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February 3, 2022 22:15
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== 2022-02-03 22:14:01,848 easyblock.py:295 INFO This is EasyBuild 4.5.0-rce21bd8758bda3e28ace9d4e3c7527e50077cd81 (framework: 4.5.0-rbe97b6553afcefae7f1731e6e0e75462bb032218, easyblocks: 4.5.0-rce21bd8758bda3e28ace9d4e3c7527e50077cd81) on host build-node.computecanada.ca. | |
== 2022-02-03 22:14:01,848 easyblock.py:301 INFO This is easyblock MakeCp from module easybuild.easyblocks.generic.makecp (/cvmfs/soft.computecanada.ca/easybuild/site-packages/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py) | |
== 2022-02-03 22:14:01,849 easyblock.py:971 INFO Build dir set to /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0 | |
== 2022-02-03 22:14:01,850 easyblock.py:1031 INFO Software install dir set to /home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0 | |
== 2022-02-03 22:14:01,850 easyblock.py:1036 INFO Module install dir set to /home/mboisson/.local/easybuild/modules/2020/ | |
== 2022-02-03 22:14:01,850 easyblock.py:280 INFO Init completed for application name rvtests version 2.1.0 | |
== 2022-02-03 22:14:01,850 easyblock.py:3937 INFO Obtained application instance of for rvtests (easyblock: MakeCp) | |
== 2022-02-03 22:14:01,850 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:01,851 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:01,852 one.py:175 INFO Skipping reformatting value for parameter 'toolchain' | |
== 2022-02-03 22:14:01,852 filetools.py:1870 INFO Creating directory /tmp/eb-7_4x5zsi/reprod_20220203221401_16100 (parents: True, set_gid: False, sticky: False) | |
== 2022-02-03 22:14:01,853 easyblock.py:4183 INFO Dumped easyconfig instance to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/rvtests-2.1.0-GCCcore-9.3.0.eb | |
== 2022-02-03 22:14:01,853 filetools.py:1870 INFO Creating directory /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks (parents: True, set_gid: False, sticky: False) | |
== 2022-02-03 22:14:01,853 filetools.py:2383 INFO /cvmfs/soft.computecanada.ca/easybuild/site-packages/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks/configuremake.py | |
== 2022-02-03 22:14:01,854 easyblock.py:4163 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks | |
== 2022-02-03 22:14:01,855 filetools.py:2383 INFO /cvmfs/soft.computecanada.ca/easybuild/site-packages/easybuild-easyblocks/easybuild/easyblocks/generic/makecp.py copied to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks/makecp.py | |
== 2022-02-03 22:14:01,856 easyblock.py:4163 INFO Dumped easyblock makecp.py required for reproduction to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/easyblocks | |
== 2022-02-03 22:14:01,856 filetools.py:1870 INFO Creating directory /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/hooks (parents: True, set_gid: False, sticky: False) | |
== 2022-02-03 22:14:01,856 filetools.py:2383 INFO /cvmfs/soft.computecanada.ca/easybuild/cc_hooks_gentoo.py copied to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/hooks/cc_hooks_gentoo.py | |
== 2022-02-03 22:14:01,856 easyblock.py:4195 INFO Dumped hooks file /cvmfs/soft.computecanada.ca/easybuild/cc_hooks_gentoo.py which is (potentially) required for reproduction to /tmp/eb-7_4x5zsi/reprod_20220203221401_16100/hooks/cc_hooks_gentoo.py | |
== 2022-02-03 22:14:01,857 easyblock.py:2018 INFO Number of iterations to perform for central part of installation procedure: 1 | |
== 2022-02-03 22:14:01,857 build_log.py:266 INFO building and installing avx2/Core/rvtests/2.1.0... | |
== 2022-02-03 22:14:01,862 filetools.py:1963 INFO Lock /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock does not exist | |
== 2022-02-03 22:14:01,862 filetools.py:1904 INFO Creating lock at /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock... | |
== 2022-02-03 22:14:01,862 filetools.py:1870 INFO Creating directory /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock (parents: True, set_gid: False, sticky: False) | |
== 2022-02-03 22:14:01,863 filetools.py:1913 INFO Lock created: /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock | |
== 2022-02-03 22:14:01,863 build_log.py:266 INFO fetching files... | |
== 2022-02-03 22:14:01,865 easyblock.py:3648 INFO Starting fetch step | |
== 2022-02-03 22:14:01,865 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:01,865 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:01,865 hooks.py:166 INFO Found pre_fetch_hook hook | |
== 2022-02-03 22:14:01,866 hooks.py:198 INFO Running 'pre_fetch_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])... | |
== 2022-02-03 22:14:01,866 easyblock.py:3656 INFO Running method fetch_step part of step fetch | |
== 2022-02-03 22:14:01,866 easyblock.py:2140 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version | |
== 2022-02-03 22:14:01,866 tools.py:271 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /cvmfs/soft.computecanada.ca/easybuild/framework/eb | |
== 2022-02-03 22:14:01,866 tools.py:287 INFO Not considering /cvmfs/soft.computecanada.ca/easybuild (no easybuild/easyconfigs subdir found) | |
== 2022-02-03 22:14:01,866 tools.py:295 INFO Also considering installation prefix /cvmfs/soft.computecanada.ca/easybuild/site-packages (via resolved path to 'eb')... | |
== 2022-02-03 22:14:01,867 easyblock.py:788 INFO Found file checksums.json at /home/mboisson/git/easybuild-easyconfigs/easybuild/easyconfigs/r/rvtests/checksums.json | |
== 2022-02-03 22:14:01,867 easyblock.py:377 INFO Loading checksums from file /home/mboisson/git/easybuild-easyconfigs/easybuild/easyconfigs/r/rvtests/checksums.json | |
== 2022-02-03 22:14:01,868 tools.py:271 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /cvmfs/soft.computecanada.ca/easybuild/framework/eb | |
== 2022-02-03 22:14:01,868 tools.py:287 INFO Not considering /cvmfs/soft.computecanada.ca/easybuild (no easybuild/easyconfigs subdir found) | |
== 2022-02-03 22:14:01,868 tools.py:295 INFO Also considering installation prefix /cvmfs/soft.computecanada.ca/easybuild/site-packages (via resolved path to 'eb')... | |
== 2022-02-03 22:14:01,869 easyblock.py:788 INFO Found file v2.1.0.tar.gz at /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz | |
== 2022-02-03 22:14:01,869 easyblock.py:470 INFO Added sources: [{'name': 'v2.1.0.tar.gz', 'path': '/home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz', 'cmd': None, 'checksum': 'bc05cd1ab1cbeda62bd79fd3ba0f46b8e304a1bc1bea556316baa2c38ef1fcf3', 'finalpath': '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0'}] | |
== 2022-02-03 22:14:01,869 easyblock.py:2183 INFO no patches provided | |
== 2022-02-03 22:14:01,931 easyblock.py:2193 INFO md5 checksum for /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz: 4a671a2ae942458bf2494e6c2f96408f | |
== 2022-02-03 22:14:01,995 easyblock.py:2193 INFO sha256 checksum for /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz: bc05cd1ab1cbeda62bd79fd3ba0f46b8e304a1bc1bea556316baa2c38ef1fcf3 | |
== 2022-02-03 22:14:01,996 easyblock.py:2228 INFO Checking dirs that need to be created: ['/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', '/home/mboisson/.local/easybuild/modules/2020/avx2/Core/rvtests'] | |
== 2022-02-03 22:14:01,997 configuremake.py:94 INFO config.guess version: 2018-08-29 (last updated: 2022-02-02T14:30:45.237457, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c) | |
== 2022-02-03 22:14:01,997 configuremake.py:149 INFO Found config.guess at /home/mboisson/.local/easybuild/sources/generic/eb_v4.5.0/ConfigureMake/config.guess | |
== 2022-02-03 22:14:01,997 build_log.py:266 INFO creating build dir, resetting environment... | |
== 2022-02-03 22:14:02,000 easyblock.py:3648 INFO Starting ready step | |
== 2022-02-03 22:14:02,000 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:02,000 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:02,001 easyblock.py:3656 INFO Running method check_readiness_step part of step ready | |
== 2022-02-03 22:14:02,001 easyblock.py:2037 INFO Setting parallelism: 8 | |
== 2022-02-03 22:14:02,048 easyblock.py:2089 WARNING Loaded modules detected: ['gentoo/2020'] | |
== 2022-02-03 22:14:02,049 easyblock.py:3656 INFO Running method make_builddir part of step ready | |
== 2022-02-03 22:14:02,049 easyblock.py:1056 INFO Found old directory /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0 | |
== 2022-02-03 22:14:02,189 filetools.py:380 INFO Path /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0 successfully removed. | |
== 2022-02-03 22:14:02,190 easyblock.py:1064 INFO Removed old directory /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0 | |
== 2022-02-03 22:14:02,190 filetools.py:1870 INFO Creating directory /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0 (parents: True, set_gid: False, sticky: False) | |
== 2022-02-03 22:14:02,190 easyblock.py:3656 INFO Running method reset_env part of step ready | |
== 2022-02-03 22:14:02,191 easyblock.py:3656 INFO Running method handle_iterate_opts part of step ready | |
== 2022-02-03 22:14:02,191 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:02,191 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:02,192 build_log.py:266 INFO unpacking... | |
== 2022-02-03 22:14:02,195 easyblock.py:3648 INFO Starting source step | |
== 2022-02-03 22:14:02,195 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:02,195 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:02,195 easyblock.py:3656 INFO Running method checksum_step part of step source | |
== 2022-02-03 22:14:02,285 easyblock.py:2246 INFO Checksum verification for /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz using bc05cd1ab1cbeda62bd79fd3ba0f46b8e304a1bc1bea556316baa2c38ef1fcf3 passed. | |
== 2022-02-03 22:14:02,286 easyblock.py:3656 INFO Running method extract_step part of step source | |
== 2022-02-03 22:14:02,286 easyblock.py:2349 INFO Unpacking source v2.1.0.tar.gz | |
== 2022-02-03 22:14:02,287 run.py:233 INFO running cmd: tar xzf /home/mboisson/.local/easybuild/sources/r/rvtests/v2.1.0.tar.gz | |
== 2022-02-03 22:14:02,562 build_log.py:266 INFO patching... | |
== 2022-02-03 22:14:02,565 easyblock.py:3648 INFO Starting patch step | |
== 2022-02-03 22:14:02,565 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:02,565 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:02,565 easyblock.py:3656 INFO Running method patch_step part of step patch | |
== 2022-02-03 22:14:02,565 build_log.py:266 INFO preparing... | |
== 2022-02-03 22:14:02,568 easyblock.py:3648 INFO Starting prepare step | |
== 2022-02-03 22:14:02,568 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:02,568 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:02,568 hooks.py:166 INFO Found pre_prepare_hook hook | |
== 2022-02-03 22:14:02,568 hooks.py:198 INFO Running 'pre_prepare_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])... | |
== 2022-02-03 22:14:02,568 environment.py:91 INFO Environment variable EBROOTLIBXML2 set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,568 environment.py:91 INFO Environment variable EBROOTLIBJPEGMINTURBO set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTLIBPNG set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTLIBTIFF set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTZLIB set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTLIBGLU set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTMESA set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTFLTK set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTTCL set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTTK set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTBZIP2 set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTZSTD set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTFREETYPE set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,569 environment.py:91 INFO Environment variable EBROOTGLIB set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTSZIP set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTLIBXMLPLUSPLUS set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTSQLITE3 set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBROOTLIBEVENT set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr (previously undefined) | |
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBVERSIONTCL set to 8.6 (previously undefined) | |
== 2022-02-03 22:14:02,570 environment.py:91 INFO Environment variable EBVERSIONTK set to 8.6 (previously undefined) | |
== 2022-02-03 22:14:02,570 easyblock.py:3656 INFO Running method prepare_step part of step prepare | |
== 2022-02-03 22:14:02,571 environment.py:91 INFO Environment variable PKG_CONFIG_PATH set to /cvmfs/soft.computecanada.ca/gentoo/2020/usr/lib/pkgconfig (previously undefined) | |
== 2022-02-03 22:14:03,511 modules.py:626 INFO Checking whether Core/gcccore/.9.3.0 exists... | |
== 2022-02-03 22:14:03,511 modules.py:638 INFO Checking whether hidden module Core/gcccore/.9.3.0 exists via 'show'... | |
== 2022-02-03 22:14:04,197 modules.py:654 INFO Result for existence check of Core/gcccore/.9.3.0 module: True | |
== 2022-02-03 22:14:05,062 modules.py:626 INFO Checking whether gcccore/.9.3.0 exists... | |
== 2022-02-03 22:14:05,062 modules.py:638 INFO Checking whether hidden module gcccore/.9.3.0 exists via 'show'... | |
== 2022-02-03 22:14:05,752 modules.py:654 INFO Result for existence check of gcccore/.9.3.0 module: True | |
== 2022-02-03 22:14:05,753 toolchain.py:760 INFO List of toolchain dependency modules and toolchain definition match! | |
== 2022-02-03 22:14:05,755 compiler.py:361 INFO _set_optimal_architecture: using march=core-avx2 as optarch for x86_64. | |
== 2022-02-03 22:14:05,757 environment.py:91 INFO Environment variable CC set to gcc (previously undefined) | |
== 2022-02-03 22:14:05,757 environment.py:91 INFO Environment variable EBVARCC set to gcc (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable CXX set to g++ (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARCXX set to g++ (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable F77 set to gfortran (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARF77 set to gfortran (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable F90 set to gfortran (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARF90 set to gfortran (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable FC set to gfortran (previously undefined) | |
== 2022-02-03 22:14:05,758 environment.py:91 INFO Environment variable EBVARFC set to gfortran (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable FLIBS set to -lgfortran (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable LDFLAGS set to -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARLDFLAGS set to -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=core-avx2 (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=core-avx2 (previously undefined) | |
== 2022-02-03 22:14:05,759 environment.py:91 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) | |
== 2022-02-03 22:14:05,760 toolchain.py:910 INFO Using ccache for these compiler commands: gcc, g++ | |
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable CCACHE_DIR set to /cvmfs/local/ccache (previously undefined) | |
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable CCACHE_TEMPDIR set to /tmp/eb-7_4x5zsi/tmpxetixyh3 (previously undefined) | |
== 2022-02-03 22:14:05,760 filetools.py:520 INFO Command ccache found at /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/ccache | |
== 2022-02-03 22:14:05,760 environment.py:91 INFO Environment variable PATH set to /tmp/eb-7_4x5zsi/tmpip3lj4zh:/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin (previous value: '/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/bin:/cvmfs/soft.computecanada.ca/easybuild/bin:/cvmfs/soft.computecanada.ca/custom/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin:/cvmfs/soft.computecanada.ca/gentoo/2020/sbin:/cvmfs/soft.computecanada.ca/gentoo/2020/bin') | |
== 2022-02-03 22:14:05,761 filetools.py:520 INFO Command gcc found at /tmp/eb-7_4x5zsi/tmpip3lj4zh/gcc | |
== 2022-02-03 22:14:05,761 filetools.py:520 INFO Command g++ found at /tmp/eb-7_4x5zsi/tmpip3lj4zh/g++ | |
== 2022-02-03 22:14:05,761 toolchain.py:789 INFO Commands symlinked to /cvmfs/soft.computecanada.ca/gentoo/2020/usr/bin/ccache via /tmp/eb-7_4x5zsi/tmpip3lj4zh: gcc, g++ | |
== 2022-02-03 22:14:05,761 easyblock.py:1921 INFO Using /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/ as start dir | |
== 2022-02-03 22:14:05,761 hooks.py:166 INFO Found post_prepare_hook hook | |
== 2022-02-03 22:14:05,762 hooks.py:198 INFO Running 'post_prepare_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])... | |
== 2022-02-03 22:14:05,762 build_log.py:266 INFO ... (took 3 secs) | |
== 2022-02-03 22:14:05,764 build_log.py:266 INFO configuring... | |
== 2022-02-03 22:14:05,767 easyblock.py:3648 INFO Starting configure step | |
== 2022-02-03 22:14:05,767 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:05,767 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:05,768 hooks.py:166 INFO Found pre_configure_hook hook | |
== 2022-02-03 22:14:05,768 hooks.py:198 INFO Running 'pre_configure_hook' hook function (arguments: [<easybuild.easyblocks.generic.makecp.MakeCp object at 0x2adbdf81fb10>])... | |
== 2022-02-03 22:14:05,768 easyconfig.py:1892 INFO Derived full easyblock module path for MakeCp: easybuild.easyblocks.generic.makecp | |
== 2022-02-03 22:14:05,768 easyconfig.py:1939 INFO Successfully obtained class 'MakeCp' for easyblock 'MakeCp' (software name 'rvtests') | |
== 2022-02-03 22:14:05,768 easyblock.py:3656 INFO Running method configure_step part of step configure | |
== 2022-02-03 22:14:05,768 build_log.py:266 INFO building... | |
== 2022-02-03 22:14:05,770 easyblock.py:3648 INFO Starting build step | |
== 2022-02-03 22:14:05,770 easyconfig.py:1686 INFO Generating template values... | |
== 2022-02-03 22:14:05,771 easyconfig.py:1705 INFO Template values: arch='x86_64', bitbucket_account='rvtests', builddir='/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0', cuda_cc_semicolon_sep='6.0;7.0;7.5;8.0', cuda_cc_space_sep='6.0 7.0 7.5 8.0', cuda_compute_capabilities='6.0,7.0,7.5,8.0', cuda_sm_comma_sep='sm_60,sm_70,sm_75,sm_80', cuda_sm_space_sep='sm_60 sm_70 sm_75 sm_80', github_account='rvtests', installdir='/home/mboisson/.local/easybuild/software/2020/avx2/Core/rvtests/2.1.0', module_name='rvtests/2.1.0', name='rvtests', nameletter='r', nameletterlower='r', namelower='rvtests', parallel='8', toolchain_name='GCCcore', toolchain_version='9.3.0', version='2.1.0', version_major='2', version_major_minor='2.1', version_minor='1', versionprefix='', versionsuffix='' | |
== 2022-02-03 22:14:05,771 easyblock.py:3656 INFO Running method build_step part of step build | |
== 2022-02-03 22:14:05,771 configuremake.py:338 INFO Building target '' | |
== 2022-02-03 22:14:05,771 run.py:233 INFO running cmd: make -j 8 | |
== 2022-02-03 22:14:17,738 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/site-packages/easybuild-framework/easybuild/base/exceptions.py:124 in __init__): cmd " make -j 8 " exited with exit code 2 and output: | |
fatal: not a git repository (or any parent up to mount point /) | |
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third cnpy | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third zstd | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
unzip -o cnpy.zip ## -o: overwrite existing file | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third sqlite | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
echo "obtain zstd" | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third nlopt | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
obtain zstd | |
echo "obtain sqlite" | |
wget --no-check-certificate https://github.com/facebook/zstd/archive/v1.3.1.tar.gz -O zstd-1.3.1.tar.gz | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third bzip2 | |
Archive: cnpy.zip | |
b39d58d3640f77c043bfe92591afeafdd82e78db | |
creating: cnpy-master/ | |
inflating: cnpy-master/CMakeLists.txt | |
inflating: cnpy-master/LICENSE | |
inflating: cnpy-master/README | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
inflating: cnpy-master/cnpy.cpp | |
inflating: cnpy-master/cnpy.h | |
inflating: cnpy-master/example1.cpp | |
inflating: cnpy-master/mat2npz | |
inflating: cnpy-master/npy2mat | |
inflating: cnpy-master/npz2mat | |
ln -s -f cnpy-master cnpy | |
obtain sqlite | |
wget --no-check-certificate https://sqlite.org/2017/sqlite-autoconf-3200100.tar.gz | |
--2022-02-03 22:14:05-- https://github.com/facebook/zstd/archive/v1.3.1.tar.gz | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third zlib | |
(cd cnpy; g++ -std=c++11 -c cnpy.cpp; ar rcs libcnpy.a cnpy.o) | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
tar zxf nlopt-2.4.2.tar.gz | |
--2022-02-03 22:14:05-- https://sqlite.org/2017/sqlite-autoconf-3200100.tar.gz | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third gsl | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
tar zxf bzip2-1.0.6.tar.gz | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third pcre | |
tar zxf zlib-1.2.8.tar.gz | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
tar zxf gsl-1.16.tar.gz | |
Resolving github.com... mv pcre-8.36.tar.gz* pcre-8.36.tar.gz | |
Resolving sqlite.org... 140.82.114.3 | |
Connecting to github.com|140.82.114.3|:443... mv: 'pcre-8.36.tar.gz' and 'pcre-8.36.tar.gz' are the same file | |
make[1]: [Makefile:14: pcre] Error 1 (ignored) | |
tar zxf pcre-8.36.tar.gz | |
(DIR=`pwd`; cd nlopt-2.4.2; ./configure --prefix="${DIR}"/nlopt; make -j; make install) | |
(DIR=`pwd`; cd pcre-8.36; ./configure --prefix="${DIR}"/pcre; make -j; make install) | |
ln -s -f zlib-1.2.8 zlib | |
(cd zlib; ./configure; make) | |
connected. | |
45.33.6.223, 2600:3c00::f03c:91ff:fe96:b959 | |
Connecting to sqlite.org|45.33.6.223|:443... ln -s -f bzip2-1.0.6 bzip2 | |
(cd bzip2-1.0.6; make) | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/bzip2-1.0.6' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
If compilation produces errors, or a large number of warnings, | |
please read README.COMPILATION.PROBLEMS -- you might be able to | |
adjust the flags in this Makefile to improve matters. | |
Also in README.COMPILATION.PROBLEMS are some hints that may help | |
if your build produces an executable which is unable to correctly | |
handle so-called 'large files' -- files of size 2GB or more. | |
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c blocksort.c | |
checking for a BSD-compatible install... /cvmfs/soft.computecanada.ca/custom/bin/install -c | |
checking whether build environment is sane... yes | |
(DIR=`pwd`; cd gsl-1.16; ./configure --prefix="${DIR}"/gsl; make -j; make install) | |
HTTP request sent, awaiting response... checking for a thread-safe mkdir -p... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p | |
checking for gawk... gawk | |
checking whether make sets $(MAKE)... yes | |
connected. | |
checking whether make supports nested variables... checking for a BSD-compatible install... yes | |
checking whether to enable maintainer-specific portions of Makefiles... no | |
checking for gcc... gcc | |
/cvmfs/soft.computecanada.ca/custom/bin/install -c | |
checking whether build environment is sane... yes | |
checking for a thread-safe mkdir -p... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p | |
checking for gawk... gawk | |
checking whether make sets $(MAKE)... yes | |
checking whether make supports nested variables... yes | |
checking whether make supports nested variables... (cached) yes | |
checking for style of include used by make... GNU | |
checking for gcc... gcc | |
checking for a BSD-compatible install... /cvmfs/soft.computecanada.ca/custom/bin/install -c | |
checking whether build environment is sane... yes | |
checking for a thread-safe mkdir -p... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p | |
checking for gawk... gawk | |
checking whether make sets $(MAKE)... yes | |
checking whether make supports nested variables... yes | |
checking whether to enable maintainer-specific portions of Makefiles... no | |
checking for a sed that does not truncate output... /cvmfs/soft.computecanada.ca/gentoo/2020/bin/sed | |
HTTP request sent, awaiting response... checking whether make sets $(MAKE)... (cached) yes | |
checking build system type... x86_64-unknown-linux-gnu | |
checking host system type... x86_64-unknown-linux-gnu | |
checking for gcc... gcc | |
302 Found | |
Location: https://codeload.github.com/facebook/zstd/tar.gz/v1.3.1 [following] | |
--2022-02-03 22:14:06-- https://codeload.github.com/facebook/zstd/tar.gz/v1.3.1 | |
Resolving codeload.github.com... 140.82.113.9 | |
Connecting to codeload.github.com|140.82.113.9|:443... make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third pcre | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
mv pcre-8.36.tar.gz* pcre-8.36.tar.gz | |
mv: 'pcre-8.36.tar.gz' and 'pcre-8.36.tar.gz' are the same file | |
make[1]: [Makefile:14: pcre] Error 1 (ignored) | |
tar zxf pcre-8.36.tar.gz | |
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c huffman.c | |
200 OK | |
Length: 2565638 (2.4M) [application/x-gzip] | |
Saving to: sqlite-autoconf-3200100.tar.gz | |
connected. | |
(DIR=`pwd`; cd pcre-8.36; ./configure --prefix="${DIR}"/pcre; make -j; make install) | |
0K .......... .......... .......... ..HTTP request sent, awaiting response... ........ .......... 1% 408K 6s | |
50K .......... .......... ..........checking for a BSD-compatible install... /cvmfs/soft.computecanada.ca/custom/bin/install -c | |
checking whether build environment is sane... yes | |
checking for a thread-safe mkdir -p... .......... ....../cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p | |
checking for gawk... gawk | |
checking whether make sets $(MAKE)... yes | |
checking whether make supports nested variables... yes | |
.... 3% 817K 4s | |
100K .......... .......... .......... .......... .......... 5% 58.3M 3s | |
150K .......... .......... ......checking whether make supports nested variables... (cached) yes | |
.... .......... ..checking for style of include used by make... GNU | |
checking for gcc... gcc | |
........ 7% 1.29M 3s | |
200K ........gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c crctable.c | |
.. .......... .......... .......... .......... 9% 1.91M 2s | |
250K .......... .......... .......... .......... .......... 11% 218M 2s | |
300K .......... .......... .......... .......... .......... 13% 212M 2s | |
350K .......... .......... ...checking whether the C compiler works... ....... .......... .......... 15% 13.2M 1sno | |
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2': | |
configure: error: C compiler cannot create executables | |
See `config.log' for more details | |
400K .......... .......... .......... .......... ........make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2' | |
make[2]: warning: -jN forced in submake: disabling jobserver mode. | |
make[2]: *** No targets specified and no makefile found. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2' | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
make[2]: *** No rule to make target 'install'. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/nlopt-2.4.2' | |
make[1]: [Makefile:46: nlopt] Error 2 (ignored) | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third tabix | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
mv tabix-0.2.6.tar.bz2* tabix-0.2.6.tar.bz2 | |
mv: 'tabix-0.2.6.tar.bz2' and 'tabix-0.2.6.tar.bz2' are the same file | |
make[1]: [Makefile:7: tabix] Error 1 (ignored) | |
tar jxf tabix-0.2.6.tar.bz2 | |
checking whether the C compiler works... 200 OK | |
Length: unspecified [application/x-gzip] | |
Saving to: zstd-1.3.1.tar.gz | |
0K .......... .... 17% 854K 1s | |
450K .......... .......... .......... .......... .......... 19% 61.6M 1s | |
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750K .......... .......... .......... .......... .......... 31% 175M 1s | |
800K .......... ......no | |
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16': | |
configure: error: C compiler cannot create executables | |
See `config.log' for more details | |
Checking for shared library support... | |
.... .......... .......... .......... 33% 1.51M 1s | |
850K .......... .......... .......... .......... .......... 35% 183M 1s | |
900K .......... ..make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16' | |
make[2]: warning: -jN forced in submake: disabling jobserver mode. | |
make[2]: *** No targets specified and no makefile found. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16' | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
make[2]: *** No rule to make target 'install'. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/gsl-1.16' | |
make[1]: [Makefile:20: gsl] Error 2 (ignored) | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third samtools | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
checking whether the C compiler works... tar jxf samtools-0.1.19.tar.bz2 | |
........ .......... .......... .......... 37% 1.87M 1s | |
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1650K .......... ....no | |
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36': | |
configure: error: C compiler cannot create executables | |
See `config.log' for more details | |
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1800K .......... .......... ....make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[2]: warning: -jN forced in submake: disabling jobserver mode. | |
make[2]: *** No targets specified and no makefile found. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
make[2]: *** No rule to make target 'install'. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[1]: [Makefile:16: pcre] Error 2 (ignored) | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third samtools | |
ln -s -f tabix-0.2.6 tabix | |
sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8:' tabix/Makefile | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
(cd tabix-0.2.6; make) | |
tar jxf samtools-0.1.19.tar.bz2 | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
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1950K .......... .......... .......... ....gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c randtable.c | |
...... .......... 79% 54.1M 0s | |
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2150K .......... ...make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6' | |
..gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzf.c -o bgzf.o | |
..... .......... .......... .......... 87% 238M 0s | |
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2500K ..... 100% 193M=0.4s | |
2022-02-03 22:14:06 (5.59 MB/s) - sqlite-autoconf-3200100.tar.gz saved [2565638/2565638] | |
tar zxf sqlite-autoconf-3200100.tar.gz | |
.......... 380K | |
50K .......... .......... .......... .......... ...Building shared library libz.so.1.2.8 with gcc. | |
ln -s -f samtools-0.1.19 samtools | |
sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8 -I../../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8 -L../../zlib-1.2.8:' samtools/Makefile samtools/bcftools/Makefile | |
(cd samtools; make lib-recur) | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o | |
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c compress.c | |
ln -s -f samtools-0.1.19 samtools | |
sed -i.bak 's:^CFLAGS=:CFLAGS=-I../zlib-1.2.8 -I../../zlib-1.2.8:;s:^LIBPATH=:LIBPATH=-L../zlib-1.2.8 -L../../zlib-1.2.8:' samtools/Makefile samtools/bcftools/Makefile | |
(cd samtools; make lib-recur) | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
....... 736K | |
100K .......... .......... .......... .......... .......... 76.5M | |
150K .......... .......... .......... .......... .......... 81.9M | |
200K ..make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -DBGZF_CACHE -I. bgzf.c -o bgzf.o | |
(DIR=`pwd`; cd sqlite-autoconf-3200100; ./configure --prefix="${DIR}"/sqlite --enable-dynamic-extensions=no; make -j; make install) | |
........ ......bgzf.c: In function worker_aux: | |
bgzf.c:392:9: warning: variable tmp set but not used [-Wunused-but-set-variable] | |
392 | int i, tmp, stop = 0; | |
| ^~~ | |
bgzf.c: In function bgzf_close: | |
bgzf.c:572:11: warning: variable count set but not used [-Wunused-but-set-variable] | |
572 | int ret, count, block_length; | |
| ^~~~~ | |
bgzf.c: In function worker_aux: | |
bgzf.c:392:9: warning: variable tmp set but not used [-Wunused-but-set-variable] | |
392 | int i, tmp, stop = 0; | |
| ^~~ | |
bgzf.c: In function bgzf_close: | |
bgzf.c:572:11: warning: variable count set but not used [-Wunused-but-set-variable] | |
572 | int ret, count, block_length; | |
| ^~~~~ | |
.... .......... .......... .......... 769K | |
250K .......... .......... .......... .......... .......... 78.2M | |
300K ..........gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kstring.c -o kstring.o | |
bgzf.c: In function bgzf_close: | |
bgzf.c:435:11: warning: variable count set but not used [-Wunused-but-set-variable] | |
435 | int ret, count, block_length; | |
| ^~~~~ | |
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE kstring.c -o kstring.o | |
Checking for off64_t... Yes. | |
Checking for fseeko... Yes. | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_aux.c -o bam_aux.o | |
.......... .......... .......... .......... 792K | |
350K .......... .......... .......... .......... .......... 25.1M | |
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500K .......... .......... .......... .......... .......... 199M | |
550K .......... .......... .......... .......... .......... 131M | |
600K .......gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE knetfile.c -o knetfile.o | |
checking for a BSD-compatible install... gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c decompress.c | |
/cvmfs/soft.computecanada.ca/custom/bin/install -c | |
checking whether build environment is sane... yes | |
Checking for strerror... Yes. | |
checking for a thread-safe mkdir -p... ... .......... .......... .......... .......... 791K | |
650K .......... .......... .......... .......... .......... 177M | |
700K .......... .......... .......... .......... .......... 213M | |
750K .......... .......... .......... .../cvmfs/soft.computecanada.ca/gentoo/2020/bin/mkdir -p | |
....... .........checking for gawk... . 91.8M | |
800K .......... .....gawk | |
checking whether make sets $(MAKE)... ..... .......... .......... .......... 78.9M | |
850K .......... .......... .......... .......... .......... 238M | |
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1100K .......... .......... .......... .......... .......... 240M | |
1150K .......... .......... .......... .......... ........yes | |
checking whether make supports nested variables... yes | |
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE index.c -o index.o | |
checking for style of include used by make... GNU | |
checking for gcc... gcc | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam.c -o bam.o | |
.. 799K | |
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1350K .......... .......... .......... .......... .......... 205M | |
1400K .......... .......... .......... .......... .......... 223M | |
1450K .......... .......... ........ 153M=0.5s | |
2022-02-03 22:14:07 (3.11 MB/s) - zstd-1.3.1.tar.gz saved [1513767] | |
tar zxf zstd-1.3.1.tar.gz | |
Checking for unistd.h... Yes. | |
cat: confdefs.h: No such file or directory | |
checking whether the C compiler works... checking whether the C compiler works... gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzlib.c | |
no | |
no | |
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36': | |
configure: error: C compiler cannot create executables | |
See `config.log' for more details | |
configure: error: in `/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100': | |
configure: error: C compiler cannot create executables | |
See `config.log' for more details | |
ln -s -f zstd-1.3.1 zstd | |
(cd zstd; make) | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1/lib' | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100' | |
make[2]: warning: -jN forced in submake: disabling jobserver mode. | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[2]: warning: -jN forced in submake: disabling jobserver mode. | |
make[2]: *** No targets specified and no makefile found. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100' | |
make[2]: *** No targets specified and no makefile found. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
make[2]: *** No rule to make target 'install'. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/sqlite-autoconf-3200100' | |
make[2]: *** No rule to make target 'install'. Stop. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/pcre-8.36' | |
make[1]: [Makefile:55: sqlite] Error 2 (ignored) | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make[1]: [Makefile:16: pcre] Error 2 (ignored) | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third eigen | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
echo "obtain Eigen..." | |
make[1]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base' | |
Checking for stdarg.h... Yes. | |
obtain Eigen... | |
wget --no-check-certificate http://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2 -O eigen-3.3.7.tar.bz2 | |
URL transformed to HTTPS due to an HSTS policy | |
--2022-02-03 22:14:07-- https://bitbucket.org/eigen/eigen/get/3.3.7.tar.bz2 | |
fatal: not a git repository (or any parent up to mount point /) | |
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). | |
Resolving bitbucket.org... make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third eigen | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
rm -rf eigen-eigen* | |
rm -f libbz2.a | |
tar jxf eigen-3.3.7.tar.bz2 | |
ar cq libbz2.a blocksort.o huffman.o crctable.o randtable.o compress.o decompress.o bzlib.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/entropy_common.o common/entropy_common.c | |
bzip2: Compressed file ends unexpectedly; | |
perhaps it is corrupted? *Possible* reason follows. | |
bzip2: Inappropriate ioctl for device | |
Input file = (stdin), output file = (stdout) | |
It is possible that the compressed file(s) have become corrupted. | |
You can use the -tvv option to test integrity of such files. | |
You can use the `bzip2recover' program to attempt to recover | |
data from undamaged sections of corrupted files. | |
tar: Child returned status 2 | |
tar: Error is not recoverable: exiting now | |
make[2]: *** [Makefile:24: eigen] Error 2 | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make[1]: *** [/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/Makefile.lib:18: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/eigen] Error 2 | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base' | |
make: *** [Makefile.lib:42: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/base/lib-base.a] Error 2 | |
make: *** Waiting for unfinished jobs.... | |
ranlib libbz2.a | |
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2.c | |
104.192.141.1, 2406:da00:ff00::22c0:3470, 2406:da00:ff00::22c5:2ef4, ... | |
Connecting to bitbucket.org|104.192.141.1|:443... connected. | |
bam.c: In function bam_header_write: | |
bam.c:128:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] | |
128 | strncpy(buf, "BAM\001", 4); | |
| ^~~~~~~~~~~~~~~~~~~~~~~~~~ | |
bam.c: In function bam_header_write: | |
bam.c:128:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] | |
128 | strncpy(buf, "BAM\001", 4); | |
| ^~~~~~~~~~~~~~~~~~~~~~~~~~ | |
HTTP request sent, awaiting response... bzip2.c: In function testStream: | |
bzip2.c:557:37: warning: variable nread set but not used [-Wunused-but-set-variable] | |
557 | Int32 bzerr, bzerr_dummy, ret, nread, streamNo, i; | |
| ^~~~~ | |
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2 bzip2.o -L. -lbz2 | |
404 Not Found | |
2022-02-03 22:14:07 ERROR 404: Not Found. | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/pool.o common/pool.c | |
make[1]: *** [Makefile:84: eigen-3.3.7.tar.bz2] Error 8 | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make: *** [Makefile.lib:18: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/eigen] Error 2 | |
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -c bzip2recover.c | |
gcc -Wall -Winline -O2 -g -D_FILE_OFFSET_BITS=64 -o bzip2recover bzip2recover.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/error_private.o common/error_private.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_import.c -o bam_import.o | |
Doing 6 tests (3 compress, 3 uncompress) ... | |
If there's a problem, things might stop at this point. | |
./bzip2 -1 < sample1.ref > sample1.rb2 | |
./bzip2 -2 < sample2.ref > sample2.rb2 | |
./bzip2 -3 < sample3.ref > sample3.rb2 | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/xxhash.o common/xxhash.c | |
./bzip2 -d < sample1.bz2 > sample1.tst | |
./bzip2 -d < sample2.bz2 > sample2.tst | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam.c -o sam.o | |
./bzip2 -ds < sample3.bz2 > sample3.tst | |
cmp sample1.bz2 sample1.rb2 | |
cmp sample2.bz2 sample2.rb2 | |
cmp sample3.bz2 sample3.rb2 | |
cmp sample1.tst sample1.ref | |
cmp sample2.tst sample2.ref | |
cmp sample3.tst sample3.ref | |
If you got this far and the 'cmp's didn't complain, it looks | |
like you're in business. | |
To install in /usr/local/bin, /usr/local/lib, /usr/local/man and | |
/usr/local/include, type | |
make install | |
To install somewhere else, eg, /xxx/yyy/{bin,lib,man,include}, type | |
make install PREFIX=/xxx/yyy | |
If you are (justifiably) paranoid and want to see what 'make install' | |
is going to do, you can first do | |
make -n install or | |
make -n install PREFIX=/xxx/yyy respectively. | |
The -n instructs make to show the commands it would execute, but | |
not actually execute them. | |
Instructions for use are in the preformatted manual page, in the file | |
bzip2.txt. For more detailed documentation, read the full manual. | |
It is available in Postscript form (manual.ps), PDF form (manual.pdf), | |
and HTML form (manual.html). | |
You can also do "bzip2 --help" to see some helpful information. | |
"bzip2 -L" displays the software license. | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/bzip2-1.0.6' | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_index.c -o bam_index.o | |
Checking whether to use vs[n]printf() or s[n]printf()... using vs[n]printf(). | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/fse_decompress.o common/fse_decompress.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_pileup.c -o bam_pileup.o | |
Checking for vsnprintf() in stdio.h... Yes. | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/threading.o common/threading.c | |
Checking for return value of vsnprintf()... Yes. | |
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bedidx.c -o bedidx.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o common/zstd_common.o common/zstd_common.c | |
bam_pileup.c: In function resolve_cigar2: | |
bam_pileup.c:75:9: warning: variable is_head set but not used [-Wunused-but-set-variable] | |
75 | int k, is_head = 0; | |
| ^~~~~~~ | |
bam_pileup.c: In function resolve_cigar2: | |
bam_pileup.c:75:9: warning: variable is_head set but not used [-Wunused-but-set-variable] | |
75 | int k, is_head = 0; | |
| ^~~~~~~ | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_lpileup.c -o bam_lpileup.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o compress/huf_compress.o compress/huf_compress.c | |
ar -csru libtabix.a bgzf.o kstring.o knetfile.o index.o bedidx.o | |
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE main.c -o main.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o | |
Checking for attribute(visibility) support... Yes. | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -I. -I./common -DXXH_NAMESPACE=ZSTD_ -I./legacy -DZSTD_LEGACY_SUPPORT=4 -c -o compress/zstdmt_compress.o compress/zstdmt_compress.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_md.c -o bam_md.o | |
make[2]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zlib-1.2.8' | |
make[2]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o example.o test/example.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. razf.c -o razf.o | |
main.c: In function main: | |
main.c:161:5: warning: this if clause does not guard... [-Wmisleading-indentation] | |
161 | if ( conf_ptr ) | |
| ^~ | |
main.c:164:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the if | |
164 | if (skip >= 0) conf.line_skip = skip; | |
| ^~ | |
main.c:181:5: warning: this if clause does not guard... [-Wmisleading-indentation] | |
181 | if (reheader) | |
| ^~ | |
main.c:184:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the if | |
184 | struct stat stat_tbi,stat_vcf; | |
| ^~~~~~ | |
gcc -I../zlib-1.2.8 -g -Wall -O2 -fPIC -o tabix main.o -L. -ltabix -lm -L../zlib-1.2.8 -lz | |
gcc -c -I../zlib-1.2.8 -g -Wall -O2 -fPIC -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -DBGZF_CACHE bgzip.c -o bgzip.o | |
razf.c: In function razf_open_w: | |
razf.c:178:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] | |
178 | strncpy((char*)rz->header->extra, "RAZF", 4); | |
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
razf.c: In function razf_open_w: | |
razf.c:178:2: warning: strncpy output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation] | |
178 | strncpy((char*)rz->header->extra, "RAZF", 4); | |
| ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o adler32.o adler32.c | |
gcc -I../zlib-1.2.8 -g -Wall -O2 -fPIC -o bgzip bgzip.o bgzf.o knetfile.o -lz | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6' | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/tabix-0.2.6' | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
In file included from compress/zstdmt_compress.c:25: | |
./common/threading.h:82:25: error: expected ;, identifier or ( before int | |
82 | #define pthread_mutex_t int /* #define rather than typedef, because sometimes pthread support is implicit, resulting in duplicated symbols */ | |
| ^~~ | |
./common/threading.h:82:25: warning: useless type name in empty declaration | |
In file included from compress/zstdmt_compress.c:25: | |
./common/threading.h:88:24: error: expected ;, identifier or ( before int | |
88 | #define pthread_cond_t int | |
| ^~~ | |
./common/threading.h:88:24: warning: useless type name in empty declaration | |
make[3]: *** [<builtin>: compress/zstdmt_compress.o] Error 1 | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1/lib' | |
make[2]: *** [Makefile:56: lib-release] Error 2 | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd-1.3.1' | |
make[1]: *** [Makefile:60: zstd] Error 2 | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make: *** [Makefile.lib:36: /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zstd/lib/libzstd.a] Error 2 | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o crc32.o crc32.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. faidx.c -o faidx.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o deflate.o deflate.c | |
faidx.c: In function fai_load: | |
faidx.c:277:5: warning: this else clause does not guard... [-Wmisleading-indentation] | |
277 | else | |
| ^~~~ | |
faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else | |
280 | if (fp == 0) { | |
| ^~ | |
faidx.c: In function fai_load: | |
faidx.c:277:5: warning: this else clause does not guard... [-Wmisleading-indentation] | |
277 | else | |
| ^~~~ | |
faidx.c:280:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else | |
280 | if (fp == 0) { | |
| ^~ | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bedidx.c -o bedidx.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o infback.o infback.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_sort.c -o bam_sort.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inffast.o inffast.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. sam_header.c -o sam_header.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_reheader.c -o bam_reheader.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inflate.o inflate.c | |
bam_reheader.c: In function bam_reheader: | |
bam_reheader.c:12:16: warning: variable old set but not used [-Wunused-but-set-variable] | |
12 | bam_header_t *old; | |
| ^~~ | |
bam_reheader.c: In function bam_reheader: | |
bam_reheader.c:12:16: warning: variable old set but not used [-Wunused-but-set-variable] | |
12 | bam_header_t *old; | |
| ^~~ | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. kprobaln.c -o kprobaln.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o inftrees.o inftrees.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o trees.o trees.c | |
kprobaln.c: In function kpa_glocal: | |
kprobaln.c:78:21: warning: variable is_diff set but not used [-Wunused-but-set-variable] | |
78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | |
| ^~~~~~~ | |
kprobaln.c: In function kpa_glocal: | |
kprobaln.c:78:21: warning: variable is_diff set but not used [-Wunused-but-set-variable] | |
78 | int bw, bw2, i, k, is_diff = 0, is_backward = 1, Pr; | |
| ^~~~~~~ | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_cat.c -o bam_cat.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o zutil.o zutil.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o compress.o compress.c | |
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o | |
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools' | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools' | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf.c -o bcf.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o uncompr.o uncompr.c | |
bcf.c: In function bcf_fmt_core: | |
bcf.c:233:9: warning: variable iPL set but not used [-Wunused-but-set-variable] | |
233 | int iPL = -1; | |
| ^~~ | |
bcf.c: In function bcf_fmt_core: | |
bcf.c:233:9: warning: variable iPL set but not used [-Wunused-but-set-variable] | |
233 | int iPL = -1; | |
| ^~~ | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzclose.o gzclose.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. vcf.c -o vcf.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcfutils.c -o bcfutils.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzlib.o gzlib.c | |
bcfutils.c: In function bcf_fit_alt: | |
bcfutils.c:119:9: warning: variable ipl set but not used [-Wunused-but-set-variable] | |
119 | int ipl=-1, igt=-1; | |
| ^~~ | |
bcfutils.c: In function bcf_fix_gt: | |
bcfutils.c:254:5: warning: this else clause does not guard... [-Wmisleading-indentation] | |
254 | else | |
| ^~~~ | |
bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else | |
256 | b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':'; | |
| ^ | |
bcfutils.c: In function bcf_fit_alt: | |
bcfutils.c:119:9: warning: variable ipl set but not used [-Wunused-but-set-variable] | |
119 | int ipl=-1, igt=-1; | |
| ^~~ | |
bcfutils.c: In function bcf_fix_gt: | |
bcfutils.c:254:5: warning: this else clause does not guard... [-Wmisleading-indentation] | |
254 | else | |
| ^~~~ | |
bcfutils.c:256:2: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the else | |
256 | b->fmt[0] = 'G'; b->fmt[1] = 'T'; b->fmt[2] = ':'; | |
| ^ | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. prob1.c -o prob1.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzread.o gzread.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. em.c -o em.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -c -o gzwrite.o gzwrite.c | |
em.c: In function bcf_em1: | |
em.c:174:12: warning: variable n2 set but not used [-Wunused-but-set-variable] | |
174 | int i, n, n2; | |
| ^~ | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kfunc.c -o kfunc.o | |
ar rc libz.a adler32.o crc32.o deflate.o infback.o inffast.o inflate.o inftrees.o trees.o zutil.o compress.o uncompr.o gzclose.o gzlib.o gzread.o gzwrite.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. kmin.c -o kmin.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example example.o -L. libz.a | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -c -o minigzip.o test/minigzip.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. index.c -o index.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip minigzip.o -L. libz.a | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. fet.c -o fet.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/adler32.o adler32.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. mut.c -o mut.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/crc32.o crc32.c | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o | |
gcc -c -I../zlib-1.2.8 -I../../zlib-1.2.8-I../zlib-1.2.8 -I../../zlib-1.2.8 -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I.. -I. bcf2qcall.c -o bcf2qcall.o | |
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/deflate.o deflate.c | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools' | |
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc' | |
make[3]: Nothing to be done for 'lib'. | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc' | |
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/bcftools' | |
make[3]: Entering directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc' | |
make[3]: Nothing to be done for 'lib'. | |
make[3]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19/misc' | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/samtools-0.1.19' | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/infback.o infback.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inffast.o inffast.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inflate.o inflate.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/inftrees.o inftrees.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/trees.o trees.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/zutil.o zutil.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/compress.o compress.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/uncompr.o uncompr.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzclose.o gzclose.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzlib.o gzlib.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzread.o gzread.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -DPIC -c -o objs/gzwrite.o gzwrite.c | |
gcc -shared -Wl,-soname,libz.so.1,--version-script,zlib.map -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -fPIC -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o libz.so.1.2.8 adler32.lo crc32.lo deflate.lo infback.lo inffast.lo inflate.lo inftrees.lo trees.lo zutil.lo compress.lo uncompr.lo gzclose.lo gzlib.lo gzread.lo gzwrite.lo -lc -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib64 -L/cvmfs/soft.computecanada.ca/easybuild/software/2020/Core/gcccore/9.3.0/lib | |
rm -f libz.so libz.so.1 | |
ln -s libz.so.1.2.8 libz.so | |
ln -s libz.so.1.2.8 libz.so.1 | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o examplesh example.o -L. libz.so.1.2.8 | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzipsh minigzip.o -L. libz.so.1.2.8 | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o example64.o test/example.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o example64 example64.o -L. libz.a | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -I. -D_FILE_OFFSET_BITS=64 -c -o minigzip64.o test/minigzip.c | |
gcc -O2 -ftree-vectorize -march=core-avx2 -fno-math-errno -D_LARGEFILE64_SOURCE=1 -DHAVE_HIDDEN -o minigzip64 minigzip64.o -L. libz.a | |
make[2]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third/zlib-1.2.8' | |
make[1]: Leaving directory '/tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third' | |
(at easybuild/site-packages/easybuild-framework/easybuild/tools/run.py:618 in parse_cmd_output) | |
== 2022-02-03 22:14:17,739 build_log.py:266 INFO ... (took 11 secs) | |
== 2022-02-03 22:14:17,742 filetools.py:1971 INFO Removing lock /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock... | |
== 2022-02-03 22:14:17,743 filetools.py:380 INFO Path /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock successfully removed. | |
== 2022-02-03 22:14:17,744 filetools.py:1975 INFO Lock removed: /home/mboisson/.local/easybuild/software/2020/.locks/_home_mboisson_.local_easybuild_software_2020_avx2_Core_rvtests_2.1.0.lock | |
== 2022-02-03 22:14:17,744 easyblock.py:3986 WARNING build failed (first 300 chars): cmd " make -j 8 " exited with exit code 2 and output: | |
fatal: not a git repository (or any parent up to mount point /) | |
Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). | |
make -C /tmp/mboisson/avx2/rvtests/2.1.0/GCCcore-9.3.0/rvtests-2.1.0/third cnpy | |
make -C /tmp/mboisson/av | |
== 2022-02-03 22:14:17,744 easyblock.py:310 INFO Closing log for application name rvtests version 2.1.0 |
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