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  1. == 2018-06-23 16:45:20,859 easyblock.py:266 INFO This is EasyBuild 3.6.2.dev0 (framework: 3.6.2.dev0, easyblocks: 3.6.2.dev0) on host node3100.skitty.os.
  2. == 2018-06-23 16:45:20,860 easyblock.py:272 INFO This is easyblock EB_netCDF from module easybuild.easyblocks.netcdf (/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyblocks-3.6.2.dev0-py2.7.egg/easybuild/easyblocks/n/netcdf.pyo)
  3. == 2018-06-23 16:45:20,860 easyblock.py:818 INFO Build dir set to /tmp/vsc40023/easybuild_build/netCDF/4.6.0/foss-2018a
  4. == 2018-06-23 16:45:20,860 config.py:486 DEBUG software install path as specified by 'installpath' and 'subdir_software': /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/software
  5. == 2018-06-23 16:45:20,860 easyconfig.py:1697 DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1f2cf50>
  6. == 2018-06-23 16:45:20,860 easyconfig.py:1703 DEBUG Obtained subdir netCDF/4.6.0-foss-2018a
  7. == 2018-06-23 16:45:20,860 easyblock.py:859 INFO Software install dir set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/software/netCDF/4.6.0-foss-2018a
  8. == 2018-06-23 16:45:20,860 config.py:486 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules
  9. == 2018-06-23 16:45:20,860 easyblock.py:864 INFO Module install dir set to /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all
  10. == 2018-06-23 16:45:20,860 easyblock.py:251 INFO Init completed for application name netCDF version 4.6.0
  11. == 2018-06-23 16:45:20,860 easyblock.py:2754 INFO Obtained application instance of for netCDF (easyblock: None)
  12. == 2018-06-23 16:45:20,860 easyblock.py:2767 DEBUG Skip set to False
  13. == 2018-06-23 16:45:20,861 build_log.py:233 INFO building and installing netCDF/4.6.0-foss-2018a...
  14. == 2018-06-23 16:45:20,861 easyblock.py:2524 DEBUG Not skipping fetch step (skippable: False, skip: None, skipsteps: [], module_only: False, force: True
  15. == 2018-06-23 16:45:20,861 build_log.py:233 INFO fetching files...
  16. == 2018-06-23 16:45:20,861 easyblock.py:2532 INFO Starting fetch step
  17. == 2018-06-23 16:45:20,861 templates.py:153 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1f2cf50>
  18. == 2018-06-23 16:45:20,861 templates.py:177 DEBUG version found in easyconfig is 4.6.0
  19. == 2018-06-23 16:45:20,861 templates.py:221 DEBUG name: github_account, config: None
  20. == 2018-06-23 16:45:20,861 templates.py:221 DEBUG name: name, config: netCDF
  21. == 2018-06-23 16:45:20,861 templates.py:221 DEBUG name: version, config: 4.6.0
  22. == 2018-06-23 16:45:20,861 templates.py:221 DEBUG name: versionsuffix, config:
  23. == 2018-06-23 16:45:20,861 templates.py:221 DEBUG name: versionprefix, config:
  24. == 2018-06-23 16:45:20,861 templates.py:153 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1f2cf50>
  25. == 2018-06-23 16:45:20,861 templates.py:177 DEBUG version found in easyconfig is 4.6.0
  26. == 2018-06-23 16:45:20,862 templates.py:221 DEBUG name: github_account, config: None
  27. == 2018-06-23 16:45:20,862 templates.py:221 DEBUG name: name, config: netCDF
  28. == 2018-06-23 16:45:20,862 templates.py:221 DEBUG name: version, config: 4.6.0
  29. == 2018-06-23 16:45:20,862 templates.py:221 DEBUG name: versionsuffix, config:
  30. == 2018-06-23 16:45:20,862 templates.py:221 DEBUG name: versionprefix, config:
  31. == 2018-06-23 16:45:20,862 easyblock.py:2538 INFO Running method fetch_step part of step fetch
  32. == 2018-06-23 16:45:20,862 easyblock.py:1581 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
  33. == 2018-06-23 16:45:20,862 filetools.py:343 INFO Command eb found at /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/bin/eb
  34. == 2018-06-23 16:45:20,862 tools.py:263 DEBUG Also considering installation prefix /kyukon/data/gent/gvo000/gvo00002/vsc40023/easybuild_easy_installed...
  35. == 2018-06-23 16:45:20,862 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.2.dev0-py2.7.egg/easybuild/easyconfigs/easybuild/easyconfigs
  36. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-k8v8Xc/files_pr6496/easybuild/easyconfigs
  37. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/site-packages/git/ext/gitdb/easybuild/easyconfigs
  38. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
  39. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/home/gent/vsc400/vsc40023/.local/python-dateutil/lib/python2.7/site-packages/python_dateutil-2.6.1-py2.7.egg/easybuild/easyconfigs
  40. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/vsc_base-2.5.8-py2.7.egg/easybuild/easyconfigs
  41. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyblocks-3.6.2.dev0-py2.7.egg/easybuild/easyconfigs
  42. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.2.dev0-py2.7.egg/easybuild/easyconfigs
  43. == 2018-06-23 16:45:20,863 tools.py:272 DEBUG Added /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.6.2.dev0-py2.7.egg/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
  44. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_framework-3.6.2.dev0-py2.7.egg/easybuild/easyconfigs
  45. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/data/gent/gvo000/gvo00002/JUBE/easybuild/easyconfigs
  46. == 2018-06-23 16:45:20,863 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/home/gent/vsc400/vsc40023/.local/python-dateutil/lib/python2.7/site-packages/easybuild/easyconfigs
  47. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/home/gent/vsc400/vsc40023/.local/keyring/lib/python2.7/site-packages/keyring-3.8/easybuild/easyconfigs
  48. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild/easyconfigs
  49. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /kyukon/home/gent/vsc400/vsc40023/easybuild/easyconfigs
  50. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python27.zip/easybuild/easyconfigs
  51. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python2.7/easybuild/easyconfigs
  52. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python2.7/plat-linux2/easybuild/easyconfigs
  53. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python2.7/lib-tk/easybuild/easyconfigs
  54. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python2.7/lib-old/easybuild/easyconfigs
  55. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python2.7/lib-dynload/easybuild/easyconfigs
  56. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /user/home/gent/vsc400/vsc40023/.local/lib/python2.7/site-packages/easybuild/easyconfigs
  57. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python2.7/site-packages/easybuild/easyconfigs
  58. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python2.7/site-packages/easybuild/easyconfigs
  59. == 2018-06-23 16:45:20,864 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python2.7/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
  60. == 2018-06-23 16:45:20,865 tools.py:268 DEBUG Checking for easybuild/easyconfigs at /kyukon/data/gent/gvo000/gvo00002/vsc40023/easybuild_easy_installed/easybuild/easyconfigs
  61. == 2018-06-23 16:45:20,871 easyblock.py:649 INFO Found file v4.6.0.tar.gz at /user/data/gent/vsc400/vsc40023/EasyBuild/sources/n/netCDF/v4.6.0.tar.gz
  62. == 2018-06-23 16:45:20,871 easyblock.py:366 DEBUG File /user/data/gent/vsc400/vsc40023/EasyBuild/sources/n/netCDF/v4.6.0.tar.gz found for source v4.6.0.tar.gz
  63. == 2018-06-23 16:45:20,872 easyblock.py:378 INFO Added sources: [{'path': '/user/data/gent/vsc400/vsc40023/EasyBuild/sources/n/netCDF/v4.6.0.tar.gz', 'cmd': None, 'finalpath': '/tmp/vsc40023/easybuild_build/netCDF/4.6.0/foss-2018a', 'name': 'v4.6.0.tar.gz', 'checksum': '6d740356399aac12290650325a05aec2fe92c1905df10761b2b0100994197725'}]
  64. == 2018-06-23 16:45:20,872 easyblock.py:1622 INFO no patches provided
  65. == 2018-06-23 16:45:20,872 filetools.py:653 DEBUG Using blocksize 16777216 for calculating the checksum
  66. == 2018-06-23 16:45:20,937 easyblock.py:1632 INFO md5 checksum for /user/data/gent/vsc400/vsc40023/EasyBuild/sources/n/netCDF/v4.6.0.tar.gz: a0268d3afe99cf202986b6dbe86c2f04
  67. == 2018-06-23 16:45:20,937 filetools.py:653 DEBUG Using blocksize 16777216 for calculating the checksum
  68. == 2018-06-23 16:45:20,989 easyblock.py:1632 INFO sha256 checksum for /user/data/gent/vsc400/vsc40023/EasyBuild/sources/n/netCDF/v4.6.0.tar.gz: 6d740356399aac12290650325a05aec2fe92c1905df10761b2b0100994197725
  69. == 2018-06-23 16:45:20,990 easyconfig.py:1685 DEBUG Determining full module name for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1f2cf50> (force_visible: False)
  70. == 2018-06-23 16:45:20,990 easyconfig.py:1665 DEBUG No alternative software name specified to determine module name with
  71. == 2018-06-23 16:45:20,990 utilities.py:103 DEBUG Module name netCDF/4.6.0-foss-2018a validated
  72. == 2018-06-23 16:45:20,990 easyconfig.py:1692 DEBUG Obtained valid full module name netCDF/4.6.0-foss-2018a
  73. == 2018-06-23 16:45:20,991 config.py:486 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules
  74. == 2018-06-23 16:45:20,991 easyblock.py:1665 INFO Checking dirs that need to be created: ['/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/software/netCDF/4.6.0-foss-2018a', '/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all/netCDF', '/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/data/netCDF']
  75. == 2018-06-23 16:45:20,993 filetools.py:1108 INFO Creating directory /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/software/netCDF/4.6.0-foss-2018a (parents: True, set_gid: False, sticky: False)
  76. == 2018-06-23 16:45:20,998 filetools.py:1136 DEBUG Not creating existing path /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all/netCDF
  77. == 2018-06-23 16:45:20,998 filetools.py:1136 DEBUG Not creating existing path /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/data/netCDF
  78. == 2018-06-23 16:45:20,998 easyblock.py:2524 DEBUG Not skipping ready step (skippable: False, skip: None, skipsteps: [], module_only: False, force: True
  79. == 2018-06-23 16:45:20,998 build_log.py:233 INFO creating build dir, resetting environment...
  80. == 2018-06-23 16:45:20,999 easyblock.py:2532 INFO Starting ready step
  81. == 2018-06-23 16:45:20,999 templates.py:153 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1f2cf50>
  82. == 2018-06-23 16:45:20,999 templates.py:177 DEBUG version found in easyconfig is 4.6.0
  83. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: github_account, config: None
  84. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: name, config: netCDF
  85. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: version, config: 4.6.0
  86. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: versionsuffix, config:
  87. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: versionprefix, config:
  88. == 2018-06-23 16:45:20,999 templates.py:153 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x1f2cf50>
  89. == 2018-06-23 16:45:20,999 templates.py:177 DEBUG version found in easyconfig is 4.6.0
  90. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: github_account, config: None
  91. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: name, config: netCDF
  92. == 2018-06-23 16:45:20,999 templates.py:221 DEBUG name: version, config: 4.6.0
  93. == 2018-06-23 16:45:21,000 templates.py:221 DEBUG name: versionsuffix, config:
  94. == 2018-06-23 16:45:21,000 templates.py:221 DEBUG name: versionprefix, config:
  95. == 2018-06-23 16:45:21,000 easyblock.py:2538 INFO Running method check_readiness_step part of step ready
  96. == 2018-06-23 16:45:21,000 easyblock.py:1518 DEBUG Desired parallelism specified via 'parallel' build option: None
  97. == 2018-06-23 16:45:21,000 affinity.py:211 DEBUG sched_getaffinity for pid 49118 returned cpuset 0,4,8,12,16,20,24,28,32
  98. == 2018-06-23 16:45:21,000 run.py:84 DEBUG Using cached value for command 'ulimit -u': ('4096\n', 0)
  99. == 2018-06-23 16:45:21,001 easyblock.py:1521 INFO Setting parallelism: 9
  100. == 2018-06-23 16:45:21,001 modules.py:648 DEBUG Current MODULEPATH: /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc
  101. == 2018-06-23 16:45:21,001 modules.py:655 DEBUG Changing LD_LIBRARY_PATH from '' to '' in environment for module command
  102. == 2018-06-23 16:45:21,001 modules.py:655 DEBUG Changing LD_PRELOAD from '' to '' in environment for module command
  103. == 2018-06-23 16:45:21,001 modules.py:659 DEBUG Running module command '/usr/share/lmod/lmod/libexec/lmod python --terse list' from /kyukon/home/gent/vsc400/vsc40023
  104. == 2018-06-23 16:45:21,038 modules.py:665 DEBUG Output of module command '/usr/share/lmod/lmod/libexec/lmod python --terse list': stdout: os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc";
  105. os.environ["_ModuleTable001_"] = "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";
  106. os.environ["_ModuleTable002_"] = "YW5weXNjcmF0Y2gvQ083L3NreWxha2UtaWIvbW9kdWxlcy9hbGwiLCIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfQ==";
  107. os.environ["_ModuleTable_Sz_"] = "2";
  108. ; stderr: cluster/skitty
  109.  
  110. == 2018-06-23 16:45:21,038 modules.py:1137 DEBUG Output found in stdout, seems like '/usr/share/lmod/lmod/libexec/lmod python --terse list' ran fine
  111. == 2018-06-23 16:45:21,038 modules.py:702 DEBUG Correcting paths in $LD_LIBRARY_PATH from [''] to []
  112. == 2018-06-23 16:45:21,039 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '')
  113. == 2018-06-23 16:45:21,039 modules.py:702 DEBUG Correcting paths in $LD_PRELOAD from [''] to []
  114. == 2018-06-23 16:45:21,039 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '')
  115. == 2018-06-23 16:45:21,039 easyblock.py:1526 WARNING Loaded modules detected: ['cluster/skitty']
  116. == 2018-06-23 16:45:21,039 easyconfig.py:612 DEBUG Dependencies BEFORE filtering: [{'external_module_metadata': {}, 'full_mod_name': 'HDF5/1.10.1-foss-2018a', 'toolchain': {'version': '2018a', 'name': 'foss'}, 'name': 'HDF5', 'dummy': False, 'short_mod_name': 'HDF5/1.10.1-foss-2018a', 'external_module': False, 'versionsuffix': '', 'version': '1.10.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'cURL/7.58.0-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'cURL', 'dummy': False, 'short_mod_name': 'cURL/7.58.0-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '7.58.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'Szip/2.1.1-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'Szip', 'dummy': False, 'short_mod_name': 'Szip/2.1.1-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '2.1.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'Autotools/20170619-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'Autotools', 'dummy': False, 'short_mod_name': 'Autotools/20170619-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '20170619', 'toolchain_inherited': True, 'hidden': False, 'build_only': True}, {'external_module_metadata': {}, 'full_mod_name': 'CMake/3.10.2-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'CMake', 'dummy': False, 'short_mod_name': 'CMake/3.10.2-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '3.10.2', 'toolchain_inherited': True, 'hidden': False, 'build_only': True}, {'external_module_metadata': {}, 'full_mod_name': 'Doxygen/1.8.13-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'Doxygen', 'dummy': False, 'short_mod_name': 'Doxygen/1.8.13-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '1.8.13', 'toolchain_inherited': True, 'hidden': False, 'build_only': True}]
  117. == 2018-06-23 16:45:21,039 toolchain.py:376 DEBUG add_dependencies: adding toolchain dependencies [{'external_module_metadata': {}, 'full_mod_name': 'HDF5/1.10.1-foss-2018a', 'toolchain': {'version': '2018a', 'name': 'foss'}, 'name': 'HDF5', 'dummy': False, 'short_mod_name': 'HDF5/1.10.1-foss-2018a', 'external_module': False, 'versionsuffix': '', 'version': '1.10.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'cURL/7.58.0-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'cURL', 'dummy': False, 'short_mod_name': 'cURL/7.58.0-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '7.58.0', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'Szip/2.1.1-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'Szip', 'dummy': False, 'short_mod_name': 'Szip/2.1.1-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '2.1.1', 'toolchain_inherited': True, 'hidden': False, 'build_only': False}, {'external_module_metadata': {}, 'full_mod_name': 'Autotools/20170619-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'Autotools', 'dummy': False, 'short_mod_name': 'Autotools/20170619-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '20170619', 'toolchain_inherited': True, 'hidden': False, 'build_only': True}, {'external_module_metadata': {}, 'full_mod_name': 'CMake/3.10.2-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'CMake', 'dummy': False, 'short_mod_name': 'CMake/3.10.2-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '3.10.2', 'toolchain_inherited': True, 'hidden': False, 'build_only': True}, {'external_module_metadata': {}, 'full_mod_name': 'Doxygen/1.8.13-GCCcore-6.4.0', 'toolchain': {'version': '6.4.0', 'name': 'GCCcore'}, 'name': 'Doxygen', 'dummy': False, 'short_mod_name': 'Doxygen/1.8.13-GCCcore-6.4.0', 'external_module': False, 'versionsuffix': '', 'version': '1.8.13', 'toolchain_inherited': True, 'hidden': False, 'build_only': True}]
  118. == 2018-06-23 16:45:21,039 toolchain.py:386 DEBUG add_dependencies: MODULEPATH: /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc
  119. == 2018-06-23 16:45:21,040 modules.py:444 DEBUG Found cached result for 'module avail' with key '('MODULEPATH=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc', 'lmod', '--show-hidden')': ['ABINIT/8.6.3-intel-2018a', 'ANTLR/2.7.7-foss-2018a-Python-2.7.14', 'ASE/3.16.2-iomkl-2018.02-Python-3.6.4', 'Autoconf/2.69-GCCcore-6.4.0', 'Autoconf/2.69-GCCcore-7.3.0', 'Automake/1.15.1-GCCcore-6.4.0', 'Automake/1.16.1-GCCcore-7.3.0', 'Autotools/20170619-GCCcore-6.4.0', 'Autotools/20180311-GCCcore-7.3.0', 'BamUtil/1.0.14-intel-2018a', 'Bazel/0.10.0-GCCcore-6.4.0', 'Bazel/0.12.0-GCCcore-6.4.0', 'Biopython/1.71-intel-2018a-Python-3.6.4', 'Bison/3.0.4', 'Bison/3.0.4-GCCcore-6.4.0', 'Bison/3.0.4-GCCcore-7.3.0', 'Bison/3.0.4-GCCcore-8.1.0', 'Bison/3.0.5-GCCcore-7.3.0', 'Boost/1.63.0-foss-2018a-Python-2.7.14', 'Boost/1.66.0-foss-2018a', 'Boost/1.66.0-intel-2018a', 'Boost/1.67.0-intel-2018a', 'CGAL/4.11.1-foss-2018a-Python-2.7.14', 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'libffi/3.2.1-GCCcore-6.4.0', 'libffi/3.2.1-GCCcore-7.3.0', 'libgtextutils/0.7-intel-2018a', 'libjpeg-turbo/1.5.2-GCCcore-6.4.0', 'libjpeg-turbo/1.5.3-GCCcore-6.4.0', 'libmatheval/1.1.11-GCCcore-6.4.0', 'libpng/1.6.32-GCCcore-6.4.0', 'libpng/1.6.34-GCCcore-6.4.0', 'libpng/1.6.34-GCCcore-7.3.0', 'libreadline/7.0-GCCcore-6.4.0', 'libreadline/7.0-GCCcore-7.3.0', 'libsndfile/1.0.28-GCCcore-6.4.0', 'libtool/2.4.6-GCCcore-6.4.0', 'libtool/2.4.6-GCCcore-7.3.0', 'libunistring/0.9.7-GCCcore-6.4.0', 'libxc/3.0.1-foss-2018a', 'libxc/3.0.1-intel-2018a', 'libxml2/2.9.4-GCCcore-6.4.0', 'libxml2/2.9.7-GCCcore-6.4.0', 'libxml2/2.9.8-GCCcore-7.3.0', 'libxslt/1.1.32-GCCcore-6.4.0', 'libxsmm/1.8.3-foss-2018a', 'libxsmm/1.8.3-intel-2018a', 'libyaml/0.1.7-GCCcore-6.4.0', 'lxml/4.2.0-intel-2018a-Python-2.7.14', 'matplotlib/2.1.2-intel-2018a-Python-2.7.14', 'matplotlib/2.1.2-intel-2018a-Python-3.6.4', 'matplotlib/2.1.2-iomkl-2018.02-Python-3.6.4', 'mympingpong/0.8.0-foss-2018a-Python-2.7.14', 'mympingpong/0.8.0-intel-2018a-Python-2.7.14', 'nanopolish/0.9.2-intel-2018a', 'ncurses/6.0', 'ncurses/6.0-GCCcore-6.4.0', 'ncurses/6.1-GCCcore-7.3.0', 'netCDF-Fortran/4.4.4-intel-2018a', 'netCDF/4.4.1.1-intel-2017b-HDF5-1.8.19', 'netCDF/4.5.0-intel-2017b', 'netCDF/4.6.0-intel-2018a', 'netCDF/4.6.0-iomkl-2018a', 'nettle/3.4-iomkl-2018a', 'numactl/2.0.11-GCCcore-6.4.0', 'numactl/2.0.11-GCCcore-7.3.0', 'phonopy/1.13.0.64-intel-2018a-Python-2.7.14', 'pixman/0.34.0-GCCcore-6.4.0', 'pkg-config/0.29.2-GCCcore-6.4.0', 'pkg-config/0.29.2-GCCcore-7.3.0', 'pkgconfig/1.3.1-intel-2018a-Python-2.7.14', 'pkgconfig/1.3.1-intel-2018a-Python-3.6.4', 'poretools/0.6.0-intel-2018a-Python-2.7.14', 'pyslurm/17.11.0.7', 'scikit-learn/0.19.1-intel-2018a-Python-3.6.4', 'setuptools/1.4.2', 'util-linux/2.31-GCCcore-6.4.0', 'util-linux/2.31.1-GCCcore-6.4.0', 'vsc-base/2.8.0', 'vsc-base/2.8.0dev', 'vsc-install/0.11.1', 'vsc-mympirun/4.1.1dev', 'vsc-mympirun/4.1.2dev', 'vsc-mympirun/4.1.4', 'vsc-mympirun/4.1.4dev', 'wheel/0.30.0-intel-2017b-Python-3.6.3', 'wheel/0.31.0-foss-2018a-Python-3.6.4', 'worker/1.6.8-intel-2018a', 'zlib/1.2.11', 'zlib/1.2.11-GCCcore-6.4.0', 'zlib/1.2.11-GCCcore-7.3.0', 'zlib/1.2.11-GCCcore-8.1.0', 'zlib/1.2.8']
  120. == 2018-06-23 16:45:21,040 modules.py:648 DEBUG Current MODULEPATH: /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc
  121. == 2018-06-23 16:45:21,040 modules.py:655 DEBUG Changing LD_LIBRARY_PATH from '' to '' in environment for module command
  122. == 2018-06-23 16:45:21,040 modules.py:655 DEBUG Changing LD_PRELOAD from '' to '' in environment for module command
  123. == 2018-06-23 16:45:21,040 modules.py:659 DEBUG Running module command '/usr/share/lmod/lmod/libexec/lmod python show HDF5/1.10.1-foss-2018a' from /kyukon/home/gent/vsc400/vsc40023
  124. == 2018-06-23 16:45:21,134 modules.py:665 DEBUG Output of module command '/usr/share/lmod/lmod/libexec/lmod python show HDF5/1.10.1-foss-2018a': stdout: os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc";
  125. os.environ["_ModuleTable001_"] = "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";
  126. os.environ["_ModuleTable002_"] = "YW5weXNjcmF0Y2gvQ083L3NreWxha2UtaWIvbW9kdWxlcy9hbGwiLCIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfQ==";
  127. os.environ["_ModuleTable_Sz_"] = "2";
  128. ; stderr:
  129. == 2018-06-23 16:45:21,134 modules.py:561 DEBUG Cached result for 'module show HDF5/1.10.1-foss-2018a' with key '('MODULEPATH=/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc', 'lmod', 'HDF5/1.10.1-foss-2018a')': os.environ["MODULEPATH"] = "/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc";
  130. os.environ["_ModuleTable001_"] = "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";
  131. os.environ["_ModuleTable002_"] = "YW5weXNjcmF0Y2gvQ083L3NreWxha2UtaWIvbW9kdWxlcy9hbGwiLCIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfQ==";
  132. os.environ["_ModuleTable_Sz_"] = "2";
  133.  
  134. == 2018-06-23 16:45:21,154 build_log.py:158 ERROR EasyBuild crashed with an error (at ?:124 in __init__): Missing modules for one or more dependencies: HDF5/1.10.1-foss-2018a (at easybuild/tools/toolchain/toolchain.py:401 in add_dependencies)
  135. == 2018-06-23 16:45:21,154 easyblock.py:2780 WARNING build failed (first 300 chars): Missing modules for one or more dependencies: HDF5/1.10.1-foss-2018a
  136. == 2018-06-23 16:45:21,154 easyblock.py:281 INFO Closing log for application name netCDF version 4.6.0
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