Skip to content

Commit

Permalink
Merge pull request #16239 from easybuilders/4.6.x
Browse files Browse the repository at this point in the history
release EasyBuild 4.6.1
  • Loading branch information
migueldiascosta committed Sep 12, 2022
2 parents 798448d + 4969826 commit 1a6c875
Show file tree
Hide file tree
Showing 578 changed files with 20,024 additions and 728 deletions.
2 changes: 1 addition & 1 deletion .github/workflows/linting.yml
Expand Up @@ -2,7 +2,7 @@ name: Static Analysis
on: [push, pull_request]
jobs:
python-linting:
runs-on: ubuntu-18.04
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@v2

Expand Down
4 changes: 2 additions & 2 deletions .github/workflows/unit_tests.yml
Expand Up @@ -2,7 +2,7 @@ name: easyconfigs unit tests
on: [push, pull_request]
jobs:
test-suite:
runs-on: ubuntu-18.04
runs-on: ubuntu-20.04
strategy:
matrix:
python: [2.7, 3.6]
Expand Down Expand Up @@ -148,7 +148,7 @@ jobs:
eb --prefix /tmp/$USER/$GITHUB_SHA --sourcepath /tmp/sources M4-1.4.18.eb
test-sdist:
runs-on: ubuntu-18.04
runs-on: ubuntu-20.04
strategy:
matrix:
python: [2.7, 3.6, 3.7]
Expand Down
94 changes: 93 additions & 1 deletion RELEASE_NOTES
Expand Up @@ -3,10 +3,102 @@ 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 15,020 easyconfig files, for 2,736 different software packages,
The latest version of easybuild-easyconfig provides 15,332 easyconfig files, for 2,773 different software packages,
incl. 37 different (compiler) toolchains.


v4.6.1 (September 12th 2022)
----------------------------

update/bugfix release

- added example easyconfig files for 37 new software packages:
- AptaSUITE (#8583), BigDFT (#15860), colossalai (#15971), CrystFEL (#8407), Dakota (#15883, #16210),
FastFold (#15972), fastparquet (#15020), FOX-Toolkit (#15986), GLM-AED (#15879), hiredis (#16071),
how_are_we_stranded_here (#16220, #16227), indicators (#16209), JavaFX (#8583), json-fortran (#15979),
jupyter-resource-usage (#15834), libev (#16086), libmad (#16067), libplinkio (#13040), LuaJIT2-OpenResty (#16047),
MetaMorpheus (#15825), mgltools (#16226), miniasm (#15858), muMerge (#16115), nano (#16198), nghttp3 (#16097),
olaFlow (#16021), OpenFAST (#15983, #15983), OpenFold (#15971), Phantompeakqualtools (#15871),
pyGenomeTracks (#16143), QuickPIC (#15978), RheoTool (#16077), Satsuma2 (#16068), SMC++ (#16017), stripy (#15866),
UCC-CUDA (#15956), VESTA (#16217)
- added additional easyconfigs for various supported software packages, including:
- alevin-fry 0.6.0, AmberTools 22.3, arrow-R 8.0.0, ASE 3.22.1, BBMap 38.98, BCFtools 1.15.1, binutils 2.39,
BLAST+ 2.13.0, Bowtie2 2.4.5, BUSCO 5.4.3, CapnProto 0.10.2, Cartopy 0.20.3, ccache 4.6.1, cclib 1.7.2, CDO 2.0.5,
CellRanger-ATAC 2.1.0, CoordgenLibs 3.0.1, cURL 7.84.0, cuTENSOR 1.6.0.3, einops 0.4.1, Elk 8.5.2, Emacs 28.1,
Embree 3.13.4, FFmpeg 4.4.2 + 5.0.1, fio 3.32, Flask 2.2.2, Flye 2.9.1, fmt 9.1.0, FORD 6.1.15, FreeSurfer 7.3.2,
GATE 9.2, GATK 4.2.6.1, GCC(core) 12.2.0, GDB 12.1, Geant4 11.0.2, GetOrganelle 1.7.6.1, gifsicle 1.93, GLFW 3.3.8,
glib-networking 2.72.1, Globus-CLI 3.6.0, gnuplot 5.4.4, gperftools 2.10, Graphviz 5.0.0, Gurobi 9.5.2, HDF5 1.12.2,
HTSlib 1.15.1, Hypre 2.25.0, Jansson 2.14, jax 0.3.14, Kalign 3.3.2, kim-api 2.3.0, LAMMPS 23Jun2022, libcerf 2.1,
libdwarf 0.4.1, Libint 2.7.2, libQGLViewer 2.8.0, LibSoup 2.74.0, libzip 1.9.2, Lua 5.4.4, lxml 4.9.1,
maeparser 1.3.0, matplotlib 3.5.2, MATSim 14.0, MDAnalysis 2.2.0, medaka 1.6.0, Megalodon 2.5.0, Mercurial 6.2,
MetaEuk 6, Mini-XML-3.3.1, MUMmer 4.0.0rc1, MUMPS 5.5.1, netCDF-Fortran 4.6.0, NGSpeciesID 0.1.2.1,
ont-remora 1.0.0, OpenFOAM v2206, OTF2 3.0, parallel 20220722, ParaView 5.10.1, patchelf 0.15.0, Perl 5.36.0,
pftoolsV3 3.2.12, PLINK 2.00a3.6, pretty-yaml 21.10.1, PRSice 2.3.5, pugixml 1.12.1, Pyomo 6.4.2,
PyOpenCL 2021.2.13, Pysam 0.19.1, PyStan 3.5.0, PyYAML 6.0, RDKit 2022.03.5, scikit-bio 0.5.7, scikit-build 0.15.0,
scikit-learn 1.1.2, scikit-optimize 0.9.0, SCOTCH 7.0.1, SIONlib 1.7.7, SISSO 3.1, spglib-python 2.0.0, Stacks 2.62,
Stata 17, SUMO 1.14.1, tbb 2021.5.0, tqdm 4.64.0, Transformers 4.21.1, Trycycler 0.5.3, Unicycler 0.5.0,
Valgrind 3.19.0, ViennaRNA 2.5.1, VTune 2022.3.0.eb, wxPython 4.1.1, x264 20220620, Z3 4.10.2, zfp 1.0.0
- minor enhancements, including:
- add alternate download URL for Voro++ (#15898)
- add extra symlinks and sanity checks for libtinfo in ncurses (#15903)
- include some easyconfig constants in flake8 configuration file (#16040)
- add pigz dependency for cutadapt v3.4 + v3.5 (#16056)
- add sanity check commands for recent gettext versions (>= 0.20.x) (#16091)
- various bug fixes, including:
- use correct Matlab Runtime Compiler (v8.4) for FreeSurfer v7.1.1 (#13375)
- fix set-alias statements for MaxQuant v2.0.3.0 (#15743)
- add Autotools build dependency to R 4.2.0 w/ foss 2021b (#15822)
- add patch for BLIS to fix auto-detection of POWER (#15826)
- downgrade SPAdes dependency to v3.13.1 for Unicycler 0.4.9 since v3.15.3 is too new (#15840)
- explicitly enable HDF5 from kallisto v0.46.2 onwards (#15843)
- add CVE patch for XZ 5.2.5 + attempt to fix symbol patch for all OSs (#15856)
- use build enviroment set by EasyBuild and add missing dependency on zlib to minimap2 (#15859)
- add missing dependencies and execute tests on Trycycler v0.5.2 (#15864)
- add patch for AlphaFold v2.2.2 to fix NaN problem with jax 0.3.9 (#15874)
- exclude (flaky) fault_tolerance_test and fix non-x86 build for TensorFlow 2.7.1 (#15882)
- work around miscompilation of OpenBLAS on POWER by compiling with -fstack-protector-strong (#15885)
- fix tests on POWER9 for BLIS 0.9.0 + fix auto-detect for POWER10 for BLIS (AMD) v2.0 + v3.0 (#15889)
- add and fix patches for PyTorch 1.9.0 on POWER (#15919)
- exclude Binary, PackedBinary and JAR easyblocks from binutils build requirements (#15932)
- consistently add libffi + elfutils dependencies to recent Clang easyconfigs (#15935, #16225)
- add patch to fix broken test on POWER for numpy in SciPy-bundle 2022.05 (#15968)
- refactor checksum test for extensions to use collect_exts_file_info (#15973)
- fix dependency on FOX Toolkit in SUMO (#15986)
- add missing SciPy-bundle dependency for rMATS-turbo (#15988)
- explictely download wannier90 source tarball from wannier90 GitHub repository in QuantumESPRESSO 7.1 easyconfigs (#15993)
- restore ploteig in EIGENSOFT 7.2.1 (#15996)
- add alternative checksum for plot3Drgl extension in R v4.1.x + v4.2.0 easyconfigs (#16011)
- add patch to fix missing sync in LINCS and SETTLE CUDA kernels for GROMACS 2020 (#16027) and 2021 (#16026)
- exclude failing test in TensorFlow 2.4.1 (#16042)
- skip NASA performance and remote server tests in netCDF v4.9.0 (#16050, #16158)
- use versioned symbols in ncurses built with system toolchain (by adding --with-versioned-syms configure option) (#16064)
- add patch to fix pkgconfig file for Blitz++ v1.0.2 (#16102)
- add missing BCFtools dependency for recent medaka versions (#16107)
- add GTK2 v2.24.33 as a dependency for Ghostscript v9.56.1 (#16112)
- fix checksum for Stacks v2.62 (due to silent re-release without version bump) (#16134)
- fix libsanitzer for glibc 2.36 to build GCCcore 11.3.0 (#16145)
- fix top level Makefile for AmberTools 20 and enable tests (#16150)
- add missing patches + enable running tests for AmberTools 21 with intel/2021a (#16151) and intel/2021b (#16152)
- replace HDF5 v1.13.1 with v1.12.1 as dependency, since we shouldn't use odd minor versions of HDF5 which are not stable releases (#16153)
- remove modextrapaths to add top-level install directory to $PATH for recent InterProScan easyconfigs (now done by default by Binary easyblock) (#16167)
- fix sources + source URL + homepage for Molekel v5.4.0 (#16219)
- consistently add maeparser + CoordgenLibs dependencies to OpenBabel 3.1.1 easyconfigs (#16231)
- fix checksum for CUDA 11.4.1 aarch64 installer (#16234)
- remove incorrect comment for Boost dependency in OpenBabel 3.1.1 easyconfigs (#16238)
- add direct Pango dependency in recent ImageMagick easyconfigs (#16237)
- other changes:
- remove superflous -DCMAKE_BUILD_TYPE=Release, use of 'build_type = Release', or enabling separate_build_dir from easyconfigs using CMakeMake easyblock (#13384)
- synchronize ncurses easyconfigs using system toolchain (#15903)
- stick to Java/11 as dependency for Bazel 5.1.1 (which is available for x86_64, aarch64, ppc64le) (#15906)
- speed up OpenMPI 4.1.4 configure by not running "autogen.pl --force", but only running required Autotools commands (#15957)
- replace sed commands by upstreamed patches for BLIS built with intel-compilers toolchain (#15958)
- simplify AlphaFold foss/2021a easyconfigs by using a fleshed out patched OpenMM dependency (#15981)
- update Java/11 to 11.0.16 and Java/17 to 17.0.4 (#16001)
- remove unecessary patch in recent JupyterLab (#16030)
- update CI workflows to use Ubuntu 20.04 (since Ubuntu 18.04 is deprecated) (#16070)
- make check for toolchain value in dependency spec in easyconfigs test suite aware that dumped easyconfig uses SYSTEM constant (#16126)


v4.6.0 (July 8th 2022)
----------------------

Expand Down
@@ -0,0 +1,73 @@
# Based on ADIOS-1.13.1-foss-2019a-Python-2.7.15.eb
# Updated to foss-2020a toolchain and switched to ConfigureMake
# Mini-XML updated to latest 2.x. version
# Author: J. Sassmannshausen (Imperial College London/UK)

easyblock = 'ConfigureMake'

name = 'ADIOS'
version = '1.13.1'
versionsuffix = '-Python-%(pyver)s'

homepage = 'https://www.olcf.ornl.gov/center-projects/adios/'
description = """The Adaptable IO System (ADIOS) provides a simple,
flexible way for scientists to describe the data in their code that may
need to be written, read, or processed outside of the running
simulation."""

toolchain = {'name': 'foss', 'version': '2020a'}
toolchainopts = {'usempi': True, 'pic': True}

github_account = 'ornladios'
source_urls = [GITHUB_SOURCE]
sources = ['v%(version)s.tar.gz']
patches = [
'%(name)s-%(version)s_force_use_of_mpi.patch',
'%(name)s-%(version)s_fix_missing_thread_lib.patch',
'%(name)s-%(version)s_fix_search_for_szip.patch',
]
checksums = [
'b1c6949918f5e69f701cabfe5987c0b286793f1057d4690f04747852544e157b', # v1.13.1.tar.gz
'81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch
'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch
'2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch
]

builddependencies = [
('Autotools', '20180311'),
]

dependencies = [
('Python', '3.8.2'),
('SciPy-bundle', '2020.03', versionsuffix),
('zlib', '1.2.11'),
('bzip2', '1.0.8'),
('Szip', '2.1.1'),
('lz4', '1.9.2'),
('netCDF', '4.7.4'),
('Mini-XML', '2.12'),
]

preconfigopts = ' autoreconf -i && '
configopts = '--with-zlib=$EBROOTZLIB -with-bzip2=$EBROOTBZIP2 --with-netcdf==$EBROOTNETCDF '
configopts += '--with-lz4=$EBROOTLZ4 --with-mxml=$EBROOTMINIMINXML --with-phdf5=$EBROOTHDF5 '

fix_python_shebang_for = ['bin/gpp.py']

runtest = ' check'

sanity_check_paths = {
'files': ['bin/adios_list_methods', 'bin/bpappend'],
'dirs': ['etc/skel/templates', 'lib/python'],
}

sanity_check_commands = [
'adios_list_methods',
'bpappend -h',
]

modextrapaths = {
'PYTHONPATH': 'lib/python',
}

moduleclass = 'data'
@@ -0,0 +1,78 @@
# Based on ADIOS-1.13.1-foss-2019a-Python-2.7.15.eb
# Updated to foss-2020a toolchain and switched to ConfigureMake
# Latest version from GitHub
# Mini-XML updated to latest 2.x. version
# Author: J. Sassmannshausen (Imperial College London/UK)

easyblock = 'ConfigureMake'

name = 'ADIOS'
version = '20210804'
local_commit = 'de85222'
versionsuffix = '-Python-%(pyver)s'

homepage = 'https://www.olcf.ornl.gov/center-projects/adios/'
description = """The Adaptable IO System (ADIOS) provides a simple,
flexible way for scientists to describe the data in their code that may
need to be written, read, or processed outside of the running
simulation."""

toolchain = {'name': 'foss', 'version': '2020a'}
toolchainopts = {'usempi': True, 'pic': True}

github_account = 'ornladios'
source_urls = [GITHUB_SOURCE]
sources = ['%s.tar.gz' % local_commit]

patches = [
'%(name)s-1.13.1_force_use_of_mpi.patch',
'%(name)s-1.13.1_fix_missing_thread_lib.patch',
'%(name)s-1.13.1_fix_search_for_szip.patch',
]
checksums = [
'c58af40cbdb13843de2c2c157379d069880835c9b932ad05e774910ec23a468f', # de85222.tar.gz
'81b9b0a77b23d6137f08900a3ecda4471b806c384cf4ad19c4370fc7ca8d9a82', # ADIOS-1.13.1_force_use_of_mpi.patch
'a66fab38e5daf40978f9e961d810f9cbf189de8db924a403ae42a01d405f6fdc', # ADIOS-1.13.1_fix_missing_thread_lib.patch
'2e21a5041822c8b57554eb977a3135637c2714d377eee3b0194d377f1458cdab', # ADIOS-1.13.1_fix_search_for_szip.patch
]

builddependencies = [
('Autotools', '20180311'),
]

dependencies = [
('Python', '3.8.2'),
('SciPy-bundle', '2020.03', versionsuffix),
('zlib', '1.2.11'),
('bzip2', '1.0.8'),
('Szip', '2.1.1'),
('lz4', '1.9.2'),
('netCDF', '4.7.4'),
('Mini-XML', '2.12'),
('zfp', '1.0.0'),
]

preconfigopts = ' autoreconf -i && export LIBS="-lgomp" && '
configopts = '--with-zlib=$EBROOTZLIB -with-bzip2=$EBROOTBZIP2 --with-netcdf==$EBROOTNETCDF '
configopts += '--with-lz4=$EBROOTLZ4 --with-mxml=$EBROOTMINIMINXML --with-phdf5=$EBROOTHDF5 '
configopts += '--with-zfp=$EBROOTZFP '

fix_python_shebang_for = ['bin/gpp.py']

runtest = ' check'

sanity_check_paths = {
'files': ['bin/adios_list_methods', 'bin/bpappend'],
'dirs': ['etc/skel/templates', 'lib/python'],
}

sanity_check_commands = [
'adios_list_methods',
'bpappend -h',
]

modextrapaths = {
'PYTHONPATH': 'lib/python',
}

moduleclass = 'data'
@@ -0,0 +1,36 @@
easyblock = 'ConfigureMake'

name = 'ANTLR'
version = '2.7.7'
versionsuffix = '-Java-%(javaver)s'

homepage = 'https://www.antlr2.org/'
description = """ANTLR, ANother Tool for Language Recognition, (formerly PCCTS)
is a language tool that provides a framework for constructing recognizers,
compilers, and translators from grammatical descriptions containing
Java, C#, C++, or Python actions."""

toolchain = {'name': 'GCCcore', 'version': '11.3.0'}

source_urls = ['https://www.antlr2.org/download/']
sources = [SOURCELOWER_TAR_GZ]
patches = ['%(name)s-%(version)s_includes.patch']
checksums = [
'853aeb021aef7586bda29e74a6b03006bcb565a755c86b66032d8ec31b67dbb9', # antlr-2.7.7.tar.gz
'd167d3248a03301bc93efcb37d5df959aae6794968e42231af0b0dd26d6a2e66', # ANTLR-2.7.7_includes.patch
]

builddependencies = [('binutils', '2.38')]

dependencies = [('Java', '11', '', True)]

configopts = '--disable-examples --disable-csharp --disable-python'

sanity_check_paths = {
'files': ['bin/antlr', 'bin/antlr-config'],
'dirs': ['include'],
}

sanity_check_commands = ["antlr --help"]

moduleclass = 'tools'
Expand Up @@ -24,8 +24,8 @@ dependencies = [
('VTK', '6.3.0', versionsuffix),
]

configopts = '-DCMAKE_BUILD_TYPE=Release -DUSE_SYSTEM_ITK=ON '
configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF'
configopts = '-DUSE_SYSTEM_ITK=ON '
configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON -DITK_DIR=$EBROOTITK/lib/cmake/ITK-%s' % local_itkshortver

skipsteps = ['install']
Expand Down
Expand Up @@ -24,8 +24,7 @@ dependencies = [

separate_build_dir = True

configopts = '-DCMAKE_BUILD_TYPE=Release '
configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON '
configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF'

Expand Down
Expand Up @@ -24,8 +24,7 @@ dependencies = [

separate_build_dir = True

configopts = '-DCMAKE_BUILD_TYPE=Release '
configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON '
configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF'

Expand Down
Expand Up @@ -28,8 +28,7 @@ dependencies = [

separate_build_dir = True

configopts = '-DCMAKE_BUILD_TYPE=Release '
configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON '
configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF'

Expand Down
Expand Up @@ -33,8 +33,7 @@ dependencies = [

separate_build_dir = True

configopts = '-DCMAKE_BUILD_TYPE=Release '
configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON '
configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF'

Expand Down
5 changes: 1 addition & 4 deletions easybuild/easyconfigs/a/ANTs/ANTs-2.3.5-foss-2021a.eb
Expand Up @@ -21,10 +21,7 @@ dependencies = [
('VTK', '9.0.1'),
]

separate_build_dir = True

configopts = '-DCMAKE_BUILD_TYPE=Release '
configopts += '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts = '-DBUILD_SHARED_LIBS=ON -DBUILD_TESTING=OFF '
configopts += '-DUSE_VTK=ON -DUSE_SYSTEM_VTK=ON '
configopts += '-DSuperBuild_ANTS_USE_GIT_PROTOCOL=OFF'

Expand Down

0 comments on commit 1a6c875

Please sign in to comment.