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boegel/gompi-2017a_partial.log

Created January 4, 2017 14:12
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(partial) EasyBuild log for failed build of /tmp/eb-nkl3do/files_pr3968/g/gompi/gompi-2017a.eb (PR #3968)
Raw
gompi-2017a_partial.log
== 2017-01-04 15:11:37,960 easyblock.py:261 INFO This is EasyBuild 3.0.2 (framework: 3.0.2, easyblocks: 3.0.2) on host node2519.golett.os.
== 2017-01-04 15:11:37,960 easyblock.py:267 INFO This is easyblock Toolchain from module easybuild.easyblocks.generic.toolchain (/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyblocks-3.0.2-py2.6.egg/easybuild/easyblocks/generic/toolchain.pyo)
== 2017-01-04 15:11:37,960 easyblock.py:753 INFO Build dir set to /tmp/vsc40023/easybuild_build/gompi/2017a/dummy-dummy
== 2017-01-04 15:11:37,960 config.py:423 DEBUG software install path as specified by 'installpath' and 'subdir_software': /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software
== 2017-01-04 15:11:37,960 easyconfig.py:1650 DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1330d90>
== 2017-01-04 15:11:37,960 easyconfig.py:1656 DEBUG Obtained subdir gompi/2017a
== 2017-01-04 15:11:37,961 easyblock.py:792 INFO Software install dir set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/gompi/2017a
== 2017-01-04 15:11:37,961 config.py:423 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules
== 2017-01-04 15:11:37,961 easyblock.py:797 INFO Module install dir set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all
== 2017-01-04 15:11:37,961 easyblock.py:246 INFO Init completed for application name gompi version 2017a
== 2017-01-04 15:11:37,961 easyblock.py:2477 INFO Obtained application instance of for gompi (easyblock: Toolchain)
== 2017-01-04 15:11:37,961 easyblock.py:2490 DEBUG Skip set to False
== 2017-01-04 15:11:37,961 build_log.py:216 INFO building and installing gompi/2017a...
== 2017-01-04 15:11:37,962 easyblock.py:2263 DEBUG Not skipping fetch step (skippable: False, skip: None, skipsteps: [], module_only: False, force: True
== 2017-01-04 15:11:37,962 build_log.py:216 INFO fetching files...
== 2017-01-04 15:11:37,962 easyblock.py:2271 INFO Starting fetch step
== 2017-01-04 15:11:37,962 templates.py:151 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1330d90>
== 2017-01-04 15:11:37,962 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,962 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,962 templates.py:219 DEBUG name: github_account, config: None
== 2017-01-04 15:11:37,962 templates.py:219 DEBUG name: name, config: gompi
== 2017-01-04 15:11:37,963 templates.py:219 DEBUG name: version, config: 2017a
== 2017-01-04 15:11:37,963 templates.py:219 DEBUG name: versionsuffix, config:
== 2017-01-04 15:11:37,963 templates.py:219 DEBUG name: versionprefix, config:
== 2017-01-04 15:11:37,963 templates.py:151 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1330d90>
== 2017-01-04 15:11:37,963 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,963 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,963 templates.py:219 DEBUG name: github_account, config: None
== 2017-01-04 15:11:37,963 templates.py:219 DEBUG name: name, config: gompi
== 2017-01-04 15:11:37,964 templates.py:219 DEBUG name: version, config: 2017a
== 2017-01-04 15:11:37,964 templates.py:219 DEBUG name: versionsuffix, config:
== 2017-01-04 15:11:37,964 templates.py:219 DEBUG name: versionprefix, config:
== 2017-01-04 15:11:37,964 easyblock.py:2274 INFO Running method fetch_step part of step fetch
== 2017-01-04 15:11:37,964 easyblock.py:1446 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2017-01-04 15:11:37,964 easyblock.py:1472 INFO no sources provided
== 2017-01-04 15:11:37,964 easyblock.py:1487 INFO no patches provided
== 2017-01-04 15:11:37,964 config.py:423 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules
== 2017-01-04 15:11:37,964 easyblock.py:1513 INFO Checking dirs that need to be created: ['/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/gompi/2017a', '/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all/gompi', '/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/toolchain/gompi']
== 2017-01-04 15:11:37,966 filetools.py:995 DEBUG Not creating existing path /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/software/gompi/2017a
== 2017-01-04 15:11:37,967 filetools.py:995 DEBUG Not creating existing path /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all/gompi
== 2017-01-04 15:11:37,968 filetools.py:995 DEBUG Not creating existing path /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/toolchain/gompi
== 2017-01-04 15:11:37,968 easyblock.py:2263 DEBUG Not skipping ready step (skippable: False, skip: None, skipsteps: [], module_only: False, force: True
== 2017-01-04 15:11:37,968 build_log.py:216 INFO creating build dir, resetting environment...
== 2017-01-04 15:11:37,968 easyblock.py:2271 INFO Starting ready step
== 2017-01-04 15:11:37,968 templates.py:151 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1330d90>
== 2017-01-04 15:11:37,968 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,968 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,968 templates.py:219 DEBUG name: github_account, config: None
== 2017-01-04 15:11:37,969 templates.py:219 DEBUG name: name, config: gompi
== 2017-01-04 15:11:37,969 templates.py:219 DEBUG name: version, config: 2017a
== 2017-01-04 15:11:37,969 templates.py:219 DEBUG name: versionsuffix, config:
== 2017-01-04 15:11:37,969 templates.py:219 DEBUG name: versionprefix, config:
== 2017-01-04 15:11:37,969 templates.py:151 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1330d90>
== 2017-01-04 15:11:37,969 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,969 templates.py:175 DEBUG version found in easyconfig is 2017a
== 2017-01-04 15:11:37,969 templates.py:219 DEBUG name: github_account, config: None
== 2017-01-04 15:11:37,970 templates.py:219 DEBUG name: name, config: gompi
== 2017-01-04 15:11:37,970 templates.py:219 DEBUG name: version, config: 2017a
== 2017-01-04 15:11:37,970 templates.py:219 DEBUG name: versionsuffix, config:
== 2017-01-04 15:11:37,970 templates.py:219 DEBUG name: versionprefix, config:
== 2017-01-04 15:11:37,970 easyblock.py:2274 INFO Running method check_readiness_step part of step ready
== 2017-01-04 15:11:37,970 easyblock.py:1401 DEBUG Desired parallelism specified via 'parallel' build option: None
== 2017-01-04 15:11:37,971 affinity.py:209 DEBUG sched_getaffinity for pid 19678 returned cpuset 0-23
== 2017-01-04 15:11:37,971 run.py:86 DEBUG Using cached value for command 'ulimit -u': ('4096\n', 0)
== 2017-01-04 15:11:37,971 easyblock.py:1404 INFO Setting parallelism: 24
== 2017-01-04 15:11:37,971 modules.py:634 DEBUG Current MODULEPATH: /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc
== 2017-01-04 15:11:37,971 modules.py:641 DEBUG Changing LD_LIBRARY_PATH from '' to '' in environment for module command
== 2017-01-04 15:11:37,972 modules.py:641 DEBUG Changing LD_PRELOAD from '' to '' in environment for module command
== 2017-01-04 15:11:37,972 modules.py:645 DEBUG Running module command '/usr/share/lmod/lmod/libexec/lmod python --terse list' from /vscmnt/gent_vulpix/_/user/home/gent/vsc400/vsc40023/2017a
== 2017-01-04 15:11:38,004 modules.py:651 DEBUG Output of module command '/usr/share/lmod/lmod/libexec/lmod python --terse list': stdout: os.environ["LMOD_DEFAULT_MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["LMOD_DEFAULT_MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["_ModuleTable001_"] = "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";
os.environ["_ModuleTable002_"] = "LH0sfSxbInNob3J0Il09ImNsdXN0ZXIiLFsic3RhdHVzIl09ImFjdGl2ZSIsfSx9LG1wYXRoQT17Ii91c2VyL2hvbWUvZ2VudC92c2M0MDAvdnNjNDAwMjMvZWJfcGhhbnB5c2NyYXRjaC9DTzcvaGFzd2VsbC1pYi9tb2R1bGVzL2FsbCIsIi9ldGMvbW9kdWxlZmlsZXMvdnNjIix9LFsic3lzdGVtQmFzZU1QQVRIIl09Ii9ldGMvbW9kdWxlZmlsZXMvdnNjIixbInZlcnNpb24iXT0yLH0=";
os.environ["_ModuleTable_Sz_"] = "2";
; stderr: cluster/golett
== 2017-01-04 15:11:38,004 modules.py:968 DEBUG Output found in stdout, seems like '/usr/share/lmod/lmod/libexec/lmod python --terse list' ran fine
== 2017-01-04 15:11:38,005 modules.py:682 DEBUG Correcting paths in $LD_LIBRARY_PATH from [''] to []
== 2017-01-04 15:11:38,005 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '')
== 2017-01-04 15:11:38,005 modules.py:682 DEBUG Correcting paths in $LD_PRELOAD from [''] to []
== 2017-01-04 15:11:38,005 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '')
== 2017-01-04 15:11:38,005 easyblock.py:1409 WARNING Loaded modules detected: ['cluster/golett']
== 2017-01-04 15:11:38,005 utilities.py:101 DEBUG Skipping importing of toolchain modules, processing of toolchain constants is already done.
== 2017-01-04 15:11:38,006 utilities.py:140 DEBUG Obtained new toolchain instance for ('dummy', 'dummy'): {'dummy': True, 'versionsuffix': '', 'version': 'dummy', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'dummy', 'full_mod_name': None, 'hidden': False, 'parsed': True, 'short_mod_name': None}
== 2017-01-04 15:11:38,007 options.py:64 DEBUG _add_options: adding options {'precise': (False, 'High precision'), 'verbose': (False, 'Verbose output'), 'rpath': (True, 'Use RPATH wrappers when --rpath is enabled in EasyBuild configuration'), 'pic': (False, 'Use PIC'), 'static': (False, 'Build static library'), 'optarch': (True, 'Enable architecture optimizations'), 'ieee': (False, 'Adhere to IEEE-754 rules'), 'veryloose': (False, 'Very loose precision'), 'strict': (False, 'Strict (highest) precision'), 'unroll': (False, 'Unroll loops'), 'lowopt': (False, 'Low compiler optimizations'), 'shared': (False, 'Build shared library'), 'opt': (False, 'High compiler optimizations'), 'i8': (False, 'Integers are 8 byte integers'), 'loose': (False, 'Loose precision'), 'cstd': (None, 'Specify C standard'), 'defaultprec': (False, 'Default precision'), 'openmp': (False, 'Enable OpenMP'), 'noopt': (False, 'Disable compiler optimizations'), 'packed-linker-options': (False, 'Pack the linker options as comma separated list'), 'r8': (False, 'Real is 8 byte real'), 'cciscxx': (False, 'Use CC as CXX'), '32bit': (False, 'Compile 32bit target'), 'debug': (False, 'Enable debug'), 'defaultopt': (False, 'Default compiler optimizations')}
== 2017-01-04 15:11:38,007 systemtools.py:208 DEBUG Determined CPU architecture: x86_64
== 2017-01-04 15:11:38,007 systemtools.py:244 DEBUG Determined CPU vendor on Linux as being 'Intel' via regex 'vendor_id\s+:\s*(\S+)' in /proc/cpuinfo
== 2017-01-04 15:11:38,007 systemtools.py:270 DEBUG Using vendor as CPU family: Intel
== 2017-01-04 15:11:38,008 compiler.py:147 DEBUG _compiler_set_options: compiler toolchain options {'precise': False, 'verbose': False, 'rpath': True, 'pic': False, 'static': False, 'optarch': True, 'ieee': False, 'veryloose': False, 'strict': False, 'unroll': False, 'lowopt': False, 'shared': False, 'opt': False, 'i8': False, 'loose': False, 'cstd': None, 'defaultprec': False, 'openmp': False, 'noopt': False, 'packed-linker-options': False, 'r8': False, 'cciscxx': False, '32bit': False, 'debug': False, 'defaultopt': False}
== 2017-01-04 15:11:38,008 easyconfig.py:666 DEBUG Initialized toolchain: {'dummy': True, 'versionsuffix': '', 'version': 'dummy', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'dummy', 'full_mod_name': None, 'hidden': False, 'parsed': True, 'short_mod_name': None} (opts: None)
== 2017-01-04 15:11:38,008 easyconfig.py:608 DEBUG Dependencies BEFORE filtering: [{'external_module_metadata': {}, 'full_mod_name': 'GCC/6.3.0-2.27', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'GCC', 'dummy': True, 'short_mod_name': 'GCC/6.3.0-2.27', 'external_module': False, 'versionsuffix': '', 'version': '6.3.0-2.27', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'OpenMPI/2.0.2-GCC-6.3.0-2.27', 'toolchain': {'version': '6.3.0-2.27', 'name': 'GCC'}, 'name': 'OpenMPI', 'dummy': False, 'short_mod_name': 'OpenMPI/2.0.2-GCC-6.3.0-2.27', 'external_module': False, 'versionsuffix': '', 'version': '2.0.2', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}]
== 2017-01-04 15:11:38,008 toolchain.py:375 DEBUG add_dependencies: adding toolchain dependencies [{'external_module_metadata': {}, 'full_mod_name': 'GCC/6.3.0-2.27', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'GCC', 'dummy': True, 'short_mod_name': 'GCC/6.3.0-2.27', 'external_module': False, 'versionsuffix': '', 'version': '6.3.0-2.27', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'OpenMPI/2.0.2-GCC-6.3.0-2.27', 'toolchain': {'version': '6.3.0-2.27', 'name': 'GCC'}, 'name': 'OpenMPI', 'dummy': False, 'short_mod_name': 'OpenMPI/2.0.2-GCC-6.3.0-2.27', 'external_module': False, 'versionsuffix': '', 'version': '2.0.2', 'toolchain_inherited': False, 'hidden': False, 'build_only': False}]
== 2017-01-04 15:11:38,008 modules.py:418 DEBUG Found cached result for 'module avail' with key '('MODULEPATH=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc', 'lmod', '--show-hidden')': ['3to2/1.1.1-intel-2016b-Python-2.7.12', 'ABINIT/8.0.8b-intel-2016b', 'ART/2016.06.05-intel-2016b', 'ASE/3.11.0-intel-2016b-Python-2.7.12', 'ATK/2.22.0-intel-2016b', 'Autoconf/2.69-foss-2016b', 'Autoconf/2.69-foss-2017a', 'Autoconf/2.69-intel-2016b', 'Automake/1.15-foss-2016b', 'Automake/1.15-foss-2017a', 'Automake/1.15-intel-2016b', 'Autotools/20150215-foss-2016b', 'Autotools/20150215-foss-2017a', 'Autotools/20150215-intel-2016b', 'BBMap/36.62-intel-2016b-Java-1.8.0_112', 'BEDTools/2.26.0-intel-2016b', 'BWA/0.7.15-intel-2016b', 'BamTools/2.4.0-foss-2016b', 'BamUtil/1.0.13-intel-2016b', 'BioPerl/1.7.0-foss-2016b-Perl-5.24.0', 'Biopython/1.68-foss-2016b-Python-2.7.12', 'Biopython/1.68-intel-2016b-Python-2.7.12', 'Biopython/1.68-intel-2016b-Python-3.5.2', 'Bison/2.7', 'Bison/3.0.4', 'Bison/3.0.4-GCCcore-5.4.0', 'Bison/3.0.4-GCCcore-6.3.0', 'Bison/3.0.4-foss-2016b', 'Bison/3.0.4-intel-2016b', 'Blender/2.77a-intel-2016b-Python-3.5.2', 'Blosc/1.11.1-intel-2016b', 'Boost/1.61.0-foss-2016b', 'Boost/1.61.0-foss-2016b-Python-2.7.12', 'Boost/1.61.0-intel-2016b', 'Boost/1.61.0-intel-2016b-Python-2.7.12', 'CBLAS/20110120-foss-2016b', 'CDO/1.7.2-intel-2016b', 'CGAL/4.8.1-intel-2016b', 'CGAL/4.8.1-intel-2016b-Python-2.7.12', 'CMake/3.4.3-foss-2016b', 'CMake/3.5.2-foss-2016b', 'CMake/3.5.2-intel-2016b', 'CMake/3.6.1-foss-2016b', 'CMake/3.6.1-intel-2016b', 'CMake/3.6.2-foss-2016b', 'CMake/3.6.2-intel-2016b', 'CMake/3.7.1-intel-2016b', 'CP2K/3.0-intel-2016b', 'CP2K/3.0-intel-2016b-psmp', 'Cantera/2.2.1-intel-2016b-Python-2.7.12', 'Cargo/0.13.0-foss-2016b', 'CheMPS2/1.8-intel-2016b', 'Clustal-Omega/1.2.0-foss-2016b', 'ClustalW2/2.1-foss-2016b', 'CryptoMiniSat/5.0.1-intel-2016b-Python-2.7.12', 'Cufflinks/2.2.1-foss-2016b', 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'minieigen/0.5.3-intel-2016b-Python-2.7.12', 'mpi4py/1.3.1-intel-2016b-Python-2.7.12-timed-pingpong', 'mpi4py/2.0.0-intel-2016b-Python-2.7.12', 'mympingpong/0.7.1-intel-2016b-Python-2.7.12', 'mypy/0.4.5-intel-2016b', 'ncbi-vdb/2.5.8-1-foss-2016b', 'ncbi-vdb/2.7.0-foss-2016b', 'ncurses/6.0', 'ncurses/6.0-foss-2016b', 'ncurses/6.0-foss-2017a', 'ncurses/6.0-intel-2016b', 'ncview/2.1.7-intel-2016b', 'netCDF-C++4/4.3.0-intel-2016b', 'netCDF-Fortran/4.4.4-foss-2016b', 'netCDF-Fortran/4.4.4-intel-2016b', 'netCDF/4.4.1-foss-2016b', 'netCDF/4.4.1-intel-2016b', 'netCDF/4.4.1.1-foss-2016b', 'nettle/3.2-foss-2016b', 'nettle/3.2-intel-2016b', 'nose-parameterized/0.5.0-intel-2016b-Python-3.5.2', 'numactl/2.0.11-GCC-5.4.0-2.26', 'numactl/2.0.11-GCC-6.3.0-2.27', 'numactl/2.0.11-intel-2016b', 'numexpr/2.6.1-intel-2016b-Python-2.7.12', 'numexpr/2.6.1-intel-2016b-Python-3.5.2', 'numpy/1.9.2-intel-2016b-Python-2.7.12', 'pandas/0.18.1-intel-2016b-Python-2.7.12', 'pandas/0.18.1-intel-2016b-Python-3.5.2', 'pandas/0.19.0-foss-2016b-Python-2.7.12', 'pandas/0.19.0-foss-2016b-Python-3.5.2', 'pandas/0.19.0-intel-2016b-Python-2.7.12', 'pandas/0.19.0-intel-2016b-Python-3.5.2', 'pandas/0.19.1-intel-2016b-Python-2.7.12', 'pandas/0.19.1-intel-2016b-Python-3.5.2', 'path.py/8.2.1-intel-2016b-Python-2.7.12', 'path.py/8.2.1-intel-2016b-Python-3.5.2', 'pbs_python/4.6.0-intel-2016b-Python-2.7.12', 'pip/8.1.2-intel-2016b-Python-2.7.12', 'pixman/0.34.0-intel-2016b', 'pkg-config/0.29.1-foss-2016b', 'pkg-config/0.29.1-intel-2016b', 'pkgconfig/1.1.0-foss-2016b-Python-2.7.12', 'pkgconfig/1.1.0-foss-2016b-Python-3.5.2', 'pkgconfig/1.1.0-intel-2016b-Python-2.7.12', 'pkgconfig/1.1.0-intel-2016b-Python-3.5.2', 'prokka/1.11-foss-2016b-BioPerl-1.7.0', 'prompt-toolkit/1.0.6-intel-2016b-Python-2.7.12', 'prompt-toolkit/1.0.6-intel-2016b-Python-3.5.2', 'pymatgen/4.1.1-intel-2016b-Python-2.7.12', 'pymatgen/4.3.2-intel-2016b-Python-2.7.12', 'qrupdate/1.1.2-intel-2016b', 'requests/2.11.1-intel-2016b-Python-2.7.12', 'requests/2.11.1-intel-2016b-Python-3.5.2', 'scikit-image/0.12.3-intel-2016b-Python-2.7.12', 'scikit-image/0.12.3-intel-2016b-Python-3.5.2', 'scikit-learn/0.17.1-intel-2016b-Python-2.7.12', 'scikit-learn/0.18-intel-2016b-Python-2.7.12', 'scikit-learn/0.18-intel-2016b-Python-3.5.2', 'scipy/0.16.0-intel-2016b-Python-2.7.12', 'seqtk/1.2-foss-2016b', 'setuptools/1.4.2', 'spglib-python/1.9.4.2-intel-2016b-Python-2.7.12', 'spglib-python/1.9.5-intel-2016b-Python-2.7.12', 'tabix/0.2.6-intel-2016b', 'taco/0.5.1-intel-2016b-Python-2.7.12', 'testpath/0.3-intel-2016b-Python-2.7.12', 'testpath/0.3-intel-2016b-Python-3.5.2', 'util-linux/2.28.1-intel-2016b', 'util-linux/2.29-foss-2016b', 'util-linux/2.29-intel-2016b', 'vsc-base/2.5.1-intel-2016b-Python-2.7.12', 'vsc-install/0.10.11-intel-2016b-Python-2.7.12', 'vsc-mympirun/3.4.3-intel-2016b-Python-2.7.12', 'wcwidth/0.1.7-intel-2016b-Python-2.7.12', 'wcwidth/0.1.7-intel-2016b-Python-3.5.2', 'wget/1.17.1-foss-2016b', 'worker/1.6.6-intel-2016b', 'worker/1.6.7-intel-2016b', 'wxPython/3.0.2.0-intel-2016b-Python-2.7.12', 'x264/20160614-intel-2016b', 'xprop/1.2.2-foss-2016b', 'xprop/1.2.2-intel-2016b', 'zlib/1.2.10', 'zlib/1.2.10-GCCcore-6.3.0', 'zlib/1.2.8', 'zlib/1.2.8-GCCcore-5.4.0', 'zlib/1.2.8-GCCcore-6.3.0', 'zlib/1.2.8-foss-2016b', 'zlib/1.2.8-intel-2016b']
== 2017-01-04 15:11:38,009 modules.py:634 DEBUG Current MODULEPATH: /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc
== 2017-01-04 15:11:38,010 modules.py:641 DEBUG Changing LD_LIBRARY_PATH from '' to '' in environment for module command
== 2017-01-04 15:11:38,010 modules.py:641 DEBUG Changing LD_PRELOAD from '' to '' in environment for module command
== 2017-01-04 15:11:38,010 modules.py:645 DEBUG Running module command '/usr/share/lmod/lmod/libexec/lmod python show OpenMPI/2.0.2-GCC-6.3.0-2.27' from /vscmnt/gent_vulpix/_/user/home/gent/vsc400/vsc40023/2017a
== 2017-01-04 15:11:38,139 modules.py:651 DEBUG Output of module command '/usr/share/lmod/lmod/libexec/lmod python show OpenMPI/2.0.2-GCC-6.3.0-2.27': stdout: os.environ["LMOD_DEFAULT_MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["LMOD_DEFAULT_MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["_ModuleTable001_"] = "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";
os.environ["_ModuleTable002_"] = "LH0sfSxbInNob3J0Il09ImNsdXN0ZXIiLFsic3RhdHVzIl09ImFjdGl2ZSIsfSx9LG1wYXRoQT17Ii91c2VyL2hvbWUvZ2VudC92c2M0MDAvdnNjNDAwMjMvZWJfcGhhbnB5c2NyYXRjaC9DTzcvaGFzd2VsbC1pYi9tb2R1bGVzL2FsbCIsIi9ldGMvbW9kdWxlZmlsZXMvdnNjIix9LFsic3lzdGVtQmFzZU1QQVRIIl09Ii9ldGMvbW9kdWxlZmlsZXMvdnNjIixbInZlcnNpb24iXT0yLH0=";
os.environ["_ModuleTable_Sz_"] = "2";
; stderr: Failed to find the following module(s): "OpenMPI/2.0.2-GCC-6.3.0-2.27" in your MODULEPATH
Try:
"module spider OpenMPI/2.0.2-GCC-6.3.0-2.27"
to see if the module(s) are available across all compilers and MPI implementations.
== 2017-01-04 15:11:38,139 modules.py:968 DEBUG Output found in stdout, seems like '/usr/share/lmod/lmod/libexec/lmod python show OpenMPI/2.0.2-GCC-6.3.0-2.27' ran fine
== 2017-01-04 15:11:38,139 modules.py:539 DEBUG Cached result for 'module show OpenMPI/2.0.2-GCC-6.3.0-2.27' with key '('MODULEPATH=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc', 'lmod', 'OpenMPI/2.0.2-GCC-6.3.0-2.27')': os.environ["LMOD_DEFAULT_MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["LMOD_DEFAULT_MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc";
os.environ["_ModuleTable001_"] = "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";
os.environ["_ModuleTable002_"] = "LH0sfSxbInNob3J0Il09ImNsdXN0ZXIiLFsic3RhdHVzIl09ImFjdGl2ZSIsfSx9LG1wYXRoQT17Ii91c2VyL2hvbWUvZ2VudC92c2M0MDAvdnNjNDAwMjMvZWJfcGhhbnB5c2NyYXRjaC9DTzcvaGFzd2VsbC1pYi9tb2R1bGVzL2FsbCIsIi9ldGMvbW9kdWxlZmlsZXMvdnNjIix9LFsic3lzdGVtQmFzZU1QQVRIIl09Ii9ldGMvbW9kdWxlZmlsZXMvdnNjIixbInZlcnNpb24iXT0yLH0=";
os.environ["_ModuleTable_Sz_"] = "2";
Failed to find the following module(s): "OpenMPI/2.0.2-GCC-6.3.0-2.27" in your MODULEPATH
Try:
"module spider OpenMPI/2.0.2-GCC-6.3.0-2.27"
to see if the module(s) are available across all compilers and MPI implementations.
== 2017-01-04 15:11:38,140 toolchain.py:392 DEBUG add_dependencies: MODULEPATH: /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc
== 2017-01-04 15:11:38,140 toolchain.py:395 DEBUG add_dependencies: added toolchain dependency {'external_module_metadata': {}, 'full_mod_name': 'GCC/6.3.0-2.27', 'toolchain': {'version': 'dummy', 'name': 'dummy'}, 'name': 'GCC', 'dummy': True, 'short_mod_name': 'GCC/6.3.0-2.27', 'external_module': False, 'versionsuffix': '', 'version': '6.3.0-2.27', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}
== 2017-01-04 15:11:38,140 toolchain.py:392 DEBUG add_dependencies: MODULEPATH: /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/haswell-ib/modules/all:/etc/modulefiles/vsc
== 2017-01-04 15:11:38,141 build_log.py:147 ERROR EasyBuild crashed with an error (at ?:124 in __init__): Missing modules for one or more dependencies: OpenMPI/2.0.2-GCC-6.3.0-2.27 (at easybuild/tools/toolchain/toolchain.py:400 in add_dependencies)
== 2017-01-04 15:11:38,141 easyblock.py:2503 WARNING build failed (first 300 chars): Missing modules for one or more dependencies: OpenMPI/2.0.2-GCC-6.3.0-2.27
== 2017-01-04 15:11:38,141 easyblock.py:276 INFO Closing log for application name gompi version 2017a
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