Created
May 8, 2019 09:59
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(partial) EasyBuild log for failed build of /scratch/eb-zWJAgO/files_pr5803/h/HDF5/HDF5-1.10.1-iomkl-2017b.eb (PR #5803)
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| == 2019-05-08 11:59:18,773 easyblock.py:278 INFO This is EasyBuild 3.9.0 (framework: 3.9.0, easyblocks: 3.9.0) on host login20.cluster.bc2.ch. | |
| == 2019-05-08 11:59:18,773 easyblock.py:284 INFO This is easyblock EB_HDF5 from module easybuild.easyblocks.hdf5 (/scicore/soft/apps/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/h/hdf5.py) | |
| == 2019-05-08 11:59:18,774 easyblock.py:834 INFO Build dir set to /scicore/home/scicore/escobar/.local/easybuild/build/HDF5/1.10.1/iomkl-2017b | |
| == 2019-05-08 11:59:18,774 easyblock.py:894 INFO Software install dir set to /scicore/home/scicore/escobar/.local/easybuild/software/HDF5/1.10.1-iomkl-2017b | |
| == 2019-05-08 11:59:18,774 easyblock.py:899 INFO Module install dir set to /scicore/home/scicore/escobar/.local/easybuild/modules/all | |
| == 2019-05-08 11:59:18,775 easyblock.py:263 INFO Init completed for application name HDF5 version 1.10.1 | |
| == 2019-05-08 11:59:18,775 easyblock.py:2980 INFO Obtained application instance of for HDF5 (easyblock: None) | |
| == 2019-05-08 11:59:18,776 one.py:146 INFO Skipping reformatting value for parameter 'toolchain' | |
| == 2019-05-08 11:59:18,777 one.py:146 INFO Skipping reformatting value for parameter 'toolchainopts' | |
| == 2019-05-08 11:59:18,780 filetools.py:1200 INFO Creating directory /scratch/eb-zWJAgO/reprod_20190508115918_4320 (parents: True, set_gid: False, sticky: False) | |
| == 2019-05-08 11:59:18,780 easyblock.py:3150 INFO Dumped easyconfig instance to /scratch/eb-zWJAgO/reprod_20190508115918_4320/HDF5-1.10.1-iomkl-2017b.eb | |
| == 2019-05-08 11:59:18,781 filetools.py:1200 INFO Creating directory /scratch/eb-zWJAgO/reprod_20190508115918_4320/easyblocks (parents: True, set_gid: False, sticky: False) | |
| == 2019-05-08 11:59:18,782 filetools.py:1670 INFO /scicore/soft/apps/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/h/hdf5.py copied to /scratch/eb-zWJAgO/reprod_20190508115918_4320/easyblocks/hdf5.py | |
| == 2019-05-08 11:59:18,782 easyblock.py:3165 INFO Dumped easyblock hdf5.py required for reproduction to /scratch/eb-zWJAgO/reprod_20190508115918_4320/easyblocks | |
| == 2019-05-08 11:59:18,783 filetools.py:1670 INFO /scicore/soft/apps/EasyBuild/3.9.0/lib/python2.7/site-packages/easybuild_easyblocks-3.9.0-py2.7.egg/easybuild/easyblocks/generic/configuremake.py copied to /scratch/eb-zWJAgO/reprod_20190508115918_4320/easyblocks/configuremake.py | |
| == 2019-05-08 11:59:18,783 easyblock.py:3165 INFO Dumped easyblock configuremake.py required for reproduction to /scratch/eb-zWJAgO/reprod_20190508115918_4320/easyblocks | |
| == 2019-05-08 11:59:18,784 easyblock.py:1590 INFO Number of iterations to perform for central part of installation procedure: 1 | |
| == 2019-05-08 11:59:18,784 build_log.py:252 INFO building and installing HDF5/1.10.1-iomkl-2017b... | |
| == 2019-05-08 11:59:18,785 build_log.py:252 INFO fetching files... | |
| == 2019-05-08 11:59:18,785 easyblock.py:2760 INFO Starting fetch step | |
| == 2019-05-08 11:59:18,786 easyblock.py:2766 INFO Running method fetch_step part of step fetch | |
| == 2019-05-08 11:59:18,786 easyblock.py:1671 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version | |
| == 2019-05-08 11:59:18,786 filetools.py:394 INFO Command eb found at /scicore/soft/apps/EasyBuild/3.9.0/bin/eb | |
| == 2019-05-08 11:59:47,342 filetools.py:532 INFO Downloaded file hdf5-1.10.1.tar.gz from url https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz to /scicore/home/scicore/escobar/.local/easybuild/sources/h/HDF5/hdf5-1.10.1.tar.gz | |
| == 2019-05-08 11:59:47,343 filetools.py:562 INFO Successful download of file hdf5-1.10.1.tar.gz from url https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz to path /scicore/home/scicore/escobar/.local/easybuild/sources/h/HDF5/hdf5-1.10.1.tar.gz | |
| == 2019-05-08 11:59:47,343 easyblock.py:746 INFO Successfully downloaded source file hdf5-1.10.1.tar.gz from https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-1.10/hdf5-1.10.1/src/hdf5-1.10.1.tar.gz | |
| == 2019-05-08 11:59:47,343 easyblock.py:392 INFO Added sources: [{'path': '/scicore/home/scicore/escobar/.local/easybuild/sources/h/HDF5/hdf5-1.10.1.tar.gz', 'cmd': None, 'finalpath': '/scicore/home/scicore/escobar/.local/easybuild/build/HDF5/1.10.1/iomkl-2017b', 'name': 'hdf5-1.10.1.tar.gz', 'checksum': '048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172'}] | |
| == 2019-05-08 11:59:47,344 easyblock.py:1712 INFO no patches provided | |
| == 2019-05-08 11:59:47,445 easyblock.py:1722 INFO md5 checksum for /scicore/home/scicore/escobar/.local/easybuild/sources/h/HDF5/hdf5-1.10.1.tar.gz: 43a2f9466702fb1db31df98ae6677f15 | |
| == 2019-05-08 11:59:47,513 easyblock.py:1722 INFO sha256 checksum for /scicore/home/scicore/escobar/.local/easybuild/sources/h/HDF5/hdf5-1.10.1.tar.gz: 048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172 | |
| == 2019-05-08 11:59:47,514 easyblock.py:1757 INFO Checking dirs that need to be created: ['/scicore/home/scicore/escobar/.local/easybuild/software/HDF5/1.10.1-iomkl-2017b', '/scicore/home/scicore/escobar/.local/easybuild/modules/all/HDF5', '/scicore/home/scicore/escobar/.local/easybuild/modules/data/HDF5'] | |
| == 2019-05-08 11:59:47,517 filetools.py:1200 INFO Creating directory /scicore/home/scicore/escobar/.local/easybuild/software/HDF5/1.10.1-iomkl-2017b (parents: True, set_gid: False, sticky: False) | |
| == 2019-05-08 11:59:47,518 filetools.py:1200 INFO Creating directory /scicore/home/scicore/escobar/.local/easybuild/modules/all/HDF5 (parents: True, set_gid: False, sticky: False) | |
| == 2019-05-08 11:59:47,519 filetools.py:1200 INFO Creating directory /scicore/home/scicore/escobar/.local/easybuild/modules/data/HDF5 (parents: True, set_gid: False, sticky: False) | |
| == 2019-05-08 11:59:47,521 configuremake.py:123 INFO Found recent config.guess at /scicore/home/scicore/escobar/.local/easybuild/sources/generic/eb_v3.9.0/ConfigureMake/config.guess, using it if required | |
| == 2019-05-08 11:59:47,521 build_log.py:252 INFO creating build dir, resetting environment... | |
| == 2019-05-08 11:59:47,522 easyblock.py:2760 INFO Starting ready step | |
| == 2019-05-08 11:59:47,522 easyblock.py:2766 INFO Running method check_readiness_step part of step ready | |
| == 2019-05-08 11:59:47,523 easyblock.py:1609 INFO Setting parallelism: 20 | |
| == 2019-05-08 11:59:47,598 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '') | |
| == 2019-05-08 11:59:47,598 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '') | |
| == 2019-05-08 11:59:47,598 easyblock.py:1623 WARNING Loaded modules detected: ['EasyBuild/3.9.0'] | |
| == 2019-05-08 11:59:47,599 easyblock.py:2766 INFO Running method make_builddir part of step ready | |
| == 2019-05-08 11:59:47,599 filetools.py:1200 INFO Creating directory /scicore/home/scicore/escobar/.local/easybuild/build/HDF5/1.10.1/iomkl-2017b (parents: True, set_gid: False, sticky: False) | |
| == 2019-05-08 11:59:47,601 easyblock.py:2766 INFO Running method reset_env part of step ready | |
| == 2019-05-08 11:59:47,601 easyblock.py:2766 INFO Running method handle_iterate_opts part of step ready | |
| == 2019-05-08 11:59:47,601 build_log.py:252 INFO unpacking... | |
| == 2019-05-08 11:59:47,602 easyblock.py:2760 INFO Starting source step | |
| == 2019-05-08 11:59:47,602 easyblock.py:2766 INFO Running method checksum_step part of step source | |
| == 2019-05-08 11:59:47,672 easyblock.py:1773 INFO Checksum verification for /scicore/home/scicore/escobar/.local/easybuild/sources/h/HDF5/hdf5-1.10.1.tar.gz using 048a9d149fb99aaa1680a712963f5a78e9c43b588d0e79d55e06760ec377c172 passed. | |
| == 2019-05-08 11:59:47,672 easyblock.py:2766 INFO Running method extract_step part of step source | |
| == 2019-05-08 11:59:47,672 easyblock.py:1841 INFO Unpacking source hdf5-1.10.1.tar.gz | |
| == 2019-05-08 11:59:47,673 run.py:192 INFO running cmd: tar xzf /scicore/home/scicore/escobar/.local/easybuild/sources/h/HDF5/hdf5-1.10.1.tar.gz | |
| == 2019-05-08 11:59:50,594 build_log.py:252 INFO patching... | |
| == 2019-05-08 11:59:50,595 easyblock.py:2760 INFO Starting patch step | |
| == 2019-05-08 11:59:50,595 easyblock.py:2766 INFO Running method patch_step part of step patch | |
| == 2019-05-08 11:59:50,595 build_log.py:252 INFO preparing... | |
| == 2019-05-08 11:59:50,595 easyblock.py:2760 INFO Starting prepare step | |
| == 2019-05-08 11:59:50,596 easyblock.py:2766 INFO Running method prepare_step part of step prepare | |
| == 2019-05-08 11:59:51,860 build_log.py:163 ERROR EasyBuild crashed with an error (at ?:124 in __init__): Missing modules for dependencies (use --robot?): zlib/1.2.11-GCCcore-6.4.0, Szip/2.1.1-GCCcore-6.4.0, libxml2/2.9.7-GCCcore-6.4.0 (at easybuild/tools/toolchain/toolchain.py:420 in _check_dependencies) | |
| == 2019-05-08 11:59:51,861 easyblock.py:3010 WARNING build failed (first 300 chars): Missing modules for dependencies (use --robot?): zlib/1.2.11-GCCcore-6.4.0, Szip/2.1.1-GCCcore-6.4.0, libxml2/2.9.7-GCCcore-6.4.0 | |
| == 2019-05-08 11:59:51,861 easyblock.py:293 INFO Closing log for application name HDF5 version 1.10.1 |
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