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June 20, 2024 06:02
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(partial) EasyBuild log for failed build of /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb (PR(s) #20809)
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| == 2024-06-20 08:02:58,282 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 08:02:58,282 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 08:02:58,282 easyblock.py:1056 INFO Build dir set to /dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0 | |
| == 2024-06-20 08:02:58,282 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 08:02:58,282 easyconfig.py:2655 DEBUG Determining software installation subdir for GROMACS EasyConfig @ /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | |
| == 2024-06-20 08:02:58,282 easyconfig.py:2658 DEBUG Using fixed naming software installation subdir: GROMACS/2024.2-foss-2023b-CUDA-12.5.0 | |
| == 2024-06-20 08:02:58,282 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 08:02:58,282 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 08:02:58,282 easyblock.py:1118 INFO Module install dir set to /home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules/all | |
| == 2024-06-20 08:02:58,282 easyblock.py:288 INFO Init completed for application name GROMACS version 2024.2 | |
| == 2024-06-20 08:02:58,282 easyblock.py:4228 INFO Obtained application instance of for GROMACS (easyblock: None) | |
| == 2024-06-20 08:02:58,283 easyblock.py:4241 DEBUG Skip set to False | |
| == 2024-06-20 08:02:58,283 easyconfig.py:1702 INFO Generating template values... | |
| == 2024-06-20 08:02:58,283 templates.py:201 DEBUG config: GROMACS EasyConfig @ /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | |
| == 2024-06-20 08:02:58,283 templates.py:231 DEBUG version found in easyconfig is 2024.2 | |
| == 2024-06-20 08:02:58,283 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s | |
| == 2024-06-20 08:02:58,283 templates.py:333 DEBUG name: github_account, config: %(namelower)s | |
| == 2024-06-20 08:02:58,283 templates.py:333 DEBUG name: name, config: GROMACS | |
| == 2024-06-20 08:02:58,283 templates.py:333 DEBUG name: parallel, config: None | |
| == 2024-06-20 08:02:58,283 templates.py:333 DEBUG name: version, config: 2024.2 | |
| == 2024-06-20 08:02:58,283 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s | |
| == 2024-06-20 08:02:58,283 templates.py:333 DEBUG name: versionprefix, config: | |
| == 2024-06-20 08:02:58,283 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' | |
| == 2024-06-20 08:02:58,284 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 08:02:58,284 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 08:02:58,284 one.py:150 DEBUG Not copying '__builtins__' variable from parsed easyconfig | |
| == 2024-06-20 08:02:58,285 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 08:02:58,285 one.py:180 INFO Skipping reformatting value for parameter 'toolchain' | |
| == 2024-06-20 08:02:58,285 one.py:180 INFO Skipping reformatting value for parameter 'toolchainopts' | |
| == 2024-06-20 08:02:58,286 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 08:02:58,286 filetools.py:1912 INFO Creating directory /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864 (parents: True, set_gid: False, sticky: False) | |
| == 2024-06-20 08:02:58,286 easyblock.py:4482 INFO Dumped easyconfig instance to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | |
| == 2024-06-20 08:02:58,287 filetools.py:1912 INFO Creating directory /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks (parents: True, set_gid: False, sticky: False) | |
| == 2024-06-20 08:02:58,290 filetools.py:2425 INFO /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks/configuremake.py | |
| == 2024-06-20 08:02:58,290 easyblock.py:4462 INFO Dumped easyblock configuremake.py required for reproduction to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks | |
| == 2024-06-20 08:02:58,290 filetools.py:1931 DEBUG Not creating existing path /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks | |
| == 2024-06-20 08:02:58,293 filetools.py:2425 INFO /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyblocks/generic/cmakemake.py copied to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks/cmakemake.py | |
| == 2024-06-20 08:02:58,293 easyblock.py:4462 INFO Dumped easyblock cmakemake.py required for reproduction to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks | |
| == 2024-06-20 08:02:58,293 filetools.py:1931 DEBUG Not creating existing path /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks | |
| == 2024-06-20 08:02:58,309 filetools.py:2425 INFO /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyblocks/g/gromacs.py copied to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks/gromacs.py | |
| == 2024-06-20 08:02:58,310 easyblock.py:4462 INFO Dumped easyblock gromacs.py required for reproduction to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/easyblocks | |
| == 2024-06-20 08:02:58,310 filetools.py:1912 INFO Creating directory /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/hooks (parents: True, set_gid: False, sticky: False) | |
| == 2024-06-20 08:02:58,311 filetools.py:2425 INFO /hpc2n/eb/custom/easyhooks/hpc2n_hooks.py copied to /dev/shm/ake/tmp/eb-27x4ay8y/reprod_20240620080258_666864/hooks/hpc2n_hooks.py | |
| == 2024-06-20 08:02:58,311 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-27x4ay8y/reprod_20240620080258_666864/hooks/hpc2n_hooks.py | |
| == 2024-06-20 08:02:58,314 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 08:02:58,314 gromacs.py:776 INFO Building these variants of GROMACS: single precision nompi, single precision mpi, double precision nompi, double precision mpi | |
| == 2024-06-20 08:02:58,314 easyblock.py:2236 INFO Number of iterations to perform for central part of installation procedure: 4 | |
| == 2024-06-20 08:02:58,314 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 08:02:58,314 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 08:02:58,315 filetools.py:2005 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 does not exist | |
| == 2024-06-20 08:02:58,315 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 08:02:58,315 filetools.py:1946 INFO Creating lock at /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... | |
| == 2024-06-20 08:02:58,315 filetools.py:1912 INFO Creating directory /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 (parents: True, set_gid: False, sticky: False) | |
| == 2024-06-20 08:02:58,317 filetools.py:1955 INFO Lock created: /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 | |
| == 2024-06-20 08:02:58,317 easyblock.py:3941 DEBUG Not skipping fetch step (skippable: False, skip: None, skipsteps: [], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False) | |
| == 2024-06-20 08:02:58,317 build_log.py:267 INFO fetching files... | |
| == 2024-06-20 08:02:58,317 easyblock.py:3950 INFO Starting fetch step | |
| == 2024-06-20 08:02:58,317 easyconfig.py:1702 INFO Generating template values... | |
| == 2024-06-20 08:02:58,317 templates.py:201 DEBUG config: GROMACS EasyConfig @ /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | |
| == 2024-06-20 08:02:58,317 templates.py:231 DEBUG version found in easyconfig is 2024.2 | |
| == 2024-06-20 08:02:58,318 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s | |
| == 2024-06-20 08:02:58,318 templates.py:333 DEBUG name: github_account, config: %(namelower)s | |
| == 2024-06-20 08:02:58,318 templates.py:333 DEBUG name: name, config: GROMACS | |
| == 2024-06-20 08:02:58,318 templates.py:333 DEBUG name: parallel, config: None | |
| == 2024-06-20 08:02:58,318 templates.py:333 DEBUG name: version, config: 2024.2 | |
| == 2024-06-20 08:02:58,318 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s | |
| == 2024-06-20 08:02:58,318 templates.py:333 DEBUG name: versionprefix, config: | |
| == 2024-06-20 08:02:58,318 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' | |
| == 2024-06-20 08:02:58,318 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 08:02:58,318 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='gromacs', builddir='/dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0', 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', installdir='/home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/GROMACS/2024.2-foss-2023b-CUDA-12.5.0', 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', start_dir='None', 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 08:02:58,318 easyblock.py:3958 INFO Running method fetch_step part of step fetch | |
| == 2024-06-20 08:02:58,318 easyblock.py:2358 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version | |
| == 2024-06-20 08:02:58,319 easyblock.py:809 INFO Considering directory in which easyconfig file is located when searching for gromacs-2024.2.tar.gz: /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS | |
| == 2024-06-20 08:02:58,319 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /home/a/ake/Projects/easybuild-dev/easybuild-framework/eb | |
| == 2024-06-20 08:02:58,319 tools.py:290 INFO Not considering /home/a/ake/Projects/easybuild-dev (no easybuild/easyconfigs subdir found) | |
| == 2024-06-20 08:02:58,319 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /afs/hpc2n.umu.se/home/a/ake/Projects/git-repos/easybuild/easybuild_common/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,319 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /hpc2n/eb/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,320 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,320 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,320 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/fake_vsc_p7v0k1cs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,320 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/included-easyblocks-y0jubo6i/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,320 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,320 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/git/ext/gitdb/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:307 DEBUG Added /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs to list of paths for easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-framework/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-install/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-base/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python310.zip/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/lib-dynload/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/.local/lib/python3.10/site-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.10/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,321 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/gitdb/ext/smmap/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,333 easyblock.py:851 INFO Found file gromacs-2024.2.tar.gz at /home/a/ake/easybuild-src/sources/g/GROMACS/gromacs-2024.2.tar.gz | |
| == 2024-06-20 08:02:58,334 easyblock.py:452 DEBUG File /home/a/ake/easybuild-src/sources/g/GROMACS/gromacs-2024.2.tar.gz found for source gromacs-2024.2.tar.gz | |
| == 2024-06-20 08:02:58,334 easyblock.py:496 INFO Added sources: [{'name': 'gromacs-2024.2.tar.gz', 'path': '/home/a/ake/easybuild-src/sources/g/GROMACS/gromacs-2024.2.tar.gz', 'cmd': None, 'checksum': {'gromacs-2024.2.tar.gz': '802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b'}, 'finalpath': '/dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0'}] | |
| == 2024-06-20 08:02:58,334 easyblock.py:809 INFO Considering directory in which easyconfig file is located when searching for GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch: /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS | |
| == 2024-06-20 08:02:58,334 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /home/a/ake/Projects/easybuild-dev/easybuild-framework/eb | |
| == 2024-06-20 08:02:58,334 tools.py:290 INFO Not considering /home/a/ake/Projects/easybuild-dev (no easybuild/easyconfigs subdir found) | |
| == 2024-06-20 08:02:58,334 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /afs/hpc2n.umu.se/home/a/ake/Projects/git-repos/easybuild/easybuild_common/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /hpc2n/eb/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/fake_vsc_p7v0k1cs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/included-easyblocks-y0jubo6i/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/git/ext/gitdb/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:307 DEBUG Added /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs to list of paths for easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-framework/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-install/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,335 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-base/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python310.zip/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/lib-dynload/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/.local/lib/python3.10/site-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.10/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/gitdb/ext/smmap/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,336 easyblock.py:851 INFO Found file GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch at /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch | |
| == 2024-06-20 08:02:58,336 easyblock.py:520 DEBUG File /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch found for patch GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch | |
| == 2024-06-20 08:02:58,336 easyblock.py:809 INFO Considering directory in which easyconfig file is located when searching for GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch: /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS | |
| == 2024-06-20 08:02:58,336 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /home/a/ake/Projects/easybuild-dev/easybuild-framework/eb | |
| == 2024-06-20 08:02:58,336 tools.py:290 INFO Not considering /home/a/ake/Projects/easybuild-dev (no easybuild/easyconfigs subdir found) | |
| == 2024-06-20 08:02:58,336 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /afs/hpc2n.umu.se/home/a/ake/Projects/git-repos/easybuild/easybuild_common/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /hpc2n/eb/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/fake_vsc_p7v0k1cs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/included-easyblocks-y0jubo6i/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/git/ext/gitdb/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:307 DEBUG Added /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs to list of paths for easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-framework/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-install/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,337 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-base/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python310.zip/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/lib-dynload/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/.local/lib/python3.10/site-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.10/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/gitdb/ext/smmap/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,338 easyblock.py:851 INFO Found file GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch at /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch | |
| == 2024-06-20 08:02:58,338 easyblock.py:520 DEBUG File /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch found for patch GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch | |
| == 2024-06-20 08:02:58,338 easyblock.py:535 INFO Added patches: [{'name': 'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', 'postinstall': False, 'path': '/dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', 'checksum': {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}}, {'name': 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', 'postinstall': False, 'path': '/dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch', 'checksum': {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}}] | |
| == 2024-06-20 08:02:58,338 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:58,502 easyblock.py:2411 INFO md5 checksum for /home/a/ake/easybuild-src/sources/g/GROMACS/gromacs-2024.2.tar.gz: b1caec2a81e221d68b3a58c53f1add40 | |
| == 2024-06-20 08:02:58,503 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:58,556 easyblock.py:2411 INFO sha256 checksum for /home/a/ake/easybuild-src/sources/g/GROMACS/gromacs-2024.2.tar.gz: 802a7e335f2e895770f57b159e4ec368ebb0ff2ce6daccf706c6e8025c36852b | |
| == 2024-06-20 08:02:58,557 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:58,557 easyblock.py:2411 INFO md5 checksum for /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch: ec290a307b2cdbdfc66b1f89d3904728 | |
| == 2024-06-20 08:02:58,557 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:58,557 easyblock.py:2411 INFO sha256 checksum for /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch: 7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199 | |
| == 2024-06-20 08:02:58,557 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:58,557 easyblock.py:2411 INFO md5 checksum for /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch: b7dc2e8f04a15189dccad5be41581045 | |
| == 2024-06-20 08:02:58,557 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:58,557 easyblock.py:2411 INFO sha256 checksum for /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch: 6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1 | |
| == 2024-06-20 08:02:58,558 templates.py:201 DEBUG config: {'name': 'gmxapi', 'version': '0.4.2', 'options': {'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True, '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']}, 'easyblock': None} | |
| == 2024-06-20 08:02:58,558 templates.py:231 DEBUG version found in easyconfig is 0.4.2 | |
| == 2024-06-20 08:02:58,558 templates.py:333 DEBUG name: name, config: gmxapi | |
| == 2024-06-20 08:02:58,558 templates.py:333 DEBUG name: version, config: 0.4.2 | |
| == 2024-06-20 08:02:58,558 easyblock.py:809 INFO Considering directory in which easyconfig file is located when searching for gromacs-2023.3.tar.gz: /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS | |
| == 2024-06-20 08:02:58,558 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /home/a/ake/Projects/easybuild-dev/easybuild-framework/eb | |
| == 2024-06-20 08:02:58,558 tools.py:290 INFO Not considering /home/a/ake/Projects/easybuild-dev (no easybuild/easyconfigs subdir found) | |
| == 2024-06-20 08:02:58,558 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /afs/hpc2n.umu.se/home/a/ake/Projects/git-repos/easybuild/easybuild_common/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /hpc2n/eb/custom/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/fake_vsc_p7v0k1cs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /dev/shm/ake/tmp/eb-27x4ay8y/included-easyblocks-y0jubo6i/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/git/ext/gitdb/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:307 DEBUG Added /home/a/ake/Projects/easybuild-dev/easybuild-easyconfigs/easybuild/easyconfigs to list of paths for easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-easyblocks/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,559 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/easybuild-framework/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-install/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/Projects/easybuild-dev/vsc-base/lib/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python310.zip/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.10/lib-dynload/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/a/ake/.local/lib/python3.10/site-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.10/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,560 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3/dist-packages/gitdb/ext/smmap/easybuild/easyconfigs | |
| == 2024-06-20 08:02:58,766 easyblock.py:851 INFO Found file gromacs-2023.3.tar.gz at /pfs/data/software/open_sources/g/GROMACS/gromacs-2023.3.tar.gz | |
| == 2024-06-20 08:02:58,972 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:59,208 easyblock.py:679 INFO md5 checksum for /pfs/data/software/open_sources/g/GROMACS/gromacs-2023.3.tar.gz: 2c9cdd8252ba9aa89a05d7c2d9b07509 | |
| == 2024-06-20 08:02:59,208 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:59,269 easyblock.py:679 INFO sha256 checksum for /pfs/data/software/open_sources/g/GROMACS/gromacs-2023.3.tar.gz: 4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb | |
| == 2024-06-20 08:02:59,270 easyblock.py:682 DEBUG Verifying checksums for extension source... | |
| == 2024-06-20 08:02:59,270 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:59,329 filetools.py:1307 DEBUG Computed sha256 checksum for /pfs/data/software/open_sources/g/GROMACS/gromacs-2023.3.tar.gz: 4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb (correct checksum: 4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb) | |
| == 2024-06-20 08:02:59,329 easyblock.py:685 INFO Checksum for extension source gromacs-2023.3.tar.gz verified | |
| == 2024-06-20 08:02:59,329 easyblock.py:532 INFO Fetched extension patches: [] | |
| == 2024-06-20 08:02:59,329 easyblock.py:726 DEBUG No patches found for extension gmxapi. | |
| == 2024-06-20 08:02:59,329 easyconfig.py:2642 DEBUG Determining full module name for GROMACS EasyConfig @ /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb (force_visible: False) | |
| == 2024-06-20 08:02:59,329 easyconfig.py:2619 DEBUG No alternative software name specified to determine module name with | |
| == 2024-06-20 08:02:59,330 toolchain.py:592 DEBUG Toolchain definition for {'name': 'foss', 'version': '2023b', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/foss/2023b', 'short_mod_name': 'foss/2023b', 'system': True}: {'BLACS': ['BLACS'], 'BLAS': ['FlexiBLAS'], 'COMPILER': ['GCC'], 'FFT': ['FFTW'], 'LAPACK': ['FlexiBLAS'], 'MPI': ['OpenMPI'], 'SCALAPACK': ['ScaLAPACK']} | |
| == 2024-06-20 08:02:59,330 toolchain.py:61 DEBUG Obtained details for 'GCC' in toolchain '{'name': 'foss', 'version': '2023b', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/foss/2023b', 'short_mod_name': 'foss/2023b', 'system': True}' from cache | |
| == 2024-06-20 08:02:59,330 toolchain.py:136 DEBUG Found compilers [{'full_mod_name': 'Core/GCC/13.2.0', 'short_mod_name': 'GCC/13.2.0', 'name': 'GCC', 'version': '13.2.0', 'versionsuffix': '', 'toolchain': {'name': 'system', 'version': 'system'}, 'toolchain_inherited': True, 'system': True, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}}] for toolchain foss ({'name': 'foss', 'version': '2023b', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/foss/2023b', 'short_mod_name': 'foss/2023b', 'system': True}) | |
| == 2024-06-20 08:02:59,330 toolchain.py:592 DEBUG Toolchain definition for {'name': 'foss', 'version': '2023b', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/foss/2023b', 'short_mod_name': 'foss/2023b', 'system': True}: {'BLACS': ['BLACS'], 'BLAS': ['FlexiBLAS'], 'COMPILER': ['GCC'], 'FFT': ['FFTW'], 'LAPACK': ['FlexiBLAS'], 'MPI': ['OpenMPI'], 'SCALAPACK': ['ScaLAPACK']} | |
| == 2024-06-20 08:02:59,330 toolchain.py:61 DEBUG Obtained details for 'OpenMPI' in toolchain '{'name': 'foss', 'version': '2023b', 'toolchain': {'name': 'system', 'version': ''}, 'versionsuffix': '', 'parsed': True, 'hidden': False, 'full_mod_name': 'Core/foss/2023b', 'short_mod_name': 'foss/2023b', 'system': True}' from cache | |
| == 2024-06-20 08:02:59,330 utilities.py:115 DEBUG Module name MPI/GCC/13.2.0/OpenMPI/4.1.6/GROMACS/2024.2-CUDA-12.5.0 validated | |
| == 2024-06-20 08:02:59,330 easyconfig.py:2650 DEBUG Obtained valid full module name MPI/GCC/13.2.0/OpenMPI/4.1.6/GROMACS/2024.2-CUDA-12.5.0 | |
| == 2024-06-20 08:02:59,330 easyblock.py:2446 INFO Checking dirs that need to be created: ['/home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/GROMACS/2024.2-foss-2023b-CUDA-12.5.0', '/home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules/all/MPI/GCC/13.2.0/OpenMPI/4.1.6/GROMACS'] | |
| == 2024-06-20 08:02:59,330 filetools.py:1931 DEBUG Not creating existing path /home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/GROMACS/2024.2-foss-2023b-CUDA-12.5.0 | |
| == 2024-06-20 08:02:59,331 filetools.py:1931 DEBUG Not creating existing path /home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules/all/MPI/GCC/13.2.0/OpenMPI/4.1.6/GROMACS | |
| == 2024-06-20 08:02:59,387 filetools.py:1233 DEBUG Using blocksize 16777216 for calculating the checksum | |
| == 2024-06-20 08:02:59,390 configuremake.py:95 INFO config.guess version: 2018-08-29 (last updated: 2024-06-19T12:50:32, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c) | |
| == 2024-06-20 08:02:59,391 configuremake.py:151 INFO Found config.guess at /pfs/data/software/open_sources/generic/eb_v4.9.3.dev0/ConfigureMake/config.guess | |
| == 2024-06-20 08:02:59,391 build_log.py:267 INFO ... (took 1 secs) | |
| == 2024-06-20 08:02:59,391 easyblock.py:3941 DEBUG Not skipping ready step (skippable: False, skip: None, skipsteps: [], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False) | |
| == 2024-06-20 08:02:59,391 build_log.py:267 INFO creating build dir, resetting environment... | |
| == 2024-06-20 08:02:59,391 easyblock.py:3950 INFO Starting ready step | |
| == 2024-06-20 08:02:59,391 easyconfig.py:1702 INFO Generating template values... | |
| == 2024-06-20 08:02:59,391 templates.py:201 DEBUG config: GROMACS EasyConfig @ /dev/shm/ake/tmp/eb-27x4ay8y/files_pr20809/g/GROMACS/GROMACS-2024.2-foss-2023b-CUDA-12.5.0.eb | |
| == 2024-06-20 08:02:59,391 templates.py:231 DEBUG version found in easyconfig is 2024.2 | |
| == 2024-06-20 08:02:59,391 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s | |
| == 2024-06-20 08:02:59,391 templates.py:333 DEBUG name: github_account, config: %(namelower)s | |
| == 2024-06-20 08:02:59,392 templates.py:333 DEBUG name: name, config: GROMACS | |
| == 2024-06-20 08:02:59,392 templates.py:333 DEBUG name: parallel, config: None | |
| == 2024-06-20 08:02:59,392 templates.py:333 DEBUG name: version, config: 2024.2 | |
| == 2024-06-20 08:02:59,392 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s | |
| == 2024-06-20 08:02:59,392 templates.py:333 DEBUG name: versionprefix, config: | |
| == 2024-06-20 08:02:59,392 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' | |
| == 2024-06-20 08:02:59,392 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 08:02:59,392 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='gromacs', builddir='/dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0', 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', installdir='/home/a/ake/easybuild-amd64_ubuntu2204_zen4/software/GROMACS/2024.2-foss-2023b-CUDA-12.5.0', 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', start_dir='None', 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 08:02:59,392 easyblock.py:3958 INFO Running method check_readiness_step part of step ready | |
| == 2024-06-20 08:02:59,392 easyblock.py:2246 DEBUG Desired parallelism specified via 'parallel' build option: None | |
| == 2024-06-20 08:02:59,398 systemtools.py:247 DEBUG sched_getaffinity for pid 666864 successful | |
| == 2024-06-20 08:02:59,398 run.py:221 DEBUG run_cmd: running cmd ulimit -u (in /home/a/ake) | |
| == 2024-06-20 08:02:59,398 run.py:247 INFO running cmd: ulimit -u | |
| == 2024-06-20 08:02:59,404 run.py:689 DEBUG cmd "ulimit -u" exited with exit code 0 and output: | |
| 1545675 | |
| == 2024-06-20 08:02:59,404 run.py:725 DEBUG Using default regular expression: (?<![(,-]|\w)(?:error|segmentation fault|failed)(?![(,-]|\.?\w) | |
| == 2024-06-20 08:02:59,404 easyblock.py:2255 INFO Setting parallelism: 48 | |
| == 2024-06-20 08:02:59,404 modules.py:814 DEBUG Current MODULEPATH: /home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules/all:/hpc2n/eb/modules/all:/home/a/ake/Projects/easybuild-dev/modules:/home/a/ake/easybuild/modules/all/Core:/home/a/ake/easybuild-dev/modules/all/Core:/hpc2n/eb/modules/all/Core:/hpc2n/eb/software/lmod/lmod/modulefiles/Core | |
| == 2024-06-20 08:02:59,405 modules.py:828 DEBUG Running module command '/hpc2n/eb/software/lmod/lmod/libexec/lmod python --terse list' from /home/a/ake | |
| == 2024-06-20 08:02:59,479 modules.py:835 DEBUG Output of module command '/hpc2n/eb/software/lmod/lmod/libexec/lmod python --terse list': stdout: import os | |
| os.environ["MODULEPATH"] = "/home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules/all:/hpc2n/eb/modules/all:/home/a/ake/Projects/easybuild-dev/modules:/home/a/ake/easybuild/modules/all/Core:/home/a/ake/easybuild-dev/modules/all/Core:/hpc2n/eb/modules/all/Core:/hpc2n/eb/software/lmod/lmod/modulefiles/Core"; | |
| os.environ["_ModuleTable001_"] = "X01vZHVsZVRhYmxlXyA9IHsKTVR2ZXJzaW9uID0gMywKY19yZWJ1aWxkVGltZSA9IDcyMDAuMCwKY19zaG9ydFRpbWUgPSAwLjAzNzI4MTAzNjM3Njk1MywKZGVwdGhUID0ge30sCmZhbWlseSA9IHt9LAptVCA9IHsKWyJFYXN5QnVpbGQtZGV2ZWxvcCJdID0gewpmbiA9ICIvaG9tZS9hL2FrZS9Qcm9qZWN0cy9lYXN5YnVpbGQtZGV2L21vZHVsZXMvRWFzeUJ1aWxkLWRldmVsb3AiLApmdWxsTmFtZSA9ICJFYXN5QnVpbGQtZGV2ZWxvcCIsCmxvYWRPcmRlciA9IDMsCnByb3BUID0ge30sCnN0YWNrRGVwdGggPSAxLApzdGF0dXMgPSAiYWN0aXZlIiwKdXNlck5hbWUgPSAiRWFzeUJ1aWxkLWRldmVsb3AiLAp3ViA9ICJNLip6ZmluYWwiLAp9LApTb2Z0SW5zdCA9IHsKZm4gPSAi"; | |
| os.environ["_ModuleTable002_"] = "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"; | |
| os.environ["_ModuleTable003_"] = "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"; | |
| os.environ["_ModuleTable004_"] = "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"; | |
| os.environ["_ModuleTable005_"] = "YWxsL0NvcmUiLCAiL2hwYzJuL2ViL21vZHVsZXMvYWxsL0NvcmUiLCAiL2hwYzJuL2ViL3NvZnR3YXJlL2xtb2QvbG1vZC9tb2R1bGVmaWxlcy9Db3JlIiwKfSwKc3lzdGVtQmFzZU1QQVRIID0gIi9ocGMybi9lYi9tb2R1bGVzL2FsbC9Db3JlOi9ocGMybi9lYi9zb2Z0d2FyZS9sbW9kL2xtb2QvbW9kdWxlZmlsZXMvQ29yZSIsCn0K"; | |
| os.environ["_ModuleTable_Sz_"] = "5"; | |
| _mlstatus = True | |
| ; stderr: snicenvironment | |
| systemdefault | |
| EasyBuild-develop | |
| eb_user/develop | |
| SoftInst/develop | |
| == 2024-06-20 08:02:59,480 modules.py:1471 DEBUG Output found in stdout, seems like '/hpc2n/eb/software/lmod/lmod/libexec/lmod python --terse list' ran fine | |
| == 2024-06-20 08:02:59,480 easyblock.py:2307 WARNING Loaded modules detected: ['snicenvironment', 'systemdefault', 'EasyBuild-develop', 'eb_user/develop', 'SoftInst/develop'] | |
| == 2024-06-20 08:02:59,481 easyblock.py:2280 INFO Removing existing module file /home/a/ake/easybuild-amd64_ubuntu2204_zen4/modules/all/MPI/GCC/13.2.0/OpenMPI/4.1.6/GROMACS/2024.2-CUDA-12.5.0.lua | |
| == 2024-06-20 08:02:59,484 easyblock.py:3958 INFO Running method make_builddir part of step ready | |
| == 2024-06-20 08:02:59,485 easyblock.py:1066 DEBUG Creating the build directory /dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0 (cleanup: True) | |
| == 2024-06-20 08:02:59,485 filetools.py:1912 INFO Creating directory /dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0 (parents: True, set_gid: False, sticky: False) | |
| == 2024-06-20 08:02:59,565 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): Failed to create directory /dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0: [Errno 13] Permission denied: '/dev/shm7ake' (at easybuild/tools/filetools.py:1924 in mkdir) | |
| == 2024-06-20 08:02:59,566 build_log.py:267 INFO ... (took < 1 sec) | |
| == 2024-06-20 08:02:59,566 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 08:02:59,566 filetools.py:2013 INFO Removing 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... | |
| == 2024-06-20 08:02:59,570 filetools.py:383 INFO Path /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 successfully removed. | |
| == 2024-06-20 08:02:59,570 filetools.py:2017 INFO Lock removed: /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 | |
| == 2024-06-20 08:02:59,570 easyblock.py:4285 WARNING build failed (first 300 chars): Failed to create directory /dev/shm7ake/build/GROMACS/2024.2/foss-2023b-CUDA-12.5.0: [Errno 13] Permission denied: '/dev/shm7ake' | |
| == 2024-06-20 08:02:59,570 easyblock.py:328 INFO Closing log for application name GROMACS version 2024.2 |
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