From bdd2cc2c57f05111606efbfbef809fb88b883601 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Jan 2024 11:58:32 +0100 Subject: [PATCH 001/116] adding easyconfigs: GROMACS-2023.4-foss-2023a.eb --- .../g/GROMACS/GROMACS-2023.4-foss-2023a.eb | 86 +++++++++++++++++++ 1 file changed, 86 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb new file mode 100644 index 00000000000..2eecebb2ae3 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb @@ -0,0 +1,86 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2023.4' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2023.4.tar.gz': 'e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), + ('scikit-build', '0.17.6'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('networkx', '3.1'), + ('mpi4py', '3.1.4'), +] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'source_tmpl': 'gromacs-2023.4.tar.gz', + 'start_dir': 'python_packaging/gmxapi', + 'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 47ce27b1fd766bf2665955ae6fc4aa4eca5ade99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 26 Jan 2024 12:00:29 +0100 Subject: [PATCH 002/116] split long line --- easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb index 2eecebb2ae3..e8c0d929bd9 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.4-foss-2023a.eb @@ -72,7 +72,8 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.2', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'source_tmpl': 'gromacs-2023.4.tar.gz', 'start_dir': 'python_packaging/gmxapi', 'checksums': ['e5d6c4d9e7ccacfaccb0888619bd21b5ea8911f82b410e68d6db5d40f695f231'], From 03b4db7bf7e3ee1aecf374f15bb39981419be358 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Mar 2024 11:43:32 +0100 Subject: [PATCH 003/116] strip Suprressor out of ResistanceGA --- .../Circuitscape-5.12.3-Julia-1.9.2.eb | 4 +++- ...-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 12 +++------- ...GA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 17 ++------------ .../Suppressor-0.2.4-Julia-1.9.2.eb | 22 +++++++++++++++++++ 4 files changed, 30 insertions(+), 25 deletions(-) create mode 100644 easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb index a6649359df9..f9909fe5c7a 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb @@ -403,6 +403,8 @@ exts_list = [ }), ] -sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"] +sanity_check_commands = [ + """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", +] moduleclass = 'lib' diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index a7789bd8358..4da1b0f58aa 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -16,8 +16,6 @@ dependencies = [ ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), ] -preinstallopts = "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && " - exts_default_options = { 'source_tmpl': 'v%(version)s.tar.gz', } @@ -224,17 +222,13 @@ exts_list = [ }), ] -sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"%(name)s\")'"] +sanity_check_commands = [ + """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", +] sanity_check_paths = { 'files': [], 'dirs': ['packages/%(name)s'], } -# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly -# This is a workaround to make Julia find the correct libraries -modluafooter = """ -prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") -""" - moduleclass = 'tools' diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 83987de1e5a..cd1ffb55617 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -14,8 +14,9 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('R', '4.2.1'), ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), + ('RCall', '0.13.17', versionsuffix), # order matters! RCall must be loaded before Circuitscape (#19281) ('Circuitscape', '5.12.3', '-Julia-%s' % local_juliaver, SYSTEM), - ('RCall', '0.13.17', versionsuffix), + ('Suppressor', '0.2.4', '-Julia-%s' % local_juliaver, SYSTEM), ] exts_defaultclass = 'RPackage' @@ -31,14 +32,6 @@ exts_default_options = { } exts_list = [ - ('Suppressor', '0.2.4', { - 'easyblock': 'JuliaPackage', - 'exts_filter': ("julia -e 'using %(ext_name)s'", ''), - 'preinstallopts': "export LD_LIBRARY_PATH=$EBROOTJULIA/lib/julia:$LD_LIBRARY_PATH && ", - 'source_tmpl': 'v%(version)s.tar.gz', - 'source_urls': ['https://github.com/JuliaIO/Suppressor.jl/archive/'], - 'checksums': ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'], - }), ('GA', '3.2.2', { 'checksums': ['6245c634a11b8414bde7ed326b8c615512645489b19969619484c865e900bf8c'], }), @@ -73,12 +66,6 @@ modextrapaths = { 'R_LIBS_SITE': '', } -# When loading R and Julia, there seems to be a library collision and Julia (namely Pkg module) doesn't work properly -# This is a workaround to make Julia find the correct libraries -modluafooter = """ -prepend_path("LD_LIBRARY_PATH", os.getenv("EBROOTJULIA") .. "/lib/julia") -""" - sanity_check_paths = { 'files': [], 'dirs': ['%(name)s'], diff --git a/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb b/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb new file mode 100644 index 00000000000..5b443b3fac5 --- /dev/null +++ b/easybuild/easyconfigs/s/Suppressor/Suppressor-0.2.4-Julia-1.9.2.eb @@ -0,0 +1,22 @@ +easyblock = 'JuliaPackage' + +name = 'Suppressor' +version = '0.2.4' +_julia_ver = '1.9.2' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/JuliaIO/Suppressor.jl' +description = """Julia macros for suppressing and/or capturing output (STDOUT), +warnings (STDERR) or both streams at the same time.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/JuliaIO/Suppressor.jl/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['5075b06ed6aa0956c786e5b5fe3d77571a4dd34e6d63b45e113c312729384cf4'] + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), +] + +moduleclass = 'lib' From 210f57ecfaf72ab3ad6416849c96b721247acbde Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Wed, 13 Mar 2024 17:02:40 +0100 Subject: [PATCH 004/116] fix codestyle in ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb --- .../ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb index cd1ffb55617..03e40a493f2 100644 --- a/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/ResistanceGA/ResistanceGA-4.2-5-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -14,7 +14,7 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('R', '4.2.1'), ('Julia', local_juliaver, '-linux-%s' % ARCH, SYSTEM), - ('RCall', '0.13.17', versionsuffix), # order matters! RCall must be loaded before Circuitscape (#19281) + ('RCall', '0.13.17', versionsuffix), # order matters! RCall must be loaded before Circuitscape (#19281) ('Circuitscape', '5.12.3', '-Julia-%s' % local_juliaver, SYSTEM), ('Suppressor', '0.2.4', '-Julia-%s' % local_juliaver, SYSTEM), ] From ac616dc76259925429a595e1a52bd5657cb79089 Mon Sep 17 00:00:00 2001 From: satishk Date: Wed, 27 Mar 2024 16:43:24 +0100 Subject: [PATCH 005/116] adding easyconfigs: Paraver-4.11.4-foss-2023a.eb --- .../p/Paraver/Paraver-4.11.4-foss-2023a.eb | 21 +++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb new file mode 100644 index 00000000000..e92b712357a --- /dev/null +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb @@ -0,0 +1,21 @@ +name = 'Paraver' +version = '4.11.4' + +homepage = 'https://tools.bsc.es/paraver' +description = """A very powerful performance visualization and analysis tool based on + traces that can be used to analyse any information that is expressed on its input trace format. + Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] +sources = ['wxparaver-%(version)s-src.tar.bz2'] +checksums = ['8f65fbeacaef003b544ecc0244a4ed9a99e9521cdd027889106fbce0b052fd8d'] + +dependencies = [ + ('zlib', '1.2.13'), + ('Boost', '1.82.0'), + ('wxWidgets', '3.2.2.1'), +] + +moduleclass = 'perf' From 8a12c59b37315a2adae17bce4264a893237f59d2 Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Thu, 25 Jul 2024 14:46:03 +0100 Subject: [PATCH 006/116] adding easyconfigs: OpenMM-8.1.2-foss-2023b.eb --- .../o/OpenMM/OpenMM-8.1.2-foss-2023b.eb | 60 +++++++++++++++++++ 1 file changed, 60 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb diff --git a/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb new file mode 100644 index 00000000000..7b4e30add53 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMM/OpenMM-8.1.2-foss-2023b.eb @@ -0,0 +1,60 @@ +# 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 +# Update to 7.5.1 +# J. Sassmannshausen / GSTT + +easyblock = 'CMakeMake' + +name = 'OpenMM' +version = '8.1.2' + +homepage = 'https://openmm.org' +description = "OpenMM is a toolkit for molecular simulation." + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'opt': True} + +source_urls = ['https://github.com/openmm/openmm/archive/'] +sources = ['%(version)s.tar.gz'] +checksums = ['afc888a4e46486d8d68dac4d403e2b0b28f51b95e52e821e34c38e8b428e040e'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Doxygen', '1.9.8'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('SWIG', '4.1.1'), +] + +pretestopts = " CTEST_OUTPUT_ON_FAILURE=1" +local_ignore_pattern = "(Integrator)|(Thermostat)|(Barostat)|(Rpmd)|(Amoeba)" +runtest = """test -e ARGS="-E \'%s\'" """ % local_ignore_pattern + +preinstallopts = ' export OPENMM_INCLUDE_PATH=%(installdir)s/include && ' +preinstallopts += ' export OPENMM_LIB_PATH=%(installdir)s/lib && ' + +# required to install the python API +installopts = ' && cd python && python setup.py build && python setup.py install --prefix=%(installdir)s' + +sanity_check_paths = { + 'files': ['lib/libOpenMM.%s' % SHLIB_EXT], + 'dirs': ['lib/python%(pyshortver)s/site-packages'] +} + +sanity_check_commands = [ + "python -c 'import simtk.openmm'", + "python -m openmm.testInstallation", +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages/OpenMM-%(version)s-py%(pyshortver)s-linux-%(arch)s.egg', + 'OPENMM_INCLUDE_PATH': 'include', + 'OPENMM_LIB_PATH': 'lib', +} + +moduleclass = 'bio' From d55ea57137f846e1197c501b208d24aaaa2589d0 Mon Sep 17 00:00:00 2001 From: software Date: Thu, 15 Aug 2024 14:56:04 +0000 Subject: [PATCH 007/116] adding easyconfigs: BGEN-enkre-1.1.7-GCC-12.3.0.eb, Boost-1.55.0-GCC-12.3.0.eb --- .../BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb | 73 +++++++++++++++++++ .../b/Boost/Boost-1.55.0-GCC-12.3.0.eb | 21 ++++++ 2 files changed, 94 insertions(+) create mode 100644 easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb diff --git a/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb new file mode 100644 index 00000000000..bf5a35b052b --- /dev/null +++ b/easybuild/easyconfigs/b/BGEN-enkre/BGEN-enkre-1.1.7-GCC-12.3.0.eb @@ -0,0 +1,73 @@ +# Contribution from the NIHR Biomedical Research Centre +# Guy's and St Thomas' NHS Foundation Trust and King's College London +# uploaded by J. Sassmannshausen +# we recommend to use --download-timeout=1000 when fetching the files + +easyblock = 'CmdCp' + +name = 'BGEN-enkre' +version = '1.1.7' + +homepage = 'https://enkre.net/cgi-bin/code/bgen/dir?ci=trunk' +description = """This repository contains a reference implementation +of the BGEN format, written in C++. The library can be used as the +basis for BGEN support in other software, or as a reference for +developers writing their own implementations of the BGEN format. +Please cite: +Band, G. and Marchini, J., "BGEN: a binary file format for imputed genotype and haplotype data", +bioArxiv 308296; doi: https://doi.org/10.1101/308296 +""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://code.enkre.net/bgen/tarball/v%(version)s/'] +sources = ['v%(version)s.tgz'] +patches = [ + '3rd-party-removal.patch', + 'BGEN-enkre_streampos.patch', +] + +checksums = [ + ('6476b077af6c8e98e85fd7e09f58cb3fdf143ff91850c984248fd4dc2d74a8c3', # v1.1.7.tgz + 'b922ac22c1c0e365d0de6054f6ce2ad911bc81db5bcd8ca915bae750f57bd0a7'), + '0269b91d21976f38a9cf9bf7811375d16bf35be587d903ab1d846b2001b7d767', # 3rd-party-removal.patch + '61c05ae5f7363d5b7b6015f0a015b93f149dbda4b23b9f48f9517a6ce93d5869', # BGEN-enkre_streampos.patch +] + +builddependencies = [ + ('Python', '3.11.3'), +] + +dependencies = [ + ('SQLite', '3.42.0'), + ('zstd', '1.5.5'), + ('Boost', '1.55.0'), +] + +cmds_map = [ + ('.*', "./waf configure && echo LIB_zstd = [\\'zstd\\'] >> build/c4che/_cache.py &&" + " echo LIB_sqlite3 = [\\'sqlite3\\'] >> build/c4che/_cache.py &&" + "echo LIB_boost = [\\'boost_system\\', \\'boost_filesystem\\', \\'boost_thread\\', \\'boost_timer\\'] " + " >> build/c4che/_cache.py && ./waf"), +] + +files_to_copy = [ + (['build/apps/edit-bgen', 'build/apps/bgenix', 'build/apps/cat-bgen'], 'bin'), + (['build/db/libdb.a', 'build/libbgen.a'], 'lib'), + (['genfile/include/*', 'db/include/*'], 'include'), +] + +postinstallcmds = ['./build/test/unit/test_bgen'] + +sanity_check_paths = { + 'files': ['bin/edit-bgen', 'bin/bgenix', 'bin/cat-bgen'], + 'dirs': ['bin', 'lib', 'include'], +} + +sanity_check_commands = [ + 'bgenix -help', + 'cat-bgen -help', + 'edit-bgen -help', +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb new file mode 100644 index 00000000000..e7cdaf16fbd --- /dev/null +++ b/easybuild/easyconfigs/b/Boost/Boost-1.55.0-GCC-12.3.0.eb @@ -0,0 +1,21 @@ +name = 'Boost' +version = '1.55.0' + +homepage = 'http://www.boost.org/' +description = """Boost provides free peer-reviewed portable C++ source libraries.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} +toolchainopts = {'pic': True} + +source_urls = [SOURCEFORGE_SOURCE] +sources = ['%%(namelower)s_%s.tar.gz' % '_'.join(version.split('.'))] +checksums = ['19c4305cd6669f2216260258802a7abc73c1624758294b2cad209d45cc13a767'] + +dependencies = [ + ('bzip2', '1.0.8'), + ('zlib', '1.2.13'), +] + +configopts = '--without-libraries=python' + +moduleclass = 'devel' From c78a22ade13ce1646520d32861fe5aeb3db12c53 Mon Sep 17 00:00:00 2001 From: Chia-Jung Hsu Date: Wed, 21 Aug 2024 10:14:40 +0000 Subject: [PATCH 008/116] adding easyconfigs: Safetensors-0.4.4-gfbf-2023b.eb, tokenizers-0.19.1-GCCcore-13.2.0.eb, Transformers-4.44.0-gfbf-2023b.eb --- .../Safetensors-0.4.4-gfbf-2023b.eb | 153 +++++ .../Transformers-4.44.0-gfbf-2023b.eb | 36 ++ .../tokenizers-0.19.1-GCCcore-13.2.0.eb | 567 ++++++++++++++++++ 3 files changed, 756 insertions(+) create mode 100644 easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb create mode 100644 easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb new file mode 100644 index 00000000000..50ead1b54c1 --- /dev/null +++ b/easybuild/easyconfigs/s/Safetensors/Safetensors-0.4.4-gfbf-2023b.eb @@ -0,0 +1,153 @@ +easyblock = "CargoPythonBundle" + +name = 'Safetensors' +version = '0.4.4' +_rustver = '1.76.0' + +homepage = 'https://huggingface.co/docs/safetensors' +description = """Safetensors is a new simple format for storing tensors safely (as opposed to +pickle) and that is still fast (zero-copy). Safetensors is really fast. + +This variant of Safetensors is installed with support for numpy and PyTorch +""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +builddependencies = [ + ('Rust', _rustver), + ('maturin', '1.5.0', '-Rust-' + _rustver), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), +] + +# crates generated on 2024-08-21 from directories savetensors/ and bindings/python/ +crates = [ + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstyle', '1.0.8'), + ('autocfg', '1.3.0'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('cast', '0.3.0'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.16'), + ('clap_builder', '4.5.15'), + ('clap_lex', '0.7.2'), + ('criterion', '0.5.1'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('either', '1.13.0'), + ('errno', '0.3.9'), + ('fastrand', '2.1.0'), + ('fnv', '1.0.7'), + ('getrandom', '0.2.15'), + ('half', '2.4.1'), + ('heck', '0.5.0'), + ('hermit-abi', '0.4.0'), + ('indoc', '2.0.5'), + ('is-terminal', '0.4.13'), + ('itertools', '0.10.5'), + ('itoa', '1.0.11'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.155'), + ('libc', '0.2.158'), + ('libm', '0.2.8'), + ('linux-raw-sys', '0.4.14'), + ('log', '0.4.22'), + ('memchr', '2.7.4'), + ('memmap2', '0.9.4'), + ('memoffset', '0.9.1'), + ('num-traits', '0.2.19'), + ('once_cell', '1.19.0'), + ('oorandom', '11.1.4'), + ('plotters', '0.3.6'), + ('plotters-backend', '0.3.6'), + ('plotters-svg', '0.3.6'), + ('portable-atomic', '1.7.0'), + ('ppv-lite86', '0.2.20'), + ('proc-macro2', '1.0.86'), + ('proptest', '1.5.0'), + ('pyo3', '0.22.2'), + ('pyo3-build-config', '0.22.2'), + ('pyo3-ffi', '0.22.2'), + ('pyo3-macros', '0.22.2'), + ('pyo3-macros-backend', '0.22.2'), + ('quick-error', '1.2.3'), + ('quote', '1.0.36'), + ('rand', '0.8.5'), + ('rand_chacha', '0.3.1'), + ('rand_core', '0.6.4'), + ('rand_xorshift', '0.3.0'), + ('rayon', '1.10.0'), + ('rayon-core', '1.12.1'), + ('regex', '1.10.6'), + ('regex-automata', '0.4.7'), + ('regex-syntax', '0.8.4'), + ('rustix', '0.38.34'), + ('rusty-fork', '0.3.0'), + ('ryu', '1.0.18'), + ('same-file', '1.0.6'), + ('serde', '1.0.204'), + ('serde', '1.0.208'), + ('serde_derive', '1.0.204'), + ('serde_derive', '1.0.208'), + ('serde_json', '1.0.122'), + ('serde_json', '1.0.125'), + ('syn', '2.0.72'), + ('syn', '2.0.75'), + ('target-lexicon', '0.12.16'), + ('tempfile', '3.12.0'), + ('tinytemplate', '1.2.1'), + ('unarray', '0.1.4'), + ('unicode-ident', '1.0.12'), + ('unindent', '0.2.3'), + ('wait-timeout', '0.2.0'), + ('walkdir', '2.5.0'), + ('wasi', '0.11.0+wasi-snapshot-preview1'), + ('wasm-bindgen', '0.2.93'), + ('wasm-bindgen-backend', '0.2.93'), + ('wasm-bindgen-macro', '0.2.93'), + ('wasm-bindgen-macro-support', '0.2.93'), + ('wasm-bindgen-shared', '0.2.93'), + ('web-sys', '0.3.70'), + ('winapi-util', '0.1.9'), + ('windows-sys', '0.52.0'), + ('windows-sys', '0.59.0'), + ('windows-targets', '0.52.6'), + ('windows_aarch64_gnullvm', '0.52.6'), + ('windows_aarch64_msvc', '0.52.6'), + ('windows_i686_gnu', '0.52.6'), + ('windows_i686_gnullvm', '0.52.6'), + ('windows_i686_msvc', '0.52.6'), + ('windows_x86_64_gnu', '0.52.6'), + ('windows_x86_64_gnullvm', '0.52.6'), + ('windows_x86_64_msvc', '0.52.6'), + ('zerocopy', '0.7.35'), + ('zerocopy-derive', '0.7.35'), +] + + +use_pip = True + +exts_list = [ + ('safetensors', version, { + 'checksums': ['5fe3e9b705250d0172ed4e100a811543108653fb2b66b9e702a088ad03772a07'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb b/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb new file mode 100644 index 00000000000..94a257d4b18 --- /dev/null +++ b/easybuild/easyconfigs/t/Transformers/Transformers-4.44.0-gfbf-2023b.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'Transformers' +version = '4.44.0' + +homepage = 'https://github.com/huggingface/transformers' +description = """State-of-the-art Natural Language Processing for PyTorch and TensorFlow 2.0""" + +toolchain = {'name': 'gfbf', 'version': '2023b'} + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('PyYAML', '6.0.1'), + ('tqdm', '4.66.2'), + ('tokenizers', '0.19.1'), # tokenizers>=0.19,<0.20 + ('Safetensors', '0.4.4'), # safetensors>=0.4.1 +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('regex', '2024.7.24', { + 'checksums': ['9cfd009eed1a46b27c14039ad5bbc5e71b6367c5b2e6d5f5da0ea91600817506'], + }), + ('transformers', version, { + 'checksums': ['75699495e30b7635ca444d8d372e138c687ab51a875b387e33f1fb759c37f196'], + }), +] + +sanity_check_commands = [ + "python -c 'from transformers import AutoTokenizer'", +] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..3b5675b24df --- /dev/null +++ b/easybuild/easyconfigs/t/tokenizers/tokenizers-0.19.1-GCCcore-13.2.0.eb @@ -0,0 +1,567 @@ +easyblock = 'CargoPythonBundle' + +name = 'tokenizers' +version = '0.19.1' + +homepage = 'https://github.com/huggingface/tokenizers' +description = "Fast State-of-the-Art Tokenizers optimized for Research and Production" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +crates = [ + ('adler2', '2.0.0'), + ('aho-corasick', '1.1.3'), + ('anes', '0.1.6'), + ('anstream', '0.6.13'), + ('anstyle', '1.0.6'), + ('anstyle', '1.0.8'), + ('anstyle-parse', '0.2.3'), + ('anstyle-query', '1.0.2'), + ('anstyle-wincon', '3.0.2'), + ('assert_approx_eq', '1.1.0'), + ('autocfg', '1.2.0'), + ('autocfg', '1.3.0'), + ('base64', '0.13.1'), + ('base64', '0.22.1'), + ('bit-set', '0.5.3'), + ('bit-vec', '0.6.3'), + ('bitflags', '1.3.2'), + ('bitflags', '2.5.0'), + ('bitflags', '2.6.0'), + ('bumpalo', '3.16.0'), + ('byteorder', '1.5.0'), + ('cast', '0.3.0'), + ('cc', '1.0.94'), + ('cc', '1.1.13'), + ('cfg-if', '1.0.0'), + ('ciborium', '0.2.2'), + ('ciborium-io', '0.2.2'), + ('ciborium-ll', '0.2.2'), + ('clap', '4.5.16'), + ('clap_builder', '4.5.15'), + ('clap_lex', '0.7.2'), + ('colorchoice', '1.0.0'), + ('console', '0.15.8'), + ('core-foundation', '0.9.4'), + ('core-foundation-sys', '0.8.7'), + ('crc32fast', '1.4.2'), + ('criterion', '0.5.1'), + ('criterion-plot', '0.5.0'), + ('crossbeam-deque', '0.8.5'), + ('crossbeam-epoch', '0.9.18'), + ('crossbeam-utils', '0.8.19'), + ('crossbeam-utils', '0.8.20'), + ('crunchy', '0.2.2'), + ('darling', '0.20.8'), + ('darling', '0.20.10'), + ('darling_core', '0.20.8'), + ('darling_core', '0.20.10'), + ('darling_macro', '0.20.8'), + ('darling_macro', '0.20.10'), + ('derive_builder', '0.20.0'), + ('derive_builder_core', '0.20.0'), + ('derive_builder_macro', '0.20.0'), + ('dirs', '5.0.1'), + ('dirs-sys', '0.4.1'), + ('either', '1.11.0'), + ('either', '1.13.0'), + ('encode_unicode', '0.3.6'), + ('env_filter', '0.1.0'), + ('env_logger', '0.11.3'), + ('errno', '0.3.8'), + ('errno', '0.3.9'), + ('esaxx-rs', '0.1.10'), + ('fancy-regex', '0.13.0'), + ('fastrand', '2.0.2'), + ('fastrand', '2.1.0'), + ('flate2', '1.0.32'), + ('fnv', '1.0.7'), + ('foreign-types', '0.3.2'), + ('foreign-types-shared', '0.1.1'), + ('form_urlencoded', '1.2.1'), + ('getrandom', '0.2.14'), + ('getrandom', '0.2.15'), + ('half', '2.4.1'), + ('heck', '0.4.1'), + ('hermit-abi', '0.4.0'), + ('hf-hub', '0.3.2'), + ('humantime', '2.1.0'), + ('ident_case', '1.0.1'), + ('idna', '0.5.0'), + ('indicatif', '0.17.8'), + ('indoc', '2.0.5'), + ('instant', '0.1.12'), + ('instant', '0.1.13'), + ('is-terminal', '0.4.13'), + ('itertools', '0.10.5'), + ('itertools', '0.11.0'), + ('itertools', '0.12.1'), + ('itoa', '1.0.11'), + ('js-sys', '0.3.70'), + ('lazy_static', '1.4.0'), + ('lazy_static', '1.5.0'), + ('libc', '0.2.153'), + ('libc', '0.2.158'), + ('libredox', '0.1.3'), + ('linux-raw-sys', '0.4.13'), + ('linux-raw-sys', '0.4.14'), + ('lock_api', '0.4.11'), + ('log', '0.4.21'), + ('log', '0.4.22'), + ('macro_rules_attribute', '0.2.0'), + ('macro_rules_attribute-proc_macro', '0.2.0'), + ('matrixmultiply', '0.3.8'), + ('memchr', '2.7.2'), + ('memchr', '2.7.4'), + ('memoffset', '0.9.1'), + ('minimal-lexical', '0.2.1'), + ('miniz_oxide', '0.8.0'), + ('monostate', '0.1.12'), + ('monostate', '0.1.13'), + ('monostate-impl', '0.1.12'), + ('monostate-impl', '0.1.13'), + ('native-tls', '0.2.12'), + ('ndarray', '0.15.6'), + ('nom', '7.1.3'), + ('num-complex', '0.4.5'), + ('num-integer', '0.1.46'), + ('num-traits', '0.2.18'), + ('num-traits', '0.2.19'), + ('number_prefix', '0.4.0'), + ('numpy', '0.21.0'), + ('once_cell', '1.19.0'), + ('onig', '6.4.0'), + ('onig_sys', '69.8.1'), + 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'afc340c74d9005395cf9dd098506f7f44e38f2b4a21c6aaacf9a105ea5e1e836'}, + {'wasm-bindgen-shared-0.2.93.tar.gz': 'c62a0a307cb4a311d3a07867860911ca130c3494e8c2719593806c08bc5d0484'}, + {'web-sys-0.3.70.tar.gz': '26fdeaafd9bd129f65e7c031593c24d62186301e0c72c8978fa1678be7d532c0'}, + {'webpki-roots-0.26.3.tar.gz': 'bd7c23921eeb1713a4e851530e9b9756e4fb0e89978582942612524cf09f01cd'}, + {'winapi-util-0.1.9.tar.gz': 'cf221c93e13a30d793f7645a0e7762c55d169dbb0a49671918a2319d289b10bb'}, + {'windows-sys-0.48.0.tar.gz': '677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9'}, + {'windows-sys-0.52.0.tar.gz': '282be5f36a8ce781fad8c8ae18fa3f9beff57ec1b52cb3de0789201425d9a33d'}, + {'windows-sys-0.59.0.tar.gz': '1e38bc4d79ed67fd075bcc251a1c39b32a1776bbe92e5bef1f0bf1f8c531853b'}, + {'windows-targets-0.48.5.tar.gz': '9a2fa6e2155d7247be68c096456083145c183cbbbc2764150dda45a87197940c'}, + {'windows-targets-0.52.5.tar.gz': '6f0713a46559409d202e70e28227288446bf7841d3211583a4b53e3f6d96e7eb'}, + {'windows-targets-0.52.6.tar.gz': '9b724f72796e036ab90c1021d4780d4d3d648aca59e491e6b98e725b84e99973'}, + {'windows_aarch64_gnullvm-0.48.5.tar.gz': '2b38e32f0abccf9987a4e3079dfb67dcd799fb61361e53e2882c3cbaf0d905d8'}, + {'windows_aarch64_gnullvm-0.52.5.tar.gz': '7088eed71e8b8dda258ecc8bac5fb1153c5cffaf2578fc8ff5d61e23578d3263'}, + {'windows_aarch64_gnullvm-0.52.6.tar.gz': '32a4622180e7a0ec044bb555404c800bc9fd9ec262ec147edd5989ccd0c02cd3'}, + {'windows_aarch64_msvc-0.48.5.tar.gz': 'dc35310971f3b2dbbf3f0690a219f40e2d9afcf64f9ab7cc1be722937c26b4bc'}, + {'windows_aarch64_msvc-0.52.5.tar.gz': '9985fd1504e250c615ca5f281c3f7a6da76213ebd5ccc9561496568a2752afb6'}, + {'windows_aarch64_msvc-0.52.6.tar.gz': '09ec2a7bb152e2252b53fa7803150007879548bc709c039df7627cabbd05d469'}, + {'windows_i686_gnu-0.48.5.tar.gz': 'a75915e7def60c94dcef72200b9a8e58e5091744960da64ec734a6c6e9b3743e'}, + {'windows_i686_gnu-0.52.5.tar.gz': '88ba073cf16d5372720ec942a8ccbf61626074c6d4dd2e745299726ce8b89670'}, + {'windows_i686_gnu-0.52.6.tar.gz': '8e9b5ad5ab802e97eb8e295ac6720e509ee4c243f69d781394014ebfe8bbfa0b'}, + {'windows_i686_gnullvm-0.52.5.tar.gz': '87f4261229030a858f36b459e748ae97545d6f1ec60e5e0d6a3d32e0dc232ee9'}, + {'windows_i686_gnullvm-0.52.6.tar.gz': '0eee52d38c090b3caa76c563b86c3a4bd71ef1a819287c19d586d7334ae8ed66'}, + {'windows_i686_msvc-0.48.5.tar.gz': '8f55c233f70c4b27f66c523580f78f1004e8b5a8b659e05a4eb49d4166cca406'}, + {'windows_i686_msvc-0.52.5.tar.gz': 'db3c2bf3d13d5b658be73463284eaf12830ac9a26a90c717b7f771dfe97487bf'}, + {'windows_i686_msvc-0.52.6.tar.gz': '240948bc05c5e7c6dabba28bf89d89ffce3e303022809e73deaefe4f6ec56c66'}, + {'windows_x86_64_gnu-0.48.5.tar.gz': '53d40abd2583d23e4718fddf1ebec84dbff8381c07cae67ff7768bbf19c6718e'}, + {'windows_x86_64_gnu-0.52.5.tar.gz': '4e4246f76bdeff09eb48875a0fd3e2af6aada79d409d33011886d3e1581517d9'}, + {'windows_x86_64_gnu-0.52.6.tar.gz': '147a5c80aabfbf0c7d901cb5895d1de30ef2907eb21fbbab29ca94c5b08b1a78'}, + {'windows_x86_64_gnullvm-0.48.5.tar.gz': '0b7b52767868a23d5bab768e390dc5f5c55825b6d30b86c844ff2dc7414044cc'}, + {'windows_x86_64_gnullvm-0.52.5.tar.gz': '852298e482cd67c356ddd9570386e2862b5673c85bd5f88df9ab6802b334c596'}, + {'windows_x86_64_gnullvm-0.52.6.tar.gz': '24d5b23dc417412679681396f2b49f3de8c1473deb516bd34410872eff51ed0d'}, + {'windows_x86_64_msvc-0.48.5.tar.gz': 'ed94fce61571a4006852b7389a063ab983c02eb1bb37b47f8272ce92d06d9538'}, + {'windows_x86_64_msvc-0.52.5.tar.gz': 'bec47e5bfd1bff0eeaf6d8b485cc1074891a197ab4225d504cb7a1ab88b02bf0'}, + {'windows_x86_64_msvc-0.52.6.tar.gz': '589f6da84c646204747d1270a2a5661ea66ed1cced2631d546fdfb155959f9ec'}, + {'zerocopy-0.7.35.tar.gz': '1b9b4fd18abc82b8136838da5d50bae7bdea537c574d8dc1a34ed098d6c166f0'}, + {'zerocopy-derive-0.7.35.tar.gz': 'fa4f8080344d4671fb4e831a13ad1e68092748387dfc4f55e356242fae12ce3e'}, + {'zeroize-1.8.1.tar.gz': 'ced3678a2879b30306d323f4542626697a464a97c0a07c9aebf7ebca65cd4dde'}, +] + +_rust_ver = '1.76.0' +builddependencies = [ + ('binutils', '2.40'), + ('Rust', _rust_ver), + ('maturin', '1.5.0', '-Rust-%s' % _rust_ver), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), # fsspec, filelock used by hf-hub + ('PyYAML', '6.0.1'), # used by hf-hub + ('tqdm', '4.66.2'), # used by hf-hub +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('huggingface-hub', '0.24.6', { + 'source_tmpl': 'huggingface_hub-%(version)s.tar.gz', + 'checksums': ['cc2579e761d070713eaa9c323e3debe39d5b464ae3a7261c39a9195b27bb8000'], + }), + (name, version, { + 'checksums': ['ee59e6680ed0fdbe6b724cf38bd70400a0c1dd623b07ac729087270caeac88e3'], + }), +] + +moduleclass = 'lib' From 835f4109d8d591389a9cfab5f7943e3df4990367 Mon Sep 17 00:00:00 2001 From: Simon Pinches Date: Thu, 29 Aug 2024 19:42:45 +0200 Subject: [PATCH 009/116] adding easyconfigs: SPRNG-5.0-gompi-2023b.eb, SPRNG-5.0-iimpi-2023b.eb, TestU01-1.2.3-GCCcore-13.2.0.eb and patches: SPRNG-5.0_MPI-lmpicxx.patch, SPRNG-5.0_MPI-lmpi.patch --- .../s/SPRNG/SPRNG-5.0-gompi-2023b.eb | 35 +++++++++++++++++++ .../s/SPRNG/SPRNG-5.0-iimpi-2023b.eb | 35 +++++++++++++++++++ .../s/SPRNG/SPRNG-5.0_MPI-lmpi.patch | 12 +++++++ .../s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch | 12 +++++++ .../t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb | 23 ++++++++++++ 5 files changed, 117 insertions(+) create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch create mode 100644 easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch create mode 100644 easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb new file mode 100644 index 00000000000..bf9aa5e5827 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-gompi-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'SPRNG' +version = '5.0' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'gompi', 'version': '2023b'} +toolchainopts = {'pic': True, 'opt': True, 'usempi': True, 'cstd': 'c++14'} + +source_urls = ['http://www.sprng.org/Version%(version)s/'] +sources = ['%(namelower)s%(version_major)s.tar.bz2'] +patches = ['%(name)s-%(version)s_MPI-lmpi.patch'] +checksums = [ + {'sprng5.tar.bz2': '696ef452bdd998d2e66586e73d81dac875082e35d08de419cede1a1bb2555b59'}, + {'SPRNG-5.0_MPI-lmpi.patch': 'a6bb936b2e7cf9efd74e0bf06702bf444c98ecb11877492308a3551c5b9dff5c'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('TestU01', '1.2.3'), +] + +preconfigopts = 'autoreconf -f -i && ' +configopts = '--with-fortran=yes --with-mpi=yes --with-testu01=$EBROOTTESTU01' + +sanity_check_paths = { + 'files': ['bin/checksprng', 'include/sprng.h', 'include/sprng_f.h', 'lib/libsprng.a'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ['cd %(builddir)s/sprng5/check && checksprng'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb new file mode 100644 index 00000000000..ea7f852cd44 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0-iimpi-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'SPRNG' +version = '5.0' + +homepage = 'http://www.sprng.org/' +description = "Scalable Parallel Pseudo Random Number Generators Library" + +toolchain = {'name': 'iimpi', 'version': '2023b'} +toolchainopts = {'pic': True, 'opt': True, 'usempi': True, 'cstd': 'c++14'} + +source_urls = ['http://www.sprng.org/Version%(version)s/'] +sources = ['%(namelower)s%(version_major)s.tar.bz2'] +patches = ['%(name)s-%(version)s_MPI-lmpicxx.patch'] +checksums = [ + {'sprng5.tar.bz2': '696ef452bdd998d2e66586e73d81dac875082e35d08de419cede1a1bb2555b59'}, + {'SPRNG-5.0_MPI-lmpicxx.patch': 'fc0903d81886a76a8cf2af73930b0347e3bcc047ad32215fdafd5a936f519545'}, +] + +builddependencies = [ + ('Autotools', '20220317'), + ('TestU01', '1.2.3'), +] + +preconfigopts = 'autoreconf -f -i && ' +configopts = '--with-fortran=yes --with-mpi=yes --with-testu01=$EBROOTTESTU01' + +sanity_check_paths = { + 'files': ['bin/checksprng', 'include/sprng.h', 'include/sprng_f.h', 'lib/libsprng.a'], + 'dirs': ['bin', 'include', 'lib', 'share'], +} + +sanity_check_commands = ['cd %(builddir)s/sprng5/check && checksprng'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch new file mode 100644 index 00000000000..c09f74fa073 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpi.patch @@ -0,0 +1,12 @@ +diff -Nru sprng5-orig/configure.ac sprng5/configure.ac +--- sprng5-orig/configure.ac 2021-06-08 18:37:02.000000000 +0200 ++++ sprng5/configure.ac 2024-08-29 19:21:40.393998554 +0200 +@@ -89,7 +89,7 @@ + + if test $use_mpi = y; then + MPI_DEF="-DSPRNG_MPI" +- MPI_CXXLIB="-lmpi_cxx" ++ MPI_CXXLIB="-lmpi" + else + MPI_DEF="" + MPI_CXXLIB="" diff --git a/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch new file mode 100644 index 00000000000..a45691c9b04 --- /dev/null +++ b/easybuild/easyconfigs/s/SPRNG/SPRNG-5.0_MPI-lmpicxx.patch @@ -0,0 +1,12 @@ +diff -Nru sprng5-orig/configure.ac sprng5/configure.ac +--- sprng5-orig/configure.ac 2021-06-08 18:37:02.000000000 +0200 ++++ sprng5/configure.ac 2024-08-29 19:18:56.124716693 +0200 +@@ -89,7 +89,7 @@ + + if test $use_mpi = y; then + MPI_DEF="-DSPRNG_MPI" +- MPI_CXXLIB="-lmpi_cxx" ++ MPI_CXXLIB="-lmpicxx" + else + MPI_DEF="" + MPI_CXXLIB="" diff --git a/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb b/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..08b769c2f8d --- /dev/null +++ b/easybuild/easyconfigs/t/TestU01/TestU01-1.2.3-GCCcore-13.2.0.eb @@ -0,0 +1,23 @@ +easyblock = 'ConfigureMake' + +name = 'TestU01' +version = '1.2.3' + +homepage = 'https://simul.iro.umontreal.ca/testu01/tu01.html' +description = "Utilities for the empirical statistical testing of uniform random number generators" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +source_urls = ['https://simul.iro.umontreal.ca/testu01/'] +sources = ['%(name)s.zip'] +checksums = ['bc1d1dd2aea7ed3b3d28eaad2c8ee55913f11ce67aec8fe4f643c1c0d2ed1cac'] + +builddependencies = [('binutils', '2.40')] + +sanity_check_paths = { + 'files': ['bin/tcode', 'lib/libmylib.%s' % SHLIB_EXT, + 'lib/libprobdist.%s' % SHLIB_EXT, 'lib/libtestu01.%s' % SHLIB_EXT], + 'dirs': ['bin', 'include', 'lib', 'share/TestU01/doc'], +} + +moduleclass = 'tools' From fe1d7d50fb0d777a7d14bac349e5a77d387f6c5a Mon Sep 17 00:00:00 2001 From: maximm Date: Tue, 1 Oct 2024 14:09:21 +0200 Subject: [PATCH 010/116] adding easyconfigs: VTune-2024.3.0.eb --- .../easyconfigs/v/VTune/VTune-2024.3.0.eb | 25 +++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb new file mode 100644 index 00000000000..850f62f204a --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb @@ -0,0 +1,25 @@ + +name = 'VTune' +version = '2024.3.0' + +homepage = 'https://www.intel.com/content/www/us/en/developer/tools/oneapi/vtune-profiler.html' +description = """Intel® VTune™ Profiler optimizes application performance, system performance, + and system configuration for HPC, cloud, IoT, media, storage, and more.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/dfae6f23-6c90-4b9f-80e2-fa2a5037fe36/'] +sources = ['l_oneapi_vtune_p_%(version)s.31_offline.sh'] +checksums = ['da9f45ee4a5ea337756e85e58e40b235417cffbca6813cf224db49061947253d'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'tools' From c84acefcb93ab1e74659cd7b35ba11f5bf082369 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 2 Oct 2024 14:40:33 +0200 Subject: [PATCH 011/116] Fixed download URL --- easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb index 850f62f204a..a7340fe52b8 100644 --- a/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb +++ b/easybuild/easyconfigs/v/VTune/VTune-2024.3.0.eb @@ -11,7 +11,7 @@ toolchain = SYSTEM # By downloading, you accept the Intel End User License Agreement # (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) # accept_eula = True -source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/dfae6f23-6c90-4b9f-80e2-fa2a5037fe36/'] +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/d7e1fdb1-cfc7-40fb-bf46-3719e9372d67/'] sources = ['l_oneapi_vtune_p_%(version)s.31_offline.sh'] checksums = ['da9f45ee4a5ea337756e85e58e40b235417cffbca6813cf224db49061947253d'] From 0a1e4603bf9c8afbba9954105a0ce7ec5f0fde8e Mon Sep 17 00:00:00 2001 From: tanmoy1989 Date: Thu, 3 Oct 2024 15:47:08 +0100 Subject: [PATCH 012/116] adding easyconfigs: CASTEP-24.1-foss-2023b.eb --- .../c/CASTEP/CASTEP-24.1-foss-2023b.eb | 49 +++++++++++++++++++ 1 file changed, 49 insertions(+) create mode 100644 easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb diff --git a/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb b/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb new file mode 100644 index 00000000000..678f4e7df25 --- /dev/null +++ b/easybuild/easyconfigs/c/CASTEP/CASTEP-24.1-foss-2023b.eb @@ -0,0 +1,49 @@ +easyblock = 'ConfigureMake' + +name = 'CASTEP' +version = '24.1' + +homepage = 'http://www.castep.org' +description = """ +CASTEP is an electronic structure materials modelling code based on density +functional theory (DFT), with functionality including geometry optimization +molecular dynamics, phonons, NMR chemical shifts and much more. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} + +download_instructions = """CASTEP is proprietary software, available under a free-of-charge license for academic use +only. Visit http://www.castep.org and navigate to "Getting Castep" to apply for a license.""" + +sources = [SOURCE_TAR_GZ] +checksums = ['97d77a4f3ce3f5c5b87e812f15a2c2cb23918acd7034c91a872b6d66ea0f7dbb'] + +dependencies = [ + ('Perl', '5.38.0'), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), # for elastic constants and castepconv utility +] + +skipsteps = ['configure'] + +_generic_opts = ' COMMS_ARCH=mpi FFT=fftw3 MATH_LIBS="-lflexiblas" ' + +buildopts = _generic_opts + 'FFTLIBDIR=$FFT_LIB_DIR MATHLIBDIR=$BLAS_LIB_DIR' +buildopts += ' castep tools utilities' + +preinstallopts = 'mkdir -p %(installdir)s/bin &&' +installopts = _generic_opts + 'INSTALL_DIR="%(installdir)s/bin"' +installopts += ' install-castep install-tools install-utilities' + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['castep.mpi', 'optados.mpi', 'orbitals2bands', 'dispersion.pl', + 'elastics.py', 'ceteprouts.pm']], + 'dirs': [], +} + +sanity_check_commands = [ + 'castep.mpi --help', + 'optados.mpi --help', +] + +moduleclass = 'phys' From 0ad9dd9c7e1bd4f412bb015d62e0795afd29d3c6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Fri, 4 Oct 2024 16:30:47 +0200 Subject: [PATCH 013/116] {lib}[GCCcore/13.3.0] Add NCCL 2.22.3 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..0534e538faa --- /dev/null +++ b/easybuild/easyconfigs/n/NCCL/NCCL-2.22.3-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,26 @@ +name = 'NCCL' +version = '2.22.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/nccl' +description = """The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective +communication primitives that are performance optimized for NVIDIA GPUs.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +github_account = 'NVIDIA' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s-1.tar.gz'] +checksums = ['45151629a9494460e73375281e8b0fe379141528879301899ece9b776faca024'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', versionsuffix), +] + +# default CUDA compute capabilities to use (override via --cuda-compute-capabilities) +cuda_compute_capabilities = ['5.0', '6.0', '7.0', '7.5', '8.0', '8.6', '9.0'] + +moduleclass = 'lib' From 01c1b0484b84331c7d8d9d83ca50ea3c64ca09c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Fri, 4 Oct 2024 16:31:29 +0200 Subject: [PATCH 014/116] {lib}[GCCcore/13.3.0] Add UCC-CUDA 1.3.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- ...C-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb | 55 +++++++++++++++++++ ...1.3.0_link_against_existing_UCC_libs.patch | 27 +++++++++ 2 files changed, 82 insertions(+) create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..a0b4865a721 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'UCC-CUDA' +version = '1.3.0' +versionsuffix = '-CUDA-%(cudaver)s' + +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. + +This module adds the UCC CUDA support. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/openucx/ucc/archive/refs/tags'] +sources = ['v%(version)s.tar.gz'] +patches = [ + '%(name)s-%(version)s_link_against_existing_UCC_libs.patch', +] +checksums = [ + {'v1.3.0.tar.gz': 'b56379abe5f1c125bfa83be305d78d81a64aa271b7b5fff0ac17b86725ff3acf'}, + {'UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch': + '758228357ce2a6ae50fb26a0b43e9176feaf379e266365f38205ce679267fc0d'}, +] + +builddependencies = [ + ('binutils', '2.42'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('UCC', version), + ('CUDA', '12.6.0', '', SYSTEM), + ('UCX-CUDA', '1.16.0', '-CUDA-%(cudaver)s'), + ('NCCL', '2.22.3', '-CUDA-%(cudaver)s'), +] + +preconfigopts = "./autogen.sh && " + +buildopts = '-C src/components/mc/cuda V=1 && make -C src/components/tl/nccl V=1' +installopts = '-C src/components/mc/cuda && make -C src/components/tl/nccl install' + +sanity_check_paths = { + 'files': ['lib/ucc/libucc_mc_cuda.%s' % SHLIB_EXT, 'lib/ucc/libucc_tl_nccl.%s' % SHLIB_EXT], + 'dirs': ['lib'] +} + +sanity_check_commands = ["ucc_info -c"] + +modextrapaths = {'EB_UCC_EXTRA_COMPONENT_PATH': 'lib/ucc'} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch new file mode 100644 index 00000000000..5d005e067f7 --- /dev/null +++ b/easybuild/easyconfigs/u/UCC-CUDA/UCC-CUDA-1.3.0_link_against_existing_UCC_libs.patch @@ -0,0 +1,27 @@ +Make CUDA/NCCL plugins link against the existing ucc libraries. + +Bart Oldeman, 2022-08-02 +Mikael OEhman, 2023-06-16 +diff -ur ucc-1.3.0.orig/src/components/mc/cuda/Makefile.am ucc-1.3.0/src/components/ec/cuda/Makefile.am +--- ucc-1.3.0.orig/src/components/mc/cuda/Makefile.am.orig 2023-06-16 12:56:53.205939925 +0200 ++++ ucc-1.3.0/src/components/mc/cuda/Makefile.am 2023-06-16 13:02:21.716110609 +0200 +@@ -14,7 +14,7 @@ + libucc_mc_cuda_la_CFLAGS = $(BASE_CFLAGS) + libucc_mc_cuda_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) + libucc_mc_cuda_la_LIBADD = $(CUDA_LIBS) \ +- $(UCC_TOP_BUILDDIR)/src/libucc.la ++ -lucc + + include $(top_srcdir)/config/module.am + endif +diff -ur ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am ucc-1.0.0/src/components/tl/nccl/Makefile.am +--- ucc-1.0.0.orig/src/components/tl/nccl/Makefile.am 2022-04-15 12:43:33.000000000 +0000 ++++ ucc-1.0.0/src/components/tl/nccl/Makefile.am 2022-08-02 12:13:59.334795989 +0000 +@@ -21,6 +21,6 @@ + libucc_tl_nccl_la_CPPFLAGS = $(AM_CPPFLAGS) $(BASE_CPPFLAGS) $(CUDA_CPPFLAGS) $(NCCL_CPPFLAGS) + libucc_tl_nccl_la_CFLAGS = $(BASE_CFLAGS) + libucc_tl_nccl_la_LDFLAGS = -version-info $(SOVERSION) --as-needed $(CUDA_LDFLAGS) $(NCCL_LDFLAGS) +-libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) $(UCC_TOP_BUILDDIR)/src/libucc.la ++libucc_tl_nccl_la_LIBADD = $(CUDA_LIBS) $(NCCL_LIBADD) -lucc + + include $(top_srcdir)/config/module.am From fb92d714a597135d8818b1255b49d151edaa9bde Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 4 Oct 2024 17:30:55 +0200 Subject: [PATCH 015/116] adding easyconfigs: GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb --- .../GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb | 91 +++++++++++++++++++ 1 file changed, 91 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb new file mode 100644 index 00000000000..ebc1ba1601a --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb @@ -0,0 +1,91 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', versionsuffix), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From a06dbe8bb1f34fe17ae2b3ca16ce2540f9873cf5 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Oct 2024 12:51:14 +0200 Subject: [PATCH 016/116] adding easyconfigs: p7zip-17.05-GCCcore-13.3.0.eb --- .../p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb | 47 +++++++++++++++++++ 1 file changed, 47 insertions(+) create mode 100644 easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..990ec0677d4 --- /dev/null +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'MakeCp' + +name = 'p7zip' +version = '17.05' + +homepage = 'https://github.com/p7zip-project/p7zip/' +description = """p7zip is a quick port of 7z.exe and 7za.exe (CLI version of +7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GITHUB_LOWER_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['d2788f892571058c08d27095c22154579dfefb807ebe357d145ab2ddddefb1a6'] + +builddependencies = [ + ('binutils', '2.42'), +] + +prebuildopts = "cp makefile.linux_amd64 makefile.linux &&" +buildopts = 'all3 CC="$CC" CXX="$CXX" OPTFLAGS="$CFLAGS"' + +github_account = '%(name)s-project' +# put script in place for 7z, since it *must* be called full path, to ensure that 7z.so is found in the same directory +# see also http://sourceforge.net/p/p7zip/discussion/383044/thread/5e4085ab/ +postinstallcmds = [ + """echo '#!/bin/sh +%(installdir)s/libexec/7z $@' > %(installdir)s/bin/7z""", + "chmod +x %(installdir)s/bin/7z", # set execution bits according to current umask +] +files_to_copy = [ + (['bin/7za', 'bin/7zr', 'bin/7zCon.sfx'], 'bin'), # stand-alone binaries + (['bin/7z', 'bin/7z.so', 'bin/Codecs'], 'libexec'), +] # 7z requires 7z.so plugin in same directory + +sanity_check_paths = { + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'dirs': ['libexec/Codecs'], +} + +sanity_check_commands = [ + "7z --help", + "7z x || test $? -gt 0", + """! 7z i | grep -q "Can't load" """, +] + +moduleclass = 'tools' From 085e15c0b615abbad0c373c0cf5ffad8f06acda1 Mon Sep 17 00:00:00 2001 From: maximm Date: Mon, 7 Oct 2024 13:05:36 +0200 Subject: [PATCH 017/116] adding easyconfigs: likwid-5.3.0-GCC-13.3.0.eb --- .../l/likwid/likwid-5.3.0-GCC-13.3.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb new file mode 100644 index 00000000000..a23dea7326c --- /dev/null +++ b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb @@ -0,0 +1,55 @@ +easyblock = 'ConfigureMake' + +name = 'likwid' +version = '5.3.0' + +homepage = 'https://github.com/RRZE-HPC/likwid' +description = """ +Likwid stands for Like I knew what I am doing. This project contributes easy +to use command line tools for Linux to support programmers in developing high +performance multi threaded programs. +""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/RRZE-HPC/%(name)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['c290e554c4253124ac2ab8b056e14ee4d23966b8c9fbfa10ba81f75ae543ce4e'] + +builddependencies = [ + ('Perl', '5.38.2'), +] +dependencies = [ + ('hwloc', '2.10.0'), +] + +# include_GCC.mk is using ifort by default. +# Changing it to gfortran, to be consistent with GCC toolchain +prebuildopts = "sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && " +prebuildopts += "sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' make/include_GCC.mk " +prebuildopts += "&& " + +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' +buildopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' + +installopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' +installopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' +installopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +installopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' +installopts += 'INSTALL_CHOWN="" ' + +maxparallel = 1 + +skipsteps = ['configure'] + +sanity_check_paths = { + 'files': ['bin/%(name)s-memsweeper', 'bin/%(name)s-mpirun', 'bin/%(name)s-perfctr', 'bin/%(name)s-perfscope', + 'bin/%(name)s-pin', 'bin/%(name)s-powermeter', 'bin/%(name)s-topology', 'lib/liblikwidpin.so', + 'lib/liblikwid.so', 'include/%(name)s.mod'], + 'dirs': ['man/man1'], +} + +moduleclass = 'tools' From 43321a606ff07af181432e122a59fe53599ab71b Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Wed, 9 Oct 2024 13:38:35 +0200 Subject: [PATCH 018/116] Added bokeh to the gfbf-2024a toolchain and tornado (dep of bokeh) to the GCCcore-13.3.0 toolchain --- .../b/bokeh/bokeh-3.6.0-gfbf-2024a.eb | 46 +++++++++++++++++++ .../t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb | 29 ++++++++++++ 2 files changed, 75 insertions(+) create mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb create mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb new file mode 100644 index 00000000000..fbdb34a71b6 --- /dev/null +++ b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'PythonBundle' + +name = 'bokeh' +version = '3.6.0' + +homepage = 'https://github.com/bokeh/bokeh' +description = "Statistical and novel interactive HTML plots for Python" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +builddependencies = [ + ('meson-python', '0.16.0'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('SciPy-bundle', '2024.05'), + ('matplotlib', '3.9.2'), + ('PyYAML', '6.0.2'), + ('Pillow-SIMD', '10.4.0'), + ('tornado', '6.4.1'), +] + +use_pip = True + +exts_list = [ + ('xyzservices', '2024.4.0', { + 'checksums': ['6a04f11487a6fb77d92a98984cd107fbd9157fd5e65f929add9c3d6e604ee88c'], + }), + (name, version, { + 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, + 'checksums': ['0032dc1e76ad097b07626e51584685ff48c65481fbaaad105663b1046165867a'], + }), +] + +sanity_check_paths = { + 'files': ['bin/bokeh'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = ["bokeh --help"] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d4266c8c1c9 --- /dev/null +++ b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,29 @@ +easyblock = "PythonPackage" + +name = "tornado" +version = "6.4.1" + +homepage = "https://github.com/tornadoweb/tornado" +description = "Tornado is a Python web framework and asynchronous networking library." + +toolchain = {"name": "GCCcore", "version": "13.3.0"} + +sources = [SOURCE_TAR_GZ] +patches = ['tornado-6.1_increase-default-timeouts.patch'] +checksums = [ + {'tornado-6.4.1.tar.gz': '92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9'}, + {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, +] + +builddependencies = [ + ("binutils", "2.42"), +] +dependencies = [ + ("Python", "3.12.3"), +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = "lib" From f53954b22d6477e9c725e319e25e89592b7bca3d Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:23:52 +0200 Subject: [PATCH 019/116] Add gnuplot --- .../g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 47 +++++++++++++++++++ .../l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb | 28 +++++++++++ .../l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb | 36 ++++++++++++++ 3 files changed, 111 insertions(+) create mode 100644 easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..049c6e4a741 --- /dev/null +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -0,0 +1,47 @@ +easyblock = 'ConfigureMake' + +name = 'gnuplot' +version = '6.0.1' + +homepage = 'http://gnuplot.sourceforge.net' +description = "Portable interactive, function plotting utility" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [('https://sourceforge.net/projects/%(name)s/files/%(name)s/%(version)s', 'download')] +sources = [SOURCE_TAR_GZ] +checksums = ['e85a660c1a2a1808ff24f7e69981ffcbac66a45c9dcf711b65610b26ea71379a'] + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Autotools', '20231222'), +] +dependencies = [ + ('ncurses', '6.5'), + ('cairo', '1.18.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('libgd', '2.3.3'), + ('Pango', '1.54.0'), + ('libcerf', '2.4'), + ('X11', '20240607'), + ('Qt6', '6.7.2'), + ('Lua', '5.4.7'), +] + +preconfigopts = 'autoreconf && export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' +preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' +#configopts = "--with-qt=qt5 --without-latex --disable-wxwidgets" +configopts = "--without-latex --disable-wxwidgets" + + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +# make sure that pdf terminal type is available +sanity_check_commands = ["%(name)s -e 'set terminal pdf'"] + +moduleclass = 'vis' diff --git a/easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..98e622129cd --- /dev/null +++ b/easybuild/easyconfigs/l/Lua/Lua-5.4.7-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +name = 'Lua' +version = '5.4.7' + +homepage = 'https://www.lua.org/' +description = """Lua is a powerful, fast, lightweight, embeddable scripting language. + Lua combines simple procedural syntax with powerful data description constructs based + on associative arrays and extensible semantics. Lua is dynamically typed, + runs by interpreting bytecode for a register-based virtual machine, + and has automatic memory management with incremental garbage collection, + making it ideal for configuration, scripting, and rapid prototyping.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://www.%(namelower)s.org/ftp/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['9fbf5e28ef86c69858f6d3d34eccc32e911c1a28b4120ff3e84aaa70cfbf1e30'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('ncurses', '6.5'), + ('libreadline', '8.2'), +] + + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..28e596386fd --- /dev/null +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'libgd' +version = '2.3.3' + +homepage = 'https://libgd.github.io' +description = "GD is an open source code library for the dynamic creation of images by programmers." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/%(name)s/%(name)s/releases/download/gd-%(version)s/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['dd3f1f0bb016edcc0b2d082e8229c822ad1d02223511997c80461481759b1ed2'] + +builddependencies = [ + ('binutils', '2.42'), +] +dependencies = [ + ('fontconfig', '2.15.0'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), +] + +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" + + +sanity_check_paths = { + 'files': ['lib/%(name)s.a', 'lib/%(name)s.so'], + 'dirs': ['bin', 'include'], +} + +sanity_check_commands = ['webpng --help'] + +moduleclass = 'lib' From e5644822f6c8086473968a499955bf0530d1516e Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 9 Oct 2024 18:55:29 +0200 Subject: [PATCH 020/116] Fix style --- easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb index 28e596386fd..2c03aa92105 100644 --- a/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/l/libgd/libgd-2.3.3-GCCcore-13.3.0.eb @@ -23,8 +23,8 @@ dependencies = [ ('zlib', '1.3.1'), ] -configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO --with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" - +configopts = "--with-fontconfig=$EBROOTFONTCONFIG --with-jpeg=$EBROOTLIBJPEGMINTURBO " +configopts += "--with-png=$EBROOTLIBPNG --with-zlib=$EBROOTZLIB" sanity_check_paths = { 'files': ['lib/%(name)s.a', 'lib/%(name)s.so'], From df0790f5535260a6edd4438ac6284494ba8bd442 Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 9 Oct 2024 23:11:09 +0200 Subject: [PATCH 021/116] Update gnuplot-6.0.1-GCCcore-13.3.0.eb --- easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb index 049c6e4a741..684924b80d1 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -32,7 +32,6 @@ dependencies = [ preconfigopts = 'autoreconf && export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' -#configopts = "--with-qt=qt5 --without-latex --disable-wxwidgets" configopts = "--without-latex --disable-wxwidgets" From ca2fc7f4a43480ca9e5cbc4eb83f0c661182c808 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 10 Oct 2024 10:09:33 +0200 Subject: [PATCH 022/116] Fix style --- .../easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb index 684924b80d1..c0f7a2a4d89 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -30,8 +30,12 @@ dependencies = [ ('Lua', '5.4.7'), ] -preconfigopts = 'autoreconf && export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' +preconfigopts = 'autoreconf && ' + +# make sure that right Lua library is used (bypassing pkg-config) +preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' + configopts = "--without-latex --disable-wxwidgets" From c454e67956564a6f760c7a5407434ec921cd3a6f Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Thu, 10 Oct 2024 10:22:00 +0200 Subject: [PATCH 023/116] Add comment --- .../easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb index c0f7a2a4d89..e27fc37776f 100644 --- a/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/gnuplot/gnuplot-6.0.1-GCCcore-13.3.0.eb @@ -34,11 +34,12 @@ preconfigopts = 'autoreconf && ' # make sure that right Lua library is used (bypassing pkg-config) preconfigopts += 'export LUA_CFLAGS="-I$EBROOTLUA/include" && export LUA_LIBS="$EBROOTLUA/lib/liblua.a" && ' + +# fix undefined reference to symbol 'libiconv_open' preconfigopts += ' export LDFLAGS="-Wl,--copy-dt-needed-entries" && ' configopts = "--without-latex --disable-wxwidgets" - sanity_check_paths = { 'files': ['bin/%(name)s'], 'dirs': [], From 71273e489e5d13584714557a6ac328b308ada47a Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 10 Oct 2024 11:19:11 +0200 Subject: [PATCH 024/116] Added cuDNN and cuTENSOR --- .../c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb | 32 +++++++++++++++ .../c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb | 40 +++++++++++++++++++ 2 files changed, 72 insertions(+) create mode 100644 easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb new file mode 100644 index 00000000000..a6cbe9ef7e7 --- /dev/null +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb @@ -0,0 +1,32 @@ +name = 'cuDNN' +version = '9.5.0.50' +versionsuffix = '-CUDA-%(cudaver)s' +homepage = 'https://developer.nvidia.com/cudnn' +description = """The NVIDIA CUDA Deep Neural Network library (cuDNN) is +a GPU-accelerated library of primitives for deep neural networks.""" + +toolchain = SYSTEM + +# note: cuDNN is tied to specific to CUDA versions, +# see also https://docs.nvidia.com/deeplearning/cudnn/support-matrix/index.html#cudnn-cuda-hardware-versions +local_short_ver = '.'.join(version.split('.')[:3]) +local_cuda_major = '12' + +source_urls = [ + 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' +] +sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] +checksums = ['86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d'] + +dependencies = [('CUDA', '12.6.0')] + +sanity_check_paths = { + 'files': [ + 'include/cudnn.h', 'lib64/libcudnn_adv_static.a', 'lib64/libcudnn_cnn_static.a', + 'lib64/libcudnn_engines_precompiled_static.a', 'lib64/libcudnn_engines_runtime_compiled_static.a', + 'lib64/libcudnn_graph_static.a', 'lib64/libcudnn_heuristic_static.a', 'lib64/libcudnn_ops_static.a', + ], + 'dirs': ['include', 'lib64'], +} + +moduleclass = 'numlib' diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb new file mode 100644 index 00000000000..fe7b69ac9b0 --- /dev/null +++ b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb @@ -0,0 +1,40 @@ +easyblock = 'Tarball' + +name = 'cuTENSOR' +version = '2.0.2.5' +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-%(arch)s/' +] +sources = ['libcutensor-linux-%(arch)s-%(version)s-archive.tar.xz'] + +checksums = [{ + 'libcutensor-linux-sbsa-%(version)s-archive.tar.xz': + '5163dd40f11f328e469a6d9b0056c8346f5d59ed538c18d6b954e4ae657c69cc', + 'libcutensor-linux-x86_64-%(version)s-archive.tar.xz': + '0e957ae7b352f599de34b6fa1ba999b0617887f885d7436ac5737d71a6b83baa', +}] + +local_cudamajver = '12' +dependencies = [('CUDA', '12.6.0')] + +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 8314b835231f14a146e2b5d199d4b66199e0389e Mon Sep 17 00:00:00 2001 From: ankekreuzer Date: Thu, 10 Oct 2024 12:28:29 +0200 Subject: [PATCH 025/116] Fixed typo in filename of cuTENSOR --- ...uTENSOR-2.0.2.5-CUDA-12.eb => cuTENSOR-2.0.2.5-CUDA-12.6.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/c/cuTENSOR/{cuTENSOR-2.0.2.5-CUDA-12.eb => cuTENSOR-2.0.2.5-CUDA-12.6.0.eb} (100%) diff --git a/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb b/easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.6.0.eb similarity index 100% rename from easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.eb rename to easybuild/easyconfigs/c/cuTENSOR/cuTENSOR-2.0.2.5-CUDA-12.6.0.eb From 677666a2b785d8961cfa75f2a1292753e2c48d23 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 10 Oct 2024 15:49:13 +0200 Subject: [PATCH 026/116] adding easyconfigs: PySCF-2.7.0-foss-2023a.eb, NECI-20230620-foss-2023a.eb, tblis-20230422-foss-2023a.eb --- .../n/NECI/NECI-20230620-foss-2023a.eb | 51 +++++++ .../p/PySCF/PySCF-2.7.0-foss-2023a.eb | 138 ++++++++++++++++++ .../t/tblis/tblis-20230422-foss-2023a.eb | 26 ++++ 3 files changed, 215 insertions(+) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb new file mode 100644 index 00000000000..cc48f534ee8 --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -0,0 +1,51 @@ +easyblock = 'CMakeMakeCp' +name = 'NECI' +version = '20230620' +_commit = '558e88c5ae6c30d0505a9badbc69111be0866ba1' + +homepage = 'https://github.com/ghb24/NECI_STABLE' +description = """Standalone NECI codebase designed for FCIQMC and other stochastic quantum +chemistry methods.""" + +toolchain = {'name': 'foss', 'version': '2023a'} +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', '3.26.3'), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +dependencies = [ + ('HDF5', '1.14.0'), +] + +# disable tests ending up with SEGFAULT +preconfigopts = "sed -i '/back_spawn_excit_gen/d' '%(builddir)s/NECI_STABLE/unit_tests/CMakeLists.txt' && " + +# 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' diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb new file mode 100644 index 00000000000..72432ce1b97 --- /dev/null +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb @@ -0,0 +1,138 @@ +easyblock = 'CMakeMakeCp' +name = 'PySCF' +version = '2.7.0' + +homepage = 'http://www.pyscf.org' +description = "PySCF is an open-source collection of electronic structure modules powered by Python." + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/pyscf/pyscf/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['f2f94e6dae8556085bb765eb5250f61589e977b4f12540c748241101d40da241'] + +builddependencies = [ + ('CMake', '3.26.3'), + ('pybind11', '2.11.1'), # needed by zquatev +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), # for numpy, scipy + ('h5py', '3.9.0'), + ('libcint', '5.4.0'), + ('libxc', '6.2.2'), + ('XCFun', '2.1.1'), + ('CPPE', '0.3.3a0'), # extra + ('PyBerny', '0.6.3'), # extra + ('PyCheMPS2', '1.8.12'), # needed by dmrgscf + ('Block', '1.5.3-20200525'), # needed by dmrgscf + ('NECI', '20230620'), # needed by fciqmc + ('Dice', '20240702'), # needed by icmpspt + ('tblis', '20230422'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'modulename': 'pyscf.%(name)s', + 'source_urls': ['https://github.com/pyscf/%(name)s/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], +} + +# The following list of extensions is equivalent to installing PySCF with extras: +# all + dmrgscf + fciqmcscf + hci + mbd + tblis + zquatev +exts_list = [ + ('dftd3', '94091d8', { + 'checksums': ['a69ae44b3d02d2c06fd531373f20ee1251ef27fc932d40a7cafea6c09d8784fc'], + }), + ('doci', '08079a9', { + 'checksums': ['f492ba45dfe50c9b459e53a946a677528af0dc2097ff77ea3767aa4f46c5d9ba'], + }), + ('icmpspt', '50c386e', { + 'patches': [('PySCF-2.1.1_icmpspt-exe-path.patch', 0)], + 'checksums': [ + {'icmpspt-50c386e.tar.gz': '08029863ae8740939a730fe5e104661c67d8dd0b8a8555b603fc8a0777096d48'}, + {'PySCF-2.1.1_icmpspt-exe-path.patch': 'e972e377b34b964c48a99909301bf21a9c73d8eb9ecb96a889621d71471c56c9'}, + ], + }), + ('properties', '8b94d8d', { + 'modulename': 'pyscf.prop', + 'checksums': ['b40e071472a6bdfcaec8cd358c7c58c58748c59d8b188fdca09d6eca63329914'], + }), + ('qsdopt', '3ad2c02', { + 'checksums': ['cc639150e5f9efad8ffe496b3dccd2952a1f60fdad51f611cffba701892b384e'], + }), + ('semiempirical', '470d716', { + 'checksums': ['0bbe304867fd053ed647445ac84c4c76787ad23def9f72415aec297740121eef'], + }), + ('shciscf', '7edb54d', { + 'checksums': ['ae54265f6600b73a350b00274c95bb0de940ddcd6e1b47b434594e18136b1bed'], + }), + ('MCfun', '0.2.3', { + 'modulename': 'mcfun', + 'source_urls': ['https://github.com/Multi-collinear/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['3741b49b839df0fde891d51292520ed9094fa1d3c9b5d9c042d4f26087cf6a13'], + }), + ('pyqmc', '0.6.0', { + 'modulename': 'pyqmc', + 'source_urls': ['https://github.com/WagnerGroup/%(name)s/archive/'], + 'sources': [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['6e9f612c2d0bf2198154520e01dce57cf3a6e474840c1892466de3171eaeb7db'], + }), + ('dmrgscf', 'a03f7b6', { + 'patches': [('PySCF-2.1.1_dmrgscf-settings.patch', 0)], + 'checksums': [ + {'dmrgscf-a03f7b6.tar.gz': 'dee40abe3d2aebab7a2d0eade4e464a6ae851b4c2b49a2cde4c3aa88f0651b04'}, + {'PySCF-2.1.1_dmrgscf-settings.patch': 'a0310a2a90e96bd64d1560b2cc73a805717e129d2921e91cc5e6038b9f153677'}, + ], + }), + ('fciqmc', 'ee98fb4', { + 'modulename': 'pyscf.fciqmcscf', + 'checksums': ['b2f081ac295df0e622c6d1b3bff6d7834f97131f1f0fc87ec8bcff2137ef4199'], + }), + ('mbd', '485c18c', { + 'patches': [('PySCF-2.1.1_mbd-fix-init.patch', 0)], + 'checksums': [ + {'mbd-485c18c.tar.gz': 'de1fb14650fcb87909cae33dc318d2e213653ac4393ced7e070dfa6308d95846'}, + {'PySCF-2.1.1_mbd-fix-init.patch': '4f8e4b2e39b77428187851c4b6ced39401561bc81f4f3a4605da5d5c7b798cbc'}, + ], + }), + ('naive-hci', '0c28d6e', { + 'modulename': 'pyscf.hci', + 'checksums': ['de247d17b80133655df5966341e5adb691b0df150cd9b0f1980cf62ec55229d5'], + }), + ('tblis', 'c67c8af', { + 'modulename': 'pyscf.tblis_einsum', + # Use our `tblis`. + 'preinstallopts': 'CMAKE_CONFIGURE_ARGS="-DVENDOR_TBLIS=off" ', + 'source_urls': ['https://github.com/pyscf/pyscf-tblis/archive/'], + 'checksums': ['9a40a760e3be1d0b7f49faab5897388dcdf75094f75e06b4c344b3642a0401d6'], + }), + ('zquatev', '4eb41b1', { + 'modulename': 'zquatev', + 'preinstallopts': "sed -i 's/add_subdirectory(pybind11)/find_package(pybind11 REQUIRED)/' CMakeLists.txt && ", + 'source_urls': ['https://github.com/sunqm/%(name)s/archive/'], + 'checksums': ['4caf08e3831a5d86e6bc22f3b4028cc159101cb9658d09de16e382e268a5a2e9'], + }), +] + +start_dir = 'pyscf/lib' +configopts = "-DBUILD_LIBCINT=OFF -DBUILD_LIBXC=OFF -DBUILD_XCFUN=OFF" +prebuildopts = "export PYSCF_INC_DIR=$EBROOTQCINT/include:$EBROOTLIBXC/lib && " + +_py_site_packages = 'lib/python%(pyshortver)s/site-packages' +files_to_copy = [(['pyscf'], _py_site_packages)] + +sanity_check_paths = { + 'files': [_py_site_packages + '/pyscf/__init__.py'], + 'dirs': [_py_site_packages + d for d in ['/pyscf/data', '/pyscf/lib']], +} + +sanity_check_commands = ["python -c 'import pyscf'"] + +modextrapaths = {'PYTHONPATH': _py_site_packages} + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb new file mode 100644 index 00000000000..a9853cde523 --- /dev/null +++ b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb @@ -0,0 +1,26 @@ +easyblock = 'ConfigureMake' + +name = 'tblis' +version = '20230422' +local_commit = '4de1919' + +homepage = "https://github.com/devinamatthews/tblis" +description = """TBLIS is a library and framework for performing tensor + operations, especially tensor contraction, using native algorithms.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCE_TAR_GZ] +source_urls = ['https://github.com/devinamatthews/tblis/archive/'] +sources = ['%s.tar.gz' % local_commit] +checksums = ['85b72884022edd2612e3a0b3ed12aa6237d3989b581091d21f58124a7450aaeb'] + +sanity_check_paths = { + 'files': [ + 'include/tblis/tblis.h', + 'lib/libtblis.%s' % SHLIB_EXT, + ], + 'dirs': [] +} + +moduleclass = 'lib' From 256cbef1db43fe7491b09204d300a7b41ce43f00 Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Thu, 10 Oct 2024 17:55:46 +0200 Subject: [PATCH 027/116] adding easyconfigs: EvidentialGene-2018.01.01-gompi-2023a.eb --- .../EvidentialGene-2018.01.01-gompi-2023a.eb | 40 +++++++++++++++++++ 1 file changed, 40 insertions(+) create mode 100644 easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb diff --git a/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb new file mode 100644 index 00000000000..15d8b4dc07c --- /dev/null +++ b/easybuild/easyconfigs/e/EvidentialGene/EvidentialGene-2018.01.01-gompi-2023a.eb @@ -0,0 +1,40 @@ +easyblock = "PackedBinary" + +name = "EvidentialGene" +version = '2018.01.01' +local_month = ['', 'jan', 'feb', 'mar', 'apr', 'may', 'jun', 'jul', 'aug', 'sep', 'oct', 'nov', 'dec'] +local_dlver = version.split('.')[0][-2:] + local_month[int(version.split('.')[1])] + version.split('.')[2] + +homepage = 'http://arthropods.eugenes.org/EvidentialGene/' +description = """EvidentialGene is a genome informatics project for + "Evidence Directed Gene Construction for Eukaryotes", + for constructing high quality, accurate gene sets for + animals and plants (any eukaryotes), being developed by + Don Gilbert at Indiana University, gilbertd at indiana edu.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +source_urls = [ + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/', + 'http://arthropods.eugenes.org/EvidentialGene/other/evigene_old/evigene_older/', +] +sources = ['evigene%s.tar' % local_dlver] +checksums = ['6972108112cdb1fb106da11321d06b09f518b544e4739d0bf19da1984131e221'] + +dependencies = [ + ('Perl', '5.36.1'), + ('Exonerate', '2.4.0'), + ('CD-HIT', '4.8.1'), + ('BLAST+', '2.14.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl', 'scripts/*/*.pl', 'scripts/*/*/*.pl'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['scripts/'], +} + +modextravars = {'evigene': '%(installdir)s'} + +moduleclass = 'bio' From d153d6e46ace73687250fdad86c2d49d654d9f69 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 17 Oct 2024 19:09:54 +0200 Subject: [PATCH 028/116] adding easyconfigs: scTIE-20231205-foss-2023a-CUDA-12.1.1.eb, POT-0.9.3-foss-2023a-CUDA-12.1.1.eb, CVXOPT-1.3.2-foss-2023a.eb --- .../c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb | 49 +++++++++++++++++++ .../p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb | 47 ++++++++++++++++++ .../scTIE-20231205-foss-2023a-CUDA-12.1.1.eb | 46 +++++++++++++++++ 3 files changed, 142 insertions(+) create mode 100644 easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb diff --git a/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb new file mode 100644 index 00000000000..d6793ad49bb --- /dev/null +++ b/easybuild/easyconfigs/c/CVXOPT/CVXOPT-1.3.2-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'PythonPackage' + +name = 'CVXOPT' +version = '1.3.2' + +homepage = 'https://cvxopt.org' +description = """CVXOPT is a free software package for convex optimization based on the Python programming language. + Its main purpose is to make the development of software for convex optimization applications straightforward by + building on Python's extensive standard library and on the strengths of Python as a high-level programming language. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'pic': True} + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] + +patches = ['CVXOPT-1.3.1_fix-setup-py.patch'] + +checksums = [ + '3461fa42c1b2240ba4da1d985ca73503914157fc4c77417327ed6d7d85acdbe6', # cvxopt-1.3.2.tar.gz + '350904c0427d4652fc73b95b7e0d78a17c917cb94ed6c356dbbbfb07f2173849', # CVXOPT-1.3.1_fix-setup-py.patch +] + +dependencies = [ + ('Python', '3.11.3'), + ('SuiteSparse', '7.1.0'), + ('GSL', '2.7'), +] + +use_pip = True +sanity_pip_check = True +download_dep_fail = True + +preinstallopts = " ".join([ + 'CVXOPT_BUILD_FFTW=1', + 'CVXOPT_BUILD_GSL=1', + 'CVXOPT_BLAS_EXTRA_LINK_ARGS="$LIBBLAS"', + 'CVXOPT_LAPACK_EXTRA_LINK_ARGS="$LIBLAPACK"', + 'CVXOPT_FFTW_EXTRA_LINK_ARGS="$LIBFFT"', + 'CVXOPT_SUITESPARSE_LIB_DIR=$EBROOTSUITESPARSE/lib', + 'CVXOPT_SUITESPARSE_INC_DIR=$EBROOTSUITESPARSE/include', +]) + +installopts = ' --no-binary cvxopt' + +sanity_check_commands = ['cd %(builddir)s/%(namelower)s-%(version)s && python -m unittest discover -s tests'] + +moduleclass = 'math' diff --git a/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..1eddcba72f5 --- /dev/null +++ b/easybuild/easyconfigs/p/POT/POT-0.9.3-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,47 @@ +easyblock = 'PythonBundle' + +name = 'POT' +version = '0.9.3' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/rflamary/POT' +description = """POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems + related to Optimal Transport for signal, image processing and machine learning.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('matplotlib', '3.7.2'), + ('scikit-learn', '1.3.1'), + ('CUDA', '12.1.1', '', SYSTEM), + ('PyTorch', '2.1.2', versionsuffix), + ('jax', '0.4.25', versionsuffix), + ('CVXOPT', '1.3.2'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('autograd', '1.7.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['49680300f842f3a8722b060ac0d3ed7aca071d1ad4d3d38c9fdadafdcc73c30b'], + }), + ('versioneer', '0.29', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['0f1a137bb5d6811e96a79bb0486798aeae9b9c6efc24b389659cebb0ee396cb9'], + }), + ('pymanopt', '2.2.1', { + # Requirements forbid some versions of `scipy` which are known to have a bug but we have fixed it. + # see `scipy-1.11.1_vectorization_error.patch` + 'preinstallopts': """sed -i 's/"scipy>=1.0[^"]*"/"scipy>=1.0"/g' pyproject.toml && """, + 'checksums': ['c784929a436eb06d73371b53ae5db3cdc19c5e60280f8131553bc805cbf7a1da'], + }), + (name, version, { + 'modulename': 'ot', + 'checksums': ['eecf2394390a73472e727ef75f7c801fc47509039f00c40f8fc64fdeea617c86'], + }), +] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..375e693aeba --- /dev/null +++ b/easybuild/easyconfigs/s/scTIE/scTIE-20231205-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,46 @@ +easyblock = 'Tarball' + +name = 'scTIE' +version = '20231205' +local_commit = '044d91a' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/SydneyBioX/scTIE' +description = """scTIE (single-cell Temporal Integration and inference of multimodal Experiments) + is an autoencoder-based method for integrating multimodal profiling of scRNA-seq and scATAC-seq + data over a time course and inferring cell-type specific GRNs. scTIE projects cells from all time + points into a common embedding space, followed by extracting interpretable information from this + space to predict cell trajectories.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = 'SydneyBioX' +source_urls = [GITHUB_SOURCE] +sources = ['%s.tar.gz' % local_commit] +checksums = ['bcbf7c846539d0f04e7bbf3cc6ae2fe075a4ba11e3a4388c29def943d39af53e'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2', versionsuffix), + ('SciPy-bundle', '2023.07'), + ('CUDA', '12.1.1', '', SYSTEM), + ('POT', '0.9.3', versionsuffix), +] + +postinstallcmds = ['cd %(installdir)s && mkdir bin && ln -r -s main.py bin/sctie && chmod a+x main.py'] + +fix_python_shebang_for = ['main.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': '', +} + +sanity_check_paths = { + 'files': ['bin/sctie'], + 'dirs': [], +} + +sanity_check_commands = ['sctie --help'] + +moduleclass = 'bio' From 51f07a06857955ff44197f8a67cfa05af06b6370 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Oct 2024 12:07:03 +0200 Subject: [PATCH 029/116] adding easyconfigs: LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb, LightGBM-4.5.0-foss-2023a.eb, LightGBM-4.5.0-foss-2023a.eb --- .../LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb | 56 +++++++++++++++++++ .../l/LightGBM/LightGBM-4.5.0-foss-2023a.eb | 32 +++++++++++ 2 files changed, 88 insertions(+) create mode 100644 easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb create mode 100644 easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb new file mode 100644 index 00000000000..79b61c8d87b --- /dev/null +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb @@ -0,0 +1,56 @@ +easyblock = 'PythonBundle' + +name = "LightGBM" +version = "4.5.0" +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = "https://lightgbm.readthedocs.io" +description = """A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM +or MART) framework based on decision tree algorithms, used for ranking, +classification and many other machine learning tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('scikit-build-core', '0.9.3'), + ('wget', '1.24.5'), +] + +dependencies = [ + ('CUDA', '12.1.1', '', SYSTEM), + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Arrow', '14.0.1'), # optional + ('dask', '2023.9.2'), # optional + ('scikit-learn', '1.3.1'), # optional +] + +use_pip = True + +# example files are not distributed with the sources +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_cmds_pre = " && ".join([ + "mkdir regression", + "wget -P regression %s/regression/regression.test" % _test_repo_url, + "wget -P regression %s/regression/regression.train" % _test_repo_url, + "mkdir test", + "cd test", + "wget %s/python-guide/simple_example.py" % _test_repo_url, + "", +]) + +exts_list = [ + ('lightgbm', version, { + 'checksums': ['e1cd7baf0318d4e308a26575a63a4635f08df866ad3622a9d8e3d71d9637a1ba'], + 'installopts': "--config-settings=cmake.define.USE_CUDA=ON", + 'use_pip_extras': "arrow,dask,pandas,scikit-learn", + 'pretestopts': _test_cmds_pre, + 'runtest': 'python', + 'testopts': "simple_example.py", + 'testinstall': True, + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb new file mode 100644 index 00000000000..0cf659abfae --- /dev/null +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb @@ -0,0 +1,32 @@ +easyblock = 'PythonBundle' + +name = "LightGBM" +version = "4.5.0" + +homepage = "https://lightgbm.readthedocs.io" +description = """A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM +or MART) framework based on decision tree algorithms, used for ranking, +classification and many other machine learning tasks.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), +] + +use_pip = True + +exts_list = [ + ('lightgbm', version, { + 'checksums': ['0000000000000000000000000000000000000000000000000000000000000000'], + }), +] + +sanity_pip_check = True + +moduleclass = 'ai' From 819ed9cf8eb306e0abf92020b81ffd96d9aa4331 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Oct 2024 12:14:58 +0200 Subject: [PATCH 030/116] fix LightGBM-4.5.0-foss-2023a.eb --- .../l/LightGBM/LightGBM-4.5.0-foss-2023a.eb | 26 +++++++++++++++++-- 1 file changed, 24 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb index 0cf659abfae..fdbf6f54f1d 100644 --- a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb @@ -11,19 +11,41 @@ classification and many other machine learning tasks.""" toolchain = {'name': 'foss', 'version': '2023a'} builddependencies = [ - ('CMake', '3.26.3'), + ('scikit-build-core', '0.9.3'), + ('wget', '1.24.5'), ] dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), + ('Arrow', '14.0.1'), # optional + ('dask', '2023.9.2'), # optional + ('scikit-learn', '1.3.1'), # optional ] use_pip = True +# example files are not distributed with the sources +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_cmds_pre = " && ".join([ + "mkdir regression", + "wget -P regression %s/regression/regression.test" % _test_repo_url, + "wget -P regression %s/regression/regression.train" % _test_repo_url, + "mkdir test", + "cd test", + "wget %s/python-guide/simple_example.py" % _test_repo_url, + "", +]) + exts_list = [ ('lightgbm', version, { - 'checksums': ['0000000000000000000000000000000000000000000000000000000000000000'], + 'checksums': ['e1cd7baf0318d4e308a26575a63a4635f08df866ad3622a9d8e3d71d9637a1ba'], + 'installopts': "--config-settings=cmake.define.USE_MPI=ON", + 'use_pip_extras': "arrow,dask,pandas,scikit-learn", + 'pretestopts': _test_cmds_pre, + 'runtest': 'python', + 'testopts': "simple_example.py", + 'testinstall': True, }), ] From 02e8e5a5273a118571ac0c65ec5da5faea38e4cb Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 18 Oct 2024 12:15:35 +0200 Subject: [PATCH 031/116] adding easyconfig: scikit-build-core-0.9.3-GCCcore-12.3.0.eb --- .../scikit-build-core-0.9.3-GCCcore-12.3.0.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..a17cdb279fe --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-build-core/scikit-build-core-0.9.3-GCCcore-12.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'scikit-build-core' +version = '0.9.3' + +homepage = 'https://scikit-build.readthedocs.io/en/latest/' +description = """Scikit-build-core is a complete ground-up rewrite of scikit-build on top of +modern packaging APIs. It provides a bridge between CMake and the Python build +system, allowing you to make Python modules with CMake.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('hatchling', '1.18.0'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('CMake', '3.26.3'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('pyproject-metadata', '0.8.0', { + 'sources': ['pyproject_metadata-%(version)s.tar.gz'], + 'checksums': ['376d5a00764ac29440a54579f88e66b7d9cb7e629d35c35a1c7248bfebc9b455'], + }), + ('scikit_build_core', version, { + 'checksums': ['341d113e473a5409dc62522e8b1b1b8b1647a0b95557ad15f6be2a36071fd390'], + }), +] + +moduleclass = 'lib' From fdb168155c6facf9c2c5c26c92df5079be48e4fe Mon Sep 17 00:00:00 2001 From: Maxim Date: Fri, 18 Oct 2024 14:33:22 +0200 Subject: [PATCH 032/116] fix likwid-5.3.0-GCC-13.3.0.eb --- .../l/likwid/likwid-5.3.0-GCC-13.3.0.eb | 33 +++++++++---------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb index a23dea7326c..b9d22fc36dc 100644 --- a/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/l/likwid/likwid-5.3.0-GCC-13.3.0.eb @@ -4,6 +4,7 @@ name = 'likwid' version = '5.3.0' homepage = 'https://github.com/RRZE-HPC/likwid' + description = """ Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high @@ -15,6 +16,7 @@ toolchainopts = {'pic': True} source_urls = ['https://github.com/RRZE-HPC/%(name)s/archive/'] sources = ['v%(version)s.tar.gz'] + checksums = ['c290e554c4253124ac2ab8b056e14ee4d23966b8c9fbfa10ba81f75ae543ce4e'] builddependencies = [ @@ -24,32 +26,29 @@ dependencies = [ ('hwloc', '2.10.0'), ] +skipsteps = ['configure'] + # include_GCC.mk is using ifort by default. # Changing it to gfortran, to be consistent with GCC toolchain -prebuildopts = "sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && " -prebuildopts += "sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' make/include_GCC.mk " -prebuildopts += "&& " +prebuildopts = """sed -i 's@FC = ifort@FC = gfortran@g' make/include_GCC.mk && """ +prebuildopts += """sed -i 's@FCFLAGS = -module ./ # ifort@FCFLAGS = -J ./ -fsyntax-only #gfortran@g' """ +prebuildopts += """ make/include_GCC.mk && """ -buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' -buildopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' -buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' +buildopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event ' +buildopts += 'FORTRAN_INTERFACE=true ' +buildopts += 'CFG_FILE_PATH=%(installdir)s/etc/likwid.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' buildopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' -installopts = 'CC="$CC" CFLAGS="$CFLAGS -std=c99" ' -installopts += 'PREFIX=%(installdir)s BUILDFREQ="" ACCESSMODE=perf_event FORTRAN_INTERFACE=true ' -installopts += 'CFG_FILE_PATH=%(installdir)s/etc/%(name)s.cfg TOPO_FILE_PATH=%(installdir)s/etc/likwid_topo.cfg ' -installopts += 'HWLOC_INCLUDE_DIR=$EBROOTHWLOC/include HWLOC_LIB_DIR=$EBROOTHWLOC/lib HWLOC_LIB_NAME=hwloc ' -installopts += 'INSTALL_CHOWN="" ' - maxparallel = 1 -skipsteps = ['configure'] +installopts = buildopts + 'INSTALL_CHOWN="" ' sanity_check_paths = { - 'files': ['bin/%(name)s-memsweeper', 'bin/%(name)s-mpirun', 'bin/%(name)s-perfctr', 'bin/%(name)s-perfscope', - 'bin/%(name)s-pin', 'bin/%(name)s-powermeter', 'bin/%(name)s-topology', 'lib/liblikwidpin.so', - 'lib/liblikwid.so', 'include/%(name)s.mod'], - 'dirs': ['man/man1'], + 'files': ['bin/likwid-memsweeper', 'bin/likwid-mpirun', 'bin/likwid-perfctr', + 'bin/likwid-perfscope', 'bin/likwid-pin', 'bin/likwid-powermeter', + 'bin/likwid-topology', 'lib/liblikwidpin.%s' % SHLIB_EXT, + 'lib/liblikwid.%s' % SHLIB_EXT, 'include/likwid.mod'], + 'dirs': ['man/man1'] } moduleclass = 'tools' From 0f31ea0f359f895fb05ab51b95ff94fe3668ef11 Mon Sep 17 00:00:00 2001 From: benjamic Date: Mon, 21 Oct 2024 16:18:04 +0200 Subject: [PATCH 033/116] adding easyconfigs: pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb --- .../pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb | 33 +++++++++++++++++++ 1 file changed, 33 insertions(+) create mode 100644 easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb new file mode 100644 index 00000000000..aceab404bda --- /dev/null +++ b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -0,0 +1,33 @@ +easyblock = 'CMakeMake' + +name = 'pmt' +version = '1.3.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://git.astron.nl/RD/pmt' +description = """PMT is a high-level software library capable of + collecting power consumption measurements on various hardware.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://git.astron.nl/RD/pmt/-/archive/%(version)s'] +sources = ['pmt-%(version)s.tar.gz'] +checksums = ['cf8c669ffb0fda4cb594550fb233f9654252db50671b59147826eadc0a3d5565'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +dependencies = [ + ('CUDA', '12.6.0', '', SYSTEM) +] + +configopts = '-DPMT_BUILD_RAPL=1 -DPMT_BUILD_NVML=1 -DPMT_BUILD_NVIDIA=1' + +sanity_check_paths = { + 'files': ["lib/libpmt.so", "include/pmt/NVIDIA.h", "include/pmt/Rapl.h", "include/pmt/NVML.h"], + 'dirs': ["lib", "include"], +} + +moduleclass = 'lib' From 7f55ef3d35ca7dd5df6fe1e855d8a3a18bd12c4d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Tue, 22 Oct 2024 12:01:02 +0200 Subject: [PATCH 034/116] try the tests which are segfaulting on `donphan` --- easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb | 3 --- 1 file changed, 3 deletions(-) diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb index cc48f534ee8..becc50b238e 100644 --- a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -31,9 +31,6 @@ dependencies = [ ('HDF5', '1.14.0'), ] -# disable tests ending up with SEGFAULT -preconfigopts = "sed -i '/back_spawn_excit_gen/d' '%(builddir)s/NECI_STABLE/unit_tests/CMakeLists.txt' && " - # enable support for HDF5 configopts = "-DENABLE_HDF5=ON" From e75f5985718e06932c820f3112d5d2afa175b7a7 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Wed, 23 Oct 2024 18:23:24 +0200 Subject: [PATCH 035/116] Add PRSice --- .../p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb | 44 ++++ .../p/PRSice/PRSice-2.3.5_remove_sysctl.patch | 194 ++++++++++++++++++ 2 files changed, 238 insertions(+) create mode 100644 easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..85f8b20972c --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +# 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 = 'CMakeMakeCp' + +name = 'PRSice' +version = '2.3.5' + +homepage = 'https://choishingwan.github.io/PRSice/' +description = """PRSice (pronounced 'precise') is a Polygenic Risk +Score software for calculating, applying, evaluating and +plotting the results of polygenic risk scores (PRS) analyses.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/choishingwan/%(name)s/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['PRSice-2.3.5_remove_sysctl.patch'] +checksums = [ + '0a7e649ddebe4e969cd8400c5ad977a7b900be4f5c920a84483cb8930367354d', # 2.3.5.tar.gz + 'ab8286e8a0700ea163f552de66458e409c396e06b57c9adfff3b7f63083f7798', # PRSice-2.3.5_remove_sysctl.patch +] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), + ('Eigen', '3.4.0'), +] + +files_to_copy = [ + (['bin/%(name)s'], 'bin'), + 'README.md', + 'LICENSE', +] + +sanity_check_paths = { + 'files': ['bin/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ['%(name)s --help'] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch new file mode 100644 index 00000000000..04a71e26a8b --- /dev/null +++ b/easybuild/easyconfigs/p/PRSice/PRSice-2.3.5_remove_sysctl.patch @@ -0,0 +1,194 @@ +# What: sysctl.h is removed in glibc v2.32. This patch is based on the following commits +# from https://github.com/choishingwan/PRSice: +# f285b243856b857a461d9a2b27e1f2f0ac25216e +# 53641c11750a7e0bdd06a925fbf28c1e3978ee72 +# Also see issue https://github.com/choishingwan/PRSice/issues/338 and PR https://github.com/choishingwan/PRSice/pull/243 +# Author: maxim-masterov (SURF) + +diff -Nru PRSice-2.3.5.orig/inc/misc.hpp PRSice-2.3.5/inc/misc.hpp +--- PRSice-2.3.5.orig/inc/misc.hpp 2024-10-23 18:13:58.539539000 +0200 ++++ PRSice-2.3.5/inc/misc.hpp 2024-10-23 18:14:29.383991502 +0200 +@@ -38,7 +38,6 @@ + #include + #include + #include +-#include + #elif defined _WIN32 + #include + // psapi must go after windows, or will generate error +@@ -48,7 +47,6 @@ + #include "stdlib.h" + #include "string.h" + #include +-#include + #include + #include + #endif +@@ -86,9 +84,6 @@ + #include + #include + #include +-#if defined(BSD) +-#include +-#endif + + #else + #error "Unable to define getMemorySize( ) for an unknown OS." +@@ -170,73 +165,7 @@ + // TODO: Delete this, doesn't seems to give robust answer + inline size_t current_ram_usage() { return 0; } + // TODO: Delete this, doesn't seems to give robust answer +-inline size_t total_ram_available() +-{ +-#ifdef __APPLE__ +- int32_t mib[2]; +- size_t sztmp; +-#endif +- unsigned char* bigstack_ua = nullptr; // ua = unaligned +- int64_t llxx; +- intptr_t default_alloc_mb; +- intptr_t malloc_size_mb = 0; +-#ifdef __APPLE__ +- mib[0] = CTL_HW; +- mib[1] = HW_MEMSIZE; +- llxx = 0; +- +- sztmp = sizeof(int64_t); +- sysctl(mib, 2, &llxx, &sztmp, nullptr, 0); +- llxx /= 1048576; +-#else +-#ifdef _WIN32 +- MEMORYSTATUSEX memstatus; +- memstatus.dwLength = sizeof(memstatus); +- GlobalMemoryStatusEx(&memstatus); +- llxx = memstatus.ullTotalPhys / 1048576; +-#else +- llxx = ((uint64_t) sysconf(_SC_PHYS_PAGES)) +- * ((size_t) sysconf(_SC_PAGESIZE)) / 1048576; +-#endif +-#endif +- if (!llxx) { default_alloc_mb = BIGSTACK_DEFAULT_MB; } +- else if (llxx < (BIGSTACK_MIN_MB * 2)) +- { +- default_alloc_mb = BIGSTACK_MIN_MB; +- } +- else +- { +- default_alloc_mb = llxx / 2; +- } +- if (!malloc_size_mb) { malloc_size_mb = default_alloc_mb; } +- else if (malloc_size_mb < BIGSTACK_MIN_MB) +- { +- malloc_size_mb = BIGSTACK_MIN_MB; +- } +- std::string message = ""; +-#ifndef __LP64__ +- if (malloc_size_mb > 2047) { malloc_size_mb = 2047; } +-#endif +- bigstack_ua = +- (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); +- // if fail, return nullptr which will then get into the while loop +- while (!bigstack_ua) +- { +- malloc_size_mb = (malloc_size_mb * 3) / 4; +- if (malloc_size_mb < BIGSTACK_MIN_MB) +- { malloc_size_mb = BIGSTACK_MIN_MB; } +- bigstack_ua = +- (unsigned char*) malloc(malloc_size_mb * 1048576 * sizeof(char)); +- if (bigstack_ua) {} +- else if (malloc_size_mb == BIGSTACK_MIN_MB) +- { +- throw std::runtime_error("Failed to allocate required memory"); +- } +- } +- free(bigstack_ua); +- bigstack_ua = nullptr; +- return malloc_size_mb * 1024 * 1024; +-} ++ + // function from John D.Cook + // https://www.johndcook.com/blog/standard_deviation/ + class RunningStat +@@ -1398,82 +1327,5 @@ + return (size_t) 0L; /* Unsupported. */ + #endif + } +- +- +-/** +- * Returns the size of physical memory (RAM) in bytes. +- */ +-inline size_t getMemorySize() +-{ +-#if defined(_WIN32) && (defined(__CYGWIN__) || defined(__CYGWIN32__)) +- /* Cygwin under Windows. ------------------------------------ */ +- /* New 64-bit MEMORYSTATUSEX isn't available. Use old 32.bit */ +- MEMORYSTATUS status; +- status.dwLength = sizeof(status); +- GlobalMemoryStatus(&status); +- return (size_t) status.dwTotalPhys; +- +-#elif defined(_WIN32) +- /* Windows. ------------------------------------------------- */ +- /* Use new 64-bit MEMORYSTATUSEX, not old 32-bit MEMORYSTATUS */ +- MEMORYSTATUSEX status; +- status.dwLength = sizeof(status); +- GlobalMemoryStatusEx(&status); +- return (size_t) status.ullTotalPhys; +- +-#elif defined(__unix__) || defined(__unix) || defined(unix) \ +- || (defined(__APPLE__) && defined(__MACH__)) +- /* UNIX variants. ------------------------------------------- */ +- /* Prefer sysctl() over sysconf() except sysctl() HW_REALMEM and HW_PHYSMEM +- */ +- +-#if defined(CTL_HW) && (defined(HW_MEMSIZE) || defined(HW_PHYSMEM64)) +- int mib[2]; +- mib[0] = CTL_HW; +-#if defined(HW_MEMSIZE) +- mib[1] = HW_MEMSIZE; /* OSX. --------------------- */ +-#elif defined(HW_PHYSMEM64) +- mib[1] = HW_PHYSMEM64; /* NetBSD, OpenBSD. --------- */ +-#endif +- int64_t size = 0; /* 64-bit */ +- size_t len = sizeof(size); +- if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; +- return 0L; /* Failed? */ +- +-#elif defined(_SC_AIX_REALMEM) +- /* AIX. ----------------------------------------------------- */ +- return (size_t) sysconf(_SC_AIX_REALMEM) * (size_t) 1024L; +- +-#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGESIZE) +- /* FreeBSD, Linux, OpenBSD, and Solaris. -------------------- */ +- return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGESIZE); +- +-#elif defined(_SC_PHYS_PAGES) && defined(_SC_PAGE_SIZE) +- /* Legacy. -------------------------------------------------- */ +- return (size_t) sysconf(_SC_PHYS_PAGES) * (size_t) sysconf(_SC_PAGE_SIZE); +- +-#elif defined(CTL_HW) && (defined(HW_PHYSMEM) || defined(HW_REALMEM)) +- /* DragonFly BSD, FreeBSD, NetBSD, OpenBSD, and OSX. -------- */ +- int mib[2]; +- mib[0] = CTL_HW; +-#if defined(HW_REALMEM) +- mib[1] = HW_REALMEM; /* FreeBSD. ----------------- */ +-#elif defined(HW_PYSMEM) +- mib[1] = HW_PHYSMEM; /* Others. ------------------ */ +-#endif +- unsigned int size = 0; /* 32-bit */ +- size_t len = sizeof(size); +- if (sysctl(mib, 2, &size, &len, NULL, 0) == 0) return (size_t) size; +- return 0L; /* Failed? */ +-#endif /* sysctl and sysconf variants */ +- +-#else +- return 0L; /* Unknown OS. */ +-#endif + } + +-inline unsigned long long remain_memory(const double& adjFactor = 0.8) +-{ +- return (misc::getMemorySize() * adjFactor - getCurrentRSS()); +-} +-} From b86d803bc5e243d48dc48f74ea2be47a261fea8e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Thu, 24 Oct 2024 20:43:56 +0200 Subject: [PATCH 036/116] adding easyconfigs: Java-21.0.5.eb and bumping version in Java-21.eb --- easybuild/easyconfigs/j/Java/Java-21.0.5.eb | 32 +++++++++++++++++++++ easybuild/easyconfigs/j/Java/Java-21.eb | 2 +- 2 files changed, 33 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/j/Java/Java-21.0.5.eb diff --git a/easybuild/easyconfigs/j/Java/Java-21.0.5.eb b/easybuild/easyconfigs/j/Java/Java-21.0.5.eb new file mode 100644 index 00000000000..932318fd336 --- /dev/null +++ b/easybuild/easyconfigs/j/Java/Java-21.0.5.eb @@ -0,0 +1,32 @@ +name = 'Java' +version = '21.0.5' +local_build = '11' + +homepage = 'https://openjdk.org' +description = """Java Platform, Standard Edition (Java SE) lets you develop and deploy +Java applications on desktops and servers.""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'OpenJDK%%(version_major)sU-jdk_%s_linux_hotspot_%%(version)s_%s.tar.gz' + +# Using the Adoptium Eclipse Temurin builds, recommended by https://whichjdk.com/#distributions + +source_urls = ['https://github.com/adoptium/temurin%%(version_major)s-binaries/releases/download/jdk-%%(version)s+%s/' + % local_build] +sources = [local_tarball_tmpl % ('%(jdkarch)s', local_build)] + +checksums = [ + { + local_tarball_tmpl % ('x64', local_build): + '3c654d98404c073b8a7e66bffb27f4ae3e7ede47d13284c132d40a83144bfd8c', + local_tarball_tmpl % ('aarch64', local_build): + '6482639ed9fd22aa2e704cc366848b1b3e1586d2bf1213869c43e80bca58fe5c', + local_tarball_tmpl % ('ppc64le', local_build): + '3c6f4c358facfb6c19d90faf02bfe0fc7512d6b0e80ac18146bbd7e0d01deeef', + local_tarball_tmpl % ('riscv64', local_build): + '2f1b3e401e36de803398dfb9818861f9f14ca8ae7db650ea0946ab048fefe3b9', + } +] + +moduleclass = 'lang' diff --git a/easybuild/easyconfigs/j/Java/Java-21.eb b/easybuild/easyconfigs/j/Java/Java-21.eb index 46e84105b35..c7aef391c20 100644 --- a/easybuild/easyconfigs/j/Java/Java-21.eb +++ b/easybuild/easyconfigs/j/Java/Java-21.eb @@ -9,6 +9,6 @@ Java applications on desktops and servers.""" toolchain = SYSTEM -dependencies = [('Java', '%(version)s.0.2')] +dependencies = [('Java', '%(version)s.0.5')] moduleclass = 'lang' From dfe49901484dafe9a04fc473aae54e7ea49aa947 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 25 Oct 2024 18:20:18 +0200 Subject: [PATCH 037/116] adding easyconfigs: Trinotate-4.0.2-foss-2023a.eb, TransDecoder-5.7.1-GCC-12.3.0.eb, PyBioLib-1.1.2250-GCCcore-12.3.0.eb --- .../PyBioLib-1.1.2250-GCCcore-12.3.0.eb | 54 ++++++++++++++++++ .../TransDecoder-5.7.1-GCC-12.3.0.eb | 35 ++++++++++++ .../t/Trinotate/Trinotate-4.0.2-foss-2023a.eb | 55 +++++++++++++++++++ 3 files changed, 144 insertions(+) create mode 100644 easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb create mode 100644 easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb diff --git a/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..02c4c54ce07 --- /dev/null +++ b/easybuild/easyconfigs/p/PyBioLib/PyBioLib-1.1.2250-GCCcore-12.3.0.eb @@ -0,0 +1,54 @@ +easyblock = "PythonBundle" + +name = 'PyBioLib' +version = '1.1.2250' + +homepage = 'https://biolib.com/' +description = """PyBioLib is a Python package for running BioLib applications from Python +scripts and the command line. +BioLib is a library of biological data science applications. Applications on +BioLib range from small bioinformatics utilities to state-of-the-art machine +learning algorithms for predicting characteristics of biological molecules.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +builddependencies = [ + ('binutils', '2.40'), + ('poetry', '1.5.1'), +] + +dependencies = [ + ('Python', '3.11.3'), + ('Python-bundle-PyPI', '2023.06'), + ('Flask', '2.3.3'), + ('PyYAML', '6.0'), +] + +use_pip = True + +exts_list = [ + ('websocket_client', '1.8.0', { + 'modulename': 'websocket', + 'checksums': ['3239df9f44da632f96012472805d40a23281a991027ce11d2f45a6f24ac4c3da'], + }), + ('docker', '7.1.0', { + 'checksums': ['ad8c70e6e3f8926cb8a92619b832b4ea5299e2831c14284663184e200546fa6c'], + }), + ('PyJWT', '2.9.0', { + 'modulename': 'jwt', + 'source_tmpl': SOURCELOWER_TAR_GZ, + 'checksums': ['7e1e5b56cc735432a7369cbfa0efe50fa113ebecdc04ae6922deba8b84582d0c'], + }), + ('gunicorn', '23.0.0', { + 'checksums': ['f014447a0101dc57e294f6c18ca6b40227a4c90e9bdb586042628030cba004ec'], + }), + ('pybiolib', version, { + 'modulename': 'biolib', + 'preinstallopts': "sed -i 's/< 8.1.0/< 8.2.0/' pyproject.toml &", + 'checksums': ['1a0fb4a0256bfa8345b881ac9697cf94a50bcab2caa9ad063689dfc0035fe5a2'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb new file mode 100644 index 00000000000..3f1bbc6fe83 --- /dev/null +++ b/easybuild/easyconfigs/t/TransDecoder/TransDecoder-5.7.1-GCC-12.3.0.eb @@ -0,0 +1,35 @@ +easyblock = 'Tarball' + +name = 'TransDecoder' +version = '5.7.1' + +homepage = 'https://github.com/TransDecoder/TransDecoder/wiki' +description = """TransDecoder identifies candidate coding regions within transcript sequences, + such as those generated by de novo RNA-Seq transcript assembly using Trinity, + or constructed based on RNA-Seq alignments to the genome using + Tophat and Cufflinks.""" + +toolchain = {'name': 'GCC', 'version': '12.3.0'} + +source_urls = ['https://github.com/TransDecoder/TransDecoder/archive/'] +sources = ['TransDecoder-v%(version)s.tar.gz'] +checksums = ['41dd5e95f6ba946ff21340417d867e5e99f123b4035779b25d3cffd20b828a30'] + +dependencies = [ + ('Perl', '5.36.1'), + ('CD-HIT', '4.8.1'), +] + +sanity_check_paths = { + 'files': ['TransDecoder.LongOrfs', 'TransDecoder.Predict'], + 'dirs': ['PerlLib', 'sample_data', 'util'], +} + +sanity_check_commands = [] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb new file mode 100644 index 00000000000..b5c3d27e371 --- /dev/null +++ b/easybuild/easyconfigs/t/Trinotate/Trinotate-4.0.2-foss-2023a.eb @@ -0,0 +1,55 @@ +easyblock = 'Tarball' +name = 'Trinotate' +version = '4.0.2' + +homepage = 'https://github.com/Trinotate/Trinotate/wiki' +description = """Trinotate is a comprehensive annotation suite designed for automatic functional +annotation of transcriptomes, particularly de novo assembled transcriptomes, +from model or non-model organisms. Trinotate makes use of a number of different +well referenced methods for functional annotation including homology search to +known sequence data (BLAST+/SwissProt), protein domain identification +(HMMER/PFAM), protein signal peptide and transmembrane domain prediction +(signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg +databases). All functional annotation data derived from the analysis of +transcripts is integrated into a SQLite database which allows fast efficient +searching for terms with specific qualities related to a desired scientific +hypothesis or a means to create a whole annotation report for a transcriptome.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +github_account = '%(name)s' +source_urls = [GITHUB_SOURCE] +sources = ['%(name)s-v%(version)s.tar.gz'] +checksums = ['2f633df2e05e5d22e19159aa147060be7884a057314cad3e6db91dba8910fad1'] + +# # for reference, list of dependencies in the container image used upstream: +# # https://github.com/Trinotate/Trinotate/blob/master/Docker/Dockerfile +dependencies = [ + ('Perl', '5.36.1'), + ('Python', '3.11.3'), + ('Trinity', '2.15.2'), + ('BLAST+', '2.14.1'), + ('DIAMOND', '2.1.8'), + ('eggnog-mapper', '2.1.12'), + ('HMMER', '3.4'), + ('Infernal', '1.1.5'), + ('PyBioLib', '1.1.2250'), + ('SAMtools', '1.18'), + ('TransDecoder', '5.7.1'), +] + +sanity_check_paths = { + 'files': ['Trinotate', 'run_TrinotateWebserver.pl'], + 'dirs': ['PerlLib', 'resources', 'testing', 'util'], +} + +sanity_check_commands = [ + 'Trinotate --help 2>&1 | grep -q "Trinotate --db "', +] + +modextrapaths = { + 'PATH': '', + 'PERL5LIB': 'PerlLib', +} + +moduleclass = 'bio' From 7996631f92066680d5e77b27e085b7ba1c9c7d30 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 25 Oct 2024 20:33:02 +0200 Subject: [PATCH 038/116] lower the `CPPE` dependency version --- easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb index 72432ce1b97..d2efdfa6e27 100644 --- a/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb +++ b/easybuild/easyconfigs/p/PySCF/PySCF-2.7.0-foss-2023a.eb @@ -23,7 +23,7 @@ dependencies = [ ('libcint', '5.4.0'), ('libxc', '6.2.2'), ('XCFun', '2.1.1'), - ('CPPE', '0.3.3a0'), # extra + ('CPPE', '0.3.1'), # extra ('PyBerny', '0.6.3'), # extra ('PyCheMPS2', '1.8.12'), # needed by dmrgscf ('Block', '1.5.3-20200525'), # needed by dmrgscf From c3b3f1def78b489f45b60f55ad3f439c56285ca4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 31 Oct 2024 13:42:42 +0100 Subject: [PATCH 039/116] fix parameter redefinition --- easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb | 1 - 1 file changed, 1 deletion(-) diff --git a/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb index a9853cde523..77e022aa0cf 100644 --- a/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb +++ b/easybuild/easyconfigs/t/tblis/tblis-20230422-foss-2023a.eb @@ -10,7 +10,6 @@ description = """TBLIS is a library and framework for performing tensor toolchain = {'name': 'foss', 'version': '2023a'} -sources = [SOURCE_TAR_GZ] source_urls = ['https://github.com/devinamatthews/tblis/archive/'] sources = ['%s.tar.gz' % local_commit] checksums = ['85b72884022edd2612e3a0b3ed12aa6237d3989b581091d21f58124a7450aaeb'] From 2f6468662289f25498348091851ca3732f2ef54b Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 5 Nov 2024 16:08:35 +0000 Subject: [PATCH 040/116] adding easyconfigs: RAxML-NG-1.2.2-GCC-13.2.0.eb --- .../r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb | 44 +++++++++++++++++++ 1 file changed, 44 insertions(+) create mode 100644 easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb new file mode 100644 index 00000000000..e4a2c353676 --- /dev/null +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb @@ -0,0 +1,44 @@ +# EasyBuild easyconfig +# +# Contributed from Fred Hutchinson Cancer Research Center, Seattle WA, US +# John Dey jfdey@fredhutch.org +# +easyblock = 'CMakeMake' + +name = 'RAxML-NG' +version = '1.2.2' + +homepage = 'https://github.com/amkozlov/raxml-ng' +description = """RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) + optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree + Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +sources = [{ + 'filename': '%(version)s.tar.gz', + 'git_config': { + 'url': 'https://github.com/amkozlov', + 'repo_name': '%(namelower)s', + 'tag': '%(version)s', + 'recursive': True, + 'keep_git_dir': True, + } +}] +checksums = [None] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Bison', '3.8.2'), + ('flex', '2.6.4'), + ('GMP', '6.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/raxml-ng'], + 'dirs': [], +} + +sanity_check_commands = ["raxml-ng --help"] + +moduleclass = 'bio' From fd5dcd3eb38f36c56fb8d4b2fe3cf5476cedf841 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Wed, 6 Nov 2024 14:44:32 +0100 Subject: [PATCH 041/116] adding easyconfigs: BindCraft-1.1.0-foss-2023a.eb, PyRosetta-4.release-387-gompi-2023a.eb, dm-haiku-0.0.13-foss-2023a.eb --- .../b/BindCraft/BindCraft-1.1.0-foss-2023a.eb | 89 +++++++++++++++++++ .../d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb | 34 +++++++ .../PyRosetta-4.release-387-gompi-2023a.eb | 38 ++++++++ 3 files changed, 161 insertions(+) create mode 100644 easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb create mode 100644 easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb create mode 100644 easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb diff --git a/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb new file mode 100644 index 00000000000..49345e486d8 --- /dev/null +++ b/easybuild/easyconfigs/b/BindCraft/BindCraft-1.1.0-foss-2023a.eb @@ -0,0 +1,89 @@ +easyblock = 'Tarball' + +name = 'BindCraft' +version = '1.1.0' + +homepage = 'https://github.com/martinpacesa/BindCraft' +description = """Simple binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. + Select your target and let the script do the rest of the work and finish once you have enough designs to order!""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +source_urls = ['https://github.com/martinpacesa/BindCraft/archive/refs/tags/'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}] +checksums = ['c682f59501f0bcfbb8289fd066362dcea37ed8553cdff5c794a2baa6d4149ce7'] + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('Biopython', '1.83'), + ('Seaborn', '0.13.2'), + ('tqdm', '4.66.1'), + ('OpenMM', '8.0.0'), + ('FFmpeg', '6.0'), + ('matplotlib', '3.7.2'), + ('PyRosetta', '4.release-387'), + ('jax', '0.4.25'), + ('dm-haiku', '0.0.13'), + ('dm-tree', '0.1.8'), + ('ml-collections', '0.1.1'), + ('Optax', '0.2.2'), + ('py3Dmol', '2.1.0'), + ('JupyterLab', '4.0.5'), + ('hatchling', '1.18.0'), + ('Flax', '0.8.4'), +] + +exts_defaultclass = 'PythonPackage' +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} +exts_list = [ + ('PDBFixer', '1.9', { + 'source_urls': ['https://github.com/openmm/pdbfixer/archive/'], + 'sources': [{'download_filename': '%(version)s.tar.gz', 'filename': '%(name)s-%(version)s.tar.gz'}], + 'checksums': ['88b9a77e50655f89d0eb2075093773e82c27a4cef842cb7d735c877b20cd39fb'], + }), + ('jupyter_console', '6.6.3', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['309d33409fcc92ffdad25f0bcdf9a4a9daa61b6f341177570fdac03de5352485'], + }), + # older version compatible with `jupyterlab-4.0.5` + ('notebook', '7.0.8', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['7f421b3fd46a17d91830e724b94e8e9ae922af152ebfd48b1e13ae4a07d8193c'], + }), + ('jupyter', '1.1.1', { + 'source_tmpl': SOURCE_WHL, + 'checksums': ['7a59533c22af65439b24bbe60373a4e95af8f16ac65a6c00820ad378e3f7cc83'], + }), + ('immutabledict', '4.2.0', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['d728b2c2410d698d95e6200237feb50a695584d20289ad3379a439aa3d90baba'], + }), + ('colabdesign', '1.1.1', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['8f556fb575d2bbef79fa1789698d55221f2cc51df38f2cc054f38cb6ecc08e27'], + }), +] + +fix_python_shebang_for = ['bindcraft.py'] + +postinstallcmds = ['chmod a+x %(installdir)s/bindcraft.py'] + +modextrapaths = { + 'PATH': '', + 'PYTHONPATH': ['', 'lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_paths = { + 'files': ['bindcraft.py'], + 'dirs': [], +} + +sanity_check_commands = ["bindcraft.py --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb new file mode 100644 index 00000000000..532f9092e79 --- /dev/null +++ b/easybuild/easyconfigs/d/dm-haiku/dm-haiku-0.0.13-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonBundle' + +name = 'dm-haiku' +version = '0.0.13' + +homepage = 'https://github.com/deepmind/dm-haiku' +description = """Haiku is a simple neural network library for JAX developed by some of the authors of Sonnet, a neural +network library for TensorFlow.""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('jax', '0.4.25'), # required by jmp, also provides absl-py +] + +use_pip = True + +exts_list = [ + ('jmp', '0.0.4', { + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['6aa7adbddf2bd574b28c7faf6e81a735eb11f53386447896909c6968dc36807d'], + }), + ('dm_haiku', version, { + 'modulename': 'haiku', + 'source_tmpl': SOURCE_PY3_WHL, + 'checksums': ['ee9562c68a059f146ad07f555ca591cb8c11ef751afecc38353863562bd23f43'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb new file mode 100644 index 00000000000..c37102d5a81 --- /dev/null +++ b/easybuild/easyconfigs/p/PyRosetta/PyRosetta-4.release-387-gompi-2023a.eb @@ -0,0 +1,38 @@ +easyblock = 'PythonBundle' + +name = 'PyRosetta' +version = '4.release-387' + +homepage = 'https://www.pyrosetta.org/' +description = """ +PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling +suite. It enables users to design their own custom molecular modeling algorithms using Rosetta +sampling methods and energy functions. +""" + +toolchain = {'name': 'gompi', 'version': '2023a'} +toolchainopts = {'usempi': True} + +builddependencies = [('binutils', '2.40')] + +dependencies = [ + ('Python', '3.11.3'), +] + +use_pip = True + +local_source_tmpl = '%(name)s%(version_major)s.Release.python%(pymajver)s%(pyminver)s.linux.%(version_minor)s.tar.bz2' +local_source_urls = 'https://graylab.jhu.edu/download/PyRosetta4/archive/release/PyRosetta4.Release.python311.linux/' + +exts_list = [ + (name, version, { + 'source_tmpl': local_source_tmpl, + 'source_urls': [local_source_urls], + 'start_dir': 'setup', + 'checksums': ['42a10efd16cba7739d87a5c4035a2cd8792bc193804963fc26bb2f82f7ac2a1a'], + }), +] + +sanity_pip_check = True + +moduleclass = 'bio' From f837d974757a4bcf8813501477d2bdcc939b624f Mon Sep 17 00:00:00 2001 From: Ake Sandgren Date: Thu, 7 Nov 2024 13:12:07 +0100 Subject: [PATCH 042/116] adding easyconfigs: GROMACS-LS-2016.3-foss-2023a.eb, MDStress-20191228-gfbf-2023a.eb and patches: GROMACS-LS-2016.3_fix_typo.patch, MDStress-20191228_use_external_voro++_and_EB_lapack.patch --- .../GROMACS-LS-2016.3-foss-2023a.eb | 49 ++++++++++++ .../GROMACS-LS-2016.3_fix_typo.patch | 38 +++++++++ .../MDStress/MDStress-20191228-gfbf-2023a.eb | 41 ++++++++++ ...28_use_external_voro++_and_EB_lapack.patch | 80 +++++++++++++++++++ 4 files changed, 208 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch create mode 100644 easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb create mode 100644 easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch diff --git a/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb new file mode 100644 index 00000000000..e47a07b97f8 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3-foss-2023a.eb @@ -0,0 +1,49 @@ +easyblock = 'EB_GROMACS' + +name = 'GROMACS-LS' +version = '2016.3' + +homepage = 'https://vanegaslab.org/software' +description = """ +GROMACS-LS and the MDStress library enable the calculation of local +stress fields from molecular dynamics simulations. + +This is a double precision only CPU only build. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = ['https://vanegaslab.org/files'] +sources = ['gromacs-ls-2016.3-12282019.tar.gz'] +patches = [ + 'GROMACS-LS-2016.3_fix_typo.patch', +] +checksums = [ + {'gromacs-ls-2016.3-12282019.tar.gz': '20f4d4f255800432be188abe41b7fec923cacc5fc895914b3beac0808ddf1919'}, + {'GROMACS-LS-2016.3_fix_typo.patch': '4b9945476405a358bc64784984c51f08ab1aa3a598fb981b2dad8e0c61665fe0'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('MDStress', '20191228'), +] + +# GROMACS-LS can only be built with double precision +single_precision = False + +# GROMACS-LS can only handle hwloc version < 2 +configopts = '-DGMX_HWLOC=OFF' + +# The tests have not been rewritten to handle the mdstress changes +skipsteps = ['test'] + +sanity_check_paths = { + 'files': ['bin/gmx_LS', 'lib/libgromacs_LS.a'], + 'dirs': [], +} + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch new file mode 100644 index 00000000000..2529da617ed --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS-LS/GROMACS-LS-2016.3_fix_typo.patch @@ -0,0 +1,38 @@ +Fix a couple of smaller problems + +Åke Sandgren, 2024-11-07 +diff -ru gromacs-ls-2016.3.orig/cmake/gmxTestCXX11.cmake gromacs-ls-2016.3/cmake/gmxTestCXX11.cmake +--- gromacs-ls-2016.3.orig/cmake/gmxTestCXX11.cmake 2019-12-28 15:42:21.000000000 +0100 ++++ gromacs-ls-2016.3/cmake/gmxTestCXX11.cmake 2024-11-07 10:45:40.060210373 +0100 +@@ -49,7 +49,7 @@ + elseif(CYGWIN) + set(CXX11_CXX_FLAG "-std=gnu++0x") #required for strdup + else() +- set(CXX11_CXX_FLAG "-std=c++0x") ++ set(CXX11_CXX_FLAG "-std=c++11") + endif() + CHECK_CXX_COMPILER_FLAG("${CXX11_CXX_FLAG}" CXXFLAG_STD_CXX0X) + if(NOT CXXFLAG_STD_CXX0X) +diff -ru gromacs-ls-2016.3.orig/src/gromacs/mdlib/minimize.cpp gromacs-ls-2016.3/src/gromacs/mdlib/minimize.cpp +--- gromacs-ls-2016.3.orig/src/gromacs/mdlib/minimize.cpp 2019-12-28 15:42:28.000000000 +0100 ++++ gromacs-ls-2016.3/src/gromacs/mdlib/minimize.cpp 2024-11-07 10:55:06.668206192 +0100 +@@ -54,6 +54,7 @@ + + #include + #include ++#include + + #include "gromacs/commandline/filenm.h" + #include "gromacs/domdec/domdec.h" +diff -ru gromacs-ls-2016.3.orig/src/programs/mdrun/runner.cpp gromacs-ls-2016.3/src/programs/mdrun/runner.cpp +--- gromacs-ls-2016.3.orig/src/programs/mdrun/runner.cpp 2019-12-28 15:42:30.000000000 +0100 ++++ gromacs-ls-2016.3/src/programs/mdrun/runner.cpp 2024-11-07 10:33:22.588969615 +0100 +@@ -175,7 +175,7 @@ + int localsspatialatom; + int localsdispcor; + int localspbc; +- real localsmindihang; ++ real localsmindihangle; + unsigned long Flags; + }; + diff --git a/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb b/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb new file mode 100644 index 00000000000..7be20fe7e5b --- /dev/null +++ b/easybuild/easyconfigs/m/MDStress/MDStress-20191228-gfbf-2023a.eb @@ -0,0 +1,41 @@ +easyblock = 'CMakeMake' + +name = 'MDStress' +version = '20191228' + +homepage = 'https://vanegaslab.org/software' +description = """MDStress library enable the calculation of local stress +fields from molecular dynamics simulations""" + +toolchain = {'name': 'gfbf', 'version': '2023a'} + +source_urls = ['https://vanegaslab.org/files'] +sources = ['mdstress-library-12282019.tar.gz'] +patches = [ + 'MDStress-20191228_use_external_voro++_and_EB_lapack.patch', +] +checksums = [ + {'mdstress-library-12282019.tar.gz': 'abea62dca77ca4645463415bec219a42554146cc0eefd480c760222e423c7db3'}, + {'MDStress-20191228_use_external_voro++_and_EB_lapack.patch': + '566c181f9a6784c81b04226d360ed71d96f99310a231a88919e7fac37e515e92'}, +] + +builddependencies = [ + ('CMake', '3.26.3'), +] + +dependencies = [ + ('Voro++', '0.4.6'), + ('Python', '3.11.3'), +] + +sanity_check_paths = { + 'files': ['bin/tensortools', 'include/mdstress/mds_basicops.h', 'lib/libmdstress.%s' % SHLIB_EXT], + 'dirs': [], +} + +modextrapaths = { + 'PYTHONPATH': 'bin', +} + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch b/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch new file mode 100644 index 00000000000..fd2458812bc --- /dev/null +++ b/easybuild/easyconfigs/m/MDStress/MDStress-20191228_use_external_voro++_and_EB_lapack.patch @@ -0,0 +1,80 @@ +use external EB Voro++ and flexi/openblas as needed + +Åke Sandgren, 2024-11-07 +diff -ru mdstress-library.orig/CMakeLists.txt mdstress-library/CMakeLists.txt +--- mdstress-library.orig/CMakeLists.txt 2019-12-28 15:48:10.000000000 +0100 ++++ mdstress-library/CMakeLists.txt 2024-11-07 11:19:48.125912695 +0100 +@@ -1,4 +1,5 @@ +-cmake_minimum_required(VERSION 2.8) ++cmake_minimum_required(VERSION 3.0) ++project('MDStress') + + enable_language(C) + enable_language(CXX) +@@ -27,42 +28,28 @@ + # COMMAND tar xaf voro++-0.4.6.tar.gz + # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/contrib) + #endif() +-FILE(GLOB VORO_SOURCES_HH include/voro++/*.hh) +-FILE(GLOB VORO_SOURCES_CC contrib/voro++/src/*.cc) +-#FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) +-#FILE(COPY ${VORO_SOURCES_HH} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) +-LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/voro++.cc) +-LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/v_base_wl.cc) ++#FILE(GLOB VORO_SOURCES_HH include/voro++/*.hh) ++#FILE(GLOB VORO_SOURCES_CC contrib/voro++/src/*.cc) ++##FILE(MAKE_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) ++##FILE(COPY ${VORO_SOURCES_HH} DESTINATION ${CMAKE_CURRENT_SOURCE_DIR}/include/voro++) ++#LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/voro++.cc) ++#LIST(REMOVE_ITEM VORO_SOURCES_CC ${CMAKE_CURRENT_SOURCE_DIR}/contrib/voro++/src/v_base_wl.cc) + +-SET(MDSTRESS_SOURCES ${MDSTRESS_SOURCES_CPP} ${MDSTRESS_SOURCES_H} ${VORO_SOURCES_CC} ${VORO_SOURCES_HH}) ++SET(MDSTRESS_SOURCES ${MDSTRESS_SOURCES_CPP} ${MDSTRESS_SOURCES_H}) + + INCLUDE_DIRECTORIES(include/mdstress) +-INCLUDE_DIRECTORIES(include/voro++) ++#INCLUDE_DIRECTORIES(include/voro++) + + # attempt to find LAPACK library +-FIND_LIBRARY(LAPACK_LIBRARY_SYS NAMES lapack liblapack HINTS /usr/lib REQUIRED) +-if (NOT LAPACK_LIBRARY_SYS) +- UNSET(LAPACK_LIBRARY_SYS-NOTFOUND) +- UNSET(LAPACK_LIBRARY_SYS) +- # check to see if we need to download LAPACK +- SET(LAPACK_URL http://www.netlib.org/lapack/lapack-3.8.0.tar.gz) +- SET(LAPACK_DOWNLOAD_PATH ${CMAKE_CURRENT_SOURCE_DIR}/contrib/lapack-3.8.0.tar.gz) +- FILE(DOWNLOAD ${LAPACK_URL} ${LAPACK_DOWNLOAD_PATH}) +- EXECUTE_PROCESS( +- COMMAND tar xaf lapack-3.8.0.tar.gz +- WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/contrib) +- ADD_SUBDIRECTORY(contrib/lapack-3.8.0) +-else() +- FIND_LIBRARY(LAPACK_LIBRARY NAMES lapack liblapack HINTS /usr/lib REQUIRED) +-endif() ++FIND_LIBRARY(LAPACK_LIBRARY NAMES flexiblas openblas lapack liblapack REQUIRED) + + ADD_LIBRARY(mdstress SHARED ${MDSTRESS_SOURCES}) +-TARGET_LINK_LIBRARIES(mdstress ${LAPACK_LIBRARY} ${PYTHON_LIBRARIES}) ++TARGET_LINK_LIBRARIES(mdstress ${LAPACK_LIBRARY} ${PYTHON_LIBRARIES} voro++) + +-INSTALL(TARGETS mdstress RUNTIME DESTINATION bin LIBRARY DESTINATION lib ARCHIVE DESTINATION lib/static) ++INSTALL(TARGETS mdstress RUNTIME DESTINATION bin LIBRARY DESTINATION lib ARCHIVE DESTINATION lib) + + INSTALL(FILES ${MDSTRESS_SOURCES_H} DESTINATION include/mdstress) +-INSTALL(FILES ${VORO_SOURCES_HH} DESTINATION include/voro++) ++#INSTALL(FILES ${VORO_SOURCES_HH} DESTINATION include/voro++) + + # only process python bindings if requested + if(MDS_BOOSTPYTHON) +diff -ru mdstress-library.orig/src/mds_stressgrid.cpp mdstress-library/src/mds_stressgrid.cpp +--- mdstress-library.orig/src/mds_stressgrid.cpp 2019-12-28 15:48:10.000000000 +0100 ++++ mdstress-library/src/mds_stressgrid.cpp 2024-11-07 09:08:35.761694010 +0100 +@@ -21,7 +21,7 @@ + =========================================================================*/ + + #include "mds_stressgrid.h" +-#include "voro++.hh" ++#include "voro++/voro++.hh" + + using namespace mds; + From 36404a365b6ce03113407ede23549a3031634682 Mon Sep 17 00:00:00 2001 From: Loris Bennett Date: Thu, 7 Nov 2024 17:43:11 +0100 Subject: [PATCH 043/116] adding easyconfigs: ORCA-6.0.1-gompi-2023b-avx2.eb --- .../o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb | 23 +++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb new file mode 100644 index 00000000000..854f0424abb --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb @@ -0,0 +1,23 @@ +name = 'ORCA' +version = '6.0.1' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] + +# orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz +checksums = ['f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2'] + +moduleclass = 'chem' From 648993b683788bad98c6532c49138ad8bf9a206c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Fri, 8 Nov 2024 14:00:59 +0100 Subject: [PATCH 044/116] bugfix of `HTSplotter-2.11` --- .../h/HTSplotter/HTSplotter-2.11-foss-2023a.eb | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb index 5a631178a6b..75808cd8e7a 100644 --- a/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb +++ b/easybuild/easyconfigs/h/HTSplotter/HTSplotter-2.11-foss-2023a.eb @@ -50,8 +50,12 @@ exts_list = [ }), (name, version, { 'modulename': 'HTSplotter', - 'source_tmpl': SOURCE_PY3_WHL, - 'checksums': ['6067735d14f15ca2fd35963701a96e39edaf0899742bfa7ccc8f9867a0279346'], + # Fixes the following error. + # `TypeError: rv_generic_interval() missing 1 required positional argument: 'confidence'` + # see https://github.com/KatherLab/marugoto/issues/14 + # see also scipy release notes https://docs.scipy.org/doc/scipy/release/1.9.0-notes.html#deprecated-features + 'preinstallopts': "sed -i 's/alpha/confidence/g' HTSplotter/save_hdf5brfiles.py && ", + 'checksums': ['51c0cee4e8eeecfd03f32dd707e0fa433cec91abb9334ec1d28e7f82615dbe29'], }), ] From 36cdeed114491b10eec90c8e6f40cc1bb02bb0d1 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Fri, 8 Nov 2024 16:13:57 +0100 Subject: [PATCH 045/116] withelist JuliaPackage from test_pr_sanity_check_paths --- test/easyconfigs/easyconfigs.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/test/easyconfigs/easyconfigs.py b/test/easyconfigs/easyconfigs.py index 74f98af5cf8..c44a70cce8b 100644 --- a/test/easyconfigs/easyconfigs.py +++ b/test/easyconfigs/easyconfigs.py @@ -1210,12 +1210,12 @@ 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 CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle, PerlBundle, + # including CargoPythonPackage, CMakePythonPackage, GoPackage, JuliaBundle & JuliaPackage, PerlBundle, # PythonBundle & PythonPackage; # BuildEnv, ModuleRC and Toolchain easyblocks doesn't install anything so there is nothing to check. whitelist = ['BuildEnv', 'CargoPythonBundle', 'CargoPythonPackage', 'CMakePythonPackage', - 'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'ModuleRC', - 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] + 'ConfigureMakePythonPackage', 'CrayToolchain', 'GoPackage', 'JuliaBundle', 'JuliaPackage', + 'ModuleRC', 'PerlBundle', 'PythonBundle', 'PythonPackage', 'Toolchain'] # Bundles of dependencies without files of their own # Autotools: Autoconf + Automake + libtool, (recent) GCC: GCCcore + binutils, CUDA: GCC + CUDAcore, # CESM-deps: Python + Perl + netCDF + ESMF + git, FEniCS: DOLFIN and co, From d6a2e48763ba3577cc0e89112a429094bd28e8fa Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Sat, 9 Nov 2024 12:08:21 +0100 Subject: [PATCH 046/116] test examples from installed version of LightGBM --- .../l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb | 2 +- easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb index 79b61c8d87b..638330e8866 100644 --- a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb @@ -28,7 +28,7 @@ dependencies = [ use_pip = True # example files are not distributed with the sources -_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/tags/v%(version)s/examples" _test_cmds_pre = " && ".join([ "mkdir regression", "wget -P regression %s/regression/regression.test" % _test_repo_url, diff --git a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb index fdbf6f54f1d..b6a03faf9ca 100644 --- a/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb +++ b/easybuild/easyconfigs/l/LightGBM/LightGBM-4.5.0-foss-2023a.eb @@ -26,7 +26,7 @@ dependencies = [ use_pip = True # example files are not distributed with the sources -_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/heads/master/examples" +_test_repo_url = "https://raw.githubusercontent.com/microsoft/LightGBM/refs/tags/v%(version)s/examples" _test_cmds_pre = " && ".join([ "mkdir regression", "wget -P regression %s/regression/regression.test" % _test_repo_url, From 27965a2d8e3824c3f14c9282ec2e6320d44a5901 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 11 Nov 2024 10:46:04 +0100 Subject: [PATCH 047/116] add Sniffles and necessary deps --- .../p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb | 33 +++++++++++++++++ .../s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb | 37 +++++++++++++++++++ 2 files changed, 70 insertions(+) create mode 100644 easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb create mode 100644 easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb new file mode 100644 index 00000000000..2920aeda78e --- /dev/null +++ b/easybuild/easyconfigs/p/Pysam/Pysam-0.22.1-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonPackage' + +name = 'Pysam' +version = '0.22.1' + +homepage = 'https://github.com/pysam-developers/pysam' +description = """Pysam is a python module for reading and manipulating Samfiles. + It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +source_urls = ['https://github.com/pysam-developers/pysam/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e4981524d7627c53fa0d3f8cbec2bd65c2ea7520092f25e1029af12cb7b82ff6'] + +builddependencies = [ + ('Cython', '3.0.10') +] + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + ('ncurses', '6.5'), + ('cURL', '8.7.1'), + ('XZ', '5.4.5'), +] + +download_dep_fail = True +use_pip = True + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb new file mode 100644 index 00000000000..394a3863539 --- /dev/null +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb @@ -0,0 +1,37 @@ +easyblock = 'PythonBundle' + +name = 'Sniffles' +version = '2.0.7' + +homepage = 'https://github.com/fritzsedlazeck/Sniffles' +description = """A fast structural variant caller for long-read sequencing, + Sniffles2 accurately detect SVs on germline, somatic and population-level for PacBio and Oxford Nanopore read data.""" + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +dependencies = [ + ('Python', '3.12.3'), + ('Pysam', '0.22.1'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'sources': [SOURCELOWER_TAR_GZ], + 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], + }), +] + +sanity_check_paths = { + 'files': ['bin/sniffles'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "python -c 'from sniffles import sv'", + "sniffles --help", +] + +moduleclass = 'bio' From f62e1d18451322f19af0668c906074867b83d1f5 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann Date: Mon, 11 Nov 2024 11:16:45 +0100 Subject: [PATCH 048/116] correct version and add new dep --- .../e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb | 33 +++++++++++++++++++ .../s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb | 5 +-- 2 files changed, 36 insertions(+), 2 deletions(-) create mode 100644 easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb new file mode 100644 index 00000000000..1630a181fbc --- /dev/null +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb @@ -0,0 +1,33 @@ +easyblock = 'PythonBundle' + +name = 'edlib' +version = '1.3.9.post1' + +homepage = 'https://martinsos.github.io/edlib' +description = "Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance." + +toolchain = {'name': 'GCC', 'version': '13.3.0'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + ('cogapp', '3.4.1', { + 'checksums': ['a806d5db9e318a1a2d3fce988008179168e7db13e5e55b19b79763f9bb9d2982'], + }), + (name, version, { + # 'source_urls': ['https://github.com/Martinsos/edlib/archive/'], + # 'source_tmpl': '%(version)s.tar.gz', + # fixes `edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory` + # see https://github.com/Martinsos/edlib/issues/217#issuecomment-1736234091 + # 'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ', + 'checksums': ['b0fb6e85882cab02208ccd6daa46f80cb9ff1d05764e91bf22920a01d7a6fbfa'], + }), +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb index 394a3863539..ad8e962950a 100644 --- a/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/s/Sniffles/Sniffles-2.4-GCC-13.3.0.eb @@ -1,7 +1,7 @@ easyblock = 'PythonBundle' name = 'Sniffles' -version = '2.0.7' +version = '2.4' homepage = 'https://github.com/fritzsedlazeck/Sniffles' description = """A fast structural variant caller for long-read sequencing, @@ -12,6 +12,7 @@ toolchain = {'name': 'GCC', 'version': '13.3.0'} dependencies = [ ('Python', '3.12.3'), ('Pysam', '0.22.1'), + ('edlib', '1.3.9.post1'), ] use_pip = True @@ -20,7 +21,7 @@ sanity_pip_check = True exts_list = [ (name, version, { 'sources': [SOURCELOWER_TAR_GZ], - 'checksums': ['bf532eb0b3aaeaee840100a3bb3339f1d5175ba98adfe3cf19685b0abb0885a1'], + 'checksums': ['e3c2f552105cd5f5941d6291b9ee9dbfe634ad19b5e7a64fa26b9e2daa6547d4'], }), ] From e7757ee7ccce2af45a30680c1f86f237dd2ff877 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 10:58:08 +0000 Subject: [PATCH 049/116] adding easyconfigs: Greenlet-3.1.1-GCCcore-13.3.0.eb --- .../Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..b54b7ecfcc3 --- /dev/null +++ b/easybuild/easyconfigs/g/Greenlet/Greenlet-3.1.1-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonPackage' + +name = 'Greenlet' +version = '3.1.1' + +homepage = 'https://github.com/python-greenlet/greenlet' + +description = """The greenlet package is a spin-off of Stackless, a version of CPython that +supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single +or a few OS-level threads) and are synchronized with data exchanges on "channels". +A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit +scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. +""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] +dependencies = [('Python', '3.12.3')] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +source_urls = [PYPI_LOWER_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4ce3ac6cdb6adf7946475d7ef31777c26d94bccc377e070a7986bd2d5c515467'] + +moduleclass = 'devel' From 43cd0efbd7737b0d363ab9a1405a79a7301f73ad Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 10:58:49 +0000 Subject: [PATCH 050/116] adding easyconfigs: SQLAlchemy-2.0.36-GCCcore-13.3.0.eb --- .../SQLAlchemy-2.0.36-GCCcore-13.3.0.eb | 45 +++++++++++++++++++ 1 file changed, 45 insertions(+) create mode 100644 easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..293b3bf2452 --- /dev/null +++ b/easybuild/easyconfigs/s/SQLAlchemy/SQLAlchemy-2.0.36-GCCcore-13.3.0.eb @@ -0,0 +1,45 @@ +easyblock = 'PythonBundle' + +name = 'SQLAlchemy' +version = '2.0.36' + +homepage = 'https://www.sqlalchemy.org/' +description = """SQLAlchemy is the Python SQL toolkit and Object Relational Mapper that gives +application developers the full power and flexibility of SQL. SQLAlchemy +provides a full suite of well known enterprise-level persistence patterns, +designed for efficient and high-performing database access, adapted into a +simple and Pythonic domain language.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [ + ('Python', '3.12.3'), + ('Greenlet', '3.1.1'), + ('psycopg', '3.2.3'), # optional, postgresql extra + ('Mako', '1.3.5'), # needed by alembic +] + +use_pip = True + +exts_list = [ + ('async-timeout', '5.0.1', { + 'sources': ['async_timeout-%(version)s.tar.gz'], + 'checksums': ['d9321a7a3d5a6a5e187e824d2fa0793ce379a202935782d555d6e9d2735677d3'], + }), + ('asyncpg', '0.30.0', { + 'checksums': ['c551e9928ab6707602f44811817f82ba3c446e018bfe1d3abecc8ba5f3eac851'], + }), + ('sqlalchemy', version, { + 'use_pip_extras': 'asyncio,postgresql,postgresql_asyncpg', + 'checksums': ['7f2767680b6d2398aea7082e45a774b2b0767b5c8d8ffb9c8b683088ea9b29c5'], + }), + ('alembic', '1.14.0', { + 'checksums': ['b00892b53b3642d0b8dbedba234dbf1924b69be83a9a769d5a624b01094e304b'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 1c3a748bdd64175839fcc5ac0acf4d63aba76b7d Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 10:59:37 +0000 Subject: [PATCH 051/116] adding easyconfigs: psycopg-3.2.3-GCCcore-13.3.0.eb --- .../p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..28b9128ff66 --- /dev/null +++ b/easybuild/easyconfigs/p/psycopg/psycopg-3.2.3-GCCcore-13.3.0.eb @@ -0,0 +1,24 @@ +easyblock = 'PythonPackage' + +name = 'psycopg' +version = '3.2.3' + +homepage = 'https://psycopg.org/' +description = "Psycopg is the most popular PostgreSQL adapter for the Python programming language." + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +sources = [SOURCE_TAR_GZ] +checksums = ['a5764f67c27bec8bfac85764d23c534af2c27b893550377e37ce59c12aac47a2'] + +builddependencies = [('binutils', '2.42')] +dependencies = [ + ('Python', '3.12.3'), + ('PostgreSQL', '16.4'), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'lib' From deaa03540ae965a2ca865186507898fba16b71db Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 11:02:05 +0000 Subject: [PATCH 052/116] adding easyconfigs: scikit-learn-1.5.2-gfbf-2024a.eb --- .../scikit-learn-1.5.2-gfbf-2024a.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb new file mode 100644 index 00000000000..aba5adaf848 --- /dev/null +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonBundle' + +name = 'scikit-learn' +version = '1.5.2' + +homepage = 'https://scikit-learn.org/stable/index.html' +description = """Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, +building upon numpy, scipy, and matplotlib. As a machine-learning module, +it provides versatile tools for data mining and analysis in any field of science and engineering. +It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.""" + +toolchain = {'name': 'gfbf', 'version': '2024a'} + +dependencies = [ + ('Python', '3.12.3'), + ('Python-bundle-PyPI', '2024.06'), + # Build requires "Cython>=3.0.8" + # Cython included with Python-bundle-PyPI (0.29.35) is too old + ('SciPy-bundle', '2024.05'), +] + +use_pip = True +sanity_pip_check = True + +exts_list = [ + (name, version, { + 'modulename': 'sklearn', + 'sources': ['scikit_learn-%(version)s.tar.gz'], + 'checksums': ['b4237ed7b3fdd0a4882792e68ef2545d5baa50aca3bb45aa7df468138ad8f94d'], + }), + ('sklearn', '0.0', { + 'checksums': ['e23001573aa194b834122d2b9562459bf5ae494a2d59ca6b8aa22c85a44c0e31'], + }), +] + +moduleclass = 'data' From 18cf679f8a480937c6beeb5a7a94340b9ad91da7 Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 11:08:49 +0000 Subject: [PATCH 053/116] added cython builddep --- .../s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb index aba5adaf848..9c2ba9c310f 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb @@ -11,11 +11,13 @@ It strives to be simple and efficient, accessible to everybody, and reusable in toolchain = {'name': 'gfbf', 'version': '2024a'} +builddependencies = [ + ('Cython', '3.0.10'), +] + dependencies = [ ('Python', '3.12.3'), ('Python-bundle-PyPI', '2024.06'), - # Build requires "Cython>=3.0.8" - # Cython included with Python-bundle-PyPI (0.29.35) is too old ('SciPy-bundle', '2024.05'), ] From 82b2bc31ed777ad75b669183e8f513d13955acdb Mon Sep 17 00:00:00 2001 From: Leonard Nielsen Date: Mon, 11 Nov 2024 11:19:41 +0000 Subject: [PATCH 054/116] added mesonpy --- .../easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb index 9c2ba9c310f..be9c3fd844c 100644 --- a/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb +++ b/easybuild/easyconfigs/s/scikit-learn/scikit-learn-1.5.2-gfbf-2024a.eb @@ -13,6 +13,7 @@ toolchain = {'name': 'gfbf', 'version': '2024a'} builddependencies = [ ('Cython', '3.0.10'), + ('meson-python', '0.16.0'), ] dependencies = [ From 1df0fa8e74def46713e4ff0857d8565876bd5132 Mon Sep 17 00:00:00 2001 From: software Date: Mon, 11 Nov 2024 11:54:46 +0000 Subject: [PATCH 055/116] adding easyconfigs: rapidNJ-2.3.3-GCCcore-12.3.0.eb --- .../r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb | 41 +++++++++++++++++++ 1 file changed, 41 insertions(+) create mode 100644 easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb diff --git a/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..5a6e44436d9 --- /dev/null +++ b/easybuild/easyconfigs/r/rapidNJ/rapidNJ-2.3.3-GCCcore-12.3.0.eb @@ -0,0 +1,41 @@ +# This seems to be actively maintained version of the code by the looks of it. +# See issue #5 +# https://github.com/somme89/rapidNJ/issues/5 +# why -march=native will not be used +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'MakeCp' + +name = 'rapidNJ' +version = '2.3.3' + +homepage = 'https://github.com/somme89/rapidNJ' +description = """RapidNJ is an algorithmic engineered implementation of canonical +neighbour-joining. It uses an efficient search heuristic to speed-up the core +computations of the neighbour-joining method that enables RapidNJ to +outperform other state-of-the-art neighbour-joining implementations.""" + +citing = """Rapid Neighbour Joining. Martin Simonsen, Thomas Mailund and Christian N. S. Pedersen. +In: Proceedings of the 8th Workshop in Algorithms in Bioinformatics (WABI), LNBI 5251, 113-122, +Springer Verlag, October 2008. +doi: 10.1007/978-3-540-87361-7_10""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/somme89/rapidNJ/archive/'] +sources = [{'filename': 'v%(version)s.tar.gz', 'download_filename': 'latest.tar.gz'}] +checksums = ['662f864cc3e5bc68aea23129f02e0062cac9ebd37e414b54c5c5e616ff4f245d'] + +builddependencies = [('binutils', '2.40')] + +files_to_copy = [(['bin/rapidnj'], 'bin')] + +# That is returning 1 instead of 0, so disabled for now +# sanity_check_commands = ['rapidnj --help'] + +sanity_check_paths = { + 'files': ['bin/rapidnj'], + 'dirs': [], +} + +moduleclass = 'bio' From 1f53f29e706015d48cb7051ce1e48ea01c23ed4b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Tue, 12 Nov 2024 14:47:51 +0100 Subject: [PATCH 056/116] bump to 2024.4 --- .../g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb index ebc1ba1601a..d93065bbed6 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb @@ -15,7 +15,7 @@ # License:: MIT/GPL name = 'GROMACS' -version = '2024.3' +version = '2024.4' versionsuffix = '-CUDA-%(cudaver)s' homepage = 'https://www.gromacs.org' @@ -42,7 +42,7 @@ patches = [ 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', ] checksums = [ - {'gromacs-2024.3.tar.gz': 'bbda056ee59390be7d58d84c13a9ec0d4e3635617adf2eb747034922cba1f029'}, + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': From 223f2c1b9e7599599bfb406d4510ea237098b057 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Tue, 12 Nov 2024 19:09:01 +0100 Subject: [PATCH 057/116] adding easyconfigs: VTune-2025.0.0.eb --- .../easyconfigs/v/VTune/VTune-2025.0.0.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb diff --git a/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb b/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb new file mode 100644 index 00000000000..1be37c7d69e --- /dev/null +++ b/easybuild/easyconfigs/v/VTune/VTune-2025.0.0.eb @@ -0,0 +1,24 @@ +name = 'VTune' +version = '2025.0.0' + +homepage = 'https://software.intel.com/en-us/vtune' +description = """Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, + Assembly and Java.""" + +toolchain = SYSTEM + +# By downloading, you accept the Intel End User License Agreement +# (https://software.intel.com/content/www/us/en/develop/articles/end-user-license-agreement.html) +# accept_eula = True +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/e7797b12-ce87-4df0-aa09-df4a272fc5d9/'] +sources = ['intel-vtune-%(version)s.1130_offline.sh'] +checksums = ['6742e5c6b1cd6e4efb794bde5d995ba738be1a991ac84678e0efca04fc080074'] + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/amplxe-perf'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'tools' From dcd7be3f781dda9ac582124e4a9f444f0724f0a0 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Nov 2024 22:13:01 +0100 Subject: [PATCH 058/116] adding easyconfigs: rclone-1.68.1.eb --- .../easyconfigs/r/rclone/rclone-1.68.1.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb diff --git a/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb b/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb new file mode 100644 index 00000000000..12c72ff4ab8 --- /dev/null +++ b/easybuild/easyconfigs/r/rclone/rclone-1.68.1.eb @@ -0,0 +1,34 @@ +easyblock = 'GoPackage' + +name = 'rclone' +version = '1.68.1' + +homepage = 'https://rclone.org' + +description = """ + Rclone is a command line program to sync files and directories to and from + a variety of online storage services +""" + +toolchain = SYSTEM + +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['26259526855a12499d00e3a3135ee95e7aeb3ecf2f85886d8c837a2e7b236226'] + +builddependencies = [('Go', '1.22.1', '', SYSTEM)] + +postinstallcmds = [ + "mkdir -p %(installdir)s/share/{doc,man/man1}", + "cp README.* MANUAL.* %(installdir)s/share/doc/", + "cp rclone.1 %(installdir)s/share/man/man1/", +] + +sanity_check_paths = { + 'files': ['bin/rclone', 'share/doc/README.md', 'share/man/man1/rclone.1'], + 'dirs': [] +} + +sanity_check_commands = ['rclone --version'] + +moduleclass = 'tools' From 0d1c1ff4772169260adca47a4e9e0c6752f556ce Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Nov 2024 22:30:44 +0100 Subject: [PATCH 059/116] adding easyconfigs: ORCA-6.0.1-gompi-2023a-avx2.eb --- .../o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb new file mode 100644 index 00000000000..bc34fff4fe8 --- /dev/null +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023a-avx2.eb @@ -0,0 +1,24 @@ +name = 'ORCA' +version = '6.0.1' +versionsuffix = '-avx2' + +homepage = 'https://orcaforum.kofo.mpg.de' +description = """ +ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum +chemistry with specific emphasis on spectroscopic properties of open-shell +molecules. It features a wide variety of standard quantum chemical methods +ranging from semiempirical methods to DFT to single- and multireference +correlated ab initio methods. It can also treat environmental and relativistic +effects.""" + +toolchain = {'name': 'gompi', 'version': '2023a'} + +download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" +# mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) +sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] +checksums = [ + # orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz + 'f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2', +] + +moduleclass = 'chem' From 5d01bc54db00977ba3019b8e217ba5908042b30e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 12 Nov 2024 22:42:09 +0100 Subject: [PATCH 060/116] revert format change of checksums in ORCA-6.0.1-gompi-2023b-avx2.eb --- .../easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb index 854f0424abb..6194413a4f1 100644 --- a/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb +++ b/easybuild/easyconfigs/o/ORCA/ORCA-6.0.1-gompi-2023b-avx2.eb @@ -16,8 +16,9 @@ toolchain = {'name': 'gompi', 'version': '2023b'} download_instructions = "Shared build of ORCA: download from https://orcaforum.kofo.mpg.de" # mostly dynamically linked (SCALAPACK, OpenBLAS are still embedded) sources = ['%%(namelower)s_%s_linux_%%(orcaarch)s_shared_openmpi416_avx2.tar.xz' % version.replace('.', '_')] - -# orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz -checksums = ['f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2'] +checksums = [ + # orca_6_0_1_linux_x86-64_shared_openmpi416_avx2.tar.xz + 'f31f98256a0c6727b6ddfe50aa3ac64c45549981138d670a57e90114b4b9c9d2', +] moduleclass = 'chem' From d4a8224ef3654a709f0ce9cd0541797d6e1d992f Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 10:44:24 +0100 Subject: [PATCH 061/116] fix name for easyconfig file for GROMACS 2024.4 --- ...3b-CUDA-12.4.0.eb => GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/g/GROMACS/{GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb => GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb} (100%) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb similarity index 100% rename from easybuild/easyconfigs/g/GROMACS/GROMACS-2024.3-foss-2023b-CUDA-12.4.0.eb rename to easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0.eb From 754b3141f1ed8be2fd8397aecbe832b644e6b6eb Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 10:58:11 +0100 Subject: [PATCH 062/116] add missing hatchling build dependency for scArches 0.6.1 w/ foss/2023a --- .../s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb | 4 ++++ easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb | 4 ++++ 2 files changed, 8 insertions(+) diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb index cb33b614f6f..bcabab4cc73 100644 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a-CUDA-12.1.1.eb @@ -10,6 +10,10 @@ description = """Single-cell architecture surgery (scArches) is a package for re toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), diff --git a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb index bdcb1ab880c..e6b6f8d4e59 100644 --- a/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb +++ b/easybuild/easyconfigs/s/scArches/scArches-0.6.1-foss-2023a.eb @@ -9,6 +9,10 @@ description = """Single-cell architecture surgery (scArches) is a package for re toolchain = {'name': 'foss', 'version': '2023a'} +builddependencies = [ + ('hatchling', '1.18.0'), +] + dependencies = [ ('Python', '3.11.3'), ('SciPy-bundle', '2023.07'), From 345ea907f238d887390bcd0268d0a8be5a5e52bf Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 11:58:11 +0100 Subject: [PATCH 063/116] adding easyconfigs: GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb --- ...4.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb new file mode 100644 index 00000000000..7a3c8faccba --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb @@ -0,0 +1,97 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' +local_plumedver = '2.9.2' +versionsuffix = '-CUDA-%%(cudaver)s-PLUMED-%s' % local_plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a GPU enabled build, containing both MPI and threadMPI binaries. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + 'GROMACS-2023.3_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('CUDA', '12.4.0', '', SYSTEM), + ('UCX-CUDA', '1.15.0', '-CUDA-%(cudaver)s'), + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), + ('PLUMED', local_plumedver), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too +ignore_plumed_version_check = True + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From c8fdb0fb74ed55979ecce8a2143eb2f0fa7f0885 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Wed, 13 Nov 2024 14:43:48 +0100 Subject: [PATCH 064/116] [gomkl/2023b] DFT-D4 multicharge wannier90 libxc-nofhc --- .../d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb | 41 ++++++++++++++ easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb | 19 +++++++ .../l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb | 53 +++++++++++++++++++ .../multicharge-0.3.0-gomkl-2023b.eb | 39 ++++++++++++++ .../Wannier90/Wannier90-3.1.0-gomkl-2023b.eb | 35 ++++++++++++ 5 files changed, 187 insertions(+) create mode 100644 easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb create mode 100644 easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb create mode 100644 easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb create mode 100644 easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb new file mode 100644 index 00000000000..a59c07c17dc --- /dev/null +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb @@ -0,0 +1,41 @@ +easyblock = 'MesonNinja' + +name = 'DFT-D4' +version = '3.7.0' + +homepage = 'https://www.chemie.uni-bonn.de/pctc/mulliken-center/software/dftd4' +description = """Generally Applicable Atomic-Charge Dependent London Dispersion Correction.""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} + +source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] +sources = ['v%(version)s.tar.gz'] +patches = ['DFT-D4-3.2.0-remove_module_id.patch'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('Meson', '1.2.3'), + ('pkgconf', '2.0.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('cffi', '1.15.1'), + ('mstore', '0.3.0'), + ('mctc-lib', '0.3.1'), + ('multicharge', '0.3.0'), +] + +configopts = '-Dpython=true -Dapi_v2=true ' +# if not intel compiler used, lapack mkl is not found. +configopts += '-Dlapack=mkl ' + +sanity_check_paths = { + 'files': ['bin/dftd4', 'lib/libdftd4.a', 'lib/libdftd4.%s' % SHLIB_EXT, 'include/dftd4.mod'], + 'dirs': [], +} + +sanity_check_commands = ["dftd4 --version"] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb new file mode 100644 index 00000000000..d5b856a6fe9 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2023b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '13.2.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.1.6', '', local_comp), + ('imkl', '2023.2.0', '', ('gompi', version)), +] + +moduleclass = 'toolchain' diff --git a/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb new file mode 100644 index 00000000000..709703f2949 --- /dev/null +++ b/easybuild/easyconfigs/l/libxc/libxc-6.2.2-GCC-13.2.0-nofhc.eb @@ -0,0 +1,53 @@ +easyblock = 'CMakeMake' + +name = 'libxc' +version = '6.2.2' +versionsuffix = '-nofhc' + +homepage = 'https://libxc.gitlab.io' +description = """Libxc is a library of exchange-correlation functionals for density-functional theory. + The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals.""" + +toolchain = {'name': 'GCC', 'version': '13.2.0'} + +source_urls = ['https://gitlab.com/libxc/libxc/-/archive/%(version)s/'] +sources = [SOURCE_TAR_GZ] +checksums = [('a0f6f1bba7ba5c0c85b2bfe65aca1591025f509a7f11471b4cd651a79491b045', + '3b0523924579cf494cafc6fea92945257f35692b004217d3dfd3ea7ca780e8dc')] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Perl', '5.38.0'), +] + +local_common_configopts = "-DENABLE_FORTRAN=ON -DENABLE_XHOST=OFF " + +# don't disable building of third and fourth derivates, since it's required by some software that depends on libxc +# (like ABINIT, which requires "3rd derivatives of energy") +# see also https://github.com/pyscf/pyscf/issues/1103 +local_common_configopts += "-DDISABLE_KXC=OFF -DDISABLE_LXC=OFF" + +# Disable fhc, this needs to support codes (like VASP) relying on the projector augmented wave (PAW) approach +local_common_configopts += ' -DDISABLE_FHC=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', +] + +# make sure that built libraries (libxc*.so*) in build directory are picked when running tests +# this is required when RPATH linking is used +pretestopts = "export LD_LIBRARY_PATH=%(builddir)s/easybuild_obj:$LD_LIBRARY_PATH && " + +runtest = 'test' + +sanity_check_paths = { + 'files': ['bin/xc-info'] + + ['lib/libxc%s.%s' % (x, y) for x in ['', 'f03', 'f90'] for y in ['a', SHLIB_EXT]], + 'dirs': ['include', 'lib/pkgconfig', 'lib/cmake/Libxc'], +} + +sanity_check_commands = ['xc-info 1'] + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb new file mode 100644 index 00000000000..298e08395e3 --- /dev/null +++ b/easybuild/easyconfigs/m/multicharge/multicharge-0.3.0-gomkl-2023b.eb @@ -0,0 +1,39 @@ +# Author: J. Sassmannshausen (Imperial College London/UK) + +easyblock = 'CMakeNinja' + +name = 'multicharge' +version = '0.3.0' + +homepage = 'https://github.com/grimme-lab/multicharge' +description = """Electronegativity equilibration model for atomic partial charges.""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} + +github_account = 'grimme-lab' +source_urls = [GITHUB_SOURCE] +sources = ['v%(version)s.tar.gz'] +checksums = ['2fcc1f80871f404f005e9db458ffaec95bb28a19516a0245278cd3175b63a6b2'] + +builddependencies = [ + ('CMake', '3.27.6'), + ('Ninja', '1.11.1'), + ('binutils', '2.40'), +] + +dependencies = [ + ('mctc-lib', '0.3.1'), + ('mstore', '0.3.0'), +] + +sanity_check_paths = { + 'files': ['bin/multicharge', 'lib/libmulticharge.a'], + 'dirs': ['include/%(name)s', 'lib/cmake', 'lib/pkgconfig'], +} + +sanity_check_commands = ["multicharge --help"] + +# run suite of tests with ctest +runtest = True + +moduleclass = 'chem' diff --git a/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb new file mode 100644 index 00000000000..e1bedb6ba07 --- /dev/null +++ b/easybuild/easyconfigs/w/Wannier90/Wannier90-3.1.0-gomkl-2023b.eb @@ -0,0 +1,35 @@ +easyblock = 'MakeCp' + +name = 'Wannier90' +version = '3.1.0' + +homepage = 'http://www.wannier.org' +description = """A tool for obtaining maximally-localised Wannier functions""" + +toolchain = {'name': 'gomkl', 'version': '2023b'} +toolchainopts = {'usempi': True} + +github_account = 'wannier-developers' +source_urls = [GITHUB_LOWER_SOURCE] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCELOWER_TAR_GZ}] +patches = ['Wannier90_3x_ignore_makeinc.patch'] +checksums = [ + '40651a9832eb93dec20a8360dd535262c261c34e13c41b6755fa6915c936b254', # wannier90-3.1.0.tar.gz + '561c0d296e0e30b8bb303702cd6e41ded54c153d9b9e6cd9cab73858e5e2945e', # Wannier90_3x_ignore_makeinc.patch +] + +# The -fallow-argument-mismatch allows MPI communication calls to be +# called with arrays of different types at different places in the +# code. This otherwise cause an error in GCC 10.X +buildopts = 'all F90=$F90 MPIF90=$MPIF90 FCOPTS="$FFLAGS -fallow-argument-mismatch" LDOPTS="$FFLAGS" ' +buildopts += 'LIBDIR="$LAPACK_LIB_DIR" LIBS="$LIBLAPACK" ' +buildopts += 'COMMS=mpi' + +files_to_copy = [(['wannier90.x', 'postw90.x'], 'bin'), (['libwannier.a'], 'lib')] + +sanity_check_paths = { + 'files': ['bin/wannier90.x', 'bin/postw90.x', 'lib/libwannier.a'], + 'dirs': [] +} + +moduleclass = 'chem' From a316bc83f3482518ad6259d159593ef24372f709 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Nov 2024 15:05:45 +0100 Subject: [PATCH 065/116] Remove bokeh, because it's already merged --- .../b/bokeh/bokeh-3.6.0-gfbf-2024a.eb | 46 ------------------- 1 file changed, 46 deletions(-) delete mode 100644 easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb diff --git a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb b/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb deleted file mode 100644 index fbdb34a71b6..00000000000 --- a/easybuild/easyconfigs/b/bokeh/bokeh-3.6.0-gfbf-2024a.eb +++ /dev/null @@ -1,46 +0,0 @@ -easyblock = 'PythonBundle' - -name = 'bokeh' -version = '3.6.0' - -homepage = 'https://github.com/bokeh/bokeh' -description = "Statistical and novel interactive HTML plots for Python" - -toolchain = {'name': 'gfbf', 'version': '2024a'} - -builddependencies = [ - ('meson-python', '0.16.0'), -] - -dependencies = [ - ('Python', '3.12.3'), - ('Python-bundle-PyPI', '2024.06'), - ('SciPy-bundle', '2024.05'), - ('matplotlib', '3.9.2'), - ('PyYAML', '6.0.2'), - ('Pillow-SIMD', '10.4.0'), - ('tornado', '6.4.1'), -] - -use_pip = True - -exts_list = [ - ('xyzservices', '2024.4.0', { - 'checksums': ['6a04f11487a6fb77d92a98984cd107fbd9157fd5e65f929add9c3d6e604ee88c'], - }), - (name, version, { - 'preinstallopts': """sed -i 's/setup(/setup(version="%(version)s",/g' setup.py && """, - 'checksums': ['0032dc1e76ad097b07626e51584685ff48c65481fbaaad105663b1046165867a'], - }), -] - -sanity_check_paths = { - 'files': ['bin/bokeh'], - 'dirs': ['lib/python%(pyshortver)s/site-packages'], -} - -sanity_check_commands = ["bokeh --help"] - -sanity_pip_check = True - -moduleclass = 'tools' From 9bd5bb154ee97c686e5eaa054f941c8f8e49803f Mon Sep 17 00:00:00 2001 From: SebastianAchilles Date: Wed, 13 Nov 2024 15:14:47 +0100 Subject: [PATCH 066/116] update cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb add sbsa checksum --- .../easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb index a6cbe9ef7e7..76340a4e654 100644 --- a/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb +++ b/easybuild/easyconfigs/c/cuDNN/cuDNN-9.5.0.50-CUDA-12.6.0.eb @@ -16,7 +16,12 @@ source_urls = [ 'https://developer.download.nvidia.com/compute/cudnn/redist/cudnn/linux-%(cudnnarch)s/' ] sources = ['%%(namelower)s-linux-%%(cudnnarch)s-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major] -checksums = ['86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d'] +checksums = [{ + '%%(namelower)s-linux-sbsa-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '494b640a69feb40ce806a726aa63a1de6b2ec459acbe6a116ef6fe3e6b27877d', + '%%(namelower)s-linux-x86_64-%%(version)s_cuda%s-archive.tar.xz' % local_cuda_major: + '86e4e4f4c09b31d3850b402d94ea52741a2f94c2f717ddc8899a14aca96e032d', +}] dependencies = [('CUDA', '12.6.0')] From 0753acb96039f9096c697ef2ecd7f245293564f6 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 15:34:21 +0100 Subject: [PATCH 067/116] adding easyconfigs: GROMACS-2024.4-foss-2023b.eb --- .../g/GROMACS/GROMACS-2024.4-foss-2023b.eb | 89 +++++++++++++++++++ 1 file changed, 89 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb new file mode 100644 index 00000000000..778af16ba08 --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b.eb @@ -0,0 +1,89 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), +] + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 3976ba038ec6081e2f06b2ec2f7773fb1810eb57 Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Wed, 13 Nov 2024 16:01:24 +0100 Subject: [PATCH 068/116] Remove tornado, because it's already merged --- .../t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb | 29 ------------------- 1 file changed, 29 deletions(-) delete mode 100644 easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb deleted file mode 100644 index d4266c8c1c9..00000000000 --- a/easybuild/easyconfigs/t/tornado/tornado-6.4.1-GCCcore-13.3.0.eb +++ /dev/null @@ -1,29 +0,0 @@ -easyblock = "PythonPackage" - -name = "tornado" -version = "6.4.1" - -homepage = "https://github.com/tornadoweb/tornado" -description = "Tornado is a Python web framework and asynchronous networking library." - -toolchain = {"name": "GCCcore", "version": "13.3.0"} - -sources = [SOURCE_TAR_GZ] -patches = ['tornado-6.1_increase-default-timeouts.patch'] -checksums = [ - {'tornado-6.4.1.tar.gz': '92d3ab53183d8c50f8204a51e6f91d18a15d5ef261e84d452800d4ff6fc504e9'}, - {'tornado-6.1_increase-default-timeouts.patch': '32e09dd8243acb8c55162f361880dc294d76770a7ff083c05aef6b8660e3bfb9'}, -] - -builddependencies = [ - ("binutils", "2.42"), -] -dependencies = [ - ("Python", "3.12.3"), -] - -download_dep_fail = True -sanity_pip_check = True -use_pip = True - -moduleclass = "lib" From e389efbfd4760141acc8910b8eeb9777d62eae9d Mon Sep 17 00:00:00 2001 From: Maxim Date: Wed, 13 Nov 2024 16:35:44 +0100 Subject: [PATCH 069/116] Update easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb index 990ec0677d4..f691f95e191 100644 --- a/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/p/p7zip/p7zip-17.05-GCCcore-13.3.0.eb @@ -34,7 +34,7 @@ files_to_copy = [ ] # 7z requires 7z.so plugin in same directory sanity_check_paths = { - 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.so'], + 'files': ['bin/7z', 'bin/7za', 'bin/7zCon.sfx', 'bin/7zr', 'libexec/7z', 'libexec/7z.%s' % SHLIB_EXT], 'dirs': ['libexec/Codecs'], } From 663e776c639e64216155230db594a24df2047c6d Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 18:35:36 +0100 Subject: [PATCH 070/116] fix long line in easyconfig for GROMACS 2024.4 w/ CUDA 12.4.0 + PLUMED 2.9.2 --- .../GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb index 7a3c8faccba..1fc7764f5a7 100644 --- a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-CUDA-12.4.0-PLUMED-2.9.2.eb @@ -85,7 +85,8 @@ exts_default_options = { exts_list = [ ('gmxapi', '0.4.2', { - 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], }), ] From 419397286785ee360048ffac175c5283a8b70ca3 Mon Sep 17 00:00:00 2001 From: Kenneth Hoste Date: Wed, 13 Nov 2024 19:39:38 +0100 Subject: [PATCH 071/116] adding easyconfigs: GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb --- .../GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb | 97 +++++++++++++++++++ 1 file changed, 97 insertions(+) create mode 100644 easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb diff --git a/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb new file mode 100644 index 00000000000..5920405282c --- /dev/null +++ b/easybuild/easyconfigs/g/GROMACS/GROMACS-2024.4-foss-2023b-PLUMED-2.9.2.eb @@ -0,0 +1,97 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2016 University of Luxembourg / LCSB, Cyprus Institute / CaSToRC, +# Ghent University / The Francis Crick Institute +# Authors:: +# * Wiktor Jurkowski +# * Fotis Georgatos +# * George Tsouloupas +# * Kenneth Hoste +# * Adam Huffman +# * Ake Sandgren +# * J. Sassmannshausen +# * Dugan Witherick +# * Christoph Siegert +# License:: MIT/GPL + +name = 'GROMACS' +version = '2024.4' +local_plumedver = '2.9.2' +versionsuffix = '-PLUMED-%s' % local_plumedver + +homepage = 'https://www.gromacs.org' +description = """ +GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the +Newtonian equations of motion for systems with hundreds to millions of +particles. + +This is a CPU only build, containing both MPI and threadMPI binaries +for both single and double precision. + +It also contains the gmxapi extension for the single precision MPI build. +""" + +toolchain = {'name': 'foss', 'version': '2023b'} +toolchainopts = {'openmp': True, 'usempi': True} + +source_urls = [ + 'https://ftp.gromacs.org/pub/gromacs/', + 'ftp://ftp.gromacs.org/pub/gromacs/', +] +sources = [SOURCELOWER_TAR_GZ] +patches = [ + 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', + 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', + 'GROMACS-2023.3_skip_test_for_plumed.patch', +] +checksums = [ + {'gromacs-2024.4.tar.gz': 'ac618ece2e58afa86b536c5a2c4fcb937f0760318f12d18f10346b6bdebd86a8'}, + {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': + '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, + {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': + '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, + {'GROMACS-2023.3_skip_test_for_plumed.patch': '6c541ee74f71f6a63950134d9d0e3afb176a2e25e76e017b4d1986a59163c083'}, +] + +builddependencies = [ + ('CMake', '3.27.6'), + ('scikit-build-core', '0.9.3'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('SciPy-bundle', '2023.11'), + ('networkx', '3.2.1'), + ('mpi4py', '3.1.5'), + ('PLUMED', local_plumedver), +] + +# PLUMED 2.9.2 is compatible with GROMACS 2024.2; 2024.4 seems to work fine too +ignore_plumed_version_check = True + +# be a bit more forgiving w.r.t. timeouts for GROMACS test suite, +# see also https://gitlab.com/gromacs/gromacs/-/issues/5062 +configopts = "-DGMX_TEST_TIMEOUT_FACTOR=3" + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'source_urls': [PYPI_SOURCE], + 'use_pip': True, + 'download_dep_fail': True, + 'sanity_pip_check': True, +} + +exts_list = [ + ('gmxapi', '0.4.2', { + 'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s ' + + '-C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', + 'checksums': ['c746c6498c73a75913d7fcb01c13cc001d4bcb82999e9bf91d63578565ed1a1f'], + }), +] + +modextrapaths = { + 'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', +} + +moduleclass = 'bio' From 7ee1b3bf760307573be48e9a99793a5473199c97 Mon Sep 17 00:00:00 2001 From: satishk Date: Thu, 14 Nov 2024 10:55:28 +0100 Subject: [PATCH 072/116] adding easyconfigs: Valgrind-3.24.0-gompi-2024a.eb --- .../v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb | 46 +++++++++++++++++++ 1 file changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb diff --git a/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb new file mode 100644 index 00000000000..2c2922383b6 --- /dev/null +++ b/easybuild/easyconfigs/v/Valgrind/Valgrind-3.24.0-gompi-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'ConfigureMake' + +name = 'Valgrind' +version = '3.24.0' + +homepage = 'https://valgrind.org' +description = "Valgrind: Debugging and profiling tools" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'optarch': True} + +source_urls = [ + 'https://sourceware.org/pub/valgrind/', + 'https://www.mirrorservice.org/sites/sourceware.org/pub/valgrind/', +] +sources = [SOURCELOWER_TAR_BZ2] +checksums = ['71aee202bdef1ae73898ccf7e9c315134fa7db6c246063afc503aef702ec03bd'] + +dependencies = [ + ('Perl', '5.38.2'), + ('Python', '3.12.3'), +] + +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': [] +} + +sanity_check_commands = [ + 'callgrind_annotate --version 2>&1 | grep "%(version)s"', + 'cg_annotate --help', + 'ms_print --version 2>&1 | grep "%(version)s"', + 'valgrind --help', + 'vgdb --help', +] + +moduleclass = 'debugger' From 8831dd2891bd4b15b7ea2d91ead3724e146a046e Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 13:20:55 +0100 Subject: [PATCH 073/116] add checksum for dft-d4 --- easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb index a59c07c17dc..02f10d2d9dc 100644 --- a/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb +++ b/easybuild/easyconfigs/d/DFT-D4/DFT-D4-3.7.0-gomkl-2023b.eb @@ -11,6 +11,10 @@ toolchain = {'name': 'gomkl', 'version': '2023b'} source_urls = ['https://github.com/dftd4/dftd4/archive/refs/tags/'] sources = ['v%(version)s.tar.gz'] patches = ['DFT-D4-3.2.0-remove_module_id.patch'] +checksums = [ + {'v3.7.0.tar.gz': 'f00b244759eff2c4f54b80a40673440ce951b6ddfa5eee1f46124297e056f69c'}, + {'DFT-D4-3.2.0-remove_module_id.patch': '8c3c81338cb57972580e4cf3db307aa2e44b8b3f6d1ba7ae24fa9d807490a93b'}, +] builddependencies = [ ('CMake', '3.27.6'), From da5266453dd983cc1f1edb250bd1df421bdf8fa0 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Thu, 14 Nov 2024 19:23:52 +0100 Subject: [PATCH 074/116] adding easyconfigs: trusTEr-0.1.1-20241025-foss-2023a.eb, subset-bam-1.1.0.eb, bamtofastq-1.4.1-GCCcore-12.3.0.eb, TEtranscripts-2.2.3-foss-2023a.eb --- .../bamtofastq-1.4.1-GCCcore-12.3.0.eb | 220 ++++++++++++++++++ .../s/subset-bam/subset-bam-1.1.0.eb | 24 ++ .../TEtranscripts-2.2.3-foss-2023a.eb | 42 ++++ .../trusTEr-0.1.1-20241025-foss-2023a.eb | 36 +++ 4 files changed, 322 insertions(+) create mode 100644 easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb create mode 100644 easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb create mode 100644 easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb create mode 100644 easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb diff --git a/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb new file mode 100644 index 00000000000..8759374058b --- /dev/null +++ b/easybuild/easyconfigs/b/bamtofastq/bamtofastq-1.4.1-GCCcore-12.3.0.eb @@ -0,0 +1,220 @@ +easyblock = 'Cargo' + +name = 'bamtofastq' +version = '1.4.1' + +homepage = 'https://github.com/10XGenomics/bamtofastq' +description = """Convert 10x BAM files to the original FASTQs compatible with 10x pipelines.""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://github.com/10XGenomics/bamtofastq/archive/refs/tags'] +sources = [{'download_filename': 'v%(version)s.tar.gz', 'filename': SOURCE_TAR_GZ}] + +builddependencies = [ + ('binutils', '2.40'), + ('Rust', '1.75.0'), + ('CMake', '3.26.3'), +] + +dependencies = [('bzip2', '1.0.8')] + +crates = [ + ('addr2line', '0.17.0'), + ('adler', '1.0.2'), + ('aho-corasick', '0.7.18'), + ('anyhow', '1.0.53'), + ('autocfg', '1.0.1'), + ('backtrace', '0.3.63'), + ('bincode', '1.3.3'), + ('bio-types', '0.12.0'), + ('bitflags', '1.3.2'), + ('bstr', '0.2.17'), + ('byteorder', '1.4.3'), + ('bzip2-sys', '0.1.11+1.0.8'), + ('cc', '1.0.71'), + ('cfg-if', '1.0.0'), + ('cmake', '0.1.45'), + ('crc32fast', '1.2.1'), + ('crossbeam-channel', '0.5.1'), + ('crossbeam-utils', '0.8.5'), + ('csv', '1.1.6'), + ('csv-core', '0.1.10'), + ('curl-sys', '0.4.49+curl-7.79.1'), + ('custom_derive', '0.1.7'), + ('derive-new', '0.5.9'), + ('docopt', '1.1.1'), + ('either', '1.6.1'), + ('fastrand', '1.7.0'), + ('flate2', '1.0.22'), + ('form_urlencoded', '1.0.1'), + ('fs-utils', '1.1.4'), + ('gimli', '0.26.0'), + ('glob', '0.3.0'), + ('heck', '0.3.3'), + ('hts-sys', '2.0.2'), + ('idna', '0.2.3'), + ('ieee754', '0.2.6'), + ('instant', '0.1.12'), + ('itertools', '0.10.3'), + ('itoa', '0.4.8'), + ('jobserver', '0.1.24'), + ('lazy_static', '1.4.0'), + ('libc', '0.2.103'), + ('libdeflate-sys', '0.5.0'), + ('libz-sys', '1.1.3'), + ('linear-map', '1.2.0'), + ('log', '0.4.14'), + ('lz4', '1.23.2'), + ('lz4-sys', '1.9.2'), + ('lzma-sys', '0.1.17'), + ('matches', '0.1.9'), + ('memchr', '2.4.1'), + ('min-max-heap', '1.3.0'), + ('miniz_oxide', '0.4.4'), + ('newtype_derive', '0.1.6'), + ('object', '0.27.1'), + ('openssl-src', '111.16.0+1.1.1l'), + ('openssl-sys', '0.9.67'), + ('percent-encoding', '2.1.0'), + ('pkg-config', '0.3.20'), + ('proc-macro2', '1.0.29'), + ('quick-error', '1.2.3'), + ('quote', '1.0.10'), + ('redox_syscall', '0.2.10'), + ('regex', '1.5.4'), + ('regex-automata', '0.1.10'), + ('regex-syntax', '0.6.25'), + ('remove_dir_all', '0.5.3'), + ('rust-htslib', '0.38.2'), + ('rustc-demangle', '0.1.21'), + ('rustc_version', '0.1.7'), + ('ryu', '1.0.5'), + ('semver', '0.1.20'), + ('serde', '1.0.135'), + ('serde_bytes', '0.11.5'), + ('serde_derive', '1.0.135'), + ('shardio', '0.8.2'), + ('strsim', '0.10.0'), + ('strum_macros', '0.20.1'), + ('syn', '1.0.80'), + ('tempfile', '3.3.0'), + ('thiserror', '1.0.29'), + ('thiserror-impl', '1.0.29'), + ('tinyvec', '1.5.0'), + ('tinyvec_macros', '0.1.0'), + ('unicode-bidi', '0.3.7'), + ('unicode-normalization', '0.1.19'), + ('unicode-segmentation', '1.8.0'), + ('unicode-xid', '0.2.2'), + ('url', '2.2.2'), + ('vcpkg', '0.2.15'), + ('winapi', '0.3.9'), + ('winapi-i686-pc-windows-gnu', '0.4.0'), + ('winapi-x86_64-pc-windows-gnu', '0.4.0'), +] + +sanity_check_paths = { + 'files': ['bin/%(namelower)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(namelower)s --help"] + +checksums = [ + {'bamtofastq-1.4.1.tar.gz': 'cebf968b0eff8911df65102e2be5884e6cd7312f1cb0aba6718bfc2d9407d543'}, + {'addr2line-0.17.0.tar.gz': 'b9ecd88a8c8378ca913a680cd98f0f13ac67383d35993f86c90a70e3f137816b'}, + {'adler-1.0.2.tar.gz': 'f26201604c87b1e01bd3d98f8d5d9a8fcbb815e8cedb41ffccbeb4bf593a35fe'}, + {'aho-corasick-0.7.18.tar.gz': '1e37cfd5e7657ada45f742d6e99ca5788580b5c529dc78faf11ece6dc702656f'}, + {'anyhow-1.0.53.tar.gz': '94a45b455c14666b85fc40a019e8ab9eb75e3a124e05494f5397122bc9eb06e0'}, + {'autocfg-1.0.1.tar.gz': 'cdb031dd78e28731d87d56cc8ffef4a8f36ca26c38fe2de700543e627f8a464a'}, + {'backtrace-0.3.63.tar.gz': '321629d8ba6513061f26707241fa9bc89524ff1cd7a915a97ef0c62c666ce1b6'}, + {'bincode-1.3.3.tar.gz': 'b1f45e9417d87227c7a56d22e471c6206462cba514c7590c09aff4cf6d1ddcad'}, + {'bio-types-0.12.0.tar.gz': 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{'syn-1.0.80.tar.gz': 'd010a1623fbd906d51d650a9916aaefc05ffa0e4053ff7fe601167f3e715d194'}, + {'tempfile-3.3.0.tar.gz': '5cdb1ef4eaeeaddc8fbd371e5017057064af0911902ef36b39801f67cc6d79e4'}, + {'thiserror-1.0.29.tar.gz': '602eca064b2d83369e2b2f34b09c70b605402801927c65c11071ac911d299b88'}, + {'thiserror-impl-1.0.29.tar.gz': 'bad553cc2c78e8de258400763a647e80e6d1b31ee237275d756f6836d204494c'}, + {'tinyvec-1.5.0.tar.gz': 'f83b2a3d4d9091d0abd7eba4dc2710b1718583bd4d8992e2190720ea38f391f7'}, + {'tinyvec_macros-0.1.0.tar.gz': 'cda74da7e1a664f795bb1f8a87ec406fb89a02522cf6e50620d016add6dbbf5c'}, + {'unicode-bidi-0.3.7.tar.gz': '1a01404663e3db436ed2746d9fefef640d868edae3cceb81c3b8d5732fda678f'}, + {'unicode-normalization-0.1.19.tar.gz': 'd54590932941a9e9266f0832deed84ebe1bf2e4c9e4a3554d393d18f5e854bf9'}, + {'unicode-segmentation-1.8.0.tar.gz': '8895849a949e7845e06bd6dc1aa51731a103c42707010a5b591c0038fb73385b'}, + {'unicode-xid-0.2.2.tar.gz': '8ccb82d61f80a663efe1f787a51b16b5a51e3314d6ac365b08639f52387b33f3'}, + {'url-2.2.2.tar.gz': 'a507c383b2d33b5fc35d1861e77e6b383d158b2da5e14fe51b83dfedf6fd578c'}, + {'vcpkg-0.2.15.tar.gz': 'accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426'}, + {'winapi-0.3.9.tar.gz': '5c839a674fcd7a98952e593242ea400abe93992746761e38641405d28b00f419'}, + {'winapi-i686-pc-windows-gnu-0.4.0.tar.gz': 'ac3b87c63620426dd9b991e5ce0329eff545bccbbb34f3be09ff6fb6ab51b7b6'}, + {'winapi-x86_64-pc-windows-gnu-0.4.0.tar.gz': '712e227841d057c1ee1cd2fb22fa7e5a5461ae8e48fa2ca79ec42cfc1931183f'}, +] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb new file mode 100644 index 00000000000..f9e6778cec2 --- /dev/null +++ b/easybuild/easyconfigs/s/subset-bam/subset-bam-1.1.0.eb @@ -0,0 +1,24 @@ +easyblock = 'Binary' + +name = 'subset-bam' +version = '1.1.0' + +homepage = 'https://github.com/10XGenomics/subset-bam' +description = """subset-bam is a tool to subset a 10x Genomics BAM file based on a tag, +most commonly the cell barcode tag.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/10XGenomics/subset-bam/releases/download/v%(version)s/'] + +sources = [{'download_filename': 'subset-bam_linux', 'filename': name}] +checksums = ['05496ea56d52becdb7972528af0a486be1d52c1749e35bea9ae4c41215ed0a1b'] + +sanity_check_paths = { + 'dirs': [], + 'files': [name], +} + +sanity_check_commands = ["%(name)s --help"] + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb b/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb new file mode 100644 index 00000000000..ab7aa3071a8 --- /dev/null +++ b/easybuild/easyconfigs/t/TEtranscripts/TEtranscripts-2.2.3-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonPackage' + +name = 'TEtranscripts' +version = '2.2.3' + +homepage = 'https://github.com/mhammell-laboratory/TEtranscripts' +description = """TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads +to both genes & transposable elements. +TEtranscripts then performs differential analysis using DESeq2.""" + +sources = [SOURCE_TAR_GZ] +checksums = ['e53577e8e73e41c6495fb819977e3e537bbeac7b2fa1635029201a37ee0bf7b8'] + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Pysam', '0.22.0'), + ('R', '4.3.2'), + ('R-bundle-Bioconductor', '3.18', '-R-%(rver)s'), +] + +use_pip = True +download_dep_fail = True + +options = {'modulename': 'TEToolkit'} + +fix_python_shebang_for = ['bin/*'] + +sanity_check_paths = { + 'files': ['bin/TEtranscripts', 'bin/TEcount'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + 'TEtranscripts --version', + 'TEcount --version', +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb new file mode 100644 index 00000000000..7cc222efe16 --- /dev/null +++ b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb @@ -0,0 +1,36 @@ +easyblock = 'PythonPackage' + +name = 'trusTEr' +version = '0.1.1-20241025' +local_commit = '6358eef' + +homepage = 'https://github.com/raquelgarza/truster' +description = """Takes fastq files from 10x single cell RNA sequencing, clusters cells using Seurat, +and can be used to produce read count matrices in a cluster level. +You can also quantify reads per cluster having predefined clusters.""" + +source_urls = ['https://github.com/raquelgarza/truster/archive/'] +sources = [{'download_filename': '%s.tar.gz' % local_commit, 'filename': SOURCE_TAR_GZ}] +checksums = ['ef6f454a73f545e5f90a28a80d388afb763a43ac1256f3c182bf947728b4e39a'] + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('SciPy-bundle', '2023.07'), + ('CellRanger', '8.0.1', '', SYSTEM), + ('R', '4.3.2'), + ('R-bundle-CRAN', '2023.12'), + ('Seurat', '5.1.0', '-R-%(rver)s'), + ('STAR', '2.7.11a'), + ('velocyto', '0.17.17'), + ('TEtranscripts','2.2.3'), + ('bamtofastq','1.4.1'), + ('subset-bam', '1.1.0-', '', SYSTEM), +] + +use_pip = True +download_dep_fail = True +sanity_pip_check = True + +moduleclass = 'bio' From 9d1614cc9c8896507ababec14ab509a666414912 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 20:05:15 +0100 Subject: [PATCH 075/116] put toolchain in a different pr --- easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb | 19 ------------------- 1 file changed, 19 deletions(-) delete mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb deleted file mode 100644 index d5b856a6fe9..00000000000 --- a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb +++ /dev/null @@ -1,19 +0,0 @@ -easyblock = "Toolchain" - -name = 'gomkl' -version = '2023b' - -homepage = '(none)' -description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" - -toolchain = SYSTEM - -local_comp = ('GCC', '13.2.0') - -dependencies = [ - local_comp, - ('OpenMPI', '4.1.6', '', local_comp), - ('imkl', '2023.2.0', '', ('gompi', version)), -] - -moduleclass = 'toolchain' From 07234dfa0d4766a6f9743b1612d04b533a4582b3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 20:07:37 +0100 Subject: [PATCH 076/116] {toolchain}[gomkl-2023b] gomkl/2023b --- easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb diff --git a/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb new file mode 100644 index 00000000000..d5b856a6fe9 --- /dev/null +++ b/easybuild/easyconfigs/g/gomkl/gomkl-2023b.eb @@ -0,0 +1,19 @@ +easyblock = "Toolchain" + +name = 'gomkl' +version = '2023b' + +homepage = '(none)' +description = """GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL""" + +toolchain = SYSTEM + +local_comp = ('GCC', '13.2.0') + +dependencies = [ + local_comp, + ('OpenMPI', '4.1.6', '', local_comp), + ('imkl', '2023.2.0', '', ('gompi', version)), +] + +moduleclass = 'toolchain' From fb7ffabc5dc8fe3264a0f8f2fd31d1999924fdd3 Mon Sep 17 00:00:00 2001 From: Balazs Hajgato Date: Thu, 14 Nov 2024 21:05:11 +0100 Subject: [PATCH 077/116] add imkl --- .../i/imkl/imkl-2023.2.0-gompi-2023b.eb | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb diff --git a/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb new file mode 100644 index 00000000000..e194f389253 --- /dev/null +++ b/easybuild/easyconfigs/i/imkl/imkl-2023.2.0-gompi-2023b.eb @@ -0,0 +1,18 @@ +name = 'imkl' +version = '2023.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/onemkl.html' +description = "Intel oneAPI Math Kernel Library" + +toolchain = {'name': 'gompi', 'version': '2023b'} + +# 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/adb8a02c-4ee7-4882-97d6-a524150da358/'] +sources = ['l_onemkl_p_%(version)s.49497_offline.sh'] +checksums = ['4a0d93da85a94d92e0ad35dc0fc3b3ab7f040bd55ad374c4d5ec81a57a2b872b'] + +interfaces = False + +installopts = "--download-cache=%(builddir)s/cache --download-dir=%(builddir)s/download --log-dir=%(builddir)s/log" + +moduleclass = 'numlib' From 69034cbc04e07aa1cd3cc8945bb5b8474de1d7d5 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek Date: Fri, 15 Nov 2024 11:33:14 +0100 Subject: [PATCH 078/116] truster ec - fix whitespace --- .../t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb index 7cc222efe16..9c26af4b15c 100644 --- a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb +++ b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb @@ -24,8 +24,8 @@ dependencies = [ ('Seurat', '5.1.0', '-R-%(rver)s'), ('STAR', '2.7.11a'), ('velocyto', '0.17.17'), - ('TEtranscripts','2.2.3'), - ('bamtofastq','1.4.1'), + ('TEtranscripts', '2.2.3'), + ('bamtofastq', '1.4.1'), ('subset-bam', '1.1.0-', '', SYSTEM), ] From 997fd8a94f3b4678c4b58b6631493ad62a9ea9f3 Mon Sep 17 00:00:00 2001 From: Pavel Tomanek <99190809+pavelToman@users.noreply.github.com> Date: Fri, 15 Nov 2024 11:51:36 +0100 Subject: [PATCH 079/116] Update trusTEr-0.1.1-20241025-foss-2023a.eb - fix typo --- .../easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb index 9c26af4b15c..3bea1107bfc 100644 --- a/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb +++ b/easybuild/easyconfigs/t/trusTEr/trusTEr-0.1.1-20241025-foss-2023a.eb @@ -26,7 +26,7 @@ dependencies = [ ('velocyto', '0.17.17'), ('TEtranscripts', '2.2.3'), ('bamtofastq', '1.4.1'), - ('subset-bam', '1.1.0-', '', SYSTEM), + ('subset-bam', '1.1.0', '', SYSTEM), ] use_pip = True From e58d753e9b1a905165cdfe0dcefdf00c9a7d6180 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 15 Nov 2024 15:10:11 +0100 Subject: [PATCH 080/116] eccodes --- .../e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb | 46 +++++++++++++++++++ .../l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb | 36 +++++++++++++++ .../libaec/libaec-1.1.3_install_binary.patch | 11 +++++ 3 files changed, 93 insertions(+) create mode 100644 easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb create mode 100644 easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch diff --git a/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb new file mode 100644 index 00000000000..2aa0915ea2e --- /dev/null +++ b/easybuild/easyconfigs/e/ecCodes/ecCodes-2.38.3-gompi-2024a.eb @@ -0,0 +1,46 @@ +easyblock = 'CMakeMake' + +name = 'ecCodes' +version = '2.38.3' + +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': '2024a'} +toolchainopts = {'usempi': False} + +source_urls = ['https://github.com/ecmwf/eccodes/archive/refs/tags/'] +sources = [{'download_filename': '%(version)s.tar.gz', 'filename': '%(namelower)s-%(version)s.tar.gz'}] +checksums = ['2f13adc4fbdfa3ea11f75ce4ed8937bf40a8fcedd760a519b15e4e17dedc9424'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('ecBuild', '3.8.5'), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('JasPer', '4.2.4'), + ('libjpeg-turbo', '3.0.1'), + ('libpng', '1.6.43'), + ('zlib', '1.3.1'), + ('libaec', '1.1.3'), +] + +# Python bindings are provided by a separate package 'eccodes-python' +configopts = "-DENABLE_NETCDF=ON -DENABLE_PNG=ON -DENABLE_PYTHON=OFF -DENABLE_JPG=ON " +configopts += "-DENABLE_JPG_LIBJASPER=ON -DENABLE_ECCODES_THREADS=ON" + + +sanity_check_paths = { + 'files': ['bin/bufr_compare', 'bin/bufr_copy', 'bin/bufr_dump', 'bin/bufr_filter', 'bin/bufr_get', 'bin/bufr_ls', + 'bin/grib_compare', 'bin/grib_copy', 'bin/grib_dump', 'bin/grib_filter', 'bin/grib_get', 'bin/grib_ls', + 'bin/gts_compare', 'bin/gts_copy', 'bin/gts_dump', 'bin/gts_filter', 'bin/gts_get', 'bin/gts_ls', + 'bin/metar_compare', 'bin/metar_copy', 'bin/metar_dump', 'bin/metar_filter', 'bin/metar_get', + 'bin/metar_ls', 'bin/codes_count', 'bin/codes_info', 'bin/codes_split_file', + 'lib/libeccodes_f90.%s' % SHLIB_EXT, 'lib/libeccodes.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +moduleclass = 'tools' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb b/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..267acc5aa3d --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.1.3-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Denis Kristak +easyblock = 'CMakeMake' + +name = 'libaec' +version = '1.1.3' + +homepage = 'https://gitlab.dkrz.de/k202009/libaec' +description = """Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers +(samples). The library achieves best results for low entropy data as often encountered in space imaging +instrument data or numerical model output from weather or climate simulations. While floating point representations +are not directly supported, they can also be efficiently coded by grouping exponents and mantissa.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://gitlab.dkrz.de/k202009/%(namelower)s/-/archive/v%(version)s'] +sources = [SOURCELOWER_TAR_GZ] +patches = ["libaec-1.1.3_install_binary.patch"] + +checksums = ['453de44eb6ea2500843a4cf4d2e97d1be251d2df7beae6c2ebe374edcb11e378', + '52fcdeacd9c27108dffafd8109012902fa63fb2e39803670a3ba16f313628f4c'] + +builddependencies = [ + ('CMake', '3.29.3'), + ('binutils', '2.42'), +] + +sanity_check_paths = { + 'files': ['bin/graec', 'include/%(name)s.h', 'include/szlib.h', + 'lib/libaec.a', 'lib/libaec.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ['graec --help'] + +moduleclass = 'lib' diff --git a/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch b/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch new file mode 100644 index 00000000000..29d7f8e0c7b --- /dev/null +++ b/easybuild/easyconfigs/l/libaec/libaec-1.1.3_install_binary.patch @@ -0,0 +1,11 @@ +# The binary is not installed by default which caused the sanity check to fail +# @author Stefan Wolfsheimer, SURF + +diff -uNr libaec-v1.1.3.orig/src/CMakeLists.txt libaec-v1.1.3/src/CMakeLists.txt +--- libaec-v1.1.3.orig/src/CMakeLists.txt 2024-11-15 14:21:05.177185441 +0100 ++++ libaec-v1.1.3/src/CMakeLists.txt 2024-11-15 14:21:39.702841450 +0100 +@@ -76,3 +76,4 @@ + COMPILE_DEFINITIONS "${libaec_COMPILE_DEFINITIONS}") + + install(TARGETS aec_static aec_shared sz_static sz_shared) ++install(TARGETS graec RUNTIME DESTINATION bin) From 9ae86e469e511278d39658b5c54b28f403b30901 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 15 Nov 2024 15:32:05 +0100 Subject: [PATCH 081/116] add CDO UDUNITS --- .../c/CDO/CDO-2.4.4-gompi-2024a.eb | 57 +++++++++++++++++++ .../UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb | 44 ++++++++++++++ 2 files changed, 101 insertions(+) create mode 100644 easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb b/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb new file mode 100644 index 00000000000..57b6de8e609 --- /dev/null +++ b/easybuild/easyconfigs/c/CDO/CDO-2.4.4-gompi-2024a.eb @@ -0,0 +1,57 @@ +# 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 = '2.4.4' + + +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': '2024a'} +toolchainopts = {'cstd': 'c++20', 'usempi': True} + +source_urls = ['https://code.mpimet.mpg.de/attachments/download/29649/'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['49f50bd18dacd585e9518cfd4f55548f692426edfb3b27ddcd1c653eab53d063'] + +builddependencies = [ + ('pkgconf', '2.2.0'), +] + +dependencies = [ + ('cURL', '8.7.1'), + ('ecCodes', '2.38.3'), + ('FFTW', '3.3.10'), + ('HDF5', '1.14.5'), + ('libxml2', '2.12.7'), + ('netCDF', '4.9.2'), + ('PROJ', '9.4.1'), + ('Szip', '2.1.1'), + ('UDUNITS', '2.2.28'), + ('util-linux', '2.40'), +] + +# 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 " + +# Make sure that right Fortran compiler is used, also on non-x86_64 architectures +configopts += 'CPPFLAGS="$CPPFLAGS -DgFortran" ' + +sanity_check_paths = { + 'files': ['bin/cdo', 'lib/libcdi.a', 'lib/libcdi.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +sanity_check_commands = ["cdo --version 2>&1 | grep 'Climate Data Operators version %(version)s'"] + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..12a51d8afd4 --- /dev/null +++ b/easybuild/easyconfigs/u/UDUNITS/UDUNITS-2.2.28-GCCcore-13.3.0.eb @@ -0,0 +1,44 @@ +## +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# +# Copyright:: Copyright 2012-2013 University of Luxembourg, Ghent University +# Authors:: Fotis Georgatos , Kenneth Hoste (Ghent University) +# License:: MIT/GPL +# $Id$ +# +# This work implements a part of the HPCBIOS project and is a component of the policy: +# http://hpcbios.readthedocs.org/en/latest/HPCBIOS_2012-97.html +## + +easyblock = 'ConfigureMake' + +name = 'UDUNITS' +version = '2.2.28' + +homepage = 'https://www.unidata.ucar.edu/software/udunits/' +description = """UDUNITS supports conversion of unit specifications between formatted and binary forms, + arithmetic manipulation of units, and conversion of values between compatible scales of measurement.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} +toolchainopts = {'pic': True} + +source_urls = [ + 'https://artifacts.unidata.ucar.edu/repository/downloads-udunits/%(version)s/', + 'https://sources.easybuild.io/u/UDUNITS/', +] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['590baec83161a3fd62c00efa66f6113cec8a7c461e3f61a5182167e0cc5d579e'] + +builddependencies = [('binutils', '2.42')] + +dependencies = [('expat', '2.6.2')] + +sanity_check_paths = { + 'files': ['bin/udunits2', 'include/converter.h', 'include/udunits2.h', 'include/udunits.h', + 'lib/libudunits2.a', 'lib/libudunits2.%s' % SHLIB_EXT], + 'dirs': ['share'], +} + +parallel = 1 + +moduleclass = 'phys' From 2b970e1df3d9f56f30766d5b9e65098437eba11f Mon Sep 17 00:00:00 2001 From: sassy Date: Fri, 15 Nov 2024 16:48:14 +0000 Subject: [PATCH 082/116] tests added, GMP added correctly --- .../easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb index e4a2c353676..a181d6523c8 100644 --- a/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb +++ b/easybuild/easyconfigs/r/RAxML-NG/RAxML-NG-1.2.2-GCC-13.2.0.eb @@ -31,9 +31,18 @@ builddependencies = [ ('CMake', '3.27.6'), ('Bison', '3.8.2'), ('flex', '2.6.4'), + ('googletest', '1.14.0'), +] + +dependencies = [ ('GMP', '6.3.0'), ] +preconfigopts = "sed -i 's/c++11/c++14/g' %(builddir)s/raxml-ng/CMakeLists.txt && " +configopts = '-DUSE_GMP=ON ' + +runtest = 'test ' + sanity_check_paths = { 'files': ['bin/raxml-ng'], 'dirs': [], From c993951349521a83803336a4735f671377dcdf61 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Sun, 17 Nov 2024 15:46:03 +0100 Subject: [PATCH 083/116] Add netCDF --- .../netCDF-C++4-4.3.1-gompi-2024a.eb | 28 +++++++++ .../netCDF-Fortran-4.6.1-gompi-2024a.eb | 28 +++++++++ .../n/netCDF/netCDF-4.9.2-gompi-2024a.eb | 54 +++++++++++++++++ .../netcdf4-python-1.7.1.post2-foss-2024a.eb | 58 +++++++++++++++++++ ...st2_relax_tolerance_compression_test.patch | 15 +++++ .../p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb | 35 +++++++++++ 6 files changed, 218 insertions(+) create mode 100644 easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb create mode 100644 easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch create mode 100644 easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb new file mode 100644 index 00000000000..1b9a80b189c --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +easyblock = 'ConfigureMake' + +name = 'netCDF-C++4' +version = '4.3.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True} + +source_urls = ['https://github.com/Unidata/netcdf-cxx4/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['e3fe3d2ec06c1c2772555bf1208d220aab5fee186d04bd265219b0bc7a978edc'] + +dependencies = [ + ('netCDF', '4.9.2'), +] + + +sanity_check_paths = { + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'dirs': [], +} + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb new file mode 100644 index 00000000000..2bc6e207794 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF-Fortran/netCDF-Fortran-4.6.1-gompi-2024a.eb @@ -0,0 +1,28 @@ +name = 'netCDF-Fortran' +version = '4.6.1' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s/archive/'] +sources = ['v%(version)s.tar.gz'] +checksums = ['40b534e0c81b853081c67ccde095367bd8a5eead2ee883431331674e7aa9509f'] + +builddependencies = [ + ('M4', '1.4.19'), +] +dependencies = [ + ('netCDF', '4.9.2'), + ('bzip2', '1.0.8'), +] + +# (too) parallel build fails, but single-core build is fairly quick anyway (~1min) +parallel = 1 + + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb new file mode 100644 index 00000000000..86160357109 --- /dev/null +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb @@ -0,0 +1,54 @@ +name = 'netCDF' +version = '4.9.2' + +homepage = 'https://www.unidata.ucar.edu/software/netcdf/' +description = """NetCDF (network Common Data Form) is a set of software libraries + and machine-independent data formats that support the creation, access, and sharing of array-oriented + scientific data.""" + +toolchain = {'name': 'gompi', 'version': '2024a'} +toolchainopts = {'pic': True, 'usempi': True} + +source_urls = ['https://github.com/Unidata/%(namelower)s-c/archive/'] +sources = ['v%(version)s.tar.gz'] +patches = ['%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch'] +checksums = [ + {'v4.9.2.tar.gz': 'bc104d101278c68b303359b3dc4192f81592ae8640f1aee486921138f7f88cb7'}, + {'%(name)s-%(version_major_minor)s.0_skip-nasa-test.patch': + '19d99e03c048b037dc01f03f5b8ddc910ebaceb076d0f050540d348f26dfcd2a'}, +] + +builddependencies = [ + ('Autotools', '20231222'), + ('CMake', '3.29.3'), + ('Doxygen', '1.11.0'), +] +dependencies = [ + ('HDF5', '1.14.5'), + ('cURL', '8.7.1'), + ('Szip', '2.1.1'), + ('zstd', '1.5.6'), + ('bzip2', '1.0.8'), + ('libxml2', '2.12.7'), +] + +# disable Szip, zlib parallel I/O tests, since these can hang on some systems, e.g. generoso +# see: https://github.com/easybuilders/easybuild-easyconfigs/pull/16834 +# and https://github.com/easybuilders/easybuild-easyconfigs/pull/17107#issuecomment-1432947172 +preconfigopts = ("sed -i -e 's|@MPIEXEC@ -n 4 ./tst_parallel5|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_zlib|echo \"skipped by EasyBuild\"|g'" + " -e 's|@MPIEXEC@ -n 4 ./tst_parallel_compress|echo \"skipped by EasyBuild\"|g'" + " %(builddir)s/%(namelower)s-c-%(version)s/nc_test4/run_par_test.sh.in &&") + +# make sure both static and shared libs are built +# and disable "remote" tests that access a unreliable external test server over internet +configopts = [ + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=OFF", + "-DENABLE_DAP_REMOTE_TESTS=OFF -DBUILD_SHARED_LIBS=ON", +] + +# some tests try to start 16 MPI ranks, so we need to allow oversubscription to avoid failing tests +pretestopts = "OMPI_MCA_rmaps_base_oversubscribe=1 " +runtest = 'test' + +moduleclass = 'data' diff --git a/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb new file mode 100644 index 00000000000..912e23a55b7 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2-foss-2024a.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonBundle' + +name = 'netcdf4-python' +version = '1.7.1.post2' + + +homepage = 'https://unidata.github.io/netcdf4-python/' +description = "Python/numpy interface to netCDF." + +toolchain = {'name': 'foss', 'version': '2024a'} +toolchainopts = {'usempi': True} + +builddependencies = [ + ('Cython', '3.0.10'), +] + +dependencies = [ + ('Python', '3.12.3'), + ('SciPy-bundle', '2024.05'), + ('netCDF', '4.9.2'), + ('cURL', '8.7.1'), + ('mpi4py', '4.0.1'), +] + +fix_python_shebang_for = ['bin/*'] +sanity_pip_check = True +use_pip = True + +exts_list = [ + ('cftime', '1.6.4', { + 'checksums': ['e325406193758a7ed67308deb52e727782a19e384e183378e7ff62098be0aedc'], + }), + (name, version, { + 'patches': [ + 'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch', + ], + 'source_tmpl': 'netcdf4-%(version)s.tar.gz', + 'source_urls': ['https://pypi.python.org/packages/source/n/netCDF4'], + 'checksums': [ + {'netcdf4-1.7.1.post2.tar.gz': '37d557e36654889d7020192bfb56f9d5f93894cb32997eb837ae586c538fd7b6'}, + {'netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch': + '7faa7e839ad1e816ffd0153e4b76b43ebce3e14d35f0534f812168dfaa78316c'}, + ], + }), +] + +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-1.7.1.post2_relax_tolerance_compression_test.patch b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch new file mode 100644 index 00000000000..be4deb77f96 --- /dev/null +++ b/easybuild/easyconfigs/n/netcdf4-python/netcdf4-python-1.7.1.post2_relax_tolerance_compression_test.patch @@ -0,0 +1,15 @@ +# Relax tolerance in the compression_szip test to avoid fails on some systems. +# author: maxim-masterov (SURF) +# +diff -Nru netcdf4-1.7.1.post2.orig/test/test_compression_szip.py netcdf4-1.7.1.post2/test/test_compression_szip.py +--- netcdf4-1.7.1.post2.orig/test/test_compression_szip.py 2024-10-07 16:01:21.276893761 +0200 ++++ netcdf4-1.7.1.post2/test/test_compression_szip.py 2024-10-07 16:27:47.424436617 +0200 +@@ -35,7 +35,7 @@ + assert_almost_equal(datarr,f.variables['data'][:]) + assert f.variables['data'].filters() ==\ + {'zlib':False,'szip':False,'zstd':False,'bzip2':False,'blosc':False,'shuffle':False,'complevel':0,'fletcher32':False} +- assert_almost_equal(datarr,f.variables['data_szip'][:]) ++ assert_almost_equal(datarr,f.variables['data_szip'][:], 6) + dtest = {'zlib': False, 'szip': {'coding': 'ec', 'pixels_per_block': 32}, 'zstd': False, 'bzip2': False, 'blosc': False, 'shuffle': False, 'complevel': 0, 'fletcher32': False} + assert f.variables['data_szip'].filters() == dtest + f.close() diff --git a/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb new file mode 100644 index 00000000000..b586cfd0da4 --- /dev/null +++ b/easybuild/easyconfigs/p/PnetCDF/PnetCDF-1.13.0-gompi-2024a.eb @@ -0,0 +1,35 @@ +easyblock = 'ConfigureMake' + +name = 'PnetCDF' +version = '1.13.0' + +homepage = 'https://parallel-netcdf.github.io/' +description = "Parallel netCDF: A Parallel I/O Library for NetCDF File Access" + +toolchain = {'name': 'gompi', 'version': '2024a'} + +source_urls = ['https://parallel-netcdf.github.io/Release'] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['aba0f1c77a51990ba359d0f6388569ff77e530ee574e40592a1e206ed9b2c491'] + +builddependencies = [ + ('Autotools', '20231222'), + ('Perl', '5.38.2'), +] + +preconfigopts = "autoreconf -f -i && " +configopts = [ + '', + '--enable-shared', +] + +sanity_check_paths = { + 'files': ['bin/%s' % x for x in ['ncmpidiff', 'ncmpidump', 'ncmpigen', 'ncoffsets', + 'ncvalidator', 'pnetcdf-config', 'pnetcdf_version']] + + ['lib/lib%(namelower)s.a', 'lib/lib%%(namelower)s.%s' % SHLIB_EXT], + 'dirs': ['include'], +} + +modextrapaths = {'PNETCDF': ''} + +moduleclass = 'data' From a1e39b0d7469ebd98596e5b067eb9584d2979e51 Mon Sep 17 00:00:00 2001 From: maxim-masterov Date: Sun, 17 Nov 2024 17:27:02 +0100 Subject: [PATCH 084/116] Move file to the right folder --- .../{netCDF-C++ => netCDF-C++4}/netCDF-C++4-4.3.1-gompi-2024a.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/n/{netCDF-C++ => netCDF-C++4}/netCDF-C++4-4.3.1-gompi-2024a.eb (100%) diff --git a/easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb similarity index 100% rename from easybuild/easyconfigs/n/netCDF-C++/netCDF-C++4-4.3.1-gompi-2024a.eb rename to easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb From fdd8fbe49a8a973cccd7977bdc86c10840d58dc5 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sun, 17 Nov 2024 17:46:33 +0100 Subject: [PATCH 085/116] use SHLIB_EXT --- .../easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb index aceab404bda..695a90190e0 100644 --- a/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb +++ b/easybuild/easyconfigs/p/pmt/pmt-1.3.1-GCCcore-13.3.0-CUDA-12.6.0.eb @@ -26,7 +26,7 @@ dependencies = [ configopts = '-DPMT_BUILD_RAPL=1 -DPMT_BUILD_NVML=1 -DPMT_BUILD_NVIDIA=1' sanity_check_paths = { - 'files': ["lib/libpmt.so", "include/pmt/NVIDIA.h", "include/pmt/Rapl.h", "include/pmt/NVML.h"], + 'files': ["lib/libpmt.%s" % SHLIB_EXT, "include/pmt/NVIDIA.h", "include/pmt/Rapl.h", "include/pmt/NVML.h"], 'dirs': ["lib", "include"], } From e983a3225e16ec05b5da3829fd859d5a621f6788 Mon Sep 17 00:00:00 2001 From: Sam Moors Date: Sun, 17 Nov 2024 21:00:35 +0100 Subject: [PATCH 086/116] use SHLIB_EXT --- .../easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb index 1b9a80b189c..909bd06a674 100644 --- a/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb +++ b/easybuild/easyconfigs/n/netCDF-C++4/netCDF-C++4-4.3.1-gompi-2024a.eb @@ -21,7 +21,7 @@ dependencies = [ sanity_check_paths = { - 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.so'], + 'files': ['include/netcdf', 'lib/libnetcdf_c++4.a', 'lib/libnetcdf_c++4.%s' % SHLIB_EXT], 'dirs': [], } From 35786a0873e32877a694ac76179cf872ff7122a5 Mon Sep 17 00:00:00 2001 From: Justus Kuhlmann <82444481+jkuhl-uni@users.noreply.github.com> Date: Mon, 18 Nov 2024 10:28:09 +0100 Subject: [PATCH 087/116] remove unnecessary comments --- .../easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb | 5 ----- 1 file changed, 5 deletions(-) diff --git a/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb index 1630a181fbc..96672c2751b 100644 --- a/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb +++ b/easybuild/easyconfigs/e/edlib/edlib-1.3.9.post1-GCC-13.3.0.eb @@ -21,11 +21,6 @@ exts_list = [ 'checksums': ['a806d5db9e318a1a2d3fce988008179168e7db13e5e55b19b79763f9bb9d2982'], }), (name, version, { - # 'source_urls': ['https://github.com/Martinsos/edlib/archive/'], - # 'source_tmpl': '%(version)s.tar.gz', - # fixes `edlib.bycython.cpp:198:12: fatal error: longintrepr.h: No such file or directory` - # see https://github.com/Martinsos/edlib/issues/217#issuecomment-1736234091 - # 'preinstallopts': 'cd bindings/python && make && python -m cogapp -d -o README.rst README-tmpl.rst && ', 'checksums': ['b0fb6e85882cab02208ccd6daa46f80cb9ff1d05764e91bf22920a01d7a6fbfa'], }), ] From f7a10c1213920e079ad3c3d86dde85e37ac1542d Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 14:21:03 +0100 Subject: [PATCH 088/116] adding easyconfigs: snpEff-5.2c-GCCcore-12.3.0-Java-11.eb --- .../snpEff-5.2c-GCCcore-12.3.0-Java-11.eb | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) create mode 100644 easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb diff --git a/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb new file mode 100644 index 00000000000..c9f29979a1d --- /dev/null +++ b/easybuild/easyconfigs/s/snpEff/snpEff-5.2c-GCCcore-12.3.0-Java-11.eb @@ -0,0 +1,37 @@ +easyblock = 'Tarball' + +name = 'snpEff' +version = '5.2c' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://pcingola.github.io/SnpEff/' +description = """SnpEff is a variant annotation and effect prediction tool. + It annotates and predicts the effects of genetic variants (such as amino acid changes).""" + +toolchain = {'name': 'GCCcore', 'version': '12.3.0'} + +source_urls = ['https://snpeff.blob.core.windows.net/versions/'] +sources = ['%%(name)s_v%s_core.zip' % version.replace('.', '_')] +checksums = ['9926f600662707e85478940abc283ef120a909f1d41c32a036f01d958cd51232'] + +dependencies = [ + # ignore website claim that Java 12+ is required, nothing is compiled for + # anything newer than Java 11 + ('Java', '11', '', SYSTEM), + ('Python', '3.11.3'), + ('Perl', '5.36.1'), +] + +fix_perl_shebang_for = ['scripts/*.pl'] +fix_python_shebang_for = ['scripts/*.py'] + +sanity_check_paths = { + 'files': ['%(name)s.jar', 'SnpSift.jar', 'scripts/%(name)s'], + 'dirs': [], +} + +sanity_check_commands = ["%(name)s -version"] + +modextrapaths = {'PATH': 'scripts'} + +moduleclass = 'bio' From 1185b3243891dd8bfdf0078924c7644ca653e648 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 14:32:06 +0100 Subject: [PATCH 089/116] adding easyconfigs: Lightning-2.2.1-foss-2023a.eb --- .../l/Lightning/Lightning-2.2.1-foss-2023a.eb | 31 +++++++++++++++++++ 1 file changed, 31 insertions(+) create mode 100644 easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb b/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb new file mode 100644 index 00000000000..5635e783f7c --- /dev/null +++ b/easybuild/easyconfigs/l/Lightning/Lightning-2.2.1-foss-2023a.eb @@ -0,0 +1,31 @@ +easyblock = 'PythonPackage' + +name = 'Lightning' +version = '2.2.1' + +homepage = 'https://github.com/Lightning-AI/pytorch-lightning' +description = """ +The deep learning framework to pretrain, finetune and deploy AI models. +Lightning has 4 core packages: + PyTorch Lightning: Train and deploy PyTorch at scale. + Lightning Fabric: Expert control. + Lightning Data: Blazing fast, distributed streaming of training data from cloud storage. + Lightning Apps: Build AI products and ML workflows. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +sources = [SOURCELOWER_TAR_GZ] +checksums = ['b3e46d596b32cafd1fb9b21fdba1b1767df97b1af5cc702693d1c51df60b19aa'] + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyTorch-Lightning', version), +] + +download_dep_fail = True +use_pip = True +sanity_pip_check = True + +moduleclass = 'tools' From d69a35cc9263e733fb7129b391d01464235f3a33 Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 17:18:03 +0100 Subject: [PATCH 090/116] adding easyconfigs: imgaug-0.4.1-foss-2023a.eb --- .../i/imgaug/imgaug-0.4.1-foss-2023a.eb | 34 +++++++++++++++++++ 1 file changed, 34 insertions(+) create mode 100644 easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb diff --git a/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb new file mode 100644 index 00000000000..2b1f0c837e5 --- /dev/null +++ b/easybuild/easyconfigs/i/imgaug/imgaug-0.4.1-foss-2023a.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'imgaug' +version = '0.4.1' + +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': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('Pillow', '10.0.0'), + ('matplotlib', '3.7.2'), + ('scikit-image', '0.22.0'), + ('OpenCV', '4.8.1', '-contrib'), + ('Shapely', '2.0.1'), + ('imageio', '2.33.1'), +] + +source_urls = ['https://github.com/nsetzer/imgaug/archive/'] +sources = ['%(version)s.tar.gz'] +patches = ['imgaug-0.4.1_openvc_requirement.patch'] +checksums = [ + {'0.4.1.tar.gz': 'dd9655f8d871da35c37cf674ba35c76175a77aeac517e8dafe6673c8f853115f'}, + {'imgaug-0.4.1_openvc_requirement.patch': '0e0993322184c56115ea04262f8eacef4a86a9aa7b26c8cd67258ccaa441d8a7'}, +] + +download_dep_fail = True +sanity_pip_check = True +use_pip = True + +moduleclass = 'lib' From ff9dcb46d48f0ec8a2507956ca67f8dd9e0a541e Mon Sep 17 00:00:00 2001 From: Sebastian Achilles Date: Mon, 18 Nov 2024 19:30:38 +0100 Subject: [PATCH 091/116] adding easyconfigs: Advisor-2025.0.0.eb, Inspector-2024.2.0.eb --- .../easyconfigs/a/Advisor/Advisor-2025.0.0.eb | 27 +++++++++++++++++++ .../i/Inspector/Inspector-2024.2.0.eb | 19 +++++++++++++ 2 files changed, 46 insertions(+) create mode 100644 easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb create mode 100644 easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb diff --git a/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb b/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb new file mode 100644 index 00000000000..1f057b7f100 --- /dev/null +++ b/easybuild/easyconfigs/a/Advisor/Advisor-2025.0.0.eb @@ -0,0 +1,27 @@ +name = 'Advisor' +version = '2025.0.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/advisor.html' +description = """Vectorization Optimization and Thread Prototyping + - Vectorize & thread code or performance “dies” + - Easy workflow + data + tips = faster code faster + - Prioritize, Prototype & Predict performance gain + """ + +toolchain = SYSTEM + +source_urls = [ + 'https://registrationcenter-download.intel.com/akdlm/IRC_NAS/fe95ae4a-3692-4e31-919d-3e7bdf5832f1/'] +sources = ['intel-advisor-%(version)s.798_offline.sh'] +checksums = ['bf85d4b0bd199a2babdff6b4bd3885ce569a3ad0e992b99b2e14dbb30af88cd4'] + +dontcreateinstalldir = True + +sanity_check_paths = { + 'files': ['%(namelower)s/%(version_major_minor)s/bin64/advisor'], + 'dirs': ['%(namelower)s/%(version_major_minor)s/bin64', + '%(namelower)s/%(version_major_minor)s/lib64', + '%(namelower)s/%(version_major_minor)s/include/intel64'] +} + +moduleclass = 'perf' diff --git a/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb b/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb new file mode 100644 index 00000000000..0d345bc2c5e --- /dev/null +++ b/easybuild/easyconfigs/i/Inspector/Inspector-2024.2.0.eb @@ -0,0 +1,19 @@ + +name = 'Inspector' +version = '2024.2.0' + +homepage = 'https://software.intel.com/content/www/us/en/develop/tools/oneapi/components/inspector.html' +description = """Intel Inspector is a dynamic memory and threading error + checking tool for users developing serial and parallel applications""" + +toolchain = SYSTEM + +source_urls = ['https://registrationcenter-download.intel.com/akdlm/IRC_NAS/1549c5b3-cf23-4595-9593-b5d0460a8dcd/'] +sources = ['l_inspector_oneapi_p_%(version)s.22_offline.sh'] +checksums = ['e2aab9b1b428d0c23184beae8caac55fa3d3f973ac51a6b6908eb38b0d9097ed'] + +dontcreateinstalldir = True + +requires_runtime_license = False + +moduleclass = 'tools' From 2e8f6f6d75af079b396043f05e2a154a4c81327d Mon Sep 17 00:00:00 2001 From: Maxim Date: Mon, 18 Nov 2024 16:48:28 -0500 Subject: [PATCH 092/116] Update easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb Co-authored-by: SebastianAchilles --- easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb index 86160357109..95e48775eeb 100644 --- a/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb +++ b/easybuild/easyconfigs/n/netCDF/netCDF-4.9.2-gompi-2024a.eb @@ -48,7 +48,7 @@ configopts = [ ] # 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 " +pretestopts = "PRTE_MCA_rmaps_default_mapping_policy=:oversubscribe " runtest = 'test' moduleclass = 'data' From f991c85b6845e65063133c9a31c1eb962775b3ef Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Mon, 18 Nov 2024 23:59:40 +0100 Subject: [PATCH 093/116] adding easyconfigs: timm-1.0.8-foss-2023a.eb --- .../t/timm/timm-1.0.8-foss-2023a.eb | 42 +++++++++++++++++++ 1 file changed, 42 insertions(+) create mode 100644 easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb diff --git a/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb new file mode 100644 index 00000000000..a954aa9e443 --- /dev/null +++ b/easybuild/easyconfigs/t/timm/timm-1.0.8-foss-2023a.eb @@ -0,0 +1,42 @@ +easyblock = 'PythonBundle' + +name = 'timm' +version = '1.0.8' + +homepage = 'https://huggingface.co/docs/timm' +description = """ +timm is a library containing SOTA computer vision models, layers, utilities, +optimizers, schedulers, data-loaders, augmentations, and training/evaluation +scripts. It comes packaged with >700 pretrained models, and is designed to be +flexible and easy to use. +""" + +toolchain = {'name': 'foss', 'version': '2023a'} + +dependencies = [ + ('Python', '3.11.3'), + ('PyTorch', '2.1.2'), + ('PyYAML', '6.0'), + ('tqdm', '4.66.1'), + ('torchvision', '0.16.0'), + ('Safetensors', '0.4.3'), +] + +builddependencies = [ + ('PDM', '2.12.4'), +] + +use_pip = True + +exts_list = [ + ('huggingface_hub', '0.24.5', { + 'checksums': ['7b45d6744dd53ce9cbf9880957de00e9d10a9ae837f1c9b7255fc8fa4e8264f3'], + }), + (name, version, { + 'checksums': ['f54a579f1cc39c43d99a4b03603e39c4cee87d4f0a08aba9c22e19064b30bf95'], + }), +] + +sanity_pip_check = True + +moduleclass = 'lib' From 5a5f662d3272c63b5523bb87e8c966554e15906e Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 19 Nov 2024 00:45:48 +0100 Subject: [PATCH 094/116] use dynamic environment name based on Julia version in RCall v0.13.17 --- .../r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb index 4da1b0f58aa..bb9b6221bf8 100644 --- a/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/r/RCall/RCall-0.13.17-foss-2022a-R-4.2.1-Julia-1.9.2.eb @@ -222,8 +222,10 @@ exts_list = [ }), ] +local_julia_env = "%(installdir)s/environments/v" + '.'.join(local_juliaver.split('.')[:2]) + sanity_check_commands = [ - """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", + """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % local_julia_env, ] sanity_check_paths = { From ac70aacc13cb3bb9ec2b47313c4f9cc351f9f9df Mon Sep 17 00:00:00 2001 From: Alex Domingo Date: Tue, 19 Nov 2024 01:48:43 +0100 Subject: [PATCH 095/116] use dynamic environment name based on Julia version in Circuitscape v5.12.3 --- .../c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb index f9909fe5c7a..8e8e7e2f86b 100644 --- a/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb +++ b/easybuild/easyconfigs/c/Circuitscape/Circuitscape-5.12.3-Julia-1.9.2.eb @@ -403,8 +403,10 @@ exts_list = [ }), ] +_julia_env = "%(installdir)s/environments/v" + '.'.join(_julia_ver.split('.')[:2]) + sanity_check_commands = [ - """julia -e 'using Pkg; Pkg.activate("%(installdir)s/environments/v1.9"); Pkg.test("%(name)s")'""", + """julia -e 'using Pkg; Pkg.activate("%s"); Pkg.test("%%(name)s")'""" % _julia_env, ] moduleclass = 'lib' From 26dca3a8cff05d2264c881b9d200cf634d10a1db Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Tue, 19 Nov 2024 09:31:15 +0100 Subject: [PATCH 096/116] {compiler}[system/system] NVHPC-24.11-CUDA-12.6.0 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb | 73 +++++++++++++++++++ 1 file changed, 73 insertions(+) create mode 100644 easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb diff --git a/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb new file mode 100644 index 00000000000..546b28e7147 --- /dev/null +++ b/easybuild/easyconfigs/n/NVHPC/NVHPC-24.11-CUDA-12.6.0.eb @@ -0,0 +1,73 @@ +name = 'NVHPC' +version = '24.11' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://developer.nvidia.com/hpc-sdk/' +description = """C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI)""" + +toolchain = SYSTEM + +local_tarball_tmpl = 'nvhpc_2024_%%(version_major)s%%(version_minor)s_Linux_%s_cuda_multi.tar.gz' +# By downloading, you accept the HPC SDK Software License Agreement +# https://docs.nvidia.com/hpc-sdk/eula/index.html +# accept_eula = True +source_urls = ['https://developer.download.nvidia.com/hpc-sdk/%(version)s/'] +sources = [local_tarball_tmpl % '%(arch)s'] +checksums = [ + { + local_tarball_tmpl % 'aarch64': + 'f2f64e5dec5e90dad5e12a31a992172b0aa19abf872ef1c54a1a437c7008eefb', + local_tarball_tmpl % 'x86_64': + '0c27d66ed0e2d3007d30ac904922a9abf96475197dc0f4dcc6316d235a1dc0c3', + } +] + +local_gccver = '13.3.0' +dependencies = [ + ('GCCcore', local_gccver), + ('binutils', '2.42', '', ('GCCcore', local_gccver)), + # This is necessary to avoid cases where just libnuma.so.1 is present in the system and -lnuma fails + ('numactl', '2.0.18', '', ('GCCcore', local_gccver)), + ('CUDA', '12.6.0', '', SYSTEM), +] + +module_add_cuda = False + +# specify default CUDA version that should be used by NVHPC +# should match one of the CUDA versions that are included with this NVHPC version +# (see install_components/Linux_x86_64/$version/cuda/) where $version is the NVHPC version +# this version can be tweaked from the EasyBuild command line with +# --try-amend=default_cuda_version="11.0" (for example) +default_cuda_version = '%(cudaver)s' + +# NVHPC EasyBlock supports some features, which can be set via CLI or this easyconfig. +# The following list gives examples for the easyconfig +# +# NVHPC needs CUDA to work. Two options are available: 1) Use NVHPC-bundled CUDA, 2) use system CUDA +# 1) Bundled CUDA +# If no easybuild dependency to CUDA is present, the bundled CUDA is taken. A version needs to be specified with +# default_cuda_version = "11.0" +# in this easyconfig file; alternatively, it can be specified through the command line during installation with +# --try-amend=default_cuda_version="10.2" +# 2) CUDA provided via EasyBuild +# Use CUDA as a dependency, for example +# dependencies = [('CUDA', '11.5.0')] +# The parameter default_cuda_version still can be set as above. +# If not set, it will be deduced from the CUDA module (via $EBVERSIONCUDA) +# +# Define a NVHPC-default Compute Capability +# cuda_compute_capabilities = "8.0" +# Can also be specified on the EasyBuild command line via --cuda-compute-capabilities=8.0 +# Only single values supported, not lists of values! +# +# Options to add/remove things to/from environment module (defaults shown) +# module_byo_compilers = False # Remove compilers from PATH (Bring-your-own compilers) +# module_nvhpc_own_mpi = False # Add NVHPC's own pre-compiled OpenMPI +# module_add_math_libs = False # Add NVHPC's math libraries (which should be there from CUDA anyway) +# module_add_profilers = False # Add NVHPC's NVIDIA Profilers +# module_add_nccl = False # Add NVHPC's NCCL library +# module_add_nvshmem = False # Add NVHPC's NVSHMEM library +# module_add_cuda = False # Add NVHPC's bundled CUDA + +# this bundle serves as a compiler-only toolchain, so it should be marked as compiler (important for HMNS) +moduleclass = 'compiler' From 589c7197cb718d1ec78f20992f5f81a995387d9d Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 19 Nov 2024 10:48:04 +0100 Subject: [PATCH 097/116] adding easyconfigs: absl-py-2.1.0-GCCcore-13.3.0.eb --- .../a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..fb76611558b --- /dev/null +++ b/easybuild/easyconfigs/a/absl-py/absl-py-2.1.0-GCCcore-13.3.0.eb @@ -0,0 +1,28 @@ +easyblock = 'PythonBundle' + +name = 'absl-py' +version = '2.1.0' + +homepage = 'https://github.com/abseil/abseil-py' +description = """absl-py is a collection of Python library code for building Python +applications. The code is collected from Google's own Python code base, and has +been extensively tested and used in production.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [('binutils', '2.42')] + +dependencies = [('Python', '3.12.3')] + +use_pip = True + +exts_list = [ + ('absl-py', version, { + 'modulename': 'absl', + 'checksums': ['7820790efbb316739cde8b4e19357243fc3608a152024288513dd968d7d959ff'], + }), +] + +sanity_pip_check = True + +moduleclass = 'tools' From ba767f37bcd4f71579732320a9a9a13c09a2fef4 Mon Sep 17 00:00:00 2001 From: sassy Date: Tue, 19 Nov 2024 10:32:23 +0000 Subject: [PATCH 098/116] adding easyconfigs: MATLAB-2024b.eb --- .../easyconfigs/m/MATLAB/MATLAB-2024b.eb | 28 +++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb diff --git a/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb b/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb new file mode 100644 index 00000000000..c53c320205f --- /dev/null +++ b/easybuild/easyconfigs/m/MATLAB/MATLAB-2024b.eb @@ -0,0 +1,28 @@ +name = 'MATLAB' +version = '2024b' + +homepage = 'https://www.mathworks.com/products/matlab' +description = """MATLAB is a high-level language and interactive environment + that enables you to perform computationally intensive tasks faster than with + traditional programming languages such as C, C++, and Fortran.""" + +toolchain = SYSTEM + +sources = ['R%s_Linux.iso' % (version)] +checksums = ['4e4499d93b4909b750ee2a6444af107cd5c1c62e75020c3e1625e946c6693573'] + +download_instructions = 'Download %s from mathworks.com' % sources[0] + +java_options = '-Xmx2048m' + +osdependencies = [('p7zip-plugins', 'p7zip-full')] # for extracting iso-files + +# Use EB_MATLAB_KEY environment variable or uncomment and modify license key +# key = '00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000-00000' + +# Use EB_MATLAB_LICENSE_SERVER and EB_MATLAB_LICENSE_SERVER_PORT environment variables or +# uncomment and modify the following variables for installation with floating license server +# license_file = 'my-license-file' +# license_server_port = 'XXXXX' + +moduleclass = 'math' From 8e62edadb9fc10f348b6cb21ceab0c3813a2efef Mon Sep 17 00:00:00 2001 From: thoffman Date: Tue, 19 Nov 2024 15:08:09 +0100 Subject: [PATCH 099/116] adding easyconfigs: Bazel-7.4.1-GCCcore-13.3.0.eb --- .../b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb | 26 +++++++++++++++++++ 1 file changed, 26 insertions(+) create mode 100644 easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb b/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..1fc72e512e2 --- /dev/null +++ b/easybuild/easyconfigs/b/Bazel/Bazel-7.4.1-GCCcore-13.3.0.eb @@ -0,0 +1,26 @@ +name = 'Bazel' +version = '7.4.1' + +homepage = 'https://bazel.io/' +description = """Bazel is a build tool that builds code quickly and reliably. +It is used to build the majority of Google's software.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = ['https://github.com/bazelbuild/%(namelower)s/releases/download/%(version)s'] +sources = ['%(namelower)s-%(version)s-dist.zip'] +checksums = ['83386618bc489f4da36266ef2620ec64a526c686cf07041332caff7c953afaf5'] + +builddependencies = [ + ('binutils', '2.42'), + ('Python', '3.12.3'), + ('Zip', '3.0'), +] +dependencies = [ + ('Java', '21.0.2', '', SYSTEM), +] + +runtest = True +testopts = "-- //examples/cpp:hello-success_test //examples/py/... //examples/py_native:test //examples/shell/..." + +moduleclass = 'devel' From 70b7ff659f79b10b645b8284cc29f9740fb42a9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Petr=20Kr=C3=A1l?= Date: Thu, 21 Nov 2024 15:21:21 +0100 Subject: [PATCH 100/116] patch a segfaulting test for `NECI` --- .../n/NECI/NECI-20230620-foss-2023a.eb | 6 +++++- .../n/NECI/NECI-20230620_segfault.patch | 21 +++++++++++++++++++ 2 files changed, 26 insertions(+), 1 deletion(-) create mode 100644 easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb index becc50b238e..09dce5c1aab 100644 --- a/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620-foss-2023a.eb @@ -19,7 +19,11 @@ sources = [{ }, 'filename': SOURCE_TAR_GZ, }] -checksums = [None] +patches = ['NECI-20230620_segfault.patch'] +checksums = [ + None, + 'f0b5f62e115a1e07d6b90bc66ee9957a5f5d686bef65beba9c2be4bd8f29f0e4', +] builddependencies = [ ('CMake', '3.26.3'), diff --git a/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch b/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch new file mode 100644 index 00000000000..0a63b605dd3 --- /dev/null +++ b/easybuild/easyconfigs/n/NECI/NECI-20230620_segfault.patch @@ -0,0 +1,21 @@ +Fixes SEGFAULT error in tests. +See https://github.com/ghb24/NECI_STABLE/issues/18 +Author: Petr Král (INUITS) +--- unit_tests/back_spawn_excit_gen/test_back_spawn_excit_gen.F90.orig 2023-06-20 10:15:17.000000000 +0200 ++++ unit_tests/back_spawn_excit_gen/test_back_spawn_excit_gen.F90 2024-11-21 14:58:46.602604509 +0100 +@@ -64,6 +64,7 @@ + nmaxy = 2 + nmaxz = 2 + allocate(KPointToBasisFn(-nmaxx:nmaxx, -nmaxy:nmaxy, -nmaxz:nmaxz, 2)) ++ KPointToBasisFn = -1 + tOrbECutoff = .false. + + allocate(projedet(nel,1)); projedet(:,1) = [1,2] +@@ -403,6 +404,7 @@ + tOrbECutoff = .false. + niftot = 1 + allocate(KPointToBasisFn(-nmaxx:nmaxx, -nmaxy:nmaxy, -nmaxz:nmaxz, 2)) ++ KPointToBasisFn = -1 + + t_back_spawn_flex = .true. + occ_virt_level = 0 From 5dd1cdab1b8c2b952e5d5a7324e81da310124d24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Mikael=20=C3=96hman?= Date: Thu, 21 Nov 2024 16:34:58 +0000 Subject: [PATCH 101/116] Fix typo in ParaView copts --- .../p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb index 8f312f89318..340952c3338 100644 --- a/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb +++ b/easybuild/easyconfigs/p/ParaView/ParaView-5.11.1-foss-2022b-CUDA-12.2.0.eb @@ -44,7 +44,7 @@ dependencies = [ _copts = [ # Basic configuration - '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON' + '-DPARAVIEW_INSTALL_DEVELOPMENT_FILES=ON', '-DPARAVIEW_BUILD_SHARED_LIBS=ON', '-DPARAVIEW_USE_MPI=ON', '-DPARAVIEW_ENABLE_FFMPEG=ON', From d447d825a3e7448e0b0b11020d4c06ef8386d4f7 Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 22 Nov 2024 11:13:22 +0100 Subject: [PATCH 102/116] adding easyconfigs: JAGS-4.3.2-foss-2024a.eb --- .../j/JAGS/JAGS-4.3.2-foss-2024a.eb | 38 +++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb diff --git a/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb new file mode 100644 index 00000000000..1077c8fc2a9 --- /dev/null +++ b/easybuild/easyconfigs/j/JAGS/JAGS-4.3.2-foss-2024a.eb @@ -0,0 +1,38 @@ +# This file is an EasyBuild reciPY as per https://github.com/easybuilders/easybuild +# Author: Pablo Escobar Lopez +# Swiss Institute of Bioinformatics +# Biozentrum - University of Basel + +easyblock = 'ConfigureMake' + +name = 'JAGS' +version = '4.3.2' + +homepage = 'http://mcmc-jags.sourceforge.net/' +description = """JAGS is Just Another Gibbs Sampler. It is a program for analysis + of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation """ + +toolchain = {'name': 'foss', 'version': '2024a'} + +source_urls = [ + ('https://sourceforge.net/projects/mcmc-%(namelower)s/files/%(name)s/%(version_major)s.x/Source/', 'download'), +] +sources = [SOURCE_TAR_GZ] +checksums = ['871f556af403a7c2ce6a0f02f15cf85a572763e093d26658ebac55c4ab472fc8'] + +configopts = ' --with-blas="$LIBBLAS" --with-lapack="$LIBLAPACK"' + + +sanity_check_paths = { + 'files': ['bin/%(namelower)s', 'libexec/%(namelower)s-terminal', 'lib/libjags.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["echo 'list modules' | %(namelower)s"] + +modextrapaths = { + 'JAGS_INCLUDE': 'include/%(name)s', + 'JAGS_LIB': 'lib', +} + +moduleclass = 'math' From 4672cb2d36ad2be1d2270b2b3375d1f69bb3a038 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 11:52:39 +0100 Subject: [PATCH 103/116] adding easyconfigs: Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb --- .../Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb | 55 +++++++++++++++++++ 1 file changed, 55 insertions(+) create mode 100644 easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb new file mode 100644 index 00000000000..b1869b01783 --- /dev/null +++ b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb @@ -0,0 +1,55 @@ +easyblock = 'PythonBundle' + +name = 'Slurm-Viewer' +version = '1.0.1' + +homepage = 'https://gitlab.com/lkeb/slurm_viewer' +description = """View the status of a Slurm cluster, including nodes and queue.""" + +toolchain = {'name': 'GCCcore', 'version': '13.2.0'} + +builddependencies = [ + ('hatchling', '1.18.0'), + ('poetry', '1.6.1'), +] + +dependencies = [ + ('Python', '3.11.5'), + ('Python-bundle-PyPI', '2023.10'), + ('pydantic', '2.7.4'), +] + +use_pip = True + +exts_list = [ + ('plotext', '5.2.8', { + 'checksums': ['319a287baabeb8576a711995f973a2eba631c887aa6b0f33ab016f12c50ffebe'], + }), + ('textual', '0.85.2', { + 'checksums': ['2a416995c49d5381a81d0a6fd23925cb0e3f14b4f239ed05f35fa3c981bb1df2'], + }), + ('textual-plotext', '0.2.1', { + 'source_tmpl': 'textual_plotext-%(version)s.tar.gz', + 'checksums': ['bc6f2d75d8e20dda6321f8254dc3decda8f41f60e6e70a3ddd83b652b890c081'], + }), + ('asyncssh', '2.18.0', { + 'checksums': ['1a322161c01f60b9719dc8f39f80db71e61f3f5e04abbc3420ce503126d87123'], + }), + ('slurm-viewer', version, { + 'source_tmpl': 'slurm_viewer-%(version)s-py3-none-any.whl', + 'checksums': ['2e42662881458701a09770a52062cb065527e30a39aac35165056f4ccf288f52'], + }), +] + +sanity_check_paths = { + 'files': ['bin/slurm-viewer', 'bin/slurm-viewer-init'], + 'dirs': ['lib'] +} + +sanity_pip_check = True + +modloadmsg = """Slurm Viewer requires a configuration file. +You can make a default settings file in your home directory by running slurm-viewer-init, +or you can point to a settings file by setting the environment variable $SLURM_VIEW_CONFIG.""" + +moduleclass = 'tools' From d8f9f592d8e3b7c1eb0c11bac69bca570915c68f Mon Sep 17 00:00:00 2001 From: Samuel Moors Date: Fri, 22 Nov 2024 12:04:26 +0100 Subject: [PATCH 104/116] fix parallel for cppyy-cling and remove unnecessary c++std --- easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb b/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb index bcd242d9d23..89c6bc40e3d 100644 --- a/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/c/cppyy/cppyy-3.1.2-GCCcore-13.2.0.eb @@ -21,7 +21,7 @@ dependencies = [ exts_list = [ ('cppyy-cling', '6.30.0', { 'modulename': False, - 'preinstallopts': "export STDCXX=14 && ", + 'preinstallopts': 'MAKE_NPROCS=%(parallel)s', 'checksums': ['5d9e0551a4cb618eb3392001b3dc2c6294f02257f02fcd4d868999ba04f92af1'], }), ('cppyy-backend', '1.15.2', { From 76d684b9180d26d522b222d275b6a00c1b77db9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 12:20:19 +0100 Subject: [PATCH 105/116] add build dependency on binutils --- .../s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb | 1 + 1 file changed, 1 insertion(+) diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb index b1869b01783..d7fd824495b 100644 --- a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb @@ -9,6 +9,7 @@ description = """View the status of a Slurm cluster, including nodes and queue." toolchain = {'name': 'GCCcore', 'version': '13.2.0'} builddependencies = [ + ('binutils', '2.40'), ('hatchling', '1.18.0'), ('poetry', '1.6.1'), ] From 0ff5111ec219a4be015fb60c04dc80ede12189fe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 13:42:47 +0100 Subject: [PATCH 106/116] Rename to SlurmViewer --- ....1-GCCcore-13.2.0.eb => SlurmViewer-1.0.1-GCCcore-13.2.0.eb} | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) rename easybuild/easyconfigs/s/Slurm-Viewer/{Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb => SlurmViewer-1.0.1-GCCcore-13.2.0.eb} (98%) diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb similarity index 98% rename from easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb index d7fd824495b..371a8d85eea 100644 --- a/easybuild/easyconfigs/s/Slurm-Viewer/Slurm-Viewer-1.0.1-GCCcore-13.2.0.eb +++ b/easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb @@ -1,6 +1,6 @@ easyblock = 'PythonBundle' -name = 'Slurm-Viewer' +name = 'SlurmViewer' version = '1.0.1' homepage = 'https://gitlab.com/lkeb/slurm_viewer' From e96add3b085d31949a57b9b3a8f45e41ec0d5dcc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bob=20Dr=C3=B6ge?= Date: Fri, 22 Nov 2024 14:11:28 +0100 Subject: [PATCH 107/116] rename directory to SlurmViewer as well --- .../SlurmViewer-1.0.1-GCCcore-13.2.0.eb | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/s/{Slurm-Viewer => SlurmViewer}/SlurmViewer-1.0.1-GCCcore-13.2.0.eb (100%) diff --git a/easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb b/easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb similarity index 100% rename from easybuild/easyconfigs/s/Slurm-Viewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb rename to easybuild/easyconfigs/s/SlurmViewer/SlurmViewer-1.0.1-GCCcore-13.2.0.eb From f36cd87a6a5c90f0a1a2388b4e98b5436f3a4c0e Mon Sep 17 00:00:00 2001 From: Stefan Wolfsheimer Date: Fri, 22 Nov 2024 14:31:48 +0100 Subject: [PATCH 108/116] adding easyconfigs: R2jags-0.8-9-foss-2023a-R-4.3.2.eb --- .../R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb | 29 +++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb diff --git a/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb b/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb new file mode 100644 index 00000000000..0784b3e87c1 --- /dev/null +++ b/easybuild/easyconfigs/r/R2jags/R2jags-0.8-9-foss-2023a-R-4.3.2.eb @@ -0,0 +1,29 @@ +easyblock = 'RPackage' + +name = 'R2jags' +version = '0.8-9' +versionsuffix = '-R-%(rver)s' + +homepage = 'https://cran.r-project.org/web/packages/R2jags' +description = "Providing wrapper functions to implement Bayesian analysis in JAGS." + +toolchain = {'name': 'foss', 'version': '2023a'} + +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 +] +sources = ['%(name)s_%(version)s.tar.gz'] +checksums = ['df06b8f919eed8dd65bca29bbe7e337718142734d6a31818ce1e49db8faee14c'] + +dependencies = [ + ('R', '4.3.2'), + ('rjags', '4-15', versionsuffix), +] + +sanity_check_paths = { + 'files': [], + 'dirs': [name], +} + +moduleclass = 'math' From 16242b712e57b7dde64d5f655e98e3db26540295 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Jan=20Andr=C3=A9=20Reuter?= Date: Fri, 4 Oct 2024 16:32:05 +0200 Subject: [PATCH 109/116] {mpi}[NVHPC/24.9] Add OpenMPI 5.0.3 MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Signed-off-by: Jan André Reuter --- .../OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb | 63 +++++++++++++++++++ ...MPI-5.0.3_disable_opal_path_nfs_test.patch | 33 ++++++++++ .../OpenMPI-5.0.3_fix_hle_make_errors.patch | 25 ++++++++ 3 files changed, 121 insertions(+) create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch create mode 100644 easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb new file mode 100644 index 00000000000..e6c772bf64e --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3-NVHPC-24.9-CUDA-12.6.0.eb @@ -0,0 +1,63 @@ +name = 'OpenMPI' +version = '5.0.3' + +homepage = 'https://www.open-mpi.org/' +description = """The Open MPI Project is an open source MPI-3 implementation.""" + +toolchain = {'name': 'NVHPC', 'version': '24.9-CUDA-12.6.0'} + +source_urls = ['https://www.open-mpi.org/software/ompi/v%(version_major_minor)s/downloads'] +sources = [SOURCELOWER_TAR_BZ2] +patches = [ + 'OpenMPI-5.0.3_fix_hle_make_errors.patch', + 'OpenMPI-5.0.3_disable_opal_path_nfs_test.patch', + ('OpenMPI-5.0.2_build-with-internal-cuda-header.patch', 1) +] +checksums = [ + {'openmpi-5.0.3.tar.bz2': + '990582f206b3ab32e938aa31bbf07c639368e4405dca196fabe7f0f76eeda90b'}, + {'OpenMPI-5.0.3_fix_hle_make_errors.patch': + '881c907a9f5901d5d6af41cd33dffdcecba4a67a9e5123e602542aea57a80895'}, + {'OpenMPI-5.0.3_disable_opal_path_nfs_test.patch': + '75d4417e35252ea3a19b2792f1b06e9aeb408c253aa4921d77226d57b71dee45'}, + {'OpenMPI-5.0.2_build-with-internal-cuda-header.patch': + 'f52dc470543f35efef10d651dd159c771ae25f8f76a420d20d87abf4dc769ed7'}, +] + +builddependencies = [ + ('pkgconf', '2.2.0'), + ('Perl', '5.38.2'), + ('Autotools', '20231222'), +] + +dependencies = [ + ('zlib', '1.3.1'), + ('hwloc', '2.10.0'), + ('libevent', '2.1.12'), + ('UCX', '1.16.0'), + ('UCX-CUDA', '1.16.0', '-CUDA-%(cudaver)s'), + ('libfabric', '1.21.0'), + ('PMIx', '5.0.2'), + ('PRRTE', '3.0.5'), + ('UCC', '1.3.0'), + ('UCC-CUDA', '1.3.0', '-CUDA-%(cudaver)s'), +] + +# CUDA related patches and custom configure option can be removed if CUDA support isn't wanted. +preconfigopts = 'nvc -Iopal/mca/cuda/include -shared opal/mca/cuda/lib/cuda.c -o opal/mca/cuda/lib/libcuda.so && ' +# Update configure to include changes from the "disable_opal_path_nfs_test" patch +preconfigopts += './autogen.pl --force && ' + +configopts = '--with-cuda=%(start_dir)s/opal/mca/cuda ' +# Required to prevent internal compiler error in opal. +configopts += '--enable-alt-short-float=no ' +# Set PGI compilers manually, as NVHPC compilers are not correctly detected +configopts += 'CC=pgcc CXX=pgc++ FC=pgfortran ' + +# site specific options +# configopts += '--without-psm2 ' +# configopts += '--disable-oshmem ' +# configopts += '--with-gpfs ' +configopts += '--with-slurm ' + +moduleclass = 'mpi' diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch new file mode 100644 index 00000000000..09d9f829f06 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_disable_opal_path_nfs_test.patch @@ -0,0 +1,33 @@ +Disable opal_path_nfs test in OpenMPI 5.0.3 as this test can easily fail on some systems, +when NFS mounts are used. Generally, this test is flaky, which may prevent users +from installing OpenMPI for no apparent reason. + +diff --git a/test/util/Makefile.am b/test/util/Makefile.am +index e5ad472..33d63c4 100644 +--- a/test/util/Makefile.am ++++ b/test/util/Makefile.am +@@ -38,7 +38,6 @@ AM_CPPFLAGS = -I$(top_srcdir)/test/support + + check_PROGRAMS = \ + opal_bit_ops \ +- opal_path_nfs \ + bipartite_graph \ + opal_sha256 + +@@ -80,11 +79,11 @@ opal_bit_ops_LDADD = \ + $(top_builddir)/test/support/libsupport.a + opal_bit_ops_DEPENDENCIES = $(opal_path_nfs_LDADD) + +-opal_path_nfs_SOURCES = opal_path_nfs.c +-opal_path_nfs_LDADD = \ +- $(top_builddir)/opal/lib@OPAL_LIB_NAME@.la \ +- $(top_builddir)/test/support/libsupport.a +-opal_path_nfs_DEPENDENCIES = $(opal_path_nfs_LDADD) ++# opal_path_nfs_SOURCES = opal_path_nfs.c ++# opal_path_nfs_LDADD = \ ++# $(top_builddir)/opal/lib@OPAL_LIB_NAME@.la \ ++# $(top_builddir)/test/support/libsupport.a ++# opal_path_nfs_DEPENDENCIES = $(opal_path_nfs_LDADD) + + #opal_os_path_SOURCES = opal_os_path.c + #opal_os_path_LDADD = \ diff --git a/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch new file mode 100644 index 00000000000..dc9b0671658 --- /dev/null +++ b/easybuild/easyconfigs/o/OpenMPI/OpenMPI-5.0.3_fix_hle_make_errors.patch @@ -0,0 +1,25 @@ +On JUWELS, building OpenMPI 5.0.5 with NVHPC 24.9 fails with errors +related to `__ATOMIC_HLE_ACQUIRE` and `__ATOMIC_HLE_RELEASE` not being +defined. Add an additional macro check to let the build succeed. + +--- a/opal/include/opal/sys/gcc_builtin/atomic.h 2024-07-23 01:23:20.567556032 +0200 ++++ a/opal/include/opal/sys/gcc_builtin/atomic.h 2024-10-02 12:19:53.130698758 +0200 +@@ -187,7 +187,7 @@ + * + *********************************************************************/ + +-#if defined(__HLE__) ++#if defined(__HLE__) && defined(__ATOMIC_HLE_ACQUIRE) && defined(__ATOMIC_HLE_RELEASE) + + # include + +@@ -225,7 +225,7 @@ + __ATOMIC_RELEASE | __ATOMIC_HLE_RELEASE); + } + +-#else /* #if defined(__HLE__) */ ++#else /* #if defined(__HLE__) && defined(__ATOMIC_HLE_ACQUIRE) && defined(__ATOMIC_HLE_RELEASE) */ + + #include "opal/sys/atomic_impl_spinlock.h" + + From 8cdff853d8e2ea30250c7246d15dc88d2aac2884 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 24 Nov 2024 12:10:10 +0000 Subject: [PATCH 110/116] adding easyconfigs: GLPK-5.0-GCCcore-13.3.0.eb --- .../g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) create mode 100644 easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..e0bd3088bc8 --- /dev/null +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb @@ -0,0 +1,36 @@ +easyblock = 'ConfigureMake' + +name = 'GLPK' +version = '5.0' + +homepage = 'https://www.gnu.org/software/glpk/' +description = """The GLPK (GNU Linear Programming Kit) package is intended for + solving large-scale linear programming (LP), + mixed integer programming (MIP), and other related problems. + It is a set of routines written in ANSI C + and organized in the form of a callable library.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +source_urls = [GNU_SOURCE] +sources = [SOURCELOWER_TAR_GZ] +checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] + +builddependencies = [ + ('binutils', '2.41'), +] +dependencies = [ + ('GMP', '6.3.0'), +] + +configopts = '--with-gmp' + + +sanity_check_paths = { + 'files': ['bin/glpsol', 'include/%(namelower)s.h', 'lib/libglpk.a', 'lib/libglpk.%s' % SHLIB_EXT], + 'dirs': [], +} + +sanity_check_commands = ["glpsol --help"] + +moduleclass = 'tools' From a5fd66dbe0034c642e7f27886a85c661a85f13c8 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 12:18:23 +0000 Subject: [PATCH 111/116] binutils version --- easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb index e0bd3088bc8..ad96183a02b 100644 --- a/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/g/GLPK/GLPK-5.0-GCCcore-13.3.0.eb @@ -17,7 +17,7 @@ sources = [SOURCELOWER_TAR_GZ] checksums = ['4a1013eebb50f728fc601bdd833b0b2870333c3b3e5a816eeba921d95bec6f15'] builddependencies = [ - ('binutils', '2.41'), + ('binutils', '2.42'), ] dependencies = [ ('GMP', '6.3.0'), From cd1f1b9ed7bddd7b0b372265437199a8b7bc8a43 Mon Sep 17 00:00:00 2001 From: Simon Branford Date: Sun, 24 Nov 2024 16:00:11 +0000 Subject: [PATCH 112/116] adding easyconfigs: Xvfb-21.1.14-GCCcore-13.3.0.eb --- .../x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb | 126 ++++++++++++++++++ 1 file changed, 126 insertions(+) create mode 100644 easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb new file mode 100644 index 00000000000..d90dad9791b --- /dev/null +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb @@ -0,0 +1,126 @@ +easyblock = 'Bundle' + +name = 'Xvfb' +version = '21.1.14' + +homepage = 'https://www.x.org/releases/X11R7.6/doc/man/man1/Xvfb.1.xhtml' +description = """Xvfb is an X server that can run on machines with no display hardware and no physical input devices. + It emulates a dumb framebuffer using virtual memory.""" + +toolchain = {'name': 'GCCcore', 'version': '13.3.0'} + +builddependencies = [ + ('binutils', '2.42'), + ('pkgconf', '2.2.0'), + ('Python', '3.12.3'), + ('Meson', '1.4.0'), + ('Ninja', '1.12.1'), + ('libxslt', '1.1.42'), + ('gettext', '0.22.5'), + ('Bison', '3.8.2'), +] + +dependencies = [ + ('X11', '20240607'), + ('pixman', '0.43.4'), + ('libdrm', '2.4.122'), + ('Mesa', '24.1.3'), + ('nettle', '3.10'), + ('libunwind', '1.8.1'), + ('XZ', '5.4.5'), +] + +default_easyblock = 'ConfigureMake' + +local_xvfb_configopts = "--enable-xvfb --disable-xorg --disable-xnest --disable-xwin " +local_xvfb_configopts += "--disable-dri --disable-dri2 --disable-dri3 --disable-libunwind " +local_xvfb_configopts += "--with-fontrootdir=%(installdir)s/share/fonts/X11" + +# use 'make V=1' to see compiler commands +local_xvfb_buildopts = "V=1 " + +# use static libraries for nettle & libunwind, so avoid errors like "No rule to make target '-lnettle'" +local_xvfb_buildopts += 'SHA1_LIBS="$EBROOTNETTLE/lib*/libnettle.a" ' +local_xvfb_buildopts += 'LIBUNWIND_LIBS="$EBROOTLIBUNWIND/lib*/libunwind.a $EBROOTXZ/lib*/liblzma.a"' + +default_component_specs = { + 'sources': [SOURCE_TAR_GZ], + 'start_dir': '%(name)s-%(version)s', +} + +local_font_misc_preconfigopts = "export PKG_CONFIG_PATH=%(installdir)s/lib/pkgconfig:$PKG_CONFIG_PATH && " +local_font_misc_preconfigopts += "export PATH=%(installdir)s/bin:$PATH && " + +components = [ + ('mkfontscale', '1.2.3', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['3a026b468874eb672a1d0a57dbd3ddeda4f0df09886caf97d30097b70c2df3f8'], + }), + ('mkfontdir', '1.0.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['bccc5fb7af1b614eabe4a22766758c87bfc36d66191d08c19d2fa97674b7b5b7'], + }), + ('bdftopcf', '1.1', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['699d1a62012035b1461c7f8e3f05a51c8bd6f28f348983249fb89bbff7309b47'], + }), + ('font-util', '1.4.1', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['f029ae80cdd75d89bee7f7af61c21e07982adfb9f72344a158b99f91f77ef5ed'], + }), + ('font-misc-misc', '1.1.3', { + 'source_urls': ['https://www.x.org/archive/individual/font/'], + 'checksums': ['bece4a9482b3cb6f7fad2164fd3b394d22dfe1ad2f96f60030a703bcff30f5a5'], + 'preconfigopts': local_font_misc_preconfigopts, + }), + ('xkbcomp', '1.4.7', { + 'source_urls': ['https://www.x.org/archive/individual/app/'], + 'checksums': ['00cecc490fcbe2f789cf13c408c459673c2c33ab758d802677321cffcda35373'], + }), + ('xkeyboard-config', '2.43', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/data/xkeyboard-config/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['c810f362c82a834ee89da81e34cd1452c99789339f46f6037f4b9e227dd06c01'], + 'configopts': '-Dxorg-rules-symlinks=true', + }), + ('xauth', '1.1.3', { + 'source_urls': ['https://www.x.org/releases/individual/app/'], + 'checksums': ['88c288e0a30bf071631118644f5232cae3a79713a7c82dd31a236e8e2c6fca15'], + }), + ('libxcvt', '0.1.2', { + 'easyblock': 'MesonNinja', + 'source_urls': ['https://www.x.org/archive/individual/lib/'], + 'sources': [SOURCE_TAR_XZ], + 'checksums': ['0561690544796e25cfbd71806ba1b0d797ffe464e9796411123e79450f71db38'], + }), + (name, version, { + 'source_urls': ['https://www.x.org/releases/individual/xserver/'], + 'sources': ['xorg-server-%(version)s.tar.gz'], + 'patches': [('xvfb-run', '.')], + 'checksums': [ + 'b79dbaf668c67da25c4eb5b395eec60f2593240519aefdd3e8645023ef46226f', # xorg-server-21.1.9.tar.gz + 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run + ], + 'start_dir': 'xorg-server-%(version)s', + 'configopts': local_xvfb_configopts, + 'buildopts': local_xvfb_buildopts, + 'installopts': local_xvfb_buildopts, + }), +] + +# enable exec permissions for xvfb-run after copying; +# need to also enable user write permissions on xvfb-run to ensure that copying with preserved permissions works +postinstallcmds = ["chmod u+w xvfb-run && cp -a xvfb-run %(installdir)s/bin/ && chmod a+x %(installdir)s/bin/xvfb-run"] + +sanity_check_paths = { + 'files': ['bin/Xvfb', 'bin/xvfb-run'], + 'dirs': ['lib/xorg', 'share/fonts/X11/misc', 'share/fonts/X11/util'], +} + +sanity_check_commands = [ + "xvfb-run --help", + "xvfb-run --error-file %(builddir)s/xvfb-run-test.err echo hello", +] + +moduleclass = 'vis' From 5754839274705a354eb9b86466ad770425755008 Mon Sep 17 00:00:00 2001 From: Simon Branford <4967+branfosj@users.noreply.github.com> Date: Sun, 24 Nov 2024 16:01:35 +0000 Subject: [PATCH 113/116] Update Xvfb-21.1.14-GCCcore-13.3.0.eb --- easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb index d90dad9791b..1ee18273171 100644 --- a/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb +++ b/easybuild/easyconfigs/x/Xvfb/Xvfb-21.1.14-GCCcore-13.3.0.eb @@ -99,7 +99,7 @@ components = [ 'sources': ['xorg-server-%(version)s.tar.gz'], 'patches': [('xvfb-run', '.')], 'checksums': [ - 'b79dbaf668c67da25c4eb5b395eec60f2593240519aefdd3e8645023ef46226f', # xorg-server-21.1.9.tar.gz + 'b79dbaf668c67da25c4eb5b395eec60f2593240519aefdd3e8645023ef46226f', # xorg-server-21.1.14.tar.gz 'fd6d13182b77871d4f65fccdaebb8a72387a726426066d3f8e6aa26b010ea0e8', # xvfb-run ], 'start_dir': 'xorg-server-%(version)s', From 3075e96a66253cbe5f229c0656562b3e55237cfc Mon Sep 17 00:00:00 2001 From: satishskamath <41335185+satishskamath@users.noreply.github.com> Date: Tue, 26 Nov 2024 12:19:24 +0100 Subject: [PATCH 114/116] Update easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Bob Dröge --- easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb index e92b712357a..72f3e310448 100644 --- a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb +++ b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb @@ -6,7 +6,7 @@ description = """A very powerful performance visualization and analysis tool bas traces that can be used to analyse any information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae.""" -toolchain = {'name': 'foss', 'version': '2023a'} +toolchain = {'name': 'GCC', 'version': '12.3.0'} source_urls = ['https://ftp.tools.bsc.es/wxparaver/'] sources = ['wxparaver-%(version)s-src.tar.bz2'] From 2eceb4ba8e53f567f7816194296244d10b112fd2 Mon Sep 17 00:00:00 2001 From: satishskamath <41335185+satishskamath@users.noreply.github.com> Date: Tue, 26 Nov 2024 12:23:54 +0100 Subject: [PATCH 115/116] Rename Paraver-4.11.4-foss-2023a.eb to Paraver-4.11.4-GCC-12.3.0.eb --- ...{Paraver-4.11.4-foss-2023a.eb => Paraver-4.11.4-GCC-12.3.0.eb} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename easybuild/easyconfigs/p/Paraver/{Paraver-4.11.4-foss-2023a.eb => Paraver-4.11.4-GCC-12.3.0.eb} (100%) diff --git a/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb b/easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-12.3.0.eb similarity index 100% rename from easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-foss-2023a.eb rename to easybuild/easyconfigs/p/Paraver/Paraver-4.11.4-GCC-12.3.0.eb From 39af9ad5bac3bca314750d67b3f1cec6d423dc71 Mon Sep 17 00:00:00 2001 From: PhoenixEmik Date: Tue, 26 Nov 2024 23:24:44 +0800 Subject: [PATCH 116/116] adding easyconfigs: picard-3.3.0-Java-17.eb --- .../p/picard/picard-3.3.0-Java-17.eb | 62 +++++++++++++++++++ 1 file changed, 62 insertions(+) create mode 100644 easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb diff --git a/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb new file mode 100644 index 00000000000..8aafd645195 --- /dev/null +++ b/easybuild/easyconfigs/p/picard/picard-3.3.0-Java-17.eb @@ -0,0 +1,62 @@ +## +# This is an easyconfig file for EasyBuild, see https://github.com/easybuilders/easybuild +# +# This is a contribution from Phoenix HPC Service, The University of Adelaide, Australia +# Homepage: https://www.adelaide.edu.au/phoenix/ +# +# Copyright:: adelaide.edu.au/phoenix +# Authors:: Robert Qiao , Exe Escobedo +# License:: MIT +# +# 2.10.1: +# Adam Huffman +# The Francis Crick Institute +# 2.18.11: +# Jonas Demeulemeester +# The Francis Crick Institute +# 2.21.1 +# Pavel Grochal (INUITS) +# 2.25.1 +# J. Sassmannshausen (GSTT) +# 2.25.5 +# Erica Bianco (HPCNow!) +# 2.26.10 +# Christoph Siegert (Leipzig University) +# 3.0.0 +# Graham Derryberry (UTK) +# 3.3.0 +# Emik Lin (HKUMed CPOS) +## + +easyblock = 'JAR' + +name = 'picard' +version = '3.3.0' +versionsuffix = '-Java-%(javaver)s' + +homepage = 'https://broadinstitute.github.io/picard/' +description = """A set of tools (in Java) for working with next generation sequencing data in the BAM format.""" + +toolchain = SYSTEM + +source_urls = ['https://github.com/broadinstitute/picard/releases/download/%(version)s'] +sources = [{ + 'filename': '%(name)s-%(version)s.jar', + 'download_filename': '%(name)s.jar', +}] +checksums = ['58819a7660646b74b34e282f5d4d21c8dbaea22ddeff96e3258755dafa0f86dc'] + +postinstallcmds = ["mv %(installdir)s/%(name)s-%(version)s.jar %(installdir)s/%(name)s.jar"] + +dependencies = [('Java', '17')] + +sanity_check_commands = ['java -jar $EBROOTPICARD/picard.jar 2>&1 | grep USAGE'] + +sanity_check_paths = { + 'files': ['picard.jar'], + 'dirs': [], +} + +modloadmsg = "To execute picard run: java -jar $EBROOTPICARD/%(name)s.jar" + +moduleclass = 'bio'