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{bio}[foss/2023b] GROMACS v2024.2 w/ CUDA 12.5.0 #20809
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# 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 <wiktor.jurkowski@gmail.com> | ||
# * Fotis Georgatos <fotis@cern.ch> | ||
# * George Tsouloupas <g.tsouloupas@cyi.ac.cy> | ||
# * Kenneth Hoste <kenneth.hoste@ugent.be> | ||
# * Adam Huffman <adam.huffman@crick.ac.uk> | ||
# * Ake Sandgren <ake.sandgren@hpc2n.umu.se> | ||
# * J. Sassmannshausen <Crick HPC team> | ||
# * Dugan Witherick <dugan.witherick@warwick.ac.uk> | ||
# * Christoph Siegert <christoph.siegert@uni-leipzig.de> | ||
# License:: MIT/GPL | ||
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name = 'GROMACS' | ||
version = '2024.2' | ||
versionsuffix = '-CUDA-%(cudaver)s' | ||
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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. | ||
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This is a GPU enabled build, containing both MPI and threadMPI binaries. | ||
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It also contains the gmxapi extension for the single precision MPI build. | ||
""" | ||
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toolchain = {'name': 'foss', 'version': '2023b'} | ||
toolchainopts = {'openmp': True, 'usempi': True} | ||
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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-2024.2.tar.gz': '802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'}, | ||
{'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': | ||
'7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, | ||
{'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': | ||
'6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}, | ||
] | ||
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builddependencies = [ | ||
('CMake', '3.27.6'), | ||
('scikit-build', '0.17.6'), | ||
] | ||
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dependencies = [ | ||
('CUDA', '12.5.0', '', SYSTEM), | ||
('UCX-CUDA', '1.15.0', versionsuffix), | ||
('Python', '3.11.5'), | ||
('SciPy-bundle', '2023.11'), | ||
('networkx', '3.2.1'), | ||
('mpi4py', '3.1.5'), | ||
] | ||
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exts_defaultclass = 'PythonPackage' | ||
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exts_default_options = { | ||
'source_urls': [PYPI_SOURCE], | ||
'use_pip': True, | ||
'download_dep_fail': True, | ||
'sanity_pip_check': True, | ||
} | ||
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exts_list = [ | ||
('gmxapi', '0.4.2', { | ||
'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', | ||
'source_tmpl': 'gromacs-2023.3.tar.gz', | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. This should correspond to the current version (and the version of gmxapi needs to be bumped as well). There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Ugh... Fixed in 5dc1057 There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. @boegel what about the gmxapi version? I'm not completely sure what the correct version number should be. https://gitlab.com/gromacs/gromacs/-/blob/v2024.2/python_packaging/gmxapi/pyproject.toml?ref_type=tags has 0.4.1 (?!), but https://gitlab.com/gromacs/gromacs/-/blob/v2024.2/python_packaging/gmxapi/src/gmxapi/version.py?ref_type=tags and https://manual.gromacs.org/2024.2/gmxapi/index.html say 0.5.0a1. So I guess the latter?? |
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'start_dir': 'python_packaging/gmxapi', | ||
'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'], | ||
}), | ||
] | ||
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modextrapaths = { | ||
'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages', | ||
} | ||
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moduleclass = 'bio' |
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I was recently looking into GROMACS 2024.2 as well, and was wondering if this patch is still required. https://gitlab.com/gromacs/gromacs/-/merge_requests/4093 may solve the same or at least similar issue. Looks like @akesandgren added this patch, so maybe he knows?
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GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch should still be relevant as long as it passes patching.
Especially the "Don't drop relevant PYTHONPATH and LD_LIBRARY_PATH settings." part is vital.
I haven't looked at 2024.2 but I assume they haven't fixed those parts yet.
And GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch is just an extra precaution to keep OMMP_NUM_THREADS and --ntomp in sync.