(partial) EasyBuild log for failed build of /dev/shm/ake/tmp/eb-dfk3ajys/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb (PR(s) #20809)

GROMACS-2024.2-foss-2023b-CUDA-12.5.0_partial.log

== 2024-06-20 07:24:49,013 easyblock.py:313 INFO This is EasyBuild 4.9.3.dev0-rd4098ba35371823fd3b92f5732e2227b66092fa8 (framework: 4.9.3.dev0-rd4098ba35371823fd3b92f5732e2227b66092fa8, easyblocks: 4.9.3.dev0-rd1f2231b2de4f8548c75c7367456873a8c33b5f9) on host b-cn1604.hpc2n.umu.se.
== 2024-06-20 07:24:49,013 easyblock.py:319 INFO This is easyblock EB_GROMACS from module easybuild.easyblocks.gromacs (/home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyblocks/g/gromacs.py)
== 2024-06-20 07:24:49,013 easyblock.py:1056 INFO Build dir set to /dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0
== 2024-06-20 07:24:49,013 config.py:700 DEBUG software install path as specified by 'installpath' and 'subdir_software': /home/a/ake/easybuild-amd64_ubuntu2204_zen4/software
== 2024-06-20 07:24:49,013 easyconfig.py:2655 DEBUG Determining software installation subdir for GROMACS EasyConfig @ /dev/shm/ake/tmp/eb-dfk3ajys/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
== 2024-06-20 07:24:49,013 easyconfig.py:2658 DEBUG Using fixed naming software installation subdir: GROMACS/2024.2-foss-2023b-CUDA-12.5.0
== 2024-06-20 07:24:49,014 easyblock.py:1113 INFO Software install dir set to /home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/GROMACS/2024.2-foss-2023b-CUDA-12.5.0
== 2024-06-20 07:24:49,014 config.py:700 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules
== 2024-06-20 07:24:49,014 easyblock.py:1118 INFO Module install dir set to /home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules/all
== 2024-06-20 07:24:49,014 easyblock.py:288 INFO Init completed for application name GROMACS version 2024.2
== 2024-06-20 07:24:49,014 easyblock.py:4228 INFO Obtained application instance of for GROMACS (easyblock: None)
== 2024-06-20 07:24:49,014 easyblock.py:4241 DEBUG Skip set to False
== 2024-06-20 07:24:49,014 easyconfig.py:1702 INFO Generating template values...
== 2024-06-20 07:24:49,015 templates.py:201 DEBUG config: GROMACS EasyConfig @ /dev/shm/ake/tmp/eb-dfk3ajys/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
== 2024-06-20 07:24:49,015 templates.py:231 DEBUG version found in easyconfig is 2024.2
== 2024-06-20 07:24:49,015 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-06-20 07:24:49,015 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-06-20 07:24:49,015 templates.py:333 DEBUG name: name, config: GROMACS
== 2024-06-20 07:24:49,015 templates.py:333 DEBUG name: parallel, config: None
== 2024-06-20 07:24:49,015 templates.py:333 DEBUG name: version, config: 2024.2
== 2024-06-20 07:24:49,015 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-06-20 07:24:49,016 templates.py:333 DEBUG name: versionprefix, config: 
== 2024-06-20 07:24:49,016 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-06-20 07:24:49,016 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-06-20 07:24:49,016 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='gromacs', cuda_cc_cmake='70;80;86;89;90', cuda_cc_semicolon_sep='7.0;8.0;8.6;8.9;9.0', cuda_cc_space_sep='7.0 8.0 8.6 8.9 9.0', cuda_compute_capabilities='7.0,8.0,8.6,8.9,9.0', cuda_sm_comma_sep='sm_70,sm_80,sm_86,sm_89,sm_90', cuda_sm_space_sep='sm_70 sm_80 sm_86 sm_89 sm_90', cudamajver='12', cudaminver='5', cudashortver='12.5', cudaver='12.5.0', github_account='gromacs', module_name='GROMACS/2024.2-CUDA-12.5.0', mpi_cmd_prefix='mpirun -n 1', name='GROMACS', nameletter='G', nameletterlower='g', namelower='gromacs', pymajver='3', pyminver='11', pyshortver='3.11', pyver='3.11.5', sysroot='', toolchain_name='foss', toolchain_version='2023b', version='2024.2', version_major='2024', version_major_minor='2024.2', version_minor='2', versionprefix='', versionsuffix='-CUDA-12.5.0'
== 2024-06-20 07:24:49,016 one.py:150 DEBUG Not copying '__builtins__' variable from parsed easyconfig
== 2024-06-20 07:24:49,017 one.py:529 DEBUG Extracted comments:
{'above': {},
 'header': ['# 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',
            ''],
 'inline': {},
 'iterabove': {},
 'iterinline': {},
 'tail': []}
== 2024-06-20 07:24:49,018 one.py:180 INFO Skipping reformatting value for parameter 'toolchain'
== 2024-06-20 07:24:49,018 one.py:180 INFO Skipping reformatting value for parameter 'toolchainopts'
== 2024-06-20 07:24:49,020 easyconfig.py:1265 DEBUG Dumped easyconfig: # 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

name = 'GROMACS'
version = '2024.2'
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.%(namelower)s.org/pub/%(namelower)s/',
    'ftp://ftp.%(namelower)s.org/pub/%(namelower)s/',
]
sources = [SOURCELOWER_TAR_GZ]
patches = [
    '%(name)s-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch',
    '%(name)s-2023.1_fix_tests_for_gmx_thread_mpi.patch',
]
checksums = [
    {SOURCELOWER_TAR_GZ: '802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'},
    {'%(name)s-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'},
    {'%(name)s-2023.1_fix_tests_for_gmx_thread_mpi.patch': '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'},
]

builddependencies = [
    ('CMake', '3.27.6', '', ('GCCcore', '13.2.0')),
    ('scikit-build', '0.17.6', '', ('GCCcore', '13.2.0')),
]
dependencies = [
    ('CUDA', '12.5.0', '', SYSTEM),
    ('UCX-CUDA', '1.15.0', '-CUDA-%(cudaver)s', ('GCCcore', '13.2.0')),
    ('Python', '3.11.5', '', ('GCCcore', '13.2.0')),
    ('SciPy-bundle', '2023.11', '', ('gfbf', '2023b')),
    ('networkx', '3.2.1', '', ('gfbf', '2023b')),
    ('mpi4py', '3.1.5', '', ('gompi', '2023b')),
]

exts_defaultclass = 'PythonPackage'
build_shared_libs = True

exts_default_options = {
    'download_dep_fail': True,
    'sanity_pip_check': True,
    'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'],
    'use_pip': True,
}

exts_list = [
    ('gmxapi', '0.4.2', {'preinstallopts': 'export CMAKE_ARGS="-Dgmxapi_ROOT=%(installdir)s -C %(installdir)s/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && ', 'source_tmpl': 'gromacs-2023.3.tar.gz', 'start_dir': 'python_packaging/gmxapi', 'checksums': ['4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb']}),
]

modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'}

moduleclass = 'bio'

== 2024-06-20 07:24:49,020 filetools.py:1912 INFO Creating directory /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401 (parents: True, set_gid: False, sticky: False)
== 2024-06-20 07:24:49,020 easyblock.py:4482 INFO Dumped easyconfig instance to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb
== 2024-06-20 07:24:49,021 filetools.py:1912 INFO Creating directory /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks (parents: True, set_gid: False, sticky: False)
== 2024-06-20 07:24:49,024 filetools.py:2425 INFO /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyblocks/generic/cmakemake.py copied to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks/cmakemake.py
== 2024-06-20 07:24:49,024 easyblock.py:4462 INFO Dumped easyblock cmakemake.py required for reproduction to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks
== 2024-06-20 07:24:49,025 filetools.py:1931 DEBUG Not creating existing path /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks
== 2024-06-20 07:24:49,028 filetools.py:2425 INFO /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks/configuremake.py
== 2024-06-20 07:24:49,028 easyblock.py:4462 INFO Dumped easyblock configuremake.py required for reproduction to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks
== 2024-06-20 07:24:49,029 filetools.py:1931 DEBUG Not creating existing path /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks
== 2024-06-20 07:24:49,057 filetools.py:2425 INFO /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyblocks/g/gromacs.py copied to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks/gromacs.py
== 2024-06-20 07:24:49,057 easyblock.py:4462 INFO Dumped easyblock gromacs.py required for reproduction to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/easyblocks
== 2024-06-20 07:24:49,058 filetools.py:1912 INFO Creating directory /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/hooks (parents: True, set_gid: False, sticky: False)
== 2024-06-20 07:24:49,061 filetools.py:2425 INFO /hpc2n/eb/custom/easyhooks/hpc2n_hooks.py copied to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/hooks/hpc2n_hooks.py
== 2024-06-20 07:24:49,061 easyblock.py:4494 INFO Dumped hooks file /hpc2n/eb/custom/easyhooks/hpc2n_hooks.py which is (potentially) required for reproduction to /dev/shm/ake/tmp/eb-dfk3ajys/reprod_20240620072449_663401/hooks/hpc2n_hooks.py
== 2024-06-20 07:24:49,064 gromacs.py:775 DEBUG List of configure options to iterate over: ['-DGMX_MPI=OFF -DGMX_THREAD_MPI=ON -DGMX_DOUBLE=OFF ', '-DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_DOUBLE=OFF ', '-DGMX_MPI=OFF -DGMX_THREAD_MPI=ON -DGMX_DOUBLE=ON ', '-DGMX_MPI=ON -DGMX_THREAD_MPI=OFF -DGMX_DOUBLE=ON ']
== 2024-06-20 07:24:49,064 gromacs.py:776 INFO Building these variants of GROMACS: single precision nompi, single precision mpi, double precision nompi, double precision mpi
== 2024-06-20 07:24:49,064 easyblock.py:2236 INFO Number of iterations to perform for central part of installation procedure: 4
== 2024-06-20 07:24:49,065 build_log.py:267 INFO building and installing MPI/GCC/13.2.0/OpenMPI/4.1.6/GROMACS/2024.2-CUDA-12.5.0...
== 2024-06-20 07:24:49,065 config.py:700 DEBUG software install path as specified by 'installpath' and 'subdir_software': /home/a/ake/easybuild-amd64_ubuntu2204_zen4/software
== 2024-06-20 07:24:49,066 filetools.py:1967 INFO Lock /home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/.locks/_home_a_ake_easybuild-amd64_ubuntu2204_zen4_software_GROMACS_2024.2-foss-2023b-CUDA-12.5.0.lock exists!
== 2024-06-20 07:24:49,258 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): Lock /home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/.locks/_home_a_ake_easybuild-amd64_ubuntu2204_zen4_software_GROMACS_2024.2-foss-2023b-CUDA-12.5.0.lock already exists, aborting! (at easybuild/tools/filetools.py:2003 in check_lock)
== 2024-06-20 07:24:49,258 easyblock.py:4285 WARNING build failed (first 300 chars): Lock /home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/.locks/_home_a_ake_easybuild-amd64_ubuntu2204_zen4_software_GROMACS_2024.2-foss-2023b-CUDA-12.5.0.lock already exists, aborting!
== 2024-06-20 07:24:49,258 easyblock.py:328 INFO Closing log for application name GROMACS version 2024.2