Created
December 10, 2025 01:14
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(partial) EasyBuild log for failed build of /dev/shm/eb-g52rb05_/files_pr24784/g/gemmi/gemmi-0.7.4-GCC-14.3.0.eb (PR(s) #24784)
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| == 2025-12-10 02:14:24,573 easyblock.py:371 INFO This is EasyBuild 5.1.2 (framework: 5.1.2, easyblocks: 5.1.2) on host vera-icelake-build. | |
| == 2025-12-10 02:14:24,574 easyblock.py:377 INFO This is easyblock CMakePythonPackage from module easybuild.easyblocks.generic.cmakepythonpackage (/apps/Common/software/EasyBuild/5.1.2/lib/python3.9/site-packages/easybuild/easyblocks/generic/cmakepythonpackage.py) | |
| == 2025-12-10 02:14:24,574 easyblock.py:1162 INFO Build dir set to /dev/shm/gemmi/0.7.4/GCC-14.3.0 | |
| == 2025-12-10 02:14:24,574 easyblock.py:1225 INFO Software install dir set to /apps/Test/software/gemmi/0.7.4-GCC-14.3.0 | |
| == 2025-12-10 02:14:24,574 easyblock.py:1230 INFO Module install dir set to /apps/Test/fmodules/all | |
| == 2025-12-10 02:14:24,574 easyblock.py:345 INFO Init completed for application name gemmi version 0.7.4 | |
| == 2025-12-10 02:14:24,574 pythonpackage.py:472 INFO Using default value for expected module name (lowercase software name): 'gemmi' | |
| == 2025-12-10 02:14:24,574 pythonpackage.py:518 INFO Using pip with --no-deps option | |
| == 2025-12-10 02:14:24,574 pythonpackage.py:546 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command | |
| == 2025-12-10 02:14:24,574 environment.py:95 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) | |
| == 2025-12-10 02:14:24,574 environment.py:95 INFO Environment variable PIP_REQUIRE_VIRTUALENV set to false (previously undefined) | |
| == 2025-12-10 02:14:24,574 environment.py:95 INFO Environment variable PIP_DISABLE_PIP_VERSION_CHECK set to true (previously undefined) | |
| == 2025-12-10 02:14:24,574 environment.py:95 INFO Environment variable XDG_CACHE_HOME set to /dev/shm/eb-g52rb05_/xdg-cache-home (previously undefined) | |
| == 2025-12-10 02:14:24,574 python.py:273 INFO Using /dev/shm/eb-g52rb05_/xdg-cache-home as pip cache directory | |
| == 2025-12-10 02:14:24,574 easyblock.py:5034 INFO Obtained application instance for gemmi (easyblock: CMakePythonPackage) | |
| == 2025-12-10 02:14:24,575 easyconfig.py:1812 INFO Generating template values... | |
| == 2025-12-10 02:14:24,575 easyconfig.py:1831 INFO Template values: arch='x86_64', bitbucket_account='gemmi', cuda_cc_cmake='80;86', cuda_cc_semicolon_sep='8.0;8.6', cuda_cc_space_sep='8.0 8.6', cuda_cc_space_sep_no_period='80 86', cuda_compute_capabilities='8.0,8.6', cuda_int_comma_sep='80,86', cuda_int_semicolon_sep='80;86', cuda_int_space_sep='80 86', cuda_sm_comma_sep='sm_80,sm_86', cuda_sm_space_sep='sm_80 sm_86', github_account='project-gemmi', module_name='gemmi/0.7.4-GCC-14.3.0', name='gemmi', nameletter='g', nameletterlower='g', namelower='gemmi', pymajver='3', pyminver='13', pyshortver='3.13', pyver='3.13.5', rpath_enabled='true', software_commit='', sysroot='', toolchain_name='GCC', toolchain_version='14.3.0', version='0.7.4', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='' | |
| == 2025-12-10 02:14:24,576 one.py:179 INFO Skipping reformatting value for parameter 'toolchain' | |
| == 2025-12-10 02:14:24,576 one.py:179 INFO Skipping reformatting value for parameter 'toolchainopts' | |
| == 2025-12-10 02:14:24,577 filetools.py:2061 INFO Creating directory /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824 (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:24,577 easyblock.py:5315 INFO Dumped easyconfig instance to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/gemmi-0.7.4-GCC-14.3.0.eb | |
| == 2025-12-10 02:14:24,577 filetools.py:2061 INFO Creating directory /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:24,580 filetools.py:2545 INFO /apps/Common/software/EasyBuild/5.1.2/lib/python3.9/site-packages/easybuild/easyblocks/generic/cmakepythonpackage.py copied to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks/cmakepythonpackage.py | |
| == 2025-12-10 02:14:24,580 easyblock.py:5295 INFO Dumped easyblock cmakepythonpackage.py required for reproduction to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks | |
| == 2025-12-10 02:14:24,582 filetools.py:2545 INFO /apps/Common/software/EasyBuild/5.1.2/lib/python3.9/site-packages/easybuild/easyblocks/generic/configuremake.py copied to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks/configuremake.py | |
| == 2025-12-10 02:14:24,582 easyblock.py:5295 INFO Dumped easyblock configuremake.py required for reproduction to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks | |
| == 2025-12-10 02:14:24,584 filetools.py:2545 INFO /apps/Common/software/EasyBuild/5.1.2/lib/python3.9/site-packages/easybuild/easyblocks/generic/cmakemake.py copied to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks/cmakemake.py | |
| == 2025-12-10 02:14:24,584 easyblock.py:5295 INFO Dumped easyblock cmakemake.py required for reproduction to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks | |
| == 2025-12-10 02:14:24,585 filetools.py:2545 INFO /apps/Common/software/EasyBuild/5.1.2/lib/python3.9/site-packages/easybuild/easyblocks/generic/pythonpackage.py copied to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks/pythonpackage.py | |
| == 2025-12-10 02:14:24,586 easyblock.py:5295 INFO Dumped easyblock pythonpackage.py required for reproduction to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/easyblocks | |
| == 2025-12-10 02:14:24,586 filetools.py:2061 INFO Creating directory /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/hooks (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:24,587 filetools.py:2545 INFO /apps/c3se_hooks.py copied to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/hooks/c3se_hooks.py | |
| == 2025-12-10 02:14:24,587 easyblock.py:5327 INFO Dumped hooks file /apps/c3se_hooks.py which is (potentially) required for reproduction to /dev/shm/eb-g52rb05_/reprod_20251210021424_1708824/hooks/c3se_hooks.py | |
| == 2025-12-10 02:14:24,588 easyblock.py:2481 INFO Number of iterations to perform for central part of installation procedure: 2 | |
| == 2025-12-10 02:14:24,588 build_log.py:322 INFO building and installing gemmi/0.7.4-GCC-14.3.0... | |
| == 2025-12-10 02:14:24,593 filetools.py:2144 INFO Lock /apps/Test/software/.locks/_apps_Test_software_gemmi_0.7.4-GCC-14.3.0.lock does not exist | |
| == 2025-12-10 02:14:24,593 filetools.py:2101 INFO Creating lock at /apps/Test/software/.locks/_apps_Test_software_gemmi_0.7.4-GCC-14.3.0.lock... | |
| == 2025-12-10 02:14:24,593 filetools.py:2061 INFO Creating directory /apps/Test/software/.locks/_apps_Test_software_gemmi_0.7.4-GCC-14.3.0.lock (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:24,597 filetools.py:2110 INFO Lock created: /apps/Test/software/.locks/_apps_Test_software_gemmi_0.7.4-GCC-14.3.0.lock | |
| == 2025-12-10 02:14:24,597 easyblock.py:2517 INFO Setting parallelism: 16 | |
| == 2025-12-10 02:14:24,597 build_log.py:322 INFO fetching files and verifying checksums... | |
| == 2025-12-10 02:14:24,598 easyblock.py:4705 INFO Starting fetch step | |
| == 2025-12-10 02:14:24,599 easyconfig.py:1812 INFO Generating template values... | |
| == 2025-12-10 02:14:24,599 easyconfig.py:1831 INFO Template values: arch='x86_64', bitbucket_account='gemmi', builddir='/dev/shm/gemmi/0.7.4/GCC-14.3.0', cuda_cc_cmake='80;86', cuda_cc_semicolon_sep='8.0;8.6', cuda_cc_space_sep='8.0 8.6', cuda_cc_space_sep_no_period='80 86', cuda_compute_capabilities='8.0,8.6', cuda_int_comma_sep='80,86', cuda_int_semicolon_sep='80;86', cuda_int_space_sep='80 86', cuda_sm_comma_sep='sm_80,sm_86', cuda_sm_space_sep='sm_80 sm_86', github_account='project-gemmi', installdir='/apps/Test/software/gemmi/0.7.4-GCC-14.3.0', module_name='gemmi/0.7.4-GCC-14.3.0', name='gemmi', nameletter='g', nameletterlower='g', namelower='gemmi', parallel='16', pymajver='3', pyminver='13', pyshortver='3.13', pyver='3.13.5', rpath_enabled='true', software_commit='', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='14.3.0', version='0.7.4', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='' | |
| == 2025-12-10 02:14:24,599 easyblock.py:4716 INFO Running method fetch_step part of step fetch | |
| == 2025-12-10 02:14:24,599 easyblock.py:2618 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version | |
| == 2025-12-10 02:14:24,599 easyblock.py:905 INFO Considering directory in which easyconfig file is located when searching for v0.7.4.tar.gz: /dev/shm/eb-g52rb05_/files_pr24784/g/gemmi | |
| == 2025-12-10 02:14:24,599 tools.py:275 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /apps/Common/software/EasyBuild/5.1.2/bin/eb | |
| == 2025-12-10 02:14:24,599 tools.py:289 INFO Also considering installation prefix /apps/Common/software/EasyBuild/5.1.2 (determined via path to 'eb' script)... | |
| == 2025-12-10 02:14:25,155 filetools.py:899 INFO File size for https://github.com/project-gemmi/gemmi/archive/v0.7.4.tar.gz: None | |
| == 2025-12-10 02:14:25,357 filetools.py:906 INFO Downloaded file v0.7.4.tar.gz from url https://github.com/project-gemmi/gemmi/archive/v0.7.4.tar.gz to /apps/sources/g/gemmi/v0.7.4.tar.gz | |
| == 2025-12-10 02:14:25,357 filetools.py:950 INFO Successful download of file v0.7.4.tar.gz from url https://github.com/project-gemmi/gemmi/archive/v0.7.4.tar.gz to path /apps/sources/g/gemmi/v0.7.4.tar.gz | |
| == 2025-12-10 02:14:25,360 easyblock.py:1056 INFO Successfully downloaded source file v0.7.4.tar.gz from https://github.com/project-gemmi/gemmi/archive/v0.7.4.tar.gz | |
| == 2025-12-10 02:14:25,360 easyblock.py:579 INFO Added sources: [{'name': 'v0.7.4.tar.gz', 'path': '/apps/sources/g/gemmi/v0.7.4.tar.gz', 'cmd': None, 'checksum': '58ed9023e0f75033ebec1da630461bc6e1af661f29f0c41deed66c20315ebe2a', 'finalpath': '/dev/shm/gemmi/0.7.4/GCC-14.3.0'}] | |
| == 2025-12-10 02:14:25,360 easyblock.py:2663 INFO no patches provided | |
| == 2025-12-10 02:14:25,367 easyblock.py:2672 INFO sha256 checksum for /apps/sources/g/gemmi/v0.7.4.tar.gz: 58ed9023e0f75033ebec1da630461bc6e1af661f29f0c41deed66c20315ebe2a | |
| == 2025-12-10 02:14:25,372 easyblock.py:622 INFO Fetched extension patches: [] | |
| == 2025-12-10 02:14:25,372 easyblock.py:2707 INFO Checking dirs that need to be created: ['/apps/Test/software/gemmi/0.7.4-GCC-14.3.0', '/apps/Test/fmodules/all/gemmi', '/apps/Test/fmodules/bio/gemmi'] | |
| == 2025-12-10 02:14:25,372 filetools.py:2061 INFO Creating directory /apps/Test/software/gemmi/0.7.4-GCC-14.3.0 (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:25,378 filetools.py:2061 INFO Creating directory /apps/Test/fmodules/all/gemmi (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:25,382 filetools.py:2061 INFO Creating directory /apps/Test/fmodules/bio/gemmi (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:25,393 configuremake.py:96 INFO config.guess version: 2023-08-22 (last updated: 2025-09-27T00:29:31.495180, SHA256 checksum: ec2577614252326f889df1de97b9a457c03a9a94811048563c211a44496d8ba3) | |
| == 2025-12-10 02:14:25,393 configuremake.py:152 INFO Found config.guess at /apps/sources/generic/eb_v5.1.2/ConfigureMake/config.guess | |
| == 2025-12-10 02:14:25,393 easyblock.py:4716 INFO Running method checksum_step part of step fetch | |
| == 2025-12-10 02:14:25,396 easyblock.py:2725 INFO Checksum verification for /apps/sources/g/gemmi/v0.7.4.tar.gz using 58ed9023e0f75033ebec1da630461bc6e1af661f29f0c41deed66c20315ebe2a passed. | |
| == 2025-12-10 02:14:25,396 build_log.py:322 INFO ... (took < 1 sec) | |
| == 2025-12-10 02:14:25,398 build_log.py:322 INFO creating build dir, resetting environment... | |
| == 2025-12-10 02:14:25,400 easyblock.py:4705 INFO Starting ready step | |
| == 2025-12-10 02:14:25,400 easyconfig.py:1812 INFO Generating template values... | |
| == 2025-12-10 02:14:25,400 easyconfig.py:1831 INFO Template values: arch='x86_64', bitbucket_account='gemmi', builddir='/dev/shm/gemmi/0.7.4/GCC-14.3.0', cuda_cc_cmake='80;86', cuda_cc_semicolon_sep='8.0;8.6', cuda_cc_space_sep='8.0 8.6', cuda_cc_space_sep_no_period='80 86', cuda_compute_capabilities='8.0,8.6', cuda_int_comma_sep='80,86', cuda_int_semicolon_sep='80;86', cuda_int_space_sep='80 86', cuda_sm_comma_sep='sm_80,sm_86', cuda_sm_space_sep='sm_80 sm_86', github_account='project-gemmi', installdir='/apps/Test/software/gemmi/0.7.4-GCC-14.3.0', module_name='gemmi/0.7.4-GCC-14.3.0', name='gemmi', nameletter='g', nameletterlower='g', namelower='gemmi', parallel='16', pymajver='3', pyminver='13', pyshortver='3.13', pyver='3.13.5', rpath_enabled='true', software_commit='', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='14.3.0', version='0.7.4', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='' | |
| == 2025-12-10 02:14:25,400 easyblock.py:4716 INFO Running method check_readiness_step part of step ready | |
| == 2025-12-10 02:14:25,401 run.py:508 INFO Running shell command '/usr/share/lmod/lmod/libexec/lmod python --terse list' in /apps/c3se-test-easyconfigs | |
| == 2025-12-10 02:14:25,440 run.py:622 INFO Shell command completed successfully: /usr/share/lmod/lmod/libexec/lmod python --terse list | |
| == 2025-12-10 02:14:25,440 run.py:624 INFO Output of '/usr/share/lmod/lmod/libexec/lmod ...' shell command (stdout only): | |
| import os | |
| os.environ["MODULEPATH"] = "/apps/Test/fmodules/all:/apps/Common/fmodules/all"; | |
| os.environ["_ModuleTable001_"] = "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"; | |
| os.environ["_ModuleTable002_"] = "dWxlcy9hbGwiLCAiL2FwcHMvQ29tbW9uL2Ztb2R1bGVzL2FsbCIsCn0sCnN5c3RlbUJhc2VNUEFUSCA9ICIvYXBwcy9BcmNoL2Ztb2R1bGVzL2FsbDovYXBwcy9Db21tb24vZm1vZHVsZXMvYWxsIiwKfQo="; | |
| os.environ["_ModuleTable_Sz_"] = "2"; | |
| _mlstatus = True | |
| Warnings and errors of '/usr/share/lmod/lmod/libexec/lmod ...' shell command (stderr only): | |
| EasyBuild/5.1.2 | |
| == 2025-12-10 02:14:25,441 easyblock.py:2567 WARNING Loaded modules detected: ['EasyBuild/5.1.2'] | |
| == 2025-12-10 02:14:25,446 easyblock.py:4716 INFO Running method make_builddir part of step ready | |
| == 2025-12-10 02:14:25,446 filetools.py:2061 INFO Creating directory /dev/shm/gemmi/0.7.4/GCC-14.3.0 (parents: True, set_gid: False, sticky: False) | |
| == 2025-12-10 02:14:25,448 easyblock.py:4716 INFO Running method reset_env part of step ready | |
| == 2025-12-10 02:14:25,448 easyblock.py:4716 INFO Running method handle_iterate_opts part of step ready | |
| == 2025-12-10 02:14:25,448 build_log.py:322 INFO starting iteration 1/2 ... | |
| == 2025-12-10 02:14:25,450 easyblock.py:2435 INFO Current iteration index: 0 | |
| == 2025-12-10 02:14:25,451 easyconfig.py:1812 INFO Generating template values... | |
| == 2025-12-10 02:14:25,451 easyconfig.py:1831 INFO Template values: arch='x86_64', bitbucket_account='gemmi', builddir='/dev/shm/gemmi/0.7.4/GCC-14.3.0', cuda_cc_cmake='80;86', cuda_cc_semicolon_sep='8.0;8.6', cuda_cc_space_sep='8.0 8.6', cuda_cc_space_sep_no_period='80 86', cuda_compute_capabilities='8.0,8.6', cuda_int_comma_sep='80,86', cuda_int_semicolon_sep='80;86', cuda_int_space_sep='80 86', cuda_sm_comma_sep='sm_80,sm_86', cuda_sm_space_sep='sm_80 sm_86', github_account='project-gemmi', installdir='/apps/Test/software/gemmi/0.7.4-GCC-14.3.0', module_name='gemmi/0.7.4-GCC-14.3.0', name='gemmi', nameletter='g', nameletterlower='g', namelower='gemmi', parallel='16', pymajver='3', pyminver='13', pyshortver='3.13', pyver='3.13.5', rpath_enabled='true', software_commit='', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='14.3.0', version='0.7.4', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='' | |
| == 2025-12-10 02:14:25,451 build_log.py:322 INFO ... (took < 1 sec) | |
| == 2025-12-10 02:14:25,453 build_log.py:322 INFO unpacking... | |
| == 2025-12-10 02:14:25,454 easyblock.py:4705 INFO Starting extract step | |
| == 2025-12-10 02:14:25,454 easyconfig.py:1812 INFO Generating template values... | |
| == 2025-12-10 02:14:25,455 easyconfig.py:1831 INFO Template values: arch='x86_64', bitbucket_account='gemmi', builddir='/dev/shm/gemmi/0.7.4/GCC-14.3.0', cuda_cc_cmake='80;86', cuda_cc_semicolon_sep='8.0;8.6', cuda_cc_space_sep='8.0 8.6', cuda_cc_space_sep_no_period='80 86', cuda_compute_capabilities='8.0,8.6', cuda_int_comma_sep='80,86', cuda_int_semicolon_sep='80;86', cuda_int_space_sep='80 86', cuda_sm_comma_sep='sm_80,sm_86', cuda_sm_space_sep='sm_80 sm_86', github_account='project-gemmi', installdir='/apps/Test/software/gemmi/0.7.4-GCC-14.3.0', module_name='gemmi/0.7.4-GCC-14.3.0', name='gemmi', nameletter='g', nameletterlower='g', namelower='gemmi', parallel='16', pymajver='3', pyminver='13', pyshortver='3.13', pyver='3.13.5', rpath_enabled='true', software_commit='', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='14.3.0', version='0.7.4', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='' | |
| == 2025-12-10 02:14:25,455 easyblock.py:4716 INFO Running method extract_step part of step extract | |
| == 2025-12-10 02:14:25,455 easyblock.py:2856 INFO Unpacking source v0.7.4.tar.gz | |
| == 2025-12-10 02:14:25,455 run.py:457 INFO run_shell_cmd: command environment of "tar xzf /apps/sources/g/gemmi/v0.7.4.tar.gz" will be saved to /dev/shm/eb-g52rb05_/run-shell-cmd-output/tar-h4bhp2ch | |
| == 2025-12-10 02:14:25,455 run.py:460 INFO run_shell_cmd: Output of "tar xzf /apps/sources/g/gemmi/v0.7.4.tar.gz" will be logged to /dev/shm/eb-g52rb05_/run-shell-cmd-output/tar-h4bhp2ch/out.txt | |
| == 2025-12-10 02:14:25,475 run.py:494 INFO Path to bash that will be used to run shell commands: /usr/bin/bash | |
| == 2025-12-10 02:14:25,475 run.py:508 INFO Running shell command 'tar xzf /apps/sources/g/gemmi/v0.7.4.tar.gz' in /dev/shm/gemmi/0.7.4/GCC-14.3.0 | |
| == 2025-12-10 02:14:25,533 run.py:622 INFO Shell command completed successfully: tar xzf /apps/sources/g/gemmi/v0.7.4.tar.gz | |
| == 2025-12-10 02:14:25,533 run.py:624 INFO Output of 'tar ...' shell command (stdout + stderr): | |
| == 2025-12-10 02:14:25,536 build_log.py:322 INFO ... (took < 1 sec) | |
| == 2025-12-10 02:14:25,538 build_log.py:322 INFO patching... | |
| == 2025-12-10 02:14:25,540 easyblock.py:4705 INFO Starting patch step | |
| == 2025-12-10 02:14:25,540 easyconfig.py:1812 INFO Generating template values... | |
| == 2025-12-10 02:14:25,540 easyconfig.py:1831 INFO Template values: arch='x86_64', bitbucket_account='gemmi', builddir='/dev/shm/gemmi/0.7.4/GCC-14.3.0', cuda_cc_cmake='80;86', cuda_cc_semicolon_sep='8.0;8.6', cuda_cc_space_sep='8.0 8.6', cuda_cc_space_sep_no_period='80 86', cuda_compute_capabilities='8.0,8.6', cuda_int_comma_sep='80,86', cuda_int_semicolon_sep='80;86', cuda_int_space_sep='80 86', cuda_sm_comma_sep='sm_80,sm_86', cuda_sm_space_sep='sm_80 sm_86', github_account='project-gemmi', installdir='/apps/Test/software/gemmi/0.7.4-GCC-14.3.0', module_name='gemmi/0.7.4-GCC-14.3.0', name='gemmi', nameletter='g', nameletterlower='g', namelower='gemmi', parallel='16', pymajver='3', pyminver='13', pyshortver='3.13', pyver='3.13.5', rpath_enabled='true', software_commit='', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='14.3.0', version='0.7.4', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='' | |
| == 2025-12-10 02:14:25,540 easyblock.py:4716 INFO Running method patch_step part of step patch | |
| == 2025-12-10 02:14:25,540 build_log.py:322 INFO ... (took < 1 sec) | |
| == 2025-12-10 02:14:25,542 build_log.py:322 INFO preparing... | |
| == 2025-12-10 02:14:25,544 easyblock.py:4705 INFO Starting prepare step | |
| == 2025-12-10 02:14:25,544 easyconfig.py:1812 INFO Generating template values... | |
| == 2025-12-10 02:14:25,544 easyconfig.py:1831 INFO Template values: arch='x86_64', bitbucket_account='gemmi', builddir='/dev/shm/gemmi/0.7.4/GCC-14.3.0', cuda_cc_cmake='80;86', cuda_cc_semicolon_sep='8.0;8.6', cuda_cc_space_sep='8.0 8.6', cuda_cc_space_sep_no_period='80 86', cuda_compute_capabilities='8.0,8.6', cuda_int_comma_sep='80,86', cuda_int_semicolon_sep='80;86', cuda_int_space_sep='80 86', cuda_sm_comma_sep='sm_80,sm_86', cuda_sm_space_sep='sm_80 sm_86', github_account='project-gemmi', installdir='/apps/Test/software/gemmi/0.7.4-GCC-14.3.0', module_name='gemmi/0.7.4-GCC-14.3.0', name='gemmi', nameletter='g', nameletterlower='g', namelower='gemmi', parallel='16', pymajver='3', pyminver='13', pyshortver='3.13', pyver='3.13.5', rpath_enabled='true', software_commit='', start_dir='None', sysroot='', toolchain_name='GCC', toolchain_version='14.3.0', version='0.7.4', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='' | |
| == 2025-12-10 02:14:25,544 easyblock.py:4716 INFO Running method prepare_step part of step prepare | |
| == 2025-12-10 02:14:25,545 modules.py:1054 INFO Checking whether pybind11/3.0.0-GCC-14.3.0 exists... | |
| == 2025-12-10 02:14:25,546 modules.py:1059 INFO Module pybind11/3.0.0-GCC-14.3.0 exists (found in list of available modules) | |
| == 2025-12-10 02:14:25,546 modules.py:1082 INFO Result for existence check of pybind11/3.0.0-GCC-14.3.0 module: True | |
| == 2025-12-10 02:14:25,546 modules.py:1054 INFO Checking whether pybind11-stubgen/2.5.5-GCCcore-14.3.0 exists... | |
| == 2025-12-10 02:14:25,546 modules.py:1061 INFO Module pybind11-stubgen/2.5.5-GCCcore-14.3.0 not found in list of available modules, checking via 'module show'... | |
| == 2025-12-10 02:14:25,546 run.py:508 INFO Running shell command '/usr/share/lmod/lmod/libexec/lmod python show pybind11-stubgen/2.5.5-GCCcore-14.3.0' in /dev/shm/gemmi/0.7.4/GCC-14.3.0/gemmi-0.7.4 | |
| == 2025-12-10 02:14:26,158 run.py:622 INFO Shell command completed successfully: /usr/share/lmod/lmod/libexec/lmod python show pybind11-stubgen/2.5.5-GCCcore-14.3.0 | |
| == 2025-12-10 02:14:26,159 run.py:624 INFO Output of '/usr/share/lmod/lmod/libexec/lmod ...' shell command (stdout only): | |
| import os | |
| os.environ["MODULEPATH"] = "/apps/Test/fmodules/all:/apps/Common/fmodules/all"; | |
| os.environ["_ModuleTable001_"] = "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"; | |
| os.environ["_ModuleTable002_"] = "dWxlcy9hbGwiLCAiL2FwcHMvQ29tbW9uL2Ztb2R1bGVzL2FsbCIsCn0sCnN5c3RlbUJhc2VNUEFUSCA9ICIvYXBwcy9BcmNoL2Ztb2R1bGVzL2FsbDovYXBwcy9Db21tb24vZm1vZHVsZXMvYWxsIiwKfQo="; | |
| os.environ["_ModuleTable_Sz_"] = "2"; | |
| _mlstatus = True | |
| Warnings and errors of '/usr/share/lmod/lmod/libexec/lmod ...' shell command (stderr only): | |
| == 2025-12-10 02:14:26,159 modules.py:1075 INFO Module pybind11-stubgen/2.5.5-GCCcore-14.3.0 not found via module avail/show, checking whether it is a wrapper | |
| == 2025-12-10 02:14:26,161 modules.py:1082 INFO Result for existence check of pybind11-stubgen/2.5.5-GCCcore-14.3.0 module: False | |
| == 2025-12-10 02:14:26,161 modules.py:1054 INFO Checking whether scikit-build-core/0.11.5-GCCcore-14.3.0 exists... | |
| == 2025-12-10 02:14:26,162 modules.py:1059 INFO Module scikit-build-core/0.11.5-GCCcore-14.3.0 exists (found in list of available modules) | |
| == 2025-12-10 02:14:26,162 modules.py:1082 INFO Result for existence check of scikit-build-core/0.11.5-GCCcore-14.3.0 module: True | |
| == 2025-12-10 02:14:26,162 modules.py:1054 INFO Checking whether meson-python/0.18.0-GCCcore-14.3.0 exists... | |
| == 2025-12-10 02:14:26,162 modules.py:1059 INFO Module meson-python/0.18.0-GCCcore-14.3.0 exists (found in list of available modules) | |
| == 2025-12-10 02:14:26,162 modules.py:1082 INFO Result for existence check of meson-python/0.18.0-GCCcore-14.3.0 module: True | |
| == 2025-12-10 02:14:26,162 modules.py:1054 INFO Checking whether nanobind/2.9.2-GCCcore-14.3.0 exists... | |
| == 2025-12-10 02:14:26,162 modules.py:1059 INFO Module nanobind/2.9.2-GCCcore-14.3.0 exists (found in list of available modules) | |
| == 2025-12-10 02:14:26,162 modules.py:1082 INFO Result for existence check of nanobind/2.9.2-GCCcore-14.3.0 module: True | |
| == 2025-12-10 02:14:26,162 modules.py:1054 INFO Checking whether CMake/4.0.3-GCCcore-14.3.0 exists... | |
| == 2025-12-10 02:14:26,162 modules.py:1059 INFO Module CMake/4.0.3-GCCcore-14.3.0 exists (found in list of available modules) | |
| == 2025-12-10 02:14:26,162 modules.py:1082 INFO Result for existence check of CMake/4.0.3-GCCcore-14.3.0 module: True | |
| == 2025-12-10 02:14:26,162 modules.py:1054 INFO Checking whether Python/3.13.5-GCCcore-14.3.0 exists... | |
| == 2025-12-10 02:14:26,162 modules.py:1059 INFO Module Python/3.13.5-GCCcore-14.3.0 exists (found in list of available modules) | |
| == 2025-12-10 02:14:26,162 modules.py:1082 INFO Result for existence check of Python/3.13.5-GCCcore-14.3.0 module: True | |
| == 2025-12-10 02:14:26,179 build_log.py:226 ERROR EasyBuild encountered an error (at easybuild/base/exceptions.py:126 in __init__): Missing modules for dependencies (use --robot?): pybind11-stubgen/2.5.5-GCCcore-14.3.0 (at easybuild/tools/toolchain/toolchain.py:576 in _check_dependencies) | |
| == 2025-12-10 02:14:26,179 build_log.py:322 INFO ... (took < 1 sec) | |
| == 2025-12-10 02:14:26,182 filetools.py:2152 INFO Removing lock /apps/Test/software/.locks/_apps_Test_software_gemmi_0.7.4-GCC-14.3.0.lock... | |
| == 2025-12-10 02:14:26,189 filetools.py:423 INFO Path /apps/Test/software/.locks/_apps_Test_software_gemmi_0.7.4-GCC-14.3.0.lock successfully removed. | |
| == 2025-12-10 02:14:26,190 filetools.py:2156 INFO Lock removed: /apps/Test/software/.locks/_apps_Test_software_gemmi_0.7.4-GCC-14.3.0.lock | |
| == 2025-12-10 02:14:26,190 easyblock.py:389 INFO Closing log for application name gemmi version 0.7.4 |
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