fosscuda-2019b-R-3.6.2-Python-3.7.4.eb @@ -44,7 +44,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel local_kerneldir = '%(installdir)s/IRkernel' @@ -53,8 +56,6 @@ postinstallcmds = [ 'cp %s/kernelspec/* %s/kernels/ir' % (local_kerneldir, local_kerneldir) ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb index 51142541134e..6aba48fcb510 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2020a-R-4.0.0-Python-3.8.2.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], diff --git a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb index 4f72aab2b802..33da48260c8d 100644 --- a/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/i/IRkernel/IRkernel-1.2-foss-2021a-R-4.1.0.eb @@ -45,7 +45,10 @@ exts_list = [ }), ] -modextrapaths = {'R_LIBS_SITE': ''} +modextrapaths = { + 'R_LIBS_SITE': '', + 'JUPYTER_PATH': '%(name)s' +} # IPython notebook looks for the json kernel file in kernels/IRkernel # We start the kernel with default bitmapType 'cairo'. This is a more sensible default @@ -58,8 +61,6 @@ postinstallcmds = [ ' %s/kernels/ir/kernel.json') % local_kerneldir ] -modextravars = {'JUPYTER_PATH': local_kerneldir} - sanity_check_paths = { 'files': ['%s/kernels/ir/kernel.json' % local_kerneldir], 'dirs': [name], From 387ad47802fbfa21167d87cf8b90506d20f8e71c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 5 Jul 2022 11:12:03 +0200 Subject: [PATCH 043/939] adding easyconfigs: ReFrame-3.12.0.eb --- .../easyconfigs/r/ReFrame/ReFrame-3.12.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb new file mode 100644 index 000000000000..d7a99ed1584f --- /dev/null +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'PythonBundle' + +name = 'ReFrame' +version = '3.12.0' + +homepage = 'https://github.com/reframe-hpc/reframe' +description = '''ReFrame is a framework for writing regression tests for HPC systems.''' + +toolchain = SYSTEM + +allow_system_deps = [('Python', SYS_PYTHON_VERSION)] + +req_py_majver = 3 +req_py_minver = 6 + +use_pip = True + +exts_list = [ + ('pip', '21.3.1', { + 'use_pip': False, + 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], + }), + ('wheel', '0.37.1', { + 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], + }), + ('setuptools', '60.0.3', { + 'source_tmpl': 'setuptools-%(version)s.tar.gz', + 'checksums': ['989ab2d3e632ba23358b8d43950bd46babde5bbb1516760dc5f5ccfe7accdd45'], + }), + ('reframe', version, { + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], + 'checksums': ['425cc546e24edd5b2dbfcdcb61dbbf723ca1a2a2977948e359e893514f5eb10f'], + }), +] + +postinstallcmds = [ + "cp -a hpctestlib tools tutorials %(installdir)s", + "mkdir -p %(installdir)s/share && cp -a share/completions %(installdir)s/share/completions", + r"sed -i 's@/\(python[0-9.]*\)$@/\1 -S@g' %(installdir)s/bin/reframe", +] + +sanity_check_paths = { + 'files': ['bin/reframe', + 'share/completions/reframe.bash', + 'share/completions/reframe.fish', + 'share/completions/reframe.tcsh'], + 'dirs': ['external', 'hpctestlib', 'lib', 'tools', 'tutorials'] +} + +sanity_check_commands = ['reframe -V'] + +sanity_pip_check = True + +modextrapaths = { + # bootstrap script installs required dependencies to 'external' subdirectory + 'PYTHONPATH': 'external', +} + +moduleclass = 'devel' From 3cb8fec4354873d16578f876acf44995983c1c85 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 5 Jul 2022 12:54:35 +0200 Subject: [PATCH 044/939] Fix long line. --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb index d7a99ed1584f..99e8c56629b1 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb @@ -32,7 +32,9 @@ exts_list = [ 'checksums': ['989ab2d3e632ba23358b8d43950bd46babde5bbb1516760dc5f5ccfe7accdd45'], }), ('reframe', version, { - 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && ./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", + 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " + "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " + "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/reframe-hpc/reframe/archive/'], 'checksums': ['425cc546e24edd5b2dbfcdcb61dbbf723ca1a2a2977948e359e893514f5eb10f'], From a8367c5ae50698c54b1abe3c266e0667e1147a14 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 2 Aug 2022 14:18:03 +0200 Subject: [PATCH 045/939] Add Score-P and dependencies --- .../c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 62 +++++++++++++++++++ .../c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb | 55 ++++++++++++++++ .../CubeWriter-4.7-GCCcore-11.3.0.eb | 53 ++++++++++++++++ .../o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb | 44 +++++++++++++ .../p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb | 37 +++++++++++ .../s/Score-P/Score-P-7.1-gompi-2022a.eb | 59 ++++++++++++++++++ 6 files changed, 310 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..270db629dc65 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: 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 = 'CubeGUI' +version = '4.7' + +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 graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +# patches = ['CubeGUI-4.6_qtlibs_symlink_realpath.patch'] +checksums = [ + '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz + # '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch +] + +preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('Autotools', '20220317'), +! ('CubeLib', '4.7'), +] + +dependencies = [ + ('Qt5', '5.15.5'), +] + +configopts = [ + "--with-qt=$EBROOTQT5" +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..bef3ea7d344e --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb @@ -0,0 +1,55 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: 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 = 'CubeLib' +version = '4.7' + +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': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e44352c80a25a49b0fa0748792ccc9f1be31300a96c32de982b92477a8740938'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + # ('pkg-config', '0.29.2'), + ('pkgconfig', '1.5.5'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +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-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..87eb56e48b93 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: 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 = 'CubeWriter' +version = '4.7' + +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': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['a7c7fca13e6cb252f08d4380223d7c56a8e86a67de147bcc0279ebb849c884a5'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('pkgconfig', '1.5.5'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +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/OPARI2-2.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..acc02a8fc51a --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.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 = '2.0.6' + +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': '11.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +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/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..6a7954de21b7 --- /dev/null +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# # +# 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 = '3.25.1' + +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': '11.3.0'} + +source_urls = ['http://tau.uoregon.edu/pdt_releases/'] +sources = ['pdtoolkit-%(version)s.tar.gz'] +checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb new file mode 100644 index 000000000000..773bcc6594bb --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb @@ -0,0 +1,59 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '7.1' + +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': '2022a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['98dea497982001fb82da3429ca55669b2917a0858c71abe2cfe7cd113381f1f7'] + +dependencies = [ + ('CubeLib', '4.7'), + ('CubeWriter', '4.7'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.6'), + ('OTF2', '3.0'), + # Hardware counter support (optional): + ('PAPI', '6.0.0.1'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +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 d86d1d56f84b09fa280ea5d3b2450714ac08dd35 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 2 Aug 2022 14:24:42 +0200 Subject: [PATCH 046/939] Cleaning --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 2 +- easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb | 3 +-- .../easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb index 270db629dc65..91b272b19e38 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -42,7 +42,7 @@ builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.38'), ('Autotools', '20220317'), -! ('CubeLib', '4.7'), + ('CubeLib', '4.7'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb index bef3ea7d344e..d48598c1cf57 100644 --- a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb @@ -36,8 +36,7 @@ checksums = ['e44352c80a25a49b0fa0748792ccc9f1be31300a96c32de982b92477a8740938'] builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.38'), - # ('pkg-config', '0.29.2'), - ('pkgconfig', '1.5.5'), + ('pkgconf', '1.8.0'), ] dependencies = [ diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb index 87eb56e48b93..6649e72f03ea 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb @@ -35,7 +35,7 @@ checksums = ['a7c7fca13e6cb252f08d4380223d7c56a8e86a67de147bcc0279ebb849c884a5'] builddependencies = [ # use same binutils version that was used when building GCCcore ('binutils', '2.38'), - ('pkgconfig', '1.5.5'), + ('pkgconf', '1.8.0'), ] dependencies = [ From fca4c21a47464bca1872ef293aa8b4d0f4397e84 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 5 Aug 2022 12:14:11 +0200 Subject: [PATCH 047/939] Fix binutils version --- easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb index 6a7954de21b7..49e5f3b335f7 100644 --- a/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PDT/PDT-3.25.1-GCCcore-11.3.0.eb @@ -30,7 +30,7 @@ sources = ['pdtoolkit-%(version)s.tar.gz'] checksums = ['0b6f8a6b8769c181b2ae6cae7298f04b8e3e3d68066f598ed24574e19500bc97'] builddependencies = [ - ('binutils', '2.36.1'), + ('binutils', '2.38'), ] From 1b6fc26b3057b6cd0f7771dad09448d803c03209 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 5 Aug 2022 21:23:47 +0200 Subject: [PATCH 048/939] Add WRF and WPS --- .../t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb | 45 +++ .../t/time/time-1.9-GCCcore-11.3.0.eb | 27 ++ .../w/WPS/WPS-4.4-foss-2022a-dmpar.eb | 38 +++ ...WPS-4.4_netCDF-Fortran_separate_path.patch | 91 ++++++ .../w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 51 ++++ ...WRF-4.4_netCDF-Fortran_separate_path.patch | 266 ++++++++++++++++++ 6 files changed, 518 insertions(+) create mode 100644 easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb create mode 100644 easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch diff --git a/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..27ca241e481d --- /dev/null +++ b/easybuild/easyconfigs/t/tcsh/tcsh-6.24.01-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg/Computer Science and Communications Research Unit +# Authors:: Valentin Plugaru +# 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_05-06.html +## +easyblock = 'ConfigureMake' + +name = 'tcsh' +version = '6.24.01' + +homepage = 'https://www.tcsh.org' +description = """Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). + It is a command language interpreter usable both as an interactive login shell and a shell script command + processor. It includes a command-line editor, programmable word completion, spelling correction, a history + mechanism, job control and a C-like syntax.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://astron.com/pub/%(namelower)s', + 'https://astron.com/pub/%(namelower)s/old', + 'ftp://ftp.astron.com/pub/%(namelower)s', + 'ftp://ftp.astron.com/pub/%(namelower)s/old', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['5659a1b973b1f947e36238cb17a00210ac4cff3b496f8f851acd77172ab91d7e'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('ncurses', '6.3')] + +postinstallcmds = ["ln -s tcsh %(installdir)s/bin/csh"] + +sanity_check_paths = { + 'files': ["bin/tcsh", "bin/csh"], + 'dirs': [] +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..d0b426f3ff87 --- /dev/null +++ b/easybuild/easyconfigs/t/time/time-1.9-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'time' +version = '1.9' + +homepage = 'https://www.gnu.org/software/time/' +description = """The `time' command runs another program, then displays information about the resources used by that + program, collected by the system while the program was running.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['fbacf0c81e62429df3e33bda4cee38756604f18e01d977338e23306a3e3b521e'] + +builddependencies = [('binutils', '2.38')] + +postinstallcmds = ["ln -s %(installdir)s/bin/%(name)s %(installdir)s/bin/gtime"] + +sanity_check_paths = { + 'files': ['bin/gtime', 'bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["time echo test"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb new file mode 100644 index 000000000000..f42560bc809c --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.4-foss-2022a-dmpar.eb @@ -0,0 +1,38 @@ +name = 'WPS' +version = '4.4' + +homepage = 'http://www.wrf-model.org' +description = """WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is + a next-generation mesoscale numerical weather prediction system designed to serve both operational + forecasting and atmospheric research needs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/wrf-model/WPS/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'WPS-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + 'fe9c8d8a9a4abbf800b30e6cbb378604c6040e4536f5594b8e2dae43e942e2b3', # v4.4.tar.gz + '751bb744bf8e5386b3bcf9c3c92dbd06183acf4007d061a3c10da808387bb0a8', # WPS-4.4_netCDF-Fortran_separate_path.patch +] + +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +builddependencies = [ + ('Perl', '5.34.1'), +] + +dependencies = [ + ('WRF', '4.4', versionsuffix), + ('JasPer', '2.0.33'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch new file mode 100644 index 000000000000..71d67030c7e1 --- /dev/null +++ b/easybuild/easyconfigs/w/WPS/WPS-4.4_netCDF-Fortran_separate_path.patch @@ -0,0 +1,91 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since 2013; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WPSv4 and foss toolchain +# +# updated for WPS v4.1 by Kenneth Hoste (HPC-UGent) +# updated for WPS v4.2 by Åke Sandgren (HPC2N) +# updated for WPS v4.4 by Maxim Masterov (SURF) + +diff -Nru WPS-4.4.orig/arch/Config.pl WPS-4.4/arch/Config.pl +--- WPS-4.4.orig/arch/Config.pl 2022-08-05 20:46:38.790818000 +0200 ++++ WPS-4.4/arch/Config.pl 2022-08-05 20:47:19.544741000 +0200 +@@ -42,6 +42,7 @@ + if(substr( $ARGV[0], 1, 8 ) eq "netcdff=") + { + $sw_netcdff_lib = substr( $ARGV[0], 9); ++ $sw_netcdff_lib =~ s/!/ /g ; + } + if(substr( $ARGV[0], 1, 6 ) eq "phdf5=") + { +diff -Nru WPS-4.4.orig/arch/preamble WPS-4.4/arch/preamble +--- WPS-4.4.orig/arch/preamble 2022-08-05 20:46:38.792313000 +0200 ++++ WPS-4.4/arch/preamble 2022-08-05 20:47:40.331112000 +0200 +@@ -39,7 +39,7 @@ + -I$(WRF_DIR)/external/io_grib1 \ + -I$(WRF_DIR)/external/io_int \ + -I$(WRF_DIR)/inc \ +- -I$(NETCDF)/include ++ -I$(NETCDF)/include -I$(NETCDFF)/include + + WRF_LIB = -L$(WRF_DIR)/external/io_grib1 -lio_grib1 \ + -L$(WRF_DIR)/external/io_grib_share -lio_grib_share \ +diff -Nru WPS-4.4.orig/configure WPS-4.4/configure +--- WPS-4.4.orig/configure 2022-08-05 20:46:38.790086000 +0200 ++++ WPS-4.4/configure 2022-08-05 20:48:51.938951000 +0200 +@@ -138,9 +138,14 @@ + echo "Will use NETCDF in dir: $NETCDF" + # for 3.6.2 and greater there might be a second library, libnetcdff.a . Check for this and use + # if available +- NETCDFF=" " +- if [ -f "$NETCDF/lib/libnetcdff.a" ] ; then +- NETCDFF="-lnetcdff" ++ USENETCDFF=" " ++ # for netCDF 4.2 and greater, the Fortran library is a seperate install ++ if [ -z "$NETCDFF" ] ++ then ++ NETCDFF=$NETCDF ++ fi ++ if [ -f "$NETCDFF/lib/libnetcdff.a" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-lnetcdff" + fi + else + echo "Will configure for use without NetCDF" +@@ -239,7 +244,7 @@ + fi + + # Found perl, so proceed with configuration +-perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$NETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir -grib2dir=$grib2dir ++perl arch/Config.pl -perl=$PERL -netcdf=$NETCDF -netcdff=$USENETCDFF -os=$os -mach=$mach -wrfdir=$wrf_dir + + + #Checking cross-compiling capability for some particular environment +@@ -405,9 +410,9 @@ + end program + EOF + FFLAGS=`grep ^FFLAGS configure.wps | cut -d"=" -f2-` +- cp $NETCDF/include/netcdf.inc . ++ cp $NETCDFF/include/netcdf.inc . + FC=`grep ^SFC configure.wps | cut -d"=" -f2-` +- $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib $NETCDFF -lnetcdf > /dev/null 2>&1 ++ $FC ${FFLAGS} fort_netcdf.f -o fort_netcdf -L${NETCDF}/lib -lnetcdf $USENETCDFF > /dev/null 2>&1 + if [ -f "fort_netcdf" ] ; then + ./fort_netcdf > /dev/null 2>&1 + if [ $? = 0 ]; then +diff -Nru WPS-4.4.orig/util/src/Makefile WPS-4.4/util/src/Makefile +--- WPS-4.4.orig/util/src/Makefile 2022-08-05 20:46:38.503642000 +0200 ++++ WPS-4.4/util/src/Makefile 2022-08-05 20:52:25.200578000 +0200 +@@ -41,11 +41,11 @@ + write_met_module.o misc_definitions_module.o met_data_module.o + $(SFC) $(LDFLAGS) -o $@ elev_angle.o cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o met_data_module.o \ +- -L$(NETCDF)/lib -I$(NETCDF)/include -lnetcdf ++ -L$(NETCDFF)/lib -I$(NETCDFF)/include -lnetcdff + + elev_angle.o: elev_angle.F cio.o module_debug.o gridinfo_module.o \ + write_met_module.o misc_definitions_module.o +- $(SFC) -c elev_angle.F -I$(NETCDF)/include ++ $(SFC) -c elev_angle.F -I$(NETCDFF)/include + + calc_ecmwf_p.exe: calc_ecmwf_p.o cio.o module_debug.o module_stringutil.o gridinfo_module.o read_met_module.o \ + write_met_module.o module_date_pack.o misc_definitions_module.o met_data_module.o constants_module.o diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb new file mode 100644 index 000000000000..f5772f50f246 --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -0,0 +1,51 @@ +name = 'WRF' +version = '4.4' +buildtype = "dmpar" +versionsuffix = '-%s' % buildtype + +homepage = 'https://www.wrf-model.org' +description = """The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale + numerical weather prediction system designed to serve both operational forecasting and atmospheric + research needs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'opt': False} # don't use agressive optimization, stick to -O2 + +source_urls = ['https://github.com/wrf-model/WRF/archive/'] +# sources = ['v%(version)s.tar.gz'] +sources = [{ + 'filename': 'v4.4.tar.gz', + 'git_config': { + 'url': 'https://github.com/wrf-model', + 'repo_name': 'WRF', + 'tag': 'v4.4', + 'clone_into': 'WRF-4.4', + 'recursive': True, + }, +}] +patches = [ + 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', +] +checksums = [ + '92f87fd769867a12dc0bda9778a2ec5319249bc335cbda87043a873d9139088d', # v4.4.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] + +# csh is used by WRF install scripts +builddependencies = [ + ('Autotools', '20220317'), + ('tcsh', '6.24.01'), + ('time', '1.9'), + ('Perl', '5.34.1'), +] + +dependencies = [ + ('JasPer', '2.0.33'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), +] + +# limit parallel build to 20 +maxparallel = 20 + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch b/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch new file mode 100644 index 000000000000..34e03618a66f --- /dev/null +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4_netCDF-Fortran_separate_path.patch @@ -0,0 +1,266 @@ +# Allow netCDF library with separate directories for C and Fortran +# ============================================================================ +# This patch has been around in EasyBuild since WRF3.5; it was committed by +# @boegel then. Adapted by @andreas-h to accomodate WRFv4 and foss toolchain +# +# updated for WPS v4.4 by Maxim Masterov (SURF) + +diff -Nru WRF-4.4.orig/arch/Config.pl WRF-4.4/arch/Config.pl +--- WRF-4.4.orig/arch/Config.pl 2022-08-05 12:50:41.026673000 +0200 ++++ WRF-4.4/arch/Config.pl 2022-08-05 12:53:16.487608000 +0200 +@@ -11,6 +11,7 @@ + select((select(STDOUT), $|=1)[0]); + $sw_perl_path = perl ; + $sw_netcdf_path = "" ; ++$sw_netcdff_path = "" ; # for netCDF 4.2 and greater, Fortran lib might be in a different path + $sw_pnetcdf_path = "" ; + $sw_netcdfpar_path = "" ; + $sw_hdf5_path=""; +@@ -95,6 +96,10 @@ + } + } + } ++ if ( substr( $ARGV[0], 1, 8 ) eq "netcdff=" ) ++ { ++ $sw_netcdff_path = substr( $ARGV[0], 9 ) ; ++ } + if ( substr( $ARGV[0], 1, 8 ) eq "pnetcdf=" ) + { + $sw_pnetcdf_path = substr( $ARGV[0], 9 ) ; +@@ -126,6 +131,7 @@ + if ( substr( $ARGV[0], 1, 11 ) eq "USENETCDFF=" ) + { + $sw_usenetcdff = substr( $ARGV[0], 12 ) ; ++ $sw_usenetcdff =~ s/!/ /g ; + } + if ( substr( $ARGV[0], 1, 10 ) eq "USENETCDF=" ) + { +@@ -610,6 +616,7 @@ + { + $_ =~ s/CONFIGURE_PERL_PATH/$sw_perl_path/g ; + $_ =~ s/CONFIGURE_NETCDF_PATH/$sw_netcdf_path/g ; ++ $_ =~ s/CONFIGURE_NETCDFF_PATH/$sw_netcdff_path/g ; + $_ =~ s/CONFIGURE_PNETCDF_PATH/$sw_pnetcdf_path/g ; + $_ =~ s/CONFIGURE_NETCDFPAR_PATH/$sw_netcdfpar_path/g ; + $_ =~ s/CONFIGURE_HDF5_PATH/$sw_hdf5_path/g ; +@@ -678,7 +685,7 @@ + } elsif ( $sw_os eq "Interix" ) { + $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf/libwrfio_nf.a -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; + } else { +- $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdf_path/lib $sw_usenetcdff $sw_usenetcdf : ; ++ $_ =~ s:CONFIGURE_NETCDF_LIB_PATH:-L\$\(WRF_SRC_ROOT_DIR\)/external/io_netcdf -lwrfio_nf -L$sw_netcdff_path/lib -L$sw_netcdf_path/lib64 $sw_usenetcdff $sw_usenetcdf : ; + } + } + else +diff -Nru WRF-4.4.orig/arch/configure.defaults WRF-4.4/arch/configure.defaults +--- WRF-4.4.orig/arch/configure.defaults 2022-08-05 12:50:41.028943000 +0200 ++++ WRF-4.4/arch/configure.defaults 2022-08-05 12:53:38.767002000 +0200 +@@ -1636,6 +1636,7 @@ + + LIB_EXTERNAL = \ + ../external/io_netcdf/libwrfio_nf.a CONFIGURE_NETCDF_PATH/lib/libnetcdf.lib \ ++ CONFIGURE_NETCDFF_PATH/lib/libnetcdff.lib \ + ../external/wavelet/libWavelet.a ../external/wavelet/lib_wavelet.a + ESMF_IO_LIB = ../external/esmf_time_f90/libesmf_time.a + LIB_BUNDLED = \ +diff -Nru WRF-4.4.orig/arch/conf_tokens WRF-4.4/arch/conf_tokens +--- WRF-4.4.orig/arch/conf_tokens 2022-08-05 12:50:41.028607000 +0200 ++++ WRF-4.4/arch/conf_tokens 2022-08-05 12:53:57.832914000 +0200 +@@ -5,6 +5,7 @@ + CONFIGURE_DMPARALLEL + CONFIGURE_RWORDSIZE + CONFIGURE_NETCDF_FLAG ++CONFIGURE_NETCDFF_FLAG + CONFIGURE_GRIB2_FLAG + CONFIGURE_NETCDF_LIB_PATH + CONFIGURE_GRIB2_LIB +@@ -13,4 +14,5 @@ + CONFIGURE_WRFIO_NF + CONFIGURE_WRFIO_GRIB2 + CONFIGURE_NETCDF_PATH ++CONFIGURE_NETCDFF_PATH + CONFIGURE_GRIB2_INC +diff -Nru WRF-4.4.orig/arch/postamble WRF-4.4/arch/postamble +--- WRF-4.4.orig/arch/postamble 2022-08-05 12:50:41.031770000 +0200 ++++ WRF-4.4/arch/postamble 2022-08-05 12:54:52.759085000 +0200 +@@ -53,6 +53,7 @@ + -I$(WRF_SRC_ROOT_DIR)/phys \ + -I$(WRF_SRC_ROOT_DIR)/wrftladj \ + -I$(WRF_SRC_ROOT_DIR)/chem -I$(WRF_SRC_ROOT_DIR)/inc \ ++ -I$(NETCDFPATH)/include -I$(NETCDFFPATH)/include \ + -I$(NETCDFPATH)/include \ + CONFIGURE_RTTOV_INC CONFIGURE_CTSM_INC + REGISTRY = Registry +@@ -63,6 +64,7 @@ + ENVCOMPDEFS = CONFIGURE_COMPILEFLAGS + CPPFLAGS = $(ARCHFLAGS) $(ENVCOMPDEFS) -I$(LIBINCLUDE) $(TRADFLAG) CONFIGURE_COMMS_INCLUDE + NETCDFPATH = CONFIGURE_NETCDF_PATH ++NETCDFFPATH = CONFIGURE_NETCDFF_PATH + HDF5PATH = CONFIGURE_HDF5_PATH + WRFPLUSPATH = CONFIGURE_WRFPLUS_PATH + RTTOVPATH = CONFIGURE_RTTOV_PATH +@@ -94,7 +96,7 @@ + + wrfio_nf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_netcdf ; \ +- make $(J) NETCDFPATH="$(NETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ ++ make $(J) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP)" \ + CC="$(SCC)" CFLAGS="$(CFLAGS)" \ + FC="$(SFC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + +@@ -105,7 +107,7 @@ + + wrfio_pnf : + ( cd $(WRF_SRC_ROOT_DIR)/external/io_pnetcdf ; \ +- make $(J) NETCDFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ ++ make $(J) NETCDFPATH="$(PNETCDFPATH)" NETCDFFPATH="$(PNETCDFPATH)" RANLIB="$(RANLIB)" CPP="$(CPP) $(ARCHFLAGS)" \ + FC="$(FC) $(PROMOTION) $(OMP) $(FCFLAGS)" TRADFLAG="$(TRADFLAG)" AR="$(AR)" ARFLAGS="$(ARFLAGS)" ) + + wrfio_grib_share : +diff -Nru WRF-4.4.orig/configure WRF-4.4/configure +--- WRF-4.4.orig/configure 2022-08-05 12:50:41.453325000 +0200 ++++ WRF-4.4/configure 2022-08-05 12:57:14.821614000 +0200 +@@ -222,9 +222,13 @@ + if [ -f "$NETCDF/lib/libnetcdff.a" -o -f "$NETCDF/lib/libnetcdff.so" -o -f "$NETCDF/lib/libnetcdff.dll.a" ] ; then + USENETCDFF="-lnetcdff" + else +- USENETCDFF=" " ++ if [ -f "$NETCDFF/lib/libnetcdff.a" -o -f "$NETCDFF/lib/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" -o -f "$NETCDFF/lib64/libnetcdff.so" ] ; then ++ USENETCDFF="-L$NETCDFF/lib!-L$NETCDFF/lib64!-lnetcdff" # ! will be replaced with space ++ else ++ USENETCDFF=" " ++ fi + fi +- if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib/libnetcdf.dll.a" ] ; then ++ if [ -f "$NETCDF/lib/libnetcdf.a" -o -f "$NETCDF/lib/libnetcdf.so" -o -f "$NETCDF/lib64/libnetcdf.a" -o -f "$NETCDF/lib64/libnetcdf.so" ] ; then + USENETCDF="-lnetcdf" + else + USENETCDF=" " +@@ -566,7 +570,7 @@ + srch=`grep -i "^#ARCH.*$os" arch/configure.defaults | grep -i "$mach"` + if [ -n "$srch" ] ; then + $PERL arch/Config.pl -dmparallel=$COMMLIB -ompparallel=$OMP -perl=$PERL \ +- -netcdf=$NETCDF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ ++ -netcdf=$NETCDF -netcdff=$NETCDFF -pnetcdf=$PNETCDF -netcdfpar=$NETCDFPAR -hdf5=$HDF5 -phdf5=$PHDF5 -os=$os -mach=$mach -ldflags=$ldflags \ + -compileflags=$compileflags -opt_level=$opt_level -USENETCDFF=$USENETCDFF -USENETCDF=$USENETCDF \ + -time=$FORTRAN_COMPILER_TIMER -tfl="$TFL" -cfl="$CFL" -config_line="$config_line" \ + -wrf_core=$wrf_core -gpfs=$GPFS_PATH -curl=$CURL_PATH -dep_lib_path="$DEP_LIB_PATH" +@@ -648,14 +652,14 @@ + echo "If you wish to change the default options, edit the file:" + echo " arch/configure.defaults" + +-if test -n "$NETCDF" ; then +- if [ ! -f $NETCDF/include/netcdf.inc ] ; then ++if test -n "$NETCDFF" ; then ++ if [ ! -f $NETCDFF/include/netcdf.inc ] ; then + echo +- echo "Error : Not found $NETCDF/include/netcdf.inc" ++ echo "Error : Not found $NETCDFF/include/netcdf.inc" + echo " Please check this installation of NetCDF and re-run this configure script" + exit -1 + fi +- grep nf_format_64bit $NETCDF/include/netcdf.inc > /dev/null ++ grep nf_format_64bit $NETCDFF/include/netcdf.inc > /dev/null + configure_aaaa=$? ; export configure_aaaa + if [ $configure_aaaa -a -z "$WRFIO_NCD_NO_LARGE_FILE_SUPPORT" ] ; then + echo "NetCDF users note:" +diff -Nru WRF-4.4.orig/external/io_netcdf/makefile WRF-4.4/external/io_netcdf/makefile +--- WRF-4.4.orig/external/io_netcdf/makefile 2022-08-05 12:50:41.676471000 +0200 ++++ WRF-4.4/external/io_netcdf/makefile 2022-08-05 15:32:21.053573000 +0200 +@@ -3,9 +3,9 @@ + OBJSL = wrf_io.o field_routines.o module_wrfsi_static.o + OBJS = $(OBJSL) + CODE = ext_ncd_get_dom_ti.code ext_ncd_get_var_td.code ext_ncd_get_var_ti.code ext_ncd_put_dom_ti.code ext_ncd_put_var_td.code ext_ncd_put_var_ti.code transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdf +-LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -lnetcdf ++LIBFFS = $(LIB_LOCAL) -L$(NETCDFPATH)/lib -L$(NETCDFPATH)/lib64 -L$(NETCDFFPATH)/lib -L$(NETCDFFPATH)/lib64 -lnetcdff -lnetcdf $(NETCDF4_DEP_LIB) + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -24,7 +24,7 @@ + $(RANLIB) $@ + + wrf_io.o: wrf_io.F90 $(CODE) +- grep nf_format_64bit $(NETCDFPATH)/include/netcdf.inc ;\ ++ grep nf_format_64bit $(NETCDFFPATH)/include/netcdf.inc ;\ + a=$$? ; export a ; \ + if [ $$a -a "$$WRFIO_NCD_LARGE_FILE_SUPPORT" = "1" ] ; then \ + $(CPP1) -DWRFIO_NCD_LARGE_FILE_SUPPORT -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ; \ +@@ -43,14 +43,14 @@ + x=`echo "$(FC)" | awk '{print $$1}'` ; export x ; \ + if [ $$x = "gfortran" ] ; then \ + echo removing external declaration of iargc for gfortran ; \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 | sed '/integer *, *external.*iargc/d' > diffwrf.f ;\ + else \ +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share diffwrf.F90 > diffwrf.f ; \ + fi + $(FC) -c $(FFLAGS) diffwrf.f + @if [ \( -f ../../frame/wrf_debug.o \) -a \( -f ../../frame/module_wrf_error.o \) -a \( -f $(ESMF_MOD_DEPENDENCE) \) -a \( -f ../../frame/clog.o \) ] ; then \ + echo "diffwrf io_netcdf is being built now. " ; \ +- if [ \( -f $(NETCDFPATH)/lib/libnetcdff.a -o -f $(NETCDFPATH)/lib/libnetcdff.so -o -f $(NETCDFPATH)/lib/libnetcdff.dll.a \) ] ; then \ ++ if [ \( -f $(NETCDFFPATH)/lib/libnetcdff.a -o -f $(NETCDFFPATH)/lib/libnetcdff.so -o -f $(NETCDFFPATH)/lib64/libnetcdff.a -o -f $(NETCDFFPATH)/lib64/libnetcdff.so \) ] ; then \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBFFS) ;\ + else \ + $(FC) $(FFLAGS) $(LDFLAGS) -o diffwrf diffwrf.o $(OBJSL) ../../frame/wrf_debug.o ../../frame/module_wrf_error.o ../../frame/clog.o $(ESMF_IO_LIB_EXT) $(LIBS) ;\ +diff -Nru WRF-4.4.orig/external/io_pnetcdf/Makefile WRF-4.4/external/io_pnetcdf/Makefile +--- WRF-4.4.orig/external/io_pnetcdf/Makefile 2022-08-05 12:50:41.688872000 +0200 ++++ WRF-4.4/external/io_pnetcdf/Makefile 2022-08-05 13:00:28.273185000 +0200 +@@ -9,8 +9,8 @@ + ext_pnc_put_var_td.code \ + ext_pnc_put_var_ti.code \ + transpose.code +-FFLAGS = $(FCFLAGS) -I$(NETCDFPATH)/include -I../ioapi_share +-LIBS = -L$(NETCDFPATH)/lib -lpnetcdf ++FFLAGS = $(FCFLAGS) -I$(NETCDFFPATH)/include -I../ioapi_share ++LIBS = -L$(NETCDFFPATH)/lib -lpnetcdf + CPP1 = $(CPP) -P $(TRADFLAG) + M4 = m4 -Uinclude -Uindex -Ulen + AR = ar +@@ -25,15 +25,15 @@ + $(RANLIB) libwrfio_pnf.a + + wrf_io.o: wrf_io.F90 $(CODE) +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share wrf_io.F90 | $(M4) - > wrf_io.f + $(FC) $(FFLAGS) -c wrf_io.f + + module_wrfsi_static.o: module_wrfsi_static.F90 +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share module_wrfsi_static.F90 > module_wrfsi_static.f + $(FC) $(FFLAGS) -c module_wrfsi_static.f + + field_routines.o: field_routines.F90 wrf_io.o +- $(CPP1) -I$(NETCDFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f ++ $(CPP1) -I$(NETCDFFPATH)/include -I../ioapi_share field_routines.F90 > field_routines.f + $(FC) $(FFLAGS) -c field_routines.f + + superclean: +diff -Nru WRF-4.4.orig/Makefile WRF-4.4/Makefile +--- WRF-4.4.orig/Makefile 2022-08-05 12:50:40.979120000 +0200 ++++ WRF-4.4/Makefile 2022-08-05 13:03:38.672102000 +0200 +@@ -923,7 +923,7 @@ + @ echo '--------------------------------------' + ( cd frame ; $(MAKE) $(J) LLIST="$(LINKLIST)" framework ; \ + cd ../external/io_netcdf ; \ +- $(MAKE) NETCDFPATH="$(NETCDFPATH)" \ ++ $(MAKE) NETCDFPATH="$(NETCDFPATH)" NETCDFFPATH="$(NETCDFFPATH)" \ + FC="$(FC) $(FCBASEOPTS) $(PROMOTION) $(FCDEBUG) $(OMP)" RANLIB="$(RANLIB)" \ + CPP="$(CPP)" LDFLAGS="$(LDFLAGS)" TRADFLAG="$(TRADFLAG)" ESMF_IO_LIB_EXT="$(ESMF_IO_LIB_EXT)" \ + LIB_LOCAL="$(LIB_LOCAL)" \ +@@ -1070,9 +1070,9 @@ + # rule used by configure to test if this will compile with netcdf4 + nc4_test: + if [ $(USENETCDFPAR) -eq 0 ] ; then \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(SCC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + else \ +- ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ ++ ( cd tools ; /bin/rm -f nc4_test.{exe,nc,o} ; $(DM_CC) -o nc4_test.exe nc4_test.c -I$(NETCDF)/include -L$(NETCDF)/lib64 -lnetcdf $(NETCDF4_DEP_LIB) ; cd .. ) ; \ + fi + + # rule used by configure to test if Fortran 2003 IEEE signaling is available From ff9d2f1f6fb14ea00fe8159fe432e31af8f93038 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 8 Aug 2022 14:19:50 +0200 Subject: [PATCH 049/939] Fix checksum --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index f5772f50f246..170cb7b35b90 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,7 +27,7 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] checksums = [ - '92f87fd769867a12dc0bda9778a2ec5319249bc335cbda87043a873d9139088d', # v4.4.tar.gz + '5332c78f5ea8d1a4475c7cd749e8f22a40b4cc5290bdf0c1c9fb051c8e6e9037', # v4.4.tar.gz '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch ] From 0e1b1f0583615fbac0453f9716a82fb41e1286a5 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 8 Aug 2022 17:14:54 +0200 Subject: [PATCH 050/939] Update WRF-4.4-foss-2022a-dmpar.eb --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index 170cb7b35b90..8fdfe98201af 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,7 +27,6 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] checksums = [ - '5332c78f5ea8d1a4475c7cd749e8f22a40b4cc5290bdf0c1c9fb051c8e6e9037', # v4.4.tar.gz '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch ] From 840c2593870ff11da7dc7d8a2a0fbf34122140fd Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 8 Aug 2022 17:32:37 +0200 Subject: [PATCH 051/939] Update WRF-4.4-foss-2022a-dmpar.eb --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index 8fdfe98201af..b59ecf9d60f4 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -26,9 +26,11 @@ sources = [{ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] -checksums = [ - '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch -] +# The problem: sources from git clone have different checksum every time +# checksums = [ +# '0d68df19766ad03041126c1531cb115e2d2a69043df96314fd30d897cfca9e4c', # v4.4.tar.gz +# '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +# ] # csh is used by WRF install scripts builddependencies = [ From 7d080fa309387da9f03bf3bc426e395660533034 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 9 Aug 2022 15:25:12 +0200 Subject: [PATCH 052/939] WIP: CubeGUI --- .../easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb index 91b272b19e38..9dd77a59d31a 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -30,10 +30,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] -# patches = ['CubeGUI-4.6_qtlibs_symlink_realpath.patch'] +patches = [ +# 'CubeGUI-4.6_qtlibs_symlink_realpath.patch', + ('CubeGUI-4.7_missing_compile_file.patch', 1), +] checksums = [ '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz - # '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch +# '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch + 'b451c8570322e5d805573afb4823d689dcad5fbe38b2b286c48b0c41070f115d', # CubeGUI-4.7_missing_compile_file.patch ] preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' From da063110b1f9e6a3789a5c3015c35a9b82d8fa4f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 9 Aug 2022 21:40:23 +0200 Subject: [PATCH 053/939] Fix CubeGUI --- .../c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 6 +- .../CubeGUI-4.7_missing_compile_file.patch | 356 ++++++++++++++++++ 2 files changed, 358 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb index 9dd77a59d31a..790b55187fd1 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb @@ -31,13 +31,11 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] sources = [SOURCELOWER_TAR_GZ] patches = [ -# 'CubeGUI-4.6_qtlibs_symlink_realpath.patch', ('CubeGUI-4.7_missing_compile_file.patch', 1), ] checksums = [ '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz -# '0b382346251b82792393e44103ddb44f9b1665dd3c652670171a0833984e8987', # CubeGUI-4.6_qtlibs_symlink_realpath.patch - 'b451c8570322e5d805573afb4823d689dcad5fbe38b2b286c48b0c41070f115d', # CubeGUI-4.7_missing_compile_file.patch + '0a3072decf1d4b9f8544331647bb160723733f3579b9d8c64906c45fcf4ce669', # CubeGUI-4.7_missing_compile_file.patch ] preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' @@ -54,7 +52,7 @@ dependencies = [ ] configopts = [ - "--with-qt=$EBROOTQT5" + 'CXX="g++" --with-qt=$EBROOTQT5/bin ', ] sanity_check_paths = { diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch new file mode 100644 index 000000000000..7b08da87205e --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch @@ -0,0 +1,356 @@ +# This patch adds the "build-config/compile" file that is missing in v4.7. +# The file is copied "as is" from CubeGUI v4.6. +# +# Author: maxim-masterov (SURF) + +diff -Nru cubegui-4.7.orig/build-config/compile cubegui-4.7/build-config/compile +--- cubegui-4.7.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 ++++ cubegui-4.7/build-config/compile 2022-08-09 11:33:06.528166000 +0200 +@@ -0,0 +1,347 @@ ++#! /bin/sh ++# Wrapper for compilers which do not understand '-c -o'. ++ ++scriptversion=2012-10-14.11; # UTC ++ ++# Copyright (C) 1999-2013 Free Software Foundation, Inc. ++# Written by Tom Tromey . ++# ++# This program is free software; you can redistribute it and/or modify ++# it under the terms of the GNU General Public License as published by ++# the Free Software Foundation; either version 2, or (at your option) ++# any later version. ++# ++# This program is distributed in the hope that it will be useful, ++# but WITHOUT ANY WARRANTY; without even the implied warranty of ++# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the ++# GNU General Public License for more details. ++# ++# You should have received a copy of the GNU General Public License ++# along with this program. If not, see . ++ ++# As a special exception to the GNU General Public License, if you ++# distribute this file as part of a program that contains a ++# configuration script generated by Autoconf, you may include it under ++# the same distribution terms that you use for the rest of that program. ++ ++# This file is maintained in Automake, please report ++# bugs to or send patches to ++# . ++ ++nl=' ++' ++ ++# We need space, tab and new line, in precisely that order. Quoting is ++# there to prevent tools from complaining about whitespace usage. ++IFS=" "" $nl" ++ ++file_conv= ++ ++# func_file_conv build_file lazy ++# Convert a $build file to $host form and store it in $file ++# Currently only supports Windows hosts. If the determined conversion ++# type is listed in (the comma separated) LAZY, no conversion will ++# take place. ++func_file_conv () ++{ ++ file=$1 ++ case $file in ++ / | /[!/]*) # absolute file, and not a UNC file ++ if test -z "$file_conv"; then ++ # lazily determine how to convert abs files ++ case `uname -s` in ++ MINGW*) ++ file_conv=mingw ++ ;; ++ CYGWIN*) ++ file_conv=cygwin ++ ;; ++ *) ++ file_conv=wine ++ ;; ++ esac ++ fi ++ case $file_conv/,$2, in ++ *,$file_conv,*) ++ ;; ++ mingw/*) ++ file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'` ++ ;; ++ cygwin/*) ++ file=`cygpath -m "$file" || echo "$file"` ++ ;; ++ wine/*) ++ file=`winepath -w "$file" || echo "$file"` ++ ;; ++ esac ++ ;; ++ esac ++} ++ ++# func_cl_dashL linkdir ++# Make cl look for libraries in LINKDIR ++func_cl_dashL () ++{ ++ func_file_conv "$1" ++ if test -z "$lib_path"; then ++ lib_path=$file ++ else ++ lib_path="$lib_path;$file" ++ fi ++ linker_opts="$linker_opts -LIBPATH:$file" ++} ++ ++# func_cl_dashl library ++# Do a library search-path lookup for cl ++func_cl_dashl () ++{ ++ lib=$1 ++ found=no ++ save_IFS=$IFS ++ IFS=';' ++ for dir in $lib_path $LIB ++ do ++ IFS=$save_IFS ++ if $shared && test -f "$dir/$lib.dll.lib"; then ++ found=yes ++ lib=$dir/$lib.dll.lib ++ break ++ fi ++ if test -f "$dir/$lib.lib"; then ++ found=yes ++ lib=$dir/$lib.lib ++ break ++ fi ++ if test -f "$dir/lib$lib.a"; then ++ found=yes ++ lib=$dir/lib$lib.a ++ break ++ fi ++ done ++ IFS=$save_IFS ++ ++ if test "$found" != yes; then ++ lib=$lib.lib ++ fi ++} ++ ++# func_cl_wrapper cl arg... ++# Adjust compile command to suit cl ++func_cl_wrapper () ++{ ++ # Assume a capable shell ++ lib_path= ++ shared=: ++ linker_opts= ++ for arg ++ do ++ if test -n "$eat"; then ++ eat= ++ else ++ case $1 in ++ -o) ++ # configure might choose to run compile as 'compile cc -o foo foo.c'. ++ eat=1 ++ case $2 in ++ *.o | *.[oO][bB][jJ]) ++ func_file_conv "$2" ++ set x "$@" -Fo"$file" ++ shift ++ ;; ++ *) ++ func_file_conv "$2" ++ set x "$@" -Fe"$file" ++ shift ++ ;; ++ esac ++ ;; ++ -I) ++ eat=1 ++ func_file_conv "$2" mingw ++ set x "$@" -I"$file" ++ shift ++ ;; ++ -I*) ++ func_file_conv "${1#-I}" mingw ++ set x "$@" -I"$file" ++ shift ++ ;; ++ -l) ++ eat=1 ++ func_cl_dashl "$2" ++ set x "$@" "$lib" ++ shift ++ ;; ++ -l*) ++ func_cl_dashl "${1#-l}" ++ set x "$@" "$lib" ++ shift ++ ;; ++ -L) ++ eat=1 ++ func_cl_dashL "$2" ++ ;; ++ -L*) ++ func_cl_dashL "${1#-L}" ++ ;; ++ -static) ++ shared=false ++ ;; ++ -Wl,*) ++ arg=${1#-Wl,} ++ save_ifs="$IFS"; IFS=',' ++ for flag in $arg; do ++ IFS="$save_ifs" ++ linker_opts="$linker_opts $flag" ++ done ++ IFS="$save_ifs" ++ ;; ++ -Xlinker) ++ eat=1 ++ linker_opts="$linker_opts $2" ++ ;; ++ -*) ++ set x "$@" "$1" ++ shift ++ ;; ++ *.cc | *.CC | *.cxx | *.CXX | *.[cC]++) ++ func_file_conv "$1" ++ set x "$@" -Tp"$file" ++ shift ++ ;; ++ *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO]) ++ func_file_conv "$1" mingw ++ set x "$@" "$file" ++ shift ++ ;; ++ *) ++ set x "$@" "$1" ++ shift ++ ;; ++ esac ++ fi ++ shift ++ done ++ if test -n "$linker_opts"; then ++ linker_opts="-link$linker_opts" ++ fi ++ exec "$@" $linker_opts ++ exit 1 ++} ++ ++eat= ++ ++case $1 in ++ '') ++ echo "$0: No command. Try '$0 --help' for more information." 1>&2 ++ exit 1; ++ ;; ++ -h | --h*) ++ cat <<\EOF ++Usage: compile [--help] [--version] PROGRAM [ARGS] ++ ++Wrapper for compilers which do not understand '-c -o'. ++Remove '-o dest.o' from ARGS, run PROGRAM with the remaining ++arguments, and rename the output as expected. ++ ++If you are trying to build a whole package this is not the ++right script to run: please start by reading the file 'INSTALL'. ++ ++Report bugs to . ++EOF ++ exit $? ++ ;; ++ -v | --v*) ++ echo "compile $scriptversion" ++ exit $? ++ ;; ++ cl | *[/\\]cl | cl.exe | *[/\\]cl.exe ) ++ func_cl_wrapper "$@" # Doesn't return... ++ ;; ++esac ++ ++ofile= ++cfile= ++ ++for arg ++do ++ if test -n "$eat"; then ++ eat= ++ else ++ case $1 in ++ -o) ++ # configure might choose to run compile as 'compile cc -o foo foo.c'. ++ # So we strip '-o arg' only if arg is an object. ++ eat=1 ++ case $2 in ++ *.o | *.obj) ++ ofile=$2 ++ ;; ++ *) ++ set x "$@" -o "$2" ++ shift ++ ;; ++ esac ++ ;; ++ *.c) ++ cfile=$1 ++ set x "$@" "$1" ++ shift ++ ;; ++ *) ++ set x "$@" "$1" ++ shift ++ ;; ++ esac ++ fi ++ shift ++done ++ ++if test -z "$ofile" || test -z "$cfile"; then ++ # If no '-o' option was seen then we might have been invoked from a ++ # pattern rule where we don't need one. That is ok -- this is a ++ # normal compilation that the losing compiler can handle. If no ++ # '.c' file was seen then we are probably linking. That is also ++ # ok. ++ exec "$@" ++fi ++ ++# Name of file we expect compiler to create. ++cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'` ++ ++# Create the lock directory. ++# Note: use '[/\\:.-]' here to ensure that we don't use the same name ++# that we are using for the .o file. Also, base the name on the expected ++# object file name, since that is what matters with a parallel build. ++lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d ++while true; do ++ if mkdir "$lockdir" >/dev/null 2>&1; then ++ break ++ fi ++ sleep 1 ++done ++# FIXME: race condition here if user kills between mkdir and trap. ++trap "rmdir '$lockdir'; exit 1" 1 2 15 ++ ++# Run the compile. ++"$@" ++ret=$? ++ ++if test -f "$cofile"; then ++ test "$cofile" = "$ofile" || mv "$cofile" "$ofile" ++elif test -f "${cofile}bj"; then ++ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile" ++fi ++ ++rmdir "$lockdir" ++exit $ret ++ ++# Local Variables: ++# mode: shell-script ++# sh-indentation: 2 ++# eval: (add-hook 'write-file-hooks 'time-stamp) ++# time-stamp-start: "scriptversion=" ++# time-stamp-format: "%:y-%02m-%02d.%02H" ++# time-stamp-time-zone: "UTC" ++# time-stamp-end: "; # UTC" ++# End: From e6b1ccccd867ad20e44ee44fe3b5c8dc26b27e4a Mon Sep 17 00:00:00 2001 From: Maxim Date: Tue, 9 Aug 2022 21:42:02 +0200 Subject: [PATCH 054/939] Update easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb index b59ecf9d60f4..b2412e3eb97d 100644 --- a/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb +++ b/easybuild/easyconfigs/w/WRF/WRF-4.4-foss-2022a-dmpar.eb @@ -27,10 +27,10 @@ patches = [ 'WRF-%(version)s_netCDF-Fortran_separate_path.patch', ] # The problem: sources from git clone have different checksum every time -# checksums = [ -# '0d68df19766ad03041126c1531cb115e2d2a69043df96314fd30d897cfca9e4c', # v4.4.tar.gz -# '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch -# ] +checksums = [ + None, # v4.4.tar.gz + '0e37c8a7bb4d25947083bdb6d0f2a9f4fdb825c88f6cb10c59b7580fe3d129ff', # WRF-4.4_netCDF-Fortran_separate_path.patch +] # csh is used by WRF install scripts builddependencies = [ From e6dff443e3848535791e3cf0c5c2fcecca58a134 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 16 Aug 2022 09:19:42 +0200 Subject: [PATCH 055/939] Restore comments dropped by inject-checksums and lower version of setuptools to retain compat with Py3.6. --- easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb index 99e8c56629b1..34fd85c49e02 100644 --- a/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb +++ b/easybuild/easyconfigs/r/ReFrame/ReFrame-3.12.0.eb @@ -19,6 +19,7 @@ req_py_minver = 6 use_pip = True exts_list = [ + # stick to pip < 22.0, to maintain compatibility with Python 3.6 ('pip', '21.3.1', { 'use_pip': False, 'checksums': ['fd11ba3d0fdb4c07fbc5ecbba0b1b719809420f25038f8ee3cd913d3faa3033a'], @@ -27,11 +28,13 @@ exts_list = [ 'source_tmpl': 'wheel-%(version)s-py2.py3-none-any.whl', 'checksums': ['4bdcd7d840138086126cd09254dc6195fb4fc6f01c050a1d7236f2630db1d22a'], }), - ('setuptools', '60.0.3', { + # stick to setuptools < 59.7.0, to maintain compatibility with Python 3.6 + ('setuptools', '59.6.0', { 'source_tmpl': 'setuptools-%(version)s.tar.gz', - 'checksums': ['989ab2d3e632ba23358b8d43950bd46babde5bbb1516760dc5f5ccfe7accdd45'], + 'checksums': ['22c7348c6d2976a52632c67f7ab0cdf40147db7789f9aed18734643fe9cf3373'], }), ('reframe', version, { + # need to add 'bin' subdir to $PATH explicitly to ensure right 'pip' command is used for installing packages 'preinstallopts': "export PATH=%(installdir)s/bin:$PATH && " "./bootstrap.sh +docs +pygelf && cp -r external %(installdir)s && " "PYTHONPATH=%(builddir)s/reframe/reframe-%(version)s/external:$PYTHONPATH ", From bb8536851f88f810d5a922e2eefe06de44f598a1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Tue, 9 Aug 2022 14:39:56 +0200 Subject: [PATCH 056/939] adding easyconfigs: netCDF-Fortran-4.6.0-iimpi-2022a.eb, netCDF-4.9.0-iimpi-2022a.eb --- .../netCDF-Fortran-4.6.0-iimpi-2022a.eb | 28 +++++++++++ .../n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 48 +++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb new file mode 100644 index 000000000000..6ccd8e612712 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.0-iimpi-2022a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.0' + +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': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-fortran/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8194aa70e400c0adfc456127c1d97af2c6489207171d13b10cd754a16da8b0ca'] + +builddependencies = [ + ('M4', '1.4.19'), +] + +dependencies = [ + ('netCDF', '4.9.0'), + ('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-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb new file mode 100644 index 000000000000..b13202347f8c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -0,0 +1,48 @@ +name = 'netCDF' +version = '4.9.0' + +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': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.13.1'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), +] + +# make sure both static and shared libs are built +configopts = [ + "-DBUILD_SHARED_LIBS=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 1acfc6c5de84bb2bb7e0bc2e47736e54f158cdab Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 18 Aug 2022 18:43:52 +0200 Subject: [PATCH 057/939] Add netCDF-4.9.0_skip-nasa-test.patch to netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index b13202347f8c..e8aeb8b93a8c 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -14,11 +14,13 @@ sources = ['v%(version)s.tar.gz'] patches = [ 'netCDF-%(version)s_fix-lib-name.patch', 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', ] checksums = [ '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch ] builddependencies = [ From 79e0cc97cdf70b8044d7e8f8aa61f3967e839c18 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 18 Aug 2022 19:26:01 +0200 Subject: [PATCH 058/939] Add NWChem and GlobalArrays --- .../GlobalArrays-5.8.1-intel-2022a.eb | 30 +++++++++++++++ .../n/NWChem/NWChem-7.0.2-intel-2022a.eb | 37 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb 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 new file mode 100644 index 000000000000..f2b34303ae90 --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.1-intel-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.1' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +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 += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb new file mode 100644 index 000000000000..e54015561491 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb @@ -0,0 +1,37 @@ +name = 'NWChem' +version = '7.0.2' +local_verdate = '2020-10-12' +local_revision = 'b9985dfa' + +homepage = 'https://www.nwchem-sw.org' +description = """NWChem aims to provide its users with computational chemistry tools that are scalable both in + their ability to treat large scientific computational chemistry problems efficiently, and in their use of available + parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. + NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all + combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties + and relativity.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'i8': True} + +source_urls = ['https://github.com/nwchemgit/nwchem/releases/download/v%(version)s-release/'] +sources = ['nwchem-%%(version)s-release.revision-%s-src.%s.tar.bz2' % (local_revision, local_verdate)] +patches = [ + 'NWChem-7.0.2_fix_gnumakefile.patch', +] +checksums = [ + # nwchem-7.0.2-release.revision-b9985dfa-src.2020-10-12.tar.bz2 + 'd9d19d87e70abf43d61b2d34e60c293371af60d14df4a6333bf40ea63f6dc8ce', + '89c634a652d4c8c358f8388ac01ee441659e3c0256c39b6494e2885c91f9aca4', # NWChem-7.0.2_fix_gnumakefile.patch +] + +dependencies = [ + ('GlobalArrays', '5.8.1'), + ('Python', '3.10.4'), +] + +preconfigopts = 'export EXTRA_LIBS=-lutil && ' + +modules = 'all python' + +moduleclass = 'chem' From d8418629678ffd5860ef6b7e05caef5714b4a96f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Fri, 19 Aug 2022 10:57:50 +0200 Subject: [PATCH 059/939] Add patch to fix build with python-3.10 --- .../n/NWChem/NWChem-7.0.2-intel-2022a.eb | 2 + .../NWChem-7.0.2_fix_for_python_3_10.patch | 41 +++++++++++++++++++ 2 files changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb index e54015561491..25d9440384bb 100644 --- a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2-intel-2022a.eb @@ -18,11 +18,13 @@ source_urls = ['https://github.com/nwchemgit/nwchem/releases/download/v%(version sources = ['nwchem-%%(version)s-release.revision-%s-src.%s.tar.bz2' % (local_revision, local_verdate)] patches = [ 'NWChem-7.0.2_fix_gnumakefile.patch', + 'NWChem-7.0.2_fix_for_python_3_10.patch', ] checksums = [ # nwchem-7.0.2-release.revision-b9985dfa-src.2020-10-12.tar.bz2 'd9d19d87e70abf43d61b2d34e60c293371af60d14df4a6333bf40ea63f6dc8ce', '89c634a652d4c8c358f8388ac01ee441659e3c0256c39b6494e2885c91f9aca4', # NWChem-7.0.2_fix_gnumakefile.patch + '2da647217ad72d929f1d495386871a32b7176beb52cbc3dabebbb56abb407e36', # NWChem-7.0.2_fix_for_python_3_10.patch ] dependencies = [ diff --git a/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch new file mode 100644 index 000000000000..e733ea890526 --- /dev/null +++ b/easybuild/easyconfigs/n/NWChem/NWChem-7.0.2_fix_for_python_3_10.patch @@ -0,0 +1,41 @@ +# This patch fixes compatibility with Python-3.10. In particular the problem that +# the "graminit.h" header is removed from Python-3.10 together with the "parser" +# module. +# See https://github.com/nwchemgit/nwchem/issues/271 for more info +# +# Author: maxim-masterov (SURF) +# +diff -Nru nwchem-7.0.2.orig/src/config/makefile.h nwchem-7.0.2/src/config/makefile.h +--- nwchem-7.0.2.orig/src/config/makefile.h 2022-08-19 10:47:57.584912000 +0200 ++++ nwchem-7.0.2/src/config/makefile.h 2022-08-19 10:50:18.158831536 +0200 +@@ -2618,12 +2618,12 @@ + GOTPYTHON2 := $(shell command -v python2 2> /dev/null) + GOTPYTHON := $(shell command -v python 2> /dev/null) + ifdef GOTPYTHON3 +- PYTHONVERSION=$(shell python3 -V 2>&1 |cut -c 8-10) ++ PYTHONVERSION=$(shell python3 -c 'import sys; print("{}.{}".format(sys.version_info.major, sys.version_info.minor))') + else ifdef GOTPYTHON2 +- PYTHONVERSION=$(shell python2 -V 2>&1 |cut -c 8-10) ++ PYTHONVERSION=$(shell python2 -c 'import sys; print("{}.{}".format(sys.version_info.major, sys.version_info.minor))') + else ifdef GOTPYTHON + #last try at python2 +- PYTHONVERSION=$(shell python -V 2>&1 |cut -c 8-10) ++ PYTHONVERSION=$(shell python -c 'import sys; print("{}.{}".format(sys.version_info.major, sys.version_info.minor))') + else + errorpython3: + $(info ) +diff -Nru nwchem-7.0.2.orig/src/python/task_python.c nwchem-7.0.2/src/python/task_python.c +--- nwchem-7.0.2.orig/src/python/task_python.c 2022-08-19 10:47:58.966129000 +0200 ++++ nwchem-7.0.2/src/python/task_python.c 2022-08-19 10:51:34.311283000 +0200 +@@ -6,7 +6,11 @@ + #include "ga.h" + + #include ++#if ( PY_MAJOR_VERSION >= 3 && PY_MINOR_VERSION >= 9) ++/* might require new headers and code */ ++#else + #include ++#endif + #include + #include + #include "typesf2c.h" From 5626a6fd306371c1d2b73d81474a1007fe76fff1 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 23 Aug 2022 10:51:01 +0200 Subject: [PATCH 060/939] adding easyconfigs: EGTtools-0.1.10.dev2-foss-2021b.eb and patches: EGTtools-0.1.10.dev2_fix_include.patch --- .../EGTtools-0.1.10.dev2-foss-2021b.eb | 45 +++++++++++++++++++ .../EGTtools-0.1.10.dev2_fix_include.patch | 13 ++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb create mode 100644 easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb new file mode 100644 index 000000000000..b721a288373f --- /dev/null +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2-foss-2021b.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'EGTtools' +version = '0.1.10.dev2' + +homepage = 'https://github.com/Socrats/EGTTools' +description = """ +EGTtools provides a centralized repository with analytical and numerical +methods to study/model game theoretical problems under the Evolutionary Game +Theory (EGT) framework.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +builddependencies = [ + ('CMake', '3.21.1'), + ('Ninja', '1.10.2'), + ('scikit-build', '0.11.1'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('networkx', '2.6.3'), + ('Seaborn', '0.11.2'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'patches': ['%(name)s-%(version)s_fix_include.patch'], + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': [ + '0ae38d9945ecd5cb49e8bdd0dcedcd938e3380e5db93fdf74c681ac8abd2317e', # egttools-0.1.10.dev2.tar.gz + # EGTtools-0.1.10.dev2_fix_include.patch + '6237d0ad05d8aca7c9eccc6627f6e91a3511d3a4adbb72c6e881553f088f6c9a', + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch new file mode 100644 index 000000000000..9dd130a6f83c --- /dev/null +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.10.dev2_fix_include.patch @@ -0,0 +1,13 @@ +Add missing include to avoid build error: "shared_ptr in namespace std does not name a template type" +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur egttools-0.1.10.dev2.orig/include/egttools/finite_populations/behaviors/NFGStrategies.hpp egttools-0.1.10.dev2/include/egttools/finite_populations/behaviors/NFGStrategies.hpp +--- egttools-0.1.10.dev2.orig/include/egttools/finite_populations/behaviors/NFGStrategies.hpp 2022-08-06 16:35:37.000000000 +0200 ++++ egttools-0.1.10.dev2/include/egttools/finite_populations/behaviors/NFGStrategies.hpp 2022-08-12 17:22:35.065010288 +0200 +@@ -25,6 +25,7 @@ + + #include + #include ++#include + #include + #include + From 845936e6bcea7ee1bcc45d3f89d0f4b6e36f9473 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:01:48 +0100 Subject: [PATCH 061/939] adding easyconfigs: libwpe-1.13.3-GCCcore-11.2.0.eb --- .../l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..90c0db43eefa --- /dev/null +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb @@ -0,0 +1,43 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'libwpe' +version = '1.13.3' + +homepage = 'https://webkit.org/wpe' +description = """WPE is the reference WebKit port for embedded and +low-consumption computer devices. It has been designed from the +ground-up with performance, small footprint, accelerated content +rendering, and simplicity of deployment in mind, bringing the +excellence of the WebKit engine to countless platforms and target devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] + +checksums = [ + '05f871922f6ca750c5689a38a346c3fba130417d3490dd52362b4fe22f334e96', # libwpe-1.13.3.tar.xz +] + +builddependencies = [ + ('binutils', '2.37'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('Meson', '0.58.2'), +] + +dependencies = [ + ('glew', '2.2.0', '-egl'), +] + +parallel = 2 + +sanity_check_paths = { + 'files': ['lib/libwpe-1.0.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 86c002427aa49cb0a166b121b4ebe81d0575e781 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 11:34:59 +0100 Subject: [PATCH 062/939] adding easyconfigs: wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb --- .../wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..e675f510aa13 --- /dev/null +++ b/easybuild/easyconfigs/w/wpebackend-fdo/wpebackend-fdo-1.13.1-GCCcore-11.2.0.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MesonNinja' + +name = 'wpebackend-fdo' +version = '1.13.1' + +homepage = 'https://wpewebkit.org/' +description = """WPE WebKit allows embedders to create simple and performant +systems based on Web platform technologies. It is a WebKit port designed with +flexibility and hardware acceleration in mind, leveraging common 3D graphics +APIs for best performance.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://wpewebkit.org/releases'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['d61ca47ec52d7cd1d6f869f66d6ea247a53092acfad1a8cbab71836a82d3a0ae'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), + ('Meson', '0.58.2'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Waylandpp', '1.0.0'), + ('libepoxy', '1.5.8'), + ('glib-networking', '2.72.1'), + ('libwpe', '1.13.3'), +] + +sanity_check_paths = { + 'files': ['lib/libWPEBackend-fdo-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From bb88dd5d72b3b79eb55818e58a0096960affcfae Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 23 Aug 2022 18:04:18 +0100 Subject: [PATCH 063/939] adding easyconfigs: WebKitGTK+-2.37.1-GCC-11.2.0.eb --- .../WebKitGTK+-2.37.1-GCC-11.2.0.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..1ede0f20a549 --- /dev/null +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -0,0 +1,86 @@ +# Updated from WebKitGTK+-2.27.4-GCC-8.3.0.eb with more modules added +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'WebKitGTK+' +version = '2.37.1' + +homepage = 'https://webkitgtk.org/' +description = """WebKitGTK+ is a full-featured port of the WebKit +rendering engine, suitable for projects requiring any kind of web +integration, from hybrid HTML/CSS applications to full-fledged web +browsers. It offers WebKit's full functionality and is useful in a wide +range of systems from desktop computers to embedded systems like phones, +tablets, and televisions.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://webkitgtk.org/releases'] +sources = ['webkitgtk-%(version)s.tar.xz'] +checksums = [ + 'c53326b1751f8c6da3db2f4bfa91c1801755893e287d0e1f6c07344589d4a6a7', # webkitgtk-2.37.1.tar.xz +] + +osdependencies = [ + # Would be better to use the system package due to security reasons + # But we need at least libgcrypt 1.7.0 and Ubuntu 16.04 and RH 7.5 + # are both using a too old version. + # Update: Libcrypt 1.9.3 from EasyBuild added (J.S) + # ('libgcrypt-dev', 'libgcrypt20-dev', 'libgcrypt-devel'), + # libsecret is not actually needed since USE_LIBSECRET option is disabled + # ('libsecret-1-dev', 'libsecret-devel'), +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('Python', '3.9.6'), + ('Perl', '5.34.0', '-minimal'), + ('GObject-Introspection', '1.68.0'), + ('pkg-config', '0.29.2'), + ('ccache', '4.6.1', '', True), +] +dependencies = [ + ('GLib', '2.69.1'), + ('gperf', '3.1'), + ('cairo', '1.16.0'), + ('GTK3', '3.24.31'), + ('LibSoup', '3.0.7'), + ('ATK', '2.36.0'), + ('libgcrypt', '1.9.3'), + ('libwebp', '1.2.0'), + ('libxslt', '1.1.34'), + ('libtasn1', '4.18.0'), + ('GStreamer', '1.18.5'), + ('OpenJPEG', '2.4.0'), + ('Ruby', '3.0.1'), + ('GSL', '2.7'), + ('glew', '2.2.0', '-egl'), + ('libwpe', '1.13.3'), + ('pugixml', '1.12.1'), + ('Wayland', '1.20.0'), + ('Waylandpp', '1.0.0'), + ('wpebackend-fdo', '1.13.1'), + ('enchant-2', '2.3.3'), + ('LittleCMS', '2.12'), + ('GST-plugins-base', '1.18.5'), +] + +# The build takes around 2.5 hours on 24 cores on AMD Rome! +# So be patient! + +# Instead of using a patch file, we are disabling problematic builds in the command line. +# At least this way, if something is not needed it can be turned off, without looking into +# a patch file. +configopts = "-DCMAKE_VERBOSE_MAKEFILE=ON -DPORT=GTK -DCMAKE_FIND_USE_PACKAGE_REGISTRY=FALSE " +configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " +configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " +configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " + +sanity_check_paths = { + 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, + 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], + 'dirs': ['include/webkitgtk-4.1/webkit2', 'libexec/webkit2gtk-4.1'], +} + +moduleclass = 'lib' From 96aabade8a3b104d292fafa6869feedeae386937 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 24 Aug 2022 17:12:52 +0200 Subject: [PATCH 064/939] adding easyconfigs: MATLAB-Engine-2021a-GCCcore-10.2.0.eb, MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 32 +++++++++++++++++++ .../MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..14525297b2fd --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021a' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.8.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..629c793528c1 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021a' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.9.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' From 4038b236aafc832399534ee095d4119d5d8d6c00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 24 Aug 2022 17:59:45 +0200 Subject: [PATCH 065/939] Add sanity pip check --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 2 ++ .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 2 ++ 2 files changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb index 14525297b2fd..3418f6ddc565 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -27,6 +27,8 @@ skipsteps = ['install'] # Test that connection with MATLAB can be established successfully sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +sanity_pip_check = True + options = {'modulename': 'matlab.engine'} moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index 629c793528c1..9380e93ff8a9 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -27,6 +27,8 @@ skipsteps = ['install'] # Test that connection with MATLAB can be established successfully sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] +sanity_pip_check = True + options = {'modulename': 'matlab.engine'} moduleclass = 'math' From a98ad52edd784d3791f323858958622a29c1f449 Mon Sep 17 00:00:00 2001 From: Bob Date: Thu, 25 Aug 2022 10:29:51 +0200 Subject: [PATCH 066/939] adding easyconfigs: Amber-22.0-foss-2021b-AmberTools-22.3.eb and patches: Amber-22_remove_undeclared_redundant_variable.patch, AmberTools-22_fix_cuda_version_check.patch --- .../Amber-22.0-foss-2021b-AmberTools-22.3.eb | 74 +++++++++++++++++++ ...remove_undeclared_redundant_variable.patch | 27 +++++++ ...AmberTools-22_fix_cuda_version_check.patch | 18 +++++ 3 files changed, 119 insertions(+) create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb create mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch create mode 100644 easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb new file mode 100644 index 000000000000..9389944b7fd3 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb @@ -0,0 +1,74 @@ +name = 'Amber' +local_amber_ver = 22 +local_ambertools_ver = 22 +# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +patchlevels = (3, 0) # (AmberTools, Amber) +version = '%s.%s' % (local_amber_ver, patchlevels[1]) +versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) + +homepage = 'http://ambermd.org/amber.html' +description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing + molecular dynamics and structure prediction.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'openmp': True} + +sources = [ + '%%(name)s%s.tar.bz2' % local_amber_ver, + 'AmberTools-%s.tar.bz2' % local_ambertools_ver, +] +patches = [ + 'Amber-22_remove_undeclared_redundant_variable.patch', + 'AmberTools-20_cmake-locate-netcdf.patch', + 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', + 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + 'AmberTools-21_CMake-FlexiBLAS.patch', + 'AmberTools-22_fix_cuda_version_check.patch', +] +checksums = [ + '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2 + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools-22.tar.bz2 + # Amber-22_remove_undeclared_redundant_variable.patch + 'f2e21002e00534f14caa00bc5bbf3b1e68acb71aa8dbcfea275d67192e32c15f', + '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch + # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch + '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + # AmberTools-20_fix_xblas_missing_make_dependency.patch + 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', + '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + '3fc08a2cf61f3eefd094554e60c88b14c9f5071f94e0a0a15c6b55fe321bfc78', # AmberTools-22_fix_cuda_version_check.patch +] + +builddependencies = [ + ('Bison', '3.7.6'), + ('pkg-config', '0.29.2'), + ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('make', '4.3'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), # mpi4py required for MMPBSA + ('Perl', '5.34.0'), + ('Boost', '1.77.0'), + ('libreadline', '8.1'), + ('matplotlib', '3.4.3'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PnetCDF', '1.12.3'), + ('arpack-ng', '3.8.0'), + ('Tkinter', '3.9.6'), + ('X11', '20210802'), + ('CUDA', '11.4.1', '', True), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), +] + +# Some CUDA tests differs from expected results +runtest = False + +static = False + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch new file mode 100644 index 000000000000..3bfe94fd93ae --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch @@ -0,0 +1,27 @@ +Remove the undeclared (and unused) variable i from the private clause +in an OpenMP pragma, which otherwise results in an error: + + 93 | !$omp parallel do private(ihkl,i,f,angle) + | 1 +Error: Symbol i at (1) has no IMPLICIT type + +Bob Dröge, University of Groningen, 2022-08-18 +--- amber22_src.orig/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:24.807724049 +0200 ++++ amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:42.039809811 +0200 +@@ -90,7 +90,7 @@ + call check_precondition(size(frac, 2) == size(scatter_type_index)) + call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1)) + +- !$omp parallel do private(ihkl,i,f,angle) ++ !$omp parallel do private(ihkl,f,angle) + do ihkl = 1, size(hkl, 2) + + ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ), +@@ -127,4 +127,4 @@ + end subroutine calc_f_non_bulk + + +-end module xray_non_bulk_impl_cpu_module +\ No newline at end of file ++end module xray_non_bulk_impl_cpu_module + diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch b/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch new file mode 100644 index 000000000000..de3b0b115df9 --- /dev/null +++ b/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch @@ -0,0 +1,18 @@ +The CUDA_VERSION returned by CMake's FindCUDA module only contains +the major and minor version number, not the patch release. +This makes the check if CUDA_VERSION is less than 11.4.1 broken, +even though only CUDA 11.4.1 supports GCC 11 (11.4.0 does not). +As we know which GCC and CUDA we're using, this patch just compares it to 11.4 anyway. + +Bob Dröge, University of Groningen, 2022-08-18 +--- amber20_src.orig/cmake/CudaConfig.cmake 2022-08-18 08:25:28.236089267 +0200 ++++ amber20_src/cmake/CudaConfig.cmake 2022-08-18 08:24:27.122766862 +0200 +@@ -82,7 +82,7 @@ + # VERSION_EQUAL 10 means 10.0, so use a range for comparing major version. + if ( "${CMAKE_C_COMPILER_ID}" STREQUAL "GNU" AND ( + ( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 12 +- AND CUDA_VERSION VERSION_GREATER_EQUAL 11.4.1 ++ AND CUDA_VERSION VERSION_GREATER_EQUAL 11.4 + AND CUDA_VERSION VERSION_LESS_EQUAL 11.7 ) + OR ( CMAKE_CXX_COMPILER_VERSION VERSION_LESS 11 + AND CUDA_VERSION VERSION_GREATER_EQUAL 11.1 From c17607e3c0aee1fb3401a349ea31253300e37f24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 25 Aug 2022 10:36:53 +0200 Subject: [PATCH 067/939] Add CUDA to versionsuffix and filename --- ....eb => Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/a/Amber/{Amber-22.0-foss-2021b-AmberTools-22.3.eb => Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb} (96%) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb similarity index 96% rename from easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb rename to easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 9389944b7fd3..2630ac530481 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -4,7 +4,7 @@ local_ambertools_ver = 22 # Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php patchlevels = (3, 0) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) -versionsuffix = '-AmberTools-%s.%s' % (local_ambertools_ver, patchlevels[0]) +versionsuffix = '-AmberTools-%s.%s-CUDA-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0]) homepage = 'http://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing From 54cb4c25ed29632a67e8a2679044ba950ad757cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Aug 2022 08:24:24 +0200 Subject: [PATCH 068/939] use alt_location for ambertools patch --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 2630ac530481..6182fcd8066b 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -22,7 +22,7 @@ patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_fix_xblas_missing_make_dependency.patch', - 'AmberTools-21_CMake-FlexiBLAS.patch', + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'} 'AmberTools-22_fix_cuda_version_check.patch', ] checksums = [ From 1dd09cafb532ba6cdc8003433567bb489f8dc180 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Aug 2022 08:50:05 +0200 Subject: [PATCH 069/939] add missing comma --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 6182fcd8066b..a1dde04b0752 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -22,7 +22,7 @@ patches = [ 'AmberTools-20_cmake-locate-netcdf.patch', 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'AmberTools-20_fix_xblas_missing_make_dependency.patch', - {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'} + {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, 'AmberTools-22_fix_cuda_version_check.patch', ] checksums = [ From 3339fed38d65f0188b5a635b32c3e0e2e4be1448 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 29 Aug 2022 15:30:09 +0200 Subject: [PATCH 070/939] Add Cartopy and dependencies --- .../c/Cartopy/Cartopy-0.20.3-foss-2022a.eb | 50 +++++++++++++++++++ .../f/Fiona/Fiona-1.8.21-foss-2022a.eb | 48 ++++++++++++++++++ .../p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb | 37 ++++++++++++++ .../s/Shapely/Shapely-1.8.2-foss-2022a.eb | 30 +++++++++++ 4 files changed, 165 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb new file mode 100644 index 000000000000..f8c63257d0fe --- /dev/null +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +easyblock = 'PythonBundle' + +name = 'Cartopy' +version = '0.20.3' + +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Fiona', '1.8.21'), + ('GDAL', '3.5.0'), + ('GEOS', '3.10.3'), + ('matplotlib', '3.5.2'), + ('pyproj', '3.3.1'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), + ('lxml', '4.9.1'), + ('Pillow', '9.1.1'), + ('PROJ', '9.0.0'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('OWSLib', '0.27.2', { + 'checksums': ['e102aa2444dfe0c8439ab1e1776cc0fa47cea28c09b8a28212c893c6017c179b'], + }), + ('pyepsg', '0.4.0', { + 'checksums': ['2d08fad1e7a8b47a90a4e43da485ba95705923425aefc4e2a3efa540dbd470d7'], + }), + ('pykdtree', '1.3.5', { + 'checksums': ['7342f75e731103e653fc1f6b9fdabc2410cf92b6e7b06160804a75786c9b5747'], + }), + ('pyshp', '2.3.1', { + 'modulename': 'shapefile', + 'checksums': ['4caec82fd8dd096feba8217858068bacb2a3b5950f43c048c6dc32a3489d5af1'], + }), + (name, version, { + 'checksums': ['0d60fa2e2fbd77c4d1f6b1f9d3b588966147f07c1b179d2d34570ac1e1b49006'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb new file mode 100644 index 000000000000..a1a8ffdd7e09 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiona/Fiona-1.8.21-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'Fiona' +version = '1.8.21' + +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('GDAL', '3.5.0'), + ('Shapely', '1.8.2'), # optional for 'calc' extras +] + +use_pip = True + +exts_list = [ + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + (name, version, { + 'checksums': ['3a0edca2a7a070db405d71187214a43d2333a57b4097544a3fcc282066a58bfc'], + 'use_pip_extras': 'calc', + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/fio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["fio --help"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..d70aee5e640c --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.3.1-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.3.1' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b3d8e14d91cc95fb3dbc03a9d0588ac58326803eefa5bbb0978d109de3304fbe'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PROJ', '9.0.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb new file mode 100644 index 000000000000..1a79d23c7529 --- /dev/null +++ b/easybuild/easyconfigs/s/Shapely/Shapely-1.8.2-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonPackage' + +name = 'Shapely' +version = '1.8.2' + +homepage = 'https://github.com/Toblerity/Shapely' +description = """Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. +It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['572af9d5006fd5e3213e37ee548912b0341fb26724d6dc8a4e3950c10197ebb6'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # needed by shapely.vectorized + ('GEOS', '3.10.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = [ + "python -c 'import shapely'", + "python -c 'import shapely.vectorized'", +] + +moduleclass = 'math' From 5611a5ea008664b69564eb1034cc56c72380c897 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 29 Aug 2022 20:02:55 +0200 Subject: [PATCH 071/939] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Disable DAP remote tests Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index e8aeb8b93a8c..7e7c2186c132 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -38,8 +38,8 @@ dependencies = [ # make sure both static and shared libs are built configopts = [ - "-DBUILD_SHARED_LIBS=OFF", - "-DBUILD_SHARED_LIBS=ON", + "-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 From 98b8631cf5f2a49a7906967a13f7cea4b651ced0 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 17:35:43 +0100 Subject: [PATCH 072/939] texinfo replaced with makeinfo, pkgconf used instead of pkg-config, optim plugin added as needed by dynare --- .../easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index 03d83437388f..d440fc720136 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -1,3 +1,6 @@ +# 'optim' plugin added which is required for dynare +# Author: J. Sassmannshausen (Imperial College London/UK) + name = 'Octave' version = '7.1.0' @@ -16,7 +19,7 @@ builddependencies = [ ('flex', '2.6.4'), ('Autotools', '20210726'), ('gperf', '3.1'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ] dependencies = [ @@ -41,7 +44,7 @@ dependencies = [ ('HDF5', '1.12.1'), ('qrupdate', '1.1.2'), ('SuiteSparse', '5.10.1', '-METIS-5.1.0'), - ('texinfo', '6.8'), + ('makeinfo', '6.8'), ('libsndfile', '1.0.31'), ('GraphicsMagick', '1.3.36'), ] @@ -73,6 +76,9 @@ exts_list = [ ('struct', '1.0.17', { 'checksums': ['0137bbb5df650f29104f6243502f3a2302aaaa5e42ea9f02d8a3943aaf668433'], }), + ('optim', '1.6.2', { + 'checksums': ['554a8e18bb7195ae861f5059c14f1a557844265c1addb5bfbf3ab9885524787e'], + }), ] moduleclass = 'math' From 9828c960664e9e72c06504b5f45dd7a744c648ef Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 30 Aug 2022 18:18:38 +0100 Subject: [PATCH 073/939] Java version downgraded to 11 --- easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index d440fc720136..f6c073f2b97f 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -35,7 +35,7 @@ dependencies = [ ('GLPK', '5.0'), ('GL2PS', '1.4.2'), ('gnuplot', '5.4.2'), - ('Java', '17', '', True), + ('Java', '11', '', True), ('zlib', '1.2.11'), ('Mesa', '21.1.7'), ('libGLU', '9.0.2'), From 588565ac1d08edc52f067178cca57b2d9da1e853 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 09:57:35 +0200 Subject: [PATCH 074/939] Sync with non-CUDA version from PR #16166 --- ...-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 46 +++++++++++++++---- 1 file changed, 36 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index a1dde04b0752..03ebe87e5228 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -18,30 +18,56 @@ sources = [ 'AmberTools-%s.tar.bz2' % local_ambertools_ver, ] patches = [ - 'Amber-22_remove_undeclared_redundant_variable.patch', - 'AmberTools-20_cmake-locate-netcdf.patch', - 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', - 'AmberTools-20_fix_xblas_missing_make_dependency.patch', + {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_missing_MPI_LIBRARY_error.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-20_fix_xblas_missing_make_dependency.patch', 'alt_location': 'AmberTools'}, {'name': 'AmberTools-21_CMake-FlexiBLAS.patch', 'alt_location': 'AmberTools'}, - 'AmberTools-22_fix_cuda_version_check.patch', + {'name': 'AmberTools-21_fix_DGESVD_workspace_query.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_dvout_call.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_incorrect_mexit_calls.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_more_blas_argument_problems.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_multiple_definition.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_potential_use_before_init.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_rism_argument_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-21_fix_xray_fftpack_arg_mismatch.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'}, + {'name': 'AmberTools-22_fix_cuda_version_check.patch', 'alt_location': 'AmberTools'}, + 'Amber-22_remove_undeclared_redundant_variable.patch', ] checksums = [ '3c887ccbad690fc76ff0b120a3448eae023c08e76582aac07900d4a9708ebd16', # Amber22.tar.bz2 - '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools-22.tar.bz2 - # Amber-22_remove_undeclared_redundant_variable.patch - 'f2e21002e00534f14caa00bc5bbf3b1e68acb71aa8dbcfea275d67192e32c15f', + '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch + # AmberTools-21_fix_DGESVD_workspace_query.patch + '560c73e9d8bd159c609098c63a0256cdee78f49e524d06ea94d16d3146f69bcd', + '1054d4007f5c79126a41582e1e80514267cf406416ed6c471574cd708b16319b', # AmberTools-21_fix_incorrect_dvout_call.patch + 'd1de8c596119dcedbb809515816f0c98762306c469e9caf2c0b878d9b0a1095f', # AmberTools-21_fix_incorrect_mexit_calls.patch + # AmberTools-21_fix_more_blas_argument_problems.patch + 'c6279b57752239184b942d37f760749494ae0eff95236f3368c76ac0d2726a7c', + 'ce30eeaba9feea53aa115e4b0dcc5be943b8a55abe322480c807ca7ea963d83b', # AmberTools-21_fix_multiple_definition.patch + # AmberTools-21_fix_potential_use_before_init.patch + '377e645b5bd2c91ebb4d0b6fbca0407a94289e5ddc5b1e7ed0cb0b0724ad2139', + # AmberTools-21_fix_rism_argument_mismatch.patch + '14255e5739cec39303df570f06820c7532f7395e1b73b1e4104377984e2c9fc1', + # AmberTools-21_fix_xray_fftpack_arg_mismatch.patch + '99c954e693659efc2a1d121f91510f56408006f0751d91595f45a34b03364e2f', + 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch + # AmberTools-22_fix_missing_error_check_on_test_run.patch + 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', + 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch '3fc08a2cf61f3eefd094554e60c88b14c9f5071f94e0a0a15c6b55fe321bfc78', # AmberTools-22_fix_cuda_version_check.patch + # Amber-22_remove_undeclared_redundant_variable.patch + 'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', ] builddependencies = [ ('Bison', '3.7.6'), - ('pkg-config', '0.29.2'), ('CMake', '3.22.1'), ('flex', '2.6.4'), ('make', '4.3'), @@ -67,7 +93,7 @@ dependencies = [ ] # Some CUDA tests differs from expected results -runtest = False +runtest = True static = False From 8320dd1cadbbea86aac4155fd16a930d80ac3ddb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 09:59:11 +0200 Subject: [PATCH 075/939] move AmberTools patch to AmberTools directory --- .../AmberTools-22_fix_cuda_version_check.patch | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/a/{Amber => AmberTools}/AmberTools-22_fix_cuda_version_check.patch (100%) diff --git a/easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch b/easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_cuda_version_check.patch similarity index 100% rename from easybuild/easyconfigs/a/Amber/AmberTools-22_fix_cuda_version_check.patch rename to easybuild/easyconfigs/a/AmberTools/AmberTools-22_fix_cuda_version_check.patch From 82e827952f45379703fedb20e5372191523b3e0b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:00:26 +0200 Subject: [PATCH 076/939] find ambertools source in ambertools dir --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 03ebe87e5228..9eba64d3c397 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -16,6 +16,7 @@ toolchainopts = {'usempi': True, 'openmp': True} sources = [ '%%(name)s%s.tar.bz2' % local_amber_ver, 'AmberTools-%s.tar.bz2' % local_ambertools_ver, + {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'}, ] patches = [ {'name': 'AmberTools-20_cmake-locate-netcdf.patch', 'alt_location': 'AmberTools'}, From 72f24fbf0856fee47c67ded7f7650df252640ba8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:03:24 +0200 Subject: [PATCH 077/939] remove old ambertools source specification --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 9eba64d3c397..13780bbfe859 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -15,7 +15,6 @@ toolchainopts = {'usempi': True, 'openmp': True} sources = [ '%%(name)s%s.tar.bz2' % local_amber_ver, - 'AmberTools-%s.tar.bz2' % local_ambertools_ver, {'filename': 'AmberTools%s.tar.bz2' % local_ambertools_ver, 'alt_location': 'AmberTools'}, ] patches = [ From f50784be53981ae6ebdc754fefdacec443ab257a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:04:11 +0200 Subject: [PATCH 078/939] add extra patch --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 13780bbfe859..5c54f0d06061 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -33,6 +33,7 @@ patches = [ {'name': 'AmberTools-22_fix_test_missing_cuda_dir.patch', 'alt_location': 'AmberTools'}, {'name': 'AmberTools-22_fix_missing_error_check_on_test_run.patch', 'alt_location': 'AmberTools'}, {'name': 'AmberTools-22_fix_cuda_version_check.patch', 'alt_location': 'AmberTools'}, + 'Amber-22_reduce_precision_of_kmmd_test.patch', 'Amber-22_remove_undeclared_redundant_variable.patch', ] checksums = [ From ed944c10a1e245b48d4b4e00e9cfb5e394912134 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:07:21 +0200 Subject: [PATCH 079/939] use cmake 3.21.1 --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 5c54f0d06061..83a7a2f96023 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -69,7 +69,7 @@ checksums = [ builddependencies = [ ('Bison', '3.7.6'), - ('CMake', '3.22.1'), + ('CMake', '3.21.1'), ('flex', '2.6.4'), ('make', '4.3'), ] From e58782014fc47e71c1c372582ea466694e941869 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 10:29:25 +0200 Subject: [PATCH 080/939] use https --- .../Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 83a7a2f96023..f13532135fba 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -1,12 +1,12 @@ name = 'Amber' local_amber_ver = 22 local_ambertools_ver = 22 -# Patch levels from http://ambermd.org/AmberPatches.php and http://ambermd.org/ATPatches.php +# Patch levels from https://ambermd.org/AmberPatches.php and https://ambermd.org/ATPatches.php patchlevels = (3, 0) # (AmberTools, Amber) version = '%s.%s' % (local_amber_ver, patchlevels[1]) versionsuffix = '-AmberTools-%s.%s-CUDA-%%(cudaver)s' % (local_ambertools_ver, patchlevels[0]) -homepage = 'http://ambermd.org/amber.html' +homepage = 'https://ambermd.org/amber.html' description = """Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction.""" From 4be80fca99362fce0f11d7fd4fd79ba017d1580b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 31 Aug 2022 11:28:42 +0200 Subject: [PATCH 081/939] remove optional arpack dep --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index f13532135fba..475f93c1e0cf 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -86,7 +86,6 @@ dependencies = [ ('netCDF', '4.8.1'), ('netCDF-Fortran', '4.5.3'), ('PnetCDF', '1.12.3'), - ('arpack-ng', '3.8.0'), ('Tkinter', '3.9.6'), ('X11', '20210802'), ('CUDA', '11.4.1', '', True), From 4aaed5877b77349fb0be94d4ded97f421f81850d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 1 Sep 2022 11:52:37 +0200 Subject: [PATCH 082/939] Add openMolcas --- .../OpenMolcas-22.06-intel-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb new file mode 100644 index 000000000000..e318c625a36f --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '22.06' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = "OpenMolcas is a quantum chemistry software package" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] +patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] +checksums = [ + '45daca1e6465d59a43479d5509315bca9c19dedbb0a2d4bb4f26f0b443b7670d', # OpenMolcas-v22.06.tar.gz + '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # OpenMolcas-21.06_mcpdft_deps.patch +] + +dependencies = [ + ('GlobalArrays', '5.8.1'), + ('HDF5', '1.13.1'), + ('Python', '3.10.4'), +] + +builddependencies = [('CMake', '3.23.1')] + +separate_build_dir = True + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' +configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' +configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' From 55adfaeaf7d8e949ae6e47bf0e0caed18d0c254a Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 1 Sep 2022 13:03:23 +0200 Subject: [PATCH 083/939] Downgrade HDF5 --- .../easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb index e318c625a36f..77b806ac4f47 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -19,7 +19,7 @@ checksums = [ dependencies = [ ('GlobalArrays', '5.8.1'), - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('Python', '3.10.4'), ] From 9acd4fec75feb2b80c2c0a1dabc538f21a3953f5 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Mon, 5 Sep 2022 13:48:22 +0200 Subject: [PATCH 084/939] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Mikael Öhman --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index 7e7c2186c132..182023f46912 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -30,7 +30,7 @@ builddependencies = [ ] dependencies = [ - ('HDF5', '1.13.1'), + ('HDF5', '1.12.2'), ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), From d5b88d121287db77419e3962188d3781c036d8b1 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 9 Sep 2022 14:43:55 +0100 Subject: [PATCH 085/939] SUNDIALS and gawk added, make check enabled --- easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index f6c073f2b97f..8bc5d81d9226 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -20,6 +20,7 @@ builddependencies = [ ('Autotools', '20210726'), ('gperf', '3.1'), ('pkgconf', '1.8.0'), + ('gawk', '5.1.1'), ] dependencies = [ @@ -47,6 +48,7 @@ dependencies = [ ('makeinfo', '6.8'), ('libsndfile', '1.0.31'), ('GraphicsMagick', '1.3.36'), + ('SUNDIALS', '6.3.0'), ] configopts = '--disable-docs ' @@ -81,4 +83,6 @@ exts_list = [ }), ] +runtest = 'check' + moduleclass = 'math' From e17c8a4ad9c8b7189651a207f71e127b9ff42275 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 16 Sep 2022 10:09:49 +0100 Subject: [PATCH 086/939] Corrected version of Wayland to 1.21.0 --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 1ede0f20a549..9026c3b2c207 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -58,7 +58,7 @@ dependencies = [ ('glew', '2.2.0', '-egl'), ('libwpe', '1.13.3'), ('pugixml', '1.12.1'), - ('Wayland', '1.20.0'), + ('Wayland', '1.21.0'), ('Waylandpp', '1.0.0'), ('wpebackend-fdo', '1.13.1'), ('enchant-2', '2.3.3'), From 275e58ef65766731d4ae7ef93d768e916ae9991f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 16 Sep 2022 13:26:20 +0200 Subject: [PATCH 087/939] Update chksum for AmberTools-20_fix_missing_MPI_LIBRARY_error.patch --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 475f93c1e0cf..9d5139c40a32 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -41,7 +41,7 @@ checksums = [ '1571d4e0f7d45b2a71dce5999fa875aea8c90ee219eb218d7916bf30ea229121', # AmberTools22.tar.bz2 '473e07c53b6f641d96d333974a6af2e03413fecef79f879d3fdecf7fecaab4d0', # AmberTools-20_cmake-locate-netcdf.patch # AmberTools-20_fix_missing_MPI_LIBRARY_error.patch - '185040c79c8799d4f2d75139b7c648a1863f3484c4e1baab3470d2cf8d660b65', + '0b89a0624167bc23876bcdefcb1055f591e38e3bd559a71d5749e342bd311acc', # AmberTools-20_fix_xblas_missing_make_dependency.patch 'ff25e91fdc72347a778c3837b581e174d6a8c71efa5b46e11391b18bca84fd65', '9543812c24c4b7842f64f1f8abaf2c92b5c4c0fadcdbd9811e76b81a778f0d36', # AmberTools-21_CMake-FlexiBLAS.patch From deec58b847dffa1b64da3abb6acd949c32e2bca3 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 16 Sep 2022 16:28:22 +0200 Subject: [PATCH 088/939] add download_instructions --- .../n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb index 908356d7fdae..ba7dbd9499e9 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -14,7 +14,10 @@ and operations on CUDA streams. toolchain = {'name': 'gompi', 'version': '2021b'} -# You need to download the source manully from https://developer.nvidia.com/nvshmem-downloads +download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for +their (free) developer program: +https://developer.nvidia.com/nvshmem-downloads""" + sources = ['%(namelower)s_src_%(version)s-3.txz'] checksums = ['8b6c0eab321b6352911e470f9e81a777a49e58148ec3728453b9522446dba178'] From de272ce0ffe470dcf6bc3e695fa31c2216b1246c Mon Sep 17 00:00:00 2001 From: swadmin Date: Mon, 19 Sep 2022 20:02:45 +0200 Subject: [PATCH 089/939] adding easyconfigs: OpenFOAM-10-foss-2022a.eb and patches: OpenFOAM-10-ThirdParty.patch --- .../o/OpenFOAM/OpenFOAM-10-ThirdParty.patch | 276 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-10-foss-2022a.eb | 37 +++ 2 files changed, 313 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch new file mode 100644 index 000000000000..4a2dd8f3b77e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-ThirdParty.patch @@ -0,0 +1,276 @@ +# This patch removes all need for the ThirdParty files of OpenFOAM: +# we use EB dependencies for everything. It adjusts the paths, variables, etc +# We also let the install dir, compiler, etc be set by EB. +# Aligned hunks by Leon Kos. Based on patch for OpenFOAM 5.0 and 4.1 by +# Kenneth Hoste (HPC-UGent) and Ward Poelmans + +diff -ru OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake +--- OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/Allwmake 2022-09-19 11:34:37.930703275 +0200 +@@ -17,8 +17,8 @@ + fi + + # Ensure CMake gets the correct C/C++ compilers +-[ -n "$WM_CC" ] && export CC="$WM_CC" +-[ -n "$WM_CXX" ] && export CXX="$WM_CXX" ++#[ -n "$WM_CC" ] && export CC="$WM_CC" ++#[ -n "$WM_CXX" ] && export CXX="$WM_CXX" + + wmake $targetType vtkPVblockMesh + wmake $targetType vtkPVFoam +diff -ru OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt +--- OpenFOAM-10-version-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/applications/utilities/postProcessing/graphics/PVReaders/CMakeLists.txt 2022-09-19 11:34:37.932703249 +0200 +@@ -2,6 +2,8 @@ + + PROJECT(PVReaders) + ++FIND_PACKAGE(MPI REQUIRED) ++ + FIND_PACKAGE(ParaView REQUIRED) + + INCLUDE(GNUInstallDirs) +diff -ru OpenFOAM-10-version-10/etc/bashrc OpenFOAM-10/etc/bashrc +--- OpenFOAM-10-version-10/etc/bashrc 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/bashrc 2022-09-19 11:34:37.934703223 +0200 +@@ -43,8 +43,9 @@ + # Please set to the appropriate path if the default is not correct. + # + [ "$BASH" -o "$ZSH_NAME" ] && \ +-export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ +-export FOAM_INST_DIR=$HOME/$WM_PROJECT ++#export FOAM_INST_DIR=$(cd $(dirname ${BASH_SOURCE:-$0})/../.. && pwd -P) || \ ++#export FOAM_INST_DIR=$HOME/$WM_PROJECT ++# For Easybuild: set by the module + # export FOAM_INST_DIR=~$WM_PROJECT + # export FOAM_INST_DIR=/opt/$WM_PROJECT + # export FOAM_INST_DIR=/usr/local/$WM_PROJECT +diff -ru OpenFOAM-10-version-10/etc/config.sh/CGAL OpenFOAM-10/etc/config.sh/CGAL +--- OpenFOAM-10-version-10/etc/config.sh/CGAL 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/CGAL 2022-09-19 11:34:37.935703211 +0200 +@@ -39,22 +39,7 @@ + # + #------------------------------------------------------------------------------ + +-boost_version=boost-system +-#boost_version=boost-1.55.0 +-#boost_version=boost-1.72.0 +- +-cgal_version=cgal-system +-#cgal_version=CGAL-4.10 +-#cgal_version=CGAL-5.0.2 +- +-if [ "$boost_version" != "boost-system" ] +-then +- export BOOST_ARCH_PATH=$WM_THIRD_PARTY_DIR/$boost_version +-fi +- +-if [ "$cgal_version" != "cgal-system" ] +-then +- export CGAL_ARCH_PATH=$WM_THIRD_PARTY_DIR/$cgal_version +-fi ++export CGAL_ARCH_PATH=$EBROOTCGAL ++export BOOST_ARCH_PATH=$EBROOTBOOST + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/gperftools OpenFOAM-10/etc/config.sh/gperftools +--- OpenFOAM-10-version-10/etc/config.sh/gperftools 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/gperftools 2022-09-19 11:34:37.937703185 +0200 +@@ -29,13 +29,7 @@ + # + #------------------------------------------------------------------------------ + +-version=svn +-gperftools_install=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER +- +-GPERFTOOLS_VERSION=gperftools-$version +-GPERFTOOLS_ARCH_PATH=$gperftools_install/$GPERFTOOLS_VERSION +- +-export PATH=$GPERFTOOLS_ARCH_PATH/bin:$PATH +-export LD_LIBRARY_PATH=$GPERFTOOLS_ARCH_PATH/lib:$LD_LIBRARY_PATH ++GPERFTOOLS_VERSION=gperftools-$EBVERSIONGPERFTOOLS ++GPERFTOOLS_ARCH_PATH=$EBROOTGPERFTOOLS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/metis OpenFOAM-10/etc/config.sh/metis +--- OpenFOAM-10-version-10/etc/config.sh/metis 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/metis 2022-09-19 11:34:37.938703172 +0200 +@@ -34,7 +34,7 @@ + # + #------------------------------------------------------------------------------ + +-export METIS_VERSION=metis-5.1.0 +-export METIS_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$METIS_VERSION ++export METIS_VERSION=metis-$EBVERSIONMETIS ++export METIS_ARCH_PATH=$EBROOTMETIS + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/mpi OpenFOAM-10/etc/config.sh/mpi +--- OpenFOAM-10-version-10/etc/config.sh/mpi 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/mpi 2022-09-19 11:34:37.939703159 +0200 +@@ -254,6 +254,9 @@ + _foamAddPath $MPI_ARCH_PATH/bin64 + _foamAddLib $MPI_ARCH_PATH/lib/release + ;; ++EASYBUILDMPI) ++ export FOAM_MPI=mpi ++ ;; + *) + export FOAM_MPI=dummy + ;; +diff -ru OpenFOAM-10-version-10/etc/config.sh/paraview OpenFOAM-10/etc/config.sh/paraview +--- OpenFOAM-10-version-10/etc/config.sh/paraview 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/paraview 2022-09-19 11:34:37.941703134 +0200 +@@ -41,25 +41,6 @@ + ) \ + && PATH="$cleaned" + +-# Determine the cmake to be used. Take the most recent. +-unset CMAKE_HOME CMAKE_ROOT +-for cmake in $WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/cmake-* +-do +- if [ -d $cmake ] +- then +- if [ -z $CMAKE_HOME ] || \ +- $WM_PROJECT_DIR/bin/tools/foamVersionCompare $CMAKE_HOME lt $cmake +- then +- export CMAKE_HOME=$cmake +- export CMAKE_ROOT=$cmake +- fi +- fi +-done +-if [ -n $CMAKE_HOME ] +-then +- export PATH=$cmake/bin:$PATH +-fi +- + #- ParaView version, automatically determine major version + #export ParaView_VERSION=4.0.1 + #export ParaView_VERSION=4.1.0 +@@ -69,7 +50,8 @@ + #export ParaView_VERSION=5.0.1 + #export ParaView_VERSION=5.4.0 + #export ParaView_VERSION=5.5.0 +-export ParaView_VERSION=5.6.3 ++#export ParaView_VERSION=5.6.3 ++export ParaView_VERSION=$EBVERSIONPARAVIEW + export ParaView_MAJOR=detect + + #export ParaView_GL=system +@@ -109,7 +91,8 @@ + export ParaView_VERSION ParaView_MAJOR + + # Set the binary and source directories +-export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++# export ParaView_DIR=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER/ParaView-$ParaView_VERSION ++export ParaView_DIR=$EBROOTPARAVIEW + paraviewSrcDir=$WM_THIRD_PARTY_DIR/ParaView-$ParaView_VERSION + + # Set paths if binaries or source are present +@@ -129,8 +112,6 @@ + fi + export ParaView_LIB_DIR=$ParaView_DIR/lib$paraviewArch$paraviewLibSubDir + +- export PATH=$ParaView_DIR/bin:$PATH +- export LD_LIBRARY_PATH=$ParaView_LIB_DIR:$LD_LIBRARY_PATH + export PV_PLUGIN_PATH=$FOAM_LIBBIN/paraview-$ParaView_MAJOR + + if [ "$FOAM_VERBOSE" -a "$PS1" ] +@@ -142,18 +123,6 @@ + echo " PV_PLUGIN_PATH : $PV_PLUGIN_PATH" + fi + +- # Add in python libraries if required +- paraviewPython=$ParaView_DIR/Utilities/VTKPythonWrapping +- if [ -r $paraviewPython ] +- then +- if [ "$PYTHONPATH" ] +- then +- export PYTHONPATH=$PYTHONPATH:$paraviewPython:$ParaView_LIB_DIR +- else +- export PYTHONPATH=$paraviewPython:$ParaView_LIB_DIR +- fi +- fi +- + # Alias paraview to launch with mesa if necessary + if [ "$ParaView_GL" = mesa ] + then +diff -ru OpenFOAM-10-version-10/etc/config.sh/scotch OpenFOAM-10/etc/config.sh/scotch +--- OpenFOAM-10-version-10/etc/config.sh/scotch 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/scotch 2022-09-19 11:34:37.942703121 +0200 +@@ -37,7 +37,7 @@ + # + #------------------------------------------------------------------------------ + +-export SCOTCH_VERSION=scotch_6.0.9 +-export SCOTCH_ARCH_PATH=$WM_THIRD_PARTY_DIR/platforms/$WM_ARCH$WM_COMPILER$WM_PRECISION_OPTION$WM_LABEL_OPTION/$SCOTCH_VERSION ++export SCOTCH_VERSION=scotch_$EBVERSIONSCOTCH ++export SCOTCH_ARCH_PATH=$EBROOTSCOTCH + + #------------------------------------------------------------------------------ +diff -ru OpenFOAM-10-version-10/etc/config.sh/settings OpenFOAM-10/etc/config.sh/settings +--- OpenFOAM-10-version-10/etc/config.sh/settings 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/etc/config.sh/settings 2022-09-19 11:34:37.943703108 +0200 +@@ -61,11 +61,11 @@ + 64) + WM_ARCH=linux64 + export WM_COMPILER_LIB_ARCH=64 +- export WM_CC='gcc' +- export WM_CXX='g++' +- export WM_CFLAGS='-m64 -fPIC' +- export WM_CXXFLAGS='-m64 -fPIC -std=c++0x' +- export WM_LDFLAGS='-m64' ++ export WM_CC=$CC ++ export WM_CXX=$CXX ++ export WM_CFLAGS=$CFLAGS ++ export WM_CXXFLAGS=$CXXFLAGS ++ export WM_LDFLAGS=$LDFLAGS + ;; + *) + echo "Unknown WM_ARCH_OPTION '$WM_ARCH_OPTION', should be 32 or 64"\ +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/Make/options OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/Make/options +--- OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/Make/options 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/Make/options 2022-09-19 11:34:37.945703082 +0200 +@@ -4,14 +4,7 @@ + $(PFLAGS) $(PINC) \ + -I$(FOAM_SRC)/Pstream/mpi/lnInclude \ + -I$(SCOTCH_ARCH_PATH)/include/$(FOAM_MPI) \ +- -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ +- -L$(SCOTCH_ARCH_PATH)/lib \ +- -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) \ +- -lptscotch \ +- -lptscotcherrexit \ +- -lscotch \ +- -lrt ++ -L$(SCOTCH_ARCH_PATH)/lib -L$(FOAM_EXT_LIBBIN)/$(FOAM_MPI) -lptscotch -lptscotcherrexit -lscotch ${LINK_FLAGS} -lrt +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C +--- OpenFOAM-10-version-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/ptscotchDecomp/ptscotchDecomp.C 2022-09-19 11:34:37.947703057 +0200 +@@ -31,10 +31,11 @@ + #include "SubField.H" + #include "PstreamGlobals.H" + ++#include ++ + extern "C" + { + #include +- #include + #include "ptscotch.h" + } + +diff -ru OpenFOAM-10-version-10/src/parallel/decompose/scotchDecomp/Make/options OpenFOAM-10/src/parallel/decompose/scotchDecomp/Make/options +--- OpenFOAM-10-version-10/src/parallel/decompose/scotchDecomp/Make/options 2022-07-11 13:18:29.000000000 +0200 ++++ OpenFOAM-10/src/parallel/decompose/scotchDecomp/Make/options 2022-09-19 11:34:37.948703044 +0200 +@@ -6,7 +6,6 @@ + EXE_INC = \ + $(PFLAGS) $(PINC) \ + -I$(SCOTCH_ARCH_PATH)/include \ +- -I/usr/include/scotch \ + -I../decompositionMethods/lnInclude + + LIB_LIBS = \ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb new file mode 100644 index 000000000000..ac915d6fce39 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb @@ -0,0 +1,37 @@ +name = 'OpenFOAM' +version = '10' + +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'} + +source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] +sources = ['version-%(version)s.tar.gz'] +patches = ['OpenFOAM-%(version)s-ThirdParty.patch'] +checksums = [ + '59d712ba798ca44b989b6ac50bcb7c534eeccb82bcf961e10ec19fc8d84000cf', # version-10.tar.gz + '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43', # OpenFOAM-10-ThirdParty.patch + '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch +] + +builddependencies = [ + ('Bison', '3.8.2'), + ('CMake', '3.23.1'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('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 46719281db5b742329591c02af287c5d92a61a3e Mon Sep 17 00:00:00 2001 From: Alex Date: Tue, 20 Sep 2022 12:15:20 +0200 Subject: [PATCH 090/939] build: harden linting.yml permissions Signed-off-by: Alex --- .github/workflows/linting.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 6346d959773f..b041561e9e4f 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,5 +1,7 @@ name: Static Analysis on: [push, pull_request] +permissions: + contents: read # to fetch code (actions/checkout) jobs: python-linting: runs-on: ubuntu-20.04 From a1d8f4898de7d5ece15122a73ff5c06f2f3edf4e Mon Sep 17 00:00:00 2001 From: Alex Date: Tue, 20 Sep 2022 12:16:14 +0200 Subject: [PATCH 091/939] build: harden unit_tests.yml permissions Signed-off-by: Alex --- .github/workflows/unit_tests.yml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 1a8e16547f51..4ce590ffa1f4 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -1,5 +1,7 @@ name: easyconfigs unit tests on: [push, pull_request] +permissions: + contents: read # to fetch code (actions/checkout) jobs: test-suite: runs-on: ubuntu-20.04 From 12016618ef7f89ae78b0554263c5a21f3dcc38f1 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Tue, 20 Sep 2022 18:24:15 +0200 Subject: [PATCH 092/939] ADD CDO --- .../c/CDO/CDO-2.0.6-gompi-2022a.eb | 46 +++++++++++++++++++ .../e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb | 44 ++++++++++++++++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb 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 new file mode 100644 index 000000000000..caccb37e4987 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'CDO' +version = '2.0.6' + +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': '2022a'} +toolchainopts = {'cstd': 'c++17', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/27276/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ef120dea9032b1be80a4cfa201958c3b910107205beb6674195675f1ee8ed402'] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('ecCodes', '2.27.0'), + ('FFTW', '3.3.10'), + ('HDF5', '1.12.2'), + ('libxml2', '2.9.13'), + ('netCDF', '4.9.0'), + ('PROJ', '9.0.0'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.38'), +] + +# 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'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb new file mode 100644 index 000000000000..742bdb55b84d --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.27.0' + +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': '2022a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://confluence.ecmwf.int/download/attachments/45757960/'] +sources = ['eccodes-%(version)s-Source.tar.gz'] +checksums = ['ede5b3ffd503967a5eac89100e8ead5e16a881b7585d02f033584ed0c4269c99'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('JasPer', '2.0.33'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('zlib', '1.2.12'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF " +configopts += "-DENABLE_JPG=ON -DENABLE_JPG_LIBJASPER=ON " +configopts += "-DENABLE_ECCODES_THREADS=ON" # multi-threading with pthreads + +local_exes = ['%s_%s' % (a, b) + for a in ['bufr', 'grib', 'gts', 'metar'] + for b in ['compare', 'copy', 'dump', 'filter', 'get', 'ls']] +local_exes += ['codes_%s' % c for c in ['count', 'info', 'split_file']] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_exes] + + ['lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' From 84b816b4bf3f165bdd9be22ee2141d4b89f97d23 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 21 Sep 2022 08:14:08 +0200 Subject: [PATCH 093/939] adding easyconfigs: Theano-1.0.4-foss-2018b-Python-3.6.6.eb --- .../Theano-1.0.4-foss-2018b-Python-3.6.6.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb new file mode 100644 index 000000000000..92874d5552d0 --- /dev/null +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Theano' +version = "1.0.4" +versionsuffix = '-Python-%(pyver)s' + +homepage = 'http://deeplearning.net/software/theano' +description = """Theano is a Python library that allows you to define, optimize, +and evaluate mathematical expressions involving multi-dimensional arrays efficiently.""" + +toolchain = {'name': 'foss', 'version': '2018b'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] + +dependencies = [('Python', '3.6.6')] + +use_pip = True +download_dep_fail = True + +sanity_check_paths = { + 'files': ['bin/theano-cache', 'bin/theano-nose'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'math' From f8f34d0004023f046b3df614ac7ad921fd8719e5 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Wed, 21 Sep 2022 08:48:34 +0200 Subject: [PATCH 094/939] improvements from linter --- .../t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb index 92874d5552d0..ed46151ae767 100644 --- a/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb +++ b/easybuild/easyconfigs/t/Theano/Theano-1.0.4-foss-2018b-Python-3.6.6.eb @@ -10,7 +10,6 @@ and evaluate mathematical expressions involving multi-dimensional arrays efficie toolchain = {'name': 'foss', 'version': '2018b'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['35c9bbef56b61ffa299265a42a4e8f8cb5a07b2997dabaef0f8830b397086913'] @@ -18,6 +17,7 @@ dependencies = [('Python', '3.6.6')] use_pip = True download_dep_fail = True +sanity_pip_check = True sanity_check_paths = { 'files': ['bin/theano-cache', 'bin/theano-nose'], From 50f2d3e230b994a3210247845eebb521afcc6021 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 21 Sep 2022 15:11:41 +0200 Subject: [PATCH 095/939] Add NCO --- .../l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb | 37 ++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb | 44 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..237260a43f78 --- /dev/null +++ b/easybuild/easyconfigs/l/libdap/libdap-3.20.11-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'libdap' +version = '3.20.11' + +homepage = 'https://www.opendap.org/software/libdap' +description = """A C++ SDK which contains an implementation of DAP 2.0 and + DAP4.0. This includes both Client- and Server-side support classes.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.opendap.org/pub/source/'] +sources = [SOURCE_TAR_GZ] +checksums = ['850debf6ee6991350bf31051308093bee35ddd2121e4002be7e130a319de1415'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('cURL', '7.83.0'), + ('libxml2', '2.9.13'), + ('libtirpc', '1.3.2'), + ('PCRE', '8.45'), + ('util-linux', '2.38'), +] + +configopts = 'TIRPC_LIBS="-ltirpc"' + +sanity_check_paths = { + 'files': ['bin/getdap', 'bin/getdap4', 'bin/dap-config', 'lib/libdap.a', 'lib/libdap.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb new file mode 100644 index 000000000000..81047083a23a --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.0-foss-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.0' + +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': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['6f0ba812e0684881a85ebf3385117761cffbba36ba842889cc96f111157f89c2'] + +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 dab8df24e7744ef755ba274f0a4ffaa8d6612272 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 22 Sep 2022 12:59:01 +0200 Subject: [PATCH 096/939] Add QIIME2 and deps --- .../m/Miniconda3/Miniconda3-4.12.0.eb | 17 ++++++++++ .../easyconfigs/q/QIIME2/QIIME2-2022.8.eb | 31 +++++++++++++++++++ 2 files changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb create mode 100644 easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb diff --git a/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb new file mode 100644 index 000000000000..5521f6fcca45 --- /dev/null +++ b/easybuild/easyconfigs/m/Miniconda3/Miniconda3-4.12.0.eb @@ -0,0 +1,17 @@ +easyblock = 'EB_Anaconda' + +name = 'Miniconda3' +version = '4.12.0' + +homepage = 'https://docs.conda.io/en/latest/miniconda.html' +description = """Miniconda is a free minimal installer for conda. It is a small, + bootstrap version of Anaconda that includes only conda, Python, the packages they + depend on, and a small number of other useful packages.""" + +toolchain = SYSTEM + +source_urls = ['https://repo.anaconda.com/miniconda/'] +sources = ['%(name)s-py38_%(version)s-Linux-x86_64.sh'] +checksums = ['3190da6626f86eee8abf1b2fd7a5af492994eb2667357ee4243975cdbb175d7a'] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb new file mode 100644 index 000000000000..30c12abc3c2e --- /dev/null +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb @@ -0,0 +1,31 @@ +# EasyBuild recipy for QIIME2 +# Author: Caspar van Leeuwen +# SURFsara - The Netherlands + +easyblock = 'Conda' + +name = 'QIIME2' +version = '2022.8' + +homepage = 'http://qiime2.org/' +description = """QIIME is an open-source bioinformatics pipeline for performing microbiome analysis + from raw DNA sequencing data.""" + +source_urls = ['https://data.qiime2.org/distro/core/'] +sources = ['qiime2-%(version)s-py38-linux-conda.yml'] +checksums = ['454bb219f928c7f4ec0097888db27ab439ba2ef7e4294f38b7033327cb3dafb8'] + +toolchain = SYSTEM + +builddependencies = [('Miniconda3', '4.12.0')] + +environment_file = 'qiime2-%(version)s-py38-linux-conda.yml' + +sanity_check_commands = ['qiime info'] + +sanity_check_paths = { + 'files': ["bin/qiime"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'bio' From 4770a3875fe686548fda2cc062a10dd207170515 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 27 Sep 2022 09:40:01 +0100 Subject: [PATCH 097/939] Entry for ccache corrected so GCCcore will be used --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 9026c3b2c207..5e41bdddcfba 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -38,7 +38,7 @@ builddependencies = [ ('Perl', '5.34.0', '-minimal'), ('GObject-Introspection', '1.68.0'), ('pkg-config', '0.29.2'), - ('ccache', '4.6.1', '', True), + ('ccache', '4.6.1'), ] dependencies = [ ('GLib', '2.69.1'), From 5bf85e732ec71c1e9ad92dc8da3e5f2866c88b76 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 13:27:06 +0200 Subject: [PATCH 098/939] adding easyconfigs: ASAP-2.1-foss-2022a.eb, DCMTK-3.6.7-GCCcore-11.3.0.eb, OpenJPEG-2.5.0-GCCcore-11.3.0.eb, OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb, pugixml-1.12.1-GCCcore-11.3.0.eb and patches: ASAP-2.1-libjpeg.patch, ASAP-2.1-pugixml.patch, ASAP-2.1-cmath.patch --- .../easyconfigs/a/ASAP/ASAP-2.1-cmath.patch | 12 +++ .../easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb | 72 ++++++++++++++ .../easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch | 35 +++++++ .../easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch | 52 ++++++++++ .../d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 56 +++++++++++ .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 44 +++++++++ .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 94 +++++++++++++++++++ .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 36 +++++++ .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 ++++++++++ ...enSlide-3.4.1-GCCcore-11.3.0-largefiles.eb | 56 +++++++++++ .../pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 29 ++++++ 11 files changed, 533 insertions(+) create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch create mode 100644 easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch create mode 100644 easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb create mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb create mode 100644 easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch new file mode 100644 index 000000000000..b4ca984d4214 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch @@ -0,0 +1,12 @@ +diff --git a/annotation/ImageScopeRepository.cpp b/annotation/ImageScopeRepository.cpp +index 6916a58..c135cb3 100644 +--- a/annotation/ImageScopeRepository.cpp ++++ b/annotation/ImageScopeRepository.cpp +@@ -9,6 +9,7 @@ + #include + #include "pugixml.hpp" + #include ++#include + + ImageScopeRepository::ImageScopeRepository(const std::shared_ptr& list) : + Repository(list), diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb new file mode 100644 index 000000000000..7dd82903d65e --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'CMakeMake' + +name = 'ASAP' +version = '2.1' + +homepage = 'https://computationalpathologygroup.github.io/ASAP/' +description = """ASAP focuses on fast and fluid image viewing with an easy-to-use interface +for making annotations. It consists of two main components: an IO library for reading and writing +multi-resolution images and a viewer component for visualizing such images.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/computationalpathologygroup/%(name)s/archive'] +sources = [SOURCE_TAR_GZ] +patches = [ + 'ASAP-2.1-libjpeg.patch', + 'ASAP-2.1-pugixml.patch', + 'ASAP-2.1-cmath.patch', +] +checksums = [ + '7ba9f39d09bada808f760c5dc9ac0cda0d221fd1393a0a3f9decfd6b5e913b3c', # ASAP-2.1.tar.gz + 'dbdf26324a7521b4beaa7ec2c0585f0816619cd73b3125efd313eb48c4813a43', # ASAP-2.1-libjpeg.patch + 'f578bb3ec4cbce573d4b9acd695eb55446592f4ac00551656a06f113ba09a9a7', # ASAP-2.1-pugixml.patch + 'e33d83853e0bd51113a886d0793504ce0abfb15fdf88410a19287d46fafd33c4', # ASAP-2.1-cmath.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('Boost', '1.79.0'), + ('Python', '3.10.4'), + ('OpenCV', '4.6.0', '-contrib'), + ('Qt5', '5.15.5'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('JasPer', '2.0.33'), + ('DCMTK', '3.6.7'), + ('SWIG', '4.0.2'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('pugixml', '1.12.1'), + ('zlib', '1.2.12'), +] + +configopts = " ".join([ + "-DOPENSLIDE_INCLUDE_DIR=$EBROOTOPENSLIDE/include/openslide", + "-DPugiXML_INCLUDE_DIR=$EBROOTPUGIXML/include", + "-DDCMTKJPEG_INCLUDE_DIR=$EBROOTDCMTK/include", + "-DWRAP_MULTIRESOLUTIONIMAGEINTERFACE_PYTHON=TRUE", + "-DBUILD_ASAP=TRUE", + "-DBUILD_EXECUTABLES=TRUE", + "-DBUILD_IMAGEPROCESSING=TRUE", + "-DBUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT=TRUE", + "-DSWIG_EXECUTABLE=$EBROOTSWIG/bin/swig" +]) + + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s', + 'bin/multiresolutionimageinterface.py', + 'lib/libmultiresolutionimageinterface.%s' % SHLIB_EXT], + 'dirs': ['bin'], +} + +sanity_check_commands = ['python -c "import multiresolutionimageinterface"'] + +# ASAP installs its python interface in bin. Ugly, but we'll need to add it to PYTHONPATH +modextrapaths = {'PYTHONPATH': ['bin']} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch new file mode 100644 index 000000000000..eeab7c051442 --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch @@ -0,0 +1,35 @@ +diff --git a/multiresolutionimageinterface/VSIImage.cpp b/multiresolutionimageinterface/VSIImage.cpp +index 509bb18..1763201 100644 +--- a/multiresolutionimageinterface/VSIImage.cpp ++++ b/multiresolutionimageinterface/VSIImage.cpp +@@ -11,7 +11,7 @@ + // Include DCMTK LIBJPEG for lossy and lossless JPEG compression + extern "C" { + #define boolean ijg_boolean +-#include "dcmtk/dcmjpeg/libijg8/jpeglib8.h" ++#include "jpeglib.h" + #include "jpeg_mem_src.h" + #undef boolean + #undef const +@@ -234,7 +234,7 @@ char* VSIImage::decodeTile(int no, int row, int col) const { + jpeg_source_mgr src_mem; + jpeg_create_decompress(&cinfo); + cinfo.err = jpeg_std_error(&jerr); +- jpeg_mem_src(&cinfo, &src_mem, (void*)buf, size); ++ jpeg_mem_src_asap(&cinfo, &src_mem, (void*)buf, size); + jpeg_read_header(&cinfo, true); + if (_compressionType == 2) { + cinfo.jpeg_color_space = JCS_YCbCr; +diff --git a/multiresolutionimageinterface/jpeg_mem_src.h b/multiresolutionimageinterface/jpeg_mem_src.h +index b9b91e9..13b9040 100644 +--- a/multiresolutionimageinterface/jpeg_mem_src.h ++++ b/multiresolutionimageinterface/jpeg_mem_src.h +@@ -47,7 +47,7 @@ static void mem_skip_input_data( j_decompress_ptr cinfo, long num_bytes ) + } + } + +-static void jpeg_mem_src( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) ++static void jpeg_mem_src_asap( j_decompress_ptr cinfo, jpeg_source_mgr * const src, void const * const buffer, long nbytes ) + { + src->init_source = mem_init_source; + src->fill_input_buffer = mem_fill_input_buffer; diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch new file mode 100644 index 000000000000..2b4a652369fe --- /dev/null +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch @@ -0,0 +1,52 @@ +diff --git a/annotation/CMakeLists.txt b/annotation/CMakeLists.txt +index 114babe..2156cd3 100644 +--- a/annotation/CMakeLists.txt ++++ b/annotation/CMakeLists.txt +@@ -25,10 +25,9 @@ set(ANNOTATION_SOURCE + ) + + add_library(annotation SHARED ${ANNOTATION_SOURCE} ${ANNOTATION_HEADERS}) +-target_compile_definitions(annotation PRIVATE "PUGIXML_HEADER_ONLY") + generate_export_header(annotation) + target_include_directories(annotation PUBLIC $ $ PRIVATE ${DIAGPathology_SOURCE_DIR} ${CMAKE_CURRENT_SOURCE_DIR} ${Boost_INCLUDE_DIRS} ${PugiXML_INCLUDE_DIR}) +-target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface) ++target_link_libraries(annotation PUBLIC core PRIVATE multiresolutionimageinterface ${PUGIXML_LIBRARY}) + set_target_properties(annotation PROPERTIES DEBUG_POSTFIX _d) + + IF(APPLE) +diff --git a/cmakemodules/FindPugiXML.cmake b/cmakemodules/FindPugiXML.cmake +index ccffcc4..9afcfb4 100644 +--- a/cmakemodules/FindPugiXML.cmake ++++ b/cmakemodules/FindPugiXML.cmake +@@ -5,11 +5,12 @@ + # PugiXML_FOUND, If false, do not try to use PugiXML. + + find_path(PugiXML_INCLUDE_DIR pugixml.hpp) ++find_library(PUGIXML_LIBRARY NAMES pugixml) + + # handle the QUIETLY and REQUIRED arguments and set PugiXML_FOUND to TRUE if + # all listed variables are TRUE + include(${CMAKE_ROOT}/Modules/FindPackageHandleStandardArgs.cmake) + FIND_PACKAGE_HANDLE_STANDARD_ARGS(PugiXML +- REQUIRED_VARS PugiXML_INCLUDE_DIR) ++ REQUIRED_VARS PUGIXML_LIBRARY PugiXML_INCLUDE_DIR) + +-mark_as_advanced(PugiXML_INCLUDE_DIR) ++mark_as_advanced(PugiXML_INCLUDE_DIR PUGIXML_LIBRARY) +diff --git a/multiresolutionimageinterface/CMakeLists.txt b/multiresolutionimageinterface/CMakeLists.txt +index 132e6ef..8d24176 100644 +--- a/multiresolutionimageinterface/CMakeLists.txt ++++ b/multiresolutionimageinterface/CMakeLists.txt +@@ -87,11 +87,10 @@ endif(BUILD_MULTIRESOLUTIONIMAGEINTERFACE_VSI_SUPPORT) + + add_library(multiresolutionimageinterface SHARED ${MULTIRESOLUTIONIMAGEINTERFACE_SRCS} ${MULTIRESOLUTIONIMAGEINTERFACE_HS} ${VSI_SOURCE_HS} ${VSI_SOURCE_SRCS}) + target_include_directories(multiresolutionimageinterface PUBLIC $ $ $ $ PRIVATE ${PugiXML_INCLUDE_DIR} ${TIFF_INCLUDE_DIR}) +-target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff) ++target_link_libraries(multiresolutionimageinterface PUBLIC core PRIVATE jpeg2kcodec libtiff ${PUGIXML_LIBRARY}) + IF(NOT WIN32) + target_link_libraries(multiresolutionimageinterface PRIVATE dl) + ENDIF(NOT WIN32) +-target_compile_definitions(multiresolutionimageinterface PRIVATE PUGIXML_HEADER_ONLY) + generate_export_header(multiresolutionimageinterface) + set_target_properties(multiresolutionimageinterface PROPERTIES DEBUG_POSTFIX _d) + diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..6bffa6ad7b90 --- /dev/null +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'CMakeMake' + +name = 'DCMTK' +version = '3.6.7' + +homepage = 'https://dicom.offis.de/dcmtk' +description = """DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. +It includes software for examining, constructing and converting DICOM image files, handling offline media, sending +and receiving images over a network connection, as well as demonstrative image storage and worklist servers.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +local_stripped_version = version.replace('.', '') + +source_urls = ['https://dicom.offis.de/download/%(namelower)s/dcmtk{}/'.format(local_stripped_version)] +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('libpng', '1.6.37'), + ('libxml2', '2.9.13'), + ('libiconv', '1.17'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=OFF', + '-DBUILD_SHARED_LIBS=ON' +] + + +sanity_check_paths = { + 'files': ['bin/dcmdump', 'bin/dcmj2pnm'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + 'dcmdata_tests | grep " 0 failed"', + 'dcmect_tests | grep " 0 failed"', + 'dcmfg_tests | grep " 0 failed"', + 'dcmiod_tests | grep " 0 failed"', + 'dcmnet_tests | grep " 0 failed"', + 'dcmrt_tests | grep " 0 failed"', + 'dcmseg_tests | grep " 0 failed"', + 'dcmsr_tests | grep " 0 failed"', + 'dcmtls_tests | grep " 0 failed"', + 'ofstd_tests | grep " 0 failed"', +] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..0c0b2fbef392 --- /dev/null +++ b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'libwebp' +version = '1.2.4' + +homepage = 'https://developers.google.com/speed/webp/' +description = """WebP is a modern image format that provides superior +lossless and lossy compression for images on the web. Using WebP, +webmasters and web developers can create smaller, richer images that +make the web faster.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('giflib', '5.2.1'), +] + +configopts = '--enable-libwebpmux' + +local_headers, local_libs = ( + ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], + ['webp', 'webpdemux', 'webpmux'] +) + +sanity_check_paths = { + 'files': ( + ['include/webp/%s' % h for h in local_headers] + + ['lib/lib%s.a' % s for s in local_libs] + + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + ), + 'dirs': ['lib/'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb new file mode 100644 index 000000000000..48f3aa8178e4 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb @@ -0,0 +1,94 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '5.0.1'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '11', '', True), + ('ant', '1.10.12', '-Java-%(javaver)s', True), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.12.2'), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", +]) + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..d607a01b64d8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'OpenEXR' +version = '3.1.5' + +homepage = 'https://www.openexr.com/' +description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic + for use in computer imaging applications""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' + +local_libs, local_bins = [ + ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], + ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] +] + +sanity_check_paths = { + 'files': ( + ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + + ['bin/exr%s' % b for b in local_bins] + ), + 'dirs': ['include/%(name)s', 'share'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..6c76dae7c5db --- /dev/null +++ b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,47 @@ +# easybuild easyconfig +# +# John Dey jfdey@fredhutch.org +# +# Fred Hutchenson Cancer Research Center Seattle WA +easyblock = 'CMakeMake' + +name = 'OpenJPEG' +version = '2.5.0' + +homepage = 'https://www.openjpeg.org/' +description = """OpenJPEG is an open-source JPEG 2000 codec written in + C language. It has been developed in order to promote the use of JPEG 2000, + a still-image compression standard from the Joint Photographic Experts Group + (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as + a JPEG 2000 Reference Software.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] +# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), +] + +sanity_check_paths = { + 'files': [ + 'bin/opj_compress', + 'bin/opj_decompress', + 'bin/opj_dump', + 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', + 'lib/libopenjp2.%s' % SHLIB_EXT + ], + 'dirs': ['bin', 'include', 'lib'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb new file mode 100644 index 000000000000..b39f32e43c66 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSlide/OpenSlide-3.4.1-GCCcore-11.3.0-largefiles.eb @@ -0,0 +1,56 @@ +easyblock = 'ConfigureMake' + +name = 'OpenSlide' +version = '3.4.1' +versionsuffix = '-largefiles' + +homepage = 'https://openslide.org/' +description = """OpenSlide is a C library that provides a simple interface to +read whole-slide images (also known as virtual slides).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_large_file_support.patch'] +checksums = [ + # v3.4.1.tar.gz + 'a5d869916e370125421535dcce778b2ba625dc50d920aa4ca93bbaaa6a7b470c', + # %(name)s-%(version_major_minor)s.1_large_file_support.patch + 'cb618053f4ae6c3ce37d1b8b0e4ef7c55fd17378776d13be4aa4efab91706b8c', +] + +builddependencies = [ + ('Autotools', '20220317'), + ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('OpenJPEG', '2.5.0'), + ('libxml2', '2.9.13'), + ('SQLite', '3.38.3'), + ('cairo', '1.17.4'), + ('Gdk-Pixbuf', '2.42.8'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': [ + 'bin/openslide-quickhash1sum', + 'bin/openslide-show-properties', + 'bin/openslide-write-png', + 'lib/libopenslide.la', + 'lib/libopenslide.%s' % SHLIB_EXT + ], + 'dirs': ['include/openslide'] +} + + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1e32278858c5 --- /dev/null +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'CMakeMake' + +name = 'pugixml' +version = '1.12.1' + +homepage = 'https://pugixml.org/' +description = "pugixml is a light-weight C++ XML processing library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/zeux/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.4_pugixml_remove_headeronly.patch'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +configopts = "-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True " + + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib'], +} + +moduleclass = 'data' From edccc61548f18e5fa1076fc6f39a62627e3150a8 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 13:35:17 +0200 Subject: [PATCH 099/939] deleted OpenCV ec and its deps --- .../l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb | 44 --------- .../OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb | 94 ------------------- .../o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb | 36 ------- 3 files changed, 174 deletions(-) delete mode 100644 easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb delete mode 100644 easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb deleted file mode 100644 index 0c0b2fbef392..000000000000 --- a/easybuild/easyconfigs/l/libwebp/libwebp-1.2.4-GCCcore-11.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'libwebp' -version = '1.2.4' - -homepage = 'https://developers.google.com/speed/webp/' -description = """WebP is a modern image format that provides superior -lossless and lossy compression for images on the web. Using WebP, -webmasters and web developers can create smaller, richer images that -make the web faster.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://storage.googleapis.com/downloads.webmproject.org/releases/webp'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['7bf5a8a28cc69bcfa8cb214f2c3095703c6b73ac5fba4d5480c205331d9494df'] - -builddependencies = [ - ('binutils', '2.38'), -] -dependencies = [ - ('libjpeg-turbo', '2.1.3'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), - ('giflib', '5.2.1'), -] - -configopts = '--enable-libwebpmux' - -local_headers, local_libs = ( - ['decode.h', 'demux.h', 'encode.h', 'mux.h', 'mux_types.h', 'types.h'], - ['webp', 'webpdemux', 'webpmux'] -) - -sanity_check_paths = { - 'files': ( - ['include/webp/%s' % h for h in local_headers] + - ['lib/lib%s.a' % s for s in local_libs] + - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] - ), - 'dirs': ['lib/'] -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb deleted file mode 100644 index 48f3aa8178e4..000000000000 --- a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-contrib.eb +++ /dev/null @@ -1,94 +0,0 @@ -name = 'OpenCV' -version = '4.6.0' -versionsuffix = '-contrib' - -# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake -local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' - -homepage = 'https://opencv.org/' -description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision - and machine learning software library. OpenCV was built to provide - a common infrastructure for computer vision applications and to accelerate - the use of machine perception in the commercial products. - Includes extra modules for OpenCV from the contrib repository.""" - -toolchain = {'name': 'foss', 'version': '2022a'} - -sources = [ - { - 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], - 'download_filename': '%(version)s.zip', - 'filename': SOURCELOWER_ZIP - }, - { - 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], - 'download_filename': '%(version)s.zip', - 'filename': '%(namelower)s_contrib-%(version)s.zip' - }, - { - 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], - 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', - 'extract_cmd': 'cp %s %(builddir)s' - }, -] -checksums = [ - '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip - '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip - '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz -] - -builddependencies = [ - ('CMake', '3.23.1'), -] -dependencies = [ - ('Python', '3.10.4'), - ('SciPy-bundle', '2022.05'), - ('zlib', '1.2.12'), - ('FFmpeg', '5.0.1'), - ('freetype', '2.12.1'), - ('HarfBuzz', '4.2.1'), - ('libjpeg-turbo', '2.1.3'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), - ('libwebp', '1.2.4'), - ('OpenEXR', '3.1.5'), - ('JasPer', '2.0.33'), - ('Java', '11', '', True), - ('ant', '1.10.12', '-Java-%(javaver)s', True), - ('GLib', '2.72.1'), - ('GTK4', '4.7.0'), - ('HDF5', '1.12.2'), -] - -# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz -# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 -configopts = " ".join([ - "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", - "-DFREETYPE_FOUND=ON", - "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", - "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", - "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", - "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", - "-DHARFBUZZ_FOUND=ON", - "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", - "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", - "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", - "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", - "-DBUILD_opencv_python2=OFF", -]) - -enhance_sanity_check = True - -local_contrib_libs = [ - 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', - 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', - 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', - 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' -] - -sanity_check_paths = { - 'files': ['lib64/libopencv_%s.%s' % (s, SHLIB_EXT) for s in local_contrib_libs], - 'dirs': [], -} - -moduleclass = 'vis' diff --git a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb deleted file mode 100644 index d607a01b64d8..000000000000 --- a/easybuild/easyconfigs/o/OpenEXR/OpenEXR-3.1.5-GCCcore-11.3.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'CMakeMake' - -name = 'OpenEXR' -version = '3.1.5' - -homepage = 'https://www.openexr.com/' -description = """OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic - for use in computer imaging applications""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] -sources = ['v%(version)s.tar.gz'] -checksums = ['93925805c1fc4f8162b35f0ae109c4a75344e6decae5a240afdfce25f8a433ec'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] - -configopts = '-DOPENEXR_BUILD_PYTHON_LIBS=OFF' - -local_libs, local_bins = [ - ['Iex', 'IlmThread', 'Imath', 'OpenEXR', 'OpenEXRUtil'], - ['envmap', 'header', 'makepreview', 'maketiled', 'multipart', 'multiview', 'stdattr'] -] - -sanity_check_paths = { - 'files': ( - ['lib/lib%s.%s' % (s, SHLIB_EXT) for s in local_libs] + - ['bin/exr%s' % b for b in local_bins] - ), - 'dirs': ['include/%(name)s', 'share'], -} - -moduleclass = 'vis' From ce611aa982d47c19d0f078bf2a13f8ac80ddeaa7 Mon Sep 17 00:00:00 2001 From: robogast Date: Wed, 28 Sep 2022 14:41:18 +0200 Subject: [PATCH 100/939] removed pugixml header only --- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index 1e32278858c5..1cf51118427d 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -9,21 +9,24 @@ description = "pugixml is a light-weight C++ XML processing library" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://github.com/zeux/%(name)s/archive/'] +source_urls = ['https://github.com/zeux/pugixml/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['%(name)s-%(version_major_minor)s.4_pugixml_remove_headeronly.patch'] +checksums = ['1e28ab24b6e04e013d96f45d25e9f2d04c921dc68c613fd010ecaaad3892c14d'] builddependencies = [ ('binutils', '2.38'), ('CMake', '3.23.1'), ] -configopts = "-DBUILD_SHARED_AND_STATIC_LIBS=ON -DPUGIXML_HEADER_ONLY=True " - +configopts = " ".join([ + "-DBUILD_SHARED_LIBS=ON", + "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", +]) sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], + 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'dirs': ['lib/cmake/pugixml'], } moduleclass = 'data' From 5b9ad1f5ecd5dae77dcbc1b351f87b3174e93b9b Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 28 Sep 2022 16:30:17 +0200 Subject: [PATCH 101/939] adding easyconfigs: netCDF-4.9.0-iimpi-2022a.eb, netcdf4-python-1.6.1-foss-2022a.eb, netcdf4-python-1.6.1-intel-2022a.eb, xarray-2022.6.0-foss-2022a.eb, xarray-2022.6.0-intel-2022a.eb, ArviZ-0.12.1-foss-2022a.eb, ArviZ-0.12.1-intel-2022a.eb --- .../a/ArviZ/ArviZ-0.12.1-foss-2022a.eb | 34 +++++++++++++ .../a/ArviZ/ArviZ-0.12.1-intel-2022a.eb | 34 +++++++++++++ .../n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 50 ++++++++++++++++++ .../netcdf4-python-1.6.1-foss-2022a.eb | 51 +++++++++++++++++++ .../netcdf4-python-1.6.1-intel-2022a.eb | 51 +++++++++++++++++++ .../x/xarray/xarray-2022.6.0-foss-2022a.eb | 25 +++++++++ .../x/xarray/xarray-2022.6.0-intel-2022a.eb | 25 +++++++++ 7 files changed, 270 insertions(+) create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb new file mode 100644 index 000000000000..bc9c93cbf77a --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.12.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.6.0'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.3.0', { + 'checksums': ['81217c145218479327469f1669f34763b7e149ed6789fd596cc90ff2d772098e'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['57d80eacc51909f18e6ab63c96a6b02227c3b077c5ffa406d5f4dabe03b8f019'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb new file mode 100644 index 000000000000..ac8ac445dc2a --- /dev/null +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'ArviZ' +version = '0.12.1' + +homepage = 'https://github.com/arviz-devs/arviz' +description = "Exploratory analysis of Bayesian models with Python" + +toolchain = {'name': 'intel', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy, scipy, pandas + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.6.0'), + ('matplotlib', '3.5.2'), +] + +download_dep_fail = True +use_pip = True + +exts_list = [ + ('xarray-einstats', '0.3.0', { + 'checksums': ['81217c145218479327469f1669f34763b7e149ed6789fd596cc90ff2d772098e'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['57d80eacc51909f18e6ab63c96a6b02227c3b077c5ffa406d5f4dabe03b8f019'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb new file mode 100644 index 000000000000..182023f46912 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -0,0 +1,50 @@ +name = 'netCDF' +version = '4.9.0' + +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': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/netcdf-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = [ + 'netCDF-%(version)s_fix-lib-name.patch', + 'netCDF-%(version)s_fix-linking-errors.patch', + 'netCDF-%(version)s_skip-nasa-test.patch', +] +checksums = [ + '9f4cb864f3ab54adb75409984c6202323d2fc66c003e5308f3cdf224ed41c0a6', # v4.9.0.tar.gz + 'ed45ae6c49cf8dcddaadef4c5cf403049bf3f761187413d7b03754d319345d6a', # netCDF-4.9.0_fix-lib-name.patch + '2b9579c149579d137eb16ae5d790787774033dcec49c0d4993d9859f224e7b15', # netCDF-4.9.0_fix-linking-errors.patch + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a', # netCDF-4.9.0_skip-nasa-test.patch +] + +builddependencies = [ + ('Autotools', '20220317'), + ('CMake', '3.23.1'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('HDF5', '1.12.2'), + ('cURL', '7.83.0'), + ('Szip', '2.1.1'), + ('zstd', '1.5.2'), +] + +# make sure both static and shared libs are built +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' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb new file mode 100644 index 000000000000..e4909b8b62d2 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +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'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +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' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb new file mode 100644 index 000000000000..60eb9cd8eefd --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.6.1' + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = """Python/numpy interface to netCDF.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('netCDF', '4.9.0'), + ('cURL', '7.83.0'), +] + +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'], + 'source_tmpl': 'netCDF4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz + # netcdf4-python-1.1.8-avoid-diskless-test.patch + 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + ], + }), +] + +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' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb new file mode 100644 index 000000000000..6b557c9ef71c --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '2022.6.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1028d198493f66bb15bd35dcfdd11defd831cbee3af6589fff16f41bddd67e84'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb new file mode 100644 index 000000000000..a0756e083cc8 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.6.0-intel-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'xarray' +version = '2022.6.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['1028d198493f66bb15bd35dcfdd11defd831cbee3af6589fff16f41bddd67e84'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # required for numpy, pandas +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'data' From de07c62b780e3c92d11971d7c9473b743f802846 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Wed, 28 Sep 2022 16:51:44 +0200 Subject: [PATCH 102/939] ArviZ v0.12.1 - Remove download_dep_fail --- easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb | 1 - easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb index bc9c93cbf77a..12bc8838f20e 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-foss-2022a.eb @@ -16,7 +16,6 @@ dependencies = [ ('matplotlib', '3.5.2'), ] -download_dep_fail = True use_pip = True exts_list = [ diff --git a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb index ac8ac445dc2a..365dbb5575c0 100644 --- a/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb +++ b/easybuild/easyconfigs/a/ArviZ/ArviZ-0.12.1-intel-2022a.eb @@ -16,7 +16,6 @@ dependencies = [ ('matplotlib', '3.5.2'), ] -download_dep_fail = True use_pip = True exts_list = [ From de74f8c244d5bd864c589857e93aee80f2293ff5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 29 Sep 2022 14:47:44 +0200 Subject: [PATCH 103/939] adding easyconfigs: Infernal-1.1.4-foss-2021a.eb --- .../i/Infernal/Infernal-1.1.4-foss-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb new file mode 100644 index 000000000000..2f490f5de246 --- /dev/null +++ b/easybuild/easyconfigs/i/Infernal/Infernal-1.1.4-foss-2021a.eb @@ -0,0 +1,40 @@ +## +# 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:: BSD +# Updated:: Denis Kristak (INUITS) +# Updated:: Sebastien Moretti (SIB) +# $Id$ +# +# 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 = 'Infernal' +version = "1.1.4" + +homepage = 'http://eddylab.org/infernal/' +description = """Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases + for RNA structure and sequence similarities.""" + +toolchain = {'name': 'foss', 'version': '2021a'} +toolchainopts = {'pic': True} + +source_urls = ['http://eddylab.org/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f9493c7dee9fbf25f6405706818883d24b9f5e455121a0662c96c8f0307f95fc'] + +local_bins = ['align', 'build', 'calibrate', 'convert', 'emit', 'fetch', 'press', 'scan', 'search', 'stat'] + +sanity_check_paths = { + 'files': ['bin/cm%s' % x for x in local_bins], + 'dirs': [] +} + +sanity_check_commands = ['cm%s -h' % x for x in local_bins] + +moduleclass = 'bio' From 7b72fe8a83006b85204350f18210a0212627a9b7 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 29 Sep 2022 17:25:19 +0200 Subject: [PATCH 104/939] DCMTK added hash, pugixml fixed E121 --- .../d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 13 +++---------- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 13 +++++++++---- 2 files changed, 12 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb index 6bffa6ad7b90..5d7107ed0910 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -15,6 +15,7 @@ local_stripped_version = version.replace('.', '') source_urls = ['https://dicom.offis.de/download/%(namelower)s/dcmtk{}/'.format(local_stripped_version)] sources = [SOURCELOWER_TAR_GZ] +checksums = ['7c58298e3e8d60232ee6fc8408cfadd14463cc11a3c4ca4c59af5988c7e9710a'] builddependencies = [ ('binutils', '2.38'), @@ -40,17 +41,9 @@ sanity_check_paths = { 'dirs': ['lib'], } +local_test_modules = ['dcmdata', 'dcmect', 'dcmfg', 'dcmiod', 'dcmnet', 'dcmrt', 'dcmseg', 'dcmsr', 'dcmtls', 'ofstd'] sanity_check_commands = [ - 'dcmdata_tests | grep " 0 failed"', - 'dcmect_tests | grep " 0 failed"', - 'dcmfg_tests | grep " 0 failed"', - 'dcmiod_tests | grep " 0 failed"', - 'dcmnet_tests | grep " 0 failed"', - 'dcmrt_tests | grep " 0 failed"', - 'dcmseg_tests | grep " 0 failed"', - 'dcmsr_tests | grep " 0 failed"', - 'dcmtls_tests | grep " 0 failed"', - 'ofstd_tests | grep " 0 failed"', + '%s_tests | grep " 0 failed"' % s for s in local_test_modules ] moduleclass = 'data' diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index 1cf51118427d..c171baaaab17 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -19,13 +19,18 @@ builddependencies = [ ] configopts = " ".join([ - "-DBUILD_SHARED_LIBS=ON", - "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", + "-DBUILD_SHARED_LIBS=ON", + "-DPUGIXML_BUILD_SHARED_AND_STATIC_LIBS=ON", ]) sanity_check_paths = { - 'files': ['include/pugiconfig.hpp', 'include/pugixml.hpp', 'lib/libpugixml.a', - 'lib/libpugixml.%s' % SHLIB_EXT, 'lib/pkgconfig/pugixml.pc'], + 'files': [ + 'include/pugiconfig.hpp', + 'include/pugixml.hpp', + 'lib/libpugixml.a', + 'lib/libpugixml.%s' % SHLIB_EXT, + 'lib/pkgconfig/pugixml.pc' + ], 'dirs': ['lib/cmake/pugixml'], } From e04259dadf79a42c8eb92e006130a636c36a9d7d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:12:26 +0200 Subject: [PATCH 105/939] Add back the authors info --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) 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 caccb37e4987..1a8eb57f3612 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 @@ -1,3 +1,8 @@ +# 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' From ce120776e83ff72e910fe540daa623fb18724fdd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 12:46:17 +0200 Subject: [PATCH 106/939] Restore sanity check command --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) 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 1a8eb57f3612..8c3b14ced525 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 @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : 2.0.6'"] + moduleclass = 'data' From dafb1e51c4a19b002095a72e5d064316e21e0966 Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 3 Oct 2022 13:37:01 +0200 Subject: [PATCH 107/939] Update easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb Co-authored-by: Sam Moors --- easybuild/easyconfigs/c/CDO/CDO-2.0.6-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 8c3b14ced525..2cca13754df1 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 @@ -48,6 +48,6 @@ sanity_check_paths = { 'dirs': ['include'], } -sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : 2.0.6'"] +sanity_check_commands = ["cdo --version 2>&1 | grep 'CDI library version : %(version)s'"] moduleclass = 'data' From 4356dc7b95e3473949f09e4ff7ce4df472f6a203 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 3 Oct 2022 14:02:15 +0200 Subject: [PATCH 108/939] adding easyconfigs: bcl-convert-4.0.3-2el7.x86_64.eb --- .../bcl-convert-4.0.3-2el7.x86_64.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb diff --git a/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb new file mode 100644 index 000000000000..e06bf2fdde60 --- /dev/null +++ b/easybuild/easyconfigs/b/bcl-convert/bcl-convert-4.0.3-2el7.x86_64.eb @@ -0,0 +1,24 @@ +easyblock = 'Rpm' + +name = 'bcl-convert' +version = '4.0.3-2' +versionsuffix = 'el7.x86_64' + +homepage = 'https://support.illumina.com/sequencing/sequencing_software/bcl-convert.html' +description = """The Illumina BCL Convert v4.0 is a standalone local software app that converts the + Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files.""" + +toolchain = SYSTEM + +source_urls = ['https://webdata.illumina.com/downloads/software/bcl-convert/'] +sources = ['bcl-convert-%(version)s.%(versionsuffix)s.rpm'] +checksums = ['be4f3d1d31cb36618f909cdbc0ed0fe70ef57a645e46b421b6e1a7f90c6c9430'] + +sanity_check_paths = { + 'files': ['usr/bin/bcl-convert'], + 'dirs': [], +} + +sanity_check_commands = ["bcl-convert --help"] + +moduleclass = 'bio' From b0544535e41fc941a6399e244680c6c0c1ed65cb Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 3 Oct 2022 15:53:32 +0200 Subject: [PATCH 109/939] Add libaec as a dependency --- easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb index 742bdb55b84d..1f313a6f013a 100644 --- a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.27.0-gompi-2022a.eb @@ -23,6 +23,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ('libpng', '1.6.37'), ('zlib', '1.2.12'), + ('libaec', '1.0.6'), ] # Python bindings are provided by a separate package 'eccodes-python' From bf8be24d19496c1f0fcc0765ea4c78c400748ae2 Mon Sep 17 00:00:00 2001 From: satishk Date: Tue, 4 Oct 2022 12:43:48 +0200 Subject: [PATCH 110/939] adding easyconfigs: PETSc-3.17.4-foss-2022a.eb --- .../p/PETSc/PETSc-3.17.4-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb new file mode 100644 index 000000000000..058019a15f9a --- /dev/null +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb @@ -0,0 +1,51 @@ +## +# Author: Robert Mijakovic +# Author: Jasper Grimm (UoY) +## +name = 'PETSc' +version = '3.17.4' + +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': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True, 'pic': True} + +source_urls = [ + 'https://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', + 'ftp://ftp.mcs.anl.gov/pub/petsc/release-snapshots/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'PETSc_ranlib-fix.patch', +] +checksums = [ + '99c127486722a3ffd95a268b4ceb0976cbf217926c681a9631bd7246eab8cb2a', # petsc-3.17.4.tar.gz + '64cf9d5008d5e92117e65bdec5316d991b6a6b8c8ecf7ea46eb790a498266297', # PETSc_ranlib-fix.patch +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Boost', '1.79.0'), + ('METIS', '5.1.0'), + ('SCOTCH', '7.0.1'), + ('MUMPS', '5.5.1', '-metis'), + ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), + ('Hypre', '2.25.0'), +] + +# enabling --with-mpi4py seems to be totally broken, leads to make errors like: +# No rule to make target 'mpi4py-build' +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' From d877bb14838740f7a6be1a636077463a8d5f2a34 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 5 Oct 2022 17:09:00 +0200 Subject: [PATCH 111/939] adding easyconfigs: openpyxl-3.0.10-GCCcore-11.3.0.eb --- .../openpyxl-3.0.10-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..bc8a63f9df38 --- /dev/null +++ b/easybuild/easyconfigs/o/openpyxl/openpyxl-3.0.10-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'openpyxl' +version = '3.0.10' + +homepage = 'https://openpyxl.readthedocs.io' +description = "A Python library to read/write Excel 2010 xlsx/xlsm files" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('lxml', '4.9.1'), + ('Pillow', '9.1.1'), +] + +use_pip = True + +exts_list = [ + ('et_xmlfile', '1.1.0', { + 'checksums': ['8eb9e2bc2f8c97e37a2dc85a09ecdcdec9d8a396530a6d5a33b30b9a92da0c5c'], + }), + ('jdcal', '1.4.1', { + 'checksums': ['472872e096eb8df219c23f2689fc336668bdb43d194094b5cc1707e1640acfc8'], + }), + (name, version, { + 'checksums': ['e47805627aebcf860edb4edf7987b1309c1b3632f3750538ed962bbcc3bd7449'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From e85a350aeb28ba6501b4f5674430b996de6120e7 Mon Sep 17 00:00:00 2001 From: robogast Date: Thu, 6 Oct 2022 16:09:16 +0200 Subject: [PATCH 112/939] moved OpenJPEG dep to PR #16276 --- .../OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb deleted file mode 100644 index 6c76dae7c5db..000000000000 --- a/easybuild/easyconfigs/o/OpenJPEG/OpenJPEG-2.5.0-GCCcore-11.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -# easybuild easyconfig -# -# John Dey jfdey@fredhutch.org -# -# Fred Hutchenson Cancer Research Center Seattle WA -easyblock = 'CMakeMake' - -name = 'OpenJPEG' -version = '2.5.0' - -homepage = 'https://www.openjpeg.org/' -description = """OpenJPEG is an open-source JPEG 2000 codec written in - C language. It has been developed in order to promote the use of JPEG 2000, - a still-image compression standard from the Joint Photographic Experts Group - (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as - a JPEG 2000 Reference Software.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/uclouvain/%(namelower)s/archive'] -sources = ['v%(version)s.tar.gz'] -checksums = ['0333806d6adecc6f7a91243b2b839ff4d2053823634d4f6ed7a59bc87409122a'] - -builddependencies = [ - ('binutils', '2.38'), - ('CMake', '3.23.1'), -] -# for running the binary of openjpeg like opj_compress you need the libraries like zlib etc. -dependencies = [ - ('zlib', '1.2.12'), - ('libpng', '1.6.37'), - ('LibTIFF', '4.3.0'), -] - -sanity_check_paths = { - 'files': [ - 'bin/opj_compress', - 'bin/opj_decompress', - 'bin/opj_dump', - 'include/openjpeg-%(version_major)s.%(version_minor)s/openjpeg.h', - 'lib/libopenjp2.%s' % SHLIB_EXT - ], - 'dirs': ['bin', 'include', 'lib'], -} - -moduleclass = 'lib' From 903cb2de9cc708dac83ba7a5cfc85726d10660a9 Mon Sep 17 00:00:00 2001 From: rocky_build Date: Thu, 6 Oct 2022 14:51:34 -0400 Subject: [PATCH 113/939] adding easyconfigs: ncbi-vdb-3.0.0-gompi-2022a.eb --- .../f/file/file-5.43-GCCcore-11.3.0.eb | 28 +++++++++ .../h/HDF5/HDF5-1.10.8-gompi-2022a.eb | 28 +++++++++ .../n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb | 58 +++++++++++++++++++ 3 files changed, 114 insertions(+) create mode 100644 easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1128c37d6ac6 --- /dev/null +++ b/easybuild/easyconfigs/f/file/file-5.43-GCCcore-11.3.0.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': '11.3.0'} + +source_urls = ['ftp://ftp.astron.com/pub/file/'] +sources = [SOURCE_TAR_GZ] +checksums = ['8c8015e91ae0e8d0321d94c78239892ef9dbc70c4ade0008c0e95894abfb1991'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), +] + +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/h/HDF5/HDF5-1.10.8-gompi-2022a.eb b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb new file mode 100644 index 000000000000..3091b947d74a --- /dev/null +++ b/easybuild/easyconfigs/h/HDF5/HDF5-1.10.8-gompi-2022a.eb @@ -0,0 +1,28 @@ +# Updated to version 1.10.8, needed for HISAT2-2.2.1 +# J. Sassmannshausen + +name = 'HDF5' +version = '1.10.8' + +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': '2022a'} +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_BZ2] +checksums = ['66ec544b195a4cb9f6ffed034fd82e52429d6112747c2996ab69853f606e546b'] + +dependencies = [ + ('zlib', '1.2.12'), + ('Szip', '2.1.1'), +] + +# needed to build HL-tools: gif2h5 gif2h5 and h5watch +# beware that gif tools are affected by multiple CVEs: CVE-2018-17433, CVE-2018-17436, CVE-2020-10809 +# configopts = "--enable-hltools" + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb new file mode 100644 index 000000000000..b02b422d181a --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-3.0.0-gompi-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'CMakeMake' + +name = 'ncbi-vdb' +version = '3.0.0' + +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': '2022a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = [ + 'ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch', + 'ncbi-vdb-cstdlib.patch', +] +checksums = [ + '154317ef265104861fe8d3d2e439939ae98f33b1e28da3c45f32ae8534dbfad7', # ncbi-vdb-3.0.0.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch + 'db3d563262ca9b14e7b9a94a0be6683a9eef41a498c9c064aa05c2a6785f1655', # ncbi-vdb-cstdlib.patch +] + +builddependencies = [ + ('Perl', '5.34.1', '-minimal'), + ('Python', '3.10.4', '-bare'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('file', '5.43'), # provides libmagic + ('HDF5', '1.10.8'), # version 1.12.x has changes to API and is not compatible + ('libxml2', '2.9.13'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/'" +preconfigopts += " %(builddir)s/%(namelower)s-%(version)s/setup/konfigure.perl &&" + +configopts = '' +configopts += ' -DHDF5_LIBDIR=$EBROOTHDF5/lib -DXML2_LIBDIR=$EBROOTLIBXML2/lib' +configopts += ' -DHDF5_INCDIR=$EBROOTHDF5/include -DXML2_INCDIR=$EBROOTLIBXML2/include' + + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find %(builddir)s/%(namelower)s-%(version)s/build/ -name \"Makefile*\" " +prebuildopts += "-exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': [('lib/libncbi-%s.%s' % (k, e), 'lib64/libncbi-%s.%s' % (k, e)) + for k in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From 1937a12077392134a19cea2b599cfb54d0c864a3 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 12 Oct 2022 14:12:56 +0100 Subject: [PATCH 114/939] adding easyconfigs: DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 68 +++++++++++++++++++ 1 file changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..1d6063dbbd94 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,68 @@ +# Loosely based on PR #7680 +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'DeepLabCut' +version = '2.2.0.6' +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': '2021a'} +toolchainopts = {'pic': True} + +dependencies = [ + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('Python', '3.9.5'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), + ('TensorFlow', '2.6.0', versionsuffix), + ('PyYAML', '5.4.1'), + ('PyTables', '3.6.1'), + ('wxPython', '4.1.1'), + ('OpenCV', '4.5.3', local_version), + ('numba', '0.53.1'), + ('libyaml', '0.2.5'), + ('imgaug', '0.4.0', versionsuffix), + ('tqdm', '4.61.2'), + ('ruamel.yaml', '0.17.21'), + ('PyYAML', '5.4.1'), + ('statsmodels', '0.12.2'), + ('PyTorch', '1.10.0', versionsuffix), +] + +use_pip = True + +exts_list = [ + ('filterpy', '1.4.5', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], + }), + ('pandas', '1.3.3', { + 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], + }), + ('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'], + }), + ('msgpack-numpy', '0.4.8', { + 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], + 'sources': ['msgpack-numpy-0.4.8.tar.gz'], + }), + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + }), +] + +moduleclass = 'lib' From d3779ab7745e23d7fa84a8e26923c1bf3ea3fe97 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 13 Oct 2022 13:09:54 +0200 Subject: [PATCH 115/939] Update QIIME2-2022.8.eb --- easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb index 30c12abc3c2e..ecd065061276 100644 --- a/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb +++ b/easybuild/easyconfigs/q/QIIME2/QIIME2-2022.8.eb @@ -13,7 +13,7 @@ description = """QIIME is an open-source bioinformatics pipeline for performing source_urls = ['https://data.qiime2.org/distro/core/'] sources = ['qiime2-%(version)s-py38-linux-conda.yml'] -checksums = ['454bb219f928c7f4ec0097888db27ab439ba2ef7e4294f38b7033327cb3dafb8'] +checksums = ['e43bffad08dfd8ab9054f1530e501258525a7b9a3f3079ac04fad701d797c90b'] toolchain = SYSTEM From fce73ff22f18fc49d84d1a7493d29a9d36eb0324 Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 13 Oct 2022 16:40:09 +0100 Subject: [PATCH 116/939] True changed to SYSTEM --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 1d6063dbbd94..086b4db09131 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -15,8 +15,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), From 1ba6b33dbd674864db989db72bcaa032a87f39de Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 13 Oct 2022 17:49:45 +0100 Subject: [PATCH 117/939] True replaced with SYSTEM --- easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb index 8bc5d81d9226..a22e3ec40930 100644 --- a/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb +++ b/easybuild/easyconfigs/o/Octave/Octave-7.1.0-foss-2021b.eb @@ -36,7 +36,7 @@ dependencies = [ ('GLPK', '5.0'), ('GL2PS', '1.4.2'), ('gnuplot', '5.4.2'), - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('zlib', '1.2.11'), ('Mesa', '21.1.7'), ('libGLU', '9.0.2'), From bf2fc71d7727c27bd735dc3c8d240b2996a91498 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 09:48:18 +0100 Subject: [PATCH 118/939] pandas removed as already in SciPy-bundle --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 086b4db09131..26c7449b3c69 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -44,9 +44,6 @@ exts_list = [ 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['4f2a4d39e4ea601b9ab42b2db08b5918a9538c168cff1c6895ae26646f3d73b1'], }), - ('pandas', '1.3.3', { - 'checksums': ['272c8cb14aa9793eada6b1ebe81994616e647b5892a370c7135efb2924b701df'], - }), ('tensorpack', '0.11', { 'checksums': ['022b610e416e62e3575424cd08e60af27808a5fb6914294615391caf582cbd4f'], }), From c282fb2ec3b963795ecbc29b12ecfb2e759a60ab Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 25 Jul 2022 09:15:03 +0200 Subject: [PATCH 119/939] Fix PyTorch 1.10.0 build on PPC --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 53 +++++--- .../p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 47 ++++--- .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 53 +++++--- ...ch-1.10.0_add-dummy-bfloat16-for-ppc.patch | 116 ++++++++++++++++++ ...> PyTorch-1.10.0_fix-faulty-asserts.patch} | 21 +--- ...orch-1.10.0_fix-missing-VSX-dispatch.patch | 26 ++++ ...rch-1.10.0_remove-vec-dump-functions.patch | 114 +++++++++++++++++ 7 files changed, 356 insertions(+), 74 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch rename easybuild/easyconfigs/p/PyTorch/{PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch => PyTorch-1.10.0_fix-faulty-asserts.patch} (88%) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index 3dedead0354d..fbed10499470 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -8,15 +8,9 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', @@ -24,18 +18,25 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', - 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -45,24 +46,38 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', - # PyTorch-1.10.0_skip_cmake_rpath.patch - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index c05632ab43ff..27db7713d1db 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -7,32 +7,33 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'foss', 'version': '2021a'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', 'PyTorch-1.7.1_correctly-pass-jit_opt_level.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -41,22 +42,36 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 938b94c4f938..450db866c3a4 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -7,15 +7,9 @@ PyTorch is a deep learning framework that puts Python first.""" toolchain = {'name': 'fosscuda', 'version': '2020b'} -sources = [{ - 'filename': '%(name)s-%(version)s.tar.gz', - 'git_config': { - 'url': 'https://github.com/pytorch', - 'repo_name': 'pytorch', - 'tag': 'v%(version)s', - 'recursive': True, - }, -}] +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', @@ -23,18 +17,25 @@ patches = [ 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.8.1_increase-distributed-test-timeout.patch', 'PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch', - 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', - 'PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch', + 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', 'PyTorch-1.10.0_fix-vnni-detection.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_fix-XNNPACK-tests.patch', 'PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch', + 'PyTorch-1.10.0_remove-vec-dump-functions.patch', + 'PyTorch-1.10.0_skip_cmake_rpath.patch', 'PyTorch-1.10.0_skip_failing_ops_tests.patch', 'PyTorch-1.10.0_skip_nan_tests_openblas.patch', - 'PyTorch-1.10.0_skip_cmake_rpath.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', ] checksums = [ - None, # can't add proper SHA256 checksum, because source tarball is created locally after recursive 'git clone' + '1970225700d1f9791eb553855ad3c22e7c9fd69cff2765d532506b33e449831e', # pytorch-v1.10.0.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch # PyTorch-1.7.1_correctly-pass-jit_opt_level.patch @@ -44,24 +45,38 @@ checksums = [ '7a6e512274f0b8673f4f207a5bc53387d88be7e79833f42d20365668b2118071', # PyTorch-1.9.0_limit-world-size-for-zero-redundancy-opt-test.patch 'ff573660913ce055e24cfd194ce747ba5685091c631cfd443eae2a99d56b57ea', - # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch - '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch + '0c8bf4b284c5c2cb4d175645d44bed674cca5218de741a8ea698cef2884a86da', # PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', - # PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch - '67152215e4530a9b1d7349fb20864445fd815288f04ab9e96e45c73b2d87827a', + # PyTorch-1.10.0_fix-faulty-asserts.patch + '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch + '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch '51f83f5d5ef69656ef35b73f17e0671e70113798421be11ea4c7b56ffcc4da03', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', # PyTorch-1.10.0_fix-vnni-detection.patch '1f3664c0febfa2a3fc4c0cd3bae185f289716ac0b6c3d7e8fa1cee19ba62b7cc', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_fix-XNNPACK-tests.patch + 'd3e749a2a42efce463e3b8a1aebb21f0edf2256682c4417297d9a44a6210e5f8', # PyTorch-1.10.0_increase_zero_optimizer_test_tolerance.patch 'e65afb01786f7f030ccb5faada1eb474bb0c418bcadcf1baaa71a4fa2f3f4240', + # PyTorch-1.10.0_remove-vec-dump-functions.patch + '5e796c83f74e77aa193fef2720a7a41e3e0eb39df726a6f0a2a1c55d37d8fcc8', + # PyTorch-1.10.0_skip_cmake_rpath.patch + 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', # PyTorch-1.10.0_skip_failing_ops_tests.patch '399af94ffcef4a6db5226552c46f11e9b0f0f371b2d7924b9e5764d2281581ab', # PyTorch-1.10.0_skip_nan_tests_openblas.patch '7d3f83e3056d9e47a460790313238f28708beb596cafaa7ae55e374d368bbedf', - # PyTorch-1.10.0_skip_cmake_rpath.patch - 'ac05943bb205623f91ef140aa00869efc5fe844184bd666bebf5405808610448', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch new file mode 100644 index 000000000000..8e74d538e621 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch @@ -0,0 +1,116 @@ +Fix missing `vec_scalar_t` on PPC during compilation. + +From https://github.com/pytorch/pytorch/pull/67331 + +From: Nikita Shulga +Date: Wed, 27 Oct 2021 08:04:08 -0700 +Subject: [PATCH] Add dummy bfloat16 VSX implementation + +Just a copy of DEFAULT bfloat16 implementation and revert restriction +introduced by https://github.com/pytorch/pytorch/pull/61630 + +Fixes https://github.com/pytorch/pytorch/issues/66867 and https://github.com/pytorch/pytorch/issues/62016 +--- + aten/src/ATen/cpu/vec/functional.h | 2 - + .../cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h | 54 +++++++++++++++++++ + .../cpu/vec/vec256/vsx/vec256_common_vsx.h | 6 +++ + 3 files changed, 60 insertions(+), 2 deletions(-) + create mode 100644 aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h + +diff --git a/aten/src/ATen/cpu/vec/functional.h b/aten/src/ATen/cpu/vec/functional.h +index 210ae9e9e883..388b3170d5b5 100644 +--- a/aten/src/ATen/cpu/vec/functional.h ++++ b/aten/src/ATen/cpu/vec/functional.h +@@ -1,6 +1,4 @@ + #pragma once + + #include +-#if !defined(__VSX__) || !defined(CPU_CAPABILITY_VSX) + #include +-#endif +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h +new file mode 100644 +index 000000000000..ee8ca997a20e +--- /dev/null ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_bfloat16_vsx.h +@@ -0,0 +1,54 @@ ++#pragma once ++ ++#include ++#include ++#include ++namespace at { ++namespace vec { ++// See Note [Acceptable use of anonymous namespace in header] ++namespace { ++ ++inline std::tuple, Vectorized> convert_bfloat16_float( ++ const Vectorized& a) { ++ constexpr int64_t K = Vectorized::size(); ++ __at_align__ float arr[K]; ++ __at_align__ BFloat16 arr2[K]; ++ a.store(arr2); ++ convert(arr2, arr, K); ++ return std::make_tuple( ++ Vectorized::loadu(arr), ++ Vectorized::loadu(arr + Vectorized::size())); ++} ++ ++inline Vectorized convert_float_bfloat16( ++ const Vectorized& a, ++ const Vectorized& b) { ++ constexpr int64_t K = Vectorized::size(); ++ __at_align__ float arr[K]; ++ __at_align__ BFloat16 arr2[K]; ++ a.store(arr); ++ b.store(arr + Vectorized::size()); ++ convert(arr, arr2, K); ++ return Vectorized::loadu(arr2); ++} ++ ++void load_fp32_from_bf16(const c10::BFloat16* data, Vectorized& out) { ++ __at_align__ float values[Vectorized::size()]; ++ for (int k = 0; k < Vectorized::size(); ++k) { ++ values[k] = data[k]; ++ } ++ out = Vectorized::loadu(values); ++} ++ ++C10_UNUSED void load_fp32_from_bf16( ++ const c10::BFloat16* data, ++ Vectorized& out1, ++ Vectorized& out2) { ++ load_fp32_from_bf16(data, out1); ++ data += Vectorized::size(); ++ load_fp32_from_bf16(data, out2); ++} ++ ++} // namespace ++} // namespace vec ++} // namespace at +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h +index 3d798a7f6268..b06f6a4bd1b5 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_common_vsx.h +@@ -3,6 +3,8 @@ + #include + #include + #include ++ ++// Note: header order is important here + #include + #include + #include +@@ -11,8 +13,12 @@ + #include + #include + #include ++ + #include + #include ++ ++#include ++ + namespace at { + namespace vec { + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch similarity index 88% rename from easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch rename to easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch index eab07090d2ab..1ba71564df77 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts-and-skip-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-faulty-asserts.patch @@ -1,6 +1,6 @@ From: Alexander Grund Date: Tue, 18 May 2021 15:08:41 +0200 -Subject: [PATCH 1/2] Fix usage of TORCH_INTERNAL_ASSERT with message +Subject: Fix usage of TORCH_INTERNAL_ASSERT with message Using only a string as the argument for TORCH_INTERNAL_ASSERT will never trigger a failure as a string is always a truethy value. @@ -8,11 +8,6 @@ This hides actual bugs and makes users and devs think all worked while it did not. Change to use TORCH_INTERNAL_ASSERT(false, "msg") -Subject: [PATCH 2/2] Add missing skip decorator for -test_preserve_bundled_inputs_methods - -This test uses optimize_for_mobile which requires NNPACK to work - diff --git a/aten/src/ATen/native/BinaryOps.cpp b/aten/src/ATen/native/BinaryOps.cpp index c4edadb03e..e889cd03a8 100644 --- a/aten/src/ATen/native/BinaryOps.cpp @@ -83,20 +78,6 @@ index 6de646acfe..66341c959d 100644 } for (int i = num_output_channels; i < num_output_channels_padded; ++i) { weight_scales_data[i] = 1.f; -diff --git a/test/test_mobile_optimizer.py b/test/test_mobile_optimizer.py -index 11ef019a26..7b5ac1a239 100644 ---- a/test/test_mobile_optimizer.py -+++ b/test/test_mobile_optimizer.py -@@ -269,6 +269,9 @@ class TestOptimizer(TestCase): - bi_module_lint_list = generate_mobile_module_lints(bi_module) - self.assertEqual(len(bi_module_lint_list), 0) - -+ @unittest.skipUnless(torch.backends.xnnpack.enabled, -+ " XNNPACK must be enabled for these tests." -+ " Please build with USE_XNNPACK=1.") - def test_preserve_bundled_inputs_methods(self): - class MyBundledInputModule(torch.nn.Module): - def __init__(self): diff --git a/torch/csrc/jit/api/module.cpp b/torch/csrc/jit/api/module.cpp index 38592b80b9..8f9508321b 100644 --- a/torch/csrc/jit/api/module.cpp diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch new file mode 100644 index 000000000000..dcc0eac4bf06 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-missing-VSX-dispatch.patch @@ -0,0 +1,26 @@ + +Fix for following error on PPC: +> undefined reference to `at::native::DispatchStub, c10::ArrayRef, c10::ArrayRef, void const*, c10::ArrayRef, void*), at::native::fft_fill_with_conjugate_symmetry_stub>::VSX' + +From https://github.com/pytorch/pytorch/pull/68914 + +From: Deepali Chourasia +Date: Thu, 25 Nov 2021 12:29:50 +0000 +Subject: [PATCH] add VSX dispatch for fft_fill_with_conjugate_symmetry_stub + +--- + aten/src/ATen/native/mkl/SpectralOps.cpp | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/aten/src/ATen/native/mkl/SpectralOps.cpp b/aten/src/ATen/native/mkl/SpectralOps.cpp +index 0625110a04ff..2bd05ca19cac 100644 +--- a/aten/src/ATen/native/mkl/SpectralOps.cpp ++++ b/aten/src/ATen/native/mkl/SpectralOps.cpp +@@ -151,6 +151,7 @@ static void _fft_fill_with_conjugate_symmetry_cpu_( + REGISTER_ARCH_DISPATCH(fft_fill_with_conjugate_symmetry_stub, DEFAULT, &_fft_fill_with_conjugate_symmetry_cpu_) + REGISTER_AVX2_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) + REGISTER_AVX512_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) ++REGISTER_VSX_DISPATCH(fft_fill_with_conjugate_symmetry_stub, &_fft_fill_with_conjugate_symmetry_cpu_) + + // _out variants can be shared between PocketFFT and MKL + Tensor& _fft_r2c_mkl_out(const Tensor& self, IntArrayRef dim, int64_t normalization, diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch new file mode 100644 index 000000000000..b6e2100a1789 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_remove-vec-dump-functions.patch @@ -0,0 +1,114 @@ +Fix compilation on PPC due to missing include + +From https://patch-diff.githubusercontent.com/raw/pytorch/pytorch/pull/66085 + +From e0fa15d188986e2a68973e3facf9d794f6cfc5df Mon Sep 17 00:00:00 2001 +From: Nikita Shulga +Date: Mon, 4 Oct 2021 09:26:37 -0700 +Subject: [PATCH] Remove unused `dump` method from VSX vec256 methods + +Follow up after https://github.com/pytorch/pytorch/pull/63533 + +Probably fixes https://github.com/pytorch/pytorch/issues/65956 +--- + .../ATen/cpu/vec/vec256/vsx/vec256_complex_double_vsx.h | 5 ----- + .../ATen/cpu/vec/vec256/vsx/vec256_complex_float_vsx.h | 8 -------- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h | 3 --- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h | 7 ------- + aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h | 9 --------- + 5 files changed, 32 deletions(-) + +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 888f2f0b932b..3a3e0daade09 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 +@@ -356,11 +356,6 @@ class Vectorized { + return {vec_sqrt(_vec0), vec_sqrt(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << std::endl; +- } +- + Vectorized sqrt() const { + return map(std::sqrt); + } +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 0aa726b9bfdd..712de24597dc 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 +@@ -144,7 +144,6 @@ class Vectorized { + // convert std::complex index mask to V index mask: xy -> xxyy + auto mask_complex = Vectorized( + vec_mergeh(mask._vec0, mask._vec0), vec_mergeh(mask._vec1, mask._vec1)); +- // mask_complex.dump(); + return { + vec_sel(a._vec0, b._vec0, mask_complex._vec0), + vec_sel(a._vec1, b._vec1, mask_complex._vec1), +@@ -409,13 +408,6 @@ class Vectorized { + return {vec_sqrt(_vec0), vec_sqrt(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec0[2] << "," +- << _vec0[3] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << "," << _vec1[2] << "," +- << _vec1[3] << std::endl; +- } +- + Vectorized sqrt() const { + return map(std::sqrt); + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +index 29616182fe12..0d5b5cb39384 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +@@ -188,9 +188,6 @@ class Vectorized { + } + const double& operator[](int idx) const = delete; + double& operator[](int idx) = delete; +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec1[0] << "," << _vec1[1] << std::endl; +- } + Vectorized map(double (*const f)(double)) const { + Vectorized ret; + for (int i = 0; i < size()/2; i++) { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 2427276bcea2..58d4b057b507 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -436,13 +436,6 @@ class Vectorized { + return {vec_neg(_vec0), vec_neg(_vec1)}; + } + +- void dump() const { +- std::cout << _vec0[0] << "," << _vec0[1] << "," << _vec0[2] << "," +- << _vec0[3] << ","; +- std::cout << _vec1[0] << "," << _vec1[1] << "," << _vec1[2] << "," +- << _vec1[3] << std::endl; +- } +- + Vectorized C10_ALWAYS_INLINE round() const { + return {vec_round(_vec0), vec_round(_vec1)}; + } +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +index c335ace0ced6..2482af6ec232 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_quint8_vsx.h +@@ -369,15 +369,6 @@ struct Vectorized { + return {vec0, vec1}; + } + +- void dump() const { +- value_type vals[size()]; +- store((void*)vals); +- for (int i = 0; i < size(); ++i) { +- std::cout << (int)(vals[i]) << " "; +- } +- std::cout << std::endl; +- } +- + DEFINE_MEMBER_OP(operator==, c10::quint8, vec_cmpeq) + DEFINE_MEMBER_OP(operator!=, c10::quint8, vec_cmpne) + DEFINE_MEMBER_OP(operator<, c10::quint8, vec_cmplt) From 642d33b48aae5ea6aef3a5ecebbcafa4e6fc8644 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Sep 2022 16:40:19 +0200 Subject: [PATCH 120/939] Fix FP16 quantization (fixes test_quantization) --- .../PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 ++ .../p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 3 ++ .../PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 ++ ...fix-fp16-quantization-without-fbgemm.patch | 43 +++++++++++++++++++ 4 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index fbed10499470..f16073d89568 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -52,6 +53,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index 27db7713d1db..20e9c720a352 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -19,6 +19,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -48,6 +49,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 450db866c3a4..412066dcf6f8 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -20,6 +20,7 @@ patches = [ 'PyTorch-1.10.0_add-dummy-bfloat16-for-ppc.patch', 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', + 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -51,6 +52,8 @@ checksums = [ '426c9ead1a74b656748d4c8bf8afd4303d8b9f2394ad22b21a845d07c8ca1d12', # PyTorch-1.10.0_fix-faulty-asserts.patch '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', + # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch + 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch new file mode 100644 index 000000000000..b62f757853f1 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch @@ -0,0 +1,43 @@ +From https://github.com/pytorch/pytorch/pull/84750 + +From d5480f56374e7612d4400e845b05bc3a4507d87c Mon Sep 17 00:00:00 2001 +From: Alexander Grund +Date: Fri, 9 Sep 2022 14:39:49 +0200 +Subject: [PATCH] Fix Use-after-Free in qembeddingbag_byte_prepack_out + +When FBGEMM is not used (either manually disabled or on platforms such +as POWER where it isn't supported at all) the fallback code requests a +`data_ptr` on a `Tensor` object returned by +`to(ScalarType::Float)` in the same line. This object will be destroyed +at the end of the line leading to a dangling pointer. + +On some platforms this manifests in wrong results being returned as the +memory gets overwritten. + +Fix this by binding the temporary object (or initial object) to a const +value reference which extents its lifetime and getting the `data_ptr` +from that. + +Fixes #84748 +--- + .../ATen/native/quantized/cpu/qembeddingbag_prepack.cpp | 7 ++++--- + 1 file changed, 4 insertions(+), 3 deletions(-) + +diff --git a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +index 614e274b54..6c04d0ae12 100644 +--- a/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp ++++ b/aten/src/ATen/native/quantized/cpu/qembeddingbag_prepack.cpp +@@ -242,9 +242,10 @@ Tensor& qembeddingbag_byte_prepack_out(Tensor& output, const Tensor& weight) { + } + + #else +- const auto weight_data = weight_contig->scalar_type() == at::ScalarType::Half +- ? weight_contig->to(at::ScalarType::Float).data_ptr() +- : weight_contig->data_ptr(); ++ const Tensor& float_weight = weight_contig->scalar_type() == at::ScalarType::Half ++ ? weight_contig->to(at::ScalarType::Float) ++ : *weight_contig; ++ const auto weight_data = float_weight.data_ptr(); + constexpr float kEpsilon = 1e-8f; + for (auto row: c10::irange(embedding_rows)) { + const float* input_row = weight_data + row * embedding_cols; From c1f6e508906b9a59d2ce250b896d5b46474bd1c9 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 22 Sep 2022 11:04:57 +0200 Subject: [PATCH 121/939] Add PyTorch-1.10.0_fix-kineto-crash.patch --- .../p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb | 3 +++ easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb | 3 +++ .../easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb | 3 +++ 3 files changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb index f16073d89568..33304aa7d22f 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -22,6 +22,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -55,6 +56,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb index 20e9c720a352..208a35c065af 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-foss-2021a.eb @@ -20,6 +20,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -51,6 +52,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb index 412066dcf6f8..ffbf98f586c5 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.10.0-fosscuda-2020b.eb @@ -21,6 +21,7 @@ patches = [ 'PyTorch-1.10.0_fix-alias-violation-in-bitwise-ops.patch', 'PyTorch-1.10.0_fix-faulty-asserts.patch', 'PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-missing-VSX-dispatch.patch', 'PyTorch-1.10.0_fix-test-cond-cpu.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', @@ -54,6 +55,8 @@ checksums = [ '44d2bb998ec3b3b65659f3327894745888a58f957a191cb524b4003018db51a2', # PyTorch-1.10.0_fix-fp16-quantization-without-fbgemm.patch 'dfc09c2e787e757191a0ebf68ace46e2a90d71263ba84e2ee764b596d2ee6769', + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-missing-VSX-dispatch.patch '29368e69e98cb16659a2043b7a0df0411c99bc57a70405f8b5300f68c25f3ee9', # PyTorch-1.10.0_fix-test-cond-cpu.patch From 28080783312808a6655707e2e179679577067b9a Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 10:22:14 +0100 Subject: [PATCH 122/939] Duplicated PyYAML removed --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 26c7449b3c69..b210c0f94191 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -32,7 +32,6 @@ dependencies = [ ('imgaug', '0.4.0', versionsuffix), ('tqdm', '4.61.2'), ('ruamel.yaml', '0.17.21'), - ('PyYAML', '5.4.1'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0', versionsuffix), ] From 6506f62a95d89a03b51d048c05931f2eba66fc32 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:14:56 +0100 Subject: [PATCH 123/939] pip_sanity_check added --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index b210c0f94191..3349b849e4f8 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -36,6 +36,8 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ] +download_dep_fail = True +sanity_pip_check = True use_pip = True exts_list = [ From 3b822c4244353022b1da082f570d12e30f2b3398 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 17 Oct 2022 11:44:21 +0100 Subject: [PATCH 124/939] download_dep removed as PythonBundle being used --- .../d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 3349b849e4f8..9416f4eee394 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -36,7 +36,6 @@ dependencies = [ ('PyTorch', '1.10.0', versionsuffix), ] -download_dep_fail = True sanity_pip_check = True use_pip = True From 35cf91b72ca9ff877866ada47660b6383c0dc954 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 17 Oct 2022 13:54:33 +0200 Subject: [PATCH 125/939] adding easyconfigs: TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb --- ...w-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..38e8358f8829 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow-Datasets' +version = '4.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.tensorflow.org/datasets' +description = """ +TensorFlow Datasets is a collection of datasets ready to use, with TensorFlow or other Python ML frameworks, such as +Jax. All datasets are exposed as tf.data.Datasets , enabling easy-to-use and high-performance input pipelines. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('tqdm', '4.61.2'), + ('TensorFlow', '2.6.0', '-CUDA-%(cudaver)s'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('googleapis-common-protos', '1.56.4', { + 'modulename': 'google', + 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], + }), + ('tensorflow-metadata', '1.10.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_urls': [ + 'https://files.pythonhosted.org/packages/3a/86/' + + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' + + 'tensorflow_metadata-1.10.0-py3-none-any.whl' + + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3', + ], + 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'download_filename': 'v(%version)s.tar.gz', + 'filename': '%(name)s-v(%version)s.tar.gz', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/datasets/archive'], + 'checksums': ['ed7c3b959d10ba762137e18b93631ab42f4ed0915bc3d9ce98ee66eef9c61418'], + }), +] + +moduleclass = 'lib' From 4fcf6ec98a14756f8b9b327f178df5b1833edb43 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 17 Oct 2022 15:42:03 +0200 Subject: [PATCH 126/939] Add missing parenthesis --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 38e8358f8829..667bb710d9e5 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -32,12 +32,12 @@ exts_list = [ }), ('tensorflow-metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'source_urls': [ + 'source_urls': [( 'https://files.pythonhosted.org/packages/3a/86/' + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' + 'tensorflow_metadata-1.10.0-py3-none-any.whl' - + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3', - ], + + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3' + )], 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), ('etils', '0.8.0', { From 14e91fc4df7d2d9dc7f286b1c514492b8a3b9032 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 09:41:25 +0200 Subject: [PATCH 127/939] tfds to pypi version Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 667bb710d9e5..60233e3f9fff 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -44,11 +44,8 @@ exts_list = [ 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], }), (name, version, { - 'download_filename': 'v(%version)s.tar.gz', - 'filename': '%(name)s-v(%version)s.tar.gz', - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/tensorflow/datasets/archive'], - 'checksums': ['ed7c3b959d10ba762137e18b93631ab42f4ed0915bc3d9ce98ee66eef9c61418'], + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['590faf3763bc14757906b36c718389eeded533ee8ae4d030ede140db86aca4cd'], }), ] From 367f739096267f6f81fee2e1ab0fac847d124aae Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 09:41:53 +0200 Subject: [PATCH 128/939] Update easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 60233e3f9fff..08ec6bcebe19 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -16,7 +16,7 @@ dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('tqdm', '4.61.2'), - ('TensorFlow', '2.6.0', '-CUDA-%(cudaver)s'), + ('TensorFlow', '2.6.0', versionsuffix), ] sanity_pip_check = True From a80dadb4d8639b292ac7ce2c8759b1f7733432c0 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Tue, 18 Oct 2022 10:27:03 +0200 Subject: [PATCH 129/939] Remove url specification for tf metadata Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 6 ------ 1 file changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 08ec6bcebe19..4242b5cd1ae1 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -32,12 +32,6 @@ exts_list = [ }), ('tensorflow-metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', - 'source_urls': [( - 'https://files.pythonhosted.org/packages/3a/86/' - + '2b3251bb560068f31817d9b678588098e28f396c1f6b88c57cf5d28670af/' - + 'tensorflow_metadata-1.10.0-py3-none-any.whl' - + '#sha256=e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3' - )], 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), ('etils', '0.8.0', { From 8bc993e53c3199e287655db2cc92b1d773582762 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 18 Oct 2022 12:40:30 +0200 Subject: [PATCH 130/939] adding easyconfigs: MIGRATE-N-5.0.4-foss-2021b.eb and patches: migrate-5.0.4_install.patch, migrate-5.0.4_locale.patch --- .../m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 41 +++++++++++++++++++ .../m/MIGRATE-N/migrate-5.0.4_install.patch | 14 +++++++ .../m/MIGRATE-N/migrate-5.0.4_locale.patch | 15 +++++++ 3 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch create mode 100644 easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb new file mode 100644 index 000000000000..5abedc1fb588 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'MIGRATE-N' +version = '5.0.4' + +homepage = 'https://peterbeerli.com/migrate-html5/index.html' +description = """ +Migrate estimates population parameters, effective population sizes +and migration rates of n populations, using genetic data. It +uses a coalescent theory approach taking into account history of +mutations and uncertainty of the genealogy. +""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] +sources = ['migrate-%(version)s.src.tar.gz'] +patches = [ + 'migrate-%(version)s_install.patch', + 'migrate-%(version)s_locale.patch', +] + +dependencies = [ + ('zlib', '1.2.11'), +] + +configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++' +prebuildopts = 'make mpis && make clean &&' +installopts = "&& make clean && make installmpi" + +parallel = 1 + +start_dir = 'src' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch new file mode 100644 index 000000000000..ba33af1af0ab --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_install.patch @@ -0,0 +1,14 @@ +Create parent directories during install +Author: B. Hajgato +Updated: Orient Kružík (INUITS) +--- migrate-5.0.3_orig/src/configure 2021-11-08 22:48:21.000000000 +0100 ++++ migrate-5.0.3/src/configure 2022-05-09 17:15:29.368752420 +0200 +@@ -4104,7 +4104,7 @@ + test -s conftest.dir/conftest.one && + test -s conftest.dir/conftest.two + then +- ac_cv_path_install="$as_dir$ac_prog$ac_exec_ext -c" ++ ac_cv_path_install="$as_dir$ac_prog$ac_exec_ext -c -D" + break 3 + fi + fi \ No newline at end of file diff --git a/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch new file mode 100644 index 000000000000..29cd65e5d996 --- /dev/null +++ b/easybuild/easyconfigs/m/MIGRATE-N/migrate-5.0.4_locale.patch @@ -0,0 +1,15 @@ +Don't use the xlocale.h header since it is an OS package and not always provided. +Author: R. van Dijk, 2018-03-07 +Updated by: Orient Kružík (INUITS) +--- migrate-5.0.3_orig/src/src/data.c 2022-04-03 00:11:20.000000000 +0200 ++++ migrate-5.0.3/src/src/data.c 2022-05-09 17:17:46.836503576 +0200 +@@ -53,9 +53,6 @@ + + #include + #include +-#ifndef WIN32 +-#include +-#endif + #include "migration.h" + #include "sighandler.h" + #include "tools.h" \ No newline at end of file From 330da15302a5eeb245d5e9617af746e8740f1c93 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Tue, 18 Oct 2022 13:02:23 +0200 Subject: [PATCH 131/939] Fixed style error --- .../easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb index 5abedc1fb588..624706433b6c 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -17,8 +17,8 @@ toolchainopts = {'usempi': True} source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] sources = ['migrate-%(version)s.src.tar.gz'] patches = [ - 'migrate-%(version)s_install.patch', - 'migrate-%(version)s_locale.patch', + 'migrate-%(version)s_install.patch', + 'migrate-%(version)s_locale.patch', ] dependencies = [ From ef9535969aa1b9b3bd4e797f0debedcb840f093d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 18 Oct 2022 19:55:27 +0200 Subject: [PATCH 132/939] adding easyconfigs: biogeme-3.2.6-foss-2022a.eb --- .../b/biogeme/biogeme-3.2.6-foss-2022a.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb new file mode 100644 index 000000000000..21a1c2ddb5e1 --- /dev/null +++ b/easybuild/easyconfigs/b/biogeme/biogeme-3.2.6-foss-2022a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'biogeme' +version = '3.2.6' + +homepage = 'https://pypi.python.org/pypi/biogeme' +description = """Biogeme is a open source Python package designed for +the maximum likelihood estimation of parametric models in general, +with a special emphasis on discrete choice models.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('Unidecode', '1.3.6', { + 'checksums': ['fed09cf0be8cf415b391642c2a5addfc72194407caee4f98719e40ec2a72b830'], + }), + (name, version, { + 'checksums': ['ff8d492019e15aecdfe7c72cff3b2616845cdf80bd2f1bde9031d94601f3faf7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 0cd66fd8614e50df8389ad31436706564b755021 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:39:37 +0200 Subject: [PATCH 133/939] adding easyconfigs: python-telegram-bot-20.0a0-GCCcore-10.2.0.eb --- ...thon-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..925a1086d5ae --- /dev/null +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -0,0 +1,97 @@ +easyblock = 'PythonBundle' + +name = 'python-telegram-bot' +version = '20.0a0' + +homepage = 'https://python-telegram-bot.org/' +description = """This library provides a pure Python, asynchronous interface for the Telegram Bot API. + It's compatible with Python versions 3.7+.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('Python', '3.8.6'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('APScheduler', '3.9.1', { + 'checksums': ['65e6574b6395498d371d045f2a8a7e4f7d50c6ad21ef7313d15b1c7cf20df1e3'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('backports.zoneinfo', '0.2.1', { + 'checksums': ['fadbfe37f74051d024037f223b8e001611eac868b5c5b06144ef4d8b799862f2'], + }), + ('cachetools', '5.0.0', { + 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], + }), + ('certifi', '2022.9.24', { + 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], + }), + ('charset-normalizer', '2.1.1', { + 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.14.7', { + 'checksums': ['7503ec1c0f559066e7e39bc4003fd2ce023d01cf51793e3c173b864eb456ead1'], + }), + ('httpx', '0.22.0', { + 'checksums': ['d8e778f76d9bbd46af49e7f062467e3157a5a3d2ae4876a4bbfd8a51ed9c9cb4'], + }), + ('idna', '3.4', { + 'checksums': ['814f528e8dead7d329833b91c5faa87d60bf71824cd12a7530b5526063d02cb4'], + }), + ('pytz_deprecation_shim', '0.1.0.post0', { + 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], + }), + ('pytz', '2022.4', { + 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], + }), + ('requests', '2.28.1', { + 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('ruffus', '2.8.4', { + 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], + }), + ('setuptools', '65.5.0', { + 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + ('tzdata', '2022.5', { + 'checksums': ['e15b2b3005e2546108af42a0eb4ccab4d9e225e2dfbf4f77aad50c70a4b1f3ab'], + }), + ('tzlocal', '4.2', { + 'checksums': ['ee5842fa3a795f023514ac2d801c4a81d1743bbe642e3940143326b3a00addd7'], + }), + (name, version, { + 'modulename': 'telegram', + 'checksums': ['a182a3d081071f1ea34833bc68ed7d0843c1fe0d6dca1d260a0e2d253b150f71'], + }), +] + +sanity_check_commands = [ + "python -c 'from telegram import Update'", + "python -c 'from telegram.ext import ApplicationBuilder, CommandHandler, ContextTypes'", +] + +moduleclass = 'lib' From 13b10372e9ce58d1d5abf4cc937c6bd79e7ee0b1 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 19 Oct 2022 16:55:57 +0200 Subject: [PATCH 134/939] added binutils as builddependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 925a1086d5ae..f98289dd3bcc 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -13,6 +13,8 @@ dependencies = [ ('Python', '3.8.6'), ] +builddependencies = [('binutils', '2.35')] + use_pip = True sanity_pip_check = True From dca1c0e2cbc9fcb628ec070b71c6e48f3b0731fa Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 19 Oct 2022 21:34:44 +0200 Subject: [PATCH 135/939] adding easyconfigs: archspec-0.1.4-GCCcore-11.3.0.eb --- .../archspec/archspec-0.1.4-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..710f53f822e4 --- /dev/null +++ b/easybuild/easyconfigs/a/archspec/archspec-0.1.4-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'archspec' +version = '0.1.4' + +homepage = 'https://github.com/archspec/archspec' +description = "A library for detecting, labeling, and reasoning about microarchitectures" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['b8d5eeb4caf892790ff1aa8ccef442a84187986aeab4da29417c9fe35532d94c'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +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 314650e894a8b06fab1448e9b54fb31a5f600db8 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 07:06:39 +0200 Subject: [PATCH 136/939] removed ruffus as dependency --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index f98289dd3bcc..34c1581e97c2 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -64,9 +64,6 @@ exts_list = [ ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('ruffus', '2.8.4', { - 'checksums': ['6cd3d96e459a1aedcc10341f14fddedfdc13664551757fcd429a241de63826aa'], - }), ('setuptools', '65.5.0', { 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], }), From 47ac220bd54bdf003b4e7530393d8f3d5203bc98 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 20 Oct 2022 09:55:25 +0200 Subject: [PATCH 137/939] removed unnecessary dependencies --- .../python-telegram-bot-20.0a0-GCCcore-10.2.0.eb | 13 +------------ 1 file changed, 1 insertion(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb index 34c1581e97c2..dfb7a16b6ba8 100644 --- a/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/python-telegram-bot/python-telegram-bot-20.0a0-GCCcore-10.2.0.eb @@ -31,9 +31,6 @@ exts_list = [ ('cachetools', '5.0.0', { 'checksums': ['486471dfa8799eb7ec503a8059e263db000cdda20075ce5e48903087f79d5fd6'], }), - ('certifi', '2022.9.24', { - 'checksums': ['0d9c601124e5a6ba9712dbc60d9c53c21e34f5f641fe83002317394311bdce14'], - }), ('charset-normalizer', '2.1.1', { 'checksums': ['5a3d016c7c547f69d6f81fb0db9449ce888b418b5b9952cc5e6e66843e9dd845'], }), @@ -55,21 +52,13 @@ exts_list = [ ('pytz_deprecation_shim', '0.1.0.post0', { 'checksums': ['af097bae1b616dde5c5744441e2ddc69e74dfdcb0c263129610d85b87445a59d'], }), - ('pytz', '2022.4', { - 'checksums': ['48ce799d83b6f8aab2020e369b627446696619e79645419610b9facd909b3174'], - }), + # to overwrite Python's requests requirement which requires older version of idna ('requests', '2.28.1', { 'checksums': ['7c5599b102feddaa661c826c56ab4fee28bfd17f5abca1ebbe3e7f19d7c97983'], }), ('rfc3986', '1.5.0', { 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], }), - ('setuptools', '65.5.0', { - 'checksums': ['512e5536220e38146176efb833d4a62aa726b7bbff82cfbc8ba9eaa3996e0b17'], - }), - ('six', '1.16.0', { - 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], - }), ('sniffio', '1.3.0', { 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], }), From 37d77d518b1a4dc9e2d40d894900a1198d8c8f54 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 10:35:49 +0200 Subject: [PATCH 138/939] adding easyconfigs: pyWannier90-2021-12-07-foss-2021a.eb --- .../pyWannier90-2021-12-07-foss-2021a.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb new file mode 100644 index 000000000000..ec32ef804a95 --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = '8354e91' +version = '2021-12-07' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'foss', 'version': '2021a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2021-12-07.tar.gz': '27233891fe39e0f45914dfa756b28319ebd4c3b5ec2124f4c9d1d3816fc0887e'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.6.2'), +] + +local_pymaj = '3' +local_pymin = '9' +local_pymajmin = local_pymaj + local_pymin + +dependencies = [ + ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('SciPy-bundle', '2021.05'), + ('PySCF', '1.7.6'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && pwd && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 85dbd36904fe1f0ee5709fdd5df2292c27c42c73 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 10:40:38 +0200 Subject: [PATCH 139/939] adding easyconfigs: SciPy-bundle-2021.05-gomkl-2021a.eb --- .../SciPy-bundle-2021.05-gomkl-2021a.eb | 71 +++++++++++++++++++ 1 file changed, 71 insertions(+) create mode 100644 easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb new file mode 100644 index 000000000000..89b95c194e83 --- /dev/null +++ b/easybuild/easyconfigs/s/SciPy-bundle/SciPy-bundle-2021.05-gomkl-2021a.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'SciPy-bundle' +version = '2021.05' + +homepage = 'https://python.org/' +description = "Bundle of Python packages for scientific software" + +toolchain = {'name': 'gomkl', 'version': '2021a'} +toolchainopts = {'pic': True, 'lowopt': True, 'strict': True} + +builddependencies = [('hypothesis', '6.13.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('pybind11', '2.6.2'), # required by scipy +] + +use_pip = True + +# order is important! +exts_list = [ + ('numpy', '1.20.3', { + 'patches': [ + 'numpy-1.18.2-mkl.patch', + 'numpy-1.20.3_disable-broken-override-test.patch', + 'numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch', + 'numpy-1.20.3_fix-target-test-ccompiler-opt.patch', + 'numpy-1.20.3_disable_fortran_callback_test.patch', + ], + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': [ + 'e55185e51b18d788e49fe8305fd73ef4470596b33fc2c1ceb304566b99c71a69', # numpy-1.20.3.zip + 'ea25ad5c0148c1398d282f0424e642fb9815a1a80f4512659b018e2adc378bcf', # numpy-1.18.2-mkl.patch + # numpy-1.20.3_disable-broken-override-test.patch + '43cc2e675c52db1776efcc6c84ebd5fc008b48e6355c81087420d5e790e4af9b', + # numpy-1.20.3_fix-cpu-feature-detection-intel-compilers.patch + '4c0b194c9d2e2c6b9798ebc271d4517f4c3cdbf2b3cbd68de16c7d4b068bb046', + # numpy-1.20.3_fix-target-test-ccompiler-opt.patch + '3d84e8b7d48387778974a5f6ae342a690ab5989547206b6add9d9667f8d7572a', + # numpy-1.20.3_disable_fortran_callback_test.patch + '44975a944544fd0e771b7e63c32590d257a3713070f8f7fdf60105dc516f1d75', + ], + }), + ('scipy', '1.6.3', { + 'checksums': ['a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707'], + }), + ('mpi4py', '3.0.3', { + 'checksums': ['012d716c8b9ed1e513fcc4b18e5af16a8791f51e6d1716baccf988ad355c5a1f'], + }), + ('numexpr', '2.7.3', { + 'checksums': ['43616529f9b7d1afc83386f943dc66c4da5e052f00217ba7e3ad8dd1b5f3a825'], + }), + ('Bottleneck', '1.3.2', { + 'checksums': ['20179f0b66359792ea283b69aa16366419132f3b6cf3adadc0c48e2e8118e573'], + }), + ('pandas', '1.2.4', { + 'preinstallopts': """sed -i 's@extra_compile_args = \["-Werror"\]@extra_compile_args = []@g' setup.py && """, + 'checksums': ['649ecab692fade3cbfcf967ff936496b0cfba0af00a55dfaacd82bdda5cb2279'], + }), + ('mpmath', '1.2.1', { + 'checksums': ['79ffb45cf9f4b101a807595bcb3e72e0396202e0b1d25d689134b48c4216a81a'], + }), + ('deap', '1.3.1', { + 'checksums': ['11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 67f9f8c3fdd341ecc78eb28dfe00497a08271dc7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 11:14:45 +0200 Subject: [PATCH 140/939] {chem}[gomkl/2021a] pyWannier90 v2021-12-07, PySCF v1.7.6, h5py v3.2.1, libcint v4.4.0 w/ Python 3.9.5 --- .../h/h5py/h5py-3.2.1-gomkl-2021a.eb | 34 +++++++++ .../l/libcint/libcint-4.4.0-gomkl-2021a.eb | 39 ++++++++++ .../p/PySCF/PySCF-1.7.6-gomkl-2021a.eb | 45 +++++++++++ .../pyWannier90-2021-12-07-gomkl-2021a.eb | 76 +++++++++++++++++++ 4 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb new file mode 100644 index 000000000000..a21aff6972d6 --- /dev/null +++ b/easybuild/easyconfigs/h/h5py/h5py-3.2.1-gomkl-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'h5py' +version = '3.2.1' + +homepage = 'https://www.h5py.org/' +description = """HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, + version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous + amounts of data.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} +toolchainopts = {'usempi': True} + +sources = [SOURCE_TAR_GZ] +checksums = ['89474be911bfcdb34cbf0d98b8ec48b578c27a89fdb1ae4ee7513f1ef8d9249e'] + +builddependencies = [('pkgconfig', '1.5.4', '-python')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('HDF5', '1.10.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +# h5py's setup.py will disable setup_requires if H5PY_SETUP_REQUIRES is set to 0 +# without this environment variable, pip will fetch the minimum numpy version h5py supports during install, +# even though SciPy-bundle provides a newer version that satisfies h5py's install_requires dependency. +preinstallopts = 'HDF5_MPI=ON HDF5_DIR="$EBROOTHDF5" H5PY_SETUP_REQUIRES=0 ' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb new file mode 100644 index 000000000000..8dc84fd9e8f7 --- /dev/null +++ b/easybuild/easyconfigs/l/libcint/libcint-4.4.0-gomkl-2021a.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'libcint' +version = '4.4.0' + +homepage = 'https://github.com/sunqm/libcint' +description = """libcint is an open source library for analytical Gaussian integrals.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/sunqm/libcint/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_remove_pyscftest.patch'] +checksums = [ + '39a831e9131395e7ac312608981495aed3e44d0511b0700b2a1fb163b32c89c1', # v4.4.0.tar.gz + '6449297a6aee30fef3d6a268aa892dea8dd5c3ca9669a50ae694ab9bcf17842d', # libcint-4.4.0_remove_pyscftest.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + # Python with numpy only required for 'make test' + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +separate_build_dir = False # Must use the same directory for tests + +configopts = '-DWITH_RANGE_COULOMB=on -DWITH_COULOMB_ERF=on -DWITH_F12=on -DENABLE_TEST=on' + +buildopts = "VERBOSE=1" + +runtest = 'test ' + +sanity_check_paths = { + 'files': ['include/cint.h', 'lib/libcint.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb new file mode 100644 index 000000000000..cf0c6a26ccc9 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-1.7.6-gomkl-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMakeCp' + +name = 'PySCF' +version = '1.7.6' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['1805819557cf78fb5938a2141a429c74dabb3ba664b60420032584d7a876c2ab'] + +builddependencies = [('CMake', '3.20.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # for numpy, scipy + ('h5py', '3.2.1'), + ('libcint', '4.4.0'), + ('libxc', '5.1.5'), + ('XCFun', '2.1.1'), +] + +start_dir = 'pyscf/lib' + +separate_build_dir = True + +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" + +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +files_to_copy = ['pyscf'] + +sanity_check_paths = { + 'files': ['pyscf/__init__.py'], + 'dirs': ['pyscf/data', 'pyscf/lib'], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': ''} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb new file mode 100644 index 000000000000..2a045c216cc2 --- /dev/null +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb @@ -0,0 +1,76 @@ +easyblock = 'MakeCp' + +name = 'pyWannier90' +local_commit = '8354e91' +version = '2021-12-07' + +homepage = 'https://github.com/hungpham2017/pyWannier90' +description = "A Wannier90 Python interface for VASP and PySCF" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +local_wannier90_version = '3.1.0' + +sources = [ + { + 'source_urls': ['https://github.com/hungpham2017/pyWannier90/archive/'], + 'download_filename': '%s.tar.gz' % local_commit, + 'filename': SOURCE_TAR_GZ + }, + { + 'source_urls': ['https://github.com/wannier-developers/wannier90/archive/'], + 'download_filename': 'v%s.tar.gz' % local_wannier90_version, + 'filename': 'Wannier90-%s.tar.gz' % local_wannier90_version, + }, +] +checksums = [ + {'pyWannier90-2021-12-07.tar.gz': '27233891fe39e0f45914dfa756b28319ebd4c3b5ec2124f4c9d1d3816fc0887e'}, + {'Wannier90-3.1.0.tar.gz': '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254'}, +] + +builddependencies = [ + ('pybind11', '2.6.2'), +] + +local_pymaj = '3' +local_pymin = '9' +local_pymajmin = local_pymaj + local_pymin + +dependencies = [ + ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('SciPy-bundle', '2021.05'), + ('PySCF', '1.7.6'), +] + +local_wannier90_make = 'make -j %(parallel)s F90="$F90" FCOPTS="$FFLAGS -fPIC" LDOPTS="$FFLAGS" ' +local_wannier90_make += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK"' + +prebuildopts = "cd %%(builddir)s/wannier90-%s && touch make.inc && " % local_wannier90_version +prebuildopts += "cp %(builddir)s/pyWannier90-*/src/wannier_lib.F90 src/wannier_lib.F90 && " +prebuildopts += local_wannier90_make + " && " +prebuildopts += local_wannier90_make + " lib && " +prebuildopts += "cd %(builddir)s/pyWannier90-*/src && pwd && " + +buildopts = 'CPP="$CXX" LIBS="-L%%(builddir)s/wannier90-%s $LIBLAPACK -lwannier" ' % local_wannier90_version +# with Intel compilers, use libwannier90_intel as make target +# with GCC compilers, use libwannier90_gf as make target +buildopts += "libwannier90_gf && " +buildopts += """sed -i "s@W90LIB = .*@W90LIB = '%(installdir)s'@g" pywannier90.py""" + +files_to_copy = [ + (['src/pywannier90.py', 'src/libwannier90.*.%s' % SHLIB_EXT], 'lib/python%(pyshortver)s/site-packages'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import libwannier90'", + "python -c 'import pywannier90'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'chem' From 54770a0d7116397f9b4e09cb94fa36193bccc97f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 17:13:02 +0200 Subject: [PATCH 141/939] adding easyconfigs: jax-0.3.23-foss-2022a.eb --- .../j/jax/jax-0.3.23-foss-2022a.eb | 109 ++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb new file mode 100644 index 000000000000..23d90b71f8b2 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -0,0 +1,109 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.23' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Bazel', '5.1.1'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', '0.3.22', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.22.tar.gz + '680a6f5265ba26d5515617a95ae47244005366f879a5c321782fde60f34e6d0d', + # tensorflow-cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057.tar.gz + '9a7a7a87356bdeef5874fae135de380466482b593469035be3609a9cd2c153c4', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'patches': [ + 'jax-0.3.9_relax-test-tolerance.patch', + ], + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': [ + {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, + {'jax-0.3.9_relax-test-tolerance.patch': + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 44f8c71cb913161c41e8d43cb63f6740291b5145 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 17:44:25 +0200 Subject: [PATCH 142/939] {bio}[foss/2021a] scvi-tools v0.16.4, scikit-misc v0.1.4 w/ Python 3.9.5 --- .../scikit-misc-0.1.4-foss-2021a.eb | 25 +++++ .../scvi-tools-0.16.4-foss-2021a.eb | 92 +++++++++++++++++++ 2 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb new file mode 100644 index 000000000000..d50466cda7d4 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-misc/scikit-misc-0.1.4-foss-2021a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'scikit-misc' +version = '0.1.4' + +homepage = 'https://github.com/has2k1/scikit-misc' +description = "Miscellaneous tools for data analysis and scientific computing" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['f7746a0347811063e1ecf9121df94835785003953c38b5ba84f63fc508c22911'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'skmisc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb new file mode 100644 index 000000000000..39b2aa92da3a --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a.eb @@ -0,0 +1,92 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '0.16.4' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('jax', '0.3.9'), + ('openpyxl', '3.0.7'), + ('PyTorch-Lightning', '1.5.9'), + ('scikit-learn', '0.24.2'), + ('dm-tree', '0.1.6'), + ('scanpy', '1.8.1'), + ('scikit-misc', '0.1.4'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + # stick to flax v0.5.2, which does not require tensorstore (which is built with Bazel) or a very recent jax yet... + ('flax', '0.5.2', { + 'checksums': ['5f07775fd4ba1926192ab6eb48c9adbd5658ddaf8585fb0c561741400d5599ff'], + }), + ('multipledispatch', '0.6.0', { + 'checksums': ['a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea'], + }), + ('numpyro', '0.10.1', { + 'checksums': ['dfa896f01c8df43ddd41663af2b3e2fc4aea73489e669474e83329b183b29150'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.5', { + 'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'], + }), + ('optax', '0.1.3', { + 'checksums': ['159e954405c3ba2072c2add7cec5532be7399bcafab3039acbf608b11844a879'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + ('pyro-ppl', '1.8.0', { + 'modulename': 'pyro', + 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '11.1.0', { + 'checksums': ['43e03d8eec12e21beaecc22c828a41c4247356414a12d5879834863d4ad53816'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('mudata', '0.2.0', { + 'checksums': ['6eef13ec2165340cd6d79fe4aabe687e9c53867c818c8dbe1cf0b6be0e5d1e75'], + }), + (name, version, { + 'modulename': 'scvi', + 'checksums': ['95c67870ecfa1d0e0b80027d3239bb47ca6cd3db2f2524985f5d31903b766eeb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 77049b4165359c8246354200de75b6b2ab6024e8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 17:51:30 +0200 Subject: [PATCH 143/939] {bio}[foss/2021a] scvi-tools v0.16.4 w/ Python 3.9.5 + CUDA 11.3.1 --- ...cvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..a5b9c930ebd5 --- /dev/null +++ b/easybuild/easyconfigs/s/scvi-tools/scvi-tools-0.16.4-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'scvi-tools' +version = '0.16.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/scverse/scvi-tools' +description = """scvi-tools (single-cell variational inference tools) is a package for probabilistic modeling and +analysis of single-cell omics data, built on top of PyTorch and AnnData.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('h5py', '3.2.1'), + ('IPython', '7.25.0'), + ('jax', '0.3.9', versionsuffix), + ('openpyxl', '3.0.7'), + ('PyTorch-Lightning', '1.5.9', versionsuffix), + ('scikit-learn', '0.24.2'), + ('dm-tree', '0.1.6'), + ('scanpy', '1.8.1'), + ('scikit-misc', '0.1.4'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + # stick to flax v0.5.2, which does not require tensorstore (which is built with Bazel) or a very recent jax yet... + ('flax', '0.5.2', { + 'checksums': ['5f07775fd4ba1926192ab6eb48c9adbd5658ddaf8585fb0c561741400d5599ff'], + }), + ('multipledispatch', '0.6.0', { + 'checksums': ['a7ab1451fd0bf9b92cab3edbd7b205622fb767aeefb4fb536c2e3de9e0a38bea'], + }), + ('numpyro', '0.10.1', { + 'checksums': ['dfa896f01c8df43ddd41663af2b3e2fc4aea73489e669474e83329b183b29150'], + }), + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('chex', '0.1.5', { + 'checksums': ['686858320f8f220c82a6c7eeb54dcdcaa4f3d7f66690dacd13a24baa1ee8299e'], + }), + ('optax', '0.1.3', { + 'checksums': ['159e954405c3ba2072c2add7cec5532be7399bcafab3039acbf608b11844a879'], + }), + ('pyro-api', '0.1.2', { + 'modulename': 'pyroapi', + 'checksums': ['a1b900d9580aa1c2fab3b123ab7ff33413744da7c5f440bd4aadc4d40d14d920'], + }), + ('pyro-ppl', '1.8.0', { + 'modulename': 'pyro', + 'checksums': ['68e4ea30f219227dd88e55de2550d3f8c20a20adbdb67ad1e13b50868bb2ac0c'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '11.1.0', { + 'checksums': ['43e03d8eec12e21beaecc22c828a41c4247356414a12d5879834863d4ad53816'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.1', { + 'checksums': ['3fefcc72ec433aa1e5d32307a3e474bbb67f405be814ea52a2166bfc9dbe68cc'], + }), + ('mudata', '0.2.0', { + 'checksums': ['6eef13ec2165340cd6d79fe4aabe687e9c53867c818c8dbe1cf0b6be0e5d1e75'], + }), + (name, version, { + 'modulename': 'scvi', + 'checksums': ['95c67870ecfa1d0e0b80027d3239bb47ca6cd3db2f2524985f5d31903b766eeb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 934e5be97e2f87044b863f3c682192d40b984c2f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:14:21 +0200 Subject: [PATCH 144/939] adding easyconfigs: Fiji-2.9.0-Java-1.8.eb --- .../easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb new file mode 100644 index 000000000000..c655cd165402 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-1.8.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.9.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-2.1.0 and Fiji-2.1.1""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/'] +sources = ['fiji-%(version)s-nojre.zip'] +checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42'] + +dependencies = [('Java', '1.8', '', SYSTEM)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' https://sites.imagej.net/Tboudier/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"' + ' https://sites.imagej.net/Ilastik/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' https://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ +Additional plugins can be installed in your $HOME/.plugins folder or requested to user support +Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` +More information at https://imagej.net/Headless +""" + +moduleclass = 'vis' From aad5dd9d48c61292e060975d9453fa51e3bb820f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:35:17 +0200 Subject: [PATCH 145/939] allow use of jax 0.3.9 as dependency for scvi-tools --- 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 45c9bcfa7122..2e63f19e967b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -485,7 +485,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # some software packages require a specific (older/newer) version of a particular dependency alt_dep_versions = { - 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-'])], + 'jax': [(r'0\.3\.9', [r'AlphaFold-2\.2\.2-foss-2021a', r'scvi-tools-0\.16\.4-foss-2021a'])], # arrow-R 6.0.0.2 is used for two R/R-bundle-Bioconductor sets (4.1.2/3.14 and 4.2.0/3.15) 'arrow-R': [('6.0.0.2', [r'R-bundle-Bioconductor-'])], # EMAN2 2.3 requires Boost(.Python) 1.64.0 From d184b5d302a432d653c4e1709e1d87d6469fa689 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 20 Oct 2022 18:24:45 +0200 Subject: [PATCH 146/939] add exception for egl dependency variant of glew --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 518f5594e1d0..4eb56e770a7d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -473,6 +473,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], + # egl variant of glew is required by libwpe + 'glew': [('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0'])], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [(r'1\.10\.', [r'ncbi-vdb-2\.11\.', r'HISAT2-2\.2\.', r'SKESA-2\.4\.', r'shovill-1\.1\.'])], From f11d34b8b40d453c80eaff9bbfdee60c9fd69eb0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 21 Oct 2022 10:58:59 +0200 Subject: [PATCH 147/939] bump version to 4.6.3dev --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 0528da1ca3fd..75d8dacffe3c 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 = '4.6.2' +VERSION = '4.6.3.dev0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From acd1e0442d09ab4cc9f01210f6f84313776a1260 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 21 Oct 2022 11:48:47 +0200 Subject: [PATCH 148/939] adding easyconfigs: torchsampler-0.1.2-foss-2022a.eb, torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb --- ...rchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb | 30 +++++++++++++++++++ .../torchsampler-0.1.2-foss-2022a.eb | 28 +++++++++++++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..30864489390d --- /dev/null +++ b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'torchsampler' +version = '0.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/ufoym/imbalanced-dataset-sampler' +description = """ +A (PyTorch) imbalanced dataset sampler for oversampling low classes and +undersampling high frequent ones.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('PyTorch', '1.12.0', versionsuffix), + ('torchvision', '0.13.1', versionsuffix), +] + +exts_list = [ + (name, version, { + 'checksums': ['6503acf0ff76888905595006a45c2a2fa017f7a13fffbfcddb3827ef8226ea78'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb new file mode 100644 index 000000000000..3b4a760bfbc9 --- /dev/null +++ b/easybuild/easyconfigs/t/torchsampler/torchsampler-0.1.2-foss-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'torchsampler' +version = '0.1.2' + +homepage = 'https://github.com/ufoym/imbalanced-dataset-sampler' +description = """ +A (PyTorch) imbalanced dataset sampler for oversampling low classes and +undersampling high frequent ones.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('torchvision', '0.13.1'), +] + +exts_list = [ + (name, version, { + 'checksums': ['6503acf0ff76888905595006a45c2a2fa017f7a13fffbfcddb3827ef8226ea78'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'devel' From d15b1ead95141beae65f0c396f9c9d1a59062081 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 11:20:46 +0100 Subject: [PATCH 149/939] Add patch for correctly skipping a test and add matplotlib builddep --- .../easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 5 +++++ ...-0.3.23_correctly-skip-from_dlpack-tests.patch | 15 +++++++++++++++ 2 files changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index 23d90b71f8b2..54a86884e763 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -17,6 +17,7 @@ builddependencies = [ ('pytest-xdist', '2.5.0'), # git 2.x required to fetch repository 'io_bazel_rules_docker' ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), # required for tests/lobpcg_test.py ] dependencies = [ @@ -93,6 +94,7 @@ exts_list = [ (name, version, { 'patches': [ 'jax-0.3.9_relax-test-tolerance.patch', + 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', ], 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], @@ -100,7 +102,10 @@ exts_list = [ {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, {'jax-0.3.9_relax-test-tolerance.patch': '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': + 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, ], + 'runtest': "pytest -n %(parallel)s tests", }), ] diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch new file mode 100644 index 000000000000..7354e39c8e3e --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_correctly-skip-from_dlpack-tests.patch @@ -0,0 +1,15 @@ +np.from_dlpack was not added until numpy 1.23 +Patch based off https://github.com/google/jax/pull/12900 and added by Simon Branford (University of Birmingham) +diff --git a/tests/array_interoperability_test.py b/tests/array_interoperability_test.py +index cc2f3a6c08d..ac04ee637c8 100644 +--- a/tests/array_interoperability_test.py ++++ b/tests/array_interoperability_test.py +@@ -200,7 +200,7 @@ def testNumpyToJax(self, shape, dtype): + "shape": shape, "dtype": dtype} + for shape in all_shapes + for dtype in torch_dtypes)) +- @unittest.skipIf(numpy_version < (1, 22, 0), "Requires numpy 1.22 or newer") ++ @unittest.skipIf(numpy_version < (1, 23, 0), "Requires numpy 1.23 or newer") + @jtu.skip_on_devices("gpu") + def testJaxToNumpy(self, shape, dtype): + rng = jtu.rand_default(self.rng()) From 430735ccd8c455694dcca5aa2f6e18e4756f3d91 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 21 Oct 2022 18:24:29 +0800 Subject: [PATCH 150/939] adding easyconfigs: EasyBuild-4.6.2.eb --- .../e/EasyBuild/EasyBuild-4.6.2.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb diff --git a/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb new file mode 100644 index 000000000000..6168661c256c --- /dev/null +++ b/easybuild/easyconfigs/e/EasyBuild/EasyBuild-4.6.2.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_EasyBuildMeta' + +name = 'EasyBuild' +version = '4.6.2' + +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/88/7f/67dd44ae3204cba36c66578b14e284ce5210d8217fb383eb24c1691a1bfd/', + # easybuild-easyblocks + 'https://files.pythonhosted.org/packages/fe/52/2609eb0d2b9e9678670c2faec23b14c9c180b4a1d2494fd91c29df2a9a5e/', + # easybuild-easyconfigs + 'https://files.pythonhosted.org/packages/5c/6b/1ead89a64a19717e5b0a0c8453458e7186928a36280e9592092ee6d58273/', + +] +sources = [ + 'easybuild-framework-%(version)s.tar.gz', + 'easybuild-easyblocks-%(version)s.tar.gz', + 'easybuild-easyconfigs-%(version)s.tar.gz', +] +checksums = [ + '136a49ed40b4d7fed1b3d3d47f0f2804cb7744fd886eb9887672e85f7e820499', # easybuild-framework-4.6.2.tar.gz + 'b88059feeb2a97c944f6a71dc88cec683fef650ac081f8563b3f312cf8fe2794', # easybuild-easyblocks-4.6.2.tar.gz + 'b9a305200c8874852cfa3d07d72ed7295481c1b532f7579dcf1212deebcd393b', # easybuild-easyconfigs-4.6.2.tar.gz +] + +# 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 116bd8f61120841cc0809ad734c9d3c682e8890c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 21 Oct 2022 12:25:38 +0200 Subject: [PATCH 151/939] add torchvision dep easyconfig --- .../torchvision-0.13.1-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb new file mode 100644 index 000000000000..26cf963f6dad --- /dev/null +++ b/easybuild/easyconfigs/t/torchvision/torchvision-0.13.1-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'torchvision' +version = '0.13.1' + +homepage = 'https://github.com/pytorch/vision' +description = " Datasets, Transforms and Models specific to Computer Vision" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/pytorch/vision/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c32fab734e62c7744dadeb82f7510ff58cc3bca1189d17b16aa99b08afc42249'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('Pillow-SIMD', '9.2.0'), + ('PyTorch', '1.12.0'), +] + +moduleclass = 'vis' From 0335eb886702eb91e125f6513bea4a2f863097aa Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 12:32:28 +0200 Subject: [PATCH 152/939] adding easyconfigs: sfftk-0.7.4-foss-2021a.eb --- .../s/sfftk/sfftk-0.7.4-foss-2021a.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb diff --git a/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb b/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb new file mode 100644 index 000000000000..b27366815440 --- /dev/null +++ b/easybuild/easyconfigs/s/sfftk/sfftk-0.7.4-foss-2021a.eb @@ -0,0 +1,70 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 +easyblock = 'PythonBundle' + +name = 'sfftk' +version = '0.7.4' + +homepage = 'https://emdb-empiar.github.io/EMDB-SFF/' +description = """ +sfftk is a set of utilities that facilitate creation, conversion and +modification of Electron Microscopy Data Bank - Segmentation File Format +(EMDB-SFF) files. EMDB-SFF is an open, community-driven file format to handle +annotated segmentations and subtomogram averages that facilitates segmentation +file interchange. It is written in Python and provides both a command-line suite +of commands and a Python API.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('mrcfile', '1.3.0'), + ('lxml', '4.6.3'), + ('h5py', '3.2.1'), + ('scikit-image', '0.18.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bitarray', '2.6.0', { + 'checksums': ['56d3f16dd807b1c56732a244ce071c135ee973d3edc9929418c1b24c5439a0fd'], + }), + ('ahds', '0.2.4', { + 'checksums': ['3356115351f7f6089f44c6f6503daa4985f158b7dfb730ef88ab3c6a7f8cc1a6'], + }), + ('styled', '0.2.0', { + 'checksums': ['91ab8022913de87fe1a614d3caeebafe046fd20cdd7d821a61738c1ce86e7276'], + }), + ('numpy-stl', '2.17.1', { + 'modulename': 'stl', + 'checksums': ['36c920192f445dd57f091a63629bdda5a9274d47513a33ac2efad12737394b7a'], + }), + ('python-utils', '3.3.3', { + 'checksums': ['3b1c8b706e40e91280eec5fa72ea730880a166cee99afa5555b863d55664478d'], + }), + ('RandomWords', '0.4.0', { + 'modulename': 'random_words', + 'checksums': ['0bb64dc14f7f5d96597e9a08e185b874a3ea20955a1acce632b87122d66d3d6b'], + }), + ('SimpleParse', '2.2.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['2c1b130017e708a2c87b3a6119b5844f08a0d53b9e4c9d48da5e6c409798e979'], + }), + ('sfftk-rw', '0.7.2', { + 'modulename': 'sfftkrw', + 'source_urls': ['https://github.com/emdb-empiar/sfftk-rw/archive/refs/tags/'], + 'sources': [{'filename': '%(name)s-%(version)s.tar.gz', 'download_filename': 'v%(version)s.tar.gz'}], + 'checksums': ['c858377d987090aa08984e8ae8dd09d5553eabc3bbea5c0ecc9994c06d474500'], + }), + (name, version, { + 'checksums': ['f165d377d4b7d42bc800a08f220169b7baf5e2faafe337beb77ee0754d52e038'], + }), +] + +sanity_check_commands = [ + "sff -h", +] + +moduleclass = 'tools' From 46c3331eb2937e72122b4dac931e73b9132d0f35 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 12:48:45 +0200 Subject: [PATCH 153/939] add mrcfile-1.3.0-foss-2021a.eb --- .../m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb new file mode 100644 index 000000000000..4597b91cf822 --- /dev/null +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -0,0 +1,22 @@ +#Thomas Hoffmann, EMBL Heidelberg, 2022/10 +easyblock = 'PythonPackage' +name = 'mrcfile' +version = '1.3.0' +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': '2021a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +dependencies = [ + ('Python','3.9.5'), + ('SciPy-bundle','2021.05'), + ] + +use_pip=True +moduleclass = 'bio' From bc45390a1d7bad6fe4260be2c3c97b149edca089 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:25:25 +0200 Subject: [PATCH 154/939] mrcfile-1.3.0-foss-2021a.eb: fixed style --- .../m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 25 +++++++++++++------ 1 file changed, 17 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index 4597b91cf822..6222f530615f 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -1,22 +1,31 @@ -#Thomas Hoffmann, EMBL Heidelberg, 2022/10 +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 easyblock = 'PythonPackage' name = 'mrcfile' version = '1.3.0' 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. +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. +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. """ +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': '2021a'} source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] +checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] + dependencies = [ - ('Python','3.9.5'), - ('SciPy-bundle','2021.05'), - ] + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] -use_pip=True +use_pip = True moduleclass = 'bio' From 9bf9b3af85b2b2e4def1ac14c68105585482e10f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:31:45 +0200 Subject: [PATCH 155/939] adding easyconfigs: napari-0.4.15-foss-2021a.eb --- .../n/napari/napari-0.4.15-foss-2021a.eb | 161 ++++++++++++++++++ 1 file changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb new file mode 100644 index 000000000000..2eb76e76f3ed --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb @@ -0,0 +1,161 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/06 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.15' + +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': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('PyQt5', '5.15.4', '-tools'), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('dask', '2021.9.1'), + ('PyOpenGL', '3.1.5'), + ('imageio', '2.10.5'), # ext + ('tqdm', '4.61.1'), + ('IPython', '7.25.0'), + # ('VisPy', '0.6.6'), + # ('Qtconsole', '5.0.2'), + ('typing-extensions', '3.10.0.0'), + # ('scikit-image', '0.19.1') # ext . + ('networkx', '2.5.1'), # req. for scikit-image ext + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True +exts_list = [ + ('pytomlpp', '1.0.10', { + 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], + }), + ('freetype_py', '2.3.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-%(version)s.zip'], + 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', '0.10.0', { + 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], + }), + ('qtconsole', '5.3.1', { + 'checksums': ['b73723fac43938b684dcb237a88510dc7721c43a726cea8ade179a2927c0a2f3'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('docstring-parser', '0.14.1', { + 'sources': 'docstring_parser-%(version)s.tar.gz', + 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], + }), + ('pep517', '0.12.0', { + 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('magicgui', '0.5.1', { + 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], + }), + ('napari-console', '0.0.4', { + 'modulename': 'napari_console', + 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.6', { + 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], + }), + ('Pint', '0.19.2', { + 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], + }), + ('build', '0.8.0', { + 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], + }), + ('psygnal', '0.3.5', { + 'patches': ['http://two.embl.de/psygnal-0.3.5_python3.8.patch'], + 'checksums': [ + '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz + 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch + ], + }), + ('pydantic', '1.9.1', { + 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], + }), + ('typer', '0.4.1', { + 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], + }), + ('npe2', '0.5.0', { + 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], + }), + ('numpydoc', '1.4.0', { + 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], + }), + ('QtPy', '2.1.0', { + 'checksums': ['ca8cd4217175186344299ee4c0f7e7adcf362c70852ba35b255a534077025c06'], + }), + ('superqt', '0.3.2', { + 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], + }), + ('tifffile', '2022.5.4', { + 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], + }), + ('pandas', '1.3.0', { + 'checksums': ['c554e6c9cf2d5ea1aba5979cc837b3649539ced0e18ece186f055450c86622e2'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + ('PyWavelets', '1.2.0', { + 'modulename': 'pywt', + 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('scikit-image', '0.19.1', { + 'modulename': 'skimage', + 'checksums': ['48f00ee1e8ec2818ae6a152c72df15f4db7f566e839f5c34e1a0c3c9e5210138'], + }), + (name, version, { + 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], + }), +] + +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' From 8bdd165cf0f944d2c3f96df5da2bd117789ad1b9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 13:34:21 +0200 Subject: [PATCH 156/939] add psygnal-0.3.5_python3.8.patch --- .../n/napari/psygnal-0.3.5_python3.8.patch | 12 ++++++++++++ 1 file changed, 12 insertions(+) create mode 100644 easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch diff --git a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch new file mode 100644 index 000000000000..9ef096a19a41 --- /dev/null +++ b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch @@ -0,0 +1,12 @@ +#Thomas Hoffmann, EMLB Heidelberg, structures-it@embl.de +#python > 3.7: prevent comple error future feature annotations is not defined +diff -ru psygnal-0.3.5/psygnal/_evented_model.py psygnal-0.3.5_python3.8/psygnal/_evented_model.py +--- psygnal-0.3.5/psygnal/_evented_model.py 2022-05-26 02:03:19.000000000 +0200 ++++ psygnal-0.3.5_python3.8/psygnal/_evented_model.py 2022-06-23 10:41:46.536586585 +0200 +@@ -1,5 +1,4 @@ +-from __future__ import annotations +- ++import annotations + import operator + import sys + import warnings From 0c145a2e2ae761c89ff06b8ecb15cc7b20d450e4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:46:04 +0200 Subject: [PATCH 157/939] add PyQt5-5.15.4-GCCcore-10.3.0-tools.eb --- .../PyQt5-5.15.4-GCCcore-10.3.0-tools.eb | 104 ++++++++++++++++++ 1 file changed, 104 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb new file mode 100644 index 000000000000..12f9c77e512f --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb @@ -0,0 +1,104 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.4' +versionsuffix = '-tools' +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': '10.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.36.1')] +dependencies = [ + ('Python', '3.9.5'), + ('Qt5', '5.15.2'), +] + +default_easyblock = 'PythonPackage' + +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.5.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.10.1', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.9.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + # run python configure.py in order to set bindir, which is no possible with sip-install: + 'configopts': local_pyqt_configopts, + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', + 'QT_INSTALL_DATA': 'qsci', +} + +moduleclass = 'vis' From 3f22cdee665855a679086f6f28e6daa97af3798a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 13:49:45 +0200 Subject: [PATCH 158/939] fix mrcfile-1.3.0-foss-2021a.eb --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index 6222f530615f..aff2c2636c7e 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -18,7 +18,6 @@ provide basic MRC file I/O functions. """ toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = [PYPI_SOURCE] sources = [SOURCELOWER_TAR_GZ] checksums = ['3a113042d24820b9dfc6902cb9d93bcbebdee22beb40552f2c35303ace4b0547'] @@ -27,5 +26,8 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ] +download_dep_fail = True +sanity_pip_check = True + use_pip = True moduleclass = 'bio' From 128ef1d53bdeafdb44043b28a1545c2b60b725e6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 14:15:37 +0200 Subject: [PATCH 159/939] fix patch url --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb index 2eb76e76f3ed..3f04fc5590d0 100644 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb @@ -87,7 +87,7 @@ exts_list = [ 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], }), ('psygnal', '0.3.5', { - 'patches': ['http://two.embl.de/psygnal-0.3.5_python3.8.patch'], + 'patches': ['psygnal-0.3.5_python3.8.patch'], 'checksums': [ '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch From a4b320225ccaf553e112b3088604ca69f156aab0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 14:27:20 +0200 Subject: [PATCH 160/939] mrcfile-1.3.0-foss-2021a.eb: fix style --- easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb index aff2c2636c7e..c6e040ded1b2 100644 --- a/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/mrcfile/mrcfile-1.3.0-foss-2021a.eb @@ -27,7 +27,7 @@ dependencies = [ ] download_dep_fail = True -sanity_pip_check = True +sanity_pip_check = True use_pip = True moduleclass = 'bio' From 81d20f68a5a96294b2d1c0db2b034dec7172278a Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 13:37:49 +0100 Subject: [PATCH 161/939] relax tolerance of testPoly5 --- .../easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 3 +++ .../jax/jax-0.3.23_relax-testPoly5-tolerance.patch | 14 ++++++++++++++ 2 files changed, 17 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index 54a86884e763..d5c28009d974 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -95,6 +95,7 @@ exts_list = [ 'patches': [ 'jax-0.3.9_relax-test-tolerance.patch', 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', + 'jax-0.3.23_relax-testPoly5-tolerance.patch', ], 'source_tmpl': '%(name)s-v%(version)s.tar.gz', 'source_urls': ['https://github.com/google/jax/archive/'], @@ -104,6 +105,8 @@ exts_list = [ '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + '47e74771049364e8db9743f8c5f3d0d784e1e4d21595bdd07da94d5b9b42b83d'}, ], 'runtest': "pytest -n %(parallel)s tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch new file mode 100644 index 000000000000..7df1c1dfe7f5 --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch @@ -0,0 +1,14 @@ +Relax the tolerance for the testPoly5 test +Patch by Simon Branford (University of Birmingham) +--- tmp/jax-jax-v0.3.23/tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 ++++ lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 +@@ -1277,6 +1277,9 @@ + if jtu.device_under_test() == "tpu": + tol[np.int32] = tol[np.float32] = 1e-1 + tol = jtu.tolerance(dtype, tol) ++ if rank == 2 and dtype == np.int8 and a_shape == (12,): ++ # relax tolerance (from 1e-3) for testPoly5 ++ tol = 2e-3 + args_maker = lambda: [rng(a_shape * rank, dtype)] + self._CheckAgainstNumpy(np.poly, jnp.poly, args_maker, check_dtypes=False, tol=tol) + self._CompileAndCheck(jnp.poly, args_maker, check_dtypes=True, rtol=tol, atol=tol) From bcf403138bd737fdfabae7cd10805a8efaf3fe83 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 21 Oct 2022 13:43:55 +0100 Subject: [PATCH 162/939] correctly generate the patch --- easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb | 2 +- .../j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb index d5c28009d974..769a042f02fa 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2022a.eb @@ -106,7 +106,7 @@ exts_list = [ {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, {'jax-0.3.23_relax-testPoly5-tolerance.patch': - '47e74771049364e8db9743f8c5f3d0d784e1e4d21595bdd07da94d5b9b42b83d'}, + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, ], 'runtest': "pytest -n %(parallel)s tests", }), diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch index 7df1c1dfe7f5..38729edac87c 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23_relax-testPoly5-tolerance.patch @@ -1,7 +1,7 @@ Relax the tolerance for the testPoly5 test Patch by Simon Branford (University of Birmingham) ---- tmp/jax-jax-v0.3.23/tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 -+++ lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 +--- tests/lax_numpy_test.py 2022-10-12 16:23:43.000000000 +0100 ++++ tests/lax_numpy_test.py 2022-10-21 13:33:59.871417000 +0100 @@ -1277,6 +1277,9 @@ if jtu.device_under_test() == "tpu": tol[np.int32] = tol[np.float32] = 1e-1 From 8360dbde5376958b38cd69763d93758860ec5014 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:09:10 +0200 Subject: [PATCH 163/939] build missing tool pyrcc5 --- .../p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 23 ++++++++++++++----- 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index 186141973332..e21ab740946b 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -18,15 +18,26 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.5.0' @@ -57,10 +68,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], @@ -75,7 +86,7 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From 8cac0b4b373bf6eb09bcc8dcd47de39ff9927d6a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:17:52 +0200 Subject: [PATCH 164/939] adding easyconfigs: QtPy-2.2.1-GCCcore-11.2.0.eb --- .../q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..deb1b3231ed4 --- /dev/null +++ b/easybuild/easyconfigs/q/QtPy/QtPy-2.2.1-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'QtPy' +version = '2.2.1' + +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': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7d5231133b772e40b4ee514b6673aca558331e4b88ca038b26c9e16c5c95524f'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4') +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 6687320ff6d271c5b89489d0fea56c9493ab4fe6 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:20:19 +0200 Subject: [PATCH 165/939] adding easyconfigs: Qtconsole-5.3.2-GCCcore-11.2.0.eb --- .../Qtconsole-5.3.2-GCCcore-11.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..cd750a04be55 --- /dev/null +++ b/easybuild/easyconfigs/q/Qtconsole/Qtconsole-5.3.2-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Qtconsole' +version = '5.3.2' + +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': '11.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['8eadf012e83ab018295803c247c6ab7eacd3d5ab1e1d88a0f37fdcfdab9295a3'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('IPython', '7.26.0'), + ('QtPy', '2.2.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'vis' From 4e648e638a1d845d6361bbb0c0b628f8f00c9f3c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Fri, 21 Oct 2022 17:24:23 +0200 Subject: [PATCH 166/939] bump to foss/2021b --- .../n/napari/napari-0.4.15-foss-2021b.eb | 136 ++++++++++++++++++ .../n/napari/psygnal-0.3.5_python3.8.patch | 2 +- 2 files changed, 137 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb 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 new file mode 100644 index 000000000000..1326a9f443b1 --- /dev/null +++ b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb @@ -0,0 +1,136 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/10 +easyblock = 'PythonBundle' + +name = 'napari' +version = '0.4.15' + +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': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4'), + ('SciPy-bundle', '2021.10'), + ('PyYAML', '5.4.1'), + ('dask', '2022.1.0'), + ('PyOpenGL', '3.1.6'), + ('imageio', '2.13.5'), + ('tqdm', '4.62.3'), + ('IPython', '7.26.0'), + ('Qtconsole', '5.3.2'), + ('typing-extensions', '3.10.0.2'), + ('scikit-image', '0.19.1'), + ('matplotlib', '3.4.3'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True +exts_list = [ + ('pytomlpp', '1.0.10', { + 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], + }), + ('freetype_py', '2.3.0', { + 'modulename': 'freetype', + 'sources': ['freetype-py-%(version)s.zip'], + 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], + }), + ('hsluv', '5.0.3', { + 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], + }), + ('vispy', '0.10.0', { + 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], + }), + ('wrapt', '1.12.1', { + 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], + }), + ('cachey', '0.2.1', { + 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], + }), + ('docstring-parser', '0.14.1', { + 'sources': 'docstring_parser-%(version)s.tar.gz', + 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], + }), + ('pep517', '0.12.0', { + 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + ('magicgui', '0.5.1', { + 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], + }), + ('napari-console', '0.0.4', { + 'modulename': 'napari_console', + 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], + }), + ('napari-plugin-engine', '0.2.0', { + 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], + }), + ('napari-svg', '0.1.6', { + 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], + }), + ('Pint', '0.19.2', { + 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], + }), + ('build', '0.8.0', { + 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], + }), + ('psygnal', '0.3.5', { + 'patches': ['psygnal-0.3.5_python3.8.patch'], + 'checksums': [ + '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz + '34c36af20b555c7201da1c4cd26180aa446d9670f55a6e89a27152e4f50e0e29', # psygnal-0.3.5_python3.8.patch + ], + }), + ('pydantic', '1.9.1', { + 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], + }), + ('typer', '0.4.1', { + 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], + }), + ('npe2', '0.5.0', { + 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], + }), + ('numpydoc', '1.4.0', { + 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], + }), + ('superqt', '0.3.2', { + 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], + }), + ('tifffile', '2022.5.4', { + 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], + }), + ('beniget', '0.4.1', { + 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], + }), + ('ply', '3.11', { + 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], + }), + ('gast', '0.5.3', { + 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], + }), + ('pythran', '0.10.0', { + 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], + }), + (name, version, { + 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], + }), +] + +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/n/napari/psygnal-0.3.5_python3.8.patch b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch index 9ef096a19a41..b8f4bace8b27 100644 --- a/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch +++ b/easybuild/easyconfigs/n/napari/psygnal-0.3.5_python3.8.patch @@ -1,4 +1,4 @@ -#Thomas Hoffmann, EMLB Heidelberg, structures-it@embl.de +#Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 #python > 3.7: prevent comple error future feature annotations is not defined diff -ru psygnal-0.3.5/psygnal/_evented_model.py psygnal-0.3.5_python3.8/psygnal/_evented_model.py --- psygnal-0.3.5/psygnal/_evented_model.py 2022-05-26 02:03:19.000000000 +0200 From 07e39d076f350b7b76461fbcc5d205bc73539b2f Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 17:28:42 +0200 Subject: [PATCH 167/939] Delete PyQt5-5.15.4-GCCcore-10.3.0-tools.eb see #16469 --- .../PyQt5-5.15.4-GCCcore-10.3.0-tools.eb | 104 ------------------ 1 file changed, 104 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb deleted file mode 100644 index 12f9c77e512f..000000000000 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0-tools.eb +++ /dev/null @@ -1,104 +0,0 @@ -easyblock = 'Bundle' - -name = 'PyQt5' -version = '5.15.4' -versionsuffix = '-tools' -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': '10.3.0'} -toolchainopts = {'cstd': 'c++11'} - -builddependencies = [('binutils', '2.36.1')] -dependencies = [ - ('Python', '3.9.5'), - ('Qt5', '5.15.2'), -] - -default_easyblock = 'PythonPackage' - -local_sipdir = '%(installdir)s/share/sip' - -local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' - -local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " - -local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " -local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--no-stubs --no-dist-info" - -local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir -local_pyqt_configopts += "--no-stubs " -local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " -# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: -local_pyqt_configopts += "--bindir=%(installdir)s/bin " -local_pyqt_configopts += "--sipdir=%s " % local_sipdir - -local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " -local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " -local_sipver = '5.5.0' -components = [ - ('SIP', local_sipver, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], - 'start_dir': 'sip-%s' % local_sipver, - 'use_pip': True, - 'options': {'modulename': 'PyQt5.sip'}, - }), - ('PyQt-builder', '1.10.1', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['967b0c7bac0331597e9f8c5b336660f173a9896830b721d6d025e14bde647e17'], - 'start_dir': 'PyQt-builder-%(version)s', - 'use_pip': True, - }), - ('PyQt5_sip', '12.9.0', { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['d3e4489d7c2b0ece9d203ae66e573939f7f60d4d29e089c9f11daa17cfeaae32'], - 'start_dir': 'PyQt5_sip-%(version)s', - 'use_pip': True, - }), - (name, version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'ConfigureMakePythonPackage', - 'start_dir': '%(name)s-%(version)s', - 'preconfigopts': local_setup_env, - # run python configure.py in order to set bindir, which is no possible with sip-install: - 'configopts': local_pyqt_configopts, - }), - ('PyQtWebEngine', version, { - 'source_urls': [PYPI_SOURCE], - 'sources': [SOURCE_TAR_GZ], - 'checksums': ['cedc28f54165f4b8067652145aec7f732a17eadf6736835852868cf76119cc19'], - 'easyblock': 'ConfigureMakePythonPackage', - 'start_dir': '%(name)s-%(version)s', - 'preconfigopts': local_setup_env, - 'configopts': local_pyqtweb_configopts, - 'options': {'modulename': 'PyQt5.QtWebEngine'}, - }), -] - -sanity_check_paths = { - 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = [ - "python -c 'import PyQt5.QtCore'", - "sip5 --help", -] - -modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', - 'QT_INSTALL_DATA': 'qsci', -} - -moduleclass = 'vis' From 46ba80c925e0af2188ce63c74612d4a3fb718cff Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 21 Oct 2022 17:44:13 +0200 Subject: [PATCH 168/939] Delete napari-0.4.15-foss-2021a.eb --- .../n/napari/napari-0.4.15-foss-2021a.eb | 161 ------------------ 1 file changed, 161 deletions(-) delete mode 100644 easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb b/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb deleted file mode 100644 index 3f04fc5590d0..000000000000 --- a/easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021a.eb +++ /dev/null @@ -1,161 +0,0 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/06 -easyblock = 'PythonBundle' - -name = 'napari' -version = '0.4.15' - -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': '2021a'} - -dependencies = [ - ('Python', '3.9.5'), - ('PyQt5', '5.15.4', '-tools'), - ('SciPy-bundle', '2021.05'), - ('PyYAML', '5.4.1'), - ('dask', '2021.9.1'), - ('PyOpenGL', '3.1.5'), - ('imageio', '2.10.5'), # ext - ('tqdm', '4.61.1'), - ('IPython', '7.25.0'), - # ('VisPy', '0.6.6'), - # ('Qtconsole', '5.0.2'), - ('typing-extensions', '3.10.0.0'), - # ('scikit-image', '0.19.1') # ext . - ('networkx', '2.5.1'), # req. for scikit-image ext - ('matplotlib', '3.4.2'), -] - -use_pip = True -sanity_pip_check = True -download_dep_fail = True -exts_list = [ - ('pytomlpp', '1.0.10', { - 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], - }), - ('freetype_py', '2.3.0', { - 'modulename': 'freetype', - 'sources': ['freetype-py-%(version)s.zip'], - 'checksums': ['f9b64ce3272a5c358dcee824800a32d70997fb872a0965a557adca20fce7a5d0'], - }), - ('hsluv', '5.0.3', { - 'checksums': ['2586bcb61d29d76e89e563a6836df24d86939961c9657f129a59f7617de45377'], - }), - ('vispy', '0.10.0', { - 'checksums': ['b76ad6f3eacadbfc4944cfb8211eadb6ea8417a590993ece5aa7caac082cffc2'], - }), - ('qtconsole', '5.3.1', { - 'checksums': ['b73723fac43938b684dcb237a88510dc7721c43a726cea8ade179a2927c0a2f3'], - }), - ('wrapt', '1.12.1', { - 'checksums': ['b62ffa81fb85f4332a4f609cab4ac40709470da05643a082ec1eb88e6d9b97d7'], - }), - ('cachey', '0.2.1', { - 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], - }), - ('docstring-parser', '0.14.1', { - 'sources': 'docstring_parser-%(version)s.tar.gz', - 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], - }), - ('pep517', '0.12.0', { - 'checksums': ['931378d93d11b298cf511dd634cf5ea4cb249a28ef84160b3247ee9afb4e8ab0'], - }), - ('tomli', '2.0.1', { - 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], - }), - ('magicgui', '0.5.1', { - 'checksums': ['dcd05c4c9bbd55bdeb72d41069b2d4304952dabe04c2aac7bdd43f5a4e3a8a94'], - }), - ('napari-console', '0.0.4', { - 'modulename': 'napari_console', - 'checksums': ['ea0e30fbfdd76542adda44be457f1306a65146fe7578f95838e28d62874f4c45'], - }), - ('napari-plugin-engine', '0.2.0', { - 'checksums': ['fa926f869d70e0d652c005661948cd0c7fee5508ae17d437937f34f5287590b3'], - }), - ('napari-svg', '0.1.6', { - 'checksums': ['12fa5c64995fc7179349969a39316355496b463858c3b0815e3b3e7ffcdced34'], - }), - ('Pint', '0.19.2', { - 'checksums': ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'], - }), - ('build', '0.8.0', { - 'checksums': ['887a6d471c901b1a6e6574ebaeeebb45e5269a79d095fe9a8f88d6614ed2e5f0'], - }), - ('psygnal', '0.3.5', { - 'patches': ['psygnal-0.3.5_python3.8.patch'], - 'checksums': [ - '5abf84f0da9f487be68299854c4eb39de0765236407736d201f97ef39913a548', # psygnal-0.3.5.tar.gz - 'c55cc07c646cb66e8c5d2ea227249216dbd1a1a9405acbd330d70105a3fd8890', # psygnal-0.3.5_python3.8.patch - ], - }), - ('pydantic', '1.9.1', { - 'checksums': ['1ed987c3ff29fff7fd8c3ea3a3ea877ad310aae2ef9889a119e22d3f2db0691a'], - }), - ('typer', '0.4.1', { - 'checksums': ['5646aef0d936b2c761a10393f0384ee6b5c7fe0bb3e5cd710b17134ca1d99cff'], - }), - ('npe2', '0.5.0', { - 'checksums': ['3d3d43b99bbd3b189fedd7313589c89642a4af0f14b24b9763eb134ba6a5548c'], - }), - ('numpydoc', '1.4.0', { - 'checksums': ['9494daf1c7612f59905fa09e65c9b8a90bbacb3804d91f7a94e778831e6fcfa5'], - }), - ('QtPy', '2.1.0', { - 'checksums': ['ca8cd4217175186344299ee4c0f7e7adcf362c70852ba35b255a534077025c06'], - }), - ('superqt', '0.3.2', { - 'checksums': ['a37df244a2d6e4387e865cdedabe925798b3352ab9cdc52f60701eb12d907960'], - }), - ('tifffile', '2022.5.4', { - 'checksums': ['b03147a15862b7c1d90d47435197f149bef7a52c25ad67cf1f9b465faa71b8d2'], - }), - ('pandas', '1.3.0', { - 'checksums': ['c554e6c9cf2d5ea1aba5979cc837b3649539ced0e18ece186f055450c86622e2'], - }), - ('beniget', '0.4.1', { - 'checksums': ['75554b3b8ad0553ce2f607627dad3d95c60c441189875b98e097528f8e23ac0c'], - }), - ('ply', '3.11', { - 'checksums': ['00c7c1aaa88358b9c765b6d3000c6eec0ba42abca5351b095321aef446081da3'], - }), - ('gast', '0.5.3', { - 'checksums': ['cfbea25820e653af9c7d1807f659ce0a0a9c64f2439421a7bba4f0983f532dea'], - }), - ('pythran', '0.10.0', { - 'checksums': ['9dac8e1d50f33d4676003e350b1f0c878ce113e6f907920e92dc103352cac5bf'], - }), - ('PyWavelets', '1.2.0', { - 'modulename': 'pywt', - 'checksums': ['6cbd69b047bb4e00873097472133425f5f08a4e6bc8b3f0ae709274d4d5e9a8d'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('scikit-image', '0.19.1', { - 'modulename': 'skimage', - 'checksums': ['48f00ee1e8ec2818ae6a152c72df15f4db7f566e839f5c34e1a0c3c9e5210138'], - }), - (name, version, { - 'checksums': ['0d4cf6067d2112c78a705917aa5e74371463982d80147a898c6b5d2f0b514baa'], - }), -] - -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' From b5fb3cea9f0d353188d0430cb139a6f61641a707 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:46:08 +0100 Subject: [PATCH 169/939] adding easyconfigs: HTSeq-2.0.2-foss-2022a.eb --- .../h/HTSeq/HTSeq-2.0.2-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb new file mode 100644 index 000000000000..912a85950377 --- /dev/null +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb @@ -0,0 +1,42 @@ +# Updated to PythonBundle and latest version from Pypi +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'HTSeq' +version = '2.0.2' + +homepage = 'https://github.com/simon-anders/htseq' +description = """HTSeq is a Python library to facilitate processing and analysis + of data from high-throughput sequencing (HTS) experiments.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [('SWIG', '4.0.2')] + +dependencies = [ + ('Python', '3.10.4'), + ('Pysam', '0.19.1'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['e2c7442d6ff3f97293cfa0da276576f0996eae0a66eb3c2006332ef198f7ea09'], + 'modulename': '%(name)s', + }), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-count', 'bin/%(namelower)s-qa'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s/scripts'], +} + +sanity_check_commands = ['%(namelower)s-count --help'] + +moduleclass = 'bio' From 390bd6fef6998dc0f5701e8617ce384600f55aef Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:50:10 +0100 Subject: [PATCH 170/939] adding easyconfigs: psutil-5.9.3-GCCcore-11.3.0.eb --- .../p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..c8b8ea559e1b --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.3' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' From f9de54bbd6b5cff81931c993c093cf37f0bb15c1 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:52:27 +0100 Subject: [PATCH 171/939] adding easyconfigs: pybedtools-0.9.0-GCC-11.3.0.eb --- .../pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..80c02fc63c7f --- /dev/null +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'pybedtools' +version = '0.9.0' + +homepage = 'https://daler.github.io/pybedtools' +description = "pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python." + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('BEDTools', '2.30.0'), + ('Pysam', '0.19.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://daler.github.io/pybedtools/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['9267c92cd764173449d9c31baedac0659b4eccc3d7c05e22ec378f86c0fc30a3'], + }), +] + +moduleclass = 'bio' From 767f5978691fc05f090417bfe2980802277b0345 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 18:55:27 +0100 Subject: [PATCH 172/939] adding easyconfigs: TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb and patches: tfea-1.1.4-README.md.patch --- .../TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 67 ++ .../t/TFEA/tfea-1.1.4-README.md.patch | 754 ++++++++++++++++++ 2 files changed, 821 insertions(+) create mode 100644 easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb create mode 100644 easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb new file mode 100644 index 000000000000..94610d8bfd03 --- /dev/null +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -0,0 +1,67 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'TFEA' +version = '1.1.4' +_mumergever = '1.1.0' +versionsuffix = '-muMerge-%s' % _mumergever + + +homepage = 'https://github.com/Dowell-Lab/TFEA' +description = """Transcription Factor Enrichment Analysis """ + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('matplotlib', '3.5.1'), + ('SciPy-bundle', '2020.11'), + ('pybedtools', '0.8.2'), + ('psutil', '5.9.3'), + ('SWIG', '4.0.2'), + ('ncurses', '6.2'), + ('cURL', '7.72.0'), + ('XZ', '5.2.5'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +exts_list = [ + ('ujson', '5.5.0', { + 'checksums': ['b25077a971c7da47bd6846a912a747f6963776d90720c88603b1b55d81790780'], + }), + ('pysam', '0.15.2', { + 'checksums': ['d049efd91ed5b1af515aa30280bc9cb46a92ddd15d546c9b21ee68a6ed4055d9'], + }), + ('HTSeq', '2.0.2', { + 'checksums': ['e2c7442d6ff3f97293cfa0da276576f0996eae0a66eb3c2006332ef198f7ea09'], + 'modulename': '%(name)s', + }), + ('mumerge', '1.1.0', { + 'source_urls': ['https://github.com/Dowell-Lab/mumerge/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['f8afd360800567ddb4e7b602ed63ef30d22eb41d7bfbd1dc323295cdc8a98bf3'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'patches': ['tfea-1.1.4-README.md.patch'], + 'checksums': [('fa74d0e4ab11fa7ca125d86b76ee1cb66480374a220ab01d61433d4302cb9b3a'), + ('92e53d05c2422e422e6744d42afdd04ffc267a743f6a39c9c6957be3c6bf3b30')], + 'modulename': 'TFEA' + }), +] + +sanity_check_paths = { + 'files': ['bin/TFEA', 'bin/TFEA-annotate', 'bin/TFEA-simulate'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "TFEA --help", + "TFEA-simulate -h", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch b/easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch new file mode 100644 index 000000000000..4cf540c49214 --- /dev/null +++ b/easybuild/easyconfigs/t/TFEA/tfea-1.1.4-README.md.patch @@ -0,0 +1,754 @@ +Missing README.md added +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/tfea-1.1.4.orig/setup.py b/tfea-1.1.4/setup.py +index 416aa4e..14d21ff 100644 +--- a/tfea-1.1.4.orig/setup.py ++++ b/tfea-1.1.4/setup.py +@@ -3,7 +3,7 @@ import TFEA + + with open("README.md", "r") as fh: + long_description = fh.read() +- ++ + setuptools.setup( + name="tfea", + version=TFEA.__version__, #Version read from __init__.py +diff --git a/tfea-1.1.4/README.md b/tfea-1.1.4/README.md +new file mode 100644 +index 0000000..5e3975a +--- /dev/null ++++ b/tfea-1.1.4/README.md +@@ -0,0 +1,733 @@ ++

Transcription Factor Enrichment Analysis (TFEA)

++

Table of Contents

++ ++1. Pipeline ++2. Installation and Requirements ++ - TFEA ++ - DESeq ++ - Bedtools ++ - Samtools ++ - MEME Suite ++ - Image Magick ++ - FIJI Modules ++4. Basic Usage ++ - Testing TFEA ++ - Running TFEA ++5. Advanced Usage ++ - Configuration File ++ - Using SBATCH ++ - Pre-Processed Inputs ++ - Secondary Analysis (MD, MDD) ++ - Measuring TF FPKM ++ - Generating Simulated Data ++ - Rerunning TFEA ++ - Help Message ++6. Example Output ++7. Contact Information ++ ++

++ ++

TFEA Pipeline

++ ++![TFEA Pipeline](https://github.com/jdrubin91/TFEA/blob/master/README_images/TFEAPipelinev5.png) ++ ++

++ ++

Installation and Requirements

++ ++

TFEA

++ ++To install, this package and all python3 dependencies: ++ ++``` ++python3 -m pip install tfea ++``` ++ ++This should take no longer than several minutes. ++ ++Once successfully installed, you should be able to run the tfea command from anywhere, try: ++ ++``` ++TFEA --help ++``` ++ ++*Note:* If you plan to run TFEA only on FIJI using the --sbatch flag, then you only need to install DESeq and DESeq2. Otherwise, follow the instructions below for installing all TFEA dependencies. ++ ++

DESeq

++ TFEA uses DESeq or DESeq2 (depending on replicate number) to rank inputted bed files based on fold change significance. If on FIJI, make sure all gcc modules are unloaded before installing DESeq or DESeq2. This can be accomplished with: ++ ++ ``` ++ module unload gcc ++ ``` ++ ++ or ++ ++ ``` ++ module purge ++ ``` ++ ++ To install DESeq and DESeq2 type in your terminal: ++ ++ ``` ++ R ++ ++ > if (!requireNamespace("BiocManager", quietly = TRUE)) ++ > install.packages("BiocManager") ++ ++ > BiocManager::install("DESeq") ++ > BiocManager::install("DESeq2") ++ ``` ++ ++

Bedtools

++ TFEA uses Bedtools to do several genomic computations. Instructions for installing bedtools can be found here: ++ ++ Bedtools Installation ++ ++ If you are on FIJI compute cluster, bedtools is available as a module: ++ ++ ``` ++ module load bedtools/2.25.0 ++ ``` ++ ++

Samtools

++ TFEA uses samtools to index bam files. Samtools download and install instructions can be found here: ++ Samtools Download and Install ++ ++ If you are on FIJI compute cluster, bedtools is available as a module: ++ ++ ``` ++ module load samtools/1.8 ++ ``` ++ ++

MEME Suite

++ TFEA uses the MEME suite to scan sequences from inputted bed files for motif hits using the background atcg distribution form inputted bed file regions. TFEA also uses the MEME suite to generate motif logos for html display. Instructions for downloading and installing the MEME suite can be found here: ++ ++ MEME Download and Installation ++ ++ If you are on FIJI compute cluster, the meme suite is available as a module: ++ ++ ``` ++ module load meme/5.0.3 ++ ``` ++ ++

Image Magick

++ TFEA uses the meme2images script within MEME to produce motif logo figures. This requires Image Magick, which is a common linux utility package sometimes pre-installed on machines. To check if you have Image Magick installed try: ++ ++ ``` ++ identify -version ++ ``` ++ ++ If you do not have Image Magick installed, follow these instructions: ++ ++ Image Magick Download and Installation ++ ++

FIJI Modules

++ Below is a summary of all FIJI modules needed to run TFEA. ++ ++ ``` ++ module load python/3.6.3 ++ module load python/3.6.3/matplotlib/1.5.1 ++ module load python/3.6.3/scipy/0.17.1 ++ module load python/3.6.3/numpy/1.14.1 ++ module load python/3.6.3/htseq/0.9.1 ++ module load python/3.6.3/pybedtools/0.7.10 ++ ++ module load samtools/1.8 ++ module load bedtools/2.25.0 ++ module load meme/5.0.3 ++ ``` ++ ++

++

BasicUsage

++

Testing TFEA

++To make sure TFEA is installed properly, run the following tests: ++ ++*Note:* If you chose to skip installations because you were going to run TFEA using the --sbatch flag, make sure you load the appropriate modules on FIJI or these tests will fail. ++ ++``` ++TFEA --test-install ++TFEA --test-full ++``` ++ ++These should each take no longer than several minutes to run ++ ++If on a compute cluster with slurm the --sbatch flag is compatible with --test-full and is recommended on FIJI. Execute like so: ++ ++``` ++TFEA --test-full --sbatch your_email@address.com ++``` ++ ++

Running TFEA

++Once you've run the above tests successfully, you should be ready to run the full version of TFEA. Below are the minimum required inputs to run the full TFEA pipeline. Test files are provided in './TFEA/test/test_files' within this repository. ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--bed1 ./TFEA/test/test_files/SRR1105736.tfit_bidirs.chr22.bed ./TFEA/test/test_files/SRR1105737.tfit_bidirs.chr22.bed \ ++--bed2 ./TFEA/test/test_files/SRR1105738.tfit_bidirs.chr22.bed ./TFEA/test/test_files/SRR1105739.tfit_bidirs.chr22.bed \ ++--bam1 ./TFEA/test/test_files/SRR1105736.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105737.sorted.chr22.subsample.bam \ ++--bam2 ./TFEA/test/test_files/SRR1105738.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105739.sorted.chr22.subsample.bam \ ++--label1 DMSO --label2 Nutlin \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

Advanced Usage

++

Configuration File

++TFEA can be run exclusively through the command line using flags. Alternatively, TFEA can be run using a configuration file (.ini) that takes in flags as variables. For example: ++ ++``` ++TFEA --config ./TFEA/test/test_files/test_config.ini ++``` ++ ++This can be helpful to keep track of different TFEA runs and because you can use variables within the config file to clean up your input. For documentation on config files and what you can do with them see Supported INI File Structure and Interpolation of values (ExtendedInterpolation) ++ ++*Notes:* ++ ++1. Section headers (ex: `[OUTPUT]`) don't matter but you need to have at least ONE section header to be a viable .ini file. ++2. Capitalization of variables doesn't matter. ++3. Feel free to specify any additional variables you like (variables are bash-like), TFEA will only parse variables that match a flag input. ++4. If an input is provided both as a flag and in a configuration file, TFEA prioritizes the command line flag input. ++ ++Below is an example of a configuration file (./test_files/test_config.ini): ++ ++ ```bash ++[OUTPUT] ++OUTPUT='./TFEA/test/test_files/test_output/' ++LABEL1='Condition 1' ++LABEL2='Condition 2' ++ ++[DATA] ++TEST_FILES='./TFEA/test/test_files/' ++BED1=[${TEST_FILES}+'SRR1105736.tfit_bidirs.chr22.bed',${TEST_FILES}+'SRR1105737.tfit_bidirs.chr22.bed'] ++BED2=[${TEST_FILES}+'SRR1105738.tfit_bidirs.chr22.bed',${TEST_FILES}+'SRR1105739.tfit_bidirs.chr22.bed'] ++BAM1=[${TEST_FILES}+'SRR1105736.sorted.chr22.subsample.bam', ${TEST_FILES}+'SRR1105737.sorted.chr22.subsample.bam'] ++BAM2=[${TEST_FILES}+'SRR1105738.sorted.chr22.subsample.bam', ${TEST_FILES}+'SRR1105739.sorted.chr22.subsample.bam'] ++ ++[MODULES] ++TEST_FILES='./TFEA/test/test_files/' #You need to re-initialize variables within each [MODULE] ++FIMO_MOTIFS=${TEST_FILES}+'test_database.meme' ++GENOMEFASTA=${TEST_FILES}+'chr22.fa' ++ ++[OPTIONS] ++OUTPUT_TYPE='html' ++PLOTALL=True ++``` ++ ++ ++

Using SBATCH

++Specifying the `--sbatch` flag will submit TFEA to a compute cluster assuming you are logged into one. If the `--sbatch` flag is specified, it MUST be followed by an e-mail address to send job information to. For example: ++ ++ ++``` ++TFEA --config ./TFEA/test/test_files/test_config.ini --sbatch your_email@address.com ++``` ++ ++Additionally, the following flags can be used to change some of the job parameters: ++ ++``` ++ --cpus CPUS Number of processes to run in parallel. Warning: ++ Increasing this value will significantly increase ++ memory footprint. Default: 1 ++ --mem MEM Amount of memory to request forsbatch script. Default: ++ 50gb ++``` ++ ++*Note:* `--cpus` also works without the `--sbatch` flag ++ ++ ++

Using Pre-processed Inputs

++TFEA has several pipeline elements to it that a user may bypass by providing downstream pre-processed files. These files can be generated by TFEA if running the full pipeline and may also be used to speed up reruns of TFEA. Below are the three types of pre-processed inputs, short descriptions, an example of the file, and a usage example with TFEA (in some cases there are other inputs needed to go along with the pre-processed file). If multiple pre-processed inputs specified, TFEA will use the most downstream one. ++ ++

combined_file

++ ++A sorted (by chrom, start, stop) bed file containing regions of interest ++ ++Example (./test_files/test_combined_file.bed) ++``` ++#chrom start stop ++chr22 10683195 10683999 ++chr22 16609343 16609405 ++chr22 16901069 16902599 ++chr22 17036962 17037636 ++chr22 17158022 17160214 ++... ++``` ++ ++Usage with TFEA ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--combined_file ./TFEA/test/test_files/test_combined_file.bed \ ++--bam1 ./TFEA/test/test_files/SRR1105736.sorted.chr22.subsample.bam ./test_files/SRR1105737.sorted.chr22.subsample.bam \ ++--bam2 ./TFEA/test/test_files/SRR1105738.sorted.chr22.subsample.bam ./test_files/SRR1105739.sorted.chr22.subsample.bam \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

ranked_file

++ ++A ranked bed file with regions of interest. ++ ++*Note:* Specifying a ranked_file turns off some plotting functionality ++ ++Example (./test_files/test_ranked_file.bed) ++ ++``` ++#chrom start stop ++chr22 50794870 50797870 ++chr22 21554591 21557591 ++chr22 50304644 50307644 ++chr22 39096295 39099295 ++chr22 31176104 31179104 ++... ++``` ++ ++Usage with TFEA ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--ranked_file ./TFEA/test/test_files/test_ranked_file.bed \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

fasta_file

++ ++A ranked fasta file with regions of interest (sequences must have unique names but these names aren't used for anything). ++ ++*Note:* Specifying a fasta_file turns off some plotting functionality ++ ++Example (./test_files/test_fasta_file.bed) ++ ++``` ++>chr22:50794870-50797870 ++ccgccccacactgacgcagt...ccgcctcagcctcctaaa ++>chr22:21554591-21557591 ++cttggggagagcagaagcca...gtgcagtggtgcaatctt ++>chr22:50304644-50307644 ++CTGAGCACCCCCCACCAGCCA...GGAGACGGGGCCTTTGT ++... ++``` ++ ++Usage with TFEA ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--fasta_file ./TFEA/test/test_files/test_fasta_file.fa \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme ++``` ++ ++

Secondary Analysis

++TFEA can also perform MD-Score analysis and differential MD-Score analysis. This can be switched on easily if running the full pipeline: ++ ++``` ++TFEA --output ./TFEA/test/test_files/test_output \ ++--combined_file ./TFEA/test/test_files/test_combined_file.bed \ ++--bam1 ./TFEA/test/test_files/SRR1105736.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105737.sorted.chr22.subsample.bam \ ++--bam2 ./TFEA/test/test_files/SRR1105738.sorted.chr22.subsample.bam ./TFEA/test/test_files/SRR1105739.sorted.chr22.subsample.bam \ ++--label1 condition1 --label2 condition2 \ ++--genomefasta ./TFEA/test/test_files/chr22.fa \ ++--fimo_motifs ./TFEA/test/test_files/test_database.meme \ ++--md --mdd ++``` ++ ++These secondary analyses can also take pre-processed input similar to TFEA. See the 'Secondary Analysis Inputs' section in the help message for more information. ++ ++

Measuring TF FPKM

++TFEA will also measure the FPKM of TF genes within your data if desired. This requires input into the `--motif_annotations` flag which is a bed file with motif names as the 4th column. Example: ++ ++``` ++chr1 3698045 3733079 P73_HUMAN.H11MO.0.A 0 + ++chr1 6579990 6589212 ZBT48_HUMAN.H11MO.0.C 0 + ++chr1 15941868 15948495 ZBT17_HUMAN.H11MO.0.A 0 - ++chr1 23359447 23368005 ZN436_HUMAN.H11MO.0.C 0 - ++``` ++ ++This special bed file can be generated from a .meme database file using a tab-separated 2-column file containing motif names to gene names and a gene annotation file: ++ ++Example of a motif_to_gene.tsv (this was generated on the HOCOMOCO v11 website): ++ ++``` ++Model Transcription factor ++ANDR_HUMAN.H11MO.0.A AR ++AP2A_HUMAN.H11MO.0.A TFAP2A ++AP2C_HUMAN.H11MO.0.A TFAP2C ++ASCL1_HUMAN.H11MO.0.A ASCL1 ++``` ++ ++Example of gene annotations: ++ ++``` ++chr1 11873 14409 DDX11L1;NR_046018;chr1:11873-14409 0 + ++chr1 14361 29370 WASH7P;NR_024540;chr1:14361-29370 0 - ++chr1 17368 17436 MIR6859-1;NR_106918;chr1:17368-17436 0 - ++chr1 17368 17436 MIR6859-4;NR_128720;chr1:17368-17436 0 - ++chr1 17368 17436 MIR6859-3;NR_107063;chr1:17368-17436 0 - ++``` ++ ++The script works by looking for gene names that correspond to each motif within the 4th column of the gene annotation file. It expects the 4th column to be ';' delimited. ++ ++Already generated motif_annotation.bed files (and also intermediate .tsv files) are located within './motif_files/' ++ ++

Generating Simulated Data

++TFEA has a subpackage that is capable of generating simulated data for testing. If you have installed TFEA, it can be invoked with: ++ ++```TFEA-simulate --help``` ++ ++The purpose of this subpackage is to embed motif instances into fasta sequences that can be generated randomly or be from an experimental dataset (e.g. untreated control sample). There are several key flags that control this process (each of these may be a comma-delimited list of values that would indicate multiple instances of motif adding): ++ ++`--distance_mu` : This flag controls where the center of the distribution is located (note: only normal distributions are supported at this point) ++ ++`--distance_sigma` : Controls the standard deviation of the normal distribution ++ ++`--rank_range` : Controls the range of sequences in which to add a motif ++ ++`--motif_number` : Controls the number of motifs to add to your range of sequences ++ ++ ++

Rerunning TFEA

++TFEA can be easily rerun given one or multiple TFEA output folders. This works simply by rerunning the rerun.sh script which contains all command-line flag inputs. TFEA also automatically creates a copy of your configuration file (if used) within the output folder which is then also used when rerunning (so no need to worry about editing the original configuration file). To rerun a single TFEA output folder: ++ ++``` ++TFEA --rerun ./TFEA/test/test_files/test_output ++``` ++ ++The `--rerun` flag also supports patterns containing wildcards to rerun all TFEA output folders that match. For example: ++ ++``` ++TFEA --rerun ./TFEA/test/test_files/test* ++``` ++ ++This works by looking recursively into all folders and subfolders for rerun.sh scripts and then executing `sh rerun.sh`, so use with caution! ++ ++

Help Message

++Below are all the possible flags that can be provided to TFEA with a short description and default values. ++ ++``` ++usage: TFEA [-h] [--output DIR] ++ [--bed1 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]]] ++ [--bed2 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]]] ++ [--bam1 [BAM1 [BAM1 ...]]] [--bam2 [BAM2 [BAM2 ...]]] ++ [--label1 LABEL1] [--label2 LABEL2] [--config CONFIG] ++ [--sbatch SBATCH] [--test-install] [--test-full] ++ [--combined_file COMBINED_FILE] [--ranked_file RANKED_FILE] ++ [--fasta_file FASTA_FILE] [--md] [--mdd] ++ [--md_bedfile1 MD_BEDFILE1] [--md_bedfile2 MD_BEDFILE2] ++ [--mdd_bedfile1 MDD_BEDFILE1] [--mdd_bedfile2 MDD_BEDFILE2] ++ [--md_fasta1 MD_FASTA1] [--md_fasta2 MD_FASTA2] ++ [--mdd_fasta1 MDD_FASTA1] [--mdd_fasta2 MDD_FASTA2] ++ [--mdd_pval MDD_PVAL] [--mdd_percent MDD_PERCENT] ++ [--combine {intersect/merge,merge all,tfit clean,tfit remove small,False}] ++ [--rank {deseq,fc,False}] [--scanner {fimo,genome hits}] ++ [--enrichment {auc,auc_bgcorrect}] [--debug] ++ [--genomefasta GENOMEFASTA] [--fimo_motifs FIMO_MOTIFS] ++ [--fimo_thresh FIMO_THRESH] [--fimo_background FIMO_BACKGROUND] ++ [--genomehits GENOMEHITS] [--singlemotif SINGLEMOTIF] ++ [--permutations PERMUTATIONS] [--largewindow LARGEWINDOW] ++ [--smallwindow SMALLWINDOW] [--dpi DPI] [--padjcutoff PADJCUTOFF] ++ [--plotall] [--output_type {txt,html}] [--cpus CPUS] [--mem MEM] ++ [--motif_annotations MOTIF_ANNOTATIONS] [--bootstrap BOOTSTRAP] ++ [--basemean_cut BASEMEAN_CUT] [--rerun [RERUN [RERUN ...]]] ++ [--gc GC] ++ ++Transcription Factor Enrichment Analysis (TFEA) ++ ++optional arguments: ++ -h, --help show this help message and exit ++ ++Main Inputs: ++ Inputs required for full pipeline ++ ++ --output DIR, -o DIR Full path to output directory. If it exists, overwrite ++ its contents. ++ --bed1 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]] ++ Bed files associated with condition 1 ++ --bed2 [FILE1 FILE2 ... FILEN [FILE1 FILE2 ... FILEN ...]] ++ Bed files associated with condition 2 ++ --bam1 [BAM1 [BAM1 ...]] ++ Sorted bam files associated with condition 1. Must be ++ indexed. ++ --bam2 [BAM2 [BAM2 ...]] ++ Sorted bam files associated with condition 2. Must be ++ indexed. ++ --label1 LABEL1 An informative label for condition 1 ++ --label2 LABEL2 An informative label for condition 2 ++ --config CONFIG, -c CONFIG ++ A configuration file that a user may use instead of ++ specifying flags. Command line flags will overwrite ++ options within the config file. See examples in the ++ config_files folder. ++ --sbatch SBATCH, -s SBATCH ++ Submits an sbatch (slurm) job. If specified, input an ++ e-mail address. ++ --test-install, -ti Checks whether all requirements are installed and ++ command-line runnable. ++ --test-full, -t Performs unit testing on full TFEA pipeline. ++ ++Processed Inputs: ++ Input options for pre-processed data ++ ++ --combined_file COMBINED_FILE ++ A single bed file combining regions of interest. ++ --ranked_file RANKED_FILE ++ A bed file containing each regions rank as the 4th ++ column. ++ --fasta_file FASTA_FILE ++ A fasta file containing sequences to be analyzed, ++ ranked by the user. ++ ++Secondary Analysis Inputs: ++ Input options for performing MD-Score and Differential MD-Score analysis ++ ++ --md Switch that controls whether to perform MD analysis. ++ --mdd Switch that controls whether to perform differential ++ MD analysis. ++ --md_bedfile1 MD_BEDFILE1 ++ A bed file for MD-Score analysis associated with ++ condition 1. ++ --md_bedfile2 MD_BEDFILE2 ++ A bed file for MD-Score analysis associated with ++ condition 2. ++ --mdd_bedfile1 MDD_BEDFILE1 ++ A bed file for Differential MD-Score analysis ++ associated with condition 1. ++ --mdd_bedfile2 MDD_BEDFILE2 ++ A bed file for Differential MD-Score analysis ++ associated with condition 2. ++ --md_fasta1 MD_FASTA1 ++ A fasta file for MD-Score analysis associated with ++ condition 1. ++ --md_fasta2 MD_FASTA2 ++ A fasta file for MD-Score analysis associated with ++ condition 2. ++ --mdd_fasta1 MDD_FASTA1 ++ A fasta file for Differential MD-Score analysis ++ associated with condition 1. ++ --mdd_fasta2 MDD_FASTA2 ++ A fasta file for Differential MD-Score analysis ++ associated with condition 2. ++ --mdd_pval MDD_PVAL P-value cutoff for retaining differential regions. ++ Default: 0.2 ++ --mdd_percent MDD_PERCENT ++ Percentage cutoff for retaining differential regions. ++ Default: False ++ ++Module Switches: ++ Switches for different modules ++ ++ --combine {intersect/merge,merge all,tfit clean,tfit remove small,False} ++ Method for combining input bed files ++ --rank {deseq,fc,False} ++ Method for ranking combined bed file ++ --scanner {fimo,genome hits} ++ Method for scanning fasta files for motifs ++ --enrichment {auc,auc_bgcorrect} ++ Method for calculating enrichment ++ --debug Print memory and CPU usage to stderr ++ ++Scanner Options: ++ Options for performing motif scanning ++ ++ --genomefasta GENOMEFASTA ++ Genomic fasta file ++ --fimo_motifs FIMO_MOTIFS ++ Full path to a .meme formatted motif databse file. ++ Some databases included in motif_databases folder. ++ --fimo_thresh FIMO_THRESH ++ P-value threshold for calling FIMO motif hits. ++ Default: 1e-6 ++ --fimo_background FIMO_BACKGROUND ++ Options for choosing mononucleotide background ++ distribution to use with FIMO. {'largewindow', ++ 'smallwindow', int, file} ++ --genomehits GENOMEHITS ++ A folder containing bed files with pre-calculated ++ motif hits to a genome. For use with 'genome hits' ++ scanner option. ++ --singlemotif SINGLEMOTIF ++ Option to run analysis on a subset of motifs within ++ specified motif database or genome hits. Can be a ++ single motif or a comma-separated list of motifs. ++ ++Enrichment Options: ++ Options for performing enrichment analysis ++ ++ --permutations PERMUTATIONS ++ Number of permutations to perfrom for calculating ++ p-value. Default: 1000 ++ --largewindow LARGEWINDOW ++ The size (bp) of a large window around input regions ++ that captures background. Default: 1500 ++ --smallwindow SMALLWINDOW ++ The size (bp) of a small window arount input regions ++ that captures signal. Default: 150 ++ ++Output Options: ++ Options for the output. ++ ++ --dpi DPI Resolution of output figures. Default: 100 ++ --padjcutoff PADJCUTOFF ++ A p-adjusted cutoff value that determines some ++ plotting output. ++ --plotall Plot graphs for all motifs.Warning: This will make ++ TFEA run much slower andwill result in a large output ++ folder. ++ --output_type {txt,html} ++ Specify output type. Selecting html will increase ++ processing time and memory usage. Default: txt ++ ++Miscellaneous Options: ++ Other options. ++ ++ --cpus CPUS Number of processes to run in parallel. Note: ++ Increasing this value will significantly increase ++ memory footprint. Default: 1 ++ --mem MEM Amount of memory to request forsbatch script. Default: ++ 50gb ++ --motif_annotations MOTIF_ANNOTATIONS ++ A bed file specifying genomic coordinates for genes ++ corresponding to motifs. Motif name must be in the 4th ++ column and match what is in the database. ++ --bootstrap BOOTSTRAP ++ Amount to subsample motifhits to. Set to False to turn ++ off. Default: False ++ --basemean_cut BASEMEAN_CUT ++ Basemean cutoff value for inputted regions. Default: 0 ++ --rerun [RERUN [RERUN ...]] ++ Rerun TFEA in all folders of aspecified directory. ++ Default: False ++ --gc GC Perform GC-correction. Default: True ++``` ++ ++

++ ++

Example Output

++TFEA will output all files and folders into the directory specified by the `--output` flag. The output directory structure is as follows: ++ ++``` ++./TFEA/test/test_output ++│ rerun.sh ++│ test_config.ini ++│ inputs.txt ++│ results.txt ++│ md_results.txt ++│ mdd_results.txt ++│ results.html ++│ ++└───e_and_o ++│ TFEA_test_output.err ++│ TFEA_test_output.out ++│ ++└───plots ++│ logo_rcMOTIF.eps ++│ logo_rcMOTIF.png ++│ logoMOTIF.eps ++│ logoMOTIF.png ++│ MOTIF_enrichment_plot.png ++│ MOTIF_simulation_plot.png ++│ MOTIF.results.html ++│ ++└───temp_files ++ combined_file.mergeall.bed ++ count_file.bed ++ count_file.header.bed ++ DESeq.R ++ DESeq.Rout ++ DESeq.res.txt ++ markov_background.txt ++ ranked_file.bed ++ ranked_file.fa ++``` ++ ++A brief description of the files contained within this output directory are below: ++ ++

rerun.sh

++This bash script can be used at any time to regenerate a TFEA output folder in its entirety, run it using: ++ ++``` ++sh ./TFEA/test/test_output/rerun.sh ++``` ++ ++

test_config.ini

++ ++TFEA copies the config file you are using into the output directoy. This file is then referenced by rerun.sh. ++ ++ ++

inputs.txt

++ ++A .txt file that contains all user-provided inputs into TFEA ++ ++

results.txt

++Contains TFEA results tab-delimited in .txt format. For example: ++ ++``` ++#TF AUC Events p-val p-adj ++P53_HUMAN.H11MO.0.A 0.2795355012578686 5 0.02464223619276762 0.04928447238553524 ++SP2_HUMAN.H11MO.0.A -0.04994116666412335 114 0.027169601555608307 0.054339203111216615 ++``` ++ ++TF = The name of the motif analyzed ++ ++AUC = Area under the curve ++ ++Events = Number of motif hits within smallwindow ++ ++p-val = P-value ++ ++p-adj = adjusted p-value (Bonferroni) ++ ++

md_results.txt and mdd_results.txt

++Contains tab-delimited results for secondary MD-Score (MDS) and Differential MD-Score (MDD) analysis if these flags were specified ++ ++

results.html

++ ++The main results html (if `--output_type 'html'` specified). For example: ++ ++![TFEA Pipeline](https://github.com/jdrubin91/TFEA/blob/master/README_images/ExampleResults.png) ++ ++1. TFEA MA-plot - An MA-like plot with each dot representing a TF motif analyzed (red=significant below specified p-adj cutoff). On the y-axis is the area under the curve (AUC) which is the main TFEA statistic. On the x-axis is the log10 of the number of motif hits within the largewindow input ++ ++2. TFEA Volcano Plot - Similar to the MA-Plot, each dot is a TF motif (red=significant below specified p-adj cutoff). X-axis = area under the curve (AUC). Y-axis = -log10 of the p-adjusted value. Dashed line is the specified p-adjusted cutoff. ++ ++3. DE-Seq MA-plot - An actual MA-plot where each dot represents a region specified by the user. On the x-axis is the log10 of the average expression across conditions and replicates. On the y-axis is the log2 fold change between both conditions. The dots on this plot are colored based on how they are ranked. ++ ++4. Link to inputs.txt file, MD MA-plot and volcano (if `--md` specified), MDD MA-plot and volcano (if `--mdd` specified), and a table of time to perform each module in TFEA and the total time to run TFEA. ++ ++5. A list of TF motifs analyzed that have positive AUC values (headers correspond to the same headers as in results.txt). If red, then this TF motif was significant below the p-adj cutoff. Clickable links will direct to a separate MOTIF.results.html file contained within the plots/ directory in output. ++ ++6. A list of TF motifs analyzed that have negative AUC values (headers correspond to the same headers as in results.txt). If red, then this TF motif was significant below the p-adj cutoff. Clickable links will direct to a separate MOTIF.results.html file contained within the plots/ directory in output. ++ ++

MOTIF.results.html

++ ++Each signficant TF motif (or all motifs if `--plotall` specified) will produce its own MOTIF.results.html file contained within the plots/ directory in the specified output directory. All images are also self-contained within the plots/ folder. For example: ++ ++![TFEA Pipeline](https://github.com/jdrubin91/TFEA/blob/master/README_images/ExampleMotifResults.png) ++ ++1. Results for this specific motif (identical to what's reported in results.html) ++ ++2. Enrichment line plot - The running sum statistic (green) for the specified TF motif. The blue dashed line indicates the random background expectation. The area under the curve (AUC) is calculated as the area between the green and dashed blue line (directional). ++ ++3. Score bar plot - Quantification of the amount added to the running sum statistic at any given point. ++ ++4. Motif hit scatter plot - The actual motif hits for each region centered on the region and bounded by the largewindow input. ++ ++5. Rank metric fill plot - A visual representation of the ranking metric used (log10(DE-Seq p-value) with direction dependent on fold change) ++ ++6. Meta plot - A meta plot of read coverage over regions separated by quartiles. ++ ++7. Heat map - A heatmap of motif hits for each quartile ++ ++8. The forward motif logo ++ ++9. The reverse complement motif logo ++ ++10. Simulation plot - The distribution of simulated AUC values (number of simulations specified with `--permutations` flag). The observed AUC is the red bar. ++ ++

++ ++

Contact Information

++Jonathan.Rubin@colorado.edu ++ From 756cca0dc2ae8128d92391352646f9e80bf1f14b Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:31:04 +0100 Subject: [PATCH 173/939] download_dep_fail removed as PythonBundle --- easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb index 912a85950377..241a26b0ee64 100644 --- a/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb +++ b/easybuild/easyconfigs/h/HTSeq/HTSeq-2.0.2-foss-2022a.eb @@ -22,7 +22,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From fb21f3d920704c4fa21a24cbba474254ecf5e83c Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:33:45 +0100 Subject: [PATCH 174/939] download_dep_fail removed, sanity_pip_check added --- easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb index c8b8ea559e1b..062ec65ec9a7 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-11.3.0.eb @@ -13,7 +13,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [('Python', '3.10.4')] use_pip = True -download_dep_fail = True +sanity_pip_check = True exts_list = [ (name, version, { From 0b76dbb3ae04ff41c0c8aed5ca4dcc4c1760b917 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:34:55 +0100 Subject: [PATCH 175/939] download_dep_fail removed as PythonBundle --- .../easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb index 94610d8bfd03..ef3a56457dff 100644 --- a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -26,7 +26,6 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True exts_list = [ From 6986e0ef3950f7ff15acd1a0deb46ccb414f16a3 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 21 Oct 2022 22:36:39 +0100 Subject: [PATCH 176/939] download_dep_fail removed as PythonBundle --- .../easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb index 80c02fc63c7f..4b4c5f400234 100644 --- a/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pybedtools/pybedtools-0.9.0-GCC-11.3.0.eb @@ -14,7 +14,6 @@ dependencies = [ ('Pysam', '0.19.1'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 5954dcafb701f24464d162c15db74a06b7cc8006 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sat, 22 Oct 2022 10:27:25 +0200 Subject: [PATCH 177/939] adding easyconfigs: captum-0.5.0-foss-2022a-CUDA-11.7.0.eb, captum-0.5.0-foss-2022a.eb --- .../captum-0.5.0-foss-2022a-CUDA-11.7.0.eb | 33 +++++++++++++++++++ .../c/captum/captum-0.5.0-foss-2022a.eb | 31 +++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..cb2d2bdffbec --- /dev/null +++ b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'captum' +version = '0.5.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://captum.ai/' +description = """ +Captum is a model interpretability and understanding library for PyTorch. +Captum means comprehension in Latin and contains general purpose +implementations of integrated gradients, saliency maps, smoothgrad, vargrad and +others for PyTorch models. It has quick integration for models built with +domain-specific libraries such as torchvision, torchtext, and others.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['84af2c8793d34c440a351793b5ca705b8542745e2dc8bc24afb1d9b86f3bf6ec'], + }), +] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb new file mode 100644 index 000000000000..7836096aaf7c --- /dev/null +++ b/easybuild/easyconfigs/c/captum/captum-0.5.0-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'captum' +version = '0.5.0' + +homepage = 'https://captum.ai/' +description = """ +Captum is a model interpretability and understanding library for PyTorch. +Captum means comprehension in Latin and contains general purpose +implementations of integrated gradients, saliency maps, smoothgrad, vargrad and +others for PyTorch models. It has quick integration for models built with +domain-specific libraries such as torchvision, torchtext, and others.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['84af2c8793d34c440a351793b5ca705b8542745e2dc8bc24afb1d9b86f3bf6ec'], + }), +] + +moduleclass = 'ai' From ba3741e917188f3b0e2573509f515d35a63282d2 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Sat, 22 Oct 2022 11:09:12 +0200 Subject: [PATCH 178/939] Update napari-0.4.15-foss-2021b.eb remove download_dep_fail --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) 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 1326a9f443b1..914242860a4f 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 @@ -30,7 +30,6 @@ dependencies = [ use_pip = True sanity_pip_check = True -download_dep_fail = True exts_list = [ ('pytomlpp', '1.0.10', { 'checksums': ['6de110c8fe43f46c52b2041d5fbaa0522677a712234832ffd8cbb51cff50804e'], From ed4dd1f420b4222632beb2dd1b06aa94272ae6ef Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 10:29:52 +0200 Subject: [PATCH 179/939] adding easyconfigs: RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb and patches: RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch, RStudio-Server-2022.07.1+554_fix-libsoci-search.patch, RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch --- ...2022.07.1+554_allow-disabling-quarto.patch | 46 ++++++++ ...ver-2022.07.1+554_fix-libsoci-search.patch | 27 +++++ ...ver-2022.07.1+554_use-XDG_CACHE_HOME.patch | 71 +++++++++++ ...022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb | 111 ++++++++++++++++++ 4 files changed, 255 insertions(+) create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch create mode 100644 easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch new file mode 100644 index 000000000000..f57b688b6a5b --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch @@ -0,0 +1,46 @@ +From 9b7ac4b2952a47568d23f6cbfed4a797798ee161 Mon Sep 17 00:00:00 2001 +From: Kevin Ushey +Date: Fri, 19 Aug 2022 10:01:14 -0700 +Subject: [PATCH] make it possible to control QUARTO_ENABLED from command line + +--- + CMakeGlobals.txt | 26 ++++++++++++++------------ + 1 file changed, 14 insertions(+), 12 deletions(-) + +diff --git a/CMakeGlobals.txt b/CMakeGlobals.txt +index 6dfe1017a9a..cbd8e865672 100644 +--- a/CMakeGlobals.txt ++++ b/CMakeGlobals.txt +@@ -244,18 +244,20 @@ if(LINUX AND EXISTS "/etc/centos-release") + endif() + + # quarto support +-if(LINUX AND UNAME_M STREQUAL aarch64) +- # disabled on linux aarch64 +- message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") +- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") +-elseif(IS_CENTOS7) +- # disable quarto on Centos 7 +- message(STATUS "quarto is not supported on Centos7; disabling quarto") +- set(QUARTO_ENABLED FALSE CACHE INTERNAL "") +-else() +- # enable by default +- set(QUARTO_ENABLED TRUE CACHE INTERNAL "") +- add_definitions(-DQUARTO_ENABLED) ++if(NOT DEFINED QUARTO_ENABLED) ++ if(LINUX AND UNAME_M STREQUAL aarch64) ++ # disabled on linux aarch64 ++ message(STATUS "quarto does not yet support aarch64 builds of Linux; disabling quarto") ++ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") ++ elseif(IS_CENTOS7) ++ # disable quarto on Centos 7 ++ message(STATUS "quarto is not supported on Centos7; disabling quarto") ++ set(QUARTO_ENABLED FALSE CACHE INTERNAL "") ++ else() ++ # enable by default ++ set(QUARTO_ENABLED TRUE CACHE INTERNAL "") ++ add_definitions(-DQUARTO_ENABLED) ++ endif() + endif() + + # install freedesktop integration files if we are installing into /usr diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch new file mode 100644 index 000000000000..25cae4ea6dbe --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_fix-libsoci-search.patch @@ -0,0 +1,27 @@ +Allow to find system SOCI_* libraries + +Add a second `find_library` call which will find the SOCI libraries in default locations if it hasn't been found already in `SOCI_LIBRARY_DIR` +See https://github.com/rstudio/rstudio/pull/11691 + +Author: Alexander Grund (TU Dresden) + +diff --git a/src/cpp/CMakeLists.txt b/src/cpp/CMakeLists.txt +index d2be417b40..6a42b4614d 100644 +--- a/src/cpp/CMakeLists.txt ++++ b/src/cpp/CMakeLists.txt +@@ -467,12 +467,12 @@ endif() + # find SOCI libraries + if(UNIX) + set(SOCI_LIBRARY_DIR "${RSTUDIO_TOOLS_SOCI}/build/lib") +- if(NOT APPLE AND RSTUDIO_USE_SYSTEM_SOCI) +- set(SOCI_LIBRARY_DIR "/usr/lib") +- endif() + find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_CORE_LIB NAMES "libsoci_core.a" "soci_core") + find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_SQLITE_LIB NAMES "libsoci_sqlite3.a" "soci_sqlite3") + find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql" PATHS "${SOCI_LIBRARY_DIR}" NO_DEFAULT_PATH) ++ find_library(SOCI_POSTGRESQL_LIB NAMES "libsoci_postgresql.a" "soci_postgresql") + find_library(DL_LIB "dl") + find_library(SQLITE_LIB "sqlite3") + get_filename_component(SQLITE_LIB "${SQLITE_LIB}" REALPATH) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch new file mode 100644 index 000000000000..9df3a006a82e --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch @@ -0,0 +1,71 @@ +From https://github.com/rstudio/rstudio/pull/11976 + +From c131989e8ecb19733fe274fe7ad8a18d490fdcf9 Mon Sep 17 00:00:00 2001 +From: Jonathan McPherson +Date: Mon, 19 Sep 2022 14:34:18 -0700 +Subject: [PATCH] use XDG_CACHE_HOME for secure cookie key in low privilege + mode + +--- + src/cpp/core/include/core/system/Xdg.hpp | 7 +++++++ + src/cpp/core/system/Xdg.cpp | 15 +++++++++++++++ + src/cpp/server_core/SecureKeyFile.cpp | 2 +- + 3 files changed, 23 insertions(+), 1 deletion(-) + +diff --git a/src/cpp/core/include/core/system/Xdg.hpp b/src/cpp/core/include/core/system/Xdg.hpp +index 71cb2a8d50f..ed848ca2476 100644 +--- a/src/cpp/core/include/core/system/Xdg.hpp ++++ b/src/cpp/core/include/core/system/Xdg.hpp +@@ -66,6 +66,13 @@ FilePath userDataDir(const boost::optional& user = boost::none, + // Returns the user-specific logging directory underneath the userDataDir + FilePath userLogDir(); + ++// Returns the RStudio XDG user cache directory. ++// ++// On Unix-alikes, this is ~/.cache, or XDG_CACHE_HOME. ++// On Windows, this is 'FOLDERID_InternetCache' (typically 'AppData/Local/Microsoft/Windows/Temporary Files') ++FilePath userCacheDir(const boost::optional& user = boost::none, ++ const boost::optional& homeDir = boost::none); ++ + // This function verifies that the userConfigDir() and userDataDir() exist and are owned by the running user. + // + // It should be invoked once. Any issues with these directories will be emitted to the session log. +diff --git a/src/cpp/core/system/Xdg.cpp b/src/cpp/core/system/Xdg.cpp +index 3866f286437..ca1e7923ac5 100644 +--- a/src/cpp/core/system/Xdg.cpp ++++ b/src/cpp/core/system/Xdg.cpp +@@ -218,6 +218,21 @@ FilePath userDataDir( + ); + } + ++FilePath userCacheDir( ++ const boost::optional& user, ++ const boost::optional& homeDir) ++{ ++ return resolveXdgDir("RSTUDIO_CACHE_HOME", ++ "XDG_CACHE_HOME", ++#ifdef _WIN32 ++ FOLDERID_InternetCache, ++#endif ++ "~/.cache", ++ user, ++ homeDir ++ ); ++} ++ + FilePath userLogDir() + { + return userDataDir().completePath("log"); +diff --git a/src/cpp/server_core/SecureKeyFile.cpp b/src/cpp/server_core/SecureKeyFile.cpp +index d3a5e37c1bd..cbc3a91a44c 100644 +--- a/src/cpp/server_core/SecureKeyFile.cpp ++++ b/src/cpp/server_core/SecureKeyFile.cpp +@@ -113,7 +113,7 @@ core::Error readSecureKeyFile(const std::string& filename, + } + else + { +- secureKeyPath = core::FilePath("/tmp/rstudio-server").completePath(filename); ++ secureKeyPath = core::system::xdg::userCacheDir().completePath(filename); + if (secureKeyPath.exists()) + { + LOG_INFO_MESSAGE("Running without privilege; using secure key at " + secureKeyPath.getAbsolutePath()); diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb new file mode 100644 index 000000000000..1f49f98c15c5 --- /dev/null +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb @@ -0,0 +1,111 @@ +easyblock = 'CMakeNinja' + +name = 'RStudio-Server' +version = '2022.07.2+576' +versionsuffix = '-Java-%(javaver)s-R-%(rver)s' +local_git_rev = '7872775ebddc40635780ca1ed238934c3345c5de' + +homepage = 'https://www.rstudio.com/' +description = """This is the RStudio Server version. +RStudio is a set of integrated tools designed to help you be more productive with R. + +The server can be started with: + rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) + +If you need a database config one can be created with: + MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" +and then used with: + rserver ... --database-config-file "${MYTMP}/db.conf" +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/rstudio/rstudio/archive'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-2022.07.1+554_allow-disabling-quarto.patch', + '%(name)s-2022.07.1+554_fix-libsoci-search.patch', + '%(name)s-2022.07.1+554_use-XDG_CACHE_HOME.patch', +] +checksums = [ + '55705c36a9b826064b4d9aa87b58c40bb9f7cd2f149b16d554e20136306ce301', + # RStudio-Server-2022.07.1+554_allow-disabling-quarto.patch + '165306d976c7b851e1e6a2d1f0c2967984b0cd203006aa834a1a6ff17894cf81', + # RStudio-Server-2022.07.1+554_fix-libsoci-search.patch + '0dafd9fa45d745d350c0c852fe03e3e1e77558d94baae2b5c595d97765002cd5', + # RStudio-Server-2022.07.1+554_use-XDG_CACHE_HOME.patch + 'd033a383c8518a85dcdf45baf14d0a9d6283d03a28576a6eb03bbfb3682d2b00', +] + +builddependencies = [ + ('ant', '1.10.11', '-Java-%(javaver)s', SYSTEM), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('Java', '11', '', SYSTEM), + ('R', '4.2.1'), + ('SOCI', '4.0.3'), + ('yaml-cpp', '0.7.0'), +] + +osdependencies = [ + ('pam-devel', 'libpam0g-dev') +] + +# Required until https://github.com/easybuilders/easybuild-framework/pull/4035 +local_start_dir = "%(builddir)s/rstudio-" + version.replace("+", "-") + +preconfigopts = " && ".join([ + # Install dependencies via scripts. Done in subshell to preserve PWD + "(export RSTUDIO_TOOLS_ROOT='%(builddir)s'", + "cd '%s/dependencies/common'" % local_start_dir, + "./install-cef", + "./install-dictionaries", + "./install-mathjax", + "./install-pandoc", + "./install-packages", + "./install-npm-dependencies)", + "" +]) + +configopts = " ".join([ + "-DRSTUDIO_TOOLS_ROOT='%(builddir)s'", + "-DRSTUDIO_TARGET=Server", + "-DRSTUDIO_USE_SYSTEM_BOOST=ON", + "-DRSTUDIO_USE_SYSTEM_SOCI=ON", + "-DRSTUDIO_USE_SYSTEM_YAML_CPP=ON", + "-DQUARTO_ENABLED=OFF", # Not available on all archs, use pandoc fallback + "-DRSTUDIO_GIT_REVISION_HASH=" + local_git_rev +]) + +sanity_check_commands = [ + # RSession requires environment variables R_HOME and R_DOC_DIR + 'R_HOME="$EBROOTR/lib64/R" R_DOC_DIR="$R_HOME/doc" rsession --verify-installation=1', + # RServer requires a db conf (this may also be needed for live use) + # Also create and set a soem dirs so it doesn't try to use $HOME + 'MYTMP=`mktemp -d`' + ' && export RSTUDIO_CONFIG_DIR="$MYTMP"' + ' && export XDG_DATA_HOME="$MYTMP/.data"' + ' && export XDG_CACHE_HOME="$MYTMP/.cache"' + ' && mkdir "$XDG_DATA_HOME" "$XDG_CACHE_HOME"' + ' && export RS_LOG_DIR="$MYTMP/log"' + ' && echo -e "provider=sqlite\\ndirectory=$MYTMP/db" >> "$MYTMP/db.conf"' + ' && rserver ' + ' '.join([ + '--verify-installation=1', + '--server-user="$USER"', + '--database-config-file="$MYTMP/db.conf"', + '--server-data-dir="$MYTMP/sdd"', + '--secure-cookie-key-file="$MYTMP/secure-cookie-key"', + ]), +] + +sanity_check_paths = { + 'files': ['bin/rstudio-server'], + 'dirs': ['bin', 'extras', 'resources', 'www', 'www-symbolmaps', 'R'], +} + +moduleclass = 'lang' From d46d46113fd3c6840f138d95449051eac2ffa601 Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg <35767167+VRehnberg@users.noreply.github.com> Date: Mon, 24 Oct 2022 12:03:25 +0200 Subject: [PATCH 180/939] Typo dependency name "-" -> "_" Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb index 4242b5cd1ae1..f6ed3b365e2b 100644 --- a/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/t/TensorFlow-Datasets/TensorFlow-Datasets-4.7.0-foss-2021a-CUDA-11.3.1.eb @@ -30,7 +30,7 @@ exts_list = [ 'modulename': 'google', 'checksums': ['c25873c47279387cfdcbdafa36149887901d36202cb645a0e4f29686bf6e4417'], }), - ('tensorflow-metadata', '1.10.0', { + ('tensorflow_metadata', '1.10.0', { 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', 'checksums': ['e3ff528496105c0d73b2a402877525b1695635378fbe5c1b47ac7b3780816bb3'], }), From 1e50f35c8b4072935096f4275f9e9f7dfae5aa64 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 11:13:29 +0100 Subject: [PATCH 181/939] adding easyconfigs: MoviePy-1.0.3-foss-2021a.eb and patches: moviepy-1.0.3-setup.py.patch --- .../m/MoviePy/MoviePy-1.0.3-foss-2021a.eb | 42 +++++++++++++++++++ .../m/MoviePy/moviepy-1.0.3-setup.py.patch | 16 +++++++ 2 files changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb create mode 100644 easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch diff --git a/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb new file mode 100644 index 000000000000..a5a678669695 --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/MoviePy-1.0.3-foss-2021a.eb @@ -0,0 +1,42 @@ +# This easyconfig was created by Simon Branford of the BEAR Software team at the University of Birmingham. +# Updated to foss 2021a: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MoviePy' +version = '1.0.3' + +homepage = "https://zulko.github.io/moviepy/" +description = """MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, + title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('FFmpeg', '4.3.2'), + ('Python', '3.9.5'), + ('Pillow', '8.2.0'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), + ('imageio', '2.10.5'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('imageio-ffmpeg', '0.4.7', { + 'checksums': ['7a08838f97f363e37ca41821b864fd3fdc99ab1fe2421040c78eb5f56a9e723e'], + }), + ('proglog', '0.1.10', { + 'checksums': ['658c28c9c82e4caeb2f25f488fff9ceace22f8d69b15d0c1c86d64275e4ddab4'], + }), + (name, version, { + 'source_tmpl': 'moviepy-%(version)s.tar.gz', + 'patches': ['moviepy-1.0.3-setup.py.patch'], + 'checksums': [('2884e35d1788077db3ff89e763c5ba7bfddbd7ae9108c9bc809e7ba58fa433f5'), + ('beca82ff8dfbc9cd0b97296f310de3ddfc43e2e49344a32375d4438485c3f3df')], + }), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch b/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch new file mode 100644 index 000000000000..ce24edbfaea7 --- /dev/null +++ b/easybuild/easyconfigs/m/MoviePy/moviepy-1.0.3-setup.py.patch @@ -0,0 +1,16 @@ +Changed the max. version of decorator to <6.0 +https://github.com/Zulko/moviepy/blob/master/setup.py +Author: J. Sassmannshausen +diff --git a/moviepy-1.0.3.orig/setup.py b/moviepy-1.0.3/setup.py +index f8088bb..feb7da7 100644 +--- a/moviepy-1.0.3.orig/setup.py ++++ b/moviepy-1.0.3/setup.py +@@ -62,7 +62,7 @@ exec(open('moviepy/version.py').read()) # loads __version__ + + # Define the requirements for specific execution needs. + requires = [ +- 'decorator>=4.0.2,<5.0', ++ 'decorator>=4.0.2,<6.0', + "imageio>=2.5,<3.0; python_version>='3.4'", + "imageio>=2.0,<2.5; python_version<'3.4'", + "imageio_ffmpeg>=0.2.0; python_version>='3.4'", From a00e25f72c3e369e977d91da33be44b6deb3b8da Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:13:47 +0100 Subject: [PATCH 182/939] GCCcore-10.2.0 EasyConfig file added --- .../p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..9bae7e1c2bad --- /dev/null +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'psutil' +version = '5.9.3' + +homepage = 'https://github.com/giampaolo/psutil' +description = """A cross-platform process and system utilities module for Python""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +builddependencies = [('binutils', '2.35')] + +dependencies = [('Python', '3.8.6')] + +use_pip = True +download_dep_fail = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/giampaolo/psutil/archive'], + 'sources': [SOURCE_TAR_GZ], + 'checksums': ['7ccfcdfea4fc4b0a02ca2c31de7fcd186beb9cff8207800e14ab66f79c773af6'], + }), +] + +moduleclass = 'lib' From 09b501df5ed25a2b5a89c9d1e0e6a8603c753e87 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 12:36:28 +0100 Subject: [PATCH 183/939] MoviePi added, scikit-image downgraded --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 34 +++++++++++++++++-- 1 file changed, 31 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 9416f4eee394..0a0782a73aff 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -1,4 +1,6 @@ # Loosely based on PR #7680 +# Scikit-image is added as an extension to avoid problems with imageio, +# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -15,13 +17,12 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', SYSTEM), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), + ('CUDA', '11.3.1', '', True), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), - ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0', versionsuffix), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -34,6 +35,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('statsmodels', '0.12.2'), ('PyTorch', '1.10.0', versionsuffix), + ('MoviePy', '1.0.3'), ] sanity_pip_check = True @@ -56,6 +58,32 @@ exts_list = [ 'checksums': ['c667d3180513422f9c7545be5eec5d296dcbb357e06f72ed39cc683797556e69'], 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), + + # this is for scikit-image + ('PyWavelets', '1.1.1', { + 'modulename': 'pywt', + 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.5.2', { + 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], + }), + ('tifffile', '2021.10.12', { + 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], + }), + ('scikit-image', '0.18.1', { + 'modulename': 'skimage', + 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], + 'checksums': [ + 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz + # scikit-image-0.18.1_fix-README-cache-perms.patch + '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', + ], + }), + # end of scikit-image + (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], From 03c6a0b337b37f16a536474ef3f62640e119bd6c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 13:58:39 +0200 Subject: [PATCH 184/939] Remove superflous example parameter --- ...RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb index 1f49f98c15c5..b63011c23f4a 100644 --- a/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/RStudio-Server/RStudio-Server-2022.07.2+576-foss-2022a-Java-11-R-4.2.1.eb @@ -10,12 +10,12 @@ description = """This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: - rserver --server-daemonize=0 --www-port 8787 --rsession-which-r=$(which R) + rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: - rserver ... --database-config-file "${MYTMP}/db.conf" + rserver ... --database-config-file="${MYTMP}/db.conf" """ toolchain = {'name': 'foss', 'version': '2022a'} From 3fcbcc9a601c1fe03a7f05e0b0724dc85d0a8b6e Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 24 Oct 2022 14:00:56 +0200 Subject: [PATCH 185/939] Add dependencies --- .../s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb | 52 +++++++ .../yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb | 30 ++++ .../yaml-cpp-0.7.0_fix-cmake-export.patch | 143 ++++++++++++++++++ 3 files changed, 225 insertions(+) create mode 100644 easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch diff --git a/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..63024d01cc2b --- /dev/null +++ b/easybuild/easyconfigs/s/SOCI/SOCI-4.0.3-GCC-11.3.0.eb @@ -0,0 +1,52 @@ +easyblock = 'CMakeMake' + +name = 'SOCI' +version = '4.0.3' + +homepage = 'http://soci.sourceforge.net/' +description = """SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the + regular C++ code, staying entirely within the Standard C++.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/SOCI/soci/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['4b1ff9c8545c5d802fbe06ee6cd2886630e5c03bf740e269bb625b45cf934928'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Boost', '1.79.0'), + ('SQLite', '3.38.3'), + ('PostgreSQL', '14.4'), +] + +# Matches RStudio (1.4.1717) install options +# https://github.com/rstudio/rstudio/blob/ddcd7191ec89c4da00e77afae7e9f27e61e87c36/dependencies/common/install-soci +configopts = "-DCMAKE_POSITION_INDEPENDENT_CODE:BOOL=true " +configopts += "-DSOCI_TESTS=OFF " +configopts += "-DSOCI_CXX11=ON " +configopts += "-DSOCI_EMPTY=OFF " +configopts += '-DCMAKE_INCLUDE_PATH="$EBROOTBOOST/include" ' +configopts += "-DBoost_USE_STATIC_LIBS=ON " +configopts += '-DCMAKE_LIBRARY_PATH="$EBROOTBOOST/lib" ' +configopts += "-DWITH_BOOST=ON " +configopts += "-DWITH_POSTGRESQL=ON " +configopts += "-DWITH_SQLITE3=ON " +configopts += "-DWITH_DB2=OFF " +configopts += "-DWITH_MYSQL=OFF " +configopts += "-DWITH_ORACLE=OFF " +configopts += "-DWITH_FIREBIRD=OFF " +configopts += "-DWITH_ODBC=OFF " +configopts += "-DBoost_DEBUG=1 " + +local_dbs = ['postgresql', 'sqlite3'] + +sanity_check_paths = { + 'files': ['lib/libsoci_%s.%s' % (x, SHLIB_EXT) for x in local_dbs + ['core']], + 'dirs': ['include/soci/%s' % x for x in local_dbs], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..c218e476fb71 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'CMakeMake' +name = 'yaml-cpp' +version = '0.7.0' + +homepage = "https://github.com/jbeder/yaml-cpp" +description = """yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/jbeder/%(name)s/archive/'] +sources = ['%(name)s-%(version)s.tar.gz'] +patches = ['%(name)s-%(version)s_fix-cmake-export.patch'] +checksums = [ + '43e6a9fcb146ad871515f0d0873947e5d497a1c9c60c58cb102a97b47208b7c3', + 'c562a575bbb161af478795e43bfd9073e3f874bea07134a321c1063cd7098c1c', # yaml-cpp-0.7.0_fix-cmake-export.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1') +] + +sanity_check_paths = { + 'files': ['lib/libyaml-cpp.a', 'include/yaml-cpp/yaml.h'], + 'dirs': ['lib', 'include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch new file mode 100644 index 000000000000..45933bb69621 --- /dev/null +++ b/easybuild/easyconfigs/y/yaml-cpp/yaml-cpp-0.7.0_fix-cmake-export.patch @@ -0,0 +1,143 @@ +Fix installed CMake config files. +From https://patch-diff.githubusercontent.com/raw/jbeder/yaml-cpp/pull/1077 + +From a339bea6bb7bd461a41e874f78b46a5af98277ff Mon Sep 17 00:00:00 2001 +From: Felix +Date: Thu, 30 Dec 2021 12:53:31 +0100 +Subject: [PATCH 1/2] untabify CMakeLists.txt in some places + +This is to align with the other code parts in this file. +--- + CMakeLists.txt | 16 ++++++++-------- + 1 file changed, 8 insertions(+), 8 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index f65efefa..6adbf45a 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -141,30 +141,30 @@ write_basic_package_version_file( + configure_file(yaml-cpp.pc.in yaml-cpp.pc @ONLY) + + if (YAML_CPP_INSTALL) +- install(TARGETS yaml-cpp ++ install(TARGETS yaml-cpp + EXPORT yaml-cpp-targets + RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR} + LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR} + ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}) +- install(DIRECTORY ${PROJECT_SOURCE_DIR}/include/ ++ install(DIRECTORY ${PROJECT_SOURCE_DIR}/include/ + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} +- FILES_MATCHING PATTERN "*.h") ++ FILES_MATCHING PATTERN "*.h") + install(EXPORT yaml-cpp-targets + DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") +- install(FILES +- "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" ++ install(FILES ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" + DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") + install(FILES "${PROJECT_BINARY_DIR}/yaml-cpp.pc" + DESTINATION ${CMAKE_INSTALL_DATADIR}/pkgconfig) + endif() + + if(YAML_CPP_BUILD_TESTS) +- add_subdirectory(test) ++ add_subdirectory(test) + endif() + + if(YAML_CPP_BUILD_TOOLS) +- add_subdirectory(util) ++ add_subdirectory(util) + endif() + + if (YAML_CPP_CLANG_FORMAT_EXE) + +From c1f987850a6282435f499bee76b12e32d7472f12 Mon Sep 17 00:00:00 2001 +From: Felix +Date: Thu, 30 Dec 2021 15:35:54 +0100 +Subject: [PATCH 2/2] fix cmake export + +After configure the file `yaml-cpp-config.cmake.in` the result ends up with +empty variables. (see also the discussion in #774). + +Rework this file and the call to `configure_package_config_file` according the +cmake documentation +(https://cmake.org/cmake/help/v3.22/module/CMakePackageConfigHelpers.html?highlight=configure_package_config#command:configure_package_config_file) +to overcome this issue and allow a simple `find_package` after install. + +As there was some discussion about the place where to install the +`yaml-cpp-config.cmake` file, e.g. #1055, factor out the install location into +an extra variable to make it easier changing this location in the future. +--- + CMakeLists.txt | 17 ++++++++++++----- + yaml-cpp-config.cmake.in | 10 ++++++---- + 2 files changed, 18 insertions(+), 9 deletions(-) + +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 6adbf45a..e9310792 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -129,10 +129,16 @@ set_target_properties(yaml-cpp PROPERTIES + PROJECT_LABEL "yaml-cpp ${yaml-cpp-label-postfix}" + DEBUG_POSTFIX "${CMAKE_DEBUG_POSTFIX}") + ++# FIXME(felix2012): A more common place for the cmake export would be ++# `CMAKE_INSTALL_LIBDIR`, as e.g. done in ubuntu or in this project for GTest ++set(CONFIG_EXPORT_DIR "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++set(EXPORT_TARGETS yaml-cpp) + configure_package_config_file( + "${PROJECT_SOURCE_DIR}/yaml-cpp-config.cmake.in" + "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- INSTALL_DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ INSTALL_DESTINATION "${CONFIG_EXPORT_DIR}" ++ PATH_VARS CMAKE_INSTALL_INCLUDEDIR CONFIG_EXPORT_DIR) ++unset(EXPORT_TARGETS) + + write_basic_package_version_file( + "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" +@@ -150,14 +156,15 @@ if (YAML_CPP_INSTALL) + DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} + FILES_MATCHING PATTERN "*.h") + install(EXPORT yaml-cpp-targets +- DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ DESTINATION "${CONFIG_EXPORT_DIR}") + install(FILES +- "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" +- "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" +- DESTINATION "${CMAKE_INSTALL_DATADIR}/cmake/yaml-cpp") ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config.cmake" ++ "${PROJECT_BINARY_DIR}/yaml-cpp-config-version.cmake" ++ DESTINATION "${CONFIG_EXPORT_DIR}") + install(FILES "${PROJECT_BINARY_DIR}/yaml-cpp.pc" + DESTINATION ${CMAKE_INSTALL_DATADIR}/pkgconfig) + endif() ++unset(CONFIG_EXPORT_DIR) + + if(YAML_CPP_BUILD_TESTS) + add_subdirectory(test) +diff --git a/yaml-cpp-config.cmake.in b/yaml-cpp-config.cmake.in +index 7b41e3f3..a7ace3dc 100644 +--- a/yaml-cpp-config.cmake.in ++++ b/yaml-cpp-config.cmake.in +@@ -3,12 +3,14 @@ + # YAML_CPP_INCLUDE_DIR - include directory + # YAML_CPP_LIBRARIES - libraries to link against + +-# Compute paths +-get_filename_component(YAML_CPP_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH) +-set(YAML_CPP_INCLUDE_DIR "@CONFIG_INCLUDE_DIRS@") ++@PACKAGE_INIT@ ++ ++set_and_check(YAML_CPP_INCLUDE_DIR "@PACKAGE_CMAKE_INSTALL_INCLUDEDIR@") + + # Our library dependencies (contains definitions for IMPORTED targets) +-include("${YAML_CPP_CMAKE_DIR}/yaml-cpp-targets.cmake") ++include(@PACKAGE_CONFIG_EXPORT_DIR@/yaml-cpp-targets.cmake) + + # These are IMPORTED targets created by yaml-cpp-targets.cmake + set(YAML_CPP_LIBRARIES "@EXPORT_TARGETS@") ++ ++check_required_components(@EXPORT_TARGETS@) From 7211d86c16354a8e7c0e084c94e148ddd2911ffc Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 24 Oct 2022 15:18:55 +0200 Subject: [PATCH 186/939] Update napari-0.4.15-foss-2021b.eb typo --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 914242860a4f..f439e3019c21 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 @@ -1,4 +1,4 @@ -# Thomas Hoffmann, EMBL Heidelberg, structures-it@emblde, 2022/10 +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 easyblock = 'PythonBundle' name = 'napari' From 9102b2e16bb86cd14d65df2ab77d435b79bb83ba Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:32:09 +0100 Subject: [PATCH 187/939] True reverted to system, scikit-image readded and setup.py patched to newer version of scikit-image --- ...epLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb | 37 ++++--------------- 1 file changed, 7 insertions(+), 30 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb index 0a0782a73aff..ce1fb1bf8a9c 100644 --- a/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/d/DeepLabCut/DeepLabCut-2.2.0.6-foss-2021a-CUDA-11.3.1.eb @@ -1,6 +1,4 @@ # Loosely based on PR #7680 -# Scikit-image is added as an extension to avoid problems with imageio, -# which comes in from MoviePy # J. Sassmannshausen (Imperial College London/UK) easyblock = 'PythonBundle' @@ -17,12 +15,13 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True} dependencies = [ - ('CUDA', '11.3.1', '', True), - ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', True), + ('CUDA', '11.3.1', '', SYSTEM), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), ('Python', '3.9.5'), ('h5py', '3.2.1'), ('IPython', '7.25.0'), ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), ('TensorFlow', '2.6.0', versionsuffix), ('PyYAML', '5.4.1'), ('PyTables', '3.6.1'), @@ -59,34 +58,12 @@ exts_list = [ 'sources': ['msgpack-numpy-0.4.8.tar.gz'], }), - # this is for scikit-image - ('PyWavelets', '1.1.1', { - 'modulename': 'pywt', - 'checksums': ['1a64b40f6acb4ffbaccce0545d7fc641744f95351f62e4c6aaa40549326008c9'], - }), - ('imread', '0.7.4', { - 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], - }), - ('pooch', '1.5.2', { - 'checksums': ['5969b2f1defbdc405df932767e05e0b536e2771c27f1f95d7f260bc99bf13581'], - }), - ('tifffile', '2021.10.12', { - 'checksums': ['0a78268a2d844af94929512d28b39bd1ea6fe46de4124103840b5fe4e1c555cd'], - }), - ('scikit-image', '0.18.1', { - 'modulename': 'skimage', - 'patches': ['scikit-image-0.18.1_fix-README-cache-perms.patch'], - 'checksums': [ - 'fbb618ca911867bce45574c1639618cdfb5d94e207432b19bc19563d80d2f171', # scikit-image-0.18.1.tar.gz - # scikit-image-0.18.1_fix-README-cache-perms.patch - '3a941401231403808963d488aaf498a712c428c3b19a1752652be9972d82b7b8', - ], - }), - # end of scikit-image - (name, version, { 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', - 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84'], + 'patches': ['deeplabcut-2.2.0.6-setup.py.patch'], + 'checksums': ['4aa6694201e2aa56b9bd3e97ab27b0bc54f1364303167216174d2376d8ae0f84', + # deeplabcut-2.2.0.6-setup.py.patch: + '1dbef23575b105a6b2fa39f28d67bf926701d4c0b4f48bed7a6b179b7e5df2b0'], }), ] From 6edee6bab09760d21ddd8c6e7f6d3fe89767571c Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 14:35:40 +0100 Subject: [PATCH 188/939] patchfile added --- .../DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch diff --git a/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch new file mode 100644 index 000000000000..9bef2d46b0c7 --- /dev/null +++ b/easybuild/easyconfigs/d/DeepLabCut/deeplabcut-2.2.0.6-setup.py.patch @@ -0,0 +1,15 @@ +scikit-imiage version bumped to 0.18.3 to use the one in EasyBuild +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/deeplabcut-2.2.0.6.orig/setup.py b/deeplabcut-2.2.0.6/setup.py +index 3bff4f2..2e0926b 100644 +--- a/deeplabcut-2.2.0.6.orig/setup.py ++++ b/deeplabcut-2.2.0.6/setup.py +@@ -33,7 +33,7 @@ setuptools.setup( + "networkx", + "numpy", + "pandas>=1.0.1", +- "scikit-image>=0.17,<=0.18.1", ++ "scikit-image>=0.17,<=0.18.3", + "scikit-learn", + "scipy>=1.4", + "statsmodels>=0.11", From 4bf1cbefb5f7888caddb40fa7a3d9f64f168e403 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 24 Oct 2022 16:13:09 +0200 Subject: [PATCH 189/939] adding easyconfigs: Seurat-4.2.0-foss-2022a-R-4.2.1.eb --- .../Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..af03c5702855 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.2.0-foss-2022a-R-4.2.1.eb @@ -0,0 +1,51 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.2.0' +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': '2022a'} + +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 +] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('Matrix', '1.5-1', { + 'checksums': ['557dba0358172d67dc63eb5db90841915bb5ce1528f941a8005ae808d635575d'], + }), + ('SeuratObject', '4.1.2', { + 'checksums': ['6a5945f501b573dbe44a15e7d969e63fd5be0c4f8e9d716b71ca29f695236d0d'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('uwot', '0.1.14', { + 'checksums': ['8016e8192b7e72604ca71840cbe43fa1d2caed8a8ad7cbf20e85cd3b384a9fe0'], + }), + (name, version, { + 'checksums': ['22a3d22a9ba255c4db5b37339b183fdfb91e2d37a8b8d58a9ff45b1bc414ebef'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 9042e641ac937d534e88989b4ff4f67f9c79b9c0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Mon, 24 Oct 2022 16:31:52 +0200 Subject: [PATCH 190/939] Update PyQt5-5.15.4-GCCcore-11.2.0.eb add sanity check commands for pyuic5, pylupdate5, and pyrcc5 --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index e21ab740946b..97b56cff0b2b 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -93,6 +93,9 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { From bbd4bb4620ef1ee9029a862ee85207370aa1f06b Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 24 Oct 2022 15:58:10 +0100 Subject: [PATCH 191/939] download_dep_fail removed sanity_pip_check added --- easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb index 9bae7e1c2bad..6cb55d20405b 100644 --- a/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/psutil/psutil-5.9.3-GCCcore-10.2.0.eb @@ -13,7 +13,7 @@ builddependencies = [('binutils', '2.35')] dependencies = [('Python', '3.8.6')] use_pip = True -download_dep_fail = True +sanity_pip_check = True exts_list = [ (name, version, { From 29b3e49e44732deeb4ce465b77061370a363b6f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 10:06:01 +0200 Subject: [PATCH 192/939] extend acceptance of -egl dependency variant of glew to wpebackend-fdo and WebKitGTK+ --- test/easyconfigs/easyconfigs.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index f9a7d053f839..374e82ddb0c0 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -493,8 +493,12 @@ def check_dep_vars(self, gen, dep, dep_vars): 'Boost.Python': [('1.64.0;', [r'EMAN2-2\.3-'])], # GATE 9.2 requires CHLEP 2.4.5.1 and Geant4 11.0.x 'CLHEP': [('2.4.5.1;', [r'GATE-9\.2-foss-2021b'])], - # egl variant of glew is required by libwpe - 'glew': [('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0'])], + # egl variant of glew is required by libwpe, wpebackend-fdo + WebKitGTK+ depend on libwpe + 'glew': [ + ('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0', + r'wpebackend-fdo-1\.13\.1-GCCcore-11\.2\.0', + r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0']), + ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) 'HDF5': [ From 4aa4c45da8ac56279c7ac80143398e9e61fcd963 Mon Sep 17 00:00:00 2001 From: Caspar van Leeuwen Date: Tue, 25 Oct 2022 14:27:15 +0200 Subject: [PATCH 193/939] Fixed style issues --- .../p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb index c171baaaab17..d507f7f7f305 100644 --- a/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/pugixml/pugixml-1.12.1-GCCcore-11.3.0.eb @@ -25,11 +25,11 @@ configopts = " ".join([ sanity_check_paths = { 'files': [ - 'include/pugiconfig.hpp', - 'include/pugixml.hpp', - 'lib/libpugixml.a', + 'include/pugiconfig.hpp', + 'include/pugixml.hpp', + 'lib/libpugixml.a', 'lib/libpugixml.%s' % SHLIB_EXT, - 'lib/pkgconfig/pugixml.pc' + 'lib/pkgconfig/pugixml.pc' ], 'dirs': ['lib/cmake/pugixml'], } From d2341f47d675a5576b6774dff5b616606dc485fa Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 Oct 2022 15:37:31 +0200 Subject: [PATCH 194/939] @jfgrimm added sanity check commands for tools pyuic5, pylupdate5, and pyrcc5; port changes to recent-ish easyconfigs. --- ...PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 19 ++++++++++-- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb | 29 ++++++++++++++----- .../p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb | 27 +++++++++++++---- .../p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb | 3 +- 4 files changed, 60 insertions(+), 18 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 2122c835fcae..400130674cd9 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -19,15 +19,24 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' @@ -76,13 +85,17 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb index b04ed87846ee..775d1c1a6e62 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.2.0.eb @@ -19,20 +19,28 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " - local_sipver = '5.5.0' - components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], @@ -63,10 +71,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { @@ -82,13 +90,18 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip-wheel'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip-wheel --help", + "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb index 54c02ccf1914..01de04b02086 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-10.3.0.eb @@ -18,15 +18,26 @@ dependencies = [ default_easyblock = 'PythonPackage' +local_sipdir = '%(installdir)s/share/sip' + local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir local_pyqtweb_configopts += "--no-stubs --no-dist-info" +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.5.0' @@ -57,10 +68,10 @@ components = [ 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], 'checksums': ['2a69597e0dd11caabe75fae133feca66387819fc9bc050f547e5551bce97e5be'], - 'easyblock': 'Binary', + 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', - 'skipsteps': ['configure', 'build'], - 'install_cmd': local_setup_env + local_pyqt5_sip_install, + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts }), ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], @@ -75,13 +86,17 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", + "pyuic5 --help", + "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", + "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb index 97b56cff0b2b..cc175935b12c 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.4-GCCcore-11.2.0.eb @@ -86,7 +86,8 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/pyrcc5', 'bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } From c26186efb83d45bc17bf86faf76942aa68ab3174 Mon Sep 17 00:00:00 2001 From: Orient Date: Tue, 25 Oct 2022 16:20:32 +0200 Subject: [PATCH 195/939] Switched to MakeCp easyblock and applied instructions from README --- .../m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb | 22 +++++++++++++------ 1 file changed, 15 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb index 624706433b6c..b27d825a42d5 100644 --- a/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb +++ b/easybuild/easyconfigs/m/MIGRATE-N/MIGRATE-N-5.0.4-foss-2021b.eb @@ -1,4 +1,4 @@ -easyblock = 'ConfigureMake' +easyblock = 'MakeCp' name = 'MIGRATE-N' version = '5.0.4' @@ -12,7 +12,6 @@ mutations and uncertainty of the genealogy. """ toolchain = {'name': 'foss', 'version': '2021b'} -toolchainopts = {'usempi': True} source_urls = ["https://peterbeerli.com/migrate-html5/download_version4"] sources = ['migrate-%(version)s.src.tar.gz'] @@ -20,22 +19,31 @@ patches = [ 'migrate-%(version)s_install.patch', 'migrate-%(version)s_locale.patch', ] +checksums = [ + 'd25ba8ed112b81ee5fdc77759a5886b0f50ece834fd8db445b9c833742c3a1b9', # migrate-5.0.4.src.tar.gz + 'aaba4dbd8d868f80afd9645ae84d5b8c153de85a4f616a8585950593655d6fcf', # migrate-5.0.4_install.patch + '67f2dec0a2fcd432e12747f979a381f7d5e5ad73b885b485c829e50613aba35b', # migrate-5.0.4_locale.patch +] dependencies = [ ('zlib', '1.2.11'), ] -configopts = '--enable-A4 "CC=$CC" STDCPLUS=-lstdc++' -prebuildopts = 'make mpis && make clean &&' -installopts = "&& make clean && make installmpi" - parallel = 1 - start_dir = 'src' +prebuildopts = './configure --prefix=%(installdir)s --enable-A4 "CC=$CC" STDCPLUS=-lstdc++ && ' +buildopts = ' && make mpis CC="$MPICC"' +files_to_copy = [(['migrate-n', 'migrate-n-mpi'], 'bin')] + sanity_check_paths = { 'files': ['bin/%s' % x for x in ['migrate-n', 'migrate-n-mpi']], 'dirs': [], } +sanity_check_commands = [ + "echo Q | migrate-n", + "echo Q | mpirun -np 1 migrate-n-mpi", +] + moduleclass = 'bio' From cdc56f3ff989905cf61c0d04acbd2c0533db7171 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 17:09:48 +0200 Subject: [PATCH 196/939] fix installation of Python 2.7.18 with GCCcore/11.2.0 (fixes #16467) --- easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb index 40d1364f4e58..6cae29ec4ff5 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-11.2.0.eb @@ -175,6 +175,7 @@ exts_list = [ }), ('backports.entry_points_selectable', '1.1.0', { 'checksums': ['988468260ec1c196dab6ae1149260e2f5472c9110334e5d51adcb77867361f6a'], + 'preinstallopts': "sed -i 's/^author =.*/version = %(version)s/g' setup.cfg && ", }), ('virtualenv', '20.7.0', { 'checksums': ['97066a978431ec096d163e72771df5357c5c898ffdd587048f45e0aecc228094'], @@ -245,6 +246,7 @@ exts_list = [ }), ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], + 'preinstallopts': "sed -i 's/^author .*/version = %(version)s/g' setup.cfg && ", }), ('wcwidth', '0.2.5', { 'checksums': ['c4d647b99872929fdb7bdcaa4fbe7f01413ed3d98077df798530e5b04f116c83'], @@ -306,6 +308,7 @@ exts_list = [ }), ('singledispatch', '3.7.0', { 'checksums': ['c1a4d5c1da310c3fd8fccfb8d4e1cb7df076148fd5d858a819e37fffe44f3092'], + 'preinstallopts': "sed -i 's/^author .*/version = %(version)s/g' setup.cfg && ", }), ('sortedcontainers', '2.4.0', { 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], From 5e900a1aa53fc1dc8540e063ecda03a05b4d5c8d Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:17:07 +0200 Subject: [PATCH 197/939] Backport glibc-2.34 SIGSTKSZ patch --- .../easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 7 +- .../m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 8 +- .../m/M4/M4-1.4.18-GCCcore-system.eb | 7 +- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 7 +- .../m/M4/M4-1.4.18_glibc_2.34.patch | 106 ++++++++++++++++++ 24 files changed, 257 insertions(+), 23 deletions(-) create mode 100644 easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb index bc8af908fd78..6daf6b4d3ccb 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'FCC', 'version': '4.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use binutils from the OS, since M4 is itself a dependency of the easybuilt binutils (via flex and Bison) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index bd7b15d0f996..c2cdc5682d3d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index 40d8acc91af4..eb7a850b087c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index aaa4eda2c913..691dd0696ef2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index c1852324b5bd..6730f48fb80f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '11.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index 90f3441ae31f..d63b26090395 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '5.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 44174916f398..9c980305317f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -13,11 +13,17 @@ toolchain = {'name': 'GCCcore', 'version': '5.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] + # use same binutils version that was used when building GCC toolchain builddependencies = [('binutils', '2.26', '', SYSTEM)] diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index bb84008fe0db..4b63035ae7b7 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '5.5.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 42ac05376423..9a72c72b661c 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '6.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index abedf0b58b2c..c5d9b7af082d 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -16,10 +16,16 @@ toolchain = {'name': 'GCCcore', 'version': '6.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index 70675bd26d41..d6b25a708e01 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index 95c1d432cdf2..20fed34dea2e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index d435d9cf19f1..692b6fd6d431 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '7.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index 18817b26e322..e0164f7af7fc 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '7.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index f268c01aaed7..59a6abb4da21 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '8.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-%(version)s_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index cdf833ca3941..b294b3ad96ad 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index b21fcafc4f7f..c5bded456032 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index 30d2b32da00a..f8bc2dc62b3e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '8.4.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index aac98bc3c120..464d943e7b56 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '9.1.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index c70532aeb1f7..031f28e5ef49 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -13,10 +13,15 @@ toolchain = {'name': 'GCCcore', 'version': '9.2.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 61100b9eb44c..96842f7085be 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -12,10 +12,16 @@ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] + +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # use same binutils version that was used when building GCC toolchain diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb index 72020d962547..03d16d2f2b28 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb @@ -15,10 +15,15 @@ toolchainopts = {'optarch': False} sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 79f53be742fb..1c23e05d6149 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -17,10 +17,15 @@ toolchain = SYSTEM source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] -patches = ['M4-1.4.18_glibc_2.28.patch'] +patches = [ + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', +] + checksums = [ 'ab2633921a5cd38e48797bf5521ad259bdc4b979078034a3b790d7fec5493fab', # m4-1.4.18.tar.gz 'a613c18f00b1a3caa46ae4b8b849a0f4f71095ad860f4fcd6c6bb4ae211681fa', # M4-1.4.18_glibc_2.28.patch + '75f0ccc981bf313f5eb4e203a9f8b1ef9e633d840064587405cf360107d4915a', # M4-1.4.18_glibc_2.34.patch ] # '-fgnu89-inline' is required to avoid linking errors with older glibc's, diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch b/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch new file mode 100644 index 000000000000..9935b43323ac --- /dev/null +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18_glibc_2.34.patch @@ -0,0 +1,106 @@ +c-stack: stop using SIGSTKSZ + +It’s been proposed to stop making SIGSTKSZ an integer constant: +https://sourceware.org/pipermail/libc-alpha/2020-September/118028.html +Also, using SIGSTKSZ in #if did not conform to current POSIX. +Also, avoiding SIGSTKSZ makes the code simpler and easier to grok. +* lib/c-stack.c (SIGSTKSZ): Remove. +(alternate_signal_stack): Now a 64 KiB array, for simplicity. +All uses changed. + +[Retrieved (and backported) from: +https://git.savannah.gnu.org/cgit/gnulib.git/patch/?id=f9e2b20a12a230efa30f1d479563ae07d276a94b] +Signed-off-by: Fabrice Fontaine + +diff -Nura m4-1.4.18.orig/lib/c-stack.c m4-1.4.18/lib/c-stack.c +--- m4-1.4.18.orig/lib/c-stack.c 2021-04-11 19:12:14.086494029 +0200 ++++ m4-1.4.18/lib/c-stack.c 2021-04-11 19:48:46.316862760 +0200 +@@ -50,15 +50,16 @@ + #if ! HAVE_STACK_T && ! defined stack_t + typedef struct sigaltstack stack_t; + #endif +-#ifndef SIGSTKSZ +-# define SIGSTKSZ 16384 +-#elif HAVE_LIBSIGSEGV && SIGSTKSZ < 16384 +-/* libsigsegv 2.6 through 2.8 have a bug where some architectures use +- more than the Linux default of an 8k alternate stack when deciding +- if a fault was caused by stack overflow. */ +-# undef SIGSTKSZ +-# define SIGSTKSZ 16384 +-#endif ++ ++/* Storage for the alternate signal stack. ++ 64 KiB is not too large for Gnulib-using apps, and is large enough ++ for all known platforms. Smaller sizes may run into trouble. ++ For example, libsigsegv 2.6 through 2.8 have a bug where some ++ architectures use more than the Linux default of an 8 KiB alternate ++ stack when deciding if a fault was caused by stack overflow. */ ++static max_align_t alternate_signal_stack[(64 * 1024 ++ + sizeof (max_align_t) - 1) ++ / sizeof (max_align_t)]; + + #include + #include +@@ -128,19 +129,6 @@ + #if (HAVE_SIGALTSTACK && HAVE_DECL_SIGALTSTACK \ + && HAVE_STACK_OVERFLOW_HANDLING) || HAVE_LIBSIGSEGV + +-/* Storage for the alternate signal stack. */ +-static union +-{ +- char buffer[SIGSTKSZ]; +- +- /* These other members are for proper alignment. There's no +- standard way to guarantee stack alignment, but this seems enough +- in practice. */ +- long double ld; +- long l; +- void *p; +-} alternate_signal_stack; +- + static void + null_action (int signo __attribute__ ((unused))) + { +@@ -205,8 +193,8 @@ + + /* Always install the overflow handler. */ + if (stackoverflow_install_handler (overflow_handler, +- alternate_signal_stack.buffer, +- sizeof alternate_signal_stack.buffer)) ++ alternate_signal_stack, ++ sizeof alternate_signal_stack)) + { + errno = ENOTSUP; + return -1; +@@ -279,14 +267,14 @@ + stack_t st; + struct sigaction act; + st.ss_flags = 0; ++ st.ss_sp = alternate_signal_stack; ++ st.ss_size = sizeof alternate_signal_stack; + # if SIGALTSTACK_SS_REVERSED + /* Irix mistakenly treats ss_sp as the upper bound, rather than + lower bound, of the alternate stack. */ +- st.ss_sp = alternate_signal_stack.buffer + SIGSTKSZ - sizeof (void *); +- st.ss_size = sizeof alternate_signal_stack.buffer - sizeof (void *); +-# else +- st.ss_sp = alternate_signal_stack.buffer; +- st.ss_size = sizeof alternate_signal_stack.buffer; ++ st.ss_size -= sizeof (void *); ++ char *ss_sp = st.ss_sp; ++ st.ss_sp = ss_sp + st.ss_size; + # endif + r = sigaltstack (&st, NULL); + if (r != 0) +diff -Nura m4-1.4.18.orig/lib/c-stack.h m4-1.4.18/lib/c-stack.h +--- m4-1.4.18.orig/lib/c-stack.h 2021-04-11 19:12:14.098494042 +0200 ++++ m4-1.4.18/lib/c-stack.h 2021-04-11 19:17:42.138848378 +0200 +@@ -34,7 +34,7 @@ + A null ACTION acts like an action that does nothing. + + ACTION must be async-signal-safe. ACTION together with its callees +- must not require more than SIGSTKSZ bytes of stack space. Also, ++ must not require more than 64 KiB bytes of stack space. Also, + ACTION should not call longjmp, because this implementation does + not guarantee that it is safe to return to the original stack. + From bb3ab265775f54661775dd52f1b834ee4e674399 Mon Sep 17 00:00:00 2001 From: easybuild Date: Tue, 25 Oct 2022 17:42:52 +0200 Subject: [PATCH 198/939] Fix mixed spaces/tabs --- easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb | 4 ++-- easybuild/easyconfigs/m/M4/M4-1.4.18.eb | 4 ++-- 23 files changed, 46 insertions(+), 46 deletions(-) diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb index 6daf6b4d3ccb..bc86a842bf04 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-FCC-4.5.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb index c2cdc5682d3d..23e948da86e3 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb index eb7a850b087c..a8d9bfb51943 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb index 691dd0696ef2..70575029ae0f 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-10.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb index 6730f48fb80f..63f864a0d850 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-11.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb index d63b26090395..43408ff8facf 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb index 9c980305317f..7c7bb607dc63 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb index 4b63035ae7b7..1c0ae73d6d81 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-5.5.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb index 9a72c72b661c..9b67783cc40e 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb index c5d9b7af082d..5bb8c4176746 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-6.4.0.eb @@ -18,8 +18,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb index d6b25a708e01..43b5a9979944 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb index 20fed34dea2e..c6ea670638e2 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb index 692b6fd6d431..0fd28aca84fe 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb index e0164f7af7fc..3957e4980e2b 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-7.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb index 59a6abb4da21..3ae81595fa91 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb index b294b3ad96ad..a646315f4d9a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb index c5bded456032..bba6ee5bb818 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb index f8bc2dc62b3e..84ace55818bd 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-8.4.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb index 464d943e7b56..abe9dbefd210 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.1.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb index 031f28e5ef49..2db382b93212 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.2.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb index 96842f7085be..e0dffd89a28a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-9.3.0.eb @@ -14,8 +14,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb index 03d16d2f2b28..6df13418cc39 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18-GCCcore-system.eb @@ -16,8 +16,8 @@ sources = [SOURCELOWER_TAR_GZ] source_urls = [GNU_SOURCE] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ diff --git a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb index 1c23e05d6149..d181fe31631a 100644 --- a/easybuild/easyconfigs/m/M4/M4-1.4.18.eb +++ b/easybuild/easyconfigs/m/M4/M4-1.4.18.eb @@ -18,8 +18,8 @@ source_urls = [GNU_SOURCE] sources = [SOURCELOWER_TAR_GZ] patches = [ - 'M4-1.4.18_glibc_2.28.patch', - 'M4-1.4.18_glibc_2.34.patch', + 'M4-1.4.18_glibc_2.28.patch', + 'M4-1.4.18_glibc_2.34.patch', ] checksums = [ From 8657f4aa2c7c65aa9a4aa66aa3ef599667319c04 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Tue, 25 Oct 2022 18:04:47 +0200 Subject: [PATCH 199/939] @jfgrimm revert PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb --- ...PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb | 19 +++---------------- 1 file changed, 3 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb index 400130674cd9..2122c835fcae 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.1-GCCcore-9.3.0-Python-3.8.2.eb @@ -19,24 +19,15 @@ dependencies = [ default_easyblock = 'PythonPackage' -local_sipdir = '%(installdir)s/share/sip' local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " -local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin --no-tools" local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir -local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " -local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir -local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci --pyqt-sipdir=%(builddir)s/PyQt5-%(version)s/sip " local_pyqtweb_configopts += "--no-stubs --no-dist-info" -local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir -local_pyqt_configopts += "--no-stubs " -local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " -# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: -local_pyqt_configopts += "--bindir=%(installdir)s/bin " -local_pyqt_configopts += "--sipdir=%s " % local_sipdir local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_sipver = '5.4.0' @@ -85,17 +76,13 @@ components = [ ] sanity_check_paths = { - 'files': ['bin/%s' % x for x in [ - 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], + 'files': ['bin/pyqt-bundle', 'bin/sip-build', 'bin/sip-install', 'bin/sip5'], 'dirs': ['lib/python%(pyshortver)s/site-packages'], } sanity_check_commands = [ "python -c 'import PyQt5.QtCore'", "sip5 --help", - "pyuic5 --help", - "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", - "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", ] modextrapaths = { From 781250e6de3b80c19a25a58abc3e59e0ddb949d0 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 25 Oct 2022 18:50:40 +0100 Subject: [PATCH 200/939] Patch added to ensure test-jobs are not failing due to blanks (https://github.com/pybind/pybind11/issues/3680) --- ...04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch | 121 ++++++++++++++++++ .../pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 11 +- 2 files changed, 131 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch diff --git a/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch b/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch new file mode 100644 index 000000000000..5d0bcd18dba0 --- /dev/null +++ b/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch @@ -0,0 +1,121 @@ +From 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5 Mon Sep 17 00:00:00 2001 +From: =?UTF-8?q?Micha=C5=82=20G=C3=B3rny?= +Date: Thu, 3 Feb 2022 18:29:46 +0100 +URL: https://github.com/pybind/pybind11/commit/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch +Subject: [PATCH] test: Strip whitespace when comparing numpy dtypes for 1.22 + compat (#3682) + +* test: Strip whitespace when comparing numpy dtypes for 1.22 compat + +Strip whitespace when comparing numpy dtype str() in order to preserve +test compatibility with both numpy 1.22 and older versions whose output +differ by whitespace. + +Fixes #3680 + +diff --git a/pybind11-2.6.0.orig/tests/test_numpy_dtypes.py b/pybind11-2.6.0/tests/test_numpy_dtypes.py +index f56b776..228ef63 100644 +--- a/pybind11-2.6.0.orig/tests/test_numpy_dtypes.py ++++ b/pybind11-2.6.0/tests/test_numpy_dtypes.py +@@ -33,8 +33,8 @@ def dt_fmt(): + e = "<" if byteorder == "little" else ">" + return ( + "{{'names':['bool_','uint_','float_','ldbl_']," +- " 'formats':['?','" + e + "u4','" + e + "f4','" + e + "f{}']," +- " 'offsets':[0,4,8,{}], 'itemsize':{}}}" ++ "'formats':['?','" + e + "u4','" + e + "f4','" + e + "f{}']," ++ "'offsets':[0,4,8,{}],'itemsize':{}}}" + ) + + +@@ -47,7 +47,7 @@ def simple_dtype_fmt(): + def packed_dtype_fmt(): + from sys import byteorder + +- return "[('bool_', '?'), ('uint_', '{e}u4'), ('float_', '{e}f4'), ('ldbl_', '{e}f{}')]".format( ++ return "[('bool_','?'),('uint_','{e}u4'),('float_','{e}f4'),('ldbl_','{e}f{}')]".format( + np.dtype("longdouble").itemsize, e="<" if byteorder == "little" else ">" + ) + +@@ -72,7 +72,7 @@ def partial_nested_fmt(): + partial_nested_off = 8 + 8 * (ld.alignment > 8) + partial_ld_off = partial_ld_offset() + partial_nested_size = partial_nested_off * 2 + partial_ld_off + ld.itemsize +- return "{{'names':['a'], 'formats':[{}], 'offsets':[{}], 'itemsize':{}}}".format( ++ return "{{'names':['a'],'formats':[{}],'offsets':[{}],'itemsize':{}}}".format( + partial_dtype_fmt(), partial_nested_off, partial_nested_size + ) + +@@ -116,25 +116,25 @@ def test_dtype(simple_dtype): + + e = "<" if byteorder == "little" else ">" + +- assert m.print_dtypes() == [ ++ assert [x.replace(" ", "") for x in m.print_dtypes()] == [ + simple_dtype_fmt(), + packed_dtype_fmt(), +- "[('a', {}), ('b', {})]".format(simple_dtype_fmt(), packed_dtype_fmt()), ++ "[('a',{}),('b',{})]".format(simple_dtype_fmt(), packed_dtype_fmt()), + partial_dtype_fmt(), + partial_nested_fmt(), +- "[('a', 'S3'), ('b', 'S3')]", ++ "[('a','S3'),('b','S3')]", + ( +- "{{'names':['a','b','c','d'], " +- + "'formats':[('S4', (3,)),('" ++ "{{'names':['a','b','c','d']," ++ + "'formats':[('S4',(3,)),('" + + e +- + "i4', (2,)),('u1', (3,)),('" ++ + "i4',(2,)),('u1',(3,)),('" + + e +- + "f4', (4, 2))], " +- + "'offsets':[0,12,20,24], 'itemsize':56}}" ++ + "f4',(4,2))]," ++ + "'offsets':[0,12,20,24],'itemsize':56}}" + ).format(e=e), +- "[('e1', '" + e + "i8'), ('e2', 'u1')]", +- "[('x', 'i1'), ('y', '" + e + "u8')]", +- "[('cflt', '" + e + "c8'), ('cdbl', '" + e + "c16')]", ++ "[('e1','" + e + "i8'),('e2','u1')]", ++ "[('x','i1'),('y','" + e + "u8')]", ++ "[('cflt','" + e + "c8'),('cdbl','" + e + "c16')]", + ] + + d1 = np.dtype( +@@ -228,7 +228,7 @@ def test_recarray(simple_dtype, packed_dtype): + ] + + arr = m.create_rec_partial(3) +- assert str(arr.dtype) == partial_dtype_fmt() ++ assert str(arr.dtype).replace(" ", "") == partial_dtype_fmt() + partial_dtype = arr.dtype + assert "" not in arr.dtype.fields + assert partial_dtype.itemsize > simple_dtype.itemsize +@@ -236,7 +236,7 @@ def test_recarray(simple_dtype, packed_dtype): + assert_equal(arr, elements, packed_dtype) + + arr = m.create_rec_partial_nested(3) +- assert str(arr.dtype) == partial_nested_fmt() ++ assert str(arr.dtype).replace(" ", "") == partial_nested_fmt() + assert "" not in arr.dtype.fields + assert "" not in arr.dtype.fields["a"][0].fields + assert arr.dtype.itemsize > partial_dtype.itemsize +@@ -275,12 +275,12 @@ def test_array_array(): + e = "<" if byteorder == "little" else ">" + + arr = m.create_array_array(3) +- assert str(arr.dtype) == ( +- "{{'names':['a','b','c','d'], " +- + "'formats':[('S4', (3,)),('" ++ assert str(arr.dtype).replace(" ", "") == ( ++ "{{'names':['a','b','c','d']," ++ + "'formats':[('S4',(3,)),('" + + e +- + "i4', (2,)),('u1', (3,)),('{e}f4', (4, 2))], " +- + "'offsets':[0,12,20,24], 'itemsize':56}}" ++ + "i4',(2,)),('u1',(3,)),('{e}f4',(4,2))]," ++ + "'offsets':[0,12,20,24],'itemsize':56}}" + ).format(e=e) + assert m.print_array_array(arr) == [ + "a={{A,B,C,D},{K,L,M,N},{U,V,W,X}},b={0,1}," diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 60135a6d7f6b..8e9b6e72bfe2 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -1,3 +1,7 @@ +# include patch to fix failing test jobs due to additional white space +# see https://github.com/pybind/pybind11/issues/3680 +# Authors: J. Sassmannshausen / Alexander Grund + name = 'pybind11' version = '2.6.0' @@ -9,7 +13,12 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -checksums = ['90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571'] +patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +checksums = [ + '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', + # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', +] builddependencies = [ ('binutils', '2.35'), From ad17fc07ee1bdc8748cff9da1619b117e3443e44 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 25 Oct 2022 21:55:37 +0200 Subject: [PATCH 201/939] work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml --- .../easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb index 630fe512e041..7dfe39787ec1 100644 --- a/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-2.7.16-GCCcore-8.3.0.eb @@ -37,6 +37,11 @@ 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 = """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 Sept 13th 2019 exts_list = [ @@ -125,6 +130,7 @@ exts_list = [ ('PyNaCl', '1.3.0', { 'modulename': 'nacl', 'checksums': ['0c6100edd16fefd1557da078c7a31e7b7d7a52ce39fdca2bec29d4f7b6e7600c'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('bcrypt', '3.1.7', { 'checksums': ['0b0069c752ec14172c5f78208f1863d7ad6755a6fae6fe76ec2c80d13be41e42'], @@ -209,9 +215,11 @@ exts_list = [ }), ('importlib_metadata', '0.22', { 'checksums': ['652234b6ab8f2506ae58e528b6fbcc668831d3cc758e1bc01ef438d328b68cdb'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), ('pluggy', '0.13.0', { 'checksums': ['fa5fa1622fa6dd5c030e9cad086fa19ef6a0cf6d7a2d12318e10cb49d6d68f34'], + 'preinstallopts': local_fix_pyproject_toml_cmd, }), # more-itertools 5.0.0 is the most recent version still supporting Python 2.x ('more-itertools', '5.0.0', { From 36183b5d248d5dfa112a3414b38b6c92c83dccfe Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 26 Oct 2022 09:41:15 +0200 Subject: [PATCH 202/939] avoid that ~/.ccache is used when building/installing WebKitGTK+ --- .../easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb index 5e41bdddcfba..d944a2691e6e 100644 --- a/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/w/WebKitGTK+/WebKitGTK+-2.37.1-GCC-11.2.0.eb @@ -77,6 +77,9 @@ configopts += "-DENABLE_GAMEPAD=OFF -DUSE_LIBSECRET=OFF -DUSE_LIBHYPHEN=OFF " configopts += "-DUSE_WOFF2=OFF -DENABLE_JOURNALD_LOG=OFF -DENABLE_BUBBLEWRAP_SANDBOX=OFF " configopts += "-DENABLE_INTROSPECTION=OFF -DUSE_LIBNOTIFY=OFF " +prebuildopts = "export CCACHE_DIR=%(builddir)s/ccache && " +preinstallopts = prebuildopts + sanity_check_paths = { 'files': ['bin/WebKitWebDriver', 'lib/libwebkit2gtk-4.1.%s' % SHLIB_EXT, 'lib/libjavascriptcoregtk-4.1.%s' % SHLIB_EXT], From f02b3d7184ab235372c4de70876b1e83bd5b8818 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 26 Oct 2022 09:42:51 +0100 Subject: [PATCH 203/939] remove ExomeDepth from recent R-bundle-Bioconductor --- .../R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 --- 3 files changed, 9 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb index b7133459ca43..761944fd152e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.14-foss-2021b-R-4.1.2.eb @@ -1075,9 +1075,6 @@ exts_list = [ ('M3Drop', '1.20.0', { 'checksums': ['b82772303c624ff01418e66cefd751a0f6f9d819ea2cf3c9c20a9acd1fc106e5'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.30.0', { 'checksums': ['2dada40e222d4f42510deeb99c24043078420a4d3d214d4cc3409d428cfb60c4'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 15af98e6e4b4..1c4ffc3555e8 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1060,9 +1060,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 209068efaa57..e9595a58dd46 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1059,9 +1059,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), From ace549bec0cd223ae2c0b2885306453f59cb9945 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 11:49:59 +0200 Subject: [PATCH 204/939] adding easyconfigs: NiBabel-4.0.2-foss-2022a.eb, pydicom-2.3.0-GCCcore-11.3.0.eb --- .../n/NiBabel/NiBabel-4.0.2-foss-2022a.eb | 46 +++++++++++++++++++ .../p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb | 26 +++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb b/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb new file mode 100644 index 000000000000..2691a91e34a9 --- /dev/null +++ b/easybuild/easyconfigs/n/NiBabel/NiBabel-4.0.2-foss-2022a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'NiBabel' +version = '4.0.2' + +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), + ('pydicom', '2.3.0'), +] + +use_pip = True + +exts_list = [ + ('bz2file', '0.98', { + 'checksums': ['64c1f811e31556ba9931953c8ec7b397488726c63e09a4c67004f43bdd28da88'], + }), + ('nibabel', version, { + 'checksums': ['45c49b5349351b45f6c045a91aa02b4f0d367686ff3284632ef95ac65b930786'], + }), +] + +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-2.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a92eebf56b97 --- /dev/null +++ b/easybuild/easyconfigs/p/pydicom/pydicom-2.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'pydicom' +version = '2.3.0' + +homepage = 'https://pydicom.github.io/' +description = "Pure python package for DICOM medical file reading and writing." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['e50dfa6bc44516816248c750a93b07fa577b867433bd8bf4fd3319a4a19259a5'] + +builddependencies = [ + ('binutils', '2.38'), +] +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' From 1f1ddd397839cc246317b5cfa9333199ad7068ff Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 26 Oct 2022 12:20:49 +0200 Subject: [PATCH 205/939] adding easyconfigs: IJulia-1.23.3-Julia-1.6.7.eb --- .../i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb new file mode 100644 index 000000000000..54566147c74f --- /dev/null +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb @@ -0,0 +1,87 @@ +easyblock = 'Bundle' + +name = 'IJulia' +version = '1.23.3' +_julia_ver = '1.6.7' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaLang/IJulia.jl' +description = "Julia kernel for Jupyter" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +exts_defaultclass = 'JuliaPackage' +exts_filter = ("julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + +exts_list = [ + ('Parsers', '2.4.2', { + 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], + 'checksums': ['44036a59b047f704d6b7841e3edf12fe2a53aa797254086fdd0709f0cdebac89'], + }), + ('JSON', '0.21.3', { + 'source_urls': ['https://github.com/JuliaIO/JSON.jl/archive/'], + 'checksums': ['bd02a015da24b03f79d55967b29f5ceaba2477b559242576d74f02623bb1b6b1'], + }), + ('MbedTLS', '1.1.7', { + 'source_urls': ['https://github.com/JuliaLang/MbedTLS.jl/archive/'], + 'checksums': ['3df27a16ea31acf4eaf6cc9f3bd25b81960c10662722ffa22b13cb0e6ac11b12'], + }), + ('VersionParsing', '1.3.0', { + 'source_urls': ['https://github.com/JuliaInterop/VersionParsing.jl/archive/'], + 'checksums': ['f90fe419e1a40ef0eccfaaed1d1b7792d9115a059a82d0c23e3c04c944d0f8ca'], + }), + ('Conda', '1.7.0', { + 'source_urls': ['https://github.com/JuliaPy/Conda.jl/archive/'], + 'checksums': ['2077b1192e1cfa206caf441d9d91b0ca83aa935db89918f1fd69cd25c2415ced'], + }), + ('SoftGlobalScope', '1.1.0', { + 'source_urls': ['https://github.com/stevengj/SoftGlobalScope.jl/archive/'], + 'checksums': ['8d4264386c859403938498cd9ddd5e94e10181deba4a3e71d391b16750e3848b'], + }), + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], + }), + ('libsodium_jll', '1.0.20+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libsodium_jll.jl/archive/'], + 'sources': [{'filename': 'libsodium-v%(version)s.tar.gz'}], + 'checksums': ['f7c3a17acc3a478ec10a4a49a0dd04694140f4483644ec9db638706ea9844aba'], + }), + ('ZeroMQ_jll', '4.3.4+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/ZeroMQ_jll.jl/archive/'], + 'sources': [{'filename': 'ZeroMQ-v%(version)s.tar.gz'}], + 'checksums': ['aa98ae3c7e050fc6bdf0b0132bb607dea2f6c062da7870b1ecada9f3c8ea8d72'], + }), + ('ZMQ', '1.2.1', { + 'source_urls': ['https://github.com/JuliaInterop/ZMQ.jl/archive/'], + 'checksums': ['8b42555340d0208e5a36cd5e8f29a3f0d44c13c064382d4b1e5d00c1c4a9dd96'], + }), + (name, version, { + 'source_urls': ['https://github.com/JuliaLang/IJulia.jl/archive/'], + 'checksums': ['1471ed94093efd24bae5e6ff1d3f7fa61901bf8834a737eeae2a9e620f50f07c'], + 'preinstallopts': "mkdir -p %(installdir)s/jupyter && export JUPYTER_DATA_DIR=%(installdir)s/jupyter && ", + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['packages'], +} + +modextrapaths = { + 'JULIA_DEPOT_PATH': '', + 'JUPYTER_PATH': 'jupyter', +} + +moduleclass = 'lib' From 3b68a7b68e8b390f477d58adca126af3e4e24aa8 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 12:18:12 +0100 Subject: [PATCH 206/939] Name of patchfile changed --- .../easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb | 4 ++-- ...5.patch => pybind11-2.6.0_fix-test-extra-whitespace.patch} | 0 2 files changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/p/pybind11/{1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch => pybind11-2.6.0_fix-test-extra-whitespace.patch} (100%) diff --git a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb index 8e9b6e72bfe2..9eddf8c8ef26 100644 --- a/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0-GCCcore-10.2.0.eb @@ -13,10 +13,10 @@ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} source_urls = ['https://github.com/pybind/pybind11/archive/'] sources = ['v%(version)s.tar.gz'] -patches = ['1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch'] +patches = ['pybind11-2.6.0_fix-test-extra-whitespace.patch'] checksums = [ '90b705137b69ee3b5fc655eaca66d0dc9862ea1759226f7ccd3098425ae69571', - # 1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch: + # pybind11-2.6.0_fix-test-extra-whitespace.patch: 'f0ff7416d14f9589b5d100ad021e18690cb08cb662df9d0ac21327d04bdb96fc', ] diff --git a/easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch b/easybuild/easyconfigs/p/pybind11/pybind11-2.6.0_fix-test-extra-whitespace.patch similarity index 100% rename from easybuild/easyconfigs/p/pybind11/1d3b04e805c8a7dd4d8b68e2a311c75a66cae1d5.patch rename to easybuild/easyconfigs/p/pybind11/pybind11-2.6.0_fix-test-extra-whitespace.patch From 4ddd6621d457e813acbaa22d94b5d1e69e3c46b0 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 13:51:19 +0200 Subject: [PATCH 207/939] adding easyconfigs: dask-2022.10.0-foss-2022a.eb, bokeh-2.4.3-foss-2022a.eb --- .../b/bokeh/bokeh-2.4.3-foss-2022a.eb | 38 ++++++++++ .../d/dask/dask-2022.10.0-foss-2022a.eb | 72 +++++++++++++++++++ 2 files changed, 110 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb create mode 100644 easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb new file mode 100644 index 000000000000..4f2830449ae5 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-2.4.3-foss-2022a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '2.4.3' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('Pillow', '9.1.1'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True + +exts_list = [ + ('tornado', '6.1', { + 'checksums': ['33c6e81d7bd55b468d2e793517c909b139960b6c790a60b7991b9b6b76fb9791'], + }), + (name, version, { + 'checksums': ['ef33801161af379665ab7a34684f2209861e3aefd5c803a21fbbb99d94874b03'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb b/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb new file mode 100644 index 000000000000..ab9413891e94 --- /dev/null +++ b/easybuild/easyconfigs/d/dask/dask-2022.10.0-foss-2022a.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'dask' +version = '2022.10.0' + +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), + ('SciPy-bundle', '2022.05'), + ('bokeh', '2.4.3'), +] + +use_pip = True + +exts_list = [ + ('toolz', '0.12.0', { + 'checksums': ['88c570861c440ee3f2f6037c4654613228ff40c93a6c25e0eba70d17282c6194'], + }), + ('locket', '1.0.0', { + 'checksums': ['5c0d4c052a8bbbf750e056a8e65ccd309086f4f0f18a2eac306a8dfa4112a632'], + }), + ('partd', '1.3.0', { + 'checksums': ['ce91abcdc6178d668bcaa431791a5a917d902341cb193f543fe445d494660485'], + }), + ('fsspec', '2021.7.0', { + 'checksums': ['792ebd3b54de0b30f1ce73f0ba0a8bcc864724f2d9f248cb8d0ece47db0cbde8'], + }), + ('HeapDict', '1.0.1', { + 'checksums': ['8495f57b3e03d8e46d5f1b2cc62ca881aca392fd5cc048dc0aa2e1a6d23ecdb6'], + }), + ('zict', '2.2.0', { + 'checksums': ['d7366c2e2293314112dcf2432108428a67b927b00005619feefc310d12d833f3'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'checksums': ['f277a3b300ecc1d0be232a339f346dff686e0becdb0843c0aaf2ae943d5492d3'], + }), + ('distributed', version, { + 'checksums': ['dcfbc9c528bcd9e4f9686e673956a90172826395ac5b258039e580777d50782f'], + }), + ('dask-mpi', '2022.4.0', { + 'checksums': ['0a04f1d7d35a06cdff506593330d4414ea242c9172498ce191f5742eac499e17'], + }), + ('docrep', '0.3.2', { + 'checksums': ['ed8a17e201abd829ef8da78a0b6f4d51fb99a4cbd0554adbed3309297f964314'], + }), + ('dask-jobqueue', '0.8.1', { + 'checksums': ['16fd1b646a073ad3de75dde12a0dfe529b836f21a3bdbcee2a88bef24e9112a7'], + }), +] + +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 9a1bce2ff7b11da801999840338254fca578060d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Wed, 26 Oct 2022 17:32:55 +0200 Subject: [PATCH 208/939] adding easyconfigs: ITK-5.2.1-foss-2022a.eb --- .../easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb new file mode 100644 index 000000000000..22f773b4840c --- /dev/null +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb @@ -0,0 +1,59 @@ +# Contributors: +# Fenglai Liu (fenglai@accre.vanderbilt.edu) - Vanderbilt University +# Alex Domingo (alex.domingo.toro@vub.be) - Vrije Universiteit Brussel (VUB) +# Denis Kristak (INUITS) +# +easyblock = 'CMakeMake' + +name = 'ITK' +version = '5.2.1' + +homepage = 'https://itk.org' +description = """Insight Segmentation and Registration Toolkit (ITK) provides + an extensive suite of software tools for registering and segmenting + multidimensional imaging data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +github_account = 'InsightSoftwareConsortium' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['6022b2b64624b8bcec3333fe48d5f74ff6ebceb3bdf98258ba7d7fbbc76b99ab'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Bison', '3.8.2'), + ('Eigen', '3.4.0'), +] +dependencies = [ + ('expat', '2.4.8'), + ('HDF5', '1.12.2'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('VTK', '9.2.0.rc2'), + ('zlib', '1.2.12'), +] + +local_sys_deps = ['EIGEN', 'EXPAT', 'HDF5', 'JPEG', 'PNG', 'TIFF', 'ZLIB'] +local_sys_cmake = ['-DITK_USE_SYSTEM_%s=ON' % d for d in local_sys_deps] + +configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF ' +configopts += '-DModule_ITKReview=ON -DModule_ITKVtkGlue=ON -DModule_SimpleITKFilters=ON ' +configopts += '-DITK_WRAP_PYTHON:BOOL=OFF ' +configopts += '-DITK_LEGACY_REMOVE:BOOL=OFF ' # needed by SimpleITK +configopts += ' '.join(local_sys_cmake) + +prebuildopts = "LC_ALL=C " + +local_lib_names = ['ITKCommon', 'ITKIOHDF5', 'ITKIOJPEG', 'ITKIOPNG', 'ITKIOTIFF', + 'ITKReview', 'ITKVTK', 'ITKVtkGlue', 'itkSimpleITKFilters'] + +sanity_check_paths = { + 'files': ['bin/itkTestDriver'] + + ['lib/lib%s-%%(version_major)s.%%(version_minor)s.%s' % (l, SHLIB_EXT) for l in local_lib_names], + 'dirs': ['include/ITK-%(version_major)s.%(version_minor)s', 'share'], +} + +moduleclass = 'data' From 806133fd03c318084c697007ecc50286d54a788c Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 26 Oct 2022 20:38:38 +0100 Subject: [PATCH 209/939] adding easyconfigs: TBA-1.0-foss-2020b.eb --- .../easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb new file mode 100644 index 000000000000..d6d7f6ff551c --- /dev/null +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -0,0 +1,65 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'Tarball' + +name = 'TBA' +version = '1.0' + +homepage = 'https://github.com/jenhantao/tba' +description = """TBA (a Transcription factor Binding Analysis): +TBA is a multi-functional machine learning tool for identifying +transcription factors associated with genomic features""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +source_urls = ['https://github.com/jenhantao/tba/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['97acb78e045bbd066d67213c84417f2af7f48fde1f513be22cbb46ad2966ae2c'] + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('Biopython', '1.78'), + ('scikit-learn', '0.23.2'), + ('Seaborn', '0.11.1'), + ('matplotlib', '3.5.1'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('idr', '2.0.3', { + 'source_urls': ['https://github.com/nboley/idr/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['63e3be099b2deadfa8c7ccc3ab83659afe683f6a35bd41b2319c6ad58ca74de6'], + }), + ('joblib', '1.2.0', { + 'checksums': ['e1cee4a79e4af22881164f218d4311f60074197fb707e082e803b61f6d137018'], + }), +] + +postinstallcmds = [ + "mv %(installdir)s/model_training/* %(installdir)s/bin ", + "mv %(installdir)s/default_motifs %(installdir)s/share ", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +sanity_check_paths = { + 'files': ['bin/train_model_default.sh', 'bin/train_classifier.py', + 'bin/create_features.py', 'bin/idr'], + 'dirs': ['share'], +} + +sanity_check_commands = [ + "idr --version", + "train_classifier.py -h", +] + +moduleclass = 'bio' From 1410906635e24073738aa8d0e83af731e6c5aca3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Wed, 26 Oct 2022 21:40:11 +0100 Subject: [PATCH 210/939] Update TBA-1.0-foss-2020b.eb matplotlib demoted to 3.3.3 to avoid conflicts --- easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb index d6d7f6ff551c..c3f0e23f2d8a 100644 --- a/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TBA/TBA-1.0-foss-2020b.eb @@ -22,7 +22,7 @@ dependencies = [ ('Biopython', '1.78'), ('scikit-learn', '0.23.2'), ('Seaborn', '0.11.1'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ] exts_defaultclass = 'PythonPackage' From 3404ec4b937e3ceb332d2b6ccff5fd61b91041da Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 11:16:17 +0200 Subject: [PATCH 211/939] adding easyconfigs: Xmipp-3.22.07-Helios-foss-2022a.eb and patches: Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch, Xmipp-3.22.07-Helios_dont_add_useless_libs.patch, Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch, Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch, Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch, XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch, XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch --- .../Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb | 87 +++++++++++++++++++ ...-Helios_correct_order_of_cu_includes.patch | 19 ++++ ...3.22.07-Helios_dont_add_useless_libs.patch | 21 +++++ ...07-Helios_dont_change_EB_build_flags.patch | 41 +++++++++ ...Helios_drop_useless_CXXFLAGS_setting.patch | 18 ++++ ...07-Helios_fix_scons_Environent_calls.patch | 37 ++++++++ ...07-Helios_fix_scons_Environent_calls.patch | 28 ++++++ ...-3.22.07-Helios_use_CXXFLAGS_from_EB.patch | 24 +++++ ...07-Helios_fix_scons_Environent_calls.patch | 28 ++++++ ...-3.22.07-Helios_use_CXXFLAGS_from_EB.patch | 25 ++++++ 10 files changed, 328 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb new file mode 100644 index 000000000000..9174334361ed --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a.eb @@ -0,0 +1,87 @@ +name = 'Xmipp' +version = '3.22.07-Helios' + +homepage = 'https://github.com/I2PC/scipion/wiki' +description = """Scipion is an image processing framework to obtain 3D +models of macromolecular complexes using Electron Microscopy (3DEM). It +integrates several software packages and presents an unified interface +for both biologists and developers. Scipion allows to execute workflows +combining different software tools, while taking care of formats and +conversions. Additionally, all steps are tracked and can be reproduced +later on. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/I2PC/xmipp/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(namelower)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippCore/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippCore-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippViz/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippViz-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, +] +patches = [ + '%(name)s-%(version)s_fix_scons_Environent_calls.patch', + '%(name)s-%(version)s_drop_useless_CXXFLAGS_setting.patch', + '%(name)s-%(version)s_correct_order_of_cu_includes.patch', + '%(name)s-%(version)s_dont_add_useless_libs.patch', + '%(name)s-%(version)s_dont_change_EB_build_flags.patch', + ('XmippCore-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippCore'), + ('XmippCore-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippCore'), + ('XmippViz-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippViz'), + ('XmippViz-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippViz'), +] +checksums = [ + {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, + {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, + {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': + '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, + {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': + '34ed0cb591e1e2788acd3e58696b1f45ce9210836d14ed1c99de1e574e4824e6'}, + {'Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch': + '2b0b2ddf349003be4112f4dca623586a03235214d6e64d232deb26468b52f0e3'}, + {'Xmipp-3.22.07-Helios_dont_add_useless_libs.patch': + '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, + {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': + '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': + '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, + {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'd86b0d3ecc339b81c9aa7a33d2b44b428643aa7e2e686529b4bb6b16d36805c2'}, + {'XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch': + '7724fc3953d9c4c308a5755f54229259425fdbad5a909153bd173292434407b9'}, + {'XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'a8bea23c243174fb27a140a34a064a622cc96f0e7231fd31caf20f90c7ba9555'}, +] + +builddependencies = [ + ('SCons', '4.4.0'), + ('CTPL', '0.0.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Java', '11', '', SYSTEM), + ('OpenCV', '4.6.0', '-contrib'), + ('SQLite', '3.38.3'), + ('HDF5', '1.12.2'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('LIBSVM', '3.30'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch new file mode 100644 index 000000000000..8b61aa946131 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch @@ -0,0 +1,19 @@ +commit baac03018283296f90c08366e0e092c95d25173b +Author: Ake Sandgren +Date: Tue Oct 18 14:34:34 2022 +0200 + + cuda_gpu_multidim_array.cu is just an include file containing templates. + Needs to be before cuda_gpu_geo_transformer.cu + +diff --git xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp +index f7e5178c..8ccbefd3 100644 +--- xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp ++++ xmipp-3.22.07-Helios/src/xmipp/libraries/reconstruction_cuda/cuda_all.cpp +@@ -31,6 +31,6 @@ + */ + + #include "cuda_gpu_bilib.cu" ++#include "cuda_gpu_multidim_array.cu" + #include "cuda_gpu_geo_transformer.cu" + #include "cuda_gpu_iirconvolve.cu" +-#include "cuda_gpu_multidim_array.cu" diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch new file mode 100644 index 000000000000..a0ad7920a2d6 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_add_useless_libs.patch @@ -0,0 +1,21 @@ +commit 4c1e2d678c5a33eae2ddb9f0558523d6d697e2b6 +Author: Ake Sandgren +Date: Thu Oct 27 08:04:04 2022 +0200 + + Don't add useless libraries to XmippInterfaceCuda and XmippParallelCuda + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index e70ea2cd..077541e8 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -209,9 +209,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + """ + _libs = list(libs) + _libpath = list(libpath)+external_libdirs +- if name == "XmippInterfaceCuda": +- _libs.append("XmippCuda") +- if "Cuda" in name: ++ if name == "XmippCuda": + _libs.append("cudart") + #_libs.append("cuda") + _libs.append("cufft") diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch new file mode 100644 index 000000000000..3c7171f617a2 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch @@ -0,0 +1,41 @@ +commit e53881505ae212fa913fc536e60869e9b8e7f73c +Author: Ake Sandgren +Date: Thu Oct 27 09:45:11 2022 +0200 + + Don't change flags from what EasyBuild has decided to use. + +diff --git xmipp-3.22.07-Helios/scripts/config.py xmipp-3.22.07-Helios/scripts/config.py +index 0f58cbe3..b442a035 100644 +--- xmipp-3.22.07-Helios/scripts/config.py ++++ xmipp-3.22.07-Helios/scripts/config.py +@@ -293,7 +293,7 @@ class Config: + self.configDict["CCFLAGS"] += " -std=c99" + if 'g++' in self.get(Config.KEY_CXX): + # optimize for current machine +- self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto" ++ #self.configDict["CXXFLAGS"] += " -mtune=native -march=native -flto" + if "-std=c99" not in self.configDict["CXXFLAGS"]: + self.configDict["CXXFLAGS"] += " -std=c++17" + if isCIBuild(): +@@ -301,8 +301,8 @@ class Config: + self.configDict["CXXFLAGS"] += " -Werror" + # don't optimize, as it slows down the build + self.configDict["CXXFLAGS"] += " -O0" +- else: +- self.configDict["CXXFLAGS"] += " -O3" ++ #else: ++ # self.configDict["CXXFLAGS"] += " -O3" + if self.is_true("DEBUG"): + self.configDict["CXXFLAGS"] += " -g" + +@@ -315,8 +315,8 @@ class Config: + if self.configDict["LIBDIRFLAGS"] == "": + # /usr/local/lib or /path/to/virtEnv/lib + localLib = "%s/lib" % info['data'] +- self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib +- self.environment.update(LD_LIBRARY_PATH=localLib) ++ #self.configDict["LIBDIRFLAGS"] = "-L%s" % localLib ++ #self.environment.update(LD_LIBRARY_PATH=localLib) + + # extra libs + hdf5InLocalLib = findFileInDirList("libhdf5*", localLib) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch new file mode 100644 index 000000000000..7e4c86186258 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch @@ -0,0 +1,18 @@ +commit f647cd54c8fa2b0894f347cbf7f13aacc0b8c785 +Author: Ake Sandgren +Date: Tue Oct 18 14:30:08 2022 +0200 + + Drop redundant setting of env var CXXFLAGS to what it already is. + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index c921c3c5..e70ea2cd 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -148,7 +148,6 @@ env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 000000000000..3eb4c9cf326c --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,37 @@ +commit 8ff0a1295743fae1eb069fe8242e524f348f5937 +Author: Ake Sandgren +Date: Tue Oct 18 14:28:47 2022 +0200 + + Make sure SCons sees the complete environment from EasyBuild. + +diff --git xmipp-3.22.07-Helios/src/xmipp/SConstruct xmipp-3.22.07-Helios/src/xmipp/SConstruct +index 22ea72cf..c921c3c5 100644 +--- xmipp-3.22.07-Helios/src/xmipp/SConstruct ++++ xmipp-3.22.07-Helios/src/xmipp/SConstruct +@@ -236,7 +236,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + # the reason is a compilation error for CUDA, which results in a multiple symbol detection + # when the order is different. This has to be fixed in the future by changing the CUDA + # build system FIXME David Strelak +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + env2['CXXFLAGS']=list(env['CXXFLAGS']) # list(.) causes a true copy and not just a pointer + env2['LINKFLAGS']=list(env['LINKFLAGS']) +@@ -425,7 +425,7 @@ def addProgram(env, name, src=None, pattern=None, installDir=None, + ldLibraryPathCopy = [env['LIBPATH']] + appendUnique(libPathsCopy, external_libdirs) # This order is important, because if we should use Scipion libs, these will be before the system libs + appendUnique(libPathsCopy, env.get('LIBPATH', '').split(os.pathsep)) +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['LD_LIBRARY_PATH'] = env['ENV'].get('LD_LIBRARY_PATH', '') + env2['ENV']['PATH'] = env['ENV']['PATH'] + +@@ -486,7 +486,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS','')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS','')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 000000000000..06c3697efcb8 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,28 @@ +commit 901b41d324b351995b9256d7ee6b370276274497 +Author: Ake Sandgren +Date: Tue Oct 18 14:21:03 2022 +0200 + + Make sure SCons sees the complete environment from EasyBuild. + +diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct +index 1c5fec3..40ed01f 100644 +--- xmippCore-3.22.07-Helios/SConstruct ++++ xmippCore-3.22.07-Helios/SConstruct +@@ -207,7 +207,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + if not sources and env.TargetInBuild(name): + Exit('No sources found for Library: %s. Exiting!!!' % name) + +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + env2['CXX'] = env['CXX'] + +@@ -363,7 +363,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS','')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS','')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch new file mode 100644 index 000000000000..f1ac9fff312e --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch @@ -0,0 +1,24 @@ +commit 36ca78858e442f1df23f5cb6b87c877a864eff44 +Author: Ake Sandgren +Date: Tue Oct 18 14:23:16 2022 +0200 + + Only use CXXFLAGS from EasyBuild. + +diff --git xmippCore-3.22.07-Helios/SConstruct xmippCore-3.22.07-Helios/SConstruct +index 40ed01f..277443d 100644 +--- xmippCore-3.22.07-Helios/SConstruct ++++ xmippCore-3.22.07-Helios/SConstruct +@@ -136,13 +136,7 @@ env['CXX'] = os.environ.get('CXX') + env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') +-if os.environ.get('DEBUG', '0') == 'True': #FIXME, use 1, true, yes... +- cxxFlags += ' -g' +-else: +- if cxxFlags.find("-O")==-1: +- cxxFlags += (" -O3" if 'TRAVIS' not in os.environ else " -O0") #don't optimize on Travis, as it slows down the build + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + diff --git a/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch new file mode 100644 index 000000000000..1cdd9c3add53 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch @@ -0,0 +1,28 @@ +commit 0e749b55db29360c9804f8c5e07094b7a5bf0597 +Author: Ake Sandgren +Date: Tue Oct 18 14:25:17 2022 +0200 + + Make sure scons sees the complete environment from EasyBuild. + +diff --git xmippViz-3.22.07-Helios/SConstruct xmippViz-3.22.07-Helios/SConstruct +index dc0a809..32c75be 100644 +--- xmippViz-3.22.07-Helios/SConstruct ++++ xmippViz-3.22.07-Helios/SConstruct +@@ -237,7 +237,7 @@ def addCppLibrary(env, name, dirs=[], tars=[], untarTargets=['configure'], patte + if not sources and env.TargetInBuild(name): + Exit('No sources found for Library: %s. Exiting!!!' % name) + +- env2 = Environment() ++ env2 = Environment(ENV=os.environ) + env2['ENV']['PATH'] = env['ENV']['PATH'] + + mpiArgs = {} +@@ -474,7 +474,7 @@ def compilerConfig(env): + + def libraryTest(env, name, lang='c'): + """Check the existence of a concrete C/C++ library.""" +- env2 = Environment(LIBS=env.get('LIBS', '')) ++ env2 = Environment(ENV=os.environ,LIBS=env.get('LIBS', '')) + conf = Configure(env2) + conf.CheckLib(name, language=lang) + env2 = conf.Finish() diff --git a/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch new file mode 100644 index 000000000000..6d8802ccb21d --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch @@ -0,0 +1,25 @@ +commit 3d1e0e6e6da7aa7cc605be2a699f02b6cfbf4ca5 +Author: Ake Sandgren +Date: Tue Oct 18 14:26:22 2022 +0200 + + Only use CXXFLAGS from EasyBuild. + +diff --git xmippViz-3.22.07-Helios/SConstruct xmippViz-3.22.07-Helios/SConstruct +index 32c75be..fecd394 100644 +--- xmippViz-3.22.07-Helios/SConstruct ++++ xmippViz-3.22.07-Helios/SConstruct +@@ -143,14 +143,7 @@ env['CXX'] = os.environ.get('CXX') + env['LINKERFORPROGRAMS'] = os.environ.get('LINKERFORPROGRAMS') + env['CCFLAGS'] = os.environ.get('CCFLAGS', '').split() + cxxFlags = os.environ.get('CXXFLAGS', '') +-if os.environ.get('DEBUG', '0') == 'True': # FIXME, use 1, true, yes... +- cxxFlags += ' -g' +-else: +- if cxxFlags.find("-O") == -1: +- cxxFlags += ( +- " -O3" if 'TRAVIS' not in os.environ else " -O0") # don't optimize on Travis, as it slows down the build + env['CXXFLAGS'] = cxxFlags.split() +-os.environ['CXXFLAGS'] = cxxFlags # FIXME use only env or os.environ in the rest of the code + env['LINKFLAGS'] = os.environ.get('LINKFLAGS', '').split() + + for path in ['JAVA_HOME', 'JAVA_BINDIR']: From 265e2707a3dbc3ef9d9278d71806d80703f5302b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 11:39:09 +0200 Subject: [PATCH 212/939] Add missing CTPL dep --- .../c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb new file mode 100644 index 000000000000..360aea103ca1 --- /dev/null +++ b/easybuild/easyconfigs/c/CTPL/CTPL-0.0.2-GCC-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CmdCp' + +name = 'CTPL' +version = '0.0.2' + +homepage = 'https://github.com/vit-vit/CTPL.git' + +description = "Modern and efficient C++ Thread Pool Library" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'vit-vit' +source_urls = [GITHUB_SOURCE] +sources = ['%(namelower)s_v.%(version)s.tar.gz'] +checksums = ['8c1cec7c570d6d84be1d29283af5039ea27c3e69703bd446d396424bf619816e'] + +dependencies = [ + ('Boost', '1.79.0'), +] + +cmds_map = [('.*', "echo Nothing to build")] + +files_to_copy = [(['ctpl.h', 'ctpl_stl.h'], 'include/CTPL'), 'LICENSE', 'example.cpp'] + +sanity_check_paths = { + 'files': ['include/CTPL/%s' % x for x in ['ctpl.h', 'ctpl_stl.h']], + 'dirs': [] +} + +moduleclass = 'devel' From 191e0c22e05b8d60b8b193c98dc025be20cbf535 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 12:33:45 +0200 Subject: [PATCH 213/939] Add missing SCons dep --- .../s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ ...ns-4.4.0_install_man_pages_correctly.patch | 15 ++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..8b3bae7755a0 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'SCons' +version = '4.4.0' + +homepage = 'https://www.scons.org/' +description = "SCons is a software construction tool." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +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-4.4.0.tar.gz': '7703c4e9d2200b4854a31800c1dbd4587e1fa86e75f58795c740bcfa7eca7eaa'}, + {'SCons-4.4.0_install_man_pages_correctly.patch': + '9d216c2ea8e152ae1531593b17adc4042eb88f1d9524d7f3b08ace5137d6d5e7'}, + ], + }), +] + +sanity_check_paths = { + 'files': ['bin/scons', 'bin/sconsign'], + 'dirs': ['lib/pythoni%(pyshortver)s/site-packages/%(name)s'], +} + +sanity_check_commands = ["scons --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch b/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch new file mode 100644 index 000000000000..4c482a86c5e9 --- /dev/null +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0_install_man_pages_correctly.patch @@ -0,0 +1,15 @@ +Install the man pages in the correct directory. + +Åke Sandgren, 2022-10-27 +diff -ru SCons-4.4.0.orig/setup.cfg SCons-4.4.0/setup.cfg +--- SCons-4.4.0.orig/setup.cfg 2022-07-30 23:16:02.000000000 +0200 ++++ SCons-4.4.0/setup.cfg 2022-10-27 11:55:33.457877253 +0200 +@@ -58,7 +58,7 @@ + SCons.Tool.docbook = *.* + + [options.data_files] +-. = scons.1 ++man/man1 = scons.1 + scons-time.1 + sconsign.1 + From 1edcba7fa4d21e5bc98fef154cf4ddf231c4b8ca Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 12:38:52 +0200 Subject: [PATCH 214/939] SCons: Fix typo --- easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb index 8b3bae7755a0..22668b263b2b 100644 --- a/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SCons/SCons-4.4.0-GCCcore-11.3.0.eb @@ -29,7 +29,7 @@ exts_list = [ sanity_check_paths = { 'files': ['bin/scons', 'bin/sconsign'], - 'dirs': ['lib/pythoni%(pyshortver)s/site-packages/%(name)s'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], } sanity_check_commands = ["scons --help"] From 882d3673c93229c62dca34816d4b42936ebd190f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 18:39:34 +0200 Subject: [PATCH 215/939] adding easyconfigs: PyQt5-5.15.5-GCCcore-11.3.0.eb --- .../p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 102 ++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a052b69a2df3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -0,0 +1,102 @@ +easyblock = 'Bundle' + +name = 'PyQt5' +version = '5.15.5' + +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': '11.3.0'} +toolchainopts = {'cstd': 'c++11'} + +builddependencies = [('binutils', '2.38')] +dependencies = [ + ('Python', '3.10.4'), + ('Qt5', '5.15.5'), +] + +default_easyblock = 'PythonPackage' + +local_sipdir = '%(installdir)s/share/sip' + +local_pylibdir = '%(installdir)s/lib/python%(pyshortver)s/site-packages' + +local_pyqt5_sip_install = "sip-install --verbose --target-dir " + local_pylibdir + " " +local_pyqt5_sip_install += "--confirm-license --no-designer-plugin --no-qml-plugin " + +local_pyqtweb_configopts = "configure.py --verbose --destdir=%s/PyQt5 " % local_pylibdir +local_pyqtweb_configopts += "--apidir=%(installdir)s/qsci " +local_pyqtweb_configopts += "--pyqt-sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--sipdir=%s " % local_sipdir +local_pyqtweb_configopts += "--no-stubs --no-dist-info" + +local_pyqt_configopts = "configure.py --verbose --destdir=%s " % local_pylibdir +local_pyqt_configopts += "--no-stubs " +local_pyqt_configopts += "--confirm-license --no-designer-plugin --no-qml-plugin " +# prevent installing pyrcc5 and other tools into $EBROOTPYTHON/bin: +local_pyqt_configopts += "--bindir=%(installdir)s/bin " +local_pyqt_configopts += "--sipdir=%s " % local_sipdir + +local_setup_env = "export PATH=%(installdir)s/bin:$PATH && " +local_setup_env += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " +local_sipver = '5.5.0' +components = [ + ('SIP', local_sipver, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCELOWER_TAR_GZ], + 'start_dir': 'sip-%s' % local_sipver, + 'use_pip': True, + 'options': {'modulename': 'PyQt5.sip'}, + }), + ('PyQt-builder', '1.14.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': 'PyQt-builder-%(version)s', + 'use_pip': True, + }), + ('PyQt5_sip', '12.11.0', { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'start_dir': 'PyQt5_sip-%(version)s', + 'use_pip': True, + }), + (name, version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqt_configopts + }), + ('PyQtWebEngine', version, { + 'source_urls': [PYPI_SOURCE], + 'sources': [SOURCE_TAR_GZ], + 'easyblock': 'ConfigureMakePythonPackage', + 'start_dir': '%(name)s-%(version)s', + 'preconfigopts': local_setup_env, + 'configopts': local_pyqtweb_configopts, + 'options': {'modulename': 'PyQt5.QtWebEngine'}, + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in [ + 'pyrcc5', 'pyuic5', 'pylupdate5', 'pyqt-bundle', 'sip-build', 'sip-install', 'sip5']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'import PyQt5.QtCore'", + "sip5 --help", + "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' From 0b6b8131e2b2f73363367341f60edbf47079e721 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 27 Oct 2022 19:48:44 +0200 Subject: [PATCH 216/939] Add missing checksums --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index a052b69a2df3..594f66926ccf 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -45,6 +45,7 @@ components = [ ('SIP', local_sipver, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5d024c419b30fea8a6de8c71a560c7ab0bc3c221fbfb14d55a5b865bd58eaac5'], 'start_dir': 'sip-%s' % local_sipver, 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, @@ -52,18 +53,21 @@ components = [ ('PyQt-builder', '1.14.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['6755931c6d2f8940553e0334d10c933ce5cc18b64425e94fda1accf4ff774f59'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), ('PyQt5_sip', '12.11.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['b4710fd85b57edef716cc55fae45bfd5bfac6fc7ba91036f1dcc3f331ca0eb39'], 'start_dir': 'PyQt5_sip-%(version)s', 'use_pip': True, }), (name, version, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['b411b7a8fa03901c9feb1dcbac7ea1fc3ce20b9ae682762b777cd5398749ca2b'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', 'preconfigopts': local_setup_env, @@ -72,6 +76,7 @@ components = [ ('PyQtWebEngine', version, { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['ab47608dccf2b5e4b950d5a3cc704b17711af035024d07a9b71ad29fc103b941'], 'easyblock': 'ConfigureMakePythonPackage', 'start_dir': '%(name)s-%(version)s', 'preconfigopts': local_setup_env, From d56c22e819ef39fad047ae05b6f62527f1961c3c Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 28 Oct 2022 07:46:55 +0200 Subject: [PATCH 217/939] adding easyconfigs: PyOpenGL-3.1.6-GCCcore-11.3.0.eb --- .../PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..202415c4bdc6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyOpenGL/PyOpenGL-3.1.6-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = 'PyOpenGL' +version = '3.1.6' + +homepage = 'http://pyopengl.sourceforge.net' +description = """PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + + +builddependencies = [ + ('binutils', '2.38'), + ('bzip2', '1.0.8'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Mesa', '22.0.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'OpenGL', + 'checksums': ['8ea6c8773927eda7405bffc6f5bb93be81569a7b05c8cac50cd94e969dce5e27'], + }), +] + +moduleclass = 'vis' From e3925ab4dfc73f8c851ed9ea864821152998b6c4 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 28 Oct 2022 08:45:04 +0100 Subject: [PATCH 218/939] fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x --- .../easyconfigs/g/GCCcore/GCCcore-10.1.0.eb | 21 ++++++----- .../easyconfigs/g/GCCcore/GCCcore-10.2.0.eb | 36 ++++++++++--------- .../easyconfigs/g/GCCcore/GCCcore-10.3.0.eb | 29 ++++++++------- .../easyconfigs/g/GCCcore/GCCcore-11.1.0.eb | 2 ++ .../easyconfigs/g/GCCcore/GCCcore-11.2.0.eb | 2 ++ 5 files changed, 52 insertions(+), 38 deletions(-) diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb index 23a101c3f9f8..5ad494800692 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.1.0.eb @@ -31,17 +31,20 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900', # gcc-10.1.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc', # mpfr-4.0.2.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.1.0.tar.gz': '954057239c89d25bc7a62bfbceb58026363ad74f079c63fdba27f95abbf60900'}, + {'gmp-6.2.0.tar.bz2': 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'}, + {'mpfr-4.0.2.tar.bz2': 'c05e3f02d09e0e9019384cdd58e0f19c64e6db1fd6f5ecf77b4b1c61ca253acc'}, + {'mpc-1.1.0.tar.gz': '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'}, + {'isl-0.22.1.tar.bz2': '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb index d6d21047a9c1..880ff3864f6b 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.2.0.eb @@ -39,24 +39,28 @@ patches = [ 'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d', # gcc-10.2.0.tar.gz - 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea', # gmp-6.2.0.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e', # mpc-1.1.0.tar.gz - '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd', # isl-0.22.1.tar.bz2 - '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66', # newlib-3.3.0.tar.gz - 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705', # nvptx-tools-20180301.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6', # GCCcore-10.2.0_fix-has-include-Fortran.patch - '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278', # GCCcore-10.2.0_fix-ice-on-arm.patch - # GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch - 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962', - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.2.0.tar.gz': '27e879dccc639cd7b0cc08ed575c1669492579529b53c9ff27b0b96265fa867d'}, + {'gmp-6.2.0.tar.bz2': 'f51c99cb114deb21a60075ffb494c1a210eb9d7cb729ed042ddb7de9534451ea'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.1.0.tar.gz': '6985c538143c1208dcb1ac42cedad6ff52e267b47e5f970183a3e75125b43c2e'}, + {'isl-0.22.1.tar.bz2': '1a668ef92eb181a7c021e8531a3ca89fd71aa1b3744db56f68365ab0a224c5cd'}, + {'newlib-3.3.0.tar.gz': '58dd9e3eaedf519360d92d84205c3deef0b3fc286685d1c562e245914ef72c66'}, + {'nvptx-tools-20180301.tar.gz': 'a25b6f7761bb61c0d8e2a183bcf51fbaaeeac26868dcfc015e3b16a33fe11705'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.3.0_nvptx_sm_35_default.patch': '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108'}, + {'GCCcore-10.2.0_fix-has-include-Fortran.patch': + 'f94fa117f3401b28fda0741f3f45439c09dc956d1ed27f9a3ebe40c0e7e404b6'}, + {'GCCcore-10.2.0_fix-ice-on-arm.patch': '44edbf1cddb2d7037f9606b6995d9ef20ff664b810a3e3ef383420a4366ed278'}, + {'GCCcore-10.2.0_fix-vec-builtins-conversion-on-ppc.patch': + 'fb160374ba691d8267a19dee4268305a6e34123cab9e65176b5168c36e9f0962'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb index a3826b1579cb..7f9079c65c0e 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-10.3.0.eb @@ -37,21 +37,24 @@ patches = [ 'gcc-10.3.0_fix-ice-in-tsubst.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', ] checksums = [ - '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16', # gcc-10.3.0.tar.gz - 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c', # gmp-6.2.1.tar.bz2 - 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926', # mpfr-4.1.0.tar.bz2 - '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459', # mpc-1.2.1.tar.gz - 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d', # isl-0.23.tar.bz2 - 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154', # newlib-4.1.0.tar.gz - '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2', # nvptx-tools-20210115.tar.gz - '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68', # GCCcore-6.2.0-fix-find-isl.patch - '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e', # GCCcore-9.3.0_gmp-c99.patch - '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108', # GCCcore-9.3.0_nvptx_sm_35_default.patch - '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717', # gcc-10.3.0_fix-ice-in-tsubst.patch - '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4', # GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch - 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832', # GCC-10.x_fix-libsanitizer-cyclades.patch + {'gcc-10.3.0.tar.gz': '8fcf994811ad4e5c7ac908e8cf62af2c1982319e5551f62ae72016064dacdf16'}, + {'gmp-6.2.1.tar.bz2': 'eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'}, + {'mpfr-4.1.0.tar.bz2': 'feced2d430dd5a97805fa289fed3fc8ff2b094c02d05287fd6133e7f1f0ec926'}, + {'mpc-1.2.1.tar.gz': '17503d2c395dfcf106b622dc142683c1199431d095367c6aacba6eec30340459'}, + {'isl-0.23.tar.bz2': 'c58922c14ae7d0791a77932f377840890f19bc486b653fa64eba7f1026fb214d'}, + {'newlib-4.1.0.tar.gz': 'f296e372f51324224d387cc116dc37a6bd397198756746f93a2b02e9a5d40154'}, + {'nvptx-tools-20210115.tar.gz': '466abe1cef9cf294318ecb3c221593356f7a9e1674be987d576bc70d833d84a2'}, + {'GCCcore-6.2.0-fix-find-isl.patch': '5ad909606d17d851c6ad629b4fddb6c1621844218b8d139fed18c502a7696c68'}, + {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, + {'GCCcore-9.3.0_nvptx_sm_35_default.patch': '8d8b9834a570b5789d47296311953b6307d4427957a73e102de43cca7a6fa108'}, + {'gcc-10.3.0_fix-ice-in-tsubst.patch': '74e6e019458aa2feb36ae3c45f45e164725ca5edd66f4fe9f873c8ee78c35717'}, + {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': + '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb index a5a301639481..dde91967953c 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.1.0.eb @@ -35,6 +35,7 @@ patches = [ 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', 'GCC-10.x_fix-libsanitizer-cyclades.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -50,6 +51,7 @@ checksums = [ {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, {'GCC-10.x_fix-libsanitizer-cyclades.patch': 'ba1f1cdc3a370281a9c1a45758db48b7edbddb70a9f6b10951fe8a77e4931832'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] diff --git a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb index 5efade9fb398..9d40637c25c6 100644 --- a/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GCCcore/GCCcore-11.2.0.eb @@ -34,6 +34,7 @@ patches = [ 'GCCcore-6.2.0-fix-find-isl.patch', 'GCCcore-9.3.0_gmp-c99.patch', 'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch', + 'GCCcore-11_fix-libsanitzer-glibc-2.36.patch', 'GCCcore-11.3.0_fix-vectorizer.patch', ] checksums = [ @@ -48,6 +49,7 @@ checksums = [ {'GCCcore-9.3.0_gmp-c99.patch': '0e135e1cc7cec701beea9d7d17a61bab34cfd496b4b555930016b98db99f922e'}, {'GCCcore-9.x-11.x_fix-unsigned-fpe-traps.patch': '03a2e4aeda78d398edd680d6a1ba842b8ceb29c126ebb7fe2e3541ddfe4fbed4'}, + {'GCCcore-11_fix-libsanitzer-glibc-2.36.patch': '5c6c3b4655883a23dd9da7ef99751e5db23f35189c03689d2ab755b22cb39a60'}, {'GCCcore-11.3.0_fix-vectorizer.patch': '7dff25b678e2f65b81d9bf0c8402ad46c25a04b0c0d610db50b763ecc5f9ef98'}, ] From b4320eab9ed3f4b592917353cb6d3ac4e21607ed Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 13:54:11 +0200 Subject: [PATCH 219/939] adding easyconfigs: cwltool-3.1.20221018083734-GCCcore-10.3.0.eb --- ...ltool-3.1.20221018083734-GCCcore-10.3.0.eb | 115 ++++++++++++++++++ 1 file changed, 115 insertions(+) create mode 100644 easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..cfc690a27ae6 --- /dev/null +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -0,0 +1,115 @@ +## +# 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 = 'PythonBundle' + +name = 'cwltool' +version = '3.1.20221018083734' + +homepage = 'https://github.com/common-workflow-language/cwltool' +description = """Common workflow language (CWL) reference implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('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'), +] + +# The Qt5 dependency of Graphviz (required by pydot) may be long to build and +# requires a lot of disk space and memory! +dependencies = [ + ('Python', '3.9.5'), + ('typing-extensions', '3.10.0.0'), + ('pydot', '1.4.2'), + ('lxml', '4.6.3'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('argcomplete', '2.0.0', { + 'checksums': ['6372ad78c89d662035101418ae253668445b391755cfe94ea52f1b9d22425b20'], + }), + ('humanfriendly', '10.0', { + 'checksums': ['6b0b831ce8f15f7300721aa49829fc4e83921a9a301cc7f606be6686a2288ddc'], + }), + ('coloredlogs', '15.0.1', { + 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], + }), + ('ruamel.yaml.clib', '0.2.7', { + 'modulename': 'ruamel.yaml', + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + }), + ('ruamel.yaml', '0.17.14', { + 'modulename': 'ruamel', + 'checksums': ['4185fcfa9e037fea9ffd0bb6172354a03ec98c21e462355d72e068c74e493512'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', '6.2.0', { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), + ('mistune', '0.8.4', { + 'checksums': ['59a3429db53c50b5c6bcc8a07f8848cb00d7dc8bdb431a4ab41920d201d4756e'], + }), + ('schema-salad', '8.3.20221016151607', { + 'modulename': 'schema_salad', + 'checksums': ['c61a517c945cd383445ebecbc085b00766913a3fdd7df9699a0fa4c41728ca1f'], + }), + ('shellescape', '3.8.1', { + 'checksums': ['40b310b30479be771bf3ab28bd8d40753778488bd46ea0969ba0b35038c3ec26'], + }), + ('cwlformat', '2022.2.18', { + 'modulename': 'cwlformat', + 'source_tmpl': 'cwlformat-%(version)s-py3-none-any.whl', + 'checksums': ['d3e2dca192ce10e703ed4eb0bae26539db08d8ddd7c6a6fe9d1406c3f1b53cda'], + }), + ('cwl-upgrader', '1.2.4', { + 'modulename': 'cwlupgrader', + 'checksums': ['b25fc236407343d44cc830ac3f63eed395b8d872fc7e17db92cde583d4a3b2ec'], + }), + ('cwl-utils', '0.20', { + 'modulename': 'cwl_utils', + 'checksums': ['28472aaba50ab4e8380c29f31c27beb63f60a1af1690369ab7bb7e31e71e66d9'], + }), + ('mypy-extensions', '0.4.3', { + 'modulename': 'mypy_extensions', + 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', + 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], + }), + ('networkx', '2.8.7', { + 'checksums': ['815383fd52ece0a7024b5fd8408cc13a389ea350cd912178b82eed8b96f82cd3'], + }), + ('prov', '1.5.1', { + 'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'], + }), + ('bagit', '1.8.1', { + 'checksums': ['37df1330d2e8640c8dee8ab6d0073ac701f0614d25f5252f9e05263409cee60c'], + }), + ('cwltool', '3.1.20221018083734', { + 'checksums': ['06d08f390ed7577ac66c6eef0c98f915363b5e36c04daa1353e3f2d0c5e19f17'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cwltool'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cwltool --version"] + +moduleclass = 'tools' From 9daea5ff0b20098eb2870fcc0dadc296fbb7d437 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 15:28:51 +0200 Subject: [PATCH 220/939] Add missing sanity_pip_check --- .../c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb index cfc690a27ae6..1d9ccc685eb8 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -112,4 +112,6 @@ sanity_check_paths = { sanity_check_commands = ["cwltool --version"] +sanity_pip_check = True + moduleclass = 'tools' From 07493ac0283d1ff8b447a97e020d44fdc92f317b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 28 Oct 2022 17:02:56 +0200 Subject: [PATCH 221/939] Use ruamel.yaml and networkx from EB --- .../cwltool-3.1.20221018083734-GCCcore-10.3.0.eb | 13 ++----------- 1 file changed, 2 insertions(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb index 1d9ccc685eb8..b40b9c1e883b 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb @@ -34,6 +34,8 @@ dependencies = [ ('typing-extensions', '3.10.0.0'), ('pydot', '1.4.2'), ('lxml', '4.6.3'), + ('ruamel.yaml', '0.17.21'), + ('networkx', '2.6.3', '', ('foss', '2021a')), ] use_pip = True @@ -49,14 +51,6 @@ exts_list = [ ('coloredlogs', '15.0.1', { 'checksums': ['7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0'], }), - ('ruamel.yaml.clib', '0.2.7', { - 'modulename': 'ruamel.yaml', - 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], - }), - ('ruamel.yaml', '0.17.14', { - 'modulename': 'ruamel', - 'checksums': ['4185fcfa9e037fea9ffd0bb6172354a03ec98c21e462355d72e068c74e493512'], - }), ('isodate', '0.6.1', { 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], }), @@ -91,9 +85,6 @@ exts_list = [ 'source_tmpl': 'mypy_extensions-%(version)s.tar.gz', 'checksums': ['2d82818f5bb3e369420cb3c4060a7970edba416647068eb4c5343488a6c604a8'], }), - ('networkx', '2.8.7', { - 'checksums': ['815383fd52ece0a7024b5fd8408cc13a389ea350cd912178b82eed8b96f82cd3'], - }), ('prov', '1.5.1', { 'checksums': ['7a2d72b0df43cd9c6e374d815c8ce3cd5ca371d54f98f837853ac9fcc98aee4c'], }), From 5822cf971248270b67fcdf12b3f057eff278950d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 28 Oct 2022 18:10:36 +0200 Subject: [PATCH 222/939] Update napari-0.4.15-foss-2021b.eb fox sources list docstring-parser --- easybuild/easyconfigs/n/napari/napari-0.4.15-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 f439e3019c21..18337a90cfdb 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 @@ -52,7 +52,7 @@ exts_list = [ 'checksums': ['0310ba8afe52729fa7626325c8d8356a8421c434bf887ac851e58dcf7cf056a6'], }), ('docstring-parser', '0.14.1', { - 'sources': 'docstring_parser-%(version)s.tar.gz', + 'sources': ['docstring_parser-%(version)s.tar.gz'], 'checksums': ['2c77522e31b7c88b1ab457a1f3c9ae38947ad719732260ba77ee8a3deb58622a'], }), ('pep517', '0.12.0', { From 560d52ba93aaf34f7137c70d30baa99999553367 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:31:57 +0100 Subject: [PATCH 223/939] adding easyconfigs: svist4get-1.3.1-foss-2020b.eb --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb new file mode 100644 index 000000000000..8ec2b2b00609 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -0,0 +1,59 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'svist4get' +version = '1.3.1' + +homepage = 'https://github.com/art-egorov/svist4get' +description = """Svist4get is a simple bioinformatics tool for visualization of +genomic signal tracks in user-defined genomic windows, either arbitrary selected +by genomic coordinates or anchored to particular transcripts or genes.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('pybedtools', '0.8.2'), + ('Biopython', '1.78'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('reportlab', '3.6.9', { + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + }), + + ('configs', '3.0.3', { + 'sources': ['%(name)s-%(version)s.zip'], + 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], + }), + ('argparse', '1.4.0', { + 'checksums': ['62b089a55be1d8949cd2bc7e0df0bddb9e028faefc8c32038cc84862aefdd6e4'], + }), + ('Wand', '0.6.10', { + 'checksums': ['373f4a7f2866c868c31ce910e1f9b36a92d132640a20068ec17cea3284fedc57'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + + (name, version, { + 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/svist4get', 'bin/svist4get_copier'], + 'dirs': ['lib'], +} + +sanity_check_commands = [ + "svist4get --help", + "svist4get -v", +] + +moduleclass = 'bio' From d12f1b147c7ad739e4603458a4aef74285b2c013 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 18:33:08 +0100 Subject: [PATCH 224/939] adding easyconfigs: TOBIAS-0.14.0-foss-2020b.eb --- .../t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb new file mode 100644 index 000000000000..124583e843d8 --- /dev/null +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -0,0 +1,83 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'TOBIAS' +version = '0.14.0' + +homepage = 'https://github.com/loosolab/TOBIAS' +description = """TOBIAS is a collection of command-line bioinformatics tools +for performing footprinting analysis on ATAC-seq data.""" + +toolchain = {'name': 'foss', 'version': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('Seaborn', '0.11.1'), + ('pybedtools', '0.8.2'), + ('pyBigWig', '0.3.18'), + ('scikit-learn', '0.23.2'), + ('PyYAML', '5.3.1'), + ('XlsxWriter', '1.4.0'), + ('svist4get', '1.3.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('adjustText', '0.7.3', { + 'checksums': ['b90e275a95b4d980cbbac7967914b8d66477c09bc346a0b3c9e2125bba664b06'], + 'modulename': 'adjustText', + }), + ('botocore', '1.28.2', { + 'checksums': ['9890005735652555d1183b44bad729603d26922dc08e261e1e0a35a7bf26ba38'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.6.0', { + 'checksums': ['2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947'], + }), + ('boto3', '1.25.2', { + 'checksums': ['43a93f8cecd882cccb2815cd76fc07a73b076027ab092a1c7cede89cb9b075f8'], + }), + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('logomaker', '0.8', { + 'checksums': ['d8c7501a7d6d7961cd68e5a44e939000ebf1b0c4197a0c9198351e1d681d3f6d'], + }), + ('MOODS-python', '1.9.4.1', { + 'checksums': ['b3b5e080cb0cd13c0fd175d0ee0d453fde3e42794fa7ac39a4f6db1ac5ddb4cc'], + 'modulename': 'MOODS', + }), + ('flit_core', '3.7.1', { + 'checksums': ['14955af340c43035dbfa96b5ee47407e377ee337f69e70f73064940d27d0a44f'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('PyPDF2', '2.11.1', { + 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], + 'modulename': 'PyPDF2', + }), + + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], + }), +] + +sanity_check_paths = { + 'files': ['bin/TOBIAS', 'bin/cluster_sites_by_overlap.py', 'bin/moods-dna.py', 'bin/jp.py'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "TOBIAS --help", +] + +moduleclass = 'bio' From c5c6cdf960b42a6c5df9d32ae61befdf7973b5bf Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:37:54 +0100 Subject: [PATCH 225/939] reportlab patched so it finds EB fontconfig instead system one --- .../s/svist4get/svist4get-1.3.1-foss-2020b.eb | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index 8ec2b2b00609..c228ca9af49a 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,17 +16,19 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '8.0.1'), + ('Pillow', '9.2.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.9', { - 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84'], + ('reportlab', '3.6.12', { + 'patches': ['reportlab-3.6.12-fontconfig.patch'], + 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + # reportlab-3.6.12-fontconfig.patch: + '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), - ('configs', '3.0.3', { 'sources': ['%(name)s-%(version)s.zip'], 'checksums': ['a5ab09e04e441dac6aa856a71fbf5ffc62954352630f79d311b8f8a31d9ce19c'], @@ -40,7 +42,6 @@ exts_list = [ ('statistics', '1.0.3.5', { 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], }), - (name, version, { 'checksums': ['22311fdc956cca531dac7ba924744e8f870a57bc6f27cbe4e8ba9854117e720c'], }), @@ -52,7 +53,7 @@ sanity_check_paths = { } sanity_check_commands = [ - "svist4get --help", + "svist4get --help", "svist4get -v", ] From 479ed72ae7168d43ea554240fc34c381c8c88929 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:39:29 +0100 Subject: [PATCH 226/939] adding easyconfigs: Pillow-9.2.0-GCCcore-10.2.0.eb --- .../p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..38e7492daf9f --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.2.0-GCCcore-10.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.2.0' + +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': '10.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = [ + '75e636fd3e0fb872693f23ccb8a5ff2cd578801251f3a4f6854c6a5d437d3c04', # Pillow-8.0.1.tar.gz +] + +builddependencies = [('binutils', '2.35')] + +dependencies = [ + ('Python', '3.8.6'), + ('libjpeg-turbo', '2.0.5'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.1.0'), + ('freetype', '2.10.3') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From af342d68b218ed49e52240d56a5d750c226b883f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 28 Oct 2022 23:49:12 +0100 Subject: [PATCH 227/939] Patchfile added --- .../reportlab-3.6.12-fontconfig.patch | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch diff --git a/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch b/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch new file mode 100644 index 000000000000..92e6ce513694 --- /dev/null +++ b/easybuild/easyconfigs/s/svist4get/reportlab-3.6.12-fontconfig.patch @@ -0,0 +1,25 @@ +Patch to make sure the fontconfig from EasyBuild will be found +Author: J. Sassmannshausen (Imperial College London/UK) +diff --git a/reportlab-3.6.12.orig/setup.py b/reportlab-3.6.12/setup.py +index 4b380b6..2ccfa93 100644 +--- a/reportlab-3.6.12.orig/setup.py ++++ b/reportlab-3.6.12/setup.py +@@ -277,14 +277,11 @@ class inc_lib_dirs: + # darwin ports installation directories + aDir(L, "/opt/local/lib") + aDir(I, "/opt/local/include") +- aDir(I, "/usr/local/include") +- aDir(L, "/usr/local/lib") +- aDir(I, "/usr/include") +- aDir(L, "/usr/lib") +- aDir(I, "/usr/include/freetype2") + if addrSize==64: +- aDir(L, "/usr/lib/lib64") +- aDir(L, "/usr/lib/x86_64-linux-gnu") ++ freepath = os.getenv("EBROOTFREETYPE") ++ aDir(L, pjoin(freepath, "lib64")) ++ aDir(I, pjoin(freepath, "include/freetype2")) ++ + else: + aDir(L, "/usr/lib/lib32") + prefix = sysconfig.get_config_var("prefix") From 160c1da84942a6311bb12c0a5e0e90835668b57c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:38:28 +0100 Subject: [PATCH 228/939] Update svist4get-1.3.1-foss-2020b.eb Missing ImageMagick added (picked up OS installation before) --- easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index c228ca9af49a..d9b689ae40e6 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -17,6 +17,7 @@ dependencies = [ ('pybedtools', '0.8.2'), ('Biopython', '1.78'), ('Pillow', '9.2.0'), + ('ImageMagick', '7.0.10-35'), ] use_pip = True From ca066e8f6222f3c8ab16b502e2d614d92ebf7af2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 00:53:11 +0100 Subject: [PATCH 229/939] Update svist4get-1.3.1-foss-2020b.eb Pillow downgraded to 8.0.1, reportlab downgraded to 3.6.9 due to conflicts with TOBIAS --- .../easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb index d9b689ae40e6..a6339d51f19e 100644 --- a/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb +++ b/easybuild/easyconfigs/s/svist4get/svist4get-1.3.1-foss-2020b.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.8.6'), ('pybedtools', '0.8.2'), ('Biopython', '1.78'), - ('Pillow', '9.2.0'), + ('Pillow', '8.0.1'), ('ImageMagick', '7.0.10-35'), ] @@ -24,9 +24,9 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('reportlab', '3.6.12', { + ('reportlab', '3.6.9', { 'patches': ['reportlab-3.6.12-fontconfig.patch'], - 'checksums': ['b13cebf4e397bba14542bcd023338b6ff2c151a3a12aabca89eecbf972cb361a', + 'checksums': ['5d0cc3682456ad213150f6dbffe7d47eab737d809e517c316103376be548fb84', # reportlab-3.6.12-fontconfig.patch: '2cc9b40e09650b7404ee9c4d72b134739acc89bacac3da58131cef2308726297'], }), From d9798882dc8f2681816c6e473b6107257f534715 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?J=C3=B6rg=20Sa=C3=9Fmannshausen?= <43338785+sassy-crick@users.noreply.github.com> Date: Sat, 29 Oct 2022 09:12:32 +0100 Subject: [PATCH 230/939] Update TOBIAS-0.14.0-foss-2020b.eb Empty line removed --- easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb index 124583e843d8..862d4fe55c1f 100644 --- a/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb +++ b/easybuild/easyconfigs/t/TOBIAS/TOBIAS-0.14.0-foss-2020b.eb @@ -64,7 +64,6 @@ exts_list = [ 'checksums': ['3c7badd512c21711eb1789c2eadbf96279289c0f94452ee54a86473bfbefd732'], 'modulename': 'PyPDF2', }), - (name, version, { 'sources': ['%(namelower)s-%(version)s.tar.gz'], 'checksums': ['ac74c35f981d499425147054f82142d22e52858d402d0c63ab7e8481bd156589'], From 769fde96b1588d61317942682d27a64a0f4a25b1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 29 Oct 2022 12:14:17 +0200 Subject: [PATCH 231/939] adding easyconfigs: make-4.3-GCCcore-11.3.0.eb, tmux-3.3a-GCCcore-11.3.0.eb --- .../m/make/make-4.3-GCCcore-11.3.0.eb | 29 +++++++++++++++ .../t/tmux/tmux-3.3a-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 2 files changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..508f420c75eb --- /dev/null +++ b/easybuild/easyconfigs/m/make/make-4.3-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'make' +version = '4.3' + +homepage = 'https://www.gnu.org/software/make/make.html' +description = "GNU version of make utility" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e05fdde47c5f7ca45cb697e973894ff4f5d79e13b750ed57d7b66d8defc78e19'] + +builddependencies = [('binutils', '2.38')] + +postinstallcmds = ["cd %(installdir)s/bin && ln -s make gmake"] + +sanity_check_paths = { + 'files': ['bin/gmake', 'bin/make'], + 'dirs': [] +} + +sanity_check_commands = [ + "gmake --help", + "make --help", +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..de3e3e02e01f --- /dev/null +++ b/easybuild/easyconfigs/t/tmux/tmux-3.3a-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'tmux' +version = '3.3a' + +homepage = 'https://github.com/tmux/tmux/' +description = """tmux is a terminal multiplexer: it enables a number of +terminals to be created, accessed, and controlled from a single screen. tmux +may be detached from a screen and continue running in the background, then +later reattached.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'optarch': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e4fd347843bd0772c4f48d6dde625b0b109b7a380ff15db21e97c11a4dcdf93f'] + +builddependencies = [ + ('binutils', '2.38'), + ('Bison', '3.8.2'), + ('make', '4.3'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('libevent', '2.1.12'), + ('ncurses', '6.3'), +] + +sanity_check_paths = { + 'files': ['bin/tmux'], + 'dirs': [] +} + +moduleclass = 'tools' From b40096676f0a96b0c47cb55a576e3f489cc73ac3 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Mon, 31 Oct 2022 02:29:29 +0000 Subject: [PATCH 232/939] Add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot --- .../o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb | 5 ++ .../o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb | 5 ++ .../OpenBLAS-0.3.21_avoid-crash-in-zdot.patch | 19 ++++++ ...AS-0.3.21_disable-fma-in-cscal-zscal.patch | 68 +++++++++++++++++++ 6 files changed, 107 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb index 93e65aa92218..c4b29c67422f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.17-GCC-11.2.0.eb @@ -19,6 +19,8 @@ patches = [ 'OpenBLAS-%(version)s_workaround-gcc11-miscompiling-C-ZBLAS3-tests.patch', 'OpenBLAS-%(version)s_fix-segfault-ztrsv.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.17.tar.gz': 'df2934fa33d04fd84d839ca698280df55c690c86a5a1133b3f7266fce1de279f'}, @@ -31,6 +33,9 @@ checksums = [ {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb index 866cd7de5151..762a9558bfb9 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.18-GCC-11.2.0.eb @@ -18,6 +18,8 @@ patches = [ 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.18.tar.gz': '1632c1e8cca62d8bed064b37747e331a1796fc46f688626337362bf0d16aeadb'}, @@ -28,6 +30,9 @@ checksums = [ {'OpenBLAS-0.3.17_fix-segfault-ztrsv.patch': 'b1f89d90cc46b486534069135854e6081994b5a1a88370d32dae982e0f040111'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb index c654f92e7003..98f44c83e7ce 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.2.0.eb @@ -17,6 +17,8 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -26,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb index bb82984319e4..4496c0bc5b3f 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-GCC-11.3.0.eb @@ -17,6 +17,8 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, @@ -26,6 +28,9 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch new file mode 100644 index 000000000000..d96341d6de58 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_avoid-crash-in-zdot.patch @@ -0,0 +1,19 @@ +Avoid crash with GCC 11's vectorizer involving 256-bit ymm registers. + +See https://gcc.gnu.org/bugzilla/show_bug.cgi?id=107451 + +Bart Oldeman + +diff --git a/kernel/x86_64/zdot.c b/kernel/x86_64/zdot.c +index 27397ccf..e1d43be1 100644 +--- a/kernel/x86_64/zdot.c ++++ b/kernel/x86_64/zdot.c +@@ -97,7 +97,7 @@ extern int blas_level1_thread_with_return_value(int mode, BLASLONG m, BLASLONG n + + + +-static void zdot_compute (BLASLONG n, FLOAT *x, BLASLONG inc_x, FLOAT *y, BLASLONG inc_y,OPENBLAS_COMPLEX_FLOAT *result) ++__attribute__((target("prefer-vector-width=128"))) static void zdot_compute (BLASLONG n, FLOAT *x, BLASLONG inc_x, FLOAT *y, BLASLONG inc_y,OPENBLAS_COMPLEX_FLOAT *result) + { + BLASLONG i; + BLASLONG ix,iy; diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch new file mode 100644 index 000000000000..6e2cb2e62e08 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch @@ -0,0 +1,68 @@ +From e7e3aa29482281edba46a27fcd452d7ed630f46a Mon Sep 17 00:00:00 2001 +From: Bart Oldeman +Date: Thu, 27 Oct 2022 17:20:44 -0400 +Subject: [PATCH] x86_64: prevent GCC and Clang from generating FMAs in + cscal/zscal. + +If e.g. -march=haswell is set in CFLAGS, GCC generates FMAs by default, which +is inconsistent with the microkernels, none of which use FMAs. These +inconsistencies cause a few failures in the LAPACK testcases, where +eigenvalue results with/without eigenvectors are compared. + +Moreover using FMAs for multiplication of complex numbers can give surprising +results, see 22aa81f for more information. + +This uses the same syntax as used in 22aa81f for zarch (s390x). +--- + kernel/x86_64/cscal.c | 13 +++++++++++++ + kernel/x86_64/zscal.c | 13 +++++++++++++ + 2 files changed, 26 insertions(+) + +diff --git a/kernel/x86_64/cscal.c b/kernel/x86_64/cscal.c +index dc3f688c69..6ae66d9731 100644 +--- a/kernel/x86_64/cscal.c ++++ b/kernel/x86_64/cscal.c +@@ -25,6 +25,19 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + +diff --git a/kernel/x86_64/zscal.c b/kernel/x86_64/zscal.c +index 3744c98bb7..dfdb4230b6 100644 +--- a/kernel/x86_64/zscal.c ++++ b/kernel/x86_64/zscal.c +@@ -25,6 +25,19 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + From e2abe951628c519b1dc970064b3c36682e02d0ec Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 31 Oct 2022 11:28:16 +0100 Subject: [PATCH 233/939] adding easyconfigs: MotionCor2-1.5.0-GCCcore-11.3.0.eb --- .../MotionCor2-1.5.0-GCCcore-11.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..6c70f59b67b7 --- /dev/null +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,44 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Ake Sandgren +# HPC2N +# Umea University + +name = 'MotionCor2' +version = '1.5.0' + +homepage = 'https://msg.ucsf.edu/' +description = """MotionCor2 correct anisotropic image motion at the +single pixel level across the whole frame, suitable for both single +particle and tomographic images. Iterative, patch-based motion detection +is combined with spatial and temporal constraints and dose weighting. + +Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, +Yifan Cheng and David A. Agard (2016) Anisotropic Correction of +Beam-induced Motion for Improved Single-particle Electron +Cryo-microscopy, Nature Methods, submitted. +BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +# No longer directly downloadable, available from https://msg.ucsf.edu/software +sources = [ + '%(name)s_%(version)s.zip', +] +checksums = ['cdb7b9aceb42d52e2a4c7a5e80270371376aea412d21fa1f1f28d4cc71c81834'] + +# CUDA is a build dependency to make sure it gets installed. +# It's actually a runtime dependency, but that's handled in the wrapper to +# make sure it doesn't conflict with whatever toolchain happens to be loaded. +# Change CUDA version to match the latest one used in this version +# of MotionCor2 +builddependencies = [ + ('binutils', '2.38'), + ('CUDA', '11.6.0', '', SYSTEM), +] + +dependencies = [ + ('LibTIFF', '4.3.0'), +] + +moduleclass = 'bio' From e71962b1ce6e45abbd51a7b7372828216bde1819 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Oct 2022 11:57:54 +0100 Subject: [PATCH 234/939] add LMERConvenienceFunctions extension for R v4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 6 ++++++ 1 file changed, 6 insertions(+) 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 49b9a97d1a05..e3da8a7d9fa6 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 @@ -3358,6 +3358,12 @@ exts_list = [ ('AMAPVox', '0.12.0', { 'checksums': ['b30fefef8661e27ffe3883665204b623eda2143dbcd3084a1d5810f8ea834c85'], }), + ('LCFdata', '2.0', { + 'checksums': ['b58f4d93b9023dd1ba2db96a59ddfc058397085933d8de4cdb38ee064d5e7bf4'], + }), + ('LMERConvenienceFunctions', '3.0', { + 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], + }), ] moduleclass = 'lang' From abc4ba47ae726bf6f7b18947f076e352b596221a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Mon, 31 Oct 2022 12:50:33 +0100 Subject: [PATCH 235/939] Update easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb index 6c70f59b67b7..13e710f1fd7c 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -26,6 +26,7 @@ sources = [ '%(name)s_%(version)s.zip', ] checksums = ['cdb7b9aceb42d52e2a4c7a5e80270371376aea412d21fa1f1f28d4cc71c81834'] +download_instructions = """Visit https://msg.ucsf.edu/software and fill in the form to download %s""" % sources[0] # CUDA is a build dependency to make sure it gets installed. # It's actually a runtime dependency, but that's handled in the wrapper to From 32c0d75f717c18624bb44eceae50c0ba5636bc62 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?=C3=85ke=20Sandgren?= Date: Mon, 31 Oct 2022 12:50:45 +0100 Subject: [PATCH 236/939] Update easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- .../easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb index 13e710f1fd7c..1ce57f532b7b 100644 --- a/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/MotionCor2/MotionCor2-1.5.0-GCCcore-11.3.0.eb @@ -21,7 +21,6 @@ BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -# No longer directly downloadable, available from https://msg.ucsf.edu/software sources = [ '%(name)s_%(version)s.zip', ] From ed75daa514deeb52189905dac31b76e6fcb6ab07 Mon Sep 17 00:00:00 2001 From: Ben Langenberg Date: Mon, 31 Oct 2022 13:35:42 +0100 Subject: [PATCH 237/939] favor decision in https://github.com/easybuilders/easybuild-easyconfigs/issues/16330 --- easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb index f2e75d38711c..fabca76f18fa 100644 --- a/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb +++ b/easybuild/easyconfigs/t/Trinity/Trinity-2.9.1-foss-2020b.eb @@ -29,8 +29,8 @@ builddependencies = [ ] dependencies = [ - ('Java', '11', '', True), - ('ant', '1.10.9', '-Java-%(javaver)s', True), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.9', '-Java-%(javaver)s', SYSTEM), ('Perl', '5.32.0'), ('Python', '3.8.6'), ('SciPy-bundle', '2020.11'), From 64400bf1141f3e8e49a6f2b590870a6284356a57 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 31 Oct 2022 15:14:37 +0100 Subject: [PATCH 238/939] adding easyconfigs: cdsapi-0.5.1-GCCcore-11.3.0.eb --- .../c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..c70d2401d595 --- /dev/null +++ b/easybuild/easyconfigs/c/cdsapi/cdsapi-0.5.1-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'cdsapi' +version = '0.5.1' + +homepage = 'https://pypi.org/project/cdsapi' +description = "Climate Data Store API" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['19f3e92f1996cc1115d0b0281617edeaecf3eefca03fbd384cfbc520d5f0476d'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('tqdm', '4.64.0'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From bdf19a088b0c99038d13c2911447c4b78f81d8e3 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 1 Nov 2022 08:37:25 +0100 Subject: [PATCH 239/939] add missing build dependency on Perl for GStreamer. And make sure to not make files suid. --- .../GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb | 9 +++++++- .../g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb | 9 +++++++- .../GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb | 9 +++++++- .../GStreamer-1.18_fix_bad_suid.patch | 22 +++++++++++++++++++ .../GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb | 9 +++++++- 7 files changed, 70 insertions(+), 6 deletions(-) create mode 100644 easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb index 3c94c21acaee..1e320e100bf1 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.0-GCC-8.2.0-2.31.1.eb @@ -13,9 +13,16 @@ toolchain = {'name': 'GCC', 'version': '8.2.0-2.31.1'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.16.0.tar.xz': '0e8e2f7118be437cba879353970cf83c2acced825ecb9275ba05d9186ef07c00'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ + ('Perl', '5.28.1'), ('Bison', '3.0.5'), ('flex', '2.6.4'), ('GObject-Introspection', '1.60.1', '-Python-3.7.2'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb index 92e0c55eca28..370fa85b4cf4 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.16.2-GCC-8.3.0.eb @@ -13,9 +13,16 @@ toolchain = {'name': 'GCC', 'version': '8.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['e3f044246783fd685439647373fa13ba14f7ab0b346eadd06437092f8419e94e'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.16.2.tar.xz': 'e3f044246783fd685439647373fa13ba14f7ab0b346eadd06437092f8419e94e'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ + ('Perl', '5.30.0'), ('Bison', '3.3.2'), ('flex', '2.6.4'), ('GObject-Introspection', '1.63.1', '-Python-3.7.4'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb index a4c5be909161..cc7e4f4623c5 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.2.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '10.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.4.tar.xz': '9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.55.3'), ('Ninja', '1.10.1'), + ('Perl', '5.32.0'), ('Bison', '3.7.1'), ('flex', '2.6.4'), ('GObject-Introspection', '1.66.1'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb index 2c38b4b9151b..11f4d5afc2e8 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.4-GCC-10.3.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.4.tar.xz': '9aeec99b38e310817012aa2d1d76573b787af47f8a725a65b833880a094dfbc5'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.58.0'), ('Ninja', '1.10.2'), + ('Perl', '5.32.1'), ('Bison', '3.7.6'), ('flex', '2.6.4'), ('GObject-Introspection', '1.68.0'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb index 7d550bd31b6a..45f9ea5e5d02 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18.5-GCC-11.2.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['55862232a63459bbf56abebde3085ca9aec211b478e891dacea4d6df8cafe80a'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.18.5.tar.xz': '55862232a63459bbf56abebde3085ca9aec211b478e891dacea4d6df8cafe80a'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.58.2'), ('Ninja', '1.10.2'), + ('Perl', '5.34.0'), ('Bison', '3.7.6'), ('flex', '2.6.4'), ('GObject-Introspection', '1.68.0'), diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch new file mode 100644 index 000000000000..4fff14d8b7af --- /dev/null +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.18_fix_bad_suid.patch @@ -0,0 +1,22 @@ +Do NOT make files setuid or try to do setcap. +That's a recipe for disaster. + +Åke Sandgren, 20221031 +diff -ru gstreamer-1.20.2.orig/libs/gst/helpers/ptp_helper_post_install.sh gstreamer-1.20.2/libs/gst/helpers/ptp_helper_post_install.sh +--- gstreamer-1.20.2.orig/libs/gst/helpers/ptp_helper_post_install.sh 2022-05-03 00:29:29.000000000 +0200 ++++ gstreamer-1.20.2/libs/gst/helpers/ptp_helper_post_install.sh 2022-10-31 16:39:11.959435316 +0100 +@@ -11,14 +11,10 @@ + setuid-root) + echo "$0: permissions before: " + ls -l "$ptp_helper" +- chown root "$ptp_helper" || true +- chmod u+s "$ptp_helper" || true + echo "$0: permissions after: " + ls -l "$ptp_helper" + ;; + capabilities) +- echo "Calling $setcap cap_net_bind_service,cap_net_admin+ep $ptp_helper" +- $setcap cap_net_bind_service,cap_net_admin+ep "$ptp_helper" || true + ;; + none) + echo "No perms/caps to set for $ptp_helper" diff --git a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb index df69820328fd..d942105b5f7d 100644 --- a/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/g/GStreamer/GStreamer-1.20.2-GCC-11.3.0.eb @@ -13,11 +13,18 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://gstreamer.freedesktop.org/src/gstreamer'] sources = [SOURCELOWER_TAR_XZ] -checksums = ['df24e8792691a02dfe003b3833a51f1dbc6c3331ae625d143b17da939ceb5e0a'] +patches = [ + '%(name)s-1.18_fix_bad_suid.patch', +] +checksums = [ + {'gstreamer-1.20.2.tar.xz': 'df24e8792691a02dfe003b3833a51f1dbc6c3331ae625d143b17da939ceb5e0a'}, + {'GStreamer-1.18_fix_bad_suid.patch': '3d963ffdaf157ed92f46a071c4ef46f548c0b19186427e8404cb066705bbb61a'}, +] builddependencies = [ ('Meson', '0.62.1'), ('Ninja', '1.10.2'), + ('Perl', '5.34.1'), ('Bison', '3.8.2'), ('flex', '2.6.4'), ('GObject-Introspection', '1.72.0'), From 9914b1c520060e5cea9fdc0621f431d86ae42fbb Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:10:58 +0100 Subject: [PATCH 240/939] adding easyconfigs: wandb-0.13.4-GCCcore-11.3.0.eb --- .../w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb | 66 +++++++++++++++++++ 1 file changed, 66 insertions(+) create mode 100644 easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1fdb7113a4e8 --- /dev/null +++ b/easybuild/easyconfigs/w/wandb/wandb-0.13.4-GCCcore-11.3.0.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'wandb' +version = '0.13.4' + +homepage = 'https://www.wandb.com/' +description = """ +CLI and Python API for Weights and Biases: a tool for visualizing and tracking +your machine learning experiments.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('GitPython', '3.1.27'), + ('PyYAML', '6.0'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('yaspin', '2.1.0', { + 'checksums': ['c8d34eca9fda3f4dfbe59f57f3cf0f3641af3eefbf1544fbeb9b3bacf82c580a'], + }), + ('shortuuid', '1.0.9', { + 'checksums': ['459f12fa1acc34ff213b1371467c0325169645a31ed989e268872339af7563d5'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + ('sentry-sdk', '1.8.0', { + 'checksums': ['9c68e82f7b1ad78aee6cdef57c2c0f6781ddd9ffa8848f4503c5a8e02b360eea'], + }), + ('charset-normalizer', '2.0.12', { + 'checksums': ['2857e29ff0d34db842cd7ca3230549d1a697f96ee6d3fb071cfa6c7393832597'], + }), + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('docker-pycreds', '0.4.0', { + 'modulename': 'dockerpycreds', + 'checksums': ['6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4'], + }), + (name, version, { + 'checksums': ['51e2672e12cca94680f6bcff0af80822d562e6b7846036050fc5bdd00240ea75'], + }), +] + +sanity_check_paths = { + 'files': ['bin/wandb', 'bin/wb'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = ['wandb --help'] + +moduleclass = 'tools' From 20cbc3a794cc30e10944f430a07c2a336a9782d7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:15:17 +0100 Subject: [PATCH 241/939] adding easyconfigs: SimpleITK-2.1.1.2-foss-2022a.eb --- .../SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb new file mode 100644 index 000000000000..9a0f8d8c8e2b --- /dev/null +++ b/easybuild/easyconfigs/s/SimpleITK/SimpleITK-2.1.1.2-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'CMakeMake' + +name = 'SimpleITK' +version = '2.1.1.2' + +homepage = 'https://www.simpleitk.org' +description = """SimpleITK is a simplified programming interface to the algorithms and data structures of + the Insight Toolkit (ITK).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_allow-lua54-for-code-generation.patch'] +checksums = [ + '5c0689b007d449ce0ce17a9ea322152315fb17ed32949005a974d3d9c2f58da3', # SimpleITK-2.1.1.2.tar.gz + # SimpleITK-2.1.1.2_allow-lua54-for-code-generation.patch + 'd1a45b1b64a226b3c22bf83c2f40f7f0e8f0a7d74bea1b2e7f5c5b6ed88b1522', +] + +builddependencies = [ + ('CMake', '3.23.1'), + ('SWIG', '4.0.2'), + ('Lua', '5.4.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('ITK', '5.2.1'), + ('scikit-build', '0.15.0'), +] + +start_dir = 'SimpleITK' + +configopts = "-DWRAP_DEFAULT:BOOL=OFF -DWRAP_PYTHON=BOOL:ON " + +postinstallcmds = [ + "cd %(builddir)s/easybuild_obj/Wrapping/Python && " + "pip install --ignore-installed --no-deps --prefix=%(installdir)s . ", +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +sanity_check_paths = { + 'files': ['lib/libSimpleITK_ITKBiasCorrection-%(version_major_minor)s.a'], + 'dirs': ['include/%(name)s-%(version_major_minor)s', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["python -c 'import %(name)s'"] + +moduleclass = 'tools' From c5c539d4f0362b6f0d87358de38fb0948af5030b Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:17:03 +0100 Subject: [PATCH 242/939] adding easyconfigs: MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb, MONAI-1.0.1-foss-2022a.eb, einops-0.4.1-GCCcore-11.3.0.eb --- .../e/einops/einops-0.4.1-GCCcore-11.3.0.eb | 29 +++++++++++ .../MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 50 +++++++++++++++++++ .../m/MONAI/MONAI-1.0.1-foss-2022a.eb | 48 ++++++++++++++++++ 3 files changed, 127 insertions(+) create mode 100644 easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..e31c2fbbbba2 --- /dev/null +++ b/easybuild/easyconfigs/e/einops/einops-0.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'einops' +version = '0.4.1' + +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': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['65ede824fa54ce99ba969c61152f9948eb8cad08d5f0ca97c95e3804bafcce48'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..bd6d8765a06a --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,50 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +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': '2022a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('einops', '0.4.1'), + ('ITK', '5.2.1'), + ('NiBabel', '4.0.2'), + ('scikit-image', '0.19.3'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1', versionsuffix), + ('tqdm', '4.64.0'), +] + +exts_list = [ + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + }), +] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb new file mode 100644 index 000000000000..0d272341e2ce --- /dev/null +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'MONAI' +version = '1.0.1' + +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': '2022a'} + +github_account = 'Project-MONAI' + +dependencies = [ + ('Python', '3.10.4'), + ('PyTorch', '1.12.0'), + ('einops', '0.4.1'), + ('ITK', '5.2.1'), + ('NiBabel', '4.0.2'), + ('scikit-image', '0.19.3'), + ('tensorboard', '2.10.0'), + ('torchvision', '0.13.1'), + ('tqdm', '4.64.0'), +] + +exts_list = [ + (name, version, { + 'preinstallopts': 'BUILD_MONAI=1', + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'checksums': ['dc961e0adbe1b0c87b85f69377267d60c835f24eb03c8982a21b23a93c6ec36b'], + }), +] + +use_pip = True + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] + +sanity_check_paths = { + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], + 'dirs': [''], +} + +moduleclass = 'vis' From 269db8f055bb836dc74be57f242a48c0a75e1f53 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 1 Nov 2022 15:22:48 +0100 Subject: [PATCH 243/939] adding easyconfigs: scikit-image-0.19.3-foss-2022a.eb, imageio-2.22.2-foss-2022a.eb --- .../i/imageio/imageio-2.22.2-foss-2022a.eb | 25 +++++++++++ .../scikit-image-0.19.3-foss-2022a.eb | 43 +++++++++++++++++++ 2 files changed, 68 insertions(+) create mode 100644 easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb b/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb new file mode 100644 index 000000000000..a340e81b29ed --- /dev/null +++ b/easybuild/easyconfigs/i/imageio/imageio-2.22.2-foss-2022a.eb @@ -0,0 +1,25 @@ +easyblock = 'PythonPackage' + +name = 'imageio' +version = '2.22.2' + +homepage = 'https://imageio.github.io' +description = """Imageio is a Python library that provides an easy interface to read and write a wide range of + image data, including animated images, video, volumetric data, and scientific formats.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['db7010cd10712518819a4187baf61b05988361ea20c23e829918727b27acb977'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Pillow', '9.1.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb new file mode 100644 index 000000000000..2cc7bce06b1f --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-image/scikit-image-0.19.3-foss-2022a.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'scikit-image' +version = '0.19.3' + +homepage = 'https://scikit-image.org/' +description = "scikit-image is a collection of algorithms for image processing." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('Pillow', '9.1.1'), + ('networkx', '2.8.4'), + ('dask', '2022.10.0'), + ('imageio', '2.22.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('PyWavelets', '1.4.1', { + 'modulename': 'pywt', + 'checksums': ['6437af3ddf083118c26d8f97ab43b0724b956c9f958e9ea788659f6a2834ba93'], + }), + ('imread', '0.7.4', { + 'checksums': ['0487adef11a22168700968c1727020361a72f6132b6ced2b8826b02d8cbf744f'], + }), + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + (name, version, { + 'modulename': 'skimage', + 'checksums': ['24b5367de1762da6ee126dd8f30cc4e7efda474e0d7d70685433f0e3aa2ec450'], + }), +] + +moduleclass = 'vis' From beaed9282b95ecc76803630bfad3d7c46d1fce1c Mon Sep 17 00:00:00 2001 From: robogast Date: Tue, 1 Nov 2022 17:07:18 +0100 Subject: [PATCH 244/939] added comments to ASAP patch files, updated checksums accordingly --- easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch | 4 ++++ easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb | 6 +++--- easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch | 6 ++++++ easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch | 3 +++ 4 files changed, 16 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch index b4ca984d4214..d836a0466d22 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-cmath.patch @@ -1,3 +1,7 @@ +# Author: Robert Jan Schlimbach (SURF) +# ASAP/2.1 forgets a few headers, in this case cmath +# Possibly fixed if https://github.com/computationalpathologygroup/ASAP/pull/241 gets merged + diff --git a/annotation/ImageScopeRepository.cpp b/annotation/ImageScopeRepository.cpp index 6916a58..c135cb3 100644 --- a/annotation/ImageScopeRepository.cpp diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb index 7dd82903d65e..1a9c9bccc8b0 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-foss-2022a.eb @@ -19,9 +19,9 @@ patches = [ ] checksums = [ '7ba9f39d09bada808f760c5dc9ac0cda0d221fd1393a0a3f9decfd6b5e913b3c', # ASAP-2.1.tar.gz - 'dbdf26324a7521b4beaa7ec2c0585f0816619cd73b3125efd313eb48c4813a43', # ASAP-2.1-libjpeg.patch - 'f578bb3ec4cbce573d4b9acd695eb55446592f4ac00551656a06f113ba09a9a7', # ASAP-2.1-pugixml.patch - 'e33d83853e0bd51113a886d0793504ce0abfb15fdf88410a19287d46fafd33c4', # ASAP-2.1-cmath.patch + '78337d0250c567335f1a356f8761587000170b71a87b3e546b6b9330d3236b0f', # ASAP-2.1-libjpeg.patch + 'ab6104fb19515d0b042944bbe95fa67f55f47ef3bf18a91d337e0ca476c7385d', # ASAP-2.1-pugixml.patch + '15cf6bf2ab65ce37338ea571d80ced59b4e35cf82e434b2ccec7b534778f4a33', # ASAP-2.1-cmath.patch ] builddependencies = [ diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch index eeab7c051442..b20303038721 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-libjpeg.patch @@ -1,3 +1,9 @@ +# Author: Robert Jan Schlimbach (SURF) +# ASAP/2.1 uses DCMKT jpeg sources directly by manually setting a PATH +# see https://github.com/computationalpathologygroup/ASAP/issues/32 +# we simply replace DCMTK jpeg with the default jpeglib header. +# Need to rename jpeg_mem_src to avoid a resulting name conflic. + diff --git a/multiresolutionimageinterface/VSIImage.cpp b/multiresolutionimageinterface/VSIImage.cpp index 509bb18..1763201 100644 --- a/multiresolutionimageinterface/VSIImage.cpp diff --git a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch index 2b4a652369fe..751d179cb193 100644 --- a/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch +++ b/easybuild/easyconfigs/a/ASAP/ASAP-2.1-pugixml.patch @@ -1,3 +1,6 @@ +# Author: Robert Jan Schlimbach (SURF) +# Patch to make ASAP/2.1 accept pugixml as non-header-only shared lib + diff --git a/annotation/CMakeLists.txt b/annotation/CMakeLists.txt index 114babe..2156cd3 100644 --- a/annotation/CMakeLists.txt From a0732b63add05a61e1f72e0aa5d57bf2af2c8e94 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Wed, 2 Nov 2022 15:53:44 +0100 Subject: [PATCH 245/939] adding easyconfigs: ESM-2-2.0.0-foss-2021a.eb --- .../e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb new file mode 100644 index 000000000000..d33ee519c80a --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +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': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] +sources = ['fair-esm-%(version)s.tar.gz'] +checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] + +dependencies = [ + ('Python', '3.9.5'), + ('PyTorch', '1.10.0'), +] + +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'esm'} + +sanity_check_commands = [ + "python -c 'import esm.pretrained'", +] + +moduleclass = 'bio' From d73fe2ec878074d495f94b2e8e7889ecb91cafa5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 00:34:10 +0100 Subject: [PATCH 246/939] build nodejs with external OpenSSL and ICU --- .../n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 32 +++++++++++++------ .../n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 25 ++++++++++----- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 25 ++++++++++----- 3 files changed, 57 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index deaf600ec198..b75eb3495ef0 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.0' # LTS on 2021-06-03 -local_libversion = '83' +_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -14,11 +14,16 @@ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} source_urls = ['http://%(name)s.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-argument-list-too-long.patch'] +patches = [ + '%(name)s-%(version)s_fix-argument-list-too-long.patch', + '%(name)s-%(version)s_use_new_icu69_calls.patch', +] checksums = [ '6114e82d3256136dc85a509d835442fbdf2f8430dcd8bfa7c304097344d06fb7', # node-v14.17.0.tar.gz # nodejs-14.17.0_fix-argument-list-too-long.patch 'b0eac4b478a9268c8902ec701f99e1445eeba2a70927bfacdeb5ba243e668550', + # nodejs-14.17.0_use_new_icu69_calls.patch + '24fbc749d225b395184aa9c4c3880665026ced898474d77259c597f6b790e290', ] builddependencies = [ @@ -26,21 +31,30 @@ builddependencies = [ ('Python', '3.9.5'), ] +dependencies = [ + ('ICU', '69.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index 569932aa4527..e81302ffc403 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.6' # LTS on 2020-08-31 -local_libversion = '83' +_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.9.6', '-bare'), ] +dependencies = [ + ('ICU', '69.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 3fe69b1af4cf..73aeb628575c 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '16.15.1' # LTS on 2022-06-12 -local_libversion = '93' +_libversion = '93' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.10.4', '-bare'), ] +dependencies = [ + ('ICU', '71.1'), + ('OpenSSL', '1.1', '', True), +] + +# Use ICU and OpenSSL from EasyBuild +_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + _common_configopts, # Static build + '--shared %s' % _common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] +_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From 9a403292a75a1d9a16753c4ac9404a04da4446a7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 00:43:07 +0100 Subject: [PATCH 247/939] add patch to fix ICU v69 support in nodejs v14 --- .../nodejs-14.17.0_use_new_icu69_calls.patch | 92 +++++++++++++++++++ 1 file changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch new file mode 100644 index 000000000000..9b635d20f3d8 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0_use_new_icu69_calls.patch @@ -0,0 +1,92 @@ +From 035c305ce7761f51328b45f1bd83e26aef267c9d Mon Sep 17 00:00:00 2001 +From: Frank Tang +Date: Thu, 15 Oct 2020 22:44:27 -0700 +Subject: [PATCH] [Intl] call new ListFormatter::createInstance + +The one we currently using is now marked as internal and to be removed +for 68. Migrating to the style which already avaiable in ICU 67-1. + +Bug: v8:11031 +Change-Id: I668382a2e1b8602ddca02bf231c5008a6c92bf2d +Reviewed-on: https://chromium-review.googlesource.com/c/v8/v8/+/2477751 +Reviewed-by: Jakob Kummerow +Commit-Queue: Frank Tang +Cr-Commit-Position: refs/heads/master@{#70638} +--- + +diff --git a/deps/v8/src/objects/js-list-format.cc b/deps/v8/src/objects/js-list-format.cc +index b17d38c..e48a387 100644 +--- a/deps/v8/src/objects/js-list-format.cc ++++ b/deps/v8/src/objects/js-list-format.cc +@@ -29,46 +29,27 @@ + namespace internal { + + namespace { +-const char* kStandard = "standard"; +-const char* kOr = "or"; +-const char* kUnit = "unit"; +-const char* kStandardShort = "standard-short"; +-const char* kOrShort = "or-short"; +-const char* kUnitShort = "unit-short"; +-const char* kStandardNarrow = "standard-narrow"; +-const char* kOrNarrow = "or-narrow"; +-const char* kUnitNarrow = "unit-narrow"; + +-const char* GetIcuStyleString(JSListFormat::Style style, +- JSListFormat::Type type) { ++UListFormatterWidth GetIcuWidth(JSListFormat::Style style) { ++ switch (style) { ++ case JSListFormat::Style::LONG: ++ return ULISTFMT_WIDTH_WIDE; ++ case JSListFormat::Style::SHORT: ++ return ULISTFMT_WIDTH_SHORT; ++ case JSListFormat::Style::NARROW: ++ return ULISTFMT_WIDTH_NARROW; ++ } ++ UNREACHABLE(); ++} ++ ++UListFormatterType GetIcuType(JSListFormat::Type type) { + switch (type) { + case JSListFormat::Type::CONJUNCTION: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kStandard; +- case JSListFormat::Style::SHORT: +- return kStandardShort; +- case JSListFormat::Style::NARROW: +- return kStandardNarrow; +- } ++ return ULISTFMT_TYPE_AND; + case JSListFormat::Type::DISJUNCTION: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kOr; +- case JSListFormat::Style::SHORT: +- return kOrShort; +- case JSListFormat::Style::NARROW: +- return kOrNarrow; +- } ++ return ULISTFMT_TYPE_OR; + case JSListFormat::Type::UNIT: +- switch (style) { +- case JSListFormat::Style::LONG: +- return kUnit; +- case JSListFormat::Style::SHORT: +- return kUnitShort; +- case JSListFormat::Style::NARROW: +- return kUnitNarrow; +- } ++ return ULISTFMT_TYPE_UNITS; + } + UNREACHABLE(); + } +@@ -143,7 +124,7 @@ + icu::Locale icu_locale = r.icu_locale; + UErrorCode status = U_ZERO_ERROR; + icu::ListFormatter* formatter = icu::ListFormatter::createInstance( +- icu_locale, GetIcuStyleString(style_enum, type_enum), status); ++ icu_locale, GetIcuType(type_enum), GetIcuWidth(style_enum), status); + if (U_FAILURE(status) || formatter == nullptr) { + delete formatter; + THROW_NEW_ERROR(isolate, NewRangeError(MessageTemplate::kIcuError), From d2457c0740f4846fa8f8224974ed8a2ab3712e04 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 3 Nov 2022 01:02:47 +0100 Subject: [PATCH 248/939] fix dependency on OpenSSL to use SYSTEM template --- easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index b75eb3495ef0..bf1db1aa052c 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -33,7 +33,7 @@ builddependencies = [ dependencies = [ ('ICU', '69.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index e81302ffc403..a6fe9b552ba3 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('ICU', '69.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 73aeb628575c..bcd9c8dded13 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -23,7 +23,7 @@ builddependencies = [ dependencies = [ ('ICU', '71.1'), - ('OpenSSL', '1.1', '', True), + ('OpenSSL', '1.1', '', SYSTEM), ] # Use ICU and OpenSSL from EasyBuild From 8da47cb621791fe7fce2c92e31742c0306ee1850 Mon Sep 17 00:00:00 2001 From: vsc45304 Date: Thu, 3 Nov 2022 08:28:15 +0100 Subject: [PATCH 249/939] added download_dep_fail --- easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb index d33ee519c80a..e3ea302ffec7 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -20,6 +20,7 @@ dependencies = [ ] use_pip = True +download_dep_fail = True sanity_pip_check = True options = {'modulename': 'esm'} From 0273721033e985b841678403fb7827b93ba087e9 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 3 Nov 2022 08:39:24 +0100 Subject: [PATCH 250/939] adding easyconfigs: ctffind-4.1.14-foss-2022a.eb --- .../c/ctffind/ctffind-4.1.14-foss-2022a.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb new file mode 100644 index 000000000000..59e562d1e6b8 --- /dev/null +++ b/easybuild/easyconfigs/c/ctffind/ctffind-4.1.14-foss-2022a.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# sciCORE - University of Basel +# SIB Swiss Institute of Bioinformatics +# +# Author: Ake Sandgren, HPC2N, Umea University +# +# Author: Thomas Hoffmann, EMBL Heidelberg + +easyblock = 'ConfigureMake' + +name = 'ctffind' +version = '4.1.14' + +homepage = 'https://grigoriefflab.umassmed.edu/ctffind4' +description = """Program for finding CTFs of electron micrographs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True} + +source_urls = ['https://grigoriefflab.umassmed.edu/sites/default/files/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + '%(name)s-%(version)s_asm-fix.patch', + '%(name)s-%(version)s_void-functions.patch' +] +checksums = [ + 'db17b2ebeb3c3b2b3764e42b820cd50d19ccccf6956c64257bfe5d5ba6b40cb5', # ctffind-4.1.14.tar.gz + 'e6d468b3f1569e2d42e077573529dbc3035a03715c436d2349ccaaab63b64f28', # ctffind-4.1.14_asm-fix.patch + '0a578328062881d86b10585f1b0efa81b7a1826baf3e7bcc5c749bba73e96d10', # ctffind-4.1.14_void-functions.patch +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('GSL', '2.7',), + ('wxWidgets', '3.2.1'), +] + +configopts = '--enable-openmp ' + +parallel = 1 + +sanity_check_paths = { + 'files': ['bin/ctffind'], + 'dirs': [], +} + +moduleclass = 'bio' From c92ba4b925937d47cbd836691b10c67e665dcd88 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Thu, 3 Nov 2022 11:30:49 +0100 Subject: [PATCH 251/939] adding easyconfigs: Nextflow-22.10.1.eb --- .../n/Nextflow/Nextflow-22.10.1.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb new file mode 100644 index 000000000000..896a6c321e37 --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb @@ -0,0 +1,33 @@ +easyblock = 'Binary' + +name = 'Nextflow' +version = '22.10.1' + +homepage = 'https://www.%(namelower)s.io/' +description = """Nextflow is a reactive workflow framework and a programming DSL + that eases writing computational pipelines with complex data""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/download/v%(version)s/'] +sources = ['%(namelower)s-%(version)s-all'] +checksums = ['c5edc9fc81d9c6eb4f628505f14f8bb4fe044d4fc7d9ef60654ba0d73abf5a80'] + +dependencies = [('Java', '11', '', True)] + +install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" +install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" +install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" +install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" + +sanity_check_paths = { + 'files': ['bin/%(namelower)s-%(version)s-all', 'bin/%(namelower)s'], + 'dirs': [] +} + +sanity_check_commands = [ + "%(namelower)s -v", + "%(namelower)s help", +] + +moduleclass = 'tools' From 88a15c893eb2a0f1767a8255c201dba3c630e450 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 3 Nov 2022 12:07:54 +0100 Subject: [PATCH 252/939] adding easyconfigs: DRAGMAP-1.3.0-foss-2021b.eb --- .../d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb new file mode 100644 index 000000000000..23c3faed318c --- /dev/null +++ b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'DRAGMAP' +version = '1.3.0' + +homepage = 'https://github.com/Illumina/DRAGMAP' +description = 'Dragmap is the Dragen mapper/aligner Open Source Software.' + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/Illumina/DRAGMAP/archive/refs/tags/'] +sources = ['%(version)s.tar.gz'] +checksums = ['baf546c2f53b13e2bce4c937201e38459f3ce2f1069722ca670d8726a4bae224'] + +skipsteps = ['configure'] +prebuildopts = 'sed -i "s|-msse4.2 -mavx2|$CXXFLAGS|g" config.mk &&' +buildopts = 'CC="$CC" CXX="$CXX"' +preinstallopts = 'mkdir %(installdir)s/bin &&' +installopts = 'DESTDIR=%(installdir)s' + +dependencies = { + ('Boost', '1.77.0'), + ('googletest', '1.11.0'), +} + +sanity_check_paths = { + 'files': ['bin/dragen-os'], + 'dirs': [] +} + +sanity_check_commands = ['dragen-os --help'] + +moduleclass = 'bio' From fb6f9fc133fc94006fca6494e9a68f2f99d09e78 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 3 Nov 2022 11:12:18 +0000 Subject: [PATCH 253/939] adding easyconfigs: bsddb3-6.2.9-GCCcore-11.3.0.eb --- .../b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..8a366485ad04 --- /dev/null +++ b/easybuild/easyconfigs/b/bsddb3/bsddb3-6.2.9-GCCcore-11.3.0.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'bsddb3' +version = '6.2.9' + +homepage = 'https://pypi.org/project/bsddb3/' +description = """bsddb3 is a nearly complete Python binding of the +Oracle/Sleepycat C API for the Database Environment, Database, Cursor, +Log Cursor, Sequence and Transaction objects.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +components = [ + ('DB', '5.3.28', { + 'source_urls': ['https://github.com/berkeleydb/libdb/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['e0a992d740709892e81f9d93f06daf305cf73fb81b545afe72478043172c3628'], + 'start_dir': '%(namelower)s-%(version)s', + }), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'preinstallopts': "unset LIBS && BERKELEYDB_DIR=%(installdir)s/ ", + 'checksums': ['70d05ec8dc568f42e70fc919a442e0daadc2a905a1cfb7ca77f549d49d6e7801'], + }), +] + +sanity_check_paths = { + 'files': ['bin/db_archive', 'include/db.h', 'lib/libdb.a', + 'lib/libdb.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(name)s'], +} + +moduleclass = 'data' From 67d85f9f722bc9647453bb01ba96719498c7a932 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 16:04:49 +0200 Subject: [PATCH 254/939] adding easyconfigs: cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb --- .../cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..b741f7e44e09 --- /dev/null +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,58 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 +easyblock = 'PythonBundle' + +name = 'cryoCARE' +version = '0.2.1' +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': '2021a'} + + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('SciPy-bundle', '2021.05'), + ('TensorFlow', '2.6.0', versionsuffix), + ('mrcfile', '1.3.0'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + ('csbdeep', '0.7.2', { + 'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'], + }), + (name, version, { + 'checksums': ['b66989acb6eadf771de08a46e4860d041113527205eebb2cf5d13ae3dc9cb43b'], + }), +] + +sanity_check_commands = [ + 'cryoCARE_extract_train_data.py --help', + 'cryoCARE_train.py --help', + 'cryoCARE_predict.py --help', +] + +moduleclass = 'vis' From 053b93f8ca8694203aa7c111e8a746696fa43c3d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 16:11:08 +0200 Subject: [PATCH 255/939] adding easyconfigs: n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb --- .../n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..7a91bbffaf40 --- /dev/null +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,61 @@ +# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2022/10 +easyblock = 'PythonBundle' + +name = 'n2v' +version = '0.3.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/juglab/cryoCARE_pip' +description = """ +Noise2Void - Learning Denoising from Single Noisy Images +The field of image denoising is currently dominated by discriminative deep +learning methods that are trained on pairs of noisy input and clean target +images. Recently it has been shown that such methods can also be trained without +clean targets. Instead, independent pairs of noisy images can be used, in an +approach known as NOISE2NOISE (N2N). Here, we introduce NOISE2VOID (N2V), a +training scheme that takes this idea one step further. It does not require noisy +image pairs, nor clean target images. Consequently, N2V allows us to train +directly on the body of data to be denoised and can therefore be applied when +other methods cannot. Especially interesting is the application to biomedical +image data, where the acquisition of training targets, clean or noisy, is +frequently not possible. We compare the performance of N2V to approaches that +have either clean target images and/or noisy image pairs available. Intuitively, +N2V cannot be expected to outperform methods that have more information +available during training. Still, we observe that the denoising performance of +NOISE2VOID drops in moderation and compares favorably to training-free denoising +methods.""" +toolchain = {'name': 'foss', 'version': '2021a'} + + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', True), + ('TensorFlow', '2.6.0', versionsuffix), + ('mrcfile', '1.3.0'), + ('tqdm', '4.61.2'), + ('matplotlib', '3.4.2'), + ('ruamel.yaml', '0.17.21'), + ('imagecodecs', '2022.9.26'), + ('JupyterLab', '3.0.16'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('tifffile', '2022.10.10', { + 'checksums': ['50b61ba943b866d191295bc38a00191c9fdab23ece063544c7f1a264e3f6aa8e'], + }), + ('csbdeep', '0.7.2', { + 'checksums': ['8a000eb71d04aa753f52ffe81a34c0a30a06ee986d20b9986d76272253e2fd53'], + }), + (name, version, { + 'checksums': ['8662aa5e903e170a1c9769882da241d669b6e7efd8b164b68723c675539ec06f'], + }), +] + +sanity_check_commands = [ + '%s --help' % x for x in ['care_predict', 'trainN2V.py', 'care_predict'] +] + +moduleclass = 'bio' From 606d0f82fb5779f1b553693e80a525a8f776d338 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Nov 2022 15:25:34 +0100 Subject: [PATCH 256/939] Update cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb --- .../c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb index b741f7e44e09..81b96e34eb71 100644 --- a/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/cryoCARE/cryoCARE-0.2.1-foss-2021a-CUDA-11.3.1.eb @@ -26,7 +26,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('SciPy-bundle', '2021.05'), ('TensorFlow', '2.6.0', versionsuffix), ('mrcfile', '1.3.0'), From f5063794a4ff1dab9dda71a411593e0f825abfd9 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Thu, 3 Nov 2022 15:27:05 +0100 Subject: [PATCH 257/939] Update n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb --- easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb index 7a91bbffaf40..a6c09399b711 100644 --- a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb @@ -29,7 +29,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ ('Python', '3.9.5'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('TensorFlow', '2.6.0', versionsuffix), ('mrcfile', '1.3.0'), ('tqdm', '4.61.2'), From d81b3437d6dc0a92a91c540fcaab2d9e9c5cb279 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:15:40 +0200 Subject: [PATCH 258/939] adding easyconfigs: imagecodecs-2022.9.26-foss-2021a.eb --- .../imagecodecs-2022.9.26-foss-2021a.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb new file mode 100644 index 000000000000..55bf95340ffe --- /dev/null +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -0,0 +1,72 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'imagecodecs' +version = '2022.9.26' + +homepage = 'https://github.com/cgohlke/imagecodecs' +description = """Imagecodecs is a Python library that provides block-oriented, in-memory buffer transformation, +compression, and decompression functions for use in the tifffile, czifile, zarr, and other +scientific image input/output modules.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +local_openjpeg_maj_min = '2.4' +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), # required for numpy + ('matplotlib', '3.4.2'), + ('Brotli', '1.0.9'), + ('bzip2', '1.0.8'), + ('Blosc', '1.21.0'), + ('Blosc2', '2.0.4'), + ('CFITSIO', '3.49'), + ('CharLS', '2.3.4'), + ('giflib', '5.2.1'), + ('jxrlib', '1.1'), + ('LittleCMS', '2.12'), + ('LERC', '3.0'), + ('libaec', '1.0.6'), + ('libavif', '0.11.1'), + ('libdeflate', '1.8'), + ('libjpeg-turbo', '2.0.6'), + ('libjxl', '0.5'), + ('LibLZF', '3.6'), + ('libpng', '1.6.37'), + ('XZ', '5.2.5'), + ('LibTIFF', '4.2.0'), + ('libwebp', '1.2.0'), + ('lz4', '1.9.3'), + ('OpenJPEG', local_openjpeg_maj_min + '.0'), + ('snappy', '1.1.8'), + ('zlib', '1.2.11'), + ('zlib-ng', '2.0.6'), + ('Zopfli', '1.0.3'), + ('zfp', '1.0.0'), + ('zstd', '1.4.9'), + ('Brunsli', '0.1'), + ('HDF5', '1.12.1'), + ('h5py', '3.2.1'), + ('libheif', '1.12.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('bitshuffle', '0.3.5', { + 'source_urls': ['https://github.com/kiyo-masui/bitshuffle/archive/'], + 'sources': ['%(version)s.tar.gz'], + 'checksums': ['c3f4461d8013e3d9db0d58defec77b143164652de505a1fba3df088eaa19be2f'], + }), + (name, version, { + 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.4/:$CPATH && ", + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'checksums': ['04d5757d8fd7819844b0f8d9eed05025dca4962f280d0010b42c7c9c993fe371'], + }), +] + +moduleclass = 'lib' From 5ee258f18cb9d63a4c80caa2564e33f4403711c4 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:33:37 +0200 Subject: [PATCH 259/939] adding easyconfigs: Blosc2-2.0.4-GCCcore-10.3.0.eb --- .../b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..7736eae49119 --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.0.4-GCCcore-10.3.0.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 = '2.0.4' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc2/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['90c78edcc262759dd16d243141513310624bb4fda3d98ac34dcfb78255e151c1'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 341cb16b6e28ac08e6907fc122a61c5535e5b2af Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:36:30 +0200 Subject: [PATCH 260/939] adding easyconfigs: CFITSIO-3.49-GCCcore-10.3.0.eb --- .../c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..1b080d809352 --- /dev/null +++ b/easybuild/easyconfigs/c/CFITSIO/CFITSIO-3.49-GCCcore-10.3.0.eb @@ -0,0 +1,42 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'ConfigureMake' + +name = 'CFITSIO' +version = '3.49' + +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': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://heasarc.gsfc.nasa.gov/FTP/software/fitsio/c/'] +sources = ['%%(namelower)s-%s.tar.gz' % version] +patches = ['CFITSIO-3.48_install_test_data.patch'] +checksums = [ + '5b65a20d5c53494ec8f638267fca4a629836b7ac8dd0ef0266834eab270ed4b3', # cfitsio-3.49.tar.gz + 'dbf16f857f133468fc1e6a793c6e89fca66d54796593e03606f2722a2a980c0c', # CFITSIO-3.48_install_test_data.patch +] + +# curl for HTTPs support +dependencies = [('cURL', '7.76.0')] + +builddependencies = [('binutils', '2.36.1')] + +# 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.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + ('cd %(installdir)s/share && testprog'), +] + +moduleclass = 'lib' From e34a43b98c10d409280e46bb0ac8151e9bcb5c8c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:39:12 +0200 Subject: [PATCH 261/939] adding easyconfigs: jxrlib-1.1-GCCcore-10.3.0.eb --- .../j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..6257a6cbb8be --- /dev/null +++ b/easybuild/easyconfigs/j/jxrlib/jxrlib-1.1-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author:: Denis Kristak (INUITS) +# Update: Thomas Hoffmann (EMBL) +## + +easyblock = 'CMakeMake' + +name = 'jxrlib' +version = '1.1' + +homepage = 'https://github.com/4creators/jxrlib' +description = """Open source implementation of jpegxr""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://deb.debian.org/debian/pool/main/j/jxrlib/'] +sources = ['%(name)s_%(version)s.orig.tar.gz'] +patches = [('jxrlib-%(version)s_cmake.patch', 1)] +checksums = [ + 'c7287b86780befa0914f2eeb8be2ac83e672ebd4bd16dc5574a36a59d9708303', # jxrlib_1.1.orig.tar.gz + 'e96ea8b418fdab10e9cbc2f4cad95ca1f59a826ce7379c6a3192882050689a74', # jxrlib-1.1_cmake.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +sanity_check_paths = { + 'files': ['bin/JxrDecApp', 'bin/JxrEncApp', "lib/libjpegxr.%s" % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['JxrDecApp', 'JxrEncApp'] + +modextrapaths = {'CPATH': 'include/jxrlib'} + +moduleclass = 'lib' From 133d1c682e91c11e2605e369b85a4fd5620a2e93 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:40:26 +0200 Subject: [PATCH 262/939] adding easyconfigs: LERC-3.0-GCCcore-10.3.0.eb --- .../l/LERC/LERC-3.0-GCCcore-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..b1976a9c3c2b --- /dev/null +++ b/easybuild/easyconfigs/l/LERC/LERC-3.0-GCCcore-10.3.0.eb @@ -0,0 +1,39 @@ +# 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 = '3.0' + +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': '10.3.0'} + +source_urls = ['https://github.com/Esri/lerc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8c0148f5c22d823eff7b2c999b0781f8095e49a7d3195f13c68c5541dd5740a1'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), +] + +postinstallcmds = [ + "cd %(builddir)s/lerc-%(version)s/src/LercTest && sed -i -e 's@../LercLib/include/@@' main.cpp", + "cp %(builddir)s/lerc-%(version)s/src/LercTest/main.cpp %(installdir)s/test.c", +] + +sanity_check_commands = [ + "mkdir -p %(builddir)s && cd %(builddir)s && g++ %(installdir)s/test.c -o lerctest -lLerc && ./lerctest", +] + +sanity_check_paths = { + 'files': ['include/Lerc_c_api.h', 'include/Lerc_types.h', 'lib/libLerc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 8745875102720aad4cfb7057f4d6c948f013bd65 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:41:40 +0200 Subject: [PATCH 263/939] adding easyconfigs: libaec-1.0.6-GCCcore-10.3.0.eb --- .../l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..7ed6541d6830 --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +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': '10.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['abab8c237d85c982bb4d6bde9b03c1f3d611dcacbd58bca55afac2496d61d4be'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +sanity_check_paths = { + 'files': ['bin/aec', 'include/libaec.h', 'include/szlib.h', 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["aec --help"] + +moduleclass = 'lib' From 558ec0d37917214b025769dc27d7b9f58d21c91d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:42:44 +0200 Subject: [PATCH 264/939] adding easyconfigs: libavif-0.11.1-foss-2021a.eb --- .../l/libavif/libavif-0.11.1-foss-2021a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb new file mode 100644 index 000000000000..2f4ed93c1c9e --- /dev/null +++ b/easybuild/easyconfigs/l/libavif/libavif-0.11.1-foss-2021a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'libavif' +version = '0.11.1' + +homepage = 'https://github.com/AOMediaCodec/libavif' +description = """This library aims to be a friendly, portable C implementation of the AV1 Image File Format, +as described here: https://aomediacodec.github.io/av1-avif/ +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/AOMediaCodec/libavif/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['0eb49965562a0e5e5de58389650d434cff32af84c34185b6c9b7b2fccae06d4e'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('NASM', '2.15.05'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('Rust', '1.52.1'), +] + +sanity_check_paths = { + 'files': ['lib/libavif.%s' % SHLIB_EXT, 'include/avif/avif.h'], + 'dirs': [], +} + +moduleclass = 'tools' From a24bdbaeacba00b74f4fde6ee3551355c153b925 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:46:49 +0200 Subject: [PATCH 265/939] adding easyconfigs: LibLZF-3.6-GCCcore-10.3.0.eb --- .../l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..635408463486 --- /dev/null +++ b/easybuild/easyconfigs/l/LibLZF/LibLZF-3.6-GCCcore-10.3.0.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 = 'ConfigureMake' + +name = 'LibLZF' +version = '3.6' + +homepage = 'http://oldhome.schmorp.de/marc/liblzf.html' +description = """LibLZF is a very small data compression library. It consists of only two .c and two .h files +and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still +written in portable C.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['http://dist.schmorp.de/liblzf/Attic/'] +sources = ['liblzf-%(version)s.tar.gz'] +checksums = ['9c5de01f7b9ccae40c3f619d26a7abec9986c06c36d260c179cedd04b89fb46a'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +sanity_check_commands = ['lzf -h'] + +sanity_check_paths = { + 'files': ['bin/lzf', 'lib/liblzf.a'], + 'dirs': ['bin', 'lib'], +} + +moduleclass = 'lib' From 06597b301e85a56bda66dce126cb5e90bb3a4909 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:47:53 +0200 Subject: [PATCH 266/939] adding easyconfigs: zlib-ng-2.0.6-GCCcore-10.3.0.eb --- .../z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..529355b3749d --- /dev/null +++ b/easybuild/easyconfigs/z/zlib-ng/zlib-ng-2.0.6-GCCcore-10.3.0.eb @@ -0,0 +1,30 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'zlib-ng' +version = '2.0.6' + +homepage = 'https://github.com/zlib-ng/zlib-ng' +description = """zlib data compression library for the next generation systems""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/zlib-ng/zlib-ng/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['8258b75a72303b661a238047cb348203d88d9dddf85d480ed885f375916fcab6'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +configopts = ' -DZLIB_ENABLE_TESTS=True ' + +sanity_check_paths = { + 'files': ['include/zconf-ng.h', 'include/zlib-ng.h', 'lib/libz-ng.a', 'lib/libz-ng.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' From 3e4cb429acf96e8bee8dff44e638024f2cd727f0 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:49:01 +0200 Subject: [PATCH 267/939] adding easyconfigs: Zopfli-1.0.3-GCCcore-10.3.0.eb --- .../z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..d08922dc6c90 --- /dev/null +++ b/easybuild/easyconfigs/z/Zopfli/Zopfli-1.0.3-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Updated: Denis Kristak +# Updated: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Zopfli' +version = '1.0.3' + +homepage = 'https://github.com/google/zopfli' +description = """Zopfli Compression Algorithm is a compression library programmed in C to perform +very good, but slow, deflate or zlib compression.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/google/zopfli/archive/refs/tags/'] +sources = ['%(namelower)s-%(version)s.tar.gz'] +checksums = ['e955a7739f71af37ef3349c4fa141c648e8775bceb2195be07e86f8e638814bd'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +configopts = [ + '-DBUILD_SHARED_LIBS=ON', + '-DBUILD_SHARED_LIBS=OFF', +] + +sanity_check_paths = { + 'files': ['bin/zopfli', 'include/zopfli.h', 'lib/libzopfli.a', 'lib/libzopfli.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["zopfli --help"] + +moduleclass = 'tools' From 1ec9bfdd271c08ac548e4c04e30cc65abc656207 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:50:02 +0200 Subject: [PATCH 268/939] adding easyconfigs: zfp-1.0.0-GCCcore-10.3.0.eb --- .../z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..3901a6550a23 --- /dev/null +++ b/easybuild/easyconfigs/z/zfp/zfp-1.0.0-GCCcore-10.3.0.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Update: Thomas Hoffmann (EMBL) +easyblock = 'MakeCp' + +name = 'zfp' +version = '1.0.0' + +homepage = 'https://github.com/LLNL/zfp' +description = """zfp is a compressed format for representing multidimensional floating-point and integer arrays. +zfp provides compressed-array classes that support high throughput read and write random access to individual array +elements. zfp also supports serial and parallel (OpenMP and CUDA) compression of whole arrays, e.g., for applications +that read and write large data sets to and from disk.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/LLNL/zfp/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['fe13b03141ee9b571692aed42ff76cf37c9dcda40f9a43a808870dca3558a57c'] + +builddependencies = [ + ('binutils', '2.36.1'), +] + +prebuildopts = "sed -i 's/FLAGS = -O3/FLAGS = $CFLAGS/g' Makefile && " +buildopts = 'ZFP_WITH_OPENMP=1' + +runtest = 'test' + +files_to_copy = ['bin', 'include', 'lib'] + +sanity_check_paths = { + 'files': ['bin/zfp', 'bin/testzfp', 'include/zfp.h', 'lib/libzfp.a'], + 'dirs': ['include/zfp'], +} + +sanity_check_commands = ["zfp --help 2>&1 | grep 'Usage: zfp'"] + +moduleclass = 'lib' From 9fe9959d6f35c302b56e8636f829179890846879 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:51:37 +0200 Subject: [PATCH 269/939] adding easyconfigs: Brunsli-0.1-GCCcore-10.3.0.eb --- .../b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..20cd4b20aef4 --- /dev/null +++ b/easybuild/easyconfigs/b/Brunsli/Brunsli-0.1-GCCcore-10.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# update: Thomas Hoffmann (EMBL) +easyblock = 'CMakeMake' + +name = 'Brunsli' +version = '0.1' + +homepage = 'https://github.com/google/brunsli/' +description = """Brunsli is a lossless JPEG repacking library.""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/google/brunsli/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['62762dc740f9fcc9706449c078f12c2a366416486d2882be50a9f201f99ac0bc'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1'), +] + +dependencies = [ + ('Brotli', '1.0.9'), + ('Highway', '0.12.2'), +] + +# skip use of third_party directory, since we provide Brotli via a proper dependency +preconfigopts = "sed -i 's/add_subdirectory(third_party)//g' ../brunsli-%(version)s/CMakeLists.txt && " + +configopts = '-DCMAKE_CXX_FLAGS="$CXXFLAGS -lbrotlienc -lbrotlidec -lbrotlicommon"' + +buildopts = "BROTLI_DIR=$EBROOTBROTLI BROTLI_INCLUDE=$EBROOTBROTLI/include" + +# also install dbrunsli binary and missing libraries +postinstallcmds = [ + "mkdir %(installdir)s/bin", + "cp dbrunsli %(installdir)s/bin/", + "cp libbrunsli*.a %(installdir)s/lib*/", + "cp libbrunsli*.%s %%(installdir)s/lib*/" % SHLIB_EXT, +] + +sanity_check_paths = { + 'files': ['bin/dbrunsli'], + 'dirs': ['include/brunsli', 'lib'], +} + +sanity_check_commands = ['dbrunsli 2>&1 | grep Usage'] + +moduleclass = 'lib' From 21102edbd215c924de05f0e9fde3c45ea1049084 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 17:52:42 +0200 Subject: [PATCH 270/939] adding easyconfigs: libheif-1.12.0-GCC-10.3.0.eb --- .../l/libheif/libheif-1.12.0-GCC-10.3.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb new file mode 100644 index 000000000000..bb5cb6bf57c1 --- /dev/null +++ b/easybuild/easyconfigs/l/libheif/libheif-1.12.0-GCC-10.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'libheif' +version = '1.12.0' + +homepage = 'https://github.com/strukturag/libheif' +description = "libheif is an HEIF and AVIF file format decoder and encoder" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/strukturag/libheif/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['e1ac2abb354fdc8ccdca71363ebad7503ad731c84022cf460837f0839e171718'] + +builddependencies = [ + ('CMake', '3.20.1'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.0.6'), + ('libde265', '1.0.8'), + ('x265', '3.5'), + ('Gdk-Pixbuf', '2.42.6'), +] + +# build both static and shared libraries +configopts = [ + "-DBUILD_SHARED_LIBS=OFF", + "-DBUILD_SHARED_LIBS=ON", +] + +sanity_check_paths = { + 'files': ['bin/heif-info', 'lib/libheif.a', 'lib/libheif.%s' % SHLIB_EXT, 'lib/pkgconfig/libheif.pc'], + 'dirs': ['include/libheif'], +} + +sanity_check_commands = ["heif-info --help"] + +moduleclass = 'tools' From f1d51b596f316a30aad8436d5d0715de30c16f56 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 3 Nov 2022 17:51:18 +0100 Subject: [PATCH 271/939] Rename package name --- .../Chemaxon-Marvin-21.14.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/{Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb => Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb} (99%) diff --git a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb similarity index 99% rename from easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb rename to easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb index adadbfe31a00..69f794a1422e 100644 --- a/easybuild/easyconfigs/c/Chemaxon_Marvin/Chemaxon_Marvin-21.14.eb +++ b/easybuild/easyconfigs/c/Chemaxon-Marvin/Chemaxon-Marvin-21.14.eb @@ -10,7 +10,7 @@ # Summary and License fields must be present in package: (main package) easyblock = 'Binary' -name = 'Chemaxon_Marvin' +name = 'Chemaxon-Marvin' version = '21.14' homepage = 'https://chemaxon.com/products/marvin' From 1da56a693b2a047860ea239717bb1698d7a6aff3 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Thu, 3 Nov 2022 19:11:22 +0200 Subject: [PATCH 272/939] adding easyconfigs: libde265-1.0.8-GCC-10.3.0.eb --- .../l/libde265/libde265-1.0.8-GCC-10.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb new file mode 100644 index 000000000000..647d345e73e2 --- /dev/null +++ b/easybuild/easyconfigs/l/libde265/libde265-1.0.8-GCC-10.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'libde265' +version = '1.0.8' + +homepage = 'https://github.com/strukturag/libde265' +description = "libde265 is an open source implementation of the h.265 video codec" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/strukturag/libde265/releases/download/v%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['24c791dd334fa521762320ff54f0febfd3c09fc978880a8c5fbc40a88f21d905'] + +builddependencies = [('CMake', '3.20.1')] + +sanity_check_paths = { + 'files': ['bin/dec265', 'bin/enc265', 'lib/liblibde265.%s' % SHLIB_EXT], + 'dirs': ['include/libde265', 'lib/cmake/libde265'], +} + +sanity_check_commands = [ + "dec265 --help", + "enc265 --help", +] + +moduleclass = 'tools' From afd61fb09cc2d8ed5970973f8b96f842e415f025 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jurij=20Pe=C4=8Dar?= Date: Thu, 3 Nov 2022 20:21:06 +0100 Subject: [PATCH 273/939] shortened Java dependency and removed test -d --- easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb index 896a6c321e37..cb17ec4556a6 100644 --- a/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb +++ b/easybuild/easyconfigs/n/Nextflow/Nextflow-22.10.1.eb @@ -13,9 +13,9 @@ source_urls = ['https://github.com/%(namelower)s-io/%(namelower)s/releases/downl sources = ['%(namelower)s-%(version)s-all'] checksums = ['c5edc9fc81d9c6eb4f628505f14f8bb4fe044d4fc7d9ef60654ba0d73abf5a80'] -dependencies = [('Java', '11', '', True)] +dependencies = [('Java', '11')] -install_cmd = "[ -d %(builddir)s/bin ] || mkdir -p %(installdir)s/bin &&" +install_cmd = "mkdir -p %(installdir)s/bin &&" install_cmd += "cp %(builddir)s/%(namelower)s-%(version)s-all %(installdir)s/bin &&" install_cmd += "cd %(installdir)s/bin && ln -s %(namelower)s-%(version)s-all %(namelower)s &&" install_cmd += "chmod +x %(installdir)s/bin/%(namelower)s-%(version)s-all" From db3c378611f30e7b425ea94e91f13d8f62b69c6c Mon Sep 17 00:00:00 2001 From: sassy Date: Thu, 3 Nov 2022 20:56:45 +0000 Subject: [PATCH 274/939] adding easyconfigs: KITE-1.1-gompi-2022a.eb --- .../k/KITE/KITE-1.1-gompi-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb new file mode 100644 index 000000000000..d1f4c2ad3a1d --- /dev/null +++ b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb @@ -0,0 +1,38 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'KITE' +version = '1.1' + +homepage = 'https://github.com/quantum-kite/kite' +description = """KITE is an open-source Python/C++ software suite for efficient real-space tight-binding (TB) +simulations of electronic structure and bulk quantum transport properties of disordered systems scalable to +multi billions of atomic orbitals.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/quantum-kite/kite/archive/'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'a480fe46f2220ab6c2d6b9914e0673580121de703523dc22658fe50dc676e47e', # 1.1.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Eigen', '3.4.0'), + ('HDF5', '1.12.2'), +] + +sanity_check_paths = { + 'files': ['bin/KITEx'], + 'dirs': [], +} + +moduleclass = 'chem' From 3efeea3c0dc2ebb94dd4b36bbc782b97b232c8fe Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 4 Nov 2022 10:55:52 +0100 Subject: [PATCH 275/939] Move to toolchain foss-2021a + Report issue with cwlformat upstream --- ...ore-10.3.0.eb => cwltool-3.1.20221018083734-foss-2021a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/c/cwltool/{cwltool-3.1.20221018083734-GCCcore-10.3.0.eb => cwltool-3.1.20221018083734-foss-2021a.eb} (96%) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb similarity index 96% rename from easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb index b40b9c1e883b..15b2225906c7 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb @@ -14,7 +14,7 @@ version = '3.1.20221018083734' homepage = 'https://github.com/common-workflow-language/cwltool' description = """Common workflow language (CWL) reference implementation.""" -toolchain = {'name': 'GCCcore', 'version': '10.3.0'} +toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('binutils', '2.36.1'), @@ -35,7 +35,7 @@ dependencies = [ ('pydot', '1.4.2'), ('lxml', '4.6.3'), ('ruamel.yaml', '0.17.21'), - ('networkx', '2.6.3', '', ('foss', '2021a')), + ('networkx', '2.6.3'), ] use_pip = True From 1d8333aba2e19716d792229dd353060d401c30a6 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 14:44:45 +0100 Subject: [PATCH 276/939] adding easyconfigs: CUDA-11.8.0.eb, cuDNN-8.6.0.163-CUDA-11.8.0.eb, NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb, UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb, GDRCopy-2.3-GCCcore-12.2.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb | 17 ++++++ .../c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb | 33 ++++++++++++ .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb | 24 +++++++++ ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb | 42 +++++++++++++++ 5 files changed, 168 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb new file mode 100644 index 000000000000..e0ea509fe8b6 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb @@ -0,0 +1,17 @@ +name = 'CUDA' +version = '11.8.0' +local_nv_version = '520.61.05' + +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 = ['9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb new file mode 100644 index 000000000000..23f76bb3dca1 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb @@ -0,0 +1,33 @@ +name = 'cuDNN' +version = '8.6.0.163' +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 = '11' # Is there a way to make this parametric? '%(cudaver)'.split(...) obviously doesn't work... + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = ['bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e'] + +dependencies = [('CUDA', '11.8.0')] + +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' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0fb6d9b4864f --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib prefix=%(installdir)s" + +installopts = 'prefix=%(installdir)s' + +github_account = 'NVIDIA' +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] +install_cmd = "make lib_install" + +sanity_check_paths = { + 'files': ['lib/libgdrapi.so'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb new file mode 100644 index 000000000000..eaacb2223145 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb @@ -0,0 +1,24 @@ +name = 'NCCL' +version = '2.15.5' +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': '12.2.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['f4ac3c74d469c9cd718f82e1477759785db9b9f8cc9d9ecc103485805b8394a3'] + +builddependencies = [('binutils', '2.39')] +buildopts = ['NVCC_APPEND_FLAGS="-allow-unsupported-compiler"'] # CUDA 11.8 doesn't officially support GCC 12.2 yet... + +dependencies = [ + ('CUDA', '11.8.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb new file mode 100644 index 000000000000..e2d761a00ca5 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb @@ -0,0 +1,42 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.13.1' +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': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = [ + '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', +] +checksums = [ + {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('UCX', version), + ('CUDA', '11.8.0', '', SYSTEM), + ('GDRCopy', '2.3'), +] + +moduleclass = 'lib' From faf4b17772355e79fa62b0eb7a94c5d5403199ca Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 4 Nov 2022 15:30:30 +0100 Subject: [PATCH 277/939] Move to networkx 2.5.1 to satisfy multi-variant deps for networkx in foss-2021a --- .../c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb index 15b2225906c7..170d12542ffd 100644 --- a/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb +++ b/easybuild/easyconfigs/c/cwltool/cwltool-3.1.20221018083734-foss-2021a.eb @@ -35,7 +35,7 @@ dependencies = [ ('pydot', '1.4.2'), ('lxml', '4.6.3'), ('ruamel.yaml', '0.17.21'), - ('networkx', '2.6.3'), + ('networkx', '2.5.1'), ] use_pip = True From ff022b85236ce9d0ed96a0600810d7bcc600b87f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 4 Nov 2022 17:05:23 +0100 Subject: [PATCH 278/939] set JUPYTER_CONFIG_PATH in IPython --- .../easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb | 5 ++++- .../easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb | 5 ++++- .../easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb index 0ecf20cc339b..a6f424ca75b8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.25.0-GCCcore-10.3.0.eb @@ -142,7 +142,10 @@ exts_list = [ }), ] -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} sanity_check_paths = { 'files': ['bin/ipython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb index b8a2d71f5841..ab9abddc1bf8 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-7.26.0-GCCcore-11.2.0.eb @@ -142,7 +142,10 @@ exts_list = [ }), ] -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} sanity_check_paths = { 'files': ['bin/ipython'], diff --git a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb index 4697bcfaf932..57bf257cf0c7 100644 --- a/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/i/IPython/IPython-8.5.0-GCCcore-11.3.0.eb @@ -160,7 +160,10 @@ exts_list = [ }), ] -modextrapaths = {'JUPYTER_PATH': 'share/jupyter'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} sanity_check_paths = { 'files': ['bin/ipython'], From 620492f519a44217ea0461e28baee7f421e53d64 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 17:14:30 +0100 Subject: [PATCH 279/939] removed NCCL, UCX-CUDA, GDCopy --- .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 ------------------- .../NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb | 24 --------- ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb | 42 --------------- 3 files changed, 118 deletions(-) delete mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb delete mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb delete mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb deleted file mode 100644 index 0fb6d9b4864f..000000000000 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb +++ /dev/null @@ -1,52 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'GDRCopy' -version = '2.3' - -homepage = 'https://github.com/NVIDIA/gdrcopy' -description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." - -toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s.tar.gz'] -checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] - -builddependencies = [ - ('binutils', '2.39'), - ('Autotools', '20220317'), - ('pkgconf', '1.9.3'), -] - -prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found -buildopts = "config lib prefix=%(installdir)s" - -installopts = 'prefix=%(installdir)s' - -github_account = 'NVIDIA' -# This easyconfig only installs the library of GDRCopy. Please keep in mind -# that GDRCopy also needs the following kernel modules at runtime: -# -# 1. Kernel module for GDRCopy: improves Host to GPU communication -# https://github.com/NVIDIA/gdrcopy -# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' -# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 -# -# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication -# https://github.com/Mellanox/nv_peer_memory -# RPM: 'nvidia_peer_memory' -# Requirements: Mellanox HCA with MLNX_OFED 2.1 -# -# These kernel modules are not listed as system dependencies to lower the system -# requirements to build this easyconfig, as they are not needed for the build. - -skipsteps = ['configure'] -install_cmd = "make lib_install" - -sanity_check_paths = { - 'files': ['lib/libgdrapi.so'], - 'dirs': ['include'], -} - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb deleted file mode 100644 index eaacb2223145..000000000000 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.15.5-GCCcore-12.2.0-CUDA-11.8.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'NCCL' -version = '2.15.5' -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': '12.2.0'} - -github_account = 'NVIDIA' -source_urls = [GITHUB_SOURCE] -sources = ['v%(version)s-1.tar.gz'] -checksums = ['f4ac3c74d469c9cd718f82e1477759785db9b9f8cc9d9ecc103485805b8394a3'] - -builddependencies = [('binutils', '2.39')] -buildopts = ['NVCC_APPEND_FLAGS="-allow-unsupported-compiler"'] # CUDA 11.8 doesn't officially support GCC 12.2 yet... - -dependencies = [ - ('CUDA', '11.8.0', '', SYSTEM), - ('UCX-CUDA', '1.13.1', versionsuffix), -] - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb deleted file mode 100644 index e2d761a00ca5..000000000000 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-11.8.0.eb +++ /dev/null @@ -1,42 +0,0 @@ -easyblock = 'EB_UCX_Plugins' - -name = 'UCX-CUDA' -version = '1.13.1' -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': '12.2.0'} -toolchainopts = {'pic': True} - -source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] -patches = [ - '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', -] -checksums = [ - {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, - {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, -] - -builddependencies = [ - ('binutils', '2.39'), - ('Autotools', '20220317'), - ('pkgconf', '1.9.3'), -] - -dependencies = [ - ('zlib', '1.2.12'), - ('UCX', version), - ('CUDA', '11.8.0', '', SYSTEM), - ('GDRCopy', '2.3'), -] - -moduleclass = 'lib' From 5d266b29427ef54b284728e5910e7452828143bb Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 18:24:15 +0100 Subject: [PATCH 280/939] added ppc64le & sbsa checksums --- .../easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb index 23f76bb3dca1..bc2f6803e9b3 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.6.0.163-CUDA-11.8.0.eb @@ -16,7 +16,14 @@ source_urls = [ 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] -checksums = ['bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e'] +checksums = [{ + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'bbc396df47294c657edc09c600674d608cb1bfc80b82dcf4547060c21711159e', + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'c8a25e7e3df1bb9c4e18a4f24dd5f25cfd4bbe8b7054e34008e53b2be4f58a80', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'a0202278d3cbd4f3adc3f7816bff6071621cb042b0903698b477acac8928ac06', +}] dependencies = [('CUDA', '11.8.0')] From 1a68db0bf0aba9ac35ef256bdce1d4970dad0c46 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 4 Nov 2022 18:51:21 +0100 Subject: [PATCH 281/939] added checksums for CUDA ppc and sbsa --- easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb index e0ea509fe8b6..4fc4d6173cee 100644 --- a/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb +++ b/easybuild/easyconfigs/c/CUDA/CUDA-11.8.0.eb @@ -12,6 +12,13 @@ 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 = ['9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16'] +checksums = [{ + 'cuda_%%(version)s_%s_linux.run' % local_nv_version: + '9223c4af3aebe4a7bbed9abd9b163b03a1b34b855fbc2b4a0d1b706ac09a5a16', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + 'f917fb7617033223938543ad3ae923190d99507acc08a399d752a2868e87349d', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'e6e9a8d31163c9776b5e313fd7590877c5684e1ecddee741154f95704d4ed27c' +}] moduleclass = 'system' From 96505b3dd71113eb316457251c6c5fa9d5bab799 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 5 Nov 2022 11:29:41 +0100 Subject: [PATCH 282/939] populate JUPYTER_PATH and JUPYTER_CONFIG_PATH in JupyterLab --- .../j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb | 12 +++++++++--- .../j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb | 12 +++++++++--- .../j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb | 12 +++++++++--- 3 files changed, 27 insertions(+), 9 deletions(-) mode change 100755 => 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb mode change 100755 => 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb mode change 100755 => 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb old mode 100755 new mode 100644 index adc0ec676957..83e3efa4e84f --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.0.16-GCCcore-10.3.0.eb @@ -48,14 +48,20 @@ exts_list = [ ('jupyterlab_server', '2.6.0', { 'checksums': ['f300adf6bb0a952bebe9c807a3b2a345d62da39b476b4f69ea0dc6b5f3f6b97d'], }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + ('jupyterlab', version, { 'checksums': ['7ad4fbe1f6d38255869410fd151a8b15692a663ca97c0a8146b3f5c40e275c23'], }), ] sanity_check_commands = ["jupyter lab --help"] -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb old mode 100755 new mode 100644 index 97db9ab8ef0c..d4ac5f149b9f --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.1.6-GCCcore-11.2.0.eb @@ -48,14 +48,20 @@ exts_list = [ ('jupyterlab_server', '2.7.0', { 'checksums': ['31457ef564febc42043bc539356c804f6f9144f602e2852150bf0820ed6d7e18'], }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + ('jupyterlab', version, { 'checksums': ['6d2ada6a333861f33a1b555d3cb7b07aa9d1ab80f07997b3d0c43878a98c1174'], }), ] sanity_check_commands = ["jupyter lab --help"] -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb old mode 100755 new mode 100644 index c48fd54eda30..303ede676424 --- a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.2.8-GCCcore-10.3.0.eb @@ -48,14 +48,20 @@ exts_list = [ ('jupyterlab_server', '2.10.3', { 'checksums': ['3fb84a5813d6d836ceda773fb2d4e9ef3c7944dbc1b45a8d59d98641a80de80a'], }), - (name, version, { - 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + ('jupyterlab', version, { 'checksums': ['5e4e99868c4f385372686767781408acbb9004b690b198b45597ba869802334b'], }), ] sanity_check_commands = ["jupyter lab --help"] -modextravars = {'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab'} +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} moduleclass = 'tools' From a8bcc6962a63d55b527445fd11bd1c2fb5676907 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:06:14 +0100 Subject: [PATCH 283/939] adding easyconfigs: JupyterLab-3.5.0-GCCcore-11.3.0.eb, jupyter-server-1.21.0-GCCcore-11.3.0.eb --- .../JupyterLab-3.5.0-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ .../jupyter-server-1.21.0-GCCcore-11.3.0.eb | 41 ++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb create mode 100755 easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1ce74b3d8a8c --- /dev/null +++ b/easybuild/easyconfigs/j/JupyterLab/JupyterLab-3.5.0-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = 'JupyterLab' +version = '3.5.0' + +homepage = "https://jupyter.org/" +description = """JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar + building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, + etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter + Notebook.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), + ('jupyter-server', '1.21.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('json5', '0.9.10', { + 'checksums': ['ad9f048c5b5a4c3802524474ce40a622fae789860a86f10cc4f7e5f9cf9b46ab'], + }), + ('notebook_shim', '0.1.0', { + 'checksums': ['7897e47a36d92248925a2143e3596f19c60597708f7bef50d81fcd31d7263e85'], + }), + ('nbclassic', '0.4.8', { + 'checksums': ['c74d8a500f8e058d46b576a41e5bc640711e1032cf7541dde5f73ea49497e283'], + }), + ('jupyterlab_server', '2.13.0', { + 'checksums': ['2040298a133458aa22f287a877d6bb91ff973f6298d562264f9f7b75e92a5ace'], + }), + ('jupyterlab', version, { + 'checksums': ['e02556c8ea1b386963c4b464e4618aee153c5416b07ab481425c817a033323a2'], + }), +] + +sanity_check_commands = ["jupyter lab --help"] + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} +modextravars = { + # only one path allowed as JUPYTERLAB_DIR + 'JUPYTERLAB_DIR': '%(installdir)s/share/jupyter/lab', +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb new file mode 100755 index 000000000000..b511014596ee --- /dev/null +++ b/easybuild/easyconfigs/j/jupyter-server/jupyter-server-1.21.0-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'PythonBundle' + +name = 'jupyter-server' +version = '1.21.0' + +homepage = "https://jupyter.org/" +description = """The Jupyter Server provides the backend (i.e. the core services, APIs, and REST +endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and +Voila.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('jupyter_server', version, { + 'checksums': ['d0adca19913a3763359be7f0b8c2ea8bfde356f4b8edd8e3149d7d0fbfaa248b'], + }), +] + +moduleclass = 'tools' From 735198dcf7b221a270fd93c09ec88076dc6aaddb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:13:25 +0100 Subject: [PATCH 284/939] adding easyconfigs: Panedr-0.7.0-foss-2021a.eb --- .../p/Panedr/Panedr-0.7.0-foss-2021a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb b/easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb new file mode 100644 index 000000000000..1b9dbb3a29da --- /dev/null +++ b/easybuild/easyconfigs/p/Panedr/Panedr-0.7.0-foss-2021a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonBundle' + +name = 'Panedr' +version = '0.7.0' + +homepage = 'https://github.com/MDAnalysis/panedr' +description = """Panedr uses the Pyedr library to read a Gromacs EDR binary +energy XDR file and returns its contents as a pandas dataframe.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +exts_list = [ + ('pyedr', version, { + 'checksums': ['2906fa86950a519ada711520cb18aa3bb49df5d992473f0c7b5359ba226c7ac2'], + # remove references to out-of-tree files + 'preinstallopts': "sed -i '8,10d' setup.cfg && " + }), + ('panedr', version, { + 'checksums': ['ef1f3163cd88ff5d69f9aabc1e5850a47cc5325d8421e57510bfa7cae5956838'], + # remove references to out-of-tree files + 'preinstallopts': "sed -i '8,10d' setup.cfg && " + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 8cbbb761cbf86493124b68bf8606370c00923544 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 11:14:36 +0100 Subject: [PATCH 285/939] adding easyconfigs: nglview-3.0.3-foss-2021a.eb, MDAnalysis-2.0.0-foss-2021a.eb --- .../MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb | 45 +++++++++++++++++++ .../n/nglview/nglview-3.0.3-foss-2021a.eb | 44 ++++++++++++++++++ 2 files changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb new file mode 100644 index 000000000000..64300f8f2f7f --- /dev/null +++ b/easybuild/easyconfigs/m/MDAnalysis/MDAnalysis-2.0.0-foss-2021a.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'MDAnalysis' +version = '2.0.0' + +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': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('Biopython', '1.79'), + ('networkx', '2.5.1'), + ('tqdm', '4.61.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('GridDataFormats', '0.6.0', { + 'modulename': 'gridData', + 'checksums': ['f14e00e8b795f8021f6069935e1133352224775c9bd97f395beb2bcd64a19b86'], + }), + ('gsd', '2.5.1', { + 'checksums': ['76bf228b1d8e95e7d6a334e8cc7712c0bd8c256148007f7ce88a489c21996593'], + }), + ('msgpack', '1.0.3', { + 'checksums': ['51fdc7fb93615286428ee7758cecc2f374d5ff363bdd884c7ea622a7a327a81e'], + }), + ('mmtf-python', '1.1.2', { + 'modulename': 'mmtf', + 'checksums': ['a5caa7fcd2c1eaa16638b5b1da2d3276cbd3ed3513f0c2322957912003b6a8df'], + }), + (name, version, { + 'modulename': name, + 'checksums': ['aa3079d1a82305eba58cf567fac8fc231940184ed88f9a4451be8433f4a06d3e'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb new file mode 100644 index 000000000000..f4c5a62bada9 --- /dev/null +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb @@ -0,0 +1,44 @@ +easyblock = 'PythonBundle' + +name = 'nglview' +version = '3.0.3' + +homepage = 'https://github.com/arose/nglview' +description = "IPython widget to interactively view molecular structures and trajectories." + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('IPython', '7.25.0'), + ('JupyterLab', '3.2.8'), + ('nodejs', '14.17.0'), + ('MDAnalysis', '2.0.0'), # optional +] + +use_pip = True + +exts_list = [ + ('versioneer', '0.24', { + 'checksums': ['1b8dba9e51e2f0e04c7e8545216eecdea2d63e1bd5569448ee66c549f7e7782f'], + }), + (name, version, { + 'use_pip_extras': 'MDAnalysis', + 'checksums': ['3253c44bd071e4701c288de44997471608487d5191ab3d3b7736c8651335c1af'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/nglview'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +modextrapaths = { + 'JUPYTER_PATH': 'share/jupyter', + 'JUPYTER_CONFIG_PATH': 'etc/jupyter', +} + +moduleclass = 'chem' From a2d2c2cfde8ad1f2de5a1feac758a05e809ac1ed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 7 Nov 2022 12:26:56 +0100 Subject: [PATCH 286/939] downgrade dependency of nglview-3.0.3-foss-2021a.eb on JupyterLab to v3.0.16 --- easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb index f4c5a62bada9..0d555c1e8910 100644 --- a/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nglview/nglview-3.0.3-foss-2021a.eb @@ -12,7 +12,7 @@ dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('IPython', '7.25.0'), - ('JupyterLab', '3.2.8'), + ('JupyterLab', '3.0.16'), ('nodejs', '14.17.0'), ('MDAnalysis', '2.0.0'), # optional ] From 439cb7b0e790eca1a8b3be13cce88776e67a3a91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 7 Nov 2022 14:01:02 +0100 Subject: [PATCH 287/939] adding easyconfigs: MCU-3366c85-gomkl-2021a.eb, matplotlib-3.4.2-gomkl-2021a.eb, spglib-python-1.16.1-gomkl-2021a.eb --- .../m/MCU/MCU-3366c85-gomkl-2021a.eb | 33 ++++++++++ .../matplotlib-3.4.2-gomkl-2021a.eb | 64 +++++++++++++++++++ .../spglib-python-1.16.1-gomkl-2021a.eb | 27 ++++++++ 3 files changed, 124 insertions(+) create mode 100644 easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb create mode 100644 easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb new file mode 100644 index 000000000000..74d3aa4c3889 --- /dev/null +++ b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'MCU' +version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work + +homepage = 'https://hungqpham.com/mcu/' +description = """A package for periodic wavefunction and crystallography analysis. + mcu is designed to support large scale analysis and topological descriptions for periodic wavefunction.""" + +toolchain = {'name': 'gomkl', 'version': '2021a'} + +source_urls = ['https://github.com/hungpham2017/mcu/archive/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['96553924c57ca27d2e4d8668be2c97fc6019c139f91950a798733c5575a8b44a'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('matplotlib', '3.4.2'), + ('spglib-python', '1.16.1'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'mcu'} + +sanity_check_commands = [ + "python -c 'from mcu import VASP'", +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb new file mode 100644 index 000000000000..ca47ecae3580 --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.4.2-gomkl-2021a.eb @@ -0,0 +1,64 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.4.2' + +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': 'gomkl', 'version': '2021a'} + +builddependencies = [ + ('pkg-config', '0.29.2'), + ('cppy', '1.1.0') +] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('libpng', '1.6.37'), + ('freetype', '2.10.4'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '8.2.0'), + ('Qhull', '2020.2') +] + +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' setup.cfg.template >setup.cfg && " + +_include_path = "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && " + +exts_list = [ + ('Cycler', '0.10.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'], + }), + ('kiwisolver', '1.3.1', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['950a199911a8d94683a6b10321f9345d5a3a8433ec58b217ace979e18f16e248'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['d8d994cefdff9aaba45166eb3de4f5211adb4accac85cbf97137e98f26ea0219'], + }), +] + +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-1.16.1-gomkl-2021a.eb b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb new file mode 100644 index 000000000000..6079d940a724 --- /dev/null +++ b/easybuild/easyconfigs/s/spglib-python/spglib-python-1.16.1-gomkl-2021a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'spglib-python' +version = '1.16.1' + +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': 'gomkl', 'version': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/%(nameletter)s/spglib'] +sources = ['spglib-%(version)s.tar.gz'] +checksums = ['9fd2fefbd83993b135877a69c498d8ddcf20a9980562b65b800cfb4cdadad003'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +options = {'modulename': 'spglib'} + +moduleclass = 'chem' From 1972ddbd3fce77cd788f6444cade40df3d9d2bd3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Mon, 7 Nov 2022 14:16:27 +0100 Subject: [PATCH 288/939] style fix --- easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb index 74d3aa4c3889..5a722540235a 100644 --- a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'MCU' -version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work +version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work homepage = 'https://hungqpham.com/mcu/' description = """A package for periodic wavefunction and crystallography analysis. From 088501e33cb81906978c5b9c7a678b3eaefbe120 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Mon, 7 Nov 2022 14:48:45 +0100 Subject: [PATCH 289/939] Moved dependencies to its usual place --- .../easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb index 23c3faed318c..e6bb3dd3a743 100644 --- a/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb +++ b/easybuild/easyconfigs/d/DRAGMAP/DRAGMAP-1.3.0-foss-2021b.eb @@ -12,17 +12,17 @@ source_urls = ['https://github.com/Illumina/DRAGMAP/archive/refs/tags/'] sources = ['%(version)s.tar.gz'] checksums = ['baf546c2f53b13e2bce4c937201e38459f3ce2f1069722ca670d8726a4bae224'] +dependencies = { + ('Boost', '1.77.0'), + ('googletest', '1.11.0'), +} + skipsteps = ['configure'] prebuildopts = 'sed -i "s|-msse4.2 -mavx2|$CXXFLAGS|g" config.mk &&' buildopts = 'CC="$CC" CXX="$CXX"' preinstallopts = 'mkdir %(installdir)s/bin &&' installopts = 'DESTDIR=%(installdir)s' -dependencies = { - ('Boost', '1.77.0'), - ('googletest', '1.11.0'), -} - sanity_check_paths = { 'files': ['bin/dragen-os'], 'dirs': [] From 773580293233ea6b9387985596155d641eaeadef Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 7 Nov 2022 15:55:10 +0100 Subject: [PATCH 290/939] Switched to new JuliaPackage easyblock + changed True to SYSTEM as requested --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 79 +++++++++++++++++-- 1 file changed, 71 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index ca021785912f..d9bb1bafff07 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Tarball' +easyblock = 'Bundle' name = 'MultilevelEstimators' version = '0.1.0' @@ -12,20 +12,83 @@ toolchain = {'name': 'GCC', 'version': '11.2.0'} dependencies = [ ('Python', '3.9.6'), - ('Julia', local_julia_ver, '-linux-%s' % ARCH, True), + ('Julia', local_julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -postinstallcmds = [ - "cd %(installdir)s && mkdir pkgs", - """export JULIA_DEPOT_PATH=%%(installdir)s/pkgs && - julia -e 'using Pkg;Pkg.add(url="%s")' """ % homepage +exts_defaultclass = 'JuliaPackage' +exts_filter = ("julia -e 'using %(ext_name)s'", "") +exts_default_options = { + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], +} + +exts_list = [ + ('Preferences', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + }), + ('JLLWrappers', '1.4.1', { + 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + }), + ('OpenSpecFun_jll', '0.5.5+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl/archive/'], + 'sources': ['OpenSpecFun-v%(version)s.tar.gz'], + }), + ('InverseFunctions', '0.1.8', { + 'source_urls': ['https://github.com/JuliaMath/InverseFunctions.jl/archive/'], + }), + ('DocStringExtensions', '0.9.2', { + 'source_urls': ['https://github.com/JuliaDocs/DocStringExtensions.jl/archive/'], + }), + ('IrrationalConstants', '0.1.1', { + 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + }), + ('Compat', '4.3.0', { + 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + }), + ('ChainRulesCore', '1.15.6', { + 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + }), + ('ChangesOfVariables', '0.1.4', { + 'source_urls': ['https://github.com/JuliaMath/ChangesOfVariables.jl/archive/'], + }), + ('LogExpFunctions', '0.3.18', { + 'source_urls': ['https://github.com/JuliaStats/LogExpFunctions.jl/archive/'], + }), + ('SpecialFunctions', '1.8.7', { + 'source_urls': ['https://github.com/JuliaMath/SpecialFunctions.jl/archive/'], + }), + ('TranscodingStreams', '0.9.9', { + 'source_urls': ['https://github.com/JuliaIO/TranscodingStreams.jl/archive/'], + }), + ('Reexport', '1.2.2', { + 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + }), + ('OrderedCollections', '1.4.1', { + 'source_urls': ['https://github.com/JuliaCollections/OrderedCollections.jl/archive/'], + }), + ('MacroTools', '0.5.10', { + 'source_urls': ['https://github.com/FluxML/MacroTools.jl/archive/'], + }), + ('Requires', '1.3.0', { + 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + }), + ('FileIO', '1.16.0', { + 'source_urls': ['https://github.com/JuliaIO/FileIO.jl/archive/'], + }), + ('JLD2', '0.4.24', { + 'source_urls': ['https://github.com/JuliaIO/JLD2.jl/archive/'], + }), + (name, version, { + 'source_urls': ['https://github.com/PieterjanRobbe/MultilevelEstimators.jl/archive/'], + }), ] sanity_check_paths = { 'files': [], - 'dirs': ["pkgs"] + 'dirs': ['packages'] } -modextrapaths = {'JULIA_DEPOT_PATH': 'pkgs'} +modextrapaths = { + 'JULIA_DEPOT_PATH': '', +} moduleclass = 'lib' From 04340fd1ae7c02dc8d1a01fd471374ba2ee8cced Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:00:29 +0100 Subject: [PATCH 291/939] add new SPOTlight package --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 1c4ffc3555e8..cb2f31c38216 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -43,7 +43,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # 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 4th May 2022 +# packages updated on 7th Nov 2022 exts_list = [ ('BiocGenerics', '0.42.0', { 'checksums': ['0cb6fa74a389693d253a9f61935d335fcfcc1dfe5acbba78b3cc43c1af5d6947'], @@ -1060,6 +1060,9 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), @@ -1087,6 +1090,9 @@ exts_list = [ ('CAGEr', '2.2.0', { 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], }), + ('SPOTlight', '1.0.0', { + 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 98ae750d79d281d348741e7007089e48573c348f Mon Sep 17 00:00:00 2001 From: Orient Date: Mon, 7 Nov 2022 16:01:58 +0100 Subject: [PATCH 292/939] Added checksums for all packages --- ...Estimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index d9bb1bafff07..e048be328cf0 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -24,61 +24,80 @@ exts_default_options = { exts_list = [ ('Preferences', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], + 'checksums': ['a87c1fc863fcb6240c3f4327776fa01a1f87e0d2df5a0c1850f789ce24469da2'], }), ('JLLWrappers', '1.4.1', { 'source_urls': ['https://github.com/JuliaPackaging/JLLWrappers.jl/archive/'], + 'checksums': ['2cb61d4171e8ebc74e36ee20e6e0ba959aa5525a9c2fef5547e0993566018775'], }), ('OpenSpecFun_jll', '0.5.5+0', { 'source_urls': ['https://github.com/JuliaBinaryWrappers/OpenSpecFun_jll.jl/archive/'], 'sources': ['OpenSpecFun-v%(version)s.tar.gz'], + 'checksums': ['6d1df617dd0a80fc0de5bc41a092e51f72782dbfd296c64e151707733cb57b6f'], }), ('InverseFunctions', '0.1.8', { 'source_urls': ['https://github.com/JuliaMath/InverseFunctions.jl/archive/'], + 'checksums': ['6b3e72037c2198268bc5247daeb14eaa5cf2b37f41c7c735b3cd2355bad1584b'], }), ('DocStringExtensions', '0.9.2', { 'source_urls': ['https://github.com/JuliaDocs/DocStringExtensions.jl/archive/'], + 'checksums': ['ff7869968381f17b24b3f471a88dd96b7008e8b8d7a14079d4667d87db0037dd'], }), ('IrrationalConstants', '0.1.1', { 'source_urls': ['https://github.com/JuliaMath/IrrationalConstants.jl/archive/'], + 'checksums': ['2eccfb55449d25d363d96ce116c45b39110d1572248e04e136ec4c37fe84ba96'], }), ('Compat', '4.3.0', { 'source_urls': ['https://github.com/JuliaLang/Compat.jl/archive/'], + 'checksums': ['0d792ec0912a8d3ed30329fc44073e964be3cd314671594dd16f8570c51b2c19'], }), ('ChainRulesCore', '1.15.6', { 'source_urls': ['https://github.com/JuliaDiff/ChainRulesCore.jl/archive/'], + 'checksums': ['79e22fc981fa7c44b3efc2f07903f555c5520dc38d0d3d31b6390980c786cb60'], }), ('ChangesOfVariables', '0.1.4', { 'source_urls': ['https://github.com/JuliaMath/ChangesOfVariables.jl/archive/'], + 'checksums': ['2eb2eb59711d53d284a9cc998e9facf3a1720cfde26eb672676cbe944fa9224a'], }), ('LogExpFunctions', '0.3.18', { 'source_urls': ['https://github.com/JuliaStats/LogExpFunctions.jl/archive/'], + 'checksums': ['f169c5512f79746987858dd19d05d6fdd4017f2b817d9cd8831bde3c3e398a82'], }), ('SpecialFunctions', '1.8.7', { 'source_urls': ['https://github.com/JuliaMath/SpecialFunctions.jl/archive/'], + 'checksums': ['3f2ecec0506fe47cfa5e436ac510e2a82d39f74fceaeb422572cf06d90f2096a'], }), ('TranscodingStreams', '0.9.9', { 'source_urls': ['https://github.com/JuliaIO/TranscodingStreams.jl/archive/'], + 'checksums': ['c341df1b582e6289fd5d5bd682111876b01582792687c0812fd093c085b12e68'], }), ('Reexport', '1.2.2', { 'source_urls': ['https://github.com/simonster/Reexport.jl/archive/'], + 'checksums': ['2566f7776aae9697cbf15765fc32187f46dd51200abc953a0266863ad67132b3'], }), ('OrderedCollections', '1.4.1', { 'source_urls': ['https://github.com/JuliaCollections/OrderedCollections.jl/archive/'], + 'checksums': ['ad6d191a2bf6f0c04abaf795fa93b3db6c3f3fb97498b464fcf7297b3a4bf6b6'], }), ('MacroTools', '0.5.10', { 'source_urls': ['https://github.com/FluxML/MacroTools.jl/archive/'], + 'checksums': ['0c61fe20a40346b0d1c248ff57e047b669ae47ad2d971b2ca7b91efdddff71ac'], }), ('Requires', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Requires.jl/archive/'], + 'checksums': ['8af4dac29839e796a651b8cb6a325b6f9c7eee5d5620b3e366b64f58325ebeb7'], }), ('FileIO', '1.16.0', { 'source_urls': ['https://github.com/JuliaIO/FileIO.jl/archive/'], + 'checksums': ['c447263eb2fac0bd1c7822b97b64f4274e8eeb52bdd5fdc8dc413342a547759f'], }), ('JLD2', '0.4.24', { 'source_urls': ['https://github.com/JuliaIO/JLD2.jl/archive/'], + 'checksums': ['fdcc4a9af9eaaa9013724deb2649ba00aa987ae5d3753a7af389ab7720bf19a9'], }), (name, version, { 'source_urls': ['https://github.com/PieterjanRobbe/MultilevelEstimators.jl/archive/'], + 'checksums': ['53bd629506cbe2472c9fb061a5a64523478556264e7fc98a3b6503dc1e7ef039'], }), ] From 4906ccbb280b753019ab454bea1fbca708772df4 Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:07:01 +0100 Subject: [PATCH 293/939] add it also to 2022a --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index e9595a58dd46..cac7fb0b26bc 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -45,7 +45,7 @@ exts_filter = ("R -q --no-save", "%s { %s }" % (local_ext_version_check, local_s # 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 7th July 2022 +# packages updated on 7th Nov 2022 exts_list = [ ('BiocGenerics', '0.42.0', { 'checksums': ['0cb6fa74a389693d253a9f61935d335fcfcc1dfe5acbba78b3cc43c1af5d6947'], @@ -1059,6 +1059,9 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), + ('ExomeDepth', '1.1.15', { + 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], + }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), @@ -1083,6 +1086,9 @@ exts_list = [ ('CAGEr', '2.2.0', { 'checksums': ['1cd64f6b045a5e246ae92cd709234c806edfcc25463819df0bd32fe4f4b2fd0d'], }), + ('SPOTlight', '1.0.0', { + 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 4ac5f57ff988d0e8fbf891c789b2d8f57279e5ef Mon Sep 17 00:00:00 2001 From: eb-test Date: Mon, 7 Nov 2022 16:12:58 +0100 Subject: [PATCH 294/939] remove ExomeDepth as is gone due to #16492 --- .../R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 3 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 --- 2 files changed, 6 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index cb2f31c38216..9c7b01b91376 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1060,9 +1060,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index cac7fb0b26bc..db12f43dc2b0 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1059,9 +1059,6 @@ exts_list = [ ('M3Drop', '1.22.0', { 'checksums': ['4b09b331181219980ba16d89e6c3891fc45cfa32526c7fc23900d4c9e1911841'], }), - ('ExomeDepth', '1.1.15', { - 'checksums': ['112bcb536f5766d9d0b55e064feedd6727ccab14cb1edfdba1f0d7b890e55ad2'], - }), ('bsseq', '1.32.0', { 'checksums': ['25cee0bcaf95eeb734a76ad55f4e508b1201d99363b401df3d0d9ab5c58aeeca'], }), From e303fcc683a3d7e3052020d25087157fdad982c7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2022 16:17:19 +0100 Subject: [PATCH 295/939] define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (fixes #16567) --- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb | 3 ++- .../easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb | 3 ++- .../easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb | 3 ++- 3 files changed, 6 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb index 5662fb3cc49e..61d5d7f6ffc9 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.1-GCCcore-10.3.0.eb @@ -30,7 +30,8 @@ dependencies = [ ('freetype', '2.10.4'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb index 57ecf2bd16cf..2be2036a9b2a 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-2.8.2-GCCcore-11.2.0.eb @@ -27,7 +27,8 @@ dependencies = [ ('freetype', '2.11.0'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb index af1f8d0d274e..389711e52307 100644 --- a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-4.2.1-GCCcore-11.3.0.eb @@ -27,7 +27,8 @@ dependencies = [ ('freetype', '2.12.1'), ] -preconfigopts = "./autogen.sh && " +# define $GTKDOCIZE to 'echo' as workaround for https://github.com/easybuilders/easybuild-easyconfigs/issues/16567 +preconfigopts = "GTKDOCIZE=echo ./autogen.sh && " configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " sanity_check_paths = { From 2ce828930e93303842546c5914ddb1458a4c6b7b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 7 Nov 2022 16:55:38 +0100 Subject: [PATCH 296/939] disable use of -Werror in recent NSS easyconfigs --- easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb | 5 ++++- easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb | 5 ++++- easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb | 5 ++++- 3 files changed, 12 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb index 1153b4b58a8c..cc653fd51357 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.65-GCCcore-10.3.0.eb @@ -31,8 +31,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb index 0ea01ba44d08..55fbfa38a92c 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.69-GCCcore-11.2.0.eb @@ -34,8 +34,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb index 3cea93f9ab67..40d16c445eb5 100644 --- a/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/NSS/NSS-3.79-GCCcore-11.3.0.eb @@ -32,8 +32,11 @@ dependencies = [ # building in parallel fails parallel = 1 +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " # fix for not being able to find header files -buildopts = 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' # fix c standard causing missing functions buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' # also install pkgconfig file (see patch) From 589da76b23b7828955ee9c4a8021e71a9b269e5f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 7 Nov 2022 17:50:26 +0100 Subject: [PATCH 297/939] adding easyconfigs: InParanoid-5.0.79d8e39-GCC-10.3.0.eb --- .../InParanoid-5.0.79d8e39-GCC-10.3.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb new file mode 100644 index 000000000000..61194783a6dd --- /dev/null +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb @@ -0,0 +1,65 @@ +## +# 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 = 'Tarball' + +name = 'InParanoid' +version = '5.0.79d8e39' + +homepage = 'https://inparanoid.sbc.su.se' +description = """InParanoid: ortholog groups with inparalogs.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] +sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] +checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 + +builddependencies = [('binutils', '2.36.1')] + +# NOTE some dependencies are not listed on the web site such as Java! +dependencies = [ + ('Perl', '5.32.1'), # brings libmoose-perl and libparallel-forkmanager-perl + ('BioPerl', '1.7.8'), + ('Java', '11', '', SYSTEM), + ('BLAST', '2.2.26', '-Linux_x86_64', SYSTEM), + ('DIAMOND', '2.0.13'), +] + +# NOTE inparanoid.pl uses only local (same directory) paths, so patch it +postinstallcmds = ["rm -rf %(installdir)s/docker/ %(installdir)s/singularity/ && " + "chmod a+rx %(installdir)s/*.pl && " + "chmod -x %(installdir)s/*.jar && " + "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|\./\$blastParser|\$blastParser|g' " + "%(installdir)s/inparanoid.pl && " + "perl -i -pe 's|#!.*perl|#!/usr/bin/env perl|' %(installdir)s/*.pl"] + +sanity_check_paths = { + 'files': ['inparanoid.pl', 'blast_parser.pl', 'diamondParser.pl'], + 'dirs': ['matrices'], +} + +modextrapaths = { + 'PATH': '', +} + +sanity_check_commands = ["inparanoid.pl -input-dir %(installdir)s/testInput/ && " + "rm -Rf %(installdir)s/output/"] + +moduleclass = 'bio' From e300c9937fb0e36dbf415eaea0a264063fd206a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 8 Nov 2022 09:30:36 +0100 Subject: [PATCH 298/939] fixed naming and versioning --- .../mcu-2021-04-06-gomkl-2021a.eb} | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/m/{MCU/MCU-3366c85-gomkl-2021a.eb => mcu/mcu-2021-04-06-gomkl-2021a.eb} (76%) diff --git a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb similarity index 76% rename from easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb rename to easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb index 5a722540235a..5a34c8b03a6f 100644 --- a/easybuild/easyconfigs/m/MCU/MCU-3366c85-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb @@ -1,7 +1,8 @@ easyblock = 'PythonPackage' -name = 'MCU' -version = '3366c85' # There is a 0.2 release but it's too old and it doesn't work +name = 'mcu' +local_commit = '3366c85' +version = '2021-04-06' # There is a 0.2 release but it's too old and it doesn't work homepage = 'https://hungqpham.com/mcu/' description = """A package for periodic wavefunction and crystallography analysis. @@ -10,7 +11,7 @@ description = """A package for periodic wavefunction and crystallography analysi toolchain = {'name': 'gomkl', 'version': '2021a'} source_urls = ['https://github.com/hungpham2017/mcu/archive/'] -sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['96553924c57ca27d2e4d8668be2c97fc6019c139f91950a798733c5575a8b44a'] dependencies = [ @@ -24,8 +25,6 @@ use_pip = True download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'mcu'} - sanity_check_commands = [ "python -c 'from mcu import VASP'", ] From f184bf0f4a276c02194f833960c6c5b1b42f3bc7 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 09:45:01 +0100 Subject: [PATCH 299/939] adding easyconfigs: Godon-20210913-x86_64.eb --- .../g/Godon/Godon-20210913-x86_64.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb new file mode 100644 index 000000000000..576e9b6362d9 --- /dev/null +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -0,0 +1,42 @@ +## +# This is a contribution from SIB Swiss Institute of Bioinformatics +# Homepage: https://www.sib.swiss/research-infrastructure/competence-centers/vital-it +# +# Authors:: Sebastien Moretti +# +# Compilation with GO looks to use a broken dependency +# +# SO use the pre-compiled binaries! +## + +easyblock = 'Binary' + +name = 'Godon' +version = '20210913' +versionsuffix = '-x86_64' + +software_license = 'LicenseGPLv3' + +homepage = 'https://bitbucket.org/Davydov/godon/' +description = """Godon is codon models software written in Go.""" + +toolchain = SYSTEM + +source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] +sources = ['godon-master-linux-gnu-x86_64'] +checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] + + +extract_sources = False + +postinstallcmds = ["mkdir -p %(installdir)s/bin/ && cd %(installdir)s/bin/ && " + "ln -s ../godon-master-linux-gnu-x86_64 godon"] + +sanity_check_paths = { + 'files': ["bin/godon"], + 'dirs': ['bin'], +} + +sanity_check_commands = ["godon --help"] + +moduleclass = 'bio' From 34ffbf8e8618aad39c9188e3097f1e3464e69110 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 10:18:21 +0100 Subject: [PATCH 300/939] adding easyconfigs: NanoLyse-1.2.1-foss-2021a.eb --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 56 +++++++++++++++++++ 1 file changed, 56 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb new file mode 100644 index 000000000000..a6b362f5ae55 --- /dev/null +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -0,0 +1,56 @@ +## +# 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 = 'PythonBundle' + +name = 'NanoLyse' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanolyse' +description = """Remove reads mapping to the lambda phage genome from a fastq file.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('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 = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('mappy', '2.24', { + 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + }), + ('NanoLyse', '1.2.1', { + 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], + }), +] + +sanity_check_paths = { + 'files': ['bin/NanoLyse'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoLyse --version"] + +sanity_pip_check = True + +moduleclass = 'bio' From 147604a643395b467b19273f00aeaafa1ef7a1f6 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 11:14:17 +0100 Subject: [PATCH 301/939] adding easyconfigs: PyDamage-0.70-foss-2021a.eb --- .../p/PyDamage/PyDamage-0.70-foss-2021a.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb new file mode 100644 index 000000000000..45477aba7e96 --- /dev/null +++ b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb @@ -0,0 +1,65 @@ +## +# 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 = 'PythonBundle' + +name = 'PyDamage' +version = '0.70' + +homepage = 'https://github.com/maxibor/pydamage' +description = """Pydamage, is a Python software to automate the process of +contig damage identification and estimation. After modelling the ancient DNA +damage using the C to T transitions, Pydamage uses a likelihood ratio test +to discriminate between truly ancient, and modern contigs originating from +sample contamination.""" +software_license = 'LicenseGPLv3' + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('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 = [ + ('Python', '3.9.5'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('statsmodels', '0.12.2'), + ('matplotlib', '3.4.2'), + ('tqdm', '4.61.2'), +] + +use_pip = True + +# Fetch the tar.gz, not the whl files! +exts_list = [ + ('kneed', '0.7.0', { + 'checksums': ['340d67fa183a72b0afae19846dd246a6fb7204e8d54243d8b8d3d9932f887c6e'], + }), + ('pydamage', '0.70', { + 'checksums': ['1dcd6ebae431f758c9434785c668351f82926847f9eda76413e96b7481138d78'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pydamage'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pydamage --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From ff135866cea1a5bb953de5ccdc4ee508a3a51e05 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Tue, 8 Nov 2022 11:46:10 +0100 Subject: [PATCH 302/939] Update imagecodecs-2022.9.26-foss-2021a.eb --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb index 55bf95340ffe..2a32ac22f2e1 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -47,7 +47,7 @@ dependencies = [ ('zfp', '1.0.0'), ('zstd', '1.4.9'), ('Brunsli', '0.1'), - ('HDF5', '1.12.1'), + ('HDF5', '1.10.7'), ('h5py', '3.2.1'), ('libheif', '1.12.0'), ] From 91d4154016519c6f550bbf367df983561d14aeca Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 12:02:18 +0100 Subject: [PATCH 303/939] adding easyconfigs: CAT-BAT-5.2.3-GCC-10.3.0.eb --- .../c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb new file mode 100644 index 000000000000..20b588f3e116 --- /dev/null +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-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 = 'Tarball' + +name = 'CAT-BAT' +version = '5.2.3' + +homepage = 'https://github.com/dutilh/CAT' +description = """Tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs).""" +# software_license = 'LicenseMIT' + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/dutilh/CAT/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Python', '3.9.5'), + ('DIAMOND', '2.0.13'), + ('prodigal', '2.6.3'), +] + +postinstallcmds = ["cd %(installdir)s/ && ln -s CAT_pack bin && " + "chmod a+rx %(installdir)s/CAT_pack/*.py && " + "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' " + "%(installdir)s/CAT_pack/check.py"] + +sanity_check_paths = { + 'files': ['CAT_pack/CAT', 'README.md'], + 'dirs': ['CAT_pack'], +} + +modextrapaths = { + 'PATH': '', +} + +sanity_check_commands = ["CAT --help"] + +moduleclass = 'bio' From 3e5ad955853e91bd8fee4cfd83c76779def2febc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 12:28:40 +0100 Subject: [PATCH 304/939] Fix install cmd + Remove empty line + Dont test bin/ dir already tested --- .../easyconfigs/g/Godon/Godon-20210913-x86_64.eb | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb index 576e9b6362d9..7014125e51cc 100644 --- a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -23,18 +23,19 @@ description = """Godon is codon models software written in Go.""" toolchain = SYSTEM source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] -sources = ['godon-master-linux-gnu-x86_64'] +sources = [{ + 'download_filename': 'godon-master-linux-gnu-x86_64', + 'filename': 'godon', +}] checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] - extract_sources = False -postinstallcmds = ["mkdir -p %(installdir)s/bin/ && cd %(installdir)s/bin/ && " - "ln -s ../godon-master-linux-gnu-x86_64 godon"] +install_cmd = "mkdir -p %(installdir)s/bin/ && mv godon %(installdir)s/bin/" sanity_check_paths = { 'files': ["bin/godon"], - 'dirs': ['bin'], + 'dirs': [], } sanity_check_commands = ["godon --help"] From 6ee549a5cf2a9b1d30e4e8b69786b57a1dc0fad7 Mon Sep 17 00:00:00 2001 From: eb-test Date: Tue, 8 Nov 2022 12:55:52 +0100 Subject: [PATCH 305/939] include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 --- .../easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb index d156b3c22fc1..2b39682fdb87 100644 --- a/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/i/idemux/idemux-0.1.6-GCCcore-10.2.0.eb @@ -19,15 +19,17 @@ builddependencies = [ dependencies = [ ('Python', '3.8.6'), ('coverage', '5.5'), - ('tqdm', '4.60.0'), ] use_pip = True exts_list = [ ('pytest-runner', '5.3.0', { - 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], 'modulename': 'ptr', + 'checksums': ['ca3f58ff4957e8be6c54c55d575b235725cbbcf4dc0d5091c29c6444cfc8a5fe'], + }), + ('tqdm', '4.60.0', { + 'checksums': ['ebdebdb95e3477ceea267decfc0784859aa3df3e27e22d23b83e9b272bf157ae'], }), (name, version, { 'checksums': ['590980baaf810c8a02705efd50eb4ace644c360470fc3dc4491d077bbb6b26fc'], From 3f68011737a67fa7a0e1187f937ef408406e2b9e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:06:41 +0100 Subject: [PATCH 306/939] Remove useless buildrequirements + Add missing minimap2 requirement --- .../n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 13 ++++--------- 1 file changed, 4 insertions(+), 9 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb index a6b362f5ae55..fe176ac7b263 100644 --- a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -13,31 +13,26 @@ version = '1.2.1' homepage = 'https://github.com/wdecoster/nanolyse' description = """Remove reads mapping to the lambda phage genome from a fastq file.""" +software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} builddependencies = [ ('binutils', '2.36.1'), - ('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 = [ ('Python', '3.9.5'), ('Biopython', '1.79'), + ('minimap2', '2.20'), ] use_pip = True # Fetch the tar.gz, not the whl files! exts_list = [ - ('mappy', '2.24', { - 'checksums': ['35a2fb73ef14173283d5abb31e7a318429e0330c3be95851df38dd83d4ff9af9'], + ('mappy', '2.20', { + 'checksums': ['00c8720783ac982b514b01b86349ede9809eeaccdf1328acb5a16dfeef51458b'], }), ('NanoLyse', '1.2.1', { 'checksums': ['933ee668da805fc9ec9fa86c9fca81a073438d45b5f64e23cf606c01e715b1d5'], From ee0deec486b0c0b1b2f976ef15ed3d96e0c4a1c5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:35:16 +0100 Subject: [PATCH 307/939] Remove useless buildrequirements --- easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb index fe176ac7b263..b31eb661ab9d 100644 --- a/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb +++ b/easybuild/easyconfigs/n/NanoLyse/NanoLyse-1.2.1-foss-2021a.eb @@ -17,10 +17,6 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), -] - dependencies = [ ('Python', '3.9.5'), ('Biopython', '1.79'), From ce4fe5319f93754c1005cef4e927d338322174c4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 14:53:39 +0100 Subject: [PATCH 308/939] Use postinstall cmd list + Use fix_perl_shebang_for + Test if testInput/ exists + Test outside of the install dir --- .../InParanoid-5.0.79d8e39-GCC-10.3.0.eb | 38 +++++++++---------- 1 file changed, 17 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb index 61194783a6dd..5bfa4ca673a9 100644 --- a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb @@ -21,8 +21,6 @@ source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 -builddependencies = [('binutils', '2.36.1')] - # NOTE some dependencies are not listed on the web site such as Java! dependencies = [ ('Perl', '5.32.1'), # brings libmoose-perl and libparallel-forkmanager-perl @@ -33,33 +31,31 @@ dependencies = [ ] # NOTE inparanoid.pl uses only local (same directory) paths, so patch it -postinstallcmds = ["rm -rf %(installdir)s/docker/ %(installdir)s/singularity/ && " - "chmod a+rx %(installdir)s/*.pl && " - "chmod -x %(installdir)s/*.jar && " - "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|\./\$blastParser|\$blastParser|g' " - "%(installdir)s/inparanoid.pl && " - "perl -i -pe 's|#!.*perl|#!/usr/bin/env perl|' %(installdir)s/*.pl"] +postinstallcmds = [ + "rm -rf %(installdir)s/docker/ %(installdir)s/singularity/", + "chmod a+rx %(installdir)s/*.pl", + "chmod -x %(installdir)s/*.jar", + "perl -i -pe 's|helpfile = \"help\"|helpfile = \"%(installdir)s/help\"|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|seqstat = \"|seqstat = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|blastParser = \"|blastParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|diamondParser = \"|diamondParser = \"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|copy\(\"\./|copy\(\"%(installdir)s/|' %(installdir)s/inparanoid.pl", + "perl -i -pe 's|\./\$blastParser|\$blastParser|g' %(installdir)s/inparanoid.pl", +] + +fix_perl_shebang_for = ['*.pl'] sanity_check_paths = { 'files': ['inparanoid.pl', 'blast_parser.pl', 'diamondParser.pl'], - 'dirs': ['matrices'], + 'dirs': ['matrices', 'testInput'], } modextrapaths = { 'PATH': '', } -sanity_check_commands = ["inparanoid.pl -input-dir %(installdir)s/testInput/ && " - "rm -Rf %(installdir)s/output/"] +sanity_check_commands = [ + "cd %(builddir)s && inparanoid.pl -input-dir %(installdir)s/testInput/", +] moduleclass = 'bio' From 931102f16450a7734781e26800043cb245d7c4f5 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:10:45 +0100 Subject: [PATCH 309/939] Remove useless builddependencies --- .../p/PyDamage/PyDamage-0.70-foss-2021a.eb | 11 ----------- 1 file changed, 11 deletions(-) diff --git a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb index 45477aba7e96..c2ff6ff71da0 100644 --- a/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyDamage/PyDamage-0.70-foss-2021a.eb @@ -21,17 +21,6 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'foss', 'version': '2021a'} -builddependencies = [ - ('binutils', '2.36.1'), - ('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 = [ ('Python', '3.9.5'), ('Biopython', '1.79'), From ab1ac7f2f6f502670404cc6a381cc4eb927f508b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:22:49 +0100 Subject: [PATCH 310/939] Remove useless buildrequirements + Use postinstallcmds list + Remove useless PATH extension --- .../c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 20b588f3e116..6707fbe1fc76 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -21,28 +21,23 @@ source_urls = ['https://github.com/dutilh/CAT/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] -builddependencies = [('binutils', '2.36.1')] - dependencies = [ ('Python', '3.9.5'), ('DIAMOND', '2.0.13'), ('prodigal', '2.6.3'), ] -postinstallcmds = ["cd %(installdir)s/ && ln -s CAT_pack bin && " - "chmod a+rx %(installdir)s/CAT_pack/*.py && " - "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' " - "%(installdir)s/CAT_pack/check.py"] +postinstallcmds = [ + "cd %(installdir)s/ && ln -s CAT_pack bin", + "chmod a+rx %(installdir)s/CAT_pack/*.py", + "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py", +] sanity_check_paths = { 'files': ['CAT_pack/CAT', 'README.md'], 'dirs': ['CAT_pack'], } -modextrapaths = { - 'PATH': '', -} - sanity_check_commands = ["CAT --help"] moduleclass = 'bio' From 73e4fa376f981612261e656a0101bc52eccbe3ab Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 15:48:32 +0100 Subject: [PATCH 311/939] Use version in binary name --- easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb index 7014125e51cc..aa401a18c4ff 100644 --- a/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb +++ b/easybuild/easyconfigs/g/Godon/Godon-20210913-x86_64.eb @@ -25,13 +25,14 @@ toolchain = SYSTEM source_urls = ['https://bitbucket.org/Davydov/godon/downloads'] sources = [{ 'download_filename': 'godon-master-linux-gnu-x86_64', - 'filename': 'godon', + 'filename': 'godon-%(version)s-linux-gnu-x86_64', }] checksums = ['159058f7577093548f3ced1540d1ff9fd5f7915cdfcb8f8cd7fb40f5c202fcca'] extract_sources = False -install_cmd = "mkdir -p %(installdir)s/bin/ && mv godon %(installdir)s/bin/" +install_cmd = "mkdir -p %(installdir)s/bin/ && cp -a godon-%(version)s-linux-gnu-x86_64 %(installdir)s/bin/ && " +install_cmd += "cd %(installdir)s/bin && ln -s godon-%(version)s-linux-gnu-x86_64 godon" sanity_check_paths = { 'files': ["bin/godon"], From 629be09f0cbcff3655396ddbf63e1d7b7c77c2a9 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Tue, 8 Nov 2022 15:47:37 +0000 Subject: [PATCH 312/939] Add HiCcompare and dependencies --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 33 ++++++++++++------- 1 file changed, 21 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index db12f43dc2b0..d34e406d5d8e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -222,9 +222,9 @@ exts_list = [ ('Rgraphviz', '2.40.0', { 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], 'checksums': [ - '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4', # Rgraphviz_2.40.0.tar.gz - # Rgraphviz-2.28.0_fno-tree-vectorize.patch - '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + {'Rgraphviz_2.40.0.tar.gz': '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4'}, + {'Rgraphviz-2.28.0_fno-tree-vectorize.patch': + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9'}, ], }), ('RNASeqPower', '1.36.0', { @@ -443,17 +443,17 @@ exts_list = [ ('dada2', '1.24.0', { 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], 'checksums': [ - '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b', # dada2_1.24.0.tar.gz - # dada2-1.16.0-remove-sse-on-aarch64.patch - 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + {'dada2_1.24.0.tar.gz': '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b'}, + {'dada2-1.16.0-remove-sse-on-aarch64.patch': + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935'}, ], }), ('LEA', '3.8.0', { 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], 'checksums': [ - 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774', # LEA_3.8.0.tar.gz - # LEA-3.0.0_support_aarch64_and_ppc64le.patch - 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + {'LEA_3.8.0.tar.gz': 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774'}, + {'LEA-3.0.0_support_aarch64_and_ppc64le.patch': + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881'}, ], }), ('tximport', '1.24.0', { @@ -720,9 +720,9 @@ exts_list = [ ('RProtoBufLib', '2.8.0', { 'patches': ['RProtoBufLib-2.8.0_fix-protobuf-build.patch'], 'checksums': [ - 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7', # RProtoBufLib_2.8.0.tar.gz - # RProtoBufLib-2.8.0_fix-protobuf-build.patch - '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64', + {'RProtoBufLib_2.8.0.tar.gz': 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7'}, + {'RProtoBufLib-2.8.0_fix-protobuf-build.patch': + '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64'}, ], }), ('cytolib', '2.8.0', { @@ -1086,6 +1086,15 @@ exts_list = [ ('SPOTlight', '1.0.0', { 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], }), + ('CGHcall', '2.58.0', { + 'checksums': ['c5e86b9234685462b7330c85b91ca648a801a76c99f3e98cd509ac47ee8afae2'], + }), + ('QDNAseq', '1.32.0', { + 'checksums': ['75bbde9b6cc55cd6a47b9f466358033a180b480def2144abdcc93a2a8e066668'], + }), + ('HiCcompare', '1.18.0', { + 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 09d88f791a5e9a6659f4ab7a76a4f9b1d8b24d41 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:11:16 +0100 Subject: [PATCH 313/939] adding easyconfigs: pullseq-1.0.2-GCCcore-10.3.0.eb --- .../p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..bd94483da59e --- /dev/null +++ b/easybuild/easyconfigs/p/pullseq/pullseq-1.0.2-GCCcore-10.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'pullseq' +version = '1.0.2' + +homepage = 'https://github.com/bcthomas/pullseq' +description = "Utility program for extracting sequences from a fasta/fastq file" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/bcthomas/pullseq/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['a295d7e0e2d64ed05d293d795d1716376707e465f2c42ede6454f27db586c85f'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] +dependencies = [ + ('PCRE', '8.44'), +] + +preconfigopts = "./bootstrap && " + +buildopts = 'CFLAGS="$CFLAGS -fcommon"' + +sanity_check_paths = { + 'files': ['bin/pullseq', 'bin/seqdiff'], + 'dirs': [], +} + +sanity_check_commands = [ + "pullseq --help 2>&1 | grep 'pullseq - a bioinformatics tool'", + "seqdiff --help 2>&1 | grep 'seqdiff - a bioinformatics tool'", +] + +moduleclass = 'bio' From fe12a8b8778e44b8765d8b97ead5176f1b84e1fc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:12:16 +0100 Subject: [PATCH 314/939] adding easyconfigs: IDBA-UD-1.1.3-GCC-10.3.0.eb --- .../i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb new file mode 100644 index 000000000000..6b69859e2595 --- /dev/null +++ b/easybuild/easyconfigs/i/IDBA-UD/IDBA-UD-1.1.3-GCC-10.3.0.eb @@ -0,0 +1,49 @@ +# 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 +# Updated: Pavel Grochal (INUITS) +# License: GPLv2 + +# "make install" doesnt copy all the compiled binaries so we use the "MakeCp" easyblock +# to be sure everything is copied and we run ./configure in prebuildopts + +# modified by Tom Strempel +easyblock = 'MakeCp' + +name = 'IDBA-UD' +version = '1.1.3' + +homepage = 'https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/' +description = """ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads +Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. +IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth +contigs are removed iteratively with cutoff threshold from low to high to reduce the errors +in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled +locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD +can iterate k value of de Bruijn graph to a very large value with less gaps and less branches +to form long contigs in both low-depth and high-depth regions.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/loneknightpy/idba/releases/download/%(version)s'] +sources = ['idba-%(version)s.tar.gz'] +checksums = ['030e24463c6d725c1c202baabf773b605b51e310844fd0f27f4688ecfbae26d0'] + +prebuildopts = './configure && ' + +# we delete every .o and Makefile file which is left in bin folder +buildopts = ' && rm -fr bin/*.o bin/Makefile*' + +files_to_copy = ["bin", "script", "ChangeLog", "NEWS"] + +pretestopts = "cd test && " +runtest = "check" + +sanity_check_paths = { + 'files': ["bin/%s" % x for x in ["idba", "idba_hybrid", "idba_tran", + "idba_ud", "parallel_blat", "idba_tran_test"]], + 'dirs': [""], +} + +moduleclass = 'bio' From 2ee8b1f495828d5a226a4dabd775c8ed35a00ab2 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:13:18 +0100 Subject: [PATCH 315/939] adding easyconfigs: FragGeneScan-1.31-GCCcore-10.3.0.eb --- .../FragGeneScan-1.31-GCCcore-10.3.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..4870fb3bdfaa --- /dev/null +++ b/easybuild/easyconfigs/f/FragGeneScan/FragGeneScan-1.31-GCCcore-10.3.0.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': '10.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s%(version)s.tar.gz'] +checksums = ['cd3212d0f148218eb3b17d24fcd1fc897fb9fee9b2c902682edde29f895f426c'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [("Perl", "5.32.1")] + +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' From 79d2a7ababdee961b9316a5c7d938dc14827b96c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:30:10 +0100 Subject: [PATCH 316/939] adding easyconfigs: SSW-1.1-GCCcore-10.3.0.eb --- .../s/SSW/SSW-1.1-GCCcore-10.3.0.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..f8abd16d82d3 --- /dev/null +++ b/easybuild/easyconfigs/s/SSW/SSW-1.1-GCCcore-10.3.0.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': '10.3.0'} + +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', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +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' From 50ebf6f6d3dd2e38a69642179c28121ea1c97578 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 8 Nov 2022 17:33:12 +0100 Subject: [PATCH 317/939] adding easyconfigs: fermi-lite-20190320-GCCcore-10.3.0.eb --- .../fermi-lite-20190320-GCCcore-10.3.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..6daf5a68037f --- /dev/null +++ b/easybuild/easyconfigs/f/fermi-lite/fermi-lite-20190320-GCCcore-10.3.0.eb @@ -0,0 +1,46 @@ +# 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': '10.3.0'} + +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', '2.36.1')] + +dependencies = [('zlib', '1.2.11')] + +prebuildopts = 'CFLAGS="$CFLAGS -fcommon"' + +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' From 143e7ae01b8298310d9b79667fe7e979aa8d1ef9 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 8 Nov 2022 20:55:07 +0100 Subject: [PATCH 318/939] adding easyconfigs: CMake-3.24.3-GCCcore-11.3.0.eb --- .../c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..d5b6ac8b205f --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.24.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b53aa10fa82bff84ccdb59065927b72d3bee49f4d86261249fc0984b3b367291'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('cURL', '7.83.0'), + ('libarchive', '3.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' From ae07a8f91ee2a5a1c4b720658ec2fc1fcd369551 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 8 Nov 2022 22:32:24 +0100 Subject: [PATCH 319/939] {tools}[GCCcore/12.2.0] XZ v5.2.7 --- .../easyconfigs/g/gettext/gettext-0.21.1.eb | 39 +++++++++++++++++++ .../x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb | 37 ++++++++++++++++++ 2 files changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb create mode 100644 easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb new file mode 100644 index 000000000000..9525991ab156 --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +# This is a basic stripped down version of gettext without any +# dependencies on other packages used as initial builddep for XZ +# It is the first step in the cyclic dependency chain of +# XZ -> libxml2 -> gettext -> XZ + +toolchain = SYSTEM + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +dependencies = [ + ('ncurses', '6.3'), +] + +configopts = '--without-emacs --with-included-libxml --without-xz --without-bzip2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2942a648d383 --- /dev/null +++ b/easybuild/easyconfigs/x/XZ/XZ-5.2.7-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'XZ' +version = '5.2.7' + +homepage = 'https://tukaani.org/xz/' +description = "xz: XZ utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://tukaani.org/xz/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['b65f1d0c2708e57716f4dd2216989a73847ac6fdb4168ffceb155767e22b834b'] + +builddependencies = [ + # use gettext built with system toolchain as build dep to avoid cyclic dependency (XZ -> gettext -> libxml2 -> XZ) + ('gettext', '0.21.1', '', SYSTEM), + ('binutils', '2.39'), +] + +# may become useful in non-x86 archs +# configopts = ' --disable-assembler ' + +sanity_check_paths = { + 'files': ['bin/lzmainfo', 'bin/unxz', 'bin/xz'], + 'dirs': [] +} + +sanity_check_commands = [ + "xz --help", + "unxz --help", +] + +moduleclass = 'tools' From 5c72c29cf95f639526b7bf4a98a508dc018b365f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:19:27 +0100 Subject: [PATCH 320/939] adding easyconfigs: MaxBin-2.2.7-gompi-2021a.eb --- .../m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb new file mode 100644 index 000000000000..338bf18f42b6 --- /dev/null +++ b/easybuild/easyconfigs/m/MaxBin/MaxBin-2.2.7-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'MakeCp' + +name = 'MaxBin' +version = '2.2.7' + +# https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html doesn't work +homepage = 'https://sourceforge.net/projects/maxbin/' +description = """MaxBin is software for binning assembled metagenomic sequences +based on an Expectation-Maximization algorithm.""" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['cb6429e857280c2b75823c8cd55058ed169c93bc707a46bde0c4383f2bffe09e'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [ + ('Perl', '5.32.1'), + ('Bowtie2', '2.4.4'), + ('FragGeneScan', '1.31'), + ('HMMER', '3.3.2'), + ('IDBA-UD', '1.1.3'), +] + +prebuildopts = "cd src && " + +files_to_copy = ['*'] + +fix_perl_shebang_for = ['run_MaxBin.pl'] + +sanity_check_paths = { + 'files': ['run_MaxBin.pl', 'src/MaxBin'], + 'dirs': [], +} + +modextrapaths = {'PATH': ['', 'src']} + +moduleclass = 'bio' From 54362da083f45edc31479bd1ab614bff278f0250 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:24:51 +0100 Subject: [PATCH 321/939] adding easyconfigs: DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb --- .../DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb new file mode 100644 index 000000000000..12a3da124438 --- /dev/null +++ b/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Tarball' + +name = 'DAS_Tool' +version = '1.1.1' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/cmks/DAS_Tool' +description = """DAS Tool is an automated method that integrates the results of a flexible number of binning + algorithms to calculate an optimized, non-redundant set of bins from a single assembly.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] +checksums = [ + '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch +] + +dependencies = [ + ('R', '4.1.0'), + ('Python', '3.9.5'), + ('Ruby', '3.0.1'), + ('pullseq', '1.0.2'), + ('prodigal', '2.6.3'), + ('BLAST+', '2.11.0'), +] + +exts_defaultclass = 'RPackage' + +exts_list = [ + (name, version, { + 'modulename': 'DASTool', + 'source_tmpl': 'DASTool_%(version)s.tar.gz', + 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], + 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + }), +] + +postinstallcmds = [ + "cd %(installdir)s; unzip db.zip", + "chmod a+x %(installdir)s/DAS_Tool", +] + +sanity_check_paths = { + 'files': ['DAS_Tool', 'arc.all.faa', '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 + +modextrapaths = { + 'PATH': '', + 'R_LIBS_SITE': '', +} + +moduleclass = 'bio' From e71706e9dd6b6e09e219cffb16ff75435eddb9cc Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:40:14 +0100 Subject: [PATCH 322/939] Add comment for the shebang fix + Test bin/CAT symlink --- easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 6707fbe1fc76..12d6688ec5a8 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -30,11 +30,12 @@ dependencies = [ postinstallcmds = [ "cd %(installdir)s/ && ln -s CAT_pack bin", "chmod a+rx %(installdir)s/CAT_pack/*.py", + # fix shebang in check.py script ('/env/' should be '/env') "sed -i 's@/usr/bin/env/ python3@/usr/bin/env python3@' %(installdir)s/CAT_pack/check.py", ] sanity_check_paths = { - 'files': ['CAT_pack/CAT', 'README.md'], + 'files': ['CAT_pack/CAT', 'bin/CAT', 'README.md'], 'dirs': ['CAT_pack'], } From ae21dff077b8bc7fa0551fb94f3ad0a726d41495 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:48:00 +0100 Subject: [PATCH 323/939] adding easyconfigs: MetaBAT-2.15-gompi-2021a.eb --- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb new file mode 100644 index 000000000000..a94f4f9953a4 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'CMakeMake' + +name = 'MetaBAT' +version = '2.15' + +homepage = 'https://bitbucket.org/berkeleylab/metabat' +description = "An efficient tool for accurately reconstructing single genomes from complex microbial communities" + +toolchain = {'name': 'gompi', 'version': '2021a'} + +source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('Boost', '1.76.0'), + ('zlib', '1.2.11'), + ('SAMtools', '1.13'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), +] + +fix_perl_shebang_for = ['bin/*.pl'] + +prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " + +sanity_check_paths = { + 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], + 'dirs': [""], +} + +moduleclass = 'bio' From ccc288eca099a7be7cdb8e893ae776dd3007b65e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 09:53:09 +0100 Subject: [PATCH 324/939] adding easyconfigs: MEGAHIT-1.2.9-GCCcore-10.3.0.eb --- .../m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..279dcf61042d --- /dev/null +++ b/easybuild/easyconfigs/m/MEGAHIT/MEGAHIT-1.2.9-GCCcore-10.3.0.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': '10.3.0'} + +source_urls = ['https://github.com/voutcn/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['09026eb07cc4e2d24f58b0a13f7a826ae8bb73da735a47cb1cbe6e4693118852'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('zlib', '1.2.11'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('bzip2', '1.0.8'), + ('gzip', '1.10'), +] + +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 4b5d1b297e33663fbba1e6ba9d92012874f65491 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 10:02:35 +0100 Subject: [PATCH 325/939] Rename file on download + Better version string --- ...9-GCC-10.3.0.eb => InParanoid-5.0-20220607-GCC-10.3.0.eb} | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/i/InParanoid/{InParanoid-5.0.79d8e39-GCC-10.3.0.eb => InParanoid-5.0-20220607-GCC-10.3.0.eb} (92%) diff --git a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb similarity index 92% rename from easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb rename to easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb index 5bfa4ca673a9..97e0d20fb04f 100644 --- a/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0.79d8e39-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/i/InParanoid/InParanoid-5.0-20220607-GCC-10.3.0.eb @@ -9,7 +9,8 @@ easyblock = 'Tarball' name = 'InParanoid' -version = '5.0.79d8e39' +version = '5.0-20220607' +local_commit = '79d8e39bb243d403ce57b699c1ae104a8a640389' homepage = 'https://inparanoid.sbc.su.se' description = """InParanoid: ortholog groups with inparalogs.""" @@ -18,7 +19,7 @@ software_license = 'LicenseGPLv3' toolchain = {'name': 'GCC', 'version': '10.3.0'} source_urls = ['https://bitbucket.org/sonnhammergroup/inparanoid/get/'] -sources = ['79d8e39bb243d403ce57b699c1ae104a8a640389.tar.gz'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['efe1a35bbb70608385780c4bf62969a29c46dd8132fbe472034422d23ad4b0c2'] # for commit 79d8e39 # NOTE some dependencies are not listed on the web site such as Java! From ddbbb99b4554786f94cdc18bc15a84f28b09c540 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 14:36:38 +0100 Subject: [PATCH 326/939] adding easyconfigs: typing-extensions-4.3.0-GCCcore-10.3.0.eb --- .../typing-extensions-4.3.0-GCCcore-10.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..d62b98215f8f --- /dev/null +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'typing-extensions' +version = '4.3.0' + +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': '10.3.0'} + +sources = ['typing_extensions-%(version)s.tar.gz'] +checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] + +builddependencies = [('binutils', '2.36.1')] + +dependencies = [('Python', '3.9.5')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'devel' From 29b4e32d07b930856f8c5fdac6fe5ca882efbbd1 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 9 Nov 2022 15:46:39 +0100 Subject: [PATCH 327/939] adding easyconfigs: Seaborn-0.12.1-foss-2022a.eb --- .../s/Seaborn/Seaborn-0.12.1-foss-2022a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb new file mode 100644 index 000000000000..e3f97801473d --- /dev/null +++ b/easybuild/easyconfigs/s/Seaborn/Seaborn-0.12.1-foss-2022a.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'Seaborn' +version = '0.12.1' + +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': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb1eb1d51d3097368c187c3ef089c0288ec1fe8aa1c69fb324c68aa1d02df4c1'] + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 601a39e5412437b1ef3c1358501c3fccbdc2b6d1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 15:48:32 +0100 Subject: [PATCH 328/939] adding easyconfigs: freebayes-1.3.6-foss-2021a-R-4.1.0.eb, vcflib-1.0.3-foss-2021a-R-4.1.0.eb, SeqLib-1.2.0-GCC-10.3.0.eb --- .../freebayes-1.3.6-foss-2021a-R-4.1.0.eb | 54 +++++++++++++++ .../s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb | 49 +++++++++++++ .../vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb | 69 +++++++++++++++++++ 3 files changed, 172 insertions(+) create mode 100644 easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb create mode 100644 easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb diff --git a/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb new file mode 100644 index 000000000000..cc4ea323667e --- /dev/null +++ b/easybuild/easyconfigs/f/freebayes/freebayes-1.3.6-foss-2021a-R-4.1.0.eb @@ -0,0 +1,54 @@ +easyblock = 'MesonNinja' + +name = 'freebayes' +version = '1.3.6' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/freebayes/freebayes' +description = "Bayesian haplotype-based genetic polymorphism discovery and genotyping." + +toolchain = {'name': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-1.3.6_find-external-libs.patch', + '%(name)s-1.3.5_fix-includes.patch', + '%(name)s-1.3.6_install-libs-headers.patch', +] +checksums = [ + 'd668c0b433cc0f11498ace10e48d72a7f0f40ca23b391b72e975ffafd1c13044', # v1.3.6.tar.gz + '4836a9ceaa9044e6e66b3ca0387b058a5e0505ddeaa62c428b526b5e234aff3b', # freebayes-1.3.6_find-external-libs.patch + '4c6c74b30bf3b2f04b8a50bbdef26e74f6e2412f3efbd81512226e557c2a53d1', # freebayes-1.3.5_fix-includes.patch + '5ba006ca6956905bbd81107a17e02287c515890ee25884c444ebf5b95da1caae', # freebayes-1.3.6_install-libs-headers.patch +] + +builddependencies = [ + ('CMake', '3.20.1'), + ('Meson', '0.58.0'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('R', '4.1.0'), + ('parallel', '20210622'), + ('libffi', '3.3'), + ('VCFtools', '0.1.16'), + ('vcflib', '1.0.3', versionsuffix), + ('SeqLib', '1.2.0'), +] + +configopts = "--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/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb new file mode 100644 index 000000000000..21b5647395b5 --- /dev/null +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.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': '10.3.0'} + +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', '20210128')] + +dependencies = [ + ('zlib', '1.2.11'), + ('XZ', '5.2.5'), + ('bzip2', '1.0.8'), + ('JsonCpp', '1.9.4'), + ('BWA', '0.7.17'), + ('HTSlib', '1.12'), + ('fermi-lite', '20190320'), + ('SSW', '1.1'), + ('PCRE', '8.44'), +] + +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/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb new file mode 100644 index 000000000000..1fd858e08a4b --- /dev/null +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb @@ -0,0 +1,69 @@ +# Author: Jasper Grimm (UoY) +# Updated: Denis Kristak (INUITS) +easyblock = 'CMakeMake' + +name = 'vcflib' +version = '1.0.3' +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': 'foss', 'version': '2021a'} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_use-external-deps.patch', + 'vcflib-1.0.3_fix-shared-linking.patch', +] +checksums = [ + '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz + '89f99efb35eb3a5fdc5a7fdeb96c204b1af481194bcd788c939c600a985fa8a4', # vcflib-1.0.3_use-external-deps.patch + '2584e33e447c07a66eefc46263161873498910e19035f9beed1600cbd05fd4b0', # vcflib-1.0.3_fix-shared-linking.patch +] + +builddependencies = [ + ('binutils', '2.36.1'), + ('CMake', '3.20.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('Perl', '5.32.1'), + ('R', '4.1.0'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.12'), + ('tabixpp', '1.1.0'), + ('intervaltree', '0.1'), + ('fastahack', '1.0.0'), + ('filevercmp', '20191210'), + ('fsom', '20141119'), + ('multichoose', '1.0.3'), + ('smithwaterman', '20160702'), +] + +preconfigopts = "find %(builddir)s/%(name)s-%(version)s/src -type f -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 += " -e 's|disorder.h|smithwaterman/disorder.h|g' {} \; && " + +postinstallcmds = ["cp -r %(builddir)s/%(name)s-%(version)s/scripts %(installdir)s"] + +modextrapaths = {'PATH': ['scripts']} + +sanity_check_paths = { + 'files': ['bin/vcfannotate', 'bin/vcfcombine', 'lib/libvcflib.%s' % SHLIB_EXT], + 'dirs': ['scripts'], +} + +sanity_check_commands = ["vcfremap"] + +moduleclass = 'bio' From 08832cc28564f07f4ac02d2e0166396122caae1d Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 17:16:19 +0100 Subject: [PATCH 329/939] Update to the last version --- ...re-10.3.0.eb => typing-extensions-4.4.0-GCCcore-10.3.0.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/t/typing-extensions/{typing-extensions-4.3.0-GCCcore-10.3.0.eb => typing-extensions-4.4.0-GCCcore-10.3.0.eb} (83%) diff --git a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb similarity index 83% rename from easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb rename to easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb index d62b98215f8f..ea51e13ece0f 100644 --- a/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.3.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/t/typing-extensions/typing-extensions-4.4.0-GCCcore-10.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonPackage' name = 'typing-extensions' -version = '4.3.0' +version = '4.4.0' homepage = 'https://github.com/python/typing/blob/master/typing_extensions/README.rst' description = 'Typing Extensions - Backported and Experimental Type Hints for Python' @@ -9,7 +9,7 @@ description = 'Typing Extensions - Backported and Experimental Type Hints for Py toolchain = {'name': 'GCCcore', 'version': '10.3.0'} sources = ['typing_extensions-%(version)s.tar.gz'] -checksums = ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'] +checksums = ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'] builddependencies = [('binutils', '2.36.1')] From 5781cd9d12fdde97531d3919ed60857da00b9d6f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 9 Nov 2022 17:51:19 +0100 Subject: [PATCH 330/939] templating the name, but hardcoding the patch version --- easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb | 4 ++-- .../easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb index 21b5647395b5..27a50312ce65 100644 --- a/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/s/SeqLib/SeqLib-1.2.0-GCC-10.3.0.eb @@ -14,8 +14,8 @@ 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', + '%(name)s-1.2.0_avoid-bwa-fml-namespace-conflict.patch', + '%(name)s-1.2.0_use-external-deps.patch', ] checksums = [ '6892bdb5cae88d8d8acbbfadd351cfa00004bc7c0fd1ae912dc1ff1ccfd61a70', # 1.2.0.tar.gz diff --git a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb index 1fd858e08a4b..9061ba602b32 100644 --- a/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb +++ b/easybuild/easyconfigs/v/vcflib/vcflib-1.0.3-foss-2021a-R-4.1.0.eb @@ -16,8 +16,8 @@ toolchain = {'name': 'foss', 'version': '2021a'} source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] patches = [ - '%(name)s-%(version)s_use-external-deps.patch', - 'vcflib-1.0.3_fix-shared-linking.patch', + '%(name)s-1.0.3_use-external-deps.patch', + '%(name)s-1.0.3_fix-shared-linking.patch', ] checksums = [ '5fd05f46dc251a56a322809da92c93c85318036aa9ac39a2eefc4fbd39b5df6c', # v1.0.3.tar.gz From 8c9b31f081ea5134b06804aad059bd2d6508637a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:18:46 +0100 Subject: [PATCH 331/939] adding easyconfigs: libxml2-2.10.3-GCCcore-12.2.0.eb --- .../libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..899bcfe4e7f5 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2/libxml2-2.10.3-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +name = 'libxml2' +version = '2.10.3' + +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). +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['5d2cc3d78bec3dbe212a9d7fa629ada25a7da928af432c93060ff5c17ee28a9c'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('XZ', '5.2.7'), + ('zlib', '1.2.12'), +] + +moduleclass = 'lib' From c1c8a42c28f4823a37f93e483f0a044e77353494 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:51:53 +0100 Subject: [PATCH 332/939] adding easyconfigs: Python-3.10.8-GCCcore-12.2.0-bare.eb, SQLite-3.39.4-GCCcore-12.2.0.eb, Tcl-8.6.12-GCCcore-12.2.0.eb, libffi-3.4.4-GCCcore-12.2.0.eb, bzip2-1.0.8-GCCcore-12.2.0.eb, UnZip-6.0-GCCcore-12.2.0.eb --- .../b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb | 27 ++++++++++ .../l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb | 29 +++++++++++ .../Python-3.10.8-GCCcore-12.2.0-bare.eb | 35 +++++++++++++ .../s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb | 39 ++++++++++++++ .../t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb | 41 +++++++++++++++ .../u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ 6 files changed, 223 insertions(+) create mode 100644 easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb create mode 100644 easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d2ce38e17320 --- /dev/null +++ b/easybuild/easyconfigs/b/bzip2/bzip2-1.0.8-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +name = 'bzip2' +version = '1.0.8' + +homepage = 'https://sourceware.org/bzip2' +description = """ + bzip2 is a freely available, patent free, high-quality data compressor. It + typically compresses files to within 10% to 15% of the best available + techniques (the PPM family of statistical compressors), whilst being around + twice as fast at compression and six times faster at decompression. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://sourceware.org/pub/%(name)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['bzip2-%(version)s-pkgconfig.patch'] +checksums = [ + 'ab5a03176ee106d3f0fa90e381da478ddae405918153cca248e682cd0c4a2269', # bzip2-1.0.8.tar.gz + '9299e8ee4d014ea973777b6ea90661fe329dfa991f822add4c763ea9ddb9aab1', # bzip2-1.0.8-pkgconfig.patch +] + +builddependencies = [ + ('binutils', '2.39'), +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f9c248d7fd79 --- /dev/null +++ b/easybuild/easyconfigs/l/libffi/libffi-3.4.4-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'libffi' +version = '3.4.4' + +homepage = 'https://sourceware.org/libffi/' +description = """The libffi library provides a portable, high level programming interface to + various calling conventions. This allows a programmer to call any function + specified by a call interface description at run-time.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/libffi/libffi/releases/download/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d66c56ad259a82cf2a9dfc408b32bf5da52371500b84745f7fb8b645712df676'] + +builddependencies = [ + ('binutils', '2.39'), +] + +configopts = '--disable-exec-static-tramp ' + +sanity_check_paths = { + 'files': ['lib/libffi.a', 'lib/libffi.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb new file mode 100644 index 000000000000..39fbf14affef --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0-bare.eb @@ -0,0 +1,35 @@ +name = 'Python' +version = '3.10.8' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'] + +builddependencies = [ + ('UnZip', '6.0'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..cc6b559ef739 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLite/SQLite-3.39.4-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'SQLite' +version = '3.39.4' +local_filename_version = '3390400' + +homepage = 'https://www.sqlite.org/' +description = "SQLite: SQL Database Engine in a C Library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.sqlite.org/2022/'] +sources = ['%%(namelower)s-autoconf-%s.tar.gz' % (local_filename_version)] +checksums = ['f31d445b48e67e284cf206717cc170ab63cbe4fd7f79a82793b772285e78fdbb'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('libreadline', '8.2'), + ('Tcl', '8.6.12'), +] + +# enable additional APIs that provide access to meta-data about tables and queries +# needed for GDAL when it used as a dep for QGIS +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -DSQLITE_ENABLE_COLUMN_METADATA"' + +sanity_check_paths = { + 'files': ['bin/sqlite3', 'include/sqlite3ext.h', 'include/sqlite3.h', + 'lib/libsqlite3.a', 'lib/libsqlite3.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +sanity_check_commands = [ + 'sqlite3 --version | grep ^%(version)s', +] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d86abbb9d4db --- /dev/null +++ b/easybuild/easyconfigs/t/Tcl/Tcl-8.6.12-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'Tcl' +version = '8.6.12' + +homepage = 'https://www.tcl.tk/' +description = """ + Tcl (Tool Command Language) is a very powerful but easy to learn dynamic + programming language, suitable for a very wide range of uses, including web + and desktop applications, networking, administration, testing and many more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://prdownloads.sourceforge.net/%(namelower)s'] +sources = ['%(namelower)s%(version)s-src.tar.gz'] +checksums = ['26c995dd0f167e48b11961d891ee555f680c175f7173ff8cb829f4ebcde4c1a6'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('zlib', '1.2.12'), +] + +configopts = '--enable-threads EXTRA_INSTALL="install-private-headers"' + +runtest = 'test' + +start_dir = 'unix' + +postinstallcmds = ['ln -s %(installdir)s/bin/tclsh%(version_major)s.%(version_minor)s %(installdir)s/bin/tclsh'] + +sanity_check_paths = { + 'files': ['bin/tclsh%(version_major)s.%(version_minor)s', 'bin/tclsh', + 'include/tcl.h', 'lib/libtcl%%(version_major)s.%%(version_minor)s.%s' % SHLIB_EXT, + 'lib/tclConfig.sh', 'man/man1/tclsh.1'], + 'dirs': ['share'], +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2b85900a4d8b --- /dev/null +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'UnZip' +version = '6.0' + +homepage = 'http://www.info-zip.org/UnZip.html' +description = """UnZip is an extraction utility for archives compressed +in .zip format (also called "zipfiles"). Although highly compatible both +with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's +own Zip program, our primary objectives have been portability and +non-MSDOS functionality.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://download.sourceforge.net/infozip'] +sources = ['%(namelower)s%(version_major)s%(version_minor)s.tar.gz'] +patches = [ + 'UnZip-%(version)s_various-security-and-other-fixes-from-Ubuntu.patch', +] +checksums = [ + '036d96991646d0449ed0aa952e4fbe21b476ce994abc276e49d30e686708bd37', # unzip60.tar.gz + # UnZip-6.0_various-security-and-other-fixes-from-Ubuntu.patch + '06b9307fd5aa018896bd4126818c00c1fd284a06cc3681cf0492f951ebb57ffe', +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('bzip2', '1.0.8'), +] + +skipsteps = ['configure'] + +buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' +buildopts += 'LF2="$LDFLAGS" ' +# Note: CF is multiple lines +buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' +buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' +buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' + +installopts = '-f unix/Makefile prefix=%(installdir)s ' + +sanity_check_paths = { + 'files': ['bin/unzip', 'bin/zipinfo'], + 'dirs': ['man/man1'] +} + +sanity_check_commands = ["unzip -v"] + +moduleclass = 'tools' From 4e58dc480e02a1ef47a382bc40ee872bcbc203e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:53:58 +0100 Subject: [PATCH 333/939] adding easyconfigs: cURL-7.86.0-GCCcore-12.2.0.eb --- .../c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..4e108bdbc197 --- /dev/null +++ b/easybuild/easyconfigs/c/cURL/cURL-7.86.0-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' + +name = 'cURL' +version = '7.86.0' + +homepage = 'https://curl.haxx.se' + +description = """ + libcurl is a free and easy-to-use client-side URL transfer library, + supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, + LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. + libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP + form based upload, proxies, cookies, user+password authentication (Basic, + Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling + and more. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://curl.haxx.se/download/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3dfdd39ba95e18847965cd3051ea6d22586609d9011d91df7bc5521288987a82'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = '--with-zlib ' +configopts += '--with-ssl=$EBROOTOPENSSL ' + +modextravars = {'CURL_INCLUDES': '%(installdir)s/include'} + +sanity_check_paths = { + 'files': ['bin/curl', 'lib/libcurl.a', 'lib/libcurl.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig', 'include/curl'], +} + +moduleclass = 'tools' From 8df94ddb722ef38af443951adf5ed0f462661a03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:54:12 +0100 Subject: [PATCH 334/939] adding easyconfigs: libarchive-3.6.1-GCCcore-12.2.0.eb --- .../libarchive-3.6.1-GCCcore-12.2.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb 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 new file mode 100644 index 000000000000..8cc05cbcb017 --- /dev/null +++ b/easybuild/easyconfigs/l/libarchive/libarchive-3.6.1-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'libarchive' +version = '3.6.1' + +homepage = 'https://www.libarchive.org/' + +description = """ + Multi-format archive and compression library +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.libarchive.org/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['c676146577d989189940f1959d9e3980d28513d74eedfbc6b7f15ea45fe54ee2'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('XZ', '5.2.7'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['include/archive.h', 'lib/libarchive.%s' % SHLIB_EXT], + 'dirs': ['bin', 'share/man/man3'], +} + +moduleclass = 'tools' From 4dd41bfb994262fabb743d9e4da47cd4b3ab0881 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:55:24 +0100 Subject: [PATCH 335/939] adding easyconfigs: CMake-3.24.3-GCCcore-12.2.0.eb --- .../c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..86db778efcb1 --- /dev/null +++ b/easybuild/easyconfigs/c/CMake/CMake-3.24.3-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +name = 'CMake' +version = '3.24.3' + +homepage = 'https://www.cmake.org' + +description = """ + CMake, the cross-platform, open-source build system. CMake is a family of + tools designed to build, test and package software. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.cmake.org/files/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b53aa10fa82bff84ccdb59065927b72d3bee49f4d86261249fc0984b3b367291'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('cURL', '7.86.0'), + ('libarchive', '3.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +moduleclass = 'devel' From b0f5a08b7873d0bcf346dbda7b49417980638983 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 21:57:44 +0100 Subject: [PATCH 336/939] adding easyconfigs: FlexiBLAS-3.2.1-GCC-12.2.0.eb, BLIS-0.9.0-GCC-12.2.0.eb, OpenBLAS-0.3.21-GCC-12.2.0.eb --- .../b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb | 42 ++++++++++++++ .../f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb | 58 +++++++++++++++++++ .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 47 +++++++++++++++ 3 files changed, 147 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb new file mode 100644 index 000000000000..3fdd482cf5a1 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-GCC-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] +builddependencies = [ + ('Python', '3.10.8', '-bare'), + ('Perl', '5.36.0'), +] + +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb new file mode 100644 index 000000000000..9a77c6b3a775 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.1-GCC-12.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.2.1' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +local_extra_flags = "-fstack-protector-strong -fstack-clash-protection" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.21'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['5be7e508e2dbb751b3bf372639d8e82a11f79e9ef6cbf243b64981c24a5703cf'], + 'backends': local_backends, + }), + ('LAPACK', '3.10.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' 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 new file mode 100644 index 000000000000..eee3ebc9454a --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb @@ -0,0 +1,47 @@ +name = 'OpenBLAS' +version = '0.3.21' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', +] +checksums = [ + {'v0.3.21.tar.gz': 'f36ba3d7a60e7c8bcc54cd9aaa9b1223dd42eaf02c811791c37e8ca707c241ca'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, +] + +builddependencies = [ + # required by LAPACK test suite + ('Python', '3.10.8', '-bare'), +] + +run_lapack_tests = True +max_failing_lapack_tests_num_errors = 150 + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' From b23bc8abe61cca25d721e9efdcbd8a0733275e9f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:06:22 +0100 Subject: [PATCH 337/939] adding easyconfigs: hwloc-2.8.0-GCCcore-12.2.0.eb, libpciaccess-0.17-GCCcore-12.2.0.eb, xorg-macros-1.19.3-GCCcore-12.2.0.eb --- .../h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../libpciaccess-0.17-GCCcore-12.2.0.eb | 26 +++++++++++ .../xorg-macros-1.19.3-GCCcore-12.2.0.eb | 27 +++++++++++ 3 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb 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 new file mode 100644 index 000000000000..f6483901c2b3 --- /dev/null +++ b/easybuild/easyconfigs/h/hwloc/hwloc-2.8.0-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'hwloc' +version = '2.8.0' + +homepage = 'https://www.open-mpi.org/projects/hwloc/' + +description = """ + The Portable Hardware Locality (hwloc) software package provides a portable + abstraction (across OS, versions, architectures, ...) of the hierarchical + topology of modern architectures, including NUMA memory nodes, sockets, shared + caches, cores and simultaneous multithreading. It also gathers various system + attributes such as cache and memory information as well as the locality of I/O + devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily + aims at helping applications with gathering information about modern computing + hardware so as to exploit it accordingly and efficiently. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.open-mpi.org/software/hwloc/v%(version_major_minor)s/downloads/'] +sources = [SOURCE_TAR_GZ] +checksums = ['20b2bd4df436827d8e50f7afeafb6f967259f2fb374ce7330244f8d0ed2dde6f'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('numactl', '2.0.16'), + ('libxml2', '2.10.3'), + ('libpciaccess', '0.17'), +] + +configopts = "--enable-libnuma=$EBROOTNUMACTL " +configopts += "--disable-cairo --disable-opencl --disable-cuda --disable-nvml --disable-gl --disable-libudev " + +sanity_check_paths = { + 'files': ['bin/lstopo', 'include/hwloc/linux.h', + 'lib/libhwloc.%s' % SHLIB_EXT], + 'dirs': ['share/man/man3'], +} +sanity_check_commands = ['lstopo'] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0c9005d81c08 --- /dev/null +++ b/easybuild/easyconfigs/l/libpciaccess/libpciaccess-0.17-GCCcore-12.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'libpciaccess' +version = '0.17' + +homepage = 'https://cgit.freedesktop.org/xorg/lib/libpciaccess/' +description = """Generic PCI access library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.x.org/releases/individual/lib/'] +sources = [SOURCE_TAR_GZ] +checksums = ['bf6985a77d2ecb00e2c79da3edfb26b909178ffca3f2e9d14ed0620259ab733b'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['include/pciaccess.h', 'lib/libpciaccess.a'], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..23dad904c35c --- /dev/null +++ b/easybuild/easyconfigs/x/xorg-macros/xorg-macros-1.19.3-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'xorg-macros' +version = '1.19.3' + +homepage = 'https://cgit.freedesktop.org/xorg/util/macros' +description = """X.org macros utilities.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/xorg/util/macros/-/archive/util-macros-%(version)s'] +sources = ['macros-util-macros-%(version)s.tar.gz'] +checksums = ['8205d210a580da0938f5ce4392a96b60cf1d9a5f792eaa1474fa4c1977aef4d0'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['share/pkgconfig/xorg-macros.pc'], + 'dirs': [], +} + +moduleclass = 'devel' From 7fd3bc769e202c71bff87cb387d7223b27583fc8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:34:01 +0100 Subject: [PATCH 338/939] adding easyconfigs: OpenMPI-4.1.4-GCC-12.2.0.eb, libevent-2.1.12-GCCcore-12.2.0.eb, libfabric-1.16.1-GCCcore-12.2.0.eb, PMIx-4.2.2-GCCcore-12.2.0.eb, UCC-1.1.0-GCCcore-12.2.0.eb --- .../libevent-2.1.12-GCCcore-12.2.0.eb | 38 ++++++++++++ .../libfabric-1.16.1-GCCcore-12.2.0.eb | 62 +++++++++++++++++++ .../o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb | 62 +++++++++++++++++++ .../p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb | 45 ++++++++++++++ .../u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb | 37 +++++++++++ 5 files changed, 244 insertions(+) create mode 100644 easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..99908875d8c2 --- /dev/null +++ b/easybuild/easyconfigs/l/libevent/libevent-2.1.12-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'libevent' +version = '2.1.12' + +homepage = 'https://libevent.org/' + +description = """ + The libevent API provides a mechanism to execute a callback function when + a specific event occurs on a file descriptor or after a timeout has been + reached. Furthermore, libevent also support callbacks due to signals or + regular timeouts. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/release-%(version)s-stable/'] +sources = ['%(name)s-%(version)s-stable.tar.gz'] +checksums = ['92e6de1be9ec176428fd2367677e61ceffc2ee1cb119035037a27d346b0403bb'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +sanity_check_paths = { + 'files': ['bin/event_rpcgen.py', 'include/event.h', 'include/event2/event.h', + 'lib/libevent_core.%s' % SHLIB_EXT, 'lib/pkgconfig/libevent.pc'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..97eacfc006e3 --- /dev/null +++ b/easybuild/easyconfigs/l/libfabric/libfabric-1.16.1-GCCcore-12.2.0.eb @@ -0,0 +1,62 @@ +easyblock = 'ConfigureMake' + +name = 'libfabric' +version = '1.16.1' + +homepage = 'https://ofiwg.github.io/libfabric/' +description = """ +Libfabric is a core component of OFI. It is the library that defines and exports +the user-space API of OFI, and is typically the only software that applications +deal with directly. It works in conjunction with provider libraries, which are +often integrated directly into libfabric. +""" + +# The psm3 provider (enabled by default) requires an AVX capable system to run +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/ofiwg/libfabric/releases/download/v%(version)s'] +sources = [SOURCE_TAR_BZ2] +patches = [ + '%(name)s-1.12.1_disable-psm3-avx-config.patch', +] +checksums = [ + {'libfabric-1.16.1.tar.bz2': '53f992d33f9afe94b8a4ea3d105504887f4311cf4b68cea99a24a85fcc39193f'}, + {'libfabric-1.12.1_disable-psm3-avx-config.patch': + '129be05a824b41eeb7bddac3c23aa421a13f7dde622948df942a265ccc96125a'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('numactl', '2.0.16'), +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +# Regenerate build files to pick up psm3-axv-config patch +preconfigopts = "./autogen.sh &&" + +# Disable deprecated "sockets" provider +configopts = "--disable-sockets " + +# Disable usNIC provider by default as this requires specific osdependencies +# If you want to enable this provider you need to uncomment the following line: +# osdependencies.append(('libnl3-devel', 'libnl3-dev')) +configopts += "--disable-usnic " + +buildopts = "V=1" + +sanity_check_paths = { + 'files': ['bin/fi_info', 'bin/fi_pingpong', 'bin/fi_strerror'] + + ['lib/libfabric.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/rdma', 'lib/pkgconfig', 'share'] +} + +sanity_check_commands = ['fi_info'] + +moduleclass = 'lib' 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 new file mode 100644 index 000000000000..09a6bc393d37 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-GCC-12.2.0.eb @@ -0,0 +1,62 @@ +name = 'OpenMPI' +version = '4.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.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', +] + +builddependencies = [ + ('pkgconf', '1.9.3'), + ('Perl', '5.36.0'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), + ('libevent', '2.1.12'), + ('UCX', '1.13.1'), + ('libfabric', '1.16.1'), + ('PMIx', '4.2.2'), + ('UCC', '1.1.0'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ffe8c9fba652 --- /dev/null +++ b/easybuild/easyconfigs/p/PMIx/PMIx-4.2.2-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'ConfigureMake' + +name = 'PMIx' +version = '4.2.2' + +homepage = 'https://pmix.org/' +description = """Process Management for Exascale Environments +PMI Exascale (PMIx) represents an attempt to +provide an extended version of the PMI standard specifically designed +to support clusters up to and including exascale sizes. The overall +objective of the project is not to branch the existing pseudo-standard +definitions - in fact, PMIx fully supports both of the existing PMI-1 +and PMI-2 APIs - but rather to (a) augment and extend those APIs to +eliminate some current restrictions that impact scalability, and (b) +provide a reference implementation of the PMI-server that demonstrates +the desired level of scalability. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openpmix/openpmix/releases/download/v%(version)s'] +sources = ['%(namelower)s-%(version)s.tar.bz2'] +checksums = ['935b2f492e4bc409017f1425a83366aa72a7039605ea187c9fac7bb1371cd73c'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('libevent', '2.1.12'), + ('zlib', '1.2.12'), + ('hwloc', '2.8.0'), +] + +configopts = ' --with-libevent=$EBROOTLIBEVENT --with-zlib=$EBROOTZLIB' +configopts += ' --with-hwloc=$EBROOTHWLOC' +configopts += ' --enable-pmix-binaries' + +buildopts = 'V=1' + +sanity_check_paths = { + 'files': ['bin/pevent', 'bin/plookup', 'bin/pmix_info', 'bin/pps'], + 'dirs': ['etc', 'include', 'lib', 'share'] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b5ff6ef4e426 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC/UCC-1.1.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'UCC' +version = '1.1.0' + +homepage = 'https://www.openucx.org/' +description = """UCC (Unified Collective Communication) is a collective +communication operations API and library that is flexible, complete, and +feature-rich for current and emerging programming models and runtimes. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['74c8ba75037b5bd88cb703e8c8ae55639af3fecfd4428912a433c010c97b4df7'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('UCX', '1.13.1'), +] + +preconfigopts = "./autogen.sh && " + +sanity_check_paths = { + 'files': ['bin/ucc_info'], + 'dirs': ['include', 'lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +moduleclass = 'lib' From 2fea5fff4cb20690af3a56e49a6441a8c231675e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:36:23 +0100 Subject: [PATCH 339/939] adding easyconfigs: gompi-2022.10.eb --- .../easyconfigs/g/gompi/gompi-2022.10.eb | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2022.10.eb diff --git a/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb b/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb new file mode 100644 index 000000000000..9d5e27529690 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2022.10.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2022.10' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' From b0e358cbfd08891ead6d086aadc81b452d909c49 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:37:21 +0100 Subject: [PATCH 340/939] adding easyconfigs: FFTW-3.3.10-GCC-12.2.0.eb, FFTW.MPI-3.3.10-gompi-2022.10.eb --- .../FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb | 19 +++++++++++++++++++ .../f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb | 17 +++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb new file mode 100644 index 000000000000..dacac34b6e31 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022.10.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb new file mode 100644 index 000000000000..90dce63b19c3 --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-GCC-12.2.0.eb @@ -0,0 +1,17 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +runtest = 'check' + +moduleclass = 'numlib' From 443aca94e6dfeb2c4eb16dc0f412566ccb62af31 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:39:30 +0100 Subject: [PATCH 341/939] {toolchain} foss/2022.10 --- easybuild/easyconfigs/f/foss/foss-2022.10.eb | 28 ++++++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb | 21 +++++++++ .../ScaLAPACK-2.2.0-gompi-2022.10-fb.eb | 43 +++++++++++++++++++ 3 files changed, 92 insertions(+) create mode 100644 easybuild/easyconfigs/f/foss/foss-2022.10.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb diff --git a/easybuild/easyconfigs/f/foss/foss-2022.10.eb b/easybuild/easyconfigs/f/foss/foss-2022.10.eb new file mode 100644 index 000000000000..023dc1773841 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2022.10.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2022.10' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb new file mode 100644 index 000000000000..453f6a14c839 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022.10.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022.10'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb new file mode 100644 index 000000000000..5b5a3e57d380 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022.10-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From c6a622be78d7044e477d203e1a9ddec8af7bf375 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 9 Nov 2022 22:49:33 +0100 Subject: [PATCH 342/939] construct 'buildopts' value in a more transparent way in UnZip easyconfig --- .../u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb index 2b85900a4d8b..042b74c404e8 100644 --- a/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/u/UnZip/UnZip-6.0-GCCcore-12.2.0.eb @@ -33,12 +33,19 @@ dependencies = [ skipsteps = ['configure'] -buildopts = '-f unix/Makefile CC="$CC" D_USE_BZ2=-DUSE_BZIP2 L_BZ2=-lbz2 ' -buildopts += 'LF2="$LDFLAGS" ' -# Note: CF is multiple lines -buildopts += 'CF="$CFLAGS $CPPFLAGS -I. -DACORN_FTYPE_NFS -DWILD_STOP_AT_DIR -DLARGE_FILE_SUPPORT ' -buildopts += '-DUNICODE_SUPPORT -DUNICODE_WCHAR -DUTF8_MAYBE_NATIVE -DNO_LCHMOD ' -buildopts += '-DDATE_FORMAT=DF_YMD -DUSE_BZIP2 -DIZ_HAVE_UXUIDGID -DNOMEMCPY -DNO_WORKING_ISPRINT" unzips ' +local_cf = ['$CFLAGS', '$CPPFLAGS', '-I.', '-DACORN_FTYPE_NFS', '-DWILD_STOP_AT_DIR', '-DLARGE_FILE_SUPPORT' + '-DUNICODE_SUPPORT', '-DUNICODE_WCHAR', '-DUTF8_MAYBE_NATIVE', '-DNO_LCHMOD', '-DDATE_FORMAT=DF_YMD', + '-DUSE_BZIP2', '-DIZ_HAVE_UXUIDGID', '-DNOMEMCPY', '-DNO_WORKING_ISPRINT'] + +buildopts = ' '.join([ + "-f unix/Makefile", + 'CC="$CC"', + 'D_USE_BZ2=-DUSE_BZIP2', + 'L_BZ2=-lbz2', + 'LF2="$LDFLAGS"', + 'CF="%s"' % ' '.join(local_cf), + 'unzips', +]) installopts = '-f unix/Makefile prefix=%(installdir)s ' From 2745967c83fc6c5dd3c06b2c051338d7a9b0f294 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Nov 2022 08:54:23 +0000 Subject: [PATCH 343/939] adding easyconfigs: OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb --- .../OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb new file mode 100644 index 000000000000..9326eb7240e9 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022.10.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '6.2' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022.10'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb9dbc87dcf8ec6785977a61f6fceee8febf1a682488eaab4c58cf50e4fa985f'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From a010106a159d8b9ad639128420ba6861ef42f21f Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 09:59:48 +0100 Subject: [PATCH 344/939] adding easyconfigs: python-libsbml-5.19.2-foss-2021a.eb --- .../python-libsbml-5.19.2-foss-2021a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb new file mode 100644 index 000000000000..3ff630bebf13 --- /dev/null +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb @@ -0,0 +1,51 @@ +## +# 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 = 'PythonBundle' + +name = 'python-libsbml' +version = '5.19.2' + +homepage = 'https://sbml.org/' +description = """LibSBML Python API.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + ('binutils', '2.36.1'), + ('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 = [ + ('Python', '3.9.5'), + ('libxml2', '2.9.10'), + ('libxslt', '1.1.34'), +] + +use_pip = True + +# NOTE Use version 5.19.2 because is the last one provided as tarball and not as weird whl +exts_list = [ + (name, version, { + 'modulename': 'libsbml', + 'checksums': ['b11a79a5421abba9f8874ebbc1c479cbdb3c1827697db74b687705632583a0e5'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'bio' From 2538811517d07628a0d89709afd06376df1898bb Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 10:20:48 +0100 Subject: [PATCH 345/939] Add missing sanity_pip_check --- .../p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb index 3ff630bebf13..ebe73922184f 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb @@ -48,4 +48,6 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } +sanity_pip_check = True + moduleclass = 'bio' From 23b69b499eb00902e17dd2c31bb5e82d0706b1ba Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 10 Nov 2022 10:52:08 +0000 Subject: [PATCH 346/939] switch 'www.cpan.org' to 'cpan.metacpan.org' in extension source_urls for recent Perl easyconfigs --- .../p/Perl/Perl-5.34.1-GCCcore-11.3.0.eb | 42 +++++++++---------- .../p/Perl/Perl-5.36.0-GCCcore-12.1.0.eb | 42 +++++++++---------- .../p/Perl/Perl-5.36.0-GCCcore-12.2.0.eb | 42 +++++++++---------- 3 files changed, 63 insertions(+), 63 deletions(-) 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 b998f1d93d04..9c3e8483a030 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 @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN/'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE/'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST/'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY/'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL/'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.35', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.60', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { 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 1424b9a1a56e..78044193927a 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 @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.36', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.61', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { 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 df8c81ece83f..9e66a846bc3a 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 @@ -110,47 +110,47 @@ exts_list = [ }), ('IPC::System::Simple', '1.30', { 'source_tmpl': 'IPC-System-Simple-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JK/JKEENAN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JK/JKEENAN'], 'checksums': ['22e6f5222b505ee513058fdca35ab7a1eab80539b98e5ca4a923a70a8ae9ba9e'], }), ('Importer', '0.026', { 'source_tmpl': 'Importer-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['e08fa84e13cb998b7a897fc8ec9c3459fcc1716aff25cc343e36ef875891b0ef'], }), ('Term::Table', '0.016', { 'source_tmpl': 'Term-Table-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['8fb4fbb8e96a2d6c514949eb8cfd7e66319bcb1cbf7cea0ab19af887a72d97bf'], }), ('Scope::Guard', '0.21', { 'source_tmpl': 'Scope-Guard-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CH/CHOCOLATE'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CH/CHOCOLATE'], 'checksums': ['8c9b1bea5c56448e2c3fadc65d05be9e4690a3823a80f39d2f10fdd8f777d278'], }), ('Sub::Info', '0.002', { 'source_tmpl': 'Sub-Info-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ea3056d696bdeff21a99d340d5570887d39a8cc47bff23adfc82df6758cdd0ea'], }), ('Test2::Require::Module', '0.000145', { 'source_tmpl': 'Test2-Suite-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/EX/EXODIST'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/EX/EXODIST'], 'checksums': ['ed44be739c8879fe178d3107b238f2db960d52797db0058de53be5b84600358b'], }), ('Test2::Plugin::NoWarnings', '0.09', { 'source_tmpl': 'Test2-Plugin-NoWarnings-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DR/DROLSKY'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DR/DROLSKY'], 'checksums': ['be3dd800042eef362bf17d2056cf9e934dee91ccce98e4f178b8fb5772f2fb74'], }), ('Class::Tiny', '1.008', { 'source_tmpl': 'Class-Tiny-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/D/DA/DAGOLDEN'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN'], 'checksums': ['ee058a63912fa1fcb9a72498f56ca421a2056dc7f9f4b67837446d6421815615'], }), ('Test::File::ShareDir::Dist', '1.001002', { 'source_tmpl': 'Test-File-ShareDir-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/K/KE/KENTNL'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/K/KE/KENTNL'], 'checksums': ['b33647cbb4b2f2fcfbde4f8bb4383d0ac95c2f89c4c5770eb691f1643a337aad'], }), ('DateTime::Locale', '1.36', { @@ -210,12 +210,12 @@ exts_list = [ }), ('CPAN::Meta::Check', '0.014', { 'source_tmpl': 'CPAN-Meta-Check-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LE/LEONT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LE/LEONT/'], 'checksums': ['28a0572bfc1c0678d9ce7da48cf521097ada230f96eb3d063fcbae1cfe6a351f'], }), ('Test::Without::Module', '0.20', { 'source_tmpl': 'Test-Without-Module-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/C/CO/CORION/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/C/CO/CORION/'], 'checksums': ['8e9aeb7c32a6c6d0b8a93114db2a8c072721273a9d9a2dd4f9ca86cfd28aa524'], }), ('DateTime', '1.58', { @@ -1051,7 +1051,7 @@ exts_list = [ }), ('Test::Needs', '0.002009', { 'source_tmpl': 'Test-Needs-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/H/HA/HAARG/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/H/HA/HAARG/'], 'checksums': ['571c21193ad16195df58b06b268798796a391b398c443271721d2cc0fb7c4ac3'], }), ('HTTP::Daemon', '6.14', { @@ -1131,12 +1131,12 @@ exts_list = [ }), ('Module::Runtime::Conflicts', '0.003', { 'source_tmpl': 'Module-Runtime-Conflicts-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['707cdc75038c70fe91779b888ac050f128565d3967ba96680e1b1c7cc9733875'], }), ('Test::CleanNamespaces', '0.24', { 'source_tmpl': 'Test-CleanNamespaces-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/E/ET/ETHER/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/E/ET/ETHER/'], 'checksums': ['338d5569e8e89a654935f843ec0bc84aaa486fe8dd1898fb9cab3eccecd5327a'], }), ('Moose', '2.2201', { @@ -1221,7 +1221,7 @@ exts_list = [ }), ('Test::More::UTF8', '0.05', { 'source_tmpl': 'Test-More-UTF8-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/M/MO/MONS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/M/MO/MONS/'], 'checksums': ['b9f1c4b36a97cdfefaa53ed1115dd38f4b483037775f6559ee1df14acfd1ce04'], }), ('Text::Template', '1.61', { @@ -1231,17 +1231,17 @@ exts_list = [ }), ('PadWalker', '2.5', { 'source_tmpl': 'PadWalker-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RO/ROBIN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RO/ROBIN/'], 'checksums': ['07b26abb841146af32072a8d68cb90176ffb176fd9268e6f2f7d106f817a0cd0'], }), ('Devel::Cycle', '1.12', { 'source_tmpl': 'Devel-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/L/LD/LDS/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/L/LD/LDS/'], 'checksums': ['fd3365c4d898b2b2bddbb78a46d507a18cca8490a290199547dab7f1e7390bc2'], }), ('Test::Memory::Cycle', '1.06', { 'source_tmpl': 'Test-Memory-Cycle-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/P/PE/PETDANCE/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/P/PE/PETDANCE/'], 'checksums': ['9d53ddfdc964cd8454cb0da4c695b6a3ae47b45839291c34cb9d8d1cfaab3202'], }), ('PDF::API2', '2.043', { @@ -1301,12 +1301,12 @@ exts_list = [ }), ('Set::Object', '1.42', { 'source_tmpl': 'Set-Object-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/R/RU/RURBAN/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/R/RU/RURBAN/'], 'checksums': ['d18c5a8a233eabbd0206cf3da5b00fcdd7b37febf12a93dcc3d1c026e6fdec45'], }), ('Heap', '0.80', { 'source_tmpl': 'Heap-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/J/JM/JMM/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/J/JM/JMM/'], 'checksums': ['ccda29f3c93176ad0fdfff4dd6f5e4ac90b370cba4b028386b7343bf64139bde'], }), ('Graph', '0.9725', { @@ -1376,7 +1376,7 @@ exts_list = [ }), ('Variable::Magic', '0.62', { 'source_tmpl': 'Variable-Magic-%(version)s.tar.gz', - 'source_urls': ['https://www.cpan.org/authors/id/V/VP/VPIT/'], + 'source_urls': ['https://cpan.metacpan.org/authors/id/V/VP/VPIT/'], 'checksums': ['3f9a18517e33f006a9c2fc4f43f01b54abfe6ff2eae7322424f31069296b615c'], }), ('B::Hooks::EndOfScope', '0.26', { From 6b3b897fcfa09c66a861fd71c41e229a2e3c4df5 Mon Sep 17 00:00:00 2001 From: easybuild Date: Thu, 10 Nov 2022 13:09:59 +0000 Subject: [PATCH 347/939] adding easyconfigs: Centrifuge-1.0.4-gompi-2021a.eb --- .../Centrifuge-1.0.4-gompi-2021a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb diff --git a/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb new file mode 100644 index 000000000000..d73a84e0a4c9 --- /dev/null +++ b/easybuild/easyconfigs/c/Centrifuge/Centrifuge-1.0.4-gompi-2021a.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'Centrifuge' +version = '1.0.4' + +homepage = 'https://ccb.jhu.edu/software/centrifuge' +description = 'Classifier for metagenomic sequences' + +toolchain = {'name': 'gompi', 'version': '2021a'} +toolchainopts = {'cstd': 'c++11'} + +source_urls = ['https://github.com/DaehwanKimLab/centrifuge/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = [ + '929daed0f84739f7636cc1ea2757527e83373f107107ffeb5937a403ba5201bc', # v1.0.4.tar.gz +] + +dependencies = [ + ('NGS', '2.10.9'), + ('ncbi-vdb', '2.10.9'), +] + +skipsteps = ['configure'] + +buildopts = 'CC="$CC" CPP="$CXX" RELEASE_FLAGS="$CXXFLAGS" ' +buildopts += 'USE_SRA=1 NCBI_NGS_DIR=$EBROOTNGS NCBI_VDB_DIR=$EBROOTNCBIMINUSVDB' + +installopts = "prefix=%(installdir)s" + +fix_perl_shebang_for = ['bin/centrifuge*.pl'] + +sanity_check_paths = { + 'files': ['bin/centrifuge%s' % x for x in ['', '-build', '-build-bin', '-class', '-download', + '-inspect', '-inspect-bin']], + 'dirs': [], +} + +sanity_check_commands = ["centrifuge --help"] + +moduleclass = 'bio' From 41f160ccd11862234a24aa8308ad16c8f36ecfdf Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 14:57:01 +0100 Subject: [PATCH 348/939] Update to version 1.1.3, the last one with the R tarball --- ...021a-R-4.1.0.eb => DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb} | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/d/DAS_Tool/{DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb => DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb} (88%) diff --git a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-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 similarity index 88% rename from easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-foss-2021a-R-4.1.0.eb rename to easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.3-foss-2021a-R-4.1.0.eb index 12a3da124438..8889f759be91 100644 --- a/easybuild/easyconfigs/d/DAS_Tool/DAS_Tool-1.1.1-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 @@ -1,7 +1,7 @@ easyblock = 'Tarball' name = 'DAS_Tool' -version = '1.1.1' +version = '1.1.3' versionsuffix = '-R-%(rver)s' homepage = 'https://github.com/cmks/DAS_Tool' @@ -14,7 +14,7 @@ source_urls = ['https://github.com/cmks/DAS_Tool/archive/'] sources = ['%(version)s.tar.gz'] patches = ['DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch'] checksums = [ - '2a55f67b5331251d8fd5adea867cc341363fbf7fa7ed5c3ce9c7679d8039f03a', # 1.1.1.tar.gz + 'c2d41a38a7a92d53d412ac3f2b8ab5b9fa64c56021aa5c4dd51fefd7c96b68f4', # 1.1.3.tar.gz 'dc89e6ab7129d170d24da28720cec0937b4d958b5ae46049373d57dde8b8a27a', # DAS_Tool-1.1.1-deafaultSearchEngBLAST.patch ] @@ -34,7 +34,7 @@ exts_list = [ 'modulename': 'DASTool', 'source_tmpl': 'DASTool_%(version)s.tar.gz', 'source_urls': ['https://github.com/cmks/DAS_Tool/raw/%(version)s/package/'], - 'checksums': ['8d33997baaaec00d253b2d749cf1ace004ccdea2275b763d4d0f1c969916b72b'], + 'checksums': ['050ba4fa061ceb398a6881652b4b5f14736581a35edd00ef9ae4cea986f38d18'], }), ] From b6783e1df0dcc157bccab2574dd932728a292ba7 Mon Sep 17 00:00:00 2001 From: easybuild Date: Thu, 10 Nov 2022 15:38:01 +0000 Subject: [PATCH 349/939] Fix Perl version in gompi-2021a in ncbi-vdb update --- .../n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb diff --git a/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb new file mode 100644 index 000000000000..aa5ea3306c4d --- /dev/null +++ b/easybuild/easyconfigs/n/ncbi-vdb/ncbi-vdb-2.10.9-gompi-2021a.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'ncbi-vdb' +version = '2.10.9' + +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': '2021a'} + +github_account = 'ncbi' +source_urls = [GITHUB_SOURCE] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] +patches = ['ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch'] +checksums = [ + '3707f81412dbf6ce2b29d3e65e364116c86acc534543e5a084cf8a666b81960d', # ncbi-vdb-2.10.9.tar.gz + 'e8f22dbd0c2e564e296bafdf76ba0e0e2da0d13e22be5aaf322135e5f26eb133', # ncbi-vdb-2.10.7_fix-LD_LIBRARY_PATH.patch +] + +builddependencies = [('Perl', '5.32.1')] + +dependencies = [ + ('NGS', '2.10.9'), + ('file', '5.40'), # provides libmagic + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('bzip2', '1.0.8'), +] + +# add addtional libraries needed to statically link HDF5 from EB +preconfigopts = "sed -i 's/-lhdf5 -Wl,-Bdynamic/-lhdf5 -Wl,-Bdynamic -lmpi -lsz/' setup/konfigure.perl &&" + +configopts = "--build-prefix=%(builddir)s " # change default build directory +configopts += "--with-ngs-sdk-prefix=$EBROOTNGS --with-ngs-java-prefix=$EBROOTNGS/jar/ngs-java.jar " +configopts += "--with-hdf5-prefix=$EBROOTHDF5 --with-xml2-prefix=$EBROOTLIBXML2" + +# replace hardcoded optimization flags with EB settings +prebuildopts = "find build/ -name \"Makefile*\" -exec sed -i 's/-O3/$(EBFLAGS)/g' {} + && EBFLAGS=\"$CFLAGS\" " +preinstallopts = 'EBFLAGS="$CFLAGS" ' + +sanity_check_paths = { + 'files': ['include/ncbi-vdb/NGS.hpp', ('lib/libncbi-ngs-c++.a', 'lib64/libncbi-ngs-c++.a')] + + [('lib/libncbi-%s.%s' % (l, e), 'lib64/libncbi-%s.%s' % (l, e)) + for l in ['vdb', 'wvdb'] for e in ['a', SHLIB_EXT]], + 'dirs': [], +} + +moduleclass = 'bio' From e443f54e1cfd4976395154afd6ce8e69f18b4476 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 16:44:08 +0100 Subject: [PATCH 350/939] Update to last version after fixes on the pypi side --- ...9.2-foss-2021a.eb => python-libsbml-5.19.7-foss-2021a.eb} | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/p/python-libsbml/{python-libsbml-5.19.2-foss-2021a.eb => python-libsbml-5.19.7-foss-2021a.eb} (83%) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb similarity index 83% rename from easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb rename to easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb index ebe73922184f..4fb837dd9a03 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.2-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb @@ -9,7 +9,7 @@ easyblock = 'PythonBundle' name = 'python-libsbml' -version = '5.19.2' +version = '5.19.7' homepage = 'https://sbml.org/' description = """LibSBML Python API.""" @@ -35,11 +35,10 @@ dependencies = [ use_pip = True -# NOTE Use version 5.19.2 because is the last one provided as tarball and not as weird whl exts_list = [ (name, version, { 'modulename': 'libsbml', - 'checksums': ['b11a79a5421abba9f8874ebbc1c479cbdb3c1827697db74b687705632583a0e5'], + 'checksums': ['447b1fde7aceccd11a93dc9f589ffd9319ba854d7b7583f911259a8b0127ab7b'], }), ] From 633254f688e76b47bfdba646d29240aa4541a4f8 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 17:01:26 +0100 Subject: [PATCH 351/939] adding easyconfigs: Nextflow-pipeline-20221110-foss-2021a-mag.eb --- ...xtflow-pipeline-20221110-foss-2021a-mag.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb diff --git a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb new file mode 100644 index 000000000000..d37829af6c2b --- /dev/null +++ b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.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 = 'Bundle' + +name = 'Nextflow-pipeline' +version = '20221110' +versionsuffix = '-mag' + +homepage = 'https://nf-co.re/mag' +description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +# NOTE The long reads sequencing part tools will be added later +dependencies = [ + ('Nextflow', '22.10.1', '', SYSTEM), + ('AdapterRemoval', '2.3.2'), + ('BCFtools', '1.12'), + ('Bowtie2', '2.4.4'), + ('BUSCO', '5.4.2'), + ('CAT-BAT', '5.2.3'), + ('Centrifuge', '1.0.4'), + ('DAS_Tool', '1.1.3', '', ('foss', '2021a-R-4.1.0')), + ('fastp', '0.23.2'), + ('FastQC', '0.11.9', '-Java-11', SYSTEM), + ('freebayes', '1.3.6', '', ('foss', '2021a-R-4.1.0')), + ('GTDB-Tk', '2.0.0'), + ('Kraken2', '2.1.2'), + ('KronaTools', '2.8'), + ('MaxBin', '2.2.7'), + ('MEGAHIT', '1.2.9'), + ('MetaBAT', '2.15'), + ('MultiQC', '1.11'), + ('NanoLyse', '1.2.1'), + ('prodigal', '2.6.3'), + ('prokka', '1.14.5'), + ('PyDamage', '0.70'), + ('QUAST', '5.0.2'), + ('SPAdes', '3.15.3'), +] + +moduleclass = 'bio' From d523a904efe69621d9267ed6d2519dd6fd43f5d4 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 18:30:34 +0100 Subject: [PATCH 352/939] adding easyconfigs: Filtlong-0.2.1-GCC-10.3.0.eb --- .../f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb new file mode 100644 index 000000000000..8ed16b2cc4c2 --- /dev/null +++ b/easybuild/easyconfigs/f/Filtlong/Filtlong-0.2.1-GCC-10.3.0.eb @@ -0,0 +1,39 @@ +# 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 + +easyblock = 'MakeCp' + +name = 'Filtlong' +version = '0.2.1' + +homepage = 'https://github.com/rrwick/Filtlong' +description = """Filtlong is a tool for filtering long reads by quality. It can take a set + of long reads and produce a smaller, better subset. It uses both read length (longer is better) + and read identity (higher is better) when choosing which reads pass the filter""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/rrwick/Filtlong/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e6f47675e87f98cf2481a60bef5cad38396f1e4db653a5c1673139f37770273a'] + +unpack_options = '--strip-components=1' + +parallel = 1 + +dependencies = [ + ('zlib', '1.2.11'), +] + +files_to_copy = ["*"] + +sanity_check_paths = { + 'files': ['bin/filtlong'], + 'dirs': [] +} + +sanity_check_commands = ["filtlong --help"] + +moduleclass = 'bio' From 820ea192af5b7d8eff4735f91552097e21283438 Mon Sep 17 00:00:00 2001 From: Orient Date: Thu, 10 Nov 2022 18:34:21 +0100 Subject: [PATCH 353/939] Sanity check now checks for the exact folder --- .../MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index e048be328cf0..b26dd65738ec 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -103,7 +103,7 @@ exts_list = [ sanity_check_paths = { 'files': [], - 'dirs': ['packages'] + 'dirs': ['packages/%(name)s'] } modextrapaths = { From 9e5bd95f46e0e292c61401b1810f5399b5716558 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Thu, 10 Nov 2022 18:35:04 +0100 Subject: [PATCH 354/939] Add a missing long read part software --- .../Nextflow-pipeline-20221110-foss-2021a-mag.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb index d37829af6c2b..af7cdd8d2972 100644 --- a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb +++ b/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb @@ -17,7 +17,7 @@ description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# NOTE The long reads sequencing part tools will be added later +# TODO The long reads sequencing part tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -29,6 +29,7 @@ dependencies = [ ('DAS_Tool', '1.1.3', '', ('foss', '2021a-R-4.1.0')), ('fastp', '0.23.2'), ('FastQC', '0.11.9', '-Java-11', SYSTEM), + ('Filtlong', '0.2.1'), ('freebayes', '1.3.6', '', ('foss', '2021a-R-4.1.0')), ('GTDB-Tk', '2.0.0'), ('Kraken2', '2.1.2'), From fae36b681c85e52a93d7bada9ffd39c902a7eb8f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 10 Nov 2022 21:06:20 +0100 Subject: [PATCH 355/939] strip out sanity_check_paths from python-libsbml easyconfig, PythonBundle checks by non-empty lib/python*/site-packages by default --- .../p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb index 4fb837dd9a03..04cf6dfe9e03 100644 --- a/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb +++ b/easybuild/easyconfigs/p/python-libsbml/python-libsbml-5.19.7-foss-2021a.eb @@ -42,11 +42,6 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - sanity_pip_check = True moduleclass = 'bio' From 342043332611daa94060ef014943f504a78a909a Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 09:10:51 +0100 Subject: [PATCH 356/939] adding easyconfigs: COBRApy-0.26.0-foss-2021a.eb --- .../c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 98 +++++++++++++++++++ 1 file changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb new file mode 100644 index 000000000000..7cce7c9bf0f7 --- /dev/null +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -0,0 +1,98 @@ +## +# 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 = 'PythonBundle' + +name = 'COBRApy' +version = '0.26.0' + +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': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('ruamel.yaml', '0.17.21'), + ('SciPy-bundle', '2021.05'), + ('sympy', '1.8'), + ('GLPK', '5.0'), + ('python-libsbml', '5.19.7'), +] + +use_pip = True + +exts_list = [ + ('typing-extensions', '4.4.0', { + 'source_tmpl': 'typing_extensions-%(version)s.tar.gz', + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.6.0', { + 'checksums': ['ba3a3775974105c221d31141f2c116f4fd65c5ceb0698657a11e9f295ec93fd0'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('swiglpk', '5.0.8', { + 'checksums': ['9b933d7ba17c619f5d838b6b3216647bcf8a2e22cd67ea89b0f2e2f50f7be0ae'], + }), + ('optlang', '1.6.0', { + 'checksums': ['b503b05e4f434c5c69e4aac90b2dfd3cba9fa8ae24899a9a820017ce1d3d370c'], + }), + ('importlib_resources', '5.10.0', { + 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], + }), + ('rfc3986', '1.5.0', { + 'checksums': ['270aaf10d87d0d4e095063c65bf3ddbc6ee3d0b226328ce21e036f946e421835'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.2', { + 'checksums': ['25ea0d673ae30af41a0c442f81cf3b38c7e79fdc7b60335a4c14e05eb0947421'], + }), + ('h11', '0.12.0', { + 'checksums': ['47222cb6067e4a307d535814917cd98fd0a57b6788ce715755fa2b6c28b56042'], + }), + ('httpcore', '0.15.0', { + 'checksums': ['18b68ab86a3ccf3e7dc0f43598eaddcf472b602aba29f9aa6ab85fe2ada3980b'], + }), + ('httpx', '0.23.0', { + 'checksums': ['f28eac771ec9eb4866d3fb4ab65abd42d38c424739e80c08d8d20570de60b0ef'], + }), + ('diskcache', '5.4.0', { + 'checksums': ['8879eb8c9b4a2509a5e633d2008634fb2b0b35c2b36192d89655dbde02419644'], + }), + # More recent versions of pipdeptree do not provide the same methods + ('pipdeptree', '1.0.0', { + 'checksums': ['5fe866a38113d28d527033ececc57b8e86df86b7c29edbacb33f41ee50f75b31'], + }), + ('versioneer', '0.28', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['11ffc09427ac99db4ce61bdc85785dae819618d0de28153adfce3085956125a8'], + }), + ('depinfo', '1.7.0', { + 'checksums': ['770c82e02f7f1f58c8ff87f8ad132ef3b5f5acbce586b838fadd0eb25b131340'], + }), + ('cobra', version, { + 'checksums': ['4c19ed3a1af8376479cc276b83fb3ceb3a373c75353f4d9d41995c6fe81e03ad'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'bio' From 3ffcba6d152aaf9ca2eb43b09d74aadf93ab696e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 09:50:15 +0100 Subject: [PATCH 357/939] Update bundle package name + Fix sanity_check_paths --- .../nf-core-mag-20221110-foss-2021a.eb} | 16 +++++++++++----- 1 file changed, 11 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/n/{Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb => nf-core-mag/nf-core-mag-20221110-foss-2021a.eb} (78%) diff --git a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb similarity index 78% rename from easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb rename to easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index af7cdd8d2972..ef6918ce6dfd 100644 --- a/easybuild/easyconfigs/n/Nextflow-pipeline/Nextflow-pipeline-20221110-foss-2021a-mag.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -8,16 +8,15 @@ easyblock = 'Bundle' -name = 'Nextflow-pipeline' +name = 'nf-core-mag' version = '20221110' -versionsuffix = '-mag' homepage = 'https://nf-co.re/mag' description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# TODO The long reads sequencing part tools will be added later +# TODO The long reads sequencing part (2) tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -26,11 +25,11 @@ dependencies = [ ('BUSCO', '5.4.2'), ('CAT-BAT', '5.2.3'), ('Centrifuge', '1.0.4'), - ('DAS_Tool', '1.1.3', '', ('foss', '2021a-R-4.1.0')), + ('DAS_Tool', '1.1.3', '-R-4.1.0'), ('fastp', '0.23.2'), ('FastQC', '0.11.9', '-Java-11', SYSTEM), ('Filtlong', '0.2.1'), - ('freebayes', '1.3.6', '', ('foss', '2021a-R-4.1.0')), + ('freebayes', '1.3.6', '-R-4.1.0'), ('GTDB-Tk', '2.0.0'), ('Kraken2', '2.1.2'), ('KronaTools', '2.8'), @@ -46,4 +45,11 @@ dependencies = [ ('SPAdes', '3.15.3'), ] +postinstallcmds = ["echo 'Bundle for the Nextflow pipeline https://nf-co.re/mag' > %(installdir)s/README"] + +sanity_check_paths = { + 'files': ['README'], + 'dirs': [], +} + moduleclass = 'bio' From 677f7d24e4b14f8a0453b0a17402de7d06f78230 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 10:19:56 +0100 Subject: [PATCH 358/939] Use SPAdes version already used in the toolchain --- .../n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index ef6918ce6dfd..2f394f3514e4 100644 --- a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -42,7 +42,7 @@ dependencies = [ ('prokka', '1.14.5'), ('PyDamage', '0.70'), ('QUAST', '5.0.2'), - ('SPAdes', '3.15.3'), + ('SPAdes', '3.13.0'), ] postinstallcmds = ["echo 'Bundle for the Nextflow pipeline https://nf-co.re/mag' > %(installdir)s/README"] From 1201ed530f22a9375fc7f6a6573afc42bd2b7dc1 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 10:44:25 +0100 Subject: [PATCH 359/939] adding easyconfigs: Porechop-0.2.4-GCCcore-10.3.0.eb --- .../Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb new file mode 100644 index 000000000000..066488978191 --- /dev/null +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb @@ -0,0 +1,33 @@ +# 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 + +easyblock = 'PythonPackage' + +name = 'Porechop' +version = '0.2.4' + +homepage = 'https://github.com/rrwick/Porechop' +description = """Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. + Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, + it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments + to effectively find adapters, even at low sequence identity""" + +toolchain = {'name': 'GCCcore', 'version': '10.3.0'} + +source_urls = ['https://github.com/rrwick/Porechop/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] + +dependencies = [ + ('Python', '3.9.5'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 2043a13a426aa1d8fd61052c72c9710e986dfc09 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Fri, 11 Nov 2022 11:00:31 +0100 Subject: [PATCH 360/939] Add missing binutils --- .../easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb index 066488978191..b637b6577632 100644 --- a/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/Porechop/Porechop-0.2.4-GCCcore-10.3.0.eb @@ -20,6 +20,10 @@ source_urls = ['https://github.com/rrwick/Porechop/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['44b499157d933be43f702cec198d1d693dcb9276e3c545669be63c2612493299'] +builddependencies = [ + ('binutils', '2.36.1'), +] + dependencies = [ ('Python', '3.9.5'), ] From 411efa84f07ffcf24aeae0446ead03fd5a66be93 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 11 Nov 2022 11:27:59 +0100 Subject: [PATCH 361/939] adding easyconfigs: Blender-3.3.1.eb --- .../easyconfigs/b/Blender/Blender-3.3.1.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb new file mode 100644 index 000000000000..71c7f00f840d --- /dev/null +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb @@ -0,0 +1,38 @@ +# EasyConfig based on the official Blender binaries, which should work +# on any system that has glibc >= 2.17. As the main binary is statically +# linked and includes a Python interpreter no other dependencies should +# be necessary +easyblock = 'PackedBinary' + +name = 'Blender' +version = '3.3.1' +versionsuffix = '' + +homepage = 'https://www.blender.org/' +description = """Blender is the free and open source 3D creation suite. It supports + the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, + compositing and motion tracking, even video editing and game creation.""" + +toolchain = {'name': 'system', 'version': ''} + +sources = ['blender-%(version)s-linux-x64.tar.xz'] +source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/'] +patches = [] +checksums = [ + '3089a485dd621785d7a702089aba72d07b8f733a362e901ec1449b9a379546f2' +] + +builddependencies = [] + +dependencies = [] + +sanity_check_paths = { + 'files': ['blender', 'blender-softwaregl'], + 'dirs': ['3.3'] +} + +#modextrapaths = { +# 'PATH' : '', +#} + +moduleclass = 'vis' From df9c497e8bb289ca7677ca4772bb237f6a3d41a5 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 11 Nov 2022 11:40:43 +0100 Subject: [PATCH 362/939] Clean up comments --- easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb | 8 -------- 1 file changed, 8 deletions(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb index 71c7f00f840d..fdfe525853e9 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb @@ -1,7 +1,3 @@ -# EasyConfig based on the official Blender binaries, which should work -# on any system that has glibc >= 2.17. As the main binary is statically -# linked and includes a Python interpreter no other dependencies should -# be necessary easyblock = 'PackedBinary' name = 'Blender' @@ -31,8 +27,4 @@ sanity_check_paths = { 'dirs': ['3.3'] } -#modextrapaths = { -# 'PATH' : '', -#} - moduleclass = 'vis' From 0506670629eeba206d73315aa85ce65e000d0cd3 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Fri, 11 Nov 2022 12:08:27 +0100 Subject: [PATCH 363/939] Add CUDA as depedency --- easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb index fdfe525853e9..7669c41af2be 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb @@ -20,7 +20,9 @@ checksums = [ builddependencies = [] -dependencies = [] +dependencies = [ + ('CUDA', '11.7.0') +] sanity_check_paths = { 'files': ['blender', 'blender-softwaregl'], From 94bb82b0263edae500c8a5f18340d6911d15e914 Mon Sep 17 00:00:00 2001 From: Bart Oldeman Date: Fri, 11 Nov 2022 16:34:14 +0000 Subject: [PATCH 364/939] Adjust disable-fma-in-cscal-zscal.patch for GCC 12 For some reason (GCC bug report pending) -ffp-contract=off is not sufficient for GCC 12, so we also need -mno-fma, implemented via a GCC pragma. --- .../o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0.eb | 6 +- ...CC-12.2.0_disable-fma-in-cscal-zscal.patch | 73 +++++++++++++++++++ 2 files changed, 76 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.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 eee3ebc9454a..b0244cb98cef 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 @@ -17,7 +17,7 @@ patches = [ ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', 'OpenBLAS-0.3.21_fix-order-vectorization.patch', - 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch', 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ @@ -28,8 +28,8 @@ checksums = [ 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, {'OpenBLAS-0.3.21_fix-order-vectorization.patch': '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, - {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': - 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'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'}, ] diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch new file mode 100644 index 000000000000..ff665e1300d8 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.21-GCC-12.2.0_disable-fma-in-cscal-zscal.patch @@ -0,0 +1,73 @@ +From e7e3aa29482281edba46a27fcd452d7ed630f46a Mon Sep 17 00:00:00 2001 +From: Bart Oldeman +Date: Thu, 27 Oct 2022 17:20:44 -0400 +Subject: [PATCH] x86_64: prevent GCC and Clang from generating FMAs in + cscal/zscal. + +If e.g. -march=haswell is set in CFLAGS, GCC generates FMAs by default, which +is inconsistent with the microkernels, none of which use FMAs. These +inconsistencies cause a few failures in the LAPACK testcases, where +eigenvalue results with/without eigenvectors are compared. + +Moreover using FMAs for multiplication of complex numbers can give surprising +results, see 22aa81f for more information. + +This uses the same syntax as used in 22aa81f for zarch (s390x). + +Edit: 2022-11-11: add no-fma target since fp-contract=off isn't sufficient for +GCC 12.2. +--- + kernel/x86_64/cscal.c | 14 +++++++++++++ + kernel/x86_64/zscal.c | 14 +++++++++++++ + 2 files changed, 28 insertions(+) + +diff --git a/kernel/x86_64/cscal.c b/kernel/x86_64/cscal.c +index dc3f688c69..6ae66d9731 100644 +--- a/kernel/x86_64/cscal.c ++++ b/kernel/x86_64/cscal.c +@@ -25,6 +25,20 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#pragma GCC target ("no-fma") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + +diff --git a/kernel/x86_64/zscal.c b/kernel/x86_64/zscal.c +index 3744c98bb7..dfdb4230b6 100644 +--- a/kernel/x86_64/zscal.c ++++ b/kernel/x86_64/zscal.c +@@ -25,6 +25,20 @@ OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE + USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + *****************************************************************************/ + ++/* ++ * Avoid contraction of floating point operations, specifically fused ++ * multiply-add, because they can cause unexpected results in complex ++ * multiplication. ++ */ ++#if defined(__GNUC__) && !defined(__clang__) ++#pragma GCC optimize ("fp-contract=off") ++#pragma GCC target ("no-fma") ++#endif ++ ++#if defined(__clang__) ++#pragma clang fp contract(off) ++#endif ++ + #include "common.h" + + From 984f088a26a28517e2f3979ed8f1328cef4b9d35 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 11 Nov 2022 17:42:25 +0000 Subject: [PATCH 365/939] adding easyconfigs: MITgcmutils-0.1.2-foss-2022a.eb --- .../MITgcmutils-0.1.2-foss-2022a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb new file mode 100644 index 000000000000..4459e4473f38 --- /dev/null +++ b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb @@ -0,0 +1,46 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'MITgcmutils' +version = '0.1.2' + +homepage = 'https://mitgcm.org/' +description = """A numerical model designed for study of the atmosphere, ocean, +and climate, MITgcm’s flexible non-hydrostatic formulation enables it to +efficiently simulate fluid phenomena over a wide range of scales; its adjoint +capabilities enable it to be applied to sensitivity questions and to parameter +and state estimation problems. By employing fluid equation isomorphisms, a +single dynamical kernel can be used to simulate flow of both the atmosphere +and ocean. The model is developed to perform efficiently on a wide variety of +computational platforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('tqdm', '4.64.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['5f15e0ad7a1e2451532facd3e83e8a0a2cea41d5c04df8272c4d31780e28ab2d'], + 'sources': ['%(name)s-%(version)s.tar.gz'], + 'modulename': 'MITgcmutils', + }), +] + +sanity_check_paths = { + 'files': ['bin/gluemncbig'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "gluemncbig --help", +] + +moduleclass = 'geo' From 769aeff75110baf1235fe12cb7848ba33ce3057b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 17:30:32 +0100 Subject: [PATCH 366/939] avoid that zlib + htslib are downloaded and built during installation of MetaBAT --- .../m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb | 7 ++-- .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 7 ++-- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 8 +++-- .../m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 7 ++-- .../m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch | 35 +++++++++++++++++++ 5 files changed, 56 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb index 7746c998d4c7..a40c2edb844a 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'gompi', 'version': '2019a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = [ 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2', # v2.14.tar.gz ] @@ -35,9 +36,11 @@ dependencies = [ ('bzip2', '1.0.6'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index 827c80520e1b..d8416cf32df9 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -29,9 +30,11 @@ dependencies = [ ('bzip2', '1.0.8'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index a94f4f9953a4..6ad2548c41fd 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -26,11 +27,14 @@ dependencies = [ ('SAMtools', '1.13'), ('XZ', '5.2.5'), ('bzip2', '1.0.8'), + ('zlib', '1.2.11'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 3a2f07771f63..670e4554b366 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -10,6 +10,7 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] +patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] builddependencies = [ @@ -28,9 +29,11 @@ dependencies = [ ('bzip2', '1.0.8'), ] -fix_perl_shebang_for = ['bin/*.pl'] +configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' +# SAMtools's libhts.a requires additional libraries like cURL to be linked +configopts += '-DCMAKE_EXE_LINKER_FLAGS_RELEASE="-lcurl -llzma -lbz2 -lssl -lcrypto" ' -prebuildopts = "cp -a $EBROOTSAMTOOLS samtools && " +fix_perl_shebang_for = ['bin/*.pl'] sanity_check_paths = { 'files': ['bin/aggregateBinDepths.pl', 'bin/aggregateContigOverlapsByBin.pl', 'bin/metabat', 'bin/metabat2'], diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch new file mode 100644 index 000000000000..9914848cdc07 --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_zlib-htslib.patch @@ -0,0 +1,35 @@ +avoid downloading and building of zlib and htslib, since they're provided as dependencies by EasyBuild +author: Kenneth Hoste (HPC-UGent) +--- berkeleylab-metabat-0db17a40717d/CMakeLists.txt.orig 2022-11-11 12:11:10.473978638 +0000 ++++ berkeleylab-metabat-0db17a40717d/CMakeLists.txt 2022-11-11 12:12:34.246072148 +0000 +@@ -8,8 +8,8 @@ + message("Installing ${CMAKE_BUILD_TYPE} MetaBAT into ${CMAKE_INSTALL_PREFIX}") + + include(${CMAKE_ROOT}/Modules/ExternalProject.cmake) +-include(cmake/zlib.cmake) +-include(cmake/htslib.cmake) ++set(zlib_LIB ${ZLIB_LIBRARY}) ++set(htslib_LIB ${HTSLIB_LIBRARY}) + + set(CMAKE_CXX_STANDARD 11) + set(CMAKE_CXX_STANDARD_REQUIRED ON) +--- berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt.orig 2022-11-11 12:23:52.313823937 +0000 ++++ berkeleylab-metabat-0db17a40717d/src/CMakeLists.txt 2022-11-11 12:24:18.424465217 +0000 +@@ -36,7 +36,7 @@ + foreach(target ${targets}) + + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) ++ add_dependencies(${target} check_git_repository) + target_link_libraries(${target} ${zlib_LIB} ${Boost_LIBRARIES} ${EXTRALIBS} ) + + endforeach() +@@ -48,7 +48,7 @@ + set(targets jgi_summarize_bam_contig_depths contigOverlaps) + foreach(target ${targets}) + add_executable(${target} ${target}.cpp) +- add_dependencies(${target} htslib zlib check_git_repository) ++ add_dependencies(${target} check_git_repository) + target_link_libraries(${target} ${htslib_LIB} ${zlib_LIB} ${Boost_LIBRARIES} ) + endforeach() + From 417104a83c72d19e3c91bf1101521ff57d57b4d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 18:10:03 +0100 Subject: [PATCH 367/939] add checksum for MetaBAT patch --- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb | 3 ++- .../m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 5 ++++- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 5 ++++- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 5 ++++- 4 files changed, 14 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb index a40c2edb844a..d906664f6db3 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.14-gompi-2019a.eb @@ -16,7 +16,8 @@ source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] checksums = [ - 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2', # v2.14.tar.gz + {'v2.14.tar.gz': 'd43d5e91afa8f2d211a913739127884669516bfbed870760597fcee2b513abe2'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, ] multi_deps = {'Python': ['3.7.2', '2.7.15']} diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index d8416cf32df9..de5256648329 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -12,7 +12,10 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.35'), diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index 6ad2548c41fd..5c65ffd3edda 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.36.1'), diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index 670e4554b366..ef62c68ea781 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -11,7 +11,10 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] patches = ['MetaBAT-2.15_zlib-htslib.patch'] -checksums = ['550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'] +checksums = [ + {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, + {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, +] builddependencies = [ ('binutils', '2.37'), From b6a4a54e13289acabe9a2b2bfc897082a1cfcf8d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 19:44:39 +0100 Subject: [PATCH 368/939] remove duplicate zlib dependency in MetaBAT easyconfig --- easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index 5c65ffd3edda..a552166e24f2 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -30,7 +30,6 @@ dependencies = [ ('SAMtools', '1.13'), ('XZ', '5.2.5'), ('bzip2', '1.0.8'), - ('zlib', '1.2.11'), ] configopts = '-DZLIB_LIBRARY="$EBROOTZLIB/lib/libz.a" -DHTSLIB_LIBRARY="$EBROOTSAMTOOLS/lib/libhts.a" ' From cfe4dd28c0745b9c39dbb3ad52f6d999df63a780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:39:25 +0100 Subject: [PATCH 369/939] adding easyconfigs: Python-2.7.18-GCCcore-12.2.0-bare.eb --- .../Python-2.7.18-GCCcore-12.2.0-bare.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb diff --git a/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb new file mode 100644 index 000000000000..f8c443163d48 --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-2.7.18-GCCcore-12.2.0-bare.eb @@ -0,0 +1,32 @@ +name = 'Python' +version = '2.7.18' +versionsuffix = '-bare' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['da3080e3b488f648a3d7a4560ddee895284c3380b11d6de75edb986526b9a814'] + +builddependencies = [ + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +moduleclass = 'lang' From c058550aa3096feff13dad0032c03fafa0353539 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:39:36 +0100 Subject: [PATCH 370/939] adding easyconfigs: Ninja-1.11.1-GCCcore-12.2.0.eb --- .../n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e6cefd164e7f --- /dev/null +++ b/easybuild/easyconfigs/n/Ninja/Ninja-1.11.1-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'CmdCp' + +name = 'Ninja' +version = '1.11.1' + +homepage = 'https://ninja-build.org/' +description = "Ninja is a small build system with a focus on speed." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/ninja-build/ninja/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['31747ae633213f1eda3842686f83c2aa1412e0f5691d1c14dbbcc67fe7400cea'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +cmds_map = [('.*', "./configure.py --bootstrap")] + +files_to_copy = [(['ninja'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/ninja'], + 'dirs': [], +} + +sanity_check_commands = ["ninja --version"] + +moduleclass = 'tools' From 308e86a4dc784296d2b8ab229053dece648d25bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:41:58 +0100 Subject: [PATCH 371/939] adding easyconfigs: GMP-6.2.1-GCCcore-12.2.0.eb --- .../g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..8d18902ab40d --- /dev/null +++ b/easybuild/easyconfigs/g/GMP/GMP-6.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'GMP' +version = '6.2.1' + +homepage = 'https://gmplib.org/' +description = """ + GMP is a free library for arbitrary precision arithmetic, operating on signed + integers, rational numbers, and floating point numbers. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'precise': True, 'pic': True} + +source_urls = ['https://ftp.gnu.org/gnu/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['eae9326beb4158c386e39a356818031bd28f3124cf915f8c5b1dc4c7a36b4d7c'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), +] + +# enable C++ interface +configopts = '--enable-cxx' + +# copy libgmp.so* to /lib to make sure that it is picked up by tests +# when EasyBuild is configured with --rpath, and clean up afterwards (let 'make install' do its job) +pretestopts = "mkdir -p %%(installdir)s/lib && cp -a .libs/libgmp.%s* %%(installdir)s/lib && " % SHLIB_EXT +testopts = " && rm -r %(installdir)s/lib" + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (l, e) for l in ['gmp', 'gmpxx'] for e in [SHLIB_EXT, 'a']] + + ['include/gmp.h', 'include/gmpxx.h'], + 'dirs': ['share'], +} + +moduleclass = 'math' From d4066666ae8b2a9c03a5be3c9ea6003233b5c06e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:45:21 +0100 Subject: [PATCH 372/939] adding easyconfigs: gettext-0.21.1-GCCcore-12.2.0.eb --- .../gettext/gettext-0.21.1-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a7ad515633fc --- /dev/null +++ b/easybuild/easyconfigs/g/gettext/gettext-0.21.1-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'gettext' +version = '0.21.1' + +homepage = 'https://www.gnu.org/software/gettext/' +description = """GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may +build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools +and documentation""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['e8c3650e1d8cee875c4f355642382c1df83058bd5a11ee8555c0cf276d646d45'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('libxml2', '2.10.3'), + ('ncurses', '6.3'), +] + +configopts = '--without-emacs --with-libxml2-prefix=$EBROOTLIBXML2' + +sanity_check_paths = { + 'files': ['bin/gettext', 'lib/libasprintf.a', 'lib/libasprintf.%s' % SHLIB_EXT, + 'lib/libgettextpo.a', 'lib/libgettextpo.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = [ + "gettext --help", + "msginit --help", +] + +moduleclass = 'tools' From 5d1c5cfe5d37610f8848161c87e052cf33263eea Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:45:33 +0100 Subject: [PATCH 373/939] adding easyconfigs: git-2.38.1-GCCcore-12.2.0-nodocs.eb --- .../g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb diff --git a/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb new file mode 100644 index 000000000000..7760dcfd6bd5 --- /dev/null +++ b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb @@ -0,0 +1,47 @@ +## +# Author: Robert Mijakovic +## +# updated to 2.33.1 +# J. Sassmannshausen / GSTT + +easyblock = 'ConfigureMake' + +name = 'git' +version = '2.38.1' +versionsuffix = '-nodocs' + +homepage = 'https://git-scm.com' +description = """Git is a free and open source distributed version control system designed +to handle everything from small to very large projects with speed and efficiency.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/git/git/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['91456b031324f7909f35e067dcfb907956d1a5c3d2069cfc5b4549e42089e546'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('cURL', '7.86.0'), + ('expat', '2.4.9'), + ('gettext', '0.21.1'), + ('Perl', '5.36.0'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +preconfigopts = 'make configure && ' + +# Work around git build system bug. If LIBS contains -lpthread, then configure +# will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. +configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" + +sanity_check_paths = { + 'files': ['bin/git'], + 'dirs': ['libexec/git-core', 'share'], +} + +moduleclass = 'tools' From 6b678b7965f224d22583846ef4afa0f505c71d03 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 20:55:20 +0100 Subject: [PATCH 374/939] adding easyconfigs: libpng-1.6.38-GCCcore-12.2.0.eb --- .../l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..c3a6b1c33876 --- /dev/null +++ b/easybuild/easyconfigs/l/libpng/libpng-1.6.38-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'libpng' +version = '1.6.38' + +homepage = 'http://www.libpng.org/pub/png/libpng.html' + +description = "libpng is the official PNG reference library" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e2b5e1b4329650992c041996cf1269681b341191dc07ffed816c555769cceb77'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('zlib', '1.2.12')] + +local_majminver = '%(version_major)s%(version_minor)s' + +sanity_check_paths = { + 'files': ['include/pngconf.h', 'include/png.h', 'include/pnglibconf.h', + 'lib/libpng.a', 'lib/libpng.%s' % SHLIB_EXT, + 'lib/libpng%s.a' % local_majminver, + 'lib/libpng%s.%s' % (local_majminver, SHLIB_EXT)], + 'dirs': ['bin', 'include/libpng%s' % local_majminver, 'share/man'], +} + +moduleclass = 'lib' From 9b05a53e14a92631d2f30667058f21e5f866908a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sat, 12 Nov 2022 21:29:25 +0100 Subject: [PATCH 375/939] adding easyconfigs: Rust-1.65.0-GCCcore-12.2.0.eb --- .../r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..757f1d6d4bf4 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-12.2.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.65.0' + +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-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.65.0-src.tar.gz': '5828bb67f677eabf8c384020582b0ce7af884e1c84389484f7f8d00dd82c0038'}, + {'Rust-1.60_sysroot-fix-interpreter.patch': 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), + ('Python', '3.10.8', '-bare'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From cbb0c9c3e4a057557cc1edc382a421fae6d4e1d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2022 17:25:15 +0100 Subject: [PATCH 376/939] adding easyconfigs: Python-3.10.8-GCCcore-12.2.0.eb --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 510 ++++++++++++++++++ 1 file changed, 510 insertions(+) create mode 100644 easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f0bca199736c --- /dev/null +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -0,0 +1,510 @@ +name = 'Python' +version = '3.10.8' + +homepage = 'https://python.org/' +description = """Python is a programming language that lets you work more quickly and integrate your systems + more effectively.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.python.org/ftp/%(namelower)s/%(version)s/'] +sources = [SOURCE_TGZ] +checksums = ['f400c3fb394b8bef1292f6dc1292c5fadc3533039a5bc0c3e885f3e16738029a'] + +builddependencies = [ + ('UnZip', '6.0'), + ('Rust', '1.65.0'), # required for setuptools-rust, which is needed for cryptography + ('pkgconf', '1.9.3'), + ('git', '2.38.1', '-nodocs'), # required for pbr +] + +dependencies = [ + ('binutils', '2.39'), + ('bzip2', '1.0.8'), # required for bz2 package in Python stdlib + ('zlib', '1.2.12'), + ('libreadline', '8.2'), + ('ncurses', '6.3'), + ('SQLite', '3.39.4'), + ('XZ', '5.2.7'), + ('GMP', '6.2.1'), # required for pycrypto + ('libffi', '3.4.4'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +install_pip = True + +exts_default_options = { + 'download_dep_fail': True, + 'sanity_pip_check': True, + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, +} + +# order is important! +# package versions updated 12 Nov 2022 +exts_list = [ + ('wheel', '0.38.4', { + 'checksums': ['965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac'], + }), + ('setuptools', '65.5.1', { + 'checksums': ['e197a19aa8ec9722928f2206f8de752def0e4c9fc6953527360d1c36d94ddb2f'], + }), + ('pip', '22.3.1', { + 'checksums': ['65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38'], + }), + ('blist', '1.3.6', { + 'patches': [ + 'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch', + 'Python-3.10-bist-1.3.6-compatibility.patch', + ], + 'checksums': [ + {'blist-1.3.6.tar.gz': '3a12c450b001bdf895b30ae818d4d6d3f1552096b8c995f0fe0c74bef04d1fc3'}, + {'Python-3_9-blist-1.3.6-fix-undefined_symbol_PyObject_GC_IS_TRACKED.patch': + '18a643d1d1565b05df7dcc9a612a86dcf7b3b352435032f6425a61b597f911d0'}, + {'Python-3.10-bist-1.3.6-compatibility.patch': + '0fb2d92e06b2c39bfc79e229e6fde6053f9aa9538733029377c9a743650a4741'}, + ], + }), + ('pbr', '5.11.0', { + 'checksums': ['b97bc6695b2aff02144133c2e7399d5885223d42b7912ffaec2ca3898e673bfe'], + }), + ('Cython', '0.29.32', { + 'checksums': ['8733cf4758b79304f2a4e39ebfac5e92341bce47bcceb26c1254398b2f8c1af7'], + }), + ('six', '1.16.0', { + 'checksums': ['1e61c37477a1626458e36f7b1d82aa5c9b094fa4802892072e49de9c60c4c926'], + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('flit-core', '3.8.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + 'checksums': 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+ }), + ('sphinxcontrib-qthelp', '1.0.3', { + 'modulename': 'sphinxcontrib.qthelp', + 'checksums': ['4c33767ee058b70dba89a6fc5c1892c0d57a54be67ddd3e7875a18d14cba5a72'], + }), + ('Babel', '2.11.0', { + 'checksums': ['5ef4b3226b0180dedded4229651c8b0e1a3a6a2837d45a073272f313e4cf97f6'], + }), + ('Sphinx', '5.3.0', { + 'checksums': ['51026de0a9ff9fc13c05d74913ad66047e104f56a129ff73e174eb5c3ee794b5'], + }), + ('sphinx-bootstrap-theme', '0.8.1', { + 'checksums': ['683e3b735448dadd0149f76edecf95ff4bd9157787e9e77e0d048ca6f1d680df'], + }), + ('click', '8.1.3', { + 'checksums': ['7682dc8afb30297001674575ea00d1814d808d6a36af415a82bd481d37ba7b8e'], + }), + ('psutil', '5.9.4', { + 'checksums': ['3d7f9739eb435d4b1338944abe23f49584bde5395f27487d2ee25ad9a8774a62'], + }), + ('future', '0.18.2', { + 'checksums': ['b1bead90b70cf6ec3f0710ae53a525360fa360d306a86583adc6bf83a4db537d'], + }), + ('sortedcontainers', '2.4.0', { + 'checksums': ['25caa5a06cc30b6b83d11423433f65d1f9d76c4c6a0c90e3379eaa43b9bfdb88'], + }), + ('intervaltree', '3.1.0', { + 'checksums': ['902b1b88936918f9b2a19e0e5eb7ccb430ae45cde4f39ea4b36932920d33952d'], + }), + ('pytoml', '0.1.21', { + 'checksums': ['8eecf7c8d0adcff3b375b09fe403407aa9b645c499e5ab8cac670ac4a35f61e7'], + }), + ('zipfile36', '0.1.3', { + 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], + }), + ('tomli-w', '1.0.0', { + 'sources': ['tomli_w-%(version)s.tar.gz'], + 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], + }), + ('flit', '3.8.0', { + 'checksums': ['d0f2a8f4bd45dc794befbf5839ecc0fd3830d65a57bd52b5997542fac5d5e937'], + }), + ('regex', '2022.10.31', { + 'checksums': ['a3a98921da9a1bf8457aeee6a551948a83601689e5ecdd736894ea9bbec77e83'], + }), + ('intreehooks', '1.0', { + 'checksums': ['87e600d3b16b97ed219c078681260639e77ef5a17c0e0dbdd5a302f99b4e34e1'], + }), + ('pylev', '1.4.0', { + 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], + }), + ('pastel', '0.2.1', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], + }), + ('crashtest', '0.3.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], + }), + ('clikit', '0.6.2', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], + }), + ('jeepney', '0.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], + }), + ('SecretStorage', '3.3.3', { + 'checksums': ['2403533ef369eca6d2ba81718576c5e0f564d5cca1b58f73a8b23e7d4eeebd77'], + }), + ('keyring', '23.11.0', { + 'modulename': False, + 'checksums': ['ad192263e2cdd5f12875dedc2da13534359a7e760e77f8d04b50968a821c2361'], + }), + ('jaraco.classes', '3.2.3', { + 'checksums': ['89559fa5c1d3c34eff6f631ad80bb21f378dbcbb35dd161fd2c6b93f5be2f98a'], + }), + ('keyrings.alt', '4.2.0', { + 'modulename': False, + 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], + }), + ('tomlkit', '0.11.6', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], + }), + ('shellingham', '1.5.0', { + 'checksums': ['72fb7f5c63103ca2cb91b23dee0c71fe8ad6fbfd46418ef17dbe40db51592dad'], + }), + ('requests-toolbelt', '0.9.1', { + 'checksums': ['968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0'], + }), + ('pyrsistent', '0.19.2', { + 'checksums': ['bfa0351be89c9fcbcb8c9879b826f4353be10f58f8a677efab0c017bf7137ec2'], + }), + ('pkginfo', '1.8.3', { + 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], + }), + ('ptyprocess', '0.7.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], + }), + ('pexpect', '4.8.0', { + 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], + }), + ('hatch-fancy-pypi-readme', '22.8.0', { + 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], + 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], + }), + ('jsonschema', '4.17.0', { + 'checksums': ['5bfcf2bca16a087ade17e02b282d34af7ccd749ef76241e7f9bd7c0cb8a9424d'], + }), + ('simplejson', '3.17.6', { + 'checksums': ['cf98038d2abf63a1ada5730e91e84c642ba6c225b0198c3684151b1f80c5f8a6'], + }), + ('webencodings', '0.5.1', { + 'checksums': ['b36a1c245f2d304965eb4e0a82848379241dc04b865afcc4aab16748587e1923'], + }), + ('html5lib', '1.1', { + 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], + }), + ('cleo', '1.0.0a5', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], + }), + ('cachy', '0.3.0', { + 'checksums': ['186581f4ceb42a0bbe040c407da73c14092379b1e4c0e327fdb72ae4a9b269b1'], + }), + ('msgpack', '1.0.4', { + 'checksums': ['f5d869c18f030202eb412f08b28d2afeea553d6613aee89e200d7aca7ef01f5f'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('poetry-core', '1.3.2', { + 'modulename': 'poetry.core', + 'checksums': ['0ab006a40cb38d6a38b97264f6835da2f08a96912f2728ce668e9ac6a34f686f'], + }), + ('glob2', '0.7', { + 'checksums': ['85c3dbd07c8aa26d63d7aacee34fa86e9a91a3873bc30bf62ec46e531f92ab8c'], + }), + ('dulwich', '0.20.50', { + 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], + }), + ('poetry-plugin-export', '1.2.0', { + 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], + }), + ('poetry', '1.2.2', { + 'checksums': ['6d9ed0b1b826a0a79190f2078d7d78483fa24bf2494f3b170e354eaa5e7b5ea1'], + }), + ('fsspec', '2022.11.0', { + 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], + }), + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + ('simplegeneric', '0.8.1', { + 'source_tmpl': 'simplegeneric-%(version)s.zip', + 'checksums': ['dc972e06094b9af5b855b3df4a646395e43d1c9d0d39ed345b7393560d0b9173'], + }), +] + +moduleclass = 'lang' From f67e8904af10fc8f97f28f3099d48e6275948ae1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 13 Nov 2022 17:53:44 +0100 Subject: [PATCH 377/939] add patch to fix installation of MetaBAT 2.15 on aarch64 --- .../MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb | 6 +++- .../m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch | 31 +++++++++++++++++++ 4 files changed, 46 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb index de5256648329..0852b759a008 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2020b-Python-2.7.18.eb @@ -11,10 +11,14 @@ toolchain = {'name': 'gompi', 'version': '2020b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb index a552166e24f2..dc2afdaad6f7 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021a.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'gompi', 'version': '2021a'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb index ef62c68ea781..3ffd2f882775 100644 --- a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15-gompi-2021b.eb @@ -10,10 +10,14 @@ toolchain = {'name': 'gompi', 'version': '2021b'} source_urls = ['https://bitbucket.org/berkeleylab/metabat/get/'] sources = ['v%(version)s.tar.gz'] -patches = ['MetaBAT-2.15_zlib-htslib.patch'] +patches = [ + 'MetaBAT-2.15_zlib-htslib.patch', + 'MetaBAT-2.15_fix-aarch64.patch', +] checksums = [ {'v2.15.tar.gz': '550487b66ec9b3bc53edf513d00c9deda594a584f53802165f037bde29b4d34e'}, {'MetaBAT-2.15_zlib-htslib.patch': 'f03b8d5717958df3e23dc6905155663b388ad330ec16eab546133d9cceeb5e77'}, + {'MetaBAT-2.15_fix-aarch64.patch': '061b43d6c0ac4a9acf3bd7cf3c62efc856661993a61e7d4652ed68aafb7aa7af'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch new file mode 100644 index 000000000000..b3029a247bff --- /dev/null +++ b/easybuild/easyconfigs/m/MetaBAT/MetaBAT-2.15_fix-aarch64.patch @@ -0,0 +1,31 @@ +fixes "error: impossible constraint in asm" when building on aarch64/amr64 +see https://bitbucket.org/berkeleylab/metabat/issues/151 +From a01eafa174e01f6a46ef71b63daa7695d2c3834e Mon Sep 17 00:00:00 2001 +From: Rob Egan +Date: Mon, 26 Sep 2022 09:19:32 -0700 +Subject: [PATCH] removed unused function using assembly types + +--- + src/metabat2.h | 6 ------ + 1 file changed, 6 deletions(-) + +diff --git a/src/metabat2.h b/src/metabat2.h +index b1cb5d3..7accc1a 100644 +--- a/src/metabat2.h ++++ b/src/metabat2.h +@@ -258,12 +258,6 @@ public: + + void gen_tnf_graph(Graph& g, Similarity cutoff); + +-unsigned long long rdtsc() { +- unsigned int lo, hi; +- __asm__ __volatile__ ("rdtsc" : "=a" (lo), "=d" (hi)); +- return ((unsigned long long) hi << 32) | lo; +-} +- + static void trim_fasta_label(std::string &label) { + size_t pos = label.find_first_of(" \t"); + if (pos != std::string::npos) +-- +2.38.1 + From 74a363dc9bb8126ba79a85f38bbca34ed71d2365 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 09:39:37 +0100 Subject: [PATCH 378/939] Fix DIAMOND duplicate choice in the foss-2021a toolchain --- easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb index 12d6688ec5a8..5ff808c82d1b 100644 --- a/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/c/CAT-BAT/CAT-BAT-5.2.3-GCC-10.3.0.eb @@ -23,7 +23,7 @@ checksums = ['19a8eb28c0ebd3fc5a04b006d305a916dd1af00a32b70d2f30df35f32ca2929b'] dependencies = [ ('Python', '3.9.5'), - ('DIAMOND', '2.0.13'), + ('DIAMOND', '2.0.11'), ('prodigal', '2.6.3'), ] From 63eeebd063e2da748b043d0f1db1cac6af62b2af Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Mon, 14 Nov 2022 10:52:16 +0000 Subject: [PATCH 379/939] Add ROntoTools extension to Bioconductor bundle --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index d34e406d5d8e..43c53a701843 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1095,6 +1095,9 @@ exts_list = [ ('HiCcompare', '1.18.0', { 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], }), + ('ROntoTools', '2.24.0', { + 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 6f6478bc51b997eef54222864da8107f2698ff48 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 14 Nov 2022 14:01:50 +0000 Subject: [PATCH 380/939] adding easyconfigs: xmitgcm-0.5.2-foss-2022a.eb --- .../x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb new file mode 100644 index 000000000000..aeac427c9c57 --- /dev/null +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -0,0 +1,41 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'xmitgcm' +version = '0.5.2' + +homepage = 'https://github.com/MITgcm/xmitgcm' +description = """xmitgcm is a python package for reading MITgcm binary +MDS files into xarray data structures. By storing data in dask arrays, +xmitgcm enables parallel, out-of-core analysis of MITgcm output data.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('MITgcmutils', '0.1.2'), + ('dask', '2022.10.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cachetools', '5.2.0', { + 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], + }), + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + (name, version, { + 'checksums': ['7dda45fdf6182a859f5c441cd5928a7c99d41c8bcea9fccf471b7011791b1131'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From ca10418869f217d7788ffe405fa8add40505dd1b Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 15:05:55 +0100 Subject: [PATCH 381/939] Add another long read missing tool --- .../n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index 2f394f3514e4..9699267036a4 100644 --- a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -16,7 +16,7 @@ description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# TODO The long reads sequencing part (2) tools will be added later +# TODO The long reads sequencing part (1 missing) tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -38,6 +38,7 @@ dependencies = [ ('MetaBAT', '2.15'), ('MultiQC', '1.11'), ('NanoLyse', '1.2.1'), + ('Porechop', '0.2.4'), ('prodigal', '2.6.3'), ('prokka', '1.14.5'), ('PyDamage', '0.70'), From e2a48ad045d3f29e3cf5d23f371f553569013015 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 14 Nov 2022 15:16:34 +0100 Subject: [PATCH 382/939] Add SWIG as missing requirement --- easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb index 7cce7c9bf0f7..54f52a701979 100644 --- a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -22,6 +22,7 @@ dependencies = [ ('ruamel.yaml', '0.17.21'), ('SciPy-bundle', '2021.05'), ('sympy', '1.8'), + ('SWIG', '4.0.2'), ('GLPK', '5.0'), ('python-libsbml', '5.19.7'), ] From 38ed74ce899c2df641b51fd6718d377cd98d1c68 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 16:25:41 +0100 Subject: [PATCH 383/939] adding easyconfigs: GD-2.75-GCCcore-11.3.0.eb, Circos-0.69-9-GCCcore-11.3.0.eb --- .../c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb | 41 +++++++++++++ .../g/GD/GD-2.75-GCCcore-11.3.0.eb | 57 +++++++++++++++++++ 2 files changed, 98 insertions(+) create mode 100644 easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..bdb8092c8c6c --- /dev/null +++ b/easybuild/easyconfigs/c/Circos/Circos-0.69-9-GCCcore-11.3.0.eb @@ -0,0 +1,41 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild + +easyblock = 'Tarball' + +name = 'Circos' +version = '0.69-9' + +homepage = 'http://www.circos.ca/' +description = """Circos is a software package for visualizing data and information. + It visualizes data in a circular layout - this makes Circos ideal for exploring + relationships between objects or positions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://circos.ca/distribution/'] +sources = [SOURCELOWER_TGZ] +checksums = ['34d8d7ebebf3f553d62820f8f4a0a57814b610341f836b4740c46c3057f789d2'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Perl', '5.34.1'), + ('GD', '2.75'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['lib/%(name)s'], +} + +modextrapaths = {'PERL5LIB': 'lib'} + +sanity_check_commands = [('perl', '-e "use Circos"')] + +moduleclass = 'bio' 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 new file mode 100644 index 000000000000..d889cb7d1f5c --- /dev/null +++ b/easybuild/easyconfigs/g/GD/GD-2.75-GCCcore-11.3.0.eb @@ -0,0 +1,57 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester (The Francis Crick Insitute, London, UK) +# Update to v2.71: Alex Domingo (Vrije Universiteit Brussel) +# Update to v2.73: Sebastien Moretti (SIB Swiss Institute of Bioinformatics) +# + +easyblock = 'Bundle' + +name = 'GD' +version = '2.75' + +homepage = 'https://github.com/lstein/Perl-GD' +description = """GD.pm - Interface to Gd Graphics Library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Perl', '5.34.1'), + ('X11', '20220504'), + ('libgd', '2.3.3'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), +] + +exts_defaultclass = 'PerlModule' +exts_filter = ("perldoc -lm %(ext_name)s ", "") + +exts_list = [ + ('ExtUtils::PkgConfig', '1.16', { + 'source_tmpl': 'ExtUtils-PkgConfig-%(version)s.tar.gz', + 'source_urls': ['https://cpan.metacpan.org/authors/id/X/XA/XAOC/'], + 'checksums': ['bbeaced995d7d8d10cfc51a3a5a66da41ceb2bc04fedcab50e10e6300e801c6e'], + }), + (name, version, { + 'source_tmpl': 'release_%(version_major)s_%(version_minor)s.tar.gz', + 'source_urls': ['https://github.com/lstein/Perl-GD/archive/'], + 'checksums': ['b82ca67fa67446f16ee7ba8bccee2062644816a83cb2ee4e4de2fa3ee8ab359d'], + }), +] + +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'], +} + +modextrapaths = { + 'PERL5LIB': 'lib/perl5/site_perl/%(perlver)s/', +} + +moduleclass = 'bio' From f7403cdf9b53f80c37ad83c1451761ed7dd872d1 Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 14 Nov 2022 18:43:51 +0000 Subject: [PATCH 384/939] adding easyconfigs: oceanspy-0.2.0-foss-2022a.eb --- .../o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb new file mode 100644 index 000000000000..d73a95fced80 --- /dev/null +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -0,0 +1,40 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'oceanspy' +version = '0.2.0' + +homepage = 'https://github.com/hainegroup/oceanspy' +description = """OceanSpy - A Python package to facilitate ocean model data analysis +and visualization.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('dask', '2022.10.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + ('xgcm', '0.8.0', { + 'checksums': ['99e7e2fc9268fb13827f8849dbae279eaaa4960d51872d62bc38293605b0215f'], + }), + + (name, version, { + 'checksums': ['8c684ecdfe03bade171e17f5ae6bedd422e51db6faffed0303e1839051d40614'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 2e3e7bd67c1faf07c838a1d64a13f28d22334417 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 14 Nov 2022 20:16:32 +0100 Subject: [PATCH 385/939] use new EasyBuild logo in README --- README.rst | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/README.rst b/README.rst index cb4636846acc..b06cc3cf03a3 100644 --- a/README.rst +++ b/README.rst @@ -1,7 +1,8 @@ -.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg - -.. image:: https://easybuilders.github.io/easybuild/images/easybuild_logo_small.png +.. image:: https://github.com/easybuilders/easybuild/raw/develop/logo/png/easybuild_logo_2022_horizontal_dark_bg_transparent.png :align: center + :height: 400px + +.. image:: https://github.com/easybuilders/easybuild-easyconfigs/workflows/easyconfigs%20unit%20tests/badge.svg `EasyBuild `_ is a software build and installation framework that allows you to manage (scientific) software From 09ce7360d06affcf127854d9b8eab140c80d18c4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 23:50:27 +0100 Subject: [PATCH 386/939] use new SYSTEM constant in dependencies of MATLAB-Engine-2021a-GCCcore-10.2.0.eb --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb index 3418f6ddc565..83a3d5d719c7 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb @@ -10,7 +10,7 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [ - ('MATLAB', version, '', True), + ('MATLAB', version, '', SYSTEM), ('Python', '3.8.6'), ] From a62c38ef82a9fb81bca8a34f8413b6e13ed3a465 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 14 Nov 2022 23:50:59 +0100 Subject: [PATCH 387/939] use new SYSTEM constant in dependencies of MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index 9380e93ff8a9..e60cc61f0044 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -10,7 +10,7 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '11.2.0'} dependencies = [ - ('MATLAB', version, '', True), + ('MATLAB', version, '', SYSTEM), ('Python', '3.9.6'), ] From 98b2773c34a35e4ab8ad8f3472e39ef421ad26f4 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Nov 2022 00:32:14 +0100 Subject: [PATCH 388/939] enable support in MATLAB-Engine for Python version used in EasyBuild --- .../m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb index e60cc61f0044..c1558fb7dc97 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb @@ -17,9 +17,11 @@ dependencies = [ use_pip = False download_dep_fail = True +# Enable support for this current version of Python +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +prebuildopts += "sed -i 's/^_supported_versions =.*/_supported_versions = ["%(pyshortver)s"]/' setup.py &&" # Since this setup.py does not provide a separate --build-base for the install # step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" skipsteps = ['install'] From 72f2ed94534866e8ff42ee891c4566e1644d08a2 Mon Sep 17 00:00:00 2001 From: adam Date: Tue, 15 Nov 2022 08:52:30 +0000 Subject: [PATCH 389/939] Fix modulename and add sanity_check_command --- easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb index 6e3329bd511d..5deaefa438cd 100644 --- a/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb +++ b/easybuild/easyconfigs/s/Scoary/Scoary-1.6.16-foss-2021a.eb @@ -27,7 +27,7 @@ exts_list = [ (name, version, { 'source_tmpl': 'scoary-%(version)s.tar.gz', 'checksums': ['f433343422c5805a70a20f7fe83851490ae3cdf07745c65680de5feea40a6dca'], - 'modulename': False, + 'modulename': 'scoary.methods', }), ] @@ -38,4 +38,6 @@ sanity_check_paths = { sanity_pip_check = True +sanity_check_commands = [('scoary', '--version')] + moduleclass = 'bio' From dbf74553f8ff671f9a520098289c2103b03e979a Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 10:02:33 +0000 Subject: [PATCH 390/939] adding easyconfigs: gsw-3.6.16-foss-2022a.eb --- .../g/gsw/gsw-3.6.16-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb new file mode 100644 index 000000000000..aa8438cd21e0 --- /dev/null +++ b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb @@ -0,0 +1,42 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'gsw' +version = '3.6.16' + +homepage = 'https://github.com/TEOS-10/GSW-python' +description = """This Python implementation of the Thermodynamic Equation of +Seawater 2010 (TEOS-10) is based primarily on numpy ufunc wrappers of the GSW-C +implementation. This library replaces the original python-gsw pure-python +implementation.. The primary reasons for this change are that by building on +the C implementation we reduce code duplication and we gain an immediate update +to the 75-term equation. +Additional benefits include a major increase in speed, a reduction in memory +usage, and the inclusion of more functions. The penalty is that a C +(or MSVC C++ for Windows) compiler is required to build the package from source.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + + (name, version, { + 'checksums': ['d24d820c8b43dbf72206cf5e3b0ed800b05aa85ca40afd39c9abd19849714197'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From e932e0d6366d8b05d06f1bdfd5a5db95a44e2f83 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 11:15:02 +0100 Subject: [PATCH 391/939] clean up version of Python dependency in pyWannier90 easyconfig --- .../p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb index ec32ef804a95..f4d75a875c3c 100644 --- a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-foss-2021a.eb @@ -32,12 +32,8 @@ builddependencies = [ ('pybind11', '2.6.2'), ] -local_pymaj = '3' -local_pymin = '9' -local_pymajmin = local_pymaj + local_pymin - dependencies = [ - ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PySCF', '1.7.6'), ] From e9fde4dae46df5bd922be8ec679aa7ec2cb5731d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 15 Nov 2022 11:46:23 +0100 Subject: [PATCH 392/939] Fix matlab version for 2021b --- .../MATLAB-Engine-2021b-GCCcore-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..a188c57dcad9 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'MATLAB-Engine' +version = '2021b' + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', version, '', True), + ('Python', '3.9.6'), +] + +use_pip = False +download_dep_fail = True + +# Since this setup.py does not provide a separate --build-base for the install +# step, both build and install must be performed in a single command. +prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " +buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" + +skipsteps = ['install'] + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +sanity_pip_check = True + +options = {'modulename': 'matlab.engine'} + +moduleclass = 'math' From 65119867029b4e74a665ec7013ddcaa8f4fb6b61 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 10:50:13 +0000 Subject: [PATCH 393/939] adding easyconfigs: pyproj-3.4.0-GCCcore-11.3.0.eb --- .../p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..2fecab554260 --- /dev/null +++ b/easybuild/easyconfigs/p/pyproj/pyproj-3.4.0-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonPackage' + +name = 'pyproj' +version = '3.4.0' + +homepage = 'https://pyproj4.github.io/pyproj' +description = "Python interface to PROJ4 library for cartographic transformations" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a708445927ace9857f52c3ba67d2915da7b41a8fdcd9b8f99a4c9ed60a75eb33'] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('PROJ', '9.0.0'), +] + +download_dep_fail = True +use_pip = True + +preinstallopts = "export PROJ_DIR=$EBROOTPROJ && " + +sanity_check_paths = { + 'files': ['bin/pyproj'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ['pyproj --help'] + +sanity_pip_check = True + +moduleclass = 'data' From 6481ad003ff37ddc871a31436c89826013f7e268 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Nov 2022 14:01:28 +0100 Subject: [PATCH 394/939] adding easyconfigs: Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb, OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb and patches: Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch, Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch --- ...CV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb | 99 +++++++++++++++++++ ...p-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 92 +++++++++++++++++ ...issing_cuda_compatibility.cu_include.patch | 55 +++++++++++ ....07-Helios_fix_opencv_cuda_detection.patch | 25 +++++ 4 files changed, 271 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch create mode 100644 easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch diff --git a/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb new file mode 100644 index 000000000000..70276c875266 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenCV/OpenCV-4.6.0-foss-2022a-CUDA-11.7.0-contrib.eb @@ -0,0 +1,99 @@ +name = 'OpenCV' +version = '4.6.0' +versionsuffix = '-CUDA-%(cudaver)s-contrib' + +# the hash is version dependent! see 3rdparty/ippicv/ippicv.cmake +local_ippicv_hash = 'a56b6ac6f030c312b2dce17430eef13aed9af274' + +homepage = 'https://opencv.org/' +description = """OpenCV (Open Source Computer Vision Library) is an open source computer vision + and machine learning software library. OpenCV was built to provide + a common infrastructure for computer vision applications and to accelerate + the use of machine perception in the commercial products. + Includes extra modules for OpenCV from the contrib repository.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'cstd': 'c++14'} + +sources = [ + { + 'source_urls': ['https://github.com/%(namelower)s/%(namelower)s/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': SOURCELOWER_ZIP + }, + { + 'source_urls': ['https://github.com/%(namelower)s/opencv_contrib/archive/'], + 'download_filename': '%(version)s.zip', + 'filename': '%(namelower)s_contrib-%(version)s.zip' + }, + { + 'source_urls': ['https://raw.githubusercontent.com/opencv/opencv_3rdparty/%s/ippicv' % local_ippicv_hash], + 'filename': 'ippicv_2020_lnx_intel64_20191018_general.tgz', + 'extract_cmd': 'cp %s %(builddir)s' + }, +] +checksums = [ + '158db5813a891c7eda8644259fc1dbd76b21bd1ffb9854a8b4b8115a4ceec359', # opencv-4.6.0.zip + '588ca44e3c88ccf8e3ff7f46e966e26ff63d72607968ace83b91628d3440f8a3', # opencv_contrib-4.6.0.zip + '08627fa5660d52d59309a572dd7db5b9c8aea234cfa5aee0942a1dd903554246', # ippicv_2020_lnx_intel64_20191018_general.tgz +] + +builddependencies = [ + ('CMake', '3.23.1'), +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('zlib', '1.2.12'), + ('FFmpeg', '4.4.2'), + ('freetype', '2.12.1'), + ('HarfBuzz', '4.2.1'), + ('libjpeg-turbo', '2.1.3'), + ('OpenJPEG', '2.5.0'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libwebp', '1.2.4'), + ('OpenEXR', '3.1.5'), + ('JasPer', '2.0.33'), + ('Java', '11', '', SYSTEM), + ('ant', '1.10.12', '-Java-%(javaver)s', SYSTEM), + ('GLib', '2.72.1'), + ('GTK4', '4.7.0'), + ('HDF5', '1.12.2'), + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), +] + +# XXXX in configurations is a bug fix in OpenCV because ocv_check_modules is not able to recognize freetype and harfbuzz +# ref: https://github.com/opencv/opencv/blob/6e8daaec0f46aaba9ea22e2afce47307b1dbff9f/cmake/OpenCVUtils.cmake#L861 +configopts = " ".join([ + "-DOPENCV_EXTRA_MODULES_PATH=%(builddir)s/%(namelower)s_contrib-%(version)s/modules", + "-DFREETYPE_FOUND=ON", + "-DFREETYPE_INCLUDE_DIRS=$EBROOTFREETYPE/include/freetype2/", + "-DFREETYPE_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES=$EBROOTFREETYPE/lib64/libfreetype.so", + "-DFREETYPE_LINK_LIBRARIES_XXXXX=ON", + "-DHARFBUZZ_FOUND=ON", + "-DHARFBUZZ_INCLUDE_DIRS=$EBROOTHARFBUZZ/include/harfbuzz", + "-DHARFBUZZ_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES=$EBROOTHARFBUZZ/lib64/libharfbuzz.so", + "-DHARFBUZZ_LINK_LIBRARIES_XXXXX=ON", + "-DBUILD_opencv_python2=OFF", + "-DCUDA_NVCC_FLAGS=--std=c++14", +]) + +enhance_sanity_check = True + +local_contrib_libs = [ + 'aruco', 'bgsegm', 'bioinspired', 'ccalib', 'datasets', 'dnn_objdetect', 'dnn_superres', 'dpm', 'face', 'freetype', + 'fuzzy', 'hdf', 'hfs', 'img_hash', 'line_descriptor', 'optflow', 'phase_unwrapping', 'plot', 'quality', 'reg', + 'rgbd', 'saliency', 'shape', 'stereo', 'structured_light', 'superres', 'surface_matching', 'text', 'tracking', + 'videostab', 'xfeatures2d', 'ximgproc', 'xobjdetect', 'xphoto' +] + +sanity_check_paths = { + 'files': ['lib64/libopencv_%s.%s' % (x, SHLIB_EXT) for x in local_contrib_libs], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..4093b1d0ecf6 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,92 @@ +name = 'Xmipp' +version = '3.22.07-Helios' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/I2PC/scipion/wiki' +description = """Scipion is an image processing framework to obtain 3D +models of macromolecular complexes using Electron Microscopy (3DEM). It +integrates several software packages and presents an unified interface +for both biologists and developers. Scipion allows to execute workflows +combining different software tools, while taking care of formats and +conversions. Additionally, all steps are tracked and can be reproduced +later on. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [ + { + 'source_urls': ['https://github.com/I2PC/xmipp/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': '%(namelower)s-v%(version)s.tar.gz', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippCore/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippCore-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, + { + 'source_urls': ['https://github.com/I2PC/xmippViz/archive/'], + 'download_filename': 'v%(version)s.tar.gz', + 'filename': 'xmippViz-v%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, +] +patches = [ + '%(name)s-%(version)s_fix_scons_Environent_calls.patch', + '%(name)s-%(version)s_drop_useless_CXXFLAGS_setting.patch', + '%(name)s-%(version)s_correct_order_of_cu_includes.patch', + '%(name)s-%(version)s_dont_add_useless_libs.patch', + '%(name)s-%(version)s_dont_change_EB_build_flags.patch', + '%(name)s-%(version)s_fix_missing_cuda_compatibility.cu_include.patch', + '%(name)s-%(version)s_fix_opencv_cuda_detection.patch', + ('XmippCore-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippCore'), + ('XmippCore-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippCore'), + ('XmippViz-%(version)s_fix_scons_Environent_calls.patch', 'src/xmippViz'), + ('XmippViz-%(version)s_use_CXXFLAGS_from_EB.patch', 'src/xmippViz'), +] +checksums = [ + {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, + {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, + {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': + '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, + {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': + '34ed0cb591e1e2788acd3e58696b1f45ce9210836d14ed1c99de1e574e4824e6'}, + {'Xmipp-3.22.07-Helios_correct_order_of_cu_includes.patch': + '2b0b2ddf349003be4112f4dca623586a03235214d6e64d232deb26468b52f0e3'}, + {'Xmipp-3.22.07-Helios_dont_add_useless_libs.patch': + '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, + {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': + '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': + '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, + {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'd86b0d3ecc339b81c9aa7a33d2b44b428643aa7e2e686529b4bb6b16d36805c2'}, + {'XmippViz-3.22.07-Helios_fix_scons_Environent_calls.patch': + '7724fc3953d9c4c308a5755f54229259425fdbad5a909153bd173292434407b9'}, + {'XmippViz-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': + 'a8bea23c243174fb27a140a34a064a622cc96f0e7231fd31caf20f90c7ba9555'}, +] + +builddependencies = [ + ('SCons', '4.4.0'), + ('CTPL', '0.0.2'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Java', '11', '', SYSTEM), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), + ('SQLite', '3.38.3'), + ('HDF5', '1.12.2'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('LIBSVM', '3.30'), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch new file mode 100644 index 000000000000..52dc98a12128 --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch @@ -0,0 +1,55 @@ +Fix support for CUDA arch < 6.0 + +Åke Sandgren, 2022-11-14 +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu +index 83189250..f125e47d 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.cu +@@ -28,8 +28,9 @@ + + #include "cuda_compatibility.h" + ++#if defined(__CUDA_ARCH__) + #if __CUDA_ARCH__ < 600 +-__device__ double atomicAdd(double* address, double val) ++static __inline__ __device__ double atomicAdd(double* address, double val) + { + unsigned long long int* address_as_ull = + (unsigned long long int*)address; +@@ -47,6 +48,7 @@ __device__ double atomicAdd(double* address, double val) + return __longlong_as_double(old); + } + #endif ++#endif + + + #endif /* LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_CU_ */ +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h +index 3bb44e0f..279ccbcb 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_compatibility.h +@@ -27,7 +27,11 @@ + #define LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_H_ + + +-__device__ double atomicAdd(double* address, double val); ++#if defined(__CUDA_ARCH__) ++#if __CUDA_ARCH__ < 600 ++static __inline__ __device__ double atomicAdd(double* address, double val); ++#endif ++#endif + + + #endif /* LIBRARIES_RECONSTRUCTION_CUDA_CUDA_COMPATIBILITY_H_ */ +diff --git a/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu b/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu +index c7dea8fb..9e267336 100644 +--- a/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu ++++ b/src/xmipp/libraries/reconstruction_cuda/cuda_correlation.cu +@@ -27,6 +27,7 @@ + #define LIBRARIES_RECONSTRUCTION_CUDA_CUDA_CORRELATION_CU_ + + #include "cuda_compatibility.h" ++#include "cuda_compatibility.cu" + + /** + * Function computes sum and sum squared for each 2D signal diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch new file mode 100644 index 000000000000..0575ef6a225f --- /dev/null +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch @@ -0,0 +1,25 @@ +Fix detection of OpenCV >= 3 + +Åke Sandgren, 2022-11-14 +diff --git a/src/xmipp/SConscript b/src/xmipp/SConscript +index a767fb99..89777947 100644 +--- a/src/xmipp/SConscript ++++ b/src/xmipp/SConscript +@@ -46,7 +46,7 @@ debug = get('DEBUG') + matlab = get('MATLAB') + opencv = env.GetOption('opencv') and get('OPENCV') + opencvsupportscuda = get('OPENCVSUPPORTSCUDA') +-opencv_3 = get('OPENCV3') ++opencv_ver = int(os.environ.get('OPENCV_VERSION', '0')) + starpu = get('STARPU') + + if opencv: +@@ -55,7 +55,7 @@ if opencv: + 'opencv_video', + 'libopencv_calib3d'] + if opencvsupportscuda: +- if opencv_3: ++ if opencv_ver >= 3: + opencvLibs+=['libopencv_cudaoptflow', 'libopencv_cudaarithm'] + else: + opencvLibs+=['libopencv_gpu'] From 5b850bac0acb053edd023b59e930b9216ae39022 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 14:02:35 +0100 Subject: [PATCH 395/939] adding easyconfigs: NanoPlot-1.33.0-foss-2021a.eb, nanomath-1.2.1-foss-2021a.eb, nanoget-1.18.1-foss-2021a.eb, pauvre-0.2.3-foss-2021a.eb --- .../n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb | 47 +++++++++++++++++++ .../n/nanoget/nanoget-1.18.1-foss-2021a.eb | 29 ++++++++++++ .../n/nanomath/nanomath-1.2.1-foss-2021a.eb | 33 +++++++++++++ .../p/pauvre/pauvre-0.2.3-foss-2021a.eb | 40 ++++++++++++++++ 4 files changed, 149 insertions(+) create mode 100644 easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb diff --git a/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb new file mode 100644 index 000000000000..400d3660c4df --- /dev/null +++ b/easybuild/easyconfigs/n/NanoPlot/NanoPlot-1.33.0-foss-2021a.eb @@ -0,0 +1,47 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'NanoPlot' +version = '1.33.0' + +homepage = 'https://github.com/wdecoster/NanoPlot' +description = "Plotting suite for long read sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['caf69a5789625e746814238cb4f0d510ed6768a094566e8f1dcaa77933c4d6fd'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.1'), + ('nanoget', '1.18.1'), + ('Seaborn', '0.11.2'), + ('plotly.py', '5.1.0'), + ('pauvre', '0.2.3'), + ('statsmodels', '0.12.2'), + ('Arrow', '6.0.0'), # for pyarrow + ('Kaleido', '0.2.1'), +] + +download_dep_fail = True +use_pip = True + +# replace strict Seaborn & pauvre version requirement with minimal version requirements +preinstallopts = "sed -i 's/==0/>=0/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/NanoPlot'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["NanoPlot --help"] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb new file mode 100644 index 000000000000..82b4f0b5841f --- /dev/null +++ b/easybuild/easyconfigs/n/nanoget/nanoget-1.18.1-foss-2021a.eb @@ -0,0 +1,29 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'nanoget' +version = '1.18.1' + +homepage = 'https://github.com/wdecoster/nanoget' +description = "Functions to extract information from Oxford Nanopore sequencing data and alignments" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e4fa37ab1bccc3287947f5792acad3c96fd1c02cb9c0a1f5d218d26bcdbe1632'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('Pysam', '0.16.0.1'), + ('nanomath', '1.2.1'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb new file mode 100644 index 000000000000..5d1a69c2f733 --- /dev/null +++ b/easybuild/easyconfigs/n/nanomath/nanomath-1.2.1-foss-2021a.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonBundle' + +name = 'nanomath' +version = '1.2.1' + +homepage = 'https://github.com/wdecoster/nanomath' +description = "A few simple math function for other Oxford Nanopore processing scripts" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), +] + +use_pip = True + +exts_list = [ + ('Python-Deprecated', '1.1.0', { + 'modulename': 'deprecated', + 'checksums': ['a242b3c1721f97912330b12cd5529abfa5b3876084a6c60a2c683a87d4b0dd6f'], + }), + (name, version, { + 'checksums': ['3c611c3b0a8fa364b8afe87c948f31d5d8009a212c28954382e926f36f90e060'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb b/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb new file mode 100644 index 000000000000..5bd495d2adb8 --- /dev/null +++ b/easybuild/easyconfigs/p/pauvre/pauvre-0.2.3-foss-2021a.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'PythonPackage' + +name = 'pauvre' +version = '0.2.3' + +homepage = 'https://github.com/conchoecia/pauvre' +description = "Tools for plotting Oxford Nanopore and other long-read data" + +toolchain = {'name': 'foss', 'version': '2021a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['ba756bc9025ae7edafd91092d12a57864f018958fd46b548e9eeda7167ee197d'] + +dependencies = [ + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Biopython', '1.79'), + ('scikit-learn', '0.24.2'), + ('matplotlib', '3.4.2'), +] + +download_dep_fail = True +use_pip = True + +# fix incorrect requirement, correct name is 'scikit-learn' +preinstallopts = "sed -i 's/sklearn/scikit-learn/g' setup.py && " + +sanity_check_paths = { + 'files': ['bin/pauvre'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["pauvre --help"] + +sanity_pip_check = True + +moduleclass = 'math' From d6d8efaeb2b212f224ca7aadbd451f3185d63702 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 13:04:53 +0000 Subject: [PATCH 396/939] adding easyconfigs: basemap-1.3.6-foss-2022a.eb --- .../b/basemap/basemap-1.3.6-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb new file mode 100644 index 000000000000..9b019b172c70 --- /dev/null +++ b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb @@ -0,0 +1,51 @@ +# 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 = '1.3.6' + +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('matplotlib', '3.5.2'), + ('GEOS', '3.10.3'), + ('Pillow', '9.1.1'), + ('pyproj', '3.4.0'), +] + +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=$EBROOTGEOS', + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'checksums': ['42adbd039b4afbe93ca2fa32cfab456d4fd590cb8ed1c28e4aa94dcb957b58ac'], + }), + (name, version, { + 'modulename': 'mpl_toolkits.basemap', + 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', + 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', + 'sources': ['v%(version)s.tar.gz'], + 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], + 'checksums': ['42adbd039b4afbe93ca2fa32cfab456d4fd590cb8ed1c28e4aa94dcb957b58ac'], + }), +] + +moduleclass = 'vis' From 92db9c418e97d27131129390c58cfc7b640eb856 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 15 Nov 2022 14:28:06 +0100 Subject: [PATCH 397/939] delete easyconfig MATLAB-Engine-2021a-GCCcore-11.2.0.eb --- .../MATLAB-Engine-2021a-GCCcore-11.2.0.eb | 36 ------------------- 1 file changed, 36 deletions(-) delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb deleted file mode 100644 index c1558fb7dc97..000000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-11.2.0.eb +++ /dev/null @@ -1,36 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021a' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('MATLAB', version, '', SYSTEM), - ('Python', '3.9.6'), -] - -use_pip = False -download_dep_fail = True - -# Enable support for this current version of Python -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -prebuildopts += "sed -i 's/^_supported_versions =.*/_supported_versions = ["%(pyshortver)s"]/' setup.py &&" -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From 2f5588ac858d263d70cd36b50c30f9fe558bce4d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 14:58:22 +0100 Subject: [PATCH 398/939] clean up version of Python dependency in pyWannier90 easyconfig --- .../p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb index 2a045c216cc2..3a1d4b39c481 100644 --- a/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb +++ b/easybuild/easyconfigs/p/pyWannier90/pyWannier90-2021-12-07-gomkl-2021a.eb @@ -32,12 +32,8 @@ builddependencies = [ ('pybind11', '2.6.2'), ] -local_pymaj = '3' -local_pymin = '9' -local_pymajmin = local_pymaj + local_pymin - dependencies = [ - ('Python', '%s.%s.5' % (local_pymaj, local_pymin)), + ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('PySCF', '1.7.6'), ] From 128ac0711acc1726eb87226ec706e199781e4048 Mon Sep 17 00:00:00 2001 From: alberta Date: Tue, 15 Nov 2022 15:04:34 +0100 Subject: [PATCH 399/939] adding easyconfigs: resolos-0.3.5.eb --- .../easyconfigs/r/resolos/resolos-0.3.5.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb new file mode 100644 index 000000000000..f588b3b926d5 --- /dev/null +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'resolos' +version = '0.3.5' + +homepage = 'https://gitlab.unige.ch/resolos/resolos' +description = """Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. +It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) +and time (environment preservation for long term archival). +For installation and detailed usage, check out the documentation.""" + +toolchain = {'name': 'system', 'version': ''} + +# source_urls = [PYPI_SOURCE] +# Link copy from pypi.org | PYPI_SOURCE is not working +sources = ["https://files.pythonhosted.org/packages/15/0b/fa95a349434f77d8afc775dd999152d7612b6baed52083981ac84eaa41e9/resolos-0.3.5.tar.gz"] +checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] + + +use_pip = True +use_pip_for_deps = True +moduleclass = 'data' + +sanity_check_commands = ["r3s info"] +sanity_check_paths = { + 'files': ["bin/r3s"], + 'dirs': [] +} From a55fa6e6769ed3a1a727065e23fe96017df4fda9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 15:58:30 +0100 Subject: [PATCH 400/939] Add the last missing tool of the pipeline + Sync with develop --- .../n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb index 9699267036a4..2e45780b042b 100644 --- a/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb +++ b/easybuild/easyconfigs/n/nf-core-mag/nf-core-mag-20221110-foss-2021a.eb @@ -16,7 +16,6 @@ description = """The Nextflow pipeline 'mag' ported to EasyBuild/EESSI.""" toolchain = {'name': 'foss', 'version': '2021a'} -# TODO The long reads sequencing part (1 missing) tools will be added later dependencies = [ ('Nextflow', '22.10.1', '', SYSTEM), ('AdapterRemoval', '2.3.2'), @@ -38,6 +37,7 @@ dependencies = [ ('MetaBAT', '2.15'), ('MultiQC', '1.11'), ('NanoLyse', '1.2.1'), + ('NanoPlot', '1.33.0'), ('Porechop', '0.2.4'), ('prodigal', '2.6.3'), ('prokka', '1.14.5'), From fb8f6c3b3fed32f72044265daa3bbc02ca00dca6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 15 Nov 2022 16:48:12 +0100 Subject: [PATCH 401/939] {toolchain} intel/2022.11 --- .../h/HPL/HPL-2.3-intel-2022.11.eb | 21 ++++++++++++ .../easyconfigs/i/iimpi/iimpi-2022.11.eb | 18 ++++++++++ .../imkl-FFTW-2022.2.1-iimpi-2022.11.eb | 11 +++++++ easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb | 18 ++++++++++ .../impi-2021.7.1-intel-compilers-2022.2.1.eb | 16 +++++++++ .../intel-compilers-2022.2.1.eb | 33 +++++++++++++++++++ .../easyconfigs/i/intel/intel-2022.11.eb | 22 +++++++++++++ 7 files changed, 139 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022.11.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb new file mode 100644 index 000000000000..6b5eb683de86 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022.11.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022.11'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb new file mode 100644 index 000000000000..49aa4591617b --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022.11.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022.11' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb new file mode 100644 index 000000000000..ff00372cf4e2 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022.11.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022.11'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb new file mode 100644 index 000000000000..3daf55958a30 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2022.2.1.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19038/'] +sources = ['l_onemkl_p_%(version)s.16993_offline.sh'] +checksums = ['eedd4b795720de776b1fc5f542ae0fac37ec235cdb567f7c2ee3182e73e3e59d'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb new file mode 100644 index 000000000000..68aeb9beb636 --- /dev/null +++ b/easybuild/easyconfigs/i/impi/impi-2021.7.1-intel-compilers-2022.2.1.eb @@ -0,0 +1,16 @@ +name = 'impi' +version = '2021.7.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/mpi-library.html' +description = "Intel MPI Library, compatible with MPICH ABI" + +toolchain = {'name': 'intel-compilers', 'version': '2022.2.1'} + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +source_urls = ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19010/'] +sources = ['l_mpi_oneapi_p_%(version)s.16815_offline.sh'] +checksums = ['90e7804f2367d457cd4cbf7aa29f1c5676287aa9b34f93e7c9a19e4b8583fff7'] + +dependencies = [('UCX', '1.13.1')] + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb new file mode 100644 index 000000000000..a6ae81701053 --- /dev/null +++ b/easybuild/easyconfigs/i/intel-compilers/intel-compilers-2022.2.1.eb @@ -0,0 +1,33 @@ +name = 'intel-compilers' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/hpc-toolkit.html' +description = "Intel C, C++ & Fortran compilers (classic and oneAPI)" + +toolchain = SYSTEM + +# see https://software.intel.com/content/www/us/en/develop/articles/oneapi-standalone-components.html +sources = [ + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/19030/'], + 'filename': 'l_dpcpp-cpp-compiler_p_%(version)s.16991_offline.sh', + }, + { + 'source_urls': ['https://registrationcenter-download.intel.com/akdlm/irc_nas/18998/'], + 'filename': 'l_fortran-compiler_p_%(version)s.16992_offline.sh', + }, +] +checksums = [ + {'l_dpcpp-cpp-compiler_p_2022.2.1.16991_offline.sh': + '3f0f02f9812a0cdf01922d2df9348910c6a4cb4f9dfe50fc7477a59bbb1f7173'}, + {'l_fortran-compiler_p_2022.2.1.16992_offline.sh': + '64f1d1efbcdc3ac2182bec18313ca23f800d94f69758db83a1394490d9d4b042'}, +] + +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), +] + +moduleclass = 'compiler' diff --git a/easybuild/easyconfigs/i/intel/intel-2022.11.eb b/easybuild/easyconfigs/i/intel/intel-2022.11.eb new file mode 100644 index 000000000000..9dd32ad27d5a --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022.11.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022.11' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From ed16eb8d76b55f3a37df562ae89fd33ff850c127 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 16:38:33 +0000 Subject: [PATCH 402/939] adding easyconfigs: zarr-2.13.3-foss-2022a.eb --- .../z/zarr/zarr-2.13.3-foss-2022a.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb new file mode 100644 index 000000000000..ff8bb790e8f2 --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -0,0 +1,41 @@ +easyblock = "PythonBundle" + +name = 'zarr' +version = '2.13.3' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, +chunked, N-dimensional arrays, designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('entrypoints', '0.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.10.2', { + 'checksums': ['22838c6b3fd986bd9c724039b88870057f790e22b20e6e1cbbaa0de142dd59c4'], + }), + (name, version, { + 'checksums': ['db24b090616c638f65e33a6bc5d956d642221182961515ccbc28b17fb0d0b48c'], + }), +] + +moduleclass = 'data' From 5a553631d9eab4892c2ef75825406ec479bea08e Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 15 Nov 2022 17:41:54 +0100 Subject: [PATCH 403/939] Use SWIG as builddependencies --- easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb index 54f52a701979..50daf951ccbb 100644 --- a/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb +++ b/easybuild/easyconfigs/c/COBRApy/COBRApy-0.26.0-foss-2021a.eb @@ -17,12 +17,15 @@ software_license = 'LicenseGPLv2' toolchain = {'name': 'foss', 'version': '2021a'} +builddependencies = [ + ('SWIG', '4.0.2'), +] + dependencies = [ ('Python', '3.9.5'), ('ruamel.yaml', '0.17.21'), ('SciPy-bundle', '2021.05'), ('sympy', '1.8'), - ('SWIG', '4.0.2'), ('GLPK', '5.0'), ('python-libsbml', '5.19.7'), ] From 0c896f78ee96f01b133e49d801b6a68b5c7dec48 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 15 Nov 2022 17:30:09 +0000 Subject: [PATCH 404/939] adding easyconfigs: lagrangian-filtering-0.8.3-foss-2022a.eb --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb new file mode 100644 index 000000000000..2b248447592b --- /dev/null +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -0,0 +1,83 @@ +# This installation unfortunately requires the GitHub dance, as the tarball +# is simply not installing. For that reason there is no checksum! +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'PythonBundle' + +name = 'lagrangian-filtering' +version = '0.8.3' + +homepage = 'https://github.com/angus-g/lagrangian-filtering' +description = """Temporal filtering of data in a Lagrangian frame of reference.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('dask', '2022.10.2'), + ('h5py', '3.7.0'), + ('SciPy-bundle', '2022.05'), + ('netcdf4-python', '1.6.1'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('zarr', '2.13.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('parcels', '2.4.0', { + 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], + }), + ('xarray', '2022.9.0', { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), + ('pykdtree', '1.3.6', { + 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], + }), + ('sosfilt', '1.2.0', { + 'checksums': ['b3083fd2edf723a6163f00ddc36ec3ca20fbf6112cc68573dad9356544a9d734'], + }), + ('psutil', '5.9.4', { + 'checksums': ['3d7f9739eb435d4b1338944abe23f49584bde5395f27487d2ee25ad9a8774a62'], + }), + ('progressbar2', '4.2.0', { + 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], + 'modulename': 'progressbar', + }), + ('cgen', '2020.1', { + 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], + }), + ('pymbolic', '2022.1', { + 'checksums': ['b52f451dd0b9803e03de3320af3b7ce5723070061c6d231c00216f6da4259012'], + }), + ('pytools', '2022.1.12', { + 'checksums': ['4d62875e9a2ab2a24e393a9a8b799492f1a721bffa840af3807bfd42871dd1f4'], + }), + ('python-utils', '3.4.5', { + 'checksums': ['7e329c427a6d23036cfcc4501638afb31b2ddc8896f25393562833874b8c6e0a'], + }), + + (name, version, { + 'sources': [{ + 'filename': '%(name)s-%(version)s-commit.tar.gz', + 'git_config': { + 'url': 'https://github.com/angus-g/', + 'repo_name': name, + 'commit': 'b942ff3', + 'recursive': True, + 'keep_git_dir': True, + }, + }], + 'checksums': [None], + 'modulename': 'filtering', + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' From 11f9457cddcb386b1bfd6aaf2e2759386ffb852e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 15 Nov 2022 19:13:34 +0100 Subject: [PATCH 405/939] Add missing checksums --- .../x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb index 4093b1d0ecf6..fc96f59b8600 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -60,6 +60,10 @@ checksums = [ '284b8ec1e514fb84b7680c8b3f59b3d5931b564beb444d3301504e3170e9a49e'}, {'Xmipp-3.22.07-Helios_dont_change_EB_build_flags.patch': '1514eaa5de35b38b5a10e949edf5c94ba95bbd05e0b9fbf70db2ea98967394e3'}, + {'Xmipp-3.22.07-Helios_fix_missing_cuda_compatibility.cu_include.patch': + 'b478c08a6a260021b4b91e5a8f6d9c5637eafdedcd99fcb672fe356d1744d349'}, + {'Xmipp-3.22.07-Helios_fix_opencv_cuda_detection.patch': + '9d7c90a8cdeca24dba41a0d2f11f59ab34a438ed34fa7f4850172848505ecbae'}, {'XmippCore-3.22.07-Helios_fix_scons_Environent_calls.patch': '8dcf0f3648f4b3438374ba629a9efa2e5c08eb25ae76ed420513664d21e2246b'}, {'XmippCore-3.22.07-Helios_use_CXXFLAGS_from_EB.patch': From bb635813adaecf716c61c72ac083d73e49f84177 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 02:26:55 +0100 Subject: [PATCH 406/939] update MATLAB-Engine v2021a to PyPI package v2021a-9.10.1 --- ...TLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 38 +++++++++++++++++++ .../MATLAB-Engine-2021a-GCCcore-10.2.0.eb | 34 ----------------- 2 files changed, 38 insertions(+), 34 deletions(-) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..97c48e8fad32 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MATLAB-Engine' +_matlab_version = '2021a' +_engine_version = '9.10.1' +version = "%s-%s" % (_matlab_version, _engine_version) + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.8.6'), +] + +use_pip = True + +exts_list = [ + ('matlabengine', '9.10.1', { + 'modulename': 'matlab.engine', + 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], + }), +] + +sanity_pip_check = True + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +# Systems with old glibc (e.g. CentOS7) need to preload shim library +# modluafooter = """ +# setenv("LD_PRELOAD", pathJoin(os.getenv("EBROOTMATLAB"), "bin", "glnxa64", "glibc-2.17_shim.so")) +# """ + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb deleted file mode 100644 index 83a3d5d719c7..000000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-GCCcore-10.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021a' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '10.2.0'} - -dependencies = [ - ('MATLAB', version, '', SYSTEM), - ('Python', '3.8.6'), -] - -use_pip = False -download_dep_fail = True - -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From abbb3aa220b6ab59d9720d484cb12aa0774d6ec8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 02:28:13 +0100 Subject: [PATCH 407/939] update MATLAB-Engine v2021b to PyPI package v2021b-9.11.19 --- ...LAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 38 +++++++++++++++++++ .../MATLAB-Engine-2021b-GCCcore-11.2.0.eb | 34 ----------------- 2 files changed, 38 insertions(+), 34 deletions(-) create mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb delete mode 100644 easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..c7c345f46d50 --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'MATLAB-Engine' +_matlab_version = '2021b' +_engine_version = '9.11.19' +version = "%s-%s" % (_matlab_version, _engine_version) + +homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' +description = """The MATLAB Engine API for Python provides a package for Python + to call MATLAB as a computational engine.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +dependencies = [ + ('MATLAB', _matlab_version, '', SYSTEM), + ('Python', '3.9.6'), +] + +use_pip = True + +exts_list = [ + ('matlabengine', '9.11.19', { + 'modulename': 'matlab.engine', + 'checksums': ['9385a13c27daa18f6cbfbe1669237e86692a51f317775a3f40e9e3d8090c679b'], + }), +] + +sanity_pip_check = True + +# Test that connection with MATLAB can be established successfully +sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] + +# Systems with old glibc (e.g. CentOS7) need to preload shim library +# modluafooter = """ +# setenv("LD_PRELOAD", pathJoin(os.getenv("EBROOTMATLAB"), "bin", "glnxa64", "glibc-2.17_shim.so")) +# """ + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb deleted file mode 100644 index a188c57dcad9..000000000000 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-GCCcore-11.2.0.eb +++ /dev/null @@ -1,34 +0,0 @@ -easyblock = 'PythonPackage' - -name = 'MATLAB-Engine' -version = '2021b' - -homepage = 'https://www.mathworks.com/help/matlab/matlab-engine-for-python.html' -description = """The MATLAB Engine API for Python provides a package for Python - to call MATLAB as a computational engine.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -dependencies = [ - ('MATLAB', version, '', True), - ('Python', '3.9.6'), -] - -use_pip = False -download_dep_fail = True - -# Since this setup.py does not provide a separate --build-base for the install -# step, both build and install must be performed in a single command. -prebuildopts = "cd $EBROOTMATLAB/extern/engines/python && " -buildopts = "--build-base=%(builddir)s install --prefix=%(installdir)s" - -skipsteps = ['install'] - -# Test that connection with MATLAB can be established successfully -sanity_check_commands = ["python -c 'import matlab.engine; eng = matlab.engine.start_matlab(); eng.quit()'"] - -sanity_pip_check = True - -options = {'modulename': 'matlab.engine'} - -moduleclass = 'math' From 1b69e4da4ebe89d50fdde47eb3518d14ac80572d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 08:24:15 +0100 Subject: [PATCH 408/939] adding easyconfigs: Meson-0.64.0-GCCcore-12.2.0.eb --- .../m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..167a5228187b --- /dev/null +++ b/easybuild/easyconfigs/m/Meson/Meson-0.64.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'Meson' +version = '0.64.0' + +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': '12.2.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c5e27e091c2a35b9049e152a6535045ebbd057253aeb67856de6ecbb7b917bab'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Python', '3.10.8'), # 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' From 34b52a6d8a9dfb1a127cf9091d6edac8e56994f9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 16 Nov 2022 12:32:59 +0000 Subject: [PATCH 409/939] adding easyconfigs: ANSYS-2022R2.eb --- easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb diff --git a/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb b/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb new file mode 100644 index 000000000000..5c94e25f8afd --- /dev/null +++ b/easybuild/easyconfigs/a/ANSYS/ANSYS-2022R2.eb @@ -0,0 +1,30 @@ +name = 'ANSYS' +version = '2022R2' + +homepage = 'https://www.ansys.com' +description = """ANSYS simulation software enables organizations to confidently predict + how their products will operate in the real world. We believe that every product is + a promise of something greater. """ + +toolchain = SYSTEM + +download_instructions = 'Manually obtain (ANSYS%(version)s_LINX64_DiskX.iso) from your ANSYS vendor' +# Custom extract command is used since iso sources contain duplicate file. +sources = [ + {'filename': 'ANSYS%(version)s_LINX64_Disk1.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_Disk2.iso', 'extract_cmd': '7z x -aos %s'}, + {'filename': 'ANSYS%(version)s_LINX64_Disk3.iso', 'extract_cmd': '7z x -aos %s'}, +] +checksums = [ + {'ANSYS2022R2_LINX64_Disk1.iso': '7c9b2a57dd3b87c1dabcd84c913135c83aaac46bf75fbe3fae8da61c85e78198'}, + {'ANSYS2022R2_LINX64_Disk2.iso': '7962ef251e2edb7e999bfb6a857272597973d7ac4c17c2271cfd891347fd452a'}, + {'ANSYS2022R2_LINX64_Disk3.iso': '58d4b72e90a27fe11aee3cd7db251ecd1f80b2353441e7061543c0fc21c14dac'}, +] + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Specify license_server and license_server_port here, or use EB_ANSYS_LICENSE_SERVER and EB_ANSYS_LICENSE_SERVER_PORT +# license_server = "ansys.lic.example.com" +# license_server_port = "1234:5678" + +moduleclass = 'tools' From d431b26b6874c8baec79d10637f28eef402851e8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Nov 2022 15:40:37 +0100 Subject: [PATCH 410/939] adding easyconfigs: IOR-3.3.0-gompi-2022a.eb --- .../i/IOR/IOR-3.3.0-gompi-2022a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb new file mode 100644 index 000000000000..9b3059aa2241 --- /dev/null +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Åke Sandgren, HPC2N, Umeå University + +easyblock = 'ConfigureMake' + +name = "IOR" +version = "3.3.0" + +homepage = 'https://github.com/hpc/ior' +description = """ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, + or HDF5 interfaces. """ + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/hpc/ior/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['41fe66f91aead70f7e53246de68dd194e7ade72070faf696f88efffdcf1bf68b'] + +builddependencies = [ + ('Autotools', '20220317'), + ('Perl', '5.34.1'), +] +dependencies = [ + ('HDF5', '1.12.2'), +] + +configopts = '--with-hdf5 ' +buildopts = 'V=1 ' + +sanity_check_paths = { + 'files': ["bin/ior"], + 'dirs': ["share"] +} + +moduleclass = 'tools' From 4b5e30730dc76f670816a72e2c72017ceeab7685 Mon Sep 17 00:00:00 2001 From: Bart te Lindert Date: Wed, 16 Nov 2022 15:50:27 +0100 Subject: [PATCH 411/939] adding easyconfigs: FreeSurfer-7.3.2-centos7_x86_64.eb --- .../FreeSurfer-7.3.2-centos7_x86_64.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb diff --git a/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb new file mode 100644 index 000000000000..56892c77fd0e --- /dev/null +++ b/easybuild/easyconfigs/f/FreeSurfer/FreeSurfer-7.3.2-centos7_x86_64.eb @@ -0,0 +1,33 @@ +name = 'FreeSurfer' +version = '7.3.2' +versionsuffix = '-centos7_x86_64' + +homepage = 'https://surfer.nmr.mgh.harvard.edu/' +description = """FreeSurfer is a set of tools for analysis and visualization +of structural and functional brain imaging data. FreeSurfer contains a fully +automatic structural imaging stream for processing cross sectional and +longitudinal data.""" + +toolchain = SYSTEM + +source_urls = [ + 'https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/%(version)s/', + 'https://surfer.nmr.mgh.harvard.edu/fswiki/MatlabRuntime?action=AttachFile&do=get&target=' +] +sources = [ + '%(namelower)s-linux%(versionsuffix)s-%(version)s.tar.gz', + 'runtime2014bLinux.tar.gz' +] +checksums = [ + {'freesurfer-linux-centos7_x86_64-7.3.2.tar.gz': + '58518d3ee5abd2e05109208aed2eef145c4e3b994164df8c4e0033c1343b9e56'}, + {'runtime2014bLinux.tar.gz': '944852af2b5a493f5261fd619af828c6e4afc0c90e6f7e709acfb616c5b51648'}, +] + +postinstallcmds = ['cp -a %(builddir)s/MCRv84/ %(installdir)s'] + +license_text = """email@example.com +00000 +g1bb3r1sh""" + +moduleclass = 'bio' From 70debb7b60b88734a6f13e6e6e6e4575bc2ed55e Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 14:59:19 +0000 Subject: [PATCH 412/939] adding easyconfigs: cmocean-2.0-foss-2022a.eb --- .../c/cmocean/cmocean-2.0-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb new file mode 100644 index 000000000000..3531eb020476 --- /dev/null +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -0,0 +1,31 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = "PythonBundle" + +name = 'cmocean' +version = '2.0' + +homepage = 'https://github.com/matplotlib/cmocean' +description = """This package contains colormaps for commonly-used +oceanographic variables. Most of the colormaps started from +matplotlib colormaps, but have now been adjusted using the viscm +tool to be perceptually uniform.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['13eea3c8994d8e303e32a2db0b3e686f6edfb41cb21e7b0e663c2b17eea9b03a'], + }), +] + +moduleclass = 'data' From 1f6acfd410de14901f935a58f00c6ff363dc4529 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 15:05:56 +0000 Subject: [PATCH 413/939] Sanity check added --- easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb index 3531eb020476..452ee96673d7 100644 --- a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -28,4 +28,9 @@ exts_list = [ }), ] +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + moduleclass = 'data' From e5deb360201cab927d4603083b499a16f4b871b7 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 16 Nov 2022 15:18:07 +0000 Subject: [PATCH 414/939] adding easyconfigs: astropy-5.1.1-foss-2022a.eb --- .../a/astropy/astropy-5.1.1-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb b/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb new file mode 100644 index 000000000000..1e3d64025d1b --- /dev/null +++ b/easybuild/easyconfigs/a/astropy/astropy-5.1.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = "PythonBundle" + +name = 'astropy' +version = '5.1.1' + +homepage = 'https://www.astropy.org/' +description = """The Astropy Project is a community effort to develop a common +core package for Astronomy in Python and foster an ecosystem of interoperable +astronomy packages. + +The Astropy community is committed to supporting diversity and inclusion.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyerfa', '2.0.0.1', { + 'modulename': 'erfa', + 'checksums': ['2fd4637ffe2c1e6ede7482c13f583ba7c73119d78bef90175448ce506a0ede30'], + }), + ('extension-helpers', '1.0.0', { + 'checksums': ['ca1bfac67c79cf4a7a0c09286ce2a24eec31bf17715818d0726318dd0e5050e6'], + }), + (name, version, { + 'checksums': ['ba4bd696af7090fd399b464c704bf27b5633121e461785edc70432606a94bd81'], + }), +] + +moduleclass = 'astro' From d0033ea45c9888ee61dbca3e9bb5cbb632b5ddc6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:34:47 +0100 Subject: [PATCH 415/939] adding easyconfigs: intltool-0.51.0-GCCcore-12.2.0.eb --- .../intltool-0.51.0-GCCcore-12.2.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..68c3f09136f5 --- /dev/null +++ b/easybuild/easyconfigs/i/intltool/intltool-0.51.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'intltool' +version = '0.51.0' + +homepage = 'https://freedesktop.org/wiki/Software/intltool/' +description = """intltool is a set of tools to centralize translation of + many different file formats using GNU gettext-compatible PO files.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://launchpad.net/intltool/trunk/%(version)s/+download/'] +sources = [SOURCE_TAR_GZ] +patches = ['intltool-%(version)s_fix-Perl-compat.patch'] +checksums = [ + '67c74d94196b153b774ab9f89b2fa6c6ba79352407037c8c14d5aeb334e959cd', # intltool-0.51.0.tar.gz + 'e839f7228b2b92301831bca88ed0bc7bce5dbf862568f1644642988204903db6', # intltool-0.51.0_fix-Perl-compat.patch +] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('Perl', '5.36.0'), +] + +fix_perl_shebang_for = ['bin/intltool-*'] + +sanity_check_paths = { + 'files': ['bin/intltool%s' % x for x in ['-extract', '-merge', '-prepare', '-update', 'ize']], + 'dirs': [] +} + +sanity_check_commands = ["intltool-merge --help"] + +moduleclass = 'devel' From 6ae319ac98043b85b314fcb44757bfce5ef34628 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:36:54 +0100 Subject: [PATCH 416/939] adding easyconfigs: freetype-2.12.1-GCCcore-12.2.0.eb, Brotli-1.0.9-GCCcore-12.2.0.eb --- .../b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb | 36 ++++++++++++++++ .../freetype-2.12.1-GCCcore-12.2.0.eb | 43 +++++++++++++++++++ 2 files changed, 79 insertions(+) create mode 100644 easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..8056873eb95b --- /dev/null +++ b/easybuild/easyconfigs/b/Brotli/Brotli-1.0.9-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'Brotli' +version = '1.0.9' + +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': '12.2.0'} + +source_urls = ['https://github.com/google/brotli/archive'] +sources = ['v%(version)s.tar.gz'] +patches = ['Brotli-%(version)s_pc_link_flags.patch'] +checksums = [ + 'f9e8d81d0405ba66d181529af42a3354f838c939095ff99930da6aa9cdf6fe46', # v1.0.9.tar.gz + '1a8498fe5179fa530d5e6da57632a7ca8ee98b462953b9995e3400cdac4c3d7e', # Brotli-1.0.9_pc_link_flags.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +sanity_check_paths = { + 'files': ['bin/brotli', 'lib/libbrotlidec.%s' % SHLIB_EXT, 'lib/libbrotlienc.%s' % SHLIB_EXT, + 'lib/libbrotlidec-static.a', 'lib/libbrotlienc-static.a'], + 'dirs': [], +} + +sanity_check_commands = ["brotli --help"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..4b7d4298ad18 --- /dev/null +++ b/easybuild/easyconfigs/f/freetype/freetype-2.12.1-GCCcore-12.2.0.eb @@ -0,0 +1,43 @@ +name = 'freetype' +version = '2.12.1' + +homepage = 'https://www.freetype.org' + +description = """ + FreeType 2 is a software font engine that is designed to be small, efficient, + highly customizable, and portable while capable of producing high-quality + output (glyph images). It can be used in graphics libraries, display servers, + font conversion tools, text image generation tools, and many other products + as well. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + GNU_SAVANNAH_SOURCE, + SOURCEFORGE_SOURCE, +] +sources = [SOURCE_TAR_GZ] +checksums = ['efe71fd4b8246f1b0b1b9bfca13cfff1c9ad85930340c27df469733bbb620938'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('bzip2', '1.0.8'), + ('libpng', '1.6.38'), + ('zlib', '1.2.12'), + ('Brotli', '1.0.9'), +] + +configopts = '--enable-freetype-config --with-harfbuzz=no' + +sanity_check_paths = { + 'files': ['bin/freetype-config', 'lib/libfreetype.a', + 'lib/libfreetype.%s' % SHLIB_EXT, 'lib/pkgconfig/freetype2.pc'], + 'dirs': ['include/freetype2'], +} + +sanity_check_commands = ["freetype-config --help"] + +moduleclass = 'vis' From e7441c854d59e7bc4fbe2d10743688559653681b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:37:46 +0100 Subject: [PATCH 417/939] adding easyconfigs: fontconfig-2.14.1-GCCcore-12.2.0.eb, util-linux-2.38.1-GCCcore-12.2.0.eb, gperf-3.1-GCCcore-12.2.0.eb --- .../fontconfig-2.14.1-GCCcore-12.2.0.eb | 40 ++++++++++++++++++ .../g/gperf/gperf-3.1-GCCcore-12.2.0.eb | 32 +++++++++++++++ .../util-linux-2.38.1-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 3 files changed, 113 insertions(+) create mode 100644 easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..6a514ecbd3cc --- /dev/null +++ b/easybuild/easyconfigs/f/fontconfig/fontconfig-2.14.1-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'fontconfig' +version = '2.14.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/fontconfig/' + +description = """ + Fontconfig is a library designed to provide system-wide font configuration, + customization and application access. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.freedesktop.org/software/fontconfig/release/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ae480e9ca34382790312ff062c625ec70df94d6d9a9366e2b2b3d525f7f90387'] + +builddependencies = [ + ('binutils', '2.39'), + ('gperf', '3.1'), + ('pkgconf', '1.9.3'), + ('Python', '3.10.8', '-bare'), +] + +dependencies = [ + ('expat', '2.4.9'), + ('freetype', '2.12.1'), + ('util-linux', '2.38.1'), +] + +configopts = '--disable-docs ' + +sanity_check_paths = { + 'files': ['include/fontconfig/fontconfig.h', 'lib/libfontconfig.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5f0199119757 --- /dev/null +++ b/easybuild/easyconfigs/g/gperf/gperf-3.1-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'gperf' +version = '3.1' + +homepage = 'https://www.gnu.org/software/gperf/' +description = """ + GNU gperf is a perfect hash function generator. For a given list of strings, + it produces a hash function and hash table, in form of C or C++ code, for + looking up a value depending on the input string. The hash function is + perfect, which means that the hash table has no collisions, and the hash + table lookup needs a single string comparison only. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['588546b945bba4b70b6a3a616e80b4ab466e3f33024a352fc2198112cdbb3ae2'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/gperf'], + 'dirs': [], +} + +sanity_check_commands = ["gperf --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ddc2a4e1286e --- /dev/null +++ b/easybuild/easyconfigs/u/util-linux/util-linux-2.38.1-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'util-linux' +version = '2.38.1' + +homepage = 'https://www.kernel.org/pub/linux/utils/util-linux' + +description = "Set of Linux utilities" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['%s/v%%(version_major_minor)s' % homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['0820eb8eea90408047e3715424bc6be771417047f683950fecb4bdd2e2cbbc6e'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('ncurses', '6.3'), + ('zlib', '1.2.12'), +] + +# disable account related utilities (they need OS dependent pam-devel files) +# disable wall and friends (requires group changing permissions for install user) +# install systemd service files in install dir +# install bash completion files in install dir +configopts = "--disable-chfn-chsh --disable-login --disable-su --disable-rfkill " +configopts += "--disable-wall --disable-use-tty-group " +configopts += "--disable-makeinstall-chown --disable-makeinstall-setuid " +configopts += "--with-systemdsystemunitdir='${prefix}/systemd' " +configopts += "--with-bashcompletiondir='${prefix}/share/bash-completion/completions' " +# disable building Python bindings (since we don't include Python as a dep) +configopts += "--without-python " + +sanity_check_paths = { + 'files': ['lib/lib%s.a' % x for x in ['blkid', 'mount', 'uuid']], + 'dirs': ['include', 'bin', 'share', 'sbin'], +} + +moduleclass = 'tools' From 4fe7551a558ac201f4797a64a3dd0dbf032eefff Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 16:39:26 +0100 Subject: [PATCH 418/939] replace hardcoded versions for matlabengine extensions --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 +- .../MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index 97c48e8fad32..d559c0538ddd 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True exts_list = [ - ('matlabengine', '9.10.1', { + ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', 'checksums': ['c1610690dbe58ac00e74e8cbb20406208235ede47da7960238e0c2fd3bd496c0'], }), diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb index c7c345f46d50..d1457326e93f 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -19,7 +19,7 @@ dependencies = [ use_pip = True exts_list = [ - ('matlabengine', '9.11.19', { + ('matlabengine', _engine_version, { 'modulename': 'matlab.engine', 'checksums': ['9385a13c27daa18f6cbfbe1669237e86692a51f317775a3f40e9e3d8090c679b'], }), From 36c48a24e97ca94cef58dacbb5f3aa81cbb59a6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 16:42:05 +0100 Subject: [PATCH 419/939] adding easyconfigs: X11-20221110-GCCcore-12.2.0.eb --- .../x/X11/X11-20221110-GCCcore-12.2.0.eb | 213 ++++++++++++++++++ 1 file changed, 213 insertions(+) create mode 100644 easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..ea22050d1227 --- /dev/null +++ b/easybuild/easyconfigs/x/X11/X11-20221110-GCCcore-12.2.0.eb @@ -0,0 +1,213 @@ +easyblock = 'Bundle' + +name = 'X11' +version = '20221110' + +homepage = 'https://www.x.org' +description = "The X Window System (X11) is a windowing system for bitmap displays" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + XORG_LIB_SOURCE, + XORG_PROTO_SOURCE, + 'https://xcb.freedesktop.org/dist/', + 'https://xkbcommon.org/download/', + XORG_DATA_SOURCE + '/xkeyboard-config', + XORG_DATA_SOURCE, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('Bison', '3.8.2'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('intltool', '0.51.0'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [ + ('bzip2', '1.0.8'), + ('fontconfig', '2.14.1'), + ('freetype', '2.12.1'), + ('zlib', '1.2.12'), + ('xorg-macros', '1.19.3'), + ('libpciaccess', '0.17'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + ('libpthread-stubs', '0.4', { # 2017-03-14 + 'checksums': ['50d5686b79019ccea08bcbd7b02fe5a40634abcfd4146b6e75c6420cc170e9d9'], + }), + ('xorgproto', '2022.2', { # 2022-08-11 + 'checksums': ['da351a403d07a7006d7bdc8dcfc14ddc1b588b38fb81adab9989a8eef605757b'], + }), + ('libXau', '1.0.10', { # 2022-08-26 + 'checksums': ['51a54da42475d4572a0b59979ec107c27dacf6c687c2b7b04e5cf989a7c7e60c'], + }), + ('libXdmcp', '1.1.3', { # 2019-03-16 + 'checksums': ['2ef9653d32e09d1bf1b837d0e0311024979653fe755ad3aaada8db1aa6ea180c'], + }), + ('xcb-proto', '1.15.2', { # 2022-06-17 + 'checksums': ['6b1ed9cd7cf35e37913eeecca37e5b85b14903002942b3e332f321335c27a8eb'], + }), + ('libxcb', '1.15', { # 2022-05-03 + 'checksums': ['1cb65df8543a69ec0555ac696123ee386321dfac1964a3da39976c9a05ad724d'], + }), + ('xtrans', '1.4.0', { # 2019-03-16 + 'checksums': ['48ed850ce772fef1b44ca23639b0a57e38884045ed2cbb18ab137ef33ec713f9'], + }), + ('libxkbcommon', '1.4.1', { # 2022-05-21 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['943c07a1e2198026d8102b17270a1f406e4d3d6bbc4ae105b9e1b82d7d136b39'], + 'preconfigopts': '', + 'configopts': '-Denable-wayland=false -Denable-docs=false ', + }), + ('libX11', '1.8.2', { # 2022-11-10 + 'checksums': ['f1bc56187bee0f830e1179ac5068ac93b78c51ace94eb27702ffb2efd116587b'], + }), + ('libXext', '1.3.5', { # 2022-10-29 + 'checksums': ['1a3dcda154f803be0285b46c9338515804b874b5ccc7a2b769ab7fd76f1035bd'], + }), + ('libFS', '1.0.9', { # 2022-08-26 + 'checksums': ['8bc2762f63178905228a28670539badcfa2c8793f7b6ce3f597b7741b932054a'], + }), + ('libICE', '1.0.10', { # 2019-07-14 + 'checksums': ['1116bc64c772fd127a0d0c0ffa2833479905e3d3d8197740b3abd5f292f22d2d'], + }), + ('libSM', '1.2.3', { # 2018-10-10 + 'checksums': ['1e92408417cb6c6c477a8a6104291001a40b3bb56a4a60608fdd9cd2c5a0f320'], + }), + ('libXScrnSaver', '1.2.3', { # 2018-07-05 + 'checksums': ['4f74e7e412144591d8e0616db27f433cfc9f45aae6669c6c4bb03e6bf9be809a'], + }), + ('libXt', '1.2.1', { # 2021-01-24 + 'checksums': ['6da1bfa9dd0ed87430a5ce95b129485086394df308998ebe34d98e378e3dfb33'], + }), + ('libXmu', '1.1.4', { # 2022-10-17 + 'checksums': ['3091d711cdc1d8ea0f545a13b90d1464c3c3ab64778fd121f0d789b277a80289'], + }), + ('libXpm', '3.5.13', { # 2019-12-13 + 'checksums': ['e3dfb0fb8c1f127432f2a498c7856b37ce78a61e8da73f1aab165a73dd97ad00'], + }), + ('libXaw', '1.0.14', { # 2021-03-27 + 'checksums': ['59cfed2712cc80bbfe62dd1aacf24f58d74a76dd08329a922077b134a8d8048f'], + }), + ('libXfixes', '6.0.0', { # 2021-05-11 + 'checksums': ['82045da5625350838390c9440598b90d69c882c324ca92f73af9f0e992cb57c7'], + }), + ('libXcomposite', '0.4.5', { # 2019-03-11 + 'checksums': ['581c7fc0f41a99af38b1c36b9be64bc13ef3f60091cd3f01105bbc7c01617d6c'], + }), + ('libXrender', '0.9.11', { # 2022-10-22 + 'checksums': ['6aec3ca02e4273a8cbabf811ff22106f641438eb194a12c0ae93c7e08474b667'], + }), + ('libXcursor', '1.2.1', { # 2022-04-03 + 'checksums': ['77f96b9ad0a3c422cfa826afabaf1e02b9bfbfc8908c5fa1a45094faad074b98'], + }), + ('libXdamage', '1.1.5', { # 2019-03-11 + 'checksums': ['630ec53abb8c2d6dac5cd9f06c1f73ffb4a3167f8118fdebd77afd639dbc2019'], + }), + ('libfontenc', '1.1.6', { # 2022-08-30 + 'checksums': ['c103543a47ce5c0200fb1867f32df5e754a7c3ef575bf1fe72187117eac22a53'], + }), + ('libXfont', '1.5.4', { # 2017-11-28 + 'checksums': ['59be6eab53f7b0feb6b7933c11d67d076ae2c0fd8921229c703fc7a4e9a80d6e'], + }), + ('libXfont2', '2.0.6', { # 2022-08-26 + 'checksums': ['a944df7b6837c8fa2067f6a5fc25d89b0acc4011cd0bc085106a03557fb502fc'], + }), + ('libXft', '2.3.6', { # 2022-09-10 + 'checksums': ['b7e59f69e0bbabe9438088775f7e5a7c16a572e58b11f9722519385d38192df5'], + }), + ('libXi', '1.8', { # 2021-09-15 + 'checksums': ['c80fd200a1190e4406bb4cc6958839d9651638cb47fa546a595d4bebcd3b9e2d'], + }), + ('libXinerama', '1.1.5', { # 2022-10-29 + 'checksums': ['2efa855cb42dc620eff3b77700d8655695e09aaa318f791f201fa60afa72b95c'], + }), + ('libXrandr', '1.5.2', { # 2019-03-16 + 'checksums': ['3f10813ab355e7a09f17e147d61b0ce090d898a5ea5b5519acd0ef68675dcf8e'], + }), + ('libXres', '1.2.1', { # 2021-03-31 + 'checksums': ['918fb33c3897b389a1fbb51571c5c04c6b297058df286d8b48faa5af85e88bcc'], + }), + ('libXtst', '1.2.4', { # 2022-09-27 + 'checksums': ['01366506aeb033f6dffca5326af85f670746b0cabbfd092aabefb046cf48c445'], + }), + ('libXv', '1.0.11', { # 2016-10-04 + 'checksums': ['c4112532889b210e21cf05f46f0f2f8354ff7e1b58061e12d7a76c95c0d47bb1'], + }), + ('libXvMC', '1.0.13', { # 2022-03-22 + 'checksums': ['e630b4373af8c67a7c8f07ebe626a1269a613d262d1f737b57231a06f7c34b4e'], + }), + ('libXxf86dga', '1.1.5', { # 2019-03-16 + 'checksums': ['715e2bf5caf6276f0858eb4b11a1aef1a26beeb40dce2942387339da395bef69'], + }), + ('libXxf86vm', '1.1.5', { # 2022-09-27 + 'checksums': ['f3f1c29fef8accb0adbd854900c03c6c42f1804f2bc1e4f3ad7b2e1f3b878128'], + }), + ('libdmx', '1.1.4', { # 2018-05-14 + 'checksums': ['4d05bd5b248c1f46729fa1536b7a5e4d692567327ad41564c36742fb327af925'], + }), + ('libxkbfile', '1.1.1', { # 2022-10-18 + 'checksums': ['87faee6d4873c5631e8bb53e85134084b862185da682de8617f08ca18d82e216'], + }), + ('libxshmfence', '1.3', { # 2018-02-26 + 'checksums': ['7eb3d46ad91bab444f121d475b11b39273142d090f7e9ac43e6a87f4ff5f902c'], + }), + ('xcb-util', '0.4.0', { # 2014-10-15 + 'checksums': ['0ed0934e2ef4ddff53fcc70fc64fb16fe766cd41ee00330312e20a985fd927a7'], + }), + ('xcb-util-image', '0.4.1', { # 2022-10-18 + 'checksums': ['0ebd4cf809043fdeb4f980d58cdcf2b527035018924f8c14da76d1c81001293b'], + }), + ('xcb-util-keysyms', '0.4.1', { # 2022-10-19 + 'checksums': ['1fa21c0cea3060caee7612b6577c1730da470b88cbdf846fa4e3e0ff78948e54'], + }), + ('xcb-util-renderutil', '0.3.10', { # 2022-10-19 + 'checksums': ['e04143c48e1644c5e074243fa293d88f99005b3c50d1d54358954404e635128a'], + }), + ('xcb-util-wm', '0.4.2', { # 2022-10-19 + 'checksums': ['dcecaaa535802fd57c84cceeff50c64efe7f2326bf752e16d2b77945649c8cd7'], + }), + ('xcb-util-cursor', '0.1.4', { # 2022-10-18 + 'checksums': ['cc8608ebb695742b6cf84712be29b2b66aa5f6768039528794fca0fa283022bf'], + }), + ('xkeyboard-config', '2.37', { # 2022-10-04 + 'easyblock': 'MesonNinja', + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['eb1383a5ac4b6210d7c7302b9d6fab052abdf51c5d2c9b55f1f779997ba68c6c'], + # required to overrule parent preconfigopts that runs autogen.sh if configure script is missing + 'preconfigopts': '', + }), + ('printproto', '1.0.5', { # 2011-01-06 + 'checksums': ['e8b6f405fd865f0ea7a3a2908dfbf06622f57f2f91359ec65d13b955e49843fc'], + }), + ('libXp', '1.0.4', { # 2022-09-12 + 'checksums': ['05e46af1ccb68f1752cca5879774a4fb9bf3b19fe088eb745034956e0c6fadba'], + }), + ('xbitmaps', '1.1.2', { # 2018-03-10 + 'checksums': ['27e700e8ee02c43f7206f4eca8f1953ad15236cac95d7a0f08505c3f7d99c265'], + }), +] + +preconfigopts = "if [ ! -f configure ]; then ./autogen.sh; fi && " + +sanity_check_paths = { + 'files': ['include/X11/Xlib.h', 'include/X11/Xutil.h'], + 'dirs': ['include/GL', 'include/X11', 'include/X11/extensions', 'lib/pkgconfig', + 'share/pkgconfig', 'share/X11/xkb'], +} + +moduleclass = 'vis' From 6cf1b4bf4a135e5b20243ba4cfe8f8f954cea413 Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Wed, 16 Nov 2022 16:12:15 +0000 Subject: [PATCH 420/939] adding easyconfigs: SpaceRanger-2.0.0-GCC-11.2.0.eb --- .../SpaceRanger-2.0.0-GCC-11.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb new file mode 100644 index 000000000000..b6aba4be7491 --- /dev/null +++ b/easybuild/easyconfigs/s/SpaceRanger/SpaceRanger-2.0.0-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'Tarball' + +name = 'SpaceRanger' +version = '2.0.0' + +homepage = 'https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger' +description = """ Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output +and brightfield microscope images in order to detect tissue, align reads, generate feature-spot matrices, +perform clustering and gene expression analysis, and place spots in spatial context on the slide image. """ + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +download_instructions = """ +Download sources from homepage, registration required +https://support.10xgenomics.com/spatial-gene-expression/software/downloads/latest +""" + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bdaa784e433c2e3707bed6a868042e954248e97fb4021d7179460a2b3702205c'] + +dependencies = [ + ('bcl2fastq2', '2.20.0'), +] + +allow_prepend_abs_path = True +# prepend reference databases GRCh38 and mm10 to PATH +# modextrapaths = {'PATH': '/path/to/databases/%(namelower)s-%(version)s'} + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': ['external', 'lib', 'mro'], +} + +sanity_check_commands = ['%(namelower)s -h'] + +moduleclass = 'bio' From 59a818348d8e797c2b498412f5fede03c16ae7bc Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 17:11:14 +0100 Subject: [PATCH 421/939] switch IJulia and MultilevelEstimators to JuliaBundle easyblock --- .../i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb | 14 +------------- ...elEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb | 17 +---------------- 2 files changed, 2 insertions(+), 29 deletions(-) diff --git a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb index 54566147c74f..06667a1bbf80 100644 --- a/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb +++ b/easybuild/easyconfigs/i/IJulia/IJulia-1.23.3-Julia-1.6.7.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'JuliaBundle' name = 'IJulia' version = '1.23.3' @@ -14,12 +14,6 @@ dependencies = [ ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -exts_defaultclass = 'JuliaPackage' -exts_filter = ("julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - exts_list = [ ('Parsers', '2.4.2', { 'source_urls': ['https://github.com/JuliaData/Parsers.jl/archive/'], @@ -74,13 +68,7 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['packages'], -} - modextrapaths = { - 'JULIA_DEPOT_PATH': '', 'JUPYTER_PATH': 'jupyter', } diff --git a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb index b26dd65738ec..822fe47b6474 100644 --- a/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb +++ b/easybuild/easyconfigs/m/MultilevelEstimators/MultilevelEstimators-0.1.0-GCC-11.2.0-Julia-1.7.2.eb @@ -1,4 +1,4 @@ -easyblock = 'Bundle' +easyblock = 'JuliaBundle' name = 'MultilevelEstimators' version = '0.1.0' @@ -15,12 +15,6 @@ dependencies = [ ('Julia', local_julia_ver, '-linux-%s' % ARCH, SYSTEM), ] -exts_defaultclass = 'JuliaPackage' -exts_filter = ("julia -e 'using %(ext_name)s'", "") -exts_default_options = { - 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}], -} - exts_list = [ ('Preferences', '1.3.0', { 'source_urls': ['https://github.com/JuliaPackaging/Preferences.jl/archive/'], @@ -101,13 +95,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['packages/%(name)s'] -} - -modextrapaths = { - 'JULIA_DEPOT_PATH': '', -} - moduleclass = 'lib' From f6b8d3a7a30b02164d0d60654b1412d18a3288b4 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 16 Nov 2022 17:44:51 +0100 Subject: [PATCH 422/939] IOR: Drop leftover builddep from old easyconfig. --- easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb index 9b3059aa2241..4ddd258e4403 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -18,9 +18,9 @@ sources = [SOURCELOWER_TAR_BZ2] checksums = ['41fe66f91aead70f7e53246de68dd194e7ade72070faf696f88efffdcf1bf68b'] builddependencies = [ - ('Autotools', '20220317'), ('Perl', '5.34.1'), ] + dependencies = [ ('HDF5', '1.12.2'), ] From 4849ec35cc212b948195b1f82eb9e4716b3d0c23 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 16 Nov 2022 18:31:41 +0100 Subject: [PATCH 423/939] add missing pyWannier90 dependency for mcu + enhance sanity check --- easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb index 5a34c8b03a6f..c70eb5db0f6a 100644 --- a/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb +++ b/easybuild/easyconfigs/m/mcu/mcu-2021-04-06-gomkl-2021a.eb @@ -19,14 +19,17 @@ dependencies = [ ('SciPy-bundle', '2021.05'), ('matplotlib', '3.4.2'), ('spglib-python', '1.16.1'), + ('pyWannier90', '2021-12-07'), ] -use_pip = True download_dep_fail = True -sanity_pip_check = True +use_pip = True sanity_check_commands = [ "python -c 'from mcu import VASP'", + "python -c 'import mcu.wannier90.pywannier90_vasp'", ] +sanity_pip_check = True + moduleclass = 'lib' From 40bad0fb605e2e69b99a1d12bdc7b59fb63189b6 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Wed, 16 Nov 2022 20:45:54 +0000 Subject: [PATCH 424/939] remove unused prebuildopts --- easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb index 9b019b172c70..456ebc347886 100644 --- a/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb +++ b/easybuild/easyconfigs/b/basemap/basemap-1.3.6-foss-2022a.eb @@ -40,7 +40,6 @@ exts_list = [ }), (name, version, { 'modulename': 'mpl_toolkits.basemap', - 'prebuildopts': 'GEOS_DIR=$EBROOTGEOS', 'preinstallopts': 'cd packages/%(name)s && GEOS_DIR=$EBROOTGEOS', 'sources': ['v%(version)s.tar.gz'], 'source_urls': ['https://github.com/matplotlib/basemap/archive/'], From a715b34768b61935a0d74e8dc6ec4c96b8313203 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 22:45:24 +0100 Subject: [PATCH 425/939] add build dependency on binutils to MATLAB-Engine v2021a-9.10.1 --- .../MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb index d559c0538ddd..f9fc548a6ee1 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021a-9.10.1-GCCcore-10.2.0.eb @@ -11,6 +11,8 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [ ('MATLAB', _matlab_version, '', SYSTEM), ('Python', '3.8.6'), From 5b1cfd90607afa5f3f7a31275d9669f8ad6a7850 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 16 Nov 2022 22:46:05 +0100 Subject: [PATCH 426/939] add build dependency on binutils to MATLAB-Engine v2021b-9.11.19 --- .../MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb index d1457326e93f..7bbd56299497 100644 --- a/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/MATLAB-Engine/MATLAB-Engine-2021b-9.11.19-GCCcore-11.2.0.eb @@ -11,6 +11,8 @@ description = """The MATLAB Engine API for Python provides a package for Python toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +builddependencies = [('binutils', '2.37')] + dependencies = [ ('MATLAB', _matlab_version, '', SYSTEM), ('Python', '3.9.6'), From 1880305e6208d1c6f1c9fd6736bf455b226ca87d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Nov 2022 09:40:16 +0100 Subject: [PATCH 427/939] using SYSTEM rather than True for CUDA dependency in NAMD easyconfig --- .../easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb index ba107970cf12..d89411f76ccf 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -24,7 +24,7 @@ checksums = [ # support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.11'), - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] builddependencies = [ From 09eacbe4fb9de594bcbd0b5587cd50ef6ce85159 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 17 Nov 2022 10:08:16 +0100 Subject: [PATCH 428/939] simplify 'sources' spec in NAMD 2.14 easyconfig + remove useless comment --- .../easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb index d89411f76ccf..eafa0dbcabf4 100644 --- a/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/NAMD/NAMD-2.14-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'usempi': False, 'openmp': False, 'pic': True} source_urls = ['https://www.ks.uiuc.edu/Research/namd/%(version)s/download/946183/'] -sources = [{'filename': 'NAMD_%(version)s_Source.tar.gz'}] +sources = ['NAMD_%(version)s_Source.tar.gz'] patches = [ "%(name)s-%(version)s_Linux-POWER-cuda.patch", "%(name)s-%(version)s-use_system_mremap_decl.patch" @@ -21,7 +21,6 @@ checksums = [ 'a838bd66a8f741247436687bd355c439f3d77542996d96e091b8b6bd0ccc34e2', # NAMD-2.14-use_system_mremap_decl.patch ] -# support for GCC 8+ on POWER dependencies = [ ('Tcl', '8.6.11'), ('CUDA', '11.3.1', '', SYSTEM), From 9885375556349694732e58132ba0e5411bf98b9a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 17 Nov 2022 11:04:14 +0100 Subject: [PATCH 429/939] Add missing cuFFTAdvisor source --- .../x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb index fc96f59b8600..f3e9847d3b7f 100644 --- a/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/x/Xmipp/Xmipp-3.22.07-Helios-foss-2022a-CUDA-11.7.0.eb @@ -32,6 +32,12 @@ sources = [ 'filename': 'xmippViz-v%(version)s.tar.gz', 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', }, + { + 'source_urls': ['https://github.com/DStrelak/cuFFTAdvisor/archive/'], + 'download_filename': '14523b8ca7e2f5474feae49eb5ac8ca1fa25f5cd.tar.gz', + 'filename': 'cuFFTAdvisor-20191010.tar.gz', + 'extract_cmd': 'tar -xzf %s -C %(namelower)s-%(version)s/src', + }, ] patches = [ '%(name)s-%(version)s_fix_scons_Environent_calls.patch', @@ -50,6 +56,7 @@ checksums = [ {'xmipp-v3.22.07-Helios.tar.gz': 'f62e2729130b63d18e518930dd96a7a5250219e40c155abb78942a0642237ecf'}, {'xmippCore-v3.22.07-Helios.tar.gz': '58e1143626cf807655a4756b165c21578d6f1b1777b43d363a2845d92d0bab8f'}, {'xmippViz-v3.22.07-Helios.tar.gz': 'e1ce2cbbd57d3307d38538b29194a0190d633e5e062685387a6baf0329ad05b3'}, + {'cuFFTAdvisor-20191010.tar.gz': '2d97cc1c9c955fa5bee44eb232d49f25f2c8ad164ea2be754d44c723c613be46'}, {'Xmipp-3.22.07-Helios_fix_scons_Environent_calls.patch': '5b59babad5a445ec7315a809509704d2d07232d2a5d180bfb78ebc8007bd0c95'}, {'Xmipp-3.22.07-Helios_drop_useless_CXXFLAGS_setting.patch': From 16045c6c49fc7b7d237e39facdebe7ef016b9b3a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Nov 2022 17:15:22 +0100 Subject: [PATCH 430/939] adding easyconfigs: cdo-bindings-1.5.7-foss-2021b.eb --- .../cdo-bindings-1.5.7-foss-2021b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb new file mode 100644 index 000000000000..e387e1c022c9 --- /dev/null +++ b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'cdo-bindings' +version = '1.5.7' + +homepage = 'https://github.com/Try2Code/cdo-bindings' +description = "Python interface to CDO." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('CDO', '2.0.5'), + ('netcdf4-python', '1.5.8'), + ('xarray', '0.20.1'), # optional +] + +use_pip = True + +exts_list = [ + ('cdo', version, { + 'checksums': ['898c2b0ff97ec494569e5d94302350538efa898d42998bfed76b4f52c6c16f3c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 2a8ed2478b091d20ffb02aa0242b7594ea7d1717 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 17 Nov 2022 23:32:54 +0100 Subject: [PATCH 431/939] downgrade dependency on netcdf-python from cdo-bindings v1.5.7 --- .../easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb index e387e1c022c9..b3f6ed923ba4 100644 --- a/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb +++ b/easybuild/easyconfigs/c/cdo-bindings/cdo-bindings-1.5.7-foss-2021b.eb @@ -11,7 +11,7 @@ toolchain = {'name': 'foss', 'version': '2021b'} dependencies = [ ('Python', '3.9.6'), ('CDO', '2.0.5'), - ('netcdf4-python', '1.5.8'), + ('netcdf4-python', '1.5.7'), ('xarray', '0.20.1'), # optional ] From 26c14ad2227b6a8022cff046833b5cf34a1af51d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Nov 2022 00:41:38 +0100 Subject: [PATCH 432/939] remove default sanity checks from cmocean v2.0 --- easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb index 452ee96673d7..3531eb020476 100644 --- a/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/c/cmocean/cmocean-2.0-foss-2022a.eb @@ -28,9 +28,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'data' From 84bf86d4e5b38adca88f3058f5eb06ca77b325b1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Nov 2022 02:07:59 +0100 Subject: [PATCH 433/939] remove default sanity checks from gsw v3.6.16 --- easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb | 7 ------- 1 file changed, 7 deletions(-) diff --git a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb index aa8438cd21e0..b18c6a531815 100644 --- a/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb +++ b/easybuild/easyconfigs/g/gsw/gsw-3.6.16-foss-2022a.eb @@ -21,22 +21,15 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ] use_pip = True sanity_pip_check = True exts_list = [ - (name, version, { 'checksums': ['d24d820c8b43dbf72206cf5e3b0ed800b05aa85ca40afd39c9abd19849714197'], }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' From 521a6fedbe179e49bf8ca8a79469997f26676345 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 18 Nov 2022 08:54:49 +0100 Subject: [PATCH 434/939] Add missing Authors from previous easyconfigs of IOR. --- easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb index 4ddd258e4403..770777c7b5ec 100644 --- a/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb +++ b/easybuild/easyconfigs/i/IOR/IOR-3.3.0-gompi-2022a.eb @@ -1,4 +1,8 @@ # 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 +# Author: Robert Mijakovic Date: Fri, 18 Nov 2022 10:14:48 +0100 Subject: [PATCH 435/939] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index 182023f46912..c97a027b5c34 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -34,6 +34,8 @@ dependencies = [ ('cURL', '7.83.0'), ('Szip', '2.1.1'), ('zstd', '1.5.2'), + ('bzip2', '1.0.8'), + ('libxml2', '2.9.13'), ] # make sure both static and shared libs are built From 88fc4eefb4cb7ea38b7578e57f6e7b7a1e5e7504 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 10:36:52 +0100 Subject: [PATCH 436/939] adding easyconfigs: libxml2-python-2.9.13-GCCcore-11.3.0.eb --- .../libxml2-python-2.9.13-GCCcore-11.3.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a63e21ba6345 --- /dev/null +++ b/easybuild/easyconfigs/l/libxml2-python/libxml2-python-2.9.13-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'libxml2-python' +version = '2.9.13' + +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': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.gnome.org/sources/libxml2/%(version_major_minor)s/'] +sources = ['libxml2-%(version)s.tar.xz'] +patches = [ + 'libxml2-2.9.7_fix-hardcoded-paths.patch', +] +checksums = [ + '276130602d12fe484ecc03447ee5e759d0465558fbc9d6bd144e3745306ebf0e', # libxml2-2.9.13.tar.gz + '3d5651c015fd375d855421983b7d33ffd4af797b7411f46e05cd8c57b210e542', # libxml2-2.9.7_fix-hardcoded-paths.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('XZ', '5.2.5'), + ('Python', '3.10.4'), + ('libxml2', version), + ('libiconv', '1.17'), +] + +start_dir = 'python' + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +options = {'modulename': 'libxml2'} + +moduleclass = 'lib' From b6ee6a570e2700a2ad68cb6034c3f0ba18199815 Mon Sep 17 00:00:00 2001 From: garadar Date: Fri, 18 Nov 2022 10:47:29 +0100 Subject: [PATCH 437/939] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb index f588b3b926d5..efcf60ced349 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'system', 'version': ''} # source_urls = [PYPI_SOURCE] # Link copy from pypi.org | PYPI_SOURCE is not working -sources = ["https://files.pythonhosted.org/packages/15/0b/fa95a349434f77d8afc775dd999152d7612b6baed52083981ac84eaa41e9/resolos-0.3.5.tar.gz"] +sources = [SOURCE_TAR_GZ] checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] From c41940db6347f79adba9bd48a5306c546c47c1a7 Mon Sep 17 00:00:00 2001 From: garadar Date: Fri, 18 Nov 2022 10:54:33 +0100 Subject: [PATCH 438/939] Update and rename resolos-0.3.5.eb to resolos-0.3.5-GCCcore-11.3.0.eb --- ...os-0.3.5.eb => resolos-0.3.5-GCCcore-11.3.0.eb} | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) rename easybuild/easyconfigs/r/resolos/{resolos-0.3.5.eb => resolos-0.3.5-GCCcore-11.3.0.eb} (75%) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb similarity index 75% rename from easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb rename to easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index efcf60ced349..e3cc4db884a7 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -4,18 +4,26 @@ name = 'resolos' version = '0.3.5' homepage = 'https://gitlab.unige.ch/resolos/resolos' -description = """Resolos is a toolkit written in Python for maintaining reproducible environments for scientific computations. -It's main goal is to enable researchers to easily replicate environments through space (running code on HPC environment) +description = """Resolos is a toolkit written in Python for maintaining reproducible environments +for scientific computations. +It's main goal is to enable researchers to easily replicate environments through space +(running code on HPC environment) + and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation.""" -toolchain = {'name': 'system', 'version': ''} +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} # source_urls = [PYPI_SOURCE] # Link copy from pypi.org | PYPI_SOURCE is not working sources = [SOURCE_TAR_GZ] checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] +dependencies = { + ('Python', '3.10.4'), + ('PyYAML', '6.0'), +} + use_pip = True use_pip_for_deps = True From 35f7c584e93f395a9ec79c219b6e57f9d47e82e1 Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Fri, 18 Nov 2022 12:07:04 +0100 Subject: [PATCH 439/939] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb index c97a027b5c34..8cec66eec5aa 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.0-iimpi-2022a.eb @@ -39,6 +39,7 @@ dependencies = [ ] # 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", From 2220ddf00633babcac55f4402fbef3d63b7bf304 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 12:11:56 +0100 Subject: [PATCH 440/939] adding easyconfigs: ABINIT-9.6.2-foss-2022a.eb, ABINIT-9.6.2-intel-2022a.eb --- .../a/ABINIT/ABINIT-9.6.2-foss-2022a.eb | 75 +++++++++++++++++++ .../a/ABINIT/ABINIT-9.6.2-intel-2022a.eb | 71 ++++++++++++++++++ 2 files changed, 146 insertions(+) create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb new file mode 100644 index 000000000000..7f51bbe7c76e --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb @@ -0,0 +1,75 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.6.2' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] + +builddependencies = [ + ('Python', '3.10.4'), +] +dependencies = [ + ('libxc', '5.2.3'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('HDF5', '1.12.2'), + ('Wannier90', '3.1.0'), +] + +# Needed due to changes in GCC10. +configopts = 'FCFLAGS="-fallow-argument-mismatch -ffree-line-length-none $FCFLAGS" ' +configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' + +# Ensure MPI +configopts += '--with-mpi="yes" ' +# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from OpenBLAS +configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' + +# FFTW +configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# Enable OpenMP +configopts += '--enable-openmp ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb new file mode 100644 index 000000000000..fbf7936af3ff --- /dev/null +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'ABINIT' +version = '9.6.2' + +homepage = 'https://www.abinit.org/' +description = """ +ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of +systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using +pseudopotentials and a planewave or wavelet basis. +""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'pic': True} + +source_urls = ['https://www.abinit.org/sites/default/files/packages/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b018c2ff24338a5952c5550a7e09d4c7793b62402c7aa4e09273e9a666e674fb'] + +builddependencies = [ + ('Python', '3.10.4'), +] +dependencies = [ + ('libxc', '5.2.3'), + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('HDF5', '1.12.2'), + ('Wannier90', '3.1.0'), +] + +# Ensure MPI with intel wrappers. +configopts = '--with-mpi="yes" ' +configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' + +# Enable OpenMP +configopts += '--enable-openmp="yes" ' + +# BLAS/Lapack from MKL +configopts += '--with-linalg-flavor=mkl ' + +# FFTW from MKL +configopts += '--with-fft-flavor=dfti ' + +# libxc support +configopts += '--with-libxc=${EBROOTLIBXC} ' + +# hdf5/netcdf4 support +configopts += '--with-netcdf="${EBROOTNETCDF}" ' +configopts += '--with-netcdf-fortran="${EBROOTNETCDFMINFORTRAN}" ' +configopts += '--with-hdf5="${EBROOTHDF5}" ' + +# Wannier90 +configopts += '--with-wannier90="${EBROOTWANNIER90}" ' +preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' + +# Enable double precision for GW calculations +configopts += '--enable-gw-dpc ' + +# Enable OpenMP +configopts += '--enable-openmp ' + +# 'make check' is just executing some basic unit tests. +# Also running 'make tests_v1' to have some basic validation +runtest = "check && make test_v1" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['abinit', 'aim', 'cut3d', 'conducti', 'mrgddb', 'mrgscr', 'optic']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'chem' From f951ddcf2b93259bc3a8ecf6a169075421186d90 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 13:56:21 +0100 Subject: [PATCH 441/939] adding easyconfigs: libyaml-0.2.5-GCCcore-12.2.0.eb, PyYAML-6.0-GCCcore-12.2.0.eb --- .../l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb | 25 +++++++++++++++++ .../p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..6085128a05be --- /dev/null +++ b/easybuild/easyconfigs/l/libyaml/libyaml-0.2.5-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libyaml' +version = '0.2.5' + +homepage = 'https://pyyaml.org/wiki/LibYAML' +description = "LibYAML is a YAML parser and emitter written in C." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://pyyaml.org/download/%(name)s/'] +sources = ['yaml-%(version)s.tar.gz'] +checksums = ['c642ae9b75fee120b2d96c712538bd2cf283228d2337df2cf2988e3c02678ef4'] + +builddependencies = [ + ('binutils', '2.39'), +] + + +sanity_check_paths = { + 'files': ['include/yaml.h', 'lib/libyaml.a', 'lib/libyaml.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +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 new file mode 100644 index 000000000000..6f216f2874f7 --- /dev/null +++ b/easybuild/easyconfigs/p/PyYAML/PyYAML-6.0-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'PyYAML' +version = '6.0' + +homepage = 'https://github.com/yaml/pyyaml' +description = "PyYAML is a YAML parser and emitter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['68fb519c14306fec9720a2a5b45bc9f0c8d1b9c72adf45c37baedfcd949c35a2'] + +builddependencies = [ + ('binutils', '2.39'), +] +dependencies = [ + ('Python', '3.10.8'), + ('libyaml', '0.2.5'), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True +options = {'modulename': 'yaml'} + +moduleclass = 'lib' From ab1b91e436a4ea1e46927f12c90737e6d231577c Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 14:01:30 +0100 Subject: [PATCH 442/939] adding easyconfigs: OpenStackClient-6.0.0-GCCcore-12.2.0.eb --- .../OpenStackClient-6.0.0-GCCcore-12.2.0.eb | 129 ++++++++++++++++++ 1 file changed, 129 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..4b6ae3f06fec --- /dev/null +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,129 @@ +easyblock = 'PythonBundle' + +name = 'OpenStackClient' +version = '6.0.0' + +homepage = 'https://docs.openstack.org/python-openstackclient/latest/' +description = """OpenStackClient (aka OSC) is a command-line client for OpenStack that brings the +command set for Compute, Identity, Image, Network, Object Store and Block +Storage APIs together in a single shell with a uniform command structure.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +dependencies = [ + ('Python', '3.10.8'), + ('PyYAML', '6.0'), +] +builddependencies = [('binutils', '2.39')] + +exts_default_options = { + 'use_pip': True, +} +exts_list = [ + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '5.0.0', { + 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], + }), + ('cmd2', '2.4.2', { + 'checksums': ['073e555c05853b0f6965f3d03329babdf9e38a5f2cea028e61a64cd7eeb74ad5'], + }), + ('jsonpointer', '2.3', { + 'checksums': ['97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a'], + }), + ('prettytable', '3.5.0', { + 'checksums': ['52f682ba4efe29dccb38ff0fe5bac8a23007d0780ff92a8b85af64bc4fc74d72'], + }), + ('autopage', '0.5.1', { + 'checksums': ['01be3ee61bb714e9090fcc5c10f4cf546c396331c620c6ae50a2321b28ed3199'], + }), + ('stevedore', '4.1.1', { + 'checksums': ['7f8aeb6e3f90f96832c301bff21a7eb5eefbe894c88c506483d355565d88cc1a'], + }), + ('cliff', '4.0.0', { + 'checksums': ['3b0d30e7acf50e3c214a39ee3e66aa2f2b5957e2a1de373e17bba8e98c7501a5'], + }), + ('dogpile.cache', '1.1.8', { + 'checksums': ['d844e8bb638cc4f544a4c89a834dfd36fe935400b71a16cbd744ebdfb720fd4e'], + }), + ('iso8601', '1.1.0', { + 'checksums': ['32811e7b81deee2063ea6d2e94f8819a86d1f3811e49d23623a41fa832bef03f'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('jsonpatch', '1.32', { + 'checksums': ['b6ddfe6c3db30d81a96aaeceb6baf916094ffa23d7dd5fa2c13e13f8b6e600c2'], + }), + ('os-service-types', '1.7.0', { + 'checksums': ['31800299a82239363995b91f1ebf9106ac7758542a1e4ef6dc737a5932878c6c'], + }), + ('keystoneauth1', '5.0.0', { + 'checksums': ['6ebb5f044c9dfd263087a328d51d479947d1ddc90c09daf4191df7dc71334323'], + }), + ('munch', '2.5.0', { + 'checksums': ['2d735f6f24d4dba3417fa448cae40c6e896ec1fdab6cdb5e6510999758a4dbd2'], + }), + ('requestsexceptions', '1.4.0', { + 'checksums': ['b095cbc77618f066d459a02b137b020c37da9f46d9b057704019c9f77dba3065'], + }), + ('openstacksdk', '0.102.0', { + 'modulename': 'openstack', + 'checksums': ['b2a18feba79eac2ac3469c8dafe01d4008c8ac30be3a4c6b53275b4f1c6ba2ad'], + }), + ('oslo.i18n', '5.1.0', { + 'modulename': 'oslo_i18n', + 'checksums': ['6bf111a6357d5449640852de4640eae4159b5562bbba4c90febb0034abc095d0'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('debtcollector', '2.5.0', { + 'checksums': ['dc9d1ad3f745c43f4bbedbca30f9ffe8905a8c028c9926e61077847d5ea257ab'], + }), + ('oslo.utils', '6.1.0', { + 'modulename': 'oslo_utils', + 'checksums': ['76bc0108d50aca972b68fec8298e791b5fbcbeb9a51a27c6986b41b0a6a62eeb'], + }), + ('osc-lib', '2.6.2', { + 'checksums': ['879b6c5a142f3294464748ab14adde0cba0a14a5f704a0d840c9e92144489dba'], + }), + ('oslo.serialization', '5.0.0', { + 'modulename': 'oslo_serialization', + 'checksums': ['2845328d0f47dc8a23fed2a82253e90acff0aa731dbd24f379cf8e50e6cc66ba'], + }), + ('rfc3986', '2.0.0', { + 'checksums': ['97aacf9dbd4bfd829baad6e6309fa6573aaf1be3f6fa735c8ab05e46cecb261c'], + }), + ('oslo.config', '9.0.0', { + 'modulename': 'oslo_config', + 'checksums': ['3b6b63c43cf1e09344ba850bcb11d6f2b9201086fbeb0a97a8950e7eac3f2645'], + }), + ('python-novaclient', '18.2.0', { + 'modulename': 'novaclient', + 'checksums': ['185bbf2cafb5f3d761f272e3e184a700cc7ba5cf7d51619065be7f5c4b5b7cf4'], + }), + ('python-keystoneclient', '5.0.1', { + 'modulename': 'keystoneclient', + 'checksums': ['a8bbf671f56c24aa5a37a225b98f2994b82063d73e3486657eb500a33a406d29'], + }), + ('python-cinderclient', '9.1.0', { + 'modulename': 'cinderclient', + 'checksums': ['f9b30af2e6e6e5a126c2c81f35145c5aee70c20955e6dd409919be4d1b87b343'], + }), + ('python-openstackclient', version, { + 'modulename': 'openstackclient', + 'checksums': ['91c3ac12da4b423c16b3917616f84a23e2961e750fce590d409ecc50ee0431ce'], + }), +] + +sanity_pip_check = True +enhance_sanity_check = True +sanity_check_commands = ['openstack -h'] + +sanity_check_paths = { + 'files': ['bin/openstack'], + 'dirs': ["bin", 'lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'tools' From 8b2ece0a3dc79b234c63d4b37a3cba1d48ac9ed8 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 18 Nov 2022 14:21:04 +0100 Subject: [PATCH 443/939] build nodejs with full ICU support, required for matlab-proxy --- .../a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb | 60 +++++++++++++++++++ .../matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 39 ++++++++++++ .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 9 ++- 3 files changed, 106 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a9701a121171 --- /dev/null +++ b/easybuild/easyconfigs/a/aiohttp/aiohttp-3.8.3-GCCcore-11.3.0.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'aiohttp' +version = '3.8.3' + +homepage = 'https://github.com/aio-libs/aiohttp' +description = "Asynchronous HTTP client/server framework for asyncio and Python." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +# aioredis and aiosignal do not depend on aiohttp, but are commonly used together and share dependencies +exts_list = [ + ('multidict', '6.0.2', { + 'checksums': ['5ff3bd75f38e4c43f1f470f2df7a4d430b821c4ce22be384e1459cb57d6bb013'], + }), + ('async-timeout', '4.0.2', { + 'checksums': ['2163e1640ddb52b7a8c80d0a67a08587e5d245cc9c553a74a847056bc2976b15'], + }), + ('yarl', '1.8.1', { + 'checksums': ['af887845b8c2e060eb5605ff72b6f2dd2aab7a761379373fd89d314f4752abbf'], + }), + ('frozenlist', '1.3.3', { + 'checksums': ['58bcc55721e8a90b88332d6cd441261ebb22342e238296bb330968952fbb3a6a'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + (name, version, { + 'checksums': ['3828fb41b7203176b82fe5d699e0d845435f2374750a44b480ea6b930f6be269'], + }), + ('aiohttp-jinja2', '1.5', { + 'checksums': ['7c3ba5eac060b691f4e50534af2d79fca2a75712ebd2b25e6fcb1295859f910b'], + }), + ('hiredis', '2.0.0', { + 'checksums': ['81d6d8e39695f2c37954d1011c0480ef7cf444d4e3ae24bc5e89ee5de360139a'], + }), + ('aioredis', '2.0.1', { + 'checksums': ['eaa51aaf993f2d71f54b70527c440437ba65340588afeb786cd87c55c89cd98e'], + }), + ('aiosignal', '1.3.1', { + 'checksums': ['54cd96e15e1649b75d6c87526a6ff0b6c1b0dd3459f43d9ca11d48c339b68cfc'], + }), + ('aiohttp-session', '2.12.0', { + 'checksums': ['0ccd11a7c77cb9e5a61f4daacdc9170d561112f9cfaf9e9a2d9867c0587d1950'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..ce43706b20bd --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = "PythonBundle" + +name = 'matlab-proxy' +version = '0.5.4' + +homepage = 'https://github.com/mathworks/matlab-proxy' +description = 'MATLAB Integration for Jupyter' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), + ('nodejs', '16.15.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Xvfb', '21.1.3'), + ('aiohttp', '3.8.3'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['534531135ae341bd86de6c18ce2694b38614deeedf57a57d4cba1d2079eb662e'], + }), +] + +sanity_check_paths = { + 'files': ['bin/matlab-proxy-app'], + 'dirs': ['lib64/python%(pyshortver)s/site-packages'] +} + +modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately (2020b or later)' + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 3fe69b1af4cf..00b497b22e56 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -19,11 +19,16 @@ checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] builddependencies = [ ('binutils', '2.38'), ('Python', '3.10.4', '-bare'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('ICU', '71.1'), ] configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + '--with-intl=system-icu', + '--shared --with-intl=system-icu', # Build libnode.so in a second run ] # Link libv8 libs to libnode From 4f968721d9f31ad662b58778cf8503c8444e3b3f Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Nov 2022 13:45:54 +0000 Subject: [PATCH 444/939] use _ instead of - to simplify package downloads and re-add comment for Python 3.10.8 --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 40 +++++++------------ 1 file changed, 15 insertions(+), 25 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index f0bca199736c..59243c2b5dce 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -78,8 +78,7 @@ exts_list = [ ('toml', '0.10.2', { 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], }), - ('flit-core', '3.8.0', { - 'source_tmpl': 'flit_core-%(version)s.tar.gz', + ('flit_core', '3.8.0', { 'checksums': ['b305b30c99526df5e63d6022dd2310a0a941a187bd3884f4c8ef0418df6c39f3'], }), ('tomli', '2.0.1', { @@ -88,8 +87,7 @@ exts_list = [ ('packaging', '21.3', { 'checksums': ['dd47c42927d89ab911e606518907cc2d3a1f38bbd026385970643f9c5b8ecfeb'], }), - ('setuptools-scm', '7.0.5', { - 'sources': ['setuptools_scm-%(version)s.tar.gz'], + ('setuptools_scm', '7.0.5', { 'checksums': ['031e13af771d6f892b941adb6ea04545bbf91ebc5ce68c78aaf3fff6e1fb4844'], }), ('python-dateutil', '2.8.2', { @@ -130,18 +128,18 @@ exts_list = [ ('cffi', '1.15.1', { 'checksums': ['d400bfb9a37b1351253cb402671cea7e89bdecc294e8016a707f6d1d8ac934f9'], }), - ('semantic-version', '2.10.0', { - 'sources': ['semantic_version-%(version)s.tar.gz'], + ('semantic_version', '2.10.0', { 'checksums': ['bdabb6d336998cbb378d4b9db3a4b56a1e3235701dc05ea2690d9a997ed5041c'], }), - ('typing-extensions', '4.4.0', { - 'sources': ['typing_extensions-%(version)s.tar.gz'], + ('typing_extensions', '4.4.0', { 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], }), ('setuptools-rust', '1.5.2', { 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], }), ('cryptography', '38.0.3', { + # avoid that cargo uses $HOME/.cargo, which can lead to build failures if home directory is NFS mounted, + # see https://github.com/rust-lang/cargo/issues/6652 'preinstallopts': "export CARGO_HOME=%(builddir)s/cargo && ", 'checksums': ['bfbe6ee19615b07a98b1d2287d6a6073f734735b49ee45b11324d85efc4d5cbd'], }), @@ -188,8 +186,7 @@ exts_list = [ ('zipp', '3.10.0', { 'checksums': ['7a7262fd930bd3e36c50b9a64897aec3fafff3dfdeec9623ae22b40e93f99bb8'], }), - ('importlib-metadata', '5.0.0', { - 'sources': ['importlib_metadata-%(version)s.tar.gz'], + ('importlib_metadata', '5.0.0', { 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], }), ('backports.entry-points-selectable', '1.2.0', { @@ -208,8 +205,7 @@ exts_list = [ ('hatchling', '1.11.1', { 'checksums': ['9f84361f70cf3a7ab9543b0c3ecc64211ed2ba8a606a71eb6a473c1c9b08e1d0'], }), - ('hatch-vcs', '0.2.0', { - 'sources': ['hatch_vcs-%(version)s.tar.gz'], + ('hatch_vcs', '0.2.0', { 'checksums': ['9913d733b34eec9bb0345d0626ca32165a4ad2de15d1ce643c36d09ca908abff'], }), ('platformdirs', '2.5.3', { @@ -221,8 +217,7 @@ exts_list = [ ('pathlib2', '2.3.7.post1', { 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], }), - ('importlib-resources', '5.10.0', { - 'sources': ['importlib_resources-%(version)s.tar.gz'], + ('importlib_resources', '5.10.0', { 'checksums': ['c01b1b94210d9849f286b86bb51bcea7cd56dde0600d8db721d7b81330711668'], }), ('virtualenv', '20.16.6', { @@ -252,8 +247,7 @@ exts_list = [ ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), - ('py-expression-eval', '0.3.14', { - 'sources': ['py_expression_eval-%(version)s.tar.gz'], + ('py_expression_eval', '0.3.14', { 'checksums': ['ea60f9404a18346d5a63854db21c50666dfb4274ae111000165b31c6f8ab93f1'], }), ('tabulate', '0.9.0', { @@ -275,8 +269,7 @@ exts_list = [ 'modulename': 'attr', 'checksums': ['29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6'], }), - ('backports.functools-lru-cache', '1.6.4', { - 'sources': ['backports.functools_lru_cache-%(version)s.tar.gz'], + ('backports.functools_lru_cache', '1.6.4', { 'checksums': ['d5ed2169378b67d3c545e5600d363a923b09c456dab1593914935a68ad478271'], }), ('wcwidth', '0.2.5', { @@ -288,8 +281,7 @@ exts_list = [ ('colorama', '0.4.6', { 'checksums': ['08695f5cb7ed6e0531a20572697297273c47b8cae5a63ffc6d6ed5c201be6e44'], }), - ('flit-scm', '1.7.0', { - 'sources': ['flit_scm-%(version)s.tar.gz'], + ('flit_scm', '1.7.0', { 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], }), ('exceptiongroup', '1.0.1', { @@ -377,8 +369,7 @@ exts_list = [ ('zipfile36', '0.1.3', { 'checksums': ['a78a8dddf4fa114f7fe73df76ffcce7538e23433b7a6a96c1c904023f122aead'], }), - ('tomli-w', '1.0.0', { - 'sources': ['tomli_w-%(version)s.tar.gz'], + ('tomli_w', '1.0.0', { 'checksums': ['f463434305e0336248cac9c2dc8076b707d8a12d019dd349f5c1e382dd1ae1b9'], }), ('flit', '3.8.0', { @@ -446,7 +437,7 @@ exts_list = [ ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), - ('hatch-fancy-pypi-readme', '22.8.0', { + ('hatch_fancy_pypi_readme', '22.8.0', { 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), @@ -488,8 +479,7 @@ exts_list = [ ('dulwich', '0.20.50', { 'checksums': ['50a941796b2c675be39be728d540c16b5b7ce77eb9e1b3f855650ece6832d2be'], }), - ('poetry-plugin-export', '1.2.0', { - 'sources': ['poetry_plugin_export-%(version)s.tar.gz'], + ('poetry_plugin_export', '1.2.0', { 'checksums': ['9a1dd42765408931d7831738749022651d43a2968b67c988db1b7a567dfe41ef'], }), ('poetry', '1.2.2', { From cc7a26bef21b44ae8a6ce40df5f02f6b81e23a13 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 18 Nov 2022 14:47:01 +0100 Subject: [PATCH 445/939] update easyconfig OpenStackClient-6.0.0-GCCcore-12.2.0.eb: remove importlib_metadata --- .../o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb index 4b6ae3f06fec..6b695f632798 100644 --- a/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/o/OpenStackClient/OpenStackClient-6.0.0-GCCcore-12.2.0.eb @@ -22,9 +22,6 @@ exts_list = [ ('pyperclip', '1.8.2', { 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], }), - ('importlib_metadata', '5.0.0', { - 'checksums': ['da31db32b304314d044d3c12c79bd59e307889b287ad12ff387b3500835fc2ab'], - }), ('cmd2', '2.4.2', { 'checksums': ['073e555c05853b0f6965f3d03329babdf9e38a5f2cea028e61a64cd7eeb74ad5'], }), From b87080a98c61bf43a3760d02006f9e41f748aba7 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Fri, 18 Nov 2022 13:54:01 +0000 Subject: [PATCH 446/939] use SOURCE_WHL / SOURCE_PY3_WHL --- .../p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 15 +++++++-------- 1 file changed, 7 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 59243c2b5dce..2f5d77e36712 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -385,19 +385,19 @@ exts_list = [ 'checksums': ['9e77e941042ad3a4cc305dcdf2b2dec1aec2fbe3dd9015d2698ad02b173006d1'], }), ('pastel', '0.2.1', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4349225fcdf6c2bb34d483e523475de5bb04a5c10ef711263452cb37d7dd4364'], }), ('crashtest', '0.3.1', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['300f4b0825f57688b47b6d70c6a31de33512eb2fa1ac614f780939aa0cf91680'], }), ('clikit', '0.6.2', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['71268e074e68082306e23d7369a7b99f824a0ef926e55ba2665e911f7208489e'], }), ('jeepney', '0.8.0', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['c0a454ad016ca575060802ee4d590dd912e35c122fa04e70306de3d076cce755'], }), ('SecretStorage', '3.3.3', { @@ -415,7 +415,7 @@ exts_list = [ 'checksums': ['2ba3d56441ba0637f5f9c096068f67010ac0453f9d0b626de2aa3019353b6431'], }), ('tomlkit', '0.11.6', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['07de26b0d8cfc18f871aec595fda24d95b08fef89d147caa861939f37230bf4b'], }), ('shellingham', '1.5.0', { @@ -431,14 +431,13 @@ exts_list = [ 'checksums': ['a84da4318dd86f870a9447a8c98340aa06216bfc6f2b7bdc4b8766984ae1867c'], }), ('ptyprocess', '0.7.0', { - 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'source_tmpl': SOURCE_WHL, 'checksums': ['4b41f3967fce3af57cc7e94b888626c18bf37a083e3651ca8feeb66d492fef35'], }), ('pexpect', '4.8.0', { 'checksums': ['fc65a43959d153d0114afe13997d439c22823a27cefceb5ff35c2178c6784c0c'], }), ('hatch_fancy_pypi_readme', '22.8.0', { - 'sources': ['hatch_fancy_pypi_readme-%(version)s.tar.gz'], 'checksums': ['da91282ca09601c18aded8e378daf8b578c70214866f0971156ee9bb9ce6c26a'], }), ('jsonschema', '4.17.0', { @@ -454,7 +453,7 @@ exts_list = [ 'checksums': ['b2e5b40261e20f354d198eae92afc10d750afb487ed5e50f9c4eaf07c184146f'], }), ('cleo', '1.0.0a5', { - 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'source_tmpl': SOURCE_PY3_WHL, 'checksums': ['ff53056589300976e960f75afb792dfbfc9c78dcbb5a448e207a17b643826360'], }), ('cachy', '0.3.0', { From 4283912a26d50c111ea52aae0d4ef5c1e1588dcd Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 18 Nov 2022 14:01:09 +0000 Subject: [PATCH 447/939] Version bump. New dependencies of latest tensorboard and Lightning --- ...-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..8f4749f4dae4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('tensorboard', '2.10.0'), + ('typing-extensions', '4.3.0'), +] + +exts_list = [ + ('fsspec', '2022.11.0', { + 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], + }), + ('pyDeprecate', '0.3.2', { + 'modulename': 'deprecate', + 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], + }), + ('torchmetrics', '0.10.3', { + 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], + }), + ('termcolor', '2.1.0', { + 'checksums': ['b80df54667ce4f48c03fe35df194f052dc27a541ebbf2544e4d6b47b5d6949c4'], + }), + ('fire', '0.4.0', { + 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], + }), + ('lightning-utilities', '0.3.0', { + 'checksums': ['d769ab9b76ebdee3243d1051d509aafee57d7947734ddc22977deef8a6427f2f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['480f3396cd63888c4e5ec2f21c02fe662a2b035d9634e6f31fcf1197a36ebd15'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From a6c6965a67bce61982442492260081e8108ce84a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 18 Nov 2022 15:23:05 +0100 Subject: [PATCH 448/939] drop download_dep_fail since it is the default --- .../m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb index ce43706b20bd..6628aef39431 100644 --- a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -19,7 +19,6 @@ dependencies = [ ('aiohttp', '3.8.3'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From 05cdc1aae7e190ede058643b5d7e0a0afb8494c5 Mon Sep 17 00:00:00 2001 From: Neil Douglas Date: Fri, 18 Nov 2022 14:56:07 +0000 Subject: [PATCH 449/939] adding easyconfigs: Cytoscape-3.9.1-Java-11.eb --- .../c/Cytoscape/Cytoscape-3.9.1-Java-11.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb diff --git a/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb b/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb new file mode 100644 index 000000000000..3d967783b2c0 --- /dev/null +++ b/easybuild/easyconfigs/c/Cytoscape/Cytoscape-3.9.1-Java-11.eb @@ -0,0 +1,36 @@ +easyblock = 'Binary' + +name = 'Cytoscape' +version = '3.9.1' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://cytoscape.org/' +description = """Cytoscape is an open source software platform for visualizing + complex networks and integrating these with any type of attribute data. + A lot of Apps are available for various kinds of problem domains, + including bioinformatics, social network analysis, and semantic web.""" + +toolchain = SYSTEM + +_underscore_version = version.replace('.', '_') + +# https://github.com/cytoscape/cytoscape/releases/download/3.9.1/Cytoscape_3_9_1_unix.sh +source_urls = ['https://github.com/cytoscape/cytoscape/releases/download/3.9.1/'] +sources = ['%%(name)s_%s_unix.sh' % _underscore_version] + +checksums = ['0b20ac377dc01e6b0f7067104c2e463d8f834e50ee19dc302bb101dfcbc342a1'] + +dependencies = [ + ('Java', '11'), +] + +install_cmd = "./%%(name)s_%s_unix.sh -q -dir %%(installdir)s" % _underscore_version + +sanity_check_paths = { + 'files': ['cytoscape.sh', 'Cytoscape'], + 'dirs': ['framework', 'apps', 'sampleData'], +} + +sanity_check_commands = ["%(namelower)s.sh --help"] + +moduleclass = 'bio' From 0f953f7ac202a170f232cffbe376ce437ad8c8ae Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 19 Nov 2022 16:09:59 +0100 Subject: [PATCH 450/939] adding easyconfigs: Siesta-4.1.5-foss-2022a.eb --- .../s/Siesta/Siesta-4.1.5-foss-2022a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb new file mode 100644 index 000000000000..00cced1d88a8 --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-foss-2022a.eb @@ -0,0 +1,26 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), + ('METIS', '5.1.0'), + ('ELPA', '2021.11.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' From 038dc2a87e80d8958742728a216ad5f26bb87762 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 19 Nov 2022 16:10:21 +0100 Subject: [PATCH 451/939] adding easyconfigs: Siesta-4.1.5-intel-2022a.eb --- .../s/Siesta/Siesta-4.1.5-intel-2022a.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb diff --git a/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb new file mode 100644 index 000000000000..0b269542103f --- /dev/null +++ b/easybuild/easyconfigs/s/Siesta/Siesta-4.1.5-intel-2022a.eb @@ -0,0 +1,26 @@ +name = 'Siesta' +version = '4.1.5' + +homepage = 'http://departments.icmab.es/leem/siesta' +description = """SIESTA is both a method and its computer program implementation, to perform efficient electronic + structure calculations and ab initio molecular dynamics simulations of molecules and solids.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'precise': True} + +source_urls = ['https://gitlab.com/siesta-project/siesta/-/releases/v%(version)s/downloads'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['518df31aa6213af5e24cc73abb537b2c89a925b487171f5339d743d0c7140b3f'] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), + ('METIS', '5.1.0'), + ('ELPA', '2021.11.001'), +] + +# transiesta is now siesta --electrode +with_transiesta = False + +runtest = 'check' + +moduleclass = 'phys' From 6cad70bc4ac115d05608737b4ee703af68fafe41 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:20:26 +0000 Subject: [PATCH 452/939] Correct sanity-check-command added --- easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb index d1f4c2ad3a1d..cfd3b1b4d0f9 100644 --- a/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb +++ b/easybuild/easyconfigs/k/KITE/KITE-1.1-gompi-2022a.eb @@ -35,4 +35,6 @@ sanity_check_paths = { 'dirs': [], } +sanity_check_commands = ['KITEx |grep "^Starting program..."'] + moduleclass = 'chem' From e5fad376f9c3ea85eb9cb08d0942e6b13445a32f Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:26:46 +0000 Subject: [PATCH 453/939] tqdm removed --- .../easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb index 4459e4473f38..12bc9138bfa3 100644 --- a/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MITgcmutils/MITgcmutils-0.1.2-foss-2022a.eb @@ -20,7 +20,6 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('tqdm', '4.64.0'), ] use_pip = True From 1ac26c04bb217380dde675cd83509a22cfd4476a Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:39:12 +0000 Subject: [PATCH 454/939] dask version changed to 2022.10.0 --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index 2b248447592b..fa2d8f0e9629 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ('h5py', '3.7.0'), ('SciPy-bundle', '2022.05'), ('netcdf4-python', '1.6.1'), From 2cd36bf71be4edfea029b23106457aee2d71b0f4 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:45:23 +0000 Subject: [PATCH 455/939] entrypoints added to close PR #16651 --- easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb index ff8bb790e8f2..8c6c042e34d9 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -19,6 +19,9 @@ use_pip = True sanity_pip_check = True exts_list = [ + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), ('asciitree', '0.3.3', { 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], }), From bf57a8625d1298cc3d1db2999b240ccfd0f52526 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:52:53 +0000 Subject: [PATCH 456/939] dask version changed to 2022.10.0 --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index aeac427c9c57..fbdcdebc32da 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ] use_pip = True From 7755da5e2cbe6cd064f3467fb3667de518de4a29 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 20:57:32 +0000 Subject: [PATCH 457/939] dask version changed to 2022.10.0 --- easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index d73a95fced80..55ff2f1d94f0 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -13,7 +13,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), - ('dask', '2022.10.2'), + ('dask', '2022.10.0'), ] use_pip = True From f89845cb8f9044ba73ebdb72acdc296830407741 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:10:01 +0000 Subject: [PATCH 458/939] adding easyconfigs: xarray-2022.9.0-foss-2022a.eb --- .../x/xarray/xarray-2022.9.0-foss-2022a.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb b/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb new file mode 100644 index 000000000000..5d3d2e2cf283 --- /dev/null +++ b/easybuild/easyconfigs/x/xarray/xarray-2022.9.0-foss-2022a.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonBundle' + +name = 'xarray' +version = '2022.9.0' + +homepage = 'https://github.com/pydata/xarray' +description = """xarray (formerly xray) is an open source project and Python package that aims to bring + the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the + core pandas data structures.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], + }), +] + +moduleclass = 'data' From e64a4a41ca05d7f80acbbec5ec5aaf6589e17902 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:34:20 +0000 Subject: [PATCH 459/939] xarray as dependency added, psutil removed, tag used instead of commit --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 9 ++------- 1 file changed, 2 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index fa2d8f0e9629..f057408344e3 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -21,6 +21,7 @@ dependencies = [ ('scikit-learn', '1.1.2'), ('tqdm', '4.64.0'), ('zarr', '2.13.3'), + ('xarray', '2022.9.0'), ] use_pip = True @@ -30,18 +31,12 @@ exts_list = [ ('parcels', '2.4.0', { 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], }), - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), ('pykdtree', '1.3.6', { 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], }), ('sosfilt', '1.2.0', { 'checksums': ['b3083fd2edf723a6163f00ddc36ec3ca20fbf6112cc68573dad9356544a9d734'], }), - ('psutil', '5.9.4', { - 'checksums': ['3d7f9739eb435d4b1338944abe23f49584bde5395f27487d2ee25ad9a8774a62'], - }), ('progressbar2', '4.2.0', { 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], 'modulename': 'progressbar', @@ -65,7 +60,7 @@ exts_list = [ 'git_config': { 'url': 'https://github.com/angus-g/', 'repo_name': name, - 'commit': 'b942ff3', + 'tag': version, 'recursive': True, 'keep_git_dir': True, }, From c738921011e77e1ab6057d34302597d89bc7fd22 Mon Sep 17 00:00:00 2001 From: sassy Date: Sun, 20 Nov 2022 21:38:43 +0000 Subject: [PATCH 460/939] entrypoint dependency removed --- easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb index 8c6c042e34d9..b04ea6aea021 100644 --- a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2022a.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('entrypoints', '0.4'), ] use_pip = True From ad2331ea10c39203802a22ebcb30c78e261f543a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 08:44:45 +0100 Subject: [PATCH 461/939] add scDblFinder extension to Bioconductor 3.15 --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 43c53a701843..118a0158da36 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1098,6 +1098,9 @@ exts_list = [ ('ROntoTools', '2.24.0', { 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], }), + ('scDblFinder', '1.10.0', { + 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From f3facbd38a67d9d047cddd06a6e2e7dee1f62f30 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:28:02 +0100 Subject: [PATCH 462/939] adding easyconfigs: APR-1.7.0-GCCcore-11.3.0.eb, APR-util-1.6.1-GCCcore-11.3.0.eb --- .../APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ .../a/APR/APR-1.7.0-GCCcore-11.3.0.eb | 22 +++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..52ae17f084c8 --- /dev/null +++ b/easybuild/easyconfigs/a/APR-util/APR-util-1.6.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'APR-util' +version = '1.6.1' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) util libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b65e40713da57d004123b6319828be7f1273fbc6490e145874ee1177e112c459'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('APR', '1.7.0'), + ('SQLite', '3.38.3'), + ('expat', '2.4.8'), +] + +configopts = "--with-apr=$EBROOTAPR/bin/apr-1-config --with-sqlite3=$EBROOTSQLITE --with-expat=$EBROOTEXPAT " + +sanity_check_paths = { + 'files': ["bin/apu-1-config", "lib/libaprutil-1.%s" % SHLIB_EXT, "lib/libaprutil-1.a"], + 'dirs': ["include/apr-1"], +} + +parallel = 1 + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..200453bcb549 --- /dev/null +++ b/easybuild/easyconfigs/a/APR/APR-1.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'APR' +version = '1.7.0' + +homepage = 'https://apr.apache.org/' +description = "Apache Portable Runtime (APR) libraries." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/apr/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['48e9dbf45ae3fdc7b491259ffb6ccf7d63049ffacbc1c0977cced095e4c2d5a2'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ["bin/apr-1-config", "lib/libapr-1.%s" % SHLIB_EXT, "lib/libapr-1.a"], + 'dirs': ["include/apr-1"], +} + +moduleclass = 'tools' From 3e01282dd85ef34dd215ffe5652c3f3accac5523 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:28:27 +0100 Subject: [PATCH 463/939] adding easyconfigs: Serf-1.3.9-GCCcore-11.3.0.eb --- .../s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..41c4515faddf --- /dev/null +++ b/easybuild/easyconfigs/s/Serf/Serf-1.3.9-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'SCons' +name = 'Serf' +version = '1.3.9' + +homepage = 'https://serf.apache.org/' +description = """The serf library is a high performance C-based HTTP client library + built upon the Apache Portable Runtime (APR) library""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://archive.apache.org/dist/%(namelower)s'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['Serf-%(version)s_python3_scons.patch'] +checksums = [ + '549c2d21c577a8a9c0450facb5cca809f26591f048e466552240947bdf7a87cc', # serf-1.3.9.tar.bz2 + 'db401893bfb464ddcf369b543cacb9a165a21f8ff9bf1a819e4b61550bb9d3d0', # Serf-1.3.9_python3_scons.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4'), + ('SCons', '4.4.0'), +] + +dependencies = [ + ('APR', '1.7.0'), + ('APR-util', '1.6.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +buildopts = "APR=$EBROOTAPR/bin/apr-1-config APU=$EBROOTAPRMINUTIL/bin/apu-1-config" + +sanity_check_paths = { + 'files': ['include/serf-1/serf.h'] + + ['lib/libserf-1.%s' % x for x in ['a', 'so']], + 'dirs': [], +} + +moduleclass = 'tools' From 26170fc62bc501a8c74a12e43c8cd5dc94562f4d Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 21 Nov 2022 10:38:26 +0100 Subject: [PATCH 464/939] adding easyconfigs: qrupdate-1.1.2-GCCcore-11.3.0.eb --- .../qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a0bb33bae798 --- /dev/null +++ b/easybuild/easyconfigs/q/qrupdate/qrupdate-1.1.2-GCCcore-11.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'qrupdate' +version = '1.1.2' + +homepage = 'https://sourceforge.net/projects/qrupdate/' +description = """qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-%(version)s_makeconf.patch'] +checksums = [ + 'e2a1c711dc8ebc418e21195833814cb2f84b878b90a2774365f0166402308e08', # qrupdate-1.1.2.tar.gz + '4aa0e61a18bd14c76048f7b2f1f52875f7bac4bc3426ce9a37dfdb5b2b0d2379', # qrupdate-1.1.2_makeconf.patch +] + +builddependencies = [ + ('binutils', '2.38'), +] + +buildopts = 'lib' + +files_to_copy = [(['libqrupdate.a'], 'lib')] + +sanity_check_paths = { + 'files': ['lib/libqrupdate.a'], + 'dirs': [], +} + +parallel = 1 + +moduleclass = 'numlib' From a62c303ac31f35f0295906aa9cb10c0650ef38bc Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 21 Nov 2022 10:01:36 +0000 Subject: [PATCH 465/939] adding easyconfigs: GnuTLS-3.7.8-GCCcore-11.3.0.eb, alsa-lib-1.2.8-GCCcore-11.3.0.eb, libidn-1.41-GCCcore-11.3.0.eb, libtasn1-4.19.0-GCCcore-11.3.0.eb, p11-kit-0.24.1-GCCcore-11.3.0.eb --- .../alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb | 24 +++++++++++ .../g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ .../l/libidn/libidn-1.41-GCCcore-11.3.0.eb | 22 ++++++++++ .../libtasn1-4.19.0-GCCcore-11.3.0.eb | 25 +++++++++++ .../p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb | 38 +++++++++++++++++ 5 files changed, 151 insertions(+) create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb 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 new file mode 100644 index 000000000000..1476c3783663 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.8' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] + +dependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' 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 new file mode 100644 index 000000000000..c604f1a0fa0d --- /dev/null +++ b/easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +easyblock = 'ConfigureMake' + +name = 'GnuTLS' +version = '3.7.8' + +homepage = 'https://www.gnutls.org' +description = """GnuTLS is a secure communications library implementing the SSL, TLS + and DTLS protocols and technologies around them. It provides a simple + C language application programming interface (API) to access the secure + communications protocols as well as APIs to parse and write X.509, PKCS #12, + OpenPGP and other required structures. It is aimed to be portable + and efficient with focus on security and interoperability.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.gnupg.org/ftp/gcrypt/gnutls/v%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c58ad39af0670efe6a8aee5e3a8b2331a1200418b64b7c51977fb396d4617114'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('GMP', '6.2.1'), + ('nettle', '3.8'), + ('Guile', '3.0.8'), + ('libtasn1', '4.19.0'), + ('libidn', '1.41'), + ('p11-kit', '0.24.1'), +] + +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" + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['certtool', 'gnutls-cli', 'gnutls-cli-debug', + 'gnutls-serv', 'ocsptool', 'psktool', 'srptool']] + + ['lib/libgnutls%s' % x for x in ['.%s' % SHLIB_EXT, 'xx.%s' % SHLIB_EXT, '-openssl.%s' % SHLIB_EXT]], + 'dirs': ['include/gnutls', 'lib/guile'], +} + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..7a37e088e107 --- /dev/null +++ b/easybuild/easyconfigs/l/libidn/libidn-1.41-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libidn' +version = '1.41' + +homepage = 'http://www.gnu.org/software/%(name)s' +description = """GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. +Libidn's purpose is to encode and decode internationalized domain names.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['884d706364b81abdd17bee9686d8ff2ae7431c5a14651047c68adf8b31fd8945'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/idn', 'lib/libidn.%s' % SHLIB_EXT], + 'dirs': ['include'], +} +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..be6a5c351a41 --- /dev/null +++ b/easybuild/easyconfigs/l/libtasn1/libtasn1-4.19.0-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'libtasn1' +version = '4.19.0' + +homepage = 'https://www.gnu.org/software/libtasn1/' +description = """Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and + some other packages. It was written by Fabio Fiorina, and has been shipped as + part of GnuTLS for some time but is now a proper GNU package.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['1613f0ac1cf484d6ec0ce3b8c06d56263cc7242f1c23b30d82d23de345a63f7a'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/asn1%s' % x for x in ['Coding', 'Decoding', 'Parser']] + + ['lib/libtasn1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include'], +} + +moduleclass = 'lib' 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 new file mode 100644 index 000000000000..4a07aaf936cd --- /dev/null +++ b/easybuild/easyconfigs/p/p11-kit/p11-kit-0.24.1-GCCcore-11.3.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'p11-kit' +version = '0.24.1' + +homepage = 'https://p11-glue.freedesktop.org/p11-kit.html' +description = """Provides a way to load and enumerate PKCS#11 modules. + Provides a standard configuration setup for installing + PKCS#11 modules in such a way that they're discoverable. + Also solves problems with coordinating the use of PKCS#11 + by different components or libraries living in the same process.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/p11-glue/p11-kit/releases/download/%(version)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['d8be783efd5cd4ae534cee4132338e3f40f182c3205d23b200094ec85faaaef8'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libtasn1', '4.19.0'), + ('libffi', '3.4.2'), +] + +preconfigopts = "bashcompdir=%(installdir)s/share/bash-completions " + +configopts = "--without-systemd" + +sanity_check_paths = { + 'files': ['bin/p11-kit', 'bin/trust'] + + ['lib/libp11-kit.%s' % SHLIB_EXT], + 'dirs': ['include/p11-kit-1/p11-kit'], +} + +sanity_check_commands = ["p11-kit --help"] + +moduleclass = 'lib' From 057dca5363ed71ef4b156c4925a39e890644a0b8 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 21 Nov 2022 12:13:20 +0200 Subject: [PATCH 466/939] fix source_urls --- .../c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb index c4b1c45f09f2..805ff73105f9 100644 --- a/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/colossalai/colossalai-0.1.8-foss-2021a-CUDA-11.3.1.eb @@ -46,7 +46,9 @@ exts_list = [ 'checksums': ['76f8fef59cf2061dbd849bbce4fe49bdd820884385004b0ca59136ac3db129e4'], }), (name, version, { - 'checksums': ['3a2cdd4dc2d8b4832fa132a0bd1102f86c38f6865d7f119018404069d35984b2'], + 'source_urls': ['https://github.com/hpcaitech/ColossalAI/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['e0975cd9a0860a2d00d1f725baaee3652e2f601724968628d8750021ef483320'], }), ] From 5fe59c9f66198ca47bc7f8569596fe8b5681ecda Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Mon, 21 Nov 2022 12:14:46 +0200 Subject: [PATCH 467/939] fix dllogger checksum --- .../o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb index 52743c921acc..9eec3b5f8071 100644 --- a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -71,7 +71,7 @@ exts_list = [ ('dllogger', version, { 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['43e5e3c3acf891dfe6151f7d869f3ad2424772fe57fd8dcb0a45bad06de93bf7'], + 'checksums': ['abae2b2ac73b9e176fa87144bf6c2048ddd3dae8e7002d6d5a270bc7e4da6b4d'], }), (name, version, { 'source_urls': ['https://github.com/aqlaboratory/openfold/archive/refs/tags/'], From d0b9ec13d111bdd95fff4432f3a35e69a4ec984f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 11:47:10 +0100 Subject: [PATCH 468/939] adding easyconfigs: RLCard-1.0.9-foss-2022a.eb --- .../r/RLCard/RLCard-1.0.9-foss-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb b/easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb new file mode 100644 index 000000000000..b0c6e795abf9 --- /dev/null +++ b/easybuild/easyconfigs/r/RLCard/RLCard-1.0.9-foss-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'RLCard' +version = '1.0.9' + +homepage = 'https://www.rlcard.org' +description = "RLCard is a toolkit for Reinforcement Learning (RL) in card games." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numpy + ('PyTorch', '1.12.0'), + ('GitPython', '3.1.27'), + ('matplotlib', '3.5.2'), +] + +use_pip = True + +exts_list = [ + # stick to termcolor 1.x, to avoid hatchling required dependency + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('rlcard', version, { + 'checksums': ['6454d2203220b7acff855cad35c9e24aabadfd664048aee45054a04adc842c75'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 4dfba82a0fc56d09f89ddcdb886d833b907946d3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 12:37:06 +0100 Subject: [PATCH 469/939] use same patches for netcdf4-python 1.6.1 in foss/intel easyconfigs --- .../n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb index 60eb9cd8eefd..d5d6084f968c 100644 --- a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.6.1-intel-2022a.eb @@ -24,13 +24,18 @@ exts_list = [ 'checksums': ['8614c00fb8a5046de304fdd86dbd224f99408185d7b245ac6628d0276596e6d2'], }), (name, version, { - 'patches': ['netcdf4-python-1.1.8-avoid-diskless-test.patch'], + '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': [ 'ba8dc5d65293a99f1afb8c2acf588d903fdfdc1963a62545b677fa2734262a78', # netCDF4-1.6.1.tar.gz # netcdf4-python-1.1.8-avoid-diskless-test.patch 'a8b262fa201d55f59015e1bc14466c1d113f807543bc1e05a22481ab0d216d72', + # netcdf4-python-1.6.1_relax_tolerance_compression_test.patch + '64d192a5d1e3e00af78f053da78f5a35015fa713c7f97b10b622be6a44347166', ], }), ] From 587568e5cd02e8be3360409615b99cbd377b6387 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 13:09:49 +0100 Subject: [PATCH 470/939] adding easyconfigs: ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb --- .../ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..7cde2f7f6bfc --- /dev/null +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'ESM-2' +version = '2.0.0' +versionsuffix = '-CUDA-%(cudaver)s' + +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': '2021a'} + +source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] +sources = ['fair-esm-%(version)s.tar.gz'] +checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Python', '3.9.5'), + ('PyTorch', '1.10.2', versionsuffix), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'esm'} + +sanity_check_commands = [ + "python -c 'import esm.pretrained'", +] + +moduleclass = 'bio' From 98ffbdb85b6f9ea656fe77c45bf08dc0448df20a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 13:20:13 +0100 Subject: [PATCH 471/939] rename hyperopt to Hyperopt --- .../cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- .../Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb} | 4 ++-- .../Hyperopt-0.2.5-fosscuda-2020b.eb} | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) rename easybuild/easyconfigs/h/{hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb => Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb} (97%) rename easybuild/easyconfigs/h/{hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb => Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb} (96%) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 8356b39778ad..23a780fa2a1c 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -21,7 +21,7 @@ dependencies = [ ('Java', '11', '', SYSTEM), ('SciPy-bundle', '2020.11'), ('leidenalg', '0.8.3'), - ('hyperopt', '0.2.5'), + ('Hyperopt', '0.2.5'), ('CMake', '3.18.4'), ('dill', '0.3.3'), ('IPython', '7.18.1'), diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb similarity index 97% rename from easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb rename to easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb index 4e2be23df1d7..f9b60c91c8e6 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.4-intel-2019b-Python-3.7.4-Java-1.8.eb @@ -3,7 +3,7 @@ easyblock = 'PythonBundle' -name = 'hyperopt' +name = 'Hyperopt' version = '0.2.4' local_python_versionsuffix = '-Python-%(pyver)s' local_java_versionsuffix = '-Java-%(javaver)s' @@ -43,7 +43,7 @@ exts_list = [ ('lightgbm', '2.3.1', { 'checksums': ['bd1817be401e74c0d8b049e97ea2f35d2ce155cfa130119ce4195ea207bd6388'], }), - (name, version, { + ('hyperopt', version, { 'use_pip_extras': 'SparkTrials,MongoTrials,ATPE', 'checksums': ['6e72089a42eb70cf84b0567d4552a908adff7cfc5cf6b1c38add41adc775d9c6'], }), diff --git a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb similarity index 96% rename from easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb rename to easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb index 8a744cd8d263..e78c32c2658b 100644 --- a/easybuild/easyconfigs/h/hyperopt/hyperopt-0.2.5-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/h/Hyperopt/Hyperopt-0.2.5-fosscuda-2020b.eb @@ -2,7 +2,7 @@ easyblock = 'PythonBundle' -name = 'hyperopt' +name = 'Hyperopt' version = '0.2.5' homepage = 'https://github.com/hyperopt/hyperopt' @@ -40,7 +40,7 @@ exts_list = [ ('py4j', '0.10.9.2', { 'checksums': ['624f97c363b8dd84822bc666b12fa7f7d97824632b2ff3d852cc491359ce7615'], }), - (name, version, { + ('hyperopt', version, { 'use_pip_extras': 'SparkTrials,MongoTrials,ATPE', 'checksums': ['bc6047d50f956ae64eebcb34b1fd40f186a93e214957f20e87af2f10195295cc'], }), From c491dfb6f9bf924c18a92af311a41954d4d34da8 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 13:33:38 +0100 Subject: [PATCH 472/939] use correct PyTorch version --- .../easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index 7cde2f7f6bfc..c4eb572620d7 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -18,7 +18,7 @@ checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), - ('PyTorch', '1.10.2', versionsuffix), + ('PyTorch', '1.10.0', versionsuffix), ] use_pip = True From 0dcbf4e8f71e4b7b28bd9598918cfd8c04c19376 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 13:36:55 +0100 Subject: [PATCH 473/939] adding easyconfigs: OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb --- .../OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb 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 new file mode 100644 index 000000000000..5d2f680ca42a --- /dev/null +++ b/easybuild/easyconfigs/o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'OmegaFold' +version = '1.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/HeliXonProtein/OmegaFold' +description = """OmegaFold: High-resolution de novo Structure Prediction from Primary Sequence""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.0', '-CUDA-%(cudaver)s'), + ('Biopython', '1.79'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + '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'], + }), +] + +sanity_check_paths = { + 'files': ['bin/omegafold'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/omegafold'], +} + +sanity_check_commands = [ + "omegafold --help", +] + +moduleclass = 'bio' From 92a83bf682fbc93dfc2b4b103440f6aad2ac9ef8 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 14:28:42 +0100 Subject: [PATCH 474/939] use PythonBundle with resolos v0.3.5 --- .../r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 28 +++++++++---------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index e3cc4db884a7..efe3f01dcbc8 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -1,36 +1,36 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'resolos' version = '0.3.5' homepage = 'https://gitlab.unige.ch/resolos/resolos' description = """Resolos is a toolkit written in Python for maintaining reproducible environments -for scientific computations. -It's main goal is to enable researchers to easily replicate environments through space -(running code on HPC environment) - +for scientific computations. It's main goal is to enable researchers to easily +replicate environments through space (running code on HPC environment) and time (environment preservation for long term archival). For installation and detailed usage, check out the documentation.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -# source_urls = [PYPI_SOURCE] -# Link copy from pypi.org | PYPI_SOURCE is not working -sources = [SOURCE_TAR_GZ] -checksums = ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'] - dependencies = { ('Python', '3.10.4'), ('PyYAML', '6.0'), } - use_pip = True -use_pip_for_deps = True -moduleclass = 'data' + +exts_list = [ + (name, version, { + 'checksums': ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'], + }), +] + +sanity_pip_check = True sanity_check_commands = ["r3s info"] sanity_check_paths = { 'files': ["bin/r3s"], - 'dirs': [] + 'dirs': ['lib/python%(pyshortver)s/site-packages'], } + +moduleclass = 'tools' From 9b5627504dcf2de5ba8caf1976e32804aaf69f30 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 21 Nov 2022 14:56:11 +0100 Subject: [PATCH 475/939] use SYSTEM global in flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb --- .../f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb index 1ad8d95623ed..7223c3f12601 100644 --- a/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/f/flair-NLP/flair-NLP-0.11.3-foss-2021a-CUDA-11.3.1.eb @@ -10,7 +10,7 @@ description = "A very simple framework for state-of-the-art NLP" toolchain = {'name': 'foss', 'version': '2021a'} dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ('tqdm', '4.61.2'), From 675a7ec13b0a7b359ce47aa491da28e71d126af1 Mon Sep 17 00:00:00 2001 From: garadar Date: Mon, 21 Nov 2022 15:29:06 +0100 Subject: [PATCH 476/939] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb Co-authored-by: Alex Domingo --- easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index efe3f01dcbc8..7aaeaad8e10b 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -12,6 +12,8 @@ For installation and detailed usage, check out the documentation.""" toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +builddependencies = [('binutils', '2.38')] + dependencies = { ('Python', '3.10.4'), ('PyYAML', '6.0'), From 97e7e854b4affd0d73ecc8dcb1bc18b8e6393497 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 21 Nov 2022 16:49:51 +0100 Subject: [PATCH 477/939] add missing extensions to easyconfig for R-bundle-Bioconductor v3.15 with foss/2021b --- ...bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 15 +++++++++++++++ 1 file changed, 15 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index 9c7b01b91376..b6ac8e83c455 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -1090,6 +1090,21 @@ exts_list = [ ('SPOTlight', '1.0.0', { 'checksums': ['f6baf718e468292960884a1aacdf8295f0864d771f5eb0f2088fb9a1bc00dcc0'], }), + ('CGHcall', '2.58.0', { + 'checksums': ['c5e86b9234685462b7330c85b91ca648a801a76c99f3e98cd509ac47ee8afae2'], + }), + ('QDNAseq', '1.32.0', { + 'checksums': ['75bbde9b6cc55cd6a47b9f466358033a180b480def2144abdcc93a2a8e066668'], + }), + ('HiCcompare', '1.18.0', { + 'checksums': ['b9320fa7a9f10832e2ac7ade0245f85ac4c2c26edef2580078888f5e1050ee2d'], + }), + ('ROntoTools', '2.24.0', { + 'checksums': ['dec7ec0d6d709fbdb44d595d776fc462420957e5c23c7bd6d2d63f5a44df04dd'], + }), + ('scDblFinder', '1.10.0', { + 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From 3c66bade085902d638af6a6e73852c496697d445 Mon Sep 17 00:00:00 2001 From: garadar Date: Mon, 21 Nov 2022 16:57:17 +0100 Subject: [PATCH 478/939] Update easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb Co-authored-by: Alex Domingo --- .../r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb | 13 +++++++++++++ 1 file changed, 13 insertions(+) diff --git a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb index 7aaeaad8e10b..4a7708038c77 100644 --- a/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/r/resolos/resolos-0.3.5-GCCcore-11.3.0.eb @@ -22,6 +22,19 @@ dependencies = { use_pip = True exts_list = [ + ('click-log', '0.4.0', { + 'checksums': ['3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975'], + }), + ('conda-pack', '0.6.0', { + 'checksums': ['615f41353fdc8793b0edb55702212273f17e40b43cc2c17493430e9c66d9f0b3'], + }), + ('semver', '2.13.0', { + 'checksums': ['fa0fe2722ee1c3f57eac478820c3a5ae2f624af8264cbdf9000c980ff7f75e3f'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), (name, version, { 'checksums': ['c0fb50e36866fa591f0a7ab3567e9037c97d96f34614e86ee9cad1b62c689de2'], }), From 048d1168850897b96d49c05f63752d4bd731dacf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 21:28:45 +0100 Subject: [PATCH 479/939] add comment for missing version --- .../o/OmegaFold/OmegaFold-1.1.0-foss-2022a-CUDA-11.7.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 5d2f680ca42a..0008cde884d3 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 @@ -19,9 +19,10 @@ dependencies = [ use_pip = True sanity_pip_check = True +# add missing version for OmegaFold exts_list = [ (name, version, { - 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, + 'preinstallopts': """sed -i '/^setup(/a \ version="%(version)s",' setup.py && """, # noqa: W605 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/HeliXonProtein/OmegaFold/archive/'], 'checksums': ['ab3b48fe7721539b6943b49cdbafc9799e15b4425a324cc25daf15a24e3f9e37'], From 010536c00c9d1afb9459a581c594c3c4c278dedf Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 21 Nov 2022 22:00:45 +0100 Subject: [PATCH 480/939] update pyproj version for Cartopy 0.20.3 --- easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb index f8c63257d0fe..436e9a24ca9d 100644 --- a/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb +++ b/easybuild/easyconfigs/c/Cartopy/Cartopy-0.20.3-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('GDAL', '3.5.0'), ('GEOS', '3.10.3'), ('matplotlib', '3.5.2'), - ('pyproj', '3.3.1'), + ('pyproj', '3.4.0'), ('SciPy-bundle', '2022.05'), ('Shapely', '1.8.2'), ('lxml', '4.9.1'), From f637208154f00f5670f28f9aa0830ec86b2e6cce Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 11:45:57 +0100 Subject: [PATCH 481/939] adding easyconfigs: Valgrind-3.20.0-gompi-2022a.eb --- .../v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb new file mode 100644 index 000000000000..45e2a41ecda8 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.20.0-gompi-2022a.eb @@ -0,0 +1,33 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.20.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['8536c031dbe078d342f121fa881a9ecd205cb5a78e639005ad570011bdb9f3c6'] + +configopts = ' --with-mpicc="$MPICC"' + +local_binaries = [ + 'callgrind_annotate', 'callgrind_control', 'cg_annotate', 'cg_diff', + 'cg_merge', 'ms_print', 'valgrind', 'valgrind-listener', 'vgdb' +] +local_archs = ('amd64', 'arm64', 'ppc64le') + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries] + + [['lib/valgrind/libmpiwrap-%s-linux.%s' % (a, SHLIB_EXT) for a in local_archs]], + 'dirs': [] +} + +moduleclass = 'debugger' From d9d7c82f7c936623f56403625c806f84917962ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 17:23:13 +0100 Subject: [PATCH 482/939] stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes --- easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb index 594f66926ccf..11986d885346 100644 --- a/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/p/PyQt5/PyQt5-5.15.5-GCCcore-11.3.0.eb @@ -50,10 +50,10 @@ components = [ 'use_pip': True, 'options': {'modulename': 'PyQt5.sip'}, }), - ('PyQt-builder', '1.14.0', { + ('PyQt-builder', '1.11.0', { 'source_urls': [PYPI_SOURCE], 'sources': [SOURCE_TAR_GZ], - 'checksums': ['6755931c6d2f8940553e0334d10c933ce5cc18b64425e94fda1accf4ff774f59'], + 'checksums': ['40f6df88c00e6aa9ac9a8bc5688f9fe2a4bd56c06cdb0a0b00ce8955ec34ffe5'], 'start_dir': 'PyQt-builder-%(version)s', 'use_pip': True, }), @@ -97,6 +97,7 @@ sanity_check_commands = [ "pyuic5 --help", "pylupdate5 -version 2>&1 | grep 'pylupdate5 v%(version)s'", "pyrcc5 -version 2>&1 | grep 'pyrcc5 v%(version)s'", + "pip check", ] modextrapaths = { From 0541ccc6695609f2f646ccd0810362055159a4d3 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 22 Nov 2022 17:54:54 +0100 Subject: [PATCH 483/939] adding easyconfigs: EGTtools-0.1.11-foss-2022a.eb --- .../e/EGTtools/EGTtools-0.1.11-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb new file mode 100644 index 000000000000..88ad1c992f38 --- /dev/null +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonBundle' + +name = 'EGTtools' +version = '0.1.11' + +homepage = 'https://github.com/Socrats/EGTTools' +description = """ +EGTtools provides a centralized repository with analytical and numerical +methods to study/model game theoretical problems under the Evolutionary Game +Theory (EGT) framework.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('CMake', '3.24.3'), + ('Ninja', '1.10.2'), + ('scikit-build', '0.15.0'), + ('Eigen', '3.4.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('networkx', '2.8.4'), + ('Seaborn', '0.11.2'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['b736bc00f80e11987ca51eaa11f013a29ccca835a05b6eb91b3850c1e5680e8e'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From 497ee827e02fd25aae30206316b44b04461a26be Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 22 Nov 2022 17:32:56 +0000 Subject: [PATCH 484/939] xarray added as dependency instead of extension --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index fbdcdebc32da..c8a257561183 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -16,6 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), ('dask', '2022.10.0'), + ('xarray', '2022.9.0'), ] use_pip = True @@ -25,9 +26,6 @@ exts_list = [ ('cachetools', '5.2.0', { 'checksums': ['6a94c6402995a99c3970cc7e4884bb60b4a8639938157eeed436098bf9831757'], }), - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), (name, version, { 'checksums': ['7dda45fdf6182a859f5c441cd5928a7c99d41c8bcea9fccf471b7011791b1131'], }), From 0d413469b3877fad7783bff87ba2fe9f10a22b67 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 22 Nov 2022 18:24:09 +0000 Subject: [PATCH 485/939] xarray added as dependency instead of extension --- .../easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index 55ff2f1d94f0..b81f3b845741 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -14,19 +14,16 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('dask', '2022.10.0'), + ('xarray', '2022.9.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('xarray', '2022.9.0', { - 'checksums': ['a2a5b48ec0a3890b71ef48853fe9d5107d2f75452722f319cb8ed6ff8e72e883'], - }), ('xgcm', '0.8.0', { 'checksums': ['99e7e2fc9268fb13827f8849dbae279eaaa4960d51872d62bc38293605b0215f'], }), - (name, version, { 'checksums': ['8c684ecdfe03bade171e17f5ae6bedd422e51db6faffed0303e1839051d40614'], }), From 27d802f112e033736cceb2688ef41162e673aae6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 20:20:50 +0100 Subject: [PATCH 486/939] avoid using empty string in sanity_check_paths in MONAI easyconfigs --- .../easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb | 2 +- easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb index bd6d8765a06a..c4ae75df7095 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a-CUDA-11.7.0.eb @@ -44,7 +44,7 @@ sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'" sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], - 'dirs': [''], + 'dirs': [], } moduleclass = 'vis' diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb index 0d272341e2ce..0314fc871d40 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-1.0.1-foss-2022a.eb @@ -42,7 +42,7 @@ sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'" sanity_check_paths = { 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], - 'dirs': [''], + 'dirs': [], } moduleclass = 'vis' From 704e6881b6a5d53486347b9a14eec021e2c34b54 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Tue, 22 Nov 2022 20:39:33 +0100 Subject: [PATCH 487/939] fix Seaborn version --- easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb index 88ad1c992f38..b400270aca97 100644 --- a/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb +++ b/easybuild/easyconfigs/e/EGTtools/EGTtools-0.1.11-foss-2022a.eb @@ -23,7 +23,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('matplotlib', '3.5.2'), ('networkx', '2.8.4'), - ('Seaborn', '0.11.2'), + ('Seaborn', '0.12.1'), ] use_pip = True From e9c43504d842606b3d71eb3abaed14571651d65e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 22:21:59 +0100 Subject: [PATCH 488/939] adding easyconfigs: scanpy-1.9.1-foss-2021b.eb --- .../s/scanpy/scanpy-1.9.1-foss-2021b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb new file mode 100644 index 000000000000..3967f4007cf1 --- /dev/null +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb @@ -0,0 +1,76 @@ +easyblock = 'PythonBundle' + +name = 'scanpy' +version = '1.9.1' + +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': '2021b'} +toolchainopts = {'openmp': True} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('h5py', '3.6.0'), + ('networkx', '2.6.3'), + ('numba', '0.54.1'), + ('PyTables', '3.6.1'), + ('statsmodels', '0.13.1'), + ('scikit-learn', '1.0.1'), + ('Seaborn', '0.11.2'), + ('tqdm', '4.62.3'), + ('leidenalg', '0.8.8'), +] + +use_pip = True + +exts_list = [ + ('natsort', '8.2.0', { + 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], + }), + # anndata 0.7.8 needs xlrd<2.0 + ('xlrd', '2.0.1', { + 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], + }), + ('anndata', '0.8.0', { + 'checksums': ['94d2cc6f76c0317c0ac28564e3092b313b7ad19c737d66701961f3e620b9066e'], + }), + ('pynndescent', '0.5.8', { + 'checksums': ['a7c552569bf604a101fd54bba1d27c12389e065945dee3a6777a518c63a46f2b'], + }), + ('umap-learn', '0.5.3', { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), + ('stdlib-list', '0.8.0', { + 'checksums': ['a1e503719720d71e2ed70ed809b385c60cd3fb555ba7ec046b96360d30b16d9f'], + }), + ('sinfo', '0.3.4', { + 'checksums': ['81ea91c69a875de178e10bada9476d7300a1f712e1823dbd7714f43a10baba4d'], + }), + ('session_info', '1.0.0', { + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), + (name, version, { + 'checksums': ['00c9a83b649da7e0171c91e9a08cff632102faa760614fd05cd4d1dbba4eb541'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['natsort', 'scanpy']], + 'dirs': ['lib/python%(pyshortver)s/site-packages/'], +} + +sanity_check_commands = [ + "natsort --help", + "scanpy --help", +] + +moduleclass = 'bio' From b8bed9f936c7067b63bc49aa7bca17c574f3cba7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 22 Nov 2022 22:46:18 +0100 Subject: [PATCH 489/939] avoid hardcoding OpenJPEG version in preinstallopts in imagecodecs easyconfig --- .../i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb index 2a32ac22f2e1..284a8b29cb82 100644 --- a/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb +++ b/easybuild/easyconfigs/i/imagecodecs/imagecodecs-2022.9.26-foss-2021a.eb @@ -63,7 +63,7 @@ exts_list = [ }), (name, version, { 'extract_cmd': "tar -xvf %s && find . -type f -print0 | xargs -0 dos2unix", - 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-2.4/:$CPATH && ", + 'preinstallopts': "export CPATH=$EBROOTOPENJPEG/include/openjpeg-%s/:$CPATH && " % local_openjpeg_maj_min, 'sources': ['%(name)s-%(version)s.tar.gz'], 'checksums': ['04d5757d8fd7819844b0f8d9eed05025dca4962f280d0010b42c7c9c993fe371'], }), From a8cf06cf7f9db89b306bf07aba66a5e5a84425eb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 00:31:32 +0100 Subject: [PATCH 490/939] downgrade dependency of oceanspy v0.2.0 on xarray to v2022.6.0 --- easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb index b81f3b845741..ac13454ba89e 100644 --- a/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb +++ b/easybuild/easyconfigs/o/oceanspy/oceanspy-0.2.0-foss-2022a.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('dask', '2022.10.0'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 0a9d01452b248f18dda7d527ed5be70e5733c5de Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 00:32:43 +0100 Subject: [PATCH 491/939] downgrade dependency of xmitgcm v0.5.2 on xarray to v2022.6.0 --- easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb index c8a257561183..cf4cebe8ec11 100644 --- a/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb +++ b/easybuild/easyconfigs/x/xmitgcm/xmitgcm-0.5.2-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('MITgcmutils', '0.1.2'), ('dask', '2022.10.0'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 2bf335ffc8a813774c7857fc06e8b7f78ea6fb59 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 10:29:00 +0100 Subject: [PATCH 492/939] adding easyconfigs: CheMPS2-1.8.12-foss-2022a.eb, PyCheMPS2-1.8.12-foss-2022a.eb --- .../c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb | 31 +++++++++++++++++ .../PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb | 33 +++++++++++++++++++ 2 files changed, 64 insertions(+) create mode 100644 easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb new file mode 100644 index 000000000000..91535173b689 --- /dev/null +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb @@ -0,0 +1,31 @@ +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': '2022a'} + +source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] +sources = ['v%(version)s.tar.gz'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('HDF5', '1.12.2') +] + +pretestopts = 'export OMP_NUM_THREADS=1 && ' +runtest = 'test' + +separate_build_dir = True + +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-2022a.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb new file mode 100644 index 000000000000..3226a9c3db35 --- /dev/null +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb @@ -0,0 +1,33 @@ +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('CheMPS2', version), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'source_urls': ['https://github.com/SebWouters/CheMPS2/archive/'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'install_src': './%(name)s', + 'modulename': '%(name)s', + }), +] + +sanity_pip_check = True + +moduleclass = 'chem' From 52bdfbb11e07ff946c90cb9ed25c209874c27aaa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 10:47:34 +0100 Subject: [PATCH 493/939] adding easyconfigs: infercnvpy-0.4.0-foss-2021b.eb --- .../infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb new file mode 100644 index 000000000000..afaff507ff21 --- /dev/null +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'infercnvpy' +version = '0.4.0' + +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': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('leidenalg', '0.8.8'), + ('scanpy', '1.9.1'), +] + +use_pip = True + +# avoid hatcling requirement to install infercnvpy +# (since installing it introduces conflicting version requirements with poetry included with Python) +local_preinstallopts = """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && """ +local_preinstallopts += """sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && """ +local_preinstallopts += """sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ + +exts_list = [ + ('setuptools', '65.6.0', { + 'checksums': ['d1eebf881c6114e51df1664bc2c9133d022f78d12d5f4f665b9191f084e2862d'], + }), + ('gtfparse', '1.2.1', { + 'checksums': ['559d4d36b0bd5d4494f925cab3c00cd969783ebb6408fa025df92663965834b8'], + }), + ('pyreadr', '0.4.7', { + 'checksums': ['901110d62b4bedaef288f4db81425fb696edc721fe2c34c1083f5fb11050a73c'], + }), + ('tqdm', '4.64.1', { + 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'checksums': ['00b8d78726db0a70bdb4d887fd503a484873244a60b9f58a0979aa75ba6e48cb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From 0ae557bd93cf3e13fe872f03288dfe6c2a560439 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 10:52:35 +0100 Subject: [PATCH 494/939] adding easyconfigs: nodejs-18.12.1-GCCcore-12.2.0.eb --- .../n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..46b6a0c4ae4e --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '18.12.1' # LTS on 2022-11-22 +local_libversion = '108' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['ba8174dda00d5b90943f37c6a180a1d37c861d91e04a4cb38dc1c0c74981c186'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +configopts = [ + '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library + '--shared --with-intl=none', # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +postinstallcmds = [ + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s' % SHLIB_EXT, 'lib/libv8.%s' % SHLIB_EXT], + 'dirs': ['lib/node_modules', 'include/node'] +} + +sanity_check_commands = ["node --help"] + +moduleclass = 'lang' From b8afb95e3a087af571d132b17546419eb84438eb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 11:27:18 +0100 Subject: [PATCH 495/939] add missing checksums for CheMPS2 and PyCheMPS2 v1.8.12 --- easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb | 3 +-- .../easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb | 3 ++- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb index 91535173b689..482ab997133b 100644 --- a/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CheMPS2/CheMPS2-1.8.12-foss-2022a.eb @@ -11,6 +11,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} source_urls = ['https://github.com/SebWouters/CheMPS2/archive/'] sources = ['v%(version)s.tar.gz'] +checksums = ['eef1b92d74ac07fde58c043f64e8cac02b5400c209c44dcbb51641f86e0c7c83'] builddependencies = [('CMake', '3.23.1')] @@ -21,8 +22,6 @@ dependencies = [ pretestopts = 'export OMP_NUM_THREADS=1 && ' runtest = 'test' -separate_build_dir = True - sanity_check_paths = { 'files': ['bin/chemps2', 'lib64/libchemps2.%s' % SHLIB_EXT, 'lib64/libchemps2.a'], 'dirs': ['include/chemps2'] diff --git a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb index 3226a9c3db35..ed3cf0c39be6 100644 --- a/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PyCheMPS2/PyCheMPS2-1.8.12-foss-2022a.eb @@ -21,10 +21,11 @@ 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', - 'modulename': '%(name)s', }), ] From a3c4da77a27192f4369b8e83391b990a75b358b5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 11:31:59 +0100 Subject: [PATCH 496/939] adding easyconfigs: Boost.MPI-1.79.0-gompi-2022a.eb --- .../Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb new file mode 100644 index 000000000000..be6c179e5285 --- /dev/null +++ b/easybuild/easyconfigs/b/Boost.MPI/Boost.MPI-1.79.0-gompi-2022a.eb @@ -0,0 +1,28 @@ +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': '2022a'} +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', '5.2.5'), + ('ICU', '71.1'), +] + +configopts = '--without-libraries=python' + +boost_mpi = True +tagged_layout = True + +moduleclass = 'devel' From 811ef35e395c75580ddfeec617d0cbaac2650231 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 23 Nov 2022 12:40:15 +0100 Subject: [PATCH 497/939] prefix custom parameters with local in nodejs --- .../n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb | 18 +++++++++--------- .../n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb | 18 +++++++++--------- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 18 +++++++++--------- 3 files changed, 27 insertions(+), 27 deletions(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb index bf1db1aa052c..866799bfdea0 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.0-GCCcore-10.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.0' # LTS on 2021-06-03 -_libversion = '83' +local_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -37,24 +37,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb index a6fe9b552ba3..6be4d5098780 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-14.17.6-GCCcore-11.2.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '14.17.6' # LTS on 2020-08-31 -_libversion = '83' +local_libversion = '83' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -27,24 +27,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index bcd9c8dded13..117331f1af84 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -2,7 +2,7 @@ easyblock = 'ConfigureMake' name = 'nodejs' version = '16.15.1' # LTS on 2022-06-12 -_libversion = '93' +local_libversion = '93' homepage = 'https://nodejs.org' description = """Node.js is a platform built on Chrome's JavaScript runtime @@ -27,24 +27,24 @@ dependencies = [ ] # Use ICU and OpenSSL from EasyBuild -_common_configopts = "--with-intl=system-icu --shared-openssl " +local_common_configopts = "--with-intl=system-icu --shared-openssl " configopts = [ - _common_configopts, # Static build - '--shared %s' % _common_configopts, # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode -_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] -_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in _extra_sonames] -_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, _libversion) +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) postinstallcmds = [ - "cd %%(installdir)s/lib && ln -s %s %s" % (_libnode_real, x) for x in _extra_libs + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [_libnode_real] + _extra_libs], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From d8364b3d5b9b06d6057c7e9de380ebb80a93ab00 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Wed, 23 Nov 2022 12:55:10 +0100 Subject: [PATCH 498/939] adding easyconfigs: GLM-0.9.9.8-GCCcore-11.3.0.eb --- .../g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..22d687ed0f41 --- /dev/null +++ b/easybuild/easyconfigs/g/GLM/GLM-0.9.9.8-GCCcore-11.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'GLM' +version = '0.9.9.8' + +homepage = 'https://github.com/g-truc/glm' +description = """ +OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics +software based on the OpenGL Shading Language (GLSL) specifications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/g-truc/glm/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + 'GLM-0.9.9.8_fix_missing_install.patch', +] +checksums = [ + '7d508ab72cb5d43227a3711420f06ff99b0a0cb63ee2f93631b162bfe1fe9592', # 0.9.9.8.tar.gz + '1cc199f9d66679b0b5e9a9fbe20bca0d9b15760fa172ca8759dd15bab35802ca', # GLM-0.9.9.8_fix_missing_install.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['include/glm/gtc', 'include/glm/gtx'], +} + +moduleclass = 'lib' From acff80f03c68708109802872b0db1993a9964020 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 23 Nov 2022 12:05:06 +0000 Subject: [PATCH 499/939] adding easyconfigs: libspatialindex-1.9.3-GCCcore-11.3.0.eb --- .../libspatialindex-1.9.3-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..445496497a10 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialindex/libspatialindex-1.9.3-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +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': '11.3.0'} + +source_urls = ['https://github.com/libspatialindex/libspatialindex/releases/download/%(version)s/'] +sources = ['spatialindex-src-%(version)s.tar.gz'] +checksums = ['47d8779e32477b330e46b62fb7e62cb812caee5d8e684c35cb635a42a749f3fc'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['lib/libspatialindex.%s' % SHLIB_EXT], + 'dirs': ['include/spatialindex'], +} + +moduleclass = 'lib' From 46b4c405d06e84d3fb1e72bed94dc5082e123311 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 14:30:41 +0100 Subject: [PATCH 500/939] use proper dependencies for ICU and OpenSSL for nodejs 18.12.1 --- .../i/ICU/ICU-72.1-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ .../n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb | 23 ++++++++++----- 2 files changed, 45 insertions(+), 7 deletions(-) create mode 100644 easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..9b141a4671dd --- /dev/null +++ b/easybuild/easyconfigs/i/ICU/ICU-72.1-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'ICU' +version = '72.1' + +homepage = 'https://icu.unicode.org' +description = """ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization + support for software applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/unicode-org/icu/releases/download/release-%(version_major)s-%(version_minor)s'] +sources = ['icu4c-%(version_major)s_%(version_minor)s-src.tgz'] +checksums = ['a2d2d38217092a7ed56635e34467f92f976b370e20182ad325edea6681a71d68'] + +builddependencies = [ + ('binutils', '2.39'), + ('Python', '3.10.8', '-bare'), +] + +start_dir = 'source' + +sanity_check_paths = { + 'files': ['lib/libicu%s.%s' % (x, SHLIB_EXT) for x in ['data', 'i18n', 'io', 'test', 'tu', 'uc']], + 'dirs': ['bin', 'include/unicode', 'share/icu', 'share/man'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb index 46b6a0c4ae4e..2ea5d3c974f3 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-18.12.1-GCCcore-12.2.0.eb @@ -21,21 +21,30 @@ builddependencies = [ ('Python', '3.10.8', '-bare'), ] +dependencies = [ + ('ICU', '72.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + configopts = [ - '--with-intl=none', # Fully disable ICU to avoid issues with the embedded icu-small library - '--shared --with-intl=none', # Build libnode.so in a second run + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run ] # Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs ] sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s' % SHLIB_EXT, 'lib/libv8.%s' % SHLIB_EXT], + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], 'dirs': ['lib/node_modules', 'include/node'] } From 6361e43ad12699fc7afaed695b7cc9d8a5c3f780 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 15:30:58 +0100 Subject: [PATCH 501/939] adding easyconfigs: LLVM-15.0.5-GCCcore-12.2.0.eb --- .../l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..fad97fede298 --- /dev/null +++ b/easybuild/easyconfigs/l/LLVM/LLVM-15.0.5-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +name = 'LLVM' +version = '15.0.5' + +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': '12.2.0'} +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', + 'cmake-%(version)s.src.tar.xz', +] +checksums = [ + {'llvm-15.0.5.src.tar.xz': '4428688b567ab1c9911aa9e13cb44c9bc1b14431713c14de491e10369f2b0370'}, + {'cmake-15.0.5.src.tar.xz': '61a9757f2fb7dd4c992522732531eb58b2bb031a2ca68848ff1cfda1fc07b7b3'}, +] + +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' From 09e832fc190757d9ce10f0e701ca6e9c0b521790 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Dvo=C5=99=C3=A1=C4=8Dek=20Josef?= Date: Wed, 23 Nov 2022 17:26:33 +0100 Subject: [PATCH 502/939] adding easyconfigs: libconfig-1.7.3-GCCcore-11.2.0.eb --- .../libconfig-1.7.3-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..4cf46abac377 --- /dev/null +++ b/easybuild/easyconfigs/l/libconfig/libconfig-1.7.3-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libconfig' +version = '1.7.3' + +homepage = 'https://hyperrealm.github.io/libconfig' +description = "Libconfig is a simple library for processing structured configuration files" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://hyperrealm.github.io/libconfig/dist/'] +sources = [SOURCE_TAR_GZ] +checksums = ['545166d6cac037744381d1e9cc5a5405094e7bfad16a411699bcff40bbb31ee7'] + +builddependencies = [ + ('binutils', '2.37'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +sanity_check_paths = { + 'files': ['include/libconfig.h', 'include/libconfig.h++', 'lib/libconfig.a', 'lib/libconfig++.a', + 'lib/libconfig.%s' % SHLIB_EXT, 'lib/libconfig++.%s' % SHLIB_EXT], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'lib' From b16f1b5994d5848d15ea4138af0442c5b4269c5f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 23 Nov 2022 18:49:02 +0000 Subject: [PATCH 503/939] adding easyconfigs: NVHPC-22.7-CUDA-11.7.0.eb, FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb, OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb, BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb, FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb, ScaLAPACK-2.2.0-nvompi-2022.07.eb, nvofbf-2022.07.eb --- .../BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb | 44 +++++++++++++ .../FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb | 20 ++++++ .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 59 +++++++++++++++++ .../n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb | 66 +++++++++++++++++++ .../easyconfigs/n/nvofbf/nvofbf-2022.07.eb | 25 +++++++ .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 31 +++++++++ .../ScaLAPACK-2.2.0-nvompi-2022.07.eb | 42 ++++++++++++ 7 files changed, 287 insertions(+) create mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb create mode 100644 easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 000000000000..9928532de5e7 --- /dev/null +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'BLIS' +version = '0.9.0' + +homepage = 'https://github.com/flame/blis/' +description = """BLIS is a portable software framework for instantiating high-performance +BLAS-like dense linear algebra libraries.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} + +source_urls = ['https://github.com/flame/blis/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_disable_power9_kernels.patch', + '%(name)s-%(version)s_enable_ppc_autodetect.patch', +] +checksums = [ + '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz + # BLIS-0.9.0_disable_power9_kernels.patch + 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', + # BLIS-0.9.0_enable_ppc_autodetect.patch + 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', +] +builddependencies = [ + ('Python', '3.10.4', '-bare'), + ('Perl', '5.34.1'), +] + +preconfigopts = "sed -i 's/LINKER.*/LINKER := nvc/' common.mk &&" +configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' +configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno"' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['include/blis/cblas.h', 'include/blis/blis.h', + 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'CPATH': 'include/blis'} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 000000000000..9a75ff49951c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW/FFTW-3.3.10-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,20 @@ +name = 'FFTW' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +# Does not work with nvc +with_quad_prec = False + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 000000000000..07c769edc088 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,59 @@ +easyblock = 'Bundle' + +name = 'FlexiBLAS' +version = '3.2.0' + +homepage = 'https://gitlab.mpi-magdeburg.mpg.de/software/flexiblas-release' +description = """FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation +used by a program without recompiling or relinking it.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} +local_extra_flags = "-D__ELF__" +toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': local_extra_flags} + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4', '-bare'), # required for running the tests + ('BLIS', '0.9.0'), +] + +dependencies = [ + ('OpenBLAS', '0.3.20'), +] + +# note: first listed backend will be used as default by FlexiBLAS, +# unless otherwise specified via easyconfig parameter flexiblas_default +local_backends = ['OpenBLAS', 'BLIS'] + +# imkl supplies its backend via the imkl module, not as a dependency +if ARCH == 'x86_64': + local_backends.append('imkl') + +default_component_specs = {'start_dir': '%(namelower)s-%(version)s'} +sanity_check_all_components = True + +# Also build and install LAPACKE, which FlexiBLAS does not support yet +components = [ + (name, version, { + 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904'], + 'configopts': '-DABI=Intel', + 'backends': local_backends, + }), + ('LAPACK', '3.10.1', { + 'easyblock': 'CMakeMake', + 'source_urls': ['https://github.com/Reference-LAPACK/lapack/archive/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['cd005cd021f144d7d5f7f33c943942db9f03a28d110d6a3b80d718a295f7f714'], + 'configopts': ('-DBUILD_SHARED_LIBS=ON -DUSE_OPTIMIZED_BLAS=ON -DLAPACKE=ON ' + '-DUSE_OPTIMIZED_LAPACK=ON -DBUILD_DEPRECATED=ON ' + '-DCMAKE_INSTALL_INCLUDEDIR=%(installdir)s/include/flexiblas'), + 'sanity_check_paths': { + 'files': ['lib/liblapacke.%s' % SHLIB_EXT, 'include/flexiblas/lapacke.h'], + 'dirs': [], + }, + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 000000000000..4922cc417e63 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,66 @@ +name = 'NVHPC' +version = '22.7' +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_2022_%%(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': + '2aae3fbfd2d0d2d09448a36166c42311368f5600c7c346f159c280b412fe924a', + local_tarball_tmpl % 'ppc64le': + '6dd4fd382c22769e4fa9508714119abd7d1df3dc58c69414a14b0b0dbc34564f', + local_tarball_tmpl % 'x86_64': + '3ce1c346f8bc7e50defb41c545c8907fdc012ff60b27eb8985cf3213f19d863a', + } +] + +local_gccver = '11.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.38', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.14', '', ('GCCcore', local_gccver)), + ('CUDA', '11.7.0', '', SYSTEM), +] + +# 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', '11.4.1')] +# 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 = '7.0' +# 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 = True # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = True # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = True # Add NVHPC's NVIDIA Profilers +# module_add_nccl = True # Add NVHPC's NCCL library +# module_add_nvshmem = True # 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' diff --git a/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb new file mode 100644 index 000000000000..af891ade799f --- /dev/null +++ b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb @@ -0,0 +1,25 @@ +easyblock = 'Toolchain' + +name = 'nvofbf' +version = '2022.07' + +homepage = '(none)' +description = """NVHPC based toolchain, including OpenMPI for MPI support, +OpenBLAS (via FlexiBLAS for BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_compiler = ('NVHPC', '22.7-CUDA-11.7.0') + +local_comp_mpi_tc = ('nvompi', version) + +dependencies = [ + local_compiler, + ('OpenMPI', '4.1.4', '', local_compiler), + ('FlexiBLAS', '3.2.0', '', local_compiler), + ('FFTW', '3.3.10', '', local_compiler), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb new file mode 100644 index 000000000000..a05030ce4e39 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,31 @@ +name = 'OpenBLAS' +version = '0.3.20' + +homepage = 'http://www.openblas.net/' +description = "OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version." + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} + +source_urls = [ + # order matters, trying to download the large.tgz/timing.tgz LAPACK tarballs from GitHub causes trouble + 'https://www.netlib.org/lapack/timing/', + 'https://github.com/xianyi/OpenBLAS/archive/', +] +sources = ['v%(version)s.tar.gz'] +patches = [ + ('large.tgz', '.'), + ('timing.tgz', '.'), + 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', +] +checksums = [ + '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz + 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz + '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz + # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', +] + +# extensive testing can be enabled by uncommenting the line below +# runtest = 'PATH=.:$PATH lapack-timing' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb new file mode 100644 index 000000000000..85b567d8d102 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb @@ -0,0 +1,42 @@ +name = 'ScaLAPACK' +version = '2.2.0' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'nvompi', 'version': '2022.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.0'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From ce2947aead4d9ae74e80445e06f913db4c6168f2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:44:22 +0100 Subject: [PATCH 504/939] adding easyconfigs: zstd-1.5.2-GCCcore-12.2.0.eb, gzip-1.12-GCCcore-12.2.0.eb, lz4-1.9.4-GCCcore-12.2.0.eb --- .../g/gzip/gzip-1.12-GCCcore-12.2.0.eb | 29 +++++++++++++ .../l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb | 30 ++++++++++++++ .../z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 3 files changed, 100 insertions(+) create mode 100644 easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..22956fb64c76 --- /dev/null +++ b/easybuild/easyconfigs/g/gzip/gzip-1.12-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'gzip' +version = '1.12' + +homepage = 'https://www.gnu.org/software/gzip/' +description = "gzip (GNU zip) is a popular data compression program as a replacement for compress" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +patches = ['gzip-1.12_fix-gnulib-strndup-redeclaration.patch'] +checksums = [ + '5b4fb14d38314e09f2fc8a1c510e7cd540a3ea0e3eb9b0420046b82c3bf41085', # gzip-1.12.tar.gz + # gzip-1.12_fix-gnulib-strndup-redeclaration.patch + '9c67e3e88848f7ff1f19f29d87f286bac1cc8f027f7eea9bcaf53883b95032e4', +] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ["bin/gunzip", "bin/gzip", "bin/uncompress"], + 'dirs': [], +} + +sanity_check_commands = [True, ('gzip', '--version')] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..6f3f81b768d6 --- /dev/null +++ b/easybuild/easyconfigs/l/lz4/lz4-1.9.4-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'lz4' +version = '1.9.4' + +homepage = 'https://lz4.github.io/lz4/' +description = """LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. + It features an extremely fast decoder, with speed in multiple GB/s per core.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['0b0e3aa07c8c063ddf40b082bdf7e37a1562bda40a0ff5272957f3e987e0e54b'] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'check' + +sanity_check_paths = { + 'files': ["bin/lz4", "lib/liblz4.%s" % SHLIB_EXT, "include/lz4.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..7176db3c09e4 --- /dev/null +++ b/easybuild/easyconfigs/z/zstd/zstd-1.5.2-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'zstd' +version = '1.5.2' + +homepage = 'https://facebook.github.io/zstd' +description = """Zstandard is a real-time compression algorithm, providing high compression ratios. + It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. + It also offers a special mode for small data, called dictionary compression, and can create dictionaries + from any sample set.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'facebook' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['f7de13462f7a82c29ab865820149e778cbfe01087b3a55b5332707abf9db4a6e'] + +builddependencies = [ + ('binutils', '2.39'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('gzip', '1.12'), + ('XZ', '5.2.7'), + ('lz4', '1.9.4'), +] + +skipsteps = ['configure'] + +runtest = 'check' + +installopts = "PREFIX=%(installdir)s" + +sanity_check_paths = { + 'files': ["bin/zstd", "lib/libzstd.%s" % SHLIB_EXT, "include/zstd.h"], + 'dirs': ["lib/pkgconfig"] +} + +moduleclass = 'lib' From 6266613ac52a07184c8d2b51c1fa352fabdcf366 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:46:43 +0100 Subject: [PATCH 505/939] {vis}[GCCcore/12.2.0] Mesa v22.2.4, Mako v1.2.4, libglvnd v1.6.0, libdrm v2.4.114, libunwind v1.6.2 --- .../l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb | 32 +++++++++ .../libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb | 33 +++++++++ .../libunwind-1.6.2-GCCcore-12.2.0.eb | 32 +++++++++ .../m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb | 29 ++++++++ .../m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb | 69 +++++++++++++++++++ 5 files changed, 195 insertions(+) create mode 100644 easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..613ec59df251 --- /dev/null +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'MesonNinja' + +name = 'libdrm' +version = '2.4.114' + +homepage = 'https://dri.freedesktop.org' +description = """Direct Rendering Manager runtime library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://dri.freedesktop.org/libdrm/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['3049cf843a47d12e5eeefbc3be3496d782fa09f42346bf0b7defe3d1e598d026'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] +dependencies = [('X11', '20221110')] + +# installing manpages requires an extra build dependency (docbook xsl) +configopts = '-Dman-pages=false' + +sanity_check_paths = { + 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], + 'dirs': ['include', 'lib'], +} + + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b953d44c5727 --- /dev/null +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'MesonNinja' + +name = 'libglvnd' +version = '1.6.0' + +homepage = 'https://gitlab.freedesktop.org/glvnd/libglvnd' +description = "libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] +sources = ['libglvnd-v%(version)s.tar.gz'] +checksums = ['33b8b993adf47a21bc1c46bcf970927edeb9884390d5b09b1aed051d600c0b2f'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), +] + +dependencies = [('X11', '20221110')] + +# Let EGL find system-installed vendor files in /etc/glvnd/egl_vendor.d etc. +allow_prepend_abs_path = True +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "/etc/glvnd/egl_vendor.d:/usr/share/glvnd/egl_vendor.d"} + +sanity_check_paths = { + 'files': ['lib/lib%s.%s' % (x, SHLIB_EXT) for x in ['EGL', 'GL', 'GLX', 'OpenGL']], + 'dirs': ['include/%s' % x for x in ['EGL', 'GL', 'GLES', 'GLES2', 'GLES3', 'glvnd', 'KHR']] + ['lib/pkgconfig'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5e849e316cdf --- /dev/null +++ b/easybuild/easyconfigs/l/libunwind/libunwind-1.6.2-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libunwind' +version = '1.6.2' + +homepage = 'https://www.nongnu.org/libunwind/' +description = """The primary goal of libunwind is to define a portable and efficient C programming interface + (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the + preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain + (non-local goto). The API supports both local (same-process) and remote (across-process) operation. + As such, the API is useful in a number of applications""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SAVANNAH_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['4a6aec666991fb45d0889c44aede8ad6eb108071c3554fcdff671f9c94794976'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('XZ', '5.2.7'), +] + +preconfigopts = 'export LIBS="$LIBS -llzma" && export CFLAGS="$CFLAGS -fno-common" && ' + +sanity_check_paths = { + 'files': ['include/libunwind.h', 'lib/libunwind.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5aaa05828b2f --- /dev/null +++ b/easybuild/easyconfigs/m/Mako/Mako-1.2.4-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'Mako' +version = '1.2.4' + +homepage = 'https://www.makotemplates.org' +description = """A super-fast templating language that borrows the best ideas from the existing templating languages""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['d60a3903dc3bb01a18ad6a89cdbe2e4eadc69c0bc8ef1e3773ba53d44c3f7a34'] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +builddependencies = [('binutils', '2.39')] + +dependencies = [('Python', '3.10.8')] + +sanity_check_paths = { + 'files': ['bin/mako-render'], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ["mako-render --help"] + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f59d911be6ac --- /dev/null +++ b/easybuild/easyconfigs/m/Mesa/Mesa-22.2.4-GCCcore-12.2.0.eb @@ -0,0 +1,69 @@ +# This is a Mesa using software rendering via Gallium-DRI and libglvnd +# - libglvnd can dynamically choose between system-installed NVidia +# libGLX/libEGL or the software renderers provided by this Mesa +# - EGL is available +# +# Software renderers enabled (swr deprecated as of v22): +# - llvmpipe: uses LLVM for JIT code generation (multi-threaded) +# - softpipe: a reference Gallium driver +# Default renderer is llvmpipe. To use softpipe, set the environment +# variable GALLIUM_DRIVER=softpipe + +name = 'Mesa' +version = '22.2.4' + +homepage = 'https://www.mesa3d.org/' +description = """Mesa is an open-source implementation of the OpenGL specification - + a system for rendering interactive 3D graphics.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://mesa.freedesktop.org/archive/', + 'https://mesa.freedesktop.org/archive/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x/%(version)s', + 'ftp://ftp.freedesktop.org/pub/mesa/older-versions/%(version_major)s.x', +] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['65d76b53ca5c7b46019e0e8e5b414de45d2fecd3fcd71707f6c3bc7691c9f7ab'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('pkgconf', '1.9.3'), + ('Mako', '1.2.4'), + ('libxml2', '2.10.3'), + ('expat', '2.4.9'), + ('gettext', '0.21.1'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), + ('libdrm', '2.4.114'), + ('libglvnd', '1.6.0'), + ('libunwind', '1.6.2'), + ('LLVM', '15.0.5'), + ('X11', '20221110'), +] + +configopts = "-Dplatforms=x11 -Dosmesa=true -Ddri-drivers='' -Dvulkan-drivers='' " +configopts += "-Dllvm=true -Dshared-llvm=true -Dlibunwind=true -Dglvnd=true" + +# 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 +# configopts += " -Dgallium-drivers=swrast" + +# symlink indirect to mesa GLX, similar to Debian, see +# https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=881789 +# This helps in certain X forwarding situations (e.g. XQuartz) +postinstallcmds = ["ln -s libGLX_mesa.so.0 %(installdir)s/lib/libGLX_indirect.so.0"] + +# Tells libglvnd where to find EGL libraries +modextrapaths = {"__EGL_VENDOR_LIBRARY_DIRS": "share/glvnd/egl_vendor.d"} + +moduleclass = 'vis' From 8338bf7b0d8e45eb8a6155dae9792dc14be1f10d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:52:50 +0100 Subject: [PATCH 506/939] use 'disabled' to skip installation of man pages for libdrm 2.4.114 --- easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb index 613ec59df251..40a3653b38d4 100644 --- a/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libdrm/libdrm-2.4.114-GCCcore-12.2.0.eb @@ -21,7 +21,7 @@ builddependencies = [ dependencies = [('X11', '20221110')] # installing manpages requires an extra build dependency (docbook xsl) -configopts = '-Dman-pages=false' +configopts = '-Dman-pages=disabled' sanity_check_paths = { 'files': ['lib/libdrm.%s' % SHLIB_EXT, 'include/libdrm/drm.h'], From 205429ecc30c39fab6171fe430898c5d73a1a925 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 22:54:14 +0100 Subject: [PATCH 507/939] fix checksum for libglvnd 1.6.0 --- .../easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb index b953d44c5727..6e95158d9021 100644 --- a/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libglvnd/libglvnd-1.6.0-GCCcore-12.2.0.eb @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} source_urls = ['https://gitlab.freedesktop.org/glvnd/libglvnd/-/archive/v%(version)s/'] sources = ['libglvnd-v%(version)s.tar.gz'] -checksums = ['33b8b993adf47a21bc1c46bcf970927edeb9884390d5b09b1aed051d600c0b2f'] +checksums = ['efc756ffd24b24059e1c53677a9d57b4b237b00a01c54a6f1611e1e51661d70c'] builddependencies = [ ('binutils', '2.39'), From 0dc8178599b7c7d388169d5db7797275ba873a9c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:05:33 +0100 Subject: [PATCH 508/939] adding easyconfigs: libGLU-9.0.2-GCCcore-12.2.0.eb --- .../l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2a35c328e4b4 --- /dev/null +++ b/easybuild/easyconfigs/l/libGLU/libGLU-9.0.2-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'libGLU' +version = '9.0.2' + +homepage = 'https://mesa.freedesktop.org/archive/glu/' +description = """The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://mesa.freedesktop.org/archive/glu/'] +sources = ['glu-%(version)s.tar.gz'] +checksums = ['24effdfb952453cc00e275e1c82ca9787506aba0282145fff054498e60e19a65'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('Mesa', '22.2.4'), +] + +sanity_check_paths = { + 'files': ['lib/libGLU.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From ea2ea8b366a92933d652ae53987e948b85f64687 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:22:08 +0100 Subject: [PATCH 509/939] {lib}[GCCcore/12.2.0] libjpeg-turbo v2.1.4, NASM v2.15.05 --- .../libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb | 42 +++++++++++++++++++ .../n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb | 25 +++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0117bb716bf7 --- /dev/null +++ b/easybuild/easyconfigs/l/libjpeg-turbo/libjpeg-turbo-2.1.4-GCCcore-12.2.0.eb @@ -0,0 +1,42 @@ +easyblock = 'CMakeMake' + +name = 'libjpeg-turbo' +version = '2.1.4' + +homepage = 'https://sourceforge.net/projects/libjpeg-turbo/' + +description = """ + libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to + accelerate baseline JPEG compression and decompression. libjpeg is a library + that implements JPEG image encoding, decoding and transcoding. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d3ed26a1131a13686dfca4935e520eb7c90ae76fbc45d98bb50a8dc86230342b'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +dependencies = [ + ('NASM', '2.15.05'), +] + +configopts = ' -G"Unix Makefiles" -DWITH_JPEG8=1' + +runtest = "test" + +sanity_check_paths = { + 'files': ['bin/cjpeg', 'bin/djpeg', 'bin/jpegtran', 'bin/rdjpgcom', + 'bin/tjbench', 'bin/wrjpgcom', 'lib/libjpeg.a', + 'lib/libjpeg.%s' % SHLIB_EXT, 'lib/libturbojpeg.a', + 'lib/libturbojpeg.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e4fa39b554ec --- /dev/null +++ b/easybuild/easyconfigs/n/NASM/NASM-2.15.05-GCCcore-12.2.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'NASM' +version = '2.15.05' + +homepage = 'https://www.nasm.us/' + +description = """NASM: General-purpose x86 assembler""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://www.nasm.us/pub/nasm/releasebuilds/%(version)s'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['3c4b8339e5ab54b1bcb2316101f8985a5da50a3f9e504d43fa6f35668bee2fd0'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/nasm'], + 'dirs': [], +} + +moduleclass = 'lang' From 8cdfede4b48a9bd320ece80e54808ae9ed538224 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:24:56 +0100 Subject: [PATCH 510/939] adding easyconfigs: double-conversion-3.2.1-GCCcore-12.2.0.eb --- .../double-conversion-3.2.1-GCCcore-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..d3221353d9fa --- /dev/null +++ b/easybuild/easyconfigs/d/double-conversion/double-conversion-3.2.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'double-conversion' +version = '3.2.1' + +homepage = 'https://github.com/google/double-conversion' +description = "Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/google/%(name)s/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e40d236343cad807e83d192265f139481c51fc83a1c49e406ac6ce0a0ba7cd35'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +separate_build_dir = True + +build_type = 'Release' + +# 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' From d0d8e02b7a4101b871dfe52484c14b546f85384c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:27:06 +0100 Subject: [PATCH 511/939] adding easyconfigs: cairo-1.17.4-GCCcore-12.2.0.eb, GLib-2.75.0-GCCcore-12.2.0.eb, pixman-0.42.2-GCCcore-12.2.0.eb, PCRE2-10.40-GCCcore-12.2.0.eb --- .../c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb | 49 +++++++++++++++++ .../g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb | 28 ++++++++++ .../p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb | 28 ++++++++++ 4 files changed, 157 insertions(+) create mode 100644 easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..a9661b33bce4 --- /dev/null +++ b/easybuild/easyconfigs/c/cairo/cairo-1.17.4-GCCcore-12.2.0.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'cairo' +version = '1.17.4' + +homepage = 'https://cairographics.org' +description = """Cairo is a 2D graphics library with support for multiple output devices. + Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, + PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [ + 'https://cairographics.org/releases/', + 'https://cairographics.org/snapshots/' +] +sources = [SOURCE_TAR_XZ] +checksums = ['74b24c1ed436bbe87499179a3b27c43f4143b8676d8ad237a6fa787401959705'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('pixman', '0.42.2'), + ('expat', '2.4.9'), + ('GLib', '2.75.0'), + ('X11', '20221110'), +] + +# disable symbol lookup, which requires -lbfd, to avoid link issues with (non-PIC) libiberty.a provided by GCC +configopts = "--enable-symbol-lookup=no --enable-gobject=yes --enable-svg=yes --enable-tee=yes --enable-xlib-xcb " + +sanity_check_paths = { + 'files': ['bin/cairo-trace', 'lib/cairo/libcairo-trace.%s' % SHLIB_EXT, 'lib/cairo/libcairo-trace.a', + 'lib/libcairo.a', 'lib/libcairo-gobject.a', 'lib/libcairo-script-interpreter.a', + 'lib/libcairo.%s' % SHLIB_EXT, 'lib/libcairo-gobject.%s' % SHLIB_EXT, + 'lib/libcairo-script-interpreter.%s' % SHLIB_EXT] + + ['include/cairo/cairo%s.h' % x for x in ['', '-deprecated', '-features', '-ft', '-gobject', '-pdf', '-ps', + '-script', '-script-interpreter', '-svg', '-version', '-xcb', + '-xlib', '-xlib-xrender']], + 'dirs': ['lib/pkgconfig'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0390a9a2e541 --- /dev/null +++ b/easybuild/easyconfigs/g/GLib/GLib-2.75.0-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'MesonNinja' + +name = 'GLib' +version = '2.75.0' + +homepage = 'https://www.gtk.org/' +description = """GLib is one of the base libraries of the GTK+ project""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['6dde8e55cc4a2c83d96797120b08bcffb5f645b2e212164ae22d63c40e0e6360'] + +builddependencies = [ + # Python is required for building against GLib, at least when + # gdbus-codegen or one of the other python scripts are used. + # Since Meson 0.50 and later are Python >=3.5 only we can't build + # Python specific versions of GLib that uses Python 2.x + # thus Python should not be a runtime dependency for GLib. + # Packages that use GLib should either have an explicit + # (build)dependency on Python or it will use the system version + # EasyBuild itself uses. + ('Python', '3.10.8'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libffi', '3.4.4'), + ('gettext', '0.21.1'), + ('libxml2', '2.10.3'), + ('PCRE2', '10.40'), + ('util-linux', '2.38.1'), +] + +# avoid using hardcoded path to Python binary in build step +preconfigopts = "export PYTHON=python && " + +configopts = "--buildtype=release --default-library=both " + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['lib/libglib-%(version_major)s.0.a', 'lib/libglib-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include'], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..7aed3007b9f6 --- /dev/null +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.40-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'PCRE2' +version = '10.40' + +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': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ded42661cab30ada2e72ebff9e725e745b4b16ce831993635136f2ef86177724'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--enable-shared --enable-jit --enable-pcre2-16 --enable-unicode" + +sanity_check_paths = { + 'files': ["bin/pcre2-config", "bin/pcre2grep", "bin/pcre2test", "lib/libpcre2-8.a", "lib/libpcre2-16.a"], + 'dirs': [], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..17b7e5b6432a --- /dev/null +++ b/easybuild/easyconfigs/p/pixman/pixman-0.42.2-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'pixman' +version = '0.42.2' + +homepage = 'http://www.pixman.org/' +description = """ + Pixman is a low-level software library for pixel manipulation, providing + features such as image compositing and trapezoid rasterization. Important + users of pixman are the cairo graphics library and the X server. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://cairographics.org/releases/'] +sources = [SOURCE_TAR_GZ] +checksums = ['ea1480efada2fd948bc75366f7c349e1c96d3297d09a3fe62626e38e234a625e'] + +builddependencies = [ + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['lib/libpixman-1.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From d6999f0e4958a0ce6afed3d64824c0659ea0405a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:41:12 +0100 Subject: [PATCH 512/939] adding easyconfigs: NSS-3.85-GCCcore-12.2.0.eb, NSPR-4.35-GCCcore-12.2.0.eb --- .../n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb | 30 +++++++++ .../n/NSS/NSS-3.85-GCCcore-12.2.0.eb | 61 +++++++++++++++++++ 2 files changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..1795b557f16d --- /dev/null +++ b/easybuild/easyconfigs/n/NSPR/NSPR-4.35-GCCcore-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'NSPR' +version = '4.35' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR' +description = """Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level + and libc-like functions.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/nspr/releases/v%(version)s/src/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['7ea3297ea5969b5d25a5dd8d47f2443cda88e9ee746301f6e1e1426f8a6abc8f'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--disable-debug --enable-optimize --enable-64bit" + +sanity_check_paths = { + 'files': ['bin/nspr-config', 'lib/libnspr%(version_major)s.a', 'lib/libnspr%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplc%(version_major)s.a', 'lib/libplc%%(version_major)s.%s' % SHLIB_EXT, + 'lib/libplds%(version_major)s.a', 'lib/libplds%%(version_major)s.%s' % SHLIB_EXT, + 'lib/pkgconfig/nspr.pc'], + 'dirs': ['include/nspr'], +} + +sanity_check_commands = ["nspr-config --version"] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb b/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e0d91d152f01 --- /dev/null +++ b/easybuild/easyconfigs/n/NSS/NSS-3.85-GCCcore-12.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'MakeCp' + +name = 'NSS' +version = '3.85' + +homepage = 'https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS' +description = """Network Security Services (NSS) is a set of libraries designed to support cross-platform development + of security-enabled client and server applications.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://ftp.mozilla.org/pub/security/nss/releases/NSS_%(version_major)s_%(version_minor)s_RTM/src/'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'NSS-3.39_pkgconfig.patch', + 'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch', +] +checksums = [ + {'nss-3.85.tar.gz': 'afd9d64510b1154debbd6cab3571e9ff64a3373898e03483e4c85cdada13d297'}, + {'NSS-3.39_pkgconfig.patch': '5c4b55842e5afd1e8e67b90635f6474510b89242963c4ac2622d3e3da9062774'}, + {'NSS-3.55_fix-ftbfs-glibc-invalid-oob-error.patch': + '15768297c5dd6918132af281531afcfe3e358f45a00bc2655d20a6cbe4310a9b'}, +] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('NSPR', '4.35'), + ('zlib', '1.2.12'), +] + +# building in parallel fails +parallel = 1 + +# disable use of -Werror to work around compilation errors with newer glibc versions, +# see also https://sourceware.org/bugzilla/show_bug.cgi?id=27476 +buildopts = "NSS_ENABLE_WERROR=0 " +# fix for not being able to find header files +buildopts += 'BUILD_OPT=1 USE_64=1 CPATH="$EBROOTNSPR/include/nspr:$CPATH" ' +# fix c standard causing missing functions +buildopts += 'OS_REL_CFLAGS="-D_XOPEN_SOURCE " && ' +# also install pkgconfig file (see patch) +buildopts += "cd config && make PREFIX=%(installdir)s BUILD_OPT=1 USE_64=1 && cd -" +# optional testsuite (takes a long time) +# buildopts += " && cd %(builddir)s/%(namelower)s-%(version)s/%(namelower)s/tests && BUILD_OPT=1 USE_64=1 ./all.sh " + +files_to_copy = ['../dist/Linux*.OBJ/*', (['../dist/public/*'], 'include')] + +sanity_check_paths = { + 'files': ['bin/nss-config', 'bin/multinit', 'lib/libnss.a'], + 'dirs': ['include/dbm', 'include/nss'], +} + +sanity_check_commands = [ + "multinit --help", + "nss-config --version", +] + +modextrapaths = {'CPATH': 'include/nss'} + +moduleclass = 'lib' From cbf1e6db9570125f7566c5ddb35445cc9c588fd5 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 23 Nov 2022 23:29:04 +0100 Subject: [PATCH 513/939] {vis}[GCCcore/12.2.0] HarfBuzz v5.3.1, GObject-Introspection v1.74.0 --- ...ect-Introspection-1.74.0-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ .../HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb | 38 ++++++++++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..f4d572664a79 --- /dev/null +++ b/easybuild/easyconfigs/g/GObject-Introspection/GObject-Introspection-1.74.0-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'MesonNinja' + +name = 'GObject-Introspection' +version = '1.74.0' + +homepage = 'https://gi.readthedocs.io/en/latest/' +description = """GObject introspection is a middleware layer between C libraries + (using GObject) and language bindings. The C library can be scanned at + compile time and generate a metadata file, in addition to the actual + native C library. Then at runtime, language bindings can read this + metadata and automatically provide bindings to call into the C library.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['347b3a719e68ba4c69ff2d57ee2689233ea8c07fc492205e573386779e42d653'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('flex', '2.6.4'), + ('Bison', '3.8.2'), + ('cairo', '1.17.4'), +] + +dependencies = [ + ('Python', '3.10.8'), + ('GLib', '2.75.0'), + ('libffi', '3.4.4'), + ('util-linux', '2.38.1'), +] + +preconfigopts = "env GI_SCANNER_DISABLE_CACHE=true " + +sanity_check_paths = { + 'files': ['bin/g-ir-%s' % x for x in ['annotation-tool', 'compiler', 'generate', 'scanner']] + + ['lib/libgirepository-1.0.' + SHLIB_EXT], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e39adfe0f434 --- /dev/null +++ b/easybuild/easyconfigs/h/HarfBuzz/HarfBuzz-5.3.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'ConfigureMake' + +name = 'HarfBuzz' +version = '5.3.1' + +homepage = 'https://www.freedesktop.org/wiki/Software/HarfBuzz' +description = """HarfBuzz is an OpenType text shaping engine.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'harfbuzz' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['77c8c903f4539b050a6d3a5be79705c7ccf7b1cb66d68152a651486e261edbd2'] + +builddependencies = [ + ('binutils', '2.39'), + ('GObject-Introspection', '1.74.0'), + ('pkgconf', '1.9.3'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('ICU', '72.1'), + ('cairo', '1.17.4'), + ('freetype', '2.12.1'), +] + +preconfigopts = "./autogen.sh && " +configopts = "--enable-introspection=yes --with-gobject=yes --enable-static --enable-shared --with-cairo " + +sanity_check_paths = { + 'files': ['lib/libharfbuzz.%s' % SHLIB_EXT, 'bin/hb-view'], + 'dirs': [] +} + +moduleclass = 'vis' From dce9c8a5771b6bf09e4c5f6d13cd479151df907c Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 24 Nov 2022 12:07:53 +0100 Subject: [PATCH 514/939] adding easyconfigs: OpenImageIO-2.3.17.0-GCC-11.3.0.eb --- .../OpenImageIO-2.3.17.0-GCC-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..30ccd8238c3d --- /dev/null +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'OpenImageIO' +version = '2.3.17.0' + +homepage = 'https://openimageio.org/' +description = """OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, + and applications.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['22d38347b40659d218fcafcadc9258d3f6eda0be02029b11969361c9a6fa9f5c'] +#patches = ['oiio-tiff.patch'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('git', '2.36.0', '-nodocs'), +] +dependencies = [ + ('Boost', '1.79.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('OpenEXR', '3.1.5'), + ('freetype', '2.12.1'), + ('zlib', '1.2.12'), +] + +separate_build_dir = True + +configopts = '-DSTOP_ON_WARNING=OFF -DUSE_PYTHON=OFF' + +sanity_check_paths = { + 'files': ['bin/oiiotool', 'lib/libOpenImageIO.%s' % SHLIB_EXT, 'lib/libOpenImageIO_Util.%s' % SHLIB_EXT], + 'dirs': ['include/OpenImageIO', 'share'], +} + +moduleclass = 'lib' + From 77e4bcb0d05710fdd2ce697b4401a71269815b07 Mon Sep 17 00:00:00 2001 From: Paul Melis Date: Thu, 24 Nov 2022 13:35:07 +0100 Subject: [PATCH 515/939] Fix style errors --- .../o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb index 30ccd8238c3d..9b762b8294be 100644 --- a/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/o/OpenImageIO/OpenImageIO-2.3.17.0-GCC-11.3.0.eb @@ -12,7 +12,6 @@ toolchain = {'name': 'GCC', 'version': '11.3.0'} source_urls = ['https://github.com/OpenImageIO/oiio/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['22d38347b40659d218fcafcadc9258d3f6eda0be02029b11969361c9a6fa9f5c'] -#patches = ['oiio-tiff.patch'] builddependencies = [ ('CMake', '3.23.1'), @@ -38,4 +37,3 @@ sanity_check_paths = { } moduleclass = 'lib' - From 312d9f5dde534e928abfd5c6aa93be762bb961eb Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Nov 2022 14:43:46 +0100 Subject: [PATCH 516/939] adding easyconfigs: bamFilters-2022-06-30-GCC-11.3.0.eb, SAMtools-1.13-GCC-11.3.0.eb --- .../bamFilters-2022-06-30-GCC-11.3.0.eb | 37 +++++++++++++++++++ .../s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb | 25 +++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb new file mode 100644 index 000000000000..b9a1c04fdf27 --- /dev/null +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MakeCp' + +name = 'bamFilters' +local_commit = '93e334e' +version = '2022-06-30' + +homepage = 'https://github.com/institut-de-genomique/bamFilters' +description = """A utility tool to filter alignments from bam files, + using identity percent, low complexity and read coverage.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://github.com/institut-de-genomique/bamFilters/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['63a2a57093f0d360ce21775de8bb118e60cbd8856593e02c608f930745e1b463'] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('BamTools', '2.5.2'), + ('SAMtools', '1.13'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), +] +prebuildopts = 'mkdir obj && ' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"' + +files_to_copy = [ + (['bamFilters'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/bamFilters'], + 'dirs': [] +} + +sanity_check_commands = ['bamFilters -h 2>&1 | grep "Usage"'] + diff --git a/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.eb new file mode 100644 index 000000000000..2f667a4e3e84 --- /dev/null +++ b/easybuild/easyconfigs/s/SAMtools/SAMtools-1.13-GCC-11.3.0.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': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/samtools/%(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', '6.3'), + ('zlib', '1.2.12'), + ('bzip2', '1.0.8'), + ('XZ', '5.2.5'), + ('cURL', '7.83.0'), +] + +moduleclass = 'bio' From b7fd2f640c125f4027e313f72178f03ebe931914 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Nov 2022 15:11:31 +0100 Subject: [PATCH 517/939] fixed line too long --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index b9a1c04fdf27..75f1c57d85fd 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -22,7 +22,8 @@ dependencies = [ ('bzip2', '1.0.8'), ] prebuildopts = 'mkdir obj && ' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"' +buildopts = '''CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" + LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"''' files_to_copy = [ (['bamFilters'], 'bin'), @@ -34,4 +35,3 @@ sanity_check_paths = { } sanity_check_commands = ['bamFilters -h 2>&1 | grep "Usage"'] - From cf9f3ee8f3cf666ec75061ab57c2090d11883760 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 24 Nov 2022 15:26:28 +0100 Subject: [PATCH 518/939] fixed line too long --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index 75f1c57d85fd..158a44d6dd8e 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -22,8 +22,8 @@ dependencies = [ ('bzip2', '1.0.8'), ] prebuildopts = 'mkdir obj && ' -buildopts = '''CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib" - LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"''' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" SAMTOOLS_LIBDIR="$EBROOTSAMTOOLS/lib"' +buildopts += ' LIBS="$LIBS -lhts -lbam -lz -lbz2 -lcurl -lssl -lcrypto -llzma"' files_to_copy = [ (['bamFilters'], 'bin'), From 73349af426ba4f81cfac40b3ee0fd56744983ed1 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 24 Nov 2022 15:53:21 +0100 Subject: [PATCH 519/939] adding easyconfigs: Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb --- .../Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb new file mode 100644 index 000000000000..0a9f224eba97 --- /dev/null +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'PythonBundle' + +name = 'Sphinx-RTD-Theme' +version = '1.1.1' + +homepage = 'https://sphinx-rtd-theme.readthedocs.io' +description = """Sphinx theme was designed to provide a great reader experience + for documentation users on both desktop and mobile devices""" + +toolchain = {'name': 'GCCcore', 'version': '10.2.0'} + +dependencies = [('Python', '3.8.6')] + +use_pip = True +exts_download_dep_fail = True + +exts_list = [ + ('sphinx_rtd_theme', version, { + 'checksums': ['6146c845f1e1947b3c3dd4432c28998a1693ccc742b4f9ad7c63129f0757c103'], + }), +] + +moduleclass = 'vis' From 40fa15da4cc66bea24d8f9d6b3a64baaa4a01666 Mon Sep 17 00:00:00 2001 From: guacke Date: Thu, 24 Nov 2022 16:53:28 +0100 Subject: [PATCH 520/939] adding easyconfigs: HighFive-2.6.2-foss-2021a.eb --- .../h/HighFive/HighFive-2.6.2-foss-2021a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb new file mode 100644 index 000000000000..402ae4696064 --- /dev/null +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb @@ -0,0 +1,34 @@ +easyblock = 'CMakeMake' + +name = 'HighFive' +version = '2.6.2' + +homepage = 'https://github.com/BlueBrain/HighFive' +description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" + +toolchain = {'name': 'foss', 'version' : '2021a'} + +github_account = 'BlueBrain' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ab51b9fbb49e877dd1aa7b53b4b26875f41e4e0b8ee0fc2f1d735e0d1e43d708'] + +builddependencies = [ + ('CMake', '3.20.1'), + ('binutils', '2.36.1') +] + +dependencies = [ + ('HDF5', '1.10.7'), + ('Boost', '1.76.0'), + ('Eigen', '3.3.9'), +] + +sanity_check_paths = { + 'files' : ['include/highfive/H5File.hpp'], + 'dirs' : [], +} + +configopts = '-DHIGHFIVE_USE_EIGEN=ON' + +moduleclass = 'lib' \ No newline at end of file From e1ea5df5ee45f8f4336002f90a11c0d8e272f478 Mon Sep 17 00:00:00 2001 From: Alan O'Cais Date: Thu, 24 Nov 2022 16:43:37 +0000 Subject: [PATCH 521/939] Make sure VTK finds the specified Python --- easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb | 1 + easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb | 1 + 2 files changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb index b4161f95eaf3..c92d21af64b4 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2020b.eb @@ -54,6 +54,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb index b6987d9bb81a..c2ca95e963f4 100644 --- a/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/v/VTK/VTK-9.0.1-foss-2021a.eb @@ -49,6 +49,7 @@ configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " # Python configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += '-DPython3_EXECUTABLE=$EBROOTPYTHON/bin/python ' # Other configopts += "-DVTK_USE_MPI=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib" From 231f4477cadb15978b6cec96c58320589ca7c090 Mon Sep 17 00:00:00 2001 From: guacke Date: Thu, 24 Nov 2022 19:33:53 +0100 Subject: [PATCH 522/939] style fixes --- .../easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb index 402ae4696064..8fc40328d058 100644 --- a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb @@ -6,7 +6,7 @@ version = '2.6.2' homepage = 'https://github.com/BlueBrain/HighFive' description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" -toolchain = {'name': 'foss', 'version' : '2021a'} +toolchain = {'name': 'foss', 'version': '2021a'} github_account = 'BlueBrain' source_urls = [GITHUB_SOURCE] @@ -25,10 +25,10 @@ dependencies = [ ] sanity_check_paths = { - 'files' : ['include/highfive/H5File.hpp'], - 'dirs' : [], + 'files': ['include/highfive/H5File.hpp'], + 'dirs': [], } configopts = '-DHIGHFIVE_USE_EIGEN=ON' -moduleclass = 'lib' \ No newline at end of file +moduleclass = 'lib' From 1218b03af4935fcb966673a092aa13cc8b103f45 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 24 Nov 2022 22:36:31 +0100 Subject: [PATCH 523/939] make test_pr_sanity_check_paths aware of JuliaBundle --- 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 374e82ddb0c0..82f50ce177d2 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1092,9 +1092,9 @@ def test_pr_sanity_check_paths(self): """Make sure a custom sanity_check_paths value is specified for easyconfigs that use a generic easyblock.""" # some generic easyblocks already have a decent customised sanity_check_paths, - # including CMakePythonPackage, GoPackage, PythonBundle & PythonPackage; + # including CMakePythonPackage, GoPackage, JuliaBundle, PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. - whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'ModuleRC', + whitelist = ['BuildEnv', 'CMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, From de68939a253670d92cac32fce497f5c800b59c83 Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 25 Nov 2022 11:08:01 +0100 Subject: [PATCH 524/939] adding easyconfigs: nano-7.0-GCCcore-11.3.0.eb --- .../n/nano/nano-7.0-GCCcore-11.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..37267b01fc70 --- /dev/null +++ b/easybuild/easyconfigs/n/nano/nano-7.0-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'nano' +version = '7.0' + +homepage = 'https://www.nano-editor.org/' +docurls = 'https://www.nano-editor.org/docs.php' +description = """a simple editor, inspired by Pico""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://www.nano-editor.org/dist/v%(version_major)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['767d595237a4b40b981e2daaeb31de94283d60b1fae03fbd52a67d95c454518a'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('ncurses', '6.3')] + +sanity_check_paths = { + 'files': ['bin/nano'], + 'dirs': ['bin', 'share'], +} + +sanity_check_commands = ['nano --version'] + +moduleclass = 'tools' From 32b0374e6674f9ddea4de2c3e2ff663ac24e590a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 25 Nov 2022 11:41:45 +0100 Subject: [PATCH 525/939] make SAMtools a build dependency --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index 158a44d6dd8e..82f31b5dfb2d 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -14,10 +14,11 @@ source_urls = ['https://github.com/institut-de-genomique/bamFilters/archive/'] sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] checksums = ['63a2a57093f0d360ce21775de8bb118e60cbd8856593e02c608f930745e1b463'] +builddependencies = [('SAMtools', '1.13')] # libbam.a, is provided by SAMtools only up to version 1.13 + dependencies = [ ('HTSlib', '1.15.1'), ('BamTools', '2.5.2'), - ('SAMtools', '1.13'), ('zlib', '1.2.12'), ('bzip2', '1.0.8'), ] From dd920df794a7221b7ef157295397b3a4a28341e2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Nov 2022 15:22:08 +0100 Subject: [PATCH 526/939] add HGNChelper extension to R 4.2.1 --- easybuild/easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 3 +++ 1 file changed, 3 insertions(+) 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 e3da8a7d9fa6..3e4080c1ebfb 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 @@ -3364,6 +3364,9 @@ exts_list = [ ('LMERConvenienceFunctions', '3.0', { 'checksums': ['eb430de9fbf836173f716960d60afc2de91de7f986471f406c3ca9027142e849'], }), + ('HGNChelper', '0.8.1', { + 'checksums': ['aa3f0b3a8691ed93d63bec8f36d2954c6fcfd0b8b3efc705379248544c999363'], + }), ] moduleclass = 'lang' From 5644eb72a00df067560a8e4bce84f05f30cbd10e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 25 Nov 2022 15:43:49 +0100 Subject: [PATCH 527/939] adding easyconfigs: cuTENSOR-1.6.1.5-CUDA-11.7.0.eb --- .../cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb new file mode 100644 index 000000000000..32caad1f1550 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-1.6.1.5-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +local_shortver = '1.6.1' +version = local_shortver + '.5' +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 = ['793b425c30ffd423c4f3a2e94acaf4fcb6752264aa73b74695a002dd2fe94b1a'] + +local_cudamajver = '11' +dependencies = [('CUDA', local_cudamajver + '.7.0')] + +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 f6d050dfa43a3633aa45ddf755c4342f2dda6e30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Fri, 25 Nov 2022 16:18:25 +0100 Subject: [PATCH 528/939] minor cleanup + use proper versionsuffix in Blender 3.3.1 easyconfig --- ...> Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb} | 17 +++++++---------- 1 file changed, 7 insertions(+), 10 deletions(-) rename easybuild/easyconfigs/b/Blender/{Blender-3.3.1.eb => Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb} (73%) diff --git a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb b/easybuild/easyconfigs/b/Blender/Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb similarity index 73% rename from easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb rename to easybuild/easyconfigs/b/Blender/Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb index 7669c41af2be..096a48791f5c 100644 --- a/easybuild/easyconfigs/b/Blender/Blender-3.3.1.eb +++ b/easybuild/easyconfigs/b/Blender/Blender-3.3.1-linux-x86_64-CUDA-11.7.0.eb @@ -2,23 +2,18 @@ easyblock = 'PackedBinary' name = 'Blender' version = '3.3.1' -versionsuffix = '' +versionsuffix = '-linux-x86_64-CUDA-%(cudaver)s' homepage = 'https://www.blender.org/' description = """Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation.""" -toolchain = {'name': 'system', 'version': ''} +toolchain = SYSTEM -sources = ['blender-%(version)s-linux-x64.tar.xz'] source_urls = ['https://ftp.nluug.nl/pub/graphics/blender/release/Blender%(version_major_minor)s/'] -patches = [] -checksums = [ - '3089a485dd621785d7a702089aba72d07b8f733a362e901ec1449b9a379546f2' -] - -builddependencies = [] +sources = ['blender-%(version)s-linux-x64.tar.xz'] +checksums = ['3089a485dd621785d7a702089aba72d07b8f733a362e901ec1449b9a379546f2'] dependencies = [ ('CUDA', '11.7.0') @@ -26,7 +21,9 @@ dependencies = [ sanity_check_paths = { 'files': ['blender', 'blender-softwaregl'], - 'dirs': ['3.3'] + 'dirs': ['%(version_major_minor)s'], } +sanity_check_commands = ["blender --help"] + moduleclass = 'vis' From ec57679185f46c6c2bee9b441810b158d57791bd Mon Sep 17 00:00:00 2001 From: Dugan Witherick Date: Fri, 25 Nov 2022 17:10:22 +0000 Subject: [PATCH 529/939] adding easyconfigs: Fiji-2.9.0-Java-8.eb --- .../easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb diff --git a/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb new file mode 100644 index 000000000000..a02535237205 --- /dev/null +++ b/easybuild/easyconfigs/f/Fiji/Fiji-2.9.0-Java-8.eb @@ -0,0 +1,49 @@ +easyblock = 'PackedBinary' + +name = 'Fiji' +version = '2.9.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://fiji.sc' +description = """Fiji is an image processing package—a 'batteries-included' distribution of + ImageJ, bundling a lot of plugins which facilitate scientific image analysis. +This release is based on ImageJ-2.1.0 and Fiji-2.1.1""" + +toolchain = SYSTEM + +source_urls = ['https://downloads.imagej.net/fiji/releases/%(version)s/'] +sources = ['fiji-%(version)s-nojre.zip'] +checksums = ['970fb80cf2a4fe8bfcecc2cc9a8617b9ab28f19fbe229ea6ae2f7f42674c8a42'] + +dependencies = [('Java', '8', '', SYSTEM)] + +postinstallcmds = [ + # Remove binaries for other platforms + 'rm %(installdir)s/{ImageJ-win32.exe,ImageJ-win64.exe}', + # Enable any update site (edit existing site with same parameters to enable it) + # Full list at https://imagej.github.io/list-of-update-sites/ + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ImageScience"' + ' https://sites.imagej.net/ImageScience/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "3D ImageJ Suite"' + ' https://sites.imagej.net/Tboudier/', + '%(installdir)s/ImageJ-linux64 --headless --update edit-update-site "ilastik"' + ' https://sites.imagej.net/Ilastik/', + # Add a new update site + # '%(installdir)s/ImageJ-linux64 --headless --update add-update-site "New Name"' + # ' https://site.url/NewName/', + # Update the installation + '%(installdir)s/ImageJ-linux64 --headless --update update', +] + +sanity_check_paths = { + 'files': ['ImageJ-linux64'], + 'dirs': [], +} + +modloadmsg = """ +Additional plugins can be installed in your $HOME/.plugins folder or requested to user support +Use ImageJ/Fiji in headless mode in your scripts with the command `ImageJ-linux64 --headless` +More information at https://imagej.net/Headless +""" + +moduleclass = 'vis' From cd5a96ce1bf1ee9120042544d578039f442c7c74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 25 Nov 2022 18:06:20 +0000 Subject: [PATCH 530/939] Include missing easyconfigs --- .../FFTW.MPI-3.3.10-nvompi-2022.07.eb | 19 ++++++ .../easyconfigs/n/nvompi/nvompi-2022.07.eb | 19 ++++++ .../OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb | 65 +++++++++++++++++++ 3 files changed, 103 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb create mode 100644 easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb new file mode 100644 index 000000000000..48501672627c --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-nvompi-2022.07.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'nvompi', 'version': '2022.07'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb b/easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb new file mode 100644 index 000000000000..1a1647cbfa25 --- /dev/null +++ b/easybuild/easyconfigs/n/nvompi/nvompi-2022.07.eb @@ -0,0 +1,19 @@ +easyblock = 'Toolchain' + +name = 'nvompi' +version = '2022.07' + +homepage = '(none)' +description = 'NVHPC based compiler toolchain, including OpenMPI for MPI support.' + +toolchain = SYSTEM + +local_compiler = ('NVHPC', '22.7-CUDA-11.7.0') + +dependencies = [ + local_compiler, + ('OpenMPI', '4.1.4', '', local_compiler), + ('CUDA', '11.7.0', '', SYSTEM), +] + +moduleclass = 'toolchain' 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 new file mode 100644 index 000000000000..34c4551c73e2 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-4.1.4-NVHPC-22.7-CUDA-11.7.0.eb @@ -0,0 +1,65 @@ +name = 'OpenMPI' +version = '4.1.4' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-4.1.1_build-with-internal-cuda-header.patch', + 'OpenMPI-4.1.1_opal-datatype-cuda-performance.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', +] + +builddependencies = [ + ('pkgconf', '1.8.0'), + ('Perl', '5.34.1'), + ('Autotools', '20220317'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('hwloc', '2.7.1'), + ('libevent', '2.1.12'), + ('UCX', '1.12.1'), + ('UCX-CUDA', '1.12.1', '-CUDA-%(cudaver)s'), + ('libfabric', '1.15.1'), + ('PMIx', '4.1.2'), + ('UCC', '1.0.0'), + ('UCC-CUDA', '1.0.0', '-CUDA-%(cudaver)s'), +] + +# Update configure to include changes from the "internal-cuda" patch +# by running a subset of autogen.pl sufficient to achieve this +# without doing the full, long-running regeneration. +preconfigopts = ' && '.join([ + 'cd config', + 'autom4te --language=m4sh opal_get_version.m4sh -o opal_get_version.sh', + 'cd ..', + 'autoconf', + 'autoheader', + 'aclocal', + 'automake', + '' +]) + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +configopts = '--with-cuda=internal ' +configopts += ' CC=pgcc CXX=pgc++ FC=pgfortran' + +# disable MPI1 compatibility for now, see what breaks... +# configopts += '--enable-mpi1-compatibility ' + +# to enable SLURM integration (site-specific) +# configopts += '--with-slurm --with-pmi=/usr/include/slurm --with-pmi-libdir=/usr' + +moduleclass = 'mpi' From 579c97a9f3909ffdd2bae39485db94749b454ce6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 25 Nov 2022 18:24:42 +0000 Subject: [PATCH 531/939] Fix configopts for BLIS --- .../easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb index 9928532de5e7..ec9012628361 100644 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -28,8 +28,8 @@ builddependencies = [ ] preconfigopts = "sed -i 's/LINKER.*/LINKER := nvc/' common.mk &&" -configopts = '--enable-cblas --enable-threading=openmp --enable-shared CC="$CC" auto' -configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno"' +configopts = '--enable-cblas --enable-threading=openmp --enable-shared' +configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno" auto' runtest = 'check' From 876bdb05adbbcc76565a20fa2d19fe24b079919c Mon Sep 17 00:00:00 2001 From: easybuild Date: Fri, 25 Nov 2022 22:31:59 +0100 Subject: [PATCH 532/939] adding easyconfigs: Vim-9.0.0950-GCCcore-11.3.0.eb --- .../v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..cde4ee8d0564 --- /dev/null +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb @@ -0,0 +1,34 @@ +# Last contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'ConfigureMake' + +name = 'Vim' +version = '9.0.0950' + +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': '11.3.0'} + +source_urls = ['https://github.com/vim/vim/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c53542fbec58362c3a5ed60a0fe5aa219ef49cd15d9545311ec0f6d1f03e2fdd'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('Perl', '5.34.1'), + ('PCRE', '8.45') +] + +configopts = '--with-features=huge --enable-python3interp=yes --enable-perlinterp=yes' + +sanity_check_paths = { + 'files': ['bin/vim', 'bin/vimtutor', 'bin/xxd'], + 'dirs': ['bin', 'share'], +} + +moduleclass = 'tools' From 59bcc0d5b70753a1a32b229456caedecfdf6873c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Fri, 25 Nov 2022 22:37:13 +0100 Subject: [PATCH 533/939] Update Vim-9.0.0950-GCCcore-11.3.0.eb Add basic sanity check. --- easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb index cde4ee8d0564..3ebc9ac6bd57 100644 --- a/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/v/Vim/Vim-9.0.0950-GCCcore-11.3.0.eb @@ -31,4 +31,6 @@ sanity_check_paths = { 'dirs': ['bin', 'share'], } +sanity_check_commands = ['vim --version'] + moduleclass = 'tools' From 868d0e04dbfa240714de7e71a0de7d27b156f63b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:00:18 +0100 Subject: [PATCH 534/939] adding easyconfigs: CPPE-0.3.1-GCC-11.3.0.eb --- .../c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb new file mode 100644 index 000000000000..73a254132a82 --- /dev/null +++ b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb @@ -0,0 +1,44 @@ +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': '11.3.0'} + +github_account = 'maxscheurer' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['38d4230ba3ace78936049c23ad4b1fe9e704fd250ec57cc9733cb3904b62cf7c'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pybind11', '2.9.2'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +exts_defaultclass = 'PythonPackage' +exts_list = [ + ('cppe', version, { + 'download_dep_fail': True, + 'use_pip': True, + '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' From 818c6bc1011f6f78b799ef90ce9a1ddda106c1be Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:00:55 +0100 Subject: [PATCH 535/939] adding easyconfigs: PyBerny-0.6.3-foss-2022a.eb --- .../p/PyBerny/PyBerny-0.6.3-foss-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.eb new file mode 100644 index 000000000000..1d3ffa473d14 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBerny/PyBerny-0.6.3-foss-2022a.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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +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' From 74bba6153408a470a0aa939c6f12d7e49fbacada Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:01:47 +0100 Subject: [PATCH 536/939] adding easyconfigs: NECI-20220711-foss-2022a.eb --- .../n/NECI/NECI-20220711-foss-2022a.eb | 48 +++++++++++++++++++ 1 file changed, 48 insertions(+) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb diff --git a/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb new file mode 100644 index 000000000000..71c70f8ab4a1 --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20220711-foss-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMakeCp' +name = 'NECI' +version = '20220711' +_commit = 'd7a9e87ed6a4a29479dc25fbf36a7bb556c3f5a3' + +homepage = 'https://github.com/ghb24/NECI_STABLE' +description = """Standalone NECI codebase designed for FCIQMC and other stochastic quantum +chemistry methods.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +sources = [{ + 'git_config': { + 'url': 'https://github.com/ghb24', + 'repo_name': 'NECI_STABLE', + 'recursive': True, + 'commit': _commit, + }, + 'filename': SOURCE_TAR_GZ, +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +dependencies = [ + ('HDF5', '1.12.2'), +] + +# 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 73f8903ebb2034e6f2c26f66da4c1bcc040f4077 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 17:02:57 +0100 Subject: [PATCH 537/939] adding easyconfigs: Dice-20221025-foss-2022a.eb and patches: Dice-20221025_icpt-mkl-to-flexiblas.patch --- .../d/Dice/Dice-20221025-foss-2022a.eb | 50 +++++++++++++++++++ .../Dice-20221025_icpt-mkl-to-flexiblas.patch | 23 +++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb create mode 100644 easybuild/easyconfigs/d/Dice/Dice-20221025_icpt-mkl-to-flexiblas.patch diff --git a/easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb b/easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb new file mode 100644 index 000000000000..b4315ca4f5fc --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20221025-foss-2022a.eb @@ -0,0 +1,50 @@ +easyblock = 'MakeCp' + +name = 'Dice' +version = '20221025' +_commit = 'f14e4249c69ec30b53491297049546f3ef1d8a55' + +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': '2022a'} +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'] +checksums = [ + {'Dice-20221025.tar.gz': '56da2c0f4bc3e9a786ae8c3193cb06df5cf20a90af29ee95ad39a10e525db315'}, + {'Dice-20221025_icpt-mkl-to-flexiblas.patch': 'a712913e5b372017be0ea7508479094e96f06c0cfd46d0bfe61d85ef42cd1386'}, +] + +builddependencies = [ + ('Eigen', '3.4.0'), + ('git', '2.36.0', '-nodocs'), +] + +dependencies = [ + ('Boost.MPI', '1.79.0'), + ('HDF5', '1.12.2'), +] + +# 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', 'FCIQMC', '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-20221025_icpt-mkl-to-flexiblas.patch b/easybuild/easyconfigs/d/Dice/Dice-20221025_icpt-mkl-to-flexiblas.patch new file mode 100644 index 000000000000..8cf99685cd3f --- /dev/null +++ b/easybuild/easyconfigs/d/Dice/Dice-20221025_icpt-mkl-to-flexiblas.patch @@ -0,0 +1,23 @@ +Replace Intel MKL subroutines with FlexiBLAS wrappers +author: Alex Domingo (Vrije Universiteit Brussel) +--- a/executables/ICPT.cpp 2022-10-26 01:45:54.000000000 +0200 ++++ b/executables/ICPT.cpp 2022-11-26 11:23:28.845637000 +0100 +@@ -7,8 +7,7 @@ + #include "BlockContract.h" + #include "CxDefs.h" + #include "icpt.h" +-#include "mkl.h" +-#include "mkl_cblas.h" ++#include "flexiblas_api.h" + using ct::TArray; + using ct::FMemoryStack; + using boost::format; +@@ -25,7 +24,7 @@ + // - something to split up tensors (H) and combine them (RDM) + // regarding universal indices + +- mkl_set_num_threads(numthrds); ++ flexiblas_set_num_threads(numthrds); + + FJobContext + Job; From e5ba592dd6c81aeaf2eb06682e9b47a8a27be15f Mon Sep 17 00:00:00 2001 From: anselmicz Date: Sat, 26 Nov 2022 19:03:35 +0100 Subject: [PATCH 538/939] adding easyconfigs: HyperQueue-0.13.0.eb --- .../h/HyperQueue/HyperQueue-0.13.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb diff --git a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb new file mode 100644 index 000000000000..59158297e6fc --- /dev/null +++ b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb @@ -0,0 +1,28 @@ +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 + +easyblock = 'PackedBinary' + +name = 'HyperQueue' +version = '0.13.0' + +homepage = 'https://it4innovations.github.io/hyperqueue/' +description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks +and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs +and distributes them to fully utilize allocated notes. +You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/It4innovations/hyperqueue/releases/download/v%(version)s/'] +sources = ['hq-v%(version)s-linux-x64.tar.gz'] +checksums = ['4c3dac11cc01ef2a0c222099e484fd1b23ac52d8db234855ec1f0685543b4e0d'] + +sanity_check_paths = { + 'files': ['hq'], + 'dirs': [], +} + +sanity_check_commands = ['hq --version'] + +moduleclass = 'tools' From b431022f8bb856e4a5142ea711977216caf90423 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 26 Nov 2022 19:04:46 +0100 Subject: [PATCH 539/939] move default extension parameters to exts_default_options in CPPE v0.3.1 --- easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb index 73a254132a82..b2a546120a1e 100644 --- a/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/c/CPPE/CPPE-0.3.1-GCC-11.3.0.eb @@ -26,10 +26,13 @@ dependencies = [ ] exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, +} exts_list = [ ('cppe', version, { - 'download_dep_fail': True, - 'use_pip': True, + 'source_urls': [PYPI_SOURCE], 'checksums': ['b0aef578d6919f8c103d4d4a9fcd3db481bd73c59c157985f52bf62477425d6c'], }), ] From d02193954ad5c855ba4ece63e873cf42a3a9e553 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jakub=20Krop=C3=A1=C4=8Dek?= <77022965+anselmicz@users.noreply.github.com> Date: Sat, 26 Nov 2022 19:13:47 +0100 Subject: [PATCH 540/939] Update HyperQueue-0.13.0.eb fix typo --- easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb index 59158297e6fc..bcb5f1b6be5f 100644 --- a/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb +++ b/easybuild/easyconfigs/h/HyperQueue/HyperQueue-0.13.0.eb @@ -9,7 +9,7 @@ version = '0.13.0' homepage = 'https://it4innovations.github.io/hyperqueue/' description = """HyperQueue lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups jobs into SLURM/PBS jobs -and distributes them to fully utilize allocated notes. +and distributes them to fully utilize allocated nodes. You thus do not have to manually aggregate your tasks into SLURM/PBS jobs.""" toolchain = SYSTEM From eabbbddc00ce7c196dc78f324cb843e9eb23a792 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Sun, 27 Nov 2022 01:06:48 +0100 Subject: [PATCH 541/939] Drop BLIS --- .../BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb | 44 ------------------- .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 3 +- 2 files changed, 1 insertion(+), 46 deletions(-) delete mode 100644 easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb deleted file mode 100644 index ec9012628361..000000000000 --- a/easybuild/easyconfigs/b/BLIS/BLIS-0.9.0-NVHPC-22.7-CUDA-11.7.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'BLIS' -version = '0.9.0' - -homepage = 'https://github.com/flame/blis/' -description = """BLIS is a portable software framework for instantiating high-performance -BLAS-like dense linear algebra libraries.""" - -toolchain = {'name': 'NVHPC', 'version': '22.7-CUDA-11.7.0'} - -source_urls = ['https://github.com/flame/blis/archive/'] -sources = ['%(version)s.tar.gz'] -patches = [ - '%(name)s-%(version)s_disable_power9_kernels.patch', - '%(name)s-%(version)s_enable_ppc_autodetect.patch', -] -checksums = [ - '1135f664be7355427b91025075562805cdc6cc730d3173f83533b2c5dcc2f308', # 0.9.0.tar.gz - # BLIS-0.9.0_disable_power9_kernels.patch - 'ed7a326bc5c5c21c42faefbec2fd7be609d1c7236981b466475edace39307279', - # BLIS-0.9.0_enable_ppc_autodetect.patch - 'f373fb252c0d14036fb631f048091976cceb02abb3e570a97fbaeac2fbb12328', -] -builddependencies = [ - ('Python', '3.10.4', '-bare'), - ('Perl', '5.34.1'), -] - -preconfigopts = "sed -i 's/LINKER.*/LINKER := nvc/' common.mk &&" -configopts = '--enable-cblas --enable-threading=openmp --enable-shared' -configopts += ' --complex-return=intel CC=gcc CFLAGS="-O2 -ftree-vectorize -march=native -fno-math-errno" auto' - -runtest = 'check' - -sanity_check_paths = { - 'files': ['include/blis/cblas.h', 'include/blis/blis.h', - 'lib/libblis.a', 'lib/libblis.%s' % SHLIB_EXT], - 'dirs': [], -} - -modextrapaths = {'CPATH': 'include/blis'} - -moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 07c769edc088..36c0727160b4 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -14,7 +14,6 @@ toolchainopts = {'pic': True, 'extra_cflags': local_extra_flags, 'extra_fflags': builddependencies = [ ('CMake', '3.23.1'), ('Python', '3.10.4', '-bare'), # required for running the tests - ('BLIS', '0.9.0'), ] dependencies = [ @@ -23,7 +22,7 @@ dependencies = [ # note: first listed backend will be used as default by FlexiBLAS, # unless otherwise specified via easyconfig parameter flexiblas_default -local_backends = ['OpenBLAS', 'BLIS'] +local_backends = ['OpenBLAS'] # imkl supplies its backend via the imkl module, not as a dependency if ARCH == 'x86_64': From fc26d3c11c5baeae5915e91165fb90fc8c79da53 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 20 Oct 2022 16:54:02 +0200 Subject: [PATCH 542/939] adding easyconfigs: PyTorch-1.12.1-foss-2021a.eb, PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 129 ++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 115 +++++++ ...2.1_fix-TestCudaFuser.test_unary_ops.patch | 26 ++ ...PyTorch-1.12.1_fix-TestTorch.test_to.patch | 21 ++ ...ch-1.12.1_fix-cuda-gcc-version-check.patch | 79 +++++ ...x-use-after-free-in-tensorpipe-agent.patch | 24 ++ .../PyTorch-1.12.1_fix-vsx-loadu.patch | 109 ++++++ .../PyTorch-1.12.1_fix-vsx-vector-funcs.patch | 310 ++++++++++++++++++ ...2.1_increase-test-adadelta-tolerance.patch | 22 ++ ...h-1.12.1_increase-tolerance-test_ops.patch | 27 ++ .../PyTorch-1.12.1_no-cuda-stubs-rpath.patch | 159 +++++++++ ...skip-ao-sparsity-test-without-fbgemm.patch | 26 ++ ...yTorch-1.12.1_skip-failing-grad-test.patch | 51 +++ 13 files changed, 1098 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..564c7ada0c81 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,129 @@ +name = 'PyTorch' +version = '1.12.1' +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': '2021a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('CUDA', '11.3.1', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('cuDNN', '8.2.1.32', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.1', '-CUDA-%(cudaver)s'), + ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + ] +} + +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 +# https://github.com/pytorch/pytorch/pull/87593 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' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb new file mode 100644 index 000000000000..cd38c8b8e9c8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -0,0 +1,115 @@ +name = 'PyTorch' +version = '1.12.1' + +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': '2021a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch', + 'PyTorch-1.12.1_skip-failing-grad-test.patch', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.20.1'), + ('hypothesis', '6.13.1'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.9.5'), + ('protobuf', '3.17.3'), + ('protobuf-python', '3.17.3'), + ('pybind11', '2.6.2'), + ('SciPy-bundle', '2021.05'), + ('typing-extensions', '3.10.0.0'), + ('PyYAML', '5.4.1'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.3.2'), + ('Pillow', '8.2.0'), + ('expecttest', '0.1.3'), +] + +excluded_tests = { + '': [ + # This test seems to take too long on NVIDIA Ampere at least. + 'distributed/test_distributed_spawn', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch new file mode 100644 index 000000000000..28a8238fb30e --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch @@ -0,0 +1,26 @@ +Fix test failure with a commit contained in https://github.com/pytorch/pytorch/pull/78244 + +From fade8da55e60a118c5595378896d34b862b2fcc3 Mon Sep 17 00:00:00 2001 +From: "S. Song" <41357537+shmsong@users.noreply.github.com> +Date: Mon, 23 May 2022 16:41:01 -0700 +Subject: [PATCH] patch python test for bfloat16 (#1724) + +* patch python test +--- + test/test_jit_cuda_fuser.py | 5 +++-- + 1 file changed, 3 insertions(+), 2 deletions(-) + +diff --git a/test/test_jit_cuda_fuser.py b/test/test_jit_cuda_fuser.py +index 48dd8a4659f1..324a758ff713 100644 +--- a/test/test_jit_cuda_fuser.py ++++ b/test/test_jit_cuda_fuser.py +@@ -598,7 +598,9 @@ def t(x: torch.Tensor, y: torch.Tensor): + # bfloat16 kernels instead of eager mode + # implementation, since mismatch in cast + # adds excessive noise. +- o = t(x.to(torch.float64), y.to(torch.float64)).to(torch.bfloat16) ++ o = t(x.to(torch.float64), y.to(torch.float64)) ++ if o.dtype.is_floating_point: ++ o = o.to(torch.bfloat16) + else: + o = t(x, y) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch new file mode 100644 index 000000000000..8d78d655b5b8 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-TestTorch.test_to.patch @@ -0,0 +1,21 @@ +A bug in PyTorch makes sparse Tensors report the wrong device making the test fail +when using multiple GPUs. +Fixed in 1.13 by https://github.com/pytorch/pytorch/pull/85240 + +Here change the test to only run the check with the default CUDA device. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_torch.py b/test/test_torch.py +index 0c9c00984c..99285b20dc 100644 +--- a/test/test_torch.py ++++ b/test/test_torch.py +@@ -7687,7 +7687,7 @@ tensor([[[1.+1.j, 1.+1.j, 1.+1.j, ..., 1.+1.j, 1.+1.j, 1.+1.j], + + if torch.cuda.is_available(): + for non_blocking in [True, False]: +- for cuda in ['cuda', 'cuda:0' if torch.cuda.device_count() == 1 else 'cuda:1']: ++ for cuda in ['cuda']: + b = torch.tensor(5., device=cuda) + test_copy_behavior(b, non_blocking) + self.assertEqual(b.device, b.to(cuda, non_blocking=non_blocking).device) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch new file mode 100644 index 000000000000..def8bc857bcf --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-cuda-gcc-version-check.patch @@ -0,0 +1,79 @@ +Update CUDA <-> compiler version compatibility matrix +See https://github.com/pytorch/pytorch/pull/86360 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/utils/cpp_extension.py b/torch/utils/cpp_extension.py +index aed4fd5004..fca125ce26 100644 +--- a/torch/utils/cpp_extension.py ++++ b/torch/utils/cpp_extension.py +@@ -48,20 +48,30 @@ MINIMUM_MSVC_VERSION = (19, 0, 24215) + # The following values were taken from the following GitHub gist that + # summarizes the minimum valid major versions of g++/clang++ for each supported + # CUDA version: https://gist.github.com/ax3l/9489132 ++# Or from include/crt/host_config.h in the CUDA SDK ++# The second value is the exclusive(!) upper bound, i.e. min <= version < max + CUDA_GCC_VERSIONS = { +- '10.2': (MINIMUM_GCC_VERSION, (8, 0, 0)), +- '11.1': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.2': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.3': (MINIMUM_GCC_VERSION, (10, 0, 0)), +- '11.4': ((6, 0, 0), (10, 0, 0)) ++ '10.2': (MINIMUM_GCC_VERSION, (9, 0)), ++ '11.0': (MINIMUM_GCC_VERSION, (10, 0)), ++ '11.1': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.2': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.3': (MINIMUM_GCC_VERSION, (11, 0)), ++ '11.4': ((6, 0, 0), (12, 0)), ++ '11.5': ((6, 0, 0), (12, 0)), ++ '11.6': ((6, 0, 0), (12, 0)), ++ '11.7': ((6, 0, 0), (12, 0)), + } + ++MINIMUM_CLANG_VERSION = (3, 3, 0), + CUDA_CLANG_VERSIONS = { +- '10.2': ((3, 3, 0), (8, 0, 0)), +- '11.1': ((6, 0, 0), (10, 0, 0)), +- '11.2': ((6, 0, 0), (10, 0, 0)), +- '11.3': ((6, 0, 0), (10, 0, 0)), +- '11.4': ((6, 0, 0), (10, 0, 0)) ++ '10.2': (MINIMUM_CLANG_VERSION, (9, 0)), ++ '11.1': (MINIMUM_CLANG_VERSION, (11, 0)), ++ '11.2': (MINIMUM_CLANG_VERSION, (12, 0)), ++ '11.3': (MINIMUM_CLANG_VERSION, (12, 0)), ++ '11.4': (MINIMUM_CLANG_VERSION, (13, 0)), ++ '11.5': (MINIMUM_CLANG_VERSION, (13, 0)), ++ '11.6': (MINIMUM_CLANG_VERSION, (14, 0)), ++ '11.7': (MINIMUM_CLANG_VERSION, (14, 0)), + } + + +@@ -819,12 +829,11 @@ class BuildExtension(build_ext, object): + if cuda_str_version not in cuda_compiler_bounds: + warnings.warn(f'There are no {compiler_name} version bounds defined for CUDA version {cuda_str_version}') + else: +- min_compiler_version, max_compiler_version = cuda_compiler_bounds[cuda_str_version] ++ min_compiler_version, max_excl_compiler_version = cuda_compiler_bounds[cuda_str_version] + min_compiler_version_str = '.'.join(map(str, min_compiler_version)) +- max_compiler_version_str = '.'.join(map(str, max_compiler_version)) ++ max_excl_compiler_version_str = '.'.join(map(str, max_excl_compiler_version)) + +- version_bound_str = f'>={min_compiler_version_str}' +- version_bound_str = f'{version_bound_str}, <={max_compiler_version_str}' ++ version_bound_str = f'>={min_compiler_version_str}, <{max_excl_compiler_version_str}' + + if compiler_version < TorchVersion(min_compiler_version_str): + raise RuntimeError( +@@ -832,10 +841,10 @@ class BuildExtension(build_ext, object): + f'than the minimum required version by CUDA {cuda_str_version} ({min_compiler_version_str}). ' + f'Please make sure to use an adequate version of {compiler_name} ({version_bound_str}).' + ) +- elif compiler_version > TorchVersion(max_compiler_version_str): ++ elif compiler_version >= TorchVersion(max_excl_compiler_version_str): + raise RuntimeError( + f'The current installed version of {compiler_name} ({compiler_version}) is greater ' +- f'than the maximum required version by CUDA {cuda_str_version} ({max_compiler_version_str}). ' ++ f'than the maximum required version by CUDA {cuda_str_version}. ' + f'Please make sure to use an adequate version of {compiler_name} ({version_bound_str}).' + ) + else: diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch new file mode 100644 index 000000000000..e0f643917921 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch @@ -0,0 +1,24 @@ +Fix an invalid usage of `erase` leading to a use after free. +See https://github.com/pytorch/pytorch/issues/87359 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/csrc/distributed/rpc/tensorpipe_agent.cpp b/torch/csrc/distributed/rpc/tensorpipe_agent.cpp +index 39935febe6..c160d1c771 100644 +--- a/torch/csrc/distributed/rpc/tensorpipe_agent.cpp ++++ b/torch/csrc/distributed/rpc/tensorpipe_agent.cpp +@@ -1261,9 +1261,11 @@ void TensorPipeAgent::updateGroupMembership( + workerNameToInfo_.erase(name); + workerNameToURL_.erase(name); + +- for (const auto& it : reverseDeviceMaps_) { +- if (reverseDeviceMaps.find(it.first) == reverseDeviceMaps.end()) { +- reverseDeviceMaps_.erase(it.first); ++ for(auto iter = reverseDeviceMaps_.begin(); iter != reverseDeviceMaps_.end(); ) { ++ if (reverseDeviceMaps.find(iter->first) == reverseDeviceMaps.end()) { ++ iter = reverseDeviceMaps_.erase(iter); ++ } else { ++ ++iter; + } + } + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch new file mode 100644 index 000000000000..839c6567bb2d --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-loadu.patch @@ -0,0 +1,109 @@ +Fix access to unitialized memory resulting in e.g. failures in TestNNDeviceTypeCPU.test_groupnorm_nhwc_cpu_float32 +See https://github.com/pytorch/pytorch/issues/32502 + +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 cb8bb78597..f5084f2101 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 +@@ -142,7 +142,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +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 8445a31fb3..b4e35acfb4 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 +@@ -196,7 +196,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +index c53b7c792e..810e79ebfe 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_double_vsx.h +@@ -171,7 +171,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 0267c40e1e..1a6aec7dbe 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -180,7 +180,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +index 464a13c9f5..7c300c8087 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int16_vsx.h +@@ -269,7 +269,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +index 6ef6147447..c98ab6215e 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int32_vsx.h +@@ -199,7 +199,7 @@ class Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +index c0f1146d9d..a4171026a2 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_int64_vsx.h +@@ -148,7 +148,7 @@ class Vectorized { + (vint64)vec_vsx_ld(offset16, dptr)}; + } + +- __at_align__ double tmp_values[size()]; ++ __at_align__ double tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return { +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h +index c3cec14a5b..a85730c9a6 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_qint32_vsx.h +@@ -81,7 +81,7 @@ struct Vectorized { + vec_vsx_ld(offset16, reinterpret_cast(ptr))}; + } + +- __at_align__ value_type tmp_values[size()]; ++ __at_align__ value_type tmp_values[size()] = {}; + std::memcpy(tmp_values, ptr, std::min(count, size()) * sizeof(value_type)); + + return {vec_vsx_ld(offset0, tmp_values), vec_vsx_ld(offset16, tmp_values)}; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch new file mode 100644 index 000000000000..56a02bdac0eb --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-vsx-vector-funcs.patch @@ -0,0 +1,310 @@ +That code fails for large values such as sin(1e20) producing inf. +See https://github.com/pytorch/pytorch/issues/85978 +and https://github.com/pytorch/pytorch/pull/86453 +Use the Sleef functions similar to the double variants. + +Author: Alexander Grund (TU Dresden) + +diff --git a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +index 77cf3695ab912..8fe6cc25f0ee9 100644 +--- a/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h ++++ b/aten/src/ATen/cpu/vec/vec256/vsx/vec256_float_vsx.h +@@ -256,29 +256,29 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE acos() const { +- return {Sleef_acosf4_u10vsx(_vec0), Sleef_acosf4_u10vsx(_vec1)}; ++ return {Sleef_acosf4_u10vsx(_vec0), Sleef_acosf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE asin() const { +- return {Sleef_asinf4_u10vsx(_vec0), Sleef_asinf4_u10vsx(_vec1)}; ++ return {Sleef_asinf4_u10vsx(_vec0), Sleef_asinf4_u10vsx(_vec1)}; + } + Vectorized atan() const { +- return {Sleef_atanf4_u10vsx(_vec0), Sleef_atanf4_u10vsx(_vec1)}; ++ return {Sleef_atanf4_u10vsx(_vec0), Sleef_atanf4_u10vsx(_vec1)}; + } + Vectorized atan2(const Vectorized& b) const { +- return {Sleef_atan2f4_u10vsx(_vec0, b._vec0), Sleef_atan2f4_u10vsx(_vec1, b._vec1)}; ++ return {Sleef_atan2f4_u10vsx(_vec0, b._vec0), Sleef_atan2f4_u10vsx(_vec1, b._vec1)}; + } + Vectorized copysign(const Vectorized &sign) const { + return {Sleef_copysignf4_vsx(_vec0, sign._vec0), Sleef_copysignf4_vsx(_vec1, sign._vec1)}; + } + Vectorized lgamma() const { +- return {Sleef_lgammaf4_u10vsx(_vec0), Sleef_lgammaf4_u10vsx(_vec1)}; ++ return {Sleef_lgammaf4_u10vsx(_vec0), Sleef_lgammaf4_u10vsx(_vec1)}; + } + Vectorized erf() const { +- return {Sleef_erff4_u10vsx(_vec0), Sleef_erff4_u10vsx(_vec1)}; ++ return {Sleef_erff4_u10vsx(_vec0), Sleef_erff4_u10vsx(_vec1)}; + } + + Vectorized erfc() const { +- return {Sleef_erfcf4_u15vsx(_vec0), Sleef_erfcf4_u15vsx(_vec1)}; ++ return {Sleef_erfcf4_u15vsx(_vec0), Sleef_erfcf4_u15vsx(_vec1)}; + } + + Vectorized erfinv() const { +@@ -301,133 +301,32 @@ class Vectorized { + } + + Vectorized C10_ALWAYS_INLINE exp() const { +- // implementation logic from avx_mathfun with some modifications from sleef +- // Express e**x = e**g 2**n +- /// = e**g e**( n loge(2) ) +- /// = e**( g + n loge(2) ) +- // +- auto tmp_x = *this; +- auto fx = (tmp_x * log2e_inv).round(); +- +- auto x = fx.madd(negln2f_hi, tmp_x); +- x = fx.madd(negln2f_lo, x); +- auto z = x * x; +- auto y = x.madd(exp_p0, exp_p1); +- y = y.madd(x, exp_p2); +- y = y.madd(x, exp_p3); +- y = y.madd(x, exp_p4); +- y = y.madd(x, exp_p5); +- y = y.madd(z, x) + one; +- +- // vm_pow2n 2^n +- vint32 imm0 = vec_signed(fx._vec0); +- vint32 imm1 = vec_signed(fx._vec1); +- // this pow2n logic is from Sleef code +- vint32 imm00 = imm0 >> 1; //>>1 +- vint32 imm01 = imm1 >> 1; +- vint32 imm10 = imm0 - imm00; +- vint32 imm11 = imm1 - imm01; +- imm00 = (imm00 + v0x7f) << vu_23; +- imm01 = (imm01 + v0x7f) << vu_23; +- imm10 = (imm10 + v0x7f) << vu_23; +- imm11 = (imm11 + v0x7f) << vu_23; +- // treat imm as float vector without conversion +- +- y._vec0 = (y._vec0 * (vfloat32)imm00) * (vfloat32)imm10; +- y._vec1 = (y._vec1 * (vfloat32)imm01) * (vfloat32)imm11; +- // boundary check +- auto tmp = blendv(y, v_inf, (Vectorized(exp_hi) <= tmp_x)); +- y = blendv(tmp, zero, (tmp_x < Vectorized(exp_lo))); +- +- return y; ++ return {Sleef_expf4_u10vsx(_vec0), Sleef_expf4_u10vsx(_vec1)}; + } + Vectorized expm1() const { +- return exp() - one; ++ return {Sleef_expm1f4_u10vsx(_vec0), Sleef_expm1f4_u10vsx(_vec1)}; + } + + Vectorized C10_ALWAYS_INLINE log() const { + return {Sleef_logf4_u10vsx(_vec0), Sleef_logf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log10() const { +- return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; ++ return {Sleef_log10f4_u10vsx(_vec0), Sleef_log10f4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log1p() const { +- return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; ++ return {Sleef_log1pf4_u10vsx(_vec0), Sleef_log1pf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE log2() const { +- return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; ++ return {Sleef_log2f4_u10vsx(_vec0), Sleef_log2f4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE ceil() const { + return {vec_ceil(_vec0), vec_ceil(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE cos() const { +- // take the absolute value +- auto x = abs(); +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- // scale by 4/Pi +- auto y = x * _4div_pi; +- // store the integer part of y in mm0 +- // j=(j+1) & (~1) (see the cephes sources) +- vint32 imm0 = (vec_signed(y._vec0) + vi_1) & vi_inv1; +- vint32 imm1 = (vec_signed(y._vec1) + vi_1) & vi_inv1; +- y._vec0 = vec_float(imm0); +- y._vec1 = vec_float(imm1); +- +- imm0 = imm0 - vi_2; +- imm1 = imm1 - vi_2; +- Vectorized poly_mask; +- // get the swap sign flag +- vint32 tmp0 = vec_and(vec_nand(imm0, imm0), vi_4); +- vint32 tmp1 = vec_and(vec_nand(imm1, imm1), vi_4); +- sign_bit._vecb0 = (vbool32)vec_sl(tmp0, vu_29); +- sign_bit._vecb1 = (vbool32)vec_sl(tmp1, vu_29); +- // get the polynom selection mask +- // there is one polynom for 0 <= x <= Pi / 4 +- // and another one for Pi / 4 < x <= Pi / 2 +- // Both branches will be computed. +- +- poly_mask._vecb0 = (vbool32)vec_cmpeq((imm0 & vi_2), vi_0); +- poly_mask._vecb1 = (vbool32)vec_cmpeq((imm1 & vi_2), vi_0); +- +- // The magic pass: "Extended precision modular arithmetic" +- // x = ((x - y * DP1) - y * DP2) - y * DP3; +- x = y.madd(minus_cephes_dp1, x); +- x = y.madd(minus_cephes_dp2, x); +- x = y.madd(minus_cephes_dp3, x); +- +- // Evaluate the first polynom (0 <= x <= Pi/4) +- auto z = x * x; +- y = z.madd(coscof_p0, coscof_p1); +- y = y.madd(z, coscof_p2); +- y = y * z * z; +- y = y - z * half + one; +- +- // Evaluate the second polynom (Pi/4 <= x <= 0) +- auto y_2 = z.madd(sincof_p0, sincof_p1); +- y_2 = y_2.madd(z, sincof_p2); +- y_2 = y_2 * z; +- y_2 = y_2.madd(x, x); +- +- // select the correct result from the two polynoms +- y = blendv(y, y_2, poly_mask); +- // update the sign +- y = y ^ sign_bit; +- +- return y; ++ return {Sleef_cosf4_u10vsx(_vec0), Sleef_cosf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE cosh() const { +- // cosh = 1/2 * (e^x + e^-x) +- auto x = abs(); +- auto e_x = x.exp(); +- auto ret = (e_x + Vectorized(one) / e_x) * half; +- // inf and nan checks +-#if 0 +- ret = blendv(ret, v_inf, x >= vf_89); +- ret = blendv(ret, v_inf, ret.isnan()); +- ret = blendv(ret, v_nan, this->isnan()); +-#endif +- return ret; ++ return {Sleef_coshf4_u10vsx(_vec0), Sleef_coshf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE floor() const { + return {vec_floor(_vec0), vec_floor(_vec1)}; +@@ -440,97 +339,16 @@ class Vectorized { + return {vec_round(_vec0), vec_round(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE sin() const { +- // take the absolute value and xtract sign +- auto x = abs(); +- auto sign_bit = (*this) & sign_mask; +- +- // scale by 4/Pi +- auto y = x * _4div_pi; +- // store the integer part of y in mm0 +- +- // j=(j+1) & (~1) (see the cephes sources) +- vint32 imm0 = (vec_signed(y._vec0) + vi_1) & vi_inv1; +- vint32 imm1 = (vec_signed(y._vec1) + vi_1) & vi_inv1; +- y._vec0 = vec_float(imm0); +- y._vec1 = vec_float(imm1); +- // get the swap sign flag +- Vectorized swap_sign_bit, poly_mask; +- swap_sign_bit._vecb0 = (vbool32)vec_sl(imm0 & vi_4, vu_29); +- swap_sign_bit._vecb1 = (vbool32)vec_sl(imm1 & vi_4, vu_29); +- // get the polynom selection mask +- // there is one polynom for 0 <= x <= Pi/4 +- // and another one for Pi/4 C10_ALWAYS_INLINE sinh() const { +- auto temp_abs = abs(); +- // get exponent +- auto ret = temp_abs.exp(); +- auto recp = Vectorized(half) / ret; +- auto v = ret * half - recp; +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- auto z = temp_abs * temp_abs; +- auto y = z.madd(p0, p1); +- y = y.madd(z, p2); +- y = (y * z).madd(temp_abs, temp_abs); +- // check and select +- auto result = blendv(y, v, temp_abs > one); +- return result | sign_bit; ++ return {Sleef_sinhf4_u10vsx(_vec0), Sleef_sinhf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE tan() const { +- return {Sleef_tanf4_u10vsx(_vec0), Sleef_tanf4_u10vsx(_vec1)}; ++ return {Sleef_tanf4_u10vsx(_vec0), Sleef_tanf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE tanh() const { +- auto x = *this; +- auto vabs = abs(); +- // get exponent +- auto exp2x = (vabs + vabs).exp(); +- auto vv = Vectorized(one) - Vectorized(two) / (exp2x + one); +- // extract the sign bit (upper one) +- auto sign_bit = (*this) & sign_mask; +- auto z = vabs * vabs; +- auto y = z.madd(tanh_p0, tanh_p1); +- auto tmp = y.madd(z, tanh_p2); +- y = z.madd(tmp, tanh_p3); +- tmp = y.madd(z, tanh_p4); +- y = tmp * z; +- tmp = y.madd(x, x); +- // add sign +- vv = vv | sign_bit; +- // check and select +- auto sel_mask = vabs >= tanh_0p625; +- auto max_mask = vabs > tanh_half_max; +- auto max_ret = sign_bit ^ one; +- return blendv(blendv(tmp, vv, sel_mask), max_ret, max_mask); ++ return {Sleef_tanhf4_u10vsx(_vec0), Sleef_tanhf4_u10vsx(_vec1)}; + } + Vectorized C10_ALWAYS_INLINE trunc() const { + return {vec_trunc(_vec0), vec_trunc(_vec1)}; +@@ -555,15 +373,15 @@ class Vectorized { + } + + Vectorized fmod(const Vectorized& b) const { +- return {Sleef_fmodf4_vsx(_vec0, b._vec0),Sleef_fmodf4_vsx(_vec1, b._vec1)}; ++ return {Sleef_fmodf4_vsx(_vec0, b._vec0),Sleef_fmodf4_vsx(_vec1, b._vec1)}; + } + + Vectorized hypot(const Vectorized& b) const { +- return {Sleef_hypotf4_u05vsx(_vec0, b._vec0), Sleef_hypotf4_u05vsx(_vec1, b._vec1)}; ++ return {Sleef_hypotf4_u05vsx(_vec0, b._vec0), Sleef_hypotf4_u05vsx(_vec1, b._vec1)}; + } + + Vectorized nextafter(const Vectorized& b) const { +- return {Sleef_nextafterf4_vsx(_vec0, b._vec0), Sleef_nextafterf4_vsx(_vec1, b._vec1)}; ++ return {Sleef_nextafterf4_vsx(_vec0, b._vec0), Sleef_nextafterf4_vsx(_vec1, b._vec1)}; + } + + Vectorized igamma(const Vectorized& x) const { diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch new file mode 100644 index 000000000000..6455052773f4 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-test-adadelta-tolerance.patch @@ -0,0 +1,22 @@ +TestOptim.test_adadelta fails on some systems with +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 0.0012711584568023682 at index (1, 3) (up to 1e-05 allowed) +> Greatest relative difference: 0.005316456816424191 at index (1, 3) (up to 0.004 allowed) +This is possibly related to the CUDA driver version. See also https://github.com/pytorch/pytorch/issues/51992 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_optim.py b/test/test_optim.py +index 6d587b4b35..32e5dbcc2f 100644 +--- a/test/test_optim.py ++++ b/test/test_optim.py +@@ -621,7 +621,8 @@ class TestOptim(TestCase): + # ROCm precision is too low to pass this test + def test_adadelta(self): + # Handles https://github.com/pytorch/pytorch/issues/69698 +- self.rel_tol = 4e-3 ++ self.precision = 2e-3 ++ self.rel_tol = 1e-2 + for optimizer in [optim.Adadelta, optim_mt.Adadelta]: + self._test_basic_cases( + lambda weight, bias, maximize: optimizer([weight, bias], maximize=maximize), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch new file mode 100644 index 000000000000..9a728ce288d5 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_increase-tolerance-test_ops.patch @@ -0,0 +1,27 @@ +`test_out` may fail due to slightly different values caused by different order of matrizes in SGEMM: + +> Mismatched elements: 1 / 50 (2.0%) +> Greatest absolute difference: 1.430511474609375e-05 at index (4, 5) (up to 1e-05 allowed) +> Greatest relative difference: 4.65393206065873e-06 at index (4, 5) (up to 1.3e-06 allowed) + +See https://github.com/pytorch/pytorch/pull/86365 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 00eb3f7f09..d97505ffb6 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -9984,7 +9984,11 @@ op_db: List[OpInfo] = [ + DecorateInfo( + toleranceOverride({torch.float32: tol(atol=1.3e-05, rtol=1.3e-05), + torch.complex64: tol(atol=1e-05, rtol=1.2e-03)}), +- 'TestCommon', 'test_reference_testing')], ++ 'TestCommon', 'test_reference_testing'), ++ DecorateInfo( ++ toleranceOverride({torch.float32: tol(atol=1.5e-05, rtol=1e-05)}), ++ 'TestCommon', 'test_out'), ++ ], + skips=( + # NVIDIA only assures that bfloat16 is supported by bmm if SM >= 5.3 + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes', device_type='cuda', active_if=not SM53OrLater), diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch new file mode 100644 index 000000000000..60e094561828 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_no-cuda-stubs-rpath.patch @@ -0,0 +1,159 @@ +# PyTorch's CMAKE configuration by default sets RUNPATH on libraries if they link other libraries +# that are outside the build tree, which is done because of the CMAKE config on +# https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L10. +# This provides problems, since the cuda stubs library path then also gets added to the RUNPATH. +# As a result, at runtime, the stub version of things like libcuda.so.1 gets picked up, instead of the real drivers +# See https://github.com/easybuilders/easybuild-easyconfigs/issues/14359 +# This line https://github.com/pytorch/pytorch/blob/v1.10.0/cmake/Dependencies.cmake#L16 +# Makes sure that any path that is linked, is also added to the RUNPATH. +# This has been reported upstream in https://github.com/pytorch/pytorch/issues/35418 +# and a fix was attempted in https://github.com/pytorch/pytorch/pull/37737 but it was reverted +# +# This EasyBuild patch changes behavior for the libraries that were failing, i.e. the ones in this list: +# https://github.com/easybuilders/easybuild-easyconfigs/issues/14359#issuecomment-970479904 +# This is done by setting INSTALL_RPATH_USE_LINK_PATH to false, and instead, specifying the RPATH +# explicitely by defining INSTALL_RPATH, but only adding directories that do not match to the "stubs" regex +# +# Original patch: Caspar van Leeuwen +# Updated: Alexander Grund (TU Dresden) +# +# See https://github.com/pytorch/pytorch/pull/87593 + +diff --git a/caffe2/CMakeLists.txt b/caffe2/CMakeLists.txt +index 328210c978..f06ee0bb4e 100644 +--- a/caffe2/CMakeLists.txt ++++ b/caffe2/CMakeLists.txt +@@ -643,13 +643,12 @@ if(NOT INTERN_BUILD_MOBILE OR NOT BUILD_CAFFE2_MOBILE) + if(USE_CUDA) + list(APPEND Caffe2_GPU_CU_SRCS ${Caffe2_GPU_HIP_JIT_FUSERS_SRCS}) + add_library(caffe2_nvrtc SHARED ${ATen_NVRTC_STUB_SRCS}) ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB}) + if(MSVC) + # Delay load nvcuda.dll so we can import torch compiled with cuda on a CPU-only machine +- set(DELAY_LOAD_FLAGS "-DELAYLOAD:nvcuda.dll;delayimp.lib") +- else() +- set(DELAY_LOAD_FLAGS "") ++ target_link_libraries(caffe2_nvrtc "-DELAYLOAD:nvcuda.dll;delayimp.lib") + endif() +- target_link_libraries(caffe2_nvrtc ${CUDA_NVRTC} ${CUDA_CUDA_LIB} ${CUDA_NVRTC_LIB} ${DELAY_LOAD_FLAGS}) + target_include_directories(caffe2_nvrtc PRIVATE ${CUDA_INCLUDE_DIRS}) + install(TARGETS caffe2_nvrtc DESTINATION "${TORCH_INSTALL_LIB_DIR}") + if(USE_NCCL) +diff --git a/cmake/LinkCudaLibraries.cmake b/cmake/LinkCudaLibraries.cmake +new file mode 100644 +index 0000000000..a24583bff4 +--- /dev/null ++++ b/cmake/LinkCudaLibraries.cmake +@@ -0,0 +1,33 @@ ++# Link CUDA libraries to the given target, i.e.: `target_link_libraries(target )` ++# ++# Additionally makes sure CUDA stub libs don't end up being in RPath ++# ++# Example: link_cuda_libraries(mytarget PRIVATE ${CUDA_LIBRARIES}) ++function(link_cuda_libraries target) ++ set(libs ${ARGN}) ++ set(install_rpath "") ++ set(filtered FALSE) ++ foreach(lib IN LISTS libs) ++ # CUDA stub libs are in form /prefix/lib/stubs/libcuda.so ++ # So extract the name of the parent folder, to check against "stubs" ++ # And the parent path which we need to add to the INSTALL_RPATH for non-stubs ++ get_filename_component(parent_path "${lib}" DIRECTORY) ++ get_filename_component(parent_name "${parent_path}" NAME) ++ if(parent_name STREQUAL "stubs") ++ message(STATUS "Filtering ${lib} from being set in ${target}'s RPATH, " ++ "because it appears to point to the CUDA stubs directory.") ++ set(filtered TRUE) ++ elseif(parent_path) ++ list(APPEND install_rpath ${parent_path}) ++ endif() ++ endforeach() ++ ++ # Regular link command ++ target_link_libraries(${target} ${scope} ${libs}) ++ # Manually set INSTALL_RPATH when there were any stub libs ++ if(filtered) ++ list(REMOVE_DUPLICATES install_rpath) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH_USE_LINK_PATH FALSE) ++ set_target_properties(${target} PROPERTIES INSTALL_RPATH "${install_rpath}") ++ endif() ++endfunction() +diff --git a/test/cpp/api/CMakeLists.txt b/test/cpp/api/CMakeLists.txt +index 373895a0ce..19868221cb 100644 +--- a/test/cpp/api/CMakeLists.txt ++++ b/test/cpp/api/CMakeLists.txt +@@ -58,7 +58,8 @@ if(NOT MSVC) + endif() + + if(USE_CUDA) +- target_link_libraries(test_api PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_api PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/dist_autograd/CMakeLists.txt b/test/cpp/dist_autograd/CMakeLists.txt +index 9969c63e16..356ba5be55 100644 +--- a/test/cpp/dist_autograd/CMakeLists.txt ++++ b/test/cpp/dist_autograd/CMakeLists.txt +@@ -10,7 +10,8 @@ if(USE_DISTRIBUTED AND NOT WIN32) + target_link_libraries(test_dist_autograd PRIVATE torch gtest) + + if(USE_CUDA) +- target_link_libraries(test_dist_autograd PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_dist_autograd PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/jit/CMakeLists.txt b/test/cpp/jit/CMakeLists.txt +index 60b43b81fc..57cd4422f8 100644 +--- a/test/cpp/jit/CMakeLists.txt ++++ b/test/cpp/jit/CMakeLists.txt +@@ -136,7 +137,8 @@ if(LINUX) + endif() + + if(USE_CUDA) +- target_link_libraries(test_jit PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_jit PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/rpc/CMakeLists.txt b/test/cpp/rpc/CMakeLists.txt +index 3997f8753e..21fddbc645 100644 +--- a/test/cpp/rpc/CMakeLists.txt ++++ b/test/cpp/rpc/CMakeLists.txt +@@ -33,7 +33,8 @@ target_include_directories( + target_link_libraries(test_cpp_rpc PRIVATE ${TORCH_RPC_TEST_DEPENDENCY_LIBS}) + + if(USE_CUDA) +- target_link_libraries(test_cpp_rpc PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_cpp_rpc PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} +diff --git a/test/cpp/tensorexpr/CMakeLists.txt b/test/cpp/tensorexpr/CMakeLists.txt +index 7dff70630d..ecb8300549 100644 +--- a/test/cpp/tensorexpr/CMakeLists.txt ++++ b/test/cpp/tensorexpr/CMakeLists.txt +@@ -57,14 +57,15 @@ if(USE_PTHREADPOOL) + target_link_libraries(test_tensorexpr PRIVATE pthreadpool_interface) + endif() + if(USE_CUDA) +- target_link_libraries(test_tensorexpr PRIVATE ++ include(${Torch_SOURCE_DIR}/cmake/LinkCudaLibraries.cmake) ++ link_cuda_libraries(test_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} + ${TORCH_CUDA_LIBRARIES}) + target_compile_definitions(test_tensorexpr PRIVATE USE_CUDA) + +- target_link_libraries(tutorial_tensorexpr PRIVATE ++ link_cuda_libraries(tutorial_tensorexpr PRIVATE + ${CUDA_LIBRARIES} + ${CUDA_NVRTC_LIB} + ${CUDA_CUDA_LIB} diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch new file mode 100644 index 000000000000..6b2fb2653951 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch @@ -0,0 +1,26 @@ +Those tests (from test_ao_sparsity) require FBGEMM which may not be available. +So add the skip decorator. +See https://github.com/pytorch/pytorch/issues/87364 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/ao/sparsity/test_composability.py b/test/ao/sparsity/test_composability.py +index b44c885507..b7d35343c0 100644 +--- a/test/ao/sparsity/test_composability.py ++++ b/test/ao/sparsity/test_composability.py +@@ -9,6 +9,7 @@ import torch.ao.quantization as tq + from torch import nn + from torch.ao import sparsity + from torch.testing._internal.common_utils import TestCase ++from torch.testing._internal.common_quantization import skipIfNoFBGEMM + + logging.basicConfig( + format="%(asctime)s - %(name)s - %(levelname)s - %(message)s", level=logging.INFO +@@ -23,6 +24,7 @@ sparse_defaults = { + # This series of tests are to check the composability goals for sparsity and quantization. Namely + # that performing quantization and sparsity model manipulations in various orderings + # does not cause problems ++@skipIfNoFBGEMM + class TestComposability(TestCase): + def _get_model_and_sparsifier_and_sparse_config(self, qconfig=None): + model = nn.Sequential( diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch new file mode 100644 index 000000000000..b515d8dd432b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch @@ -0,0 +1,51 @@ +Test test_fn_grad_linalg_det_singular_cpu_complex128 in test_ops_gradients fails not only on Windows, +so extend the skip marker introduced in https://github.com/pytorch/pytorch/pull/69827 + +test_forward_mode_AD_norm_inf_cpu_complex128 in test_ops_gradients fails due to NaNs. +Might be fixed by https://github.com/pytorch/pytorch/pull/80082 where a part of the changes +come from with additional skip for that test similar to other complex128 skips. + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py +index 00eb3f7f09..8d009cf280 100644 +--- a/torch/testing/_internal/common_methods_invocations.py ++++ b/torch/testing/_internal/common_methods_invocations.py +@@ -9729,11 +9729,11 @@ op_db: List[OpInfo] = [ + dtypesIfCUDA=all_types_and_complex_and(torch.bool, torch.half, torch.bfloat16, torch.chalf), + skips=( + # Inplace abs doesn't support complex inputs +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_grad', dtypes=(torch.cdouble,)), +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_gradgrad', dtypes=(torch.cdouble,)), +- DecorateInfo(unittest.expectedFailure, 'TestGradients', ++ DecorateInfo(unittest.skip("In-place abs not supported for complex tensors"), 'TestGradients', + 'test_inplace_forward_mode_AD', dtypes=(torch.cdouble,)), + DecorateInfo(unittest.skip("Skipped!"), 'TestUnaryUfuncs', 'test_reference_numerics_extremal', + device_type='cpu', dtypes=[torch.cfloat, torch.cdouble]), +@@ -11559,7 +11559,7 @@ op_db: List[OpInfo] = [ + skips=( + # These tests started breaking after touching the SVD. + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad', device_type='cpu', +- dtypes=(torch.complex128,), active_if=IS_WINDOWS), ++ dtypes=(torch.complex128,)), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + # dtypes are tested in the suite above, no need to repeat it for singular + DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), +@@ -17230,6 +17230,13 @@ op_db: List[OpInfo] = [ + device_type="cpu", + dtypes=(torch.complex128,), + ), ++ DecorateInfo( ++ unittest.skip("NaNs in analytical jacobian!"), ++ "TestGradients", ++ "test_forward_mode_AD", ++ device_type="cpu", ++ dtypes=(torch.complex128,), ++ ), + DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_fn_fwgrad_bwgrad', + dtypes=[torch.complex128]), + # AssertionError: RuntimeError not raised : Expected RuntimeError when doing an unsafe cast from a result From a51c4dcc20707b75971d9ae9df434a89c85677fd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Thu, 27 Oct 2022 13:46:48 +0200 Subject: [PATCH 543/939] Remove test which times out --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 564c7ada0c81..5c8c7675ce64 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -59,6 +60,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch From d720a6809955020093c01b5d221fb5d6d994786d Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 22 Nov 2022 15:58:48 +0100 Subject: [PATCH 544/939] Patch failure on older CUDA drivers --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 5 +-- .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 5 +-- ...h-1.12.1_fix-test_cpp_extensions_jit.patch | 31 +++++++++++++++++++ 3 files changed, 37 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 5c8c7675ce64..ae0cff605da0 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -14,7 +14,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-test-model_dump.patch', @@ -27,6 +26,7 @@ patches = [ 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', @@ -42,7 +42,6 @@ checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.10.0_fix-kineto-crash.patch 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -64,6 +63,8 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index cd38c8b8e9c8..cb1f43fa0950 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -13,7 +13,6 @@ sources = ['%(namelower)s-v%(version)s.tar.gz'] patches = [ 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', 'PyTorch-1.7.0_disable-dev-shm-test.patch', - 'PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch', 'PyTorch-1.10.0_fix-kineto-crash.patch', 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', 'PyTorch-1.10.0_fix-test-model_dump.patch', @@ -25,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', @@ -40,7 +40,6 @@ checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch - '89ac7a8e9e7df2e64cf8404fe3a279f5e9b759fee41c9de3aaff9c22f385c2c6', # PyTorch-1.8.1_dont-use-gpu-ccc-in-test.patch # PyTorch-1.10.0_fix-kineto-crash.patch 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch @@ -60,6 +59,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch new file mode 100644 index 000000000000..38dcd0c2eb6f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch @@ -0,0 +1,31 @@ +When the CUDA Toolkit (compiler...) is to new or to old for the GPU or the GPU driver +this test may fail. +See https://github.com/pytorch/pytorch/pull/89495 + +diff --git a/test/test_cpp_extensions_jit.py b/test/test_cpp_extensions_jit.py +index 2ead8d32ca179..dd350823ffef9 100644 +--- a/test/test_cpp_extensions_jit.py ++++ b/test/test_cpp_extensions_jit.py +@@ -200,7 +200,21 @@ def test_jit_cuda_archflags(self): + archflags["5.0;6.0+PTX;7.0;7.5"] = (['50', '60', '70', '75'], ['60']) + + for flags, expected in archflags.items(): +- self._run_jit_cuda_archflags(flags, expected) ++ try: ++ self._run_jit_cuda_archflags(flags, expected) ++ except RuntimeError as e: ++ # Using the device default (empty flags) may fail if the device is newer than the CUDA compiler ++ # This raises a RuntimeError with a specific message which we explictely ignore here ++ if not flags and "Error building" in str(e): ++ pass ++ else: ++ raise ++ try: ++ torch.cuda.synchronize() ++ except RuntimeError: ++ # Ignore any error, e.g. unsupported PTX code on current device ++ # to avoid errors from here leaking into other tests ++ pass + + @unittest.skipIf(not TEST_CUDNN, "CuDNN not found") + def test_jit_cudnn_extension(self): From f223ac3773b440849fe8a6c428780287e0aa75db Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 10:36:58 +0100 Subject: [PATCH 545/939] Skip test which may succeed --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 +- ...yTorch-1.12.1_skip-failing-grad-test.patch | 21 +++++++++++++++++++ 3 files changed, 23 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index ae0cff605da0..e8cea51ff733 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -79,7 +79,7 @@ checksums = [ '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', - 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index cb1f43fa0950..bb39edb055de 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -75,7 +75,7 @@ checksums = [ '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', - 'b24442e38e42ab62c340c84d9daaebd9f5a893ba8434338b97fcff6bba9ff24f', # PyTorch-1.12.1_skip-failing-grad-test.patch + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch index b515d8dd432b..a79bc9a7a5ed 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-failing-grad-test.patch @@ -5,6 +5,9 @@ test_forward_mode_AD_norm_inf_cpu_complex128 in test_ops_gradients fails due to Might be fixed by https://github.com/pytorch/pytorch/pull/80082 where a part of the changes come from with additional skip for that test similar to other complex128 skips. +Also skip test_forward_mode_AD_nn_functional_max_unpool2d_cpu_float64 & test_forward_mode_AD_nn_functional_max_unpool3d_cpu_float64 +which may unexpectably succeed. + Author: Alexander Grund (TU Dresden) diff --git a/torch/testing/_internal/common_methods_invocations.py b/torch/testing/_internal/common_methods_invocations.py @@ -35,6 +38,24 @@ index 00eb3f7f09..8d009cf280 100644 DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), # dtypes are tested in the suite above, no need to repeat it for singular DecorateInfo(unittest.skip("Skipped!"), 'TestCommon', 'test_dtypes'), +@@ -13447,7 +13447,7 @@ op_db: List[OpInfo] = [ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + )), +@@ -13481,7 +13481,7 @@ op_db: List[OpInfo] = [ + # and if there are several indices pointing to the same memory, + # gradcheck is oblivious about that and cannot perturb them all at once + # (see sample_inputs_max_unpool_grad to find out more). +- DecorateInfo(unittest.expectedFailure, 'TestGradients', 'test_forward_mode_AD'), ++ DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_forward_mode_AD'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_gradgrad'), + DecorateInfo(unittest.skip("Skipped!"), 'TestGradients', 'test_fn_grad'), + )), @@ -17230,6 +17230,13 @@ op_db: List[OpInfo] = [ device_type="cpu", dtypes=(torch.complex128,), From 6e3c238b82abe35f249701a69ca6f53c558e2038 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 11:12:42 +0100 Subject: [PATCH 546/939] Skip c10d test which times out --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 3 +++ .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 3 +++ ...skip-test_round_robin_create_destroy.patch | 26 +++++++++++++++++++ 3 files changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index e8cea51ff733..f81fea585ecf 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -37,6 +37,7 @@ patches = [ 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', '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', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -80,6 +81,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index bb39edb055de..ab67d74f8541 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -35,6 +35,7 @@ patches = [ 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', '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', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -76,6 +77,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch new file mode 100644 index 000000000000..f8e01a445dbe --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch @@ -0,0 +1,26 @@ +test_round_robin_create_destroy of distributed/test_c10d_gloo may run into timeouts. +So simply skip the on all OS (not only on Windows), the existing skip marker suggest that this is OK. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/test_c10d_gloo.py b/test/distributed/test_c10d_gloo.py +index e49d65ea33d..b4fb75a1b11 100644 +--- a/test/distributed/test_c10d_gloo.py ++++ b/test/distributed/test_c10d_gloo.py +@@ -10,6 +10,7 @@ import sys + import tempfile + from functools import reduce + from itertools import groupby ++from unittest import skip + + import torch + import torch.distributed as c10d +@@ -1438,7 +1439,7 @@ class ProcessGroupGlooTest(MultiProcessTestCase): + pg.broadcast(tensor, root=0).wait() + self.assertEqual(torch.full([100, 100], 0.0), tensor) + +- @skip_if_win32() ++ @skip("Occasionally times out") + @requires_gloo() + def test_round_robin_create_destroy(self): + store = c10d.FileStore(self.file_name, self.world_size) From ec03d0c0bd8b8bddaf3ff85655be03efe494d17a Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 25 Nov 2022 16:32:16 +0100 Subject: [PATCH 547/939] Fix test failures on 1 GPU --- .../PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 + .../p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 + .../PyTorch-1.12.1_fix-skip-decorators.patch | 118 ++++++++++++++++++ 3 files changed, 122 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index f81fea585ecf..03c04cd2a9e7 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -26,6 +26,7 @@ patches = [ 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -64,6 +65,7 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index ab67d74f8541..7fd464b8dd27 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.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-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', @@ -60,6 +61,7 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch new file mode 100644 index 000000000000..8300d0d50860 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch @@ -0,0 +1,118 @@ +The decorators are implemented to run when the function is called which is after +the test `setup` method spawned subprocesses which may use NCCL to sync failing when there are +not enough GPUs available. +So replace the custom code by calls to the `unittest` skip decorators. +See https://github.com/pytorch/pytorch/pull/89750 + +Author: Alexander Grund (TU Dresden) + +diff --git a/torch/testing/_internal/common_distributed.py b/torch/testing/_internal/common_distributed.py +index 8baf7d03d9f..3dc922ee923 100644 +--- a/torch/testing/_internal/common_distributed.py ++++ b/torch/testing/_internal/common_distributed.py +@@ -124,46 +124,11 @@ def skip_if_odd_worldsize(func): + return wrapper + + def require_n_gpus_for_nccl_backend(n, backend): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend == "nccl" and torch.cuda.device_count() < n: +- sys.exit(TEST_SKIPS[f"multi-gpu-{n}"].exit_code) +- else: +- return func(*args, **kwargs) +- +- return wrapper +- +- return decorator ++ return skip_if_lt_x_gpu(n) if backend == "nccl" else unittest.skipIf(False, None) + + + def skip_if_lt_x_gpu(x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator +- +- +-# This decorator helps avoiding initializing cuda while testing other backends +-def nccl_skip_if_lt_x_gpu(backend, x): +- def decorator(func): +- @wraps(func) +- def wrapper(*args, **kwargs): +- if backend != "nccl": +- return func(*args, **kwargs) +- if torch.cuda.is_available() and torch.cuda.device_count() >= x: +- return func(*args, **kwargs) +- sys.exit(TEST_SKIPS[f"multi-gpu-{x}"].exit_code) +- +- return wrapper +- +- return decorator ++ return unittest.skipIf(torch.cuda.device_count() < x, TEST_SKIPS[f"multi-gpu-{x}"].message) + + + def verify_ddp_error_logged(model_DDP, err_substr): +diff --git a/torch/testing/_internal/distributed/distributed_test.py b/torch/testing/_internal/distributed/distributed_test.py +index 1414a0376b1..1f6b00e6edf 100644 +--- a/torch/testing/_internal/distributed/distributed_test.py ++++ b/torch/testing/_internal/distributed/distributed_test.py +@@ -56,7 +56,6 @@ from torch.testing._internal.common_distributed import ( + skip_if_small_worldsize, + skip_if_odd_worldsize, + skip_if_lt_x_gpu, +- nccl_skip_if_lt_x_gpu, + skip_if_no_gpu, + require_n_gpus_for_nccl_backend, + requires_nccl_version, +@@ -4604,7 +4603,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4615,7 +4614,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_grad_is_view(self): + """ + Runs _test_accumulate_gradients_no_sync using default inputs +@@ -4626,7 +4625,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_allreduce_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync +@@ -4654,7 +4653,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): + """ + Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce +@@ -4688,7 +4687,7 @@ class DistributedTest: + BACKEND != "mpi" and BACKEND != "nccl" and BACKEND != "gloo", + "get_future is only supported on mpi, nccl and gloo", + ) +- @nccl_skip_if_lt_x_gpu(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(BACKEND, 2) + def test_get_future(self): + def mult(fut): + return [t * 3 for t in fut.wait()] From d159a5a3c98487a79900be700b9e49b1468b9449 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Nov 2022 13:27:16 +0100 Subject: [PATCH 548/939] Fix test failures on 1 GPU --- .../p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb | 2 +- .../easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb | 2 +- .../p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch | 10 +++++----- 3 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb index 03c04cd2a9e7..9778d40af769 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a-CUDA-11.3.1.eb @@ -65,7 +65,7 @@ checksums = [ '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', - '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb index 7fd464b8dd27..4417c0caceea 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2021a.eb @@ -61,7 +61,7 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', - '32fc722f5f93b9a89b10809c2b38718de9c847a96ffdd540d2c71eae154e4201', # PyTorch-1.12.1_fix-skip-decorators.patch + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch index 8300d0d50860..0fbe044ff32b 100644 --- a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-skip-decorators.patch @@ -76,7 +76,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync(self): """ Runs _test_accumulate_gradients_no_sync using default inputs @@ -85,7 +85,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_grad_is_view(self): """ Runs _test_accumulate_gradients_no_sync using default inputs @@ -94,7 +94,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_allreduce_hook(self): """ Runs multiple iterations on _test_accumulate_gradients_no_sync @@ -103,7 +103,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_accumulate_gradients_no_sync_allreduce_with_then_hook(self): """ Runs multiple iterations on _test_accumulate_gradients_no_sync using allreduce @@ -112,7 +112,7 @@ index 1414a0376b1..1f6b00e6edf 100644 "get_future is only supported on mpi, nccl and gloo", ) - @nccl_skip_if_lt_x_gpu(BACKEND, 2) -+ @require_n_gpus_for_nccl_backend(BACKEND, 2) ++ @require_n_gpus_for_nccl_backend(2, BACKEND) def test_get_future(self): def mult(fut): return [t * 3 for t in fut.wait()] From 1d3e6ac7b0c5015794e4d36e30c360665a1021e3 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 28 Nov 2022 14:23:57 +0100 Subject: [PATCH 549/939] Cancel old GithubAction runs --- .github/workflows/linting.yml | 5 +++++ .github/workflows/unit_tests.yml | 5 +++++ 2 files changed, 10 insertions(+) diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 6346d959773f..d7482ec3f7d2 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -1,5 +1,10 @@ name: Static Analysis on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: python-linting: runs-on: ubuntu-20.04 diff --git a/.github/workflows/unit_tests.yml b/.github/workflows/unit_tests.yml index 1a8e16547f51..620535115d90 100644 --- a/.github/workflows/unit_tests.yml +++ b/.github/workflows/unit_tests.yml @@ -1,5 +1,10 @@ name: easyconfigs unit tests on: [push, pull_request] + +concurrency: + group: ${{format('{0}:{1}:{2}', github.repository, github.ref, github.workflow)}} + cancel-in-progress: true + jobs: test-suite: runs-on: ubuntu-20.04 From abd1f7187f7c4174fe2795f1ba5755ba05ec80fb Mon Sep 17 00:00:00 2001 From: Viktor Rehnberg Date: Mon, 28 Nov 2022 15:36:00 +0100 Subject: [PATCH 550/939] adding easyconfigs: phonopy-2.16.3-foss-2022a.eb --- .../p/phonopy/phonopy-2.16.3-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb new file mode 100644 index 000000000000..d06fecee5a29 --- /dev/null +++ b/easybuild/easyconfigs/p/phonopy/phonopy-2.16.3-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'phonopy' +version = '2.16.3' + +homepage = 'https://atztogo.github.io/phonopy/' +description = """Phonopy is an open source package of phonon calculations based on the supercell approach.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCE_TAR_GZ] +checksums = ['c536d355156626f26e5d5fd158b03e10c4a13c461d6a02a26b05e3b6311b9d79'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # for numpy + ('matplotlib', '3.5.2'), + ('PyYAML', '6.0'), + ('h5py', '3.7.0'), + ('spglib-python', '2.0.0'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_paths = { + 'files': ['bin/phonopy'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["phonopy --help"] + +sanity_pip_check = True + +moduleclass = 'lib' From f5b2e1e6a85cfc4aca8269869c75a5ec0ee26aed Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 28 Nov 2022 14:48:43 +0000 Subject: [PATCH 551/939] adding easyconfigs: SPOOLES-2.2-gompi-2021a.eb and patches: SPOOLES-2.2_build-mpi-mt.patch, SPOOLES-2.2_shared-libs.patch --- .../s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb | 43 ++++++++++++++++++ .../s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch | 38 ++++++++++++++++ .../s/SPOOLES/SPOOLES-2.2_shared-libs.patch | 45 +++++++++++++++++++ 3 files changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch create mode 100644 easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb new file mode 100644 index 000000000000..b521a3c9f8e7 --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb @@ -0,0 +1,43 @@ +# 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': '2021a'} + +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': 'a4abc168c660f4af55feb865c5559304a099755e2c46ebf09fabd83bb1636d2c'}, + {'SPOOLES-2.2_shared-libs.patch': '7b767a699679740ec2a4acd12e66c4a3656a276c354f61436e82cb4d448741f4'}, +] + +builddependencies = [ + ('Perl', '5.32.1', '-minimal'), +] + +#parallel = 1 + +build_cmd_targets = 'lib' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="$MPI_LIB_DIR" MPI_INCLUDE_DIR="$MPI_INC_DIR"' + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib'], +} + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch new file mode 100644 index 000000000000..59466c19b068 --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch @@ -0,0 +1,38 @@ +Author: Jasper Grimm +Description: build multithreaded, MPI targets by default +diff -Nru spooles-2.2.orig/MPI/makefile spooles-2.2.p1/MPI/makefile +--- spooles-2.2.orig/MPI/makefile 1998-12-17 15:47:44.000000000 +0000 ++++ spooles-2.2.p1/MPI/makefile 2022-11-25 16:07:34.000000000 +0000 +@@ -2,7 +2,7 @@ + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMPI.a ++ cd src ; make makeLib + + clean : + cd src ; make clean +diff -Nru spooles-2.2.orig/MPI/src/makefile spooles-2.2.p1/MPI/src/makefile +--- spooles-2.2.orig/MPI/src/makefile 1998-12-16 21:54:41.000000000 +0000 ++++ spooles-2.2.p1/MPI/src/makefile 2022-11-25 16:08:18.000000000 +0000 +@@ -42,3 +42,8 @@ + + clean : + - rm -f *.a *.o ++ ++makelib: ++ perl ../../makeLib > makeG ++ make -f makeG ++ rm -f makeG +diff -Nru spooles-2.2.orig/MT/makefile spooles-2.2.p1/MT/makefile +--- spooles-2.2.orig/MT/makefile 1998-12-17 15:47:48.000000000 +0000 ++++ spooles-2.2.p1/MT/makefile 2022-11-25 16:08:55.000000000 +0000 +@@ -2,7 +2,7 @@ + cd drivers ; make drivers + + lib : +- cd src ; make spoolesMT.a ++ cd src ; make makeLib + + clean : + cd src ; make clean diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch new file mode 100644 index 000000000000..d94230433834 --- /dev/null +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch @@ -0,0 +1,45 @@ +Author: Jasper Grimm +Description: add targets to build shared libraries +diff -Nru spooles-2.2.p1/makefile spooles-2.2.p2/makefile +--- spooles-2.2.p1/makefile 2022-11-25 16:06:54.000000000 +0000 ++++ spooles-2.2.p2/makefile 2022-11-25 16:14:28.000000000 +0000 +@@ -123,8 +123,10 @@ + cd Utilities ; make lib + cd ZV ; make lib + cd misc ; make lib +-#cd MPI ; make lib +-#cd MT ; make lib ++ MPI ; make lib ++ MT ; make lib ++ $(CC) -shared */*/*.lo -Wl,-soname,libspooles.so.2.2 -o libspooles.so.2.2 -lmpi -lpthread -lm ++ ln -s libspooles.so.2.2 libspooles.so + + global : + cd A2/src ; make -f makeGlobalLib +diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib +--- spooles-2.2.p1/makeLib 2022-11-25 16:06:54.000000000 +0000 ++++ spooles-2.2.p2/makeLib 2022-11-25 16:13:02.000000000 +0000 +@@ -64,14 +64,21 @@ + $srcname = " \\\n " . $src ; + print $srcname ; + } ++print "\n\n.SUFFIXES: .c .o .lo .a .so" ; + print "\n\nOBJ_FILES = \$\{SRC:.c=.o\}" ; ++print "\n\nLOBJ_FILES = \$\{SRC:.c=.lo\}" ; + print "\n\n" ; + print <<'EOF' ; + .c.o : +- $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o ++ $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o $(MPI_INCLUDE_DIR) + + ../../spooles.a : ${OBJ_FILES} + $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o ++.c.lo: ++ $(PURIFY) $(CC) -c $(CFLAGS) $*.c -fPIC -DPIC -o $(OBJ)_$*.lo $(MPI_INCLUDE_DIR) ++ ++../../libspooles.a : ${OBJ_FILES} ${LOBJ_FILES} ++ $(AR) $(ARFLAGS) ../../libspooles.a $(OBJ)_*.o + rm -f $(OBJ)_*.o +- $(RANLIB) ../../spooles.a ++ $(RANLIB) ../../linspooles.a + EOF From d9d2d73dfd816ac6b1831fb7ffe1ef69c84e23f8 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Mon, 28 Nov 2022 14:51:00 +0000 Subject: [PATCH 552/939] remove commented `parallel` parameter --- easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb index b521a3c9f8e7..1713aedf476d 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb @@ -1,5 +1,4 @@ # Author: Jasper Grimm (UoY) - easyblock = 'MakeCp' name = 'SPOOLES' @@ -28,8 +27,6 @@ builddependencies = [ ('Perl', '5.32.1', '-minimal'), ] -#parallel = 1 - build_cmd_targets = 'lib' buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="$MPI_LIB_DIR" MPI_INCLUDE_DIR="$MPI_INC_DIR"' From e647457943395ee0d5e67e29bf04c4fe22bf2b34 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Mon, 28 Nov 2022 17:03:44 +0000 Subject: [PATCH 553/939] adding easyconfigs: PyImageJ-1.3.1-foss-2021a.eb --- .../p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb b/easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb new file mode 100644 index 000000000000..d1e6fb65e8a3 --- /dev/null +++ b/easybuild/easyconfigs/p/PyImageJ/PyImageJ-1.3.1-foss-2021a.eb @@ -0,0 +1,60 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonBundle' + +name = 'PyImageJ' +version = '1.3.1' + +homepage = "https://pyimagej.readthedocs.io/" +description = """PyImageJ provides a set of wrapper functions for integration between ImageJ2 and Python. It also + supports the original ImageJ API and data structures. A major advantage of this approach is the ability to combine + ImageJ and ImageJ2 with other tools available from the Python software ecosystem, including NumPy, SciPy, + scikit-image, CellProfiler, OpenCV, ITK and many more.""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('Java', '11', '', SYSTEM), + ('Maven', '3.6.3', '', SYSTEM), + ('matplotlib', '3.4.2'), + ('Pillow', '8.2.0'), + ('scikit-image', '0.18.3'), + ('SciPy-bundle', '2021.05'), + ('xarray', '0.19.0'), +] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('setuptools', '61.3.1', { + 'checksums': ['88fafba4abc2f047e08a188fd4bbc10b0e464592c37b514c19f8f8f88d94450b'], + }), + ('imglyb', '2.0.1', { + 'checksums': ['ace14759bb4201e4b1b93ff4c4aa2c90e87e0bb22095160e205792be89fee929'], + }), + ('jgo', '1.0.5', { + 'checksums': ['48cfab8ec880692d93b22c42e0239f4792c009461c121c15549c456c6a6a4eb6'], + }), + ('JPype1', '1.4.1', { + 'modulename': 'jpype', + 'checksums': ['dc8ee854073474ad79ae168d90c2f6893854f58936cfa18f3587cadae0d3696d'], + }), + ('labeling', '0.1.13', { + 'checksums': ['908d5c247d75d368422c15d0b1efcb3b9d322d0c51cf436865bfb75ce5c829f4'], + }), + ('scyjava', '1.8.1', { + 'checksums': ['de94bf2f1569af0c5c41f38eade53930ae3d17dc584eed712fac6494a7f20efc'], + }), + (name, version, { + 'modulename': 'imagej', + 'source_tmpl': '%(namelower)s-%(version)s.tar.gz', + 'checksums': ['1328c1b380315a1feff7a42c558dc85a37964a6cd7cc2e5688ec0ce54bf3ac0a'], + }), +] + +sanity_check_commands = [ + """python -c 'import imagej; ij = imagej.init("2.5.0", mode="headless"); print(ij.getVersion())'""" +] + +moduleclass = 'vis' From d22f33188db10e850b2a14fd6bd60c6d276d1872 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 28 Nov 2022 20:41:41 +0100 Subject: [PATCH 554/939] add MAD support --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index 3216a7a24e75..c1e324f3ce3a 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -1,7 +1,5 @@ -# Institution: IT4Innovations National Supercomputing Center, Czech Republic -# Author: Jakub Kropacek -# License: GPLv3 -# Year: 2022 +# Contribution from IT4Innovations National Supercomputing Center, Czech Republic +# Jakub Kropacek, 2022 easyblock = 'ConfigureMake' @@ -23,6 +21,7 @@ builddependencies = [('binutils', '2.38')] dependencies = [ ('FLAC', '1.3.4'), ('LAME', '3.100'), + ('libmad', '0.15.1b'), ('libvorbis', '1.3.7'), ('FFmpeg', '5.0.1'), ] @@ -33,6 +32,4 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], } -sanity_check_commands = ['sox --help'] - moduleclass = 'data' From f797f9a82d82cf1c87303126f57b534b3e6d2805 Mon Sep 17 00:00:00 2001 From: easybuild Date: Mon, 28 Nov 2022 20:44:14 +0100 Subject: [PATCH 555/939] return sanity check --- easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb index c1e324f3ce3a..b009ef44f7fa 100644 --- a/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/s/SoX/SoX-14.4.2-GCCcore-11.3.0.eb @@ -32,4 +32,6 @@ sanity_check_paths = { 'dirs': ['bin', 'include', 'lib', 'lib/pkgconfig', 'share/man'], } +sanity_check_commands = ['sox --help'] + moduleclass = 'data' From 2c344125936d6ba3d90415c5e36f5b1c0bc744cc Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 29 Nov 2022 11:36:08 +0100 Subject: [PATCH 556/939] drop nodejs-16.15.1-GCCcore-11.3.0.eb from this PR, a better one had already been merged --- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 47 ------------------- 1 file changed, 47 deletions(-) delete mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb deleted file mode 100644 index 00b497b22e56..000000000000 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ /dev/null @@ -1,47 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'nodejs' -version = '16.15.1' # LTS on 2022-06-12 -local_libversion = '93' - -homepage = 'https://nodejs.org' -description = """Node.js is a platform built on Chrome's JavaScript runtime - for easily building fast, scalable network applications. Node.js uses an - event-driven, non-blocking I/O model that makes it lightweight and efficient, - perfect for data-intensive real-time applications that run across distributed devices.""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://nodejs.org/dist/v%(version)s/'] -sources = ['node-v%(version)s.tar.gz'] -checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] - -builddependencies = [ - ('binutils', '2.38'), - ('Python', '3.10.4', '-bare'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('ICU', '71.1'), -] - -configopts = [ - '--with-intl=system-icu', - '--shared --with-intl=system-icu', # Build libnode.so in a second run -] - -# Link libv8 libs to libnode -postinstallcmds = [ - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libnode.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libbase.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), - "cd %%(installdir)s/lib; ln -s libnode.%s.%s libv8_libplatform.%s" % (SHLIB_EXT, local_libversion, SHLIB_EXT), -] - -sanity_check_paths = { - 'files': ['bin/node', 'bin/npm', 'lib/libnode.%s.%s' % (SHLIB_EXT, local_libversion)], - 'dirs': ['lib/node_modules', 'include/node'] -} - -moduleclass = 'lang' From 3d63fa2a387d8fa5bc64d13372a334c40f20c372 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 29 Nov 2022 11:45:02 +0100 Subject: [PATCH 557/939] add nodejs-16.15.1 from develop to clear conflict. --- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..117331f1af84 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -0,0 +1,51 @@ +easyblock = 'ConfigureMake' + +name = 'nodejs' +version = '16.15.1' # LTS on 2022-06-12 +local_libversion = '93' + +homepage = 'https://nodejs.org' +description = """Node.js is a platform built on Chrome's JavaScript runtime + for easily building fast, scalable network applications. Node.js uses an + event-driven, non-blocking I/O model that makes it lightweight and efficient, + perfect for data-intensive real-time applications that run across distributed devices.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://nodejs.org/dist/v%(version)s/'] +sources = ['node-v%(version)s.tar.gz'] +checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('ICU', '71.1'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +# Use ICU and OpenSSL from EasyBuild +local_common_configopts = "--with-intl=system-icu --shared-openssl " + +configopts = [ + local_common_configopts, # Static build + '--shared %s' % local_common_configopts, # Build libnode.so in a second run +] + +# Link libv8 libs to libnode +local_extra_sonames = ['libnode', 'libv8', 'libv8_libbase', 'libv8_libplatform'] +local_extra_libs = ['%s.%s' % (x, SHLIB_EXT) for x in local_extra_sonames] +local_libnode_real = "libnode.%s.%s" % (SHLIB_EXT, local_libversion) + +postinstallcmds = [ + "cd %%(installdir)s/lib && ln -s %s %s" % (local_libnode_real, x) for x in local_extra_libs +] + +sanity_check_paths = { + 'files': ['bin/node', 'bin/npm'] + ['lib/%s' % x for x in [local_libnode_real] + local_extra_libs], + 'dirs': ['lib/node_modules', 'include/node'] +} + +moduleclass = 'lang' From 6017f5bad23ca3a12b701954950f165c2434c508 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 13:41:46 +0100 Subject: [PATCH 558/939] adding easyconfigs: memtester-4.5.1-GCCcore-11.3.0.eb --- .../memtester-4.5.1-GCCcore-11.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..7812a2d4fedb --- /dev/null +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'MakeCp' + +name = 'memtester' +version = '4.5.1' + +homepage = 'https://pyropus.ca./software/memtester/' +description = 'A userspace utility for testing the memory subsystem for faults' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://pyropus.ca./software/memtester/old-versions/'] +sources = [SOURCE_TAR_GZ] +checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] + +builddependencies = [ + ('binutils', '2.38'), +] + +files_to_copy = [(['memtester'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/memtester'], + 'dirs': [] +} + +moduleclass = 'tools' From 6ebd52a7d602583625c3d66174a45b3570f819ac Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 14:27:11 +0100 Subject: [PATCH 559/939] Switch to ubuntu mirror --- .../m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb index 7812a2d4fedb..06490ea807a4 100644 --- a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -8,10 +8,13 @@ description = 'A userspace utility for testing the memory subsystem for faults' toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://pyropus.ca./software/memtester/old-versions/'] -sources = [SOURCE_TAR_GZ] +# Using ubuntu source mirror due to problematic URL redirects +source_urls = ['http://archive.ubuntu.com/ubuntu/pool/universe/m/memtester/'] +sources = ['memtester_%(version)s.orig.tar.gz'] checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] +insecure_download = True + builddependencies = [ ('binutils', '2.38'), ] From de50989c691cdacbe189538fc89f2da383419702 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 29 Nov 2022 15:27:52 +0100 Subject: [PATCH 560/939] Remove faulty variable --- .../easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb index 06490ea807a4..901ab911bea7 100644 --- a/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/memtester/memtester-4.5.1-GCCcore-11.3.0.eb @@ -13,8 +13,6 @@ source_urls = ['http://archive.ubuntu.com/ubuntu/pool/universe/m/memtester/'] sources = ['memtester_%(version)s.orig.tar.gz'] checksums = ['1c5fc2382576c084b314cfd334d127a66c20bd63892cac9f445bc1d8b4ca5a47'] -insecure_download = True - builddependencies = [ ('binutils', '2.38'), ] From 532daf7e39105fb151f7d466c99c8b38e9f2cd4a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 08:34:40 +0100 Subject: [PATCH 561/939] add patches to correctly run Xvfb and to pick up MATLAB license from EB installed MATLAB if available --- .../matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 14 +++++++-- .../matlab-proxy-0.5.4_fix_xvfb_startup.patch | 31 +++++++++++++++++++ ...5.4_use_lic_from_eb_installed_matlab.patch | 28 +++++++++++++++++ 3 files changed, 71 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch create mode 100644 easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb index 6628aef39431..f043052deda3 100644 --- a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -24,7 +24,17 @@ sanity_pip_check = True exts_list = [ (name, version, { - 'checksums': ['534531135ae341bd86de6c18ce2694b38614deeedf57a57d4cba1d2079eb662e'], + 'patches': [ + '%(name)s-%(version)s_use_lic_from_eb_installed_matlab.patch', + '%(name)s-%(version)s_fix_xvfb_startup.patch', + ], + 'checksums': [ + {'matlab-proxy-0.5.4.tar.gz': '534531135ae341bd86de6c18ce2694b38614deeedf57a57d4cba1d2079eb662e'}, + {'matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch': + 'f3d30ac6b82667eff81b2b0999bdb9ee8083488fdfa3960c561e3bb046acaa41'}, + {'matlab-proxy-0.5.4_fix_xvfb_startup.patch': + '4f952d6e807830d8d6a138c90bbe74981a082569b6d4e1855c789a0f6ad3e4f6'}, + ], }), ] @@ -33,6 +43,6 @@ sanity_check_paths = { 'dirs': ['lib64/python%(pyshortver)s/site-packages'] } -modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately (2020b or later)' +modloadmsg = 'matlab-proxy requires MATLAB to be loaded separately and BEFORE this module (2020b or later)' moduleclass = 'math' diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch new file mode 100644 index 000000000000..fd099bb15f93 --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_fix_xvfb_startup.patch @@ -0,0 +1,31 @@ +Fix startup of Xvfb to use EB's Xvfb and don't empty the environment. + +Åke Sandgren, 2022-11-29 +diff -ru matlab-proxy-0.5.4.orig/matlab_proxy/settings.py matlab-proxy-0.5.4/matlab_proxy/settings.py +--- matlab-proxy-0.5.4.orig/matlab_proxy/settings.py 2022-11-10 08:39:50.000000000 +0100 ++++ matlab-proxy-0.5.4/matlab_proxy/settings.py 2022-11-29 17:12:54.429102236 +0100 +@@ -239,8 +246,11 @@ + # Allow child process to use the file descriptor created by parent. + os.set_inheritable(dpipe[1], True) + ++ xvfb = shutil.which("Xvfb") ++ if xvfb is None: ++ xvfb = "Xvfb" + xvfb_cmd = [ +- "Xvfb", ++ xvfb, + "-displayfd", + # Write descriptor + str(dpipe[1]), +diff -ru matlab-proxy-0.5.4.orig/matlab_proxy/util/mw.py matlab-proxy-0.5.4/matlab_proxy/util/mw.py +--- matlab-proxy-0.5.4.orig/matlab_proxy/util/mw.py 2022-11-10 08:39:50.000000000 +0100 ++++ matlab-proxy-0.5.4/matlab_proxy/util/mw.py 2022-11-29 16:49:14.415197842 +0100 +@@ -286,7 +286,7 @@ + # Creates subprocess asynchronously with environment variables defined in matlab_env + # Pipe errors, if any, to the process object instead of stdout. + xvfb = await asyncio.create_subprocess_exec( +- *xvfb_cmd, close_fds=False, env=env, stderr=asyncio.subprocess.PIPE ++ *xvfb_cmd, close_fds=False, stderr=asyncio.subprocess.PIPE + ) + + read_descriptor, write_descriptor = pipe diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch new file mode 100644 index 000000000000..1585cca459ff --- /dev/null +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4_use_lic_from_eb_installed_matlab.patch @@ -0,0 +1,28 @@ +Use the license file from EB's MATLAB installation by default +Author: Mikael Öhman micketeer@gmail.com +diff -ru matlab-proxy-0.5.4.orig/matlab_proxy/settings.py matlab-proxy-0.5.4/matlab_proxy/settings.py +--- matlab-proxy-0.5.4.orig/matlab_proxy/settings.py 2022-11-10 08:39:50.000000000 +0100 ++++ matlab-proxy-0.5.4/matlab_proxy/settings.py 2022-11-29 17:12:54.429102236 +0100 +@@ -130,6 +130,13 @@ + return settings + + else: ++ if mwi_env.get_env_name_network_license_manager() in os.environ: ++ license_file = os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ elif 'EBROOTMATLAB' in os.environ: ++ license_file = os.environ.get('EBROOTMATLAB') + '/licenses/network.lic' ++ else: ++ license_file = None ++ + matlab_startup_file = str( + Path(__file__).resolve().parent / "matlab" / "startup.m" + ) +@@ -172,7 +179,7 @@ + "mwapikey": str(uuid.uuid4()), + "matlab_protocol": "https", + "nlm_conn_str": mwi.validators.validate_mlm_license_file( +- os.environ.get(mwi_env.get_env_name_network_license_manager()) ++ license_file + ), + "matlab_config_file": mwi_config_folder / "proxy_app_config.json", + "ws_env": ws_env, From 544b780cd6af10c2bd48d07ff0f16c13fcdaa2ef Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Tue, 25 Oct 2022 12:59:43 +0200 Subject: [PATCH 562/939] adding easyconfigs: PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb, PyTorch-1.12.1-foss-2022a.eb and patches: PyTorch-1.12.1_fix-test_wishart_log_prob.patch, PyTorch-1.12.1_python-3.10-annotation-fix.patch, PyTorch-1.12.1_python-3.10-compat.patch, PyTorch-1.12.1_remove-flaky-test-in-testnn.patch --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 148 ++++++++++++++++++ .../p/PyTorch/PyTorch-1.12.1-foss-2022a.eb | 133 ++++++++++++++++ ...rch-1.12.1_fix-test_wishart_log_prob.patch | 36 +++++ ...ch-1.12.1_python-3.10-annotation-fix.patch | 69 ++++++++ .../PyTorch-1.12.1_python-3.10-compat.patch | 115 ++++++++++++++ ...h-1.12.1_remove-flaky-test-in-testnn.patch | 22 +++ 6 files changed, 523 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch 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 new file mode 100644 index 000000000000..7f1ab7e67f8f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,148 @@ +name = 'PyTorch' +version = '1.12.1' +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': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + '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', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('cuDNN', '8.4.1.50', '-CUDA-%(cudaver)s', SYSTEM), + ('magma', '2.6.2', '-CUDA-%(cudaver)s'), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), + ('expecttest', '0.1.3'), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '3.7', '5.2', '6.0', '6.1', '7.0', '7.2', '7.5', '8.0', '8.6'] + +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', + ] +} + +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 +# https://github.com/pytorch/pytorch/pull/87593 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' 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 new file mode 100644 index 000000000000..c31da6305720 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1-foss-2022a.eb @@ -0,0 +1,133 @@ +name = 'PyTorch' +version = '1.12.1' + +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': '2022a'} + +source_urls = [GITHUB_RELEASE] +sources = ['%(namelower)s-v%(version)s.tar.gz'] + +patches = [ + 'PyTorch-1.7.0_avoid-nan-in-test-torch.patch', + 'PyTorch-1.7.0_disable-dev-shm-test.patch', + 'PyTorch-1.10.0_fix-kineto-crash.patch', + 'PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch', + 'PyTorch-1.10.0_fix-test-model_dump.patch', + 'PyTorch-1.10.0_fix-vsx-vector-functions.patch', + 'PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch', + 'PyTorch-1.11.0_fix-fsdp-fp16-test.patch', + 'PyTorch-1.11.0_fix-test_utils.patch', + 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', + 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', + 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', + 'PyTorch-1.12.1_fix-skip-decorators.patch', + 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', + 'PyTorch-1.12.1_fix-test_wishart_log_prob.patch', + 'PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch', + 'PyTorch-1.12.1_fix-TestTorch.test_to.patch', + 'PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch', + 'PyTorch-1.12.1_fix-vsx-vector-funcs.patch', + 'PyTorch-1.12.1_fix-vsx-loadu.patch', + 'PyTorch-1.12.1_increase-test-adadelta-tolerance.patch', + 'PyTorch-1.12.1_increase-tolerance-test_ops.patch', + 'PyTorch-1.12.1_no-cuda-stubs-rpath.patch', + 'PyTorch-1.12.1_python-3.10-annotation-fix.patch', + 'PyTorch-1.12.1_python-3.10-compat.patch', + 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', + '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', +] +checksums = [ + '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz + 'b899aa94d9e60f11ee75a706563312ccefa9cf432756c470caa8e623991c8f18', # PyTorch-1.7.0_avoid-nan-in-test-torch.patch + '622cb1eaeadc06e13128a862d9946bcc1f1edd3d02b259c56a9aecc4d5406b8a', # PyTorch-1.7.0_disable-dev-shm-test.patch + # PyTorch-1.10.0_fix-kineto-crash.patch + 'dc467333b28162149af8f675929d8c6bf219f23230bfc0d39af02ba4f6f882eb', + # PyTorch-1.10.0_fix-test-dataloader-fixed-affinity.patch + '313dca681f45ce3bc7c4557fdcdcbe0b77216d2c708fa30a2ec0e22c44876707', + # PyTorch-1.10.0_fix-test-model_dump.patch + '339148ae1a028cda6e750ac93fa38a599f66c7abe26586c9219f1a206ea14557', + # PyTorch-1.10.0_fix-vsx-vector-functions.patch + '7bef5f96cb83b2d655d2f76dd7468a171d446f0b3e06da2232ec7f886484d312', + # PyTorch-1.10.0_skip-nnapi-test-without-qnnpack.patch + '34ba476a7bcddec323bf9eca083cb4623d0f569d081aa3add3769c24f22849d2', + 'bb1c4e6d6fd4b0cf57ff8b824c797331b533bb1ffc63f5db0bae3aee10c3dc13', # PyTorch-1.11.0_fix-fsdp-fp16-test.patch + '4f7e25c4e2eb7094f92607df74488c6a4a35849fabf05fcf6c3655fa3f44a861', # PyTorch-1.11.0_fix-test_utils.patch + # PyTorch-1.11.0_increase_c10d_gloo_timeout.patch + '20cd4a8663f74ab326fdb032b926bf5c7e94d9750c515ab9050927ba00cf1953', + # PyTorch-1.11.0_increase-distributed-test-timeout.patch + '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', + 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch + 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', + 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch + # PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch + '1efc9850c431d702e9117d4766277d3f88c5c8b3870997c9974971bce7f2ab83', + # PyTorch-1.12.1_fix-test_wishart_log_prob.patch + 'cf475ae6e6234b96c8d1bf917597c5176c94b3ccd940b72f2e1cd0c979580f45', + # PyTorch-1.12.1_fix-TestCudaFuser.test_unary_ops.patch + '8e6e844c6b0541e0c8115911ee1a9d548613254b36dfbdada202fd723fc26aa2', + '75f27987c3f25c501e719bd2b1c70a029ae0ee28514a97fe447516aee02b1535', # PyTorch-1.12.1_fix-TestTorch.test_to.patch + # PyTorch-1.12.1_fix-use-after-free-in-tensorpipe-agent.patch + '0bd7e88b92c4c6f0fecf01746009858ba19f2df68b10b88c41485328a531875d', + 'caccbf60f62eac313896c1eaec78b08f5d0fdfcb907079087490bb13d1561aa2', # PyTorch-1.12.1_fix-vsx-vector-funcs.patch + '8bfe3c94ada1dd1f7974a1261a8b576fb7ae944050fa1c7830fca033831123b2', # PyTorch-1.12.1_fix-vsx-loadu.patch + # PyTorch-1.12.1_increase-test-adadelta-tolerance.patch + '944ed1af5ad4bbe20cbb042764a88dad1eef6cd33218617cf3d4cd90c6764695', + # PyTorch-1.12.1_increase-tolerance-test_ops.patch + '1c1fa520801e2ee5faf56a3d6dc96321e7c11664fd16bffd7c6ee437e68357fb', + '2905826ca713752b47c84e4ec8b177c90cbd91fca498ba2ba546f495c4cf70a6', # PyTorch-1.12.1_no-cuda-stubs-rpath.patch + # PyTorch-1.12.1_python-3.10-annotation-fix.patch + '11e168fd429d9e156fc79dd806b08125f3640651ad9998abd810446b2ed0c2d7', + '81402420a878b40f824778f0333fbec6504325a6a1b06a22749c4cac3eaccf67', # PyTorch-1.12.1_python-3.10-compat.patch + # PyTorch-1.12.1_remove-flaky-test-in-testnn.patch + 'e81b678e354dd137c0d6d974605cdedbf672096fdbdf567c347bc2fbfc73471d', + # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch + 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', + '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch + # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch + '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', +] + +osdependencies = [OS_PKG_IBVERBS_DEV] + +builddependencies = [ + ('CMake', '3.23.1'), + ('hypothesis', '6.46.7'), +] + +dependencies = [ + ('Ninja', '1.10.2'), # Required for JIT compilation of C++ extensions + ('Python', '3.10.4'), + ('protobuf', '3.19.4'), + ('protobuf-python', '3.19.4'), + ('pybind11', '2.9.2'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('MPFR', '4.1.0'), + ('GMP', '6.2.1'), + ('numactl', '2.0.14'), + ('FFmpeg', '4.4.2'), + ('Pillow', '9.1.1'), + ('expecttest', '0.1.3'), +] + +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', + ] +} + +runtest = 'cd test && PYTHONUNBUFFERED=1 %(python)s run_test.py --continue-through-error --verbose %(excluded_tests)s' + +tests = ['PyTorch-check-cpp-extension.py'] + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch new file mode 100644 index 000000000000..c801b4ca53fa --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-test_wishart_log_prob.patch @@ -0,0 +1,36 @@ +Fix a TestDistributions.test_wishart_log_prob failure in test_distributions +See https://github.com/pytorch/pytorch/pull/87977 + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributions/test_distributions.py b/test/distributions/test_distributions.py +index 127018516e123..219eacf4790b0 100644 +--- a/test/distributions/test_distributions.py ++++ b/test/distributions/test_distributions.py +@@ -2036,7 +2036,7 @@ def test_lowrank_multivariate_normal_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_lowrank_multivariate_normal_sample(self): +@@ -2176,7 +2176,7 @@ def test_multivariate_normal_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_multivariate_normal_sample(self): +@@ -2331,7 +2331,7 @@ def test_wishart_log_prob(self): + unbatched_prob = torch.stack([dist_unbatched[i].log_prob(x[:, i]) for i in range(5)]).t() + + self.assertEqual(batched_prob.shape, unbatched_prob.shape) +- self.assertEqual(0.0, (batched_prob - unbatched_prob).abs().max(), atol=1e-3, rtol=0) ++ self.assertEqual(batched_prob, unbatched_prob, atol=1e-3, rtol=0) + + @unittest.skipIf(not TEST_NUMPY, "NumPy not found") + def test_wishart_sample(self): diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch new file mode 100644 index 000000000000..61f04d40743f --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-annotation-fix.patch @@ -0,0 +1,69 @@ +Handle change of type annotation handling in Python 3.10 in the JIT module. +Fixes failures in e.g. test_jit. + +From https://github.com/pytorch/pytorch/pull/81334 & https://github.com/pytorch/pytorch/pull/81506 +Backport: Alexander Grund (TU Dresden) + +diff --git a/torch/_jit_internal.py b/torch/_jit_internal.py +index 3c067d5c1c5..2cc3dba89b4 100644 +--- a/torch/_jit_internal.py ++++ b/torch/_jit_internal.py +@@ -1059,11 +1059,19 @@ def _get_named_tuple_properties(obj): + if field in obj._field_defaults] + else: + defaults = [] ++ # In 3.10 recommended way to get annotations is to call `inspect.get_annotations` function ++ # Also, annotations from base class are not inherited so they need to be queried explicitly ++ if sys.version_info[:2] < (3, 10): ++ obj_annotations = getattr(obj, '__annotations__', {}) ++ else: ++ obj_annotations = inspect.get_annotations(obj) ++ if len(obj_annotations) == 0 and hasattr(obj, "__base__"): ++ obj_annotations = inspect.get_annotations(obj.__base__) ++ + annotations = [] +- has_annotations = hasattr(obj, '__annotations__') + for field in obj._fields: +- if has_annotations and field in obj.__annotations__: +- the_type = torch.jit.annotations.ann_to_type(obj.__annotations__[field], fake_range()) ++ if field in obj_annotations: ++ the_type = torch.jit.annotations.ann_to_type(obj_annotations[field], fake_range()) + annotations.append(the_type) + else: + annotations.append(torch._C.TensorType.getInferred()) +diff --git a/torch/jit/_recursive.py b/torch/jit/_recursive.py +index 8175d14fe5d..aa36a4561d4 100644 +--- a/torch/jit/_recursive.py ++++ b/torch/jit/_recursive.py +@@ -5,6 +5,7 @@ import collections + import textwrap + import functools + import warnings ++import sys + from typing import Dict, List, Set, Type + + import torch._jit_internal as _jit_internal +@@ -134,7 +135,22 @@ def infer_concrete_type_builder(nn_module, share_types=True): + if isinstance(nn_module, (torch.nn.ParameterDict)): + concrete_type_builder.set_parameter_dict() + +- class_annotations = getattr(nn_module, '__annotations__', {}) ++ def get_annotations(obj): ++ if sys.version_info < (3, 10): ++ return getattr(obj, '__annotations__', {}) ++ # In Python-3.10+ it is recommended to use inspect.get_annotations ++ # See https://docs.python.org/3.10/howto/annotations.html ++ # But also, in 3.10 annotations from base class are not inherited ++ # by unannotated derived one, so they must be manually extracted ++ annotations = inspect.get_annotations(obj) ++ if len(annotations) > 0: ++ return annotations ++ cls = obj if isinstance(obj, type) else type(obj) ++ if len(cls.__bases__) == 0: ++ return {} ++ return inspect.get_annotations(cls.__bases__[0]) ++ ++ class_annotations = get_annotations(nn_module) + if isinstance(nn_module, (torch.ao.quantization.QuantWrapper)): + class_annotations = {} + diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch new file mode 100644 index 000000000000..957a31669b00 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_python-3.10-compat.patch @@ -0,0 +1,115 @@ +Fixes some compatibility issues with Python 3.10 + +Most notably conversion from float to long which avoids: + TypeError: 'float' object cannot be interpreted as an integer +Also some test failures in test_fx & test_jit due to differences in Python 3.10. + +From https://github.com/pytorch/pytorch/pull/82329 +Backported: Alexander Grund (TU Dresden) + +diff --git a/test/jit/test_hash.py b/test/jit/test_hash.py +index cb1c1544b10..2ca1e9cda0a 100644 +--- a/test/jit/test_hash.py ++++ b/test/jit/test_hash.py +@@ -75,7 +75,10 @@ class TestHash(JitTestCase): + self.checkScript(fn, (1.2345, float("inf"))) + self.checkScript(fn, (float("inf"), float("inf"))) + self.checkScript(fn, (1.2345, float('nan'))) +- self.checkScript(fn, (float("nan"), float("nan"))) ++ if sys.version_info < (3, 10): ++ # Hash of two nans are not guaranteed to be equal. From https://docs.python.org/3/whatsnew/3.10.html : ++ # Hashes of NaN values of both float type and decimal.Decimal type now depend on object identity. ++ self.checkScript(fn, (float("nan"), float("nan"))) + self.checkScript(fn, (float("nan"), float("inf"))) + + def test_hash_int(self): +diff --git a/test/test_fx.py b/test/test_fx.py +index 625614d29a8..307b629cab3 100644 +--- a/test/test_fx.py ++++ b/test/test_fx.py +@@ -3280,6 +3280,7 @@ class TestFX(JitTestCase): + .run(scripted.code) + + @unittest.skipIf(IS_WINDOWS, "Python Windows bug? https://bugs.python.org/issue45108") ++ @unittest.skipIf(sys.version_info >= (3, 10), "Does not work on Python-3.10") + def test_assert(self): + def f(x): + assert x > 1 +@@ -4017,7 +4018,7 @@ class TestFunctionalTracing(JitTestCase): + + def functional_test(self): + if func_name in self.UNTRACEABLE_FUNCTIONALS_PY38 and \ +- sys.version_info >= (3, 8) and sys.version_info < (3, 10): ++ sys.version_info >= (3, 8) and sys.version_info < (3, 11): + exc, err = self.UNTRACEABLE_FUNCTIONALS_PY38[func_name] + with self.assertRaisesRegex(exc, err): + symbolic_trace(fn) +diff --git a/test/test_jit.py b/test/test_jit.py +index 7dbae135a9a..ea436482a55 100644 +--- a/test/test_jit.py ++++ b/test/test_jit.py +@@ -7450,6 +7450,9 @@ a") + # tensor from empty list is type float in python and annotated type in torchscript + if "annotate" in li and "dtype" not in option: + continue ++ # Skip unsigned tensor initializaton for signed values on 3.10 ++ if sys.version_info[:2] >= (3, 10) and "torch.uint8" in option and "-" in li: ++ continue + code = tensor_template.format(list_create=li, tensor_op=op, options=option) + scope = {} + exec(code, globals(), scope) +diff --git a/torch/csrc/utils/python_scalars.h b/torch/csrc/utils/python_scalars.h +index 7f454bdff82..7df0662fa2c 100644 +--- a/torch/csrc/utils/python_scalars.h ++++ b/torch/csrc/utils/python_scalars.h +@@ -1,6 +1,7 @@ + #pragma once + + #include ++#include + #include + + #include +@@ -8,13 +9,37 @@ + + namespace torch { namespace utils { + ++template ++inline T unpackIntegral(PyObject* obj, const char* type) { ++#if PY_VERSION_HEX >= 0x030a00f0 ++ // In Python-3.10 floats can no longer be silently converted to integers ++ // Keep backward compatible behavior for now ++ if (PyFloat_Check(obj)) { ++ return c10::checked_convert(THPUtils_unpackDouble(obj), type); ++ } ++ return c10::checked_convert(THPUtils_unpackLong(obj), type); ++#else ++ return static_cast(THPUtils_unpackLong(obj)); ++#endif ++} ++ + inline void store_scalar(void* data, at::ScalarType scalarType, PyObject* obj) { + switch (scalarType) { +- case at::kByte: *(uint8_t*)data = (uint8_t)THPUtils_unpackLong(obj); break; +- case at::kChar: *(int8_t*)data = (int8_t)THPUtils_unpackLong(obj); break; +- case at::kShort: *(int16_t*)data = (int16_t)THPUtils_unpackLong(obj); break; +- case at::kInt: *(int32_t*)data = (int32_t)THPUtils_unpackLong(obj); break; +- case at::kLong: *(int64_t*)data = THPUtils_unpackLong(obj); break; ++ case at::kByte: ++ *(uint8_t*)data = unpackIntegral(obj, "uint8"); ++ break; ++ case at::kChar: ++ *(int8_t*)data = unpackIntegral(obj, "int8"); ++ break; ++ case at::kShort: ++ *(int16_t*)data = unpackIntegral(obj, "int16"); ++ break; ++ case at::kInt: ++ *(int32_t*)data = unpackIntegral(obj, "int32"); ++ break; ++ case at::kLong: ++ *(int64_t*)data = unpackIntegral(obj, "int64"); ++ break; + case at::kHalf: + *(at::Half*)data = at::convert(THPUtils_unpackDouble(obj)); + break; diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch new file mode 100644 index 000000000000..31d44fb01d14 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_remove-flaky-test-in-testnn.patch @@ -0,0 +1,22 @@ +This test is flaky when run with the type float16. +I.e. TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int32_int32_float16 & + TestNNDeviceTypeCPU.test_embedding_bag_device_cpu_int64_int64_float16 +fail. +See https://github.com/pytorch/pytorch/issues/86638 +So remove the half precision test. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/test_nn.py b/test/test_nn.py +index aad884ebd4f..b514f72a3e9 100644 +--- a/test/test_nn.py ++++ b/test/test_nn.py +@@ -18236,7 +18236,7 @@ class TestNNDeviceType(NNTestCase): + self.assertRaises(RuntimeError, lambda: es(input.view(-1), offset)) + + @skipMeta +- @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double, torch.half))) ++ @dtypes(*itertools.product((torch.int, torch.long), (torch.int, torch.long), (torch.float, torch.double))) + def test_embedding_bag_device(self, device, dtypes): + self._test_EmbeddingBag(device, 'sum', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) + self._test_EmbeddingBag(device, 'mean', False, wdtype=dtypes[2], dtype=dtypes[0], odtype=dtypes[1]) From 8ee368d5a36f73e2e13a2da77a18c0f4d6238746 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Wed, 30 Nov 2022 10:09:28 +0100 Subject: [PATCH 563/939] Add Molden-7.1 --- .../m/Molden/Molden-7.1-GCCcore-11.3.0.eb | 48 +++++++++++ .../Molden/Molden-7.1_fix_arg_handling.patch | 24 ++++++ ...olden-7.1_fix_makefile_for_easybuild.patch | 82 +++++++++++++++++++ .../makedepend-1.0.7-GCCcore-11.3.0.eb | 26 ++++++ 4 files changed, 180 insertions(+) create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch create mode 100644 easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch create mode 100644 easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..305f84282e94 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +easyblock = 'MakeCp' + +name = 'Molden' +version = '7.1' + +homepage = 'https://www3.cmbi.umcn.nl/molden' +description = """Molden is a package for displaying Molecular Density from the + Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical + packages Mopac/Ampac""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden'] +sources = ['%(namelower)s%(version)s.tar.gz'] +patches = [ + 'Molden-7.1_fix_makefile_for_easybuild.patch', + 'Molden-7.1_fix_arg_handling.patch', +] +checksums = [ + '98a39f0aa1667c14c36f40c0251522984245e5ba282af8fbc8a2f06079e40d43', # molden7.1.tar.gz + '78c9dd75fdc4c62392bb4284c377fbfd8bdae51f3f867540266723c3a978789c', # Molden-7.1_fix_makefile_for_easybuild.patch + 'e69941737369ec76049b4bd5d0e008d1e200b7043e44dae83ae058144699e924', # Molden-7.1_fix_arg_handling.patch +] + +builddependencies = [ + ('binutils', '2.38'), + ('makedepend', '1.0.7'), +] + +dependencies = [ + ('X11', '20220504'), + ('libglvnd', '1.4.0'), + ('libGLU', '9.0.2'), +] + +buildopts = 'CC="$CC" FC="$F90" FFLAGS="$FFLAGS -fallow-argument-mismatch" all' + +parallel = 1 + +files_to_copy = [(['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']], 'bin'), + 'CopyRight', 'README', 'REGISTER'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ambfor', 'ambmd', 'gmolden', 'molden', 'surf']] + ['README', 'REGISTER'], + 'dirs': [], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch new file mode 100644 index 000000000000..e01ce216125a --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_arg_handling.patch @@ -0,0 +1,24 @@ +# Use F2003 functions for argument handling. +# Author: maxim-masterv (SURF) +diff -Nru molden7.1.orig/src/molden.f molden7.1/src/molden.f +--- molden7.1.orig/src/molden.f 2022-05-06 22:35:25.000000000 +0200 ++++ molden7.1/src/molden.f 2022-11-29 20:17:13.900597108 +0100 +@@ -3813,15 +3813,15 @@ + endif + + iredir = 0 +- nargs = iargc() +- call getarg(0,liris) ++ nargs = COMMAND_ARGUMENT_COUNT() ++ call GET_COMMAND_ARGUMENT(0,liris) + call parsfn(liris,linlen(liris),20) + + ntargs = 0 + n = 0 + if (nargs.gt.0) then + 2013 n = n + 1 +- call getarg(n,liris) ++ call GET_COMMAND_ARGUMENT(n,liris) + if (liris(1:1).eq.'-') then + if (liris(1:2).eq.'-5') ido5d = 1 + if (liris(1:2).eq.'-7') ido7f = 1 diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch new file mode 100644 index 000000000000..b02b9c70f558 --- /dev/null +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1_fix_makefile_for_easybuild.patch @@ -0,0 +1,82 @@ +# Make makefile EasyBuild friendly. +# Author: maxim-masterov (SURF) +diff -Nru molden7.1.orig/makefile molden7.1/makefile +--- molden7.1.orig/makefile 2022-01-21 12:28:48.000000000 +0100 ++++ molden7.1/makefile 2022-11-29 20:26:40.997854074 +0100 +@@ -13,10 +13,10 @@ + # Disregard compiler warnings on rdmolf.f + # + # +-CC = cc ++#CC = cc + LIBS = -lX11 -lm + LDR = ${FC} +-LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lXmu -lX11 -lm ++LIBSG = -lGLU -lGL -lXmu -lX11 -lm + ARCH := $(shell getconf LONG_BIT) + AFLAG= -m$(ARCH) + EXTEN= +@@ -29,20 +29,6 @@ + uname := $(shell uname -s) + os := + +-ifeq ($(uname), Linux) +- os := $(shell head -n 1 /etc/issue | cut -d" " -f1) +- ifeq ($(os), Ubuntu) +- EXTEN = exten +- EXTENZ = exten2 +- LIBSG = -L/usr/X11R6/lib -lGLU -lGL -lX11 -lm +- endif +- ifeq ($(os), Debian) +- LIBSG = -L/usr/lib/X11 -lGLU -lGL -lX11 -lm +- endif +- +- choosefc := 'yes' +-endif +- + ifneq (,$(findstring CYGWIN,$(uname))) + uname := Linux + choosefc := 'yes' +@@ -52,18 +38,6 @@ + choosefc := 'yes' + endif + +- +-ifneq ($(choosefc), $(empty)) +- comg77 := $(shell which g77 | grep -i g77) +- comgfort := $(shell which gfortran | grep -i gfortran) +- ifneq ($(comg77), $(empty)) +- FC = g77 +- endif +- ifneq ($(comgfort), $(empty)) +- FC = gfortran +- endif +-endif +- + print-% : ; @echo $* = $($*) + # + # Linux version +@@ -108,17 +82,17 @@ + EXT = ${EXTRAZ} + endif + FFLAGS = -g ${AFLAG} +-LIBS = -L/usr/X11R6/lib -lX11 -lm ++LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +-LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++LIBS = -lX11 -lm + endif + LDR = ${FC} -g ${AFLAG} +-CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -I/usr/X11R6/include -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++CFLAGS = ${AFLAG} ${EXTRAZ} -c -g -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 + ifeq ($(os), Debian) +- CFLAGS = ${AFLAG} ${EXTRAZ} -c -I/usr/include/X11 -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 +- LIBS = -L/usr/lib/X11 -lX11 -lm ++ CFLAGS = ${AFLAG} ${EXTRAZ} -c -DDOBACK -DHASTIMER -DCOLOR_OFFSET=0.0 ++ LIBS = -lX11 -lm + ifeq ($(AFLAG),"-m64") +- LIBS = -L/usr/X11R6/lib64 -lX11 -lm ++ LIBS = -lX11 -lm + endif + endif + ifeq ($(os), FreeBSD) diff --git a/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..375e2d9f2a71 --- /dev/null +++ b/easybuild/easyconfigs/m/makedepend/makedepend-1.0.7-GCCcore-11.3.0.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'makedepend' +version = '1.0.7' + +homepage = 'https://linux.die.net/man/1/makedepend' +description = "The makedepend package contains a C-preprocessor like utility to determine build-time dependencies." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [XORG_UTIL_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['17c1adf0284aaee473abfff0e8d3e754770615e1275f2a0043b9d97a00ed5cc9'] + +builddependencies = [ + ('binutils', '2.38'), + ('xproto', '7.0.31'), + ('xorg-macros', '1.19.3'), +] + +sanity_check_paths = { + 'files': ['bin/makedepend'], + 'dirs': [], +} + +moduleclass = 'devel' From e3b48de3343a89fbb35f09ae7257bf6c54607687 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Nov 2022 10:14:19 +0100 Subject: [PATCH 564/939] adding easyconfigs: PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb --- ...0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb new file mode 100644 index 000000000000..27fbf46a6064 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Geometric/PyTorch-Geometric-2.1.0-foss-2021a-PyTorch-1.12.1-CUDA-11.3.1.eb @@ -0,0 +1,60 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Geometric' +version = '2.1.0' +local_pytorchver = '1.12.1' +versionsuffix = '-PyTorch-%s-CUDA-%%(cudaver)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': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', SYSTEM), + ('PyTorch', local_pytorchver, '-CUDA-%(cudaver)s'), + ('scikit-learn', '0.24.2'), + ('scikit-image', '0.18.3'), + ('numba', '0.53.1'), + ('h5py', '3.2.1'), + ('tqdm', '4.61.2'), + ('RDFlib', '6.2.0'), + ('ASE', '3.22.0'), + ('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 7bcc8094ce3db34b1457f35102f1900eccff975a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 10:27:37 +0100 Subject: [PATCH 565/939] adding easyconfigs: GlobalArrays-5.8.2-intel-2022a.eb --- .../GlobalArrays-5.8.2-intel-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb 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 new file mode 100644 index 000000000000..4af8e53447de --- /dev/null +++ b/easybuild/easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 'GlobalArrays' +version = '5.8.2' + +homepage = 'https://hpc.pnl.gov/globalarrays' +description = "Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] +sources = ['v%(version)s/ga-%(version)s.tar.gz'] + +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 += '-lmkl_sequential -lmkl_core -lmkl_blacs_intelmpi_ilp64 -lpthread -lm -ldl"' + +# select armci network as (Comex) MPI-1 two-sided +configopts += ' --with-mpi-ts' + +sanity_check_paths = { + 'files': ['bin/adjust.x', 'bin/collisions.x', 'bin/ga-config', 'lib/libarmci.a', + 'lib/libcomex.a', 'lib/libga.a'], + 'dirs': ['include'], +} + +moduleclass = 'lib' From 94b168c6396d4713b4e96b679e54bac2b6a127ad Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 30 Nov 2022 10:48:53 +0100 Subject: [PATCH 566/939] Fix ftp address --- easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb index 305f84282e94..5a87cef7f183 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb @@ -10,7 +10,7 @@ description = """Molden is a package for displaying Molecular Density from the toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['ftp://ftp.cmbi.umcn.nl/pub/molgraph/molden'] +source_urls = ['https://ftp.science.ru.nl/Molden/'] sources = ['%(namelower)s%(version)s.tar.gz'] patches = [ 'Molden-7.1_fix_makefile_for_easybuild.patch', From 93fddda86a3291b8dc66f36dfedfe34283b1145d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 10:52:04 +0100 Subject: [PATCH 567/939] add missing checksums --- .../easyconfigs/g/GlobalArrays/GlobalArrays-5.8.2-intel-2022a.eb | 1 + 1 file changed, 1 insertion(+) 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 4af8e53447de..435986d2ef92 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 @@ -11,6 +11,7 @@ toolchainopts = {'usempi': True} source_urls = ['https://github.com/GlobalArrays/ga/releases/download/'] 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"' From 2d7958b4c6ad394947f684cffab73969af003db5 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 30 Nov 2022 11:38:43 +0100 Subject: [PATCH 568/939] adding easyconfigs: OpenMolcas-22.10-intel-2022a.eb, OpenMolcas-22.10-intel-2022a-noGA.eb --- .../OpenMolcas-22.10-intel-2022a-noGA.eb | 47 ++++++++++++++++++ .../OpenMolcas-22.10-intel-2022a.eb | 48 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb create mode 100644 easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb new file mode 100644 index 000000000000..a173700d9902 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb @@ -0,0 +1,47 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '22.10' +versionsuffix = '-noGA' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = """OpenMolcas is a quantum chemistry software package. +This build does not support MPI and can only be run on a single node.""" + +toolchain = {'name': 'intel', 'version': '2022a'} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] +patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] +checksums = [ + {'OpenMolcas-v22.10.tar.gz': 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658'}, + {'OpenMolcas-21.06_mcpdft_deps.patch': '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('HDF5', '1.12.2'), +] + +build_shared_libs = True + +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' +configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' +configopts += '-DMPI=OFF -DGA=OFF ' + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb new file mode 100644 index 000000000000..62257a69fe82 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -0,0 +1,48 @@ +easyblock = 'CMakeMake' + +name = 'OpenMolcas' +version = '22.10' + +homepage = "https://gitlab.com/Molcas/OpenMolcas" +description = "OpenMolcas is a quantum chemistry software package." + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://gitlab.com/Molcas/OpenMolcas/-/archive/v%(version)s/'] +sources = ["OpenMolcas-v%(version)s.tar.gz"] +patches = ['OpenMolcas-21.06_mcpdft_deps.patch'] +checksums = [ + {'OpenMolcas-v22.10.tar.gz': 'd1d3d6c9bd69486c36f5285a51ac18e75c03540c5b33751855e94abc764d9658'}, + {'OpenMolcas-21.06_mcpdft_deps.patch': '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('HDF5', '1.12.2'), + ('GlobalArrays', '5.8.2'), +] + +build_shared_libs = True + +preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' +configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' +configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' +configopts += '-DMPI=ON -DGA=ON ' + +modextrapaths = {'PATH': ''} +modextravars = { + 'MOLCAS': '%(installdir)s', + 'MOLCAS_DRIVER': '%(installdir)s/pymolcas', + 'MOLCAS_SOURCE': '%(installdir)s', +} + +sanity_check_paths = { + 'files': ['bin/dynamix.exe', 'bin/mpprop.exe', 'lib/libmolcas.%s' % SHLIB_EXT, + 'sbin/help_basis', 'pymolcas'], + 'dirs': ['data/', 'basis_library/'], +} + +moduleclass = 'chem' From 8d27d191d89eb52c703f9b133b39428a3c78a50c Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Wed, 30 Nov 2022 13:38:57 +0100 Subject: [PATCH 569/939] adding easyconfigs: MEMOTE-0.13.0-foss-2021a.eb --- .../m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb | 134 ++++++++++++++++++ 1 file changed, 134 insertions(+) create mode 100644 easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb diff --git a/easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb b/easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb new file mode 100644 index 000000000000..9483459e6fdb --- /dev/null +++ b/easybuild/easyconfigs/m/MEMOTE/MEMOTE-0.13.0-foss-2021a.eb @@ -0,0 +1,134 @@ +## +# 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 = 'PythonBundle' + +name = 'MEMOTE' +version = '0.13.0' + +homepage = 'https://github.com/opencobra/memote' +description = """The genome-scale metabolic model test suite""" +# software_license = 'LicenseApachev2' + +toolchain = {'name': 'foss', 'version': '2021a'} + +dependencies = [ + ('Python', '3.9.5'), + ('COBRApy', '0.26.0'), + ('GitPython', '3.1.18'), + ('boto3', '1.20.13'), + ('openpyxl', '3.0.7'), + ('PyYAML', '5.4.1'), +] + +use_pip = True + +exts_list = [ + ('click-configfile', '0.2.3', { + 'checksums': ['95beec13bee950e98f43c81dcdabef4f644091559ea66298f9dadf59351d90d1'], + }), + ('click-log', '0.4.0', { + 'checksums': ['3970f8570ac54491237bcdb3d8ab5e3eef6c057df29f8c3d1151a51a9c23b975'], + }), + ('binaryornot', '0.4.4', { + 'checksums': ['359501dfc9d40632edc9fac890e19542db1a287bbcfa58175b66658392018061'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('jinja2-time', '0.2.0', { + 'checksums': ['d14eaa4d315e7688daa4969f616f226614350c48730bfa1692d2caebd8c90d40'], + }), + ('text-unidecode', '1.3', { + 'checksums': ['bad6603bb14d279193107714b288be206cac565dfa49aa5b105294dd5c4aab93'], + }), + ('python-slugify', '7.0.0', { + 'modulename': 'slugify', + 'checksums': ['7a0f21a39fa6c1c4bf2e5984c9b9ae944483fd10b54804cb0e23a3ccd4954f0b'], + }), + ('cookiecutter', '2.1.1', { + 'checksums': ['f3982be8d9c53dac1261864013fdec7f83afd2e42ede6f6dd069c5e149c540d5'], + }), + ('numpydoc', '1.1.0', { + 'checksums': ['c36fd6cb7ffdc9b4e165a43f67bf6271a7b024d0bb6b00ac468c9e2bfc76448e'], + }), + ('click-default-group', '1.2.2', { + 'checksums': ['d9560e8e8dfa44b3562fbc9425042a0fd6d21956fcc2db0077f63f34253ab904'], + }), + ('jsonpointer', '2.3', { + 'checksums': ['97cba51526c829282218feb99dab1b1e6bdf8efd1c43dc9d57be093c0d69c99a'], + }), + ('datapackage', '1.15.2', { + 'checksums': ['1e91a18c866914dea0acfe2aec785e6ec583c33766b0682c740b30bb7de88c58'], + }), + ('simpleeval', '0.9.12', { + 'checksums': ['3e0be507486d4e21cf9d08847c7e57dd61a1603950399985f7c5a0be7fd33e36'], + }), + ('statistics', '1.0.3.5', { + 'checksums': ['2dc379b80b07bf2ddd5488cad06b2b9531da4dd31edb04dc9ec0dc226486c138'], + }), + ('greenlet', '2.0.1', { + 'checksums': ['42e602564460da0e8ee67cb6d7236363ee5e131aa15943b6670e44e5c2ed0f67'], + }), + ('SQLAlchemy', '1.4.44', { + 'modulename': 'sqlalchemy', + 'checksums': ['2dda5f96719ae89b3ec0f1b79698d86eb9aecb1d54e990abb3fdd92c04b46a90'], + }), + ('unicodecsv', '0.14.1', { + 'checksums': ['018c08037d48649a0412063ff4eda26eaa81eff1546dbffa51fa5293276ff7fc'], + }), + ('ijson', '3.1.4', { + 'checksums': ['1d1003ae3c6115ec9b587d29dd136860a81a23c7626b682e2b5b12c9fd30e4ea'], + }), + ('jsonlines', '3.1.0', { + 'checksums': ['2579cb488d96f815b0eb81629e3e6b0332da0962a18fa3532958f7ba14a5c37f'], + }), + ('linear-tsv', '1.1.0', { + 'modulename': 'tsv', + 'checksums': ['b504d78f4075615ae75de86a16e5680701a441fc84da2a2cf9f94351ab1ccbf5'], + }), + ('tabulator', '1.53.5', { + 'checksums': ['0e2887d0b36483a292e75b118d7f03e710c1337435553b5f62d2a7a891b7fe55'], + }), + ('cached-property', '1.5.2', { + 'checksums': ['9fa5755838eecbb2d234c3aa390bd80fbd3ac6b6869109bfc1b499f7bd89a130'], + }), + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('tableschema', '1.20.2', { + 'checksums': ['cfa3b0aa1c0941002384c6288794f9488cb5ea9188cf84ac700d17758cb036e7'], + }), + ('goodtables', '2.5.4', { + 'checksums': ['67c51ac98967684763adb6406f92a683571d144b3a80095b0351a65f49848027'], + }), + ('pylru', '1.2.1', { + 'checksums': ['47ad140a63ab9389648dadfbb4330700e0ffeeb28ec04664ee47d37ed133b0f4'], + }), + ('pyperclip', '1.6.0', { + 'checksums': ['ce829433a9af640e08ee89b20f7c62132714bcc5d77df114044d0fccb8c3b3b8'], + }), + ('travis-encrypt', '1.1.2', { + 'modulename': 'travis', + 'checksums': ['0eaec20d99fb7a6051dae39195a51d81c365097675ad921d6c6381eabf014ce5'], + }), + ('memote', version, { + 'checksums': ['574620e67e461c6a2003ecd2c9bda01cafe5919c4c6f1653e382b9d74d8af05c'], + }), +] + +sanity_check_paths = { + 'files': ['bin/memote'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["memote"] + +sanity_pip_check = True + +moduleclass = 'bio' From 5c8a45e5eafabd1f491f8661cfafd8b68c25afb3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 30 Nov 2022 15:54:42 +0100 Subject: [PATCH 570/939] add numbat extension and requires dependencies to R-bundle-Bioconductor 3.15 + R 4.2.1 --- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 12 +++++++++ .../easyconfigs/r/R/R-4.2.1-foss-2022a.eb | 27 +++++++++++++++++++ 2 files changed, 39 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 118a0158da36..5566af30766c 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1101,6 +1101,18 @@ exts_list = [ ('scDblFinder', '1.10.0', { 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], }), + ('treeio', '1.20.2', { + 'checksums': ['a103a6953abf2014bd1bb8b2da4f2d7375bab338724d0bf864085981a85fd5cb'], + }), + ('ggtree', '3.4.4', { + 'checksums': ['c59f4879b4e4ee1a24d61bbec9bfddced3a7a6a747c9bc537bf2c84c2ca43840'], + }), + ('scistreer', '1.0.1', { + 'checksums': ['cb2461cb97a844a1cbdd9e5ecc1961ada0fc3ef186313c73cb07658a887a16dd'], + }), + ('numbat', '1.1.0', { + 'checksums': ['3cdda07de7329e6c886a1f60b2978bb776b04133080e97d82d5772fd666efc2c'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} 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 3e4080c1ebfb..3065e42243c7 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 @@ -3367,6 +3367,33 @@ exts_list = [ ('HGNChelper', '0.8.1', { 'checksums': ['aa3f0b3a8691ed93d63bec8f36d2954c6fcfd0b8b3efc705379248544c999363'], }), + ('logger', '0.2.2', { + 'checksums': ['4f1be7d4381f2fc591f19fdbfb8f3cccbf26c9fdbae104612f6e6d5762a97e22'], + }), + ('parallelDist', '0.2.6', { + 'checksums': ['30c6b3b85cf78c04a7dcd17ea7ed64356971f6ce48d15794078a18c53b249e06'], + }), + ('roptim', '0.1.6', { + 'checksums': ['7ef0c2a2ddb3703efaabf337fa0026485875d5ffb35ba3ef5d60eb0c62c30686'], + }), + ('yulab.utils', '0.0.5', { + 'checksums': ['6ecd4dc5dae40e86b7a462fdac3ab8c0b276dcae5a284eb43390a05b01e3056b'], + }), + ('ggfun', '0.0.9', { + 'checksums': ['5c740e9d1e73b77658f41ed65e21492f4e71b12c7c9ff4b9e52ebf5f8f197612'], + }), + ('gridGraphics', '0.5-1', { + 'checksums': ['29086e94e63891884c933b186b35511aac2a2f9c56967a72e4050e2980e7da8b'], + }), + ('ggplotify', '0.1.0', { + 'checksums': ['178f73d6d3dc391c3efb1a62c95fe38587044f9e3288dffb915d3687941bb38a'], + }), + ('aplot', '0.1.9', { + 'checksums': ['af0763620a757571caac769bad5398c22a4890af6cb5646ac5fa9039a114bb12'], + }), + ('tidytree', '0.4.1', { + 'checksums': ['fbc4364d17e1b1c26ed06af0cdf36c88a5bc562fdbd4731ab179e30bba4009eb'], + }), ] moduleclass = 'lang' From f1201d60610dd411c8364e2d990ddddcbf554730 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 30 Nov 2022 18:41:41 +0100 Subject: [PATCH 571/939] adding easyconfigs: STAR-CCM+-17.06.007.eb, STAR-CCM+-17.06.007-r8.eb --- .../s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb | 14 ++++++++++++++ .../easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb | 13 +++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb create mode 100644 easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb new file mode 100644 index 000000000000..4a95d4c1766f --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007-r8.eb @@ -0,0 +1,14 @@ +name = 'STAR-CCM+' +version = '17.06.007' +versionsuffix = '-r8' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%%(name)s%%(version)s_01_linux-x86_64%s.tar.gz' % versionsuffix] +checksums = ['d6417d2b778afb5e7222d0bf174e335c158b418f530f2e860cae32d1a48e4bfa'] + +moduleclass = 'cae' diff --git a/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb new file mode 100644 index 000000000000..bace577350af --- /dev/null +++ b/easybuild/easyconfigs/s/STAR-CCM+/STAR-CCM+-17.06.007.eb @@ -0,0 +1,13 @@ +name = 'STAR-CCM+' +version = '17.06.007' + +homepage = 'https://mdx.plm.automation.siemens.com/star-ccm-plus' +description = """STAR-CCM+ is a multiphysics computational fluid dynamics (CFD) software for the simulation of products +operating under real-world conditions.""" + +toolchain = SYSTEM + +sources = ['%(name)s%(version)s_01_linux-x86_64.tar.gz'] +checksums = ['b8c9d142deffde4ff9e9d8524cc2dc20e9f0035238b0ecebb8ea25e594c9165b'] + +moduleclass = 'cae' From 38f3860ad81cc321a663b646e60b0e93f2ea0c97 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 30 Nov 2022 18:11:26 +0000 Subject: [PATCH 572/939] adding easyconfigs: TensorFlow-2.8.4-foss-2021b.eb and patches: TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch --- .../TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 202 ++++++++++++++++++ ....8.4_remove-libclang-and-io-gcs-deps.patch | 34 +++ 2 files changed, 236 insertions(+) create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb create mode 100644 easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb new file mode 100644 index 000000000000..15c5fd729ce6 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -0,0 +1,202 @@ +easyblock = 'PythonBundle' + +name = 'TensorFlow' +version = '2.8.4' + +homepage = 'https://www.tensorflow.org/' +description = "An open-source software library for Machine Intelligence" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} + +builddependencies = [ + ('Bazel', '4.2.2'), + ('protobuf', '3.17.3'), + # git 2.x required, see also https://github.com/tensorflow/tensorflow/issues/29053 + ('git', '2.33.1', '-nodocs'), + ('pybind11', '2.7.1'), + ('UnZip', '6.0'), + ('LLVM', '12.0.1'), # for debugging with llvm-symbolizer, to be removed +] +dependencies = [ + ('Python', '3.9.6'), + ('h5py', '3.6.0'), + ('cURL', '7.78.0'), + ('dill', '0.3.4'), + ('double-conversion', '3.1.5'), + ('flatbuffers', '2.0.0'), + ('giflib', '5.2.1'), + ('hwloc', '2.5.0'), + ('ICU', '69.1'), + ('JsonCpp', '1.9.4'), + ('libjpeg-turbo', '2.0.6'), + ('LMDB', '0.9.29'), + ('NASM', '2.15.05'), + ('nsync', '1.24.0'), + ('SQLite', '3.36'), + ('protobuf-python', '3.17.3'), + ('flatbuffers-python', '2.0'), + ('libpng', '1.6.37'), + ('snappy', '1.1.9'), + ('zlib', '1.2.11'), + ('networkx', '2.6.3'), # required for pythran +] + +use_pip = True +sanity_pip_check = True + +# Dependencies created and updated using findPythonDeps.sh: +# https://gist.github.com/Flamefire/49426e502cd8983757bd01a08a10ae0d +exts_list = [ + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('tensorflow_estimator', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['bee8e0520c60ae7eaf6ca8cb46c5a9f4b45725531380db8fbe38fcb48478b6bb'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('Werkzeug', '2.1.2', { + 'checksums': ['1ce08e8093ed67d638d63879fd1ba3735817f7a80de3674d293f5984f25fb6e6'], + }), + ('tensorboard_plugin_wit', '1.8.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['ff26bdd583d155aa951ee3b152b3d0cffae8005dc697f72b44a8e8c2a77a8cbe'], + }), + ('tensorboard_data_server', '0.6.1', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['809fe9887682d35c1f7d1f54f0f40f98bb1f771b14265b453ca051e2ce58fca7'], + }), + ('Markdown', '3.3.7', { + 'checksums': ['cbb516f16218e643d8e0a95b309f77eb118cb138d39a4f27851e6a63581db874'], + }), + ('grpcio', '1.46.1', { + 'modulename': 'grpc', + 'preinstallopts': "export GRPC_PYTHON_BUILD_EXT_COMPILER_JOBS=%(parallel)s && ", + 'checksums': ['4835b0f5fedbee3a3d6eea48f4e65dffd30b52c078690fa97ddc9fcea1e3b35d'], + }), + ('oauthlib', '3.2.0', { + 'checksums': ['23a8208d75b902797ea29fd31fa80a15ed9dc2c6c16fe73f5d346f83f6fa27a2'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('rsa', '4.8', { + 'checksums': ['5c6bd9dc7a543b7fe4304a631f8a8a3b674e2bbfc49c2ae96200cdbe55df6b17'], + }), + ('pyasn1-modules', '0.2.8', { + 'checksums': ['905f84c712230b2c592c19470d3ca8d552de726050d1d1716282a1f6146be65e'], + }), + ('cachetools', '5.1.0', { + 'checksums': ['8b3b8fa53f564762e5b221e9896798951e7f915513abf2ba072ce0f07f3f5a98'], + }), + ('google-auth', '2.6.6', { + 'modulename': 'google.auth', + 'checksums': ['1ba4938e032b73deb51e59c4656a00e0939cf0b1112575099f136babb4563312'], + }), + ('google-auth-oauthlib', '0.4.6', { + 'checksums': ['a90a072f6993f2c327067bf65270046384cda5a8ecb20b94ea9a687f1f233a7a'], + }), + ('tensorboard', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + 'checksums': ['65a338e4424e9079f2604923bdbe301792adce2ace1be68da6b3ddf005170def'], + }), + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('Keras_Preprocessing', '1.1.2', { + 'checksums': ['add82567c50c8bc648c14195bf544a5ce7c1f76761536956c3d2978970179ef3'], + }), + ('keras', '2.8.0', { + 'source_tmpl': '%(name)s-%(version)s-py2.py3-none-any.whl', + 'checksums': ['744d39dc6577dcd80ff4a4d41549e92b77d6a17e0edd58a431d30656e29bc94e'], + }), + ('google-pasta', '0.2.0', { + 'modulename': 'pasta', + 'checksums': ['c9f2c8dfc8f96d0d5808299920721be30c9eec37f2389f28904f454565c8a16e'], + }), + ('astunparse', '1.6.3', { + 'checksums': ['5ad93a8456f0d084c3456d059fd9a92cce667963232cbf763eac3bc5b7940872'], + }), + ('tblib', '1.7.0', { + 'checksums': ['059bd77306ea7b419d4f76016aef6d7027cc8a0785579b5aad198803435f882c'], + }), + ('portpicker', '1.5.2', { + 'checksums': ['c55683ad725f5c00a41bc7db0225223e8be024b1fa564d039ed3390e4fd48fb3'], + }), + ('absl-py', '1.0.0', { + 'modulename': 'absl', + 'checksums': ['ac511215c01ee9ae47b19716599e8ccfa746f2e18de72bdf641b79b22afa27ea'], + }), + (name, version, { + 'patches': [ + 'TensorFlow-2.1.0_fix-cuda-build.patch', + 'TensorFlow-2.4.0_add-ldl.patch', + 'TensorFlow-2.4.0_dont-use-var-lock.patch', + 'TensorFlow-2.5.0_add-support-for-large-core-systems.patch', + 'TensorFlow-2.5.0_disable-avx512-extensions.patch', + 'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch', + 'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch', + 'TensorFlow-2.5.0_fix-crash-on-shutdown.patch', + 'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch', + 'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch', + 'TensorFlow-2.7.1_fix_cpu_count.patch', + ], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], + 'test_script': 'TensorFlow-2.x_mnist-test.py', + 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_targets': [ + '//tensorflow/core/...', + '-//tensorflow/core:example_java_proto', + '-//tensorflow/core/example:example_protos_closure', + '//tensorflow/cc/...', + '//tensorflow/c/...', + '//tensorflow/python/...', + '-//tensorflow/c/eager:c_api_test_gpu', + '-//tensorflow/c/eager:c_api_distributed_test', + '-//tensorflow/c/eager:c_api_distributed_test_gpu', + '-//tensorflow/c/eager:c_api_cluster_test_gpu', + '-//tensorflow/c/eager:c_api_remote_function_test_gpu', + '-//tensorflow/c/eager:c_api_remote_test_gpu', + '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + '-//tensorflow/core/common_runtime:mkl_layout_pass_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', + ], + 'testopts': "--test_timeout=3600 --test_size_filters=small", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small --run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'with_xla': True, + 'checksums': [ + {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, + {'TensorFlow-2.1.0_fix-cuda-build.patch': + '78c20aeaa7784b8ceb46238a81e8c2461137d28e0b576deeba8357d23fbe1f5a'}, + {'TensorFlow-2.4.0_add-ldl.patch': '917ee7282e782e48673596d8917c3207e60e0851bb9acf230a2a439b067af2e3'}, + {'TensorFlow-2.4.0_dont-use-var-lock.patch': + 'b14f2493fd2edf79abd1c4f2dde6c98a3e7d5cb9c25ab9386df874d5f072d6b5'}, + {'TensorFlow-2.5.0_add-support-for-large-core-systems.patch': + '915f3477d6407fafd48269fe1e684a05ce361d9b9b85e58686682df87760f636'}, + {'TensorFlow-2.5.0_disable-avx512-extensions.patch': + '3655ce24c97569ac9738c07cac85347ba6f5c815ada95b19b606ffa46d4dda03'}, + {'TensorFlow-2.5.0-fix-alias-violation-in-absl.patch': + '12454fda3330fb45cd380377e283f04488b40e0b8ae7378e786ddf731a581f75'}, + {'TensorFlow-2.5.0_fix-arm-vector-intrinsics.patch': + '6abfadc0f67ff3b510d70430843201cb46d7bd65db045ec9b482af70e0c8c0c8'}, + {'TensorFlow-2.5.0_fix-crash-on-shutdown.patch': + '578c7493221ebd3dc25ca43d63a72cbb28fdf4112b1e2baa7390f25781bd78fd'}, + {'TensorFlow-2.7.1_remove-duplicate-gpu-tests.patch': + 'f78526a34d85f4dda59b160b576aa3a3126db7073a58c4e3b1424923f6a21483'}, + {'TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch': + '10a6daad2ef65d649a6d4a6659f97f833359b3c35d3ce15e63d2db2e331a6a35'}, + {'TensorFlow-2.7.1_fix_cpu_count.patch': + '5427a4cff0afc2fe5b24776ae9ca3616c56a79c1fde0025b37bec24837bb0698'}, + ], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch new file mode 100644 index 000000000000..b9f3afe50d02 --- /dev/null +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4_remove-libclang-and-io-gcs-deps.patch @@ -0,0 +1,34 @@ +This combines two patches from TensorFlow 2.7.1. + +tensorflow-io-gcs-filesystem is not available as a binary for all architectures and +building it requires TensorFlow to be installed, i.e. there is a cyclic dependency. +As it is not actually required (but optional) remove it from `REQUIRED_PACKAGES`. +See https://github.com/tensorflow/tensorflow/issues/56636 + +libclang was introduced in +https://github.com/tensorflow/tensorflow/commit/c211472000ff57bac7fcec9b0465cf73b37bf135 +> This is in preparation to open-source TF's TFRT backend. +> TFRT generates code using libclang python bindings as part of the build. +Hence it is not currently used and as it is not (easily) available for all architectures +simply remove it. + +Patch added by Simon Branford (University of Birmingham) + +--- tensorflow/tools/pip_package/setup.py.orig 2022-11-29 16:42:19.016145000 +0000 ++++ tensorflow/tools/pip_package/setup.py 2022-11-29 16:42:39.287641518 +0000 +@@ -78,7 +78,6 @@ + 'google_pasta >= 0.1.1', + 'h5py >= 2.9.0', + 'keras_preprocessing >= 1.1.1', # 1.1.0 needs tensorflow==1.7 +- 'libclang >= 9.0.1', + 'numpy >= 1.20', + 'opt_einsum >= 2.3.2', + # TODO(b/182876485): Protobuf 3.20 results in linker errors on Windows +@@ -101,7 +100,6 @@ + 'tensorboard >= 2.8, < 2.9', + 'tensorflow-estimator >= 2.8, < 2.9', + 'keras >= 2.8.0rc0, < 2.9', +- 'tensorflow-io-gcs-filesystem >= 0.23.1', + ] + + From 86b2154c791af929a207ef03fc95b6d7e2335cf6 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 30 Nov 2022 18:28:13 +0000 Subject: [PATCH 573/939] split long lines --- .../easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index 15c5fd729ce6..5e83ea300e9e 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -148,7 +148,8 @@ exts_list = [ 'source_urls': ['https://github.com/tensorflow/tensorflow/archive/'], 'test_script': 'TensorFlow-2.x_mnist-test.py', 'test_tag_filters_cpu': '-gpu,-tpu,-no_cuda_on_cpu_tap,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', - 'test_tag_filters_gpu': 'gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,-benchmark-test,-v1only', + 'test_tag_filters_gpu': ('gpu,-no_gpu,-nogpu,-gpu_cupti,-no_cuda11,-no_pip,-no_oss,-oss_serial,' + '-benchmark-test,-v1only'), 'test_targets': [ '//tensorflow/core/...', '-//tensorflow/core:example_java_proto', @@ -170,7 +171,8 @@ exts_list = [ '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", - 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small --run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", + 'testopts_gpu': "--test_timeout=3600 --test_size_filters=small " + + "--run_under=//tensorflow/tools/ci_build/gpu_build:parallel_gpu_execute", 'with_xla': True, 'checksums': [ {'v2.8.4.tar.gz': 'c08a222792bdbff9da299c7885561ee27b95d414d1111c426efac4ccdce92cde'}, From 6dcc9281a466822d9b15dd444c9b9ba98951b9f0 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Wed, 30 Nov 2022 18:33:02 +0000 Subject: [PATCH 574/939] return comments that --inject-checksums removed --- .../t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb index 5e83ea300e9e..a3e3a25f20d2 100644 --- a/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb +++ b/easybuild/easyconfigs/t/TensorFlow/TensorFlow-2.8.4-foss-2021b.eb @@ -157,17 +157,24 @@ exts_list = [ '//tensorflow/cc/...', '//tensorflow/c/...', '//tensorflow/python/...', + # Fails on some nodes but C API isn't installed anyway '-//tensorflow/c/eager:c_api_test_gpu', '-//tensorflow/c/eager:c_api_distributed_test', '-//tensorflow/c/eager:c_api_distributed_test_gpu', + # Race condition with port picker: https://github.com/tensorflow/tensorflow/issues/46602 '-//tensorflow/c/eager:c_api_cluster_test_gpu', '-//tensorflow/c/eager:c_api_remote_function_test_gpu', '-//tensorflow/c/eager:c_api_remote_test_gpu', + # Fails to open its own test.xml(?) '-//tensorflow/core/common_runtime:collective_param_resolver_local_test', + # Fails on non-AVX-512 systems: https://github.com/tensorflow/tensorflow/issues/46532 '-//tensorflow/core/common_runtime:mkl_layout_pass_test', '-//tensorflow/core/kernels/mkl:mkl_fused_ops_test', + # Fails on AMD EPYC systems: https://github.com/tensorflow/tensorflow/issues/52151 '-//tensorflow/core/kernels/mkl:mkl_fused_batch_norm_op_test', + # All tests in this directory fail with segfault (TensorFlow Graph IR) '-//tensorflow/core/ir/importexport/tests/roundtrip/...', + # Fails on e.g. AMD EPYC and known to be flaky on Mac: https://github.com/tensorflow/tensorflow/issues/56717 '-//tensorflow/python/data/experimental/kernel_tests/service:fault_tolerance_test', ], 'testopts': "--test_timeout=3600 --test_size_filters=small", From bb01ff5e5f8401f9ddc48f0b641117784f36da77 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Paul=20J=C3=A4hne?= Date: Thu, 1 Dec 2022 10:33:34 +0100 Subject: [PATCH 575/939] adding easyconfigs: Alfred-0.2.6-GCC-11.2.0.eb --- .../a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb b/easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb new file mode 100644 index 000000000000..63a34e4004d0 --- /dev/null +++ b/easybuild/easyconfigs/a/Alfred/Alfred-0.2.6-GCC-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Alfred' +version = '0.2.6' + +homepage = "https://www.gear-genomics.com/alfred/" +description = """Alfred is an efficient and versatile command-line application + that computes multi-sample quality control metrics in a read-group aware manner. + Alfred supports read counting, feature annotation and haplotype-resolved consensus + computation using multiple sequence alignments.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +github_account = 'tobiasrausch' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2f92cc1acc1f059a75468fca49f755c25947d59f39f2225abaaa4d145ac971a8'] + +dependencies = [ + ('Boost', '1.77.0'), + ('bzip2', '1.0.8'), + ('HTSlib', '1.14'), + ('XZ', '5.2.5'), + ('zlib', '1.2.11'), + ('zstd', '1.5.0'), +] + +files_to_copy = [(['src/%(namelower)s'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +moduleclass = 'bio' From c42a0661329ff63b1e3134267ebb81de54f1608f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 1 Dec 2022 10:34:30 +0100 Subject: [PATCH 576/939] adding easyconfigs: Bonnie++-2.00a-GCC-10.3.0.eb --- .../b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb new file mode 100644 index 000000000000..b4663ebc3f54 --- /dev/null +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb @@ -0,0 +1,31 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2014 Uni.Lu/LCSB, NTUA +# Authors:: Fotis Georgatos +# License:: MIT/GPL +# $Id$ +## + +easyblock = 'ConfigureMake' + +name = 'Bonnie++' +version = '2.00a' + +homepage = 'https://www.coker.com.au/bonnie++' +description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://www.coker.com.au/bonnie++/'] +sources = [SOURCELOWER_TGZ] +checksums = ['a8d33bbd81bc7eb559ce5bf6e584b9b53faea39ccfb4ae92e58f27257e468f0e'] + +sanity_check_paths = { + 'files': ['sbin/bonnie++'], + 'dirs': [] +} + +sanity_check_commands = ["bonnie++ --help 2>&1 | grep '^bonnie'"] + +moduleclass = 'tools' From d60aefdb6ee0fe3ae9548440999ed054d58cfd13 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Thu, 1 Dec 2022 09:54:46 +0000 Subject: [PATCH 577/939] adding easyconfigs: tensorflow-probability-0.16.0-foss-2021b.eb --- ...ensorflow-probability-0.16.0-foss-2021b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb new file mode 100644 index 000000000000..05bea7aff462 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorflow-probability/tensorflow-probability-0.16.0-foss-2021b.eb @@ -0,0 +1,46 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Authors:: Dugan Witherick (University of Warwick) +# License:: MIT/GPL +# $Id$ +# +## + +easyblock = 'PythonBundle' + +name = 'tensorflow-probability' +version = '0.16.0' + +homepage = 'https://www.tensorflow.org/probability' +description = """TensorFlow Probability (TFP) is a library for probabilistic reasoning and statistical analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'usempi': True, 'pic': True} + +dependencies = [ + ('Python', '3.9.6'), + ('TensorFlow', '2.8.4'), + ('dm-tree', '0.1.6'), +] + +use_pip = True + +exts_list = [ + ('cloudpickle', '2.2.0', { + 'checksums': ['3f4219469c55453cfe4737e564b67c2a149109dabf7f242478948b895f61106f'], + }), + (name, version, { + 'installopts': '--install-option="--release"', + 'modulename': 'tensorflow_probability', + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/tensorflow/probability/archive/'], + 'checksums': ['0c8b8bb00403af56979f5c5cfda6fb3ea6f3e5efc4530ab66889415d230ebd81'], + }), +] + +sanity_check_commands = ["python -c 'import tensorflow; import tensorflow_probability'"] + +sanity_pip_check = True + +moduleclass = 'lib' From eb30861033549b9a0861dcf3b1b8b26a62420699 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 1 Dec 2022 12:45:45 +0100 Subject: [PATCH 578/939] Downgrade version of GA to match what is already used in other PRs for this toolchain version --- .../easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb index 62257a69fe82..06c248940750 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -22,7 +22,7 @@ builddependencies = [('CMake', '3.23.1')] dependencies = [ ('Python', '3.10.4'), ('HDF5', '1.12.2'), - ('GlobalArrays', '5.8.2'), + ('GlobalArrays', '5.8.1'), ] build_shared_libs = True From 4e61d4f5ff141bb13f6488310c7b2fac0aeafb56 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 1 Dec 2022 15:03:20 +0100 Subject: [PATCH 579/939] Update OpenMolcas-22.06-intel-2022a.eb --- .../o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb index 77b806ac4f47..0cbe3d6e3df3 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -17,20 +17,21 @@ checksums = [ '708763e060aa0174bbe9c0cc336b509fbf492066465908dd919452836a7a793a', # OpenMolcas-21.06_mcpdft_deps.patch ] +builddependencies = [('CMake', '3.23.1')] + dependencies = [ ('GlobalArrays', '5.8.1'), ('HDF5', '1.12.2'), ('Python', '3.10.4'), ] -builddependencies = [('CMake', '3.23.1')] - separate_build_dir = True +build_shared_libs = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' configopts += '-DMPI=ON -DOPENMP=ON -DGA=ON ' -configopts += '-DBUILD_SHARED_LIBS=ON -DTOOLS=ON -DFDE=ON' +configopts += '-DTOOLS=ON -DFDE=ON' modextrapaths = {'PATH': ''} modextravars = { From fffe2f973ee41c2365a3381c69df7f7856ce2988 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 1 Dec 2022 17:05:43 +0100 Subject: [PATCH 580/939] delete patch (already added by PR #16166) --- ...remove_undeclared_redundant_variable.patch | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch diff --git a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch b/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch deleted file mode 100644 index 3bfe94fd93ae..000000000000 --- a/easybuild/easyconfigs/a/Amber/Amber-22_remove_undeclared_redundant_variable.patch +++ /dev/null @@ -1,27 +0,0 @@ -Remove the undeclared (and unused) variable i from the private clause -in an OpenMP pragma, which otherwise results in an error: - - 93 | !$omp parallel do private(ihkl,i,f,angle) - | 1 -Error: Symbol i at (1) has no IMPLICIT type - -Bob Dröge, University of Groningen, 2022-08-18 ---- amber22_src.orig/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:24.807724049 +0200 -+++ amber22_src/src/pmemd/src/xray/src/xray_non_bulk_impl_cpu.F90 2022-08-18 13:12:42.039809811 +0200 -@@ -90,7 +90,7 @@ - call check_precondition(size(frac, 2) == size(scatter_type_index)) - call check_precondition(size(hkl, 2) == size(atomic_scatter_factor, 1)) - -- !$omp parallel do private(ihkl,i,f,angle) -+ !$omp parallel do private(ihkl,f,angle) - do ihkl = 1, size(hkl, 2) - - ! Fhkl = SUM( fj * exp(2 * M_PI * i * (h * xj + k * yj + l * zj)) ), -@@ -127,4 +127,4 @@ - end subroutine calc_f_non_bulk - - --end module xray_non_bulk_impl_cpu_module -\ No newline at end of file -+end module xray_non_bulk_impl_cpu_module - From 0f955aeeb754a9b070da9f2eedd4161c299ae07d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Thu, 1 Dec 2022 17:07:39 +0100 Subject: [PATCH 581/939] Use SYSTEM instead of True for system-level deps --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 9d5139c40a32..036301c8c418 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -88,7 +88,7 @@ dependencies = [ ('PnetCDF', '1.12.3'), ('Tkinter', '3.9.6'), ('X11', '20210802'), - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), ] From b5810670afcfdb8ed9c7860fa649b9789fba7d87 Mon Sep 17 00:00:00 2001 From: Maxim Date: Thu, 1 Dec 2022 17:13:19 +0100 Subject: [PATCH 582/939] Update OpenMolcas-22.06-intel-2022a.eb --- .../easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb index 0cbe3d6e3df3..b8d19e00410b 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.06-intel-2022a.eb @@ -25,7 +25,6 @@ dependencies = [ ('Python', '3.10.4'), ] -separate_build_dir = True build_shared_libs = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' From 4f5688325d003ac34702632cfde3697cc0ca7915 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Thu, 1 Dec 2022 19:15:38 +0000 Subject: [PATCH 583/939] Update easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb --- easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb index b4663ebc3f54..6876b4e9f658 100644 --- a/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bonnie++/Bonnie++-2.00a-GCC-10.3.0.eb @@ -13,7 +13,7 @@ name = 'Bonnie++' version = '2.00a' homepage = 'https://www.coker.com.au/bonnie++' -description = """Bonnie++-1.97: Enhanced performance Test of Filesystem I/O""" +description = """Enhanced performance Test of Filesystem I/O""" toolchain = {'name': 'GCC', 'version': '10.3.0'} From 9a70cfc6df30558484d2421d2d6b32d81b352ce6 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 1 Dec 2022 22:15:30 +0100 Subject: [PATCH 584/939] adding easyconfigs: pysteps-1.7.1-foss-2022a.eb and patches: pysteps-1.7.1_h5py-3.7_compat.patch --- .../p/pysteps/pysteps-1.7.1-foss-2022a.eb | 52 +++++++++++++++++++ .../pysteps-1.7.1_h5py-3.7_compat.patch | 17 ++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb new file mode 100644 index 000000000000..1716b3638df0 --- /dev/null +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb @@ -0,0 +1,52 @@ +easyblock = 'PythonBundle' + +name = 'pysteps' +version = '1.7.1' + +homepage = 'https://pysteps.github.io/' +description = """ +Pysteps is an open-source and community-driven Python library for probabilistic +precipitation nowcasting, i.e. short-term ensemble prediction systems.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('OpenCV', '4.6.0', '-contrib'), + ('Pillow', '9.1.1'), + ('pyproj', '3.4.0'), + ('matplotlib', '3.5.2'), + ('dask', '2022.10.0'), + ('netcdf4-python', '1.6.1'), + ('xarray', '2022.9.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsmin', '3.0.1', { + 'checksums': ['c0959a121ef94542e807a674142606f7e90214a2b3d1eb17300244bbb5cc2bfc'], + }), + ('pyFFTW', '0.13.0', { + 'source_tmpl': '%(name)s-%(version)s.tar.gz', + 'checksums': ['da85102405c0bd95d57eb19e99b01a0729d8406cb204c3900894b873784253da'], + }), + (name, version, { + 'patches': ['pysteps-1.7.1_h5py-3.7_compat.patch'], + 'source_tmpl': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/pySTEPS/pysteps/archive/'], + 'checksums': [ + {'v1.7.1.tar.gz': '5063d7546d9995ec6ca52a5b4e50ef3f3c1ae43088a55e370af4aec18162a22f'}, + {'pysteps-1.7.1_h5py-3.7_compat.patch': 'c2b1a47d7151a7f4072dce797c6303314c0d8fd7683b0001deb43f24357ed977'}, + ], + }), + ('pysteps-nwp-importers', '6ca1582', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/pySTEPS/pysteps-nwp-importers/archive/'], + 'checksums': ['e9aea5f1c49dadf0bc878822cd9403db93cf473c8ad21d8bfda799136c87f4db'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch new file mode 100644 index 000000000000..853055ec24e2 --- /dev/null +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1_h5py-3.7_compat.patch @@ -0,0 +1,17 @@ +Fix compatibility with h5py v3.7 +Author: Samuel Moors (Vrije Universiteit Brussel) +diff -ur pysteps-1.7.1.orig/pysteps/io/importers.py pysteps-1.7.1/pysteps/io/importers.py +--- pysteps-1.7.1.orig/pysteps/io/importers.py 2022-09-25 22:49:54.000000000 +0200 ++++ pysteps-1.7.1/pysteps/io/importers.py 2022-11-25 13:00:14.948382946 +0100 +@@ -1377,7 +1377,10 @@ + raise IOError("requested quantity %s not found" % qty) + + where = f["where"] +- proj4str = where.attrs["projdef"].decode() ++ proj4str = where.attrs["projdef"] ++ if(not isinstance(proj4str, str)): ++ proj4str = proj4str.decode() ++ + pr = pyproj.Proj(proj4str) + + ll_lat = where.attrs["LL_lat"] From b8ab8ca6c3eaac0827add186726786641960b781 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 1 Dec 2022 22:45:19 +0100 Subject: [PATCH 585/939] fix xarray version --- easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb index 1716b3638df0..6c52576341fb 100644 --- a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb @@ -19,7 +19,7 @@ dependencies = [ ('matplotlib', '3.5.2'), ('dask', '2022.10.0'), ('netcdf4-python', '1.6.1'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ] use_pip = True From 25727ca728bf3a1a5514bb9ffd0195bbdfc079ce Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Fri, 2 Dec 2022 09:28:33 +0100 Subject: [PATCH 586/939] fix homepage --- easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb index a6c09399b711..4f00955fdf93 100644 --- a/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/n/n2v/n2v-0.3.2-foss-2021a-CUDA-11.3.1.eb @@ -5,7 +5,7 @@ name = 'n2v' version = '0.3.2' versionsuffix = '-CUDA-%(cudaver)s' -homepage = 'https://github.com/juglab/cryoCARE_pip' +homepage = 'https://github.com/juglab/n2v' description = """ Noise2Void - Learning Denoising from Single Noisy Images The field of image denoising is currently dominated by discriminative deep From 4b97835c4ce4af35f5412aa7cc7772c2bf18b855 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 2 Dec 2022 10:19:00 +0100 Subject: [PATCH 587/939] use correct order for patch checksums --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index 036301c8c418..c649a8f50358 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -61,8 +61,8 @@ checksums = [ 'fb1ab74314d7816169bb9f3f527b78085654aae2825c52cebf50a5760401b737', # AmberTools-22_fix_test_missing_cuda_dir.patch # AmberTools-22_fix_missing_error_check_on_test_run.patch 'a86eee60bd65c16a849469e303cb99dfc207cbadd2ae9e70b9ff580ced785475', - 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch '3fc08a2cf61f3eefd094554e60c88b14c9f5071f94e0a0a15c6b55fe321bfc78', # AmberTools-22_fix_cuda_version_check.patch + 'b5855866c63c2ee860a5e6ad6f618ac4dab7072f5caae95769d4b2457d616a8e', # Amber-22_reduce_precision_of_kmmd_test.patch # Amber-22_remove_undeclared_redundant_variable.patch 'b94900c2178dd6dbf2824b17074980a3e5e6e71b38c0b2b30e1f147e4e1ac8cb', ] From bb109fa47fc3d769e1830d032623b0216cae6f55 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 2 Dec 2022 12:31:55 +0100 Subject: [PATCH 588/939] Git subtree support Git subtree is part of git since 1.7, and is default on OS git - we shouldn't have less functionality --- easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb index 7760dcfd6bd5..001f08105d63 100644 --- a/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.38.1-GCCcore-12.2.0-nodocs.eb @@ -39,6 +39,8 @@ preconfigopts = 'make configure && ' # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" +postinstallcmds = ['cd contrib/subtree; make install'] + sanity_check_paths = { 'files': ['bin/git'], 'dirs': ['libexec/git-core', 'share'], From 901cd22c51d1eeced500c1a792ca5a09b1951049 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 2 Dec 2022 12:35:20 +0100 Subject: [PATCH 589/939] Git subtree support Git subtree is part of git since 1.7, and it gets installed by default on the OS package of git. --- easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb index 214a4cc7228a..658c91a6dd56 100644 --- a/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb +++ b/easybuild/easyconfigs/g/git/git-2.36.0-GCCcore-11.3.0-nodocs.eb @@ -39,6 +39,8 @@ preconfigopts = 'make configure && ' # will not append -lpthread to LDFLAGS, but Makefile ignores LIBS. configopts = "--with-perl=${EBROOTPERL}/bin/perl --enable-pthreads='-lpthread'" +postinstallcmds = ['cd contrib/subtree; make install'] + sanity_check_paths = { 'files': ['bin/git'], 'dirs': ['libexec/git-core', 'share'], From 4cf2c16db72886057c5a2fa8d22fb47cd81f1f96 Mon Sep 17 00:00:00 2001 From: robogast Date: Fri, 2 Dec 2022 15:30:57 +0100 Subject: [PATCH 590/939] adding easyconfigs: cuDNN-8.7.0.84-CUDA-11.8.0.eb --- .../c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb new file mode 100644 index 000000000000..8443701d7c4f --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-8.7.0.84-CUDA-11.8.0.eb @@ -0,0 +1,40 @@ +name = 'cuDNN' +version = '8.7.0.84' +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 = '11' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/cudnn/v%s/local_installers/%%(cudashortver)s/' % local_short_ver # noqa: E501 +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = [{ + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '976c4cba7233c97ae74006afab5172976300ba40f5b250a21f8cf71f59c9f76d', + '%%(namelower)s-linux-ppc64le-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '0433d6d8b6841298e049e8a542750aa330a6e046a52ad95fae0c2f75dabe5575', + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + 'cf967f78dbf6c075243cc83aa18759e370db3754aa15b12a0a14e8bf67a3a9d4', +}] + +dependencies = [('CUDA', '11.8.0')] + +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 c02eb63373defb8485ec294b7a3430a5bc4c706b Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 2 Dec 2022 20:57:38 +0100 Subject: [PATCH 591/939] adding easyconfigs: mold-1.7.1-GCCcore-12.2.0.eb --- .../m/mold/mold-1.7.1-GCCcore-12.2.0.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..7345b723f611 --- /dev/null +++ b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'mold' +version = '1.7.1' + +homepage = 'https://github.com/rui314/mold' +description = "mold is a high-performance drop-in replacement for existing Unix linkers." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/rui314/mold/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['fa2558664db79a1e20f09162578632fa856b3cde966fbcb23084c352b827dfa9'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=c++" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mold', 'lib/mold/mold-wrapper.%s' % SHLIB_EXT], + 'dirs': ['share/man'], +} + +sanity_check_commands = [ + "mold --help", + "mold --run gcc -v", +] + +moduleclass = 'tools' From 0f49063a158908cb1fef76b756e274302f32cd49 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 2 Dec 2022 23:08:03 +0100 Subject: [PATCH 592/939] update easyconfigs: NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb --- .../NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb | 46 ++++++++++--------- 1 file changed, 24 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb index ba7dbd9499e9..e59c093c9fac 100644 --- a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.4.1-gompi-2021b-CUDA-11.4.1.eb @@ -27,34 +27,36 @@ builddependencies = [ ] dependencies = [ - ('CUDA', '11.4.1', '', True), + ('CUDA', '11.4.1', '', SYSTEM), ('UCX-CUDA', '1.11.2', versionsuffix), ('NCCL', '2.10.3', versionsuffix), ] skipsteps = ['configure'] -prebuildopts = 'export NVSHMEM_USE_GDRCOPY=1 && ' -prebuildopts += 'export GDRCOPY_HOME=${EBROOTGDRCOPY} && ' - -prebuildopts += 'export MPI_HOME=${EBROOTOPENMPI} && ' -prebuildopts += 'export NVSHMEM_MPI_SUPPORT=1 && ' -prebuildopts += 'export NVSHMEMTEST_USE_MPI_LAUNCHER=1 && ' - -prebuildopts += 'export NCCL_HOME=${EBROOTNCCL} && ' -prebuildopts += 'export NVSHMEM_USE_NCCL=1 && ' - -prebuildopts += 'export NVSHMEM_BUILDDIR=%(builddir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj && ' -prebuildopts += 'export NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj && ' -prebuildopts += 'export NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj && ' - -prebuildopts += 'export NVSHMEM_PREFIX=%(installdir)s && ' -prebuildopts += 'export NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples && ' -prebuildopts += 'export NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest && ' -prebuildopts += 'export NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest && ' -prebuildopts += 'export NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test && ' +prebuildopts = 'export %s &&' % ' '.join([ + 'NVSHMEM_USE_GDRCOPY=1', + 'GDRCOPY_HOME=${EBROOTGDRCOPY}', + + 'MPI_HOME=${EBROOTOPENMPI}', + 'NVSHMEM_MPI_SUPPORT=1', + 'NVSHMEMTEST_USE_MPI_LAUNCHER=1', + + 'NCCL_HOME=${EBROOTNCCL}', + 'NVSHMEM_USE_NCCL=1', + + 'NVSHMEM_BUILDDIR=%(builddir)s', + 'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj', + 'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj', + 'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj', + 'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj', + + 'NVSHMEM_PREFIX=%(installdir)s', + 'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples', + 'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest', + 'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest', + 'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test', +]) preinstallopts = prebuildopts From 8e0c5fd34382a07bc887b96c140df72f09123581 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 2 Dec 2022 23:28:15 +0100 Subject: [PATCH 593/939] adding easyconfigs: NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb --- .../NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb | 70 +++++++++++++++++++ 1 file changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..0876e2e7643e --- /dev/null +++ b/easybuild/easyconfigs/n/NVSHMEM/NVSHMEM-2.7.0-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,70 @@ +easyblock = 'ConfigureMake' + +name = 'NVSHMEM' +version = '2.7.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nvshmem' +description = """NVSHMEM is a parallel programming interface based on OpenSHMEM that provides +efficient and scalable communication for NVIDIA GPU clusters. NVSHMEM creates a +global address space for data that spans the memory of multiple GPUs and can be +accessed with fine-grained GPU-initiated operations, CPU-initiated operations, +and operations on CUDA streams. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +download_instructions = """The sources of NVSHMEM can be downloaded at NVIDIA's webpage when you have signed up for +their (free) developer program: +https://developer.nvidia.com/nvshmem-downloads""" + +sources = ['%(namelower)s_src_%(version)s-6.txz'] +checksums = ['23ed9b0187104dc87d5d2bc1394b6f5ff29e8c19138dc019d940b109ede699df'] + +builddependencies = [ + ('Autotools', '20220317'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('UCX-CUDA', '1.12.1', versionsuffix), + ('NCCL', '2.12.12', versionsuffix), +] + +skipsteps = ['configure'] + +prebuildopts = 'export %s &&' % ' '.join([ + 'NVSHMEM_USE_GDRCOPY=1', + 'GDRCOPY_HOME=${EBROOTGDRCOPY}', + + 'MPI_HOME=${EBROOTOPENMPI}', + 'NVSHMEM_MPI_SUPPORT=1', + 'NVSHMEMTEST_USE_MPI_LAUNCHER=1', + + 'NCCL_HOME=${EBROOTNCCL}', + 'NVSHMEM_USE_NCCL=1', + + 'NVSHMEM_BUILDDIR=%(builddir)s', + 'NVSHMEM_EXAMPLES_BUILDDIR=${NVSHMEM_BUILDDIR}/examples/obj', + 'NVSHMEM_OTHERTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/othertest/obj', + 'NVSHMEM_TEST_BUILDDIR=${NVSHMEM_BUILDDIR}/test/obj', + 'NVSHMEM_PERFTEST_BUILDDIR=${NVSHMEM_BUILDDIR}/perftest/obj', + + 'NVSHMEM_PREFIX=%(installdir)s', + 'NVSHMEM_EXAMPLES_INSTALL=${NVSHMEM_PREFIX}/examples', + 'NVSHMEM_OTHERTEST_INSTALL=${NVSHMEM_PREFIX}/othertest', + 'NVSHMEM_PERFTEST_INSTALL=${NVSHMEM_PREFIX}/perftest', + 'NVSHMEM_TEST_INSTALL=${NVSHMEM_PREFIX}/test', +]) + +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['lib/libnvshmem.a', 'lib/nvshmem_bootstrap_mpi.%s' % SHLIB_EXT], + 'dirs': ['include'] +} + +modextravars = {'NVSHMEM_HOME': '%(installdir)s'} + +moduleclass = 'devel' From 8e84eb93b72ca85a67339a41e2e4a6ea04ab63d0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Sat, 3 Dec 2022 23:24:22 +0100 Subject: [PATCH 594/939] update mold-1.7.1-GCCcore-12.2.0.eb: remove not needed configsopts --- easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb index 7345b723f611..9dac36ca9146 100644 --- a/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/mold/mold-1.7.1-GCCcore-12.2.0.eb @@ -21,8 +21,6 @@ dependencies = [ ('OpenSSL', '1.1', '', SYSTEM), ] -configopts = "-DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=c++" - runtest = 'test' sanity_check_paths = { From 17e9a433cab17c63b650b749ed0f749074def2f3 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 4 Dec 2022 12:44:53 +0000 Subject: [PATCH 595/939] testsuite exception --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 9e66b9f8b2a1..3160d1b9ad9a 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -582,6 +582,8 @@ def check_dep_vars(self, gen, dep, dep_vars): ('2.5.0;', ['AlphaFold-2.1.2-']), # medaka 1.5.0 (foss/2021a) depends on TensorFlow >=2.5.2, <2.6.0 ('2.5.3;', ['medaka-1.5.0-']), + # tensorflow-probability version to TF version + ('2.8.4;', ['tensorflow-probability-0.16.0-']), ], # smooth-topk uses a newer version of torchvision 'torchvision': [('0.11.3;', ['smooth-topk-1.0-20210817-'])], From 0e44f70703a3ab2f09aa2627ae75e119b4d3e58c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 5 Dec 2022 08:11:10 +0100 Subject: [PATCH 596/939] rename sources on download --- .../easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb index 6c52576341fb..241d7b891166 100644 --- a/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb +++ b/easybuild/easyconfigs/p/pysteps/pysteps-1.7.1-foss-2022a.eb @@ -35,16 +35,16 @@ exts_list = [ }), (name, version, { 'patches': ['pysteps-1.7.1_h5py-3.7_compat.patch'], - 'source_tmpl': 'v%(version)s.tar.gz', 'source_urls': ['https://github.com/pySTEPS/pysteps/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': [ - {'v1.7.1.tar.gz': '5063d7546d9995ec6ca52a5b4e50ef3f3c1ae43088a55e370af4aec18162a22f'}, + {'pysteps-1.7.1.tar.gz': '5063d7546d9995ec6ca52a5b4e50ef3f3c1ae43088a55e370af4aec18162a22f'}, {'pysteps-1.7.1_h5py-3.7_compat.patch': 'c2b1a47d7151a7f4072dce797c6303314c0d8fd7683b0001deb43f24357ed977'}, ], }), - ('pysteps-nwp-importers', '6ca1582', { - 'source_tmpl': '%(version)s.tar.gz', + ('pysteps-nwp-importers', '20220124', { 'source_urls': ['https://github.com/pySTEPS/pysteps-nwp-importers/archive/'], + 'sources': [{'download_filename': '6ca1582.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], 'checksums': ['e9aea5f1c49dadf0bc878822cd9403db93cf473c8ad21d8bfda799136c87f4db'], }), ] From 208570f5ae1971ea5935822a09ab1dd4c2a466ce Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 5 Dec 2022 11:10:44 +0100 Subject: [PATCH 597/939] fix homepage --- easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb index 5a87cef7f183..af605779f962 100644 --- a/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/Molden/Molden-7.1-GCCcore-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'MakeCp' name = 'Molden' version = '7.1' -homepage = 'https://www3.cmbi.umcn.nl/molden' +homepage = 'https://www.theochem.ru.nl/molden/' description = """Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac""" From 41bf0895e03a05391cbd1510136f6a9cb213ff36 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 5 Dec 2022 12:23:22 +0100 Subject: [PATCH 598/939] make sure configopts does not end up with missing space between options. --- .../OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb | 13 ++++++++++--- .../o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb | 13 ++++++++++--- 2 files changed, 20 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb index a173700d9902..fb6ba76e9420 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a-noGA.eb @@ -27,9 +27,16 @@ dependencies = [ build_shared_libs = True -configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' -configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' -configopts += '-DMPI=OFF -DGA=OFF ' +_copts = [ + '-DLINALG=MKL', + '-DMKLROOT=$MKLROOT', + '-DOPENMP=ON', + '-DTOOLS=ON', + '-DFDE=ON', + '-DMPI=OFF', + '-DGA=OFF', +] +configopts = ' '.join(_copts) modextrapaths = {'PATH': ''} modextravars = { diff --git a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb index 06c248940750..412aae94403a 100644 --- a/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb +++ b/easybuild/easyconfigs/o/OpenMolcas/OpenMolcas-22.10-intel-2022a.eb @@ -28,9 +28,16 @@ dependencies = [ build_shared_libs = True preconfigopts = 'GAROOT=$EBROOTGLOBALARRAYS' -configopts = '-DLINALG=MKL -DMKLROOT=$MKLROOT ' -configopts += '-DOPENMP=ON -DTOOLS=ON -DFDE=ON' -configopts += '-DMPI=ON -DGA=ON ' +_copts = [ + '-DLINALG=MKL', + '-DMKLROOT=$MKLROOT', + '-DOPENMP=ON', + '-DTOOLS=ON', + '-DFDE=ON', + '-DMPI=ON', + '-DGA=ON', +] +configopts = ' '.join(_copts) modextrapaths = {'PATH': ''} modextravars = { From 452419edf55084e67600bda613c37c90273b91e4 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Mon, 5 Dec 2022 16:23:57 +0100 Subject: [PATCH 599/939] Skip remaining PyTorch 1.12.1 test timeout --- .../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 7f1ab7e67f8f..d70fb0603782 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 @@ -24,6 +24,7 @@ patches = [ 'PyTorch-1.11.0_increase_c10d_gloo_timeout.patch', 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', + 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -64,6 +65,8 @@ checksums = [ # PyTorch-1.11.0_increase-distributed-test-timeout.patch '087ad20163a1291773ae3457569b80523080eb3731e210946459b2333a919f3f', 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch + # PyTorch-1.11.1_skip-test_init_from_local_shards.patch + '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch From d4c8979e46f2bb5c2065e99e9e03c179baec11c7 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 6 Dec 2022 12:58:28 +0100 Subject: [PATCH 600/939] adding easyconfigs: SAP-1.1.3-GCC-11.3.0.eb --- .../easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..0b8512ddefa1 --- /dev/null +++ b/easybuild/easyconfigs/s/SAP/SAP-1.1.3-GCC-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'ConfigureMake' + +name = 'SAP' +version = '1.1.3' + +homepage = 'https://github.com/mathbio-nimr-mrc-ac-uk/SAP' +description = "SAP is a pairwise structure alignment via double dynamic programming" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +github_account = 'mathbio-nimr-mrc-ac-uk' +source_urls = [GITHUB_SOURCE] +sources = ['v.%(version)s.tar.gz'] +checksums = ['1ee5025f8a900cd9d9c490f7038b98d80a619e3015f2dc97b869ea3033c459e0'] + +builddependencies = [ + ('Autotools', '20220317'), +] + +dependencies = [ + ('Perl', '5.34.1'), +] + +preconfigopts = "autoreconf -f -i && " + +sanity_check_paths = { + 'files': ['bin/sap'], + 'dirs': [], +} + +moduleclass = 'bio' From 7e18786d5bbe93fbf3713c3292dab0efce325436 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Dec 2022 17:23:10 +0100 Subject: [PATCH 601/939] adding easyconfigs: DendroPy-4.5.2-GCCcore-11.3.0.eb --- .../DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1ffdbf30d5e3 --- /dev/null +++ b/easybuild/easyconfigs/d/DendroPy/DendroPy-4.5.2-GCCcore-11.3.0.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 = '4.5.2' + +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': '11.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['3e5d2522170058ebc8d1ee63a7f2d25b915e34957dc02693ebfdc15f347a0101'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +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' From e580ce3034dd84c87617e784fcddad7c820f8035 Mon Sep 17 00:00:00 2001 From: Fokke Dijkstra Date: Tue, 6 Dec 2022 17:24:05 +0100 Subject: [PATCH 602/939] adding easyconfigs: arpack-ng-3.8.0-foss-2022a.eb --- .../a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb new file mode 100644 index 000000000000..7aba9e12ea2f --- /dev/null +++ b/easybuild/easyconfigs/a/arpack-ng/arpack-ng-3.8.0-foss-2022a.eb @@ -0,0 +1,38 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'ConfigureMake' + +name = 'arpack-ng' +version = "3.8.0" + +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': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +github_account = 'opencollab' +source_urls = [GITHUB_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['ada5aeb3878874383307239c9235b716a8a170c6d096a6625bfd529844df003d'] + +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"' + +sanity_check_paths = { + 'files': ["lib64/libarpack.la", "lib64/libarpack.%s" % SHLIB_EXT, + "lib64/libparpack.la", "lib64/libparpack.%s" % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'numlib' From cae54a5b0b8c86e09f88c1c9ffcdca6a7d82f8d1 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Tue, 6 Dec 2022 16:40:37 +0000 Subject: [PATCH 603/939] fix patches and improve EC --- .../s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb | 23 ++++++++++++++----- .../s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch | 2 +- .../s/SPOOLES/SPOOLES-2.2_shared-libs.patch | 12 +++++----- 3 files changed, 24 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb index 1713aedf476d..dcbd212c988f 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2-gompi-2021a.eb @@ -19,22 +19,33 @@ patches = [ ] checksums = [ {'spooles.2.2.tgz': 'a84559a0e987a1e423055ef4fdf3035d55b65bbe4bf915efaa1a35bef7f8c5dd'}, - {'SPOOLES-2.2_build-mpi-mt.patch': 'a4abc168c660f4af55feb865c5559304a099755e2c46ebf09fabd83bb1636d2c'}, - {'SPOOLES-2.2_shared-libs.patch': '7b767a699679740ec2a4acd12e66c4a3656a276c354f61436e82cb4d448741f4'}, + {'SPOOLES-2.2_build-mpi-mt.patch': 'c983c7f37eb0904959cd2f6dff0b1fdb6a36440ca2a044fb2d324fd301e3dd7c'}, + {'SPOOLES-2.2_shared-libs.patch': 'bca50e13e3c552240f7494c4d9f69be8725054c9f79ebc82dbe6b7531588d09e'}, ] builddependencies = [ + ('Autotools', '20210128'), ('Perl', '5.32.1', '-minimal'), ] build_cmd_targets = 'lib' -buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="$MPI_LIB_DIR" MPI_INCLUDE_DIR="$MPI_INC_DIR"' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" MPI_LIB_PATH="-L$MPI_LIB_DIR" MPI_INCLUDE_DIR="-I$MPI_INC_DIR"' -files_to_copy = ['*'] +files_to_copy = [ + (['libspooles*'], 'lib'), +] + +# install header files, keeping relative subdirectories +_install_headers = " ".join([ + "cd %(builddir)s && mkdir -p %(installdir)s/include/spooles &&", + "find . -name '*.h' -print -exec install -D {} %(installdir)s/include/spooles/{} \;" +]) + +postinstallcmds = [_install_headers] sanity_check_paths = { - 'files': [], - 'dirs': ['lib'], + 'files': ['lib/lib%%(namelower)s.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include/spooles'], } moduleclass = 'math' diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch index 59466c19b068..29c060a2d41c 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_build-mpi-mt.patch @@ -20,7 +20,7 @@ diff -Nru spooles-2.2.orig/MPI/src/makefile spooles-2.2.p1/MPI/src/makefile clean : - rm -f *.a *.o + -+makelib: ++makeLib: + perl ../../makeLib > makeG + make -f makeG + rm -f makeG diff --git a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch index d94230433834..0de7fd03168d 100644 --- a/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch +++ b/easybuild/easyconfigs/s/SPOOLES/SPOOLES-2.2_shared-libs.patch @@ -9,8 +9,8 @@ diff -Nru spooles-2.2.p1/makefile spooles-2.2.p2/makefile cd misc ; make lib -#cd MPI ; make lib -#cd MT ; make lib -+ MPI ; make lib -+ MT ; make lib ++ cd MPI ; make lib ++ cd MT ; make lib + $(CC) -shared */*/*.lo -Wl,-soname,libspooles.so.2.2 -o libspooles.so.2.2 -lmpi -lpthread -lm + ln -s libspooles.so.2.2 libspooles.so @@ -19,7 +19,7 @@ diff -Nru spooles-2.2.p1/makefile spooles-2.2.p2/makefile diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib --- spooles-2.2.p1/makeLib 2022-11-25 16:06:54.000000000 +0000 +++ spooles-2.2.p2/makeLib 2022-11-25 16:13:02.000000000 +0000 -@@ -64,14 +64,21 @@ +@@ -64,14 +64,19 @@ $srcname = " \\\n " . $src ; print $srcname ; } @@ -32,8 +32,8 @@ diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib - $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o + $(PURIFY) $(CC) -c $(CFLAGS) $*.c -o $(OBJ)_$*.o $(MPI_INCLUDE_DIR) - ../../spooles.a : ${OBJ_FILES} - $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o +-../../spooles.a : ${OBJ_FILES} +- $(AR) $(ARFLAGS) ../../spooles.a $(OBJ)_*.o +.c.lo: + $(PURIFY) $(CC) -c $(CFLAGS) $*.c -fPIC -DPIC -o $(OBJ)_$*.lo $(MPI_INCLUDE_DIR) + @@ -41,5 +41,5 @@ diff -Nru spooles-2.2.p1/makeLib spooles-2.2.p2/makeLib + $(AR) $(ARFLAGS) ../../libspooles.a $(OBJ)_*.o rm -f $(OBJ)_*.o - $(RANLIB) ../../spooles.a -+ $(RANLIB) ../../linspooles.a ++ $(RANLIB) ../../libspooles.a EOF From 3ce55b350f7f12462f67e75d6e5cd06674f9aec5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Dec 2022 17:36:07 +0000 Subject: [PATCH 604/939] Steal Barts patches --- .../FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch | 24 + ...exiBLAS-3.0.4_fix-wrapper_blas_intel.patch | 6750 +++++++++++++++++ .../FlexiBLAS-3.0.4_remove-semicolon.patch | 15 + .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 13 +- .../FlexiBLAS-3.2.0_remove-intel-suffix.patch | 16 + 5 files changed, 6817 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch create mode 100644 easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch new file mode 100644 index 000000000000..65afad7a02a9 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-imkl.patch @@ -0,0 +1,24 @@ +CMake-related fixes to use correct backend for MKL + +Author: Bart Oldeman +diff -ur flexiblas-3.0.4/src/CMakeLists.txt flexiblas-3.0.4.new/src/CMakeLists.txt +--- flexiblas-3.0.4/src/CMakeLists.txt 2020-10-22 09:07:49.000000000 +0000 ++++ flexiblas-3.0.4.new/src/CMakeLists.txt 2021-09-28 17:28:59.862127651 +0000 +@@ -331,7 +331,7 @@ + INCLUDE(CheckFunctionExists) + + # SET(BLA_STATIC TRUE) +-MACRO(BuildBackendBlas VENDOR BACKEND_CODE) ++MACRO(BuildBackendBlas VENDOR BACKEND_CODE_PARAM) + MESSAGE(STATUS "Build additional BLAS interface: ${VENDOR}") + MESSAGE(STATUS "-- Libs: ${${VENDOR}_LIBRARY}") + MESSAGE(STATUS "-- Linker Flags: ${${VENDOR}_LINKER_FLAGS}") +@@ -356,6 +356,8 @@ + # Use the MKL Backend Code if it is MKL + IF(_MKL_VERSION) + SET(BACKEND_CODE backends/intel_mkl/backend.c) ++ ELSE() ++ SET(BACKEND_CODE ${BACKEND_CODE_PARAM}) + ENDIF() + + SET(CMAKE_REQUIRED_LIBRARIES ${__CMAKE_REQUIRED_LIBRARIES}) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch new file mode 100644 index 000000000000..ce6b2d8b3ab8 --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch @@ -0,0 +1,6750 @@ +Sync intel with gnu wrapper. The only difference should be in [cz]dot[uc]; without +these wrapper_blas_intel.c won't compile. + +Bart Oldeman +diff -ur flexiblas-3.0.4/src/wrapper_blas_intel.c flexiblas-3.0.4.new/src/wrapper_blas_intel.c +--- flexiblas-3.0.4/src/wrapper_blas_intel.c 2020-10-22 09:07:55.000000000 +0000 ++++ flexiblas-3.0.4.new/src/wrapper_blas_intel.c 2021-10-03 22:52:02.359617295 +0000 +@@ -235,6 +235,8 @@ + return 0; + } + ++static TLS_STORE uint8_t hook_pos_caxpy = 0; ++ + void FC_GLOBAL(caxpy,CAXPY)(blasint* n, float complex* ca, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* ca, void* cx, void* incx, void* cy, void* incy); +@@ -261,6 +263,40 @@ + + + ++void flexiblas_real_caxpy_(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cy, void* incy); ++ ++ fn = current_backend->blas.caxpy.f77_blas_function; ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_caxpy(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_caxpy_"))); ++ ++ ++void flexiblas_chain_caxpy_(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cy, void* incy); ++ ++ ++ ++ hook_pos_caxpy++; ++ if ( hook_pos_caxpy < __flexiblas_hooks->caxpy.nhook ) { ++ fn = __flexiblas_hooks->caxpy.f77_hook_function[hook_pos_caxpy]; ++ } else { ++ hook_pos_caxpy = 0; ++ fn = current_backend->blas.caxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_caxpy(void* n, void* ca, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_caxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ccopy = 0; ++ + void FC_GLOBAL(ccopy,CCOPY)(blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -287,6 +323,40 @@ + + + ++void flexiblas_real_ccopy_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ fn = current_backend->blas.ccopy.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_ccopy(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_ccopy_"))); ++ ++ ++void flexiblas_chain_ccopy_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ ++ ++ hook_pos_ccopy++; ++ if ( hook_pos_ccopy < __flexiblas_hooks->ccopy.nhook ) { ++ fn = __flexiblas_hooks->ccopy.f77_hook_function[hook_pos_ccopy]; ++ } else { ++ hook_pos_ccopy = 0; ++ fn = current_backend->blas.ccopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_ccopy(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_ccopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cdotc = 0; ++ + void FC_GLOBAL(cdotc,CDOTC)( float complex* returnvalue, blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -327,6 +397,56 @@ + + + ++void flexiblas_real_cdotc_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ fn = current_backend->blas.cdotc.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_cdotc( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_cdotc_"))); ++ ++ ++void flexiblas_chain_cdotc_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ ++ ++ hook_pos_cdotc++; ++ if ( hook_pos_cdotc < __flexiblas_hooks->cdotc.nhook ) { ++ fn = __flexiblas_hooks->cdotc.f77_hook_function[hook_pos_cdotc]; ++ } else { ++ hook_pos_cdotc = 0; ++ fn = current_backend->blas.cdotc.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_cdotc( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_cdotc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cdotu = 0; ++ + void FC_GLOBAL(cdotu,CDOTU)( float complex* returnvalue, blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -367,6 +487,56 @@ + + + ++void flexiblas_real_cdotu_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ fn = current_backend->blas.cdotu.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_cdotu( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_cdotu_"))); ++ ++ ++void flexiblas_chain_cdotu_( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ float complex (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ void (*fn_intel) (float complex *ret, void* n, void* cx, void* incx, void* cy, void* incy); ++ float complex ret; ++ ++ ++ ++ hook_pos_cdotu++; ++ if ( hook_pos_cdotu < __flexiblas_hooks->cdotu.nhook ) { ++ fn = __flexiblas_hooks->cdotu.f77_hook_function[hook_pos_cdotu]; ++ } else { ++ hook_pos_cdotu = 0; ++ fn = current_backend->blas.cdotu.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ } ++ ++ *((float complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_cdotu( void * returnvalue, void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_cdotu_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgbmv = 0; ++ + void FC_GLOBAL(cgbmv,CGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -393,6 +563,40 @@ + + + ++void flexiblas_real_cgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.cgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_cgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_cgbmv_"))); ++ ++ ++void flexiblas_chain_cgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_cgbmv++; ++ if ( hook_pos_cgbmv < __flexiblas_hooks->cgbmv.nhook ) { ++ fn = __flexiblas_hooks->cgbmv.f77_hook_function[hook_pos_cgbmv]; ++ } else { ++ hook_pos_cgbmv = 0; ++ fn = current_backend->blas.cgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_cgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_cgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgemm = 0; ++ + void FC_GLOBAL(cgemm,CGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -419,6 +623,40 @@ + + + ++void flexiblas_real_cgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.cgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_cgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_cgemm_"))); ++ ++ ++void flexiblas_chain_cgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_cgemm++; ++ if ( hook_pos_cgemm < __flexiblas_hooks->cgemm.nhook ) { ++ fn = __flexiblas_hooks->cgemm.f77_hook_function[hook_pos_cgemm]; ++ } else { ++ hook_pos_cgemm = 0; ++ fn = current_backend->blas.cgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_cgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_cgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgemv = 0; ++ + void FC_GLOBAL(cgemv,CGEMV)(char* trans, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -445,6 +683,40 @@ + + + ++void flexiblas_real_cgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.cgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_cgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_cgemv_"))); ++ ++ ++void flexiblas_chain_cgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_cgemv++; ++ if ( hook_pos_cgemv < __flexiblas_hooks->cgemv.nhook ) { ++ fn = __flexiblas_hooks->cgemv.f77_hook_function[hook_pos_cgemv]; ++ } else { ++ hook_pos_cgemv = 0; ++ fn = current_backend->blas.cgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_cgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_cgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgerc = 0; ++ + void FC_GLOBAL(cgerc,CGERC)(blasint* m, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -471,6 +743,40 @@ + + + ++void flexiblas_real_cgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.cgerc.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_cgerc_"))); ++ ++ ++void flexiblas_chain_cgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_cgerc++; ++ if ( hook_pos_cgerc < __flexiblas_hooks->cgerc.nhook ) { ++ fn = __flexiblas_hooks->cgerc.f77_hook_function[hook_pos_cgerc]; ++ } else { ++ hook_pos_cgerc = 0; ++ fn = current_backend->blas.cgerc.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_cgerc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgeru = 0; ++ + void FC_GLOBAL(cgeru,CGERU)(blasint* m, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -497,6 +803,40 @@ + + + ++void flexiblas_real_cgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.cgeru.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_cgeru_"))); ++ ++ ++void flexiblas_chain_cgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_cgeru++; ++ if ( hook_pos_cgeru < __flexiblas_hooks->cgeru.nhook ) { ++ fn = __flexiblas_hooks->cgeru.f77_hook_function[hook_pos_cgeru]; ++ } else { ++ hook_pos_cgeru = 0; ++ fn = current_backend->blas.cgeru.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_cgeru_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chbmv = 0; ++ + void FC_GLOBAL(chbmv,CHBMV)(char* uplo, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -523,6 +863,40 @@ + + + ++void flexiblas_real_chbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.chbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_chbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_chbmv_"))); ++ ++ ++void flexiblas_chain_chbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_chbmv++; ++ if ( hook_pos_chbmv < __flexiblas_hooks->chbmv.nhook ) { ++ fn = __flexiblas_hooks->chbmv.f77_hook_function[hook_pos_chbmv]; ++ } else { ++ hook_pos_chbmv = 0; ++ fn = current_backend->blas.chbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_chbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_chbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chemm = 0; ++ + void FC_GLOBAL(chemm,CHEMM)(char* side, char* uplo, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -549,6 +923,40 @@ + + + ++void flexiblas_real_chemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.chemm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_chemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_chemm_"))); ++ ++ ++void flexiblas_chain_chemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_chemm++; ++ if ( hook_pos_chemm < __flexiblas_hooks->chemm.nhook ) { ++ fn = __flexiblas_hooks->chemm.f77_hook_function[hook_pos_chemm]; ++ } else { ++ hook_pos_chemm = 0; ++ fn = current_backend->blas.chemm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_chemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_chemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chemv = 0; ++ + void FC_GLOBAL(chemv,CHEMV)(char* uplo, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -575,6 +983,40 @@ + + + ++void flexiblas_real_chemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.chemv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_chemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_chemv_"))); ++ ++ ++void flexiblas_chain_chemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_chemv++; ++ if ( hook_pos_chemv < __flexiblas_hooks->chemv.nhook ) { ++ fn = __flexiblas_hooks->chemv.f77_hook_function[hook_pos_chemv]; ++ } else { ++ hook_pos_chemv = 0; ++ fn = current_backend->blas.chemv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_chemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_chemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cher = 0; ++ + void FC_GLOBAL(cher,CHER)(char* uplo, blasint* n, float* alpha, float complex* x, blasint* incx, float complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -601,6 +1043,40 @@ + + + ++void flexiblas_real_cher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.cher.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_cher_"))); ++ ++ ++void flexiblas_chain_cher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_cher++; ++ if ( hook_pos_cher < __flexiblas_hooks->cher.nhook ) { ++ fn = __flexiblas_hooks->cher.f77_hook_function[hook_pos_cher]; ++ } else { ++ hook_pos_cher = 0; ++ fn = current_backend->blas.cher.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_cher_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cher2 = 0; ++ + void FC_GLOBAL(cher2,CHER2)(char* uplo, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -627,6 +1103,40 @@ + + + ++void flexiblas_real_cher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.cher2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_cher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_cher2_"))); ++ ++ ++void flexiblas_chain_cher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_cher2++; ++ if ( hook_pos_cher2 < __flexiblas_hooks->cher2.nhook ) { ++ fn = __flexiblas_hooks->cher2.f77_hook_function[hook_pos_cher2]; ++ } else { ++ hook_pos_cher2 = 0; ++ fn = current_backend->blas.cher2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_cher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_cher2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cher2k = 0; ++ + void FC_GLOBAL(cher2k,CHER2K)(char* uplo, char* trans, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -653,6 +1163,40 @@ + + + ++void flexiblas_real_cher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.cher2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_cher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_cher2k_"))); ++ ++ ++void flexiblas_chain_cher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_cher2k++; ++ if ( hook_pos_cher2k < __flexiblas_hooks->cher2k.nhook ) { ++ fn = __flexiblas_hooks->cher2k.f77_hook_function[hook_pos_cher2k]; ++ } else { ++ hook_pos_cher2k = 0; ++ fn = current_backend->blas.cher2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_cher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_cher2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cherk = 0; ++ + void FC_GLOBAL(cherk,CHERK)(char* uplo, char* trans, blasint* n, blasint* k, float* alpha, float complex* a, blasint* lda, float* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -679,6 +1223,40 @@ + + + ++void flexiblas_real_cherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.cherk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_cherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_cherk_"))); ++ ++ ++void flexiblas_chain_cherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_cherk++; ++ if ( hook_pos_cherk < __flexiblas_hooks->cherk.nhook ) { ++ fn = __flexiblas_hooks->cherk.f77_hook_function[hook_pos_cherk]; ++ } else { ++ hook_pos_cherk = 0; ++ fn = current_backend->blas.cherk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_cherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_cherk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chpmv = 0; ++ + void FC_GLOBAL(chpmv,CHPMV)(char* uplo, blasint* n, float complex* alpha, float complex* ap, float complex* x, blasint* incx, float complex* beta, float complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -705,6 +1283,40 @@ + + + ++void flexiblas_real_chpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.chpmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_chpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_chpmv_"))); ++ ++ ++void flexiblas_chain_chpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_chpmv++; ++ if ( hook_pos_chpmv < __flexiblas_hooks->chpmv.nhook ) { ++ fn = __flexiblas_hooks->chpmv.f77_hook_function[hook_pos_chpmv]; ++ } else { ++ hook_pos_chpmv = 0; ++ fn = current_backend->blas.chpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_chpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_chpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chpr = 0; ++ + void FC_GLOBAL(chpr,CHPR)(char* uplo, blasint* n, float* alpha, float complex* x, blasint* incx, float complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -731,6 +1343,40 @@ + + + ++void flexiblas_real_chpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.chpr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_chpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_chpr_"))); ++ ++ ++void flexiblas_chain_chpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_chpr++; ++ if ( hook_pos_chpr < __flexiblas_hooks->chpr.nhook ) { ++ fn = __flexiblas_hooks->chpr.f77_hook_function[hook_pos_chpr]; ++ } else { ++ hook_pos_chpr = 0; ++ fn = current_backend->blas.chpr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_chpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_chpr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_chpr2 = 0; ++ + void FC_GLOBAL(chpr2,CHPR2)(char* uplo, blasint* n, float complex* alpha, float complex* x, blasint* incx, float complex* y, blasint* incy, float complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -757,6 +1403,40 @@ + + + ++void flexiblas_real_chpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.chpr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_chpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_chpr2_"))); ++ ++ ++void flexiblas_chain_chpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_chpr2++; ++ if ( hook_pos_chpr2 < __flexiblas_hooks->chpr2.nhook ) { ++ fn = __flexiblas_hooks->chpr2.f77_hook_function[hook_pos_chpr2]; ++ } else { ++ hook_pos_chpr2 = 0; ++ fn = current_backend->blas.chpr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_chpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_chpr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_crotg = 0; ++ + void FC_GLOBAL(crotg,CROTG)(float complex* ca, float complex* cb, float* c, float complex* s) + { + void (*fn) (void* ca, void* cb, void* c, void* s); +@@ -783,6 +1463,40 @@ + + + ++void flexiblas_real_crotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ fn = current_backend->blas.crotg.f77_blas_function; ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_crotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_real_crotg_"))); ++ ++ ++void flexiblas_chain_crotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ ++ ++ hook_pos_crotg++; ++ if ( hook_pos_crotg < __flexiblas_hooks->crotg.nhook ) { ++ fn = __flexiblas_hooks->crotg.f77_hook_function[hook_pos_crotg]; ++ } else { ++ hook_pos_crotg = 0; ++ fn = current_backend->blas.crotg.f77_blas_function; ++ } ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_crotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_chain_crotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cscal = 0; ++ + void FC_GLOBAL(cscal,CSCAL)(blasint* n, float complex* ca, float complex* cx, blasint* incx) + { + void (*fn) (void* n, void* ca, void* cx, void* incx); +@@ -809,6 +1523,40 @@ + + + ++void flexiblas_real_cscal_(void* n, void* ca, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx); ++ ++ fn = current_backend->blas.cscal.f77_blas_function; ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_cscal(void* n, void* ca, void* cx, void* incx) __attribute__((alias("flexiblas_real_cscal_"))); ++ ++ ++void flexiblas_chain_cscal_(void* n, void* ca, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx); ++ ++ ++ ++ hook_pos_cscal++; ++ if ( hook_pos_cscal < __flexiblas_hooks->cscal.nhook ) { ++ fn = __flexiblas_hooks->cscal.f77_hook_function[hook_pos_cscal]; ++ } else { ++ hook_pos_cscal = 0; ++ fn = current_backend->blas.cscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_cscal(void* n, void* ca, void* cx, void* incx) __attribute__((alias("flexiblas_chain_cscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csrot = 0; ++ + void FC_GLOBAL(csrot,CSROT)(blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy, float* c, float* s) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); +@@ -835,6 +1583,40 @@ + + + ++void flexiblas_real_csrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.csrot.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_csrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_csrot_"))); ++ ++ ++void flexiblas_chain_csrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_csrot++; ++ if ( hook_pos_csrot < __flexiblas_hooks->csrot.nhook ) { ++ fn = __flexiblas_hooks->csrot.f77_hook_function[hook_pos_csrot]; ++ } else { ++ hook_pos_csrot = 0; ++ fn = current_backend->blas.csrot.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_csrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_csrot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csscal = 0; ++ + void FC_GLOBAL(csscal,CSSCAL)(blasint* n, float* sa, float complex* cx, blasint* incx) + { + void (*fn) (void* n, void* sa, void* cx, void* incx); +@@ -861,6 +1643,40 @@ + + + ++void flexiblas_real_csscal_(void* n, void* sa, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* cx, void* incx); ++ ++ fn = current_backend->blas.csscal.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_csscal(void* n, void* sa, void* cx, void* incx) __attribute__((alias("flexiblas_real_csscal_"))); ++ ++ ++void flexiblas_chain_csscal_(void* n, void* sa, void* cx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* cx, void* incx); ++ ++ ++ ++ hook_pos_csscal++; ++ if ( hook_pos_csscal < __flexiblas_hooks->csscal.nhook ) { ++ fn = __flexiblas_hooks->csscal.f77_hook_function[hook_pos_csscal]; ++ } else { ++ hook_pos_csscal = 0; ++ fn = current_backend->blas.csscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) cx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_csscal(void* n, void* sa, void* cx, void* incx) __attribute__((alias("flexiblas_chain_csscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cswap = 0; ++ + void FC_GLOBAL(cswap,CSWAP)(blasint* n, float complex* cx, blasint* incx, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); +@@ -887,6 +1703,40 @@ + + + ++void flexiblas_real_cswap_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ fn = current_backend->blas.cswap.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_cswap(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_real_cswap_"))); ++ ++ ++void flexiblas_chain_cswap_(void* n, void* cx, void* incx, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy); ++ ++ ++ ++ hook_pos_cswap++; ++ if ( hook_pos_cswap < __flexiblas_hooks->cswap.nhook ) { ++ fn = __flexiblas_hooks->cswap.f77_hook_function[hook_pos_cswap]; ++ } else { ++ hook_pos_cswap = 0; ++ fn = current_backend->blas.cswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_cswap(void* n, void* cx, void* incx, void* cy, void* incy) __attribute__((alias("flexiblas_chain_cswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csymm = 0; ++ + void FC_GLOBAL(csymm,CSYMM)(char* side, char* uplo, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -913,6 +1763,40 @@ + + + ++void flexiblas_real_csymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.csymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_csymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_csymm_"))); ++ ++ ++void flexiblas_chain_csymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_csymm++; ++ if ( hook_pos_csymm < __flexiblas_hooks->csymm.nhook ) { ++ fn = __flexiblas_hooks->csymm.f77_hook_function[hook_pos_csymm]; ++ } else { ++ hook_pos_csymm = 0; ++ fn = current_backend->blas.csymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_csymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_csymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csyr2k = 0; ++ + void FC_GLOBAL(csyr2k,CSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -939,6 +1823,40 @@ + + + ++void flexiblas_real_csyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.csyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_csyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_csyr2k_"))); ++ ++ ++void flexiblas_chain_csyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_csyr2k++; ++ if ( hook_pos_csyr2k < __flexiblas_hooks->csyr2k.nhook ) { ++ fn = __flexiblas_hooks->csyr2k.f77_hook_function[hook_pos_csyr2k]; ++ } else { ++ hook_pos_csyr2k = 0; ++ fn = current_backend->blas.csyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_csyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_csyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_csyrk = 0; ++ + void FC_GLOBAL(csyrk,CSYRK)(char* uplo, char* trans, blasint* n, blasint* k, float complex* alpha, float complex* a, blasint* lda, float complex* beta, float complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -965,6 +1883,40 @@ + + + ++void flexiblas_real_csyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.csyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_csyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_csyrk_"))); ++ ++ ++void flexiblas_chain_csyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_csyrk++; ++ if ( hook_pos_csyrk < __flexiblas_hooks->csyrk.nhook ) { ++ fn = __flexiblas_hooks->csyrk.f77_hook_function[hook_pos_csyrk]; ++ } else { ++ hook_pos_csyrk = 0; ++ fn = current_backend->blas.csyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_csyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_csyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctbmv = 0; ++ + void FC_GLOBAL(ctbmv,CTBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -991,6 +1943,40 @@ + + + ++void flexiblas_real_ctbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctbmv_"))); ++ ++ ++void flexiblas_chain_ctbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctbmv++; ++ if ( hook_pos_ctbmv < __flexiblas_hooks->ctbmv.nhook ) { ++ fn = __flexiblas_hooks->ctbmv.f77_hook_function[hook_pos_ctbmv]; ++ } else { ++ hook_pos_ctbmv = 0; ++ fn = current_backend->blas.ctbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctbsv = 0; ++ + void FC_GLOBAL(ctbsv,CTBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -1017,6 +2003,40 @@ + + + ++void flexiblas_real_ctbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctbsv_"))); ++ ++ ++void flexiblas_chain_ctbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctbsv++; ++ if ( hook_pos_ctbsv < __flexiblas_hooks->ctbsv.nhook ) { ++ fn = __flexiblas_hooks->ctbsv.f77_hook_function[hook_pos_ctbsv]; ++ } else { ++ hook_pos_ctbsv = 0; ++ fn = current_backend->blas.ctbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctpmv = 0; ++ + void FC_GLOBAL(ctpmv,CTPMV)(char* uplo, char* trans, char* diag, blasint* n, float complex* ap, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1043,6 +2063,40 @@ + + + ++void flexiblas_real_ctpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ctpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ctpmv_"))); ++ ++ ++void flexiblas_chain_ctpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctpmv++; ++ if ( hook_pos_ctpmv < __flexiblas_hooks->ctpmv.nhook ) { ++ fn = __flexiblas_hooks->ctpmv.f77_hook_function[hook_pos_ctpmv]; ++ } else { ++ hook_pos_ctpmv = 0; ++ fn = current_backend->blas.ctpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctpsv = 0; ++ + void FC_GLOBAL(ctpsv,CTPSV)(char* uplo, char* trans, char* diag, blasint* n, float complex* ap, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1069,6 +2123,40 @@ + + + ++void flexiblas_real_ctpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ctpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ctpsv_"))); ++ ++ ++void flexiblas_chain_ctpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctpsv++; ++ if ( hook_pos_ctpsv < __flexiblas_hooks->ctpsv.nhook ) { ++ fn = __flexiblas_hooks->ctpsv.f77_hook_function[hook_pos_ctpsv]; ++ } else { ++ hook_pos_ctpsv = 0; ++ fn = current_backend->blas.ctpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrmm = 0; ++ + void FC_GLOBAL(ctrmm,CTRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -1095,6 +2183,40 @@ + + + ++void flexiblas_real_ctrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ctrmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ctrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ctrmm_"))); ++ ++ ++void flexiblas_chain_ctrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ctrmm++; ++ if ( hook_pos_ctrmm < __flexiblas_hooks->ctrmm.nhook ) { ++ fn = __flexiblas_hooks->ctrmm.f77_hook_function[hook_pos_ctrmm]; ++ } else { ++ hook_pos_ctrmm = 0; ++ fn = current_backend->blas.ctrmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ctrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ctrmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrmv = 0; ++ + void FC_GLOBAL(ctrmv,CTRMV)(char* uplo, char* trans, char* diag, blasint* n, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -1121,6 +2243,40 @@ + + + ++void flexiblas_real_ctrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctrmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctrmv_"))); ++ ++ ++void flexiblas_chain_ctrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctrmv++; ++ if ( hook_pos_ctrmv < __flexiblas_hooks->ctrmv.nhook ) { ++ fn = __flexiblas_hooks->ctrmv.f77_hook_function[hook_pos_ctrmv]; ++ } else { ++ hook_pos_ctrmv = 0; ++ fn = current_backend->blas.ctrmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctrmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrsm = 0; ++ + void FC_GLOBAL(ctrsm,CTRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -1147,6 +2303,40 @@ + + + ++void flexiblas_real_ctrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ctrsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ctrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ctrsm_"))); ++ ++ ++void flexiblas_chain_ctrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ctrsm++; ++ if ( hook_pos_ctrsm < __flexiblas_hooks->ctrsm.nhook ) { ++ fn = __flexiblas_hooks->ctrsm.f77_hook_function[hook_pos_ctrsm]; ++ } else { ++ hook_pos_ctrsm = 0; ++ fn = current_backend->blas.ctrsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ctrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ctrsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ctrsv = 0; ++ + void FC_GLOBAL(ctrsv,CTRSV)(char* uplo, char* trans, char* diag, blasint* n, float complex* a, blasint* lda, float complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -1173,6 +2363,40 @@ + + + ++void flexiblas_real_ctrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ctrsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ctrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ctrsv_"))); ++ ++ ++void flexiblas_chain_ctrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ctrsv++; ++ if ( hook_pos_ctrsv < __flexiblas_hooks->ctrsv.nhook ) { ++ fn = __flexiblas_hooks->ctrsv.f77_hook_function[hook_pos_ctrsv]; ++ } else { ++ hook_pos_ctrsv = 0; ++ fn = current_backend->blas.ctrsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ctrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ctrsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dasum = 0; ++ + double FC_GLOBAL(dasum,DASUM)(blasint* n, double* dx, blasint* incx) + { + double (*fn) (void* n, void* dx, void* incx); +@@ -1200,6 +2424,42 @@ + + + ++double flexiblas_real_dasum_(void* n, void* dx, void* incx) ++{ ++ double (*fn) (void* n, void* dx, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dasum.f77_blas_function; ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dasum(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_real_dasum_"))); ++ ++ ++double flexiblas_chain_dasum_(void* n, void* dx, void* incx) ++{ ++ double (*fn) (void* n, void* dx, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dasum++; ++ if ( hook_pos_dasum < __flexiblas_hooks->dasum.nhook ) { ++ fn = __flexiblas_hooks->dasum.f77_hook_function[hook_pos_dasum]; ++ } else { ++ hook_pos_dasum = 0; ++ fn = current_backend->blas.dasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dasum(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_chain_dasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_daxpy = 0; ++ + void FC_GLOBAL(daxpy,DAXPY)(blasint* n, double* da, double* dx, blasint* incx, double* dy, blasint* incy) + { + void (*fn) (void* n, void* da, void* dx, void* incx, void* dy, void* incy); +@@ -1226,6 +2486,40 @@ + + + ++void flexiblas_real_daxpy_(void* n, void* da, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* dy, void* incy); ++ ++ fn = current_backend->blas.daxpy.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_daxpy(void* n, void* da, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_daxpy_"))); ++ ++ ++void flexiblas_chain_daxpy_(void* n, void* da, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* dy, void* incy); ++ ++ ++ ++ hook_pos_daxpy++; ++ if ( hook_pos_daxpy < __flexiblas_hooks->daxpy.nhook ) { ++ fn = __flexiblas_hooks->daxpy.f77_hook_function[hook_pos_daxpy]; ++ } else { ++ hook_pos_daxpy = 0; ++ fn = current_backend->blas.daxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_daxpy(void* n, void* da, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_daxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dcopy = 0; ++ + void FC_GLOBAL(dcopy,DCOPY)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); +@@ -1252,6 +2546,40 @@ + + + ++void flexiblas_real_dcopy_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ fn = current_backend->blas.dcopy.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dcopy(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_dcopy_"))); ++ ++ ++void flexiblas_chain_dcopy_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ ++ ++ hook_pos_dcopy++; ++ if ( hook_pos_dcopy < __flexiblas_hooks->dcopy.nhook ) { ++ fn = __flexiblas_hooks->dcopy.f77_hook_function[hook_pos_dcopy]; ++ } else { ++ hook_pos_dcopy = 0; ++ fn = current_backend->blas.dcopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dcopy(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_dcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ddot = 0; ++ + double FC_GLOBAL(ddot,DDOT)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy) + { + double (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); +@@ -1279,6 +2607,42 @@ + + + ++double flexiblas_real_ddot_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ double (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ double ret; ++ ++ fn = current_backend->blas.ddot.f77_blas_function; ++ ret = fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_real_ddot(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_ddot_"))); ++ ++ ++double flexiblas_chain_ddot_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ double (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ double ret; ++ ++ ++ ++ hook_pos_ddot++; ++ if ( hook_pos_ddot < __flexiblas_hooks->ddot.nhook ) { ++ fn = __flexiblas_hooks->ddot.f77_hook_function[hook_pos_ddot]; ++ } else { ++ hook_pos_ddot = 0; ++ fn = current_backend->blas.ddot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_chain_ddot(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_ddot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgbmv = 0; ++ + void FC_GLOBAL(dgbmv,DGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1305,6 +2669,40 @@ + + + ++void flexiblas_real_dgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dgbmv_"))); ++ ++ ++void flexiblas_chain_dgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dgbmv++; ++ if ( hook_pos_dgbmv < __flexiblas_hooks->dgbmv.nhook ) { ++ fn = __flexiblas_hooks->dgbmv.f77_hook_function[hook_pos_dgbmv]; ++ } else { ++ hook_pos_dgbmv = 0; ++ fn = current_backend->blas.dgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgemm = 0; ++ + void FC_GLOBAL(dgemm,DGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* b, blasint* ldb, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -1331,6 +2729,40 @@ + + + ++void flexiblas_real_dgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dgemm_"))); ++ ++ ++void flexiblas_chain_dgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dgemm++; ++ if ( hook_pos_dgemm < __flexiblas_hooks->dgemm.nhook ) { ++ fn = __flexiblas_hooks->dgemm.f77_hook_function[hook_pos_dgemm]; ++ } else { ++ hook_pos_dgemm = 0; ++ fn = current_backend->blas.dgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgemv = 0; ++ + void FC_GLOBAL(dgemv,DGEMV)(char* trans, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1357,6 +2789,40 @@ + + + ++void flexiblas_real_dgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dgemv_"))); ++ ++ ++void flexiblas_chain_dgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dgemv++; ++ if ( hook_pos_dgemv < __flexiblas_hooks->dgemv.nhook ) { ++ fn = __flexiblas_hooks->dgemv.f77_hook_function[hook_pos_dgemv]; ++ } else { ++ hook_pos_dgemv = 0; ++ fn = current_backend->blas.dgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dger = 0; ++ + void FC_GLOBAL(dger,DGER)(blasint* m, blasint* n, double* alpha, double* x, blasint* incx, double* y, blasint* incy, double* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -1383,6 +2849,40 @@ + + + ++void flexiblas_real_dger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.dger.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_dger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_dger_"))); ++ ++ ++void flexiblas_chain_dger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_dger++; ++ if ( hook_pos_dger < __flexiblas_hooks->dger.nhook ) { ++ fn = __flexiblas_hooks->dger.f77_hook_function[hook_pos_dger]; ++ } else { ++ hook_pos_dger = 0; ++ fn = current_backend->blas.dger.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_dger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_dger_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dnrm2 = 0; ++ + double FC_GLOBAL(dnrm2,DNRM2)(blasint* n, double* x, blasint* incx) + { + double (*fn) (void* n, void* x, void* incx); +@@ -1410,6 +2910,42 @@ + + + ++double flexiblas_real_dnrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dnrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_dnrm2_"))); ++ ++ ++double flexiblas_chain_dnrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dnrm2++; ++ if ( hook_pos_dnrm2 < __flexiblas_hooks->dnrm2.nhook ) { ++ fn = __flexiblas_hooks->dnrm2.f77_hook_function[hook_pos_dnrm2]; ++ } else { ++ hook_pos_dnrm2 = 0; ++ fn = current_backend->blas.dnrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_dnrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drot = 0; ++ + void FC_GLOBAL(drot,DROT)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy, double* c, double* s) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s); +@@ -1436,6 +2972,40 @@ + + + ++void flexiblas_real_drot_(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.drot.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_drot(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_drot_"))); ++ ++ ++void flexiblas_chain_drot_(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_drot++; ++ if ( hook_pos_drot < __flexiblas_hooks->drot.nhook ) { ++ fn = __flexiblas_hooks->drot.f77_hook_function[hook_pos_drot]; ++ } else { ++ hook_pos_drot = 0; ++ fn = current_backend->blas.drot.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_drot(void* n, void* dx, void* incx, void* dy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_drot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drotg = 0; ++ + void FC_GLOBAL(drotg,DROTG)(double* da, double* db, double* c, double* s) + { + void (*fn) (void* da, void* db, void* c, void* s); +@@ -1462,6 +3032,40 @@ + + + ++void flexiblas_real_drotg_(void* da, void* db, void* c, void* s) ++{ ++ void (*fn) (void* da, void* db, void* c, void* s); ++ ++ fn = current_backend->blas.drotg.f77_blas_function; ++ fn((void*) da, (void*) db, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_drotg(void* da, void* db, void* c, void* s) __attribute__((alias("flexiblas_real_drotg_"))); ++ ++ ++void flexiblas_chain_drotg_(void* da, void* db, void* c, void* s) ++{ ++ void (*fn) (void* da, void* db, void* c, void* s); ++ ++ ++ ++ hook_pos_drotg++; ++ if ( hook_pos_drotg < __flexiblas_hooks->drotg.nhook ) { ++ fn = __flexiblas_hooks->drotg.f77_hook_function[hook_pos_drotg]; ++ } else { ++ hook_pos_drotg = 0; ++ fn = current_backend->blas.drotg.f77_blas_function; ++ } ++ fn((void*) da, (void*) db, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_drotg(void* da, void* db, void* c, void* s) __attribute__((alias("flexiblas_chain_drotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drotm = 0; ++ + void FC_GLOBAL(drotm,DROTM)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy, double* dparam) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* dparam); +@@ -1488,6 +3092,40 @@ + + + ++void flexiblas_real_drotm_(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* dparam); ++ ++ fn = current_backend->blas.drotm.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) dparam); ++ ++ return; ++} ++void flexiblas_real_drotm(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) __attribute__((alias("flexiblas_real_drotm_"))); ++ ++ ++void flexiblas_chain_drotm_(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy, void* dparam); ++ ++ ++ ++ hook_pos_drotm++; ++ if ( hook_pos_drotm < __flexiblas_hooks->drotm.nhook ) { ++ fn = __flexiblas_hooks->drotm.f77_hook_function[hook_pos_drotm]; ++ } else { ++ hook_pos_drotm = 0; ++ fn = current_backend->blas.drotm.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy, (void*) dparam); ++ ++ return; ++} ++void flexiblas_chain_drotm(void* n, void* dx, void* incx, void* dy, void* incy, void* dparam) __attribute__((alias("flexiblas_chain_drotm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_drotmg = 0; ++ + void FC_GLOBAL(drotmg,DROTMG)(double* dd1, double* dd2, double* dx1, double* dy1, double* dparam) + { + void (*fn) (void* dd1, void* dd2, void* dx1, void* dy1, void* dparam); +@@ -1514,6 +3152,40 @@ + + + ++void flexiblas_real_drotmg_(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) ++{ ++ void (*fn) (void* dd1, void* dd2, void* dx1, void* dy1, void* dparam); ++ ++ fn = current_backend->blas.drotmg.f77_blas_function; ++ fn((void*) dd1, (void*) dd2, (void*) dx1, (void*) dy1, (void*) dparam); ++ ++ return; ++} ++void flexiblas_real_drotmg(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) __attribute__((alias("flexiblas_real_drotmg_"))); ++ ++ ++void flexiblas_chain_drotmg_(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) ++{ ++ void (*fn) (void* dd1, void* dd2, void* dx1, void* dy1, void* dparam); ++ ++ ++ ++ hook_pos_drotmg++; ++ if ( hook_pos_drotmg < __flexiblas_hooks->drotmg.nhook ) { ++ fn = __flexiblas_hooks->drotmg.f77_hook_function[hook_pos_drotmg]; ++ } else { ++ hook_pos_drotmg = 0; ++ fn = current_backend->blas.drotmg.f77_blas_function; ++ } ++ fn((void*) dd1, (void*) dd2, (void*) dx1, (void*) dy1, (void*) dparam); ++ ++ return; ++} ++void flexiblas_chain_drotmg(void* dd1, void* dd2, void* dx1, void* dy1, void* dparam) __attribute__((alias("flexiblas_chain_drotmg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsbmv = 0; ++ + void FC_GLOBAL(dsbmv,DSBMV)(char* uplo, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1540,6 +3212,40 @@ + + + ++void flexiblas_real_dsbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dsbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dsbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dsbmv_"))); ++ ++ ++void flexiblas_chain_dsbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dsbmv++; ++ if ( hook_pos_dsbmv < __flexiblas_hooks->dsbmv.nhook ) { ++ fn = __flexiblas_hooks->dsbmv.f77_hook_function[hook_pos_dsbmv]; ++ } else { ++ hook_pos_dsbmv = 0; ++ fn = current_backend->blas.dsbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dsbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dsbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dscal = 0; ++ + void FC_GLOBAL(dscal,DSCAL)(blasint* n, double* da, double* dx, blasint* incx) + { + void (*fn) (void* n, void* da, void* dx, void* incx); +@@ -1566,6 +3272,40 @@ + + + ++void flexiblas_real_dscal_(void* n, void* da, void* dx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx); ++ ++ fn = current_backend->blas.dscal.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dscal(void* n, void* da, void* dx, void* incx) __attribute__((alias("flexiblas_real_dscal_"))); ++ ++ ++void flexiblas_chain_dscal_(void* n, void* da, void* dx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx); ++ ++ ++ ++ hook_pos_dscal++; ++ if ( hook_pos_dscal < __flexiblas_hooks->dscal.nhook ) { ++ fn = __flexiblas_hooks->dscal.f77_hook_function[hook_pos_dscal]; ++ } else { ++ hook_pos_dscal = 0; ++ fn = current_backend->blas.dscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dscal(void* n, void* da, void* dx, void* incx) __attribute__((alias("flexiblas_chain_dscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsdot = 0; ++ + double FC_GLOBAL(dsdot,DSDOT)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + double (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -1593,6 +3333,42 @@ + + + ++double flexiblas_real_dsdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ double (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ double ret; ++ ++ fn = current_backend->blas.dsdot.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_real_dsdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_dsdot_"))); ++ ++ ++double flexiblas_chain_dsdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ double (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ double ret; ++ ++ ++ ++ hook_pos_dsdot++; ++ if ( hook_pos_dsdot < __flexiblas_hooks->dsdot.nhook ) { ++ fn = __flexiblas_hooks->dsdot.f77_hook_function[hook_pos_dsdot]; ++ } else { ++ hook_pos_dsdot = 0; ++ fn = current_backend->blas.dsdot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++double flexiblas_chain_dsdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_dsdot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dspmv = 0; ++ + void FC_GLOBAL(dspmv,DSPMV)(char* uplo, blasint* n, double* alpha, double* ap, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1619,6 +3395,40 @@ + + + ++void flexiblas_real_dspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dspmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dspmv_"))); ++ ++ ++void flexiblas_chain_dspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dspmv++; ++ if ( hook_pos_dspmv < __flexiblas_hooks->dspmv.nhook ) { ++ fn = __flexiblas_hooks->dspmv.f77_hook_function[hook_pos_dspmv]; ++ } else { ++ hook_pos_dspmv = 0; ++ fn = current_backend->blas.dspmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dspmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dspr = 0; ++ + void FC_GLOBAL(dspr,DSPR)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -1645,6 +3455,40 @@ + + + ++void flexiblas_real_dspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.dspr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_dspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_dspr_"))); ++ ++ ++void flexiblas_chain_dspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_dspr++; ++ if ( hook_pos_dspr < __flexiblas_hooks->dspr.nhook ) { ++ fn = __flexiblas_hooks->dspr.f77_hook_function[hook_pos_dspr]; ++ } else { ++ hook_pos_dspr = 0; ++ fn = current_backend->blas.dspr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_dspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_dspr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dspr2 = 0; ++ + void FC_GLOBAL(dspr2,DSPR2)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* y, blasint* incy, double* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -1671,6 +3515,40 @@ + + + ++void flexiblas_real_dspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.dspr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_dspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_dspr2_"))); ++ ++ ++void flexiblas_chain_dspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_dspr2++; ++ if ( hook_pos_dspr2 < __flexiblas_hooks->dspr2.nhook ) { ++ fn = __flexiblas_hooks->dspr2.f77_hook_function[hook_pos_dspr2]; ++ } else { ++ hook_pos_dspr2 = 0; ++ fn = current_backend->blas.dspr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_dspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_dspr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dswap = 0; ++ + void FC_GLOBAL(dswap,DSWAP)(blasint* n, double* dx, blasint* incx, double* dy, blasint* incy) + { + void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); +@@ -1697,6 +3575,40 @@ + + + ++void flexiblas_real_dswap_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ fn = current_backend->blas.dswap.f77_blas_function; ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dswap(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_real_dswap_"))); ++ ++ ++void flexiblas_chain_dswap_(void* n, void* dx, void* incx, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* dx, void* incx, void* dy, void* incy); ++ ++ ++ ++ hook_pos_dswap++; ++ if ( hook_pos_dswap < __flexiblas_hooks->dswap.nhook ) { ++ fn = __flexiblas_hooks->dswap.f77_hook_function[hook_pos_dswap]; ++ } else { ++ hook_pos_dswap = 0; ++ fn = current_backend->blas.dswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) dx, (void*) incx, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dswap(void* n, void* dx, void* incx, void* dy, void* incy) __attribute__((alias("flexiblas_chain_dswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsymm = 0; ++ + void FC_GLOBAL(dsymm,DSYMM)(char* side, char* uplo, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* b, blasint* ldb, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -1723,6 +3635,40 @@ + + + ++void flexiblas_real_dsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dsymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dsymm_"))); ++ ++ ++void flexiblas_chain_dsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dsymm++; ++ if ( hook_pos_dsymm < __flexiblas_hooks->dsymm.nhook ) { ++ fn = __flexiblas_hooks->dsymm.f77_hook_function[hook_pos_dsymm]; ++ } else { ++ hook_pos_dsymm = 0; ++ fn = current_backend->blas.dsymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dsymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsymv = 0; ++ + void FC_GLOBAL(dsymv,DSYMV)(char* uplo, blasint* n, double* alpha, double* a, blasint* lda, double* x, blasint* incx, double* beta, double* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -1749,6 +3695,40 @@ + + + ++void flexiblas_real_dsymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.dsymv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_dsymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_dsymv_"))); ++ ++ ++void flexiblas_chain_dsymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_dsymv++; ++ if ( hook_pos_dsymv < __flexiblas_hooks->dsymv.nhook ) { ++ fn = __flexiblas_hooks->dsymv.f77_hook_function[hook_pos_dsymv]; ++ } else { ++ hook_pos_dsymv = 0; ++ fn = current_backend->blas.dsymv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_dsymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_dsymv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyr = 0; ++ + void FC_GLOBAL(dsyr,DSYR)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -1775,6 +3755,40 @@ + + + ++void flexiblas_real_dsyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.dsyr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_dsyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_dsyr_"))); ++ ++ ++void flexiblas_chain_dsyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_dsyr++; ++ if ( hook_pos_dsyr < __flexiblas_hooks->dsyr.nhook ) { ++ fn = __flexiblas_hooks->dsyr.f77_hook_function[hook_pos_dsyr]; ++ } else { ++ hook_pos_dsyr = 0; ++ fn = current_backend->blas.dsyr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_dsyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_dsyr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyr2 = 0; ++ + void FC_GLOBAL(dsyr2,DSYR2)(char* uplo, blasint* n, double* alpha, double* x, blasint* incx, double* y, blasint* incy, double* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -1801,6 +3815,40 @@ + + + ++void flexiblas_real_dsyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.dsyr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_dsyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_dsyr2_"))); ++ ++ ++void flexiblas_chain_dsyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_dsyr2++; ++ if ( hook_pos_dsyr2 < __flexiblas_hooks->dsyr2.nhook ) { ++ fn = __flexiblas_hooks->dsyr2.f77_hook_function[hook_pos_dsyr2]; ++ } else { ++ hook_pos_dsyr2 = 0; ++ fn = current_backend->blas.dsyr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_dsyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_dsyr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyr2k = 0; ++ + void FC_GLOBAL(dsyr2k,DSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* b, blasint* ldb, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -1827,6 +3875,40 @@ + + + ++void flexiblas_real_dsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dsyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dsyr2k_"))); ++ ++ ++void flexiblas_chain_dsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dsyr2k++; ++ if ( hook_pos_dsyr2k < __flexiblas_hooks->dsyr2k.nhook ) { ++ fn = __flexiblas_hooks->dsyr2k.f77_hook_function[hook_pos_dsyr2k]; ++ } else { ++ hook_pos_dsyr2k = 0; ++ fn = current_backend->blas.dsyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dsyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dsyrk = 0; ++ + void FC_GLOBAL(dsyrk,DSYRK)(char* uplo, char* trans, blasint* n, blasint* k, double* alpha, double* a, blasint* lda, double* beta, double* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -1853,6 +3935,40 @@ + + + ++void flexiblas_real_dsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.dsyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_dsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_dsyrk_"))); ++ ++ ++void flexiblas_chain_dsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_dsyrk++; ++ if ( hook_pos_dsyrk < __flexiblas_hooks->dsyrk.nhook ) { ++ fn = __flexiblas_hooks->dsyrk.f77_hook_function[hook_pos_dsyrk]; ++ } else { ++ hook_pos_dsyrk = 0; ++ fn = current_backend->blas.dsyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_dsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_dsyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtbmv = 0; ++ + void FC_GLOBAL(dtbmv,DTBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -1879,6 +3995,40 @@ + + + ++void flexiblas_real_dtbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtbmv_"))); ++ ++ ++void flexiblas_chain_dtbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtbmv++; ++ if ( hook_pos_dtbmv < __flexiblas_hooks->dtbmv.nhook ) { ++ fn = __flexiblas_hooks->dtbmv.f77_hook_function[hook_pos_dtbmv]; ++ } else { ++ hook_pos_dtbmv = 0; ++ fn = current_backend->blas.dtbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtbsv = 0; ++ + void FC_GLOBAL(dtbsv,DTBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -1905,6 +4055,40 @@ + + + ++void flexiblas_real_dtbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtbsv_"))); ++ ++ ++void flexiblas_chain_dtbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtbsv++; ++ if ( hook_pos_dtbsv < __flexiblas_hooks->dtbsv.nhook ) { ++ fn = __flexiblas_hooks->dtbsv.f77_hook_function[hook_pos_dtbsv]; ++ } else { ++ hook_pos_dtbsv = 0; ++ fn = current_backend->blas.dtbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtpmv = 0; ++ + void FC_GLOBAL(dtpmv,DTPMV)(char* uplo, char* trans, char* diag, blasint* n, double* ap, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1931,6 +4115,40 @@ + + + ++void flexiblas_real_dtpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.dtpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_dtpmv_"))); ++ ++ ++void flexiblas_chain_dtpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtpmv++; ++ if ( hook_pos_dtpmv < __flexiblas_hooks->dtpmv.nhook ) { ++ fn = __flexiblas_hooks->dtpmv.f77_hook_function[hook_pos_dtpmv]; ++ } else { ++ hook_pos_dtpmv = 0; ++ fn = current_backend->blas.dtpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtpsv = 0; ++ + void FC_GLOBAL(dtpsv,DTPSV)(char* uplo, char* trans, char* diag, blasint* n, double* ap, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -1957,6 +4175,40 @@ + + + ++void flexiblas_real_dtpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.dtpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_dtpsv_"))); ++ ++ ++void flexiblas_chain_dtpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtpsv++; ++ if ( hook_pos_dtpsv < __flexiblas_hooks->dtpsv.nhook ) { ++ fn = __flexiblas_hooks->dtpsv.f77_hook_function[hook_pos_dtpsv]; ++ } else { ++ hook_pos_dtpsv = 0; ++ fn = current_backend->blas.dtpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrmm = 0; ++ + void FC_GLOBAL(dtrmm,DTRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -1983,6 +4235,40 @@ + + + ++void flexiblas_real_dtrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.dtrmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dtrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_dtrmm_"))); ++ ++ ++void flexiblas_chain_dtrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_dtrmm++; ++ if ( hook_pos_dtrmm < __flexiblas_hooks->dtrmm.nhook ) { ++ fn = __flexiblas_hooks->dtrmm.f77_hook_function[hook_pos_dtrmm]; ++ } else { ++ hook_pos_dtrmm = 0; ++ fn = current_backend->blas.dtrmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dtrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_dtrmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrmv = 0; ++ + void FC_GLOBAL(dtrmv,DTRMV)(char* uplo, char* trans, char* diag, blasint* n, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -2009,6 +4295,40 @@ + + + ++void flexiblas_real_dtrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtrmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtrmv_"))); ++ ++ ++void flexiblas_chain_dtrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtrmv++; ++ if ( hook_pos_dtrmv < __flexiblas_hooks->dtrmv.nhook ) { ++ fn = __flexiblas_hooks->dtrmv.f77_hook_function[hook_pos_dtrmv]; ++ } else { ++ hook_pos_dtrmv = 0; ++ fn = current_backend->blas.dtrmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtrmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrsm = 0; ++ + void FC_GLOBAL(dtrsm,DTRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -2035,6 +4355,40 @@ + + + ++void flexiblas_real_dtrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.dtrsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dtrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_dtrsm_"))); ++ ++ ++void flexiblas_chain_dtrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_dtrsm++; ++ if ( hook_pos_dtrsm < __flexiblas_hooks->dtrsm.nhook ) { ++ fn = __flexiblas_hooks->dtrsm.f77_hook_function[hook_pos_dtrsm]; ++ } else { ++ hook_pos_dtrsm = 0; ++ fn = current_backend->blas.dtrsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dtrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_dtrsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dtrsv = 0; ++ + void FC_GLOBAL(dtrsv,DTRSV)(char* uplo, char* trans, char* diag, blasint* n, double* a, blasint* lda, double* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -2061,6 +4415,40 @@ + + + ++void flexiblas_real_dtrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.dtrsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_dtrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_dtrsv_"))); ++ ++ ++void flexiblas_chain_dtrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_dtrsv++; ++ if ( hook_pos_dtrsv < __flexiblas_hooks->dtrsv.nhook ) { ++ fn = __flexiblas_hooks->dtrsv.f77_hook_function[hook_pos_dtrsv]; ++ } else { ++ hook_pos_dtrsv = 0; ++ fn = current_backend->blas.dtrsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_dtrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_dtrsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dzasum = 0; ++ + double FC_GLOBAL(dzasum,DZASUM)(blasint* n, double complex* zx, blasint* incx) + { + double (*fn) (void* n, void* zx, void* incx); +@@ -2088,6 +4476,42 @@ + + + ++double flexiblas_real_dzasum_(void* n, void* zx, void* incx) ++{ ++ double (*fn) (void* n, void* zx, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dzasum.f77_blas_function; ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dzasum(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_real_dzasum_"))); ++ ++ ++double flexiblas_chain_dzasum_(void* n, void* zx, void* incx) ++{ ++ double (*fn) (void* n, void* zx, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dzasum++; ++ if ( hook_pos_dzasum < __flexiblas_hooks->dzasum.nhook ) { ++ fn = __flexiblas_hooks->dzasum.f77_hook_function[hook_pos_dzasum]; ++ } else { ++ hook_pos_dzasum = 0; ++ fn = current_backend->blas.dzasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dzasum(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_chain_dzasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dznrm2 = 0; ++ + double FC_GLOBAL(dznrm2,DZNRM2)(blasint* n, double complex* x, blasint* incx) + { + double (*fn) (void* n, void* x, void* incx); +@@ -2115,6 +4539,42 @@ + + + ++double flexiblas_real_dznrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ fn = current_backend->blas.dznrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_real_dznrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_dznrm2_"))); ++ ++ ++double flexiblas_chain_dznrm2_(void* n, void* x, void* incx) ++{ ++ double (*fn) (void* n, void* x, void* incx); ++ double ret; ++ ++ ++ ++ hook_pos_dznrm2++; ++ if ( hook_pos_dznrm2 < __flexiblas_hooks->dznrm2.nhook ) { ++ fn = __flexiblas_hooks->dznrm2.f77_hook_function[hook_pos_dznrm2]; ++ } else { ++ hook_pos_dznrm2 = 0; ++ fn = current_backend->blas.dznrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++double flexiblas_chain_dznrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_dznrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_icamax = 0; ++ + int FC_GLOBAL(icamax,ICAMAX)(blasint* n, float complex* cx, blasint* incx) + { + blasint (*fn) (void* n, void* cx, void* incx); +@@ -2142,6 +4602,42 @@ + + + ++blasint flexiblas_real_icamax_(void* n, void* cx, void* incx) ++{ ++ blasint (*fn) (void* n, void* cx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.icamax.f77_blas_function; ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_icamax(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_real_icamax_"))); ++ ++ ++blasint flexiblas_chain_icamax_(void* n, void* cx, void* incx) ++{ ++ blasint (*fn) (void* n, void* cx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_icamax++; ++ if ( hook_pos_icamax < __flexiblas_hooks->icamax.nhook ) { ++ fn = __flexiblas_hooks->icamax.f77_hook_function[hook_pos_icamax]; ++ } else { ++ hook_pos_icamax = 0; ++ fn = current_backend->blas.icamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_icamax(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_chain_icamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_idamax = 0; ++ + int FC_GLOBAL(idamax,IDAMAX)(blasint* n, double* dx, blasint* incx) + { + blasint (*fn) (void* n, void* dx, void* incx); +@@ -2169,6 +4665,42 @@ + + + ++blasint flexiblas_real_idamax_(void* n, void* dx, void* incx) ++{ ++ blasint (*fn) (void* n, void* dx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.idamax.f77_blas_function; ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_idamax(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_real_idamax_"))); ++ ++ ++blasint flexiblas_chain_idamax_(void* n, void* dx, void* incx) ++{ ++ blasint (*fn) (void* n, void* dx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_idamax++; ++ if ( hook_pos_idamax < __flexiblas_hooks->idamax.nhook ) { ++ fn = __flexiblas_hooks->idamax.f77_hook_function[hook_pos_idamax]; ++ } else { ++ hook_pos_idamax = 0; ++ fn = current_backend->blas.idamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) dx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_idamax(void* n, void* dx, void* incx) __attribute__((alias("flexiblas_chain_idamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_isamax = 0; ++ + int FC_GLOBAL(isamax,ISAMAX)(blasint* n, float* sx, blasint* incx) + { + blasint (*fn) (void* n, void* sx, void* incx); +@@ -2196,6 +4728,42 @@ + + + ++blasint flexiblas_real_isamax_(void* n, void* sx, void* incx) ++{ ++ blasint (*fn) (void* n, void* sx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.isamax.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_isamax(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_real_isamax_"))); ++ ++ ++blasint flexiblas_chain_isamax_(void* n, void* sx, void* incx) ++{ ++ blasint (*fn) (void* n, void* sx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_isamax++; ++ if ( hook_pos_isamax < __flexiblas_hooks->isamax.nhook ) { ++ fn = __flexiblas_hooks->isamax.f77_hook_function[hook_pos_isamax]; ++ } else { ++ hook_pos_isamax = 0; ++ fn = current_backend->blas.isamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_isamax(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_chain_isamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_izamax = 0; ++ + int FC_GLOBAL(izamax,IZAMAX)(blasint* n, double complex* zx, blasint* incx) + { + blasint (*fn) (void* n, void* zx, void* incx); +@@ -2223,6 +4791,42 @@ + + + ++blasint flexiblas_real_izamax_(void* n, void* zx, void* incx) ++{ ++ blasint (*fn) (void* n, void* zx, void* incx); ++ blasint ret; ++ ++ fn = current_backend->blas.izamax.f77_blas_function; ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_real_izamax(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_real_izamax_"))); ++ ++ ++blasint flexiblas_chain_izamax_(void* n, void* zx, void* incx) ++{ ++ blasint (*fn) (void* n, void* zx, void* incx); ++ blasint ret; ++ ++ ++ ++ hook_pos_izamax++; ++ if ( hook_pos_izamax < __flexiblas_hooks->izamax.nhook ) { ++ fn = __flexiblas_hooks->izamax.f77_hook_function[hook_pos_izamax]; ++ } else { ++ hook_pos_izamax = 0; ++ fn = current_backend->blas.izamax.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) zx, (void*) incx); ++ ++ return ret; ++} ++blasint flexiblas_chain_izamax(void* n, void* zx, void* incx) __attribute__((alias("flexiblas_chain_izamax_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sasum = 0; ++ + float FC_GLOBAL(sasum,SASUM)(blasint* n, float* sx, blasint* incx) + { + float (*fn) (void* n, void* sx, void* incx); +@@ -2250,6 +4854,42 @@ + + + ++float flexiblas_real_sasum_(void* n, void* sx, void* incx) ++{ ++ float (*fn) (void* n, void* sx, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.sasum.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_sasum(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_real_sasum_"))); ++ ++ ++float flexiblas_chain_sasum_(void* n, void* sx, void* incx) ++{ ++ float (*fn) (void* n, void* sx, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_sasum++; ++ if ( hook_pos_sasum < __flexiblas_hooks->sasum.nhook ) { ++ fn = __flexiblas_hooks->sasum.f77_hook_function[hook_pos_sasum]; ++ } else { ++ hook_pos_sasum = 0; ++ fn = current_backend->blas.sasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_sasum(void* n, void* sx, void* incx) __attribute__((alias("flexiblas_chain_sasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_saxpy = 0; ++ + void FC_GLOBAL(saxpy,SAXPY)(blasint* n, float* sa, float* sx, blasint* incx, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sa, void* sx, void* incx, void* sy, void* incy); +@@ -2276,6 +4916,40 @@ + + + ++void flexiblas_real_saxpy_(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sy, void* incy); ++ ++ fn = current_backend->blas.saxpy.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_saxpy(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_saxpy_"))); ++ ++ ++void flexiblas_chain_saxpy_(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sy, void* incy); ++ ++ ++ ++ hook_pos_saxpy++; ++ if ( hook_pos_saxpy < __flexiblas_hooks->saxpy.nhook ) { ++ fn = __flexiblas_hooks->saxpy.f77_hook_function[hook_pos_saxpy]; ++ } else { ++ hook_pos_saxpy = 0; ++ fn = current_backend->blas.saxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_saxpy(void* n, void* sa, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_saxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_scasum = 0; ++ + float FC_GLOBAL(scasum,SCASUM)(blasint* n, float complex* cx, blasint* incx) + { + float (*fn) (void* n, void* cx, void* incx); +@@ -2303,6 +4977,42 @@ + + + ++float flexiblas_real_scasum_(void* n, void* cx, void* incx) ++{ ++ float (*fn) (void* n, void* cx, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.scasum.f77_blas_function; ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_scasum(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_real_scasum_"))); ++ ++ ++float flexiblas_chain_scasum_(void* n, void* cx, void* incx) ++{ ++ float (*fn) (void* n, void* cx, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_scasum++; ++ if ( hook_pos_scasum < __flexiblas_hooks->scasum.nhook ) { ++ fn = __flexiblas_hooks->scasum.f77_hook_function[hook_pos_scasum]; ++ } else { ++ hook_pos_scasum = 0; ++ fn = current_backend->blas.scasum.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) cx, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_scasum(void* n, void* cx, void* incx) __attribute__((alias("flexiblas_chain_scasum_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_scnrm2 = 0; ++ + float FC_GLOBAL(scnrm2,SCNRM2)(blasint* n, float complex* x, blasint* incx) + { + float (*fn) (void* n, void* x, void* incx); +@@ -2330,6 +5040,42 @@ + + + ++float flexiblas_real_scnrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.scnrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_scnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_scnrm2_"))); ++ ++ ++float flexiblas_chain_scnrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_scnrm2++; ++ if ( hook_pos_scnrm2 < __flexiblas_hooks->scnrm2.nhook ) { ++ fn = __flexiblas_hooks->scnrm2.f77_hook_function[hook_pos_scnrm2]; ++ } else { ++ hook_pos_scnrm2 = 0; ++ fn = current_backend->blas.scnrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_scnrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_scnrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_scopy = 0; ++ + void FC_GLOBAL(scopy,SCOPY)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -2356,6 +5102,40 @@ + + + ++void flexiblas_real_scopy_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ fn = current_backend->blas.scopy.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_scopy(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_scopy_"))); ++ ++ ++void flexiblas_chain_scopy_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ ++ ++ hook_pos_scopy++; ++ if ( hook_pos_scopy < __flexiblas_hooks->scopy.nhook ) { ++ fn = __flexiblas_hooks->scopy.f77_hook_function[hook_pos_scopy]; ++ } else { ++ hook_pos_scopy = 0; ++ fn = current_backend->blas.scopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_scopy(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_scopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sdot = 0; ++ + float FC_GLOBAL(sdot,SDOT)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + float (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -2383,6 +5163,42 @@ + + + ++float flexiblas_real_sdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ fn = current_backend->blas.sdot.f77_blas_function; ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_real_sdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_sdot_"))); ++ ++ ++float flexiblas_chain_sdot_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ ++ ++ hook_pos_sdot++; ++ if ( hook_pos_sdot < __flexiblas_hooks->sdot.nhook ) { ++ fn = __flexiblas_hooks->sdot.f77_hook_function[hook_pos_sdot]; ++ } else { ++ hook_pos_sdot = 0; ++ fn = current_backend->blas.sdot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_chain_sdot(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_sdot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sdsdot = 0; ++ + float FC_GLOBAL(sdsdot,SDSDOT)(blasint* n, float* sb, float* sx, blasint* incx, float* sy, blasint* incy) + { + float (*fn) (void* n, void* sb, void* sx, void* incx, void* sy, void* incy); +@@ -2410,6 +5226,42 @@ + + + ++float flexiblas_real_sdsdot_(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sb, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ fn = current_backend->blas.sdsdot.f77_blas_function; ++ ret = fn((void*) n, (void*) sb, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_real_sdsdot(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_sdsdot_"))); ++ ++ ++float flexiblas_chain_sdsdot_(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) ++{ ++ float (*fn) (void* n, void* sb, void* sx, void* incx, void* sy, void* incy); ++ float ret; ++ ++ ++ ++ hook_pos_sdsdot++; ++ if ( hook_pos_sdsdot < __flexiblas_hooks->sdsdot.nhook ) { ++ fn = __flexiblas_hooks->sdsdot.f77_hook_function[hook_pos_sdsdot]; ++ } else { ++ hook_pos_sdsdot = 0; ++ fn = current_backend->blas.sdsdot.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) sb, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return ret; ++} ++float flexiblas_chain_sdsdot(void* n, void* sb, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_sdsdot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgbmv = 0; ++ + void FC_GLOBAL(sgbmv,SGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2436,6 +5288,40 @@ + + + ++void flexiblas_real_sgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.sgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_sgbmv_"))); ++ ++ ++void flexiblas_chain_sgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_sgbmv++; ++ if ( hook_pos_sgbmv < __flexiblas_hooks->sgbmv.nhook ) { ++ fn = __flexiblas_hooks->sgbmv.f77_hook_function[hook_pos_sgbmv]; ++ } else { ++ hook_pos_sgbmv = 0; ++ fn = current_backend->blas.sgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_sgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgemm = 0; ++ + void FC_GLOBAL(sgemm,SGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* b, blasint* ldb, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -2462,6 +5348,40 @@ + + + ++void flexiblas_real_sgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.sgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_sgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_sgemm_"))); ++ ++ ++void flexiblas_chain_sgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_sgemm++; ++ if ( hook_pos_sgemm < __flexiblas_hooks->sgemm.nhook ) { ++ fn = __flexiblas_hooks->sgemm.f77_hook_function[hook_pos_sgemm]; ++ } else { ++ hook_pos_sgemm = 0; ++ fn = current_backend->blas.sgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_sgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_sgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgemv = 0; ++ + void FC_GLOBAL(sgemv,SGEMV)(char* trans, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2488,6 +5408,40 @@ + + + ++void flexiblas_real_sgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.sgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_sgemv_"))); ++ ++ ++void flexiblas_chain_sgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_sgemv++; ++ if ( hook_pos_sgemv < __flexiblas_hooks->sgemv.nhook ) { ++ fn = __flexiblas_hooks->sgemv.f77_hook_function[hook_pos_sgemv]; ++ } else { ++ hook_pos_sgemv = 0; ++ fn = current_backend->blas.sgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_sgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sger = 0; ++ + void FC_GLOBAL(sger,SGER)(blasint* m, blasint* n, float* alpha, float* x, blasint* incx, float* y, blasint* incy, float* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -2514,6 +5468,40 @@ + + + ++void flexiblas_real_sger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.sger.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_sger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_sger_"))); ++ ++ ++void flexiblas_chain_sger_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_sger++; ++ if ( hook_pos_sger < __flexiblas_hooks->sger.nhook ) { ++ fn = __flexiblas_hooks->sger.f77_hook_function[hook_pos_sger]; ++ } else { ++ hook_pos_sger = 0; ++ fn = current_backend->blas.sger.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_sger(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_sger_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_snrm2 = 0; ++ + float FC_GLOBAL(snrm2,SNRM2)(blasint* n, float* x, blasint* incx) + { + float (*fn) (void* n, void* x, void* incx); +@@ -2541,6 +5529,42 @@ + + + ++float flexiblas_real_snrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ fn = current_backend->blas.snrm2.f77_blas_function; ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_real_snrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_real_snrm2_"))); ++ ++ ++float flexiblas_chain_snrm2_(void* n, void* x, void* incx) ++{ ++ float (*fn) (void* n, void* x, void* incx); ++ float ret; ++ ++ ++ ++ hook_pos_snrm2++; ++ if ( hook_pos_snrm2 < __flexiblas_hooks->snrm2.nhook ) { ++ fn = __flexiblas_hooks->snrm2.f77_hook_function[hook_pos_snrm2]; ++ } else { ++ hook_pos_snrm2 = 0; ++ fn = current_backend->blas.snrm2.f77_blas_function; ++ } ++ ret = fn((void*) n, (void*) x, (void*) incx); ++ ++ return ret; ++} ++float flexiblas_chain_snrm2(void* n, void* x, void* incx) __attribute__((alias("flexiblas_chain_snrm2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srot = 0; ++ + void FC_GLOBAL(srot,SROT)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy, float* c, float* s) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s); +@@ -2567,6 +5591,40 @@ + + + ++void flexiblas_real_srot_(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.srot.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_srot(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_srot_"))); ++ ++ ++void flexiblas_chain_srot_(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_srot++; ++ if ( hook_pos_srot < __flexiblas_hooks->srot.nhook ) { ++ fn = __flexiblas_hooks->srot.f77_hook_function[hook_pos_srot]; ++ } else { ++ hook_pos_srot = 0; ++ fn = current_backend->blas.srot.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_srot(void* n, void* sx, void* incx, void* sy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_srot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srotg = 0; ++ + void FC_GLOBAL(srotg,SROTG)(float* sa, float* sb, float* c, float* s) + { + void (*fn) (void* sa, void* sb, void* c, void* s); +@@ -2593,6 +5651,40 @@ + + + ++void flexiblas_real_srotg_(void* sa, void* sb, void* c, void* s) ++{ ++ void (*fn) (void* sa, void* sb, void* c, void* s); ++ ++ fn = current_backend->blas.srotg.f77_blas_function; ++ fn((void*) sa, (void*) sb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_srotg(void* sa, void* sb, void* c, void* s) __attribute__((alias("flexiblas_real_srotg_"))); ++ ++ ++void flexiblas_chain_srotg_(void* sa, void* sb, void* c, void* s) ++{ ++ void (*fn) (void* sa, void* sb, void* c, void* s); ++ ++ ++ ++ hook_pos_srotg++; ++ if ( hook_pos_srotg < __flexiblas_hooks->srotg.nhook ) { ++ fn = __flexiblas_hooks->srotg.f77_hook_function[hook_pos_srotg]; ++ } else { ++ hook_pos_srotg = 0; ++ fn = current_backend->blas.srotg.f77_blas_function; ++ } ++ fn((void*) sa, (void*) sb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_srotg(void* sa, void* sb, void* c, void* s) __attribute__((alias("flexiblas_chain_srotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srotm = 0; ++ + void FC_GLOBAL(srotm,SROTM)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy, float* sparam) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* sparam); +@@ -2619,6 +5711,40 @@ + + + ++void flexiblas_real_srotm_(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* sparam); ++ ++ fn = current_backend->blas.srotm.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) sparam); ++ ++ return; ++} ++void flexiblas_real_srotm(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) __attribute__((alias("flexiblas_real_srotm_"))); ++ ++ ++void flexiblas_chain_srotm_(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy, void* sparam); ++ ++ ++ ++ hook_pos_srotm++; ++ if ( hook_pos_srotm < __flexiblas_hooks->srotm.nhook ) { ++ fn = __flexiblas_hooks->srotm.f77_hook_function[hook_pos_srotm]; ++ } else { ++ hook_pos_srotm = 0; ++ fn = current_backend->blas.srotm.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy, (void*) sparam); ++ ++ return; ++} ++void flexiblas_chain_srotm(void* n, void* sx, void* incx, void* sy, void* incy, void* sparam) __attribute__((alias("flexiblas_chain_srotm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_srotmg = 0; ++ + void FC_GLOBAL(srotmg,SROTMG)(float* sd1, float* sd2, float* sx1, float* sy1, float* sparam) + { + void (*fn) (void* sd1, void* sd2, void* sx1, void* sy1, void* sparam); +@@ -2645,6 +5771,40 @@ + + + ++void flexiblas_real_srotmg_(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) ++{ ++ void (*fn) (void* sd1, void* sd2, void* sx1, void* sy1, void* sparam); ++ ++ fn = current_backend->blas.srotmg.f77_blas_function; ++ fn((void*) sd1, (void*) sd2, (void*) sx1, (void*) sy1, (void*) sparam); ++ ++ return; ++} ++void flexiblas_real_srotmg(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) __attribute__((alias("flexiblas_real_srotmg_"))); ++ ++ ++void flexiblas_chain_srotmg_(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) ++{ ++ void (*fn) (void* sd1, void* sd2, void* sx1, void* sy1, void* sparam); ++ ++ ++ ++ hook_pos_srotmg++; ++ if ( hook_pos_srotmg < __flexiblas_hooks->srotmg.nhook ) { ++ fn = __flexiblas_hooks->srotmg.f77_hook_function[hook_pos_srotmg]; ++ } else { ++ hook_pos_srotmg = 0; ++ fn = current_backend->blas.srotmg.f77_blas_function; ++ } ++ fn((void*) sd1, (void*) sd2, (void*) sx1, (void*) sy1, (void*) sparam); ++ ++ return; ++} ++void flexiblas_chain_srotmg(void* sd1, void* sd2, void* sx1, void* sy1, void* sparam) __attribute__((alias("flexiblas_chain_srotmg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssbmv = 0; ++ + void FC_GLOBAL(ssbmv,SSBMV)(char* uplo, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2671,6 +5831,40 @@ + + + ++void flexiblas_real_ssbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.ssbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_ssbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_ssbmv_"))); ++ ++ ++void flexiblas_chain_ssbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_ssbmv++; ++ if ( hook_pos_ssbmv < __flexiblas_hooks->ssbmv.nhook ) { ++ fn = __flexiblas_hooks->ssbmv.f77_hook_function[hook_pos_ssbmv]; ++ } else { ++ hook_pos_ssbmv = 0; ++ fn = current_backend->blas.ssbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_ssbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_ssbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sscal = 0; ++ + void FC_GLOBAL(sscal,SSCAL)(blasint* n, float* sa, float* sx, blasint* incx) + { + void (*fn) (void* n, void* sa, void* sx, void* incx); +@@ -2697,6 +5891,40 @@ + + + ++void flexiblas_real_sscal_(void* n, void* sa, void* sx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx); ++ ++ fn = current_backend->blas.sscal.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_sscal(void* n, void* sa, void* sx, void* incx) __attribute__((alias("flexiblas_real_sscal_"))); ++ ++ ++void flexiblas_chain_sscal_(void* n, void* sa, void* sx, void* incx) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx); ++ ++ ++ ++ hook_pos_sscal++; ++ if ( hook_pos_sscal < __flexiblas_hooks->sscal.nhook ) { ++ fn = __flexiblas_hooks->sscal.f77_hook_function[hook_pos_sscal]; ++ } else { ++ hook_pos_sscal = 0; ++ fn = current_backend->blas.sscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_sscal(void* n, void* sa, void* sx, void* incx) __attribute__((alias("flexiblas_chain_sscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sspmv = 0; ++ + void FC_GLOBAL(sspmv,SSPMV)(char* uplo, blasint* n, float* alpha, float* ap, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2723,6 +5951,40 @@ + + + ++void flexiblas_real_sspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.sspmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_sspmv_"))); ++ ++ ++void flexiblas_chain_sspmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_sspmv++; ++ if ( hook_pos_sspmv < __flexiblas_hooks->sspmv.nhook ) { ++ fn = __flexiblas_hooks->sspmv.f77_hook_function[hook_pos_sspmv]; ++ } else { ++ hook_pos_sspmv = 0; ++ fn = current_backend->blas.sspmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sspmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_sspmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sspr = 0; ++ + void FC_GLOBAL(sspr,SSPR)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -2749,6 +6011,40 @@ + + + ++void flexiblas_real_sspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.sspr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_sspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_sspr_"))); ++ ++ ++void flexiblas_chain_sspr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_sspr++; ++ if ( hook_pos_sspr < __flexiblas_hooks->sspr.nhook ) { ++ fn = __flexiblas_hooks->sspr.f77_hook_function[hook_pos_sspr]; ++ } else { ++ hook_pos_sspr = 0; ++ fn = current_backend->blas.sspr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_sspr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_sspr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sspr2 = 0; ++ + void FC_GLOBAL(sspr2,SSPR2)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* y, blasint* incy, float* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -2775,6 +6071,40 @@ + + + ++void flexiblas_real_sspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.sspr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_sspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_sspr2_"))); ++ ++ ++void flexiblas_chain_sspr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_sspr2++; ++ if ( hook_pos_sspr2 < __flexiblas_hooks->sspr2.nhook ) { ++ fn = __flexiblas_hooks->sspr2.f77_hook_function[hook_pos_sspr2]; ++ } else { ++ hook_pos_sspr2 = 0; ++ fn = current_backend->blas.sspr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_sspr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_sspr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sswap = 0; ++ + void FC_GLOBAL(sswap,SSWAP)(blasint* n, float* sx, blasint* incx, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); +@@ -2801,6 +6131,40 @@ + + + ++void flexiblas_real_sswap_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ fn = current_backend->blas.sswap.f77_blas_function; ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_sswap(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_real_sswap_"))); ++ ++ ++void flexiblas_chain_sswap_(void* n, void* sx, void* incx, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sx, void* incx, void* sy, void* incy); ++ ++ ++ ++ hook_pos_sswap++; ++ if ( hook_pos_sswap < __flexiblas_hooks->sswap.nhook ) { ++ fn = __flexiblas_hooks->sswap.f77_hook_function[hook_pos_sswap]; ++ } else { ++ hook_pos_sswap = 0; ++ fn = current_backend->blas.sswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) sx, (void*) incx, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_sswap(void* n, void* sx, void* incx, void* sy, void* incy) __attribute__((alias("flexiblas_chain_sswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssymm = 0; ++ + void FC_GLOBAL(ssymm,SSYMM)(char* side, char* uplo, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* b, blasint* ldb, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -2827,6 +6191,40 @@ + + + ++void flexiblas_real_ssymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.ssymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_ssymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_ssymm_"))); ++ ++ ++void flexiblas_chain_ssymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_ssymm++; ++ if ( hook_pos_ssymm < __flexiblas_hooks->ssymm.nhook ) { ++ fn = __flexiblas_hooks->ssymm.f77_hook_function[hook_pos_ssymm]; ++ } else { ++ hook_pos_ssymm = 0; ++ fn = current_backend->blas.ssymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_ssymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_ssymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssymv = 0; ++ + void FC_GLOBAL(ssymv,SSYMV)(char* uplo, blasint* n, float* alpha, float* a, blasint* lda, float* x, blasint* incx, float* beta, float* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -2853,6 +6251,40 @@ + + + ++void flexiblas_real_ssymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.ssymv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_ssymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_ssymv_"))); ++ ++ ++void flexiblas_chain_ssymv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_ssymv++; ++ if ( hook_pos_ssymv < __flexiblas_hooks->ssymv.nhook ) { ++ fn = __flexiblas_hooks->ssymv.f77_hook_function[hook_pos_ssymv]; ++ } else { ++ hook_pos_ssymv = 0; ++ fn = current_backend->blas.ssymv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_ssymv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_ssymv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyr = 0; ++ + void FC_GLOBAL(ssyr,SSYR)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -2879,6 +6311,40 @@ + + + ++void flexiblas_real_ssyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.ssyr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_ssyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_ssyr_"))); ++ ++ ++void flexiblas_chain_ssyr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_ssyr++; ++ if ( hook_pos_ssyr < __flexiblas_hooks->ssyr.nhook ) { ++ fn = __flexiblas_hooks->ssyr.f77_hook_function[hook_pos_ssyr]; ++ } else { ++ hook_pos_ssyr = 0; ++ fn = current_backend->blas.ssyr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_ssyr(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_ssyr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyr2 = 0; ++ + void FC_GLOBAL(ssyr2,SSYR2)(char* uplo, blasint* n, float* alpha, float* x, blasint* incx, float* y, blasint* incy, float* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -2905,6 +6371,40 @@ + + + ++void flexiblas_real_ssyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.ssyr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_ssyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_ssyr2_"))); ++ ++ ++void flexiblas_chain_ssyr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_ssyr2++; ++ if ( hook_pos_ssyr2 < __flexiblas_hooks->ssyr2.nhook ) { ++ fn = __flexiblas_hooks->ssyr2.f77_hook_function[hook_pos_ssyr2]; ++ } else { ++ hook_pos_ssyr2 = 0; ++ fn = current_backend->blas.ssyr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_ssyr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_ssyr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyr2k = 0; ++ + void FC_GLOBAL(ssyr2k,SSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* b, blasint* ldb, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -2931,6 +6431,40 @@ + + + ++void flexiblas_real_ssyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.ssyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_ssyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_ssyr2k_"))); ++ ++ ++void flexiblas_chain_ssyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_ssyr2k++; ++ if ( hook_pos_ssyr2k < __flexiblas_hooks->ssyr2k.nhook ) { ++ fn = __flexiblas_hooks->ssyr2k.f77_hook_function[hook_pos_ssyr2k]; ++ } else { ++ hook_pos_ssyr2k = 0; ++ fn = current_backend->blas.ssyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_ssyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_ssyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ssyrk = 0; ++ + void FC_GLOBAL(ssyrk,SSYRK)(char* uplo, char* trans, blasint* n, blasint* k, float* alpha, float* a, blasint* lda, float* beta, float* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -2957,6 +6491,40 @@ + + + ++void flexiblas_real_ssyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.ssyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_ssyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_ssyrk_"))); ++ ++ ++void flexiblas_chain_ssyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_ssyrk++; ++ if ( hook_pos_ssyrk < __flexiblas_hooks->ssyrk.nhook ) { ++ fn = __flexiblas_hooks->ssyrk.f77_hook_function[hook_pos_ssyrk]; ++ } else { ++ hook_pos_ssyrk = 0; ++ fn = current_backend->blas.ssyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_ssyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_ssyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stbmv = 0; ++ + void FC_GLOBAL(stbmv,STBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -2983,6 +6551,40 @@ + + + ++void flexiblas_real_stbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.stbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_stbmv_"))); ++ ++ ++void flexiblas_chain_stbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_stbmv++; ++ if ( hook_pos_stbmv < __flexiblas_hooks->stbmv.nhook ) { ++ fn = __flexiblas_hooks->stbmv.f77_hook_function[hook_pos_stbmv]; ++ } else { ++ hook_pos_stbmv = 0; ++ fn = current_backend->blas.stbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_stbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stbsv = 0; ++ + void FC_GLOBAL(stbsv,STBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -3009,6 +6611,40 @@ + + + ++void flexiblas_real_stbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.stbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_stbsv_"))); ++ ++ ++void flexiblas_chain_stbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_stbsv++; ++ if ( hook_pos_stbsv < __flexiblas_hooks->stbsv.nhook ) { ++ fn = __flexiblas_hooks->stbsv.f77_hook_function[hook_pos_stbsv]; ++ } else { ++ hook_pos_stbsv = 0; ++ fn = current_backend->blas.stbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_stbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stpmv = 0; ++ + void FC_GLOBAL(stpmv,STPMV)(char* uplo, char* trans, char* diag, blasint* n, float* ap, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3035,6 +6671,40 @@ + + + ++void flexiblas_real_stpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.stpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_stpmv_"))); ++ ++ ++void flexiblas_chain_stpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_stpmv++; ++ if ( hook_pos_stpmv < __flexiblas_hooks->stpmv.nhook ) { ++ fn = __flexiblas_hooks->stpmv.f77_hook_function[hook_pos_stpmv]; ++ } else { ++ hook_pos_stpmv = 0; ++ fn = current_backend->blas.stpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_stpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_stpsv = 0; ++ + void FC_GLOBAL(stpsv,STPSV)(char* uplo, char* trans, char* diag, blasint* n, float* ap, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3061,6 +6731,40 @@ + + + ++void flexiblas_real_stpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.stpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_stpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_stpsv_"))); ++ ++ ++void flexiblas_chain_stpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_stpsv++; ++ if ( hook_pos_stpsv < __flexiblas_hooks->stpsv.nhook ) { ++ fn = __flexiblas_hooks->stpsv.f77_hook_function[hook_pos_stpsv]; ++ } else { ++ hook_pos_stpsv = 0; ++ fn = current_backend->blas.stpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_stpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_stpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strmm = 0; ++ + void FC_GLOBAL(strmm,STRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -3087,6 +6791,40 @@ + + + ++void flexiblas_real_strmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.strmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_strmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_strmm_"))); ++ ++ ++void flexiblas_chain_strmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_strmm++; ++ if ( hook_pos_strmm < __flexiblas_hooks->strmm.nhook ) { ++ fn = __flexiblas_hooks->strmm.f77_hook_function[hook_pos_strmm]; ++ } else { ++ hook_pos_strmm = 0; ++ fn = current_backend->blas.strmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_strmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_strmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strmv = 0; ++ + void FC_GLOBAL(strmv,STRMV)(char* uplo, char* trans, char* diag, blasint* n, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -3113,6 +6851,40 @@ + + + ++void flexiblas_real_strmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.strmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_strmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_strmv_"))); ++ ++ ++void flexiblas_chain_strmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_strmv++; ++ if ( hook_pos_strmv < __flexiblas_hooks->strmv.nhook ) { ++ fn = __flexiblas_hooks->strmv.f77_hook_function[hook_pos_strmv]; ++ } else { ++ hook_pos_strmv = 0; ++ fn = current_backend->blas.strmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_strmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_strmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strsm = 0; ++ + void FC_GLOBAL(strsm,STRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -3139,6 +6911,40 @@ + + + ++void flexiblas_real_strsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.strsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_strsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_strsm_"))); ++ ++ ++void flexiblas_chain_strsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_strsm++; ++ if ( hook_pos_strsm < __flexiblas_hooks->strsm.nhook ) { ++ fn = __flexiblas_hooks->strsm.f77_hook_function[hook_pos_strsm]; ++ } else { ++ hook_pos_strsm = 0; ++ fn = current_backend->blas.strsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_strsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_strsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_strsv = 0; ++ + void FC_GLOBAL(strsv,STRSV)(char* uplo, char* trans, char* diag, blasint* n, float* a, blasint* lda, float* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -3165,6 +6971,40 @@ + + + ++void flexiblas_real_strsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.strsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_strsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_strsv_"))); ++ ++ ++void flexiblas_chain_strsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_strsv++; ++ if ( hook_pos_strsv < __flexiblas_hooks->strsv.nhook ) { ++ fn = __flexiblas_hooks->strsv.f77_hook_function[hook_pos_strsv]; ++ } else { ++ hook_pos_strsv = 0; ++ fn = current_backend->blas.strsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_strsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_strsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zaxpy = 0; ++ + void FC_GLOBAL(zaxpy,ZAXPY)(blasint* n, double complex* za, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* za, void* zx, void* incx, void* zy, void* incy); +@@ -3191,6 +7031,40 @@ + + + ++void flexiblas_real_zaxpy_(void* n, void* za, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zy, void* incy); ++ ++ fn = current_backend->blas.zaxpy.f77_blas_function; ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zaxpy(void* n, void* za, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zaxpy_"))); ++ ++ ++void flexiblas_chain_zaxpy_(void* n, void* za, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zaxpy++; ++ if ( hook_pos_zaxpy < __flexiblas_hooks->zaxpy.nhook ) { ++ fn = __flexiblas_hooks->zaxpy.f77_hook_function[hook_pos_zaxpy]; ++ } else { ++ hook_pos_zaxpy = 0; ++ fn = current_backend->blas.zaxpy.f77_blas_function; ++ } ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zaxpy(void* n, void* za, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zaxpy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zcopy = 0; ++ + void FC_GLOBAL(zcopy,ZCOPY)(blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3217,6 +7091,40 @@ + + + ++void flexiblas_real_zcopy_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ fn = current_backend->blas.zcopy.f77_blas_function; ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zcopy(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zcopy_"))); ++ ++ ++void flexiblas_chain_zcopy_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zcopy++; ++ if ( hook_pos_zcopy < __flexiblas_hooks->zcopy.nhook ) { ++ fn = __flexiblas_hooks->zcopy.f77_hook_function[hook_pos_zcopy]; ++ } else { ++ hook_pos_zcopy = 0; ++ fn = current_backend->blas.zcopy.f77_blas_function; ++ } ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zcopy(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdotc = 0; ++ + void FC_GLOBAL(zdotc,ZDOTC)( double complex* returnvalue, blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3257,6 +7165,56 @@ + + + ++void flexiblas_real_zdotc_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ fn = current_backend->blas.zdotc.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_zdotc( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zdotc_"))); ++ ++ ++void flexiblas_chain_zdotc_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ ++ ++ hook_pos_zdotc++; ++ if ( hook_pos_zdotc < __flexiblas_hooks->zdotc.nhook ) { ++ fn = __flexiblas_hooks->zdotc.f77_hook_function[hook_pos_zdotc]; ++ } else { ++ hook_pos_zdotc = 0; ++ fn = current_backend->blas.zdotc.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_zdotc( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zdotc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdotu = 0; ++ + void FC_GLOBAL(zdotu,ZDOTU)( double complex* returnvalue, blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3297,6 +7255,56 @@ + + + ++void flexiblas_real_zdotu_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ fn = current_backend->blas.zdotu.f77_blas_function; fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_real_zdotu( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zdotu_"))); ++ ++ ++void flexiblas_chain_zdotu_( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ double complex (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ void (*fn_intel) (double complex *ret, void* n, void* zx, void* incx, void* zy, void* incy); ++ double complex ret; ++ ++ ++ ++ hook_pos_zdotu++; ++ if ( hook_pos_zdotu < __flexiblas_hooks->zdotu.nhook ) { ++ fn = __flexiblas_hooks->zdotu.f77_hook_function[hook_pos_zdotu]; ++ } else { ++ hook_pos_zdotu = 0; ++ fn = current_backend->blas.zdotu.f77_blas_function; ++ } fn_intel = (void *) fn; ++ ++ if(current_backend->info.intel_interface == 0 ) { ++ ret = fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } else { ++ fn_intel( &ret, (void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ } ++ ++ *((double complex *)returnvalue) = ret; ++ return; ++} ++void flexiblas_chain_zdotu( void * returnvalue, void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zdotu_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdrot = 0; ++ + void FC_GLOBAL(zdrot,ZDROT)(blasint* n, double complex* cx, blasint* incx, double complex* cy, blasint* incy, double* c, double* s) + { + void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); +@@ -3323,6 +7331,40 @@ + + + ++void flexiblas_real_zdrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ fn = current_backend->blas.zdrot.f77_blas_function; ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_zdrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_real_zdrot_"))); ++ ++ ++void flexiblas_chain_zdrot_(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) ++{ ++ void (*fn) (void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s); ++ ++ ++ ++ hook_pos_zdrot++; ++ if ( hook_pos_zdrot < __flexiblas_hooks->zdrot.nhook ) { ++ fn = __flexiblas_hooks->zdrot.f77_hook_function[hook_pos_zdrot]; ++ } else { ++ hook_pos_zdrot = 0; ++ fn = current_backend->blas.zdrot.f77_blas_function; ++ } ++ fn((void*) n, (void*) cx, (void*) incx, (void*) cy, (void*) incy, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_zdrot(void* n, void* cx, void* incx, void* cy, void* incy, void* c, void* s) __attribute__((alias("flexiblas_chain_zdrot_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zdscal = 0; ++ + void FC_GLOBAL(zdscal,ZDSCAL)(blasint* n, double* da, double complex* zx, blasint* incx) + { + void (*fn) (void* n, void* da, void* zx, void* incx); +@@ -3349,6 +7391,40 @@ + + + ++void flexiblas_real_zdscal_(void* n, void* da, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* zx, void* incx); ++ ++ fn = current_backend->blas.zdscal.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_zdscal(void* n, void* da, void* zx, void* incx) __attribute__((alias("flexiblas_real_zdscal_"))); ++ ++ ++void flexiblas_chain_zdscal_(void* n, void* da, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* da, void* zx, void* incx); ++ ++ ++ ++ hook_pos_zdscal++; ++ if ( hook_pos_zdscal < __flexiblas_hooks->zdscal.nhook ) { ++ fn = __flexiblas_hooks->zdscal.f77_hook_function[hook_pos_zdscal]; ++ } else { ++ hook_pos_zdscal = 0; ++ fn = current_backend->blas.zdscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_zdscal(void* n, void* da, void* zx, void* incx) __attribute__((alias("flexiblas_chain_zdscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgbmv = 0; ++ + void FC_GLOBAL(zgbmv,ZGBMV)(char* trans, blasint* m, blasint* n, blasint* kl, blasint* ku, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3375,6 +7451,40 @@ + + + ++void flexiblas_real_zgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zgbmv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zgbmv_"))); ++ ++ ++void flexiblas_chain_zgbmv_(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zgbmv++; ++ if ( hook_pos_zgbmv < __flexiblas_hooks->zgbmv.nhook ) { ++ fn = __flexiblas_hooks->zgbmv.f77_hook_function[hook_pos_zgbmv]; ++ } else { ++ hook_pos_zgbmv = 0; ++ fn = current_backend->blas.zgbmv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) kl, (void*) ku, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zgbmv(void* trans, void* m, void* n, void* kl, void* ku, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zgbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgemm = 0; ++ + void FC_GLOBAL(zgemm,ZGEMM)(char* transa, char* transb, blasint* m, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3401,6 +7511,40 @@ + + + ++void flexiblas_real_zgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zgemm.f77_blas_function; ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zgemm_"))); ++ ++ ++void flexiblas_chain_zgemm_(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zgemm++; ++ if ( hook_pos_zgemm < __flexiblas_hooks->zgemm.nhook ) { ++ fn = __flexiblas_hooks->zgemm.f77_hook_function[hook_pos_zgemm]; ++ } else { ++ hook_pos_zgemm = 0; ++ fn = current_backend->blas.zgemm.f77_blas_function; ++ } ++ fn((void*) transa, (void*) transb, (void*) m, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zgemm(void* transa, void* transb, void* m, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zgemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgemv = 0; ++ + void FC_GLOBAL(zgemv,ZGEMV)(char* trans, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3427,6 +7571,40 @@ + + + ++void flexiblas_real_zgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zgemv.f77_blas_function; ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zgemv_"))); ++ ++ ++void flexiblas_chain_zgemv_(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zgemv++; ++ if ( hook_pos_zgemv < __flexiblas_hooks->zgemv.nhook ) { ++ fn = __flexiblas_hooks->zgemv.f77_hook_function[hook_pos_zgemv]; ++ } else { ++ hook_pos_zgemv = 0; ++ fn = current_backend->blas.zgemv.f77_blas_function; ++ } ++ fn((void*) trans, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zgemv(void* trans, void* m, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zgemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgerc = 0; ++ + void FC_GLOBAL(zgerc,ZGERC)(blasint* m, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -3453,6 +7631,40 @@ + + + ++void flexiblas_real_zgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.zgerc.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_zgerc_"))); ++ ++ ++void flexiblas_chain_zgerc_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_zgerc++; ++ if ( hook_pos_zgerc < __flexiblas_hooks->zgerc.nhook ) { ++ fn = __flexiblas_hooks->zgerc.f77_hook_function[hook_pos_zgerc]; ++ } else { ++ hook_pos_zgerc = 0; ++ fn = current_backend->blas.zgerc.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zgerc(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_zgerc_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgeru = 0; ++ + void FC_GLOBAL(zgeru,ZGERU)(blasint* m, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* a, blasint* lda) + { + void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -3479,6 +7691,40 @@ + + + ++void flexiblas_real_zgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.zgeru.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_zgeru_"))); ++ ++ ++void flexiblas_chain_zgeru_(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_zgeru++; ++ if ( hook_pos_zgeru < __flexiblas_hooks->zgeru.nhook ) { ++ fn = __flexiblas_hooks->zgeru.f77_hook_function[hook_pos_zgeru]; ++ } else { ++ hook_pos_zgeru = 0; ++ fn = current_backend->blas.zgeru.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zgeru(void* m, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_zgeru_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhbmv = 0; ++ + void FC_GLOBAL(zhbmv,ZHBMV)(char* uplo, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3505,6 +7751,40 @@ + + + ++void flexiblas_real_zhbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zhbmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zhbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zhbmv_"))); ++ ++ ++void flexiblas_chain_zhbmv_(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zhbmv++; ++ if ( hook_pos_zhbmv < __flexiblas_hooks->zhbmv.nhook ) { ++ fn = __flexiblas_hooks->zhbmv.f77_hook_function[hook_pos_zhbmv]; ++ } else { ++ hook_pos_zhbmv = 0; ++ fn = current_backend->blas.zhbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zhbmv(void* uplo, void* n, void* k, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zhbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhemm = 0; ++ + void FC_GLOBAL(zhemm,ZHEMM)(char* side, char* uplo, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3531,6 +7811,40 @@ + + + ++void flexiblas_real_zhemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zhemm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zhemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zhemm_"))); ++ ++ ++void flexiblas_chain_zhemm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zhemm++; ++ if ( hook_pos_zhemm < __flexiblas_hooks->zhemm.nhook ) { ++ fn = __flexiblas_hooks->zhemm.f77_hook_function[hook_pos_zhemm]; ++ } else { ++ hook_pos_zhemm = 0; ++ fn = current_backend->blas.zhemm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zhemm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zhemm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhemv = 0; ++ + void FC_GLOBAL(zhemv,ZHEMV)(char* uplo, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3557,6 +7871,40 @@ + + + ++void flexiblas_real_zhemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zhemv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zhemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zhemv_"))); ++ ++ ++void flexiblas_chain_zhemv_(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zhemv++; ++ if ( hook_pos_zhemv < __flexiblas_hooks->zhemv.nhook ) { ++ fn = __flexiblas_hooks->zhemv.f77_hook_function[hook_pos_zhemv]; ++ } else { ++ hook_pos_zhemv = 0; ++ fn = current_backend->blas.zhemv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zhemv(void* uplo, void* n, void* alpha, void* a, void* lda, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zhemv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zher = 0; ++ + void FC_GLOBAL(zher,ZHER)(char* uplo, blasint* n, double* alpha, double complex* x, blasint* incx, double complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); +@@ -3583,6 +7931,40 @@ + + + ++void flexiblas_real_zher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ fn = current_backend->blas.zher.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_real_zher_"))); ++ ++ ++void flexiblas_chain_zher_(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda); ++ ++ ++ ++ hook_pos_zher++; ++ if ( hook_pos_zher < __flexiblas_hooks->zher.nhook ) { ++ fn = __flexiblas_hooks->zher.f77_hook_function[hook_pos_zher]; ++ } else { ++ hook_pos_zher = 0; ++ fn = current_backend->blas.zher.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zher(void* uplo, void* n, void* alpha, void* x, void* incx, void* a, void* lda) __attribute__((alias("flexiblas_chain_zher_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zher2 = 0; ++ + void FC_GLOBAL(zher2,ZHER2)(char* uplo, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* a, blasint* lda) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); +@@ -3609,6 +7991,40 @@ + + + ++void flexiblas_real_zher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ fn = current_backend->blas.zher2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_real_zher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_real_zher2_"))); ++ ++ ++void flexiblas_chain_zher2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda); ++ ++ ++ ++ hook_pos_zher2++; ++ if ( hook_pos_zher2 < __flexiblas_hooks->zher2.nhook ) { ++ fn = __flexiblas_hooks->zher2.f77_hook_function[hook_pos_zher2]; ++ } else { ++ hook_pos_zher2 = 0; ++ fn = current_backend->blas.zher2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) a, (void*) lda); ++ ++ return; ++} ++void flexiblas_chain_zher2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* a, void* lda) __attribute__((alias("flexiblas_chain_zher2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zher2k = 0; ++ + void FC_GLOBAL(zher2k,ZHER2K)(char* uplo, char* trans, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3635,6 +8051,40 @@ + + + ++void flexiblas_real_zher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zher2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zher2k_"))); ++ ++ ++void flexiblas_chain_zher2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zher2k++; ++ if ( hook_pos_zher2k < __flexiblas_hooks->zher2k.nhook ) { ++ fn = __flexiblas_hooks->zher2k.f77_hook_function[hook_pos_zher2k]; ++ } else { ++ hook_pos_zher2k = 0; ++ fn = current_backend->blas.zher2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zher2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zher2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zherk = 0; ++ + void FC_GLOBAL(zherk,ZHERK)(char* uplo, char* trans, blasint* n, blasint* k, double* alpha, double complex* a, blasint* lda, double* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -3661,6 +8111,40 @@ + + + ++void flexiblas_real_zherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zherk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zherk_"))); ++ ++ ++void flexiblas_chain_zherk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zherk++; ++ if ( hook_pos_zherk < __flexiblas_hooks->zherk.nhook ) { ++ fn = __flexiblas_hooks->zherk.f77_hook_function[hook_pos_zherk]; ++ } else { ++ hook_pos_zherk = 0; ++ fn = current_backend->blas.zherk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zherk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zherk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhpmv = 0; ++ + void FC_GLOBAL(zhpmv,ZHPMV)(char* uplo, blasint* n, double complex* alpha, double complex* ap, double complex* x, blasint* incx, double complex* beta, double complex* y, blasint* incy) + { + void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); +@@ -3687,6 +8171,40 @@ + + + ++void flexiblas_real_zhpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ fn = current_backend->blas.zhpmv.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zhpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_real_zhpmv_"))); ++ ++ ++void flexiblas_chain_zhpmv_(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy); ++ ++ ++ ++ hook_pos_zhpmv++; ++ if ( hook_pos_zhpmv < __flexiblas_hooks->zhpmv.nhook ) { ++ fn = __flexiblas_hooks->zhpmv.f77_hook_function[hook_pos_zhpmv]; ++ } else { ++ hook_pos_zhpmv = 0; ++ fn = current_backend->blas.zhpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) ap, (void*) x, (void*) incx, (void*) beta, (void*) y, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zhpmv(void* uplo, void* n, void* alpha, void* ap, void* x, void* incx, void* beta, void* y, void* incy) __attribute__((alias("flexiblas_chain_zhpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhpr = 0; ++ + void FC_GLOBAL(zhpr,ZHPR)(char* uplo, blasint* n, double* alpha, double complex* x, blasint* incx, double complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); +@@ -3713,6 +8231,40 @@ + + + ++void flexiblas_real_zhpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ fn = current_backend->blas.zhpr.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_zhpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_real_zhpr_"))); ++ ++ ++void flexiblas_chain_zhpr_(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* ap); ++ ++ ++ ++ hook_pos_zhpr++; ++ if ( hook_pos_zhpr < __flexiblas_hooks->zhpr.nhook ) { ++ fn = __flexiblas_hooks->zhpr.f77_hook_function[hook_pos_zhpr]; ++ } else { ++ hook_pos_zhpr = 0; ++ fn = current_backend->blas.zhpr.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_zhpr(void* uplo, void* n, void* alpha, void* x, void* incx, void* ap) __attribute__((alias("flexiblas_chain_zhpr_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zhpr2 = 0; ++ + void FC_GLOBAL(zhpr2,ZHPR2)(char* uplo, blasint* n, double complex* alpha, double complex* x, blasint* incx, double complex* y, blasint* incy, double complex* ap) + { + void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); +@@ -3739,6 +8291,40 @@ + + + ++void flexiblas_real_zhpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ fn = current_backend->blas.zhpr2.f77_blas_function; ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_real_zhpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_real_zhpr2_"))); ++ ++ ++void flexiblas_chain_zhpr2_(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) ++{ ++ void (*fn) (void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap); ++ ++ ++ ++ hook_pos_zhpr2++; ++ if ( hook_pos_zhpr2 < __flexiblas_hooks->zhpr2.nhook ) { ++ fn = __flexiblas_hooks->zhpr2.f77_hook_function[hook_pos_zhpr2]; ++ } else { ++ hook_pos_zhpr2 = 0; ++ fn = current_backend->blas.zhpr2.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) n, (void*) alpha, (void*) x, (void*) incx, (void*) y, (void*) incy, (void*) ap); ++ ++ return; ++} ++void flexiblas_chain_zhpr2(void* uplo, void* n, void* alpha, void* x, void* incx, void* y, void* incy, void* ap) __attribute__((alias("flexiblas_chain_zhpr2_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zrotg = 0; ++ + void FC_GLOBAL(zrotg,ZROTG)(double complex* ca, double complex* cb, double* c, double complex* s) + { + void (*fn) (void* ca, void* cb, void* c, void* s); +@@ -3765,6 +8351,40 @@ + + + ++void flexiblas_real_zrotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ fn = current_backend->blas.zrotg.f77_blas_function; ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_real_zrotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_real_zrotg_"))); ++ ++ ++void flexiblas_chain_zrotg_(void* ca, void* cb, void* c, void* s) ++{ ++ void (*fn) (void* ca, void* cb, void* c, void* s); ++ ++ ++ ++ hook_pos_zrotg++; ++ if ( hook_pos_zrotg < __flexiblas_hooks->zrotg.nhook ) { ++ fn = __flexiblas_hooks->zrotg.f77_hook_function[hook_pos_zrotg]; ++ } else { ++ hook_pos_zrotg = 0; ++ fn = current_backend->blas.zrotg.f77_blas_function; ++ } ++ fn((void*) ca, (void*) cb, (void*) c, (void*) s); ++ ++ return; ++} ++void flexiblas_chain_zrotg(void* ca, void* cb, void* c, void* s) __attribute__((alias("flexiblas_chain_zrotg_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zscal = 0; ++ + void FC_GLOBAL(zscal,ZSCAL)(blasint* n, double complex* za, double complex* zx, blasint* incx) + { + void (*fn) (void* n, void* za, void* zx, void* incx); +@@ -3791,6 +8411,40 @@ + + + ++void flexiblas_real_zscal_(void* n, void* za, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx); ++ ++ fn = current_backend->blas.zscal.f77_blas_function; ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_zscal(void* n, void* za, void* zx, void* incx) __attribute__((alias("flexiblas_real_zscal_"))); ++ ++ ++void flexiblas_chain_zscal_(void* n, void* za, void* zx, void* incx) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx); ++ ++ ++ ++ hook_pos_zscal++; ++ if ( hook_pos_zscal < __flexiblas_hooks->zscal.nhook ) { ++ fn = __flexiblas_hooks->zscal.f77_hook_function[hook_pos_zscal]; ++ } else { ++ hook_pos_zscal = 0; ++ fn = current_backend->blas.zscal.f77_blas_function; ++ } ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_zscal(void* n, void* za, void* zx, void* incx) __attribute__((alias("flexiblas_chain_zscal_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zswap = 0; ++ + void FC_GLOBAL(zswap,ZSWAP)(blasint* n, double complex* zx, blasint* incx, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); +@@ -3817,6 +8471,40 @@ + + + ++void flexiblas_real_zswap_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ fn = current_backend->blas.zswap.f77_blas_function; ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zswap(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_real_zswap_"))); ++ ++ ++void flexiblas_chain_zswap_(void* n, void* zx, void* incx, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* zx, void* incx, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zswap++; ++ if ( hook_pos_zswap < __flexiblas_hooks->zswap.nhook ) { ++ fn = __flexiblas_hooks->zswap.f77_hook_function[hook_pos_zswap]; ++ } else { ++ hook_pos_zswap = 0; ++ fn = current_backend->blas.zswap.f77_blas_function; ++ } ++ fn((void*) n, (void*) zx, (void*) incx, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zswap(void* n, void* zx, void* incx, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zswap_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zsymm = 0; ++ + void FC_GLOBAL(zsymm,ZSYMM)(char* side, char* uplo, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3843,6 +8531,40 @@ + + + ++void flexiblas_real_zsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zsymm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zsymm_"))); ++ ++ ++void flexiblas_chain_zsymm_(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zsymm++; ++ if ( hook_pos_zsymm < __flexiblas_hooks->zsymm.nhook ) { ++ fn = __flexiblas_hooks->zsymm.f77_hook_function[hook_pos_zsymm]; ++ } else { ++ hook_pos_zsymm = 0; ++ fn = current_backend->blas.zsymm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zsymm(void* side, void* uplo, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zsymm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zsyr2k = 0; ++ + void FC_GLOBAL(zsyr2k,ZSYR2K)(char* uplo, char* trans, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); +@@ -3869,6 +8591,40 @@ + + + ++void flexiblas_real_zsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zsyr2k.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zsyr2k_"))); ++ ++ ++void flexiblas_chain_zsyr2k_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zsyr2k++; ++ if ( hook_pos_zsyr2k < __flexiblas_hooks->zsyr2k.nhook ) { ++ fn = __flexiblas_hooks->zsyr2k.f77_hook_function[hook_pos_zsyr2k]; ++ } else { ++ hook_pos_zsyr2k = 0; ++ fn = current_backend->blas.zsyr2k.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zsyr2k(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* b, void* ldb, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zsyr2k_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zsyrk = 0; ++ + void FC_GLOBAL(zsyrk,ZSYRK)(char* uplo, char* trans, blasint* n, blasint* k, double complex* alpha, double complex* a, blasint* lda, double complex* beta, double complex* c, blasint* ldc) + { + void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); +@@ -3895,6 +8651,40 @@ + + + ++void flexiblas_real_zsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ fn = current_backend->blas.zsyrk.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_real_zsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_real_zsyrk_"))); ++ ++ ++void flexiblas_chain_zsyrk_(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) ++{ ++ void (*fn) (void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc); ++ ++ ++ ++ hook_pos_zsyrk++; ++ if ( hook_pos_zsyrk < __flexiblas_hooks->zsyrk.nhook ) { ++ fn = __flexiblas_hooks->zsyrk.f77_hook_function[hook_pos_zsyrk]; ++ } else { ++ hook_pos_zsyrk = 0; ++ fn = current_backend->blas.zsyrk.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) n, (void*) k, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) c, (void*) ldc); ++ ++ return; ++} ++void flexiblas_chain_zsyrk(void* uplo, void* trans, void* n, void* k, void* alpha, void* a, void* lda, void* beta, void* c, void* ldc) __attribute__((alias("flexiblas_chain_zsyrk_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztbmv = 0; ++ + void FC_GLOBAL(ztbmv,ZTBMV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -3921,6 +8711,40 @@ + + + ++void flexiblas_real_ztbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztbmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztbmv_"))); ++ ++ ++void flexiblas_chain_ztbmv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztbmv++; ++ if ( hook_pos_ztbmv < __flexiblas_hooks->ztbmv.nhook ) { ++ fn = __flexiblas_hooks->ztbmv.f77_hook_function[hook_pos_ztbmv]; ++ } else { ++ hook_pos_ztbmv = 0; ++ fn = current_backend->blas.ztbmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztbmv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztbmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztbsv = 0; ++ + void FC_GLOBAL(ztbsv,ZTBSV)(char* uplo, char* trans, char* diag, blasint* n, blasint* k, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); +@@ -3947,6 +8771,40 @@ + + + ++void flexiblas_real_ztbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztbsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztbsv_"))); ++ ++ ++void flexiblas_chain_ztbsv_(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztbsv++; ++ if ( hook_pos_ztbsv < __flexiblas_hooks->ztbsv.nhook ) { ++ fn = __flexiblas_hooks->ztbsv.f77_hook_function[hook_pos_ztbsv]; ++ } else { ++ hook_pos_ztbsv = 0; ++ fn = current_backend->blas.ztbsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) k, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztbsv(void* uplo, void* trans, void* diag, void* n, void* k, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztbsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztpmv = 0; ++ + void FC_GLOBAL(ztpmv,ZTPMV)(char* uplo, char* trans, char* diag, blasint* n, double complex* ap, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3973,6 +8831,40 @@ + + + ++void flexiblas_real_ztpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ztpmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ztpmv_"))); ++ ++ ++void flexiblas_chain_ztpmv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztpmv++; ++ if ( hook_pos_ztpmv < __flexiblas_hooks->ztpmv.nhook ) { ++ fn = __flexiblas_hooks->ztpmv.f77_hook_function[hook_pos_ztpmv]; ++ } else { ++ hook_pos_ztpmv = 0; ++ fn = current_backend->blas.ztpmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztpmv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztpmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztpsv = 0; ++ + void FC_GLOBAL(ztpsv,ZTPSV)(char* uplo, char* trans, char* diag, blasint* n, double complex* ap, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); +@@ -3999,6 +8891,40 @@ + + + ++void flexiblas_real_ztpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ fn = current_backend->blas.ztpsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_real_ztpsv_"))); ++ ++ ++void flexiblas_chain_ztpsv_(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztpsv++; ++ if ( hook_pos_ztpsv < __flexiblas_hooks->ztpsv.nhook ) { ++ fn = __flexiblas_hooks->ztpsv.f77_hook_function[hook_pos_ztpsv]; ++ } else { ++ hook_pos_ztpsv = 0; ++ fn = current_backend->blas.ztpsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) ap, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztpsv(void* uplo, void* trans, void* diag, void* n, void* ap, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztpsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrmm = 0; ++ + void FC_GLOBAL(ztrmm,ZTRMM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4025,6 +8951,40 @@ + + + ++void flexiblas_real_ztrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ztrmm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ztrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ztrmm_"))); ++ ++ ++void flexiblas_chain_ztrmm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ztrmm++; ++ if ( hook_pos_ztrmm < __flexiblas_hooks->ztrmm.nhook ) { ++ fn = __flexiblas_hooks->ztrmm.f77_hook_function[hook_pos_ztrmm]; ++ } else { ++ hook_pos_ztrmm = 0; ++ fn = current_backend->blas.ztrmm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ztrmm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ztrmm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrmv = 0; ++ + void FC_GLOBAL(ztrmv,ZTRMV)(char* uplo, char* trans, char* diag, blasint* n, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -4051,6 +9011,40 @@ + + + ++void flexiblas_real_ztrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztrmv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztrmv_"))); ++ ++ ++void flexiblas_chain_ztrmv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztrmv++; ++ if ( hook_pos_ztrmv < __flexiblas_hooks->ztrmv.nhook ) { ++ fn = __flexiblas_hooks->ztrmv.f77_hook_function[hook_pos_ztrmv]; ++ } else { ++ hook_pos_ztrmv = 0; ++ fn = current_backend->blas.ztrmv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztrmv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztrmv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrsm = 0; ++ + void FC_GLOBAL(ztrsm,ZTRSM)(char* side, char* uplo, char* transa, char* diag, blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb) + { + void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4077,6 +9071,40 @@ + + + ++void flexiblas_real_ztrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.ztrsm.f77_blas_function; ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_ztrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_ztrsm_"))); ++ ++ ++void flexiblas_chain_ztrsm_(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_ztrsm++; ++ if ( hook_pos_ztrsm < __flexiblas_hooks->ztrsm.nhook ) { ++ fn = __flexiblas_hooks->ztrsm.f77_hook_function[hook_pos_ztrsm]; ++ } else { ++ hook_pos_ztrsm = 0; ++ fn = current_backend->blas.ztrsm.f77_blas_function; ++ } ++ fn((void*) side, (void*) uplo, (void*) transa, (void*) diag, (void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_ztrsm(void* side, void* uplo, void* transa, void* diag, void* m, void* n, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_ztrsm_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_ztrsv = 0; ++ + void FC_GLOBAL(ztrsv,ZTRSV)(char* uplo, char* trans, char* diag, blasint* n, double complex* a, blasint* lda, double complex* x, blasint* incx) + { + void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); +@@ -4103,6 +9131,40 @@ + + + ++void flexiblas_real_ztrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ fn = current_backend->blas.ztrsv.f77_blas_function; ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_real_ztrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_real_ztrsv_"))); ++ ++ ++void flexiblas_chain_ztrsv_(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) ++{ ++ void (*fn) (void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx); ++ ++ ++ ++ hook_pos_ztrsv++; ++ if ( hook_pos_ztrsv < __flexiblas_hooks->ztrsv.nhook ) { ++ fn = __flexiblas_hooks->ztrsv.f77_hook_function[hook_pos_ztrsv]; ++ } else { ++ hook_pos_ztrsv = 0; ++ fn = current_backend->blas.ztrsv.f77_blas_function; ++ } ++ fn((void*) uplo, (void*) trans, (void*) diag, (void*) n, (void*) a, (void*) lda, (void*) x, (void*) incx); ++ ++ return; ++} ++void flexiblas_chain_ztrsv(void* uplo, void* trans, void* diag, void* n, void* a, void* lda, void* x, void* incx) __attribute__((alias("flexiblas_chain_ztrsv_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_caxpby = 0; ++ + void FC_GLOBAL(caxpby,CAXPBY)(blasint* n, float complex* ca, float complex* cx, blasint* incx, float complex* cb, float complex* cy, blasint* incy) + { + void (*fn) (void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy); +@@ -4129,6 +9191,40 @@ + + + ++void flexiblas_real_caxpby_(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy); ++ ++ fn = current_backend->blas.caxpby.f77_blas_function; ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cb, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_caxpby(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) __attribute__((alias("flexiblas_real_caxpby_"))); ++ ++ ++void flexiblas_chain_caxpby_(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) ++{ ++ void (*fn) (void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy); ++ ++ ++ ++ hook_pos_caxpby++; ++ if ( hook_pos_caxpby < __flexiblas_hooks->caxpby.nhook ) { ++ fn = __flexiblas_hooks->caxpby.f77_hook_function[hook_pos_caxpby]; ++ } else { ++ hook_pos_caxpby = 0; ++ fn = current_backend->blas.caxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) ca, (void*) cx, (void*) incx, (void*) cb, (void*) cy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_caxpby(void* n, void* ca, void* cx, void* incx, void* cb, void* cy, void* incy) __attribute__((alias("flexiblas_chain_caxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_daxpby = 0; ++ + void FC_GLOBAL(daxpby,DAXPBY)(blasint* n, double* da, double* dx, blasint* incx, double* db, double* dy, blasint* incy) + { + void (*fn) (void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy); +@@ -4155,6 +9251,40 @@ + + + ++void flexiblas_real_daxpby_(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy); ++ ++ fn = current_backend->blas.daxpby.f77_blas_function; ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) db, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_daxpby(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) __attribute__((alias("flexiblas_real_daxpby_"))); ++ ++ ++void flexiblas_chain_daxpby_(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) ++{ ++ void (*fn) (void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy); ++ ++ ++ ++ hook_pos_daxpby++; ++ if ( hook_pos_daxpby < __flexiblas_hooks->daxpby.nhook ) { ++ fn = __flexiblas_hooks->daxpby.f77_hook_function[hook_pos_daxpby]; ++ } else { ++ hook_pos_daxpby = 0; ++ fn = current_backend->blas.daxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) da, (void*) dx, (void*) incx, (void*) db, (void*) dy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_daxpby(void* n, void* da, void* dx, void* incx, void* db, void* dy, void* incy) __attribute__((alias("flexiblas_chain_daxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zaxpby = 0; ++ + void FC_GLOBAL(zaxpby,ZAXPBY)(blasint* n, double complex* za, double complex* zx, blasint* incx, double complex* zb, double complex* zy, blasint* incy) + { + void (*fn) (void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy); +@@ -4181,6 +9311,40 @@ + + + ++void flexiblas_real_zaxpby_(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy); ++ ++ fn = current_backend->blas.zaxpby.f77_blas_function; ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zb, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_zaxpby(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) __attribute__((alias("flexiblas_real_zaxpby_"))); ++ ++ ++void flexiblas_chain_zaxpby_(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) ++{ ++ void (*fn) (void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy); ++ ++ ++ ++ hook_pos_zaxpby++; ++ if ( hook_pos_zaxpby < __flexiblas_hooks->zaxpby.nhook ) { ++ fn = __flexiblas_hooks->zaxpby.f77_hook_function[hook_pos_zaxpby]; ++ } else { ++ hook_pos_zaxpby = 0; ++ fn = current_backend->blas.zaxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) za, (void*) zx, (void*) incx, (void*) zb, (void*) zy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_zaxpby(void* n, void* za, void* zx, void* incx, void* zb, void* zy, void* incy) __attribute__((alias("flexiblas_chain_zaxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_saxpby = 0; ++ + void FC_GLOBAL(saxpby,SAXPBY)(blasint* n, float* sa, float* sx, blasint* incx, float* sb, float* sy, blasint* incy) + { + void (*fn) (void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy); +@@ -4207,6 +9371,40 @@ + + + ++void flexiblas_real_saxpby_(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy); ++ ++ fn = current_backend->blas.saxpby.f77_blas_function; ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sb, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_real_saxpby(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) __attribute__((alias("flexiblas_real_saxpby_"))); ++ ++ ++void flexiblas_chain_saxpby_(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) ++{ ++ void (*fn) (void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy); ++ ++ ++ ++ hook_pos_saxpby++; ++ if ( hook_pos_saxpby < __flexiblas_hooks->saxpby.nhook ) { ++ fn = __flexiblas_hooks->saxpby.f77_hook_function[hook_pos_saxpby]; ++ } else { ++ hook_pos_saxpby = 0; ++ fn = current_backend->blas.saxpby.f77_blas_function; ++ } ++ fn((void*) n, (void*) sa, (void*) sx, (void*) incx, (void*) sb, (void*) sy, (void*) incy); ++ ++ return; ++} ++void flexiblas_chain_saxpby(void* n, void* sa, void* sx, void* incx, void* sb, void* sy, void* incy) __attribute__((alias("flexiblas_chain_saxpby_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_comatcopy = 0; ++ + void FC_GLOBAL(comatcopy,COMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float complex* alpha, float complex* a, blasint* lda, float complex* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4233,6 +9431,40 @@ + + + ++void flexiblas_real_comatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.comatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_comatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_comatcopy_"))); ++ ++ ++void flexiblas_chain_comatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_comatcopy++; ++ if ( hook_pos_comatcopy < __flexiblas_hooks->comatcopy.nhook ) { ++ fn = __flexiblas_hooks->comatcopy.f77_hook_function[hook_pos_comatcopy]; ++ } else { ++ hook_pos_comatcopy = 0; ++ fn = current_backend->blas.comatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_comatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_comatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zomatcopy = 0; ++ + void FC_GLOBAL(zomatcopy,ZOMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double complex* alpha, double complex* a, blasint* lda, double complex* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4259,6 +9491,40 @@ + + + ++void flexiblas_real_zomatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.zomatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_zomatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_zomatcopy_"))); ++ ++ ++void flexiblas_chain_zomatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_zomatcopy++; ++ if ( hook_pos_zomatcopy < __flexiblas_hooks->zomatcopy.nhook ) { ++ fn = __flexiblas_hooks->zomatcopy.f77_hook_function[hook_pos_zomatcopy]; ++ } else { ++ hook_pos_zomatcopy = 0; ++ fn = current_backend->blas.zomatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_zomatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_zomatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_domatcopy = 0; ++ + void FC_GLOBAL(domatcopy,DOMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double* alpha, double* a, blasint* lda, double* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4285,6 +9551,40 @@ + + + ++void flexiblas_real_domatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.domatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_domatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_domatcopy_"))); ++ ++ ++void flexiblas_chain_domatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_domatcopy++; ++ if ( hook_pos_domatcopy < __flexiblas_hooks->domatcopy.nhook ) { ++ fn = __flexiblas_hooks->domatcopy.f77_hook_function[hook_pos_domatcopy]; ++ } else { ++ hook_pos_domatcopy = 0; ++ fn = current_backend->blas.domatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_domatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_domatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_somatcopy = 0; ++ + void FC_GLOBAL(somatcopy,SOMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float* alpha, float* a, blasint* lda, float* b, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); +@@ -4311,6 +9611,40 @@ + + + ++void flexiblas_real_somatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ fn = current_backend->blas.somatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_somatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_real_somatcopy_"))); ++ ++ ++void flexiblas_chain_somatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb); ++ ++ ++ ++ hook_pos_somatcopy++; ++ if ( hook_pos_somatcopy < __flexiblas_hooks->somatcopy.nhook ) { ++ fn = __flexiblas_hooks->somatcopy.f77_hook_function[hook_pos_somatcopy]; ++ } else { ++ hook_pos_somatcopy = 0; ++ fn = current_backend->blas.somatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_somatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* b, void* ldb) __attribute__((alias("flexiblas_chain_somatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cimatcopy = 0; ++ + void FC_GLOBAL(cimatcopy,CIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float complex* alpha, float complex* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4337,6 +9671,40 @@ + + + ++void flexiblas_real_cimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.cimatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_cimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_cimatcopy_"))); ++ ++ ++void flexiblas_chain_cimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_cimatcopy++; ++ if ( hook_pos_cimatcopy < __flexiblas_hooks->cimatcopy.nhook ) { ++ fn = __flexiblas_hooks->cimatcopy.f77_hook_function[hook_pos_cimatcopy]; ++ } else { ++ hook_pos_cimatcopy = 0; ++ fn = current_backend->blas.cimatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_cimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_cimatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zimatcopy = 0; ++ + void FC_GLOBAL(zimatcopy,ZIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double complex* alpha, double complex* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4363,6 +9731,40 @@ + + + ++void flexiblas_real_zimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.zimatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_zimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_zimatcopy_"))); ++ ++ ++void flexiblas_chain_zimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_zimatcopy++; ++ if ( hook_pos_zimatcopy < __flexiblas_hooks->zimatcopy.nhook ) { ++ fn = __flexiblas_hooks->zimatcopy.f77_hook_function[hook_pos_zimatcopy]; ++ } else { ++ hook_pos_zimatcopy = 0; ++ fn = current_backend->blas.zimatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_zimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_zimatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dimatcopy = 0; ++ + void FC_GLOBAL(dimatcopy,DIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, double* alpha, double* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4389,6 +9791,40 @@ + + + ++void flexiblas_real_dimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.dimatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_dimatcopy_"))); ++ ++ ++void flexiblas_chain_dimatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_dimatcopy++; ++ if ( hook_pos_dimatcopy < __flexiblas_hooks->dimatcopy.nhook ) { ++ fn = __flexiblas_hooks->dimatcopy.f77_hook_function[hook_pos_dimatcopy]; ++ } else { ++ hook_pos_dimatcopy = 0; ++ fn = current_backend->blas.dimatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dimatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_dimatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_simatcopy = 0; ++ + void FC_GLOBAL(simatcopy,SIMATCOPY)(char* order, char* trans, blasint* rows, blasint* cols, float* alpha, float* a, blasint* lda, blasint* ldb) + { + void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); +@@ -4415,6 +9851,40 @@ + + + ++void flexiblas_real_simatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ fn = current_backend->blas.simatcopy.f77_blas_function; ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_simatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_real_simatcopy_"))); ++ ++ ++void flexiblas_chain_simatcopy_(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) ++{ ++ void (*fn) (void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb); ++ ++ ++ ++ hook_pos_simatcopy++; ++ if ( hook_pos_simatcopy < __flexiblas_hooks->simatcopy.nhook ) { ++ fn = __flexiblas_hooks->simatcopy.f77_hook_function[hook_pos_simatcopy]; ++ } else { ++ hook_pos_simatcopy = 0; ++ fn = current_backend->blas.simatcopy.f77_blas_function; ++ } ++ fn((void*) order, (void*) trans, (void*) rows, (void*) cols, (void*) alpha, (void*) a, (void*) lda, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_simatcopy(void* order, void* trans, void* rows, void* cols, void* alpha, void* a, void* lda, void* ldb) __attribute__((alias("flexiblas_chain_simatcopy_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_sgeadd = 0; ++ + void FC_GLOBAL(sgeadd,SGEADD)(blasint* m, blasint* n, float* alpha, float* a, blasint* lda, float* beta, float* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4441,6 +9911,40 @@ + + + ++void flexiblas_real_sgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.sgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_sgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_sgeadd_"))); ++ ++ ++void flexiblas_chain_sgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_sgeadd++; ++ if ( hook_pos_sgeadd < __flexiblas_hooks->sgeadd.nhook ) { ++ fn = __flexiblas_hooks->sgeadd.f77_hook_function[hook_pos_sgeadd]; ++ } else { ++ hook_pos_sgeadd = 0; ++ fn = current_backend->blas.sgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_sgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_sgeadd_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_dgeadd = 0; ++ + void FC_GLOBAL(dgeadd,DGEADD)(blasint* m, blasint* n, double* alpha, double* a, blasint* lda, double* beta, double* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4467,6 +9971,40 @@ + + + ++void flexiblas_real_dgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.dgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_dgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_dgeadd_"))); ++ ++ ++void flexiblas_chain_dgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_dgeadd++; ++ if ( hook_pos_dgeadd < __flexiblas_hooks->dgeadd.nhook ) { ++ fn = __flexiblas_hooks->dgeadd.f77_hook_function[hook_pos_dgeadd]; ++ } else { ++ hook_pos_dgeadd = 0; ++ fn = current_backend->blas.dgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_dgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_dgeadd_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_cgeadd = 0; ++ + void FC_GLOBAL(cgeadd,CGEADD)(blasint* m, blasint* n, float complex* alpha, float complex* a, blasint* lda, float complex* beta, float complex* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4493,6 +10031,40 @@ + + + ++void flexiblas_real_cgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.cgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_cgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_cgeadd_"))); ++ ++ ++void flexiblas_chain_cgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_cgeadd++; ++ if ( hook_pos_cgeadd < __flexiblas_hooks->cgeadd.nhook ) { ++ fn = __flexiblas_hooks->cgeadd.f77_hook_function[hook_pos_cgeadd]; ++ } else { ++ hook_pos_cgeadd = 0; ++ fn = current_backend->blas.cgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_cgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_cgeadd_"))); ++ ++ ++static TLS_STORE uint8_t hook_pos_zgeadd = 0; ++ + void FC_GLOBAL(zgeadd,ZGEADD)(blasint* m, blasint* n, double complex* alpha, double complex* a, blasint* lda, double complex* beta, double complex* b, blasint* ldb) + { + void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); +@@ -4519,4 +10091,36 @@ + + + ++void flexiblas_real_zgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ fn = current_backend->blas.zgeadd.f77_blas_function; ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_real_zgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_real_zgeadd_"))); ++ ++ ++void flexiblas_chain_zgeadd_(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) ++{ ++ void (*fn) (void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb); ++ ++ ++ ++ hook_pos_zgeadd++; ++ if ( hook_pos_zgeadd < __flexiblas_hooks->zgeadd.nhook ) { ++ fn = __flexiblas_hooks->zgeadd.f77_hook_function[hook_pos_zgeadd]; ++ } else { ++ hook_pos_zgeadd = 0; ++ fn = current_backend->blas.zgeadd.f77_blas_function; ++ } ++ fn((void*) m, (void*) n, (void*) alpha, (void*) a, (void*) lda, (void*) beta, (void*) b, (void*) ldb); ++ ++ return; ++} ++void flexiblas_chain_zgeadd(void* m, void* n, void* alpha, void* a, void* lda, void* beta, void* b, void* ldb) __attribute__((alias("flexiblas_chain_zgeadd_"))); ++ ++ + diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch new file mode 100644 index 000000000000..ed695ca92f6e --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.0.4_remove-semicolon.patch @@ -0,0 +1,15 @@ +Testing with ifort fails with this semicolon. + +https://github.com/Reference-LAPACK/lapack/commit/64e8a7500d817869e5fcde35afd39af8bc7a8086.diff +diff --git a/TESTING/dbal.in b/TESTING/dbal.in +index c00fe3e83..828629b15 100644 +--- a/test/lapack-3.9.0/dbal.in ++++ b/test/lapack-3.9.0/dbal.in +@@ -209,6 +209,6 @@ DBL: Tests DGEBAL + 0.00000000000000000000D+00 0.00000000000000000000D+00 0.00000000000000000000D+00 0.63043209914231165391D-03 0.10000000000000000000D+01 0.79310682416114036641D+03 + 0.00000000000000000000D+00 0.00000000000000000000D+00 0.00000000000000000000D+00 0.00000000000000000000D+00 0.12608641982846233078D-02 0.10000000000000000000D+01 + +- 2.494800386918399765D+291 1.582914569427869018D+175 1.004336277661868922D+59 3.186183822264904554D-58 5.053968264940243633D-175 0.40083367200179455560D-291; ++ 2.494800386918399765D+291 1.582914569427869018D+175 1.004336277661868922D+59 3.186183822264904554D-58 5.053968264940243633D-175 0.40083367200179455560D-291 + + 0 diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 36c0727160b4..3a87838891a7 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -36,7 +36,18 @@ components = [ (name, version, { 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904'], + 'patches': [ + 'FlexiBLAS-3.0.4_fix-imkl.patch', + 'FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch', + 'FlexiBLAS-3.0.4_remove-semicolon.patch', + 'FlexiBLAS-3.2.0_remove-intel-suffix.patch', + ], + 'checksums': [ + 'a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904', # flexiblas-3.2.0.tar.gz + 'a078e46ad126574cc42314abd5b40461cdc6e950af79d105dbf92875c254c87c', # FlexiBLAS-3.0.4_fix-imkl.patch + '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch + 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', # FlexiBLAS-3.0.4_remove-semicolon.patch + ], 'configopts': '-DABI=Intel', 'backends': local_backends, }), diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch new file mode 100644 index 000000000000..7fced99a11cf --- /dev/null +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0_remove-intel-suffix.patch @@ -0,0 +1,16 @@ +Avoid using the _intel suffix name for library +We can only have 1 library per version regardless, and the ABI is +determined by the toolchain like with all other stuff we compile. + +Author: micketeer@gmail.com +--- CMakeLists.txt.orig 2022-11-28 18:35:05.033932657 +0000 ++++ CMakeLists.txt 2022-11-28 18:35:20.226889430 +0000 +@@ -167,7 +167,7 @@ + ENDIF() + + IF ( ABI STREQUAL "Intel") +- SET(FLEXIBLAS_ABI_INTEL TRUE) ++ SET(FLEXIBLAS_ABI_INTEL FALSE) + SET(USE_INTERFACE_INTEL TRUE) + ELSEIF ( ABI STREQUAL "XL" ) + SET(FLEXIBLAS_ABI_IBM TRUE) From 99a7047a35bd2150d66396812c2d7f7f8daca9a0 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 6 Dec 2022 18:37:15 +0100 Subject: [PATCH 605/939] adding easyconfigs: AOCC-4.0.0-GCCcore-11.3.0.eb --- .../a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..198b56b144fb --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '4.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4'] + +clangversion = '14.0.6' + +dependencies = [ + ('binutils', '2.38'), + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('libxml2', '2.9.13'), +] + +moduleclass = 'compiler' From 5e3f10b483d97cf424d3b38737ac02ed5e4bf80e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Tue, 6 Dec 2022 18:37:35 +0100 Subject: [PATCH 606/939] adding easyconfigs: AOCC-4.0.0-GCCcore-12.2.0.eb --- .../a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..aca9ebc5b59d --- /dev/null +++ b/easybuild/easyconfigs/a/AOCC/AOCC-4.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,24 @@ +name = 'AOCC' +version = '4.0.0' + +homepage = 'https://developer.amd.com/amd-aocc/' +description = "AMD Optimized C/C++ & Fortran compilers (AOCC) based on LLVM 13.0" + +# Clang also depends on libstdc++ during runtime, but this dependency is +# already specified as the toolchain. +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['http://developer.amd.com/wordpress/media/files/'] +sources = ['aocc-compiler-%(version)s.tar'] +checksums = ['2729ec524cbc927618e479994330eeb72df5947e90cfcc49434009eee29bf7d4'] + +clangversion = '14.0.6' + +dependencies = [ + ('binutils', '2.39'), + ('ncurses', '6.3'), + ('zlib', '1.2.12'), + ('libxml2', '2.10.3'), +] + +moduleclass = 'compiler' From 6f2dcb8f85aab8194b1e343c611482179b86bf03 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Tue, 6 Dec 2022 18:33:13 +0000 Subject: [PATCH 607/939] Fix style --- .../FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 3a87838891a7..89dc1755c9d5 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -36,17 +36,19 @@ components = [ (name, version, { 'source_urls': ['https://github.com/mpimd-csc/flexiblas/releases/download/v%(version)s/'], 'sources': [SOURCELOWER_TAR_GZ], - 'patches': [ + 'patches': [ 'FlexiBLAS-3.0.4_fix-imkl.patch', 'FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch', 'FlexiBLAS-3.0.4_remove-semicolon.patch', 'FlexiBLAS-3.2.0_remove-intel-suffix.patch', ], - 'checksums': [ + 'checksums': [ 'a3f4d66a30b6fa6473e492de86d34abc5f9d4e69d4d91ba23618388e8df05904', # flexiblas-3.2.0.tar.gz 'a078e46ad126574cc42314abd5b40461cdc6e950af79d105dbf92875c254c87c', # FlexiBLAS-3.0.4_fix-imkl.patch - '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch - 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', # FlexiBLAS-3.0.4_remove-semicolon.patch + # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch + '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', + # FlexiBLAS-3.0.4_remove-semicolon.patch + 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', ], 'configopts': '-DABI=Intel', 'backends': local_backends, From 06a3ea4b8dcb56b97521cf713c6a2489cb4c452e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 09:58:18 +0100 Subject: [PATCH 608/939] adding easyconfigs: Qt5-5.15.7-GCCcore-12.2.0.eb and patches: Qt5-5.15.7_GCC-12.patch --- .../q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb | 76 +++++++++++++++++++ .../easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch | 14 ++++ 2 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch diff --git a/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..592deb7c5f5a --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7-GCCcore-12.2.0.eb @@ -0,0 +1,76 @@ +easyblock = 'EB_Qt' + +name = 'Qt5' +version = '5.15.7' + +homepage = 'https://qt.io/' +description = "Qt is a comprehensive cross-platform C++ application framework." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +# 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', + 'Qt5-5.14.1_fix-OF-Gentoo.patch', + 'Qt5-5.15.7_GCC-12.patch', +] +checksums = [ + {'qt-everywhere-opensource-src-5.15.7.tar.xz': '8a71986676a3f37a198a9113acedbfd5bc5606a459b6b85816d951458adbe9a0'}, + {'Qt5-5.13.1_fix-avx2.patch': '6f46005f056bf9e6ff3e5d012a874d18ee03b33e685941f2979c970be91a9dbc'}, + {'Qt5-5.13.1_fix-qmake-libdir.patch': '511ca9c0599ceb1989f73d8ceea9199c041512d3a26ee8c5fd870ead2c10cb63'}, + {'Qt5-5.14.1_fix-OF-Gentoo.patch': '0b9defb7ce75314d85bebe07e143db7f7de316fec64c17cbd13f7eec5d2d1afa'}, + {'Qt5-5.15.7_GCC-12.patch': '9a5bde91b223a3e2e90d3d6bec107af69a1a0f18d789593738a953080473fa68'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), + # deps for QtWebEngine + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.11.1'), + # Qt5WebEngine has build dependency on Python 2 + ('Python', '2.7.18', '-bare'), + ('re2c', '3.0'), +] + +dependencies = [ + ('double-conversion', '3.2.1'), + ('GLib', '2.75.0'), + ('PCRE2', '10.40'), + ('libpng', '1.6.38'), + ('HarfBuzz', '5.3.1'), + ('graphite2', '1.3.14'), + # deps for QtWebEngine + ('X11', '20221110'), + ('fontconfig', '2.14.1'), + ('DBus', '1.15.2'), + ('libevent', '2.1.12'), + ('libGLU', '9.0.2'), + ('libjpeg-turbo', '2.1.4'), + ('NSS', '3.85'), + ('snappy', '1.1.9'), + ('JasPer', '4.0.0'), + ('bzip2', '1.0.8'), + ('OpenSSL', '1.1', '', SYSTEM), + ('ICU', '72.1'), + ('nodejs', '18.12.1'), +] + +# 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/Qt5-5.15.7_GCC-12.patch b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch new file mode 100644 index 000000000000..02c54554ffb2 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5/Qt5-5.15.7_GCC-12.patch @@ -0,0 +1,14 @@ +add missing include to fix compilation error with GCC 12.x +../../3rdparty/chromium/third_party/skia/src/utils/SkParseColor.cpp:300:49: error: no matching function for call to begin(const char* const [140]) +cfr. https://github.com/archlinux/svntogit-packages/blob/packages/qt5-webengine/trunk/qt5-webengine-gcc12.patch +--- Qt5/5.15.7/GCCcore-12.2.0/qt-everywhere-src-5.15.7/qtwebengine/src/3rdparty/chromium/third_party/skia/src/utils/SkParseColor.cpp.orig 2021-10-19 14:46:32.000000000 +0200 ++++ Qt5/5.15.7/GCCcore-12.2.0/qt-everywhere-src-5.15.7/qtwebengine/src/3rdparty/chromium/third_party/skia/src/utils/SkParseColor.cpp 2022-11-25 14:48:38.501288572 +0100 +@@ -8,6 +8,8 @@ + + #include "include/utils/SkParse.h" + ++#include ++ + static constexpr const char* gColorNames[] = { + "aliceblue", + "antiquewhite", From e6e09e190cdc012774cef0400d6c60192730254a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Wed, 7 Dec 2022 14:34:28 +0000 Subject: [PATCH 609/939] adding easyconfigs: OVITO-3.7.11-gompi-2022a-basic.eb --- .../o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb diff --git a/easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb b/easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb new file mode 100644 index 000000000000..25186032c64f --- /dev/null +++ b/easybuild/easyconfigs/o/OVITO/OVITO-3.7.11-gompi-2022a-basic.eb @@ -0,0 +1,38 @@ +easyblock = 'CMakeMake' + +name = 'OVITO' +version = '3.7.11' +versionsuffix = '-basic' + +homepage = 'https://www.ovito.org' +description = """OVITO is a scientific visualization and data analysis solution for atomistic and other particle-based +models. It helps scientists gain meaningful and quick insights from numerical simulation results.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://gitlab.com/stuko/ovito/-/archive/v%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dc592ea59c6bc6fbc31bd750905e0767bc48d21b4c35276f3068d4479794ecec'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Qt5', '5.15.5'), + ('HDF5', '1.12.2'), + ('netCDF', '4.9.0'), + ('FFmpeg', '4.4.2'), + ('zlib', '1.2.12'), + ('Boost', '1.79.0'), + ('libglvnd', '1.4.0'), + ('Python', '3.10.4'), +] + +sanity_check_paths = { + 'files': ['bin/ovito'], + 'dirs': [] +} + +moduleclass = 'vis' From fbcd2f409f5eab4e79ede1ee98e359171d4abc30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 16:21:04 +0100 Subject: [PATCH 610/939] add missing `moduleclass` in bamFilters easyconfig --- .../b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb index 82f31b5dfb2d..f8df6c47a860 100644 --- a/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/bamFilters/bamFilters-2022-06-30-GCC-11.3.0.eb @@ -36,3 +36,5 @@ sanity_check_paths = { } sanity_check_commands = ['bamFilters -h 2>&1 | grep "Usage"'] + +moduleclass = 'bio' From a020698312201430f808046bc8a43027cc739df7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:44:44 +0000 Subject: [PATCH 611/939] adding easyconfigs: YACS-0.1.8-GCCcore-11.3.0.eb --- .../y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..f48627864998 --- /dev/null +++ b/easybuild/easyconfigs/y/YACS/YACS-0.1.8-GCCcore-11.3.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'YACS' +version = '0.1.8' + +homepage = "https://github.com/rbgirshick/yacs" +description = """YACS was created as a lightweight library to define and +manage system configurations, such as those commonly found in software +designed for scientific experimentation. These "configurations" +typically cover concepts like hyperparameters used in training a machine +learning model or configurable model hyperparameters, such as the depth +of a convolutional neural network.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['efc4c732942b3103bea904ee89af98bcd27d01f0ac12d8d4d369f1e7a2914384'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('PyYAML', '6.0'), +] + +use_pip = True +download_dep_fail = True + +sanity_pip_check = True + +moduleclass = 'lib' From 76787673d34cb9ad6810dc0b16efac6320c77b3a Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:45:35 +0000 Subject: [PATCH 612/939] adding easyconfigs: RDFlib-6.2.0-GCCcore-11.3.0.eb --- .../r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..d602151be5a0 --- /dev/null +++ b/easybuild/easyconfigs/r/RDFlib/RDFlib-6.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'RDFlib' +version = '6.2.0' + +homepage = 'https://github.com/RDFLib/rdflib' +description = """RDFLib is a Python library for working with RDF, a simple yet powerful language + for representing information.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [('Python', '3.10.4')] + +use_pip = True + +exts_list = [ + ('isodate', '0.6.1', { + 'checksums': ['48c5881de7e8b0a0d648cb024c8062dc84e7b840ed81e864c7614fd3c127bde9'], + }), + ('rdflib', version, { + 'checksums': ['62dc3c86d1712db0f55785baf8047f63731fa59b2682be03219cb89262065942'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 8694b846a2bd79449c3d91fdddee425921971260 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Wed, 7 Dec 2022 17:47:03 +0000 Subject: [PATCH 613/939] adding easyconfigs: line_profiler-4.0.0-foss-2022a.eb --- .../line_profiler-4.0.0-foss-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb new file mode 100644 index 000000000000..42ca38e1daf1 --- /dev/null +++ b/easybuild/easyconfigs/l/line_profiler/line_profiler-4.0.0-foss-2022a.eb @@ -0,0 +1,40 @@ +easyblock = 'PythonPackage' + +name = 'line_profiler' +version = '4.0.0' + +homepage = 'https://github.com/pyutils/line_profiler' +description = """line_profiler is a module for doing line-by-line profiling +of functions. kernprof is a convenient script for running either +line_profiler or the Python standard library's cProfile or profile modules, +depending on what is available.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +github_account = 'pyutils' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['ebe361a2318ac781c619573b62b3abf124881257c6b9425747dc3f1c03e708fc'] + +builddependencies = [ + ('scikit-build', '0.15.0'), + ('CMake', '3.23.1'), + ('Ninja', '1.10.2'), +] +dependencies = [ + ('Python', '3.10.4'), + ('IPython', '8.5.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/kernprof'], + 'dirs': [], +} + +sanity_check_commands = ['kernprof --help'] + +moduleclass = 'devel' From 5218261ffbfeda844673c8a580b5478ee65682c6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 18:55:56 +0100 Subject: [PATCH 614/939] fix checksum for cell2location 0.05-alpha --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 8356b39778ad..7f105e3eeb10 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -119,7 +119,7 @@ exts_list = [ (name, version, { 'source_urls': ['https://github.com/BayraktarLab/cell2location/archive/'], 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], - 'checksums': ['2df1fe2b2b4ec5fcebc6c1d6146ce0cd79115bd14059b0ae882a41f1029a4efc'], + 'checksums': ['b1d4fc0e1eb8292457793d6af8228189bd24dd87837b8f4435d0a0312ed20c6b'], }), ] From 611499730c8b4d2c2eaa0622ef9863a227646d56 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:04:54 +0100 Subject: [PATCH 615/939] adding easyconfigs: DBus-1.15.2-GCCcore-12.2.0.eb --- .../d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb b/easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e3189b0b860b --- /dev/null +++ b/easybuild/easyconfigs/d/DBus/DBus-1.15.2-GCCcore-12.2.0.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'DBus' +version = '1.15.2' + +homepage = 'https://dbus.freedesktop.org/' + +description = """ + D-Bus is a message bus system, a simple way for applications to talk + to one another. In addition to interprocess communication, D-Bus helps + coordinate process lifecycle; it makes it simple and reliable to code + a "single instance" application or daemon, and to launch applications + and daemons on demand when their services are needed. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['7e640803084af59f5e477b7ded11fd888b5380910a895c51ca3aedd63c0626ca'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('expat', '2.4.9'), +] + +configopts = '--with-systemdsystemunitdir=no ' +# disable documentation +configopts += '--disable-xml-docs --disable-doxygen-docs --disable-ducktype-docs' + +sanity_check_paths = { + 'files': ['bin/dbus-%s' % x for x in + ['cleanup-sockets', 'daemon', 'launch', 'monitor', + 'run-session', 'send', 'uuidgen']] + + ['lib/libdbus-1.%s' % x for x in ['a', SHLIB_EXT]], + 'dirs': ['include', 'share'], +} + +moduleclass = 'devel' From 0e1f5230116edefd7b0768f4470cae644ca5a41d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:05:07 +0100 Subject: [PATCH 616/939] adding easyconfigs: snappy-1.1.9-GCCcore-12.2.0.eb --- .../s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..5f980fff33b4 --- /dev/null +++ b/easybuild/easyconfigs/s/snappy/snappy-1.1.9-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'CMakeMake' + +name = 'snappy' +version = '1.1.9' + +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': '12.2.0'} + +source_urls = ['https://github.com/google/snappy/archive/'] +sources = ['%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_inline-functions.patch', + '%(name)s-%(version)s_use-default-rtti.patch', +] +checksums = [ + '75c1fbb3d618dd3a0483bff0e26d0a92b495bbe5059c8b4f1c962b478b6e06e7', # 1.1.9.tar.gz + 'ad79190b274df5ddabf14eddd2bb0d9a091ee7d44e4afde89febf9a8f783fdce', # snappy-1.1.9_inline-functions.patch + 'af56538330b2d781677c7d94576c15fc36e004ae0b4f1ac7d86bbec22b65e73d', # snappy-1.1.9_use-default-rtti.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +# 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 8e7c8153cbcb7e487c629ed6a2f524d6cc5d97ba Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:05:20 +0100 Subject: [PATCH 617/939] adding easyconfigs: graphite2-1.3.14-GCCcore-12.2.0.eb --- .../graphite2-1.3.14-GCCcore-12.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..e7e24e4484aa --- /dev/null +++ b/easybuild/easyconfigs/g/graphite2/graphite2-1.3.14-GCCcore-12.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'CMakeMake' + +name = 'graphite2' +version = '1.3.14' + +homepage = 'https://scripts.sil.org/cms/scripts/page.php?site_id=projects&item_id=graphite_home' +description = """Graphite is a "smart font" system developed specifically to + handle the complexities of lesser-known languages of the world.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/silnrsi/graphite/archive/'] +sources = ['%(version)s.zip'] +checksums = ['36e15981af3bf7a3ca3daf53295c8ffde04cf7d163e3474e4d0836e2728b4149'] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.39'), +] + +sanity_check_paths = { + 'files': ['bin/gr2fonttest'] + + ['lib/lib%%(name)s.%s' % x for x in [SHLIB_EXT, 'la']], + 'dirs': ['include/%(name)s', 'share'] +} + +moduleclass = 'lib' From 8784060ee6dae0b4409547fb1ed939bf4e1815a0 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:07:00 +0100 Subject: [PATCH 618/939] add re2c easyconfig requires as dependency for Qt5 5.15.7 --- .../r/re2c/re2c-3.0-GCCcore-12.2.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..baee86381e69 --- /dev/null +++ b/easybuild/easyconfigs/r/re2c/re2c-3.0-GCCcore-12.2.0.eb @@ -0,0 +1,29 @@ +easyblock = 'ConfigureMake' + +name = 're2c' +version = '3.0' + +homepage = 'https://re2c.org' +description = """re2c is a free and open-source lexer generator for C and C++. Its main goal is generating +fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using +traditional table-driven approach, re2c encodes the generated finite state automata directly in the form +of conditional jumps and comparisons.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/skvadrik/re2c/releases/download/%(version)s'] +sources = ['%(name)s-%(version)s.tar.xz'] +checksums = ['b3babbbb1461e13fe22c630a40c43885efcfbbbb585830c6f4c0d791cf82ba0b'] + +builddependencies = [('binutils', '2.39')] + +configopts = "--disable-rust" + +sanity_check_paths = { + 'files': ['bin/re2c'], + 'dirs': [], +} + +sanity_check_commands = ["re2c --help"] + +moduleclass = 'tools' From c264a4761e30b99b0fad496aa46d7808131f38c8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 7 Dec 2022 19:24:11 +0100 Subject: [PATCH 619/939] adding easyconfigs: pyccel-1.7.0-foss-2022a.eb --- .../p/pyccel/pyccel-1.7.0-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb b/easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb new file mode 100644 index 000000000000..efb6a2e0e29b --- /dev/null +++ b/easybuild/easyconfigs/p/pyccel/pyccel-1.7.0-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'pyccel' +version = '1.7.0' + +homepage = 'https://github.com/pyccel/pyccel' +description = "Python extension language using accelerators" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('sympy', '1.10.1'), +] + +use_pip = True + +exts_list = [ + ('textX', '3.0.0', { + 'checksums': ['cd432adb82e348960cecdcabe68dbb916fe6eb2e4cb067c4a4b68b8c9ec51acf'], + }), + ('Arpeggio', '2.0.0', { + 'checksums': ['d6b03839019bb8a68785f9292ee6a36b1954eb84b925b84a6b8a5e1e26d3ed3d'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + (name, version, { + 'preinstallopts': "PYTHONPATH=$PWD:$PYTHONPATH ", + 'checksums': ['473212328957514d7ea52e1a57cc3a4402ae2140b0bca34c904b79d52ae81bfb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lang' From 916a602eb8791efb7a51cf7c851d9635da986714 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 8 Dec 2022 09:37:07 +0100 Subject: [PATCH 620/939] Add XCfun-2.1.1-GCCcore-11.3.0 --- .../x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..16e144e63941 --- /dev/null +++ b/easybuild/easyconfigs/x/XCFun/XCFun-2.1.1-GCCcore-11.3.0.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': '11.3.0'} + +source_urls = ['https://github.com/dftlibs/xcfun/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8b602df74c7be83d501532565deafd1b7881946d94789122f24c309a669298ab'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1') +] + +modextravars = {'XCFun_DIR': '%(installdir)s/share/cmake/XCFun/'} + +sanity_check_paths = { + 'files': ['lib/libxcfun.%s' % SHLIB_EXT], + 'dirs': ['include/XCFun'] +} + +moduleclass = 'chem' From 08708c4bcefabd9d2553964c82a3d38bb9b27fb5 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 8 Dec 2022 09:37:34 +0100 Subject: [PATCH 621/939] Add MRCPP-1.4.1-foss-2022a --- .../m/MRCPP/MRCPP-1.4.1-foss-2022a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb b/easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb new file mode 100644 index 000000000000..4eb89f1dcb15 --- /dev/null +++ b/easybuild/easyconfigs/m/MRCPP/MRCPP-1.4.1-foss-2022a.eb @@ -0,0 +1,31 @@ +easyblock = 'CMakeMake' + +name = 'MRCPP' +version = '1.4.1' + +homepage = 'https://mrcpp.readthedocs.io' +description = """MultiResolution Computation Program Package""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://github.com/MRChemSoft/mrcpp/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f369d72cc37415e9a6bdc0692ec4f6c5cfcc22e34b9ce569470e656c45e5b86c'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Eigen', '3.4.0') +] + +configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libmrcpp.%s' % SHLIB_EXT], + 'dirs': ['include/MRCPP'] +} + +modextravars = {'MRCPP_DIR': '%(installdir)s/share/cmake/MRCPP/'} + +moduleclass = 'math' From 135c4f6edb5e3d2133009f3062aaca4d249c2655 Mon Sep 17 00:00:00 2001 From: Stig Rune Jensen Date: Thu, 8 Dec 2022 09:38:09 +0100 Subject: [PATCH 622/939] Add MRChem-1.1.1-foss-2022a --- .../m/MRChem/MRChem-1.1.1-foss-2022a.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb b/easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb new file mode 100644 index 000000000000..03ddfe84466c --- /dev/null +++ b/easybuild/easyconfigs/m/MRChem/MRChem-1.1.1-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'MRChem' +version = '1.1.1' + +homepage = 'https://mrchem.readthedocs.io' +description = """MRChem is a numerical real-space code for molecular electronic +structure calculations within the self-consistent field (SCF) approximations of +quantum chemistry: Hartree-Fock and Density Functional Theory.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://github.com/MRChemSoft/mrchem/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9926778edf8bb49fd4cde513faf6a887800ecf1791d1a71c0edae228ba6da646'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('Eigen', '3.4.0') +] + +dependencies = [ + ('MRCPP', '1.4.1'), + ('Python', '3.10.4'), + ('XCFun', '2.1.1') +] + +configopts = "-DENABLE_MPI=True -DENABLE_OPENMP=True" +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/mrchem', 'bin/mrchem.x'], + 'dirs': ['lib'], +} + +moduleclass = 'chem' From 20f41fdb31e923b0a496b4eb9ee3aa6e22c9f7a3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:28:07 +0100 Subject: [PATCH 623/939] adding easyconfigs: Doxygen-1.9.5-GCCcore-12.2.0.eb, libiconv-1.17-GCCcore-12.2.0.eb --- .../d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ .../libiconv/libiconv-1.17-GCCcore-12.2.0.eb | 23 ++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb 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 new file mode 100644 index 000000000000..35b262f3df87 --- /dev/null +++ b/easybuild/easyconfigs/d/Doxygen/Doxygen-1.9.5-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +name = 'Doxygen' +version = '1.9.5' + +homepage = 'https://www.doxygen.org' +description = """ + Doxygen is a documentation system for C++, C, Java, Objective-C, Python, + IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some + extent D. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(namelower)s-%(version)s.src.tar.gz'] +checksums = ['55b454b35d998229a96f3d5485d57a0a517ce2b78d025efb79d57b5a2e4b2eec'] + +builddependencies = [ + ('binutils', '2.39'), + ('Bison', '3.8.2'), + ('CMake', '3.24.3'), + ('flex', '2.6.4'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('libiconv', '1.17'), +] + +configopts = "-DICONV_DIR=$EBROOTLIBICONV -DICONV_IN_GLIBC=OFF" + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..9e0244a6104a --- /dev/null +++ b/easybuild/easyconfigs/l/libiconv/libiconv-1.17-GCCcore-12.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libiconv' +version = '1.17' + +homepage = 'https://www.gnu.org/software/libiconv' +description = "Libiconv converts from one character encoding to another through Unicode conversion" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['8f74213b56238c85a50a5329f77e06198771e70dd9a739779f4c02f65d971313'] + +builddependencies = [('binutils', '2.39')] + +sanity_check_paths = { + 'files': ['bin/iconv', 'include/iconv.h', 'include/libcharset.h', 'include/localcharset.h', + 'lib/libcharset.a', 'lib/libcharset.%s' % SHLIB_EXT, 'lib/libiconv.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +moduleclass = 'lib' From f092f55f98b01398b8e2c4830d3f2b9cf9e6c1d7 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:51:48 +0100 Subject: [PATCH 624/939] adding easyconfigs: LibTIFF-4.4.0-GCCcore-12.2.0.eb, jbigkit-2.1-GCCcore-12.2.0.eb, libdeflate-1.14-GCCcore-12.2.0.eb --- .../j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb | 45 +++++++++++++++++++ .../l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb | 35 +++++++++++++++ .../libdeflate-1.14-GCCcore-12.2.0.eb | 40 +++++++++++++++++ 3 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..8dc21fe2bd74 --- /dev/null +++ b/easybuild/easyconfigs/j/jbigkit/jbigkit-2.1-GCCcore-12.2.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'jbigkit' +version = '2.1' + +homepage = 'https://www.cl.cam.ac.uk/~mgk25/jbigkit/' +description = """JBIG-KIT is a software implementation of the JBIG1 data + compression standard (ITU-T T.82), which was designed for bi-level image + data, such as scanned documents.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.cl.cam.ac.uk/~mgk25/jbigkit/download'] +sources = [SOURCE_TAR_GZ] +patches = [ + '%(name)s-%(version)s_libpath.patch', + '%(name)s-%(version)s_shlib.patch', +] +checksums = [ + 'de7106b6bfaf495d6865c7dd7ac6ca1381bd12e0d81405ea81e7f2167263d932', # jbigkit-2.1.tar.gz + '97c88956090097b484fcdb90e12eab82212e67ddc862f035d7c6446a696786ce', # jbigkit-2.1_libpath.patch + '54ae429e8ec949eceee0f902b676f572f1cdfbff46f77c7222acdeafb643a696', # jbigkit-2.1_shlib.patch +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +files_to_copy = [ + (['libjbig/libjbig%s.%s' % (x, y) for x in ['85', ''] for y in ['a', SHLIB_EXT, SHLIB_EXT + '.0']], 'lib'), + (['libjbig/jbig85.h', 'libjbig/jbig.h', 'libjbig/jbig_ar.h'], 'include'), + (['pbmtools/pbmtojbg', 'pbmtools/jbgtopbm'], 'bin'), +] + +sanity_check_paths = { + 'files': ['lib/libjbig85.a', 'lib/libjbig.a', + 'bin/pbmtojbg', 'bin/jbgtopbm', + 'include/jbig.h', 'include/jbig_ar.h', + ], + 'dirs': ['bin', 'include', 'lib'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..bcefb663225b --- /dev/null +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'LibTIFF' +version = '4.4.0' + +homepage = 'https://libtiff.maptools.org/' +description = "tiff: Library and tools for reading and writing TIFF data files" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://download.osgeo.org/libtiff/'] +sources = ['tiff-%(version)s.tar.gz'] +checksums = ['917223b37538959aca3b790d2d73aa6e626b688e02dcda272aec24c2f498abed'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('zlib', '1.2.12'), + ('libjpeg-turbo', '2.1.4'), + ('XZ', '5.2.7'), + ('jbigkit', '2.1'), + ('zstd', '1.5.2'), + ('libdeflate', '1.14'), +] + +configopts = "--enable-ld-version-script " +configopts += '--disable-webp' + +sanity_check_paths = { + 'files': ['bin/tiffinfo'], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..37b4f66bb324 --- /dev/null +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb @@ -0,0 +1,40 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 +# Updated to 1.8 +# J. Sassmannshausen NHS/GSTT + +easyblock = 'ConfigureMake' + +name = 'libdeflate' +version = '1.14' + +homepage = 'https://github.com/ebiggers/libdeflate' +description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'ebiggers' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['89e7df898c37c3427b0f39aadcf733731321a278771d20fc553f92da8d4808ac'] + +builddependencies = [('binutils', '2.39')] + +skipsteps = ['configure'] + +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': [ + 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', + 'lib/%(name)s.a', 'lib/%%(name)s.%s' % SHLIB_EXT, + 'include/%(name)s.h', + ], + 'dirs': [], +} +sanity_check_commands = [ + '%(name)s-gzip -h', + '%(name)s-gunzip -h', +] + +moduleclass = 'system' From 8548eab176bad45b573be27bd1ec2035e056df6b Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:54:25 +0100 Subject: [PATCH 625/939] adding easyconfigs: Pango-1.50.12-GCCcore-12.2.0.eb, FriBidi-1.0.12-GCCcore-12.2.0.eb --- .../FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb | 32 +++++++++++++++ .../p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..97c8eece78b9 --- /dev/null +++ b/easybuild/easyconfigs/f/FriBidi/FriBidi-1.0.12-GCCcore-12.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'FriBidi' +version = '1.0.12' + +homepage = 'https://github.com/fribidi/fribidi' + +description = """ + The Free Implementation of the Unicode Bidirectional Algorithm. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/fribidi/fribidi/releases/download/v%(version)s'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['0cd233f97fc8c67bb3ac27ce8440def5d3ffacf516765b91c2cc654498293495'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +configopts = '--disable-docs' + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'include/%(namelower)s/%(namelower)s.h', + 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': [] +} + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2da3f6b7bf59 --- /dev/null +++ b/easybuild/easyconfigs/p/Pango/Pango-1.50.12-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'Pango' +version = '1.50.12' + +homepage = 'https://www.pango.org/' +description = """Pango is a library for laying out and rendering of text, with an emphasis on internationalization. +Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the +context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['caef96d27bbe792a6be92727c73468d832b13da57c8071ef79b9df69ee058fe3'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.74.0'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('X11', '20221110'), + ('GLib', '2.75.0'), + ('cairo', '1.17.4'), + ('HarfBuzz', '5.3.1'), + ('FriBidi', '1.0.12'), +] + +configopts = "--buildtype=release --default-library=both " + +sanity_check_paths = { + 'files': ['bin/pango-view', 'lib/libpango-1.0.%s' % SHLIB_EXT, 'lib/libpangocairo-1.0.%s' % SHLIB_EXT, + 'lib/libpangoft2-1.0.%s' % SHLIB_EXT, 'lib/libpangoxft-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' From bf9eef894096ab9c210492cf8e7c5f3b09f4dc94 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:54:37 +0100 Subject: [PATCH 626/939] adding easyconfigs: JasPer-4.0.0-GCCcore-12.2.0.eb --- .../j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..2f1a4dceeccf --- /dev/null +++ b/easybuild/easyconfigs/j/JasPer/JasPer-4.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'JasPer' +version = '4.0.0' + +homepage = 'https://www.ece.uvic.ca/~frodo/jasper/' + +description = """ + The JasPer Project is an open-source initiative to provide a free + software-based reference implementation of the codec specified in + the JPEG-2000 Part-1 standard. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +github_account = 'jasper-software' +source_urls = [GITHUB_SOURCE] +sources = ['version-%(version)s.tar.gz'] +checksums = ['977c4c2e4210f4e37313cd2232d99e73d57ab561917b3c060bcdd5e83a0a13f1'] + +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] + +configopts = '-DJAS_ENABLE_DOC=OFF ' + +sanity_check_paths = { + 'files': ['bin/jasper', ('lib/libjasper.%s' % SHLIB_EXT, 'lib64/libjasper.%s' % SHLIB_EXT)], + 'dirs': ['include'], +} + +sanity_check_commands = ['jasper --version'] + +moduleclass = 'vis' From 79030a2c0ff064bbf62ff2e0f1dd6a0c8476cc89 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 10:59:20 +0100 Subject: [PATCH 627/939] {vis}[GCCcore/12.2.0] GTK3 v3.24.35, ATK v2.38.0, at-spi2-atk v2.38.0, at-spi2-core v2.46.0, Gdk-Pixbuf v2.42.10, libepoxy v1.5.10 --- .../a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb | 39 ++++++++++ .../at-spi2-atk-2.38.0-GCCcore-12.2.0.eb | 37 +++++++++ .../at-spi2-core-2.46.0-GCCcore-12.2.0.eb | 39 ++++++++++ .../g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb | 77 +++++++++++++++++++ .../Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb | 46 +++++++++++ .../libepoxy-1.5.10-GCCcore-12.2.0.eb | 37 +++++++++ 6 files changed, 275 insertions(+) create mode 100644 easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..38922c40f8d7 --- /dev/null +++ b/easybuild/easyconfigs/a/ATK/ATK-2.38.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'ATK' +version = '2.38.0' + +homepage = 'https://developer.gnome.org/atk/' +description = """ + ATK provides the set of accessibility interfaces that are implemented by other + toolkits and applications. Using the ATK interfaces, accessibility tools have + full access to view and control running applications. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ac4de2a4ef4bd5665052952fe169657e65e895c5057dffb3c2a810f6191a0c36'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), + ('GObject-Introspection', '1.74.0'), +] + +dependencies = [ + ('GLib', '2.75.0'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dintrospection=true " + +sanity_check_paths = { + 'files': ['lib/libatk-1.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..16b32ffb2272 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-atk/at-spi2-atk-2.38.0-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-atk' +version = '2.38.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = "AT-SPI 2 toolkit bridge" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['cfa008a5af822b36ae6287f18182c40c91dd699c55faa38605881ed175ca464f'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('DBus', '1.15.2'), + ('at-spi2-core', '2.46.0'), + ('libxml2', '2.10.3'), + ('ATK', '2.38.0'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatk-bridge-2.0.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..b9f052b08264 --- /dev/null +++ b/easybuild/easyconfigs/a/at-spi2-core/at-spi2-core-2.46.0-GCCcore-12.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'MesonNinja' + +name = 'at-spi2-core' +version = '2.46.0' + +homepage = 'https://wiki.gnome.org/Accessibility' +description = """ + Assistive Technology Service Provider Interface. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['aa0c86c79f7a8d67bae49a5b7a5ab08430c608cffe6e33bf47a72f41ab03c3d0'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('DBus', '1.15.2'), + ('X11', '20221110'), +] + +configopts = "--libdir lib " + +sanity_check_paths = { + 'files': ['lib/libatspi.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'vis' 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 new file mode 100644 index 000000000000..f00f26786b05 --- /dev/null +++ b/easybuild/easyconfigs/g/GTK3/GTK3-3.24.35-GCCcore-12.2.0.eb @@ -0,0 +1,77 @@ +easyblock = 'Bundle' + +name = 'GTK3' +version = '3.24.35' + +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': '12.2.0'} + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('GObject-Introspection', '1.74.0'), + ('gettext', '0.21.1'), + ('pkgconf', '1.9.3'), + ('cairo', '1.17.4'), + ('Perl', '5.36.0'), +] +dependencies = [ + ('ATK', '2.38.0'), + ('at-spi2-atk', '2.38.0'), + ('Gdk-Pixbuf', '2.42.10'), + ('Pango', '1.50.12'), + ('libepoxy', '1.5.10'), + ('X11', '20221110'), + ('FriBidi', '1.0.12'), +] + +default_easyblock = 'ConfigureMake' + +default_component_specs = { + 'sources': [SOURCELOWER_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('GTK+', version, { + 'source_urls': [FTPGNOME_SOURCE], + '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 ", + }), + ('hicolor-icon-theme', '0.17', { + 'source_urls': ['https://icon-theme.freedesktop.org/releases/'], + 'checksums': ['317484352271d18cbbcfac3868eab798d67fff1b8402e740baa6ff41d588a9d8'], + }), + ('adwaita-icon-theme', '42.0', { + 'source_urls': ['https://ftp.gnome.org/pub/GNOME/sources/%(namelower)s/%(version_major)s'], + 'patches': ['adwaita-icon-theme-3.34.3_disable-svg-conversion.patch'], + 'checksums': [ + '5e85b5adc8dee666900fcaf271ba717f7dcb9d0a03d96dae08f9cbd27e18b1e0', + # adwaita-icon-theme-3.34.3_disable-svg-conversion.patch + 'f4b86855d50759ecfc1e8f6550ec0f3a7a4ea2c80b9f5fc1685fe8967d1c5342', + ], + 'preconfigopts': 'autoreconf -f -i && ', + }), +] + +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/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..4c2a7cd38bab --- /dev/null +++ b/easybuild/easyconfigs/g/Gdk-Pixbuf/Gdk-Pixbuf-2.42.10-GCCcore-12.2.0.eb @@ -0,0 +1,46 @@ +easyblock = 'MesonNinja' + +name = 'Gdk-Pixbuf' +version = '2.42.10' + +homepage = 'https://docs.gtk.org/gdk-pixbuf/' +description = """ + The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. + It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it + was distributed as part of GTK+ 2 but it was split off into a separate package + in preparation for the change to GTK+ 3. +""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['ee9b6c75d13ba096907a2e3c6b27b61bcd17f5c7ebeab5a5b439d2f2e39fe44b'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), + ('GObject-Introspection', '1.74.0'), +] + +dependencies = [ + ('GLib', '2.75.0'), + ('libjpeg-turbo', '2.1.4'), + ('libpng', '1.6.38'), + ('LibTIFF', '4.4.0'), + ('X11', '20221110'), +] + +configopts = "--buildtype=release --default-library=both " +configopts += "-Dgio_sniffing=false -Dintrospection=enabled -Dman=false" + +sanity_check_paths = { + 'files': ['lib/libgdk_pixbuf-%(version_major)s.0.a', 'lib/libgdk_pixbuf-%%(version_major)s.0.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include/gdk-pixbuf-%(version_major)s.0', 'lib/gdk-pixbuf-%(version_major)s.0', 'share'], +} + +sanity_check_commands = ["gdk-pixbuf-pixdata --help"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..c47fc5755521 --- /dev/null +++ b/easybuild/easyconfigs/l/libepoxy/libepoxy-1.5.10-GCCcore-12.2.0.eb @@ -0,0 +1,37 @@ +easyblock = 'MesonNinja' + +name = 'libepoxy' +version = '1.5.10' + +homepage = 'https://github.com/anholt/libepoxy' +description = "Epoxy is a library for handling OpenGL function pointer management for you" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +github_account = 'anholt' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['%(version)s.tar.gz'] +checksums = ['a7ced37f4102b745ac86d6a70a9da399cc139ff168ba6b8002b4d8d43c900c15'] + +builddependencies = [ + ('binutils', '2.39'), + ('Meson', '0.64.0'), + ('Ninja', '1.11.1'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('X11', '20221110'), + ('Mesa', '22.2.4'), +] + +configopts = '-Degl=yes --libdir %(installdir)s/lib ' + +sanity_check_paths = { + 'files': ['include/epoxy/%s.h' % x for x in ['common', 'egl_generated', 'egl', 'gl_generated', + 'gl', 'glx_generated', 'glx']] + + ['lib/libepoxy.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +moduleclass = 'lib' From 3a653403eed6740ba5f86b81a0bd958c47f60c3e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:00:12 +0100 Subject: [PATCH 628/939] adding easyconfigs: Ghostscript-10.0.0-GCCcore-12.2.0.eb --- .../Ghostscript-10.0.0-GCCcore-12.2.0.eb | 59 +++++++++++++++++++ 1 file changed, 59 insertions(+) create mode 100644 easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..33a9307aa2a2 --- /dev/null +++ b/easybuild/easyconfigs/g/Ghostscript/Ghostscript-10.0.0-GCCcore-12.2.0.eb @@ -0,0 +1,59 @@ +easyblock = 'ConfigureMake' + +name = 'Ghostscript' +version = '10.0.0' + +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': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://github.com/ArtifexSoftware/ghostpdl-downloads/releases/download/gs%s/' % version.replace('.', ''), +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['a57764d70caf85e2fc0b0f59b83b92e25775631714dcdb97cc6e0cea414bb5a3'] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.38'), + ('freetype', '2.12.1'), + ('libjpeg-turbo', '2.1.4'), + ('expat', '2.4.9'), + ('GLib', '2.75.0'), + ('cairo', '1.17.4'), + ('LibTIFF', '4.4.0'), + ('GTK3', '3.24.35'), +] + +# Do not use local copies of zlib, jpeg, freetype, and png +preconfigopts = "mv zlib zlib.no && mv jpeg jpeg.no && mv freetype freetype.no && mv libpng libpng.no && " +preconfigopts += 'export LIBS="$LIBS -L$EBROOTZLIB/lib -lz" && ' + +configopts = "--with-system-libtiff --enable-dynamic" + +# Avoid race condition in build if too much parallelism is used +maxparallel = 4 + +postinstallcmds = [ + # build and install shared libs + "make so && make soinstall", + # install header files + "mkdir -p %(installdir)s/include/ghostscript", + "install -v -m644 base/*.h %(installdir)s/include/ghostscript", + "install -v -m644 psi/*.h %(installdir)s/include/ghostscript", +] + +sanity_check_paths = { + 'files': ['bin/gs', 'lib/libgs.%s' % SHLIB_EXT], + 'dirs': ['lib/ghostscript', 'include/ghostscript', 'share/man'], +} + +moduleclass = 'tools' From c585860e4fb88d56e2e0d75ff6806582de01cf08 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:01:48 +0100 Subject: [PATCH 629/939] adding easyconfigs: ImageMagick-7.1.0-53-GCCcore-12.2.0.eb, LittleCMS-2.14-GCCcore-12.2.0.eb --- .../ImageMagick-7.1.0-53-GCCcore-12.2.0.eb | 41 +++++++++++++++++++ .../LittleCMS-2.14-GCCcore-12.2.0.eb | 28 +++++++++++++ 2 files changed, 69 insertions(+) create mode 100644 easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb 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 new file mode 100644 index 000000000000..67ede6c655f7 --- /dev/null +++ b/easybuild/easyconfigs/i/ImageMagick/ImageMagick-7.1.0-53-GCCcore-12.2.0.eb @@ -0,0 +1,41 @@ +easyblock = 'ConfigureMake' + +name = 'ImageMagick' +version = '7.1.0-53' + +homepage = 'https://www.imagemagick.org/' +description = """ImageMagick is a software suite to create, edit, compose, or convert bitmap images""" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://github.com/ImageMagick/ImageMagick/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['4d4cade8f435736b62382b472fe75206b8eef540a968860ace5476a96799b5ef'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('X11', '20221110'), + ('Ghostscript', '10.0.0'), + ('JasPer', '4.0.0'), + ('libjpeg-turbo', '2.1.4'), + ('LibTIFF', '4.4.0'), + ('LittleCMS', '2.14'), + ('Pango', '1.50.12'), +] + +builddependencies = [ + ('binutils', '2.39'), + ('pkgconf', '1.9.3'), +] + +configopts = "--with-gslib --with-x" + +sanity_check_paths = { + 'files': [], + 'dirs': ['bin', 'etc/%(name)s-%(version_major)s', + 'include/%(name)s-%(version_major)s', 'lib', 'share'], +} + +modextravars = {'MAGICK_HOME': '%(installdir)s'} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..36dfc68a3237 --- /dev/null +++ b/easybuild/easyconfigs/l/LittleCMS/LittleCMS-2.14-GCCcore-12.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'LittleCMS' +version = '2.14' + +homepage = 'https://www.littlecms.com/' +description = """ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, + with special focus on accuracy and performance. """ + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +source_urls = ['https://sourceforge.net/projects/lcms/files/lcms/%s/' % '.'.join(version.split('.')[:2])] +sources = ['lcms2-%(version)s.tar.gz'] +checksums = ['28474ea6f6591c4d4cee972123587001a4e6e353412a41b3e9e82219818d5740'] + +builddependencies = [('binutils', '2.39')] + +dependencies = [('libjpeg-turbo', '2.1.4')] + +sanity_check_paths = { + 'files': ['bin/jpgicc', 'bin/linkicc', 'bin/psicc', 'bin/transicc', 'include/lcms2.h', 'include/lcms2_plugin.h', + 'lib/liblcms2.a', 'lib/liblcms2.%s' % SHLIB_EXT, 'lib/pkgconfig/lcms2.pc'], + 'dirs': ['share/man'], +} + +sanity_check_commands = ["jpgicc --help"] + +moduleclass = 'vis' From 49480c126e3a66a9b09aff34a02f4a2d3f56955a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:15:25 +0100 Subject: [PATCH 630/939] remove outdated comment in scanpy 1.9.1 easyconfig Co-authored-by: Simon Branford <4967+branfosj@users.noreply.github.com> --- easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb index 3967f4007cf1..88ec508f7761 100644 --- a/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb +++ b/easybuild/easyconfigs/s/scanpy/scanpy-1.9.1-foss-2021b.eb @@ -33,7 +33,6 @@ exts_list = [ ('natsort', '8.2.0', { 'checksums': ['57f85b72c688b09e053cdac302dd5b5b53df5f73ae20b4874fcbffd8bf783d11'], }), - # anndata 0.7.8 needs xlrd<2.0 ('xlrd', '2.0.1', { 'checksums': ['f72f148f54442c6b056bf931dbc34f986fd0c3b0b6b5a58d013c9aef274d0c88'], }), From 21ca16420efd61fdea808e6422da1599d003e5aa Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 11:37:55 +0100 Subject: [PATCH 631/939] adding easyconfigs: wandb-0.13.6-GCC-11.3.0.eb --- .../w/wandb/wandb-0.13.6-GCC-11.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb b/easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb new file mode 100644 index 000000000000..7b9de203570d --- /dev/null +++ b/easybuild/easyconfigs/w/wandb/wandb-0.13.6-GCC-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'wandb' +version = '0.13.6' + +homepage = 'https://wandb.ai' +description = """CLI and Python API for Weights and Biases (wandb), a tool for visualizing and +tracking your machine learning experiments.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +dependencies = [ + ('Python', '3.10.4'), + ('GitPython', '3.1.27'), + ('PyYAML', '6.0'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('docker-pycreds', '0.4.0', { + 'modulename': 'dockerpycreds', + 'checksums': ['6ce3270bcaf404cc4c3e27e4b6c70d3521deae82fb508767870fdbf772d584d4'], + }), + ('pathtools', '0.1.2', { + 'checksums': ['7c35c5421a39bb82e58018febd90e3b6e5db34c5443aaaf742b3f33d4655f1c0'], + }), + ('promise', '2.3', { + 'checksums': ['dfd18337c523ba4b6a58801c164c1904a9d4d1b1747c7d5dbf45b693a49d93d0'], + }), + ('urllib3', '1.26.13', { + 'checksums': ['c083dd0dce68dbfbe1129d5271cb90f9447dea7d52097c6e0126120c521ddea8'], + }), + ('sentry-sdk', '1.11.1', { + 'checksums': ['675f6279b6bb1fea09fd61751061f9a90dca3b5929ef631dd50dc8b3aeb245e9'], + }), + ('setproctitle', '1.3.2', { + 'checksums': ['b9fb97907c830d260fa0658ed58afd48a86b2b88aac521135c352ff7fd3477fd'], + }), + ('shortuuid', '1.0.11', { + 'checksums': ['fc75f2615914815a8e4cb1501b3a513745cb66ef0fd5fc6fb9f8c3fa3481f789'], + }), + (name, version, { + 'checksums': ['0d721aea476fd013c61a516948630ad58ceba78f4283b1f4b446e931664a8a98'], + }), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['wandb', 'wb']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +moduleclass = 'ai' From 9a59864b33ce9f78858a2d660feb3d6b2cc0fec0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 15:01:31 +0100 Subject: [PATCH 632/939] add flex as build dependency of cell2location v0.05 --- .../c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb index 7f105e3eeb10..1f400b685096 100644 --- a/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb +++ b/easybuild/easyconfigs/c/cell2location/cell2location-0.05-alpha-fosscuda-2020b.eb @@ -14,6 +14,7 @@ toolchain = {'name': 'fosscuda', 'version': '2020b'} builddependencies = [ ('Bison', '3.7.1'), + ('flex', '2.6.4'), # needed by louvain ] dependencies = [ From bcc30f0ceb3e83f3a3c0a4e9ddb89862d377e35a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 15:08:23 +0100 Subject: [PATCH 633/939] adding easyconfigs: SimPEG-0.18.1-foss-2021b.eb --- .../s/SimPEG/SimPEG-0.18.1-foss-2021b.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb new file mode 100644 index 000000000000..b079a1e9c9c3 --- /dev/null +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-foss-2021b.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'SimPEG' +version = '0.18.1' + +homepage = 'https://simpeg.xyz' +description = """An open source Python package for simulation and gradient based parameter estimation in + geophysical applications.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('numba', '0.54.1'), +] + +use_pip = True + +exts_list = [ + ('pymatsolver', '0.2.0', { + 'checksums': ['df9e0444f3c7fadf57b226d7d90b7be1dea9e24718575b458ba50429736d6c45'], + }), + ('discretize', '0.8.2', { + 'checksums': ['19b2bcb57cf769ca2c225875db5d3017dc58ca8cd3ad7f44ee89ba0e1622e4a6'], + }), + ('utm', '0.7.0', { + 'checksums': ['3c9a3650e98bb6eecec535418d0dfd4db8f88c8ceaca112a0ff0787e116566e2'], + }), + ('geoana', '0.4.0', { + 'checksums': ['e95bb3974019111e0522a6955ee735cca71fa11554647fafcbdbee8b91524495'], + }), + ('empymod', '2.2.1', { + 'checksums': ['7167ca4adfc7fe737261ff4371052b8caa1c662b1aa1862822552f76734cf7ac'], + }), + (name, version, { + 'modulename': 'SimPEG', + 'checksums': ['3cbbb96640b23e9bd3311bc71e5c79fb731cefd6b3b845ecd6dad59c4a6e3600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From d92c20418997d891b843a1258252f3d261ce4128 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 15:08:37 +0100 Subject: [PATCH 634/939] adding easyconfigs: SimPEG-0.18.1-intel-2021b.eb --- .../s/SimPEG/SimPEG-0.18.1-intel-2021b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb new file mode 100644 index 000000000000..ff2cc5d5fd80 --- /dev/null +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.18.1-intel-2021b.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonBundle' + +name = 'SimPEG' +version = '0.18.1' + +homepage = 'https://simpeg.xyz' +description = """An open source Python package for simulation and gradient based parameter estimation in + geophysical applications.""" + +toolchain = {'name': 'intel', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('matplotlib', '3.4.3'), + ('scikit-learn', '1.0.1'), + ('numba', '0.54.1'), +] + +use_pip = True + +exts_list = [ + ('pydiso', '0.0.3', { + 'checksums': ['883e1c4bda04afebd4ac364f1a2992e26123be0f8965c5ac59571549c6cec608'], + }), + ('pymatsolver', '0.2.0', { + 'checksums': ['df9e0444f3c7fadf57b226d7d90b7be1dea9e24718575b458ba50429736d6c45'], + }), + ('discretize', '0.8.2', { + 'checksums': ['19b2bcb57cf769ca2c225875db5d3017dc58ca8cd3ad7f44ee89ba0e1622e4a6'], + }), + ('utm', '0.7.0', { + 'checksums': ['3c9a3650e98bb6eecec535418d0dfd4db8f88c8ceaca112a0ff0787e116566e2'], + }), + ('geoana', '0.4.0', { + 'checksums': ['e95bb3974019111e0522a6955ee735cca71fa11554647fafcbdbee8b91524495'], + }), + ('empymod', '2.2.1', { + 'checksums': ['7167ca4adfc7fe737261ff4371052b8caa1c662b1aa1862822552f76734cf7ac'], + }), + (name, version, { + 'modulename': 'SimPEG', + 'checksums': ['3cbbb96640b23e9bd3311bc71e5c79fb731cefd6b3b845ecd6dad59c4a6e3600'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 02b28ff2d19730ddf2474a144788c71aad0d6b4a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 16:25:34 +0100 Subject: [PATCH 635/939] adding easyconfigs: Parcels-2.4.0-foss-2022a.eb --- .../p/Parcels/Parcels-2.4.0-foss-2022a.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb new file mode 100644 index 000000000000..239f726f0f60 --- /dev/null +++ b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb @@ -0,0 +1,51 @@ +easyblock = 'PythonBundle' + +name = 'Parcels' +version = '2.4.0' + +homepage = 'http://www.oceanparcels.org/' +description = """Parcels (Probably A Really Computationally Efficient Lagrangian Simulator) is a +set of Python classes and methods to create customisable particle tracking +simulations using output from Ocean Circulation models. Parcels can be used to +track passive and active particulates such as water, plankton, plastic and +fish.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('dask', '2022.10.0'), + ('FFmpeg', '5.0.1'), + ('git', '2.36.0', '-nodocs'), + ('matplotlib', '3.5.2'), + ('netcdf4-python', '1.6.1'), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), + ('xarray', '2022.6.0'), + ('zarr', '2.13.3'), +] + +use_pip = True + +exts_list = [ + ('cgen', '2020.1', { + 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], + }), + ('pytools', '2022.1.13', { + 'checksums': ['c2f98359f6f281fb9d06136cdfb825a1984571598c8b437f8d6815ab80a04149'], + }), + ('pymbolic', '2022.2', { + 'checksums': ['f82776942bb3cb72329fa1f1aa2b68ec09f237db9178c95cfdc92a6aea7cec89'], + }), + ('pykdtree', '1.3.5', { + 'checksums': ['7342f75e731103e653fc1f6b9fdabc2410cf92b6e7b06160804a75786c9b5747'], + }), + ('parcels', version, { + 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 037c9b01321d1b2e3f4fc02a98e5b918ca3e4b21 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 16:39:54 +0100 Subject: [PATCH 636/939] allow up to 100 failing tests for MOOSE --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index a75bf142bb7a..003c439e93ad 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -50,8 +50,8 @@ install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " # run tests install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " -# run tests, but tolerate failures -install_cmd += "(python run_tests -j %(parallel)s --max-fails 10000 || echo 'Some tests are failing!' >&2 ) " +# run tests, but tolerate up to 100 failures +install_cmd += "python run_tests -j %(parallel)s --max-fails 100 " sanity_check_paths = { 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, From 248eac2233c0b9a740d8db973f29520149d27fcb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 17:11:03 +0100 Subject: [PATCH 637/939] upgrade dependency on libdeflate to common v1.8 on GCCcore/10.3.0 --- easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb | 2 +- easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb index ac030fc7674f..e3fa56007207 100644 --- a/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/f/fastp/fastp-0.23.2-GCC-10.3.0.eb @@ -18,7 +18,7 @@ checksums = ['185bd58732e57474fa08aae90e154fbc05f3e437ee2b434386dd2266d60d8ef6'] dependencies = [ ('zlib', '1.2.11'), ('ISA-L', '2.30.0'), - ('libdeflate', '1.7'), + ('libdeflate', '1.8'), ] skipsteps = ['configure'] diff --git a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb index e3ae717ce007..bee76f307bb5 100644 --- a/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/v/vt/vt-0.57721-GCC-10.3.0.eb @@ -41,7 +41,7 @@ dependencies = [ ('cURL', '7.76.0'), ('PCRE', '8.44'), ('PCRE2', '10.36'), - ('libdeflate', '1.7'), + ('libdeflate', '1.8'), ('libRmath', '4.2.0'), ('LIBSVM', '3.25'), ('HTSlib', '1.12'), From 97172f7a6958f8acdf7a712b76c59f2ba7d61e15 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 8 Dec 2022 17:43:59 +0100 Subject: [PATCH 638/939] MOOSE test suite always does non-zero exit if there are failing tests --- .../m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb index 003c439e93ad..a46d5626ef06 100644 --- a/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb +++ b/easybuild/easyconfigs/m/MOOSE/MOOSE-2021-05-18-foss-2019b-Python-3.7.4.eb @@ -50,8 +50,8 @@ install_cmd += "./scripts/update_and_rebuild_libmesh.sh --skip-submodule-update install_cmd += "cd test && pwd && make -j %(parallel)s && make -j %(parallel)s hit && " # run tests install_cmd += "echo 'running tests' && export PYTHONPATH=%(installdir)s/moose/moosetools/contrib/hit:$PYTHONPATH && " -# run tests, but tolerate up to 100 failures -install_cmd += "python run_tests -j %(parallel)s --max-fails 100 " +# run tests, but tolerate failures +install_cmd += "(python run_tests -j %(parallel)s --max-fails 100 || echo 'Some tests are failing!' >&2)" sanity_check_paths = { 'files': ['moose/framework/libmoose-opt.%s' % SHLIB_EXT, From 1254cffccb30ac0ee284928a1a75d3a0c34cd308 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 8 Dec 2022 18:10:26 +0100 Subject: [PATCH 639/939] adding easyconfigs: OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb --- .../OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb | 94 +++++++++++++++++++ 1 file changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb diff --git a/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 000000000000..fc4c449b8109 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFold/OpenFold-1.0.1-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,94 @@ +easyblock = 'PythonBundle' + +name = 'OpenFold' +version = '1.0.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/aqlaboratory/openfold' +description = "A faithful PyTorch reproduction of DeepMind's AlphaFold 2" + +toolchain = {'name': 'foss', 'version': '2021a'} + +builddependencies = [ + # CMake is required to build ninja Python package (included as extension) + ('CMake', '3.20.1'), +] + +dependencies = [ + ('Python', '3.9.5'), + ('CUDA', '11.3.1', '', SYSTEM), + ('SciPy-bundle', '2021.05'), + ('PyYAML', '5.4.1'), + ('Biopython', '1.79'), + ('HH-suite', '3.3.0'), + ('HMMER', '3.3.2'), + ('Kalign', '3.3.1'), + ('UCX-CUDA', '1.10.0', versionsuffix), + ('cuDNN', '8.2.1.32', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('dm-tree', '0.1.6'), + ('einops', '0.4.1'), + ('colossalai', '0.1.8', versionsuffix), + ('scikit-build', '0.11.1'), + # OpenFold also requires the AlphaFold modification to OpenMM + # https://github.com/aqlaboratory/openfold/blob/v1.0.0/scripts/install_third_party_dependencies.sh#L20-L24 + # https://github.com/aqlaboratory/openfold/blob/v1.0.0/lib/openmm.patch + ('OpenMM', '7.5.1', '-DeepMind-patch'), +] + +use_pip = True + +exts_list = [ + ('PDBFixer', '1.7', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['a0bef3c52a7bbe69a6aea5333f51f3e7d158339be5829aed19b0344bd66d4eea'], + }), + ('ninja', '1.10.2.3', { + 'checksums': ['e1b86ad50d4e681a7dbdff05fc23bb52cb773edb90bc428efba33fa027738408'], + }), + ('hjson', '3.0.2', { + 'checksums': ['2838fd7200e5839ea4516ece953f3a19892c41089f0d933ba3f68e596aacfcd5'], + }), + ('py-cpuinfo', '8.0.0', { + 'modulename': 'cpuinfo', + 'checksums': ['5f269be0e08e33fd959de96b34cd4aeeeacac014dd8305f70eb28d06de2345c5'], + }), + ('triton', '1.0.0', { + 'source_tmpl': '%(name)s-%(version)s-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['37b8d0eb36ed7631a6f9d01bd3183f900ae7dbd9e5e40112468a3568505671dc'], + }), + ('deepspeed', '0.5.9', { + 'checksums': ['7c43d151b51d346a430034e77764097c4af7637217c08503291c48c37ae7d090'], + }), + ('contextlib2', '21.6.0', { + 'checksums': ['ab1e2bfe1d01d968e1b7e8d9023bc51ef3509bba217bb730cee3827e1ee82869'], + }), + ('ml_collections', '0.1.0', { + 'preinstallopts': "touch requirements.txt && touch requirements-test.txt && ", + 'checksums': ['59a17fcd1c140153009788517f304caaddd7a94f06690f9f0ed09987beebcf3c'], + }), + ('dllogger', '1.0.0', { + 'source_urls': ['https://github.com/NVIDIA/dllogger/archive/refs/tags/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['abae2b2ac73b9e176fa87144bf6c2048ddd3dae8e7002d6d5a270bc7e4da6b4d'], + }), + (name, version, { + 'source_urls': ['https://github.com/aqlaboratory/openfold/archive/refs/tags/'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['79eee0b90280eea5ec110511d95b42c62ea6e0098e4a78678738eb21b332bd99'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdbfixer'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "pdbfixer --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' From 96e8c78bba04a7e1b12a3b69c96f02d206295410 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 8 Dec 2022 18:10:43 +0100 Subject: [PATCH 640/939] enhance ESM-2 for esmfold --- .../ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 23 +++++++++++++------ 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index c4eb572620d7..854de665b3cd 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'ESM-2' version = '2.0.0' @@ -11,10 +11,6 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] -sources = ['fair-esm-%(version)s.tar.gz'] -checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] - dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), @@ -22,13 +18,26 @@ dependencies = [ ] use_pip = True -download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'esm'} +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('fair-esm', version, { + 'modulename': 'esm', + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), +] sanity_check_commands = [ "python -c 'import esm.pretrained'", + "python -c 'import omegaconf'", ] moduleclass = 'bio' From 135d16b70b05c623fe798164f9e29818487e62d5 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 8 Dec 2022 18:16:39 +0100 Subject: [PATCH 641/939] adding easyconfigs: CliMetLab-0.12.6-foss-2022a.eb, Magics-4.13.0-gompi-2022a.eb, ecBuild-3.7.0.eb --- .../CliMetLab/CliMetLab-0.12.6-foss-2022a.eb | 84 +++++++++++++++++++ .../easyconfigs/e/ecBuild/ecBuild-3.7.0.eb | 35 ++++++++ .../m/Magics/Magics-4.13.0-gompi-2022a.eb | 44 ++++++++++ 3 files changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb create mode 100644 easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb new file mode 100644 index 000000000000..815b57a29630 --- /dev/null +++ b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb @@ -0,0 +1,84 @@ +easyblock = 'PythonBundle' + +name = 'CliMetLab' +version = '0.12.6' + +homepage = 'https://climetlab.readthedocs.io/' +description = """ +CliMetLab is a Python package aiming at simplifying access to climate and +meteorological datasets, allowing users to focus on science instead of +technical issues such as data access and data formats. It is mostly intended to +be used in Jupyter notebooks, and be interoperable with all popular data +analytic packages, such as Numpy, Pandas, Xarray, SciPy, Matplotlib, etc. as +well as machine learning frameworks, such as Tensorflow, Keras or PyTorch.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('xarray', '2022.9.0'), + ('dask', '2022.10.0'), + ('netcdf4-python', '1.6.1'), + ('tqdm', '4.64.0'), + ('ecCodes', '2.27.0'), + ('PyYAML', '6.0'), + ('Magics', '4.13.0'), + ('cdsapi', '0.5.1'), +] + +use_pip = True +sanity_pip_check = True + +# stick to termcolor 1.x, to avoid hatchling required dependency +# remove ecmwflibs requirement (provides ecCodes and Magics) +exts_list = [ + ('eccodes', '1.5.0', { + 'checksums': ['e70c8f159140c343c215fd608ddf533be652ff05ad2ff17243c7b66cf92127fa'], + }), + ('cfgrib', '0.9.10.3', { + 'checksums': ['c10806058c80c48610c201bf05eb292401807806ab9423ab4965ae23dbb6b521'], + }), + ('multiurl', '0.1.1', { + 'checksums': ['8895c51f10a9f80a80f019bee5083a975760b7bdbd6cb2e32b2376a5916aa374'], + }), + ('ecmwf-api-client', '1.6.3', { + 'modulename': 'ecmwfapi', + 'checksums': ['3a00bda34a72e2d5198c97399a4750b42a6633efdb5e1b3a5fd2b2bbaa5db0d6'], + }), + ('ecmwf-opendata', '0.1.1', { + 'modulename': 'ecmwf.opendata', + 'checksums': ['dfb5d4694fbb78b0f79799e130be0b5a56b30c075937c3d03dd6d9b68399bfdd'], + }), + ('findlibs', '0.0.2', { + 'checksums': ['6c7e038496f9a97783ab2cd5736bb68522d5bebd8b0eb17c976b6a4ae4032c8d'], + }), + ('Magics', '1.5.8', { + 'modulename': 'Magics', + 'checksums': ['7df4241802fb552ee052da18190a5266a8faff7feecc70779cb5e1809625fb90'], + }), + ('pdbufr', '0.9.0', { + 'checksums': ['c9f9e19ebae7d27e86166d72a088c699044917a66c800cfccfa72005a1cda945'], + }), + ('pyodc', '1.1.4', { + 'checksums': ['e6185117a38483b0567bf45e6a476b83e0b6b2a7d94ae110cb3ecf92e2cd900e'], + }), + ('Markdown', '3.4.1', { + 'checksums': ['3b809086bb6efad416156e00a0da66fe47618a5d6918dd688f53f40c8e4cfeff'], + }), + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('branca', '0.3.1', { + 'checksums': ['3e762c9bdf40725f3d05ea1fda8fae9b470bfada6474e43a1242c8204a7bb15e'], + }), + ('climetlab', version, { + 'preinstallopts': """sed -i 's/"ecmwflibs/# "ecmwflibs/g' setup.py & """, + 'checksums': ['5c3506e3f4223b9ddbfbee09d41dd5b4e45ecce584b90419cce9fef33f9a1de3'], + }), +] + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb new file mode 100644 index 000000000000..8a5bb9a339e2 --- /dev/null +++ b/easybuild/easyconfigs/e/ecBuild/ecBuild-3.7.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'ecBuild' +version = '3.7.0' + +homepage = 'https://ecbuild.readthedocs.io/' + +description = """ +A CMake-based build system, consisting of a collection of CMake macros and +functions that ease the managing of software build systems """ + +toolchain = SYSTEM + +github_account = 'ecmwf' +sources = [ + { + 'source_urls': [GITHUB_SOURCE], + 'filename': '%(version)s.tar.gz', + 'extract_cmd': 'tar -xzf %s --strip-components=1', + }, +] +checksums = ['44ba49b6b628e88bc0145f0cd1fdbdff37fbff2327c581f22a47cd10263a21b6'] + +buildininstalldir = True + +skipsteps = ['install'] + +sanity_check_paths = { + 'files': ['bin/ecbuild', 'cmake/ecbuild-config.cmake'], + 'dirs': ['bin', 'lib', 'share', 'cmake'], +} + +sanity_check_commands = ['ecbuild --help'] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb b/easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb new file mode 100644 index 000000000000..3d7c2d18e8f8 --- /dev/null +++ b/easybuild/easyconfigs/m/Magics/Magics-4.13.0-gompi-2022a.eb @@ -0,0 +1,44 @@ +easyblock = 'CMakeMake' + +name = 'Magics' +version = '4.13.0' + +homepage = 'https://confluence.ecmwf.int/display/MAGP/' + +description = """ +Magics is ECMWF's meteorological plotting software and can be either accessed +directly through its Python or Fortran interfaces or by using Metview.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} + +source_urls = ['https://github.com/ecmwf/magics/archive'] +sources = ['%(version)s.tar.gz'] +checksums = ['bc9653754a9d655b14effd637d13dba6ecaf048d2f45cb8b70b3e262983b37bf'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('ecBuild', '3.7.0', '', SYSTEM), +] + +dependencies = [ + ('PROJ', '9.0.0'), + ('netCDF', '4.9.0'), + ('Pango', '1.50.7'), + ('expat', '2.4.8'), + ('ecCodes', '2.27.0'), +] + +_bins = ['magics', 'magicsCompatibilityChecker', 'magjson', 'magjsonx', 'magml', 'magmlx', 'metgram', 'metgram.sh', + 'metgramx'] + +runtest = 'test' + +sanity_check_paths = { + 'files': ['lib/libMagPlus%s.%s' % (x, SHLIB_EXT) for x in ['', 'Double', 'Single']] + + ['bin/%s' % x for x in _bins], + 'dirs': ['bin', 'lib', 'include', 'share'] +} + +sanity_check_commands = ['magics 2>&1 | grep "^Usage: magics"'] + +moduleclass = 'geo' From 30411e5fe2fe94d592ea3f9e64b82a44b961e9e4 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 8 Dec 2022 20:39:41 +0100 Subject: [PATCH 642/939] Update PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb --- .../PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb index 8f4749f4dae4..d131b7ed36b5 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb @@ -29,9 +29,6 @@ exts_list = [ ('torchmetrics', '0.10.3', { 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], }), - ('termcolor', '2.1.0', { - 'checksums': ['b80df54667ce4f48c03fe35df194f052dc27a541ebbf2544e4d6b47b5d6949c4'], - }), ('fire', '0.4.0', { 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], }), From d1a466160b30784eace504f9ebe73665e089747e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 22:56:44 +0100 Subject: [PATCH 643/939] downgrade dependency on FFmpeg on Parcels v2.4.0 --- easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb index 239f726f0f60..e243e530189b 100644 --- a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb @@ -16,7 +16,7 @@ dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('dask', '2022.10.0'), - ('FFmpeg', '5.0.1'), + ('FFmpeg', '4.42'), ('git', '2.36.0', '-nodocs'), ('matplotlib', '3.5.2'), ('netcdf4-python', '1.6.1'), From 98485c1091a42fff28f8ac171d28e2ae0a0d81d8 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Thu, 8 Dec 2022 23:04:22 +0100 Subject: [PATCH 644/939] Update easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb Co-authored-by: SebastianAchilles --- .../PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb index d131b7ed36b5..e9d3bd119a41 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb @@ -29,6 +29,10 @@ exts_list = [ ('torchmetrics', '0.10.3', { 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], }), + # stick to termcolor 1.x, to avoid hatchling required dependency + ('termcolor', '1.1.0', { + 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], + }), ('fire', '0.4.0', { 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], }), From 6b6521552c504042c902f3bf5eb431600be8fc44 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 8 Dec 2022 23:39:56 +0100 Subject: [PATCH 645/939] explain origin of list of dependencies of Parcels --- easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb index e243e530189b..9061cf7b2deb 100644 --- a/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb +++ b/easybuild/easyconfigs/p/Parcels/Parcels-2.4.0-foss-2022a.eb @@ -12,11 +12,13 @@ fish.""" toolchain = {'name': 'foss', 'version': '2022a'} +# dependencies of Parcels are not listed as install_requires +# taken from https://github.com/OceanParcels/parcels/blob/v%(version)s/environment_py3_linux.yml dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('dask', '2022.10.0'), - ('FFmpeg', '4.42'), + ('FFmpeg', '4.4.2'), ('git', '2.36.0', '-nodocs'), ('matplotlib', '3.5.2'), ('netcdf4-python', '1.6.1'), From 3315fa0874034f094b65f84a9260fd4dbbc44520 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 9 Dec 2022 07:43:48 +0100 Subject: [PATCH 646/939] fix description to match package intention. --- .../m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb index f043052deda3..0381f59f5ef8 100644 --- a/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/m/matlab-proxy/matlab-proxy-0.5.4-GCCcore-11.3.0.eb @@ -4,7 +4,7 @@ name = 'matlab-proxy' version = '0.5.4' homepage = 'https://github.com/mathworks/matlab-proxy' -description = 'MATLAB Integration for Jupyter' +description = "A Python package which enables you to launch MATLAB and access it from a web browser." toolchain = {'name': 'GCCcore', 'version': '11.3.0'} From 81734287dcc0f2f53b295d278e56d06eee598809 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Dec 2022 08:28:24 +0100 Subject: [PATCH 647/939] fix xarray version --- .../easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb index 815b57a29630..7d9b35710021 100644 --- a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb @@ -17,7 +17,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), - ('xarray', '2022.9.0'), + ('xarray', '2022.6.0'), ('dask', '2022.10.0'), ('netcdf4-python', '1.6.1'), ('tqdm', '4.64.0'), From 29bc8c5ebc594184bf52d9ed003beef8a7935968 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 9 Dec 2022 09:23:20 +0100 Subject: [PATCH 648/939] also update the non-CUDA version --- .../ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 7 +----- .../e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 24 +++++++++++-------- 2 files changed, 15 insertions(+), 16 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index 854de665b3cd..572347352111 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -30,14 +30,9 @@ exts_list = [ 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], }), ('fair-esm', version, { - 'modulename': 'esm', + 'modulename': 'esm, esm.pretrained', 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], }), ] -sanity_check_commands = [ - "python -c 'import esm.pretrained'", - "python -c 'import omegaconf'", -] - moduleclass = 'bio' diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb index e3ea302ffec7..2a897513a5e9 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -1,4 +1,4 @@ -easyblock = 'PythonPackage' +easyblock = 'PythonBundle' name = 'ESM-2' version = '2.0.0' @@ -10,23 +10,27 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} -source_urls = ['https://pypi.python.org/packages/source/f/fair-esm'] -sources = ['fair-esm-%(version)s.tar.gz'] -checksums = ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'] - dependencies = [ ('Python', '3.9.5'), ('PyTorch', '1.10.0'), ] use_pip = True -download_dep_fail = True sanity_pip_check = True -options = {'modulename': 'esm'} - -sanity_check_commands = [ - "python -c 'import esm.pretrained'", +# omegaconf is required for esmfold (in addition to OpenFold-1.0.1) +exts_list = [ + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), + ('antlr4-python3-runtime', '4.9.3', { + 'modulename': 'antlr4', + 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], + }), + ('fair-esm', version, { + 'modulename': 'esm, esm.pretrained', + 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], + }), ] moduleclass = 'bio' From aea1ef2d053e30c8ad1c074384d01762a9ac6abc Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Fri, 9 Dec 2022 09:58:21 +0000 Subject: [PATCH 649/939] Adding webp support as we already have the libwebp here, it helps a lot making this library more useful --- .../p/Pillow-SIMD/Pillow-SIMD-9.2.0-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) 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 0973b9770798..c430b0e2e0a3 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 @@ -21,7 +21,8 @@ dependencies = [ ('libpng', '1.6.37'), ('zlib', '1.2.12'), ('LibTIFF', '4.3.0'), - ('freetype', '2.12.1') + ('freetype', '2.12.1'), + ('libwebp', '1.2.4'), ] use_pip = True From 8f2d4abf10dc2e5b1440802d5ecfd074866973bd Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Dec 2022 14:38:29 +0100 Subject: [PATCH 650/939] Fix test_autograd --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 3 +++ ....1_fix-autograd-thread_shutdown-test.patch | 24 +++++++++++++++++++ 2 files changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch 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 d70fb0603782..f0d3ab839eb0 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 @@ -25,6 +25,7 @@ patches = [ 'PyTorch-1.11.0_increase-distributed-test-timeout.patch', 'PyTorch-1.11.0_install-vsx-vec-headers.patch', 'PyTorch-1.11.1_skip-test_init_from_local_shards.patch', + 'PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch', 'PyTorch-1.12.1_fix-cuda-gcc-version-check.patch', 'PyTorch-1.12.1_fix-skip-decorators.patch', 'PyTorch-1.12.1_fix-test_cpp_extensions_jit.patch', @@ -67,6 +68,8 @@ checksums = [ 'f2e6b9625733d9a471bb75e1ea20e28814cf1380b4f9089aa838ee35ddecf07d', # PyTorch-1.11.0_install-vsx-vec-headers.patch # PyTorch-1.11.1_skip-test_init_from_local_shards.patch '4aeb1b0bc863d4801b0095cbce69f8794066748f0df27c6aaaf729c5ecba04b7', + # PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch + 'd97cd6b0570a167ecc3e631dc4ea884d95ace285cc38aa980566f4fec2c0d089', # PyTorch-1.12.1_fix-cuda-gcc-version-check.patch 'a650f4576f06c749f244cada52ff9c02499fa8f182019129488db3845e0756ab', 'e3ca6e42b2fa592ea095939fb59ab875668a058479407db3f3684cc5c6f4146c', # PyTorch-1.12.1_fix-skip-decorators.patch diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch new file mode 100644 index 000000000000..c82cc0604676 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_fix-autograd-thread_shutdown-test.patch @@ -0,0 +1,24 @@ +Fix flaky test_thread_shutdown in test_autograd + +From https://github.com/pytorch/pytorch/pull/86464 + +Backport: Alexander Grund (TU Dresden) + +diff --git a/test/test_autograd.py b/test/test_autograd.py +index da1e859682e..0c0bc4f1a2a 100644 +--- a/test/test_autograd.py ++++ b/test/test_autograd.py +@@ -4320,8 +4320,12 @@ class MyFunction(Function): + def backward(ctx, grad): + return grad + ++# Run on cuda if it is available to ensure that the worker thread ++# is properly initialized by the time we exit. ++device = "cuda" if torch.cuda.is_available() else "cpu" ++ + for shape in [(1,), ()]: +- v = torch.ones(shape, requires_grad=True) ++ v = torch.ones(shape, requires_grad=True, device=device) + MyFunction.apply(v).backward() + """ + s = TestCase.runWithPytorchAPIUsageStderr(code) From 5ebcb2835792626859e283c903cf944e8a72253c Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Dec 2022 14:46:00 +0100 Subject: [PATCH 651/939] Fix test_c10d_gloo --- .../PyTorch-1.12.1-foss-2022a-CUDA-11.7.0.eb | 6 ++-- ...PyTorch-1.12.1_skip-test_round_robin.patch | 35 +++++++++++++++++++ 2 files changed, 38 insertions(+), 3 deletions(-) create mode 100644 easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch 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 f0d3ab839eb0..9a11fc1e85e3 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 @@ -43,7 +43,7 @@ patches = [ 'PyTorch-1.12.1_remove-flaky-test-in-testnn.patch', '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-1.12.1_skip-test_round_robin.patch', ] checksums = [ '031c71073db73da732b5d01710220564ce6dd88d812ba053f0cc94296401eccb', # pytorch-v1.12.1.tar.gz @@ -97,8 +97,8 @@ checksums = [ # PyTorch-1.12.1_skip-ao-sparsity-test-without-fbgemm.patch 'edd464ec8c37b44c07a72008d732604f6837f2dd61c7810c391a86ba4945ca39', '1c89e7e67287fe6b9a95480a4178d3653b94d0ab2fe68edf227606c8ae548fdc', # PyTorch-1.12.1_skip-failing-grad-test.patch - # PyTorch-1.12.1_skip-test_round_robin_create_destroy.patch - '1435fcac3234edc865479199673b902eb67f6a2bd046af7d731141f03594666d', + # PyTorch-1.12.1_skip-test_round_robin.patch + '63d4849b78605aa088fdff695637d9473ea60dee603a3ff7f788690d70c55349', ] osdependencies = [OS_PKG_IBVERBS_DEV] diff --git a/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch new file mode 100644 index 000000000000..ebeec6b80b55 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch/PyTorch-1.12.1_skip-test_round_robin.patch @@ -0,0 +1,35 @@ +test_round_robin & test_round_robin_create_destroy of distributed/test_c10d_gloo may run into timeouts. +So simply skip the on all OS (not only on Windows), the existing skip marker suggest that this is OK. + +Author: Alexander Grund (TU Dresden) + +diff --git a/test/distributed/test_c10d_gloo.py b/test/distributed/test_c10d_gloo.py +index e49d65ea33d..b4fb75a1b11 100644 +--- a/test/distributed/test_c10d_gloo.py ++++ b/test/distributed/test_c10d_gloo.py +@@ -10,6 +10,7 @@ import sys + import tempfile + from functools import reduce + from itertools import groupby ++from unittest import skip + + import torch + import torch.distributed as c10d +@@ -1415,7 +1415,7 @@ class ProcessGroupGlooTest(MultiProcessTestCase): + for i, tensor in enumerate(tensors): + self.assertEqual(torch.full(size, float(i * self.world_size)), tensor) + +- @skip_if_win32() ++ @skip("Occasionally times out") + @requires_gloo() + def test_round_robin(self): + num_process_groups = 2 +@@ -1438,7 +1439,7 @@ class ProcessGroupGlooTest(MultiProcessTestCase): + pg.broadcast(tensor, root=0).wait() + self.assertEqual(torch.full([100, 100], 0.0), tensor) + +- @skip_if_win32() ++ @skip("Occasionally times out") + @requires_gloo() + def test_round_robin_create_destroy(self): + store = c10d.FileStore(self.file_name, self.world_size) From 493d0ab42b38ea02264868a719d760ac14cf8a88 Mon Sep 17 00:00:00 2001 From: Alexander Grund Date: Fri, 9 Dec 2022 15:09:03 +0100 Subject: [PATCH 652/939] Skip aborting FSDP tests --- .../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 9a11fc1e85e3..528fb6715575 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 @@ -137,6 +137,9 @@ excluded_tests = { 'distributed/test_distributed_spawn', # Broken on CUDA 11.6/11.7: https://github.com/pytorch/pytorch/issues/75375 'distributions/test_constraints', + # Those 2 abort on some machines. Skip for now + 'distributed/fsdp/test_fsdp_input', + 'distributed/fsdp/test_fsdp_mixed_precision', ] } From 1c26956e2937d1e172f2bc90d3f9936fa45f6df5 Mon Sep 17 00:00:00 2001 From: Victor Lopez Date: Fri, 9 Dec 2022 15:20:44 +0100 Subject: [PATCH 653/939] Add easyconfigs: dlb --- .../easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb | 26 +++++++++++++++++++ .../easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb | 26 +++++++++++++++++++ 2 files changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb new file mode 100644 index 000000000000..bf0987b6dd29 --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb @@ -0,0 +1,26 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.2' + +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': '2022a'} +builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] + +moduleclass = 'lib' + +configopts = '--with-mpi' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb new file mode 100644 index 000000000000..aae046e6f0b2 --- /dev/null +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb @@ -0,0 +1,26 @@ +# vim: set syntax=python: +easyblock = 'ConfigureMake' + +name = 'dlb' +version = '3.2' + +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': '2022a'} +builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] + +sources = [SOURCELOWER_TAR_GZ] +source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] + +checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] + +moduleclass = 'lib' + +configopts = '--with-mpi' From f9486579fe322aadd4571fcdbac6b40a00070654 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 9 Dec 2022 18:03:32 +0000 Subject: [PATCH 654/939] Fix missing checksum --- .../f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index 89dc1755c9d5..c15509fa214d 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -49,6 +49,8 @@ components = [ '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_remove-semicolon.patch 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', + # FlexiBLAS-3.2.0_remove-intel-suffix.patch + '98b70ac9b10c9e45cd7c2251f8b710cda704b04311b33b6fe1a56be51aa43bc4', ], 'configopts': '-DABI=Intel', 'backends': local_backends, From 2f45aeebb21c32c6bee952efa50b9812f1cbe073 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Fri, 9 Dec 2022 18:40:07 +0000 Subject: [PATCH 655/939] Trailing space --- .../f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb index c15509fa214d..0ad1849f7758 100644 --- a/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/f/FlexiBLAS/FlexiBLAS-3.2.0-NVHPC-22.7-CUDA-11.7.0.eb @@ -48,7 +48,7 @@ components = [ # FlexiBLAS-3.0.4_fix-wrapper_blas_intel.patch '30ae7d1edbcff2beb18bca9b751dcaf0bf9a996d41fbe669b0a11592ec01c7ac', # FlexiBLAS-3.0.4_remove-semicolon.patch - 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', + 'a3bbcff7aeca6f8bab989e7e3a8069f2b7b660e4559042221eecaa30dc0ce300', # FlexiBLAS-3.2.0_remove-intel-suffix.patch '98b70ac9b10c9e45cd7c2251f8b710cda704b04311b33b6fe1a56be51aa43bc4', ], From b63081a90ed5f63181fa96c4ef9fd53264be90cf Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Dec 2022 23:40:37 +0100 Subject: [PATCH 656/939] adding easyconfig deepdiff-5.8.1-GCCcore-11.3.0.eb --- .../deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..fffd39905e06 --- /dev/null +++ b/easybuild/easyconfigs/d/deepdiff/deepdiff-5.8.1-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'deepdiff' +version = '5.8.1' + +homepage = 'https://zepworks.com/deepdiff/current/' +description = """DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] +dependencies = [('Python', '3.10.4')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('jsonpickle', '2.2.0', { + 'checksums': ['7b272918b0554182e53dc340ddd62d9b7f902fec7e7b05620c04f3ccef479a0e'], + }), + ('ordered-set', '4.1.0', { + 'checksums': ['694a8e44c87657c59292ede72891eb91d34131f6531463aab3009191c77364a8'], + }), + (name, version, { + 'checksums': ['8d4eb2c4e6cbc80b811266419cb71dd95a157094a3947ccf937a94d44943c7b8'], + }), +] + +moduleclass = 'tools' From 9610492606b6a832164474256dd7b48bd5453141 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 01:05:25 +0100 Subject: [PATCH 657/939] fix parameters of Sphinx-RTD-Theme v1.1.1 PythonBundle --- .../Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb index 0a9f224eba97..b47eb8e0a276 100644 --- a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -4,15 +4,14 @@ name = 'Sphinx-RTD-Theme' version = '1.1.1' homepage = 'https://sphinx-rtd-theme.readthedocs.io' -description = """Sphinx theme was designed to provide a great reader experience - for documentation users on both desktop and mobile devices""" +description = """Sphinx theme designed to provide a great reader experience + for documentation users on both desktop and mobile devices.""" toolchain = {'name': 'GCCcore', 'version': '10.2.0'} dependencies = [('Python', '3.8.6')] use_pip = True -exts_download_dep_fail = True exts_list = [ ('sphinx_rtd_theme', version, { @@ -20,4 +19,6 @@ exts_list = [ }), ] +sanity_pip_check = True + moduleclass = 'vis' From ca35504c6975c13a3cd7244ae9cab8969fcc8d85 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 01:33:08 +0100 Subject: [PATCH 658/939] add binutils as build dependecy of Sphinx-RTD-Theme v1.1.1 --- .../s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb index b47eb8e0a276..76924dcf2299 100644 --- a/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/s/Sphinx-RTD-Theme/Sphinx-RTD-Theme-1.1.1-GCCcore-10.2.0.eb @@ -9,6 +9,8 @@ description = """Sphinx theme designed to provide a great reader experience toolchain = {'name': 'GCCcore', 'version': '10.2.0'} +builddependencies = [('binutils', '2.35')] + dependencies = [('Python', '3.8.6')] use_pip = True From d40c72fb741a95735e90e9ad9223ee4095192d36 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 10 Dec 2022 00:34:25 +0100 Subject: [PATCH 659/939] adding easyconfigs tensorboardX-2.5.1-foss-2022a.eb --- .../tensorboardX-2.5.1-foss-2022a.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb new file mode 100644 index 000000000000..8a5ba42a91c0 --- /dev/null +++ b/easybuild/easyconfigs/t/tensorboardX/tensorboardX-2.5.1-foss-2022a.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'tensorboardX' +version = '2.5.1' + +homepage = 'https://github.com/lanpa/tensorboardX' +description = "Tensorboard for PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# tensorboardX v2.x works with tensorboards generated with TensorFlow 2, +# but TensorFlow is not needed to use tensorboardX +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('protobuf-python', '3.19.4'), +] + +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': '%(name)s', + 'checksums': ['ea85a3446f22ce8a917fe4fa4d8a7a96222ef84ac835267d038c34bb99f6d61b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' From 9605baf9cb3834d492af9988b49fca58dc835788 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 9 Dec 2022 23:41:12 +0100 Subject: [PATCH 660/939] update PyTorch-Lightning v1.8.2 to v1.8.4 and use dependencies following its requirements file --- ...-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb | 50 ------- ...-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb | 124 ++++++++++++++++++ 2 files changed, 124 insertions(+), 50 deletions(-) delete mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb deleted file mode 100644 index e9d3bd119a41..000000000000 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.2-foss-2022a-CUDA-11.7.0.eb +++ /dev/null @@ -1,50 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'PyTorch-Lightning' -version = '1.8.2' -versionsuffix = '-CUDA-%(cudaver)s' - -homepage = 'https://pytorchlightning.ai' -description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." - -toolchain = {'name': 'foss', 'version': '2022a'} - -dependencies = [ - ('CUDA', '11.7.0', '', SYSTEM), - ('Python', '3.10.4'), - ('PyTorch', '1.12.0', versionsuffix), - ('tqdm', '4.64.0'), - ('tensorboard', '2.10.0'), - ('typing-extensions', '4.3.0'), -] - -exts_list = [ - ('fsspec', '2022.11.0', { - 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], - }), - ('pyDeprecate', '0.3.2', { - 'modulename': 'deprecate', - 'checksums': ['d481116cc5d7f6c473e7c4be820efdd9b90a16b594b350276e9e66a6cb5bdd29'], - }), - ('torchmetrics', '0.10.3', { - 'checksums': ['9e6ab66175f2dc13e246c37485b2c27c77931dfe47fc2b81c76217b8efdc1e57'], - }), - # stick to termcolor 1.x, to avoid hatchling required dependency - ('termcolor', '1.1.0', { - 'checksums': ['1d6d69ce66211143803fbc56652b41d73b4a400a2891d7bf7a1cdf4c02de613b'], - }), - ('fire', '0.4.0', { - 'checksums': ['c5e2b8763699d1142393a46d0e3e790c5eb2f0706082df8f647878842c216a62'], - }), - ('lightning-utilities', '0.3.0', { - 'checksums': ['d769ab9b76ebdee3243d1051d509aafee57d7947734ddc22977deef8a6427f2f'], - }), - ('pytorch-lightning', version, { - 'checksums': ['480f3396cd63888c4e5ec2f21c02fe662a2b035d9634e6f31fcf1197a36ebd15'], - }), -] - -use_pip = True -sanity_pip_check = True - -moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..532eba19c22b --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,124 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.4' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.3'), + ('BeautifulSoup', '4.10.0'), + ('deepdiff', '5.8.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), + ('tensorboardX', '2.5.1'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.5.1', { + 'checksums': ['63a5c5ce3673d3d5fbbf23cd87e11ab84b6b451436f1b7f19ec54b6bc36ed7ca'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('starlette', '0.19.1', { + 'checksums': ['c6d21096774ecb9639acad41b86b7706e52ba3bf1dc13ea4ed9ad593d47e24c7'], + }), + ('fastapi', '0.79.1', { + 'checksums': ['006862dec0f0f5683ac21fb0864af2ff12a931e7ba18920f28cc8eceed51896b'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('lightning_cloud', '0.5.12', { + 'checksums': ['5b0cf53ecfb512f9476eec3a7f425c0e174ca9d0e726673605d5e1e57074eb0c'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '1.3.0', { + 'checksums': ['8d3b509d4e6d235655f7dd495fcf0afc1bd86da84de3a8d434e6f82137ebcde8'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('croniter', '1.3.8', { + 'checksums': ['32a5ec04e97ec0837bcdf013767abd2e71cceeefd3c2e14c804098ce51ad6cd9'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('lightning-utilities', '0.4.2', { + 'checksums': ['dc6696ab180117f7e97b5488dac1d77765ab891022f7521a97a39e10d362bdb8'], + }), + ('blessed', '1.19.1', { + 'checksums': ['9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.3', { + 'checksums': ['1d920d0e9ab76ec5d42192a68d15af2562663b5dfbf4a67cf9eba520e1ca57e6'], + }), + ('inquirer', '2.10.1', { + 'checksums': ['e9876258183e24f6e8c44136b04f6f2e18dd6684aee59b86a8057c50601a6523'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.24.21', { + 'checksums': ['7e976cfd0a61601e74624ef8f5246b40a01f2cce73a011ef29cf80a6e371d0fa'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.3.4', { + 'checksums': ['6554ebea5764f66f4be544a4fcaa0953ee80e600dd7bd818ba4893d72bf12bfb'], + }), + ('s3fs', '2022.7.1', { + 'checksums': ['4883d682cb96b769fca568dbbcaa33ff457ac8077a03af221e6f253adac05771'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['c2771f966fc1b909cdfd1d603a87b8c84a3d5ff7aacf35b2c0260f697ec0c8be'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' + From 39f7d49c2f8e8187dcf1ebc086eddd728ffc7b4c Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 11 Dec 2022 01:51:14 +0100 Subject: [PATCH 661/939] remove blank lines at end of PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb --- .../PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb index 532eba19c22b..faf2e40814c4 100644 --- a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a-CUDA-11.7.0.eb @@ -121,4 +121,3 @@ exts_list = [ sanity_pip_check = True moduleclass = 'lib' - From f351308c25c4e59bb8f8e25bb95d7f9cf18a6727 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 11 Dec 2022 09:57:33 +0000 Subject: [PATCH 662/939] geo moduleclass for SimPEG --- .../s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb index 96c544367471..d8b79f635f4d 100644 --- a/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/s/SimPEG/SimPEG-0.14.1-intel-2020a-Python-3.8.2.eb @@ -56,4 +56,4 @@ exts_list = [ sanity_pip_check = True -moduleclass = 'bio' +moduleclass = 'geo' From 99d673be61df6ae52fb6413b6a24676c9f4deb40 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Sun, 11 Dec 2022 11:18:07 +0100 Subject: [PATCH 663/939] add Python 3.11 to classifiers in setup.py --- setup.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/setup.py b/setup.py index 75d8dacffe3c..6b4971a52b9f 100644 --- a/setup.py +++ b/setup.py @@ -99,6 +99,8 @@ def get_data_files(): "Programming Language :: Python :: 3.7", "Programming Language :: Python :: 3.8", "Programming Language :: Python :: 3.9", + "Programming Language :: Python :: 3.10", + "Programming Language :: Python :: 3.11", "Topic :: Software Development :: Build Tools", ], packages=[], From 9ee6150ef116266902d8e9ea85b32d06757b33f3 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Dec 2022 10:27:06 +0000 Subject: [PATCH 664/939] switch LibTiff homepage --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb | 2 +- ...1.14-GCCcore-12.2.0.eb => libdeflate-1.15-GCCcore-12.2.0.eb} | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/l/libdeflate/{libdeflate-1.14-GCCcore-12.2.0.eb => libdeflate-1.15-GCCcore-12.2.0.eb} (100%) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb index bcefb663225b..6336e1de0434 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb @@ -3,7 +3,7 @@ easyblock = 'ConfigureMake' name = 'LibTIFF' version = '4.4.0' -homepage = 'https://libtiff.maptools.org/' +homepage = 'https://libtiff.gitlab.io/libtiff/' description = "tiff: Library and tools for reading and writing TIFF data files" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb similarity index 100% rename from easybuild/easyconfigs/l/libdeflate/libdeflate-1.14-GCCcore-12.2.0.eb rename to easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb From 8c08c47901d4ff3fc0b67386e6bb7e21c6c1cc99 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Dec 2022 10:27:39 +0000 Subject: [PATCH 665/939] switch libdeflate to 1.15, which requires change to CMakeMake --- .../l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb | 10 +++------- 1 file changed, 3 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb index 37b4f66bb324..de86aeb5c08a 100644 --- a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb @@ -3,10 +3,10 @@ # Updated to 1.8 # J. Sassmannshausen NHS/GSTT -easyblock = 'ConfigureMake' +easyblock = 'CMakeMake' name = 'libdeflate' -version = '1.14' +version = '1.15' homepage = 'https://github.com/ebiggers/libdeflate' description = """Heavily optimized library for DEFLATE/zlib/gzip compression and decompression.""" @@ -16,14 +16,10 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} github_account = 'ebiggers' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] -checksums = ['89e7df898c37c3427b0f39aadcf733731321a278771d20fc553f92da8d4808ac'] +checksums = ['58b95040df7383dc0413defb700d9893c194732474283cc4c8f144b00a68154b'] builddependencies = [('binutils', '2.39')] -skipsteps = ['configure'] - -installopts = 'PREFIX=%(installdir)s' - sanity_check_paths = { 'files': [ 'bin/%(name)s-gunzip', 'bin/%(name)s-gzip', From d9119b7ce7382c3741045f50adf8245f4fd22967 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Sun, 11 Dec 2022 11:36:51 +0100 Subject: [PATCH 666/939] add Java builddep --- .../e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb | 10 +++++++--- .../easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb | 10 +++++++--- 2 files changed, 14 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb index 572347352111..b4cd134d85e0 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a-CUDA-11.3.1.eb @@ -11,6 +11,10 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + dependencies = [ ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), @@ -22,13 +26,13 @@ sanity_pip_check = True # omegaconf is required for esmfold (in addition to OpenFold-1.0.1) exts_list = [ - ('omegaconf', '2.2.3', { - 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], - }), ('antlr4-python3-runtime', '4.9.3', { 'modulename': 'antlr4', 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], }), + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), ('fair-esm', version, { 'modulename': 'esm, esm.pretrained', 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], diff --git a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb index 2a897513a5e9..3b6ec3564b0f 100644 --- a/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/e/ESM-2/ESM-2-2.0.0-foss-2021a.eb @@ -10,6 +10,10 @@ description = """ESM-2 outperforms all tested single-sequence protein language m toolchain = {'name': 'foss', 'version': '2021a'} +builddependencies = [ + ('Java', '11', '', SYSTEM), # needed by ANTLR4 runtime +] + dependencies = [ ('Python', '3.9.5'), ('PyTorch', '1.10.0'), @@ -20,13 +24,13 @@ sanity_pip_check = True # omegaconf is required for esmfold (in addition to OpenFold-1.0.1) exts_list = [ - ('omegaconf', '2.2.3', { - 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], - }), ('antlr4-python3-runtime', '4.9.3', { 'modulename': 'antlr4', 'checksums': ['f224469b4168294902bb1efa80a8bf7855f24c99aef99cbefc1bcd3cce77881b'], }), + ('omegaconf', '2.2.3', { + 'checksums': ['59ff9fba864ffbb5fb710b64e8a9ba37c68fa339a2e2bb4f1b648d6901552523'], + }), ('fair-esm', version, { 'modulename': 'esm, esm.pretrained', 'checksums': ['4ed34d4598ec75ed6550a4e581d023bf8d4a8375317ecba6269bb68135f80c85'], From 6030a7eb4eab256423c9c6bebc0cf338458a0f54 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 11 Dec 2022 10:56:58 +0000 Subject: [PATCH 667/939] switch libdeflate version in LibTIFF --- easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb index 6336e1de0434..b2fb13f5ec33 100644 --- a/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/LibTIFF/LibTIFF-4.4.0-GCCcore-12.2.0.eb @@ -21,7 +21,7 @@ dependencies = [ ('XZ', '5.2.7'), ('jbigkit', '2.1'), ('zstd', '1.5.2'), - ('libdeflate', '1.14'), + ('libdeflate', '1.15'), ] configopts = "--enable-ld-version-script " From 369c2e71a1a0c317f5b11542651c460df04b6d6a Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 11 Dec 2022 11:28:42 +0000 Subject: [PATCH 668/939] Update easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb --- .../l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb index de86aeb5c08a..386b12fc1218 100644 --- a/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/l/libdeflate/libdeflate-1.15-GCCcore-12.2.0.eb @@ -18,7 +18,10 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['58b95040df7383dc0413defb700d9893c194732474283cc4c8f144b00a68154b'] -builddependencies = [('binutils', '2.39')] +builddependencies = [ + ('binutils', '2.39'), + ('CMake', '3.24.3'), +] sanity_check_paths = { 'files': [ From b23acaa051a7497cdb395b95bf557a34b335badd Mon Sep 17 00:00:00 2001 From: robogast Date: Sun, 11 Dec 2022 18:53:56 +0100 Subject: [PATCH 669/939] adding easyconfigs: CUDA-12.0.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb | 24 +++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb new file mode 100644 index 000000000000..9b47dfcc5716 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.0.0' +local_nv_version = '525.60.13' + +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: + '905e9b9516900839fb76064719db752439f38b8cb730b49335d8bd53ddfad392', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '117fe045c71668e45d41c6119b6f27875370c78e33fc56795b6fe014c796ec60', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'cd13e9c65d4c8f895a968706f46064d536be09f9706bce081cc864b7e4fa4544' +}] + +moduleclass = 'system' From 5831891309cc6d6dd967c04064cbddc33242d203 Mon Sep 17 00:00:00 2001 From: robogast Date: Sun, 11 Dec 2022 20:39:31 +0100 Subject: [PATCH 670/939] adding easyconfigs: NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb, UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb, GDRCopy-2.3-GCCcore-12.2.0.eb --- easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb | 24 +++++++++ .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 52 +++++++++++++++++++ .../NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 42 +++++++++++++++ ...-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb | 40 ++++++++++++++ 4 files changed, 158 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb new file mode 100644 index 000000000000..9b47dfcc5716 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb @@ -0,0 +1,24 @@ +name = 'CUDA' +version = '12.0.0' +local_nv_version = '525.60.13' + +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: + '905e9b9516900839fb76064719db752439f38b8cb730b49335d8bd53ddfad392', + 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: + '117fe045c71668e45d41c6119b6f27875370c78e33fc56795b6fe014c796ec60', + 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: + 'cd13e9c65d4c8f895a968706f46064d536be09f9706bce081cc864b7e4fa4544' +}] + +moduleclass = 'system' diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..0fb6d9b4864f --- /dev/null +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -0,0 +1,52 @@ +easyblock = 'ConfigureMake' + +name = 'GDRCopy' +version = '2.3' + +homepage = 'https://github.com/NVIDIA/gdrcopy' +description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology." + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] + +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib prefix=%(installdir)s" + +installopts = 'prefix=%(installdir)s' + +github_account = 'NVIDIA' +# This easyconfig only installs the library of GDRCopy. Please keep in mind +# that GDRCopy also needs the following kernel modules at runtime: +# +# 1. Kernel module for GDRCopy: improves Host to GPU communication +# https://github.com/NVIDIA/gdrcopy +# RPM: 'gdrcopy-kmod', DEB: 'gdrdrv-dkms' +# Requirements: version of GDRCopy kernel module (gdrdrv.ko) >= 2.0 +# +# 2. (optional) Kernel module for GPUDirect RDMA: improves GPU to GPU communication +# https://github.com/Mellanox/nv_peer_memory +# RPM: 'nvidia_peer_memory' +# Requirements: Mellanox HCA with MLNX_OFED 2.1 +# +# These kernel modules are not listed as system dependencies to lower the system +# requirements to build this easyconfig, as they are not needed for the build. + +skipsteps = ['configure'] +install_cmd = "make lib_install" + +sanity_check_paths = { + 'files': ['lib/libgdrapi.so'], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb new file mode 100644 index 000000000000..3270ad6f6e00 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -0,0 +1,42 @@ +name = 'NCCL' +version = '2.16.2' +versionsuffix = '-CUDA-%(cudaver)s' +easyblock = 'Tarball' + +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': '12.2.0'} + +source_urls = [ + 'https://developer.download.nvidia.com/compute/redist/nccl/v%(version)s/' +] +sources = ['%(namelower)s_%(version)s-1+cuda%(cudashortver)s_%(arch)s.txz'] +checksums = [{ + '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_x86_64.txz': + 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', + '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_ppc64le.txz': + 'daac3b7de8d0091369cb59b59d011b494c2f16403c80478c15b97d88a9895651', + '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_aarch64.txz': + 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', +}] + +builddependencies = [('binutils', '2.39')] + +dependencies = [ + ('CUDA', '12.0.0', '', SYSTEM), + ('UCX-CUDA', '1.13.1', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +sanity_check_paths = { + 'files': [ + 'include/nccl.h', 'lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'lib/pkgconfig/nccl.pc' + ], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb new file mode 100644 index 000000000000..556fafb06852 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -0,0 +1,40 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-CUDA' +version = '1.13.1' +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': '12.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] +sources = ['ucx-%(version)s.tar.gz'] +patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] +checksums = [ + {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, +] + +builddependencies = [ + ('binutils', '2.39'), + ('Autotools', '20220317'), + ('pkgconf', '1.9.3'), +] +dependencies = [ + ('zlib', '1.2.12'), + ('UCX', '1.13.1'), + ('CUDA', '12.0.0', '', SYSTEM), + ('GDRCopy', '2.3'), +] + + +moduleclass = 'lib' From 6282b28223ecb206f3a52e47fc234c53af234338 Mon Sep 17 00:00:00 2001 From: robogast Date: Sun, 11 Dec 2022 20:43:21 +0100 Subject: [PATCH 671/939] removed CUDA/12.0.0 from PR --- easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb | 24 --------------------- 1 file changed, 24 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb diff --git a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb b/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb deleted file mode 100644 index 9b47dfcc5716..000000000000 --- a/easybuild/easyconfigs/c/CUDA/CUDA-12.0.0.eb +++ /dev/null @@ -1,24 +0,0 @@ -name = 'CUDA' -version = '12.0.0' -local_nv_version = '525.60.13' - -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: - '905e9b9516900839fb76064719db752439f38b8cb730b49335d8bd53ddfad392', - 'cuda_%%(version)s_%s_linux_ppc64le.run' % local_nv_version: - '117fe045c71668e45d41c6119b6f27875370c78e33fc56795b6fe014c796ec60', - 'cuda_%%(version)s_%s_linux_sbsa.run' % local_nv_version: - 'cd13e9c65d4c8f895a968706f46064d536be09f9706bce081cc864b7e4fa4544' -}] - -moduleclass = 'system' From a3ac06d74a1e1f6b8c5a7a05298bfeb8895fc2cf Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Sun, 11 Dec 2022 21:04:14 +0100 Subject: [PATCH 672/939] Moved easyblock var to top of file --- .../n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index 3270ad6f6e00..dc192d2fe025 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -1,7 +1,8 @@ +easyblock = 'Tarball' + name = 'NCCL' version = '2.16.2' versionsuffix = '-CUDA-%(cudaver)s' -easyblock = 'Tarball' homepage = 'https://developer.nvidia.com/nccl' description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective From e3806345201bf320a2a7628a27b4f130855876e3 Mon Sep 17 00:00:00 2001 From: Victor Lopez Herrero Date: Mon, 12 Dec 2022 10:32:11 +0100 Subject: [PATCH 673/939] Apply suggestions from code review Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb | 6 +++--- easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb | 6 +++--- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb index bf0987b6dd29..fa248865fb6b 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb @@ -14,13 +14,13 @@ homepage = 'https://pm.bsc.es/dlb/' docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] toolchain = {'name': 'gompi', 'version': '2022a'} -builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] +builddependencies = [('Python', '3.10.4', '-bare')] sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] -moduleclass = 'lib' - configopts = '--with-mpi' + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb index aae046e6f0b2..be30e500a7d2 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb @@ -14,13 +14,13 @@ homepage = 'https://pm.bsc.es/dlb/' docurls = ['https://pm.bsc.es/ftp/dlb/doc/user-guide/'] toolchain = {'name': 'iimpi', 'version': '2022a'} -builddependencies = [('Python', '3.10.4', '', ('GCCcore', '11.3.0-bare'))] +builddependencies = [('Python', '3.10.4', '-bare')] sources = [SOURCELOWER_TAR_GZ] source_urls = ['https://pm.bsc.es/ftp/dlb/releases'] checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] -moduleclass = 'lib' - configopts = '--with-mpi' + +moduleclass = 'lib' From e7286c1f1e62b42941afbd742012d5a5291e9b8d Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Mon, 12 Dec 2022 10:54:18 +0100 Subject: [PATCH 674/939] Update NCCL aarch64 checksum --- .../n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index dc192d2fe025..ec551b3f239b 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -20,7 +20,7 @@ checksums = [{ '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_ppc64le.txz': 'daac3b7de8d0091369cb59b59d011b494c2f16403c80478c15b97d88a9895651', '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_aarch64.txz': - 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', + '738d22d216266cd039610d0b87e008fcbba8ec9a93a626b958be96583d8b8b8a', }] builddependencies = [('binutils', '2.39')] From d6296fb50b469f5d9641920bc4c8a0be406e7d42 Mon Sep 17 00:00:00 2001 From: Robert Jan Schlimbach Date: Mon, 12 Dec 2022 11:40:44 +0100 Subject: [PATCH 675/939] Revert NCCL ec back to github source --- .../NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 25 +++---------------- 1 file changed, 4 insertions(+), 21 deletions(-) diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index ec551b3f239b..22b2ed8966dd 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -1,5 +1,3 @@ -easyblock = 'Tarball' - name = 'NCCL' version = '2.16.2' versionsuffix = '-CUDA-%(cudaver)s' @@ -10,18 +8,10 @@ communication primitives that are performance optimized for NVIDIA GPUs.""" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} -source_urls = [ - 'https://developer.download.nvidia.com/compute/redist/nccl/v%(version)s/' -] -sources = ['%(namelower)s_%(version)s-1+cuda%(cudashortver)s_%(arch)s.txz'] -checksums = [{ - '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_x86_64.txz': - 'fb630e2d244cdc8cf3fe2cbe07cbf0a50a5213ba546edc717bdba5d5ac757b87', - '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_ppc64le.txz': - 'daac3b7de8d0091369cb59b59d011b494c2f16403c80478c15b97d88a9895651', - '%(namelower)s_%(version)s-1+cuda%(cudashortver)s_aarch64.txz': - '738d22d216266cd039610d0b87e008fcbba8ec9a93a626b958be96583d8b8b8a', -}] +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['7f7c738511a8876403fc574d13d48e7c250d934d755598d82e14bab12236fc64'] builddependencies = [('binutils', '2.39')] @@ -33,11 +23,4 @@ dependencies = [ # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] -sanity_check_paths = { - 'files': [ - 'include/nccl.h', 'lib/libnccl.%s' % SHLIB_EXT, 'lib/libnccl_static.a', 'lib/pkgconfig/nccl.pc' - ], - 'dirs': [], -} - moduleclass = 'lib' From f3762bb5ab9a385ed75b33c42e5c13b92856cfac Mon Sep 17 00:00:00 2001 From: sassy Date: Mon, 12 Dec 2022 10:54:44 +0000 Subject: [PATCH 676/939] adding easyconfigs: SCOTCH-7.0.1-iimpi-2022a.eb --- .../s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb new file mode 100644 index 000000000000..f9abb478142d --- /dev/null +++ b/easybuild/easyconfigs/s/SCOTCH/SCOTCH-7.0.1-iimpi-2022a.eb @@ -0,0 +1,24 @@ +name = 'SCOTCH' +version = '7.0.1' + +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': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://gitlab.inria.fr/scotch/scotch/-/archive/v%(version)s/'] +sources = ['%(namelower)s-v%(version)s.tar.gz'] +checksums = ['0618e9bc33c02172ea7351600fce4fccd32fe00b3359c4aabb5e415f17c06fed'] + +builddependencies = [ + ('Bison', '3.8.2'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +moduleclass = 'math' From 6ea0eb15c898b96e4b88e0ffb466c4b5eb94e4c8 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 12 Dec 2022 12:24:42 +0100 Subject: [PATCH 677/939] Add Score-P v8 + dependencies --- .../c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb | 53 +++++++++++++++++ .../CubeWriter-4.8-GCCcore-11.3.0.eb | 53 +++++++++++++++++ .../o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb | 44 ++++++++++++++ .../o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb | 50 ++++++++++++++++ .../p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb | 49 +++++++++++++++ .../s/Score-P/Score-P-8.0-gompi-2022a.eb | 59 +++++++++++++++++++ 6 files changed, 308 insertions(+) create mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a9337f666c23 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.8-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: 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 = 'CubeLib' +version = '4.8' + +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': '11.3.0'} +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['171c93ac5afd6bc74c50a9a58efdaf8589ff5cc1e5bd773ebdfb2347b77e2f68'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +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-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..79fbfeebdd14 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb @@ -0,0 +1,53 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: 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 = 'CubeWriter' +version = '4.8' + +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': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(versions)s/dist'] +sources = ['cubew-%(version)s.tar.gz'] +checksums = ['73c7f9e9681ee45d71943b66c01cfe675b426e4816e751ed2e0b670563ca4cf3'] + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +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/OPARI2-2.0.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..c672c06de72a --- /dev/null +++ b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.7-GCCcore-11.3.0.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 = '2.0.7' + +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': '11.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['e302a4cc265eb2a4aa27c16a90eabd9e1e58cb02a191dd1c4d86f9a0df128715'] + +builddependencies = [ + ('binutils', '2.38'), +] + + +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/OTF2-3.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..61eba75f5f0f --- /dev/null +++ b/easybuild/easyconfigs/o/OTF2/OTF2-3.0.2-GCCcore-11.3.0.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 = '3.0.2' + +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': '11.3.0'} + +source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ae3a7ad83055d8f873738fee5031470652d31b9bcbf223dd556aea41f5f62303'] + +builddependencies = [ + ('binutils', '2.38'), +] +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-7.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..209e88d199b6 --- /dev/null +++ b/easybuild/easyconfigs/p/PAPI/PAPI-7.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,49 @@ +## +# Author: Robert Mijakovic +## + +easyblock = 'ConfigureMake' + +name = 'PAPI' +version = '7.0.0' + +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': '11.3.0'} + +source_urls = ['https://icl.cs.utk.edu/projects/papi/downloads/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['799dcc317a47da96beaeed445812ecb6ae49df7c0504a4569797c1f7d74c4fd2'] + +builddependencies = [ + ('binutils', '2.38'), +] + +start_dir = 'src' + +configopts = "--with-components=rapl " # for energy measurements + +parallel = 1 + +runtest = 'fulltest' + +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/s/Score-P/Score-P-8.0-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb new file mode 100644 index 000000000000..efea7c597cec --- /dev/null +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb @@ -0,0 +1,59 @@ +## +# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany +# Copyright 2020 TU Dresden, Germany +# Authors:: +# * Bernd Mohr +# * Markus Geimer +# * Alexander Grund +# * Robert Mijakovic +# License:: 3-clause BSD +# +# This work is based on experiences from the UNITE project +# http://apps.fz-juelich.de/unite/ +## + +name = 'Score-P' +version = '8.0-rc1' + +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': '2022a'} + +source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] +sources = ['scorep-%(version)s.tar.gz'] +checksums = ['d5975e69a594fff4982701f5181b4825386a238a95df68a0d5c1e1b62480add7'] + +dependencies = [ + ('CubeLib', '4.8'), + ('CubeWriter', '4.8'), + ('libunwind', '1.6.2'), + ('OPARI2', '2.0.7'), + ('OTF2', '3.0.2'), + # Hardware counter support (optional): + ('PAPI', '7.0.0'), + # PDT source-to-source instrumentation support (optional): + ('PDT', '3.25.1'), +] + +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 f368e78ecd6e4e539d46cbe82e7e869edf708416 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 12 Dec 2022 12:29:52 +0100 Subject: [PATCH 678/939] Cleaning --- .../c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb | 64 ------------------- .../c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb | 54 ---------------- .../CubeWriter-4.7-GCCcore-11.3.0.eb | 53 --------------- .../o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb | 44 ------------- .../s/Score-P/Score-P-7.1-gompi-2022a.eb | 59 ----------------- 5 files changed, 274 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb delete mode 100644 easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb deleted file mode 100644 index 790b55187fd1..000000000000 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7-GCCcore-11.3.0.eb +++ /dev/null @@ -1,64 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: 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 = 'CubeGUI' -version = '4.7' - -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 graphical report explorer. -""" - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('CubeGUI-4.7_missing_compile_file.patch', 1), -] -checksums = [ - '103fe00fa9846685746ce56231f64d850764a87737dc0407c9d0a24037590f68', # cubegui-4.7.tar.gz - '0a3072decf1d4b9f8544331647bb160723733f3579b9d8c64906c45fcf4ce669', # CubeGUI-4.7_missing_compile_file.patch -] - -preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('Autotools', '20220317'), - ('CubeLib', '4.7'), -] - -dependencies = [ - ('Qt5', '5.15.5'), -] - -configopts = [ - 'CXX="g++" --with-qt=$EBROOTQT5/bin ', -] - -sanity_check_paths = { - 'files': ['bin/cube', 'bin/cubegui-config', - 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], - 'dirs': ['include/cubegui', 'lib/cube-plugins'], -} - -moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb deleted file mode 100644 index d48598c1cf57..000000000000 --- a/easybuild/easyconfigs/c/CubeLib/CubeLib-4.7-GCCcore-11.3.0.eb +++ /dev/null @@ -1,54 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: 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 = 'CubeLib' -version = '4.7' - -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': '11.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['e44352c80a25a49b0fa0748792ccc9f1be31300a96c32de982b92477a8740938'] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('zlib', '1.2.12'), -] - -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-4.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb deleted file mode 100644 index 6649e72f03ea..000000000000 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.7-GCCcore-11.3.0.eb +++ /dev/null @@ -1,53 +0,0 @@ -## -# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild -# -# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany -# Authors:: 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 = 'CubeWriter' -version = '4.7' - -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': '11.3.0'} - -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version_major_minor)s/dist'] -sources = ['cubew-%(version)s.tar.gz'] -checksums = ['a7c7fca13e6cb252f08d4380223d7c56a8e86a67de147bcc0279ebb849c884a5'] - -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('pkgconf', '1.8.0'), -] - -dependencies = [ - ('zlib', '1.2.12'), -] - -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/OPARI2-2.0.6-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb deleted file mode 100644 index acc02a8fc51a..000000000000 --- a/easybuild/easyconfigs/o/OPARI2/OPARI2-2.0.6-GCCcore-11.3.0.eb +++ /dev/null @@ -1,44 +0,0 @@ -# # -# 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 = '2.0.6' - -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': '11.3.0'} - -source_urls = ['http://perftools.pages.jsc.fz-juelich.de/cicd/%(namelower)s/tags/%(namelower)s-%(version)s'] -sources = [SOURCELOWER_TAR_GZ] -checksums = ['55972289ce66080bb48622110c3189a36e88a12917635f049b37685b9d3bbcb0'] - -builddependencies = [ - ('binutils', '2.38'), -] - - -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/s/Score-P/Score-P-7.1-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb deleted file mode 100644 index 773bcc6594bb..000000000000 --- a/easybuild/easyconfigs/s/Score-P/Score-P-7.1-gompi-2022a.eb +++ /dev/null @@ -1,59 +0,0 @@ -## -# Copyright:: Copyright 2013-2020 Juelich Supercomputing Centre, Germany -# Copyright 2020 TU Dresden, Germany -# Authors:: -# * Bernd Mohr -# * Markus Geimer -# * Alexander Grund -# * Robert Mijakovic -# License:: 3-clause BSD -# -# This work is based on experiences from the UNITE project -# http://apps.fz-juelich.de/unite/ -## - -name = 'Score-P' -version = '7.1' - -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': '2022a'} - -source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] -sources = ['scorep-%(version)s.tar.gz'] -checksums = ['98dea497982001fb82da3429ca55669b2917a0858c71abe2cfe7cd113381f1f7'] - -dependencies = [ - ('CubeLib', '4.7'), - ('CubeWriter', '4.7'), - ('libunwind', '1.6.2'), - ('OPARI2', '2.0.6'), - ('OTF2', '3.0'), - # Hardware counter support (optional): - ('PAPI', '6.0.0.1'), - # PDT source-to-source instrumentation support (optional): - ('PDT', '3.25.1'), -] - -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 ca0d663962a7c3cf405424cfeed062f9defe7c06 Mon Sep 17 00:00:00 2001 From: alberta Date: Mon, 12 Dec 2022 12:53:05 +0100 Subject: [PATCH 679/939] adding easyconfigs: humann-3.6-foss-2022a.eb --- .../h/humann/humann-3.6-foss-2022a.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb diff --git a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb new file mode 100644 index 000000000000..8f511fe8f859 --- /dev/null +++ b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb @@ -0,0 +1,39 @@ +# Humann +easyblock = 'PythonBundle' + +name = 'humann' +version = '3.6' + +homepage = 'http://huttenhower.sph.harvard.edu/humann' + +description ="""HUMAnN v3 is a pipeline for efficiently + and accurately determining the coverage and abundance + of microbial pathways in a community from metagenomic data. +Sequencing a metagenome typically produces millions + of short DNA/RNA reads. This process, referred + to as functional profiling, aims to describe the metabolic potential + of a microbial community and its members. More generally, + functional profiling answers the question: + What are the microbes in my community-of-interest doing (or capable of doing)?""" + +toolchain = {'name': 'foss', 'version': '2022a'} + + +dependencies = { + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +} + + +exts_list = [ + (name, version, { + 'checksums': ['addce81db58bacfdd5465423455d25e385aa8dd14349253c3a7054bf7d3747dc'], + }), + +] + + +use_pip = True +sanity_pip_check = True + + From 3848fcc29388e3ad1c484aac8be2d9353c94c550 Mon Sep 17 00:00:00 2001 From: alberta Date: Mon, 12 Dec 2022 13:24:08 +0100 Subject: [PATCH 680/939] Fix files --- easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb index 8f511fe8f859..1e8577eb47da 100644 --- a/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb +++ b/easybuild/easyconfigs/h/humann/humann-3.6-foss-2022a.eb @@ -6,7 +6,7 @@ version = '3.6' homepage = 'http://huttenhower.sph.harvard.edu/humann' -description ="""HUMAnN v3 is a pipeline for efficiently +description = """HUMAnN v3 is a pipeline for efficiently and accurately determining the coverage and abundance of microbial pathways in a community from metagenomic data. Sequencing a metagenome typically produces millions @@ -35,5 +35,3 @@ exts_list = [ use_pip = True sanity_pip_check = True - - From 30c688a809bd854a4a1a93bf5cfd9ab1b7e6044d Mon Sep 17 00:00:00 2001 From: robogast Date: Mon, 12 Dec 2022 13:34:07 +0100 Subject: [PATCH 681/939] removed sm_35, updated GDRCopy to match the previous ec --- .../g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb | 14 +++++++------- .../NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb | 2 +- .../UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb | 1 + 3 files changed, 9 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb index 0fb6d9b4864f..c9c58812cf58 100644 --- a/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/g/GDRCopy/GDRCopy-2.3-GCCcore-12.2.0.eb @@ -9,6 +9,7 @@ description = "A low-latency GPU memory copy library based on NVIDIA GPUDirect R toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} +github_account = 'NVIDIA' source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['b85d15901889aa42de6c4a9233792af40dd94543e82abe0439e544c87fd79475'] @@ -19,12 +20,6 @@ builddependencies = [ ('pkgconf', '1.9.3'), ] -prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found -buildopts = "config lib prefix=%(installdir)s" - -installopts = 'prefix=%(installdir)s' - -github_account = 'NVIDIA' # This easyconfig only installs the library of GDRCopy. Please keep in mind # that GDRCopy also needs the following kernel modules at runtime: # @@ -42,10 +37,15 @@ github_account = 'NVIDIA' # requirements to build this easyconfig, as they are not needed for the build. skipsteps = ['configure'] + +local_envopts = "prefix=%(installdir)s" +prebuildopts = "PATH=$PATH:/sbin " # ensures that ldconfig is found +buildopts = "config lib %s" % local_envopts install_cmd = "make lib_install" +installopts = local_envopts sanity_check_paths = { - 'files': ['lib/libgdrapi.so'], + 'files': ['lib/libgdrapi.%s' % SHLIB_EXT], 'dirs': ['include'], } diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb index 22b2ed8966dd..cd576dcb0e7a 100644 --- a/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.16.2-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -21,6 +21,6 @@ dependencies = [ ] # default CUDA compute capabilities to use (override via --cuda-compute-capabilities) -cuda_compute_capabilities = ['3.5', '5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] +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-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb index 556fafb06852..9212315db276 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -29,6 +29,7 @@ builddependencies = [ ('Autotools', '20220317'), ('pkgconf', '1.9.3'), ] + dependencies = [ ('zlib', '1.2.12'), ('UCX', '1.13.1'), From 73837ff17c277d8690e7e59ae6f709b62dfafd48 Mon Sep 17 00:00:00 2001 From: Maxim Masterov Date: Mon, 12 Dec 2022 13:34:27 +0100 Subject: [PATCH 682/939] Add CubeGUI --- .../c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb | 64 +++++++++++++++++++ ...=> CubeGUI-4.8_missing_compile_file.patch} | 8 +-- 2 files changed, 68 insertions(+), 4 deletions(-) create mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb rename easybuild/easyconfigs/c/CubeGUI/{CubeGUI-4.7_missing_compile_file.patch => CubeGUI-4.8_missing_compile_file.patch} (97%) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..90d43bac7414 --- /dev/null +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb @@ -0,0 +1,64 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2019 Juelich Supercomputing Centre, Germany +# Authors:: 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 = 'CubeGUI' +version = '4.8' + +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 graphical report explorer. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + ('CubeGUI-4.8_missing_compile_file.patch', 1), +] +checksums = [ + '1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76', # cubegui-4.8.tar.gz + '487697669f6a9a3455fabfdb65d720699070986776c465830ad417942e25e2dc', # CubeGUI-4.8_missing_compile_file.patch +] + +preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' + +builddependencies = [ + # use same binutils version that was used when building GCCcore + ('binutils', '2.38'), + ('Autotools', '20220317'), + ('CubeLib', '4.8'), +] + +dependencies = [ + ('Qt5', '5.15.5'), +] + +configopts = [ + 'CXX="g++" --with-qt=$EBROOTQT5/bin ', +] + +sanity_check_paths = { + 'files': ['bin/cube', 'bin/cubegui-config', + 'lib/libcube4gui.a', 'lib/libcube4gui.%s' % SHLIB_EXT], + 'dirs': ['include/cubegui', 'lib/cube-plugins'], +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch similarity index 97% rename from easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch rename to easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch index 7b08da87205e..d7a92c4db957 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.7_missing_compile_file.patch +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch @@ -1,11 +1,11 @@ -# This patch adds the "build-config/compile" file that is missing in v4.7. +# This patch adds the "build-config/compile" file that is missing in v4.8 # The file is copied "as is" from CubeGUI v4.6. # # Author: maxim-masterov (SURF) -diff -Nru cubegui-4.7.orig/build-config/compile cubegui-4.7/build-config/compile ---- cubegui-4.7.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 -+++ cubegui-4.7/build-config/compile 2022-08-09 11:33:06.528166000 +0200 +diff -Nru cubegui-4.8.orig/build-config/compile cubegui-4.8/build-config/compile +--- cubegui-4.8.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 ++++ cubegui-4.8/build-config/compile 2022-12-12 13:16:45.979205634 +0100 @@ -0,0 +1,347 @@ +#! /bin/sh +# Wrapper for compilers which do not understand '-c -o'. From 615716b317d787bada42e7819dd51c3953d9eaae Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 12 Dec 2022 14:32:05 +0100 Subject: [PATCH 683/939] Rename file --- ...{Score-P-8.0-gompi-2022a.eb => Score-P-8.0-rc1-gompi-2022a.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/Score-P/{Score-P-8.0-gompi-2022a.eb => Score-P-8.0-rc1-gompi-2022a.eb} (100%) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb similarity index 100% rename from easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb rename to easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb From 86f9811903672eb61735965ac96eeaa3a9560869 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 14:15:58 +0000 Subject: [PATCH 684/939] The new g2lib moved to github and uses cmake now --- .../g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..539118743c8a --- /dev/null +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +name = 'g2clib' +version = '1.7.0' +easyblock = 'CMakeMake' + +homepage = 'https://github.com/NOAA-EMC/NCEPLIBS-g2c' +description = """Library contains GRIB2 encoder/decoder ('C' version).""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NOAA-EMC/NCEPLIBS-g2c/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['73afba9da382fed73ed8692d77fa037bb313280879cd4012a5e5697dccf55175'] + +builddependencies = [('binutils', '2.38'), + ('CMake', '3.23.1'), + ] + +dependencies = [ + ('JasPer', '2.0.33'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), +] + +parallel = 8 + +sanity_check_paths = { + 'files': ['lib/libg2c.so'], + 'dirs': ['include', 'lib'], +} + +moduleclass = 'data' From b83c31c48f4040096aa023f0bf53ca5345506e96 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 15:21:31 +0100 Subject: [PATCH 685/939] adding easyconfigs: QGIS-3.28.1-foss-2021b.eb, GRASS-8.2.0-foss-2021b.eb, Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb and patches: QGIS-3.28.1_fix-SIP-macro.patch, GRASS-8.2.0_GCC_ldlibs.patch, Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch, Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch, Qt5Webkit-5.212.0-alpha4_fix_python_path.patch, Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch --- .../attrdict3-2.0.2-GCCcore-11.2.0.eb | 26 ++++ .../e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb | 33 +++++ .../f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb | 30 ++++ .../g/GRASS/GRASS-8.2.0-foss-2021b.eb | 102 ++++++++++++++ .../g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch | 15 ++ .../l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb | 35 +++++ .../libspatialite-5.0.1-GCC-11.2.0.eb | 40 ++++++ .../m/minizip/minizip-1.1-GCCcore-11.2.0.eb | 39 ++++++ .../q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb | 39 ++++++ .../q/QGIS/QGIS-3.28.1-foss-2021b.eb | 75 ++++++++++ .../q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch | 21 +++ .../QScintilla-2.11.6-GCCcore-11.2.0.eb | 33 +++++ ...Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb | 71 ++++++++++ ....0-alpha4_dont_use_multiarch_lib_dir.patch | 26 ++++ ...fix_deprecated_encoding_in_json.load.patch | 15 ++ ...ebkit-5.212.0-alpha4_fix_python_path.patch | 66 +++++++++ ..._use_CXX_true_instead_of_TRUE_define.patch | 128 ++++++++++++++++++ .../QtKeychain-0.13.2-GCCcore-11.2.0.eb | 36 +++++ .../q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb | 39 ++++++ .../w/wxPython/wxPython-4.2.0-foss-2021b.eb | 48 +++++++ .../w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb | 71 ++++++++++ 21 files changed, 988 insertions(+) create mode 100644 easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch create mode 100644 easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb create mode 100644 easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch create mode 100644 easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch create mode 100644 easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch create mode 100644 easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb create mode 100644 easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..67c44f60b2a7 --- /dev/null +++ b/easybuild/easyconfigs/a/attrdict3/attrdict3-2.0.2-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonBundle' + +name = 'attrdict3' +version = '2.0.2' + +homepage = 'https://github.com/pirofti/AttrDict3' +description = """AttrDict is a Python library that provides mapping objects that allow their elements + to be accessed both as keys and as attributes.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Python', '3.9.6')] + +sanity_pip_check = True +use_pip = True + +exts_list = [ + (name, version, { + 'modulename': 'attrdict', + 'checksums': ['004c171ca1120cc1755701db99d7fa4944afb1e68950434efdaa542513335fe8'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..4af59f56c339 --- /dev/null +++ b/easybuild/easyconfigs/e/exiv2/exiv2-0.27.5-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'exiv2' +version = '0.27.5' + +homepage = 'https://exiv2.org' +description = "Exiv2 is a Cross-platform C++ library and a command line utility to manage image metadata." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +github_account = 'Exiv2' +source_urls = [GITHUB_RELEASE] +sources = ['%(name)s-%(version)s-Source.tar.gz'] +checksums = ['35a58618ab236a901ca4928b0ad8b31007ebdc0386d904409d825024e45ea6e2'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('expat', '2.4.1'), + ('zlib', '1.2.11'), +] + +sanity_check_paths = { + 'files': ['bin/exiv2', 'lib/libexiv2.%s' % SHLIB_EXT, 'lib/libexiv2-xmp.a', 'lib/pkgconfig/exiv2.pc'], + 'dirs': ['include/exiv2', 'lib/cmake'], +} + +sanity_check_commands = ["exiv2 --help"] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..6bc2457695b9 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeXL/FreeXL-1.0.6-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'FreeXL' +version = '1.0.6' + +homepage = 'https://www.gaia-gis.it/fossil/freexl/index' + +description = """ +FreeXL is an open source library to extract valid data from within an +Excel (.xls) spreadsheet. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gaia-gis.it/gaia-sins'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3de8b57a3d130cb2881ea52d3aa9ce1feedb1b57b7daa4eb37f751404f90fc22'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +sanity_check_paths = { + 'files': ['lib/libfreexl.a'], + 'dirs': [] +} + +moduleclass = 'lib' 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 new file mode 100644 index 000000000000..890e801c9090 --- /dev/null +++ b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb @@ -0,0 +1,102 @@ +easyblock = 'ConfigureMake' + +name = 'GRASS' +version = '8.2.0' + +homepage = "https://grass.osgeo.org" +description = """The Geographic Resources Analysis Support System - used + for geospatial data management and analysis, image processing, + graphics and maps production, spatial modeling, and visualization""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://grass.osgeo.org/grass%s/source' % ''.join(version.split('.')[:2])] +sources = [SOURCELOWER_TAR_GZ] +patches = ['%(name)s-%(version)s_GCC_ldlibs.patch'] +checksums = [ + {'grass-8.2.0.tar.gz': '621c3304a563be19c0220ae28f931a5e9ba74a53218c5556cd3f7fbfcca33a80'}, + {'GRASS-8.2.0_GCC_ldlibs.patch': '771edf64c583218d28529c53845218a6ab774179999b9b92edb4de32954edc49'}, +] + +builddependencies = [ + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('bzip2', '1.0.8'), + ('gettext', '0.21'), + ('Python', '3.9.6'), + ('libxml2', '2.9.10'), + ('libpng', '1.6.37'), + ('libreadline', '8.1'), + ('ncurses', '6.2'), + ('netCDF', '4.8.1'), + ('GDAL', '3.3.2'), + ('libspatialite', '5.0.1'), + ('GEOS', '3.9.1'), + ('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'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('wxPython', '4.2.0'), + ('zstd', '1.5.0'), +] + +preconfigopts = "sed -e 's/-lblas/$LIBBLAS/g' -e 's/-llapack/$LIBLAPACK/g' -i configure && " + +configopts = '--enable-64bit ' +configopts += '--enable-largefile=yes ' +configopts += '--with-cairo=yes ' +configopts += '--with-cxx ' +configopts += '--with-ffmpeg --with-ffmpeg-libs=$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=$LAPACK_LIB_DIR ' +configopts += '--with-lapack-includes=$LAPACK_INC_DIR ' +configopts += '--with-blas ' +configopts += '--with-blas-lib=$BLAS_LIB_DIR ' +configopts += '--with-blas-includes=$BLAS_INC_DIR ' +configopts += '--with-netcdf=$EBROOTNETCDF/bin/nc-config ' +configopts += '--without-odbc ' +configopts += '--with-opengl ' +configopts += '--with-openmp ' +configopts += '--with-png ' +configopts += '--with-png-libs="$EBROOTLIBPNG/lib $EBROOTZLIB/lib" --with-png-includes=$EBROOTLIBPNG/include ' +configopts += '--without-postgres ' +configopts += '--with-proj --with-proj-libs=$EBROOTPROJ/lib ' +configopts += '--with-proj-includes=$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-zstd --with-zstd-libs=$EBROOTZSTD/lib --with-zstd-includes=$EBROOTZSTD/include ' + +postinstallcmds = [ + 'ln -s grass%(version_major)s%(version_minor)s %(installdir)s/grass%(version_major)s', +] + +sanity_check_paths = { + 'files': [], + 'dirs': ["."] +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch new file mode 100644 index 000000000000..d8af9023033b --- /dev/null +++ b/easybuild/easyconfigs/g/GRASS/GRASS-8.2.0_GCC_ldlibs.patch @@ -0,0 +1,15 @@ +Use mathlib and threads in the LDFLAGS + +Åke Sandgren, 2022-12-07 +diff -ru grass-8.2.0.orig/configure grass-8.2.0/configure +--- grass-8.2.0.orig/configure 2022-06-03 15:27:06.000000000 +0200 ++++ grass-8.2.0/configure 2022-12-07 14:23:37.234003038 +0100 +@@ -4031,7 +4031,7 @@ + SHLIB_LD_FLAGS="-Wl,-soname,\$(notdir \$@)" + SHLIB_SUFFIX=".so" + SHLIB_LD="${CC} -shared" +- LDFLAGS="-Wl,--export-dynamic" ++ LDFLAGS="-pthread -lm -Wl,--export-dynamic" + LD_SEARCH_FLAGS='-Wl,-rpath-link,${LIB_RUNTIME_DIR} -Wl,-rpath,${INST_DIR}/lib' + LD_LIBRARY_PATH_VAR="LD_LIBRARY_PATH" + ;; diff --git a/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb new file mode 100644 index 000000000000..76f469f32a99 --- /dev/null +++ b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'librttopo' +version = '1.1.0' + +homepage = 'https://git.osgeo.org/gitea/rttopo/librttopo' +description = """The RT Topology Library exposes an API to create and +manage standard (ISO 13249 aka SQL/MM) topologies using user-provided +data stores.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://git.osgeo.org/gitea/rttopo/librttopo/archive'] +sources = [SOURCE_TAR_GZ] +checksums = ['2e2fcabb48193a712a6c76ac9a9be2a53f82e32f91a2bc834d9f1b4fa9cd879f'] + +builddependencies = [ + ('Autotools', '20210726'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GEOS', '3.9.1'), +] + +preconfigopts = './autogen.sh && ' + +sanity_check_paths = { + 'files': ['include/librttopo.h', 'lib/librttopo.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb b/easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..b908b0db7f96 --- /dev/null +++ b/easybuild/easyconfigs/l/libspatialite/libspatialite-5.0.1-GCC-11.2.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'libspatialite' +version = '5.0.1' + +homepage = "https://www.gaia-gis.it/fossil/libspatialite/home" +description = """SpatiaLite is an open source library intended to extend the SQLite core to support + fully fledged Spatial SQL capabilities.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.gaia-gis.it/gaia-sins/libspatialite-sources/'] +sources = [SOURCE_TAR_GZ] +checksums = ['eecbc94311c78012d059ebc0fae86ea5ef6eecb13303e6e82b3753c1b3409e98'] + +builddependencies = [ + ('CMake', '3.21.1'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('minizip', '1.1'), + ('FreeXL', '1.0.6'), + ('GEOS', '3.9.1'), + ('SQLite', '3.36'), + ('PROJ', '8.1.0'), + ('libxml2', '2.9.10'), + ('librttopo', '1.1.0'), +] + +configopts = '--disable-geosadvanced' + +sanity_check_paths = { + 'files': ['include/spatialite.h', 'lib/libspatialite.a', 'lib/libspatialite.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..2ccef97d5ceb --- /dev/null +++ b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +easyblock = 'ConfigureMake' + +name = 'minizip' +version = '1.1' +_zlib_version = '1.2.11' + +homepage = 'https://www.winimage.com/zLibDll/minizip.html' +description = "Mini zip and unzip based on zlib" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +# This exists in the contrib section of zlib and since it depends on +# zlib the sources will already have been downloaded +sources = [ + {'filename': 'zlib-%s.tar.gz' % _zlib_version, 'alt_location': 'zlib'}, +] +checksums = ['c3e5e9fdd5004dcb542feda5ee4f0ff0744628baf8ed2dd5d66f8ca1197cb1a1'] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), +] + +dependencies = [ + ('zlib', _zlib_version), +] + +start_dir = 'contrib/minizip' + +preconfigopts = 'autoreconf -i && ' + +sanity_check_paths = { + 'files': ['include/minizip/unzip.h', 'lib/libminizip.a', 'lib/libminizip.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' + diff --git a/easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..4261cd91c3aa --- /dev/null +++ b/easybuild/easyconfigs/q/QCA/QCA-2.3.5-GCCcore-11.2.0.eb @@ -0,0 +1,39 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QCA' +version = '2.3.5' + +homepage = 'https://userbase.kde.org/QCA' +description = """Taking a hint from the similarly-named Java Cryptography Architecture, + QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes + and conventions. QCA separates the API from the implementation, using plugins known as + Providers. The advantage of this model is to allow applications to avoid linking to or + explicitly depending on any particular cryptographic library. This allows one to easily + change or upgrade crypto implementations without even needing to recompile the + application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['http://download.kde.org/stable/qca/%(version)s/'] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['91f7d916ab3692bf5991f0a553bf8153161bfdda14bd005d480a2b4e384362e8'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1') +] +dependencies = [ + ('Qt5', '5.15.2') +] + +configopts = "-DQT5_BUILD=true" + +sanity_check_paths = { + 'files': ['bin/qcatool-qt5', 'lib/libqca-qt5.%s' % SHLIB_EXT, 'lib/pkgconfig/qca2-qt5.pc'], + 'dirs': ['include/Qca-qt5', 'lib/cmake/Qca-qt5', 'share/man'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb new file mode 100644 index 000000000000..eaac6f93058b --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb @@ -0,0 +1,75 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QGIS' +version = '3.28.1' + +homepage = 'http://www.qgis.org/' +description = "QGIS is a user friendly Open Source Geographic Information System (GIS)" + +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True, 'cstd': 'gnu++11'} + +source_urls = ['http://qgis.org/downloads/'] +sources = [SOURCELOWER_TAR_BZ2] +patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] +checksums = [ + {'qgis-3.28.1.tar.bz2': '09015bb68c45556ffe9d480272d24048e6276a6bf1c010fd77beae64329ff674'}, + {'QGIS-3.28.1_fix-SIP-macro.patch': '5da6bcd380e46969efa7718d8aec79a2548616c278853f29ed07d745fd5b043f'}, +] + +builddependencies = [ + ('CMake', '3.22.1'), + ('flex', '2.6.4'), + ('Bison', '3.7.6'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('Qt5', '5.15.2'), + ('Qt5Webkit', '5.212.0-alpha4'), + ('PyQt5', '5.15.4'), + ('PROJ', '8.1.0'), + ('GEOS', '3.9.1'), + ('SQLite', '3.36'), + ('libspatialite', '5.0.1'), + ('libspatialindex', '1.9.3'), + ('GDAL', '3.3.2'), + ('Qwt', '6.2.0'), + ('expat', '2.4.1'), + ('QCA', '2.3.5'), + # QScintilla must be listed after PyQt5 due to Python bindings 'overriding' those of PyQt5 + ('QScintilla', '2.11.6'), + ('GSL', '2.7'), + ('libzip', '1.7.3'), + ('QtKeychain', '0.13.2'), + ('ICU', '69.1'), + ('PostgreSQL', '13.4'), + ('GRASS', '8.2.0'), + ('protobuf', '3.17.3'), + ('exiv2', '0.27.5'), +] + +# specify locations that CMake can't figure out correctly +_copts = [ + "-DCMAKE_PREFIX_PATH=$EBROOTQT", + "-DQSCINTILLA_LIBRARY=$EBROOTQSCINTILLA/lib/libqscintilla2_qt5.%s" % SHLIB_EXT, + "-DQt5WebKit_DIR=$EBROOTQT5WEBKIT/lib64/cmake/Qt5WebKit", + "-DQt5WebKitWidgets_DIR=$EBROOTQT5WEBKIT/lib64/cmake/Qt5WebKitWidgets", + "-DPYQT5_SIP_DIR=$EBROOTPYQT5/share/sip", + "-DQSCI_SIP_DIR=$EBROOTQSCINTILLA/share/sip/PyQt5", + "-DGRASS_PREFIX8=$EBROOTGRASS/grass8", +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': ['bin/qgis', 'bin/qgis_bench', 'lib/libqgis_analysis.%s' % SHLIB_EXT, + 'lib/libqgis_app.%s' % SHLIB_EXT, 'lib/libqgis_core.%s' % SHLIB_EXT, 'lib/libqgis_gui.%s' % SHLIB_EXT, + 'lib/libqgis_native.%s' % SHLIB_EXT, 'lib/libqgispython.%s' % SHLIB_EXT], + 'dirs': ['include/qgis', 'man', 'share/qgis'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch new file mode 100644 index 000000000000..bae12be4ff32 --- /dev/null +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch @@ -0,0 +1,21 @@ +diff -ru qgis-3.28.1.orig/cmake/SIPMacros.cmake qgis-3.28.1/cmake/SIPMacros.cmake +--- qgis-3.28.1.orig/cmake/SIPMacros.cmake 2022-11-18 13:10:21.000000000 +0100 ++++ qgis-3.28.1/cmake/SIPMacros.cmake 2022-12-09 08:14:33.475615182 +0100 +@@ -101,7 +101,7 @@ + ENDIF( ${CONCAT_NUM} LESS ${SIP_CONCAT_PARTS} ) + ENDFOREACH(CONCAT_NUM RANGE 0 ${SIP_CONCAT_PARTS} ) + +- SET(SIPCMD ${SIP_BUILD_EXECUTABLE} --no-protected-is-public --pep484-pyi --no-make --concatenate=${SIP_CONCAT_PARTS} --qmake=${QMAKE_EXECUTABLE} --include-dir=${CMAKE_CURRENT_BINARY_DIR} --include-dir=${PYQT5_SIP_DIR} ${SIP_BUILD_EXTRA_OPTIONS}) ++ SET(SIPCMD ${SIP_BUILD_EXECUTABLE} --no-protected-is-public --pep484-pyi --no-make --concatenate=${SIP_CONCAT_PARTS} --qmake=${QMAKE_EXECUTABLE} --include-dir=${CMAKE_CURRENT_BINARY_DIR} --include-dir=${PYQT5_SIP_DIR} --include-dir=$ENV{EBROOTPYQT5}/share/sip --include-dir=$ENV{EBROOTQSCINTILLA}/share/sip/PyQt5 ${SIP_BUILD_EXTRA_OPTIONS}) + + ADD_CUSTOM_COMMAND( + OUTPUT ${_sip_output_files} +@@ -140,7 +140,7 @@ + ENDIF( ${CONCAT_NUM} LESS ${SIP_CONCAT_PARTS} ) + ENDFOREACH(CONCAT_NUM RANGE 0 ${SIP_CONCAT_PARTS} ) + +- SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} -I ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} ${_configured_module_sip}) ++ SET(SIPCMD ${SIP_BINARY_PATH} ${_sip_tags} -w -e ${_sip_x} ${SIP_EXTRA_OPTIONS} -j ${SIP_CONCAT_PARTS} -c ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} -I ${CMAKE_CURRENT_BINARY_DIR}/${_module_path} ${_sip_includes} --include-dir=$ENV{EBROOTPYQT5}/share/sip --include-dir=$ENV{EBROOTQSCINTILLA}/share/sip/PyQt5 ${_configured_module_sip}) + ADD_CUSTOM_COMMAND( + OUTPUT ${_sip_output_files} + COMMAND ${CMAKE_COMMAND} -E echo ${message} diff --git a/easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..65d4b96bf104 --- /dev/null +++ b/easybuild/easyconfigs/q/QScintilla/QScintilla-2.11.6-GCCcore-11.2.0.eb @@ -0,0 +1,33 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +name = 'QScintilla' +version = '2.11.6' + +homepage = 'https://www.riverbankcomputing.com/software/qscintilla' +description = "QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://www.riverbankcomputing.com/static/Downloads/QScintilla/%(version)s/'] +sources = [SOURCE_TAR_GZ] +patches = ['QScintilla-2.11.2_fix-link-python-bindings.patch'] +checksums = [ + {'QScintilla-2.11.6.tar.gz': 'e7346057db47d2fb384467fafccfcb13aa0741373c5d593bc72b55b2f0dd20a7'}, + {'QScintilla-2.11.2_fix-link-python-bindings.patch': + '6296efa69ce9448e43dda80573cb0a70fee72462157d3d6fc194fe61fd477803'}, +] + +builddependencies = [ + ('binutils', '2.37'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('PyQt5', '5.15.4'), +] + +prebuildopts = 'export CPATH=$EBROOTQT5/include/QtWidgets:$EBROOTQT5/include/QtPrintSupport:$CPATH && ' + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..9c4fab966b4a --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4-GCCcore-11.2.0.eb @@ -0,0 +1,71 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeNinja' + +name = 'Qt5Webkit' +# Qt5 > 5.9 required at least version 5.212.0 +# At the time of writing the latest version was 5.212.0-alpha3 +version = '5.212.0-alpha4' + +homepage = 'https://github.com/qt/qtwebkit' +description = "Qt Port of WebKit. WebKit is an open source web browser engine." +docurls = ['https://github.com/qt/qtwebkit/blob/dev/README'] + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/qtwebkit/qtwebkit/releases/download/qtwebkit-%(version)s/'] +sources = ['qtwebkit-%(version)s.tar.xz'] +patches = [ + '%(name)s-%(version)s_bison3.7.patch', + '%(name)s-%(version)s_fix_python_path.patch', + '%(name)s-%(version)s_fix_deprecated_encoding_in_json.load.patch', + '%(name)s-%(version)s_use_CXX_true_instead_of_TRUE_define.patch', + '%(name)s-%(version)s_dont_use_multiarch_lib_dir.patch', +] +checksums = [ + {'qtwebkit-5.212.0-alpha4.tar.xz': '9ca126da9273664dd23a3ccd0c9bebceb7bb534bddd743db31caf6a5a6d4a9e6'}, + {'Qt5Webkit-5.212.0-alpha4_bison3.7.patch': '34f37b53ee0bc31c63ce85ebd1ae95543a8ba28483e387b20efd50574bd813be'}, + {'Qt5Webkit-5.212.0-alpha4_fix_python_path.patch': + '126aed68cf0e22f595d3a8ae87938ba9e6a0727b53e38a92412fbf816a1687b2'}, + {'Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch': + 'e6ffe068a41af8d8aade58eeaa8352b87b731f29fc463e71bb1dc497301956c8'}, + {'Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch': + 'b952923cfe35667c69e7540d5c449d5e65301a4c2f43cdea8b33f190ab6b0403'}, + {'Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch': + '4974a348731ce80f73fbfbcce2351bddfb87a54affc7ae6dd52559a4ad93e8e8'}, +] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), + ('pkgconf', '1.8.0'), + ('Bison', '3.7.6'), + ('flex', '2.6.4'), + ('gperf', '3.1'), + ('Ninja', '1.10.2'), + ('Python', '3.9.6'), + ('Ruby', '3.0.1'), + ('Perl', '5.34.0'), +] + +dependencies = [ + ('Qt5', '5.15.2'), + ('zlib', '1.2.11'), + ('SQLite', '3.36'), + ('ICU', '69.1'), + ('libxslt', '1.1.34'), + ('libjpeg-turbo', '2.0.6'), +] + +configopts = "-DPORT=Qt -DUSE_LIBHYPHEN=OFF -DUSE_GSTREAMER=OFF " + +sanity_check_paths = { + 'files': [ + 'lib/libQt5WebKit.%s' % SHLIB_EXT, + 'lib/libQt5WebKitWidgets.%s' % SHLIB_EXT, + ], + 'dirs': ['include/QtWebKit', 'include/QtWebKitWidgets'], +} + +moduleclass = 'devel' diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch new file mode 100644 index 000000000000..6ce4a9830dda --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_dont_use_multiarch_lib_dir.patch @@ -0,0 +1,26 @@ +Don't use multiarch lib dir + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/cmake/KDEInstallDirs.cmake qtwebkit-5.212.0-alpha4/Source/cmake/KDEInstallDirs.cmake +--- qtwebkit-5.212.0-alpha4.orig/Source/cmake/KDEInstallDirs.cmake 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/cmake/KDEInstallDirs.cmake 2022-12-08 11:04:09.788027403 +0100 +@@ -210,11 +210,6 @@ + # See http://wiki.debian.org/Multiarch + if((CMAKE_SYSTEM_NAME MATCHES "Linux|kFreeBSD" OR CMAKE_SYSTEM_NAME STREQUAL "GNU") + AND NOT CMAKE_CROSSCOMPILING) +- if (EXISTS "/etc/debian_version") # is this a debian system ? +- if(CMAKE_LIBRARY_ARCHITECTURE) +- set(_LIBDIR_DEFAULT "lib/${CMAKE_LIBRARY_ARCHITECTURE}") +- endif() +- else() # not debian, rely on CMAKE_SIZEOF_VOID_P: + if(NOT DEFINED CMAKE_SIZEOF_VOID_P) + message(AUTHOR_WARNING + "Unable to determine default LIB_INSTALL_LIBDIR directory because no target architecture is known. " +@@ -224,7 +219,6 @@ + set(_LIBDIR_DEFAULT "lib64") + endif() + endif() +- endif() + endif() + + set(_gnu_install_dirs_vars diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch new file mode 100644 index 000000000000..d456d73cb1be --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_deprecated_encoding_in_json.load.patch @@ -0,0 +1,15 @@ +"enconding" kw has been deprecated in json.load since Python 3.1 and was removed completely in 3.9 + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files 2022-12-08 08:20:29.980590518 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files 2022-12-08 08:21:00.908330630 +0100 +@@ -163,7 +163,7 @@ + initBytecodesFile = openOrExit(initASMFileName, "w") + + try: +- bytecodeSections = json.load(bytecodeFile, encoding = "utf-8") ++ bytecodeSections = json.load(bytecodeFile) + except: + print("Unexpected error parsing {0}: {1}".format(bytecodeJSONFile, sys.exc_info())) + diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch new file mode 100644 index 000000000000..02a483f2f519 --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_fix_python_path.patch @@ -0,0 +1,66 @@ +Don't use hardcoded path to python + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/generate-bytecode-files 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/generate-bytecode-files 2022-12-08 07:56:12.528708137 +0100 +@@ -1,4 +1,4 @@ +-#! /usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2014 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/cssmin.py qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/cssmin.py +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/cssmin.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/cssmin.py 2022-12-08 07:56:12.528708137 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2013 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/generate-combined-inspector-json.py 2022-12-08 07:56:12.532708103 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2013 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/UpdateContents.py qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/UpdateContents.py +--- qtwebkit-5.212.0-alpha4.orig/Source/JavaScriptCore/Scripts/UpdateContents.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/JavaScriptCore/Scripts/UpdateContents.py 2022-12-08 07:56:12.532708103 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2015 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py qtwebkit-5.212.0-alpha4/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py +--- qtwebkit-5.212.0-alpha4.orig/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/ThirdParty/ANGLE/src/libANGLE/renderer/generate_new_renderer.py 2022-12-08 07:56:12.524708171 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + # + # Copyright (c) 2015 The ANGLE Project Authors. All rights reserved. + # Use of this source code is governed by a BSD-style license that can be +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/AVFoundationSupport.py qtwebkit-5.212.0-alpha4/Source/WebCore/AVFoundationSupport.py +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/AVFoundationSupport.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/AVFoundationSupport.py 2022-12-08 07:56:12.524708171 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2015 Apple Inc. All rights reserved. + # +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebInspectorUI/Scripts/cssmin.py qtwebkit-5.212.0-alpha4/Source/WebInspectorUI/Scripts/cssmin.py +--- qtwebkit-5.212.0-alpha4.orig/Source/WebInspectorUI/Scripts/cssmin.py 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebInspectorUI/Scripts/cssmin.py 2022-12-08 07:56:12.528708137 +0100 +@@ -1,4 +1,4 @@ +-#!/usr/bin/python ++#!/usr/bin/env python + + # Copyright (C) 2013 Apple Inc. All rights reserved. + # diff --git a/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch new file mode 100644 index 000000000000..3068f9bfc4bc --- /dev/null +++ b/easybuild/easyconfigs/q/Qt5Webkit/Qt5Webkit-5.212.0-alpha4_use_CXX_true_instead_of_TRUE_define.patch @@ -0,0 +1,128 @@ +Use C++ "true" value instead of the TRUE define +It is not automatically defined in later ICU vwersions + +Åke Sandgren, 2022-12-08 +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProvider.h qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProvider.h +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProvider.h 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProvider.h 2022-12-08 08:45:36.252382941 +0100 +@@ -80,12 +80,12 @@ + // Ensure chunk offset is well formed if computed offset exceeds int32_t range. + ASSERT(offset < std::numeric_limits::max()); + text->chunkOffset = offset < std::numeric_limits::max() ? static_cast(offset) : 0; +- isAccessible = TRUE; ++ isAccessible = true; + return true; + } + if (nativeIndex >= nativeLength && text->chunkNativeLimit == nativeLength) { + text->chunkOffset = text->chunkLength; +- isAccessible = FALSE; ++ isAccessible = false; + return true; + } + } else { +@@ -94,12 +94,12 @@ + // Ensure chunk offset is well formed if computed offset exceeds int32_t range. + ASSERT(offset < std::numeric_limits::max()); + text->chunkOffset = offset < std::numeric_limits::max() ? static_cast(offset) : 0; +- isAccessible = TRUE; ++ isAccessible = true; + return true; + } + if (nativeIndex <= 0 && !text->chunkNativeStart) { + text->chunkOffset = 0; +- isAccessible = FALSE; ++ isAccessible = false; + return true; + } + } +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderLatin1.cpp 2022-12-08 08:46:20.924008445 +0100 +@@ -100,23 +100,23 @@ + if (index < uText->chunkNativeLimit && index >= uText->chunkNativeStart) { + // Already inside the buffer. Set the new offset. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return TRUE; ++ return true; + } + if (index >= length && uText->chunkNativeLimit == length) { + // Off the end of the buffer, but we can't get it. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return FALSE; ++ return false; + } + } else { + if (index <= uText->chunkNativeLimit && index > uText->chunkNativeStart) { + // Already inside the buffer. Set the new offset. + uText->chunkOffset = static_cast(index - uText->chunkNativeStart); +- return TRUE; ++ return true; + } + if (!index && !uText->chunkNativeStart) { + // Already at the beginning; can't go any farther. + uText->chunkOffset = 0; +- return FALSE; ++ return false; + } + } + +@@ -144,7 +144,7 @@ + + uText->nativeIndexingLimit = uText->chunkLength; + +- return TRUE; ++ return true; + } + + static int32_t uTextLatin1Extract(UText* uText, int64_t start, int64_t limit, UChar* dest, int32_t destCapacity, UErrorCode* status) +@@ -336,7 +336,7 @@ + static UBool uTextLatin1ContextAwareAccess(UText* text, int64_t nativeIndex, UBool forward) + { + if (!text->context) +- return FALSE; ++ return false; + int64_t nativeLength = uTextLatin1ContextAwareNativeLength(text); + UBool isAccessible; + if (uTextAccessInChunkOrOutOfRange(text, nativeIndex, nativeLength, forward, isAccessible)) +@@ -356,7 +356,7 @@ + ASSERT(newContext == UTextProviderContext::PriorContext); + textLatin1ContextAwareSwitchToPriorContext(text, nativeIndex, nativeLength, forward); + } +- return TRUE; ++ return true; + } + + static int32_t uTextLatin1ContextAwareExtract(UText*, int64_t, int64_t, UChar*, int32_t, UErrorCode* errorCode) +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/icu/UTextProviderUTF16.cpp 2022-12-08 08:46:59.755682780 +0100 +@@ -125,7 +125,7 @@ + static UBool uTextUTF16ContextAwareAccess(UText* text, int64_t nativeIndex, UBool forward) + { + if (!text->context) +- return FALSE; ++ return false; + int64_t nativeLength = uTextUTF16ContextAwareNativeLength(text); + UBool isAccessible; + if (uTextAccessInChunkOrOutOfRange(text, nativeIndex, nativeLength, forward, isAccessible)) +@@ -145,7 +145,7 @@ + ASSERT(newContext == UTextProviderContext::PriorContext); + textUTF16ContextAwareSwitchToPriorContext(text, nativeIndex, nativeLength, forward); + } +- return TRUE; ++ return true; + } + + static int32_t uTextUTF16ContextAwareExtract(UText*, int64_t, int64_t, UChar*, int32_t, UErrorCode* errorCode) +diff -ru qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/TextCodecICU.cpp qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/TextCodecICU.cpp +--- qtwebkit-5.212.0-alpha4.orig/Source/WebCore/platform/text/TextCodecICU.cpp 2020-03-04 18:16:37.000000000 +0100 ++++ qtwebkit-5.212.0-alpha4/Source/WebCore/platform/text/TextCodecICU.cpp 2022-12-08 08:44:48.972780065 +0100 +@@ -308,7 +308,7 @@ + m_converterICU = ucnv_open(m_canonicalConverterName, &err); + ASSERT(U_SUCCESS(err)); + if (m_converterICU) +- ucnv_setFallback(m_converterICU, TRUE); ++ ucnv_setFallback(m_converterICU, true); + } + + int TextCodecICU::decodeToBuffer(UChar* target, UChar* targetLimit, const char*& source, const char* sourceLimit, int32_t* offsets, bool flush, UErrorCode& err) diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..0405b52686e5 --- /dev/null +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb @@ -0,0 +1,36 @@ +# Author: Pavel Grochal (INUITS) +# License: GPLv2 + +easyblock = 'CMakeMake' + +name = 'QtKeychain' +version = '0.13.2' + +homepage = 'https://github.com/frankosterfeld/qtkeychain' +description = "Platform-independent Qt API for storing passwords securely." + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://github.com/frankosterfeld/qtkeychain/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['20beeb32de7c4eb0af9039b21e18370faf847ac8697ab3045906076afbc4caa5'] + +builddependencies = [ + ('binutils', '2.37'), + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Qt5', '5.15.2'), +] + +# Need to turn off build tranlsations, it tries to put that to qt5 dir. +# The other option would be to set translations directory +configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ -DBUILD_TRANSLATIONS=OFF" + +sanity_check_paths = { + 'files': ['lib/libqt5keychain.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..2238ccf4c84a --- /dev/null +++ b/easybuild/easyconfigs/q/Qwt/Qwt-6.2.0-GCCcore-11.2.0.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': '11.2.0'} + +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', '2.37'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Qt5', '5.15.2'), +] + +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' diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb new file mode 100644 index 000000000000..274ca8152c40 --- /dev/null +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb @@ -0,0 +1,48 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +name = 'wxPython' +version = '4.2.0' + +homepage = "https://www.wxpython.org/" +description = """Wraps the wxWidgets C++ toolkit and provides access to the user interface portions of the wxWidgets +API, enabling Python applications to have a native GUI on Windows, Macs or Unix systems, with a native look and feel +and requiring very little (if any) platform specific code.""" + + +toolchain = {'name': 'foss', 'version': '2021b'} +sources = ['%(name)s-%(version)s.tar.gz'] +patches = [ + 'wxPython-4.1.1_fix_install_path.patch', + 'wxPython-4.1.1_use_bang_env_python.patch', +] +checksums = [ + {'wxPython-4.2.0.tar.gz': '663cebc4509d7e5d113518865fe274f77f95434c5d57bc386ed58d65ceed86c7'}, + {'wxPython-4.1.1_fix_install_path.patch': 'f13743877deddbf525bbb3f81c8f7a6b0c2dbf1333595926f653f696999e31ce'}, + {'wxPython-4.1.1_use_bang_env_python.patch': 'c355c60a8cce3018fc0c30ffc78623efd2481e9baf33673e22a57863e1a3ac87'}, +] + +builddependencies = [ + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('Pillow', '8.3.2'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.1'), + ('GTK3', '3.24.31'), + ('GLib', '2.69.1'), + ('GConf', '3.2.6'), + ('GST-plugins-base', '1.18.5'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('LibSoup', '3.0.7'), + ('wxWidgets', '3.2.0'), + ('WebKitGTK+', '2.37.1'), + ('attrdict3', '2.0.2'), +] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb new file mode 100644 index 000000000000..631d9b165c33 --- /dev/null +++ b/easybuild/easyconfigs/w/wxWidgets/wxWidgets-3.2.0-GCC-11.2.0.eb @@ -0,0 +1,71 @@ +easyblock = 'ConfigureMake' + +name = 'wxWidgets' +version = '3.2.0' + +homepage = 'https://www.wxwidgets.org' +description = """wxWidgets is a C++ library that lets developers create +applications for Windows, Mac OS X, Linux and other platforms with a +single code base. It has popular language bindings for Python, Perl, +Ruby and many other languages, and unlike other cross-platform toolkits, +wxWidgets gives applications a truly native look and feel because it +uses the platform's native API rather than emulating the GUI.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +github_account = 'wxWidgets' +source_urls = [GITHUB_RELEASE] +sources = [SOURCE_TAR_BZ2] +checksums = ['356e9b55f1ae3d58ae1fed61478e9b754d46b820913e3bfbc971c50377c1903a'] + +builddependencies = [ + ('gettext', '0.21'), + ('pkgconf', '1.8.0'), + ('Python', '3.9.6'), +] + +dependencies = [ + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('libjpeg-turbo', '2.0.6'), + ('XZ', '5.2.5'), + ('jbigkit', '2.1'), + ('LibTIFF', '4.3.0'), + ('expat', '2.4.1'), + ('GTK3', '3.24.31'), + ('X11', '20210802'), + ('Mesa', '21.1.7'), + ('libGLU', '9.0.2'), + ('SDL2', '2.0.20'), + ('cairo', '1.16.0'), + ('GST-plugins-base', '1.18.5'), + ('GLib', '2.69.1'), +] + +local_cpath_ext = '$EBROOTGTKPLUS/include/gtk-3.0:$EBROOTGLIB/include/glib-2.0:$EBROOTGLIB/lib/glib-2.0/include' + +preconfigopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +configopts = '--enable-intl --enable-ipv6 ' +# Options required by wxPython +configopts += '--with-gtk=3 --with-gtk-prefix=$EBROOTGTKPLUS ' +# Note: the configure step might claim to find OpenGL headers in +# /usr/include, but it will still use the ones from the Mesa dependency above +configopts += '--with-opengl ' +configopts += '--enable-unicode --enable-sound --enable-graphics_ctx ' +configopts += '--enable-mediactrl --enable-display --enable-geometry ' +configopts += '--enable-debug_flag --enable-optimise --disable-debugreport ' +configopts += '--enable-autoidman --with-sdl ' +configopts += '--disable-webview --disable-webviewwebkit ' +configopts += '--disable-tests ' + + +prebuildopts = 'CPATH=$CPATH:%s ' % local_cpath_ext + +sanity_check_paths = { + 'files': ['bin/wx-config', 'bin/wxrc'], + 'dirs': ['include/wx-%(version_major_minor)s/wx', 'lib', 'share'], +} + +moduleclass = 'vis' From 45254aa1a8236616903201636177488c101f6093 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 15:31:52 +0100 Subject: [PATCH 686/939] Pocl has *NO* https website. Only http --- easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb index d9dbdf2fa1db..06688ffbce21 100644 --- a/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/pocl/pocl-1.8-GCC-11.3.0.eb @@ -3,7 +3,7 @@ easyblock = 'CMakeNinja' name = 'pocl' version = '1.8' -homepage = 'https://portablecl.org' +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'} From d42d64a8ee59d969678f94912d789ba116f81f52 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 15:48:51 +0100 Subject: [PATCH 687/939] wxPython: clarify that wxPython 4.2 requires wxWidgets >= 3.2 --- easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb index 274ca8152c40..6a911f23dd82 100644 --- a/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb +++ b/easybuild/easyconfigs/w/wxPython/wxPython-4.2.0-foss-2021b.eb @@ -40,7 +40,7 @@ dependencies = [ ('Mesa', '21.1.7'), ('libGLU', '9.0.2'), ('LibSoup', '3.0.7'), - ('wxWidgets', '3.2.0'), + ('wxWidgets', '3.2.0'), # wxPython 4.2 depends on wxWidgets >=3.2 ('WebKitGTK+', '2.37.1'), ('attrdict3', '2.0.2'), ] From 3162d2e92ad13a33b2e3bea2784f2b4bdd6c0b0a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 16:10:47 +0100 Subject: [PATCH 688/939] QGIS: Add missing author info for patch and update checksums. --- easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb | 2 +- .../easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch | 6 ++++++ 2 files changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb index eaac6f93058b..b17b0f8cc3d4 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1-foss-2021b.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_BZ2] patches = ['QGIS-%(version)s_fix-SIP-macro.patch'] checksums = [ {'qgis-3.28.1.tar.bz2': '09015bb68c45556ffe9d480272d24048e6276a6bf1c010fd77beae64329ff674'}, - {'QGIS-3.28.1_fix-SIP-macro.patch': '5da6bcd380e46969efa7718d8aec79a2548616c278853f29ed07d745fd5b043f'}, + {'QGIS-3.28.1_fix-SIP-macro.patch': '141b7730666b3e703b9a6648d1e5a2686f8819f6a4938c6d60aa8c8d65820bd3'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch index bae12be4ff32..0b30feff7071 100644 --- a/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch +++ b/easybuild/easyconfigs/q/QGIS/QGIS-3.28.1_fix-SIP-macro.patch @@ -1,3 +1,9 @@ +include location of PyQt .sip files in SIPCMD macro + +author: Kenneth Hoste (HPC-UGent) +author: Pavel Grochal (INUITS) + +Updated to QGIS/3.28.1: Åke Sandgren, 2022-12-09 diff -ru qgis-3.28.1.orig/cmake/SIPMacros.cmake qgis-3.28.1/cmake/SIPMacros.cmake --- qgis-3.28.1.orig/cmake/SIPMacros.cmake 2022-11-18 13:10:21.000000000 +0100 +++ qgis-3.28.1/cmake/SIPMacros.cmake 2022-12-09 08:14:33.475615182 +0100 From 08716e60f488628f83f81208ac2d0f5fb3e0025d Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 12 Dec 2022 16:16:21 +0100 Subject: [PATCH 689/939] update comment about ecmwflibs --- .../easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb index 7d9b35710021..ca9f62f7e164 100644 --- a/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb +++ b/easybuild/easyconfigs/c/CliMetLab/CliMetLab-0.12.6-foss-2022a.eb @@ -31,7 +31,7 @@ use_pip = True sanity_pip_check = True # stick to termcolor 1.x, to avoid hatchling required dependency -# remove ecmwflibs requirement (provides ecCodes and Magics) +# remove ecmwflibs requirement as it just bundles ecCodes and Magics and there are no direct imports to it exts_list = [ ('eccodes', '1.5.0', { 'checksums': ['e70c8f159140c343c215fd608ddf533be652ff05ad2ff17243c7b66cf92127fa'], From 51816822c4f75604886aa23ad4556f4a03120fac Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 16:17:46 +0100 Subject: [PATCH 690/939] QtKeychain: Add osdependency on libsecret --- .../q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb index 0405b52686e5..0a91d9e6e604 100644 --- a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb @@ -15,6 +15,8 @@ source_urls = ['https://github.com/frankosterfeld/qtkeychain/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['20beeb32de7c4eb0af9039b21e18370faf847ac8697ab3045906076afbc4caa5'] +osdependencies = [('libsecret-1-dev', 'libsecret-devel')] + builddependencies = [ ('binutils', '2.37'), ('CMake', '3.22.1'), From cdba8bf1a76b4f14d2fcfe6d4b951386b83486ee Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 15:25:06 +0000 Subject: [PATCH 691/939] Trimesh is a shapely-like library used by some of our users --- .../t/trimesh/trimesh-3.17.1-foss-2022a.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb new file mode 100644 index 000000000000..10fffaef98fa --- /dev/null +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'PythonPackage' + +name = 'trimesh' +version = '3.17.1' + +homepage = 'https://trimsh.org/' +description = """Trimesh is a Python (2.7- 3.3+) library for loading and using triangular meshes with an emphasis on +watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy +manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" + + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [PYPI_SOURCE] +sources = [SOURCE_TAR_GZ] +checksums = ['025bb2fa3a2e87bdd6873f11db45a7ca19216f2f8b6aed29140fca57e32c298e'] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + + + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy required +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + + +moduleclass = 'lib' From 8dacf50912d39a13f043b0c51f2694ec90f4dd89 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 12 Dec 2022 16:35:09 +0100 Subject: [PATCH 692/939] Delete empty last line in librttopo and minizip. --- easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb | 1 - easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb | 1 - 2 files changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb index 76f469f32a99..2f125cbbd62a 100644 --- a/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/l/librttopo/librttopo-1.1.0-GCC-11.2.0.eb @@ -32,4 +32,3 @@ sanity_check_paths = { } moduleclass = 'lib' - diff --git a/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb index 2ccef97d5ceb..a5989e656474 100644 --- a/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/m/minizip/minizip-1.1-GCCcore-11.2.0.eb @@ -36,4 +36,3 @@ sanity_check_paths = { } moduleclass = 'lib' - From 34b2548c463543d5238d7f724ec6e764af7569fb Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:56:17 +0100 Subject: [PATCH 693/939] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb someone prefers this way, I guess Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 539118743c8a..84feba1ab7f7 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -1,6 +1,7 @@ +easyblock = 'CMakeMake' + name = 'g2clib' version = '1.7.0' -easyblock = 'CMakeMake' homepage = 'https://github.com/NOAA-EMC/NCEPLIBS-g2c' description = """Library contains GRIB2 encoder/decoder ('C' version).""" From 5ee143ebfd4e0afc9cbe36cb99eb6b1886064128 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:56:56 +0100 Subject: [PATCH 694/939] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb Life is too short to argue over indentation styles. Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- .../easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 84feba1ab7f7..607127c9fb6b 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -13,9 +13,10 @@ source_urls = ['https://github.com/NOAA-EMC/NCEPLIBS-g2c/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] checksums = ['73afba9da382fed73ed8692d77fa037bb313280879cd4012a5e5697dccf55175'] -builddependencies = [('binutils', '2.38'), - ('CMake', '3.23.1'), - ] +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] dependencies = [ ('JasPer', '2.0.33'), From 07615e9fe1567fecd6d5c3a7a5dc5d75d297a9d7 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:57:38 +0100 Subject: [PATCH 695/939] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb no need for parallel limitation Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 607127c9fb6b..7b19daafbd1a 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -24,8 +24,6 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ] -parallel = 8 - sanity_check_paths = { 'files': ['lib/libg2c.so'], 'dirs': ['include', 'lib'], From 2b4a4205f168c72e109d65a4ab7c9c1f0ce6b9ae Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:58:00 +0100 Subject: [PATCH 696/939] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index 7b19daafbd1a..e0b095442e08 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ dependencies = [ ] sanity_check_paths = { - 'files': ['lib/libg2c.so'], + 'files': ['lib/libg2c.%s' % SHLIB_EXT], 'dirs': ['include', 'lib'], } From c86f6bcc0a6d6da93895e48ec5e2f6a541027a96 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 17:58:06 +0100 Subject: [PATCH 697/939] Update easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb Co-authored-by: Jasper <65227842+jfgrimm@users.noreply.github.com> --- easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb index e0b095442e08..cc05f88f67a4 100644 --- a/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/g2clib/g2clib-1.7.0-GCCcore-11.3.0.eb @@ -26,7 +26,7 @@ dependencies = [ sanity_check_paths = { 'files': ['lib/libg2c.%s' % SHLIB_EXT], - 'dirs': ['include', 'lib'], + 'dirs': ['include'], } moduleclass = 'data' From 2807634baf4b7739b75e51c679ff65f1962bc1dd Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 12 Dec 2022 19:51:21 +0100 Subject: [PATCH 698/939] Fix URL --- .../easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb index 79fbfeebdd14..aea69135267c 100644 --- a/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeWriter/CubeWriter-4.8-GCCcore-11.3.0.eb @@ -28,7 +28,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} -source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(versions)s/dist'] +source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] sources = ['cubew-%(version)s.tar.gz'] checksums = ['73c7f9e9681ee45d71943b66c01cfe675b426e4816e751ed2e0b670563ca4cf3'] From 41d3f5074a76aabfb9ab0c9e39e940d8793d222e Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 20:31:53 +0100 Subject: [PATCH 699/939] Update easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb index 10fffaef98fa..fc52d8885bef 100644 --- a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb @@ -11,7 +11,6 @@ manipulation and analysis, in the style of the excellent Polygon object in the S toolchain = {'name': 'foss', 'version': '2022a'} -source_urls = [PYPI_SOURCE] sources = [SOURCE_TAR_GZ] checksums = ['025bb2fa3a2e87bdd6873f11db45a7ca19216f2f8b6aed29140fca57e32c298e'] From 7586a4d1a46c6547f2a1cab6e2e13b9dd2f02613 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Mon, 12 Dec 2022 20:32:36 +0100 Subject: [PATCH 700/939] remove spurious blank lines --- easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb | 4 ---- 1 file changed, 4 deletions(-) diff --git a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb index fc52d8885bef..ad68fc7a786f 100644 --- a/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb +++ b/easybuild/easyconfigs/t/trimesh/trimesh-3.17.1-foss-2022a.eb @@ -8,7 +8,6 @@ description = """Trimesh is a Python (2.7- 3.3+) library for loading and using t watertight meshes. The goal of the library is to provide a fully featured Trimesh object which allows for easy manipulation and analysis, in the style of the excellent Polygon object in the Shapely library.""" - toolchain = {'name': 'foss', 'version': '2022a'} sources = [SOURCE_TAR_GZ] @@ -18,8 +17,6 @@ use_pip = True download_dep_fail = True sanity_pip_check = True - - dependencies = [ ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), # numpy required @@ -30,5 +27,4 @@ sanity_check_paths = { 'dirs': ['lib/python%(pyshortver)s/site-packages'], } - moduleclass = 'lib' From 94786fc545ee4b852000aeb07a67b49584573dd0 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 09:30:30 +0100 Subject: [PATCH 701/939] add exception to test suite for wxPython 4.2.0 depending on wxWidgets 3.2.0 --- test/easyconfigs/easyconfigs.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 3160d1b9ad9a..b6c93819c945 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -592,6 +592,8 @@ def check_dep_vars(self, gen, dep, dep_vars): 'UCX': [('1.11.0;', ['UCX-CUDA-1.11.0-'])], # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], + # wxPython 4.2.0 depends on wxWidgets 3.2.0 + 'wxWidgets': [(r'3\.2\.0', ['wxPython-4.2.0'])], } if dep in alt_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From a06c1e0322d74b297661ab25aac034cc5d095d5b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 11:17:00 +0100 Subject: [PATCH 702/939] add exception to test suite for packages that depend on wxPython 4.2.0 depending on wxWidgets 3.2.0 --- 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 b6c93819c945..bbc89eacc653 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -593,7 +593,7 @@ def check_dep_vars(self, gen, dep, dep_vars): # WPS 3.9.1 requires WRF 3.9.1.1 'WRF': [(r'3\.9\.1\.1', [r'WPS-3\.9\.1'])], # wxPython 4.2.0 depends on wxWidgets 3.2.0 - 'wxWidgets': [(r'3\.2\.0', ['wxPython-4.2.0'])], + 'wxWidgets': [(r'3\.2\.0', [r'wxPython-4\.2\.0', r'GRASS-8\.2\.0', r'QGIS-3\.28\.1'])], } if dep in alt_dep_versions and len(dep_vars) > 1: for key in list(dep_vars): From 4ccb40e8c8079639fe46a83e932087b80e5d349f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 11:17:59 +0100 Subject: [PATCH 703/939] add exception to test suite for packages that have a chain dependency on glew-2.2.0-elg --- test/easyconfigs/easyconfigs.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index bbc89eacc653..63e9464d464d 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -497,7 +497,10 @@ def check_dep_vars(self, gen, dep, dep_vars): 'glew': [ ('2.2.0; versionsuffix: -egl', [r'libwpe-1\.13\.3-GCCcore-11\.2\.0', r'wpebackend-fdo-1\.13\.1-GCCcore-11\.2\.0', - r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0']), + r'WebKitGTK\+-2\.37\.1-GCC-11\.2\.0', + r'wxPython-4\.2\.0', + r'GRASS-8\.2\.0', + r'QGIS-3\.28\.1']), ], 'Geant4': [('11.0.1;', [r'GATE-9\.2-foss-2021b'])], # ncbi-vdb v2.x and v3.0.0 require HDF5 v1.10.x (HISAT2, SKESA, shovill depend on ncbi-vdb) From 2ee0d06b829844c15a1ee494b3c0f42619054e6d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 13 Dec 2022 11:31:45 +0100 Subject: [PATCH 704/939] QtKeyChain: Turn of use of libsecret. It should still use GNOME Keyring if running. --- .../q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb index 0a91d9e6e604..7cb7366cb236 100644 --- a/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/q/QtKeychain/QtKeychain-0.13.2-GCCcore-11.2.0.eb @@ -15,8 +15,6 @@ source_urls = ['https://github.com/frankosterfeld/qtkeychain/archive/'] sources = ['v%(version)s.tar.gz'] checksums = ['20beeb32de7c4eb0af9039b21e18370faf847ac8697ab3045906076afbc4caa5'] -osdependencies = [('libsecret-1-dev', 'libsecret-devel')] - builddependencies = [ ('binutils', '2.37'), ('CMake', '3.22.1'), @@ -28,7 +26,7 @@ dependencies = [ # Need to turn off build tranlsations, it tries to put that to qt5 dir. # The other option would be to set translations directory -configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ -DBUILD_TRANSLATIONS=OFF" +configopts = "-DCMAKE_INSTALL_LIBDIR=lib/ -DBUILD_TRANSLATIONS=OFF -DLIBSECRET_SUPPORT=OFF " sanity_check_paths = { 'files': ['lib/libqt5keychain.%s' % SHLIB_EXT], From 7d13d25d93b104f769ca1ed9129f9bb57052fdfd Mon Sep 17 00:00:00 2001 From: Jiri Furst Date: Tue, 13 Dec 2022 11:54:07 +0100 Subject: [PATCH 705/939] adding easyconfigs: KaHIP-3.14-gompi-2022a.eb --- .../k/KaHIP/KaHIP-3.14-gompi-2022a.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb diff --git a/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb new file mode 100644 index 000000000000..1445dd5e9251 --- /dev/null +++ b/easybuild/easyconfigs/k/KaHIP/KaHIP-3.14-gompi-2022a.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'KaHIP' +version = '3.14' + +homepage = 'https://kahip.github.io/' +description = """The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/KaHIP/KaHIP/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +checksums = ['9da04f3b0ea53b50eae670d6014ff54c0df2cb40f6679b2f6a96840c1217f242'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +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' From 449e356f75b301bfe9cb42afc6e51972233f8b78 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 13 Dec 2022 17:19:44 +0000 Subject: [PATCH 706/939] xarray removed and with Parcels from PR 16838 replaced, surplus Python extensions removed --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 12 +----------- 1 file changed, 1 insertion(+), 11 deletions(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index f057408344e3..8049e6561336 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -21,16 +21,13 @@ dependencies = [ ('scikit-learn', '1.1.2'), ('tqdm', '4.64.0'), ('zarr', '2.13.3'), - ('xarray', '2022.9.0'), + ('Parcels', '2.4.0'), ] use_pip = True sanity_pip_check = True exts_list = [ - ('parcels', '2.4.0', { - 'checksums': ['221ce49b6cb5bb4996aa3c817c0de7f022c952a4d8cb4160ca7df7dd940714b5'], - }), ('pykdtree', '1.3.6', { 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], }), @@ -41,19 +38,12 @@ exts_list = [ 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], 'modulename': 'progressbar', }), - ('cgen', '2020.1', { - 'checksums': ['4ec99d0c832d9f95f5e51dd18a629ad50df0b5464ce557ef42c6e0cd9478bfcf'], - }), - ('pymbolic', '2022.1', { - 'checksums': ['b52f451dd0b9803e03de3320af3b7ce5723070061c6d231c00216f6da4259012'], - }), ('pytools', '2022.1.12', { 'checksums': ['4d62875e9a2ab2a24e393a9a8b799492f1a721bffa840af3807bfd42871dd1f4'], }), ('python-utils', '3.4.5', { 'checksums': ['7e329c427a6d23036cfcc4501638afb31b2ddc8896f25393562833874b8c6e0a'], }), - (name, version, { 'sources': [{ 'filename': '%(name)s-%(version)s-commit.tar.gz', From af82218750da1b57c444c9c346ad88ea097ddd49 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 14 Dec 2022 10:55:05 +0100 Subject: [PATCH 707/939] remove dependencies in Parcels from lagrangian-filtering --- .../lagrangian-filtering-0.8.3-foss-2022a.eb | 27 +------------------ 1 file changed, 1 insertion(+), 26 deletions(-) diff --git a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb index 8049e6561336..986728f528fe 100644 --- a/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb +++ b/easybuild/easyconfigs/l/lagrangian-filtering/lagrangian-filtering-0.8.3-foss-2022a.eb @@ -18,9 +18,6 @@ dependencies = [ ('h5py', '3.7.0'), ('SciPy-bundle', '2022.05'), ('netcdf4-python', '1.6.1'), - ('scikit-learn', '1.1.2'), - ('tqdm', '4.64.0'), - ('zarr', '2.13.3'), ('Parcels', '2.4.0'), ] @@ -28,30 +25,13 @@ use_pip = True sanity_pip_check = True exts_list = [ - ('pykdtree', '1.3.6', { - 'checksums': ['780b693d0555b857d7aab31e35d4293bf4ebdb9dec7a45ba4bb23b4400f626dc'], - }), - ('sosfilt', '1.2.0', { - 'checksums': ['b3083fd2edf723a6163f00ddc36ec3ca20fbf6112cc68573dad9356544a9d734'], - }), - ('progressbar2', '4.2.0', { - 'checksums': ['1393922fcb64598944ad457569fbeb4b3ac189ef50b5adb9cef3284e87e394ce'], - 'modulename': 'progressbar', - }), - ('pytools', '2022.1.12', { - 'checksums': ['4d62875e9a2ab2a24e393a9a8b799492f1a721bffa840af3807bfd42871dd1f4'], - }), - ('python-utils', '3.4.5', { - 'checksums': ['7e329c427a6d23036cfcc4501638afb31b2ddc8896f25393562833874b8c6e0a'], - }), (name, version, { 'sources': [{ - 'filename': '%(name)s-%(version)s-commit.tar.gz', + 'filename': '%(name)s-%(version)s.tar.gz', 'git_config': { 'url': 'https://github.com/angus-g/', 'repo_name': name, 'tag': version, - 'recursive': True, 'keep_git_dir': True, }, }], @@ -60,9 +40,4 @@ exts_list = [ }), ] -sanity_check_paths = { - 'files': [], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - moduleclass = 'lib' From 1fc94700e80f2b860635c30dbef9a24faeaf9f23 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 14 Dec 2022 13:19:53 +0200 Subject: [PATCH 708/939] adding easyconfigs: jax-0.3.23-foss-2021b-CUDA-11.4.1.eb --- .../jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb | 125 ++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 000000000000..9bad44f1db6e --- /dev/null +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,125 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +# Updated by: Alex Domingo (Vrije Universiteit Brussel) +# Downgrade to foss/2021b: T. Hoffmann (EMBL) +easyblock = 'PythonBundle' + +name = 'jax' +version = '0.3.23' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://pypi.python.org/pypi/jax' +description = """Composable transformations of Python+NumPy programs: +differentiate, vectorize, JIT to GPU/TPU, and more""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6"] + +builddependencies = [ + ('Bazel', '3.7.2'), + ('pytest-xdist', '2.5.0'), + # git 2.x required to fetch repository 'io_bazel_rules_docker' + ('git', '2.33.1', '-nodocs'), + ('matplotlib', '3.4.3'), # required by some jax tests +] + +dependencies = [ + ('CUDA', '11.4.1', '', SYSTEM), + ('cuDNN', '8.2.2.26', versionsuffix, SYSTEM), + ('NCCL', '2.10.3', versionsuffix), + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('flatbuffers-python', '2.0'), +] + +# downloading TensorFlow tarball to avoid that Bazel downloads it during the build +# note: this *must* be the exact same commit as used in WORKSPACE +local_tf_commit = 'cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057' +local_tf_dir = 'tensorflow-%s' % local_tf_commit +local_tf_builddir = '%(builddir)s/' + local_tf_dir + +# replace remote TensorFlow repository with the local one from EB +local_jax_prebuildopts = "sed -i -f jaxlib_local-tensorflow-repo.sed WORKSPACE && " +local_jax_prebuildopts += "sed -i 's|EB_TF_REPOPATH|%s|' WORKSPACE && " % local_tf_builddir + +use_pip = True + +default_easyblock = 'PythonPackage' +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'source_urls': [PYPI_SOURCE], + 'start_dir': '%(name)s-%(version)s', + 'use_pip': True, + 'sanity_pip_check': True, + 'download_dep_fail': True, +} + +components = [ + ('absl-py', '1.3.0', { + 'options': {'modulename': 'absl'}, + 'checksums': ['463c38a08d2e4cef6c498b76ba5bd4858e4c6ef51da1a5a1f27139a022e20248'], + }), + ('jaxlib', '0.3.22', { + 'sources': [ + '%(name)s-v%(version)s.tar.gz', + { + 'download_filename': '%s.tar.gz' % local_tf_commit, + 'filename': 'tensorflow-%s.tar.gz' % local_tf_commit, + } + ], + 'source_urls': [ + 'https://github.com/google/jax/archive/', + 'https://github.com/tensorflow/tensorflow/archive/' + ], + 'patches': [ + ('jaxlib_local-tensorflow-repo.sed', '.'), + ('TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch', '../' + local_tf_dir), + ], + 'checksums': [ + # jaxlib-v0.3.22.tar.gz + '680a6f5265ba26d5515617a95ae47244005366f879a5c321782fde60f34e6d0d', + # tensorflow-cb946f223b9b3fa04efdbb7a0e6a9dabb22a7057.tar.gz + '9a7a7a87356bdeef5874fae135de380466482b593469035be3609a9cd2c153c4', + # jaxlib_local-tensorflow-repo.sed + 'abb5c3b97f4e317bce9f22ed3eeea3b9715365818d8b50720d937e2d41d5c4e5', + # TensorFlow-2.7.0_cuda-noncanonical-include-paths.patch + '0a759010c253d49755955cd5f028e75de4a4c447dcc8f5a0d9f47cce6881a9db', + ], + 'start_dir': 'jax-jaxlib-v%(version)s', + 'prebuildopts': local_jax_prebuildopts, + }), +] + +exts_list = [ + ('opt_einsum', '3.3.0', { + 'checksums': ['59f6475f77bbc37dcf7cd748519c0ec60722e91e63ca114e68821c0c54a46549'], + }), + ('etils', '0.8.0', { + 'checksums': ['d1d5af7bd9c784a273c4e1eccfaa8feaca5e0481a08717b5313fa231da22a903'], + }), + (name, version, { + 'patches': [ + 'jax-0.3.9_relax-test-tolerance.patch', + 'jax-0.3.23_correctly-skip-from_dlpack-tests.patch', + 'jax-0.3.23_relax-testPoly5-tolerance.patch', + ], + 'runtest': "NVIDIA_TF32_OVERRIDE=0 CUDA_VISIBLE_DEVICES=0 XLA_PYTHON_CLIENT_ALLOCATOR=platform " + + "JAX_ENABLE_X64=true pytest -vv tests", + 'source_tmpl': '%(name)s-v%(version)s.tar.gz', + 'source_urls': ['https://github.com/google/jax/archive/'], + 'checksums': [ + {'jax-v0.3.23.tar.gz': 'fa8c68a82fa2fcf3d272bf239c77e7028bb6077466a53349ce85f6e85ed623db'}, + {'jax-0.3.9_relax-test-tolerance.patch': + '3da3c8b4d9ff3449b51a4f39d6bbadd348ea3bd4ca493a6f1292743f86fa7b3d'}, + {'jax-0.3.23_correctly-skip-from_dlpack-tests.patch': + 'a69ce7280ca8bb42e671217f00d9147f8c64b4b7ba65dea7f05f2c6de757b279'}, + {'jax-0.3.23_relax-testPoly5-tolerance.patch': + 'be64bf36dde4884a97b6c8bb22c6b14ab5b24033cd40bfe7ce18363c55c30e87'}, + ], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 747e41bf0b2ee81af6f52d3e5bbeb3fc83830583 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 14 Dec 2022 12:35:48 +0100 Subject: [PATCH 709/939] remove cuda_compute_capabilities --- .../easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb | 2 -- 1 file changed, 2 deletions(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb index 9bad44f1db6e..48839d0ac0c1 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb @@ -14,8 +14,6 @@ differentiate, vectorize, JIT to GPU/TPU, and more""" toolchain = {'name': 'foss', 'version': '2021b'} -cuda_compute_capabilities = ["5.0", "6.0", "6.1", "7.0", "7.5", "8.0", "8.6"] - builddependencies = [ ('Bazel', '3.7.2'), ('pytest-xdist', '2.5.0'), From 3e88c0712ff553ef3b7ce784acef597602baf0c1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 13:03:46 +0100 Subject: [PATCH 710/939] adding easyconfigs: Squidpy-1.2.2-foss-2021b.eb --- .../s/Squidpy/Squidpy-1.2.2-foss-2021b.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb new file mode 100644 index 000000000000..826d06bfc4fa --- /dev/null +++ b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb @@ -0,0 +1,72 @@ +easyblock = 'PythonBundle' + +name = 'Squidpy' +version = '1.2.2' + +homepage = 'https://squidpy.readthedocs.io' +description = "Squidpy is a tool for the analysis and visualization of spatial molecular data." + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('networkx', '2.6.3'), + ('Pillow', '8.3.2'), + ('tqdm', '4.62.3'), + ('matplotlib', '3.4.3'), + ('xarray', '0.20.1'), + ('statsmodels', '0.13.1'), + ('scikit-image', '0.19.1'), + ('scikit-learn', '1.0.1'), + ('dask', '2022.1.0'), + ('scanpy', '1.9.1'), + ('numba', '0.54.1'), + ('aiohttp', '3.8.1'), + ('zarr', '2.13.3'), +] + +use_pip = True + +exts_list = [ + ('slicerator', '1.1.0', { + 'checksums': ['44010a7f5cd87680c07213b5cabe81d1fb71252962943e5373ee7d14605d6046'], + }), + ('PIMS', '0.6.1', { + 'checksums': ['e2b704461d4ea9bce8b6a22ca35836fe67d6d34537736b405341ae5547194f3b'], + }), + ('dask-image', '2022.9.0', { + 'checksums': ['f123dfd16a7d15c76662a6ac14778509ed5eed9b494f4322e5945e9b15923547'], + }), + ('matplotlib-scalebar', '0.8.1', { + 'checksums': ['14887af1093579c5e6afae51a0a1ecc3f715cdbc5c4d7ef59cdeec76ee6bb15d'], + }), + ('typing_extensions', '4.4.0', { + 'checksums': ['1511434bb92bf8dd198c12b1cc812e800d4181cfcb867674e0f8279cc93087aa'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('inflect', '6.0.2', { + 'checksums': ['f1a6bcb0105046f89619fde1a7d044c612c614c2d85ef182582d9dc9b86d309a'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('omnipath', '1.0.6', { + 'checksums': ['06f11b537cb1c2773d8eee13d906288f845d96f7b6cf86746ee50920c2651506'], + }), + ('validators', '0.20.0', { + 'checksums': ['24148ce4e64100a2d5e267233e23e7afeb55316b47d30faae7eb6e7292bc226a'], + }), + ('fsspec', '2022.11.0', { + 'checksums': ['259d5fd5c8e756ff2ea72f42e7613c32667dc2049a4ac3d84364a7ca034acb8b'], + }), + ('squidpy', version, { + 'checksums': ['b2af7e9e154aa98d6f1612f707b53e0507261b8153718f7011ba3c1b8ed8daeb'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From a3c9c20f321441966980166c621f0a987d113d98 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:13:23 +0000 Subject: [PATCH 711/939] adding easyconfigs: Pint-0.19.2-GCCcore-11.2.0.eb --- .../p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..565dc4060318 --- /dev/null +++ b/easybuild/easyconfigs/p/Pint/Pint-0.19.2-GCCcore-11.2.0.eb @@ -0,0 +1,27 @@ +easyblock = 'PythonPackage' + +name = 'Pint' +version = '0.19.2' + +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': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['e1d4989ff510b378dad64f91711e7bdabe5ca78d75b06a18569ac454678c4baf'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'numlib' From 71dc315b01714e785678849cab2a466b83d89627 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 13:14:33 +0100 Subject: [PATCH 712/939] add easyconfig for zarr dependency of Squidpy --- .../z/zarr/zarr-2.13.3-foss-2021b.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb new file mode 100644 index 000000000000..b73fbcf4961e --- /dev/null +++ b/easybuild/easyconfigs/z/zarr/zarr-2.13.3-foss-2021b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'zarr' +version = '2.13.3' + +homepage = 'https://zarr.readthedocs.io/en/stable/' +description = """Zarr is a Python package providing an implementation of compressed, +chunked, N-dimensional arrays, designed for use in parallel computing.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('entrypoints', '0.4', { + 'checksums': ['b706eddaa9218a19ebcd67b56818f05bb27589b1ca9e8d797b74affad4ccacd4'], + }), + ('asciitree', '0.3.3', { + 'checksums': ['4aa4b9b649f85e3fcb343363d97564aa1fb62e249677f2e18a96765145cc0f6e'], + }), + ('fasteners', '0.18', { + 'checksums': ['cb7c13ef91e0c7e4fe4af38ecaf6b904ec3f5ce0dda06d34924b6b74b869d953'], + }), + ('monotonic', '1.6', { + 'source_tmpl': '%(version)s.tar.gz', + 'source_urls': ['https://github.com/atdt/monotonic/archive'], + 'checksums': ['9609c249aed584fd714811014870650d08d6f6414402b5a190663c49bf83b221'], + }), + ('numcodecs', '0.10.2', { + 'checksums': ['22838c6b3fd986bd9c724039b88870057f790e22b20e6e1cbbaa0de142dd59c4'], + }), + (name, version, { + 'checksums': ['db24b090616c638f65e33a6bc5d956d642221182961515ccbc28b17fb0d0b48c'], + }), +] + +moduleclass = 'data' From d4d1f3f6319446d74db026e85a78500d75249031 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:15:23 +0000 Subject: [PATCH 713/939] adding easyconfigs: pydantic-1.10.2-GCCcore-11.2.0.eb --- .../pydantic-1.10.2-GCCcore-11.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..022227e23b0b --- /dev/null +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'PythonBundle' + +name = 'pydantic' +version = '1.10.2' + +homepage = 'https://github.com/samuelcolvin/pydantic' +description = """Data validation and settings management using Python type hinting.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('typing_extensions', '4.3.0', { + 'checksums': ['e6d2677a32f47fc7eb2795db1dd15c1f34eff616bcaf2cfb5e997f854fa1c4a6'], + }), + (name, version, { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), +] + +moduleclass = 'devel' From 1f45fb9d467f0abf8b781ec8ce34b8db700251e8 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:19:25 +0000 Subject: [PATCH 714/939] adding easyconfigs: pytest-7.1.3-GCCcore-11.2.0.eb --- .../p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb | 61 +++++++++++++++++++ 1 file changed, 61 insertions(+) create mode 100644 easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..97f957621d5e --- /dev/null +++ b/easybuild/easyconfigs/p/pytest/pytest-7.1.3-GCCcore-11.2.0.eb @@ -0,0 +1,61 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.1.3' + +homepage = 'https://pytest.org' +description = """pytest: simple powerful testing with Python""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +builddependencies = [('binutils', '2.37')] +dependencies = [('Python', '3.9.6')] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('py', '1.11.0', { + 'checksums': ['51c75c4126074b472f746a24399ad32f6053d1b34b68d2fa41e558e6f4a98719'], + }), + ('attrs', '22.1.0', { + 'modulename': 'attr', + 'checksums': ['29adc2665447e5191d0e7c568fde78b21f9672d344281d0c6e1ab085429b22b6'], + }), + ('pluggy', '1.0.0', { + 'checksums': ['4224373bacce55f955a878bf9cfa763c1e360858e330072059e10bad68531159'], + }), + ('atomicwrites', '1.4.1', { + 'checksums': ['81b2c9071a49367a7f770170e5eec8cb66567cfbbc8c73d20ce5ca4a8d71cf11'], + }), + ('more-itertools', '8.14.0', { + 'modulename': 'more_itertools', + 'checksums': ['c09443cd3d5438b8dafccd867a6bc1cb0894389e90cb53d227456b0b0bccb750'], + }), + ('scandir', '1.10.0', { + 'checksums': ['4d4631f6062e658e9007ab3149a9b914f3548cb38bfb021c64f39a025ce578ae'], + }), + ('pathlib2', '2.3.7.post1', { + 'checksums': ['9fe0edad898b83c0c3e199c842b27ed216645d2e177757b2dd67384d4113c641'], + }), + ('iniconfig', '1.1.1', { + 'checksums': ['bc3af051d7d14b2ee5ef9969666def0cd1a000e121eaea580d4a313df4b37f32'], + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """ + }), + ('toml', '0.10.2', { + 'checksums': ['b3bda1d108d5dd99f4a20d24d9c348e91c4db7ab1b749200bded2f839ccbe68f'], + }), + ('tomli', '2.0.1', { + 'checksums': ['de526c12914f0c550d15924c62d72abc48d6fe7364aa87328337a31007fe8a4f'], + }), + (name, version, { + 'checksums': ['4f365fec2dff9c1162f834d9f18af1ba13062db0c708bf7b946f8a5c76180c39'], + }), +] + +sanity_check_paths = { + 'files': ['bin/pytest'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'tools' From d2eef69054b185c31bfa02bacf998c0a2bace16d Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:28:54 +0000 Subject: [PATCH 715/939] adding easyconfigs: simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb --- ...mint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb new file mode 100644 index 000000000000..ef7429557010 --- /dev/null +++ b/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb @@ -0,0 +1,51 @@ +# For the various build options see here: +# https://www.bennyp.org/research/simint/README.txt +# lmax is set to 5 which is widely used it seems +# vec is set to avx, which should work on most platforms +# This might be changed to other values, if required +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'simint' +version = '0.7' +local_lmax = '5' +local_vec = 'avx' + +# custom configuration, to be used as dependency for PSI4 +versionsuffix = '-lmax-%s-vec-%s-psi4' % (local_lmax, local_vec) + +homepage = 'https://www.bennyp.org/research/simint/' +description = """Simint is a vectorized implementation of the Obara-Saika (OS) +method of calculating electron repulsion integrals. Speedup is gained by +vectorizing the primitive loop of the OS algorithm, with additional vectorization +and optimizations left to the compiler.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://www.bennyp.org/research/simint/download/'] +sources = ['%(name)s-v%(version)s.tar.bz2'] +checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax +local_common_configopts += '-DSIMINT_VECTOR=%s ' % local_vec +local_common_configopts += '-DENABLE_TESTS=ON ' +# 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', +] + +# run test to valicate accuracy +runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' + +sanity_check_paths = { + 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'chem' From fca54e9630b424b829639bba0bd3afd87fd892a9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 12:53:33 +0000 Subject: [PATCH 716/939] download_dep_fail removed as PythonBundle --- .../easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb index 022227e23b0b..da47b586bf1f 100644 --- a/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/pydantic/pydantic-1.10.2-GCCcore-11.2.0.eb @@ -14,7 +14,6 @@ dependencies = [ ('Python', '3.9.6'), ] -download_dep_fail = True use_pip = True sanity_pip_check = True From eeba836c0c1f4c6a7a9a5f9e2d88ff4469f1c062 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 14 Dec 2022 16:04:06 +0000 Subject: [PATCH 717/939] adding easyconfigs: SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb --- ...ignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb new file mode 100644 index 000000000000..ae2e384e07b2 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb @@ -0,0 +1,53 @@ +# 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 + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0g' +_suffix = 'fast' +_cuda_suffix = '-CUDA-%(cudaver)s' +versionsuffix = '-' + _suffix + _cuda_suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +unpack_options = '--strip-components=1' +checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] + +dependencies = [ + ('CUDA', '11.7.0', '', True), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy > 1.19.2 + ('tqdm', '4.64.0'), # tqdm > 4.46.1 + ('PyTorch', '1.12.0', _cuda_suffix), # torch > 1.7.0 + ('matplotlib', '3.5.2'), # matplotlib > 3.3.2 +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From da09c8997509458bf100b9939088cd662590be89 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Wed, 14 Dec 2022 16:05:51 +0000 Subject: [PATCH 718/939] add non-CUDA version --- .../s/SignalP/SignalP-6.0g-foss-2022a-fast.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb new file mode 100644 index 000000000000..4dcd1681be21 --- /dev/null +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast.eb @@ -0,0 +1,51 @@ +# 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 + +easyblock = 'PythonPackage' + +name = 'SignalP' +version = '6.0g' +_suffix = 'fast' +versionsuffix = '-' + _suffix + +homepage = 'https://services.healthtech.dtu.dk/software.php' +description = """SignalP predicts the presence and location of signal peptide cleavage sites +in amino acid sequences from different organisms""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +download_instructions = """ +SignalP requires registration and acceptance of licence terms (academic use only). + [1] go to: https://services.healthtech.dtu.dk/service.php?SignalP-6.0 + [2] navigate to the "Downloads" tab + [3] select "%s" type under version "%%(version)s" + [4] complete the form; you should receive a download link via email +""" % _suffix + +sources = ['%%(namelower)s-%%(version)s.%s.tar.gz' % _suffix] +unpack_options = '--strip-components=1' +checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # numpy > 1.19.2 + ('tqdm', '4.64.0'), # tqdm > 4.46.1 + ('PyTorch', '1.12.0'), # torch > 1.7.0 + ('matplotlib', '3.5.2'), # matplotlib > 3.3.2 +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +_bin = '%%(namelower)s%s' % version[0] +sanity_check_paths = { + 'files': ['bin/%s' % _bin], + 'dirs': ['lib/python%(pyshortver)s/site-packages/%(namelower)s'], +} + +sanity_check_commands = ['%s --help' % _bin] + +moduleclass = 'bio' From 0939f4a9973f5daa968acc3aab6efb38ae33bbd2 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 16:14:18 +0000 Subject: [PATCH 719/939] adding easyconfigs: TOML-Fortran-0.3.1-GCC-11.2.0.eb --- .../TOML-Fortran-0.3.1-GCC-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..5bfab710a6b5 --- /dev/null +++ b/easybuild/easyconfigs/t/TOML-Fortran/TOML-Fortran-0.3.1-GCC-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'CMakeMake' + +name = 'TOML-Fortran' +version = '0.3.1' + +homepage = 'https://github.com/toml-f/toml-f' +description = 'TOML parser for Fortran projects' + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/toml-f/toml-f/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['7586f0be7dc88dddba4d4e42059b84baa2688a2784bdc1d1f37112ab3edb88e1'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +sanity_check_paths = { + 'files': ['include/toml-f/GNU-11.2.0/tomlf.mod', 'lib/libtoml-f.a'], + 'dirs': ['include/toml-f/GNU-11.2.0', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 9d1bbb3219bc9bd115a91848e24d571fa56b3cbd Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 14 Dec 2022 16:19:36 +0000 Subject: [PATCH 720/939] adding easyconfigs: mstore-0.2.0-GCC-11.2.0.eb --- .../m/mstore/mstore-0.2.0-GCC-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb new file mode 100644 index 000000000000..df8ae82f8925 --- /dev/null +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb @@ -0,0 +1,26 @@ +# 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': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/grimme-lab/mstore/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['95edba88afbc8013f57f4c818a97c0500cc40b158bed11234c061b2b6d7e480d'] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +sanity_check_paths = { + 'files': ['bin/mstore-info', 'bin/mstore-fortranize', 'bin/mctc-convert'], + 'dirs': ['include/mstore', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'tools' From 529a5c6be3e548857975470645d406bc03256193 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 17:29:52 +0100 Subject: [PATCH 721/939] adding easyconfigs: Seurat-4.3.0-foss-2021b-R-4.2.0.eb --- .../Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb | 72 +++++++++++++++++++ 1 file changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb new file mode 100644 index 000000000000..6457985022a6 --- /dev/null +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb @@ -0,0 +1,72 @@ +easyblock = 'Bundle' + +name = 'Seurat' +version = '4.3.0' +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': '2021b'} + +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 +] + +dependencies = [ + ('R', '4.2.0'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +exts_defaultclass = 'RPackage' +exts_default_options = {'sources': ['%(name)s_%(version)s.tar.gz']} + +exts_list = [ + ('Matrix', '1.5-3', { + 'checksums': ['4e720f4edc97b1c09646a445851b1ce955caf6b1de8306a2283328b526fee00d'], + }), + ('sp', '1.5-1', { + 'checksums': ['69b9eab481d389bbb736d2adcf50c180aca248c3ffc4ebda8ffe2accc5f229df'], + }), + ('SeuratObject', '4.1.3', { + 'checksums': ['585d2754f6165a367f0f458523f0a25d4d4160c929c931b27c5603cc6bd986d3'], + }), + ('sctransform', '0.3.5', { + 'checksums': ['c08e56df05d64ed04ee53eb9e1d4d321da8aff945e36d56db1d5ceb1cd7e6e0b'], + }), + ('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'], + }), + (name, version, { + 'checksums': ['7ebacb3b86f74279de60b597f9a6e728f0668719811b0dca3425d21762fff97c'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +modextrapaths = {'R_LIBS_SITE': ''} + +moduleclass = 'bio' From 2fb486d0da9583e8dc6c1de37aa689514f1a9d80 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 17:30:36 +0100 Subject: [PATCH 722/939] stick to scanpy 1.8.2 as dependency for Squidpy --- easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb index 826d06bfc4fa..f60b9abeeab5 100644 --- a/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb +++ b/easybuild/easyconfigs/s/Squidpy/Squidpy-1.2.2-foss-2021b.eb @@ -20,7 +20,7 @@ dependencies = [ ('scikit-image', '0.19.1'), ('scikit-learn', '1.0.1'), ('dask', '2022.1.0'), - ('scanpy', '1.9.1'), + ('scanpy', '1.8.2'), ('numba', '0.54.1'), ('aiohttp', '3.8.1'), ('zarr', '2.13.3'), From df96a3095825106ca2dd972234e938a9ff692c51 Mon Sep 17 00:00:00 2001 From: Jasper <65227842+jfgrimm@users.noreply.github.com> Date: Wed, 14 Dec 2022 17:32:38 +0000 Subject: [PATCH 723/939] Update SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb --- .../s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb index ae2e384e07b2..9e3f52167c21 100644 --- a/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/s/SignalP/SignalP-6.0g-foss-2022a-fast-CUDA-11.7.0.eb @@ -30,7 +30,7 @@ unpack_options = '--strip-components=1' checksums = ['a16fcea2b30067d2622d446031978bd86927e2e1cecf29a567c7922f6861b5aa'] dependencies = [ - ('CUDA', '11.7.0', '', True), + ('CUDA', '11.7.0', '', SYSTEM), ('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), # numpy > 1.19.2 ('tqdm', '4.64.0'), # tqdm > 4.46.1 From 74cd8fe2f403943ee290756af4d52e267663d8cf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 14 Dec 2022 21:58:30 +0100 Subject: [PATCH 724/939] stick to R 4.1.2 + Bioconductor 3.14 as dependency for Seurat 4.3.0 with foss/2021b --- ...ss-2021b-R-4.2.0.eb => Seurat-4.3.0-foss-2021b-R-4.1.2.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Seurat/{Seurat-4.3.0-foss-2021b-R-4.2.0.eb => Seurat-4.3.0-foss-2021b-R-4.1.2.eb} (96%) diff --git a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb similarity index 96% rename from easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb rename to easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb index 6457985022a6..b98250be5b35 100644 --- a/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/s/Seurat/Seurat-4.3.0-foss-2021b-R-4.1.2.eb @@ -16,8 +16,8 @@ source_urls = [ ] dependencies = [ - ('R', '4.2.0'), - ('R-bundle-Bioconductor', '3.15', versionsuffix), + ('R', '4.1.2'), + ('R-bundle-Bioconductor', '3.14', versionsuffix), ] exts_defaultclass = 'RPackage' From 8fb7c15d6bd7201bcc50bf54bb66021a3c7ada42 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 14:51:31 +0800 Subject: [PATCH 725/939] adding easyconfigs: cutadapt-4.2-GCCcore-11.3.0.eb, pigz-2.7-GCCcore-11.3.0.eb, python-isal-1.1.0-GCCcore-11.3.0.eb --- .../c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb | 56 +++++++++++++++++++ .../p/pigz/pigz-2.7-GCCcore-11.3.0.eb | 45 +++++++++++++++ .../python-isal-1.1.0-GCCcore-11.3.0.eb | 36 ++++++++++++ 3 files changed, 137 insertions(+) create mode 100644 easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..e80a64e1148d --- /dev/null +++ b/easybuild/easyconfigs/c/cutadapt/cutadapt-4.2-GCCcore-11.3.0.eb @@ -0,0 +1,56 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics (SIB) +# Biozentrum - University of Basel +# Modified by: Adam Huffman, Jonas Demeulemeester +# The Francis Crick Institute +# Modified by: Albert Bogdanowicz +# Institute of Biochemistry and Biophysics PAS +# Modified by: Jasper Grimm +# University of York + +easyblock = 'PythonBundle' + +name = 'cutadapt' +version = '4.2' + +homepage = 'https://opensource.scilifelab.se/projects/cutadapt/' +description = """Cutadapt finds and removes adapter sequences, primers, poly-A tails and + other types of unwanted sequence from your high-throughput sequencing reads.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('pigz', '2.7'), + ('Python', '3.10.4'), + ('python-isal', '1.1.0'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('xopen', '1.7.0', { + 'checksums': ['901f9c8298e95ed74767a4bd76d9f4cf71d8de27b8cf296ac3e7bc1c11520d9f'], + }), + ('dnaio', '0.10.0', { + 'checksums': ['de51a50948f00b864297d74eddb588fbee5ac229855754e77564d18b24619d18'], + }), + (name, version, { + 'checksums': ['ab0ac450baecc1576cc5ccbc06eab2685be9ee7676763938237d954a644237f1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/cutadapt'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "cutadapt --help", + "cutadapt --version", +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..95cc9bff5e7c --- /dev/null +++ b/easybuild/easyconfigs/p/pigz/pigz-2.7-GCCcore-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MakeCp' + +name = 'pigz' +version = '2.7' + +homepage = 'https://zlib.net/pigz/' + +description = """ + pigz, which stands for parallel implementation of gzip, is a fully + functional replacement for gzip that exploits multiple processors and multiple + cores to the hilt when compressing data. pigz was written by Mark Adler, and + uses the zlib and pthread libraries. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [ + 'https://zlib.net/pigz/', + 'https://zlib.net/pigz/fossils/', +] +sources = [SOURCE_TAR_GZ] +patches = ['%(name)s-2.6_makefile.patch'] +checksums = [ + {'pigz-2.7.tar.gz': 'b4c9e60344a08d5db37ca7ad00a5b2c76ccb9556354b722d56d55ca7e8b1c707'}, + {'pigz-2.6_makefile.patch': '7e37175714d43c946373d07c522ec98a77c0f8572a9d448f759c41f6f060275d'}, +] + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('zlib', '1.2.12'), +] + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS" LDFLAGS="-L$EBROOTZLIB/lib"' + +files_to_copy = [(["pigz", "unpigz"], "bin")] + +sanity_check_paths = { + 'files': ['bin/pigz', 'bin/unpigz'], + 'dirs': [], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..24db46643c1d --- /dev/null +++ b/easybuild/easyconfigs/p/python-isal/python-isal-1.1.0-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +# Author: Jasper Grimm (UoY) + +easyblock = 'PythonPackage' + +name = 'python-isal' +version = '1.1.0' + +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': '11.3.0'} + +github_account = 'pycompression' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['3fa7f5ac22350cf9c4370aa725dea39c4155123864fff4bf6e6392f83976c86f'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('ISA-L', '2.30.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +preinstallopts = 'PYTHON_ISAL_LINK_DYNAMIC=true' +installopts = '--no-binary isal' + +options = {'modulename': 'isal'} + +moduleclass = 'lib' From 72cfc12469eb616cd05c7c7485dcda449400a352 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 15:03:24 +0800 Subject: [PATCH 726/939] adding easyconfigs: FastTree-2.1.11-GCCcore-11.3.0.eb --- .../FastTree-2.1.11-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..a79c7a054dab --- /dev/null +++ b/easybuild/easyconfigs/f/FastTree/FastTree-2.1.11-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +# 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': '11.3.0'} +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', '2.38')] + +cmds_map = [('%(name)s-%(version)s.c', '$CC -DOPENMP $CFLAGS $LIBS %%(source)s -o %(name)s')] + +files_to_copy = [(['FastTree'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/FastTree'], + 'dirs': [], +} + +sanity_check_commands = ['FastTree 2>&1 | grep "FastTree Version %(version)s"'] + +moduleclass = 'bio' From 7d41424849296648069cfb677fd4045d476ce732 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 15:06:40 +0800 Subject: [PATCH 727/939] adding easyconfigs: scikit-bio-0.5.7-foss-2022a.eb --- .../scikit-bio/scikit-bio-0.5.7-foss-2022a.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb new file mode 100644 index 000000000000..8c60a0e7d9fb --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2022a.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.7' + +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('scikit-learn', '1.1.2'), + ('IPython', '8.5.0'), + ('h5py', '3.7.0'), + ('Pillow', '9.1.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('msgpack', '1.0.4', { + 'checksums': ['f5d869c18f030202eb412f08b28d2afeea553d6613aee89e200d7aca7ef01f5f'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + (name, version, { + 'modulename': 'skbio', + 'checksums': ['6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9'], + }), +] + +moduleclass = 'bio' From ea130bd99d852a89c5db6faec4b0dcbf31f78659 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Thu, 15 Dec 2022 15:13:36 +0800 Subject: [PATCH 728/939] adding easyconfigs: statsmodels-0.13.1-foss-2022a.eb --- .../statsmodels-0.13.1-foss-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb new file mode 100644 index 000000000000..7b353348d047 --- /dev/null +++ b/easybuild/easyconfigs/s/statsmodels/statsmodels-0.13.1-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonBundle' + +name = 'statsmodels' +version = '0.13.1' + +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': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('patsy', '0.5.2', { + 'checksums': ['5053de7804676aba62783dbb0f23a2b3d74e35e5bfa238b88b7cbf148a38b69d'], + }), + (name, version, { + 'checksums': ['006ec8d896d238873af8178d5475203844f2c391194ed8d42ddac37f5ff77a69'], + }), +] + +moduleclass = 'math' From 404928f272ba5fe3c34c25373e8dabecf90a6647 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:24:05 +0100 Subject: [PATCH 729/939] adding easyconfigs: CodAn-1.2-foss-2021b.eb --- .../c/CodAn/CodAn-1.2-foss-2021b.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb new file mode 100644 index 000000000000..67ff7133a6be --- /dev/null +++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb @@ -0,0 +1,52 @@ +# author: Denis Kristak (INUITS) +easyblock = "Binary" + +name = "CodAn" +version = "1.2" + +homepage = "https://github.com/pedronachtigall/CodAn" +description = """CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR +regions on transcripts from any Eukaryote species.""" + +toolchain = {"name": "foss", "version": "2021b"} + +source_urls = ["https://github.com/pedronachtigall/CodAn/archive"] +sources = ["v%(version)s.tar.gz"] +checksums = ['34962ac67dc94da0bff6e032568e38388726bf1d7efceed462d6b7c841b087b7'] + +dependencies = [ + ("Python", "3.9.6"), + ("Biopython", "1.79"), + ("BioPerl", "1.7.8"), + ("Perl", "5.34.0"), +] + +extract_sources = True + +install_cmd = "cp -r %(builddir)s/* %(installdir)s/ && " +install_cmd += "tar -xf %(installdir)s/%(name)s-%(version)s/CodAn.tar.gz && " +install_cmd += "mkdir %(installdir)s/bin && " +install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && " +install_cmd += "chmod u+rwx %(installdir)s/bin/* " + + +sanity_check_paths = { + "files": ["bin/%(namelower)s.py"], + "dirs": [], +} + +local_sanity_check_cmd = "mkdir %(installdir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/models/VERT_full.zip %(installdir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/tutorial/transcripts.fa %(installdir)s/eb_test && " +local_sanity_check_cmd += "cd %(installdir)s/eb_test/ && " +local_sanity_check_cmd += "unzip VERT_full.zip && " +local_sanity_check_cmd += ( + "codan.py -t transcripts.fa -m VERT_full | grep 'prediction finished!'" +) + +sanity_check_commands = [ + "%(namelower)s.py --help", + local_sanity_check_cmd, +] + +moduleclass = "bio" From 8f94311bea61d8db3af8fcb6dde94eab78137885 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:27:40 +0100 Subject: [PATCH 730/939] adding easyconfigs: RegTools-0.5.2-foss-2021b.eb --- .../r/RegTools/RegTools-0.5.2-foss-2021b.eb | 39 +++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb new file mode 100644 index 000000000000..b1a7c9fc772a --- /dev/null +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb @@ -0,0 +1,39 @@ +# updated: Denis Kristak (INUITS) +easyblock = "CMakeMake" + +name = "RegTools" +version = "0.5.2" + +homepage = "https://regtools.readthedocs.org" +description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a +regulatory and splicing context.""" + +toolchain = {"name": "foss", "version": "2021b"} + +source_urls = ["https://github.com/griffithlab/%(namelower)s/archive"] +sources = ["%(version)s.tar.gz"] +checksums = ['24d3bc18174237e0fc2d0330839c8dc21c97cdb7d6e528c518188c10f17f3e7e'] + +builddependencies = [ + ("CMake", "3.21.1"), +] + +# required by included scripts +dependencies = [ + ("Python", "3.9.6"), + ("PyYAML", "5.4.1"), # required by create_IGVsessions.py script + ("R", "4.1.2"), +] + +# 'make install' is not supported... +install_cmd = "mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && " +install_cmd += "cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/" + +sanity_check_paths = { + "files": ["bin/regtools"], + "dirs": ["scripts"], +} + +sanity_check_commands = ["regtools --help"] + +moduleclass = "bio" From 7ae6bbd01fa2c86580091d38a88bbdaa3ef8d104 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:29:39 +0100 Subject: [PATCH 731/939] adding easyconfigs: BEDOPS-2.4.41-foss-2021b.eb --- .../b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb new file mode 100644 index 000000000000..0e4aad5edd50 --- /dev/null +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# updated: Denis Kristak (INUITS) + +easyblock = "MakeCp" + +name = "BEDOPS" +version = "2.4.41" + +homepage = "http://%(namelower)s.readthedocs.io/en/latest/index.html" +description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and + scalable Boolean and other set operations, statistical calculations, archiving, conversion and + other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for + distributing whole-genome analyses across a computational cluster.""" + +toolchain = {"name": "foss", "version": "2021b"} +toolchainopts = {"pic": True} + +source_urls = ["https://github.com/%(namelower)s/%(namelower)s/archive/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194'] + +# else build of jansson library fails with: "configure: error: C compiler cannot create executables" +prebuildopts = "unset LIBS && " +# builds all variants and copies executables to bin directory +buildopts = " all && make install" +# actually used variant is linked to via symlinks +keepsymlinks = True + +files_to_copy = ["bin"] + +sanity_check_paths = { + "files": [ + "bin/%s" % x for x in ["bam2bed", "%(namelower)s", "convert2bed", "unstarch"] + ], + "dirs": [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +moduleclass = "bio" From a5a3bf299dd84dd429dd3ec512f4c7994eb57b1b Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:39:12 +0100 Subject: [PATCH 732/939] adding easyconfigs: PsiCLASS-1.0.3-GCC-11.2.0.eb --- .../p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb new file mode 100644 index 000000000000..399609c8b90d --- /dev/null +++ b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb @@ -0,0 +1,34 @@ +# author: Denis Kristak (INUITS) +easyblock = "MakeCp" + +name = "PsiCLASS" +version = "1.0.3" + +homepage = "https://github.com/splicebox/PsiCLASS" +description = """PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.""" + +toolchain = {"name": "GCC", "version": "11.2.0"} + +source_urls = ["https://github.com/splicebox/PsiCLASS/archive/"] +sources = ["v%(version)s.tar.gz"] + +checksums = [ + "c60c0f33f9a076b97ccdba68b9140a5fb6936a5c5e309d70b3d0cf558828f73d", # v1.0.3.tar.gz +] + +parallel = 1 + +files_to_copy = ["*"] + +modextrapaths = {"PATH": [""]} + +sanity_check_paths = { + "files": ["classes", "grader", "psiclass"], + "dirs": [], +} + +sanity_check_commands = [ + "psiclass -b $EBROOTPSICLASS/example/s1.bam,$EBROOTPSICLASS/example/s2.bam" +] + +moduleclass = "bio" From 90af87a3379db6e2d2689962534f8ad76762ba8f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 10:44:16 +0100 Subject: [PATCH 733/939] adding easyconfigs: GeneMark-ET-4.71-GCCcore-11.2.0.eb, BRAKER-2.1.6-foss-2021b.eb --- .../b/BRAKER/BRAKER-2.1.6-foss-2021b.eb | 41 +++++++++++++++++++ .../GeneMark-ET-4.71-GCCcore-11.2.0.eb | 31 ++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb create mode 100644 easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb new file mode 100644 index 000000000000..a1aa7296bbc2 --- /dev/null +++ b/easybuild/easyconfigs/b/BRAKER/BRAKER-2.1.6-foss-2021b.eb @@ -0,0 +1,41 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'Tarball' + +name = 'BRAKER' +version = '2.1.6' + +homepage = 'https://github.com/Gaius-Augustus/BRAKER' +description = """BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET + and AUGUSTUS in novel eukaryotic genomes.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +source_urls = ['https://github.com/Gaius-Augustus/BRAKER/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['eef3c4037364472988a010322cbd79b5171158f9c016f4383809adade4866c06'] + +dependencies = [ + ('Perl', '5.34.0'), + ('AUGUSTUS', '3.4.0'), + ('GeneMark-ET', '4.71'), + ('BamTools', '2.5.2'), + ('SAMtools', '1.14'), + ('GenomeThreader', '1.7.3', '-Linux_x86_64-64bit', SYSTEM), + ('spaln', '2.4.12'), + ('Exonerate', '2.4.0'), + ('BLAST+', '2.12.0'), + ('Biopython', '1.79'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] + +sanity_check_paths = { + 'files': ['scripts/align2hints.pl', 'scripts/braker.pl', 'scripts/findGenesInIntrons.pl', 'scripts/startAlign.pl'], + 'dirs': ['docs', 'example'], +} + +sanity_check_commands = ["braker.pl --help"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..9d7b048917cd --- /dev/null +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb @@ -0,0 +1,31 @@ +# updated: Denis Kristak (INUITS) +easyblock = "Tarball" + +name = "GeneMark-ET" +version = "4.71" + +homepage = "http://exon.gatech.edu/GeneMark" +description = "Eukaryotic gene prediction suite with automatic training" + +toolchain = {"name": "GCCcore", "version": "11.2.0"} + +sources = ["gmes_linux_64-%(version)s.tar.gz"] +checksums = ['29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95'] + +download_instructions = """ +1. complete the license form: http://exon.gatech.edu/GeneMark/license_download.cgi +2. rename the tarball: `mv gmes_linux_64.tar.gz gmes_linux_64-%(version)s.tar.gz` +""" + +dependencies = [("Perl", "5.34.0")] + +fix_perl_shebang_for = ["*.pl"] + +sanity_check_paths = { + "files": ["gmes.cfg", "gmes_petap.pl"], + "dirs": ["lib"], +} + +modextrapaths = {"PATH": ""} + +moduleclass = "bio" From c737d4a5a6ba535628a01d037781f9f1e8e86df7 Mon Sep 17 00:00:00 2001 From: Victor Lopez Herrero Date: Thu, 15 Dec 2022 10:47:16 +0100 Subject: [PATCH 734/939] Apply suggestions from code review Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb | 9 +++++++++ easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb | 9 +++++++++ 2 files changed, 18 insertions(+) diff --git a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb index fa248865fb6b..48dba7492e10 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-gompi-2022a.eb @@ -23,4 +23,13 @@ checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] 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-3.2-iimpi-2022a.eb b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb index be30e500a7d2..523228ad6091 100644 --- a/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb +++ b/easybuild/easyconfigs/d/dlb/dlb-3.2-iimpi-2022a.eb @@ -23,4 +23,13 @@ checksums = ['b1c65ce3179b5275cfdf0bf921c0565a4a3ebcfdab72d7cef014957c17136c7e'] 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 311902b868e8598eeb5f2b5e864d99246dec8e8f Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 11:05:06 +0100 Subject: [PATCH 735/939] adding required dep to the PR --- .../s/spaln/spaln-2.4.12-GCC-11.2.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb new file mode 100644 index 000000000000..4939d85b41eb --- /dev/null +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb @@ -0,0 +1,45 @@ +# updated: Denis Kristak (INUITS) +easyblock = 'ConfigureMake' + +name = 'spaln' +version = '2.4.12' + +homepage = 'https://github.com/ogotoh/spaln' +description = """Spaln (space-efficient spliced alignment) is a stand-alone program that maps + and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} +# disable use of -march=native, which makes compilation fail due to missing header files like fwd2s1_simd.h; +# see also https://github.com/ogotoh/spaln/issues/56 +toolchainopts = {'optarch': False} + +source_urls = ['https://github.com/ogotoh/spaln/archive/'] +sources = ['ver%(version)s.tar.gz'] +checksums = ['0c5f842131409686dbaad01778960f53f1ebba8dd83d55b454ec4bf1b6bde2af'] + +dependencies = [ + ('zlib', '1.2.11'), + ('Perl', '5.34.0'), +] + +start_dir = 'src' + +# we need to make sure not to pass --prefix, otherwise the configure script gets stuck in an infinite loop... +prefix_opt = '--exec_prefix=' + +configopts = "--exec_prefix=%(installdir)s/bin --table_dir=%(installdir)s/table --alndbs_dir=%(installdir)s/seqdb " +configopts += "--use_zlib=1" +fix_perl_shebang_for = ['seqdb/*.pl'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['makdbs', 'makmdm', 'sortgrcd', 'spaln']], + 'dirs': ['seqdb', 'table'], +} + +sanity_check_commands = ["spaln -h 2>&1 | grep 'SPALN version %(version)s'"] +modextrapaths = { + 'PATH': 'seqdb', + 'PERL5LIB': 'seqdb', +} + +moduleclass = 'bio' \ No newline at end of file From 1c6299169910863889aaa9d7c98451f273d72a2e Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 11:06:06 +0100 Subject: [PATCH 736/939] adding easyconfigs: olego-1.1.9-GCC-11.2.0.eb --- .../o/olego/olego-1.1.9-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb new file mode 100644 index 000000000000..cf88a6c75093 --- /dev/null +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = "MakeCp" + +name = "olego" +version = "1.1.9" + +homepage = "https://github.com/chaolinzhanglab/olego" +description = """OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts +a seed-and-extend scheme, and does not rely on a separate external mapper.""" + +toolchain = {"name": "GCC", "version": "11.2.0"} + +source_urls = ["https://github.com/chaolinzhanglab/olego//archive/"] +sources = ["v%(version)s.tar.gz"] +checksums = ['1b6ba7a4a310ac71667052d3a6e1f073d3976302ab6b6b67041475f7ca1f4bac'] + +files_to_copy = ["*"] + +modextrapaths = {"PATH": [""]} + +sanity_check_paths = { + "files": ["olegoindex", "olego"], + "dirs": [], +} + +sanity_check_commands = ["olego"] +sanity_check_commands = ['olego 2>&1 | grep "version %(version)s"'] + +moduleclass = "bio" From 56869b3c6fd1deee9dab738a11edfee7f6b0bb90 Mon Sep 17 00:00:00 2001 From: deniskristak Date: Thu, 15 Dec 2022 11:07:20 +0100 Subject: [PATCH 737/939] adding comment --- easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb index cf88a6c75093..afb06b4f3905 100644 --- a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -1,3 +1,4 @@ +# updated by: Denis Kristak (INUITS) easyblock = "MakeCp" name = "olego" From 1f9332cdc352be25a05ced2bb26f03595d46689c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 11:26:42 +0100 Subject: [PATCH 738/939] minor cleanup in FLANN easyconfigs --- .../f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb | 9 +++------ .../f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb | 10 +++------- 2 files changed, 6 insertions(+), 13 deletions(-) diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb index 6bae64530232..34f5aaf3db5f 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.8.4-foss-2020a-Python-3.8.2.eb @@ -13,10 +13,9 @@ description = "FLANN is a library for performing fast approximate nearest neighb toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'openmp': True} - source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-%(version)s_fix-cmake.patch'] +patches = ['FLANN-%(version)s_fix-cmake.patch'] checksums = [ 'ed5843113150b3d6bc4c325fecb51337838a9fc09ad64bdb6aea79d6e610ee13', # flann-1.8.4.tar.gz @@ -29,9 +28,7 @@ dependencies = [ ('SciPy-bundle', '2020.03', '-Python-3.8.2'), ] -separate_build_dir = True - -configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} @@ -40,6 +37,6 @@ sanity_check_paths = { 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], 'dirs': ['include/flann', 'lib/pkgconfig', 'share/doc/flann', 'share/flann/python'], } -sanity_check_commands = [('python', '-c "import pyflann"')] +sanity_check_commands = ["python -c 'import pyflann'"] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb index a8e0f8d3ec09..5321fb0cc982 100644 --- a/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb +++ b/easybuild/easyconfigs/f/FLANN/FLANN-1.9.1-foss-2020a-Python-3.8.2.eb @@ -16,8 +16,7 @@ toolchainopts = {'openmp': True} source_urls = ['https://github.com/mariusmuja/flann/archive/'] sources = ['%(version)s.tar.gz'] -patches = ['%(name)s-1.8.4_fix-cmake.patch'] - +patches = ['FLANN-1.8.4_fix-cmake.patch'] checksums = [ 'b23b5f4e71139faa3bcb39e6bbcc76967fbaf308c4ee9d4f5bfbeceaa76cc5d3', # flann-1.9.1.tar.gz '179699d853440c9d4446b8f338a1fde64c3e712dd4bc305790a2d5790fb25ed6', # FLANN-1.8.4_fix-cmake.patch @@ -29,10 +28,7 @@ dependencies = [ ('SciPy-bundle', '2020.03', '-Python-3.8.2'), ] -separate_build_dir = True - - -configopts = "-DCMAKE_BUILD_TYPE=Release -DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" +configopts = "-DUSE_OPENMP=ON -DUSE_MPI=ON -DBUILD_PYTHON_BINDINGS=ON -DBUILD_C_BINDINGS=ON" modextrapaths = {'PYTHONPATH': ['share/flann/python']} @@ -41,6 +37,6 @@ sanity_check_paths = { 'lib/libflann_cpp.%s' % SHLIB_EXT, 'lib/libflann.%s' % SHLIB_EXT], 'dirs': ['include/flann', 'lib/pkgconfig', 'share/flann/python'], } -sanity_check_commands = [('python', '-c "import pyflann"')] +sanity_check_commands = ["python -c 'import pyflann'"] moduleclass = 'lib' From 67541d78b62340142970bfb7ca419605d6ae6a6a Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 11:50:39 +0100 Subject: [PATCH 739/939] Update spaln-2.4.12-GCC-11.2.0.eb code style err fix --- easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb index 4939d85b41eb..b8da6b502900 100644 --- a/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/spaln/spaln-2.4.12-GCC-11.2.0.eb @@ -42,4 +42,4 @@ modextrapaths = { 'PERL5LIB': 'seqdb', } -moduleclass = 'bio' \ No newline at end of file +moduleclass = 'bio' From 38a0bc9cecca00d99bb55f0ce47bc34314c09a47 Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 12:30:41 +0100 Subject: [PATCH 740/939] Add CUDAsamples for CUDA 11.3.1 --- .../c/CUDAsamples/CUDAsamples-11.3.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb new file mode 100644 index 000000000000..036dee8fefb3 --- /dev/null +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -0,0 +1,41 @@ +easyblock = 'MakeCp' + +name = 'CUDAsamples' +version = '11.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/cuda-samples' +description = "Samples for CUDA Developers which demonstrates features in CUDA Toolkit" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/NVIDIA/cuda-samples/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] + +dependencies = [ + ('CUDA', '11.3.1', '', True), +] + +# Get rid of pre-built Windows DLLs and only build deviceQuery for now. +# Other samples require extensive dependencies. +# If, at some point, all samples should be built, simply remove the explicit cd. +prebuildopts = "rm -r bin/win64 && cd Samples/deviceQuery && " + +files_to_copy = [ + (['bin/%s/linux/release/*' % ARCH], 'bin'), + 'LICENSE', +] + +local_binaries = ['deviceQuery'] + +# Only paths are used for sanity checks. +# Commands may fail due to missing compatibility libraries that might be needed +# to be able to use this specific CUDA version in combination with the available +# NVIDIA drivers. +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_binaries], + 'dirs': [], +} + +moduleclass = 'lang' From 7e94117be8139238213c72cbd31d0e4ea9576e12 Mon Sep 17 00:00:00 2001 From: deniskristak <35582739+deniskristak@users.noreply.github.com> Date: Thu, 15 Dec 2022 12:43:17 +0100 Subject: [PATCH 741/939] Update olego-1.1.9-GCC-11.2.0.eb removed obsolete sanity check cmd --- easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb index afb06b4f3905..89c892a1f8a8 100644 --- a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -23,7 +23,6 @@ sanity_check_paths = { "dirs": [], } -sanity_check_commands = ["olego"] sanity_check_commands = ['olego 2>&1 | grep "version %(version)s"'] moduleclass = "bio" From 68cccb51a8c4118d25d41e796b9d031993cf79f1 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 14:21:00 +0100 Subject: [PATCH 742/939] adding easyconfigs: meson-python-0.11.0-GCCcore-12.2.0.eb --- .../meson-python-0.11.0-GCCcore-12.2.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb new file mode 100644 index 000000000000..4dd4ad15f866 --- /dev/null +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonBundle' + +name = 'meson-python' +version = '0.11.0' + +homepage = 'https://github.com/mesonbuild/meson-python' +description = "Python build backend (PEP 517) for Meson projects" + +toolchain = {'name': 'GCCcore', 'version': '12.2.0'} + +dependencies = [ + ('Python', '3.10.8'), + ('Meson', '0.64.0'), +] + +use_pip = True + +exts_list = [ + ('pyproject-metadata', '0.6.1', { + 'checksums': ['b5fb09543a64a91165dfe85796759f9e415edc296beb4db33d1ecf7866a862bd'], + }), + (name, version, { + 'sources': ['meson_python-%(version)s.tar.gz'], + 'checksums': ['110258837c2ffe762f5f855c7ea5385f1edd44074e93a0f317ffefc7aab42b09'], + 'modulename': 'mesonpy', + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From af654e85a80bf05dd38cc9bf18494671b94737d8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 14:56:46 +0100 Subject: [PATCH 743/939] add missing binutils build dependency for meson-python --- .../m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb index 4dd4ad15f866..4d0193a8bd50 100644 --- a/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/m/meson-python/meson-python-0.11.0-GCCcore-12.2.0.eb @@ -8,6 +8,10 @@ description = "Python build backend (PEP 517) for Meson projects" toolchain = {'name': 'GCCcore', 'version': '12.2.0'} +builddependencies = [ + ('binutils', '2.39'), +] + dependencies = [ ('Python', '3.10.8'), ('Meson', '0.64.0'), From e87fc83ee457d4605ce5b3b1c10bde1e4ff78d9d Mon Sep 17 00:00:00 2001 From: Adam Huffman Date: Thu, 15 Dec 2022 14:17:08 +0000 Subject: [PATCH 744/939] Add HiCBricks to Bioconductor 3.15 --- ...le-Bioconductor-3.15-foss-2021b-R-4.2.0.eb | 27 ++++++++++--------- ...le-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 3 +++ 2 files changed, 18 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb index b6ac8e83c455..2cd7b030d51e 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2021b-R-4.2.0.eb @@ -220,9 +220,9 @@ exts_list = [ ('Rgraphviz', '2.40.0', { 'patches': ['Rgraphviz-2.28.0_fno-tree-vectorize.patch'], 'checksums': [ - '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4', # Rgraphviz_2.40.0.tar.gz - # Rgraphviz-2.28.0_fno-tree-vectorize.patch - '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9', + {'Rgraphviz_2.40.0.tar.gz': '94a4ce168efe39046fe10e2d75a9e459158716b4ef6ef977a0ced725f871cee4'}, + {'Rgraphviz-2.28.0_fno-tree-vectorize.patch': + '15783e9daba6f63c8e655858468a99e9f4f088468dbe3b414825e5844cf6b4a9'}, ], }), ('RNASeqPower', '1.36.0', { @@ -444,17 +444,17 @@ exts_list = [ ('dada2', '1.24.0', { 'patches': ['dada2-1.16.0-remove-sse-on-aarch64.patch'], 'checksums': [ - '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b', # dada2_1.24.0.tar.gz - # dada2-1.16.0-remove-sse-on-aarch64.patch - 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935', + {'dada2_1.24.0.tar.gz': '9dd083928fc06d53cdb0a2e2d35be7c304fac74a300f8d3c3026022859b5725b'}, + {'dada2-1.16.0-remove-sse-on-aarch64.patch': + 'ec840afde51428f6f2d1a480b7f0da16660c1d7a234699fa5e23fd6e66888935'}, ], }), ('LEA', '3.8.0', { 'patches': ['LEA-3.0.0_support_aarch64_and_ppc64le.patch'], 'checksums': [ - 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774', # LEA_3.8.0.tar.gz - # LEA-3.0.0_support_aarch64_and_ppc64le.patch - 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881', + {'LEA_3.8.0.tar.gz': 'c0fd5b5a66aff94d65b8961409c226966aa96a02eb7d1e9a9e75382226e5b774'}, + {'LEA-3.0.0_support_aarch64_and_ppc64le.patch': + 'caeaae7aa0577540bc9c03b54ce5a0fe4ff1a28ac503106e2b3acd1b9db82881'}, ], }), ('tximport', '1.24.0', { @@ -721,9 +721,9 @@ exts_list = [ ('RProtoBufLib', '2.8.0', { 'patches': ['RProtoBufLib-2.8.0_fix-protobuf-build.patch'], 'checksums': [ - 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7', # RProtoBufLib_2.8.0.tar.gz - # RProtoBufLib-2.8.0_fix-protobuf-build.patch - '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64', + {'RProtoBufLib_2.8.0.tar.gz': 'f7160c1623f50f0e23d14e7e99a2e6c018186871f7f1f68c9171031f6ae678d7'}, + {'RProtoBufLib-2.8.0_fix-protobuf-build.patch': + '8775d74e2288000c57575f4ef45a875b4a377ac02f89efa947699ea786bedf64'}, ], }), ('cytolib', '2.8.0', { @@ -1105,6 +1105,9 @@ exts_list = [ ('scDblFinder', '1.10.0', { 'checksums': ['c0834495a342c6467d64dc899ba5913354ea5d53037c9be95e639950db6e2478'], }), + ('HiCBricks', '1.14.0', { + 'checksums': ['ac998260ffa66ec93a4c34e56cbaf392f76a848ae35b9ea987f0ec15f0adc47d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index 5566af30766c..b73795d4c56b 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1113,6 +1113,9 @@ exts_list = [ ('numbat', '1.1.0', { 'checksums': ['3cdda07de7329e6c886a1f60b2978bb776b04133080e97d82d5772fd666efc2c'], }), + ('HiCBricks', '1.14.0', { + 'checksums': ['ac998260ffa66ec93a4c34e56cbaf392f76a848ae35b9ea987f0ec15f0adc47d'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From d5381729fef1a2c3588ef52bc2fbbc65771d775d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 15:20:14 +0100 Subject: [PATCH 745/939] trivial style fixes in CodAn easyconfig --- .../c/CodAn/CodAn-1.2-foss-2021b.eb | 41 +++++++++---------- 1 file changed, 19 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb index 67ff7133a6be..5d220aff8506 100644 --- a/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CodAn/CodAn-1.2-foss-2021b.eb @@ -1,24 +1,24 @@ # author: Denis Kristak (INUITS) -easyblock = "Binary" +easyblock = 'Binary' -name = "CodAn" -version = "1.2" +name = 'CodAn' +version = '1.2' -homepage = "https://github.com/pedronachtigall/CodAn" +homepage = 'https://github.com/pedronachtigall/CodAn' description = """CodAn (Coding sequence Annotator) is a computational tool designed to characterize the CDS and UTR regions on transcripts from any Eukaryote species.""" -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ["https://github.com/pedronachtigall/CodAn/archive"] -sources = ["v%(version)s.tar.gz"] +source_urls = ['https://github.com/pedronachtigall/CodAn/archive'] +sources = ['v%(version)s.tar.gz'] checksums = ['34962ac67dc94da0bff6e032568e38388726bf1d7efceed462d6b7c841b087b7'] dependencies = [ - ("Python", "3.9.6"), - ("Biopython", "1.79"), - ("BioPerl", "1.7.8"), - ("Perl", "5.34.0"), + ('Python', '3.9.6'), + ('Biopython', '1.79'), + ('BioPerl', '1.7.8'), + ('Perl', '5.34.0'), ] extract_sources = True @@ -29,24 +29,21 @@ install_cmd += "mkdir %(installdir)s/bin && " install_cmd += "mv %(installdir)s/%(name)s-%(version)s/bin/* %(installdir)s/bin && " install_cmd += "chmod u+rwx %(installdir)s/bin/* " - sanity_check_paths = { - "files": ["bin/%(namelower)s.py"], - "dirs": [], + 'files': ['bin/%(namelower)s.py'], + 'dirs': [], } -local_sanity_check_cmd = "mkdir %(installdir)s/eb_test && " -local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/models/VERT_full.zip %(installdir)s/eb_test && " -local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/tutorial/transcripts.fa %(installdir)s/eb_test && " -local_sanity_check_cmd += "cd %(installdir)s/eb_test/ && " +local_sanity_check_cmd = "mkdir %(builddir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/models/VERT_full.zip %(builddir)s/eb_test && " +local_sanity_check_cmd += "cp %(installdir)s/%(name)s-%(version)s/tutorial/transcripts.fa %(builddir)s/eb_test && " +local_sanity_check_cmd += "cd %(builddir)s/eb_test/ && " local_sanity_check_cmd += "unzip VERT_full.zip && " -local_sanity_check_cmd += ( - "codan.py -t transcripts.fa -m VERT_full | grep 'prediction finished!'" -) +local_sanity_check_cmd += "codan.py -t transcripts.fa -m VERT_full | grep 'prediction finished!'" sanity_check_commands = [ "%(namelower)s.py --help", local_sanity_check_cmd, ] -moduleclass = "bio" +moduleclass = 'bio' From 3512e1133fe5dca8673f9400630521dea74544ac Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 15:49:25 +0100 Subject: [PATCH 746/939] Build all CUDA samples except for the ones with extensive dependencies --- easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb index 036dee8fefb3..e807e85c12c1 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -18,9 +18,10 @@ dependencies = [ ] # Get rid of pre-built Windows DLLs and only build deviceQuery for now. -# Other samples require extensive dependencies. -# If, at some point, all samples should be built, simply remove the explicit cd. -prebuildopts = "rm -r bin/win64 && cd Samples/deviceQuery && " +prebuildopts = "rm -r bin/win64 && " + +# Filter out samples that require extensive dependencies. +buildopts = "HOST_COMPILER=g++ FILTER_OUT='Samples/EGLStream_CUDA_Interop/Makefile Samples/boxFilterNPP/Makefile Samples/cannyEdgeDetectorNPP/Makefile Samples/cudaNvSci/Makefile Samples/cudaNvSciNvMedia/Makefile Samples/simpleGL/Makefile Samples/warpAggregatedAtomicsCG/Makefile Samples/simpleVulkan/Makefile Samples/simpleVulkanMMAP/Makefile Samples/streamOrderedAllocationIPC/Makefile Samples/vulkanImageCUDA/Makefile'" files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), From b9350223d69f770cb999498a73de5d63c7e6201f Mon Sep 17 00:00:00 2001 From: huebner-m Date: Thu, 15 Dec 2022 16:10:25 +0100 Subject: [PATCH 747/939] Update easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb Co-authored-by: ocaisa --- .../easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb | 13 ++++++++++++- 1 file changed, 12 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb index e807e85c12c1..a8b05d0ddff6 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -21,7 +21,18 @@ dependencies = [ prebuildopts = "rm -r bin/win64 && " # Filter out samples that require extensive dependencies. -buildopts = "HOST_COMPILER=g++ FILTER_OUT='Samples/EGLStream_CUDA_Interop/Makefile Samples/boxFilterNPP/Makefile Samples/cannyEdgeDetectorNPP/Makefile Samples/cudaNvSci/Makefile Samples/cudaNvSciNvMedia/Makefile Samples/simpleGL/Makefile Samples/warpAggregatedAtomicsCG/Makefile Samples/simpleVulkan/Makefile Samples/simpleVulkanMMAP/Makefile Samples/streamOrderedAllocationIPC/Makefile Samples/vulkanImageCUDA/Makefile'" +local_filters = "Samples/EGLStream_CUDA_Interop/Makefile " +local_filters += "Samples/boxFilterNPP/Makefile " +local_filters += "Samples/cannyEdgeDetectorNPP/Makefile " +local_filters += "Samples/cudaNvSci/Makefile " +local_filters += "Samples/cudaNvSciNvMedia/Makefile " +local_filters += "Samples/simpleGL/Makefile " +local_filters += "Samples/warpAggregatedAtomicsCG/Makefile " +local_filters += "Samples/simpleVulkan/Makefile " +local_filters += "Samples/simpleVulkanMMAP/Makefile " +local_filters += "Samples/streamOrderedAllocationIPC/Makefile " +local_filters += "Samples/vulkanImageCUDA/Makefile" +buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), From 6cb6e79e60318fb28dded7fc7b35b3a38fa921d8 Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 15 Dec 2022 16:15:11 +0100 Subject: [PATCH 748/939] Update easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb --- easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb index a8b05d0ddff6..b8aaaaab878e 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb @@ -39,7 +39,7 @@ files_to_copy = [ 'LICENSE', ] -local_binaries = ['deviceQuery'] +local_binaries = ['deviceQuery', 'matrixMul', 'bandwidthTest', 'cudaOpenMP'] # Only paths are used for sanity checks. # Commands may fail due to missing compatibility libraries that might be needed From 9eef202248d2607ded45a8a172a8775bd7df7dd6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 16:19:04 +0100 Subject: [PATCH 749/939] downgrade to setuptools 63.4.3 in Python 3.10.8 easyconfig --- .../easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb index 2f5d77e36712..b9943b5441f2 100644 --- a/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb +++ b/easybuild/easyconfigs/p/Python/Python-3.10.8-GCCcore-12.2.0.eb @@ -47,8 +47,8 @@ exts_list = [ ('wheel', '0.38.4', { 'checksums': ['965f5259b566725405b05e7cf774052044b1ed30119b5d586b2703aafe8719ac'], }), - ('setuptools', '65.5.1', { - 'checksums': ['e197a19aa8ec9722928f2206f8de752def0e4c9fc6953527360d1c36d94ddb2f'], + ('setuptools', '63.4.3', { + 'checksums': ['521c833d1e5e1ef0869940e7f486a83de7773b9f029010ad0c2fe35453a9dad9'], }), ('pip', '22.3.1', { 'checksums': ['65fd48317359f3af8e593943e6ae1506b66325085ea64b706a998c6e83eeaf38'], From 94d78268ddf6acfb7d03d107203b08d4c1b27167 Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 16:28:15 +0100 Subject: [PATCH 750/939] Renaming, CUDAsamples -> CUDA-Samples --- .../CUDAsamples-11.3.eb => CUDA-Samples/CUDA-Samples-11.3.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/c/{CUDAsamples/CUDAsamples-11.3.eb => CUDA-Samples/CUDA-Samples-11.3.eb} (98%) diff --git a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb similarity index 98% rename from easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb rename to easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb index e807e85c12c1..437f61c10b3b 100644 --- a/easybuild/easyconfigs/c/CUDAsamples/CUDAsamples-11.3.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb @@ -1,6 +1,6 @@ easyblock = 'MakeCp' -name = 'CUDAsamples' +name = 'CUDA-Samples' version = '11.3' versionsuffix = '-CUDA-%(cudaver)s' From 36a989a733d3356d0c339ac3b0ee042ad7ad9beb Mon Sep 17 00:00:00 2001 From: Michael Huebner Date: Thu, 15 Dec 2022 16:31:28 +0100 Subject: [PATCH 751/939] Rename file with explicit versions --- ...amples-11.3.eb => CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/CUDA-Samples/{CUDA-Samples-11.3.eb => CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb} (100%) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb similarity index 100% rename from easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3.eb rename to easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb From 853eb8afa23522866c67c6436e72c45f77584d1b Mon Sep 17 00:00:00 2001 From: ocaisa Date: Thu, 15 Dec 2022 17:19:02 +0100 Subject: [PATCH 752/939] Tweak for tests --- .../CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb index e77aa006f900..b71d2bfad4d6 100644 --- a/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/c/CUDA-Samples/CUDA-Samples-11.3-GCC-10.3.0-CUDA-11.3.1.eb @@ -14,7 +14,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['2bee5f7c89347259aaab75aa6df6e10375059bdbbaf04cc7936f5db7d54fa3ac'] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ] # Get rid of pre-built Windows DLLs and only build deviceQuery for now. @@ -32,7 +32,7 @@ local_filters += "Samples/simpleVulkan/Makefile " local_filters += "Samples/simpleVulkanMMAP/Makefile " local_filters += "Samples/streamOrderedAllocationIPC/Makefile " local_filters += "Samples/vulkanImageCUDA/Makefile" -buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters +buildopts = "HOST_COMPILER=g++ FILTER_OUT='%s'" % local_filters files_to_copy = [ (['bin/%s/linux/release/*' % ARCH], 'bin'), From a3090ecec3def36987792f1c1c078af2aa327118 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:46:55 +0100 Subject: [PATCH 753/939] adding easyconfigs: SLEPc-3.17.2-foss-2022a.eb --- .../s/SLEPc/SLEPc-3.17.2-foss-2022a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb new file mode 100644 index 000000000000..216e5e154d29 --- /dev/null +++ b/easybuild/easyconfigs/s/SLEPc/SLEPc-3.17.2-foss-2022a.eb @@ -0,0 +1,21 @@ +name = 'SLEPc' +version = '3.17.2' + +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': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True} + +source_urls = ['https://slepc.upv.es/download/distrib'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f784cca83a14156631d6e0f5726ca0778e259e1fe40c927607d5fb12d958d705'] + +dependencies = [('PETSc', '3.17.4')] + +petsc_arch = 'installed-arch-linux2-c-opt' + +moduleclass = 'numlib' From 5f640e8f03b6d27daa731dea4e3fedf6d5ca009f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:47:08 +0100 Subject: [PATCH 754/939] adding easyconfigs: VTK-9.2.2-foss-2022a.eb --- .../easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb | 87 +++++++++++++++++++ 1 file changed, 87 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb b/easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb new file mode 100644 index 000000000000..1394917dc978 --- /dev/null +++ b/easybuild/easyconfigs/v/VTK/VTK-9.2.2-foss-2022a.eb @@ -0,0 +1,87 @@ +## +# Authors:: +# * Fotis Georgatos +# * Robert Mijakovic +## + +easyblock = 'CMakeMake' + +name = 'VTK' +version = '9.2.2' + +homepage = 'https://www.vtk.org' +description = """The Visualization Toolkit (VTK) is an open-source, freely available software system for + 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several + interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization + algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques + such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.vtk.org/files/release/%(version_major_minor)s'] +sources = [ + SOURCE_TAR_GZ, + '%(name)sData-%(version)s.tar.gz', +] +patches = [('vtk-version.egg-info', '.')] +checksums = [ + {'VTK-9.2.2.tar.gz': '1c5b0a2be71fac96ff4831af69e350f7a0ea3168981f790c000709dcf9121075'}, + {'VTKData-9.2.2.tar.gz': '4b0ac438c77773ff741fd02c0e3b0dc1406b4c51e6cbe4e8304306fa125f27bf'}, + {'vtk-version.egg-info': '787b82415ae7a4a1f815b4db0e25f7abc809a05fc85d7d219627f3a7e5d3867b'}, +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('XZ', '5.2.5'), + ('libGLU', '9.0.2'), + ('X11', '20220504'), +] + +separate_build_dir = True + +# OpenGL +configopts = "-DOPENGL_glu_LIBRARY=$EBROOTLIBGLU/lib/libGLU.%s " % SHLIB_EXT +configopts += "-DOPENGL_gl_LIBRARY=$EBROOTMESA/lib/libGL.%s " % SHLIB_EXT +configopts += "-DOPENGL_INCLUDE_DIR=$EBROOTMESA/include " +# Python +configopts += "-DVTK_WRAP_PYTHON=ON -DVTK_PYTHON_VERSION=3 -DVTK_PYTHON_OPTIONAL_LINK=OFF " +configopts += "-DPython3_ROOT_DIR=$EBROOTPYTHON " +# Other +configopts += "-DVTK_USE_MPI=ON " +configopts += "-DCMAKE_INSTALL_LIBDIR=lib" + +preinstallopts = "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " + +# Install a egg-info file so VTK is more python friendly, required for mayavi +local_egg_info_src = '%(builddir)s/VTK-%(version)s/vtk-version.egg-info' +local_egg_info_dest = '%(installdir)s/lib/python%(pyshortver)s/site-packages/vtk-%(version)s.egg-info' +postinstallcmds = [ + 'sed "s/#VTK_VERSION#/%%(version)s/" %s > %s' % (local_egg_info_src, local_egg_info_dest), +] + +modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']} + +local_vtk_exec = ['vtk%s-%%(version_major_minor)s' % x + for x in ['WrapJava', 'ParseJava', 'WrapPythonInit', 'WrapPython', 'WrapHierarchy']] +local_vtk_exec += ['vtkpython'] +local_vtk_libs = ['CommonCore', 'IONetCDF', 'ParallelCore', 'RenderingOpenGL2'] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in local_vtk_exec] + ['include/vtk-%(version_major_minor)s/vtkMPI.h'] + + ['lib/libvtk%s-%%(version_major_minor)s.%s' % (l, SHLIB_EXT) for l in local_vtk_libs], + 'dirs': ['lib/python%(pyshortver)s/site-packages/', 'include/vtk-%(version_major_minor)s'], +} + +sanity_check_commands = [ + "python -c 'import %(namelower)s'", + "python -c 'import pkg_resources; pkg_resources.get_distribution(\"vtk\")'", + # make sure that VTK Python libraries link to libpython (controlled via DVTK_PYTHON_OPTIONAL_LINK=OFF), + # see https://gitlab.kitware.com/vtk/vtk/-/issues/17881 + "ldd $EBROOTVTK/lib/libvtkPythonContext2D-%%(version_major_minor)s.%s | grep /libpython" % SHLIB_EXT, +] + +moduleclass = 'vis' From a07e1788e4dbb88c95a8d54ac04cbf0a21cb80cb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:47:21 +0100 Subject: [PATCH 755/939] adding easyconfigs: ParMETIS-4.0.3-gompi-2022a.eb --- .../p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.eb new file mode 100644 index 000000000000..5b392db9c1f2 --- /dev/null +++ b/easybuild/easyconfigs/p/ParMETIS/ParMETIS-4.0.3-gompi-2022a.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': '2022a'} +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', '3.24.3')] + +# Build static and shared libraries +configopts = ['', '-DSHARED=1'] + +moduleclass = 'math' From 7921f8853881880e926f2edf16e6f21706d117ad Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 15 Dec 2022 20:51:04 +0100 Subject: [PATCH 756/939] use VTK 9.2.2 as dependency of ITK 5.2.1 (instead of VTK 9.2.0rc2) --- easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb index 22f773b4840c..83ecef81cdc0 100644 --- a/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb +++ b/easybuild/easyconfigs/i/ITK/ITK-5.2.1-foss-2022a.eb @@ -32,7 +32,7 @@ dependencies = [ ('libjpeg-turbo', '2.1.3'), ('libpng', '1.6.37'), ('LibTIFF', '4.3.0'), - ('VTK', '9.2.0.rc2'), + ('VTK', '9.2.2'), ('zlib', '1.2.12'), ] From 6144912418a31286f4e477d434f4ac975c522009 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Thu, 15 Dec 2022 23:36:09 +0100 Subject: [PATCH 757/939] adding easyconfigs: NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb --- ...CL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb | 35 +++++++++++++++++++ 1 file changed, 35 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb diff --git a/easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..dc4b43cede09 --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL-tests/NCCL-tests-2.13.6-gompi-2022a-CUDA-11.7.0.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'NCCL-tests' +version = '2.13.6' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/NVIDIA/nccl-tests' +description = "Tests check both the performance and the correctness of NCCL operations." + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'usempi': True} + +github_account = 'NVIDIA' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['52b472a58a4918d3221a9b8c4bd9335382643d7e241983918b64692d685cc3d1'] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('NCCL', '2.12.12', '-CUDA-%(cudaver)s'), +] + +buildopts = 'VERBOSE=1 MPI=1 MPI_HOME=$EBROOTOPENMPI CUDA_HOME=$EBROOTCUDA NCCL_HOME=$EBROOTNCCL ' + +_binaries = ['all_gather_perf', 'all_reduce_perf', 'alltoall_perf', 'broadcast_perf', 'gather_perf', + 'hypercube_perf', 'reduce_perf', 'reduce_scatter_perf', 'scatter_perf', 'sendrecv_perf'] + +files_to_copy = [(['build/%s' % x for x in _binaries], 'bin')] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _binaries], + 'dirs': [], +} + +moduleclass = 'tools' From 1761f728f1fa6e6476c026bb10e74480f40a12ed Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Dec 2022 00:08:07 +0100 Subject: [PATCH 758/939] adding easyconfigs: Transformers-4.24.0-foss-2022a.eb --- .../Transformers-4.24.0-foss-2022a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb new file mode 100644 index 000000000000..47a488d49c16 --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.24.0' + +homepage = 'https://github.com/huggingface/transformers' +description = """ +State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for tokenizers +] +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('regex', '2022.10.31', { + 'checksums': ['a3a98921da9a1bf8457aeee6a551948a83601689e5ecdd736894ea9bbec77e83'], + }), + ('tokenizers', '0.13.2', { + 'checksums': ['f9525375582fd1912ac3caa2f727d36c86ff8c0c6de45ae1aaff90f87f33b907'], + }), + ('huggingface-hub', '0.10.1', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['5c188d5b16bec4b78449f8681f9975ff9d321c16046cc29bcf0d7e464ff29276'], + }), + ('transformers', version, { + 'checksums': ['486f353a8e594002e48be0e2aba723d96eda839e63bfe274702a4b5eda85559b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'math' From e4120221981e58f19da1605a83ff88578da1d02a Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Fri, 16 Dec 2022 08:10:17 +0100 Subject: [PATCH 759/939] adding easyconfigs: Bader-1.04-GCC-11.2.0.eb --- .../b/Bader/Bader-1.04-GCC-11.2.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb new file mode 100644 index 000000000000..20b55c3aed9f --- /dev/null +++ b/easybuild/easyconfigs/b/Bader/Bader-1.04-GCC-11.2.0.eb @@ -0,0 +1,28 @@ +easyblock = 'MakeCp' + +name = 'Bader' +version = '1.04' + +homepage = 'https://theory.cm.utexas.edu/henkelman/code/bader/' +description = "Bader Charge Analysis" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['http://theory.cm.utexas.edu/henkelman/code/bader/download/v%(version)s'] +sources = [{'download_filename': 'bader.tar.gz', 'filename': SOURCE_TAR_GZ}] +checksums = ['f20a0a021157d911bea06666911763b737c4ff38b39e793b8560f940fe391b8e'] + +buildopts = ' -f makefile.lnx_ifort FC=$FC FFLAGS="$FFLAGS" ' + +parallel = 1 + +files_to_copy = [ + (['bader'], 'bin'), +] + +sanity_check_paths = { + 'files': ['bin/bader'], + 'dirs': [], +} + +moduleclass = 'phys' From 8e5aab16d2b7ba5f5a4678c89134ec4d8f39bc73 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Dec 2022 15:33:46 +0800 Subject: [PATCH 760/939] adding easyconfigs: alsa-lib-1.2.8-GCCcore-11.2.0.eb --- .../alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb 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 new file mode 100644 index 000000000000..ae379c9ac316 --- /dev/null +++ b/easybuild/easyconfigs/a/alsa-lib/alsa-lib-1.2.8-GCCcore-11.2.0.eb @@ -0,0 +1,24 @@ +easyblock = 'ConfigureMake' + +name = 'alsa-lib' +version = '1.2.8' + +homepage = 'https://www.alsa-project.org' +description = """The Advanced Linux Sound Architecture (ALSA) provides audio and MIDI functionality + to the Linux operating system.""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['ftp://ftp.alsa-project.org/pub/lib/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['1ab01b74e33425ca99c2e36c0844fd6888273193bd898240fe8f93accbcbf347'] + +dependencies = [('binutils', '2.37')] + +sanity_check_paths = { + 'files': ['bin/aserver', 'include/asoundlib.h', + 'lib64/libatopology.%s' % SHLIB_EXT, 'lib64/libasound.%s' % SHLIB_EXT], + 'dirs': ['include/alsa', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lib' From c6cd9a761fb6aa4f121a057b4003ecfa5670b9b2 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Dec 2022 15:34:13 +0800 Subject: [PATCH 761/939] adding easyconfigs: bwidget-1.9.15-GCCcore-11.2.0.eb --- .../bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..aa9c67ac17a5 --- /dev/null +++ b/easybuild/easyconfigs/b/bwidget/bwidget-1.9.15-GCCcore-11.2.0.eb @@ -0,0 +1,26 @@ +easyblock = 'Tarball' + +name = 'bwidget' +version = '1.9.15' + +homepage = 'https://core.tcl-lang.org/bwidget/home' +description = 'The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces.' + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} + +source_urls = ['https://downloads.sourceforge.net/project/tcllib/BWidget/%(version)s/'] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['9c4dd648fdfd31de7cb5af44b392a1916f949dd195820684d940edcd8485ac13'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [('Tk', '8.6.11')] + +modextrapaths = {'TCLLIBPATH': '.'} + +sanity_check_paths = { + 'files': ['button.tcl'], + 'dirs': ['BWman', 'demo', 'images', 'lang', 'tests'], +} + +moduleclass = 'vis' From d8b44ca1bb29325dc51cf9aa30c8d1e8115cba26 Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Fri, 16 Dec 2022 15:34:43 +0800 Subject: [PATCH 762/939] adding easyconfigs: umap-learn-0.5.3-foss-2021b.eb --- .../umap-learn/umap-learn-0.5.3-foss-2021b.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb new file mode 100644 index 000000000000..3ddc3e129e2c --- /dev/null +++ b/easybuild/easyconfigs/u/umap-learn/umap-learn-0.5.3-foss-2021b.eb @@ -0,0 +1,41 @@ +# 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 = '0.5.3' + +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': '2021b'} +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('scikit-learn', '1.0.1'), + ('numba', '0.54.1'), + ('LLVM', '12.0.1'), + ('tqdm', '4.62.3'), +] + +use_pip = True + +exts_list = [ + ('pynndescent', '0.5.7', { + 'checksums': ['ecb395255fa36a748b5870b4ba0300ea0f7da8b1964864b8edd62577a84dfd7d'], + }), + (name, version, { + 'modulename': 'umap', + 'checksums': ['dbd57cb181c2b66d238acb5635697526bf24c798082daed0cf9b87f6a3a6c0c7'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From f9da8d33f94afc91e4102cfd0eeb7a771e062d25 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 16 Dec 2022 09:06:04 +0100 Subject: [PATCH 763/939] adding easyconfigs: TM-align-20190822-GCC-11.3.0.eb --- .../TM-align/TM-align-20190822-GCC-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb b/easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb new file mode 100644 index 000000000000..df013e222a02 --- /dev/null +++ b/easybuild/easyconfigs/t/TM-align/TM-align-20190822-GCC-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CmdCp' + +name = 'TM-align' +version = '20190822' + +homepage = 'https://zhanglab.ccmb.med.umich.edu/RNA-align/TMalign/' +description = """This package unifies protein structure alignment and RNA structure alignment + into the standard TM-align program for single chain structure alignment, MM-align program for + multi-chain structure alignment, and TM-score program for sequence dependent structure superposition.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = ['https://zhanggroup.org/TM-align/'] +sources = ['TMtools%(version)s.tar.gz'] +checksums = ['bf81b636f222f6a6960963875e9c95dc034498f8c6fbd7cd2e66b6fde9856798'] + +_cmd = '$F77 $FCFLAGS TMalign.f -o TMalign' +_cmd += ' && $F77 $FCFLAGS TMscore.f -o TMscore' + +cmds_map = [('.*', _cmd)] + +files_to_copy = [ + (['TMalign', 'TMscore'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/TMalign', 'bin/TMscore'], + 'dirs': [], +} + +sanity_check_commands = [ + 'TMalign -h', + 'TMscore -h', +] + +moduleclass = 'bio' From 8794380eb3968571e7649f571f3388f7c488997a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Dec 2022 16:21:26 +0100 Subject: [PATCH 764/939] adding easyconfigs: BWA-0.7.17-GCCcore-11.3.0.eb --- .../b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..498ebbb605e4 --- /dev/null +++ b/easybuild/easyconfigs/b/BWA/BWA-0.7.17-GCCcore-11.3.0.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': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/lh3/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['980b9591b61c60042c4a39b9e31ccaad8d17ff179d44d347997825da3fdf47fd'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Perl', '5.34.1'), + ('zlib', '1.2.12'), +] + +# 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 e9d9f02f4ad03773b6ab23870b7a5597ac1c88e5 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 16 Dec 2022 16:37:21 +0100 Subject: [PATCH 765/939] adding easyconfigs: GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb --- .../GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb new file mode 100644 index 000000000000..7c64788e3d69 --- /dev/null +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb @@ -0,0 +1,53 @@ +## +# 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 +## + +easyblock = 'Tarball' + +name = 'GATK' +version = '4.3.0.0' +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': '11.3.0'} + +source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] +sources = ['gatk-%(version)s.zip'] +checksums = ['12fbd03142311419a050dba8009d615ee8faceb32b46aad8f4448dafd61e11eb'] + +dependencies = [ + ('Java', '11', '', True), + ('Python', '3.10.4'), +] + +modextrapaths = {'PATH': ''} + +sanity_check_paths = { + 'files': ['gatk'], + 'dirs': [], +} +sanity_check_commands = [ + "gatk --help", + "gatk --list", +] + +moduleclass = 'bio' From eaf9963987de7bfb0402ac75f99a26b95d6d33be Mon Sep 17 00:00:00 2001 From: fizwit Date: Fri, 16 Dec 2022 20:01:30 -0800 Subject: [PATCH 766/939] {bio}[foss/2021b] slamdunk 0.4.3 w/Python 3.9.6 --- .../s/slamdunk/slamdunk-0.4.3-foss-2021b.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb diff --git a/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb b/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb new file mode 100644 index 000000000000..83ec0ecee9cc --- /dev/null +++ b/easybuild/easyconfigs/s/slamdunk/slamdunk-0.4.3-foss-2021b.eb @@ -0,0 +1,34 @@ + +# easybuild easyconfig +# +# John Dey Fred Hutchinson Cancer Center +# +easyblock = 'PythonBundle' + +name = 'slamdunk' +version = '0.4.3' + +homepage = 'https://t-neumann.github.io/slamdunk/' +description = """SlamDunk is a novel, fully automated software tool for automated, robust, scalable + and reproducible SLAMseq data analysis.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +dependencies = [ + ('Python', '3.9.6'), + ('HTSlib', '1.14'), + ('Biopython', '1.79'), # includes ScyPy-bundle + ('Pysam', '0.17.0'), + ('pybedtools', '0.8.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'checksums': ['8475d4cadad3defda6b11de405fc59de917a6e57468f709a1e28b8a0627f2ff5'], + }), +] + +moduleclass = 'bio' From 3ffe9a479c34d6da5dbca3e246fa4c0499f23962 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 10:11:30 +0000 Subject: [PATCH 767/939] update source_urls in MUMPS 5.3.*, 5.4.*, and 5.5.* --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb | 2 +- 7 files changed, 7 insertions(+), 7 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb index c3b9ed471b2c..788e37ba4031 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-foss-2020b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb index 3e9e86cfe09a..2ccfcf5826fc 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.3.5-intel-2020b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2020b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb index 796b2daf5239..f35a1d8bdc85 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.0-foss-2021a-metis.eb @@ -11,7 +11,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb index ce1f12d8b5d1..02f1645d955c 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-foss-2021b-metis.eb @@ -8,7 +8,7 @@ description = """A parallel sparse direct solver""" toolchain = {'name': 'foss', 'version': '2021b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-5.4.0_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb index 3971d5baaa7f..03dc589f2ea1 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.4.1-intel-2021b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2021b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-5.4.0_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb index 1b9876029cc8..8a0c06141638 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.0-foss-2021a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2021a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb index d9da01989eac..d5d20b8c5682 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.5.1-foss-2022a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2022a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD From 2bc7906676b8b9376db83721694b3f0a766bc048 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 10:23:54 +0000 Subject: [PATCH 768/939] update source_urls in MUMPS 5.1.* and 5.2.* --- easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb | 2 +- .../easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb | 2 +- .../easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb | 2 +- easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb | 2 +- 10 files changed, 10 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb index 5c4845921c06..b9872da4d0ae 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.1.2-foss-2017b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2017b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] checksums = ['eb345cda145da9aea01b851d17e54e7eef08e16bfa148100ac1f7f046cd42ae9'] diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb index ea67534b6679..75d6a04770ae 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2018b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb index 5c7d17274b37..d10d2450e7dc 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis-seq.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver. This module is for its sequentia toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': False} -source_urls = ['http://mumps.enseeiht.fr/'] # doesn't support https +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb index 718db19d94b1..6a6dbb4a649f 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb index 7d9a6bacb272..7072922653bc 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2019b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2019b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb index 849c31db3e01..6c29b89b5591 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-foss-2020a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'foss', 'version': '2020a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb index 7e3d0011f82a..1dc132a103ae 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis-seq.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver. This module is for its sequentia toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': False} -source_urls = ['http://mumps.enseeiht.fr/'] # doesn't support https +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb index 1049b760c097..4e81acee6ea8 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2019a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb index 87578164d883..1acfe3342efd 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2019b-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2019b'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD diff --git a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb index 6e411ccea17e..ca6f8b652a03 100644 --- a/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb +++ b/easybuild/easyconfigs/m/MUMPS/MUMPS-5.2.1-intel-2020a-metis.eb @@ -8,7 +8,7 @@ description = "A parallel sparse direct solver" toolchain = {'name': 'intel', 'version': '2020a'} toolchainopts = {'pic': True, 'usempi': True} -source_urls = ['http://mumps.enseeiht.fr/'] +source_urls = ['https://graal.ens-lyon.fr/MUMPS/'] sources = ['%(name)s_%(version)s.tar.gz'] patches = [ '%(name)s-%(version)s_shared-pord.patch', # builds the shared libs of PORD From 6b66c567082d1c191a3ee1aa7879f4f41bd62a3d Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 14:55:20 +0000 Subject: [PATCH 769/939] adding easyconfigs: SuperLU_DIST-8.1.0-foss-2022a.eb --- .../SuperLU_DIST-8.1.0-foss-2022a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb 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 new file mode 100644 index 000000000000..18297b94e505 --- /dev/null +++ b/easybuild/easyconfigs/s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = "EB_SuperLU" + +name = 'SuperLU_DIST' +version = '8.1.0' + +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': '2022a'} +toolchainopts = {'pic': True, 'openmp': True} + +github_account = 'xiaoyeli' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ["v%(version)s.tar.gz"] +checksums = ['9308844b99a7e762d5704934f7e9f79daf158b0bfc582994303c2e0b31518b34'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('ParMETIS', '4.0.3'), +] + +configopts = '-DTPL_PARMETIS_INCLUDE_DIRS="${EBROOTPARMETIS}/include" ' +configopts += '-DTPL_PARMETIS_LIBRARIES="${EBROOTPARMETIS}/lib/libparmetis.a;${EBROOTPARMETIS}/lib/libmetis.a" ' + +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 c9b1089d2819b6d2ca6d9980768a2ffe67d54a21 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sat, 17 Dec 2022 15:00:05 +0000 Subject: [PATCH 770/939] add ParMETIS and SuperLU_Dist deps to PETSc 3.17.4 --- easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb index 058019a15f9a..4f5e7a066713 100644 --- a/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb +++ b/easybuild/easyconfigs/p/PETSc/PETSc-3.17.4-foss-2022a.eb @@ -36,6 +36,8 @@ dependencies = [ ('MUMPS', '5.5.1', '-metis'), ('SuiteSparse', '5.13.0', '-METIS-5.1.0'), ('Hypre', '2.25.0'), + ('ParMETIS', '4.0.3'), + ('SuperLU_DIST', '8.1.0'), ] # enabling --with-mpi4py seems to be totally broken, leads to make errors like: From de048d8cdef02feeeeab939630bf7286fc603aa2 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 16:15:08 +0100 Subject: [PATCH 771/939] update checksum of GATK v4.3.0.0 Co-authored-by: SebastianAchilles --- .../easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb index 7c64788e3d69..a0b3fff12471 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb @@ -32,7 +32,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://github.com/broadinstitute/gatk/releases/download/%(version)s/'] sources = ['gatk-%(version)s.zip'] -checksums = ['12fbd03142311419a050dba8009d615ee8faceb32b46aad8f4448dafd61e11eb'] +checksums = ['e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd'] dependencies = [ ('Java', '11', '', True), From d4ce1ebdbd5c245fa1ba720057f23de4cc3d59e9 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 16:15:35 +0100 Subject: [PATCH 772/939] use SYSTEM global in Java dependency of GATK v4.3.0.0 Co-authored-by: SebastianAchilles --- .../easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb index a0b3fff12471..81e5752680fc 100644 --- a/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb +++ b/easybuild/easyconfigs/g/GATK/GATK-4.3.0.0-GCCcore-11.3.0-Java-11.eb @@ -35,7 +35,7 @@ sources = ['gatk-%(version)s.zip'] checksums = ['e2c27229b34c3e22445964adf00639a0909887bbfcc040f6910079177bc6e2dd'] dependencies = [ - ('Java', '11', '', True), + ('Java', '11', '', SYSTEM), ('Python', '3.10.4'), ] From 9025440291bc42c3fb070f3927378b85a20dd467 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 16:56:58 +0100 Subject: [PATCH 773/939] adding easyconfigs: BBMap-39.01-GCC-11.3.0.eb --- .../b/BBMap/BBMap-39.01-GCC-11.3.0.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb b/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb new file mode 100644 index 000000000000..e72ccff30e4b --- /dev/null +++ b/easybuild/easyconfigs/b/BBMap/BBMap-39.01-GCC-11.3.0.eb @@ -0,0 +1,34 @@ +easyblock = 'MakeCp' + +name = 'BBMap' +version = '39.01' + +homepage = 'https://sourceforge.net/projects/bbmap/' +description = """BBMap short read aligner, and other bioinformatic tools.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['98608da50130c47f3abd095b889cc87f60beeb8b96169b664bc9d849abe093e6'] + +dependencies = [('Java', '11', '', SYSTEM)] + +prebuildopts = 'cd jni && ' + +local_suff = {'Darwin': 'osx', 'Linux': 'linux'}[OS_TYPE] +buildopts = "-f makefile.%s" % local_suff + +files_to_copy = ['*'] + +sanity_check_paths = { + 'files': ['bbmap.sh', 'jni/libbbtoolsjni.%s' % SHLIB_EXT], + 'dirs': [] +} + +modextrapaths = {'PATH': ''} + +modloadmsg = "For improved speed, add 'usejni=t' to the command line of %(name)s tools which support the use of the" +modloadmsg += " compiled jni C code.\n" + +moduleclass = 'bio' From a8aa7f69df39a6e47648f3bc76fbdcda9224aefc Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sat, 17 Dec 2022 17:24:46 +0000 Subject: [PATCH 774/939] retain test filter --- .../s/SuperLU_DIST/SuperLU_DIST-8.1.0-foss-2022a.eb | 4 ++++ 1 file changed, 4 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 18297b94e505..1527189c23bd 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 @@ -24,6 +24,10 @@ dependencies = [ 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 ] From 6de51e947be2752c5ade623c241ef2587b11a22f Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 17 Dec 2022 18:50:13 +0100 Subject: [PATCH 775/939] adding easyconfigs: Pindel-0.2.5b9-20170508-GCC-11.3.0.eb --- .../Pindel-0.2.5b9-20170508-GCC-11.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb new file mode 100644 index 000000000000..798e6828551b --- /dev/null +++ b/easybuild/easyconfigs/p/Pindel/Pindel-0.2.5b9-20170508-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# Author: Jonas Demeulemeester +# The Francis Crick Insitute, London, UK +## + +easyblock = 'CmdCp' + +name = 'Pindel' +# no official release provided for version 0.2.5b9 (20160729), +# therefore, pull last commit (20170508) to this version from master repo +version = '0.2.5b9-20170508' +_commit = 'b706fba61' + +homepage = 'http://gmt.genome.wustl.edu/packages/pindel/' +description = """ Pindel can detect breakpoints of large deletions, medium sized + insertions, inversions, tandem duplications and other structural variants at single-based + resolution from next-gen sequence data. It uses a pattern growth approach to identify the + breakpoints of these variants from paired-end short reads. """ + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'openmp': True} + +github_account = 'genome' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': '%s.tar.gz' % _commit, 'filename': SOURCE_TAR_GZ}] +patches = ['%(name)s-%(version)s_fix-ambig-abs-compil-err.patch'] +checksums = [ + {'Pindel-0.2.5b9-20170508.tar.gz': 'd626260986270efce5a947d03785781c8fddfc922f41279cf9d4bd504c4e3690'}, + {'Pindel-0.2.5b9-20170508_fix-ambig-abs-compil-err.patch': + '216ae1145fd1568ac2187a89bf4b95c45d5c02272047a3dd5f9dfbede26c8fec'}, +] + +dependencies = [ + ('HTSlib', '1.15.1'), + ('zlib', '1.2.12') +] + +cmds_map = [('.*', "./INSTALL ${EBROOTHTSLIB}")] + +_exes = ['pindel', 'sam2pindel', 'pindel2vcf', 'bam2pindel.pl', 'Adaptor.pm'] +files_to_copy = [(_exes, 'bin'), "demo", "test", "README.md"] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in _exes], + 'dirs': ['demo', 'test'], +} + +moduleclass = 'bio' From 0489dd86fa84fb0bec14bdd2d02c4c9d7576b47a Mon Sep 17 00:00:00 2001 From: guacke Date: Sun, 18 Dec 2022 16:18:39 +0100 Subject: [PATCH 776/939] Add MPI support. --- easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb index 8fc40328d058..476b4a265c3d 100644 --- a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb @@ -29,6 +29,6 @@ sanity_check_paths = { 'dirs': [], } -configopts = '-DHIGHFIVE_USE_EIGEN=ON' +configopts = '-DHIGHFIVE_USE_EIGEN=ON -DHIGHFIVE_PARALLEL_HDF5=ON' moduleclass = 'lib' From fea694ff57c20c68f39703f5f6fdb77330d5cb73 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sun, 18 Dec 2022 18:22:43 +0100 Subject: [PATCH 777/939] adding easyconfigs: Beagle-5.4.22Jul22.46e-Java-11.eb --- .../Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb diff --git a/easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb b/easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb new file mode 100644 index 000000000000..d2afe2dfd9a8 --- /dev/null +++ b/easybuild/easyconfigs/b/Beagle/Beagle-5.4.22Jul22.46e-Java-11.eb @@ -0,0 +1,38 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# +easyblock = "JAR" + +name = 'Beagle' +_revision = '22Jul22.46e' +version = '5.4.' + _revision +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://faculty.washington.edu/browning/beagle/beagle.html' +description = """Beagle is a software package for phasing genotypes and for imputing + ungenotyped markers.""" + +toolchain = SYSTEM + +source_urls = ['https://faculty.washington.edu/browning/beagle'] +sources = ['%%(namelower)s.%s.jar' % _revision] +checksums = ['57226e441f4da7104df139d022ed24ad9804fa72cf754e45d04f5658dcef242b'] + +dependencies = [('Java', '11')] + +# add beagle.jar +postinstallcmds = ["cd %%(installdir)s && ln -s %%(namelower)s.%s.jar %%(namelower)s.jar" % _revision] + +sanity_check_paths = { + 'files': ['%%(namelower)s.%s.jar' % _revision, '%(namelower)s.jar'], + 'dirs': [] +} + +modloadmsg = """ +To execute %(name)s-%(version)s run: java -jar ${EBROOTBEAGLE}/%(namelower)s.jar +""" + +moduleclass = 'bio' From 59a6fe8ac4f61a2517f94cfc0f1b42aaaee0ce6a Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 19 Dec 2022 00:48:07 +0100 Subject: [PATCH 778/939] push HighFive frmo foss/2021a down to gompi/2021a --- ...ghFive-2.6.2-foss-2021a.eb => HighFive-2.6.2-gompi-2021a.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/h/HighFive/{HighFive-2.6.2-foss-2021a.eb => HighFive-2.6.2-gompi-2021a.eb} (93%) diff --git a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2021a.eb similarity index 93% rename from easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb rename to easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2021a.eb index 476b4a265c3d..bedb87011ed1 100644 --- a/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-foss-2021a.eb +++ b/easybuild/easyconfigs/h/HighFive/HighFive-2.6.2-gompi-2021a.eb @@ -6,7 +6,7 @@ version = '2.6.2' homepage = 'https://github.com/BlueBrain/HighFive' description = """HighFive is a modern header-only C++11 friendly interface for libhdf5.""" -toolchain = {'name': 'foss', 'version': '2021a'} +toolchain = {'name': 'gompi', 'version': '2021a'} github_account = 'BlueBrain' source_urls = [GITHUB_SOURCE] From e3eeb784225626075c33e069b9f12c71c4ee1e7c Mon Sep 17 00:00:00 2001 From: Miguel Dias Costa Date: Mon, 19 Dec 2022 15:29:21 +0800 Subject: [PATCH 779/939] adding easyconfigs: scikit-bio-0.5.7-foss-2020b.eb --- .../scikit-bio/scikit-bio-0.5.7-foss-2020b.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb diff --git a/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb new file mode 100644 index 000000000000..7ce9ef45be9d --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-bio/scikit-bio-0.5.7-foss-2020b.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'scikit-bio' +version = '0.5.7' + +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': '2020b'} + +dependencies = [ + ('Python', '3.8.6'), + ('SciPy-bundle', '2020.11'), + ('matplotlib', '3.3.3'), + ('scikit-learn', '0.23.2'), + ('IPython', '7.18.1'), + ('h5py', '3.1.0'), + ('Pillow', '8.0.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('msgpack', '1.0.1', { + 'checksums': ['7033215267a0e9f60f4a5e4fb2228a932c404f237817caff8dc3115d9e7cd975'], + }), + ('CacheControl', '0.12.11', { + 'checksums': ['a5b9fcc986b184db101aa280b42ecdcdfc524892596f606858e0b7a8b4d9e144'], + }), + ('hdmedians', '0.14.2', { + 'checksums': ['b47aecb16771e1ba0736557255d80ae0240b09156bff434321de559b359ac2d6'], + }), + ('lockfile', '0.12.2', { + 'checksums': ['6aed02de03cba24efabcd600b30540140634fc06cfa603822d508d5361e9f799'], + }), + ('natsort', '8.1.0', { + 'checksums': ['c7c1f3f27c375719a4dfcab353909fe39f26c2032a062a8c80cc844eaaca0445'], + }), + (name, version, { + 'modulename': 'skbio', + 'checksums': ['6343ca0c621e2fcc5d1c042c8be3200664c5325956a83bea751cf1bcc75d1da9'], + }), +] + +moduleclass = 'bio' From 3960ef30cb6a88b3bf7fe8ac3d920bed6ff2fd66 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Dec 2022 08:38:01 +0100 Subject: [PATCH 780/939] adding easyconfigs: CloudCompare-2.12.4-foss-2021b.eb --- .../CloudCompare-2.12.4-foss-2021b.eb | 76 +++++++++++++++++++ 1 file changed, 76 insertions(+) create mode 100644 easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb diff --git a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb new file mode 100644 index 000000000000..ebc938838cb0 --- /dev/null +++ b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb @@ -0,0 +1,76 @@ +easyblock = 'CMakeMake' + +name = 'CloudCompare' +version = '2.12.4' + +homepage = 'https://www.cloudcompare.org/' +description = "3D point cloud and mesh processing software" + +toolchain = {'name': 'foss', 'version': '2021b'} + +github_account = 'CloudCompare' +source_urls = [GITHUB_SOURCE] +sources = [ + 'v%(version)s.tar.gz', + { + 'filename': 'CCCoreLib-20220714.tar.gz', + 'git_config': { + 'url': 'https://github.com/CloudCompare', + 'repo_name': 'CCCoreLib', + 'commit': '54ecc7104ead3f203ac6454ff999afe5dac60f2c', + }, + 'extract_cmd': 'tar -C %(name)s-%(version)s/libs/qCC_db/extern -xf %s', + }, +] +checksums = [ + '31c1f4f91efbdb74619cebb36f57f999d6f1a57bb6f87b13e60d21e670c38f68', + None, +] + +builddependencies = [ + ('CMake', '3.22.1'), +] + +dependencies = [ + ('Qt5', '5.15.2'), + ('GDAL', '3.3.2'), + ('Eigen', '3.3.9'), +] + +_copts = [ + '-DEIGEN_ROOT_DIR=$EBROOTEIGEN', + '-DOpenGL_GL_PREFERENCE=GLVND', + '-DOPTION_USE_GDAL=1', + '-DPLUGIN_GL_QEDL=1', + '-DPLUGIN_GL_QSSAO=1', + '-DPLUGIN_IO_QADDITIONAL=1', + '-DPLUGIN_IO_QCSV_MATRIX=1', + '-DPLUGIN_IO_QPHOTOSCAN=1', + '-DPLUGIN_STANDARD_QBROOM=1', + '-DPLUGIN_STANDARD_QCOMPASS=1', + '-DPLUGIN_STANDARD_QCSF=1', + '-DPLUGIN_STANDARD_QFACETS=1', + '-DPLUGIN_STANDARD_QHOUGH_NORMALS=1', + '-DPLUGIN_STANDARD_QHPR=1', + '-DPLUGIN_STANDARD_QM3C2=1', + '-DPLUGIN_STANDARD_QPCV=1', + '-DPLUGIN_STANDARD_QRANSAC_SD=1', + '-DPLUGIN_STANDARD_QSRA=1', +] +configopts = ' '.join(_copts) + +sanity_check_paths = { + 'files': + ['bin/%s' % x for x in ['CloudCompare', 'ccViewer']] + + ['lib/cloudcompare/lib%s.%s' % (x, SHLIB_EXT) for x in [ + 'CCAppCommon', 'CCCoreLib', 'CC_FBO_LIB', 'CCPluginAPI', 'QCC_DB_LIB', 'QCC_GL_LIB', 'QCC_IO_LIB' + ]] + + ['lib/cloudcompare/plugins/lib%s_PLUGIN.%s' % (x, SHLIB_EXT) for x in [ + 'QCORE_IO', 'QEDL_GL', 'QSSAO_GL', 'QADDITIONAL_IO', 'QCSV_MATRIX_IO', 'QPHOTOSCAN_IO', + 'QBROOM', 'QCANUPO', 'QCOMPASS', 'QCSF', 'QFACETS', 'QHOUGH_NORMALS', 'QHPR', 'QM3C2', + 'QPCV', 'QRANSAC_SD', 'QSRA', + ]], + 'dirs': ['share/cloudcompare/shaders'], +} + +moduleclass = 'geo' From 1afc71778feb6681ff552845fd31e3ac3c2221f1 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Dec 2022 08:44:15 +0100 Subject: [PATCH 781/939] Remove check for libQCANUPO_PLUGIN since it is not built at the moment. --- .../c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb index ebc938838cb0..9262cad1523e 100644 --- a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb @@ -67,7 +67,7 @@ sanity_check_paths = { ]] + ['lib/cloudcompare/plugins/lib%s_PLUGIN.%s' % (x, SHLIB_EXT) for x in [ 'QCORE_IO', 'QEDL_GL', 'QSSAO_GL', 'QADDITIONAL_IO', 'QCSV_MATRIX_IO', 'QPHOTOSCAN_IO', - 'QBROOM', 'QCANUPO', 'QCOMPASS', 'QCSF', 'QFACETS', 'QHOUGH_NORMALS', 'QHPR', 'QM3C2', + 'QBROOM', 'QCOMPASS', 'QCSF', 'QFACETS', 'QHOUGH_NORMALS', 'QHPR', 'QM3C2', 'QPCV', 'QRANSAC_SD', 'QSRA', ]], 'dirs': ['share/cloudcompare/shaders'], From 200a26faa500f8764b58aaa700e23d542595f549 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Mon, 19 Dec 2022 10:00:53 +0100 Subject: [PATCH 782/939] CloudCompare: Update to using Eigen 3.4.0 to match other easyconfigs in 2021b. --- .../c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb index 9262cad1523e..c8b47a5dd75a 100644 --- a/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb +++ b/easybuild/easyconfigs/c/CloudCompare/CloudCompare-2.12.4-foss-2021b.eb @@ -34,7 +34,7 @@ builddependencies = [ dependencies = [ ('Qt5', '5.15.2'), ('GDAL', '3.3.2'), - ('Eigen', '3.3.9'), + ('Eigen', '3.4.0'), ] _copts = [ From a89a5a040bfeeb521f716006fe072fa672f9caf5 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 19 Dec 2022 12:59:20 +0100 Subject: [PATCH 783/939] Remove redundant patch from CubeGUI --- .../c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb | 18 +- .../CubeGUI-4.8_missing_compile_file.patch | 356 ------------------ 2 files changed, 3 insertions(+), 371 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb index 90d43bac7414..548d1fbc2c40 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb @@ -30,25 +30,13 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://apps.fz-juelich.de/scalasca/releases/cube/%(version)s/dist'] sources = [SOURCELOWER_TAR_GZ] -patches = [ - ('CubeGUI-4.8_missing_compile_file.patch', 1), -] -checksums = [ - '1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76', # cubegui-4.8.tar.gz - '487697669f6a9a3455fabfdb65d720699070986776c465830ad417942e25e2dc', # CubeGUI-4.8_missing_compile_file.patch -] - -preconfigopts = 'autoreconf && autoreconf build-frontend/ && ' +checksums = ['1df8fcaea95323e7eaf0cc010784a41243532c2123a27ce93cb7e3241557ff76'] -builddependencies = [ - # use same binutils version that was used when building GCCcore - ('binutils', '2.38'), - ('Autotools', '20220317'), - ('CubeLib', '4.8'), -] +builddependencies = [('binutils', '2.38')] dependencies = [ ('Qt5', '5.15.5'), + ('CubeLib', '4.8'), ] configopts = [ diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch deleted file mode 100644 index d7a92c4db957..000000000000 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8_missing_compile_file.patch +++ /dev/null @@ -1,356 +0,0 @@ -# This patch adds the "build-config/compile" file that is missing in v4.8 -# The file is copied "as is" from CubeGUI v4.6. -# -# Author: maxim-masterov (SURF) - -diff -Nru cubegui-4.8.orig/build-config/compile cubegui-4.8/build-config/compile ---- cubegui-4.8.orig/build-config/compile 1970-01-01 01:00:00.000000000 +0100 -+++ cubegui-4.8/build-config/compile 2022-12-12 13:16:45.979205634 +0100 -@@ -0,0 +1,347 @@ -+#! /bin/sh -+# Wrapper for compilers which do not understand '-c -o'. -+ -+scriptversion=2012-10-14.11; # UTC -+ -+# Copyright (C) 1999-2013 Free Software Foundation, Inc. -+# Written by Tom Tromey . -+# -+# This program is free software; you can redistribute it and/or modify -+# it under the terms of the GNU General Public License as published by -+# the Free Software Foundation; either version 2, or (at your option) -+# any later version. -+# -+# This program is distributed in the hope that it will be useful, -+# but WITHOUT ANY WARRANTY; without even the implied warranty of -+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -+# GNU General Public License for more details. -+# -+# You should have received a copy of the GNU General Public License -+# along with this program. If not, see . -+ -+# As a special exception to the GNU General Public License, if you -+# distribute this file as part of a program that contains a -+# configuration script generated by Autoconf, you may include it under -+# the same distribution terms that you use for the rest of that program. -+ -+# This file is maintained in Automake, please report -+# bugs to or send patches to -+# . -+ -+nl=' -+' -+ -+# We need space, tab and new line, in precisely that order. Quoting is -+# there to prevent tools from complaining about whitespace usage. -+IFS=" "" $nl" -+ -+file_conv= -+ -+# func_file_conv build_file lazy -+# Convert a $build file to $host form and store it in $file -+# Currently only supports Windows hosts. If the determined conversion -+# type is listed in (the comma separated) LAZY, no conversion will -+# take place. -+func_file_conv () -+{ -+ file=$1 -+ case $file in -+ / | /[!/]*) # absolute file, and not a UNC file -+ if test -z "$file_conv"; then -+ # lazily determine how to convert abs files -+ case `uname -s` in -+ MINGW*) -+ file_conv=mingw -+ ;; -+ CYGWIN*) -+ file_conv=cygwin -+ ;; -+ *) -+ file_conv=wine -+ ;; -+ esac -+ fi -+ case $file_conv/,$2, in -+ *,$file_conv,*) -+ ;; -+ mingw/*) -+ file=`cmd //C echo "$file " | sed -e 's/"\(.*\) " *$/\1/'` -+ ;; -+ cygwin/*) -+ file=`cygpath -m "$file" || echo "$file"` -+ ;; -+ wine/*) -+ file=`winepath -w "$file" || echo "$file"` -+ ;; -+ esac -+ ;; -+ esac -+} -+ -+# func_cl_dashL linkdir -+# Make cl look for libraries in LINKDIR -+func_cl_dashL () -+{ -+ func_file_conv "$1" -+ if test -z "$lib_path"; then -+ lib_path=$file -+ else -+ lib_path="$lib_path;$file" -+ fi -+ linker_opts="$linker_opts -LIBPATH:$file" -+} -+ -+# func_cl_dashl library -+# Do a library search-path lookup for cl -+func_cl_dashl () -+{ -+ lib=$1 -+ found=no -+ save_IFS=$IFS -+ IFS=';' -+ for dir in $lib_path $LIB -+ do -+ IFS=$save_IFS -+ if $shared && test -f "$dir/$lib.dll.lib"; then -+ found=yes -+ lib=$dir/$lib.dll.lib -+ break -+ fi -+ if test -f "$dir/$lib.lib"; then -+ found=yes -+ lib=$dir/$lib.lib -+ break -+ fi -+ if test -f "$dir/lib$lib.a"; then -+ found=yes -+ lib=$dir/lib$lib.a -+ break -+ fi -+ done -+ IFS=$save_IFS -+ -+ if test "$found" != yes; then -+ lib=$lib.lib -+ fi -+} -+ -+# func_cl_wrapper cl arg... -+# Adjust compile command to suit cl -+func_cl_wrapper () -+{ -+ # Assume a capable shell -+ lib_path= -+ shared=: -+ linker_opts= -+ for arg -+ do -+ if test -n "$eat"; then -+ eat= -+ else -+ case $1 in -+ -o) -+ # configure might choose to run compile as 'compile cc -o foo foo.c'. -+ eat=1 -+ case $2 in -+ *.o | *.[oO][bB][jJ]) -+ func_file_conv "$2" -+ set x "$@" -Fo"$file" -+ shift -+ ;; -+ *) -+ func_file_conv "$2" -+ set x "$@" -Fe"$file" -+ shift -+ ;; -+ esac -+ ;; -+ -I) -+ eat=1 -+ func_file_conv "$2" mingw -+ set x "$@" -I"$file" -+ shift -+ ;; -+ -I*) -+ func_file_conv "${1#-I}" mingw -+ set x "$@" -I"$file" -+ shift -+ ;; -+ -l) -+ eat=1 -+ func_cl_dashl "$2" -+ set x "$@" "$lib" -+ shift -+ ;; -+ -l*) -+ func_cl_dashl "${1#-l}" -+ set x "$@" "$lib" -+ shift -+ ;; -+ -L) -+ eat=1 -+ func_cl_dashL "$2" -+ ;; -+ -L*) -+ func_cl_dashL "${1#-L}" -+ ;; -+ -static) -+ shared=false -+ ;; -+ -Wl,*) -+ arg=${1#-Wl,} -+ save_ifs="$IFS"; IFS=',' -+ for flag in $arg; do -+ IFS="$save_ifs" -+ linker_opts="$linker_opts $flag" -+ done -+ IFS="$save_ifs" -+ ;; -+ -Xlinker) -+ eat=1 -+ linker_opts="$linker_opts $2" -+ ;; -+ -*) -+ set x "$@" "$1" -+ shift -+ ;; -+ *.cc | *.CC | *.cxx | *.CXX | *.[cC]++) -+ func_file_conv "$1" -+ set x "$@" -Tp"$file" -+ shift -+ ;; -+ *.c | *.cpp | *.CPP | *.lib | *.LIB | *.Lib | *.OBJ | *.obj | *.[oO]) -+ func_file_conv "$1" mingw -+ set x "$@" "$file" -+ shift -+ ;; -+ *) -+ set x "$@" "$1" -+ shift -+ ;; -+ esac -+ fi -+ shift -+ done -+ if test -n "$linker_opts"; then -+ linker_opts="-link$linker_opts" -+ fi -+ exec "$@" $linker_opts -+ exit 1 -+} -+ -+eat= -+ -+case $1 in -+ '') -+ echo "$0: No command. Try '$0 --help' for more information." 1>&2 -+ exit 1; -+ ;; -+ -h | --h*) -+ cat <<\EOF -+Usage: compile [--help] [--version] PROGRAM [ARGS] -+ -+Wrapper for compilers which do not understand '-c -o'. -+Remove '-o dest.o' from ARGS, run PROGRAM with the remaining -+arguments, and rename the output as expected. -+ -+If you are trying to build a whole package this is not the -+right script to run: please start by reading the file 'INSTALL'. -+ -+Report bugs to . -+EOF -+ exit $? -+ ;; -+ -v | --v*) -+ echo "compile $scriptversion" -+ exit $? -+ ;; -+ cl | *[/\\]cl | cl.exe | *[/\\]cl.exe ) -+ func_cl_wrapper "$@" # Doesn't return... -+ ;; -+esac -+ -+ofile= -+cfile= -+ -+for arg -+do -+ if test -n "$eat"; then -+ eat= -+ else -+ case $1 in -+ -o) -+ # configure might choose to run compile as 'compile cc -o foo foo.c'. -+ # So we strip '-o arg' only if arg is an object. -+ eat=1 -+ case $2 in -+ *.o | *.obj) -+ ofile=$2 -+ ;; -+ *) -+ set x "$@" -o "$2" -+ shift -+ ;; -+ esac -+ ;; -+ *.c) -+ cfile=$1 -+ set x "$@" "$1" -+ shift -+ ;; -+ *) -+ set x "$@" "$1" -+ shift -+ ;; -+ esac -+ fi -+ shift -+done -+ -+if test -z "$ofile" || test -z "$cfile"; then -+ # If no '-o' option was seen then we might have been invoked from a -+ # pattern rule where we don't need one. That is ok -- this is a -+ # normal compilation that the losing compiler can handle. If no -+ # '.c' file was seen then we are probably linking. That is also -+ # ok. -+ exec "$@" -+fi -+ -+# Name of file we expect compiler to create. -+cofile=`echo "$cfile" | sed 's|^.*[\\/]||; s|^[a-zA-Z]:||; s/\.c$/.o/'` -+ -+# Create the lock directory. -+# Note: use '[/\\:.-]' here to ensure that we don't use the same name -+# that we are using for the .o file. Also, base the name on the expected -+# object file name, since that is what matters with a parallel build. -+lockdir=`echo "$cofile" | sed -e 's|[/\\:.-]|_|g'`.d -+while true; do -+ if mkdir "$lockdir" >/dev/null 2>&1; then -+ break -+ fi -+ sleep 1 -+done -+# FIXME: race condition here if user kills between mkdir and trap. -+trap "rmdir '$lockdir'; exit 1" 1 2 15 -+ -+# Run the compile. -+"$@" -+ret=$? -+ -+if test -f "$cofile"; then -+ test "$cofile" = "$ofile" || mv "$cofile" "$ofile" -+elif test -f "${cofile}bj"; then -+ test "${cofile}bj" = "$ofile" || mv "${cofile}bj" "$ofile" -+fi -+ -+rmdir "$lockdir" -+exit $ret -+ -+# Local Variables: -+# mode: shell-script -+# sh-indentation: 2 -+# eval: (add-hook 'write-file-hooks 'time-stamp) -+# time-stamp-start: "scriptversion=" -+# time-stamp-format: "%:y-%02m-%02d.%02H" -+# time-stamp-time-zone: "UTC" -+# time-stamp-end: "; # UTC" -+# End: From f5aec762f9bead2c171bb79587a508fdc9ee2bdc Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 19 Dec 2022 13:25:32 +0100 Subject: [PATCH 784/939] Change version --- ...re-P-8.0-rc1-gompi-2022a.eb => Score-P-8.0-gompi-2022a.eb} | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) rename easybuild/easyconfigs/s/Score-P/{Score-P-8.0-rc1-gompi-2022a.eb => Score-P-8.0-gompi-2022a.eb} (94%) diff --git a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb similarity index 94% rename from easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb rename to easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb index efea7c597cec..3b6348b0077d 100644 --- a/easybuild/easyconfigs/s/Score-P/Score-P-8.0-rc1-gompi-2022a.eb +++ b/easybuild/easyconfigs/s/Score-P/Score-P-8.0-gompi-2022a.eb @@ -13,7 +13,7 @@ ## name = 'Score-P' -version = '8.0-rc1' +version = '8.0' homepage = 'https://www.score-p.org' description = """ @@ -26,7 +26,7 @@ toolchain = {'name': 'gompi', 'version': '2022a'} source_urls = ['https://perftools.pages.jsc.fz-juelich.de/cicd/scorep/tags/scorep-%(version)s'] sources = ['scorep-%(version)s.tar.gz'] -checksums = ['d5975e69a594fff4982701f5181b4825386a238a95df68a0d5c1e1b62480add7'] +checksums = ['4c0f34f20999f92ebe6ca1ff706d0846b8ce6cd537ffbedb49dfaef0faa66311'] dependencies = [ ('CubeLib', '4.8'), From e8803bb5798d24c757bb3bc5c1c664011fb60313 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Mon, 19 Dec 2022 13:48:45 +0100 Subject: [PATCH 785/939] Remove redundant CXX flag --- easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb index 548d1fbc2c40..516af3a8db55 100644 --- a/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/c/CubeGUI/CubeGUI-4.8-GCCcore-11.3.0.eb @@ -40,7 +40,7 @@ dependencies = [ ] configopts = [ - 'CXX="g++" --with-qt=$EBROOTQT5/bin ', + '--with-qt=$EBROOTQT5/bin ', ] sanity_check_paths = { From 4209d05fe8fc1ac58a1a9127be7a223fb59b9281 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Mon, 19 Dec 2022 15:02:50 +0100 Subject: [PATCH 786/939] Bowtie2 2.4.4+ fix for non-x86_64 systems --- .../b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb | 23 +++++++++++++++---- .../b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb | 23 +++++++++++++++---- .../b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb | 23 +++++++++++++++---- 3 files changed, 57 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb index 85afb32d7a8c..1a4e8413c88e 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb @@ -7,11 +7,13 @@ # 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 = '2.4.4' -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +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. @@ -21,9 +23,22 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin 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 = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] +source_urls = [ + ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), + 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', +] +sources = [ + '%(namelower)s-%(version)s-source.zip', + # SIMD Everywhere implementations only, for non-x86_64 systems + {'download_filename': 'master.zip', + 'filename': 'simde-no-tests.master.zip', + 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', + }, +] +checksums = [ + 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip + 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb index 24d2f6861d98..f3b249e22f35 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb @@ -7,11 +7,13 @@ # 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 = '2.4.4' -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +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. @@ -21,9 +23,22 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.2.0'} 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 = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] +source_urls = [ + ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), + 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', +] +sources = [ + '%(namelower)s-%(version)s-source.zip', + # SIMD Everywhere implementations only, for non-x86_64 systems + {'download_filename': 'master.zip', + 'filename': 'simde-no-tests.master.zip', + 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', + }, +] +checksums = [ + 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip + 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip +] dependencies = [ ('zlib', '1.2.11'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb index 23f2eb1bda77..28ade29cb7e0 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb @@ -7,11 +7,13 @@ # 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 = '2.4.5' -homepage = 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' +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. @@ -21,9 +23,22 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.3.0'} 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 = ['d3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a'] +source_urls = [ + ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), + 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', +] +sources = [ + '%(namelower)s-%(version)s-source.zip', + # SIMD Everywhere implementations only, for non-x86_64 systems + {'download_filename': 'master.zip', + 'filename': 'simde-no-tests.master.zip', + 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', + }, +] +checksums = [ + 'd3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a', # bowtie2-2.4.5-source.zip + 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip +] dependencies = [ ('zlib', '1.2.12'), From f08c670586960356ba4d49239c61d16349b815de Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Mon, 19 Dec 2022 17:21:07 +0100 Subject: [PATCH 787/939] Added support for KaHIP library --- .../o/OpenFOAM/OpenFOAM-v2206-cleanup.patch | 159 ++++++++++++++++++ .../o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb | 5 +- 2 files changed, 162 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch new file mode 100644 index 000000000000..ffc27639061b --- /dev/null +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-cleanup.patch @@ -0,0 +1,159 @@ +# 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 +# ------------------------------------------------------------------------- +--- /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="$METIS_ROOT" ++ ++##Easybuild## +--- /dev/null 2022-12-01 18:21:35.103878336 +0100 ++++ OpenFOAM-v2206/etc/easybuild/config.sh/kahip 2022-12-12 20:24:07.538408981 +0100 +@@ -0,0 +1,6 @@ ++##Easybuild## settings -*- sh -*- ++ ++KAHIP_VERSION="kahip-$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 ++ ++#------------------------------------------------------------------------------ diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb index 4c58236cb3be..e15587e68ee8 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-v2206-foss-2022a.eb @@ -16,12 +16,12 @@ 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-v2206-cleanup.patch', 1), 'OpenFOAM-v1906-wmake-ompi.patch', ] checksums = [ 'db95eda4afb97ca870733b2d4201ef539099d0778e3f3eca9a075d4f1a0eea46', # OpenFOAM-v2206.tgz - 'cdd2597a1ac1448e9bd33a364a8dfe17f51cc9ab5a8e0ab67cf92bba3ed9da43', # OpenFOAM-v2012-cleanup.patch + '25333124581acae57c173587de4ebd6e143b894b1a26e4f0326db8b7e0cb1972', # OpenFOAM-v2206-cleanup.patch '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch ] @@ -37,6 +37,7 @@ dependencies = [ # OpenFOAM requires 64 bit METIS using 32 bit indexes (array indexes) ('METIS', '5.1.0'), ('SCOTCH', '7.0.1'), + ('KaHIP', '3.14'), ('CGAL', '4.14.3'), ('ParaView', '5.10.1', '-mpi'), ('gnuplot', '5.4.4'), From b366c3526539c66753a65cf033a06a82fa374b85 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 18:46:47 +0100 Subject: [PATCH 788/939] use single rather than double quotes --- .../r/RegTools/RegTools-0.5.2-foss-2021b.eb | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb index b1a7c9fc772a..9c084bba01de 100644 --- a/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb +++ b/easybuild/easyconfigs/r/RegTools/RegTools-0.5.2-foss-2021b.eb @@ -1,39 +1,39 @@ # updated: Denis Kristak (INUITS) -easyblock = "CMakeMake" +easyblock = 'CMakeMake' -name = "RegTools" -version = "0.5.2" +name = 'RegTools' +version = '0.5.2' -homepage = "https://regtools.readthedocs.org" +homepage = 'https://regtools.readthedocs.org' description = """RegTools is a set of tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.""" -toolchain = {"name": "foss", "version": "2021b"} +toolchain = {'name': 'foss', 'version': '2021b'} -source_urls = ["https://github.com/griffithlab/%(namelower)s/archive"] -sources = ["%(version)s.tar.gz"] +source_urls = ['https://github.com/griffithlab/%(namelower)s/archive'] +sources = ['%(version)s.tar.gz'] checksums = ['24d3bc18174237e0fc2d0330839c8dc21c97cdb7d6e528c518188c10f17f3e7e'] builddependencies = [ - ("CMake", "3.21.1"), + ('CMake', '3.21.1'), ] # required by included scripts dependencies = [ - ("Python", "3.9.6"), - ("PyYAML", "5.4.1"), # required by create_IGVsessions.py script - ("R", "4.1.2"), + ('Python', '3.9.6'), + ('PyYAML', '5.4.1'), # required by create_IGVsessions.py script + ('R', '4.1.2'), ] # 'make install' is not supported... -install_cmd = "mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && " -install_cmd += "cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/" +install_cmd = 'mkdir %(installdir)s/bin && cp -a regtools %(installdir)s/bin/ && ' +install_cmd += 'cp -a %(builddir)s/regtools-%(version)s/scripts %(installdir)s/' sanity_check_paths = { - "files": ["bin/regtools"], - "dirs": ["scripts"], + 'files': ['bin/regtools'], + 'dirs': ['scripts'], } -sanity_check_commands = ["regtools --help"] +sanity_check_commands = ['regtools --help'] -moduleclass = "bio" +moduleclass = 'bio' From c737acda45339c4988df56b49b6392094bdf0645 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 18:52:35 +0100 Subject: [PATCH 789/939] use single rather than double quotes --- .../b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb index 0e4aad5edd50..2a76d9d7b501 100644 --- a/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb +++ b/easybuild/easyconfigs/b/BEDOPS/BEDOPS-2.4.41-foss-2021b.eb @@ -1,40 +1,40 @@ # This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild # updated: Denis Kristak (INUITS) -easyblock = "MakeCp" +easyblock = 'MakeCp' -name = "BEDOPS" -version = "2.4.41" +name = 'BEDOPS' +version = '2.4.41' -homepage = "http://%(namelower)s.readthedocs.io/en/latest/index.html" +homepage = 'http://%(namelower)s.readthedocs.io/en/latest/index.html' description = """BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.""" -toolchain = {"name": "foss", "version": "2021b"} -toolchainopts = {"pic": True} +toolchain = {'name': 'foss', 'version': '2021b'} +toolchainopts = {'pic': True} -source_urls = ["https://github.com/%(namelower)s/%(namelower)s/archive/"] -sources = ["v%(version)s.tar.gz"] +source_urls = ['https://github.com/%(namelower)s/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] checksums = ['3b868c820d59dd38372417efc31e9be3fbdca8cf0a6b39f13fb2b822607d6194'] -# else build of jansson library fails with: "configure: error: C compiler cannot create executables" -prebuildopts = "unset LIBS && " +# else build of jansson library fails with: 'configure: error: C compiler cannot create executables' +prebuildopts = 'unset LIBS && ' # builds all variants and copies executables to bin directory -buildopts = " all && make install" +buildopts = ' all && make install' # actually used variant is linked to via symlinks keepsymlinks = True -files_to_copy = ["bin"] +files_to_copy = ['bin'] sanity_check_paths = { - "files": [ - "bin/%s" % x for x in ["bam2bed", "%(namelower)s", "convert2bed", "unstarch"] + 'files': [ + 'bin/%s' % x for x in ['bam2bed', '%(namelower)s', 'convert2bed', 'unstarch'] ], - "dirs": [], + 'dirs': [], } -sanity_check_commands = ["%(namelower)s --help"] +sanity_check_commands = ['%(namelower)s --help'] -moduleclass = "bio" +moduleclass = 'bio' From f91335c8d9f56be34f08e50801271b699e17e39e Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 19:03:54 +0100 Subject: [PATCH 790/939] use single rather than double quotes --- .../p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb | 31 +++++++++---------- 1 file changed, 14 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb index 399609c8b90d..5a1c4f1c964c 100644 --- a/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/p/PsiCLASS/PsiCLASS-1.0.3-GCC-11.2.0.eb @@ -1,34 +1,31 @@ # author: Denis Kristak (INUITS) -easyblock = "MakeCp" +easyblock = 'MakeCp' -name = "PsiCLASS" -version = "1.0.3" +name = 'PsiCLASS' +version = '1.0.3' -homepage = "https://github.com/splicebox/PsiCLASS" +homepage = 'https://github.com/splicebox/PsiCLASS' description = """PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples.""" -toolchain = {"name": "GCC", "version": "11.2.0"} +toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ["https://github.com/splicebox/PsiCLASS/archive/"] -sources = ["v%(version)s.tar.gz"] - -checksums = [ - "c60c0f33f9a076b97ccdba68b9140a5fb6936a5c5e309d70b3d0cf558828f73d", # v1.0.3.tar.gz -] +source_urls = ['https://github.com/splicebox/PsiCLASS/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c60c0f33f9a076b97ccdba68b9140a5fb6936a5c5e309d70b3d0cf558828f73d'] parallel = 1 -files_to_copy = ["*"] +files_to_copy = ['*'] -modextrapaths = {"PATH": [""]} +modextrapaths = {'PATH': ''} sanity_check_paths = { - "files": ["classes", "grader", "psiclass"], - "dirs": [], + 'files': ['classes', 'grader', 'psiclass'], + 'dirs': [], } sanity_check_commands = [ - "psiclass -b $EBROOTPSICLASS/example/s1.bam,$EBROOTPSICLASS/example/s2.bam" + 'psiclass -b $EBROOTPSICLASS/example/s1.bam,$EBROOTPSICLASS/example/s2.bam' ] -moduleclass = "bio" +moduleclass = 'bio' From 00c182f892a0ce081653700c14652c83f299ef38 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 19:46:53 +0100 Subject: [PATCH 791/939] use single rather than double quotes --- .../GeneMark-ET-4.71-GCCcore-11.2.0.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb index 9d7b048917cd..7c3550e3cb56 100644 --- a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb @@ -1,15 +1,15 @@ # updated: Denis Kristak (INUITS) -easyblock = "Tarball" +easyblock = 'Tarball' -name = "GeneMark-ET" -version = "4.71" +name = 'GeneMark-ET' +version = '4.71' -homepage = "http://exon.gatech.edu/GeneMark" +homepage = 'http://exon.gatech.edu/GeneMark' description = "Eukaryotic gene prediction suite with automatic training" -toolchain = {"name": "GCCcore", "version": "11.2.0"} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} -sources = ["gmes_linux_64-%(version)s.tar.gz"] +sources = ['gmes_linux_64-%(version)s.tar.gz'] checksums = ['29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95'] download_instructions = """ @@ -17,15 +17,15 @@ download_instructions = """ 2. rename the tarball: `mv gmes_linux_64.tar.gz gmes_linux_64-%(version)s.tar.gz` """ -dependencies = [("Perl", "5.34.0")] +dependencies = [('Perl', '5.34.0')] -fix_perl_shebang_for = ["*.pl"] +fix_perl_shebang_for = ['*.pl'] sanity_check_paths = { - "files": ["gmes.cfg", "gmes_petap.pl"], - "dirs": ["lib"], + 'files': ['gmes.cfg', 'gmes_petap.pl'], + 'dirs': ['lib'], } -modextrapaths = {"PATH": ""} +modextrapaths = {'PATH': ''} -moduleclass = "bio" +moduleclass = 'bio' From ccdea8325804196009ff9f779fbffbbb3443f94c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 19:57:18 +0100 Subject: [PATCH 792/939] use single rather than double quotes --- .../o/olego/olego-1.1.9-GCC-11.2.0.eb | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb index 89c892a1f8a8..5bb617a46272 100644 --- a/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/o/olego/olego-1.1.9-GCC-11.2.0.eb @@ -1,28 +1,28 @@ # updated by: Denis Kristak (INUITS) -easyblock = "MakeCp" +easyblock = 'MakeCp' -name = "olego" -version = "1.1.9" +name = 'olego' +version = '1.1.9' -homepage = "https://github.com/chaolinzhanglab/olego" +homepage = 'https://github.com/chaolinzhanglab/olego' description = """OLego is a program specifically designed for de novo spliced mapping of mRNA-seq reads. OLego adopts a seed-and-extend scheme, and does not rely on a separate external mapper.""" -toolchain = {"name": "GCC", "version": "11.2.0"} +toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ["https://github.com/chaolinzhanglab/olego//archive/"] -sources = ["v%(version)s.tar.gz"] +source_urls = ['https://github.com/chaolinzhanglab/olego//archive/'] +sources = ['v%(version)s.tar.gz'] checksums = ['1b6ba7a4a310ac71667052d3a6e1f073d3976302ab6b6b67041475f7ca1f4bac'] -files_to_copy = ["*"] +files_to_copy = ['*'] -modextrapaths = {"PATH": [""]} +modextrapaths = {'PATH': ''} sanity_check_paths = { - "files": ["olegoindex", "olego"], - "dirs": [], + 'files': ['olegoindex', 'olego'], + 'dirs': [], } sanity_check_commands = ['olego 2>&1 | grep "version %(version)s"'] -moduleclass = "bio" +moduleclass = 'bio' From d40f513485de9c8af036b9451acb7460b53e87a7 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Mon, 19 Dec 2022 20:03:22 +0100 Subject: [PATCH 793/939] add alternative checksum --- .../g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb index 7c3550e3cb56..017e077aa136 100644 --- a/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/g/GeneMark-ET/GeneMark-ET-4.71-GCCcore-11.2.0.eb @@ -10,7 +10,10 @@ description = "Eukaryotic gene prediction suite with automatic training" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} sources = ['gmes_linux_64-%(version)s.tar.gz'] -checksums = ['29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95'] +checksums = [( + '29adf580ccee6f69d19045bedc3a53e7a71b4c39a95409be3e96d3e9dca83c95', + '629f430e7262bdb5df8f24413e65d26e35eb10ea34212145b692ee4689591e54', +)] download_instructions = """ 1. complete the license form: http://exon.gatech.edu/GeneMark/license_download.cgi From ae193a1c63f27f02274e944706d5adcd44ad73e7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Mon, 19 Dec 2022 20:15:14 +0100 Subject: [PATCH 794/939] adding easyconfigs: OpenSceneGraph-3.6.5-foss-2022a.eb, librsvg-2.55.1-GCCcore-11.3.0.eb, poppler-22.12.0-GCC-11.3.0.eb --- .../librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb | 40 +++++++++++++ .../OpenSceneGraph-3.6.5-foss-2022a.eb | 51 +++++++++++++++++ .../p/poppler/poppler-22.12.0-GCC-11.3.0.eb | 57 +++++++++++++++++++ 3 files changed, 148 insertions(+) create mode 100644 easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb create mode 100644 easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..8116a32cafc2 --- /dev/null +++ b/easybuild/easyconfigs/l/librsvg/librsvg-2.55.1-GCCcore-11.3.0.eb @@ -0,0 +1,40 @@ +easyblock = 'ConfigureMake' + +name = 'librsvg' +version = '2.55.1' + +homepage = 'https://wiki.gnome.org/Projects/LibRsvg' +description = "Librsvg is a library to render SVG files using cairo." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://download.gnome.org/sources/librsvg/%(version_major_minor)s/'] +sources = [SOURCE_TAR_XZ] +checksums = ['6baf48a9d3a56fd13bbfbb9f1f76759b240b70a1fa220fd238474d66a926f98c'] + +builddependencies = [ + ('binutils', '2.38'), + ('Rust', '1.60.0'), +] + +dependencies = [ + ('cairo', '1.17.4'), + ('freetype', '2.12.1'), + ('Gdk-Pixbuf', '2.42.8'), + ('HarfBuzz', '4.2.1'), + ('Pango', '1.50.7'), + ('GObject-Introspection', '1.72.0'), +] + +# 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' diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb new file mode 100644 index 000000000000..049ea1ecc5c1 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb @@ -0,0 +1,51 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Author: Jiri Furst +### + +easyblock = 'CMakeMake' + +name = 'OpenSceneGraph' +version = '3.6.5' + +homepage = 'http://www.openscenegraph.org/' +description = """The OpenSceneGraph is an open source high performance 3D graphics toolkit, +used by application developers in fields such as visual simulation, games, virtual reality, +scientific visualization and modelling. Written entirely in Standard C++ and OpenGL it runs +on all Windows platforms, OSX, GNU/Linux, IRIX, Solaris, HP-Ux, AIX and FreeBSD operating +systems. The OpenSceneGraph is now well established as the world leading scene graph +technology, used widely in the vis-sim, space, scientific, oil-gas, games and virtual +reality industries.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = [GITHUB_SOURCE] +sources = ['OpenSceneGraph-%(version)s.tar.gz'] +checksums = ['aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12'] + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('X11', '20220504'), + ('Mesa', '22.0.3'), + ('GDAL', '3.5.0'), + ('DCMTK', '3.6.7'), + ('OpenEXR', '3.1.5'), + ('SDL2', '2.0.22'), + ('poppler', '22.12.0'), + ('librsvg', '2.55.1'), + ('giflib', '5.2.1'), +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['osgarchive', 'osgconv', 'osgfilecache', 'osgversion', 'osgviewer', 'present3D']], + 'dirs': ['lib'], +} + +sanity_check_commands = ['osgversion'] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..dc7391dd572f --- /dev/null +++ b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb @@ -0,0 +1,57 @@ +easyblock = 'Bundle' + +name = 'poppler' +version = '22.12.0' + +homepage = 'https://poppler.freedesktop.org' +description = "Poppler is a PDF rendering library" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('freetype', '2.12.1'), + ('fontconfig', '2.14.0'), + ('libjpeg-turbo', '2.1.3'), + ('libpng', '1.6.37'), + ('NSS', '3.79'), + ('LibTIFF', '4.3.0'), + ('Qt5', '5.15.5'), + ('Boost', '1.79.0'), + ('cairo', '1.17.4'), + ('OpenJPEG', '2.5.0'), + ('zlib', '1.2.12'), +] + +default_easyblock = 'CMakeMake' + +default_component_specs = { + 'start_dir': '%(name)s-%(version)s', +} + +components = [ + (name, version, { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_XZ], + 'configopts': "-DENABLE_BOOST=ON", + }), + ('poppler-data', '0.4.11', { + 'source_urls': ['https://poppler.freedesktop.org/'], + 'sources': [SOURCE_TAR_GZ], + }), +] + +sanity_check_paths = { + 'files': ['bin/pdfinfo', 'lib/libpoppler.%s' % SHLIB_EXT, 'lib/libpoppler-cpp.%s' % SHLIB_EXT, + 'lib/libpoppler-glib.%s' % SHLIB_EXT, 'lib/libpoppler-qt5.%s' % SHLIB_EXT], + 'dirs': ['include/poppler', 'lib/pkgconfig', 'share'], +} + +sanity_check_commands = ["pdfinfo --help"] + +moduleclass = 'lib' From ed7bb90f0bf20a91e1056c2d01e0c24d10a50864 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Mon, 19 Dec 2022 20:50:40 +0100 Subject: [PATCH 795/939] Added missing checksums for poppler --- easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb index dc7391dd572f..ab2bab388264 100644 --- a/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/p/poppler/poppler-22.12.0-GCC-11.3.0.eb @@ -38,11 +38,13 @@ components = [ (name, version, { 'source_urls': ['https://poppler.freedesktop.org/'], 'sources': [SOURCE_TAR_XZ], + 'checksums': ['d9aa9cacdfbd0f8e98fc2b3bb008e645597ed480685757c3e7bc74b4278d15c0'], 'configopts': "-DENABLE_BOOST=ON", }), ('poppler-data', '0.4.11', { 'source_urls': ['https://poppler.freedesktop.org/'], 'sources': [SOURCE_TAR_GZ], + 'checksums': ['2cec05cd1bb03af98a8b06a1e22f6e6e1a65b1e2f3816cb3069bb0874825f08c'], }), ] From e35011389860b5a90a1748525630746a03bb6d1c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 09:29:35 +0100 Subject: [PATCH 796/939] adding easyconfigs: AdapterRemoval-2.3.3-GCC-11.3.0.eb --- .../AdapterRemoval-2.3.3-GCC-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..e93de5614246 --- /dev/null +++ b/easybuild/easyconfigs/a/AdapterRemoval/AdapterRemoval-2.3.3-GCC-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'AdapterRemoval' +version = '2.3.3' + +homepage = 'https://github.com/MikkelSchubert/adapterremoval' +description = """AdapterRemoval searches for and removes remnant adapter sequences + from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases + from the 3' end of reads following adapter removal.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'MikkelSchubert' +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['a1bdc054319ede085fc8a4e9867c23ffed7df5e97b99d52221b7c587d19418fc'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.12'), +] + +skipsteps = ['configure'] + +installopts = "PREFIX=%(installdir)s" + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': ['share'] +} + +sanity_check_commands = [('%(name)s', '--version')] + +moduleclass = 'bio' From cdbe59adaa4f98ae1a26b89c56b2653306688526 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 10:38:59 +0100 Subject: [PATCH 797/939] adding easyconfigs: CDO-2.1.1-gompi-2021a.eb, NCO-5.1.3-foss-2021a.eb --- .../c/CDO/CDO-2.1.1-gompi-2021a.eb | 53 +++++++++++++++++++ .../easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb | 44 +++++++++++++++ 2 files changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.eb create mode 100644 easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb 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 new file mode 100644 index 000000000000..33b3ae569e7e --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.1.1-gompi-2021a.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 = '2.1.1' + +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': '2021a'} +toolchainopts = {'cstd': 'c++17', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/27654'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['c29d084ccbda931d71198409fb2d14f99930db6e7a3654b3c0243ceb304755d9'] + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('cURL', '7.76.0'), + ('ecCodes', '2.22.1'), + ('FFTW', '3.3.9'), + ('HDF5', '1.10.7'), + ('libxml2', '2.9.10'), + ('netCDF', '4.8.0'), + ('PROJ', '8.0.1'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.36'), +] + +# 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 'CDI library version : %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb b/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb new file mode 100644 index 000000000000..2636620beaf8 --- /dev/null +++ b/easybuild/easyconfigs/n/NCO/NCO-5.1.3-foss-2021a.eb @@ -0,0 +1,44 @@ +easyblock = 'ConfigureMake' + +name = 'NCO' +version = '5.1.3' + +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': 'foss', 'version': '2021a'} + +source_urls = ['https://github.com/nco/nco/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f6766627dab3f067c88f2cd713e3058c324ea4f900fabf9755bdd8918c32de7b'] + +builddependencies = [ + ('Bison', '3.7.6'), + ('flex', '2.6.4'), +] + +dependencies = [ + ('UDUNITS', '2.2.28'), + ('expat', '2.2.9'), + ('ANTLR', '2.7.7', '-Java-11'), + ('libdap', '3.20.7'), + ('GSL', '2.7'), + ('netCDF', '4.8.0'), + ('ESMF', '8.1.1'), # 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 c124d09527017d24a12f761548ab352c147f2a30 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 11:20:00 +0100 Subject: [PATCH 798/939] adding easyconfigs: SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb --- ...euratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb diff --git a/easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb new file mode 100644 index 000000000000..4728174df2a5 --- /dev/null +++ b/easybuild/easyconfigs/s/SeuratDisk/SeuratDisk-0.0.0.9020-foss-2022a-R-4.2.1.eb @@ -0,0 +1,27 @@ +easyblock = 'RPackage' + +name = 'SeuratDisk' +local_commit = '9b89970' +version = '0.0.0.9020' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://github.com/mojaveazure/seurat-disk' +description = "Interfaces for HDF5-based Single Cell File Formats" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/mojaveazure/seurat-disk/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['323daf9db620fac1bbc2724e00cf89c9e496207111988bb03a592c8c2cb8dd06'] + +dependencies = [ + ('R', '4.2.1'), + ('R-bundle-Bioconductor', '3.15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'bio' From 4d1450592523ab5817cef3256899f0619828b7c2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 11:51:16 +0100 Subject: [PATCH 799/939] add zellkonverter to R-bundle-Bioconductor v3.15 w/ foss/2022a --- .../R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb index b73795d4c56b..70987c77acfe 100644 --- a/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb +++ b/easybuild/easyconfigs/r/R-bundle-Bioconductor/R-bundle-Bioconductor-3.15-foss-2022a-R-4.2.1.eb @@ -1116,6 +1116,18 @@ exts_list = [ ('HiCBricks', '1.14.0', { 'checksums': ['ac998260ffa66ec93a4c34e56cbaf392f76a848ae35b9ea987f0ec15f0adc47d'], }), + ('dir.expiry', '1.4.0', { + 'checksums': ['588f190e57f3e4a9196c48369e0f879436f1d124548b991203c75f0a51fd1c25'], + }), + ('basilisk.utils', '1.8.0', { + 'checksums': ['1356bb897401316fd0c8df916a9512ae8cb18739b447d2f211784a4a33d8d8ca'], + }), + ('basilisk', '1.8.1', { + 'checksums': ['f34a74870c59e84c3594eb2cab09a4a58ed6e994523cdb063a87161c458f9d8c'], + }), + ('zellkonverter', '1.6.5', { + 'checksums': ['669a314d8ca5f62d29a5ab42d51647c4c2a23e9ae2542921933d48a9e394b767'], + }), ] modextrapaths = {'R_LIBS_SITE': ''} From caa1c8159bfcd939ca5dc0580cb464598537db23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 20 Dec 2022 16:09:09 +0100 Subject: [PATCH 800/939] pkg-config replaced by pkgconf --- .../o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb index 049ea1ecc5c1..1b3f0538c07a 100644 --- a/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenSceneGraph/OpenSceneGraph-3.6.5-foss-2022a.eb @@ -26,7 +26,7 @@ checksums = ['aea196550f02974d6d09291c5d83b51ca6a03b3767e234a8c0e21322927d1e12'] builddependencies = [ ('CMake', '3.23.1'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ] dependencies = [ From 9901b1a1a2adc06619f0f2f7dc3d84dc60332493 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 20 Dec 2022 15:35:15 +0000 Subject: [PATCH 801/939] Demoted to GCCcore, other suggestions also added --- ...4.eb => simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb} | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/simint/{simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb => simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb} (88%) diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb similarity index 88% rename from easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb rename to easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb index ef7429557010..6198188f68f4 100644 --- a/easybuild/easyconfigs/s/simint/simint-0.7-foss-2021b-lmax-5-vec-avx-psi4.eb +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb @@ -10,6 +10,8 @@ easyblock = 'CMakeMake' name = 'simint' version = '0.7' local_lmax = '5' +# supported: {scalar, sse, avx, avxfma, micavx512} +# scalar ONLY FOR USE WITH simint-scalar (and only useful for benchmarks), micavx512 experimental! local_vec = 'avx' # custom configuration, to be used as dependency for PSI4 @@ -21,7 +23,7 @@ method of calculating electron repulsion integrals. Speedup is gained by vectorizing the primitive loop of the OS algorithm, with additional vectorization and optimizations left to the compiler.""" -toolchain = {'name': 'foss', 'version': '2021b'} +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} source_urls = ['https://www.bennyp.org/research/simint/download/'] sources = ['%(name)s-v%(version)s.tar.bz2'] @@ -29,6 +31,7 @@ checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] builddependencies = [ ('CMake', '3.22.1'), + ('binutils', '2.37'), ] local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax From 117b5cc28dadd4b5dea0fe369b4812c40c66e7cf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Tue, 20 Dec 2022 16:37:31 +0100 Subject: [PATCH 802/939] adding easyconfigs: Ruby-3.0.3-GCCcore-11.3.0.eb --- .../r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb | 163 ++++++++++++++++++ 1 file changed, 163 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb 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 new file mode 100644 index 000000000000..864a9112c6a2 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.3-GCCcore-11.3.0.eb @@ -0,0 +1,163 @@ +name = 'Ruby' +version = '3.0.3' + +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': '11.3.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac'] + +builddependencies = [('binutils', '2.38')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2022-12-20 +exts_list = [ + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.6.3', { + 'checksums': ['86aaea16adf346a2b22743d88f8dcceeb1038843989ab93cda44b5176c845459'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.23.0', { + 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.2.3', { + 'checksums': ['462979de2971b8df33c2ee797fd497731617241f9dcd93960cc3caccb2dd13d8'], + }), + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], + }), + ('faraday-net_http', '3.0.2', { + 'checksums': ['6882929abed8094e1ee30344a3369e856fe34530044630d1f652bf70ebd87e8d'], + }), + ('faraday', '1.2.0', { + 'checksums': ['bd5c138304ee53907f8d0747724660c3a1cdf77d530d1cecd70d141299194b99'], + }), + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.3.0', { + 'checksums': ['677985be912f33c90f98f229aaa0c0ddb2ef8776f21929a36eeeb25251c944da'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '5.0.1', { + 'checksums': ['65603917ff4ecb32f499f42c14951aeed2380054fa7fc51758fc0a8d455fe043'], + }), + ('addressable', '2.8.1', { + 'checksums': ['bc724a176ef02118c8a3ed6b5c04c39cf59209607ffcce77b91d0261dbadedfa'], + }), + ('concurrent-ruby', '1.1.10', { + 'checksums': ['244cb1ca0d91ec2c15ca2209507c39fb163336994428e16fbd3f465c87bd8e68'], + }), + ('i18n', '1.12.0', { + 'checksums': ['91e3cc1b97616d308707eedee413d82ee021d751c918661fb82152793e64aced'], + }), + ('minitest', '5.16.3', { + 'checksums': ['60f81ad96ca5518e1457bd29eb826db60f86fbbdf8c05eac63b4824ef1f52614'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.6.6', { + 'checksums': ['bb397b50c31127f8dab372fa9b21da1e7c453c5b57da172ed858136c6283f826'], + }), + ('activesupport', '5.2.8.1', { + 'checksums': ['f0498c616e1b243c7b56d67920c389f959c186ad7031569e80335b42e1d22564'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.16.0', { + 'checksums': ['bba0da1cea8ac3e1f5cdd7cb1cb5fc78d7ac562c33736f18f0c3eb2b63053d9e'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], + }), + ('rspec-support', '3.12.0', { + 'checksums': ['dd4d44b247ff679b95b5607ac5641d197a5f9b1d33f916123cb98fc5f917c58b'], + }), + ('rspec-mocks', '3.12.1', { + 'checksums': ['e0dd725c7d1c1417c3a1715ccc4e41c124fab6c05b2de5a91ce22d74ee301801'], + }), + ('rspec-expectations', '3.12.1', { + 'checksums': ['808b29f7f3ef4535fc897c10235b662bb6b58219406fec56158623b3a8e06c9e'], + }), + ('rspec-core', '3.12.0', { + 'checksums': ['c466f4137966526e177d2156ca45c249eeecc7ed519b23ae2fb80c4675406bc5'], + }), + ('rspec', '3.12.0', { + 'checksums': ['ccc41799a43509dc0be84070e3f0410ac95cbd480ae7b6c245543eb64162399c'], + }), + ('rack', '2.2.4', { + 'checksums': ['ea2232b638cbd919129c8c8ad8012ecaccc09f848152a7e705d2139d0137ac2b'], + }), + ('rack-protection', '3.0.5', { + 'checksums': ['3a428f9de18ee2a4080e2fab308f20f9e98d74dcbe06ed407a8035b46ba822a8'], + }), + ('tilt', '2.0.11', { + 'checksums': ['7b180fc472cbdeb186c85d31c0f2d1e61a2c0d77e1d9fd0ca28482a9d972d6a0'], + }), + ('mustermann', '3.0.0', { + 'checksums': ['6d3569aa3c3b2f048c60626f48d9b2d561cc8d2ef269296943b03da181c08b67'], + }), + ('sinatra', '3.0.5', { + 'checksums': ['40ec7643a65d01b9c25ab5f7cafc5c67ca0b9ac523fa728345d88de69392cee7'], + }), + ('rack-test', '2.0.2', { + 'checksums': ['adadd0e957f63a34199a9fdf905a920a0b0a50795735095b4ac4bd3c13385466'], + }), + ('bundler', '2.3.26', { + 'checksums': ['1ee53cdf61e728ad82c6dbff06cfcd8551d5422e88e86203f0e2dbe9ae999e09'], + })] + +moduleclass = 'lang' From 18c1eeb2e1ba0a1059f0d7be621bcfa9b84771c9 Mon Sep 17 00:00:00 2001 From: Vital-IT Date: Tue, 20 Dec 2022 17:09:42 +0100 Subject: [PATCH 803/939] Use a specific commit not the head + Download simde only if non-x86_64 --- .../b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb | 32 +++++++++---------- .../b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb | 32 +++++++++---------- .../b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb | 32 +++++++++---------- 3 files changed, 48 insertions(+), 48 deletions(-) diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb index 1a4e8413c88e..9fa06c8160c6 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-10.3.0.eb @@ -12,6 +12,8 @@ name = 'Bowtie2' version = '2.4.4' +_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 @@ -23,22 +25,20 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin 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'), - 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', -] -sources = [ - '%(namelower)s-%(version)s-source.zip', - # SIMD Everywhere implementations only, for non-x86_64 systems - {'download_filename': 'master.zip', - 'filename': 'simde-no-tests.master.zip', - 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', - }, -] -checksums = [ - 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip - 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip -] +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] + +# 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'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb index f3b249e22f35..5fc68b03499b 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.4-GCC-11.2.0.eb @@ -12,6 +12,8 @@ name = 'Bowtie2' version = '2.4.4' +_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 @@ -23,22 +25,20 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.2.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [ - ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), - 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', -] -sources = [ - '%(namelower)s-%(version)s-source.zip', - # SIMD Everywhere implementations only, for non-x86_64 systems - {'download_filename': 'master.zip', - 'filename': 'simde-no-tests.master.zip', - 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', - }, -] -checksums = [ - 'b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc', # bowtie2-2.4.4-source.zip - 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip -] +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['b9fc1d6e5b898f832c590023bcb15e2a7b76e0ffac486800a9897e7cba2175fc'] + +# 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'), diff --git a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb index 28ade29cb7e0..d7b304b4c3be 100644 --- a/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/b/Bowtie2/Bowtie2-2.4.5-GCC-11.3.0.eb @@ -12,6 +12,8 @@ name = 'Bowtie2' version = '2.4.5' +_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 @@ -23,22 +25,20 @@ description = """ Bowtie 2 is an ultrafast and memory-efficient tool for alignin toolchain = {'name': 'GCC', 'version': '11.3.0'} toolchainopts = {'pic': True, 'cstd': 'gnu++98'} -source_urls = [ - ('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download'), - 'https://github.com/simd-everywhere/simde-no-tests/archive/refs/heads', -] -sources = [ - '%(namelower)s-%(version)s-source.zip', - # SIMD Everywhere implementations only, for non-x86_64 systems - {'download_filename': 'master.zip', - 'filename': 'simde-no-tests.master.zip', - 'extract_cmd': 'unzip %s && mv simde-no-tests-master/* %(namelower)s-%(version)s/third_party/simde/', - }, -] -checksums = [ - 'd3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a', # bowtie2-2.4.5-source.zip - 'c3da65daa8fcaaeb549059c53b7bbbc31774457af189407e654210ade84f550a', # simde-no-tests.master.zip -] +source_urls = [('https://sourceforge.net/projects/bowtie-bio/files/%(namelower)s/%(version)s', 'download')] +sources = ['%(namelower)s-%(version)s-source.zip'] +checksums = ['d3cbd5f323393b5649aea10325d7c4b77f02035a8b204e5ac18eba95236e076a'] + +# 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', '1.2.12'), From aed53123302aeea7f1d9b9943c43c9a889eccbf2 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 20 Dec 2022 17:17:33 +0100 Subject: [PATCH 804/939] adding easyconfigs: FreeImage-3.18.0-GCCcore-11.3.0.eb --- .../FreeImage-3.18.0-GCCcore-11.3.0.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..11730391a1b2 --- /dev/null +++ b/easybuild/easyconfigs/f/FreeImage/FreeImage-3.18.0-GCCcore-11.3.0.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': '11.3.0'} +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', '2.38')] + +dependencies = [('zlib', '1.2.12')] + +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' From 8d6a15ec2c63f6ae029d803afbb7eb9f0c8248da Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 18:20:13 +0100 Subject: [PATCH 805/939] enable dataset support for recent versions of Arrow --- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb | 5 +++-- easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb | 5 +++-- easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb | 5 +++-- 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 +++-- 5 files changed, 15 insertions(+), 10 deletions(-) diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb index da7afc30a3a2..638d160140b5 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021a.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " @@ -48,7 +48,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -61,6 +61,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb index aca66d53dc2b..8e67baea1054 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.0-foss-2021b.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " @@ -49,7 +49,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh 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_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -62,6 +62,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb index ae4130379ec9..6b7ebcc3c0f0 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-6.0.1-foss-2021a.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " @@ -48,7 +48,7 @@ local_install_pyarrow_cmds = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfi local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pyshortver)s/site-packages:$PYTHONPATH && " local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -61,6 +61,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb index 6f01b9c72ba4..9c2d0b80319a 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022.05.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " configopts += "-DZSTD_ROOT=$EBROOTZSTD " @@ -50,7 +50,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$TMPDIR && " local_install_pyarrow_cmds += "sed -i 's/numpy==[0-9.]*/numpy/g' pyproject.toml && " local_install_pyarrow_cmds += "Python3_ROOT_DIR=$EBROOTPYTHON " -local_install_pyarrow_cmds += "PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -63,6 +63,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] diff --git a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb index 84ee66a73e28..19aac4c1a50e 100644 --- a/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb +++ b/easybuild/easyconfigs/a/Arrow/Arrow-8.0.0-foss-2022a.eb @@ -39,7 +39,7 @@ dependencies = [ start_dir = 'cpp' # see https://arrow.apache.org/docs/developers/python.html -configopts = "-DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " +configopts = "-DARROW_DATASET=on -DARROW_PYTHON=on -DARROW_PARQUET=ON -DARROW_WITH_SNAPPY=ON " configopts += "-DCMAKE_INSTALL_LIBDIR=lib -DPython3_ROOT_DIR=$EBROOTPYTHON " configopts += "-DARROW_WITH_ZLIB=ON -DARROW_WITH_BZ2=ON -DARROW_WITH_ZSTD=ON -DARROW_WITH_LZ4=ON " configopts += "-DZSTD_ROOT=$EBROOTZSTD " @@ -50,7 +50,7 @@ local_install_pyarrow_cmds += "export PYTHONPATH=%(installdir)s/lib/python%(pysh local_install_pyarrow_cmds += "cd %(builddir)s/*arrow-%(version)s/python && export XDG_CACHE_HOME=$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_PARQUET=1 pip install --prefix %(installdir)s ." +local_install_pyarrow_cmds += "PYARROW_WITH_DATASET=1 PYARROW_WITH_PARQUET=1 pip install --prefix %(installdir)s ." postinstallcmds = [local_install_pyarrow_cmds] modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} @@ -63,6 +63,7 @@ sanity_check_paths = { sanity_check_commands = [ "python -c 'import pyarrow'", + "python -c 'import pyarrow.dataset'", "python -c 'import pyarrow.parquet'", ] From 05c3f96528256ae9e836f9c7f7c30490eb58b3bd Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 20 Dec 2022 18:49:55 +0100 Subject: [PATCH 806/939] adding easyconfigs: dbus-glib-0.112-GCCcore-11.3.0.eb --- .../dbus-glib-0.112-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..68fd32c517be --- /dev/null +++ b/easybuild/easyconfigs/d/dbus-glib/dbus-glib-0.112-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'ConfigureMake' + +name = 'dbus-glib' +version = '0.112' + +homepage = 'https://dbus.freedesktop.org/doc/dbus-glib' +description = """D-Bus is a message bus system, a simple way for applications to talk to one another.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://dbus.freedesktop.org/releases/dbus-glib'] +sources = [SOURCE_TAR_GZ] +checksums = ['7d550dccdfcd286e33895501829ed971eeb65c614e73aadb4a08aeef719b143a'] + +builddependencies = [ + ('binutils', '2.38'), + ('pkgconf', '1.8.0'), + ('Python', '3.10.4', '-bare'), # Python is needed for building against GLib. +] + +dependencies = [ + ('GLib', '2.72.1'), + ('DBus', '1.14.0'), + ('expat', '2.4.8'), +] + +sanity_check_commands = [ + 'dbus-binding-tool --version', + 'dbus-binding-tool --help', +] + +sanity_check_paths = { + 'files': ['bin/dbus-binding-tool', 'lib/libdbus-glib-1.%s' % SHLIB_EXT, 'lib/libdbus-glib-1.a'], + 'dirs': ['include', 'share'] +} + +moduleclass = 'devel' From 45e309b56269ea2aef90d6a3d6768ae8f921136d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 21:29:11 +0100 Subject: [PATCH 807/939] {toolchain} foss/2022b --- .../f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb | 19 ++++++++ easybuild/easyconfigs/f/foss/foss-2022b.eb | 28 ++++++++++++ easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb | 20 +++++++++ easybuild/easyconfigs/g/gompi/gompi-2022b.eb | 20 +++++++++ .../easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb | 21 +++++++++ .../OSU-Micro-Benchmarks-6.2-gompi-2022b.eb | 26 +++++++++++ .../ScaLAPACK-2.2.0-gompi-2022b-fb.eb | 43 +++++++++++++++++++ 7 files changed, 177 insertions(+) create mode 100644 easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/f/foss/foss-2022b.eb create mode 100644 easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb create mode 100644 easybuild/easyconfigs/g/gompi/gompi-2022b.eb create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb create mode 100644 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb create mode 100644 easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb diff --git a/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb new file mode 100644 index 000000000000..a8c00b01432e --- /dev/null +++ b/easybuild/easyconfigs/f/FFTW.MPI/FFTW.MPI-3.3.10-gompi-2022b.eb @@ -0,0 +1,19 @@ +name = 'FFTW.MPI' +version = '3.3.10' + +homepage = 'https://www.fftw.org' +description = """FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) +in one or more dimensions, of arbitrary input size, and of both real and complex data.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = ['fftw-%(version)s.tar.gz'] +checksums = ['56c932549852cddcfafdab3820b0200c7742675be92179e59e6215b340e26467'] + +dependencies = [('FFTW', '3.3.10')] + +runtest = 'check' + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/f/foss/foss-2022b.eb b/easybuild/easyconfigs/f/foss/foss-2022b.eb new file mode 100644 index 000000000000..c1a658b50200 --- /dev/null +++ b/easybuild/easyconfigs/f/foss/foss-2022b.eb @@ -0,0 +1,28 @@ +easyblock = 'Toolchain' + +name = 'foss' +version = '2022b' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# toolchain used to build foss dependencies +local_comp_mpi_tc = ('gompi', version) + +# we need GCC and OpenMPI as explicit dependencies instead of gompi toolchain +# because of toolchain preparation functions +dependencies = [ + ('GCC', local_gccver), + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), + ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb b/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb new file mode 100644 index 000000000000..1ed2f9c0bad2 --- /dev/null +++ b/easybuild/easyconfigs/g/gfbf/gfbf-2022b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gfbf' +version = '2022b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, including + FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +dependencies = [ + ('GCC', local_gccver), + ('FlexiBLAS', '3.2.1', '', ('GCC', local_gccver)), + ('FFTW', '3.3.10', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/g/gompi/gompi-2022b.eb b/easybuild/easyconfigs/g/gompi/gompi-2022b.eb new file mode 100644 index 000000000000..f49f5d2e3000 --- /dev/null +++ b/easybuild/easyconfigs/g/gompi/gompi-2022b.eb @@ -0,0 +1,20 @@ +easyblock = 'Toolchain' + +name = 'gompi' +version = '2022b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain, + including OpenMPI for MPI support.""" + +toolchain = SYSTEM + +local_gccver = '12.2.0' + +# compiler toolchain dependencies +dependencies = [ + ('GCC', local_gccver), # includes both GCC and binutils + ('OpenMPI', '4.1.4', '', ('GCC', local_gccver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb new file mode 100644 index 000000000000..286030ee6568 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-foss-2022b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'foss', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb new file mode 100644 index 000000000000..b98375baf035 --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-6.2-gompi-2022b.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '6.2' + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['bb9dbc87dcf8ec6785977a61f6fceee8febf1a682488eaab4c58cf50e4fa985f'] + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb new file mode 100644 index 000000000000..fc9fc30a11c5 --- /dev/null +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-gompi-2022b-fb.eb @@ -0,0 +1,43 @@ +name = 'ScaLAPACK' +version = '2.2.0' +versionsuffix = '-fb' + +homepage = 'https://www.netlib.org/scalapack/' +description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines + redesigned for distributed memory MIMD parallel computers.""" + +toolchain = {'name': 'gompi', 'version': '2022b'} +toolchainopts = {'pic': True} + +source_urls = [homepage] +sources = [SOURCELOWER_TGZ] +patches = ['ScaLAPACK-%(version)s_fix-GCC-10.patch'] +checksums = [ + '40b9406c20735a9a3009d863318cb8d3e496fb073d201c5463df810e01ab2a57', # scalapack-2.2.0.tgz + 'f6bc3c6dee012ba4a696548a2e12b6aae932ce4fd5a142153b338839f52b5906', # ScaLAPACK-2.2.0_fix-GCC-10.patch +] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('FlexiBLAS', '3.2.1'), +] + +# Config Opts based on AOCL User Guide: +# https://developer.amd.com/wp-content/resources/AOCL_User%20Guide_2.2.pdf + +configopts = '-DBUILD_SHARED_LIBS=ON ' +configopts += '-DBLAS_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DLAPACK_LIBRARIES="$EBROOTFLEXIBLAS/lib/libflexiblas.%s" ' % SHLIB_EXT +configopts += '-DCMAKE_C_COMPILER=mpicc ' +configopts += '-DCMAKE_Fortran_COMPILER=mpif90 ' +configopts += '-DCMAKE_Fortran_FLAGS="-lpthread -fopenmp $DCMAKE_Fortran_FLAGS" ' + +sanity_check_paths = { + 'files': ['lib/libscalapack.%s' % SHLIB_EXT, 'lib64/libscalapack.%s' % SHLIB_EXT], + 'dirs': ["lib", "lib64"], +} + +moduleclass = 'numlib' From 05d20400270b1e177bd170a48a58641d1ef3dd09 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 20 Dec 2022 21:31:54 +0100 Subject: [PATCH 808/939] {toolchain} intel/2022b --- .../easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb | 21 ++++++++++++++++++ easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb | 18 +++++++++++++++ easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb | 18 +++++++++++++++ .../imkl-FFTW-2022.2.1-iimpi-2022b.eb | 11 ++++++++++ easybuild/easyconfigs/i/intel/intel-2022b.eb | 22 +++++++++++++++++++ 5 files changed, 90 insertions(+) create mode 100644 easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb create mode 100644 easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb create mode 100644 easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb create mode 100644 easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb create mode 100644 easybuild/easyconfigs/i/intel/intel-2022b.eb diff --git a/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb new file mode 100644 index 000000000000..8b309fa2a4b2 --- /dev/null +++ b/easybuild/easyconfigs/h/HPL/HPL-2.3-intel-2022b.eb @@ -0,0 +1,21 @@ +name = 'HPL' +version = '2.3' + +homepage = 'https://www.netlib.org/benchmark/hpl/' +description = """HPL is a software package that solves a (random) dense linear system in double precision (64 bits) + arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available + implementation of the High Performance Computing Linpack Benchmark.""" + +toolchain = {'name': 'intel', 'version': '2022b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://www.netlib.org/benchmark/%(namelower)s'] +sources = [SOURCELOWER_TAR_GZ] +# fix Make dependencies, so parallel build also works +patches = ['HPL_parallel-make.patch'] +checksums = [ + '32c5c17d22330e6f2337b681aded51637fb6008d3f0eb7c277b163fadd612830', # hpl-2.3.tar.gz + '2a5bf9c4f328049828ddecec7ba3f05a9e25d236f4212747c53bd22fea80c5e6', # HPL_parallel-make.patch +] + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb b/easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb new file mode 100644 index 000000000000..634c1d810929 --- /dev/null +++ b/easybuild/easyconfigs/i/iimkl/iimkl-2022b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimkl' +version = '2022b' + +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 = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('imkl', local_comp_ver, '', SYSTEM), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb b/easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb new file mode 100644 index 000000000000..91d6d4d70554 --- /dev/null +++ b/easybuild/easyconfigs/i/iimpi/iimpi-2022b.eb @@ -0,0 +1,18 @@ +# This is an easyconfig file for EasyBuild, see http://easybuilders.github.io/easybuild +easyblock = 'Toolchain' + +name = 'iimpi' +version = '2022b' + +homepage = 'https://software.intel.com/parallel-studio-xe' +description = """Intel C/C++ and Fortran compilers, alongside Intel MPI.""" + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +dependencies = [ + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb new file mode 100644 index 000000000000..91a574e686f9 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl-FFTW/imkl-FFTW-2022.2.1-iimpi-2022b.eb @@ -0,0 +1,11 @@ +name = 'imkl-FFTW' +version = '2022.2.1' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "FFTW interfaces using Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'iimpi', 'version': '2022b'} + +dependencies = [('imkl', version, '', SYSTEM)] + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/i/intel/intel-2022b.eb b/easybuild/easyconfigs/i/intel/intel-2022b.eb new file mode 100644 index 000000000000..a2553d65c7e6 --- /dev/null +++ b/easybuild/easyconfigs/i/intel/intel-2022b.eb @@ -0,0 +1,22 @@ +easyblock = 'Toolchain' + +name = 'intel' +version = '2022b' + +homepage = 'https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain' +description = "Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL)." + +toolchain = SYSTEM + +local_comp_ver = '2022.2.1' +local_gccver = '12.2.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.39', '', ('GCCcore', local_gccver)), + ('intel-compilers', local_comp_ver), + ('impi', '2021.7.1', '', ('intel-compilers', local_comp_ver)), + ('imkl', local_comp_ver, '', SYSTEM), + ('imkl-FFTW', local_comp_ver, '', ('iimpi', version)), +] + +moduleclass = 'toolchain' From 6dca59be89cfd54ead8c6a50020ebdad2204b703 Mon Sep 17 00:00:00 2001 From: eb Date: Tue, 20 Dec 2022 23:04:35 +0000 Subject: [PATCH 809/939] adding easyconfigs: XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb, XGBoost-1.7.2-foss-2022a.eb --- .../XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb | 33 +++++++++++++++++++ .../x/XGBoost/XGBoost-1.7.2-foss-2022a.eb | 29 ++++++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..7f522d922183 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f1a749aedb9330afc48007cc78b8bbbbea35ce372f48a2735f9c71bbc7b8dcfb'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('CUDA', '11.7.0', '', SYSTEM), +] + +configopts = "-DUSE_CUDA=ON -DBUILD_WITH_CUDA_CUB=ON " + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb new file mode 100644 index 000000000000..96f8e7efca12 --- /dev/null +++ b/easybuild/easyconfigs/x/XGBoost/XGBoost-1.7.2-foss-2022a.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'XGBoost' +version = '1.7.2' + +homepage = 'https://github.com/dmlc/xgboost' +description = """XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, + flexible and portable.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['f1a749aedb9330afc48007cc78b8bbbbea35ce372f48a2735f9c71bbc7b8dcfb'] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +# use the parallel parameter from EB instead of total procs in the system +preinstallopts = "sed -i 's/nproc = os.cpu_count.*$/nproc = %(parallel)s/' setup.py &&" + +moduleclass = 'lib' From b57c6e46c20961da1650f6e05b214d2f6061f8ee Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 13:14:14 +1100 Subject: [PATCH 810/939] adding easyconfigs: ESMF-8.3.0-intel-2022a.eb, netCDF-C++4-4.3.1-iimpi-2022a.eb --- .../e/ESMF/ESMF-8.3.0-intel-2022a.eb | 37 +++++++++++++++++++ .../netCDF-C++4-4.3.1-iimpi-2022a.eb | 25 +++++++++++++ 2 files changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb new file mode 100644 index 000000000000..1d6572890e3a --- /dev/null +++ b/easybuild/easyconfigs/e/ESMF/ESMF-8.3.0-intel-2022a.eb @@ -0,0 +1,37 @@ +name = 'ESMF' +version = '8.3.0' + +homepage = 'https://www.earthsystemcog.org/projects/esmf/' +description = """The Earth System Modeling Framework (ESMF) is a suite of software tools for developing + high-performance, multi-component Earth science modeling applications.""" + +toolchain = {'name': 'intel', 'version': '2022a'} +toolchainopts = {'usempi': True, 'openmp': True, 'cstd': 'c++11', 'pic': True} + +source_urls = ['https://github.com/esmf-org/esmf/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['ESMF-6.1.1_libopts.patch'] +checksums = [ + '0ff43ede83d1ac6beabd3d5e2a646f7574174b28a48d1b9f2c318a054ba268fd', # v8.3.0.tar.gz + '3851627f07c32a7da55d99072d619942bd3a1d9dd002e1557716158e7aacdaf4', # ESMF-6.1.1_libopts.patch +] + +builddependencies = [('CMake', '3.23.1')] + +dependencies = [ + ('netCDF', '4.9.0'), + ('netCDF-Fortran', '4.6.0'), + ('netCDF-C++4', '4.3.1'), + ('libarchive', '3.6.1'), +] + +# disable errors from GCC 10 on mismatches between actual and dummy argument lists (GCC 9 behaviour) +prebuildopts = 'ESMF_F90COMPILEOPTS="${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' diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.eb new file mode 100644 index 000000000000..df12f9d9a906 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-iimpi-2022a.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': '2022a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [('netCDF', '4.9.0')] + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'data' From a12ad79be1b537f95e18967f4c6ab8a60217bfd6 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 13:16:35 +1100 Subject: [PATCH 811/939] adding easyconfigs: FMS-2022.02-gompi-2022a.eb, FMS-2022.02-iimpi-2022a.eb --- .../f/FMS/FMS-2022.02-gompi-2022a.eb | 35 +++++++++++++++++++ .../f/FMS/FMS-2022.02-iimpi-2022a.eb | 35 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb create mode 100644 easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb diff --git a/easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb b/easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb new file mode 100644 index 000000000000..bb40ce9b7d38 --- /dev/null +++ b/easybuild/easyconfigs/f/FMS/FMS-2022.02-gompi-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'FMS' +version = '2022.02' + +homepage = 'https://github.com/NOAA-GFDL/FMS' +description = """The Flexible Modeling System (FMS) is a software framework for + supporting the efficient development, construction, execution, and scientific + interpretation of atmospheric, oceanic, and climate system models.""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/NOAA-GFDL/FMS/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ad4978302b219e11b883b2f52519e1ee455137ad947474abb316c8654f72c874'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), +] + +separate_build_dir = True + +configopts = "-D64BIT=ON -DOPENMP=ON -DFPIC=ON" + +sanity_check_paths = { + 'files': ['lib/libfms_%s.a' % (x) for x in ['r4', 'r8']], + 'dirs': ['include_r4', 'include_r8', 'lib/cmake'], +} + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb b/easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb new file mode 100644 index 000000000000..a121a552ee3d --- /dev/null +++ b/easybuild/easyconfigs/f/FMS/FMS-2022.02-iimpi-2022a.eb @@ -0,0 +1,35 @@ +easyblock = 'CMakeMake' + +name = 'FMS' +version = '2022.02' + +homepage = 'https://github.com/NOAA-GFDL/FMS' +description = """The Flexible Modeling System (FMS) is a software framework for + supporting the efficient development, construction, execution, and scientific + interpretation of atmospheric, oceanic, and climate system models.""" + +toolchain = {'name': 'iimpi', 'version': '2022a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/NOAA-GFDL/FMS/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['ad4978302b219e11b883b2f52519e1ee455137ad947474abb316c8654f72c874'] + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('netCDF-Fortran', '4.6.0'), +] + +separate_build_dir = True + +configopts = "-D64BIT=ON -DOPENMP=ON -DFPIC=ON" + +sanity_check_paths = { + 'files': ['lib/libfms_%s.a' % (x) for x in ['r4', 'r8']], + 'dirs': ['include_r4', 'include_r8', 'lib/cmake'], +} + +moduleclass = 'geo' From b2f44f34f86e85c4f45ff5ad3893d90f6cceff56 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:22:12 +1100 Subject: [PATCH 812/939] adding easyconfigs: fdict-0.8.0-GCC-10.3.0.eb, fdict-0.8.0-GCC-11.2.0.eb, fdict-0.8.0-intel-compilers-2021.2.0.eb, fdict-0.8.0-intel-compilers-2021.4.0.eb --- .../f/fdict/fdict-0.8.0-GCC-10.3.0.eb | 30 +++++++++++++++++++ .../f/fdict/fdict-0.8.0-GCC-11.2.0.eb | 30 +++++++++++++++++++ .../fdict-0.8.0-intel-compilers-2021.2.0.eb | 30 +++++++++++++++++++ .../fdict-0.8.0-intel-compilers-2021.4.0.eb | 30 +++++++++++++++++++ 4 files changed, 120 insertions(+) create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb create mode 100644 easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb new file mode 100644 index 000000000000..8a89448a3c83 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb new file mode 100644 index 000000000000..3b5996e2d24b --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-GCC-11.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="gnu" FFLAGS="$FFLAGS"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb new file mode 100644 index 000000000000..487ef3592c6a --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb new file mode 100644 index 000000000000..241923554191 --- /dev/null +++ b/easybuild/easyconfigs/f/fdict/fdict-0.8.0-intel-compilers-2021.4.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'fdict' +version = '0.8.0' + +homepage = 'https://github.com/zerothi/fdict' +description = """ +A variable and dictionary in pure fortran for retaining any data-type and a fast hash-table dictionary. +""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://github.com/zerothi/fdict/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['26ab63038d3c629994ec43dfecc3831a38ea85136a4cb7d574798c21b40d427c'] + +buildopts = 'VENDOR="intel" FFLAGS="$FFLAGS" FPP="$FC -E -P"' + +files_to_copy = [ + (['libfdict.a'], 'lib'), + (['variable.mod', 'dictionary.mod'], 'include'), + (['settings.bash'], 'share'), +] + +sanity_check_paths = { + 'files': ['include/dictionary.mod', 'lib/libfdict.a'], + 'dirs': ['share'], +} + +moduleclass = 'data' From 4e285b74942734612ca2a8633515b4ee0b1e5d64 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:23:26 +1100 Subject: [PATCH 813/939] adding easyconfigs: flook-0.8.1-GCC-10.3.0.eb, flook-0.8.1-intel-compilers-2021.2.0.eb --- .../f/flook/flook-0.8.1-GCC-10.3.0.eb | 36 +++++++++++++++++++ .../flook-0.8.1-intel-compilers-2021.2.0.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb new file mode 100644 index 000000000000..220d66b7494d --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-10.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb new file mode 100644 index 000000000000..99b8846126f6 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="intel" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From 1c13d9eee6462c8163e3317496ac076c5d351a5c Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:27:02 +1100 Subject: [PATCH 814/939] adding easyconfigs: libfdf-0.2.2-GCC-10.3.0-serial.eb, libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb --- .../libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb | 23 +++++++++++++++++++ ...f-0.2.2-intel-compilers-2021.2.0-serial.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb 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 new file mode 100644 index 000000000000..60424b615f6e --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-10.3.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' 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 new file mode 100644 index 000000000000..f6a353357b6c --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.2.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' From 59c7e4baf3c40f9f7f5fc284fa67141b21b096d3 Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:43:11 +1100 Subject: [PATCH 815/939] adding easyconfigs: flook-0.8.1-GCC-11.2.0.eb, flook-0.8.1-intel-compilers-2021.4.0.eb --- .../f/flook/flook-0.8.1-GCC-11.2.0.eb | 36 +++++++++++++++++++ .../flook-0.8.1-intel-compilers-2021.4.0.eb | 36 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb create mode 100644 easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..2adf960c7c51 --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-GCC-11.2.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="gnu" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb new file mode 100644 index 000000000000..bf8b3b0072eb --- /dev/null +++ b/easybuild/easyconfigs/f/flook/flook-0.8.1-intel-compilers-2021.4.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MakeCp' + +name = 'flook' +version = '0.8.1' + +homepage = 'https://github.com/ElectronicStructureLibrary/flook' +description = """The fortran-Lua-hook library.""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://github.com/ElectronicStructureLibrary/flook/archive/'] +sources = ['v%(version)s/flook-%(version)s.tar.gz'] +patches = [('flook-%(version)s_setup.make', './setup.make')] +checksums = [ + 'beb15b8cb57b7a2facc7a5094326aaa877fda4fe35f8aabac023232c2e12d97e', # flook-0.8.1.tar.gz + '6df3f53faa8a8fe61534ded997c5e748d0327c13b18972fbbf49eacbda30d6e0', # flook-0.8.1_setup.make +] + +dependencies = [('Lua', '5.4.3')] + +parallel = 1 + +local_comp_flags = 'VENDOR="intel" FFLAGS="$FFLAGS" CFLAGS="$CFLAGS"' +buildopts = 'liball %s' % local_comp_flags + +files_to_copy = [ + (['libflookall.a', 'libflook.a'], 'lib'), + (['flook.mod'], 'include'), +] + +sanity_check_paths = { + 'files': ['include/flook.mod', 'lib/libflook.a', 'lib/libflookall.a'], + 'dirs': [], +} + +moduleclass = 'data' From d21125b8675acd05c6295a8829fcd839105fb63e Mon Sep 17 00:00:00 2001 From: Micael Oliveira Date: Wed, 21 Dec 2022 15:50:11 +1100 Subject: [PATCH 816/939] adding easyconfigs: libfdf-0.2.2-GCC-11.2.0-serial.eb, libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb --- .../libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb | 23 +++++++++++++++++++ ...f-0.2.2-intel-compilers-2021.4.0-serial.eb | 23 +++++++++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb create mode 100644 easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb 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 new file mode 100644 index 000000000000..16305fbd339b --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-GCC-11.2.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' 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 new file mode 100644 index 000000000000..4277acce16ff --- /dev/null +++ b/easybuild/easyconfigs/l/libfdf/libfdf-0.2.2-intel-compilers-2021.4.0-serial.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'libfdf' +version = '0.2.2' +versionsuffix = '-serial' +homepage = 'https://launchpad.net/libfdf' +description = """LibFDF provides a Fortran API to parse files in the + Flexible Data Format (FDF).""" + +toolchain = {'name': 'intel-compilers', 'version': '2021.4.0'} + +source_urls = ['https://gitlab.com/siesta-project/libraries/libfdf/uploads/3eed96bf0701f36d49671617167a7771/'] +sources = ['libfdf-%(version)s.tar.gz'] +checksums = ['d7134ca665df94244f5bb35326b9f05aec6002c45cb1049816f33c22acf7dae0'] + +configopts = ' --without-mpi ' + +sanity_check_paths = { + 'files': ['include/fdf.mod', 'lib/libfdf.a'], + 'dirs': [''], +} + +moduleclass = 'data' From ecb0b3c12b3292a544cd27dbb80e991baf8e9233 Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 21 Dec 2022 12:05:35 +0200 Subject: [PATCH 817/939] adding easyconfigs: Pillow-9.1.1-GCCcore-11.2.0.eb --- .../p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb diff --git a/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..1d53e76e7776 --- /dev/null +++ b/easybuild/easyconfigs/p/Pillow/Pillow-9.1.1-GCCcore-11.2.0.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonPackage' + +name = 'Pillow' +version = '9.1.1' + +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': '11.2.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['7502539939b53d7565f3d11d87c78e7ec900d3c72945d4ee0e2f250d598309a0'] + +builddependencies = [('binutils', '2.37')] + +dependencies = [ + ('Python', '3.9.6'), + ('libjpeg-turbo', '2.0.6'), + ('libpng', '1.6.37'), + ('zlib', '1.2.11'), + ('LibTIFF', '4.3.0'), + ('freetype', '2.11.0') +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +options = {'modulename': 'PIL'} + +moduleclass = 'vis' From 02ef0ee642d2628146ee9b89b9471ce4e63e389d Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann Date: Wed, 21 Dec 2022 12:06:21 +0200 Subject: [PATCH 818/939] adding easyconfigs: matplotlib-3.5.2-foss-2021b.eb --- .../matplotlib/matplotlib-3.5.2-foss-2021b.eb | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb new file mode 100644 index 000000000000..84f735fc30ea --- /dev/null +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb @@ -0,0 +1,74 @@ +easyblock = 'PythonBundle' + +name = 'matplotlib' +version = '3.5.2' + +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': 'foss', 'version': '2021b'} + +builddependencies = [ + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('Python', '3.9.6'), + ('SciPy-bundle', '2021.10'), + ('libpng', '1.6.37'), + ('freetype', '2.11.0'), + ('Tkinter', '%(pyver)s'), + ('Pillow', '9.1.1'), + ('Qhull', '2020.2') +] + +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} && " + +exts_list = [ + ('fonttools', '4.34.0', { + 'modulename': 'fontTools', + 'source_tmpl': '%(name)s-%(version)s.zip', + 'checksums': ['73d3fab85790f076d56db431bfdf9ce51b566816ff74d51e050e11ab1ffa8f8b'], + }), + ('Cycler', '0.11.0', { + 'modulename': 'cycler', + 'source_tmpl': 'cycler-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'], + 'checksums': ['9c87405839a19696e837b3b818fed3f5f69f16f1eec1a1ad77e043dcea9c772f'], + }), + ('setuptools', '62.1.0', { + 'checksums': ['47c7b0c0f8fc10eec4cf1e71c6fdadf8decaa74ffa087e68cd1c20db7ad6a592'], + }), + ('cppy', '1.2.1', { + 'checksums': ['83b43bf17b1085ac15c5debdb42154f138b928234b21447358981f69d0d6fe1b'], + }), + ('kiwisolver', '1.4.3', { + 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], + 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], + }), + (name, version, { + 'preinstallopts': _fix_setup + _include_path, + 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], + 'checksums': ['48cf850ce14fa18067f2d9e0d646763681948487a8080ec0af2686468b4607a2'], + }), +] + +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' From 36e7f2f2ad21e2097d3440da7308685857156e1a Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 21 Dec 2022 11:09:59 +0100 Subject: [PATCH 819/939] update buildep matplotlib / Pillow --- .../easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb index 48839d0ac0c1..cc8ee4c2d2e8 100644 --- a/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/j/jax/jax-0.3.23-foss-2021b-CUDA-11.4.1.eb @@ -19,7 +19,7 @@ builddependencies = [ ('pytest-xdist', '2.5.0'), # git 2.x required to fetch repository 'io_bazel_rules_docker' ('git', '2.33.1', '-nodocs'), - ('matplotlib', '3.4.3'), # required by some jax tests + ('matplotlib', '3.5.2'), # required by some jax tests; also loads Pillow/9.1.1 ] dependencies = [ From 8c5174d13b4db41e02389e06fc71772b082096d2 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 11:10:11 +0100 Subject: [PATCH 820/939] adding easyconfigs: Ruby-3.0.5-GCCcore-11.3.0.eb --- .../r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb | 164 ++++++++++++++++++ 1 file changed, 164 insertions(+) create mode 100644 easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb 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 new file mode 100644 index 000000000000..114a5a627539 --- /dev/null +++ b/easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb @@ -0,0 +1,164 @@ +name = 'Ruby' +version = '3.0.5' + +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': '11.3.0'} + +source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac'] + +builddependencies = [('binutils', '2.38')] + +exts_default_options = { + 'source_urls': ['https://rubygems.org/downloads/'], + 'source_tmpl': '%(name)s-%(version)s.gem', +} + +# !! order of packages is important !! +# some packages have dependencies with minimum and maximum version requirements +# each version is picked as high as possible to fullfill all requirements +# packages updated on 2022-12-20 +exts_list = [ + ('ffi', '1.15.5', { + 'checksums': ['6f2ed2fa68047962d6072b964420cba91d82ce6fa8ee251950c17fca6af3c2a0'], + }), + ('childprocess', '4.1.0', { + 'checksums': ['3616ce99ccb242361ce7f2b19bf9ff3e6bc1d98b927c7edc29af8ca617ba6cd3'], + }), + ('json', '2.6.3', { + 'checksums': ['86aaea16adf346a2b22743d88f8dcceeb1038843989ab93cda44b5176c845459'], + }), + ('cabin', '0.9.0', { + 'checksums': ['91c5394289e993e7037a6c869e3f212f31a5984d2b1811ac934f591c87446b2c'], + }), + ('backports', '3.23.0', { + 'checksums': ['88fc26a40083a51015faa2ba02cbdc3605cb59f183cf0868f4fb3ac02900148f'], + }), + ('arr-pm', '0.0.12', { + 'checksums': ['fdff482f75239239201f4d667d93424412639aad0b3b0ad4d827e7c637e0ad39'], + }), + ('clamp', '1.3.2', { + 'checksums': ['4f6a99a8678d51abbf1650263a74d1ac50939edc11986271431d2e03a0d7a022'], + }), + ('multipart-post', '2.2.3', { + 'checksums': ['462979de2971b8df33c2ee797fd497731617241f9dcd93960cc3caccb2dd13d8'], + }), + ('ruby2_keywords', '0.0.5', { + 'checksums': ['ffd13740c573b7301cf7a2e61fc857b2a8e3d3aff32545d6f8300d8bae10e3ef'], + }), + ('faraday-net_http', '3.0.2', { + 'checksums': ['6882929abed8094e1ee30344a3369e856fe34530044630d1f652bf70ebd87e8d'], + }), + ('faraday', '1.2.0', { + 'checksums': ['bd5c138304ee53907f8d0747724660c3a1cdf77d530d1cecd70d141299194b99'], + }), + ('faraday_middleware', '1.2.0', { + 'checksums': ['ded15d574d50e92bd04448d5566913af5cb1a01b2fa311ceecc2464fa0ab88af'], + }), + ('highline', '2.0.3', { + 'checksums': ['2ddd5c127d4692721486f91737307236fe005352d12a4202e26c48614f719479'], + }), + ('net-http-pipeline', '1.0.1', { + 'checksums': ['6923ce2f28bfde589a9f385e999395eead48ccfe4376d4a85d9a77e8c7f0b22f'], + }), + ('connection_pool', '2.3.0', { + 'checksums': ['677985be912f33c90f98f229aaa0c0ddb2ef8776f21929a36eeeb25251c944da'], + }), + ('net-http-persistent', '2.9.4', { + 'checksums': ['24274d207ffe66222ef70c78a052c7ea6e66b4ff21e2e8a99e3335d095822ef9'], + }), + ('multi_json', '1.15.0', { + 'checksums': ['1fd04138b6e4a90017e8d1b804c039031399866ff3fbabb7822aea367c78615d'], + }), + ('public_suffix', '5.0.1', { + 'checksums': ['65603917ff4ecb32f499f42c14951aeed2380054fa7fc51758fc0a8d455fe043'], + }), + ('addressable', '2.8.1', { + 'checksums': ['bc724a176ef02118c8a3ed6b5c04c39cf59209607ffcce77b91d0261dbadedfa'], + }), + ('concurrent-ruby', '1.1.10', { + 'checksums': ['244cb1ca0d91ec2c15ca2209507c39fb163336994428e16fbd3f465c87bd8e68'], + }), + ('i18n', '1.12.0', { + 'checksums': ['91e3cc1b97616d308707eedee413d82ee021d751c918661fb82152793e64aced'], + }), + ('minitest', '5.16.3', { + 'checksums': ['60f81ad96ca5518e1457bd29eb826db60f86fbbdf8c05eac63b4824ef1f52614'], + }), + ('thread_safe', '0.3.6', { + 'checksums': ['9ed7072821b51c57e8d6b7011a8e282e25aeea3a4065eab326e43f66f063b05a'], + }), + ('tzinfo', '1.1.0', { + 'checksums': ['715a47c25f8e4c2f106c92d5a97e612f84eb7e85f5822bf3d6cf615b44492abc'], + }), + ('zeitwerk', '2.6.6', { + 'checksums': ['bb397b50c31127f8dab372fa9b21da1e7c453c5b57da172ed858136c6283f826'], + }), + ('activesupport', '5.2.8.1', { + 'checksums': ['f0498c616e1b243c7b56d67920c389f959c186ad7031569e80335b42e1d22564'], + }), + ('gh', '0.18.0', { + 'checksums': ['eb93f18a88db3ba92eb888610fc53fae731d9dacfe55922b58cc3f3aca776a47'], + }), + ('launchy', '2.5.0', { + 'checksums': ['954243c4255920982ce682f89a42e76372dba94770bf09c23a523e204bdebef5'], + }), + ('ethon', '0.16.0', { + 'checksums': ['bba0da1cea8ac3e1f5cdd7cb1cb5fc78d7ac562c33736f18f0c3eb2b63053d9e'], + }), + ('typhoeus', '1.4.0', { + 'checksums': ['fff9880d5dc35950e7706cf132fd297f377c049101794be1cf01c95567f642d4'], + }), + ('websocket', '1.2.9', { + 'checksums': ['884b12dee993217795bb5f58acc89c0121c88bdc99df4d1636c0505dca352b36'], + }), + ('pusher-client', '0.6.2', { + 'checksums': ['c405c931090e126c056d99f6b69a01b1bcb6cbfdde02389c93e7d547c6efd5a3'], + }), + ('diff-lcs', '1.5.0', { + 'checksums': ['49b934001c8c6aedb37ba19daec5c634da27b318a7a3c654ae979d6ba1929b67'], + }), + ('rspec-support', '3.12.0', { + 'checksums': ['dd4d44b247ff679b95b5607ac5641d197a5f9b1d33f916123cb98fc5f917c58b'], + }), + ('rspec-mocks', '3.12.1', { + 'checksums': ['e0dd725c7d1c1417c3a1715ccc4e41c124fab6c05b2de5a91ce22d74ee301801'], + }), + ('rspec-expectations', '3.12.1', { + 'checksums': ['808b29f7f3ef4535fc897c10235b662bb6b58219406fec56158623b3a8e06c9e'], + }), + ('rspec-core', '3.12.0', { + 'checksums': ['c466f4137966526e177d2156ca45c249eeecc7ed519b23ae2fb80c4675406bc5'], + }), + ('rspec', '3.12.0', { + 'checksums': ['ccc41799a43509dc0be84070e3f0410ac95cbd480ae7b6c245543eb64162399c'], + }), + ('rack', '2.2.4', { + 'checksums': ['ea2232b638cbd919129c8c8ad8012ecaccc09f848152a7e705d2139d0137ac2b'], + }), + ('rack-protection', '3.0.5', { + 'checksums': ['3a428f9de18ee2a4080e2fab308f20f9e98d74dcbe06ed407a8035b46ba822a8'], + }), + ('tilt', '2.0.11', { + 'checksums': ['7b180fc472cbdeb186c85d31c0f2d1e61a2c0d77e1d9fd0ca28482a9d972d6a0'], + }), + ('mustermann', '3.0.0', { + 'checksums': ['6d3569aa3c3b2f048c60626f48d9b2d561cc8d2ef269296943b03da181c08b67'], + }), + ('sinatra', '3.0.5', { + 'checksums': ['40ec7643a65d01b9c25ab5f7cafc5c67ca0b9ac523fa728345d88de69392cee7'], + }), + ('rack-test', '2.0.2', { + 'checksums': ['adadd0e957f63a34199a9fdf905a920a0b0a50795735095b4ac4bd3c13385466'], + }), + ('bundler', '2.3.26', { + 'checksums': ['1ee53cdf61e728ad82c6dbff06cfcd8551d5422e88e86203f0e2dbe9ae999e09'], + })] + +moduleclass = 'lang' + From e75c79b2ecedab9d0250872737fbcc45b89166a2 Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 21 Dec 2022 11:30:42 +0100 Subject: [PATCH 821/939] Update Ruby-3.0.5-GCCcore-11.3.0.eb --- easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) 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 114a5a627539..370bd16dda59 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 @@ -161,4 +161,3 @@ exts_list = [ })] moduleclass = 'lang' - From d110e6f9c378e9adcf45f53133291524c0692e5a Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 11:52:33 +0100 Subject: [PATCH 822/939] adding easyconfigs: CUnit-2.1-3-GCCcore-11.3.0.eb --- .../c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..cae0ab9fe40e --- /dev/null +++ b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CUnit' +version = '2.1-3' + +homepage = 'https://sourceforge.net/projects/cunit/' +description = "Automated testing framework for C." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], + 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lang' From 6765f3b0cd865131b2e2b0c562ded9cf85dbdd47 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:12:15 +0100 Subject: [PATCH 823/939] adding easyconfigs: libev-4.33-GCC-11.3.0.eb --- .../l/libev/libev-4.33-GCC-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb new file mode 100644 index 000000000000..bbfa103b29b1 --- /dev/null +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libev' +version = '4.33' + +homepage = 'http://software.schmorp.de/pkg/libev.html' +description = """A full-featured and high-performance (see benchmark) +event loop that is loosely modelled after libevent, but without its +limitations and bugs. It is used in GNU Virtual Private Ethernet, +rxvt-unicode, auditd, the Deliantra MORPG Server and Client, and many +other programs.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['http://dist.schmorp.de/libev/Attic'] +sources = ['%(name)s-%(version)s.tar.gz'] + +checksums = [ + '507eb7b8d1015fbec5b935f34ebed15bf346bed04a11ab82b8eee848c4205aea', # libev-4.33.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), +] + +sanity_check_paths = { + 'files': ['lib/libev.%s' % SHLIB_EXT], + 'dirs': ['include/', 'share'], +} + +moduleclass = 'lib' From 3a78383983dab4629ed17457e2296781892f9ec2 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:18:46 +0100 Subject: [PATCH 824/939] adding easyconfigs: nghttp3-0.6.0-GCCcore-11.3.0.eb --- .../n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..5d41fd671995 --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp3/nghttp3-0.6.0-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'CMakeMake' + +name = 'nghttp3' +version = '0.6.0' + +homepage = 'https://github.com/ngtcp2/nghttp3' +description = """ nghttp3 is an implementation of RFC 9114 HTTP/3 +mapping over QUIC and RFC 9204 QPACK in C. +It does not depend on any particular QUIC transport implementation.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '3cd5fa107541a2dd11b87a84f251a98fae4c7b67df9d78be7343e4adce540b7f', # v0.6.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('pkg-config', '0.29.2'), + ('CUnit', '2.1-3'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp3.a', 'lib/libnghttp3.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp3'], +} + +moduleclass = 'lib' From a038ce36bcd7bd7cef0954f6820b5801dba325b1 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:25:19 +0100 Subject: [PATCH 825/939] adding easyconfigs: ngtcp2-0.7.0-GCC-11.3.0.eb --- .../n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..75ed02edf9f3 --- /dev/null +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'CMakeMake' + +name = 'ngtcp2' +version = '0.7.0' + +homepage = 'https://github.com/ngtcp2/ngtcp2' +description = """ +'Call it TCP/2. One More Time.' + +ngtcp2 project is an effort to implement RFC9000 QUIC protocol.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'ngtcp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + 'b2015c58e6d249bb71c7f7726a1e5ec5ccc78be7d50d82938358fac14ec98ca9', # v0.6.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('CUnit', '2.1-3'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('GnuTLS', '3.7.8'), + ('nghttp3', '0.6.0'), + ('libev', '4.33'), +] + +configopts = '-DENABLE_GNUTLS=True' + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libngtcp2_static.a', 'lib/libngtcp2.%s' % SHLIB_EXT], + 'dirs': ['share/doc/ngtcp2'], +} + +moduleclass = 'lib' From 7bb26aa5a378c8049d3fa8190d600ac6fa53af0d Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:44:00 +0100 Subject: [PATCH 826/939] adding easyconfigs: nghttp2-1.48.0-GCC-11.3.0.eb --- .../n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb new file mode 100644 index 000000000000..9076065af443 --- /dev/null +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'CMakeMake' + +name = 'nghttp2' +version = '1.48.0' + +homepage = 'https://github.com/nghttp2/nghttp2' +description = """ +This is an implementation of the Hypertext Transfer Protocol version 2 in C. + +The framing layer of HTTP/2 is implemented as a reusable C library. +On top of that, we have implemented an HTTP/2 client, server and proxy. +We have also developed load test and benchmarking tools for HTTP/2. + +An HPACK encoder and decoder are available as a public API.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +github_account = 'nghttp2' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] + +checksums = [ + '946a8fa490548b67fc6074553cb225279cc6404bae96cf74551f2ad4453be637', # v1.48.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), + ('CMake', '3.23.1'), + ('CUnit', '2.1-3'), + ('Boost', '1.79.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), + ('nghttp3', '0.6.0'), + ('Python', '3.10.4'), + ('libxml2', '2.9.13'), + ('Jansson', '2.14'), + ('jemalloc', '5.3.0'), + ('ngtcp2', '0.7.0'), + ('libevent', '2.1.12'), + ('libev', '4.33'), + ('c-ares', '1.18.1'), +] + +runtest = 'check' + +sanity_check_paths = { + 'files': ['lib/libnghttp2.%s' % SHLIB_EXT], + 'dirs': ['include/nghttp2', 'share'], +} + +moduleclass = 'lib' From 2677cc183eb7e3b765fd85bc79754603e4fb9307 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:48:41 +0100 Subject: [PATCH 827/939] adding easyconfigs: libidn2-2.3.2-GCCcore-11.3.0.eb --- .../l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..5a7cd13f5c6c --- /dev/null +++ b/easybuild/easyconfigs/l/libidn2/libidn2-2.3.2-GCCcore-11.3.0.eb @@ -0,0 +1,24 @@ +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': '11.3.0'} + +source_urls = ['https://ftp.gnu.org/gnu/libidn/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['76940cd4e778e8093579a9d195b25fff5e936e9dc6242068528b437a76764f91'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/idn2', 'lib/libidn2.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["idn2 --help"] + +moduleclass = 'lib' From 53e6db443339a0dfff0b03aeb5ab2b8ac04d1b05 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 12:51:32 +0100 Subject: [PATCH 828/939] adding easyconfigs: libpsl-0.21.1-GCCcore-11.3.0.eb --- .../l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb | 32 +++++++++++++++++++ 1 file changed, 32 insertions(+) create mode 100644 easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..31149e9b2b37 --- /dev/null +++ b/easybuild/easyconfigs/l/libpsl/libpsl-0.21.1-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'libpsl' +version = '0.21.1' + +homepage = 'https://rockdaboot.github.io/libpsl' +description = "C library for the Public Suffix List" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/rockdaboot/libpsl/releases/download/%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['ac6ce1e1fbd4d0254c4ddb9d37f1fa99dec83619c1253328155206b896210d4c'] + +builddependencies = [ + ('binutils', '2.38'), + ('Python', '3.10.4', '-bare'), +] + +dependencies = [ + ('libidn2', '2.3.2'), + ('libunistring', '1.0'), +] + +sanity_check_commands = [('psl --version')] + +sanity_check_paths = { + 'files': ['bin/psl', 'lib/libpsl.a'], + 'dirs': [] +} + +moduleclass = 'lib' From 9ee828973c40175bcec729fe30df5d1c9aae0cd1 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 13:33:48 +0100 Subject: [PATCH 829/939] missing dep --- .../c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb | 27 +++++++++++++++++++ 1 file changed, 27 insertions(+) create mode 100644 easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..cae0ab9fe40e --- /dev/null +++ b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb @@ -0,0 +1,27 @@ +easyblock = 'ConfigureMake' + +name = 'CUnit' +version = '2.1-3' + +homepage = 'https://sourceforge.net/projects/cunit/' +description = "Automated testing framework for C." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCE_TAR_BZ2] +checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] + +builddependencies = [ + ('binutils', '2.38'), + ('Autotools', '20220317'), +] + +preconfigopts = "autoreconf -i && " + +sanity_check_paths = { + 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], + 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], +} + +moduleclass = 'lang' From 240ce5b43c26e25ba7c6f008e104442988ccfffe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ji=C5=99=C3=AD=20F=C3=BCrst?= Date: Wed, 21 Dec 2022 16:30:14 +0100 Subject: [PATCH 830/939] Added missing OpenSSL dependency --- easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb index 5d7107ed0910..ffc3a669e07f 100644 --- a/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/d/DCMTK/DCMTK-3.6.7-GCCcore-11.3.0.eb @@ -22,6 +22,7 @@ builddependencies = [ ('CMake', '3.23.1'), ] dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), ('zlib', '1.2.12'), ('libjpeg-turbo', '2.1.3'), ('LibTIFF', '4.3.0'), From f4a09d081c250ea095d43c230280f28aa3c564d6 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 16:38:24 +0100 Subject: [PATCH 831/939] adding easyconfigs: glib-networking-2.72.1-GCCcore-11.3.0.eb --- .../glib-networking-2.72.1-GCCcore-11.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..cb7dd92d43c8 --- /dev/null +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'MesonNinja' + +name = 'glib-networking' +version = '2.72.1' + +homepage = 'https://gitlab.gnome.org/GNOME/glib-networking' +description = "Network extensions for GLib" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gitlab.gnome.org/GNOME/glib-networking/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = ['675a654ae55d381490c5d76b84e088f684125415fbd2d46f74dfa5522c4a1268'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('GLib', '2.72.1'), + ('GnuTLS', '3.7.8'), + ('libidn2', '2.3.2'), + ('zstd', '1.5.2'), +] + +sanity_check_paths = { + 'files': ['lib/gio/modules/libgiognutls.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = {'GIO_EXTRA_MODULES': 'lib/gio/modules'} + +moduleclass = 'lib' From d8ea96641b33e343bb342ebdfdaaddad4a4c9c4c Mon Sep 17 00:00:00 2001 From: Thomas Hoffmann <81254262+ThomasHoffmann77@users.noreply.github.com> Date: Wed, 21 Dec 2022 17:02:43 +0100 Subject: [PATCH 832/939] Pillow as extension instead of dependency --- .../m/matplotlib/matplotlib-3.5.2-foss-2021b.eb | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb index 84f735fc30ea..701b39665ad0 100644 --- a/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb +++ b/easybuild/easyconfigs/m/matplotlib/matplotlib-3.5.2-foss-2021b.eb @@ -17,10 +17,12 @@ builddependencies = [ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), + ('libjpeg-turbo', '2.0.6'), # for Pillow ext. ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), # for Pillow ext, ('freetype', '2.11.0'), ('Tkinter', '%(pyver)s'), - ('Pillow', '9.1.1'), + # ('Pillow', '9.1.1'), # as extension ('Qhull', '2020.2') ] @@ -55,6 +57,10 @@ exts_list = [ 'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'], 'checksums': ['ab8a15c2750ae8d53e31f77a94f846d0a00772240f1c12817411fa2344351f86'], }), + ('Pillow', '9.1.1', { + 'modulename': 'PIL', + 'checksums': ['7502539939b53d7565f3d11d87c78e7ec900d3c72945d4ee0e2f250d598309a0'], + }), (name, version, { 'preinstallopts': _fix_setup + _include_path, 'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'], From 581ff30c525403b0591ba11da19d4f9129019a12 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 17:36:59 +0100 Subject: [PATCH 833/939] adding easyconfigs: LibSoup-3.0.8-GCC-11.3.0.eb --- .../l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb new file mode 100644 index 000000000000..98036c143ffa --- /dev/null +++ b/easybuild/easyconfigs/l/LibSoup/LibSoup-3.0.8-GCC-11.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'MesonNinja' + +name = 'LibSoup' +version = '3.0.8' + +homepage = 'https://wiki.gnome.org/Projects/libsoup' +description = """libsoup is an HTTP client/server library for GNOME. It +uses GObjects and the glib main loop, to integrate well with GNOME +applications, and also has a synchronous API, for use in threaded +applications.""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'cstd': 'gnu11'} + +source_urls = [FTPGNOME_SOURCE] +sources = [SOURCELOWER_TAR_XZ] +checksums = ['c8739dc1c23c2b1e3b816d7598b3fa1764a3e1a2a2f5257b1bc4466d867caced'] + +builddependencies = [ + ('binutils', '2.38'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkg-config', '0.29.2'), + ('GObject-Introspection', '1.72.0'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('libxml2', '2.9.13'), + ('SQLite', '3.38.3'), + ('GLib', '2.72.1'), + ('libpsl', '0.21.1'), + ('cURL', '7.83.0'), + ('GnuTLS', '3.7.8'), + ('nghttp2', '1.48.0'), + ('glib-networking', '2.72.1'), + ('Brotli', '1.0.9'), +] + +sanity_check_paths = { + 'files': ['lib/libsoup-3.0.%s' % SHLIB_EXT], + 'dirs': ['include/libsoup-3.0/libsoup/', 'lib/pkgconfig'] +} + +moduleclass = 'lib' From b96a0d8a1012bc68d1a28d3283949be4fbb1b8fb Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Wed, 21 Dec 2022 18:08:25 +0100 Subject: [PATCH 834/939] adding easyconfigs: libgpg-error-1.46-GCCcore-11.3.0.eb --- .../libgpg-error-1.46-GCCcore-11.3.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..eb147d5e586d --- /dev/null +++ b/easybuild/easyconfigs/l/libgpg-error/libgpg-error-1.46-GCCcore-11.3.0.eb @@ -0,0 +1,22 @@ +easyblock = 'ConfigureMake' + +name = 'libgpg-error' +version = '1.46' + +homepage = 'https://gnupg.org/related_software/libgpg-error/index.html' +description = """Libgpg-error is a small library that defines common error values for all GnuPG components.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://gnupg.org/ftp/gcrypt/%(name)s/'] +sources = [SOURCE_TAR_BZ2] +checksums = ['b7e11a64246bbe5ef37748de43b245abd72cfcd53c9ae5e7fc5ca59f1c81268d'] + +builddependencies = [('binutils', '2.38')] + +sanity_check_paths = { + 'files': ['bin/gpg-error', 'include/gpg-error.h', 'lib/libgpg-error.%s' % SHLIB_EXT], + 'dirs': ['share'] +} + +moduleclass = 'system' From fee31cc72f17340ddb291fb470ba7933d25d24bd Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:38:24 +0000 Subject: [PATCH 835/939] adding easyconfigs: gh-2.20.2.eb --- easybuild/easyconfigs/g/gh/gh-2.20.2.eb | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/g/gh/gh-2.20.2.eb diff --git a/easybuild/easyconfigs/g/gh/gh-2.20.2.eb b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb new file mode 100644 index 000000000000..3d63f9784263 --- /dev/null +++ b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb @@ -0,0 +1,21 @@ +easyblock = 'GoPackage' + +name = 'gh' +version = '2.20.2' + +homepage = 'https://github.com/cli/cli' +description = """gh is GitHub on the command line.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/cli/cli/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['221380a32559984b64cdda81fabb60e5d4ed00db49ffe8390ddc149bef25c5a7'] + +builddependencies = [ + ('Go', '1.18.3'), +] + +installopts = './cmd/%(namelower)s' + +moduleclass = 'tools' From 77427773828db49e8db850982d7537980f7c27b1 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:45:21 +0000 Subject: [PATCH 836/939] Updating download links to 'official home on GitHub' according to pcre.org --- easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb | 3 ++- easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb | 2 +- easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb | 2 +- 8 files changed, 9 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb index 12016d01cbe1..987673424a7a 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.21-foss-2016a.eb @@ -12,8 +12,9 @@ description = """ toolchain = {'name': 'foss', 'version': '2016a'} toolchainopts = {'optarch': True, 'pic': True} -source_urls = ['http://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] +checksums = ['1cfd43caffe07fe7f2cfafc74c8f0d87b38d80bbb63226a1193407476508e317'] configopts = "--with-pic --disable-cpp --enable-jit" diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb index 5c1b1a2eee6c..6e778809b3c2 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.31-foss-2018b.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'foss', 'version': '2018b'} toolchainopts = {'pic': True} -source_urls = ['http://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e11ebd99dd23a7bccc9127d95d9978101b5f3cf0a6e7d25a1b1ca165a97166c4'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb index 01e3fb5bfdb0..450024fdf675 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.2.0'} toolchainopts = {'pic': True} -source_urls = ['http://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e2e2899a97489fc6ad1b0cc3da7952c7cca991b4a0f7db6649b75d9721025d31'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb index 389549a78a0f..8cc0b7a65246 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.33-GCCcore-8.3.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '8.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['e2e2899a97489fc6ad1b0cc3da7952c7cca991b4a0f7db6649b75d9721025d31'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb index 964495dcb0e6..f5d596ea476c 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.34-GCCcore-9.3.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '9.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['da6aba7ba2509e918e41f4f744a59fa41a2425c59a298a232e7fe85691e00379'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb index af6d2eaca841..b44919660c67 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.35-GCCcore-10.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['8fdcef8c8f4cd735169dd0225fd010487970c1bcadd49e9b90e26c7250a33dc9'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb index 5f9348bc96c0..6f63b8cf2984 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.36-GCCcore-10.3.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '10.3.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['b95ddb9414f91a967a887d69617059fb672b914f56fa3d613812c1ee8e8a1a37'] diff --git a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb index 257c390e0b9d..e82daf409ada 100644 --- a/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/p/PCRE2/PCRE2-10.37-GCCcore-11.2.0.eb @@ -12,7 +12,7 @@ description = """ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} -source_urls = ['https://download.sourceforge.net/pcre'] +source_urls = ['https://github.com/PCRE2Project/%(namelower)s/releases/download/%(namelower)s-%(version)s'] sources = [SOURCELOWER_TAR_GZ] checksums = ['04e214c0c40a97b8a5c2b4ae88a3aa8a93e6f2e45c6b3534ddac351f26548577'] From 3d5bd6293e0d51d7ba4590d710d043560b361f19 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:48:42 +0000 Subject: [PATCH 837/939] adding easyconfigs: polars-0.15.6-foss-2022a.eb, Rust-1.65.0-GCCcore-11.3.0.eb --- .../p/polars/polars-0.15.6-foss-2022a.eb | 58 +++++++++++++++++++ .../r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb | 58 +++++++++++++++++++ 2 files changed, 116 insertions(+) create mode 100644 easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb b/easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb new file mode 100644 index 000000000000..12b58c2b3524 --- /dev/null +++ b/easybuild/easyconfigs/p/polars/polars-0.15.6-foss-2022a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'polars' +version = '0.15.6' + +homepage = 'https://pola.rs/' +description = """Lightning-fast DataFrame library for Rust and Python.""" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +builddependencies = [ + # required for setuptools-rust, which is needed for maturin + # (and is needed in a more recent version than supplied with Python 3.10.4) + ('Rust', '1.65.0'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('Arrow', '8.0.0'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('setuptools', '65.6.3', { + 'checksums': ['a7620757bf984b58deaf32fc8a4577a9bbc0850cf92c20e1ce41c38c19e5fb75'], + }), + ('setuptools-rust', '1.5.2', { + 'checksums': ['d8daccb14dc0eae1b6b6eb3ecef79675bd37b4065369f79c35393dd5c55652c7'], + }), + ('maturin', '0.14.6', { + 'checksums': ['021e0b557e907027a6c7f10968635fd4c15522eee0688fed031b1ac6240ecac4'], + }), + ('connectorx', '0.3.1', { + 'source_tmpl': 'connectorx-%(version)s-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'checksums': ['71d2c2678339fb01f89469bbe22e66e75cabcf727a52ed72d576fef5744ebc58'], + }), + ('xlsx2csv', '0.8.0', { + 'checksums': ['2c268e509b7766ca4a24f2f36302e918705c5ead2fcde3f4bd5f1ca6152f7e2c'], + }), + ('deltalake', '0.6.4', { + 'checksums': ['2f3cf70d67c17a7d5928c7da214ff795283f628311d91643602176dc50f7099e'], + }), + (name, version, { + 'checksums': ['f6d27e88b46ddd88036869f066c12dd6877192d936430b43001e092529766cee'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..245fa49d6683 --- /dev/null +++ b/easybuild/easyconfigs/r/Rust/Rust-1.65.0-GCCcore-11.3.0.eb @@ -0,0 +1,58 @@ +easyblock = 'ConfigureMake' + +name = 'Rust' +version = '1.65.0' + +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': '11.3.0'} + +source_urls = ['https://static.rust-lang.org/dist/'] +sources = ['rustc-%(version)s-src.tar.gz'] +patches = ['Rust-1.60_sysroot-fix-interpreter.patch'] +checksums = [ + {'rustc-1.65.0-src.tar.gz': '5828bb67f677eabf8c384020582b0ce7af884e1c84389484f7f8d00dd82c0038'}, + {'Rust-1.60_sysroot-fix-interpreter.patch': 'b59ed4c2591fc9098277299be21dd6752654f6f193d8652b7d21cb0fa0dd8716'}, +] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), + ('Python', '3.10.4', '-bare'), + ('pkgconf', '1.8.0'), +] + +dependencies = [ + ('OpenSSL', '1.1', '', SYSTEM), +] + +configopts = "--enable-extended --sysconfdir=%(installdir)s/etc " + +# avoid build dependency on Ninja, which requires Python, +# since Rust is a build dependency for cryptography that is included with Python +configopts += "--set=llvm.ninja=false " + +# Use ./x.py to bootstrap so that options like -j N are correctly passed through +# see: https://rustc-dev-guide.rust-lang.org/building/how-to-build-and-run.html#what-is-xpy +# (ConfigureMake already adds `-j %(parallel)s` to the `build_cmd`) +build_cmd = "./x.py build" +install_cmd = "./x.py install -j %(parallel)s" + +# avoid failure when home directory is an NFS mount, +# see https://github.com/rust-lang/cargo/issues/6652 +prebuildopts = "export CARGO_HOME=%(builddir)s/cargo && " +preinstallopts = prebuildopts + +sanity_check_paths = { + 'files': ['bin/cargo', 'bin/rustc', 'bin/rustdoc'], + 'dirs': ['lib/rustlib', 'share/doc', 'share/man'], +} + +sanity_check_commands = [ + "cargo --version", + "rustc --version", +] + +moduleclass = 'lang' From 2d2879ecebcf6bbe4b34f4489402b522a42111cb Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:52:55 +0000 Subject: [PATCH 838/939] Add `pkg-config` dependency for `icu` and adapt old argument-list-too-long.patch (long pathnames may break building `nodejs`) --- .../n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 10 +- ...s-16.15.1_fix-argument-list-too-long.patch | 107 ++++++++++++++++++ 2 files changed, 116 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index 117331f1af84..abcac90c84c4 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -14,10 +14,18 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://nodejs.org/dist/v%(version)s/'] sources = ['node-v%(version)s.tar.gz'] -checksums = ['308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'] +patches = [ + '%(name)s-%(version)s_fix-argument-list-too-long.patch', +] +checksums = [ + {'node-v16.15.1.tar.gz': '308aee7149c4092a53c87c28ef49e23a8d1606119e79ae68333062e2a1f94208'}, + {'nodejs-16.15.1_fix-argument-list-too-long.patch': + '36b5627e60fd2b861ce3dc5445b137b4fe7ec30a4f866ea540ec56bda9686405'}, +] builddependencies = [ ('binutils', '2.38'), + ('pkg-config', '0.29.2'), ('Python', '3.10.4', '-bare'), ] diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch new file mode 100644 index 000000000000..4a69b371a766 --- /dev/null +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1_fix-argument-list-too-long.patch @@ -0,0 +1,107 @@ +# +# nodejs-14.17.0_fix-argument-list-too-long.patch adjusted for v16 +# +# Source: https://github.com/nodejs/node/issues/9137 +# +diff --git a/tools/gyp/pylib/gyp/generator/make.py b/tools/gyp/pylib/gyp/generator/make.py +index d163ae31..2ce1c301 100644 +--- a/tools/gyp/pylib/gyp/generator/make.py ++++ b/tools/gyp/pylib/gyp/generator/make.py +@@ -155,6 +155,31 @@ cmd_alink_thin = rm -f $@ && $(AR.$(TOOLSET)) crsT $@ $(filter %.o,$^) + quiet_cmd_link = LINK($(TOOLSET)) $@ + cmd_link = $(LINK.$(TOOLSET)) -o $@ $(GYP_LDFLAGS) $(LDFLAGS.$(TOOLSET)) -Wl,--start-group $(LD_INPUTS) $(LIBS) -Wl,--end-group + ++# Note: this does not handle spaces in paths ++define xargs ++ $(1) $(word 1,$(2)) ++$(if $(word 2,$(2)),$(call xargs,$(1),$(wordlist 2,$(words $(2)),$(2)))) ++endef ++ ++define write-to-file ++ @: >$(1) ++$(call xargs,@printf "%s\\n" >>$(1),$(2)) ++endef ++ ++OBJ_FILE_LIST := ar-file-list ++ ++define create_archive ++ rm -f $(1) $(1).$(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crs $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ ++define create_thin_archive ++ rm -f $(1) $(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crsT $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ + # We support two kinds of shared objects (.so): + # 1) shared_library, which is just bundling together many dependent libraries + # into a link line. +@@ -199,6 +224,31 @@ cmd_alink = rm -f $@ && $(AR.$(TOOLSET)) crs $@ $(filter %.o,$^) + quiet_cmd_alink_thin = AR($(TOOLSET)) $@ + cmd_alink_thin = rm -f $@ && $(AR.$(TOOLSET)) crsT $@ $(filter %.o,$^) + ++# Note: this does not handle spaces in paths ++define xargs ++ $(1) $(word 1,$(2)) ++$(if $(word 2,$(2)),$(call xargs,$(1),$(wordlist 2,$(words $(2)),$(2)))) ++endef ++ ++define write-to-file ++ @: >$(1) ++$(call xargs,@printf "%s\\n" >>$(1),$(2)) ++endef ++ ++OBJ_FILE_LIST := ar-file-list ++ ++define create_archive ++ rm -f $(1) $(1).$(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crs $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ ++define create_thin_archive ++ rm -f $(1) $(OBJ_FILE_LIST); mkdir -p `dirname $(1)` ++ $(call write-to-file,$(1).$(OBJ_FILE_LIST),$(filter %.o,$(2))) ++ $(AR.$(TOOLSET)) crsT $(1) @$(1).$(OBJ_FILE_LIST) ++endef ++ + # Due to circular dependencies between libraries :(, we wrap the + # special "figure out circular dependencies" flags around the entire + # input list during linking. +@@ -1766,14 +1816,28 @@ $(obj).$(TOOLSET)/$(TARGET)/%%.o: $(obj)/%%%s FORCE_DO_CMD + self.flavor not in ("mac", "openbsd", "netbsd", "win") + and not self.is_standalone_static_library + ): +- self.WriteDoCmd( ++ if self.flavor in ('linux', 'android'): ++ self.WriteMakeRule( + [self.output_binary], + link_deps, +- "alink_thin", +- part_of_all, +- postbuilds=postbuilds, +- ) ++ actions = ['$(call create_thin_archive,$@,$^)'] ++ ) ++ else: ++ self.WriteDoCmd( ++ [self.output_binary], ++ link_deps, ++ "alink_thin", ++ part_of_all, ++ postbuilds=postbuilds, ++ ) + else: ++ if self.flavor in ('linux', 'android'): ++ self.WriteMakeRule( ++ [self.output_binary], ++ link_deps, ++ actions = ['$(call create_archive,$@,$^)'] ++ ) ++ else: + self.WriteDoCmd( + [self.output_binary], + link_deps, From a236f8fe9371e686895a4425af4d09e0f63e9493 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 21 Dec 2022 22:59:29 +0000 Subject: [PATCH 839/939] adding easyconfigs: rising-0.2.2-foss-2022a-CUDA-11.7.0.eb, rising-0.2.2-foss-2022a.eb --- .../rising-0.2.2-foss-2022a-CUDA-11.7.0.eb | 43 +++++++++++++++++++ .../r/rising/rising-0.2.2-foss-2022a.eb | 42 ++++++++++++++++++ 2 files changed, 85 insertions(+) create mode 100644 easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..a141be4df71a --- /dev/null +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'rising' +version = '0.2.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://rising.rtfd.io/' +description = "Provides everything needed for high performance data loading and augmentation in PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# rising archive on PyPi is incomplete as of 2022-02-05 +github_account = 'PhoenixDL' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numpy + ('PyTorch', '1.12.0', versionsuffix), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + (name, version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5294b3f9b183b4efe7e4bafb4b42caa19aa4db737e7379e8356cc575fce57662'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb new file mode 100644 index 000000000000..828dbb0e31a1 --- /dev/null +++ b/easybuild/easyconfigs/r/rising/rising-0.2.2-foss-2022a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'rising' +version = '0.2.2' + +homepage = 'https://rising.rtfd.io/' +description = "Provides everything needed for high performance data loading and augmentation in PyTorch." + +toolchain = {'name': 'foss', 'version': '2022a'} + +# rising archive on PyPi is incomplete as of 2022-02-05 +github_account = 'PhoenixDL' + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), # provides numpy + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('threadpoolctl', '3.1.0', { + 'checksums': ['a335baacfaa4400ae1f0d8e3a58d6674d2f8828e3716bb2802c44955ad391380'], + }), + (name, version, { + 'source_urls': ['https://github.com/%(github_account)s/%(name)s/archive'], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['5294b3f9b183b4efe7e4bafb4b42caa19aa4db737e7379e8356cc575fce57662'], + }), +] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_pip_check = True + +moduleclass = 'data' From 68957c2e3f712866c6c15eae149fad1ae8879174 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 22 Dec 2022 08:45:46 +0000 Subject: [PATCH 840/939] `pkg-config` -> `pkgconf` --- easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb index abcac90c84c4..87bfe5f2d358 100644 --- a/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/n/nodejs/nodejs-16.15.1-GCCcore-11.3.0.eb @@ -25,7 +25,7 @@ checksums = [ builddependencies = [ ('binutils', '2.38'), - ('pkg-config', '0.29.2'), + ('pkgconf', '1.8.0'), ('Python', '3.10.4', '-bare'), ] From bb719d64d8c530fc1cd91dc4ef6941308ca52e64 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 09:50:23 +0000 Subject: [PATCH 841/939] adding easyconfigs: TinyXML-2.6.2-GCCcore-11.2.0.eb, TinyXML-2.6.2-GCCcore-11.3.0.eb --- .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 48 +++++++++++++++++++ .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 48 +++++++++++++++++++ 2 files changed, 96 insertions(+) create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb new file mode 100644 index 000000000000..ca94bda02b9b --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'TinyXML' +version = '2.6.2' + +homepage = 'https://sourceforge.net/projects/tinyxml' +description = """TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating + into other programs. It reads XML and creates C++ objects representing the XML document. The + objects can be manipulated, changed, and saved again as XML. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] +checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] + +builddependencies = [('binutils', '2.37')] + +buildopts = ' '.join([ + 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + # build a shared library + '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', +]) + +_incs = ['tinystr.h', 'tinyxml.h'] +_libs = ['lib%(namelower)s.so.%(version)s'] + +files_to_copy = [ + (_incs, 'include'), + (_libs, 'lib'), +] + +postinstallcmds = [ + "cd %(installdir)s/lib" + " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s" + " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s" + " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so" +] + +sanity_check_paths = { + 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], + 'dirs': [], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..86a49712c2b4 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -0,0 +1,48 @@ +# Author: Jasper Grimm (UoY) +easyblock = 'MakeCp' + +name = 'TinyXML' +version = '2.6.2' + +homepage = 'https://sourceforge.net/projects/tinyxml' +description = """TinyXML is a simple, small, minimal, C++ XML parser that can be easily integrating + into other programs. It reads XML and creates C++ objects representing the XML document. The + objects can be manipulated, changed, and saved again as XML. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] +checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] + +builddependencies = [('binutils', '2.38')] + +buildopts = ' '.join([ + 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + # build a shared library + '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', +]) + +_incs = ['tinystr.h', 'tinyxml.h'] +_libs = ['lib%(namelower)s.so.%(version)s'] + +files_to_copy = [ + (_incs, 'include'), + (_libs, 'lib'), +] + +postinstallcmds = [ + "cd %(installdir)s/lib", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so", +] + +sanity_check_paths = { + 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], + 'dirs': [], +} + +moduleclass = 'lib' From f65d80fc0b3e0fa0a35dc2b24476e6ad1d7e9386 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Thu, 22 Dec 2022 11:05:37 +0100 Subject: [PATCH 842/939] Delete CUnit-2.1-3-GCCcore-11.3.0.eb this easyconfig is already merged in https://github.com/easybuilders/easybuild-easyconfigs/pull/16972 --- .../c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb | 27 ------------------- 1 file changed, 27 deletions(-) delete mode 100644 easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb deleted file mode 100644 index cae0ab9fe40e..000000000000 --- a/easybuild/easyconfigs/c/CUnit/CUnit-2.1-3-GCCcore-11.3.0.eb +++ /dev/null @@ -1,27 +0,0 @@ -easyblock = 'ConfigureMake' - -name = 'CUnit' -version = '2.1-3' - -homepage = 'https://sourceforge.net/projects/cunit/' -description = "Automated testing framework for C." - -toolchain = {'name': 'GCCcore', 'version': '11.3.0'} - -source_urls = [SOURCEFORGE_SOURCE] -sources = [SOURCE_TAR_BZ2] -checksums = ['f5b29137f845bb08b77ec60584fdb728b4e58f1023e6f249a464efa49a40f214'] - -builddependencies = [ - ('binutils', '2.38'), - ('Autotools', '20220317'), -] - -preconfigopts = "autoreconf -i && " - -sanity_check_paths = { - 'files': ['lib/libcunit.a', 'lib/libcunit.%s' % SHLIB_EXT], - 'dirs': ['include/CUnit', 'lib/pkgconfig', 'share'], -} - -moduleclass = 'lang' From 13955bc0c036944cb400bc50a914702a3c5a1484 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:17:23 +0000 Subject: [PATCH 843/939] add debian, Nektar++ patches for TinyXML --- .../TinyXML-2.6.2-CVE-2021-42260.patch | 23 ++++++++ .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 14 ++++- .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 14 ++++- .../TinyXML-2.6.2-enforce-use-stl.patch | 18 ++++++ .../TinyXML-2.6.2-entity-encoding.patch | 58 +++++++++++++++++++ .../TinyXML/TinyXML-2.6.2-tagindex-type.patch | 23 ++++++++ 6 files changed, 148 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch create mode 100644 easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch new file mode 100644 index 000000000000..d9eeb45c73b5 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-CVE-2021-42260.patch @@ -0,0 +1,23 @@ +Description: In stamp always advance the pointer if *p= 0xef + . + The current implementation only advanced if 0xef is followed + by two non-zero bytes. In case of malformed input (0xef should be + the start byte of a three byte character) this leads to an infinite + loop. (CVE-2021-42260) +Origin: https://sourceforge.net/p/tinyxml/git/merge-requests/1/ + +--- a/tinyxmlparser.cpp ++++ b/tinyxmlparser.cpp +@@ -274,6 +274,12 @@ void TiXmlParsingData::Stamp( const char* now, TiXmlEncoding encoding ) + else + { p +=3; ++col; } // A normal character. + } ++ else ++ { ++ // TIXML_UTF_LEAD_0 (239) is the start character of a 3 byte sequence, so ++ // there is something wrong here. Just advance the pointer to evade infinite loops ++ ++p; ++ } + } + else + { diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index ca94bda02b9b..c2b46986f5d1 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -15,7 +15,19 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] -checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] +patches = [ + '%(name)s-2.6.2-enforce-use-stl.patch', + '%(name)s-2.6.2-entity-encoding.patch', + '%(name)s-2.6.2-CVE-2021-42260.patch', + '%(name)s-2.6.2-tagindex-type.patch' +] +checksums = [ + {'tinyxml_2_6_2.tar.gz': '15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'}, + {'TinyXML-2.6.2-enforce-use-stl.patch': '16a5b5e842eb0336be606131e5fb12a9165970f7bd943780ba09df2e1e8b29b1'}, + {'TinyXML-2.6.2-entity-encoding.patch': 'c5128e03933cd2e22eb85554d58f615f4dbc9177bd144cae2913c0bd7b140c2b'}, + {'TinyXML-2.6.2-CVE-2021-42260.patch': '3c4a6d9606944f54be5f108f278bb9137d78c6da9aa369a3d3faf87077a0a4bd'}, + {'TinyXML-2.6.2-tagindex-type.patch': 'cd1a1888ca0be64bb2cccc0c90eb070f3c789b8b9b7e02946ab8c4d38340424d'}, +] builddependencies = [('binutils', '2.37')] diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb index 86a49712c2b4..3caed91ebaf6 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -15,7 +15,19 @@ toolchainopts = {'pic': True} source_urls = [SOURCEFORGE_SOURCE] sources = ['%%(namelower)s_%s.tar.gz' % version.replace('.', '_')] -checksums = ['15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'] +patches = [ + '%(name)s-2.6.2-enforce-use-stl.patch', + '%(name)s-2.6.2-entity-encoding.patch', + '%(name)s-2.6.2-CVE-2021-42260.patch', + '%(name)s-2.6.2-tagindex-type.patch', +] +checksums = [ + {'tinyxml_2_6_2.tar.gz': '15bdfdcec58a7da30adc87ac2b078e4417dbe5392f3afb719f9ba6d062645593'}, + {'TinyXML-2.6.2-enforce-use-stl.patch': '16a5b5e842eb0336be606131e5fb12a9165970f7bd943780ba09df2e1e8b29b1'}, + {'TinyXML-2.6.2-entity-encoding.patch': 'c5128e03933cd2e22eb85554d58f615f4dbc9177bd144cae2913c0bd7b140c2b'}, + {'TinyXML-2.6.2-CVE-2021-42260.patch': '3c4a6d9606944f54be5f108f278bb9137d78c6da9aa369a3d3faf87077a0a4bd'}, + {'TinyXML-2.6.2-tagindex-type.patch': 'cd1a1888ca0be64bb2cccc0c90eb070f3c789b8b9b7e02946ab8c4d38340424d'}, +] builddependencies = [('binutils', '2.38')] diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch new file mode 100644 index 000000000000..f930ba9c2c83 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-enforce-use-stl.patch @@ -0,0 +1,18 @@ +Description: TinyXml is built with TIXML_USE_STL, so we have to + enforce it when the library is used. +Author: Felix Geyer + +diff -Nur tinyxml-2.5.3/tinyxml.h tinyxml-2.5.3.patch/tinyxml.h +--- tinyxml-2.5.3/tinyxml.h 2007-05-07 00:41:23.000000000 +0200 ++++ tinyxml-2.5.3.patch/tinyxml.h 2009-07-08 22:32:03.000000000 +0200 +@@ -26,6 +26,10 @@ + #ifndef TINYXML_INCLUDED + #define TINYXML_INCLUDED + ++#ifndef TIXML_USE_STL ++ #define TIXML_USE_STL ++#endif ++ + #ifdef _MSC_VER + #pragma warning( push ) + #pragma warning( disable : 4530 ) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch new file mode 100644 index 000000000000..7a8d87859103 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-entity-encoding.patch @@ -0,0 +1,58 @@ +Description: TinyXML incorrectly encodes text element containing an ampersand followed by either x or #. +Origin: http://sourceforge.net/tracker/index.php?func=detail&aid=3031828&group_id=13559&atid=313559 + +diff -u -r1.105 tinyxml.cpp +--- a/tinyxml.cpp ++++ b/tinyxml.cpp +@@ -57,30 +57,7 @@ + { + unsigned char c = (unsigned char) str[i]; + +- if ( c == '&' +- && i < ( (int)str.length() - 2 ) +- && str[i+1] == '#' +- && str[i+2] == 'x' ) +- { +- // Hexadecimal character reference. +- // Pass through unchanged. +- // © -- copyright symbol, for example. +- // +- // The -1 is a bug fix from Rob Laveaux. It keeps +- // an overflow from happening if there is no ';'. +- // There are actually 2 ways to exit this loop - +- // while fails (error case) and break (semicolon found). +- // However, there is no mechanism (currently) for +- // this function to return an error. +- while ( i<(int)str.length()-1 ) +- { +- outString->append( str.c_str() + i, 1 ); +- ++i; +- if ( str[i] == ';' ) +- break; +- } +- } +- else if ( c == '&' ) ++ if ( c == '&' ) + { + outString->append( entity[0].str, entity[0].strLength ); + ++i; +diff -u -r1.89 xmltest.cpp +--- a/xmltest.cpp ++++ b/xmltest.cpp +@@ -1340,6 +1340,16 @@ + }*/ + } + ++ #ifdef TIXML_USE_STL ++ { ++ TiXmlDocument xml; ++ xml.Parse("foo&#xa+bar"); ++ std::string str; ++ str << xml; ++ XmlTest( "Entity escaping", "foo&#xa+bar", str.c_str() ); ++ } ++ #endif ++ + /* 1417717 experiment + { + TiXmlDocument xml; diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch new file mode 100644 index 000000000000..0b1d09b80432 --- /dev/null +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-tagindex-type.patch @@ -0,0 +1,23 @@ +Author: Mike +Description: use size_t for tagIndex instead of int (and casting tag->length) + https://gitlab.nektar.info/nektar/nektar/-/blob/master/cmake/scripts/tinyxml.patch +--- tinyxmlparser.cpp 2017-10-03 16:05:35.999295200 +0100 ++++ tinyxmlparser.cpp 2017-10-03 16:05:58.556565300 +0100 +@@ -655,7 +655,7 @@ + + while ( in->good() ) + { +- int tagIndex = (int) tag->length(); ++ size_t tagIndex = tag->length(); + while ( in->good() && in->peek() != '>' ) + { + int c = in->get(); +@@ -958,7 +958,7 @@ + // We should be at a "<", regardless. + if ( !in->good() ) return; + assert( in->peek() == '<' ); +- int tagIndex = (int) tag->length(); ++ size_t tagIndex = tag->length(); + + bool closingTag = false; + bool firstCharFound = false; From ab5f98c4e5df5f134a76d3e85b372a76a9e66707 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:24:19 +0000 Subject: [PATCH 844/939] ensure TIXML_USE_STL is actually passed through --- easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 2 +- easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index c2b46986f5d1..660168cf94b8 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] buildopts = ' '.join([ - 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTINYXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', # build a shared library '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', ]) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb index 3caed91ebaf6..e6c9320d31c5 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [('binutils', '2.38')] buildopts = ' '.join([ - 'TINYXML_USE_STL=YES CXXFLAGS="$CXXFLAGS $CPPFLAGS" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTIXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', # build a shared library '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', ]) From 3c51bfd38a26f63c706216df4fbc25485e7ae36c Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:26:04 +0000 Subject: [PATCH 845/939] fix typo --- easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index 660168cf94b8..20da0a912d42 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -32,7 +32,7 @@ checksums = [ builddependencies = [('binutils', '2.37')] buildopts = ' '.join([ - 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTINYXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', + 'CXXFLAGS="$CXXFLAGS $CPPFLAGS -DTIXML_USE_STL" CXX="$CXX" LDFLAGS="$LDFLAGS" LD="$LD"', # build a shared library '&& $CXX -shared -Wl,-soname,lib%(namelower)s.so.%(version)s -o lib%(namelower)s.so.%(version)s $LDFLAGS *.o', ]) From c9fc4e38ab18c83316e0422d30f424b2883d61ac Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 11:33:26 +0100 Subject: [PATCH 846/939] adding easyconfigs: glew-2.2.0-GCCcore-11.3.0-egl.eb --- .../g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb diff --git a/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb new file mode 100644 index 000000000000..0bd382da354a --- /dev/null +++ b/easybuild/easyconfigs/g/glew/glew-2.2.0-GCCcore-11.3.0-egl.eb @@ -0,0 +1,43 @@ +easyblock = 'ConfigureMake' +versionsuffix = '-egl' +# available: -glx, -osmesa, -egl +# GLEW does support GLX (onscreen or requiring VirtualGL), EGL (technically can do both onscreen and +# offscreen), and OSMESA (offscreen software only). + +name = 'glew' +version = '2.2.0' + +homepage = 'https://github.com/nigels-com/glew' +description = """The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source +C/C++ extension loading library. GLEW provides efficient run-time mechanisms +for determining which OpenGL extensions are supported on the target platform.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/nigels-com/glew/releases/download/%(name)s-%(version)s/'] +sources = ['%(name)s-%(version)s.tgz'] +checksums = ['d4fc82893cfb00109578d0a1a2337fb8ca335b3ceccf97b97e5cc7f08e4353e1'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Mesa', '22.0.3'), + ('X11', '20220504'), +] + +local_system = 'SYSTEM=linux`echo %(versionsuffix)s|sed -e "s/-glx//g"`' +buildopts = local_system + +skipsteps = ['configure'] + +preinstallopts = 'GLEW_PREFIX=%(installdir)s GLEW_DEST=%(installdir)s ' +install_cmd = 'make install.all ' + local_system + +sanity_check_paths = { + 'files': ['lib/libGLEW.a', 'lib/libGLEW.%s' % SHLIB_EXT] + + ['bin/glewinfo', 'bin/visualinfo'] + + ['include/GL/%s.h' % h for h in ['glew', 'glxew', 'wglew']], + 'dirs': [] +} + +moduleclass = 'devel' From 0ab889c69cb6396795b05cc082165142bb72b467 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 10:50:41 +0000 Subject: [PATCH 847/939] ensure GCCcore/11.3.0 version creates symlinks correctly, and match postinstallcmds --- .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb | 12 ++++++------ .../t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb index 20da0a912d42..502a6576d665 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.2.0.eb @@ -45,12 +45,12 @@ files_to_copy = [ (_libs, 'lib'), ] -postinstallcmds = [ - "cd %(installdir)s/lib" - " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s" - " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s" - " && ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so" -] +postinstallcmds = [' && '.join([ + "cd %(installdir)s/lib", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s", + "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so", +])] sanity_check_paths = { 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], diff --git a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb index e6c9320d31c5..1810c449235c 100644 --- a/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/TinyXML/TinyXML-2.6.2-GCCcore-11.3.0.eb @@ -45,12 +45,12 @@ files_to_copy = [ (_libs, 'lib'), ] -postinstallcmds = [ +postinstallcmds = [' && '.join([ "cd %(installdir)s/lib", "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major)s", "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so.%(version_major_minor)s", "ln -s lib%(namelower)s.so.%(version)s lib%(namelower)s.so", -] +])] sanity_check_paths = { 'files': ['include/%s' % i for i in _incs] + ['lib/%s' % l for l in _libs], From 2b4fd34df36198c2950db720ba3ed6a662e06dde Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:16:35 +0100 Subject: [PATCH 848/939] adding easyconfigs: Wayland-1.21.0-GCCcore-11.3.0.eb --- .../Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..eb4b2f98bb1c --- /dev/null +++ b/easybuild/easyconfigs/w/Wayland/Wayland-1.21.0-GCCcore-11.3.0.eb @@ -0,0 +1,62 @@ +# Author: Jasper Grimm (UoY) +# URL of Wayland download changed to GitLab due to changes upstream +# Author: J. Sassmannshausen (Imperial College London/UK) +easyblock = 'Bundle' + +name = 'Wayland' +version = '1.21.0' + +homepage = 'https://wayland.freedesktop.org/' +description = """ +Wayland is a project to define a protocol for a compositor to talk to + its clients as well as a library implementation of the protocol. The + compositor can be a standalone display server running on Linux kernel + modesetting and evdev input devices, an X application, or a wayland + client itself. The clients can be traditional applications, X servers + (rootless or fullscreen) or other display servers. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), + ('Meson', '0.62.1'), + ('Ninja', '1.10.2'), + ('pkgconf', '1.8.0'), + ('binutils', '2.38'), +] + +dependencies = [ + ('libffi', '3.4.2'), + ('expat', '2.4.8'), + ('libxml2', '2.9.13'), +] + +default_easyblock = 'MesonNinja' +default_component_specs = { + 'source_urls': ['https://wayland.freedesktop.org/releases'], + 'sources': [SOURCE_TAR_XZ], + 'start_dir': '%(namelower)s-%(version)s', +} + +components = [ + ('wayland', version, { + 'source_urls': ['https://gitlab.freedesktop.org/wayland/wayland/-/releases/%(version)s/downloads'], + 'checksums': ['6dc64d7fc16837a693a51cfdb2e568db538bfdc9f457d4656285bb9594ef11ac'], + 'configopts': "-Ddocumentation=false", + }), + ('wayland-protocols', '1.25', { + 'checksums': ['f1ff0f7199d0a0da337217dd8c99979967808dc37731a1e759e822b75b571460'], + 'preconfigopts': "PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH " + }), +] + +_libs = ['lib/libwayland-%s.%s' % (x, SHLIB_EXT) for x in ['client', 'cursor', 'egl', 'server']] +sanity_check_paths = { + 'files': ['bin/wayland-scanner'] + _libs, + 'dirs': ['lib'], +} + +sanity_check_commands = ["wayland-scanner --help", "wayland-scanner --version"] + +moduleclass = 'vis' From 3f5d45e882843513de55f252baecf78561337380 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:20:26 +0100 Subject: [PATCH 849/939] adding easyconfigs: Waylandpp-1.0.0-GCCcore-11.3.0.eb --- .../Waylandpp-1.0.0-GCCcore-11.3.0.eb | 52 +++++++++++++++++++ 1 file changed, 52 insertions(+) create mode 100644 easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..84e55e3290e4 --- /dev/null +++ b/easybuild/easyconfigs/w/Waylandpp/Waylandpp-1.0.0-GCCcore-11.3.0.eb @@ -0,0 +1,52 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'Waylandpp' +version = '1.0.0' + +homepage = 'https://github.com/NilsBrause/waylandpp' +description = """Wayland is an object oriented display protocol, which +features request and events. Requests can be seen as method calls on +certain objects, whereas events can be seen as signals of an object. +This makes the Wayland protocol a perfect candidate for a C++ binding. + +The goal of this library is to create such a C++ binding for Wayland +using the most modern C++ technology currently available, providing +an easy to use C++ API to Wayland.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/NilsBrause/waylandpp/archive'] +sources = ['%(version)s.tar.gz'] + +checksums = [ + 'b20b45917382c6b87e9380130c9a1a1c563da2f498de5830df12fbce326dd9f5', # 1.0.0.tar.gz +] + +builddependencies = [ + ('binutils', '2.38'), + ('pkg-config', '0.29.2'), + ('CMake', '3.23.1'), +] + +dependencies = [ + ('pugixml', '1.12.1'), + ('Wayland', '1.21.0'), + ('freeglut', '3.2.2'), +] + +sanity_check_paths = { + 'files': ['bin/wayland-scanner++', 'lib//libwayland-client-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-client++.%s' % SHLIB_EXT, + 'lib/libwayland-client-unstable++.%s' % SHLIB_EXT, + 'lib/libwayland-cursor++.%s' % SHLIB_EXT, + 'lib/libwayland-egl++.%s' % SHLIB_EXT, + 'lib/libwayland-server-extra++.%s' % SHLIB_EXT, + 'lib/libwayland-server++.%s' % SHLIB_EXT, + 'lib/libwayland-server-unstable++.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'lib' From a772b074dcc59e31c2ce34e7ca5b9ab72bb19def Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:43:17 +0100 Subject: [PATCH 850/939] adding easyconfigs: hunspell-1.7.1-GCCcore-11.3.0.eb --- .../hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..9c3d1392c26e --- /dev/null +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb @@ -0,0 +1,42 @@ +# Contribution from Imperial College London/UK +# uploaded by J. Sassmannshausen + +easyblock = 'ConfigureMake' + +name = 'hunspell' +version = '1.7.1' + +homepage = 'http://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': '11.3.0'} + +source_urls = ['https://github.com/hunspell/hunspell/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['6e3557624c608b3e6525b8bd277706db4f5a857c28fdb3cfa8d0d2b67776da8a'] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('M4', '1.4.19'), +] + +dependencies = [ + ('gettext', '0.21'), +] + +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' From 7366eeef429a66c240ec29c606633b3552c0f433 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Thu, 22 Dec 2022 12:46:14 +0100 Subject: [PATCH 851/939] adding easyconfigs: enchant-2-2.3.3-GCCcore-11.3.0.eb --- .../enchant-2-2.3.3-GCCcore-11.3.0.eb | 51 +++++++++++++++++++ 1 file changed, 51 insertions(+) create mode 100644 easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..0377d8077725 --- /dev/null +++ b/easybuild/easyconfigs/e/enchant-2/enchant-2-2.3.3-GCCcore-11.3.0.eb @@ -0,0 +1,51 @@ +# Updated from enchant-1.6.1-intel-2017a.eb +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'ConfigureMake' + +name = 'enchant-2' +version = '2.3.3' + +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': '11.3.0'} + +source_urls = ['https://github.com/AbiWord/enchant/releases/download/v%(version)s'] +sources = ['enchant-%(version)s.tar.gz'] +checksums = [ + '3da12103f11cf49c3cf2fd2ce3017575c5321a489e5b9bfa81dd91ec413f3891' +] + +builddependencies = [ + ('Autotools', '20220317'), + ('binutils', '2.38'), + ('M4', '1.4.19'), + ('pkg-config', '0.29.2'), +] + +preconfigopts = "autoreconf -vfi && " + +dependencies = [ + ('hunspell', '1.7.1'), + ('GLib', '2.72.1'), +] + +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' From 453e46345b98c82f8908c34b080fba5c9c42a084 Mon Sep 17 00:00:00 2001 From: Jasper Grimm Date: Thu, 22 Dec 2022 12:16:58 +0000 Subject: [PATCH 852/939] add patch to libwpe to avoid poisoned malloc/calloc error from string.h --- .../l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb | 16 ++++++++-------- ...wpe-1.13.3_include-string-before-poison.patch | 13 +++++++++++++ 2 files changed, 21 insertions(+), 8 deletions(-) create mode 100644 easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb index 90c0db43eefa..1aa03f9c0a0a 100644 --- a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3-GCCcore-11.2.0.eb @@ -6,10 +6,10 @@ name = 'libwpe' version = '1.13.3' homepage = 'https://webkit.org/wpe' -description = """WPE is the reference WebKit port for embedded and -low-consumption computer devices. It has been designed from the -ground-up with performance, small footprint, accelerated content -rendering, and simplicity of deployment in mind, bringing the +description = """WPE is the reference WebKit port for embedded and +low-consumption computer devices. It has been designed from the +ground-up with performance, small footprint, accelerated content +rendering, and simplicity of deployment in mind, bringing the excellence of the WebKit engine to countless platforms and target devices.""" toolchain = {'name': 'GCCcore', 'version': '11.2.0'} @@ -17,9 +17,11 @@ toolchainopts = {'pic': True} source_urls = ['https://wpewebkit.org/releases'] sources = ['%(name)s-%(version)s.tar.xz'] - +patches = ['%(name)s-1.13.3_include-string-before-poison.patch'] checksums = [ - '05f871922f6ca750c5689a38a346c3fba130417d3490dd52362b4fe22f334e96', # libwpe-1.13.3.tar.xz + {'libwpe-1.13.3.tar.xz': '05f871922f6ca750c5689a38a346c3fba130417d3490dd52362b4fe22f334e96'}, + {'libwpe-1.13.3_include-string-before-poison.patch': + '2d21ed6b2dafa758126cda162e450ab2b3a3c0b622e375ff443523ba32fc5812'}, ] builddependencies = [ @@ -33,8 +35,6 @@ dependencies = [ ('glew', '2.2.0', '-egl'), ] -parallel = 2 - sanity_check_paths = { 'files': ['lib/libwpe-1.0.%s' % SHLIB_EXT], 'dirs': ['include'], diff --git a/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch new file mode 100644 index 000000000000..ecd1030693c4 --- /dev/null +++ b/easybuild/easyconfigs/l/libwpe/libwpe-1.13.3_include-string-before-poison.patch @@ -0,0 +1,13 @@ +Author: Jasper Grimm +Description: Include string.h before poisoning {c,m}alloc +diff -ruN libwpe-1.13.3/src/alloc-private.h libwpe-1.13.3.p1/src/alloc-private.h +--- libwpe-1.13.3/src/alloc-private.h 2022-08-11 12:59:47.000000000 +0100 ++++ libwpe-1.13.3.p1/src/alloc-private.h 2022-12-22 12:01:51.000000000 +0000 +@@ -27,6 +27,7 @@ + #ifndef wpe_alloc_private_h + #define wpe_alloc_private_h + ++#include + #include + + #if defined(__has_attribute) && __has_attribute(noreturn) From 3dd26349af7c290bfba947e3d06188bae8143564 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 22 Dec 2022 12:58:58 +0000 Subject: [PATCH 853/939] Add original author info --- easybuild/easyconfigs/g/gh/gh-2.20.2.eb | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/easybuild/easyconfigs/g/gh/gh-2.20.2.eb b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb index 3d63f9784263..b78e0a508e2e 100644 --- a/easybuild/easyconfigs/g/gh/gh-2.20.2.eb +++ b/easybuild/easyconfigs/g/gh/gh-2.20.2.eb @@ -1,3 +1,9 @@ +# easybuild easyconfig +# +# John Dey +# +# Fred Hutchinson Cancer Research Center - Seattle Washington - US +# easyblock = 'GoPackage' name = 'gh' From c13a8e983b5d25d6e7d9c55c10678bdb32689cab Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 22 Dec 2022 16:38:25 +0100 Subject: [PATCH 854/939] GRASS: check for actual files/dirs in sanity_check_paths --- easybuild/easyconfigs/g/GRASS/GRASS-8.2.0-foss-2021b.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 890e801c9090..064972b3a7c9 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 @@ -95,8 +95,8 @@ postinstallcmds = [ ] sanity_check_paths = { - 'files': [], - 'dirs': ["."] + 'files': ['bin/grass'], + 'dirs': ['grass%(version_major)s%(version_minor)s'] } moduleclass = 'geo' From dbcb440d0034988ec7cdd49ed0d6ddf07fecdcc3 Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Fri, 23 Dec 2022 11:45:40 +0100 Subject: [PATCH 855/939] adding easyconfigs: ruamel.yaml-0.17.21-GCCcore-11.3.0.eb --- .../ruamel.yaml-0.17.21-GCCcore-11.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..442567f3a0cb --- /dev/null +++ b/easybuild/easyconfigs/r/ruamel.yaml/ruamel.yaml-0.17.21-GCCcore-11.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'ruamel.yaml' +version = '0.17.21' + +homepage = 'https://sourceforge.net/projects/ruamel-yaml' +description = "ruamel.yaml is a YAML 1.2 loader/dumper package for Python." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_list = [ + ('ruamel.yaml.clib', '0.2.7', { + 'checksums': ['1f08fd5a2bea9c4180db71678e850b995d2a5f4537be0e94557668cf0f5f9497'], + 'modulename': False, + }), + (name, version, { + 'checksums': ['8b7ce697a2f212752a35c1ac414471dc16c424c9573be4926b56ff3f5d23b7af'], + }), + ('configobj', '5.0.6', { + 'checksums': ['a2f5650770e1c87fb335af19a9b7eb73fc05ccf22144eb68db7d00cd2bcb0902'], + }), + ('lz4', '4.0.2', { + 'checksums': ['083b7172c2938412ae37c3a090250bfdd9e4a6e855442594f86c3608ed12729b'], + }), + ('ruamel.yaml.base', '0.3.2', { + 'checksums': ['88b6edc8ace60c12d98f05fda22e5d9d69ba9a4b531cf54783142151145b0372'], + }), + ('ruamel.yaml.convert', '0.3.2', { + 'checksums': ['065ed9492a3189291d5bc0256709afc0231b52e4a01376fc91cf1757560ac9c4'], + }), + ('ruamel.yaml.cmd', '0.6.3', { + 'checksums': ['f4ebce7d6d9d53afae84d7efd79f8d6c3dcad56e0e6be3a5d2370be0e04acea0'], + }), +] + +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 1eb2a6063d14624b830c81f6d567465d157de679 Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 23 Dec 2022 10:57:56 +0000 Subject: [PATCH 856/939] matplotlib version changed to 3.3.3 --- .../easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb index ef3a56457dff..37bf2e3548cb 100644 --- a/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb +++ b/easybuild/easyconfigs/t/TFEA/TFEA-1.1.4-foss-2020b-muMerge-1.1.0.eb @@ -15,7 +15,7 @@ toolchain = {'name': 'foss', 'version': '2020b'} dependencies = [ ('Python', '3.8.6'), - ('matplotlib', '3.5.1'), + ('matplotlib', '3.3.3'), ('SciPy-bundle', '2020.11'), ('pybedtools', '0.8.2'), ('psutil', '5.9.3'), From b17ad691d04fef6f3aff94e34e662bb0b1dcc59c Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 12:15:56 +0100 Subject: [PATCH 857/939] adding easyconfigs: DeepMod2-0.0.1-foss-2021a.eb --- .../d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 43 +++++++++++++++++++ 1 file changed, 43 insertions(+) create mode 100644 easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb new file mode 100644 index 000000000000..9f570ba7fb9f --- /dev/null +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -0,0 +1,43 @@ +easyblock = 'Tarball' + +name = 'DeepMod2' +version = '0.0.1' + +homepage = 'https://github.com/WGLab/DeepMod2' + +description = """ + DeepMod2 is a computational tool for detecting DNA methylation and modifications + from Oxford Nanopore reads. +""" + +toolchain = {'name': 'foss', 'version': '2021a'} + +github_account = 'WGLab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] + +dependencies = [ + ('CUDA', '11.7.0'), + ('Python', '3.9.5'), + ('SciPy-bundle', '2021.05'), + ('Pysam', '0.16.0.1'), + ('TensorFlow', '2.6.0'), + ('h5py', '3.2.1'), + ('tqdm', '4.61.1'), + ('numba', '0.53.1'), + ('ont-fast5-api', '4.0.0'), +] + +preinstall_cmd = "chmod a+x %(namelower)s" + +sanity_check_paths = { + 'files': ['%(namelower)s'], + 'dirs': ['src'], +} + +sanity_check_commands = ['%(namelower)s --help'] + +modextrapaths = {'PATH': ''} + +moduleclass = 'bio' From 78ef3b6592895540ba79ab2192c88d56271add7b Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 12:40:56 +0100 Subject: [PATCH 858/939] Update toolchain to fosscuda/2021a --- .../easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index 9f570ba7fb9f..a358dbd75251 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -17,8 +17,11 @@ source_urls = [GITHUB_SOURCE] sources = ['v%(version)s.tar.gz'] checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] -dependencies = [ +builddependencies = [ ('CUDA', '11.7.0'), +] + +dependencies = [ ('Python', '3.9.5'), ('SciPy-bundle', '2021.05'), ('Pysam', '0.16.0.1'), From 75ec70affeda805fb14b0fd4f87a75510baab39e Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 13:23:00 +0100 Subject: [PATCH 859/939] Update dependencies cuda version --- easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index a358dbd75251..627190a93c7b 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] builddependencies = [ - ('CUDA', '11.7.0'), + ('CUDA', '11.7.0', '', {'name': 'system', 'version': ''}), ] dependencies = [ From d9eeb9f06c6c645d185efff37725f47b729b670c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Dec 2022 13:32:44 +0100 Subject: [PATCH 860/939] use https rather than http --- .../easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb index 9c3d1392c26e..5e59a4c56308 100644 --- a/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/h/hunspell/hunspell-1.7.1-GCCcore-11.3.0.eb @@ -6,7 +6,7 @@ easyblock = 'ConfigureMake' name = 'hunspell' version = '1.7.1' -homepage = 'http://hunspell.github.io/' +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.""" From 981384f7de8929e839bededed9d1d824e2cc672c Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 23 Dec 2022 15:11:30 +0100 Subject: [PATCH 861/939] add missing zlib and zstd to GnuTLS --- easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.2-GCCcore-10.3.0.eb | 2 ++ easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.3-GCCcore-11.2.0.eb | 2 ++ easybuild/easyconfigs/g/GnuTLS/GnuTLS-3.7.8-GCCcore-11.3.0.eb | 2 ++ 3 files changed, 6 insertions(+) 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 94a5cbb5961d..fad3ae66a6f9 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 @@ -26,6 +26,8 @@ dependencies = [ ('libtasn1', '4.17.0'), ('libidn', '1.36'), ('p11-kit', '0.24.0'), + ('zlib', '1.2.11'), + ('zstd', '1.4.9'), ] configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " 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 6bcdaa9f327b..ea03e7cd2dc8 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 @@ -26,6 +26,8 @@ dependencies = [ ('libtasn1', '4.18.0'), ('libidn', '1.38'), ('p11-kit', '0.24.1'), + ('zlib', '1.2.11'), + ('zstd', '1.5.0'), ] configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " 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 c604f1a0fa0d..8660253cc57c 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 @@ -26,6 +26,8 @@ dependencies = [ ('libtasn1', '4.19.0'), ('libidn', '1.41'), ('p11-kit', '0.24.1'), + ('zlib', '1.2.12'), + ('zstd', '1.5.2'), ] configopts = "--with-guile-site-dir=%(installdir)s/lib/guile --enable-openssl-compatibility " From 0a82cfef560b795f3eb3b5ceb2668c0ac8efeea6 Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 23 Dec 2022 15:27:09 +0100 Subject: [PATCH 862/939] Update Ruby-3.0.5-GCCcore-11.3.0.eb --- easybuild/easyconfigs/r/Ruby/Ruby-3.0.5-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 370bd16dda59..13a6f73ff7b4 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 @@ -10,7 +10,7 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} source_urls = ['https://cache.ruby-lang.org/pub/ruby/%(version_major_minor)s'] sources = [SOURCELOWER_TAR_GZ] -checksums = ['3586861cb2df56970287f0fd83f274bd92058872d830d15570b36def7f1a92ac'] +checksums = ['9afc6380a027a4fe1ae1a3e2eccb6b497b9c5ac0631c12ca56f9b7beb4848776'] builddependencies = [('binutils', '2.38')] From 7bf8ff7455236684a65e15c110016045611a539d Mon Sep 17 00:00:00 2001 From: iotaka Date: Fri, 23 Dec 2022 15:28:05 +0100 Subject: [PATCH 863/939] Update libev-4.33-GCC-11.3.0.eb --- easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb index bbfa103b29b1..780a94eb1c97 100644 --- a/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/libev/libev-4.33-GCC-11.3.0.eb @@ -1,3 +1,4 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) easyblock = 'ConfigureMake' name = 'libev' From 3cedd28ede417addb242d5f0e7b6bd5e58accb7d Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Fri, 23 Dec 2022 16:07:04 +0100 Subject: [PATCH 864/939] adding easyconfigs: Blosc2-2.4.3-GCCcore-11.3.0.eb --- .../b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..585ddd2f44bb --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc2/Blosc2-2.4.3-GCCcore-11.3.0.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 = '2.4.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +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', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc2/blosc2-export.h', 'include/blosc2.h', 'lib/libblosc2.a', + 'lib/libblosc2.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From 0ea28443a7e50c2684e51a574d05ea0c85e8ebf4 Mon Sep 17 00:00:00 2001 From: alberta Date: Fri, 23 Dec 2022 20:05:20 +0100 Subject: [PATCH 865/939] Try suffix for tqdm --- easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index 627190a93c7b..a4c6aa9b0068 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -27,7 +27,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('TensorFlow', '2.6.0'), ('h5py', '3.2.1'), - ('tqdm', '4.61.1'), + ('tqdm', '4.61.1', '', {'name': 'GCCcore', 'version': '10.3.0'}), ('numba', '0.53.1'), ('ont-fast5-api', '4.0.0'), ] From 3eae11208c4719cbceae40e153be6bb43225622d Mon Sep 17 00:00:00 2001 From: alberta Date: Sat, 24 Dec 2022 00:53:23 +0100 Subject: [PATCH 866/939] adding easyconfigs: TRF-4.09.1-GCC-10.3.0.eb --- .../t/TRF/TRF-4.09.1-GCC-10.3.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb diff --git a/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb new file mode 100644 index 000000000000..c7b4a835f151 --- /dev/null +++ b/easybuild/easyconfigs/t/TRF/TRF-4.09.1-GCC-10.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'ConfigureMake' + +name = 'TRF' +version = '4.09.1' + +homepage = 'https://tandem.bu.edu/trf/trf.html' +description = """Tandem Repeats Finder: a program to analyze DNA sequences.""" + +toolchain = {'name': 'GCC', 'version': '10.3.0'} + +github_account = 'Benson-Genomics-Lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['516015b625473350c3d1c9b83cac86baea620c8418498ab64c0a67029c3fb28a'] + +builddependencies = [ + ('binutils', '2.36.1'), + ('Autotools', '20210128'), +] + +preconfigopts = "autoreconf -i -f && " + +sanity_check_paths = { + 'files': ['bin/trf'], + 'dirs': [], +} + +sanity_check_commands = ["trf -v"] + +moduleclass = 'bio' From daed5dd1c9406f267c4190186bfc73af0d32cf59 Mon Sep 17 00:00:00 2001 From: alberta Date: Sat, 24 Dec 2022 12:45:21 +0100 Subject: [PATCH 867/939] Try with tqdm 4.61.2 --- easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb index a4c6aa9b0068..2b702203a848 100644 --- a/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb +++ b/easybuild/easyconfigs/d/DeepMod2/DeepMod2-0.0.1-foss-2021a.eb @@ -18,7 +18,7 @@ sources = ['v%(version)s.tar.gz'] checksums = ['68b1e4334a0f867c513e9939c196389f7ed74be6bfa297e1e33dba314840660e'] builddependencies = [ - ('CUDA', '11.7.0', '', {'name': 'system', 'version': ''}), + ('CUDA', '11.7.0', '', SYSTEM), ] dependencies = [ @@ -27,7 +27,7 @@ dependencies = [ ('Pysam', '0.16.0.1'), ('TensorFlow', '2.6.0'), ('h5py', '3.2.1'), - ('tqdm', '4.61.1', '', {'name': 'GCCcore', 'version': '10.3.0'}), + ('tqdm', '4.61.2', '', {'name': 'GCCcore', 'version': '10.3.0'}), ('numba', '0.53.1'), ('ont-fast5-api', '4.0.0'), ] From d01a1f54e2630205bd4dbf7931d2ad684293e4aa Mon Sep 17 00:00:00 2001 From: "e.dilorenzo" Date: Tue, 27 Dec 2022 09:49:54 +0100 Subject: [PATCH 868/939] adding easyconfigs: Blosc-1.21.3-GCCcore-11.3.0.eb --- .../b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..115e49c59acd --- /dev/null +++ b/easybuild/easyconfigs/b/Blosc/Blosc-1.21.3-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'Blosc' +version = '1.21.3' + +homepage = 'https://www.blosc.org/' + +description = "Blosc, an extremely fast, multi-threaded, meta-compressor library" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True, 'cstd': 'c++11'} + +source_urls = ['https://github.com/Blosc/c-blosc/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['941016c4564bca662080bb01aea74f06630bd665e598c6f6967fd91b2e2e0bb6'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.23.1'), +] + +sanity_check_paths = { + 'files': ['include/blosc-export.h', 'include/blosc.h', 'lib/libblosc.a', + 'lib/libblosc.%s' % SHLIB_EXT], + 'dirs': [], +} + +moduleclass = 'lib' From f100c4e8eeeefa96ccef7f224885742b9b82d4e5 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 09:45:54 +0000 Subject: [PATCH 869/939] adding easyconfigs: tesseract-5.3.0-GCCcore-11.3.0.eb, Leptonica-1.83.0-GCCcore-11.3.0.eb --- .../Leptonica-1.83.0-GCCcore-11.3.0.eb | 32 ++++++++++ .../tesseract-5.3.0-GCCcore-11.3.0.eb | 63 +++++++++++++++++++ 2 files changed, 95 insertions(+) create mode 100644 easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..d4743b6cc7dd --- /dev/null +++ b/easybuild/easyconfigs/l/Leptonica/Leptonica-1.83.0-GCCcore-11.3.0.eb @@ -0,0 +1,32 @@ +easyblock = 'ConfigureMake' + +name = 'Leptonica' +version = '1.83.0' + +homepage = 'http://www.leptonica.org' +description = """Leptonica is a collection of pedagogically-oriented open source software + that is broadly useful for image processing and image analysis applications.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/DanBloomberg/leptonica/releases/download/%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['206591dd58cf84ef380836dad133b58c9d1af92491f5a9825c346a162044bcfe'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('libpng', '1.6.37'), + ('LibTIFF', '4.3.0'), + ('libjpeg-turbo', '2.1.3'), + ('giflib', '5.2.1'), + ('libwebp', '1.2.4'), + ('zlib', '1.2.12'), +] + +sanity_check_paths = { + 'files': ['bin/convertformat'], + 'dirs': ['include/leptonica', 'lib/pkgconfig'] +} + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..b01480119f01 --- /dev/null +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb @@ -0,0 +1,63 @@ +easyblock = 'CMakeMake' + +name = 'tesseract' +version = '5.3.0' + +homepage = 'https://github.com/tesseract-ocr/tesseract' +description = """Tesseract is an optical character recognition engine""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +github_account = 'tesseract-ocr' +source_urls = [GITHUB_SOURCE] +sources = [ + '%(version)s.tar.gz', + { + 'source_urls': ['https://github.com/tesseract-ocr/tessdata_best/archive/'], + 'download_filename': '4.1.0.tar.gz', + 'filename': 'tessdata_best-4.1.0.tar.gz', + }, +] +checksums = [ + {'5.3.0.tar.gz': '7e70870f8341e5ea228af2836ce79a36eefa11b01b56177b4a8997f330c014b8'}, + {'tessdata_best-4.1.0.tar.gz': 'bb05b738298ae73e7130e2913ed002b49d94cd1cea508e63be1928fe47770b32'}, +] + +builddependencies = [ + ('CMake', '3.24.3'), + ('binutils', '2.38'), + ('pkgconf', '1.8.0') +] + +dependencies = [ + ('zlib', '1.2.12'), + ('libpng', '1.6.37'), + ('libjpeg-turbo', '2.1.3'), + ('LibTIFF', '4.3.0'), + ('Leptonica', '1.83.0'), + ('libarchive', '3.6.1'), + ('ICU', '71.1'), + ('fontconfig', '2.14.0'), + ('GLib', '2.72.1'), + ('cairo', '1.17.4'), + ('Pango', '1.50.7'), +] + +separate_build_dir = True + +postinstallcmds = [ + 'rm %(builddir)s/tessdata_best-4.1.0/configs', + 'rm -rf %(builddir)s/tessdata_best-4.1.0/tessconfigs', + 'mv %(builddir)s/tessdata_best-4.1.0/* %(installdir)s/share/tessdata' +] + +modextrapaths = { + 'TESSDATA_PREFIX': 'tessdata', +} + +sanity_check_paths = { + 'files': ['bin/tesseract'], + 'dirs': ['share/tessdata', 'include/tesseract'] +} + +moduleclass = 'vis' From 6bed58c31914d7018d26e0d2d624524334eb0791 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 12:52:34 +0000 Subject: [PATCH 870/939] {math}[foss/2022a] Transformers v4.24.0 - Add missing \`pkgconf\` build dependency --- .../easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb index 47a488d49c16..0558a3731f58 100644 --- a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb @@ -10,6 +10,7 @@ State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" toolchain = {'name': 'foss', 'version': '2022a'} builddependencies = [ + ('pkgconf', '1.8.0'), # required for setuptools-rust, which is needed for tokenizers ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for tokenizers ] dependencies = [ From 9267e989bedf1dc2f1804a2517d79bd93fa993bb Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 12:54:00 +0000 Subject: [PATCH 871/939] Remove unnecessary comment --- .../t/Transformers/Transformers-4.24.0-foss-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb index 0558a3731f58..fc965d151e3f 100644 --- a/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.24.0-foss-2022a.eb @@ -10,7 +10,7 @@ State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" toolchain = {'name': 'foss', 'version': '2022a'} builddependencies = [ - ('pkgconf', '1.8.0'), # required for setuptools-rust, which is needed for tokenizers + ('pkgconf', '1.8.0'), ('Rust', '1.60.0'), # required for setuptools-rust, which is needed for tokenizers ] dependencies = [ From bbf8372d6bbaad4b98804a1acfd429bf980fa71d Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 15:00:53 +0000 Subject: [PATCH 872/939] adding easyconfigs: Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb, Albumentations-1.3.0-foss-2022a.eb, imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb, imgaug-0.4.0-foss-2022a.eb --- ...mentations-1.3.0-foss-2022a-CUDA-11.7.0.eb | 38 +++++++++++++++++++ .../Albumentations-1.3.0-foss-2022a.eb | 36 ++++++++++++++++++ .../imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb | 36 ++++++++++++++++++ .../i/imgaug/imgaug-0.4.0-foss-2022a.eb | 34 +++++++++++++++++ 4 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..b66cbc3dfe8e --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('scikit-image', '0.19.3'), + ('scikit-learn', '1.1.2'), + ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('imgaug', '0.4.0', versionsuffix), +] + +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['be1af36832c8893314f2a5550e8ac19801e04770734c1b70fa3c996b41f37bed'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb new file mode 100644 index 000000000000..cecb717c37c6 --- /dev/null +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Albumentations' +version = '1.3.0' + +homepage = 'https://albumentations.ai' +description = "Albumentations is a Python library for fast and flexible image augmentations" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('PyYAML', '6.0'), + ('scikit-image', '0.19.3'), + ('scikit-learn', '1.1.2'), + ('OpenCV', '4.6.0', '-contrib'), + ('imgaug', '0.4.0'), +] + +preinstallopts = "sed -i 's|CHOOSE_INSTALL_REQUIRES),|[]),|g' setup.py && " + +use_pip = True + +exts_list = [ + ('qudida', '0.0.4', { + 'checksums': ['db198e2887ab0c9aa0023e565afbff41dfb76b361f85fd5e13f780d75ba18cc8'], + }), + ('albumentations', version, { + 'checksums': ['be1af36832c8893314f2a5550e8ac19801e04770734c1b70fa3c996b41f37bed'], + }), +] + +sanity_pip_check = True + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb new file mode 100644 index 000000000000..44e5f993163f --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb @@ -0,0 +1,36 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), + ('matplotlib', '3.5.2'), + ('scikit-image', '0.19.3'), + ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('Shapely', '1.8.2'), + ('imageio', '2.22.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + {'imgaug-0.4.0.tar.gz': '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7'}, + {'imgaug-0.4.0_openvc_requirement.patch': '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb new file mode 100644 index 000000000000..643f7eaca510 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a.eb @@ -0,0 +1,34 @@ +# This easyconfig was created by the BEAR Software team at the University of Birmingham. +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.0' + +homepage = 'https://imgaug.readthedocs.io/en/latest/' +description = """ This python library helps you with augmenting images for your machine learning projects. + It converts a set of input images into a new, much larger set of slightly altered images. """ + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('Pillow', '9.1.1'), + ('matplotlib', '3.5.2'), + ('scikit-image', '0.19.3'), + ('OpenCV', '4.6.0', '-contrib'), + ('Shapely', '1.8.2'), + ('imageio', '2.22.2'), +] + +sources = [SOURCE_TAR_GZ] +patches = ['imgaug-0.4.0_openvc_requirement.patch'] +checksums = [ + {'imgaug-0.4.0.tar.gz': '46bab63ed38f8980630ff721a09ca2281b7dbd4d8c11258818b6ebcc69ea46c7'}, + {'imgaug-0.4.0_openvc_requirement.patch': '2ff0b66ba38fdcf5f267a3d0ad1dc2710fee3c2f8cd3d086c56ea538a2a9ffc8'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From 6342d7426d35884eceb8fbf98d20a831e64dd3aa Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 15:17:35 +0000 Subject: [PATCH 873/939] adding easyconfigs: PyTorch-Lightning-1.8.4-foss-2022a.eb --- .../PyTorch-Lightning-1.8.4-foss-2022a.eb | 121 ++++++++++++++++++ 1 file changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb new file mode 100644 index 000000000000..2a62146958f6 --- /dev/null +++ b/easybuild/easyconfigs/p/PyTorch-Lightning/PyTorch-Lightning-1.8.4-foss-2022a.eb @@ -0,0 +1,121 @@ +easyblock = 'PythonBundle' + +name = 'PyTorch-Lightning' +version = '1.8.4' + +homepage = 'https://pytorchlightning.ai' +description = "PyTorch Lightning is the lightweight PyTorch wrapper for ML researchers." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + # dependencies from requirements/app/base.txt + ('aiohttp', '3.8.3'), + ('BeautifulSoup', '4.10.0'), + ('deepdiff', '5.8.1'), + # dependencies from requirements/pytorch/base.txt + ('PyTorch', '1.12.0'), + ('tqdm', '4.64.0'), + ('tensorboardX', '2.5.1'), +] + +use_pip = True + +# dependencies from requirements/app/base.txt and requirements/pytorch/base.txt +exts_list = [ + ('commonmark', '0.9.1', { + 'checksums': ['452f9dc859be7f06631ddcb328b6919c67984aca654e5fefb3914d54691aed60'], + }), + ('rich', '12.5.1', { + 'checksums': ['63a5c5ce3673d3d5fbbf23cd87e11ab84b6b451436f1b7f19ec54b6bc36ed7ca'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('starlette', '0.19.1', { + 'checksums': ['c6d21096774ecb9639acad41b86b7706e52ba3bf1dc13ea4ed9ad593d47e24c7'], + }), + ('fastapi', '0.79.1', { + 'checksums': ['006862dec0f0f5683ac21fb0864af2ff12a931e7ba18920f28cc8eceed51896b'], + }), + ('sniffio', '1.3.0', { + 'checksums': ['e60305c5e5d314f5389259b7f22aaa33d8f7dee49763119234af3755c55b9101'], + }), + ('anyio', '3.6.1', { + 'checksums': ['413adf95f93886e442aea925f3ee43baa5a765a64a0f52c6081894f9992fdd0b'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + ('lightning_cloud', '0.5.12', { + 'checksums': ['5b0cf53ecfb512f9476eec3a7f425c0e174ca9d0e726673605d5e1e57074eb0c'], + }), + ('itsdangerous', '2.1.2', { + 'checksums': ['5dbbc68b317e5e42f327f9021763545dc3fc3bfe22e6deb96aaf1fc38874156a'], + }), + ('starsessions', '1.3.0', { + 'checksums': ['8d3b509d4e6d235655f7dd495fcf0afc1bd86da84de3a8d434e6f82137ebcde8'], + }), + ('fsspec', '2022.7.1', { + 'checksums': ['7f9fb19d811b027b97c4636c6073eb53bc4cbee2d3c4b33fa88b9f26906fd7d7'], + }), + ('croniter', '1.3.8', { + 'checksums': ['32a5ec04e97ec0837bcdf013767abd2e71cceeefd3c2e14c804098ce51ad6cd9'], + }), + ('traitlets', '5.2.0', { + 'checksums': ['60474f39bf1d39a11e0233090b99af3acee93bbc2281777e61dd8c87da8a0014'], + }), + ('arrow', '1.2.3', { + 'checksums': ['3934b30ca1b9f292376d9db15b19446088d12ec58629bc3f0da28fd55fb633a1'], + }), + ('lightning-utilities', '0.4.2', { + 'checksums': ['dc6696ab180117f7e97b5488dac1d77765ab891022f7521a97a39e10d362bdb8'], + }), + ('blessed', '1.19.1', { + 'checksums': ['9a0d099695bf621d4680dd6c73f6ad547f6a3442fbdbe80c4b1daa1edbc492fc'], + }), + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('readchar', '4.0.3', { + 'checksums': ['1d920d0e9ab76ec5d42192a68d15af2562663b5dfbf4a67cf9eba520e1ca57e6'], + }), + ('inquirer', '2.10.1', { + 'checksums': ['e9876258183e24f6e8c44136b04f6f2e18dd6684aee59b86a8057c50601a6523'], + }), + ('wrapt', '1.14.1', { + 'checksums': ['380a85cf89e0e69b7cfbe2ea9f765f004ff419f34194018a6827ac0e3edfed4d'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('botocore', '1.24.21', { + 'checksums': ['7e976cfd0a61601e74624ef8f5246b40a01f2cce73a011ef29cf80a6e371d0fa'], + }), + ('aioitertools', '0.11.0', { + 'checksums': ['42c68b8dd3a69c2bf7f2233bf7df4bb58b557bca5252ac02ed5187bbc67d6831'], + }), + ('aiobotocore', '2.3.4', { + 'checksums': ['6554ebea5764f66f4be544a4fcaa0953ee80e600dd7bd818ba4893d72bf12bfb'], + }), + ('s3fs', '2022.7.1', { + 'checksums': ['4883d682cb96b769fca568dbbcaa33ff457ac8077a03af221e6f253adac05771'], + }), + ('torchmetrics', '0.9.3', { + 'checksums': ['4ebfd2466021db26397636966ee1a195d3b340ba5d71bb258e764340dfc2476f'], + }), + ('pytorch-lightning', version, { + 'checksums': ['c2771f966fc1b909cdfd1d603a87b8c84a3d5ff7aacf35b2c0260f697ec0c8be'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 93a306b070ecf54432308493e308d92430ddba88 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 15:19:51 +0000 Subject: [PATCH 874/939] adding easyconfigs: SentencePiece-0.1.97-GCC-11.3.0.eb --- .../SentencePiece-0.1.97-GCC-11.3.0.eb | 65 +++++++++++++++++++ 1 file changed, 65 insertions(+) create mode 100644 easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb new file mode 100644 index 000000000000..21674bdab438 --- /dev/null +++ b/easybuild/easyconfigs/s/SentencePiece/SentencePiece-0.1.97-GCC-11.3.0.eb @@ -0,0 +1,65 @@ +## +# Author: Robert Mijakovic +## +easyblock = 'Bundle' + +name = 'SentencePiece' +version = '0.1.97' + +homepage = 'https://github.com/google/sentencepiece' +description = "Unsupervised text tokenizer for Neural Network-based text generation." +github_account = 'google' + +toolchain = {'name': 'GCC', 'version': '11.3.0'} + +builddependencies = [ + ('CMake', '3.23.1'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('gperftools', '2.10'), +] + +default_component_specs = { + 'source_urls': [GITHUB_LOWER_SOURCE], + 'sources': ['v%(version)s.tar.gz'], + 'checksums': ['41c3a07f315e3ac87605460c8bb8d739955bc8e7f478caec4017ef9b7d78669b'], +} + +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 7c361bd1ebc73e461bf909c9646501c94e69707b Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 17:52:30 +0000 Subject: [PATCH 875/939] adding easyconfigs: boto3-1.26.37-GCCcore-11.3.0.eb, neptune-client-0.16.2-foss-2022a.eb --- .../b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb | 39 +++++++++++ .../neptune-client-0.16.2-foss-2022a.eb | 66 +++++++++++++++++++ 2 files changed, 105 insertions(+) create mode 100644 easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb diff --git a/easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb b/easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..316623bb8778 --- /dev/null +++ b/easybuild/easyconfigs/b/boto3/boto3-1.26.37-GCCcore-11.3.0.eb @@ -0,0 +1,39 @@ +easyblock = 'PythonBundle' + +name = 'boto3' +version = '1.26.37' + +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': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +exts_list = [ + ('botocore', '1.29.37', { + 'checksums': ['3afa4fec9f7713caa05116563b38f81bec7bd20585d517155484d3f25efab5aa'], + }), + ('jmespath', '1.0.1', { + 'checksums': ['90261b206d6defd58fdd5e85f478bf633a2901798906be2ad389150c5c60edbe'], + }), + ('s3transfer', '0.6.0', { + 'checksums': ['2ed07d3866f523cc561bf4a00fc5535827981b117dd7876f036b0c1aca42c947'], + }), + (name, version, { + 'checksums': ['82b790b1dabd0746b028d2013b5d4d636a41f3aaf25520081f4c173cb6eb395d'], + }), +] + +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb new file mode 100644 index 000000000000..5914ef4527ae --- /dev/null +++ b/easybuild/easyconfigs/n/neptune-client/neptune-client-0.16.2-foss-2022a.eb @@ -0,0 +1,66 @@ +easyblock = 'PythonBundle' + +name = 'neptune-client' +version = '0.16.2' + +homepage = 'https://docs.neptune.ai' +description = """ +Neptune is an experiment tracking hub that brings organization and collaboration to your data science team. +""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('GitPython', '3.1.27'), + ('Pillow-SIMD', '9.2.0'), + ('PyYAML', '6.0'), + ('typing-extensions', '4.3.0'), + ('boto3', '1.26.37'), +] + +use_pip = True + +exts_list = [ + ('monotonic', '1.6', { + 'checksums': ['3a55207bcfed53ddd5c5bae174524062935efed17792e9de2ad0205ce9ad63f7'], + }), + ('swagger-spec-validator', '3.0.3', { + 'checksums': ['16a5ce08c772824a77b1a4a05efc047d72eef1ed53fb969dfe0a18f437ac30a8'], + }), + ('jsonref', '0.2', { + 'checksums': ['f3c45b121cf6257eafabdc3a8008763aed1cd7da06dbabc59a9e4d2a5e4e6697'], + }), + ('bravado-core', '5.17.1', { + 'checksums': ['0da9c6f3814734622a55db3f62d08db6e188b25f3ebd087de370c91afb66a7f4'], + }), + ('bravado', '11.0.3', { + 'checksums': ['1bb6ef75d84140c851fffe6420baaee5037d840070cfe11d60913be6ab8e0530'], + }), + ('PyJWT', '2.6.0', { + 'modulename': 'jwt', + 'checksums': ['69285c7e31fc44f68a1feb309e948e0df53259d579295e6cfe2b1792329f05fd'], + }), + ('blinker', '1.5', { + 'checksums': ['923e5e2f69c155f2cc42dafbbd70e16e3fde24d2d4aa2ab72fbe386238892462'], + }), + ('oauthlib', '3.2.2', { + 'checksums': ['9859c40929662bec5d64f34d01c99e093149682a3f38915dc0655d5a633dd918'], + }), + ('requests-oauthlib', '1.3.1', { + 'checksums': ['75beac4a47881eeb94d5ea5d6ad31ef88856affe2332b9aafb52c6452ccf0d7a'], + }), + ('websocket-client', '1.4.2', { + 'modulename': 'websocket', + 'checksums': ['d6e8f90ca8e2dd4e8027c4561adeb9456b54044312dba655e7cae652ceb9ae59'], + }), + (name, version, { + 'modulename': 'neptune', + 'checksums': ['7e5e0261f3ce486f45e3272c5b5e3d563f0765a921bcda159b002e70175a553b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From 0cbdb3652d50d59b2e3a55979238a225c7a29819 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 19:41:03 +0000 Subject: [PATCH 876/939] adding easyconfigs: spaCy-3.4.4-foss-2022a.eb --- .../s/spaCy/spaCy-3.4.4-foss-2022a.eb | 83 +++++++++++++++++++ 1 file changed, 83 insertions(+) create mode 100644 easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb new file mode 100644 index 000000000000..7b96e506726f --- /dev/null +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb @@ -0,0 +1,83 @@ +easyblock = 'PythonBundle' + +name = 'spaCy' +version = '3.4.4' + +homepage = 'https://spacy.io/' +description = "Industrial-strength Natural Language Processing (NLP) in Python." + +toolchain = {'name': 'foss', 'version': '2022a'} + +download_dep_fail = True +use_pip = True + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), +] + +exts_list = [ + ('spacy-legacy', '3.0.10', { + 'checksums': ['16104595d8ab1b7267f817a449ad1f986eb1f2a2edf1050748f08739a479679a'], + }), + ('spacy-loggers', '1.0.4', { + 'checksums': ['e6f983bf71230091d5bb7b11bf64bd54415eca839108d5f83d9155d0ba93bf28'], + }), + ('cymem', '2.0.7', { + 'checksums': ['e6034badb5dd4e10344211c81f16505a55553a7164adc314c75bd80cf07e57a8'], + }), + ('murmurhash', '1.0.9', { + 'checksums': ['fe7a38cb0d3d87c14ec9dddc4932ffe2dbc77d75469ab80fd5014689b0e07b58'], + }), + ('preshed', '3.0.8', { + 'checksums': ['6c74c70078809bfddda17be96483c41d06d717934b07cab7921011d81758b357'], + }), + ('blis', '0.7.9', { + 'checksums': ['29ef4c25007785a90ffc2f0ab3d3bd3b75cd2d7856a9a482b7d0dac8d511a09d'], + }), + ('confection', '0.0.3', { + 'checksums': ['4fec47190057c43c9acbecb8b1b87a9bf31c469caa0d6888a5b9384432fdba5a'], + }), + ('thinc', '8.1.6', { + 'checksums': ['9241c37761f004fe684e637d2b4d8b79addebabc64e343aa1cba144fad2c9b47'], + }), + ('ml_datasets', '0.2.0', { + 'checksums': ['3f9c8901f8d6be3dab5b23ec3a6c01e619a60d0184696b1030cde2e3086943f1'], + }), + ('wasabi', '0.10.1', { + 'checksums': ['c8e372781be19272942382b14d99314d175518d7822057cb7a97010c4259d249'], + }), + ('srsly', '2.4.5', { + 'checksums': ['c842258967baa527cea9367986e42b8143a1a890e7d4a18d25a36edc3c7a33c7'], + }), + ('catalogue', '2.0.8', { + 'checksums': ['b325c77659208bfb6af1b0d93b1a1aa4112e1bb29a4c5ced816758a722f0e388'], + }), + ('typer', '0.7.0', { + 'checksums': ['ff797846578a9f2a201b53442aedeb543319466870fbe1c701eab66dd7681165'], + }), + ('pathy', '0.10.1', { + 'checksums': ['4cd6e71b4cd5ff875cfbb949ad9fa5519d8d1dbe69d5fc1d1b23aa3cb049618b'], + }), + ('smart-open', '6.3.0', { + 'source_tmpl': 'smart_open-%(version)s.tar.gz', + 'checksums': ['d5238825fe9a9340645fac3d75b287c08fbb99fb2b422477de781c9f5f09e019'], + }), + ('tqdm', '4.64.1', { + 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], + }), + ('pydantic', '1.10.2', { + 'checksums': ['91b8e218852ef6007c2b98cd861601c6a09f1aa32bbbb74fab5b1c33d4a1e410'], + }), + ('langcodes', '3.3.0', { + 'checksums': ['794d07d5a28781231ac335a1561b8442f8648ca07cd518310aeb45d6f0807ef6'], + }), + (name, version, { + 'sources': ['%(namelower)s-%(version)s.tar.gz'], + 'checksums': ['e500cf2cb5f1849461a7928fa269703756069bdfb71559065240af6d0208b08c'], + }), +] + +sanity_pip_check = True + +moduleclass = 'data' From 9fe9691ddf2e25a54e2040000b4f7875062234e4 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 20:59:58 +0000 Subject: [PATCH 877/939] Remove `download_dep_fail` --- easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb index 7b96e506726f..80d6185e427d 100644 --- a/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb +++ b/easybuild/easyconfigs/s/spaCy/spaCy-3.4.4-foss-2022a.eb @@ -8,7 +8,6 @@ description = "Industrial-strength Natural Language Processing (NLP) in Python." toolchain = {'name': 'foss', 'version': '2022a'} -download_dep_fail = True use_pip = True dependencies = [ From 9c112de52e0041ab47ece411eb20f3ac7f43b384 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 21:33:49 +0000 Subject: [PATCH 878/939] Remove unneccessary CUDA dependency; use SHLIB_EXT --- easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb index 0d9e772ecb6e..0e9191507e1e 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -18,7 +18,6 @@ checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479' 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ - ('CUDA', '11.3.1', '', True), ('Python', '3.9.5'), ('PyTorch', '1.10.0'), ('ITK', '5.2.1'), @@ -39,7 +38,7 @@ sanity_pip_check = True sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], 'dirs': [''], } From 391f7e9761d7dec0fecc01f3b7c18166a11ac981 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 21:35:15 +0000 Subject: [PATCH 879/939] use SHLIB_EXT in `sanity_check_paths` --- .../easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb index 1315a7276424..e1b2fdd1ce12 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -19,7 +19,7 @@ checksums = [('b427c117250b24199ea88c0b3ec1a6d80a22958b4413b7c85c6318ef011f6479' 'a63df7d5a680d9641c223ea090ff843a7d6f20bdb62095bd44f3b0480a4706ed')] dependencies = [ - ('CUDA', '11.3.1', '', True), + ('CUDA', '11.3.1', '', SYSTEM), ('Python', '3.9.5'), ('PyTorch', '1.10.0', versionsuffix), ('ITK', '5.2.1'), @@ -40,7 +40,7 @@ sanity_pip_check = True sanity_check_commands = ["python -c 'import monai; monai.config.print_config()'"] sanity_check_paths = { - 'files': ['lib/python%(pyshortver)s/site-packages/%(namelower)s/_C.so'], + 'files': ['lib/python%%(pyshortver)s/site-packages/%%(namelower)s/_C.%s' % SHLIB_EXT], 'dirs': [''], } From 722976e5e8ab0ec71cb3d5bb7b5b5728c297f2f7 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 27 Dec 2022 22:47:35 +0000 Subject: [PATCH 880/939] Update torchvision to 0.11.3 --- .../easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb | 2 +- easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb index e1b2fdd1ce12..64267d63a4ab 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a-CUDA-11.3.1.eb @@ -26,7 +26,7 @@ dependencies = [ ('NiBabel', '3.2.1'), ('scikit-image', '0.18.3'), ('tensorboard', '2.8.0'), - ('torchvision', '0.11.1', versionsuffix), + ('torchvision', '0.11.3', versionsuffix), ('tqdm', '4.61.2'), ] diff --git a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb index 0e9191507e1e..2bdc812a6fe8 100644 --- a/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb +++ b/easybuild/easyconfigs/m/MONAI/MONAI-0.8.0-foss-2021a.eb @@ -24,7 +24,7 @@ dependencies = [ ('NiBabel', '3.2.1'), ('scikit-image', '0.18.3'), ('tensorboard', '2.8.0'), - ('torchvision', '0.11.1'), + ('torchvision', '0.11.3'), ('tqdm', '4.61.2'), ] From d99b96a9b41961849e2d4c45b1aa2a1ea139a73f Mon Sep 17 00:00:00 2001 From: iotaka Date: Wed, 28 Dec 2022 11:32:50 +0100 Subject: [PATCH 881/939] Update ngtcp2-0.7.0-GCC-11.3.0.eb --- easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb index 75ed02edf9f3..f5d87ac788a0 100644 --- a/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/n/ngtcp2/ngtcp2-0.7.0-GCC-11.3.0.eb @@ -1,3 +1,5 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + easyblock = 'CMakeMake' name = 'ngtcp2' From cac1071009c2429c4aef19c0799e25fc2fde7fef Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 28 Dec 2022 11:58:22 +0100 Subject: [PATCH 882/939] adding easyconfigs: LHAPDF-6.5.3-gompi-2022a.eb --- .../l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb new file mode 100644 index 000000000000..3794712a7e51 --- /dev/null +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -0,0 +1,40 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'LHAPDF' +version = '6.5.3' + +homepage = 'http://lhapdf.hepforge.org/' +description = """ +Les Houches Parton Density Function unified library + +First you need to adjust by `export LHAPDF_DATA_PATH=/local/.../path/` to your. +Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. +""" + +toolchain = {'name': 'gompi', 'version': '2022a'} +# TODO +#toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hepforge.org/archive/lhapdf/'] +sources = [SOURCE_TAR_GZ] +checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] + +dependencies = [ + ('Python', '3.10.4'), + ('Boost', '1.79.0') +] + +configopts = "--disable-static --enable-python" + +sanity_check_paths = { + 'files': ["lib/libLHAPDF.so",'bin/lhapdf-config'], + 'dirs': ["lib","share/LHAPDF"], +} + +sanity_check_commands = ["python -c 'import lhapdf'"] +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'phys' From 0ad429b4a9fb49bb037fe883b5e3c78c4e219272 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Wed, 28 Dec 2022 12:08:14 +0100 Subject: [PATCH 883/939] Remove TODO and add toolchainopts --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 3794712a7e51..5fee37a6ace4 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -15,8 +15,7 @@ Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ toolchain = {'name': 'gompi', 'version': '2022a'} -# TODO -#toolchainopts = {'optarch': True, 'pic': True} +toolchainopts = {'optarch': True, 'pic': True} source_urls = ['http://www.hepforge.org/archive/lhapdf/'] sources = [SOURCE_TAR_GZ] From 0dc4bdff01683c75da391f8cb9dcfa7787fa829a Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Wed, 28 Dec 2022 12:20:35 +0000 Subject: [PATCH 884/939] Switch to `versionsuffix` for CUDA dependencies --- .../Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb | 2 +- .../easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb index b66cbc3dfe8e..b4b6d0f7b61f 100644 --- a/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/a/Albumentations/Albumentations-1.3.0-foss-2022a-CUDA-11.7.0.eb @@ -16,7 +16,7 @@ dependencies = [ ('PyYAML', '6.0'), ('scikit-image', '0.19.3'), ('scikit-learn', '1.1.2'), - ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), ('imgaug', '0.4.0', versionsuffix), ] diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb index 44e5f993163f..565a626ba4fe 100644 --- a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.0-foss-2022a-CUDA-11.7.0.eb @@ -17,7 +17,7 @@ dependencies = [ ('Pillow', '9.1.1'), ('matplotlib', '3.5.2'), ('scikit-image', '0.19.3'), - ('OpenCV', '4.6.0', '-CUDA-%(cudaver)s' + '-contrib'), + ('OpenCV', '4.6.0', versionsuffix + '-contrib'), ('Shapely', '1.8.2'), ('imageio', '2.22.2'), ] From c2507741a6c9e9cdda9316b577ec52839044a019 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 28 Dec 2022 15:45:46 +0000 Subject: [PATCH 885/939] Toolchain changed to GCC --- ...mint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb | 54 +++++++++++++++++++ 1 file changed, 54 insertions(+) create mode 100644 easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb new file mode 100644 index 000000000000..a64ba46e9115 --- /dev/null +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb @@ -0,0 +1,54 @@ +# For the various build options see here: +# https://www.bennyp.org/research/simint/README.txt +# lmax is set to 5 which is widely used it seems +# vec is set to avx, which should work on most platforms +# This might be changed to other values, if required +# J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeMake' + +name = 'simint' +version = '0.7' +local_lmax = '5' +# supported: {scalar, sse, avx, avxfma, micavx512} +# scalar ONLY FOR USE WITH simint-scalar (and only useful for benchmarks), micavx512 experimental! +local_vec = 'avx' + +# custom configuration, to be used as dependency for PSI4 +versionsuffix = '-lmax-%s-vec-%s-psi4' % (local_lmax, local_vec) + +homepage = 'https://www.bennyp.org/research/simint/' +description = """Simint is a vectorized implementation of the Obara-Saika (OS) +method of calculating electron repulsion integrals. Speedup is gained by +vectorizing the primitive loop of the OS algorithm, with additional vectorization +and optimizations left to the compiler.""" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +source_urls = ['https://www.bennyp.org/research/simint/download/'] +sources = ['%(name)s-v%(version)s.tar.bz2'] +checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] + +builddependencies = [ + ('CMake', '3.22.1'), + ('binutils', '2.37'), +] + +local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax +local_common_configopts += '-DSIMINT_VECTOR=%s ' % local_vec +local_common_configopts += '-DENABLE_TESTS=ON ' +# 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', +] + +# run test to valicate accuracy +runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' + +sanity_check_paths = { + 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], + 'dirs': ['include', 'share'], +} + +moduleclass = 'chem' From aac090752780821eee1dd8e74a7045eb63535fb9 Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 28 Dec 2022 15:54:05 +0000 Subject: [PATCH 886/939] Addition to PR #16892 : Sanity check command added --- easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb index df8ae82f8925..96534b540932 100644 --- a/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/m/mstore/mstore-0.2.0-GCC-11.2.0.eb @@ -18,6 +18,8 @@ builddependencies = [ ('CMake', '3.22.1'), ] +sanity_check_commands = ['mstore-fortranize --help'] + sanity_check_paths = { 'files': ['bin/mstore-info', 'bin/mstore-fortranize', 'bin/mctc-convert'], 'dirs': ['include/mstore', 'lib/pkgconfig', 'share'], From 356788dd5a14e2c601f82673037dd755fc2c3837 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 29 Dec 2022 09:17:17 +0100 Subject: [PATCH 887/939] remove zstd dep (already included in GnuTLS) --- .../g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb index cb7dd92d43c8..89649bba2dd6 100644 --- a/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/g/glib-networking/glib-networking-2.72.1-GCCcore-11.3.0.eb @@ -23,7 +23,6 @@ dependencies = [ ('GLib', '2.72.1'), ('GnuTLS', '3.7.8'), ('libidn2', '2.3.2'), - ('zstd', '1.5.2'), ] sanity_check_paths = { From 6c51b07d87323bfa10b008dc95f3a3eb426be7de Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 15:51:54 +0100 Subject: [PATCH 888/939] use single sed command to fiddle with infercnvpy's pyproject.toml + fix unrolled preinstallopts --- .../i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index afaff507ff21..3ccfde57c1c5 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -19,9 +19,9 @@ use_pip = True # avoid hatcling requirement to install infercnvpy # (since installing it introduces conflicting version requirements with poetry included with Python) -local_preinstallopts = """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && """ -local_preinstallopts += """sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && """ -local_preinstallopts += """sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ +local_preinstallopts = """sed -e -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ +local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ +local_preinstallopts += """-e 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """ exts_list = [ ('setuptools', '65.6.0', { @@ -37,7 +37,7 @@ exts_list = [ 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], }), (name, version, { - 'preinstallopts': """sed -i 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' pyproject.toml && sed -i 's/^requires = .*/requires = ["setuptools"]/g' pyproject.toml && sed -i 's/dynamic = \["version"\]/version = "%(version)s"/g' pyproject.toml && """, + 'preinstallopts': local_preinstallopts, 'checksums': ['00b8d78726db0a70bdb4d887fd503a484873244a60b9f58a0979aa75ba6e48cb'], }), ] From 3c671c26fa12d4691d24d72cd49d730b5d2bf8d4 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 16:20:11 +0100 Subject: [PATCH 889/939] fix checksums in easyconfig for OpenFOAM v10 --- easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb index ac915d6fce39..7fafa63937ce 100644 --- a/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb +++ b/easybuild/easyconfigs/o/OpenFOAM/OpenFOAM-10-foss-2022a.eb @@ -13,9 +13,8 @@ source_urls = ['https://github.com/OpenFOAM/OpenFOAM-%(version_major)s/archive'] sources = ['version-%(version)s.tar.gz'] patches = ['OpenFOAM-%(version)s-ThirdParty.patch'] checksums = [ - '59d712ba798ca44b989b6ac50bcb7c534eeccb82bcf961e10ec19fc8d84000cf', # version-10.tar.gz - '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43', # OpenFOAM-10-ThirdParty.patch - '518e27683c5c41400cfbc17b31effa50b31b25916dccbf85b18b0b955f642505', # OpenFOAM-v1906-wmake-ompi.patch + {'version-10.tar.gz': '59d712ba798ca44b989b6ac50bcb7c534eeccb82bcf961e10ec19fc8d84000cf'}, + {'OpenFOAM-10-ThirdParty.patch': '307df0206cdb24533f4974378843332064f4a2d85cf0638c20fc4c87b1524b43'}, ] builddependencies = [ From 031e96b0691457b898c26a51d555ab33b11259a8 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 16:29:10 +0100 Subject: [PATCH 890/939] stick to scanpy 1.8.2 as dependency for infercnvpy --- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index 6ef3d046708a..574df806cf5e 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -12,7 +12,7 @@ dependencies = [ ('Python', '3.9.6'), ('SciPy-bundle', '2021.10'), ('leidenalg', '0.8.8'), - ('scanpy', '1.9.1'), + ('scanpy', '1.8.2'), ] use_pip = True From b4c68edddf12808ddd09e8c4469434559ea2a11e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 16:50:57 +0100 Subject: [PATCH 891/939] adding easyconfigs: SELFIES-2.1.1-GCC-11.2.0.eb --- .../s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb | 22 +++++++++++++++++++ 1 file changed, 22 insertions(+) create mode 100644 easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb diff --git a/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb new file mode 100644 index 000000000000..adcde874baab --- /dev/null +++ b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb @@ -0,0 +1,22 @@ +easyblock = 'PythonPackage' + +name = 'SELFIES' +version = '2.1.1' + +homepage = 'https://github.com/aspuru-guzik-group/selfies' +description = "Robust representation of semantically constrained graphs, in particular for molecules in chemistry" + +toolchain = {'name': 'GCC', 'version': '11.2.0'} + +dependencies = [ + ('Python', '3.9.6'), +] + +sources = [SOURCELOWER_TAR_GZ] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'chem' From 28d9815464c1185044f86e35f857e1bd7b9548d4 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:00:11 +0100 Subject: [PATCH 892/939] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 5fee37a6ace4..1aafeabaa428 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -22,8 +22,8 @@ sources = [SOURCE_TAR_GZ] checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] dependencies = [ - ('Python', '3.10.4'), - ('Boost', '1.79.0') + ('Python', '3.10.4'), + ('Boost', '1.79.0'), ] configopts = "--disable-static --enable-python" From 7e70179c870524744e67eac891244507b45982f1 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:00:32 +0100 Subject: [PATCH 893/939] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 1aafeabaa428..64e5f06400de 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -29,8 +29,8 @@ dependencies = [ configopts = "--disable-static --enable-python" sanity_check_paths = { - 'files': ["lib/libLHAPDF.so",'bin/lhapdf-config'], - 'dirs': ["lib","share/LHAPDF"], + 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], + 'dirs': ["share/LHAPDF"], } sanity_check_commands = ["python -c 'import lhapdf'"] From cf183f9646d554a14af9a4a3d85c5eb944fc521e Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:01:26 +0100 Subject: [PATCH 894/939] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 64e5f06400de..97d5f88e6327 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -33,7 +33,12 @@ sanity_check_paths = { 'dirs': ["share/LHAPDF"], } -sanity_check_commands = ["python -c 'import lhapdf'"] +sanity_check_commands = [ + "lhapd --version", + "lhapd-config --version", + "python -c 'import lhapdf'", +] + modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} moduleclass = 'phys' From ad71a3cd0683e66b43185e093996bba644549252 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:02:52 +0100 Subject: [PATCH 895/939] Update LHAPDF-6.5.3-gompi-2022a.eb --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index 97d5f88e6327..ba4620d26704 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -34,8 +34,8 @@ sanity_check_paths = { } sanity_check_commands = [ - "lhapd --version", - "lhapd-config --version", + "lhapdf --version", + "lhapdf-config --version", "python -c 'import lhapdf'", ] From 6bef77404be851710c22b83e3c5c98323a80c880 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 17:10:26 +0100 Subject: [PATCH 896/939] add missing checksum in SELFIES easyconfig --- easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb index adcde874baab..81faead483ec 100644 --- a/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb +++ b/easybuild/easyconfigs/s/SELFIES/SELFIES-2.1.1-GCC-11.2.0.eb @@ -13,6 +13,7 @@ dependencies = [ ] sources = [SOURCELOWER_TAR_GZ] +checksums = ['d8066b47e746a6ca5111143e5365ffebbb56b0b244328a61dd4e344d0125f84b'] download_dep_fail = True use_pip = True From e3ab068a3e3b7486dabc511a0fbfcbab0f0f214a Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 2 Jan 2023 17:16:01 +0100 Subject: [PATCH 897/939] add session-info as extension to easyconfig for infercnvpy 0.4.0, since it's required --- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 3 +++ 1 file changed, 3 insertions(+) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index 574df806cf5e..dd0a59c97cb9 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -36,6 +36,9 @@ exts_list = [ ('tqdm', '4.64.1', { 'checksums': ['5f4f682a004951c1b450bc753c710e9280c5746ce6ffedee253ddbcbf54cf1e4'], }), + ('session_info', '1.0.0', { + 'checksums': ['3cda5e03cca703f32ae2eadbd6bd80b6c21442cfb60e412c21cb8ad6d5cbb6b7'], + }), (name, version, { 'preinstallopts': local_preinstallopts, 'checksums': ['00b8d78726db0a70bdb4d887fd503a484873244a60b9f58a0979aa75ba6e48cb'], From 5ed2f4c964bbd6752ca5040c14c58fca400793ad Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Mon, 2 Jan 2023 17:30:48 +0100 Subject: [PATCH 898/939] Fix hatcling typo in comment --- .../easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb index dd0a59c97cb9..469957dab364 100644 --- a/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb +++ b/easybuild/easyconfigs/i/infercnvpy/infercnvpy-0.4.0-foss-2021b.eb @@ -17,7 +17,7 @@ dependencies = [ use_pip = True -# avoid hatcling requirement to install infercnvpy +# avoid hatchling requirement to install infercnvpy # (since installing it introduces conflicting version requirements with poetry included with Python) local_preinstallopts = """sed -i -e 's/^build-backend = .*/build-backend = "setuptools.build_meta"/g' """ local_preinstallopts += """-e 's/^requires = .*/requires = ["setuptools"]/g' """ From c6e49ea5041673b84815d45f90e5fad5990dd539 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 17:37:36 +0100 Subject: [PATCH 899/939] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb index ba4620d26704..99fd3cdace8f 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb @@ -31,7 +31,7 @@ configopts = "--disable-static --enable-python" sanity_check_paths = { 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], 'dirs': ["share/LHAPDF"], -} +} sanity_check_commands = [ "lhapdf --version", From e0c45cd68d64c55c0eefcd3d6921c80348d29ce8 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Mon, 2 Jan 2023 21:37:43 +0000 Subject: [PATCH 900/939] Add `sanity_check_commands` --- .../easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb index b01480119f01..fed7c2635a0f 100644 --- a/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/tesseract/tesseract-5.3.0-GCCcore-11.3.0.eb @@ -52,7 +52,7 @@ postinstallcmds = [ ] modextrapaths = { - 'TESSDATA_PREFIX': 'tessdata', + 'TESSDATA_PREFIX': 'share/tessdata', } sanity_check_paths = { @@ -60,4 +60,6 @@ sanity_check_paths = { 'dirs': ['share/tessdata', 'include/tesseract'] } +sanity_check_commands = ['tesseract --version', 'tesseract --list-langs'] + moduleclass = 'vis' From fce2cdec0fd2b53667727694d3d95f1b16a37bd8 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 22:41:09 +0100 Subject: [PATCH 901/939] add modextravars and modloadmsg --- .../l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 50 +++++++++++++++++++ 1 file changed, 50 insertions(+) create mode 100644 easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb new file mode 100644 index 000000000000..055e2cc78b25 --- /dev/null +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -0,0 +1,50 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Alexander Puck Neuwirth + +easyblock = 'ConfigureMake' + +name = 'LHAPDF' +version = '6.5.3' + +homepage = 'http://lhapdf.hepforge.org/' +description = """ +Les Houches Parton Density Function + +LHAPDF is the standard tool for evaluating parton distribution functions (PDFs) in high-energy physics. +""" + +toolchain = {'name': 'GCC', 'version': '11.3.0'} +toolchainopts = {'optarch': True, 'pic': True} + +source_urls = ['http://www.hepforge.org/archive/lhapdf/'] +sources = [SOURCE_TAR_GZ] +checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] + +dependencies = [ + ('Python', '3.10.4'), +] + +configopts = "--disable-static --enable-python" + +sanity_check_paths = { + 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], + 'dirs': ["share/LHAPDF"], +} + +sanity_check_commands = [ + "lhapdf --version", + "lhapdf-config --version", + "python -c 'import lhapdf'", +] + +modloadmsg = """ +To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/`. +Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. +""" + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} +modextravars = { + # 'LHAPDF_DATA_DIR': '/path/to/LHAPDF_DATA_DIR', # please adapt +} + +moduleclass = 'phys' From d2aecb58f7fd2ff3e45875a9fcb6940eb4350635 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 22:58:56 +0100 Subject: [PATCH 902/939] Delete LHAPDF-6.5.3-gompi-2022a.eb --- .../l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb | 44 ------------------- 1 file changed, 44 deletions(-) delete mode 100644 easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb deleted file mode 100644 index 99fd3cdace8f..000000000000 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-gompi-2022a.eb +++ /dev/null @@ -1,44 +0,0 @@ -# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild -# Author: Alexander Puck Neuwirth - -easyblock = 'ConfigureMake' - -name = 'LHAPDF' -version = '6.5.3' - -homepage = 'http://lhapdf.hepforge.org/' -description = """ -Les Houches Parton Density Function unified library - -First you need to adjust by `export LHAPDF_DATA_PATH=/local/.../path/` to your. -Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. -""" - -toolchain = {'name': 'gompi', 'version': '2022a'} -toolchainopts = {'optarch': True, 'pic': True} - -source_urls = ['http://www.hepforge.org/archive/lhapdf/'] -sources = [SOURCE_TAR_GZ] -checksums = ['57435cd695e297065d53e69bd29090765c934936b6a975ff8c559766f2230359'] - -dependencies = [ - ('Python', '3.10.4'), - ('Boost', '1.79.0'), -] - -configopts = "--disable-static --enable-python" - -sanity_check_paths = { - 'files': ["bin/lhapdf", "bin/lhapdf-config", "lib/libLHAPDF.%s" % SHLIB_EXT], - 'dirs': ["share/LHAPDF"], -} - -sanity_check_commands = [ - "lhapdf --version", - "lhapdf-config --version", - "python -c 'import lhapdf'", -] - -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} - -moduleclass = 'phys' From 93b07186ca71d0eb09ab1de3c24b7b287b2010e7 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 23:02:49 +0100 Subject: [PATCH 903/939] Update LHAPDF-6.5.3-GCC-11.3.0.eb --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index 055e2cc78b25..cef4199ee7ef 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -44,7 +44,7 @@ Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} modextravars = { - # 'LHAPDF_DATA_DIR': '/path/to/LHAPDF_DATA_DIR', # please adapt + # 'LHAPDF_DATA_PATH': '/path/to/share/LHAPDF/', # please adapt } moduleclass = 'phys' From ea52363d55aef472877a05250b64003e388d6ce5 Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Mon, 2 Jan 2023 23:07:53 +0100 Subject: [PATCH 904/939] Update LHAPDF-6.5.3-GCC-11.3.0.eb --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index cef4199ee7ef..e222dd2f1138 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -38,7 +38,7 @@ sanity_check_commands = [ ] modloadmsg = """ -To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/`. +To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/:$LHAPDF_DATA_PATH`. Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ From 5a9bc1e2fdaf5ed66570a6b4805e0598ab4f3f91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:12:04 +0100 Subject: [PATCH 905/939] add dependency on UCX-CUDA --- .../a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index c649a8f50358..ad434a512db3 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -90,6 +90,7 @@ dependencies = [ ('X11', '20210802'), ('CUDA', '11.4.1', '', SYSTEM), ('NCCL', '2.10.3', '-CUDA-%(cudaver)s'), + ('UCX-CUDA', '1.11.2', '-CUDA-%(cudaver)s'), ] # Some CUDA tests differs from expected results From 13ffa7c6062b23c6e33affacb779c1a89987661b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:12:44 +0100 Subject: [PATCH 906/939] switch order of deps to make it identical to non-cuda version --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index ad434a512db3..c9fdf6490ce0 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -68,8 +68,8 @@ checksums = [ ] builddependencies = [ - ('Bison', '3.7.6'), ('CMake', '3.21.1'), + ('Bison', '3.7.6'), ('flex', '2.6.4'), ('make', '4.3'), ] From 946b38fbed9b5772c72015bf2244f1df7cffc5fc Mon Sep 17 00:00:00 2001 From: Alexander Puck Neuwirth Date: Tue, 3 Jan 2023 10:21:02 +0100 Subject: [PATCH 907/939] Update easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index e222dd2f1138..e3b5b92532d6 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -42,8 +42,8 @@ To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ -modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} -modextravars = { +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}, # 'LHAPDF_DATA_PATH': '/path/to/share/LHAPDF/', # please adapt } From 0d54dfd986ead170809af2c320c8ffacac587878 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:25:50 +0100 Subject: [PATCH 908/939] remove redundant curly bracket --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index e3b5b92532d6..b239ef07505c 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -43,7 +43,7 @@ Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ modextrapaths = { - 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}, + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', # 'LHAPDF_DATA_PATH': '/path/to/share/LHAPDF/', # please adapt } From 0d51bb35897d82cd1da4873d83161be8022f0168 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 3 Jan 2023 10:42:38 +0100 Subject: [PATCH 909/939] Shorten line of modloadmsg --- easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb index b239ef07505c..3bcded3044d4 100644 --- a/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/l/LHAPDF/LHAPDF-6.5.3-GCC-11.3.0.eb @@ -38,7 +38,8 @@ sanity_check_commands = [ ] modloadmsg = """ -To use/install your own PDF data you need to adjust the path `export LHAPDF_DATA_PATH=/local/.../path/:$LHAPDF_DATA_PATH`. +To use/install your own PDF data, you need to adjust the $LHAPDF_DATA_PATH: +export LHAPDF_DATA_PATH=/local/.../path/:$LHAPDF_DATA_PATH` Then you can run `lhapdf update` followed by `lhapdf install your_pdf`. """ From 1dbe5f41c77050055c109bec42b4b165835f8b2d Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:47:13 +0100 Subject: [PATCH 910/939] adding easyconfigs: UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb and patches: UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch --- ...X-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb | 45 ++++++ ...OCm-1.11.2_fix_hsa+hip_include_paths.patch | 149 ++++++++++++++++++ 2 files changed, 194 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb create mode 100644 easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch diff --git a/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb new file mode 100644 index 000000000000..fda3009ae001 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2-GCCcore-11.2.0-ROCm-4.5.0.eb @@ -0,0 +1,45 @@ +easyblock = 'EB_UCX_Plugins' + +name = 'UCX-ROCm' +version = '1.11.2' +_rocm_version = '4.5.0' +versionsuffix = '-ROCm-%s' % _rocm_version + +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 ROCm support. +""" + +toolchain = {'name': 'GCCcore', 'version': '11.2.0'} +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': 'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch', 'alt_location': 'UCX-CUDA'}, + 'UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch', +] +checksums = [ + {'ucx-1.11.2.tar.gz': 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, + {'UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch': + 'a57ce314f90b170bbe6eb98d938b44ca1bb7285dbfc5891bbff56b66009ff9f9'}, +] + +builddependencies = [ + ('binutils', '2.37'), + ('Autotools', '20210726'), + ('pkg-config', '0.29.2'), +] + +dependencies = [ + ('zlib', '1.2.11'), + ('UCX', version), + ('ROCm', _rocm_version), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch new file mode 100644 index 000000000000..a29251bbc506 --- /dev/null +++ b/easybuild/easyconfigs/u/UCX-ROCm/UCX-ROCm-1.11.2_fix_hsa+hip_include_paths.patch @@ -0,0 +1,149 @@ +Fix hsa and hip include path + +Ã…ke Sandgren, 2023-01-03 +diff -ru ucx-1.11.2.orig/config/m4/rocm.m4 ucx-1.11.2/config/m4/rocm.m4 +--- ucx-1.11.2.orig/config/m4/rocm.m4 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/config/m4/rocm.m4 2023-01-03 09:23:39.310360596 +0100 +@@ -84,9 +84,9 @@ + + rocm_happy=yes + AS_IF([test "x$rocm_happy" = xyes], +- [AC_CHECK_HEADERS([hsa.h], [rocm_happy=yes], [rocm_happy=no])]) ++ [AC_CHECK_HEADERS([hsa/hsa.h], [rocm_happy=yes], [rocm_happy=no])]) + AS_IF([test "x$rocm_happy" = xyes], +- [AC_CHECK_HEADERS([hsa_ext_amd.h], [rocm_happy=yes], [rocm_happy=no])]) ++ [AC_CHECK_HEADERS([hsa/hsa_ext_amd.h], [rocm_happy=yes], [rocm_happy=no])]) + AS_IF([test "x$rocm_happy" = xyes], + [AC_CHECK_LIB([hsa-runtime64], [hsa_init], [rocm_happy=yes], [rocm_happy=no])]) + +@@ -111,7 +111,7 @@ + hip_happy=no + AC_CHECK_LIB([hip_hcc], [hipFree], [AC_MSG_WARN([Please install ROCm-3.7.0 or above])], [hip_happy=yes]) + AS_IF([test "x$hip_happy" = xyes], +- [AC_CHECK_HEADERS([hip_runtime.h], [hip_happy=yes], [hip_happy=no])]) ++ [AC_CHECK_HEADERS([hip/hip_runtime.h], [hip_happy=yes], [hip_happy=no])]) + AS_IF([test "x$hip_happy" = xyes], + [AC_CHECK_LIB([amdhip64], [hipFree], [hip_happy=yes], [hip_happy=no])]) + AS_IF([test "x$hip_happy" = xyes], [HIP_CXXFLAGS="--std=gnu++11"], []) +diff -ru ucx-1.11.2.orig/src/ucm/rocm/rocmmem.h ucx-1.11.2/src/ucm/rocm/rocmmem.h +--- ucx-1.11.2.orig/src/ucm/rocm/rocmmem.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/ucm/rocm/rocmmem.h 2023-01-03 09:25:40.289314597 +0100 +@@ -7,7 +7,7 @@ + #define UCM_ROCMMEM_H_ + + #include +-#include ++#include + + /* hsa_amd_memory_pool_allocate */ + hsa_status_t ucm_override_hsa_amd_memory_pool_allocate( +diff -ru ucx-1.11.2.orig/src/uct/rocm/base/rocm_base.h ucx-1.11.2/src/uct/rocm/base/rocm_base.h +--- ucx-1.11.2.orig/src/uct/rocm/base/rocm_base.h 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/base/rocm_base.h 2023-01-03 09:24:10.206096620 +0100 +@@ -9,8 +9,8 @@ + + #include + #include +-#include +-#include ++#include ++#include + + + hsa_status_t uct_rocm_base_init(void); +diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_ep.c ucx-1.11.2/src/uct/rocm/copy/rocm_copy_ep.c +--- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_ep.c 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_ep.c 2023-01-03 09:25:35.457356174 +0100 +@@ -19,7 +19,7 @@ + #include + #include + +-#include ++#include + + #define uct_rocm_memcpy_h2d(_d,_s,_l) memcpy((_d),(_s),(_l)) + #define uct_rocm_memcpy_d2h(_d,_s,_l) ucs_memcpy_nontemporal((_d),(_s),(_l)) +diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_iface.h ucx-1.11.2/src/uct/rocm/copy/rocm_copy_iface.h +--- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_iface.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_iface.h 2023-01-03 09:24:33.245895073 +0100 +@@ -8,7 +8,7 @@ + + #include + +-#include ++#include + + #define UCT_ROCM_COPY_TL_NAME "rocm_cpy" + +diff -ru ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_md.c ucx-1.11.2/src/uct/rocm/copy/rocm_copy_md.c +--- ucx-1.11.2.orig/src/uct/rocm/copy/rocm_copy_md.c 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/copy/rocm_copy_md.c 2023-01-03 09:25:33.073376690 +0100 +@@ -20,7 +20,7 @@ + #include + #include + +-#include ++#include + + static ucs_config_field_t uct_rocm_copy_md_config_table[] = { + {"", "", NULL, +diff -ru ucx-1.11.2.orig/src/uct/rocm/gdr/rocm_gdr_md.c ucx-1.11.2/src/uct/rocm/gdr/rocm_gdr_md.c +--- ucx-1.11.2.orig/src/uct/rocm/gdr/rocm_gdr_md.c 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/src/uct/rocm/gdr/rocm_gdr_md.c 2023-01-03 09:25:37.569338002 +0100 +@@ -18,7 +18,7 @@ + #include + #include + +-#include ++#include + + static ucs_config_field_t uct_rocm_gdr_md_config_table[] = { + {"", "", NULL, +diff -ru ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_iface.h ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_iface.h +--- ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_iface.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_iface.h 2023-01-03 09:24:27.741943217 +0100 +@@ -9,7 +9,7 @@ + + #include + +-#include ++#include + + #define UCT_ROCM_IPC_TL_NAME "rocm_ipc" + +diff -ru ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_md.h ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_md.h +--- ucx-1.11.2.orig/src/uct/rocm/ipc/rocm_ipc_md.h 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/ipc/rocm_ipc_md.h 2023-01-03 09:25:30.109402193 +0100 +@@ -7,7 +7,7 @@ + #define ROCM_IPC_MD_H + + #include +-#include ++#include + + + extern uct_component_t uct_rocm_ipc_component; +diff -ru ucx-1.11.2.orig/test/gtest/common/mem_buffer.cc ucx-1.11.2/test/gtest/common/mem_buffer.cc +--- ucx-1.11.2.orig/test/gtest/common/mem_buffer.cc 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/test/gtest/common/mem_buffer.cc 2023-01-03 09:32:23.085955061 +0100 +@@ -31,7 +31,7 @@ + #endif + + #if HAVE_ROCM +-# include ++# include + + #define ROCM_CALL(_code) \ + do { \ +diff -ru ucx-1.11.2.orig/test/gtest/ucm/rocm_hooks.cc ucx-1.11.2/test/gtest/ucm/rocm_hooks.cc +--- ucx-1.11.2.orig/test/gtest/ucm/rocm_hooks.cc 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/test/gtest/ucm/rocm_hooks.cc 2023-01-03 09:32:26.177929298 +0100 +@@ -5,7 +5,7 @@ + */ + #include + #include +-#include ++#include + + static ucm_event_t alloc_event, free_event; + From 1d711a273efbda79f36baf1d6053d06c2dbaa96b Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:49:00 +0100 Subject: [PATCH 911/939] Update UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch to fix libs for rocm libs too. --- ...-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb | 8 +-- ....11.0_link_against_existing_UCX_libs.patch | 52 ++++++++++++++----- ...-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb | 8 +-- 3 files changed, 46 insertions(+), 22 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb index ce3211904db0..ac5302556e36 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -16,14 +16,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = [ '%(name)s-%(version)s_link_against_existing_UCX_libs.patch', ] checksums = [ - 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647', # ucx-1.11.0.tar.gz - # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', + {'ucx-1.11.0.tar.gz': 'b7189b69fe0e16e3c03784ef674e45687a9c520750bd74a45125c460ede37647'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch index 765d880238ef..5020e1af7345 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch @@ -1,9 +1,9 @@ Make CUDA/ROCm plugins link against the existing ucs/ucm/uct libraries. Ã…ke Sandgren, Mikael Öhman 2021-08-09 -diff -ru ucx-1.11.0.orig/configure.ac ucx-1.11.0/configure.ac ---- ucx-1.11.0.orig/configure.ac 2021-06-26 02:05:59.632558898 +0200 -+++ ucx-1.11.0/configure.ac 2021-06-26 02:08:39.330081752 +0200 +diff -ru ucx-1.11.2.orig/configure.ac ucx-1.11.2/configure.ac +--- ucx-1.11.2.orig/configure.ac 2021-09-23 22:36:08.000000000 +0200 ++++ ucx-1.11.2/configure.ac 2023-01-03 10:29:43.816777145 +0100 @@ -29,13 +29,13 @@ AC_GNU_SOURCE AC_CONFIG_HEADERS([config.h]) @@ -25,9 +25,9 @@ diff -ru ucx-1.11.0.orig/configure.ac ucx-1.11.0/configure.ac AH_TOP([ #ifndef UCX_CONFIG_H -diff -ru ucx-1.11.0.orig/src/ucm/cuda/Makefile.am ucx-1.11.0/src/ucm/cuda/Makefile.am ---- ucx-1.11.0.orig/src/ucm/cuda/Makefile.am 2021-08-09 19:14:56.904346018 +0200 -+++ ucx-1.11.0/src/ucm/cuda/Makefile.am 2021-08-09 19:15:22.472286262 +0200 +diff -ru ucx-1.11.2.orig/src/ucm/cuda/Makefile.am ucx-1.11.2/src/ucm/cuda/Makefile.am +--- ucx-1.11.2.orig/src/ucm/cuda/Makefile.am 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/ucm/cuda/Makefile.am 2023-01-03 10:29:43.816777145 +0100 @@ -9,7 +9,7 @@ module_LTLIBRARIES = libucm_cuda.la libucm_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) @@ -37,9 +37,21 @@ diff -ru ucx-1.11.0.orig/src/ucm/cuda/Makefile.am ucx-1.11.0/src/ucm/cuda/Makefi libucm_cuda_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ $(patsubst %, -Xlinker %, $(CUDA_LDFLAGS)) \ -version-info $(SOVERSION) -diff -ru ucx-1.11.0.orig/src/uct/cuda/Makefile.am ucx-1.11.0/src/uct/cuda/Makefile.am ---- ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am 2021-08-09 19:16:59.146060323 +0200 -+++ ucx-1.11.0/src/uct/cuda/gdr_copy/Makefile.am 2021-08-09 19:17:27.915993083 +0200 +diff -ru ucx-1.11.2.orig/src/ucm/rocm/Makefile.am ucx-1.11.2/src/ucm/rocm/Makefile.am +--- ucx-1.11.2.orig/src/ucm/rocm/Makefile.am 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/ucm/rocm/Makefile.am 2023-01-03 10:32:04.931602717 +0100 +@@ -10,7 +10,7 @@ + module_LTLIBRARIES = libucm_rocm.la + libucm_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libucm_rocm_la_CFLAGS = $(BASE_CFLAGS) $(ROCM_CFLAGS) +-libucm_rocm_la_LIBADD = ../libucm.la ++libucm_rocm_la_LIBADD = -lucm + libucm_rocm_la_LDFLAGS = $(UCM_MODULE_LDFLAGS) \ + $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ +diff -ru ucx-1.11.2.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.11.2/src/uct/cuda/gdr_copy/Makefile.am +--- ucx-1.11.2.orig/src/uct/cuda/gdr_copy/Makefile.am 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/uct/cuda/gdr_copy/Makefile.am 2023-01-03 10:29:43.816777145 +0100 @@ -10,7 +10,7 @@ libuct_cuda_gdrcopy_la_CFLAGS = $(BASE_CFLAGS) libuct_cuda_gdrcopy_la_LDFLAGS = $(CUDA_LDFLAGS) $(GDR_COPY_LDFLAGS) \ @@ -48,10 +60,10 @@ diff -ru ucx-1.11.0.orig/src/uct/cuda/Makefile.am ucx-1.11.0/src/uct/cuda/Makefi +libuct_cuda_gdrcopy_la_LIBADD = -lucs \ $(top_builddir)/src/uct/cuda/libuct_cuda.la \ $(CUDA_LIBS) - -diff -ru ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.11.0/src/uct/cuda/gdr_copy/Makefile.am ---- ucx-1.11.0.orig/src/uct/cuda/Makefile.am 2021-08-09 19:16:06.472183427 +0200 -+++ ucx-1.11.0/src/uct/cuda/Makefile.am 2021-08-09 19:16:38.201109272 +0200 + +diff -ru ucx-1.11.2.orig/src/uct/cuda/Makefile.am ucx-1.11.2/src/uct/cuda/Makefile.am +--- ucx-1.11.2.orig/src/uct/cuda/Makefile.am 2021-07-10 09:59:16.000000000 +0200 ++++ ucx-1.11.2/src/uct/cuda/Makefile.am 2023-01-03 10:29:43.816777145 +0100 @@ -11,8 +11,8 @@ libuct_cuda_la_CPPFLAGS = $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) libuct_cuda_la_CFLAGS = $(BASE_CFLAGS) $(CUDA_CFLAGS) @@ -63,4 +75,16 @@ diff -ru ucx-1.11.0.orig/src/uct/cuda/gdr_copy/Makefile.am ucx-1.11.0/src/uct/cu $(CUDA_LIBS) noinst_HEADERS = \ - +diff -ru ucx-1.11.2.orig/src/uct/rocm/Makefile.am ucx-1.11.2/src/uct/rocm/Makefile.am +--- ucx-1.11.2.orig/src/uct/rocm/Makefile.am 2021-02-27 02:18:15.000000000 +0100 ++++ ucx-1.11.2/src/uct/rocm/Makefile.am 2023-01-03 10:31:38.195822390 +0100 +@@ -10,8 +10,7 @@ + module_LTLIBRARIES = libuct_rocm.la + libuct_rocm_la_CPPFLAGS = $(BASE_CPPFLAGS) $(ROCM_CPPFLAGS) + libuct_rocm_la_CFLAGS = $(BASE_CFLAGS) +-libuct_rocm_la_LIBADD = $(top_builddir)/src/ucs/libucs.la \ +- $(top_builddir)/src/uct/libuct.la ++libuct_rocm_la_LIBADD = -lucs -luct + libuct_rocm_la_LDFLAGS = $(ROCM_LDFLAGS) $(ROCM_LIBS) -version-info $(SOVERSION) \ + $(patsubst %, -Xlinker %, -L$(ROCM_ROOT)/lib -rpath $(ROCM_ROOT)/hip/lib -rpath $(ROCM_ROOT)/lib) \ + $(patsubst %, -Xlinker %, --enable-new-dtags) \ diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb index d5f4602d19fa..461a01a7509d 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.11.2-GCCcore-11.2.0-CUDA-11.4.1.eb @@ -16,14 +16,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = [ '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', ] checksums = [ - 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df', # ucx-1.11.2.tar.gz - # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', + {'ucx-1.11.2.tar.gz': 'deebf86a5344fc2bd9e55449f88c650c4514928592807c9bc6fe4190e516c6df'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ From ac34c6a4dbca0ee5916375c5e1120f326175d22e Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:50:07 +0100 Subject: [PATCH 912/939] Update checksums for UCX-CUDA-1.12/13 --- .../UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb | 8 ++++---- .../UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb | 4 ++-- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb index 0fb175ca066e..29b645b0e0a0 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.12.1-GCCcore-11.3.0-CUDA-11.7.0.eb @@ -16,14 +16,14 @@ toolchain = {'name': 'GCCcore', 'version': '11.3.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = [ '%(name)s-1.11.0_link_against_existing_UCX_libs.patch', ] checksums = [ - '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e', # ucx-1.12.1.tar.gz - # UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3', + {'ucx-1.12.1.tar.gz': '40b447c8e7da94a253f2828001b2d76021eb4ad39647107d433d62d61e18ae8e'}, + {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ diff --git a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb index 9212315db276..3025ba35f6df 100644 --- a/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb +++ b/easybuild/easyconfigs/u/UCX-CUDA/UCX-CUDA-1.13.1-GCCcore-12.2.0-CUDA-12.0.0.eb @@ -16,12 +16,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.2.0'} toolchainopts = {'pic': True} source_urls = ['https://github.com/openucx/ucx/releases/download/v%(version)s'] -sources = ['ucx-%(version)s.tar.gz'] +sources = [{'filename': 'ucx-%(version)s.tar.gz', 'alt_location': 'UCX'}] patches = ['%(name)s-1.11.0_link_against_existing_UCX_libs.patch'] checksums = [ {'ucx-1.13.1.tar.gz': 'efc37829b68e131d2acc82a3fd4334bfd611156a756837ffeb650ab9a9dd3828'}, {'UCX-CUDA-1.11.0_link_against_existing_UCX_libs.patch': - 'e61328e95e96dae1754e9ec4c26accc4695cc8d83712bd109a93589e0da35ab3'}, + '457187fa020e526609ba91e7750c9941d57bd57d60d6eed317b40ad8824aca93'}, ] builddependencies = [ From 09869837ae46ba32c4ae3c53b8748478d30d1673 Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Tue, 3 Jan 2023 11:53:01 +0100 Subject: [PATCH 913/939] adding easyconfigs: OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb --- ...o-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100755 easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb diff --git a/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb new file mode 100755 index 000000000000..a6b19ada3f2e --- /dev/null +++ b/easybuild/easyconfigs/o/OSU-Micro-Benchmarks/OSU-Micro-Benchmarks-5.9-gompi-2021b-ROCm-4.5.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'OSU-Micro-Benchmarks' +version = '5.9' +_rocm_version = '4.5.0' +versionsuffix = '-ROCm-%s' % _rocm_version + +homepage = 'https://mvapich.cse.ohio-state.edu/benchmarks/' +description = """OSU Micro-Benchmarks""" + +toolchain = {'name': 'gompi', 'version': '2021b'} +toolchainopts = {'usempi': True} + +source_urls = ['https://mvapich.cse.ohio-state.edu/download/mvapich/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['d619740a1c2cc7c02a9763931546b320d0fa4093c415ff3873c2958e121c0609'] + +dependencies = [ + ('ROCm', _rocm_version), + ('UCX-ROCm', '1.11.2', versionsuffix), +] + +configopts = ' --enable-rocm ' + +local_benchmark_dirs = [ + 'libexec/osu-micro-benchmarks/mpi/%s' % x for x in ['collective', 'one-sided', 'pt2pt', 'startup'] +] + +modextrapaths = {'PATH': local_benchmark_dirs} + +sanity_check_paths = { + 'files': [], + 'dirs': local_benchmark_dirs, +} + +moduleclass = 'perf' From 8df5225052a01d486f9d2dc5e7d117b00442a354 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Tue, 3 Jan 2023 13:12:20 +0000 Subject: [PATCH 914/939] adding easyconfigs: NanoFilt-2.8.0-foss-2021b.eb --- .../n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100755 easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb diff --git a/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb new file mode 100755 index 000000000000..e0392394b13f --- /dev/null +++ b/easybuild/easyconfigs/n/NanoFilt/NanoFilt-2.8.0-foss-2021b.eb @@ -0,0 +1,26 @@ +easyblock = 'PythonPackage' + +name = 'NanoFilt' +version = '2.8.0' + +homepage = 'https://github.com/wdecoster/nanofilt' +description = """Filtering and trimming of long read sequencing data.""" + +toolchain = {'name': 'foss', 'version': '2021b'} + +sources = [SOURCE_TAR_GZ] +checksums = ['47f4f4f8be834f011570a8d76d07cc12abe0686c8917607316a8ccfb3e20758c'] + +dependencies = [ + ('Python', '3.9.6'), + ('Biopython', '1.79'), +] + +download_dep_fail = True +use_pip = True + +sanity_check_commands = ["NanoFilt --help"] + +sanity_pip_check = True + +moduleclass = 'bio' From 27844c6d27b1f9e5eb8750323e7445b8c8001478 Mon Sep 17 00:00:00 2001 From: iotaka Date: Tue, 3 Jan 2023 15:35:51 +0100 Subject: [PATCH 915/939] Update nghttp2-1.48.0-GCC-11.3.0.eb --- easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb | 2 ++ 1 file changed, 2 insertions(+) diff --git a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb index 9076065af443..b3af8adacf8a 100644 --- a/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb +++ b/easybuild/easyconfigs/n/nghttp2/nghttp2-1.48.0-GCC-11.3.0.eb @@ -1,3 +1,5 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + easyblock = 'CMakeMake' name = 'nghttp2' From 71e297372b214b410aa0dccbb1afa94e378d43fb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Tue, 3 Jan 2023 15:36:51 +0100 Subject: [PATCH 916/939] adding easyconfigs: SNAP-2.0.1-GCC-12.2.0.eb --- .../s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) create mode 100644 easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb diff --git a/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb new file mode 100644 index 000000000000..c7b19e83bc5e --- /dev/null +++ b/easybuild/easyconfigs/s/SNAP/SNAP-2.0.1-GCC-12.2.0.eb @@ -0,0 +1,30 @@ +easyblock = 'MakeCp' + +name = 'SNAP' +version = '2.0.1' + +homepage = 'https://www.microsoft.com/en-us/research/project/snap' +description = """Scalable Nucleotide Alignment Program -- a fast and accurate read aligner for + high-throughput sequencing data""" + +toolchain = {'name': 'GCC', 'version': '12.2.0'} +toolchainopts = {'cstd': 'c++98'} + +source_urls = ['https://github.com/amplab/snap/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['30f199c583e054c50ca6f3b61f27066640b7c829e5c5e8083841596a2869c064'] + +dependencies = [('zlib', '1.2.12')] + +buildopts = 'CXX="$CXX"' + +files_to_copy = [(['snap-aligner', 'SNAPCommand'], 'bin')] + +sanity_check_paths = { + 'files': ['bin/snap-aligner', 'bin/SNAPCommand'], + 'dirs': [], +} + +sanity_check_commands = ["snap-aligner --help"] + +moduleclass = 'bio' From d72d91f641f3ccc03544d4e5cec2ea16a9296073 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 3 Jan 2023 16:11:49 +0100 Subject: [PATCH 917/939] adding easyconfigs: geopandas-0.12.2-foss-2022a.eb, rasterio-1.3.4-foss-2022a.eb, regionmask-0.9.0-foss-2022a.eb --- .../geopandas/geopandas-0.12.2-foss-2022a.eb | 37 +++++++++++++ .../r/rasterio/rasterio-1.3.4-foss-2022a.eb | 54 +++++++++++++++++++ .../regionmask/regionmask-0.9.0-foss-2022a.eb | 34 ++++++++++++ 3 files changed, 125 insertions(+) create mode 100644 easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb create mode 100644 easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb new file mode 100644 index 000000000000..74bbbede7ef4 --- /dev/null +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'geopandas' +version = '0.12.2' + +homepage = 'https://github.com/geopandas/geopandas' +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': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('Shapely', '1.8.2'), + ('Fiona', '1.8.21'), + ('pyproj', '3.4.0'), + ('networkx', '2.8.4'), # needed by mapclassify + ('scikit-learn', '1.1.2'), # needed by mapclassify +] + +use_pip = True + +exts_list = [ + ('mapclassify', '2.4.3', { + 'checksums': ['51b81e1f1ee7f64a4ca1e9f61f01216c364a3f086a48b1be38eb057199cb19bf'], + }), + (name, version, { + 'checksums': ['0acdacddefa176525e4da6d9aeeece225da26055c4becdc6e97cf40fa97c27f4'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb new file mode 100644 index 000000000000..563debbbcd1e --- /dev/null +++ b/easybuild/easyconfigs/r/rasterio/rasterio-1.3.4-foss-2022a.eb @@ -0,0 +1,54 @@ +easyblock = 'PythonBundle' + +name = 'rasterio' +version = '1.3.4' + +homepage = 'https://github.com/mapbox/rasterio' +description = "Rasterio reads and writes geospatial raster data." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('GDAL', '3.5.0'), + ('matplotlib', '3.5.2'), # plot extra + ('boto3', '1.26.37'), # s3 extra +] + +use_pip = True + +exts_list = [ + ('affine', '2.3.1', { + 'checksums': ['d676de66157ad6af99ffd94e0f54e89dfc35b0fb7252ead2ed0ad2dca431bdd0'], + }), + ('click-plugins', '1.1.1', { + 'checksums': ['46ab999744a9d831159c3411bb0c79346d94a444df9a3a3742e9ed63645f264b'], + }), + ('cligj', '0.7.2', { + 'checksums': ['a4bc13d623356b373c2c27c53dbd9c68cae5d526270bfa71f6c6fa69669c6b27'], + }), + ('snuggs', '1.4.7', { + 'checksums': ['501cf113fe3892e14e2fee76da5cd0606b7e149c411c271898e6259ebde2617b'], + }), + (name, version, { + 'checksums': ['5a8771405276ecf00b8ee927bd0a81ec21778dcfc97e4a37d0b388f10c9a41a8'], + 'use_pip_extras': 'plot,s3', + }), +] + +fix_python_shebang_for = ['bin/jp.py', 'bin/rio'] + +sanity_check_paths = { + 'files': ['bin/rio'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "jp.py --help", + "rio --help", +] + +sanity_pip_check = True + +moduleclass = 'geo' diff --git a/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb new file mode 100644 index 000000000000..6c259ec85aa1 --- /dev/null +++ b/easybuild/easyconfigs/r/regionmask/regionmask-0.9.0-foss-2022a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'regionmask' +version = '0.9.0' + +homepage = 'https://regionmask.readthedocs.io' +description = """regionmask creates masks of geographical regions. It determines to which +geographic region each grid point belongs.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('geopandas', '0.12.2'), + ('rasterio', '1.3.4'), + ('Shapely', '1.8.2'), + ('xarray', '2022.6.0'), +] + +use_pip = True + +exts_list = [ + ('pooch', '1.6.0', { + 'checksums': ['57d20ec4b10dd694d2b05bb64bc6b109c6e85a6c1405794ce87ed8b341ab3f44'], + }), + (name, version, { + 'checksums': ['8da1b6359756241867c4e967097810ef86b9dff4e06d11ca648fe1d607e9cf14'], + }), +] + +sanity_pip_check = True + +moduleclass = 'geo' From 40ec5004aa135b95302c6b69560c0938e8e50371 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 3 Jan 2023 17:38:17 +0100 Subject: [PATCH 918/939] add dependency on matplotlib to geopandas-0.12.2-foss-2022a.eb --- easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb index 74bbbede7ef4..ee3dee5c65a8 100644 --- a/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb +++ b/easybuild/easyconfigs/g/geopandas/geopandas-0.12.2-foss-2022a.eb @@ -16,6 +16,7 @@ dependencies = [ ('SciPy-bundle', '2022.05'), ('Shapely', '1.8.2'), ('Fiona', '1.8.21'), + ('matplotlib', '3.5.2'), ('pyproj', '3.4.0'), ('networkx', '2.8.4'), # needed by mapclassify ('scikit-learn', '1.1.2'), # needed by mapclassify From d4f326329a84e06bb7a56df508f9cf77fc163ca4 Mon Sep 17 00:00:00 2001 From: Alexandre Strube Date: Tue, 3 Jan 2023 18:55:31 +0000 Subject: [PATCH 919/939] adding easyconfigs: openslide-python-1.2.0-GCCcore-11.3.0.eb --- .../openslide-python-1.2.0-GCCcore-11.3.0.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..1d28069258b9 --- /dev/null +++ b/easybuild/easyconfigs/o/openslide-python/openslide-python-1.2.0-GCCcore-11.3.0.eb @@ -0,0 +1,29 @@ +easyblock = 'PythonPackage' + +name = 'openslide-python' +version = '1.2.0' + +homepage = 'https://github.com/openslide/openslide-python' +description = "OpenSlide Python is a Python interface to the OpenSlide library." + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = ['https://github.com/openslide/openslide-python/archive'] +sources = ['v%(version)s.tar.gz'] +checksums = ['8162829d3d0ea44dd82602ced7390d9b10dd339337a58f17a8eb81a30bc0883b'] + +builddependencies = [('binutils', '2.38')] + +dependencies = [ + ('Python', '3.10.4'), + ('OpenSlide', '3.4.1', '-largefiles'), + ('Pillow-SIMD', '9.2.0'), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +options = {'modulename': 'openslide'} + +moduleclass = 'vis' From fc4a4294dd69cc808fde4a86af891cc1a7d54216 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Tue, 3 Jan 2023 20:54:24 +0000 Subject: [PATCH 920/939] adding easyconfigs: dcm2niix-1.0.20220720-GCCcore-11.3.0.eb, CharLS-2.4.1-GCCcore-11.3.0.eb --- .../c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb | 30 +++++++++++++++ .../dcm2niix-1.0.20220720-GCCcore-11.3.0.eb | 37 +++++++++++++++++++ 2 files changed, 67 insertions(+) create mode 100644 easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb create mode 100644 easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..97a9eec1bdd2 --- /dev/null +++ b/easybuild/easyconfigs/c/CharLS/CharLS-2.4.1-GCCcore-11.3.0.eb @@ -0,0 +1,30 @@ +easyblock = 'CMakeMake' + +name = 'CharLS' +version = '2.4.1' + +homepage = 'https://github.com/team-charls/charls' +description = """CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image +compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 +compression ratios.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/team-charls/charls/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['f313f556b5acb9215961d9718c21235aafcd43bce6b357bf66f772e5692bba75'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3') +] + +configopts = '-DBUILD_SHARED_LIBS=ON ' + +sanity_check_paths = { + 'files': ['lib/libcharls.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..0e272245b83d --- /dev/null +++ b/easybuild/easyconfigs/d/dcm2niix/dcm2niix-1.0.20220720-GCCcore-11.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'CMakeMake' + +name = 'dcm2niix' +version = '1.0.20220720' + +homepage = 'https://github.com/rordenlab/dcm2niix' +description = """dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/rordenlab/dcm2niix/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['a095545d6d70c5ce2efd90dcd58aebe536f135410c12165a9f231532ddab8991'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +dependencies = [ + ('zlib', '1.2.12'), + ('pigz', '2.7'), + ('OpenJPEG', '2.5.0'), + ('CharLS', '2.4.1'), +] + +configopts = '-DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DOpenJPEG_DIR=$EBROOTOPENJPEG ' + +sanity_check_paths = { + 'files': ['bin/dcm2niix'], + 'dirs': [''], +} + +sanity_check_commands = ['dcm2niix -h'] + +moduleclass = 'bio' From ea19013660f6eeddc49b05c19c97aaba6bdb16eb Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Wed, 4 Jan 2023 08:32:48 +0100 Subject: [PATCH 921/939] fix Clang-AOMP/4.5.0 checksums for xxx-rocm-4.5.0.tar.gz --- .../c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb index b679ed3649ab..283883c7246a 100644 --- a/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb +++ b/easybuild/easyconfigs/c/Clang-AOMP/Clang-AOMP-4.5.0-GCCcore-11.2.0.eb @@ -40,7 +40,7 @@ default_component_specs = { components = [ ('llvm-project', 'rocm-4.5.0', { - 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296'], + 'checksums': ['b71451bf26650ba06c0c5c4c7df70f13975151eaa673ef0cc77c1ab0000ccc97'], }), ('ROCm-Device-Libs', 'rocm-4.5.0', { 'checksums': ['78412fb10ceb215952b5cc722ed08fa82501b5848d599dc00744ae1bdc196f77'], @@ -49,13 +49,13 @@ components = [ # uses same sources as llvm-project component 'sources': ['llvm-project-%(version)s.tar.gz'], 'patches': ['clang-aomp-%(version)s-openmp-remove-hardcoded-source-paths.patch'], - 'checksums': ['e33d08c8ae42a3ba394dceb8938263cd14ba45e9603b18f3502c3344814ca296', + 'checksums': ['b71451bf26650ba06c0c5c4c7df70f13975151eaa673ef0cc77c1ab0000ccc97', 'f959dfa95ec705acf0ffb8d5e85b48cc56e2bed1b15fab22d9eda1f416dd98ca'], }), ('aomp-extras', 'rocm-4.5.0', { 'source_urls': ['https://github.com/ROCm-Developer-Tools/%(name)s/archive/'], 'patches': ['clang-aomp-%(version)s-aomp-extras-remove-hardcoded-devicelib-path.patch'], - 'checksums': ['66d4d0cb4a1a05edb5f13599d8c06de4e10daf561201273cc56dc907139cb894', + 'checksums': ['a9c32fb7659c0aabba5b1e76ec05037dda485bf893cef4144279b42ef8fae416', '1ae5a1af5ccd6c5a77dbc2882d0b40f07d33a7d0021736b29a21e46ab777803a'], }), ] From 89c93739881cf6ec2d4a42c1a676da7de985bbeb Mon Sep 17 00:00:00 2001 From: sassy Date: Wed, 4 Jan 2023 11:51:51 +0000 Subject: [PATCH 922/939] Fix so short test job is running, with all tests jobs are provided as well --- ...mint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb | 28 +++++++++++++++++-- 1 file changed, 26 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb index a64ba46e9115..73ff6cd68229 100644 --- a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb @@ -43,8 +43,32 @@ configopts = [ local_common_configopts + ' -DBUILD_SHARED_LIBS=ON', ] -# run test to valicate accuracy -runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' +# Run test to valicate accuracy. +# List of all available tests. Running all of them will take quite some time! +# local_tests = [ +# 'Al2Cl6.6-31gss.mol', 'anthracene.aug-cc-pvqz.mol', 'benzene.aug-cc-pvtz.mol', 'C4H4Cl2F2.dzp.mol', +# 'ethane.roos-ano-tz.mol', 'R-camphor.roos-ano-tz.mol', 'water.sto-3g.mol', 'Al2Cl6.aug-cc-pvqz.mol', +# 'anthracene.aug-cc-pvtz.mol', 'benzene.dzp.mol', 'C4H4Cl2F2.roos-ano-tz.mol', 'ethane.sto-3g.mol', +# 'R-camphor.sto-3g.mol', 'Al2Cl6.aug-cc-pvtz.mol', 'anthracene.dzp.mol', 'benzene.roos-ano-tz.mol', +# 'C4H4Cl2F2.sto-3g.mol', 'water.6-31gss.mol', 'Al2Cl6.dzp.mol', 'anthracene.roos-ano-tz.mol', +# 'benzene.sto-3g.mol', 'ethane.6-31gss.mol', 'R-camphor.6-31gss.mol', 'water.aug-cc-pvqz.mol', +# 'Al2Cl6.roos-ano-tz.mol', 'anthracene.sto-3g.mol', 'C4H4Cl2F2.6-31gss.mol', 'ethane.aug-cc-pvqz.mol', +# 'R-camphor.aug-cc-pvqz.mol', 'water.aug-cc-pvtz.mol', 'Al2Cl6.sto-3g.mol', 'benzene.6-31gss.mol', +# 'C4H4Cl2F2.aug-cc-pvqz.mol', 'ethane.aug-cc-pvtz.mol', 'R-camphor.aug-cc-pvtz.mol water.dzp.mol', +# ] + +# This runs fast but does not give any guarantee if the installation is numerically correct! +local_tests = ['ethane.sto-3g.mol'] + +# Run selected tests: +sanity_check_commands = [ + 'cd %%(builddir)s/easybuild_obj/ && ' + 'OMP_NUM_THREADS=4 test/test_eri ../%%(name)s-v%%(version)s/test/dat/%s' % x for x in local_tests +] + +postinstallcmds = [ + "echo 'Please check the testjob manually to see if there are any errors'", +] sanity_check_paths = { 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], From 7ac9c2a80673440e62773d3364f791dd6277bd8c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2023 13:56:42 +0100 Subject: [PATCH 923/939] remove simint easyconfig using GCCcore/11.2.0 toolchain (since there's one using GCC/11.2.0) --- ...-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb | 54 ------------------- 1 file changed, 54 deletions(-) delete mode 100644 easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb deleted file mode 100644 index 6198188f68f4..000000000000 --- a/easybuild/easyconfigs/s/simint/simint-0.7-GCCcore-11.2.0-lmax-5-vec-avx-psi4.eb +++ /dev/null @@ -1,54 +0,0 @@ -# For the various build options see here: -# https://www.bennyp.org/research/simint/README.txt -# lmax is set to 5 which is widely used it seems -# vec is set to avx, which should work on most platforms -# This might be changed to other values, if required -# J. Sassmannshausen (Imperial College London/UK) - -easyblock = 'CMakeMake' - -name = 'simint' -version = '0.7' -local_lmax = '5' -# supported: {scalar, sse, avx, avxfma, micavx512} -# scalar ONLY FOR USE WITH simint-scalar (and only useful for benchmarks), micavx512 experimental! -local_vec = 'avx' - -# custom configuration, to be used as dependency for PSI4 -versionsuffix = '-lmax-%s-vec-%s-psi4' % (local_lmax, local_vec) - -homepage = 'https://www.bennyp.org/research/simint/' -description = """Simint is a vectorized implementation of the Obara-Saika (OS) -method of calculating electron repulsion integrals. Speedup is gained by -vectorizing the primitive loop of the OS algorithm, with additional vectorization -and optimizations left to the compiler.""" - -toolchain = {'name': 'GCCcore', 'version': '11.2.0'} - -source_urls = ['https://www.bennyp.org/research/simint/download/'] -sources = ['%(name)s-v%(version)s.tar.bz2'] -checksums = ['9851fa2323924d4732dd611b366219f4408c8561556abb5e4fa6dbb64a8f919c'] - -builddependencies = [ - ('CMake', '3.22.1'), - ('binutils', '2.37'), -] - -local_common_configopts = '-DSIMINT_MAXAM=%s ' % local_lmax -local_common_configopts += '-DSIMINT_VECTOR=%s ' % local_vec -local_common_configopts += '-DENABLE_TESTS=ON ' -# 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', -] - -# run test to valicate accuracy -runtest = 'OMP_NUM_THREADS=4 test/test_eri ../%(name)s-v%(version)s/test/dat/' - -sanity_check_paths = { - 'files': ['lib/libsimint.a', 'lib/libsimint.%s' % SHLIB_EXT], - 'dirs': ['include', 'share'], -} - -moduleclass = 'chem' From af73e140a3129e83bde814fa7fdf54dfd295af7c Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2023 13:57:22 +0100 Subject: [PATCH 924/939] tweak post-install msg for simint --- .../s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb index 73ff6cd68229..be3968e7c305 100644 --- a/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb +++ b/easybuild/easyconfigs/s/simint/simint-0.7-GCC-11.2.0-lmax-5-vec-avx-psi4.eb @@ -67,7 +67,7 @@ sanity_check_commands = [ ] postinstallcmds = [ - "echo 'Please check the testjob manually to see if there are any errors'", + "echo 'Please check results of the test(s) run in sanity check command manually to see if there are any errors'", ] sanity_check_paths = { From 7f2634b784cc6db60e4d88a4be2fb000617ddfdf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Wed, 4 Jan 2023 14:19:31 +0100 Subject: [PATCH 925/939] disable tests --- .../Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb index c9fdf6490ce0..cc2ae4045a44 100644 --- a/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb +++ b/easybuild/easyconfigs/a/Amber/Amber-22.0-foss-2021b-AmberTools-22.3-CUDA-11.4.1.eb @@ -94,7 +94,7 @@ dependencies = [ ] # Some CUDA tests differs from expected results -runtest = True +runtest = False static = False From 8447d9e10fb19d09f55aab50262899e3f38a610e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 4 Jan 2023 16:16:25 +0100 Subject: [PATCH 926/939] adding easyconfigs: KronaTools-2.8.1-GCCcore-11.3.0.eb --- .../KronaTools-2.8.1-GCCcore-11.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.eb b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..8eb58d4954b6 --- /dev/null +++ b/easybuild/easyconfigs/k/KronaTools/KronaTools-2.8.1-GCCcore-11.3.0.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': '11.3.0'} + +source_urls = ['https://github.com/marbl/Krona/releases/download/v%(version)s/'] +sources = ['%(name)s-%(version)s.tar'] +checksums = ['f3ab44bf172e1f846e8977c7443d2e0c9676b421b26c50e91fa996d70a6bfd10'] + +dependencies = [('Perl', '5.34.1')] + +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 72672d9561b76d27a63f70ef6cb3aca5ed7a5003 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Jan 2023 18:39:18 +0100 Subject: [PATCH 927/939] adding easyconfigs: task-spooler-1.0.2-GCCcore-11.3.0.eb --- .../task-spooler-1.0.2-GCCcore-11.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..e01e690c0c1f --- /dev/null +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -0,0 +1,25 @@ +easyblock = 'ConfigureMake' + +name = 'task-spooler' +version = '1.0.2' + +homepage = 'http://viric.name/soft/ts/' +description = 'task spooler is a Unix batch system where the tasks spooled run one after the other.' + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +source_urls = [homepage] +sources = ['ts-%(version)s.tar.gz'] +checksums = ['f73452aed80e2f9a7764883e9353aa7f40e65d3c199ad1f3be60fd58b58eafec'] + +skipsteps = ['configure'] +installopts = 'PREFIX=%(installdir)s' + +sanity_check_paths = { + 'files': ['bin/ts'], + 'dirs': [] +} + +sanity_check_commands = ["ts -h"] + +moduleclass = 'tools' \ No newline at end of file From 70f9e74b9770be4e2217039c7e3e48bb274eedf4 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Jan 2023 19:23:44 +0100 Subject: [PATCH 928/939] added newline to the EOF --- .../t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb index e01e690c0c1f..31d855d42534 100644 --- a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -22,4 +22,4 @@ sanity_check_paths = { sanity_check_commands = ["ts -h"] -moduleclass = 'tools' \ No newline at end of file +moduleclass = 'tools' From cfa4060742e3309155509593ebe96b4d9d9043d0 Mon Sep 17 00:00:00 2001 From: Orient Date: Wed, 4 Jan 2023 19:41:42 +0100 Subject: [PATCH 929/939] Added binutils as a dependency --- .../t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb index 31d855d42534..22e51f5507ec 100644 --- a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -12,6 +12,10 @@ source_urls = [homepage] sources = ['ts-%(version)s.tar.gz'] checksums = ['f73452aed80e2f9a7764883e9353aa7f40e65d3c199ad1f3be60fd58b58eafec'] +dependencies = { + ('binutils', '2.38'), +} + skipsteps = ['configure'] installopts = 'PREFIX=%(installdir)s' From 34e5626e4e44c1811da3189d835e21234bdf175b Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 4 Jan 2023 23:28:00 +0100 Subject: [PATCH 930/939] adding easyconfigs: CoSymLib-0.10.9-foss-2022a.eb --- .../c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb diff --git a/easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb b/easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb new file mode 100644 index 000000000000..6daeefb02993 --- /dev/null +++ b/easybuild/easyconfigs/c/CoSymLib/CoSymLib-0.10.9-foss-2022a.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'CoSymLib' +version = '0.10.9' + +homepage = 'https://cosymlib.readthedocs.io' +description = """Cosymlib is a python library for computing continuous symmetry & shape measures +(CSMs & CShMs). Although its main aim is to provide simple and ready-to-use +tools for the analysis of the symmetry & shape of molecules, many of the +procedures contained in cosymlib can be easily applied to any finite +geometrical object defined by a set of vertices or a by mass distribution +function.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('matplotlib', '3.5.2'), + ('PyYAML', '6.0'), +] + +use_pip = True + +# replace hardcoded library sonames for BLAS/LAPACK +_fix_linker_blas = 'sed -i \'s/libraries=.*/libraries=["flexiblas", "gfortran"],/g\' setup.py &&' + +exts_list = [ + ('symgroupy', '0.5.11', { + 'checksums': ['bf59460d29ee707289c859d5e10e3984d3cd0536e5b7b001962f428cb73b3c22'], + 'preinstallopts': _fix_linker_blas, + }), + ('wfnsympy', '0.3.5', { + 'checksums': ['f1bede9d9e4efdc79e2a1a4f62b02bd7758908ce6bf91a2641150e0f65c32a6c'], + 'preinstallopts': _fix_linker_blas, + }), + ('huckelpy', '0.2.3', { + 'checksums': ['25a4309d4997332b1179de93bb5b6437c61f8ba198a9e0bcd3aec28b6cd6ce28'], + }), + ('cosymlib', version, { + 'checksums': ['c3e74aa00570489cac609ce6f274a7b6626141948eb5a261d4b27c4e517cee94'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['cchir', 'cosym', 'esym', 'gsym', 'mosym', 'shape', + 'shape_classic', 'shape_map']], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["cosym --version"] + +moduleclass = 'chem' From ca0515c3db7128581e25c9fc867fbfafc9769d77 Mon Sep 17 00:00:00 2001 From: crubb <1574005+crubb@users.noreply.github.com> Date: Thu, 5 Jan 2023 07:34:55 +0000 Subject: [PATCH 931/939] adding easyconfigs: GDCM-3.0.20-GCCcore-11.3.0.eb --- .../g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb diff --git a/easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb new file mode 100644 index 000000000000..3f7946de5fc6 --- /dev/null +++ b/easybuild/easyconfigs/g/GDCM/GDCM-3.0.20-GCCcore-11.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'CMakeMake' + +name = 'GDCM' +version = '3.0.20' + +homepage = 'https://sourceforge.net/projects/gdcm' +description = "Grassroots DICOM: Cross-platform DICOM implementation" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['d299731e229fe7595001f17e6b81e6f9a27daac3df7295543753525242cea0b2'] + +builddependencies = [ + ('binutils', '2.38'), + ('CMake', '3.24.3'), +] + +configopts = "-DGDCM_BUILD_DOCBOOK_MANPAGES=0" + +sanity_check_paths = { + 'files': ['lib/libgdcmCommon.a', 'lib/libgdcmDICT.a'], + 'dirs': ['include/gdcm-%(version_major_minor)s', 'lib/gdcm-%(version_major_minor)s'], +} + +moduleclass = 'tools' From 5f4d34e40afec9bbcb82b828909dfa3614ed004e Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 09:14:24 +0100 Subject: [PATCH 932/939] update copyright lines for 2023 --- 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 6b4971a52b9f..3ab99c0cc89a 100644 --- a/setup.py +++ b/setup.py @@ -1,5 +1,5 @@ ## -# Copyright 2012-2022 Ghent University +# Copyright 2012-2023 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 461a6de8085a..01ba03af458f 100644 --- a/test/__init__.py +++ b/test/__init__.py @@ -1,5 +1,5 @@ ## -# Copyright 2009-2022 Ghent University +# Copyright 2009-2023 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 63e9464d464d..7cbbb83f2adf 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1,5 +1,5 @@ ## -# Copyright 2013-2022 Ghent University +# Copyright 2013-2023 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 0cbaca896617..e765cdfc3f13 100644 --- a/test/easyconfigs/styletests.py +++ b/test/easyconfigs/styletests.py @@ -1,5 +1,5 @@ ## -# Copyright 2016-2022 Ghent University +# Copyright 2016-2023 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 eae8bd6dbe3f..c058d96f0c58 100644 --- a/test/easyconfigs/suite.py +++ b/test/easyconfigs/suite.py @@ -1,6 +1,6 @@ #!/usr/bin/python ## -# Copyright 2012-2022 Ghent University +# Copyright 2012-2023 Ghent University # # This file is part of EasyBuild, # originally created by the HPC team of Ghent University (http://ugent.be/hpc/en), From 02db3463ce31b247a8c6e2dbad75fc042a12c098 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 12:15:59 +0100 Subject: [PATCH 933/939] add missing patches to OpenBLAS 0.3.20 with NVHPC/22.7 --- .../OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb index a05030ce4e39..39645058d21d 100644 --- a/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb +++ b/easybuild/easyconfigs/o/OpenBLAS/OpenBLAS-0.3.20-NVHPC-22.7-CUDA-11.7.0.eb @@ -16,13 +16,21 @@ patches = [ ('large.tgz', '.'), ('timing.tgz', '.'), 'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch', + 'OpenBLAS-0.3.21_fix-order-vectorization.patch', + 'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch', + 'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch', ] checksums = [ - '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c', # v0.3.20.tar.gz - 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1', # large.tgz - '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af', # timing.tgz - # OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch - 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971', + {'v0.3.20.tar.gz': '8495c9affc536253648e942908e88e097f2ec7753ede55aca52e5dead3029e3c'}, + {'large.tgz': 'f328d88b7fa97722f271d7d0cfea1c220e0f8e5ed5ff01d8ef1eb51d6f4243a1'}, + {'timing.tgz': '999c65f8ea8bd4eac7f1c7f3463d4946917afd20a997807300fe35d70122f3af'}, + {'OpenBLAS-0.3.15_workaround-gcc-miscompilation.patch': + 'e6b326fb8c4a8a6fd07741d9983c37a72c55c9ff9a4f74a80e1352ce5f975971'}, + {'OpenBLAS-0.3.21_fix-order-vectorization.patch': + '08af834e5d60441fd35c128758ed9c092ba6887c829e0471ecd489079539047d'}, + {'OpenBLAS-0.3.21_disable-fma-in-cscal-zscal.patch': + 'bd6836206a883208dc8bc997946f97e4c97d91d8e101fc54db414aaa56902fc3'}, + {'OpenBLAS-0.3.21_avoid-crash-in-zdot.patch': '3dac2c1ec896df574f1b37cde81a16f24550b7f1eb81fbfacb0c4449b0dc7894'}, ] # extensive testing can be enabled by uncommenting the line below From f287618c53a835ae7f64c9e9f1d276e132f368d2 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Thu, 5 Jan 2023 12:17:36 +0100 Subject: [PATCH 934/939] retain -fb versionsuffix for ScalaPACK on top of FlexiBLAS --- easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb | 2 +- ...0-nvompi-2022.07.eb => ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb} | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) rename easybuild/easyconfigs/s/ScaLAPACK/{ScaLAPACK-2.2.0-nvompi-2022.07.eb => ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb} (98%) diff --git a/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb index af891ade799f..172f0f07ea94 100644 --- a/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb +++ b/easybuild/easyconfigs/n/nvofbf/nvofbf-2022.07.eb @@ -19,7 +19,7 @@ dependencies = [ ('FlexiBLAS', '3.2.0', '', local_compiler), ('FFTW', '3.3.10', '', local_compiler), ('FFTW.MPI', '3.3.10', '', local_comp_mpi_tc), - ('ScaLAPACK', '2.2.0', '', local_comp_mpi_tc), + ('ScaLAPACK', '2.2.0', '-fb', local_comp_mpi_tc), ] moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb similarity index 98% rename from easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb rename to easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb index 85b567d8d102..ebb363f77596 100644 --- a/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07.eb +++ b/easybuild/easyconfigs/s/ScaLAPACK/ScaLAPACK-2.2.0-nvompi-2022.07-fb.eb @@ -1,5 +1,6 @@ name = 'ScaLAPACK' version = '2.2.0' +versionsuffix = '-fb' homepage = 'https://www.netlib.org/scalapack/' description = """The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines From d7df04169bde1b07e7893ef168fed8003f173a19 Mon Sep 17 00:00:00 2001 From: ItIsI-Orient <62220698+ItIsI-Orient@users.noreply.github.com> Date: Thu, 5 Jan 2023 13:57:47 +0100 Subject: [PATCH 935/939] Added required changes --- .../t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb index 22e51f5507ec..89e79d4d650a 100644 --- a/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb +++ b/easybuild/easyconfigs/t/task-spooler/task-spooler-1.0.2-GCCcore-11.3.0.eb @@ -12,9 +12,7 @@ source_urls = [homepage] sources = ['ts-%(version)s.tar.gz'] checksums = ['f73452aed80e2f9a7764883e9353aa7f40e65d3c199ad1f3be60fd58b58eafec'] -dependencies = { - ('binutils', '2.38'), -} +builddependencies = [('binutils', '2.38')] skipsteps = ['configure'] installopts = 'PREFIX=%(installdir)s' From a97bd9612cf85846260af2af0bbbbbea776e83c6 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 5 Jan 2023 15:01:55 +0100 Subject: [PATCH 936/939] update easyconfig ABINIT-9.6.2-foss-2022a.eb: fix OpenMP and FlexiBLAS option --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb | 8 ++------ 1 file changed, 2 insertions(+), 6 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb index 7f51bbe7c76e..4003b3410d57 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-foss-2022a.eb @@ -34,13 +34,12 @@ configopts += 'FFLAGS="-fallow-argument-mismatch $FFLAGS" ' # Ensure MPI configopts += '--with-mpi="yes" ' -# configopts += ' FC="mpiifort" CC="mpiicc" CXX="mpiicpc" ' # Enable OpenMP configopts += '--enable-openmp="yes" ' -# BLAS/Lapack from OpenBLAS -configopts += '--with-linalg-flavor="openblas" LINALG_LIBS="${LIBLAPACK_MT}" ' +# BLAS/Lapack from FlexiBLAS +configopts += 'LINALG_LIBS="${LIBLAPACK_MT}" ' # FFTW configopts += '--with-fft-flavor=fftw3 FFTW3_LIBS="-L${EBROOTFFTW} -lfftw3f -lfftw3" ' @@ -60,9 +59,6 @@ preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' # Enable double precision for GW calculations configopts += '--enable-gw-dpc ' -# Enable OpenMP -configopts += '--enable-openmp ' - # 'make check' is just executing some basic unit tests. # Also running 'make tests_v1' to have some basic validation runtest = "check && make test_v1" From 258ef7125f58c3e19be2a2777d798cebcc5448f9 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 5 Jan 2023 15:56:23 +0100 Subject: [PATCH 937/939] update easyconfig ABINIT-9.6.2-intel-2022a.eb: fix OpenMP option --- easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb index fbf7936af3ff..a6b50b225afc 100644 --- a/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb +++ b/easybuild/easyconfigs/a/ABINIT/ABINIT-9.6.2-intel-2022a.eb @@ -56,9 +56,6 @@ preconfigopts = 'export WANNIER90_LIBS="-L$EBROOTWANNIER90/lib -lwannier" && ' # Enable double precision for GW calculations configopts += '--enable-gw-dpc ' -# Enable OpenMP -configopts += '--enable-openmp ' - # 'make check' is just executing some basic unit tests. # Also running 'make tests_v1' to have some basic validation runtest = "check && make test_v1" From c7c09e7952389e7f3dce6c2f1b47f10cb4e747b8 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Fri, 6 Jan 2023 18:48:47 +0100 Subject: [PATCH 938/939] prepare release notes for EasyBuild v4.7.0 + bump version to 4.7.0 --- RELEASE_NOTES | 70 ++++++++++++++++++++++++++++++++++++++++++++++++++- setup.py | 2 +- 2 files changed, 70 insertions(+), 2 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 693825cf8730..722efb29a077 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,10 +3,78 @@ 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 15,535 easyconfig files, for 2,798 different software packages, +The latest version of easybuild-easyconfig provides 16,138 easyconfig files, for 2,906 different software packages, incl. 37 different (compiler) toolchains. +4.7.0 (Janurary 9th 2023) +------------------------- + +feature release + +- added easyconfigs for foss/2022a, intel/2022a common toolchains (#16961 and #16962) + - see also https://docs.easybuild.io/en/latest/Common-toolchains.html +- added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724) +- added example easyconfig files for 109 new software packages: + - Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757), captum (#16477), CAT-BAT (#16577), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842), CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749), cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391), DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704), ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853), HyperQueue (#16753), IJulia (#16494), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844), KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088), Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911), minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892), MultilevelEstimators (#15630), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751), nf-core-mag (#16613), nvofbf (#16724), nvompi (#16724), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564), Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576), PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447), resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032), SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027), Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048), TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587), torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637) +- added additional easyconfigs for various supported software packages, including: + - ABINIT 9.6.2, AdapterRemoval 2.3.3, aiohttp 3.8.3, Albumentations 1.3.0, alsa-lib 1.2.8, Amber 22.0, ANSYS 2022R2, AOCC 4.0.0, APR 1.7.0, APR-util 1.6.1, archspec 0.1.4, arpack-ng 3.8.0, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, ATK 2.38.0, at-spi2-atk 2.38.0, at-spi2-core 2.44.1, Bader 1.04, basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, biogeme 3.2.6, Blender 3.3.1, BLIS 0.9.0, Blosc 1.21.3, Blosc2 2.0.4, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, boto3 1.26.37, BRAKER 2.1.6, Brotli 1.0.9, Brunsli 0.1, bsddb3 6.2.9, BWA 0.7.17, bwidget 1.9.15, bzip2 1.0.8, cairo 1.17.4, Cartopy 0.20.3, CAT-BAT 5.2.3, CDO 2.0.6, CDO 2.1.1, cdsapi 0.5.1, Centrifuge 1.0.4, CFITSIO 3.49, CGAL 4.14.3, CharLS 2.4.1, CheMPS2 1.8.12, Circos 0.69, CMake 3.24.3, ctffind 4.1.14, CubeGUI 4.8, CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0, CUDA 12.0.0, cuDNN 8.6.0.163, cuDNN 8.7.0.84, CUnit 2.1, cURL 7.86.0, cutadapt 4.2, cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dbus-glib 0.112, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, DendroPy 4.5.2, dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, EasyBuild 4.6.2, ecCodes 2.27.0, einops 0.4.1, enchant 2, ESM 2, ESMF 8.3.0, ETE 3.1.2, exiv2 0.27.5, FastTree 2.1.11, fdict 0.8.0, fermi-lite 20190320, FFTW 3.3.10, FFTW.MPI 3.3.10, Fiji 2.9.0, Filtlong 0.2.1, Fiona 1.8.21, FLANN 1.8.4, FLANN 1.9.1, FlexiBLAS 3.2.0, FlexiBLAS 3.2.1, flook 0.8.1, fontconfig 2.14.1, FragGeneScan 1.31, freebayes 1.3.6, FreeImage 3.18.0, FreeSurfer 7.3.2, freetype 2.12.1, FreeXL 1.0.6, FriBidi 1.0.12, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, Gdk-Pixbuf 2.42.10, GDRCopy 2.3, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, git 2.38.1, glew 2.2.0, GLib 2.75.0, glib-networking 2.72.1, GLM 0.9.9.8, GlobalArrays 5.8.1, GlobalArrays 5.8.2, GMP 6.2.1, GnuTLS 3.7.8, GObject-Introspection 1.74.0, gperf 3.1, graphite2 1.3.14, GRASS 8.2.0, GTK3 3.24.35, gzip 1.12, h5py 3.2.1, HarfBuzz 5.3.1, HDF5 1.10.8, HPL 2.3, HTSeq 2.0.2, hunspell 1.7.1, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, IDBA UD, imagecodecs 2022.9.26, imageio 2.22.2, ImageMagick 7.1.0, imbalanced-learn 0.9.0, imgaug 0.4.0, imkl 2022.2.1, imkl-FFTW 2022.2.1, impi 2021.7.1, Infernal 1.1.4, intel-compilers 2022.2.1, intltool 0.51.0, IOR 3.3.0, ITK 5.2.1, JasPer 4.0.0, jax 0.3.23, jax 0.3.23, jbigkit 2.1, JupyterLab 3.5.0, jxrlib 1.1, KronaTools 2.8.1, Leptonica 1.83.0, LERC 3.0, libaec 1.0.6, libarchive 3.6.1, libavif 0.11.1, libcint 4.4.0, libconfig 1.7.3, libdap 3.20.11, libde265 1.0.8, libdeflate 1.15, libdrm 2.4.114, libepoxy 1.5.10, libev 4.33, libevent 2.1.12, libfabric 1.16.1, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libffi 3.4.4, libGLU 9.0.2, libglvnd 1.6.0, libgpg-error 1.46, libheif 1.12.0, libiconv 1.17, libidn 1.41, libidn2 2.3.2, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, libpsl 0.21.1, librsvg 2.55.1, LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libunwind 1.6.2, libxml2 2.10.3, libxml2-python 2.9.13, libyaml 0.2.5, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, make 4.3, makedepend 1.0.7, Mako 1.2.4, MATLAB-Engine 2021, matplotlib 3.4.2, matplotlib 3.5.2, MaxBin 2.2.7, MDAnalysis 2.0.0, MEGAHIT 1.2.9, Mesa 22.2.4, Meson 0.64.0, MetaBAT 2.15, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, MotionCor2 1.5.0, MoviePy 1.0.3, mrcfile 1.3.0, MRChem 1.1.1, MRCPP 1.4.1, NAMD 2.14, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, nanomath 1.2.1, NanoPlot 1.33.0, NASM 2.15.05, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.0, NCO 5.1.3, neptune-client 0.16.2, netCDF 4.9.0, netcdf4-python 1.6.1, netCDF-C++4 4.3.1, netCDF-Fortran 4.6.0, Nextflow 22.10.1, nghttp2 1.48.0, nghttp3 0.6.0, nglview 3.0.3, ngtcp2 0.7.0, NiBabel 4.0.2, Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.4.1, NVSHMEM 2.7.0, NWChem 7.0.2, Octave 7.1.0, OPARI2 2.0.7, OpenBLAS 0.3.20, OpenBLAS 0.3.21, OpenCV 4.6.0, OpenFOAM 10, OpenFOAM 9, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.06, OpenMolcas 22.10, OpenMolcas 22.10, OpenMPI 4.1.4, OpenMPI 4.1.4, openpyxl 3.0.10, OpenSceneGraph 3.6.5, OpenSlide 3.4.1, openslide-python 1.2.0, OpenStackClient 6.0.0, OSU-Micro-Benchmark 6.2, OTF2 3.0.2, p11-kit 0.24.1, Pango 1.50.12, PAPI 7.0.0, ParaView 5.9.1, ParMETIS 4.0.3, pauvre 0.2.3, PCRE2 10.40, PDT 3.25.1, PETSc 3.17.4, phonopy 2.16.3, pigz 2.7, Pillow 9.1.1, Pillow 9.2.0, Pindel 0.2.5b9, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, Porechop 0.2.4, psutil 5.9.3, psutil 5.9.3, pugixml 1.12.1, pullseq 1.0.2, pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, PyOpenGL 3.1.6, pyproj 3.3.1, pyproj 3.4.0, PyQt5 5.15.5, PySCF 1.7.6, pytest 7.1.3, Python 2.7.18, Python 3.10.8, Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, pyWannier90 2021, pyWannier90 2021, PyYAML 6.0, QCA 2.3.5, QGIS 3.28.1, QIIME2 2022.8, qrupdate 1.1.2, QScintilla 2.11.6, Qt5 5.15.7, Qt5Webkit 5.212.0, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, Qwt 6.2.0, rasterio 1.3.4, RDFlib 6.2.0, re2c 3.0, ReFrame 3.12.0, regionmask 0.9.0, RegTools 0.5.2, resolos 0.3.5, rising 0.2.2, RLCard 1.0.9, RStudio-Server 2022.07.2+576, ruamel.yaml 0.17.21, Ruby 3.0.3, Ruby 3.0.5, Rust 1.65.0, SAMtools 1.13, SAP 1.1.3, ScaLAPACK 2.2.0, scanpy 1.9.1, scikit-bio 0.5.7, scikit-image 0.19.3, SciPy-bundle 2021.05, Scoary 1.6.16, SCons 4.4.0, Score-P 8.0, SCOTCH 6.1.0, SCOTCH 7.0.1, scvi-tools 0.16.4, Seaborn 0.12.1, SELFIES 2.1.1, SentencePiece 0.1.96, SentencePiece 0.1.97, SeqLib 1.2.0, Serf 1.3.9, Seurat 4.3.0, SeuratDisk 0.0.0.9020, sfftk 0.7.4, Shapely 1.8.2, Siesta 4.1.5, SignalP 6.0g, simint 0.7, SimPEG 0.18.1, SimpleITK 2.1.1.2, SISSO++ 1.1, slamdunk 0.4.3, SLEPc 3.17.2, SNAP 2.0.1, snappy 1.1.9, SOCI 4.0.3, SpaceRanger 2.0.0, spaln 2.4.12, spglib-python 1.16.1, SQLite 3.39.4, SSW 1.1, STAR-CCM+ 17.06.007, statsmodels 0.13.1, SuperLU_DIST 8.1.0, Tcl 8.6.12, tcsh 6.24.01, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, texinfo 6.8, Theano 1.0.4, time 1.9, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, torchvision 0.13.1, Transformers 4.24.0, TRF 4.09.1, Trinity 2.9.1, typing-extensions v4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, umap-learn 0.5.3, UnZip 6.0, util-linux 2.38.1, Valgrind 3.20.0, vcflib 1.0.3, Vim 9.0.0950, VTK 9.2.2, wandb 0.13.4, wandb 0.13.6, Wayland 1.21.0, Waylandpp 1.0.0, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.6.0, xarray 2022.9.0, XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, xorg-macros 1.19.3, XZ 5.2.7, YACS 0.1.8, yaml-cpp 0.7.0, zarr 2.13.3, zfp 1.0.0, zlib-ng 2.0.6, Zopfli 1.0.3, zstd 1.5.2 +- minor enhancements, including: + - enable building of dev tools in recent PyQt5 easyconfigs(#16469) + - add LMERConvenienceFunctions extension for R v4.2.1(#16512) + - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) + - add SPOTlight packages to R-bundle-Bioconductor-3.15(#16569) + - Add HiCcompare and dependencies to Bioconductor 3.15(#16581) + - Add ROntoTools extension to Bioconductor bundle(#16636) + - add scDblFinder extension to Bioconductor 3.15(#16686) + - add HGNChelper extension to R 4.2.1(#16744) + - add HGNChelper extension to R 4.2.1(#16744) + - automatically cancel Github Action workflow runs for outdated commits (#16754) + - add libmad dependency to SoX v14.4.2 (#16758) + - add numbat extension and requires dependencies to R-bundle-Bioconductor 3.15 + R 4.2.1(#16777) + - install subtree support for git 2.36.0(#16784) + - install subtree support for git 2.38.1(#16785) + - add extensions to ESM-2 to enhance it for esmfold (#16841) + - add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (#16844) + - fix homepage for pocl v1.8 (#16857) + - add HiCBricks extension to Bioconductor 3.15(#16913) + - add ParMETIS and SuperLU_Dist dependencies to PETSc 3.17.4(#16934) + - add KaHIP dependency to OpenFOAM v2206 (#16974) + - add zellkonverter to R-bundle-Bioconductor v3.15 w/ foss/2022a(#16952) + - enable dataset support for recent versions of Arrow(#16956) + - add sanity check command added for mstore(#17029) +- various bug fixes, including: + - define $JUPYTER_PATH via modextrapaths rather than modextravars for IRkernel 1.x (#15776) + - add patches to fix PyTorch 1.10.0 build on POWER (#15904) + - fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (#16485) + - add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility(#16486) + - work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml(#16490) + - fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x(#16502) + - Add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot(#16510) + - add missing build dependency on Perl for GStreamer. And make sure to not make files suid.(#16516) + - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) + - also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs(#16556) + - define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (fixes #16567)(#16570) + - disable use of -Werror in recent NSS easyconfigs(#16571) + - use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs(#16611) + - avoid that zlib + htslib are downloaded and built during installation of MetaBAT(#16624) + - add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems(#16633) + - stick to DIAMOND 2.0.11 as dependency for CAT-BAT with GCC/10.3.0(#16634) + - add missing pyWannier90 dependency for mcu + enhance sanity check(#16667) + - fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo)(#16693) + - fix checksum for dlllogger extension in OpenFold v1.0.0(#16694) + - rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs(#16697) + - update version of pyproj dependency for Cartopy 0.20.3 (to match one used for basemap 1.3.6)(#16699) + - stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes(#16703) +- other changes: + - only give read permissions in GitHub Actions workflows (#16263) + - remove ExomeDepth from recent R-bundle-Bioconductor(#16492) + - include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0(#16578) + - switch IJulia and MultilevelEstimators to JuliaBundle easyblock(#16665) + - cleanup package names and source definitions in Python 3.10.8(#16679) + - downgrade to setuptools 63.4.3 in Python 3.10.8 easyconfig(#16915) + + 4.6.2 (October 21st 2022) ------------------------- diff --git a/setup.py b/setup.py index 3ab99c0cc89a..c39675b8edee 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 = '4.6.3.dev0' +VERSION = '4.7.0' MAJ_VER = VERSION.split('.')[0] MAJMIN_VER = '.'.join(VERSION.split('.')[0:2]) From 77fe9c3071861e283fc472706fe0ecd41b1afb82 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Mon, 9 Jan 2023 10:22:13 +0100 Subject: [PATCH 939/939] minor tweaks to release notes for EasyBuild v4.7.0 --- RELEASE_NOTES | 146 +++++++++++++++++++++++++++++++++----------------- 1 file changed, 98 insertions(+), 48 deletions(-) diff --git a/RELEASE_NOTES b/RELEASE_NOTES index 722efb29a077..5286c71d11c0 100644 --- a/RELEASE_NOTES +++ b/RELEASE_NOTES @@ -3,8 +3,8 @@ 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 16,138 easyconfig files, for 2,906 different software packages, -incl. 37 different (compiler) toolchains. +The latest version of easybuild-easyconfig provides 16,138 easyconfig files, for 2,904 different software packages, +incl. 39 different (compiler) toolchains. 4.7.0 (Janurary 9th 2023) @@ -15,64 +15,114 @@ feature release - added easyconfigs for foss/2022a, intel/2022a common toolchains (#16961 and #16962) - see also https://docs.easybuild.io/en/latest/Common-toolchains.html - added easyconfigs for NVHPC-based toolchains nvompi/2022.07 and nvofbf/2022.07 (#16724) -- added example easyconfig files for 109 new software packages: - - Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757), captum (#16477), CAT-BAT (#16577), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842), CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749), cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391), DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704), ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853), HyperQueue (#16753), IJulia (#16494), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844), KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088), Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911), minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892), MultilevelEstimators (#15630), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751), nf-core-mag (#16613), nvofbf (#16724), nvompi (#16724), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564), Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576), PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447), resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032), SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027), Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048), TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587), torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637) +- added example easyconfig files for 107 new software packages: + - Alfred (#16780), attrdict3 (#16856), bamFilters (#16735), bcl-convert (#16351), Beagle (#346), Boost.MPI (#15757), + captum (#16477), CAT-BAT (#16577, #16634), cdo-bindings (#16669), Chemaxon-Marvin (#13954), CliMetLab (#16842), + CloudCompare (#16944), cmocean (#16659), COBRApy (#16616), CodAn (#16902), CoSymLib (#17049), CPPE (#16749), + cryoCARE (#16534), CTPL (#16498), CUDA-Samples (#16914), cwltool (#16503), Cytoscape (#16682), DeepLabCut (#16391), + DeepMod2 (#17008), Dice (#16752), dlb (#16845), DRAGMAP (#16532), ecBuild (#16842), EGTtools (#16704), + ESM-2 (#16528), flair-NLP (#15588), FMS (#16965), Godon (#16574), gsw (#16643), HighFive (#16737), humann (#16853), + HyperQueue (#16753), IJulia (#16494, #16665), infercnvpy (#16712), InParanoid (#16572), jupyter-server (#14844), + KaHIP (#16861), KITE (#16550), lagrangian-filtering (#16654), LHAPDF (#17028), librttopo (#16856), libwpe (#16088), + Magics (#16842), matlab-proxy (#14270), mcu (#16566), MEMOTE (#16772), memtester (#16763), meson-python (#16911), + minizip (#16856), MITgcmutils (#16623), MONAI (#16519), MOOSE (#13824), mstore (#16892, #17029), + MultilevelEstimators (#15630, #16665), n2v (#16535), NanoLyse (#16575), napari (#16468), NECI (#16751), + nf-core-mag (#16613), oceanspy (#16640), olego (#16909), OmegaFold (#16698), OVITO (#16811), Panedr (#16564), + Parcels (#16838), polars (#16989), PsiCLASS (#16906), pyccel (#16823), PyCheMPS2 (#16710), PyDamage (#16576), + PyImageJ (#16757), pysteps (#16783), python-libsbml (#16610), python-telegram-bot (#16442), pyWannier90 (#16447), + resolos (#16649), RLCard (#16695), SAP (#5200), scikit-misc (#16457), scvi-tools (#16457), SELFIES (#17032), + SeuratDisk (#16951), sfftk (#16466), simint (#16886), SISSO++ (#15759), slamdunk (#15197), spaCy (#17027), + Sphinx-RTD-Theme (#16736), SPOOLES (#16756), Squidpy (#16880), svist4get (#16505), task-spooler (#17048), + TBA (#16497), TensorFlow-Datasets (#16421), TFEA (#16476), TinyXML (#16992), tokenizers (#15587), + torchsampler (#16464), trimesh (#16858), UCX-ROCm (#17033), wpebackend-fdo (#16093), xmitgcm (#16637) - added additional easyconfigs for various supported software packages, including: - - ABINIT 9.6.2, AdapterRemoval 2.3.3, aiohttp 3.8.3, Albumentations 1.3.0, alsa-lib 1.2.8, Amber 22.0, ANSYS 2022R2, AOCC 4.0.0, APR 1.7.0, APR-util 1.6.1, archspec 0.1.4, arpack-ng 3.8.0, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, ATK 2.38.0, at-spi2-atk 2.38.0, at-spi2-core 2.44.1, Bader 1.04, basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, biogeme 3.2.6, Blender 3.3.1, BLIS 0.9.0, Blosc 1.21.3, Blosc2 2.0.4, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, boto3 1.26.37, BRAKER 2.1.6, Brotli 1.0.9, Brunsli 0.1, bsddb3 6.2.9, BWA 0.7.17, bwidget 1.9.15, bzip2 1.0.8, cairo 1.17.4, Cartopy 0.20.3, CAT-BAT 5.2.3, CDO 2.0.6, CDO 2.1.1, cdsapi 0.5.1, Centrifuge 1.0.4, CFITSIO 3.49, CGAL 4.14.3, CharLS 2.4.1, CheMPS2 1.8.12, Circos 0.69, CMake 3.24.3, ctffind 4.1.14, CubeGUI 4.8, CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0, CUDA 12.0.0, cuDNN 8.6.0.163, cuDNN 8.7.0.84, CUnit 2.1, cURL 7.86.0, cutadapt 4.2, cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dbus-glib 0.112, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, DendroPy 4.5.2, dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, EasyBuild 4.6.2, ecCodes 2.27.0, einops 0.4.1, enchant 2, ESM 2, ESMF 8.3.0, ETE 3.1.2, exiv2 0.27.5, FastTree 2.1.11, fdict 0.8.0, fermi-lite 20190320, FFTW 3.3.10, FFTW.MPI 3.3.10, Fiji 2.9.0, Filtlong 0.2.1, Fiona 1.8.21, FLANN 1.8.4, FLANN 1.9.1, FlexiBLAS 3.2.0, FlexiBLAS 3.2.1, flook 0.8.1, fontconfig 2.14.1, FragGeneScan 1.31, freebayes 1.3.6, FreeImage 3.18.0, FreeSurfer 7.3.2, freetype 2.12.1, FreeXL 1.0.6, FriBidi 1.0.12, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, Gdk-Pixbuf 2.42.10, GDRCopy 2.3, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, git 2.38.1, glew 2.2.0, GLib 2.75.0, glib-networking 2.72.1, GLM 0.9.9.8, GlobalArrays 5.8.1, GlobalArrays 5.8.2, GMP 6.2.1, GnuTLS 3.7.8, GObject-Introspection 1.74.0, gperf 3.1, graphite2 1.3.14, GRASS 8.2.0, GTK3 3.24.35, gzip 1.12, h5py 3.2.1, HarfBuzz 5.3.1, HDF5 1.10.8, HPL 2.3, HTSeq 2.0.2, hunspell 1.7.1, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, IDBA UD, imagecodecs 2022.9.26, imageio 2.22.2, ImageMagick 7.1.0, imbalanced-learn 0.9.0, imgaug 0.4.0, imkl 2022.2.1, imkl-FFTW 2022.2.1, impi 2021.7.1, Infernal 1.1.4, intel-compilers 2022.2.1, intltool 0.51.0, IOR 3.3.0, ITK 5.2.1, JasPer 4.0.0, jax 0.3.23, jax 0.3.23, jbigkit 2.1, JupyterLab 3.5.0, jxrlib 1.1, KronaTools 2.8.1, Leptonica 1.83.0, LERC 3.0, libaec 1.0.6, libarchive 3.6.1, libavif 0.11.1, libcint 4.4.0, libconfig 1.7.3, libdap 3.20.11, libde265 1.0.8, libdeflate 1.15, libdrm 2.4.114, libepoxy 1.5.10, libev 4.33, libevent 2.1.12, libfabric 1.16.1, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libfdf 0.2.2, libffi 3.4.4, libGLU 9.0.2, libglvnd 1.6.0, libgpg-error 1.46, libheif 1.12.0, libiconv 1.17, libidn 1.41, libidn2 2.3.2, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, libpsl 0.21.1, librsvg 2.55.1, LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libunwind 1.6.2, libxml2 2.10.3, libxml2-python 2.9.13, libyaml 0.2.5, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, make 4.3, makedepend 1.0.7, Mako 1.2.4, MATLAB-Engine 2021, matplotlib 3.4.2, matplotlib 3.5.2, MaxBin 2.2.7, MDAnalysis 2.0.0, MEGAHIT 1.2.9, Mesa 22.2.4, Meson 0.64.0, MetaBAT 2.15, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, MotionCor2 1.5.0, MoviePy 1.0.3, mrcfile 1.3.0, MRChem 1.1.1, MRCPP 1.4.1, NAMD 2.14, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, nanomath 1.2.1, NanoPlot 1.33.0, NASM 2.15.05, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.0, NCO 5.1.3, neptune-client 0.16.2, netCDF 4.9.0, netcdf4-python 1.6.1, netCDF-C++4 4.3.1, netCDF-Fortran 4.6.0, Nextflow 22.10.1, nghttp2 1.48.0, nghttp3 0.6.0, nglview 3.0.3, ngtcp2 0.7.0, NiBabel 4.0.2, Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.4.1, NVSHMEM 2.7.0, NWChem 7.0.2, Octave 7.1.0, OPARI2 2.0.7, OpenBLAS 0.3.20, OpenBLAS 0.3.21, OpenCV 4.6.0, OpenFOAM 10, OpenFOAM 9, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.06, OpenMolcas 22.10, OpenMolcas 22.10, OpenMPI 4.1.4, OpenMPI 4.1.4, openpyxl 3.0.10, OpenSceneGraph 3.6.5, OpenSlide 3.4.1, openslide-python 1.2.0, OpenStackClient 6.0.0, OSU-Micro-Benchmark 6.2, OTF2 3.0.2, p11-kit 0.24.1, Pango 1.50.12, PAPI 7.0.0, ParaView 5.9.1, ParMETIS 4.0.3, pauvre 0.2.3, PCRE2 10.40, PDT 3.25.1, PETSc 3.17.4, phonopy 2.16.3, pigz 2.7, Pillow 9.1.1, Pillow 9.2.0, Pindel 0.2.5b9, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, Porechop 0.2.4, psutil 5.9.3, psutil 5.9.3, pugixml 1.12.1, pullseq 1.0.2, pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, PyOpenGL 3.1.6, pyproj 3.3.1, pyproj 3.4.0, PyQt5 5.15.5, PySCF 1.7.6, pytest 7.1.3, Python 2.7.18, Python 3.10.8, Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, pyWannier90 2021, pyWannier90 2021, PyYAML 6.0, QCA 2.3.5, QGIS 3.28.1, QIIME2 2022.8, qrupdate 1.1.2, QScintilla 2.11.6, Qt5 5.15.7, Qt5Webkit 5.212.0, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, Qwt 6.2.0, rasterio 1.3.4, RDFlib 6.2.0, re2c 3.0, ReFrame 3.12.0, regionmask 0.9.0, RegTools 0.5.2, resolos 0.3.5, rising 0.2.2, RLCard 1.0.9, RStudio-Server 2022.07.2+576, ruamel.yaml 0.17.21, Ruby 3.0.3, Ruby 3.0.5, Rust 1.65.0, SAMtools 1.13, SAP 1.1.3, ScaLAPACK 2.2.0, scanpy 1.9.1, scikit-bio 0.5.7, scikit-image 0.19.3, SciPy-bundle 2021.05, Scoary 1.6.16, SCons 4.4.0, Score-P 8.0, SCOTCH 6.1.0, SCOTCH 7.0.1, scvi-tools 0.16.4, Seaborn 0.12.1, SELFIES 2.1.1, SentencePiece 0.1.96, SentencePiece 0.1.97, SeqLib 1.2.0, Serf 1.3.9, Seurat 4.3.0, SeuratDisk 0.0.0.9020, sfftk 0.7.4, Shapely 1.8.2, Siesta 4.1.5, SignalP 6.0g, simint 0.7, SimPEG 0.18.1, SimpleITK 2.1.1.2, SISSO++ 1.1, slamdunk 0.4.3, SLEPc 3.17.2, SNAP 2.0.1, snappy 1.1.9, SOCI 4.0.3, SpaceRanger 2.0.0, spaln 2.4.12, spglib-python 1.16.1, SQLite 3.39.4, SSW 1.1, STAR-CCM+ 17.06.007, statsmodels 0.13.1, SuperLU_DIST 8.1.0, Tcl 8.6.12, tcsh 6.24.01, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, texinfo 6.8, Theano 1.0.4, time 1.9, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, torchvision 0.13.1, Transformers 4.24.0, TRF 4.09.1, Trinity 2.9.1, typing-extensions v4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, umap-learn 0.5.3, UnZip 6.0, util-linux 2.38.1, Valgrind 3.20.0, vcflib 1.0.3, Vim 9.0.0950, VTK 9.2.2, wandb 0.13.4, wandb 0.13.6, Wayland 1.21.0, Waylandpp 1.0.0, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.6.0, xarray 2022.9.0, XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, xorg-macros 1.19.3, XZ 5.2.7, YACS 0.1.8, yaml-cpp 0.7.0, zarr 2.13.3, zfp 1.0.0, zlib-ng 2.0.6, Zopfli 1.0.3, zstd 1.5.2 + - Albumentations 1.3.0, ANSYS 2022R2, AOCC 4.0.0, archspec 0.1.4, ArviZ 0.12.1, ASAP 2.1, astropy 5.1.1, + basemap 1.3.6, BBMap 39.01, BEDOPS 2.4.41, Blender 3.3.1, Blosc 1.21.3, Blosc2 2.4.3, bokeh 2.4.3, Bonnie++ 2.00a, + boto3 1.26.37, BRAKER 2.1.6, CDO 2.1.1, cdsapi 0.5.1, CharLS 2.4.1, CheMPS2 1.8.12, CMake 3.24.3, CubeGUI 4.8, + CubeLib 4.8, CubeWriter 4.8, CUDA 11.8.0 + 12.0.0, cuDNN 8.6.0.163 + 8.7.0.84, cURL 7.86.0, cutadapt 4.2, + cuTENSOR 1.6.1.5, dask 2022.10.0, DAS_Tool 1.1.3, DBus 1.15.2, dcm2niix 1.0.20220720, DCMTK 3.6.7, deepdiff 5.8.1, + dm-reverb 0.7.0, double-conversion 3.2.1, Doxygen 1.9.5, ecCodes 2.27.0, exiv2 0.27.5, Fiji 2.9.0, Filtlong 0.2.1, + FLANN 1.9.1, FlexiBLAS 3.2.1, fontconfig 2.14.1, FreeXL 1.0.6, g2clib 1.7.0, GATK 4.3.0.0, GD 2.75, GDCM 3.0.20, + Gdk-Pixbuf 2.42.10, GeneMark-ET 4.71, gensim 4.2.0, geopandas 0.12.2, gettext 0.21.1, gh 2.20.2, Ghostscript 10.0.0, + git 2.38.1, GLib 2.75.0, GlobalArrays 5.8.2, GnuTLS 3.7.8, GObject-Introspection 1.74.0, GRASS 8.2.0, GTK3 3.24.35, + HarfBuzz 5.3.1, HTSeq 2.0.2, hwloc 2.8.0, Hyperopt 0.2.7, ICU 72.1, imagecodecs 2022.9.26, imageio 2.22.2, + ImageMagick 7.1.0-53, imbalanced-learn 0.9.0, JasPer 4.0.0, jax 0.3.23, JupyterLab 3.5.0, Leptonica 1.83.0, + libavif 0.11.1, libdap 3.20.11, libdeflate 1.15, libdrm 2.4.114, libfabric 1.16.1, libffi 3.4.4, libglvnd 1.6.0, + libgpg-error 1.46, libidn 1.41, libjpeg-turbo 2.1.4, LibLZF 3.6, libpciaccess 0.17, libpng 1.6.38, librsvg 2.55.1, + LibSoup 3.0.8, libspatialindex 1.9.3, libspatialite 5.0.1, libtasn1 4.19.0, LibTIFF 4.4.0, libxml2 2.10.3, + libxml2-python 2.9.13, line_profiler 4.0.0, LittleCMS 2.14, LLVM 15.0.5, lz4 1.9.4, makedepend 1.0.7, Mako 1.2.4, + MATLAB-Engine 2021b, Mesa 22.2.4, Meson 0.64.0, MIGRATE-N 5.0.4, Miniconda3 4.12.0, mold 1.7.1, Molden 7.1, + MotionCor2 1.5.0, MoviePy 1.0.3, MRChem 1.1.1, MRCPP 1.4.1, nano 7.0, NanoFilt 2.8.0, nanoget 1.18.1, + nanomath 1.2.1, ncbi-vdb 3.0.0, NCCL 2.16.2, NCCL-tests 2.13.6, NCO 5.1.3, nglview 3.0.3, NiBabel 4.0.2, + Ninja 1.11.1, nodejs 18.12.1, NSPR 4.35, NSS 3.85, NVHPC 22.7, NVSHMEM 2.7.0, Octave 7.1.0, OPARI2 2.0.7, + OpenFOAM 10, OpenFold 1.0.1, OpenImageIO 2.3.17.0, OpenMolcas 22.10, openpyxl 3.0.10, openslide-python 1.2.0, + OpenStackClient 6.0.0, OSU-Micro-Benchmarks 6.2, OTF2 3.0.2, Pango 1.50.12, PAPI 7.0.0, pauvre 0.2.3, PETSc 3.17.4, + phonopy 2.16.3, pigz 2.7, Pillow 9.2.0, Pint 0.19.2, pixman 0.42.2, PMIx 4.2.2, poppler 22.12.0, psutil 5.9.3, + pybedtools 0.9.0, PyBerny 0.6.3, pydantic 1.10.2, pydicom 2.3.0, pyproj 3.4.0, PyQt5 5.15.5, pytest 7.1.3, + Python 3.10.8, python-isal 1.1.0, PyTorch 1.12.1, PyTorch-Geometric 2.1.0, PyTorch-Lightning 1.8.4, QCA 2.3.5, + QGIS 3.28.1, QIIME2 2022.8, QScintilla 2.11.6, Qt5 5.15.7, Qtconsole 5.3.2, QtKeychain 0.13.2, QtPy 2.2.1, + rasterio 1.3.4, re2c 3.0, ReFrame 3.12.0, RStudio-Server 2022.07.2+576, Ruby 3.0.5, Rust 1.65.0, SAP 1.1.3, + scanpy 1.9.1, scikit-image 0.19.3, SCons 4.4.0, Score-P 8.0, Seaborn 0.12.1, SentencePiece 0.1.97, Seurat 4.3.0, + SignalP 6.0g, SimPEG 0.18.1, SLEPc 3.17.2, SNAP 2.0.1, SpaceRanger 2.0.0, SQLite 3.39.4, STAR-CCM+ 17.06.007, + SuperLU_DIST 8.1.0, tensorboardX 2.5.1, TensorFlow 2.8.4, tensorflow-probability 0.16.0, tesseract 5.3.0, + texinfo 6.8, TM-align 20190822, tmux 3.3a, TOBIAS 0.14.0, TOML-Fortran 0.3.1, Transformers 4.24.0, + typing-extensions 4.4.0, UCC 1.1.0, UCX-CUDA 1.13.1, util-linux 2.38.1, Valgrind 3.20.0, Vim 9.0.0950, VTK 9.2.2, + wandb 0.13.6, WebKitGTK+ 2.37.1, WPS 4.4, WRF 4.4, wxPython 4.2.0, wxWidgets 3.2.0, X11 20221110, xarray 2022.9.0, + XCFun 2.1.1, XGBoost 1.7.2, Xmipp 3.22.07, XZ 5.2.7, yaml-cpp 0.7.0, zarr 2.13.3, zlib-ng 2.0.6 - minor enhancements, including: - - enable building of dev tools in recent PyQt5 easyconfigs(#16469) - - add LMERConvenienceFunctions extension for R v4.2.1(#16512) - - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) - - add SPOTlight packages to R-bundle-Bioconductor-3.15(#16569) - - Add HiCcompare and dependencies to Bioconductor 3.15(#16581) - - Add ROntoTools extension to Bioconductor bundle(#16636) - - add scDblFinder extension to Bioconductor 3.15(#16686) - - add HGNChelper extension to R 4.2.1(#16744) - - add HGNChelper extension to R 4.2.1(#16744) - - automatically cancel Github Action workflow runs for outdated commits (#16754) + - enable building of dev tools in recent PyQt5 easyconfigs (#16469) + - add extensions to R v4.2.1: LMERConvenienceFunctions (#16512), HGNChelper 4.2.1 (#16744) + - add extensions to R-bundle-Bioconductor 3.15: SPOTlight (#16569), HiCcompare (#16581), ROntoTools (#16636), + scDblFinder (#16686), numbat (#16777), HiCBricks (#16913), zellkonverter (#16952) - add libmad dependency to SoX v14.4.2 (#16758) - - add numbat extension and requires dependencies to R-bundle-Bioconductor 3.15 + R 4.2.1(#16777) - - install subtree support for git 2.36.0(#16784) - - install subtree support for git 2.38.1(#16785) + - also install subtree support in recent git easyconfigs (#16784, #16785) - add extensions to ESM-2 to enhance it for esmfold (#16841) - add libwebp dependency to Pillow-SIMD 9.2.0 to add webp support (#16844) - - fix homepage for pocl v1.8 (#16857) - - add HiCBricks extension to Bioconductor 3.15(#16913) - - add ParMETIS and SuperLU_Dist dependencies to PETSc 3.17.4(#16934) - add KaHIP dependency to OpenFOAM v2206 (#16974) - - add zellkonverter to R-bundle-Bioconductor v3.15 w/ foss/2022a(#16952) - - enable dataset support for recent versions of Arrow(#16956) - - add sanity check command added for mstore(#17029) + - enable dataset support for recent versions of Arrow (#16956) - various bug fixes, including: - define $JUPYTER_PATH via modextrapaths rather than modextravars for IRkernel 1.x (#15776) - add patches to fix PyTorch 1.10.0 build on POWER (#15904) - fix installation of Python 2.7.18 with GCCcore/11.2.0 (was broken due to 0.0.0 version for some extensions) (#16485) - - add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility(#16486) - - work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml(#16490) - - fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x(#16502) - - Add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot(#16510) - - add missing build dependency on Perl for GStreamer. And make sure to not make files suid.(#16516) - - build nodejs with OpenSSL and ICU provided as proper dependencies(#16529) - - also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs(#16556) - - define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (fixes #16567)(#16570) - - disable use of -Werror in recent NSS easyconfigs(#16571) - - use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs(#16611) - - avoid that zlib + htslib are downloaded and built during installation of MetaBAT(#16624) - - add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems(#16633) - - stick to DIAMOND 2.0.11 as dependency for CAT-BAT with GCC/10.3.0(#16634) - - add missing pyWannier90 dependency for mcu + enhance sanity check(#16667) - - fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo)(#16693) - - fix checksum for dlllogger extension in OpenFold v1.0.0(#16694) - - rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs(#16697) - - update version of pyproj dependency for Cartopy 0.20.3 (to match one used for basemap 1.3.6)(#16699) - - stick to older PyQt-builder in easyconfig for PyQt5 5.15.5, so that 'pip check' passes(#16703) + - add patch for M4 1.4.18 to fix glibc v2.34 SIGSTKSZ compatibility (#16486) + - add patch for pybind11 2.6.0 to fix failing test due to extra whitespace (#16487) + - work around installation problem for extensions in Python 2.7.16 easyconfig due to missing build-backend spec in pyproject.toml (#16490) + - fix libsanitzer for glibc 2.36 to build GCCcore 10.x and 11.x (#16502) + - add OpenBLAS patches to disable FMA in [cz]cal and fix crash in zdot (#16510) + - add missing Perl build dependency GStreamer + add patch to skip trying to make files suid (#16516) + - build nodejs with OpenSSL and ICU provided as proper dependencies (#16529) + - also define $JUPYTER_CONFIG_PATH in IPython and JupyterLab easyconfigs (#16556) + - define $GTKDOCIZE as 'echo' before generating configure script for recent HarfBuzz versions (#16570) + - disable use of -Werror in recent NSS easyconfigs (#16571) + - use 'cpan.metacpan.org' rather than 'www.cpan.org' in extension source_urls for recent Perl easyconfigs (#16611) + - avoid that zlib + htslib are downloaded and built during installation of MetaBAT (#16624) + - add patch to fix installation of MetaBAT 2.15 on non-x86_64 systems (#16633) + - add missing pyWannier90 dependency for mcu + enhance sanity check (#16667) + - fix source_urls for colossalai 0.1.8 (no longer available via PyPI, only via GitHub repo) (#16693) + - add patches to fix or skip PyTorch 1.12.1 tests (#16793) + - fix checksum for cell2location 0.05-alpha and add missing build dependency on flex (#16819) + - upgrade dependency on libdeflate to common v1.8 in fastp and vt easyconfigs using GCC(core)/10.3.0 (#16839) + - fix checksum for dlllogger extension in OpenFold v1.0.0 (#16694) + - make sure that Python dependency is actually used for VTK 9.0.1 (#16741) + - fix homepage for pocl v1.8 (#16857) + - fix source_urls in MUMPS easyconfigs (#16931, #16932) + - fix installation of Bowtie2 v2.4.4+ on non-x86_64 systems (#16946) + - add missing OpenSSL dependency to DCMTK 3.6.7 (#16979) + - fix source URL for PCRE2 (#16987) + - add pkgconf dependency for ICU and add patch to avoid trouble with long path names for nodejs-16.15.1/GCCcore-11.3.0 (#16990) + - add patch for libwpe 1.13.3 to avoid build issues on CentOS 7 (#17001) + - add missing zlib and zstd to GnuTLS (#17013) + - add missing pkgconf build dependency to Transformers v4.24.0 (#17020) + - fix checksums for xxx-rocm-4.5.0.tar.gz source tarballs for Clang-AOMP 4.5.0 (#17042) + - replace useless test step for simint 0.7 with (lightweight) sanity check command (#17044) - other changes: - only give read permissions in GitHub Actions workflows (#16263) - - remove ExomeDepth from recent R-bundle-Bioconductor(#16492) - - include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0(#16578) - - switch IJulia and MultilevelEstimators to JuliaBundle easyblock(#16665) - - cleanup package names and source definitions in Python 3.10.8(#16679) - - downgrade to setuptools 63.4.3 in Python 3.10.8 easyconfig(#16915) + - remove ExomeDepth from recent R-bundle-Bioconductor easyconfigs (#16492) + - include tqdm as extension in the idemux bundle to avoid multivariant deps on GCCcore-10.2.0 (#16578) + - use new EasyBuild logo in README (#16641) + - rename hyperopt to Hyperopt, to be consistent with existing Hyperopt easyconfigs (#16697) + - automatically cancel Github Action workflow runs for outdated commits (#16754) + - use geo moduleclass for SimPEG 0.14.1 (#16847) 4.6.2 (October 21st 2022)