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October 2, 2024 12:30
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(partial) EasyBuild log for failed build of /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs/g/GROMACS/GROMACS-2023.3-foss-2022a.eb (easyblock PR(s) #3463)
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| moduleclass = 'bio' | |
| == 2024-10-02 13:49:34,489 parser.py:139 INFO Type checking of easyconfig parameter values passed! | |
| == 2024-10-02 13:49:34,489 easyconfig.py:688 INFO setting easyconfig parameter builddependencies: value [('CMake', '3.24.3'), ('scikit-build', '0.15.0')] (type: <class 'list'>) | |
| == 2024-10-02 13:49:34,489 easyconfig.py:688 INFO setting easyconfig parameter checksums: value [{'gromacs-2023.3.tar.gz': '4ec8f8d0c7af76b13f8fd16db8e2c120e749de439ae9554d9f653f812d78d1cb'}, {'GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch': '7f41bda16c9c2837624265dda4be252f655d1288ddc4486b1a2422af30d5d199'}, {'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch': '6df844bb3bbc51180446a3595c61a4ef195e5f975533a04cef76841aa763aec1'}] (type: <class 'list'>) | |
| == 2024-10-02 13:49:34,489 easyconfig.py:688 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4'), ('SciPy-bundle', '2022.05'), ('networkx', '2.8.4')] (type: <class 'list'>) | |
| == 2024-10-02 13:49:34,489 easyconfig.py:688 INFO setting easyconfig parameter description: value | |
| 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. | |
| (type: <class 'str'>) | |
| == 2024-10-02 13:49:34,489 easyconfig.py:688 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletter)s/%(name)s'], 'use_pip': True, 'download_dep_fail': True, 'sanity_pip_check': True} (type: <class 'dict'>) | |
| == 2024-10-02 13:49:34,489 easyconfig.py:688 INFO setting easyconfig parameter exts_defaultclass: value PythonPackage (type: <class 'str'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter exts_list: value [('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']})] (type: <class 'list'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter homepage: value https://www.gromacs.org (type: <class 'str'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter modextrapaths: value {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} (type: <class 'dict'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter moduleclass: value bio (type: <class 'str'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter name: value GROMACS (type: <class 'str'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter patches: value ['GROMACS-2023.1_set_omp_num_threads_env_for_ntomp_tests.patch', 'GROMACS-2023.1_fix_tests_for_gmx_thread_mpi.patch'] (type: <class 'list'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter source_urls: value ['https://ftp.gromacs.org/pub/gromacs/', 'ftp://ftp.gromacs.org/pub/gromacs/'] (type: <class 'list'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter sources: value ['%(namelower)s-%(version)s.tar.gz'] (type: <class 'list'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter toolchain: value {'name': 'foss', 'version': '2022a'} (type: <class 'dict'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter toolchainopts: value {'openmp': True, 'usempi': True} (type: <class 'dict'>) | |
| == 2024-10-02 13:49:34,490 easyconfig.py:688 INFO setting easyconfig parameter version: value 2023.3 (type: <class 'str'>) | |
| == 2024-10-02 13:49:34,490 hooks.py:205 INFO Found parse_hook hook | |
| == 2024-10-02 13:49:34,490 hooks.py:239 INFO Running 'parse_hook' hook function (args: [<easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f7f02030070>], keyword args: {})... | |
| == 2024-10-02 13:49:34,492 easyconfig.py:750 INFO Parsing dependency specifications... | |
| == 2024-10-02 13:49:34,492 easyconfig.py:1705 INFO Generating template values... | |
| == 2024-10-02 13:49:34,492 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' | |
| == 2024-10-02 13:49:34,492 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) | |
| == 2024-10-02 13:49:34,492 easyconfig.py:1724 INFO Template values: arch='x86_64', bitbucket_account='gromacs', github_account='gromacs', mpi_cmd_prefix='mpirun -n 1', name='GROMACS', nameletter='G', nameletterlower='g', namelower='gromacs', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', software_commit='', sysroot='', toolchain_name='foss', toolchain_version='2022a', version='2023.3', version_major='2023', version_major_minor='2023.3', version_minor='3', versionprefix='', versionsuffix='' | |
| == 2024-10-02 13:49:36,233 modules.py:628 INFO Checking whether CMake/3.24.3-foss-2022a exists... | |
| == 2024-10-02 13:49:36,233 modules.py:649 INFO Module CMake/3.24.3-foss-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,234 modules.py:656 INFO Result for existence check of CMake/3.24.3-foss-2022a module: False | |
| == 2024-10-02 13:49:36,234 modules.py:628 INFO Checking whether CMake/3.24.3-gompi-2022a exists... | |
| == 2024-10-02 13:49:36,234 modules.py:649 INFO Module CMake/3.24.3-gompi-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,235 modules.py:656 INFO Result for existence check of CMake/3.24.3-gompi-2022a module: False | |
| == 2024-10-02 13:49:36,235 modules.py:628 INFO Checking whether CMake/3.24.3-gfbf-2022a exists... | |
| == 2024-10-02 13:49:36,235 modules.py:649 INFO Module CMake/3.24.3-gfbf-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,235 modules.py:656 INFO Result for existence check of CMake/3.24.3-gfbf-2022a module: False | |
| == 2024-10-02 13:49:36,235 modules.py:628 INFO Checking whether CMake/3.24.3-GCC-11.3.0 exists... | |
| == 2024-10-02 13:49:36,235 modules.py:649 INFO Module CMake/3.24.3-GCC-11.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,236 modules.py:656 INFO Result for existence check of CMake/3.24.3-GCC-11.3.0 module: False | |
| == 2024-10-02 13:49:36,236 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,236 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,236 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,236 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,237 easyconfig.py:2376 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'CMake', 'version': '3.24.3', 'versionsuffix': '', 'toolchain': {'name': 'foss', 'version': '2022a'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} | |
| == 2024-10-02 13:49:36,237 modules.py:628 INFO Checking whether scikit-build/0.15.0-foss-2022a exists... | |
| == 2024-10-02 13:49:36,237 modules.py:649 INFO Module scikit-build/0.15.0-foss-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,238 modules.py:656 INFO Result for existence check of scikit-build/0.15.0-foss-2022a module: False | |
| == 2024-10-02 13:49:36,238 modules.py:628 INFO Checking whether scikit-build/0.15.0-gompi-2022a exists... | |
| == 2024-10-02 13:49:36,238 modules.py:649 INFO Module scikit-build/0.15.0-gompi-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,238 modules.py:656 INFO Result for existence check of scikit-build/0.15.0-gompi-2022a module: False | |
| == 2024-10-02 13:49:36,238 modules.py:628 INFO Checking whether scikit-build/0.15.0-gfbf-2022a exists... | |
| == 2024-10-02 13:49:36,238 modules.py:649 INFO Module scikit-build/0.15.0-gfbf-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,239 modules.py:656 INFO Result for existence check of scikit-build/0.15.0-gfbf-2022a module: False | |
| == 2024-10-02 13:49:36,239 modules.py:628 INFO Checking whether scikit-build/0.15.0-GCC-11.3.0 exists... | |
| == 2024-10-02 13:49:36,239 modules.py:649 INFO Module scikit-build/0.15.0-GCC-11.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,239 modules.py:656 INFO Result for existence check of scikit-build/0.15.0-GCC-11.3.0 module: False | |
| == 2024-10-02 13:49:36,239 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,240 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,240 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,240 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,240 easyconfig.py:2376 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'scikit-build', 'version': '0.15.0', 'versionsuffix': '', 'toolchain': {'name': 'foss', 'version': '2022a'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} | |
| == 2024-10-02 13:49:36,240 modules.py:628 INFO Checking whether Python/3.10.4-foss-2022a exists... | |
| == 2024-10-02 13:49:36,241 modules.py:649 INFO Module Python/3.10.4-foss-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,241 modules.py:656 INFO Result for existence check of Python/3.10.4-foss-2022a module: False | |
| == 2024-10-02 13:49:36,241 modules.py:628 INFO Checking whether Python/3.10.4-gompi-2022a exists... | |
| == 2024-10-02 13:49:36,241 modules.py:649 INFO Module Python/3.10.4-gompi-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,242 modules.py:656 INFO Result for existence check of Python/3.10.4-gompi-2022a module: False | |
| == 2024-10-02 13:49:36,242 modules.py:628 INFO Checking whether Python/3.10.4-gfbf-2022a exists... | |
| == 2024-10-02 13:49:36,242 modules.py:649 INFO Module Python/3.10.4-gfbf-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,242 modules.py:656 INFO Result for existence check of Python/3.10.4-gfbf-2022a module: False | |
| == 2024-10-02 13:49:36,242 modules.py:628 INFO Checking whether Python/3.10.4-GCC-11.3.0 exists... | |
| == 2024-10-02 13:49:36,242 modules.py:649 INFO Module Python/3.10.4-GCC-11.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,243 modules.py:656 INFO Result for existence check of Python/3.10.4-GCC-11.3.0 module: False | |
| == 2024-10-02 13:49:36,243 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,243 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,243 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,243 easyconfig.py:2200 INFO Found loaded index for /home/s3248973/.local/EasyBuildDev/easybuild-easyconfigs/easybuild/easyconfigs | |
| == 2024-10-02 13:49:36,243 easyconfig.py:2376 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'foss', 'version': '2022a'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} | |
| == 2024-10-02 13:49:36,244 modules.py:628 INFO Checking whether SciPy-bundle/2022.05-gompi-2022a exists... | |
| == 2024-10-02 13:49:36,244 modules.py:649 INFO Module SciPy-bundle/2022.05-gompi-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,244 modules.py:656 INFO Result for existence check of SciPy-bundle/2022.05-gompi-2022a module: False | |
| == 2024-10-02 13:49:36,244 modules.py:628 INFO Checking whether SciPy-bundle/2022.05-gfbf-2022a exists... | |
| == 2024-10-02 13:49:36,245 modules.py:649 INFO Module SciPy-bundle/2022.05-gfbf-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,245 modules.py:656 INFO Result for existence check of SciPy-bundle/2022.05-gfbf-2022a module: False | |
| == 2024-10-02 13:49:36,245 modules.py:628 INFO Checking whether SciPy-bundle/2022.05-GCC-11.3.0 exists... | |
| == 2024-10-02 13:49:36,245 modules.py:649 INFO Module SciPy-bundle/2022.05-GCC-11.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,246 modules.py:656 INFO Result for existence check of SciPy-bundle/2022.05-GCC-11.3.0 module: False | |
| == 2024-10-02 13:49:36,246 modules.py:628 INFO Checking whether SciPy-bundle/2022.05-GCCcore-11.3.0 exists... | |
| == 2024-10-02 13:49:36,246 modules.py:649 INFO Module SciPy-bundle/2022.05-GCCcore-11.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,246 modules.py:656 INFO Result for existence check of SciPy-bundle/2022.05-GCCcore-11.3.0 module: False | |
| == 2024-10-02 13:49:36,246 easyconfig.py:2376 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'SciPy-bundle', 'version': '2022.05', 'versionsuffix': '', 'toolchain': {'name': 'foss', 'version': '2022a'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'foss', 'version': '2022a'} | |
| == 2024-10-02 13:49:36,247 modules.py:628 INFO Checking whether networkx/2.8.4-gompi-2022a exists... | |
| == 2024-10-02 13:49:36,247 modules.py:649 INFO Module networkx/2.8.4-gompi-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,247 modules.py:656 INFO Result for existence check of networkx/2.8.4-gompi-2022a module: False | |
| == 2024-10-02 13:49:36,247 modules.py:628 INFO Checking whether networkx/2.8.4-gfbf-2022a exists... | |
| == 2024-10-02 13:49:36,247 modules.py:649 INFO Module networkx/2.8.4-gfbf-2022a not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,248 modules.py:656 INFO Result for existence check of networkx/2.8.4-gfbf-2022a module: False | |
| == 2024-10-02 13:49:36,248 modules.py:628 INFO Checking whether networkx/2.8.4-GCC-11.3.0 exists... | |
| == 2024-10-02 13:49:36,248 modules.py:649 INFO Module networkx/2.8.4-GCC-11.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,248 modules.py:656 INFO Result for existence check of networkx/2.8.4-GCC-11.3.0 module: False | |
| == 2024-10-02 13:49:36,248 modules.py:628 INFO Checking whether networkx/2.8.4-GCCcore-11.3.0 exists... | |
| == 2024-10-02 13:49:36,249 modules.py:649 INFO Module networkx/2.8.4-GCCcore-11.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2024-10-02 13:49:36,249 modules.py:656 INFO Result for existence check of networkx/2.8.4-GCCcore-11.3.0 module: False | |
| == 2024-10-02 13:49:36,249 easyconfig.py:2376 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'networkx', 'version': '2.8.4', 'versionsuffix': '', 'toolchain': {'name': 'foss', 'version': '2022a'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'foss', 'version': '2022a'} | |
| == 2024-10-02 13:49:36,251 pythonpackage.py:423 INFO Using default value for expected module name (lowercase software name): 'gmxapi' | |
| == 2024-10-02 13:49:36,251 pythonpackage.py:459 INFO Using pip with --no-deps option | |
| == 2024-10-02 13:49:36,251 pythonpackage.py:486 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command | |
| == 2024-10-02 13:49:36,251 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) | |
| == 2024-10-02 13:49:36,251 environment.py:93 INFO Environment variable PIP_REQUIRE_VIRTUALENV set to false (previously undefined) | |
| == 2024-10-02 13:49:36,251 environment.py:93 INFO Environment variable PIP_DISABLE_PIP_VERSION_CHECK set to true (previously undefined) | |
| == 2024-10-02 13:49:36,251 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/easybuild-tmp/eb-nc_mqkpk/xdg-cache-home (previously undefined) | |
| == 2024-10-02 13:49:36,251 python.py:136 INFO Using /tmp/easybuild-tmp/eb-nc_mqkpk/xdg-cache-home as pip cache directory | |
| == 2024-10-02 13:49:36,414 easyblock.py:1908 INFO Installing extensions sequentially... | |
| == 2024-10-02 13:49:36,414 easyblock.py:1914 INFO Starting extension gmxapi | |
| == 2024-10-02 13:49:36,414 build_log.py:267 INFO installing extension gmxapi 0.4.2 (1/1)... | |
| == 2024-10-02 13:49:36,582 modules.py:628 INFO Checking whether foss/2022a exists... | |
| == 2024-10-02 13:49:36,582 modules.py:635 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... | |
| == 2024-10-02 13:49:38,949 modules.py:656 INFO Result for existence check of foss/2022a module: True | |
| == 2024-10-02 13:49:38,951 toolchain.py:766 INFO List of toolchain dependency modules and toolchain definition match! | |
| == 2024-10-02 13:49:38,953 compiler.py:338 INFO _set_optimal_architecture: no optarch found for compiler GCC. Ignoring option. | |
| == 2024-10-02 13:49:38,953 compiler.py:362 INFO _set_optimal_architecture: using march=native as optarch for x86_64/AMD. | |
| == 2024-10-02 13:49:38,960 variables.py:203 WARNING flags_for_subdirs: directory /software/rome/r23.10/ScaLAPACK/2.2.0-gompi-2022a-fb/include was not found | |
| == 2024-10-02 13:49:38,964 environment.py:93 INFO Environment variable BLAS_INC_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,964 environment.py:93 INFO Environment variable EBVARBLAS_INC_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,964 environment.py:93 INFO Environment variable BLAS_LAPACK_INC_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,964 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_INC_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_LAPACK_LIB_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_LIB_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_LIB_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable BLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARBLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable CC set to mpicc (previously undefined) | |
| == 2024-10-02 13:49:38,965 environment.py:93 INFO Environment variable EBVARCC set to mpicc (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable CC_SEQ set to gcc (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARCC_SEQ set to gcc (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable CFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable CPPFLAGS set to -I/software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/include -I/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/include -I/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable CXX set to mpicxx (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARCXX set to mpicxx (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable CXXFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable CXX_SEQ set to g++ (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARCXX_SEQ set to g++ (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable F77 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARF77 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable F77_SEQ set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARF77_SEQ set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable F90 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARF90 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable F90FLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,966 environment.py:93 INFO Environment variable F90_SEQ set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARF90_SEQ set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FC set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFC set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FCFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FC_SEQ set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFC_SEQ set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O3 -march=native -fno-math-errno -fopenmp (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFTW_INC_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/include (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFFTW_INC_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/include (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFTW_LIB_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFFTW_LIB_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS set to libfftw3_mpi.so,libfftw3.so (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS set to libfftw3_mpi.so,libfftw3.so (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS_MT set to libfftw3_omp.so,libfftw3.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS_MT set to libfftw3_omp.so,libfftw3.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS set to libfftw3_mpi.a,libfftw3.a (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3_mpi.a,libfftw3.a (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS_MT set to libfftw3_omp.a,libfftw3.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS_MT set to libfftw3_omp.a,libfftw3.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,967 environment.py:93 INFO Environment variable FFT_INC_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/include (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARFFT_INC_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/include (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable FFT_LIB_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARFFT_LIB_DIR set to /software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable FFT_SHARED_LIBS set to libfftw3_mpi.so,libfftw3.so (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS set to libfftw3_mpi.so,libfftw3.so (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable FFT_SHARED_LIBS_MT set to libfftw3_omp.so,libfftw3.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS_MT set to libfftw3_omp.so,libfftw3.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable FFT_STATIC_LIBS set to libfftw3_mpi.a,libfftw3.a (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS set to libfftw3_mpi.a,libfftw3.a (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable FFT_STATIC_LIBS_MT set to libfftw3_omp.a,libfftw3.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3_omp.a,libfftw3.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable LAPACK_INC_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARLAPACK_INC_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable LAPACK_LIB_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARLAPACK_LIB_DIR set to /software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARLAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,968 environment.py:93 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LDFLAGS set to -L/software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib64 -L/software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib -L/software/rome/r23.10/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/software/rome/r23.10/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/software/rome/r23.10/GCCcore/11.3.0/lib64 -L/software/rome/r23.10/GCCcore/11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib64 -L/software/rome/r23.10/FFTW.MPI/3.3.10-gompi-2022a/lib -L/software/rome/r23.10/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/software/rome/r23.10/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/software/rome/r23.10/GCCcore/11.3.0/lib64 -L/software/rome/r23.10/GCCcore/11.3.0/lib (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBBLAS set to -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLIBBLAS set to -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBBLAS_MT set to -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLIBBLAS_MT set to -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBFFT set to -lfftw3_mpi -lfftw3 (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLIBFFT set to -lfftw3_mpi -lfftw3 (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBFFT_MT set to -lfftw3_omp -lfftw3 -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3_omp -lfftw3 -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBLAPACK set to -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLIBLAPACK set to -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBLAPACK_MT set to -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT set to -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,969 environment.py:93 INFO Environment variable LIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable LIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lflexiblas -lgfortran -lpthread (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable MPICC set to mpicc (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARMPICC set to mpicc (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable MPICXX set to mpicxx (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARMPICXX set to mpicxx (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable MPIF77 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARMPIF77 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable MPIF90 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARMPIF90 set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable MPIFC set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable EBVARMPIFC set to mpifort (previously undefined) | |
| == 2024-10-02 13:49:38,970 environment.py:93 INFO Environment variable MPI_INC_DIR set to /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVARMPI_INC_DIR set to /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable MPI_LIB_DIR set to /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVARMPI_LIB_DIR set to /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable MPI_LIB_SHARED set to /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVARMPI_LIB_SHARED set to /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable MPI_LIB_STATIC set to (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVARMPI_LIB_STATIC set to (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable OMPI_CC set to gcc (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVAROMPI_CC set to gcc (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable OMPI_CXX set to g++ (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVAROMPI_CXX set to g++ (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable OMPI_F77 set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVAROMPI_F77 set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable OMPI_F90 set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVAROMPI_F90 set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable OMPI_FC set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVAROMPI_FC set to gfortran (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable OPTFLAGS set to -O3 -march=native (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O3 -march=native (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) | |
| == 2024-10-02 13:49:38,971 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable SCALAPACK_INC_DIR set to (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable EBVARSCALAPACK_INC_DIR set to (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable SCALAPACK_LIB_DIR set to /software/rome/r23.10/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /software/rome/r23.10/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable SCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable SCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable EBVARSCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,972 environment.py:93 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) | |
| == 2024-10-02 13:49:38,973 filetools.py:528 INFO Command python found at /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python | |
| == 2024-10-02 13:49:38,973 pythonpackage.py:545 INFO Python command being used: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python | |
| == 2024-10-02 13:49:38,973 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:38,973 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:39,048 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' | |
| == 2024-10-02 13:49:39,049 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' | |
| == 2024-10-02 13:49:39,573 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:39,574 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:39,646 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' | |
| == 2024-10-02 13:49:39,646 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' | |
| == 2024-10-02 13:49:40,153 filetools.py:1924 INFO Creating directory /dev/shm/s3248973-EasyBuild2338009/GROMACS/2023.3/foss-2022a/gmxapi (parents: True, set_gid: False, sticky: False) | |
| == 2024-10-02 13:49:40,154 run.py:251 INFO Using /bin/bash as shell for running cmd: tar xzf /data/horse/ws/s3248973-EasyBuild/sources/g/GROMACS/gromacs-2023.3.tar.gz | |
| == 2024-10-02 13:49:40,154 run.py:260 INFO running cmd: tar xzf /data/horse/ws/s3248973-EasyBuild/sources/g/GROMACS/gromacs-2023.3.tar.gz | |
| == 2024-10-02 13:49:40,889 build_log.py:267 INFO configuring... | |
| == 2024-10-02 13:49:40,892 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:40,892 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:40,959 pythonpackage.py:763 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 | |
| == 2024-10-02 13:49:40,960 pythonpackage.py:777 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') doesn't use current $CC value ('mpicc'), fixing | |
| == 2024-10-02 13:49:40,960 environment.py:93 INFO Environment variable LDSHARED set to mpicc -shared (previously undefined) | |
| == 2024-10-02 13:49:40,960 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' | |
| == 2024-10-02 13:49:40,960 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' | |
| == 2024-10-02 13:49:41,043 build_log.py:267 INFO building... | |
| == 2024-10-02 13:49:41,047 easyblock.py:3947 INFO Skipping test step as requested via skip-test-step | |
| == 2024-10-02 13:49:41,047 build_log.py:267 INFO testing [skipped] | |
| == 2024-10-02 13:49:41,049 build_log.py:267 INFO installing... | |
| == 2024-10-02 13:49:41,051 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:41,052 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' | |
| == 2024-10-02 13:49:41,116 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sysconfig; print(sysconfig.get_default_scheme())' | |
| == 2024-10-02 13:49:41,116 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sysconfig; print(sysconfig.get_default_scheme())' | |
| == 2024-10-02 13:49:41,181 pythonpackage.py:283 INFO Active Python installation scheme: posix_prefix | |
| == 2024-10-02 13:49:41,182 filetools.py:1924 INFO Creating directory /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/lib/python3.10/site-packages (parents: True, set_gid: False, sticky: False) | |
| == 2024-10-02 13:49:41,183 environment.py:93 INFO Environment variable PYTHONPATH set to /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/lib/python3.10/site-packages:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') | |
| == 2024-10-02 13:49:41,183 environment.py:93 INFO Environment variable PATH set to /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/SciPy-bundle/2022.05-foss-2022a/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/pybind11/2.9.2-GCCcore-11.3.0/bin:/software/rome/r23.10/FFTW/3.3.10-GCC-11.3.0/bin:/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/bin:/software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/bin:/software/rome/r23.10/UCC/1.0.0-GCCcore-11.3.0/bin:/software/rome/r23.10/PMIx/4.1.2-GCCcore-11.3.0/bin:/software/rome/r23.10/libfabric/1.15.1-GCCcore-11.3.0/bin:/software/rome/r23.10/UCX/1.12.1-GCCcore-11.3.0/bin:/software/rome/r23.10/libevent/2.1.12-GCCcore-11.3.0/bin:/software/rome/r23.10/hwloc/2.7.1-GCCcore-11.3.0/sbin:/software/rome/r23.10/hwloc/2.7.1-GCCcore-11.3.0/bin:/software/rome/r23.10/libxml2/2.9.13-GCCcore-11.3.0/bin:/software/rome/r23.10/XZ/5.2.5-GCCcore-11.3.0/bin:/software/rome/r23.10/numactl/2.0.14-GCCcore-11.3.0/bin:/software/rome/r23.10/binutils/2.38-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/scikit-build/0.15.0-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/CMake/3.24.3-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/libarchive/3.6.1-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/cURL/7.83.0-GCCcore-11.3.0/bin:/software/rome/r23.10/OpenSSL/1.1/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/ncurses/6.3-GCCcore-11.3.0/bin:/software/rome/r23.10/GCCcore/11.3.0/bin:/dev/shm/venv/bin:/home/s3248973/.local/EasyBuildDev/easybuild-framework:/home/s3248973/.local/bin:/home/s3248973/bin:/software/util/slurm/bin:/software/foundation/generic/bin:/software/foundation/x86_64/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/software/util/dtwrapper/bin (previous value: '/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/SciPy-bundle/2022.05-foss-2022a/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/pybind11/2.9.2-GCCcore-11.3.0/bin:/software/rome/r23.10/FFTW/3.3.10-GCC-11.3.0/bin:/software/rome/r23.10/FlexiBLAS/3.2.0-GCC-11.3.0/bin:/software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/bin:/software/rome/r23.10/UCC/1.0.0-GCCcore-11.3.0/bin:/software/rome/r23.10/PMIx/4.1.2-GCCcore-11.3.0/bin:/software/rome/r23.10/libfabric/1.15.1-GCCcore-11.3.0/bin:/software/rome/r23.10/UCX/1.12.1-GCCcore-11.3.0/bin:/software/rome/r23.10/libevent/2.1.12-GCCcore-11.3.0/bin:/software/rome/r23.10/hwloc/2.7.1-GCCcore-11.3.0/sbin:/software/rome/r23.10/hwloc/2.7.1-GCCcore-11.3.0/bin:/software/rome/r23.10/libxml2/2.9.13-GCCcore-11.3.0/bin:/software/rome/r23.10/XZ/5.2.5-GCCcore-11.3.0/bin:/software/rome/r23.10/numactl/2.0.14-GCCcore-11.3.0/bin:/software/rome/r23.10/binutils/2.38-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/scikit-build/0.15.0-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/CMake/3.24.3-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/libarchive/3.6.1-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/cURL/7.83.0-GCCcore-11.3.0/bin:/software/rome/r23.10/OpenSSL/1.1/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/ncurses/6.3-GCCcore-11.3.0/bin:/software/rome/r23.10/GCCcore/11.3.0/bin:/dev/shm/venv/bin:/home/s3248973/.local/EasyBuildDev/easybuild-framework:/home/s3248973/.local/bin:/home/s3248973/bin:/software/util/slurm/bin:/software/foundation/generic/bin:/software/foundation/x86_64/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/software/util/dtwrapper/bin') | |
| == 2024-10-02 13:49:41,184 pythonpackage.py:243 INFO Determining pip version... | |
| == 2024-10-02 13:49:41,184 run.py:251 INFO Using /bin/bash as shell for running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version | |
| == 2024-10-02 13:49:41,184 run.py:260 INFO running cmd: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version | |
| == 2024-10-02 13:49:41,825 pythonpackage.py:251 INFO Found pip version: 22.0.4 | |
| == 2024-10-02 13:49:41,826 pythonpackage.py:635 INFO Found pip version 22.0.4, OK | |
| == 2024-10-02 13:49:41,826 run.py:251 INFO Using /bin/bash as shell for running cmd: export CMAKE_ARGS="-Dgmxapi_ROOT=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a -C /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a --no-deps --ignore-installed --no-index --no-build-isolation . | |
| == 2024-10-02 13:49:41,826 run.py:260 INFO running cmd: export CMAKE_ARGS="-Dgmxapi_ROOT=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a -C /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a --no-deps --ignore-installed --no-index --no-build-isolation . | |
| == 2024-10-02 13:49:49,963 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): cmd "export CMAKE_ARGS="-Dgmxapi_ROOT=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a -C /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 1 and output: | |
| Processing /dev/shm/s3248973-EasyBuild2338009/GROMACS/2023.3/foss-2022a/gmxapi/gromacs-2023.3/python_packaging/gmxapi | |
| Preparing metadata (pyproject.toml): started | |
| Preparing metadata (pyproject.toml): finished with status 'done' | |
| Building wheels for collected packages: gmxapi | |
| Building wheel for gmxapi (pyproject.toml): started | |
| Building wheel for gmxapi (pyproject.toml): finished with status 'error' | |
| error: subprocess-exited-with-error | |
| Building wheel for gmxapi (pyproject.toml) did not run successfully. | |
| exit code: 1 | |
| > [135 lines of output] | |
| /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/config/__init__.py:28: SetuptoolsDeprecationWarning: As setuptools moves its configuration towards `pyproject.toml`, | |
| `setuptools.config.read_configuration` became deprecated. | |
| For the time being, you can use the `setuptools.config.setupcfg` module | |
| to access a backward compatible API, but this module is provisional | |
| and might be removed in the future. | |
| warnings.warn(dedent(msg), SetuptoolsDeprecationWarning) | |
| running bdist_wheel | |
| running build | |
| running build_py | |
| creating build | |
| creating build/lib.linux-x86_64-cpython-310 | |
| creating build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/exceptions.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/commandline.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/datamodel.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/operation.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/_transform.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/abc.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/_logging.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/typing.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/testsupport.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/utility.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/version.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/__init__.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| copying src/gmxapi/runtime.py -> build/lib.linux-x86_64-cpython-310/gmxapi | |
| creating build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/read_tpr.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/fileio.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/abc.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/workflow.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/context.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/modify_input.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/mdrun.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| copying src/gmxapi/simulation/__init__.py -> build/lib.linux-x86_64-cpython-310/gmxapi/simulation | |
| running build_ext | |
| loading initial cache file /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake | |
| -- The C compiler identification is GNU 11.3.0 | |
| -- The CXX compiler identification is GNU 11.3.0 | |
| -- Detecting C compiler ABI info | |
| -- Detecting C compiler ABI info - done | |
| -- Check for working C compiler: /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/bin/mpicc - skipped | |
| -- Detecting C compile features | |
| -- Detecting C compile features - done | |
| -- Detecting CXX compiler ABI info | |
| -- Detecting CXX compiler ABI info - done | |
| -- Check for working CXX compiler: /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/bin/mpicxx - skipped | |
| -- Detecting CXX compile features | |
| -- Detecting CXX compile features - done | |
| -- Could NOT find Python3 (missing: Python3_INCLUDE_DIRS Python3_LIBRARIES Development Development.Module Development.Embed) (found suitable version "3.8.17", minimum required is "3.7") | |
| -- Found PythonLibs: python3.8 | |
| -- Performing Test HAS_FLTO | |
| -- Performing Test HAS_FLTO - Success | |
| -- Found OpenMP_C: -fopenmp (found version "4.5") | |
| -- Found OpenMP_CXX: -fopenmp (found version "4.5") | |
| -- Found OpenMP: TRUE (found version "4.5") | |
| -- Found GROMACS: 2023.3 | |
| -- Configuring Python package for gmxapi version 0.4.0 | |
| -- Imported /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/bin executable. | |
| CMake Error at CMakeLists.txt:273 (message): | |
| gmxapi core features includes MPI Python bindings and mpi4py compatibility. | |
| Please install mpi4py with a compatible toolchain, then try again to | |
| install this package. | |
| The GROMACS C++ compiler appears to be compatible with | |
| /software/rome/r23.10/OpenMPI/4.1.4-GCC-11.3.0/bin/mpicxx so you might try: | |
| MPICC= pip install --upgrade --no-cache-dir mpi4py | |
| -- Configuring incomplete, errors occurred! | |
| See also "/dev/shm/s3248973-EasyBuild2338009/GROMACS/2023.3/foss-2022a/gmxapi/gromacs-2023.3/python_packaging/gmxapi/build/temp.linux-x86_64-cpython-310/CMakeFiles/CMakeOutput.log". | |
| Traceback (most recent call last): | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 363, in <module> | |
| main() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 345, in main | |
| json_out['return_val'] = hook(**hook_input['kwargs']) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/pip/_vendor/pep517/in_process/_in_process.py", line 261, in build_wheel | |
| return _build_backend().build_wheel(wheel_directory, config_settings, | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/build_meta.py", line 244, in build_wheel | |
| return self._build_with_temp_dir(['bdist_wheel'], '.whl', | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/build_meta.py", line 229, in _build_with_temp_dir | |
| self.run_setup() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/build_meta.py", line 174, in run_setup | |
| exec(compile(code, __file__, 'exec'), locals()) | |
| File "setup.py", line 415, in <module> | |
| setup( | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/__init__.py", line 87, in setup | |
| return distutils.core.setup(**attrs) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 148, in setup | |
| return run_commands(dist) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/core.py", line 163, in run_commands | |
| dist.run_commands() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 967, in run_commands | |
| self.run_command(cmd) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/dist.py", line 1214, in run_command | |
| super().run_command(command) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 986, in run_command | |
| cmd_obj.run() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/wheel/bdist_wheel.py", line 299, in run | |
| self.run_command('build') | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command | |
| self.distribution.run_command(command) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/dist.py", line 1214, in run_command | |
| super().run_command(command) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 986, in run_command | |
| cmd_obj.run() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build.py", line 136, in run | |
| self.run_command(cmd_name) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/cmd.py", line 313, in run_command | |
| self.distribution.run_command(command) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/dist.py", line 1214, in run_command | |
| super().run_command(command) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/dist.py", line 986, in run_command | |
| cmd_obj.run() | |
| File "setup.py", line 232, in run | |
| super(CMakeBuild, self).run() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/command/build_ext.py", line 79, in run | |
| _build_ext.run(self) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/Cython/Distutils/old_build_ext.py", line 186, in run | |
| _build_ext.build_ext.run(self) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 339, in run | |
| self.build_extensions() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/Cython/Distutils/old_build_ext.py", line 195, in build_extensions | |
| _build_ext.build_ext.build_extensions(self) | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 448, in build_extensions | |
| self._build_extensions_serial() | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/site-packages/setuptools/_distutils/command/build_ext.py", line 473, in _build_extensions_serial | |
| self.build_extension(ext) | |
| File "setup.py", line 210, in build_extension | |
| subprocess.check_call( | |
| File "/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/subprocess.py", line 369, in check_call | |
| raise CalledProcessError(retcode, cmd) | |
| subprocess.CalledProcessError: Command '['cmake', '/dev/shm/s3248973-EasyBuild2338009/GROMACS/2023.3/foss-2022a/gmxapi/gromacs-2023.3/python_packaging/gmxapi', '-DCMAKE_LIBRARY_OUTPUT_DIRECTORY=/dev/shm/s3248973-EasyBuild2338009/GROMACS/2023.3/foss-2022a/gmxapi/gromacs-2023.3/python_packaging/gmxapi/build/lib.linux-x86_64-cpython-310/gmxapi/', '-DCMAKE_BUILD_TYPE=Release', '-Dgmxapi_ROOT=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a', '-D_setuppy_cmake_hints=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake', '-C', '/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake', '-Dpybind11_ROOT=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/pybind11/2.9.2-GCCcore-11.3.0/lib/python3.10/site-packages/pybind11/share/cmake/pybind11']' returned non-zero exit status 1. | |
| [end of output] | |
| note: This error originates from a subprocess, and is likely not a problem with pip. | |
| ERROR: Failed building wheel for gmxapi | |
| Failed to build gmxapi | |
| ERROR: Could not build wheels for gmxapi, which is required to install pyproject.toml-based projects | |
| (at easybuild/tools/run.py:695 in parse_cmd_output) | |
| == 2024-10-02 13:49:49,963 build_log.py:267 INFO ... (took 13 secs) | |
| == 2024-10-02 13:49:49,966 build_log.py:267 INFO ... (took 23 secs) | |
| == 2024-10-02 13:49:49,968 filetools.py:2025 INFO Removing lock /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/.locks/_data_horse_ws_s3248973-EasyBuild_easybuild-rome_software_GROMACS_2023.3-foss-2022a.lock... | |
| == 2024-10-02 13:49:49,973 filetools.py:385 INFO Path /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/.locks/_data_horse_ws_s3248973-EasyBuild_easybuild-rome_software_GROMACS_2023.3-foss-2022a.lock successfully removed. | |
| == 2024-10-02 13:49:49,973 filetools.py:2029 INFO Lock removed: /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/.locks/_data_horse_ws_s3248973-EasyBuild_easybuild-rome_software_GROMACS_2023.3-foss-2022a.lock | |
| == 2024-10-02 13:49:49,973 easyblock.py:4297 WARNING build failed (first 300 chars): cmd "export CMAKE_ARGS="-Dgmxapi_ROOT=/data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a -C /data/horse/ws/s3248973-EasyBuild/easybuild-rome/software/GROMACS/2023.3-foss-2022a/share/cmake/gromacs_mpi/gromacs-hints_mpi.cmake" && /data/horse/ws/s3248973-EasyBuild/easy | |
| == 2024-10-02 13:49:49,973 easyblock.py:326 INFO Closing log for application name GROMACS version 2023.3 |
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