Created
April 8, 2020 17:53
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(partial) EasyBuild log for failed build of /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-intel-2019b.eb (PR #10346)
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| == 2020-04-08 19:53:08,527 easyblock.py:280 INFO This is EasyBuild 4.1.2 (framework: 4.1.2, easyblocks: 4.1.1) on host iris-003. | |
| == 2020-04-08 19:53:08,528 easyblock.py:286 INFO This is easyblock CMakeMake from module easybuild.easyblocks.generic.cmakemake (/work/projects/sw/resif/iris/default/local/software/EasyBuild/4.1.2/lib/python3.7/site-packages/easybuild/easyblocks/generic/cmakemake.py) | |
| == 2020-04-08 19:53:08,528 easyblock.py:843 INFO Build dir set to /dev/shm/arpackng/3.7.0/intel-2019b | |
| == 2020-04-08 19:53:08,528 easyblock.py:903 INFO Software install dir set to /work/projects/sw/resif/iris/default/local/software/arpack-ng/3.7.0-intel-2019b | |
| == 2020-04-08 19:53:08,528 easyblock.py:908 INFO Module install dir set to /work/projects/sw/resif/iris/default/local/modules/all | |
| == 2020-04-08 19:53:08,529 easyblock.py:265 INFO Init completed for application name arpack-ng version 3.7.0 | |
| == 2020-04-08 19:53:08,529 easyblock.py:3079 INFO Obtained application instance of for arpack-ng (easyblock: CMakeMake) | |
| == 2020-04-08 19:53:08,529 one.py:150 INFO Skipping reformatting value for parameter 'toolchain' | |
| == 2020-04-08 19:53:08,530 one.py:150 INFO Skipping reformatting value for parameter 'toolchainopts' | |
| == 2020-04-08 19:53:08,532 filetools.py:1296 INFO Creating directory /mnt/irisgpfs/users/svarrette/git/lab.uni.lu/svarrette/sw/logs/easybuild/reprod_20200408195308_166388 (parents: True, set_gid: False, sticky: False) | |
| == 2020-04-08 19:53:08,536 easyblock.py:3257 INFO Dumped easyconfig instance to /mnt/irisgpfs/users/svarrette/git/lab.uni.lu/svarrette/sw/logs/easybuild/reprod_20200408195308_166388/arpack-ng-3.7.0-intel-2019b.eb | |
| == 2020-04-08 19:53:08,537 filetools.py:1296 INFO Creating directory /mnt/irisgpfs/users/svarrette/git/lab.uni.lu/svarrette/sw/logs/easybuild/reprod_20200408195308_166388/easyblocks (parents: True, set_gid: False, sticky: False) | |
| == 2020-04-08 19:53:08,540 filetools.py:1773 INFO /work/projects/sw/resif/iris/default/local/software/EasyBuild/4.1.2/lib/python3.7/site-packages/easybuild/easyblocks/generic/cmakemake.py copied to /mnt/irisgpfs/users/svarrette/git/lab.uni.lu/svarrette/sw/logs/easybuild/reprod_20200408195308_166388/easyblocks/cmakemake.py | |
| == 2020-04-08 19:53:08,540 easyblock.py:3272 INFO Dumped easyblock cmakemake.py required for reproduction to /mnt/irisgpfs/users/svarrette/git/lab.uni.lu/svarrette/sw/logs/easybuild/reprod_20200408195308_166388/easyblocks | |
| == 2020-04-08 19:53:08,542 filetools.py:1773 INFO /work/projects/sw/resif/iris/default/local/software/EasyBuild/4.1.2/lib/python3.7/site-packages/easybuild/easyblocks/generic/configuremake.py copied to /mnt/irisgpfs/users/svarrette/git/lab.uni.lu/svarrette/sw/logs/easybuild/reprod_20200408195308_166388/easyblocks/configuremake.py | |
| == 2020-04-08 19:53:08,542 easyblock.py:3272 INFO Dumped easyblock configuremake.py required for reproduction to /mnt/irisgpfs/users/svarrette/git/lab.uni.lu/svarrette/sw/logs/easybuild/reprod_20200408195308_166388/easyblocks | |
| == 2020-04-08 19:53:08,542 easyblock.py:1590 INFO Number of iterations to perform for central part of installation procedure: 2 | |
| == 2020-04-08 19:53:08,542 build_log.py:265 INFO building and installing numlib/arpack-ng/3.7.0-intel-2019b... | |
| == 2020-04-08 19:53:08,543 build_log.py:265 INFO fetching files... | |
| == 2020-04-08 19:53:08,543 easyblock.py:2857 INFO Starting fetch step | |
| == 2020-04-08 19:53:08,543 easyblock.py:2863 INFO Running method fetch_step part of step fetch | |
| == 2020-04-08 19:53:08,543 easyblock.py:1699 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version | |
| == 2020-04-08 19:53:08,544 tools.py:266 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /work/projects/sw/resif/iris/default/local/software/EasyBuild/4.1.2/bin/eb | |
| == 2020-04-08 19:53:08,544 tools.py:280 INFO Also considering installation prefix /work/projects/sw/resif/iris/default/local/software/EasyBuild/4.1.2 (determined via path to 'eb' script)... | |
| == 2020-04-08 19:53:08,545 easyblock.py:671 INFO Found file 3.7.0.tar.gz at /opt/apps/sources/a/arpack-ng/3.7.0.tar.gz | |
| == 2020-04-08 19:53:08,550 easyblock.py:394 INFO Added sources: [{'name': '3.7.0.tar.gz', 'path': '/opt/apps/sources/a/arpack-ng/3.7.0.tar.gz', 'cmd': None, 'checksum': '972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6', 'finalpath': '/dev/shm/arpackng/3.7.0/intel-2019b'}] | |
| == 2020-04-08 19:53:08,550 tools.py:266 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /work/projects/sw/resif/iris/default/local/software/EasyBuild/4.1.2/bin/eb | |
| == 2020-04-08 19:53:08,551 tools.py:280 INFO Also considering installation prefix /work/projects/sw/resif/iris/default/local/software/EasyBuild/4.1.2 (determined via path to 'eb' script)... | |
| == 2020-04-08 19:53:08,551 easyblock.py:671 INFO Found file arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch at /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch | |
| == 2020-04-08 19:53:08,551 easyblock.py:460 INFO Added patches: [{'name': 'arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch', 'path': '/tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch', 'checksum': '784c473c312560994f75c4222b42f704a3504d35367964a171d51e2d9350266f'}] | |
| == 2020-04-08 19:53:08,555 easyblock.py:1750 INFO md5 checksum for /opt/apps/sources/a/arpack-ng/3.7.0.tar.gz: 6fc6c6bf78dbd4f144595ef0675c8430 | |
| == 2020-04-08 19:53:08,560 easyblock.py:1750 INFO sha256 checksum for /opt/apps/sources/a/arpack-ng/3.7.0.tar.gz: 972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6 | |
| == 2020-04-08 19:53:08,560 easyblock.py:1750 INFO md5 checksum for /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch: 6ba4bc848d882145753e12183b30e607 | |
| == 2020-04-08 19:53:08,560 easyblock.py:1750 INFO sha256 checksum for /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch: 784c473c312560994f75c4222b42f704a3504d35367964a171d51e2d9350266f | |
| == 2020-04-08 19:53:08,560 easyblock.py:1785 INFO Checking dirs that need to be created: ['/work/projects/sw/resif/iris/default/local/software/arpack-ng/3.7.0-intel-2019b', '/work/projects/sw/resif/iris/default/local/modules/all/numlib/arpack-ng', '/work/projects/sw/resif/iris/default/local/modules/numlib/numlib/arpack-ng'] | |
| == 2020-04-08 19:53:08,561 configuremake.py:125 INFO Found recent config.guess at /work/projects/sw/resif/iris/default/local/sources/generic/eb_v4.1.1/ConfigureMake/config.guess, using it if required | |
| == 2020-04-08 19:53:08,561 build_log.py:265 INFO creating build dir, resetting environment... | |
| == 2020-04-08 19:53:08,561 easyblock.py:2857 INFO Starting ready step | |
| == 2020-04-08 19:53:08,561 easyblock.py:2863 INFO Running method check_readiness_step part of step ready | |
| == 2020-04-08 19:53:08,568 run.py:219 INFO running cmd: ulimit -u | |
| == 2020-04-08 19:53:08,575 easyblock.py:1609 INFO Setting parallelism: 28 | |
| == 2020-04-08 19:53:08,648 environment.py:97 INFO Environment variable LD_LIBRARY_PATH set to (previous value: '') | |
| == 2020-04-08 19:53:08,649 environment.py:97 INFO Environment variable LD_PRELOAD set to (previous value: '') | |
| == 2020-04-08 19:53:08,649 easyblock.py:1648 WARNING Loaded modules detected: ['tools/EasyBuild/4.1.2'] | |
| == 2020-04-08 19:53:08,649 easyblock.py:2863 INFO Running method make_builddir part of step ready | |
| == 2020-04-08 19:53:08,650 easyblock.py:928 INFO Found old directory /dev/shm/arpackng/3.7.0/intel-2019b | |
| == 2020-04-08 19:53:08,650 filetools.py:1392 INFO Path /dev/shm/arpackng/3.7.0/intel-2019b successfully removed. | |
| == 2020-04-08 19:53:08,650 easyblock.py:936 INFO Removed old directory /dev/shm/arpackng/3.7.0/intel-2019b | |
| == 2020-04-08 19:53:08,651 filetools.py:1296 INFO Creating directory /dev/shm/arpackng/3.7.0/intel-2019b (parents: True, set_gid: False, sticky: False) | |
| == 2020-04-08 19:53:08,651 easyblock.py:2863 INFO Running method reset_env part of step ready | |
| == 2020-04-08 19:53:08,652 easyblock.py:2863 INFO Running method handle_iterate_opts part of step ready | |
| == 2020-04-08 19:53:08,652 build_log.py:265 INFO starting iteration #0 ... | |
| == 2020-04-08 19:53:08,652 easyblock.py:1541 INFO Current iteration index: 0 | |
| == 2020-04-08 19:53:08,653 build_log.py:265 INFO unpacking... | |
| == 2020-04-08 19:53:08,653 easyblock.py:2857 INFO Starting source step | |
| == 2020-04-08 19:53:08,653 easyblock.py:2863 INFO Running method checksum_step part of step source | |
| == 2020-04-08 19:53:08,660 easyblock.py:1801 INFO Checksum verification for /opt/apps/sources/a/arpack-ng/3.7.0.tar.gz using 972e3fc3cd0b9d6b5a737c9bf6fd07515c0d6549319d4ffb06970e64fa3cc2d6 passed. | |
| == 2020-04-08 19:53:08,661 easyblock.py:1801 INFO Checksum verification for /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch using 784c473c312560994f75c4222b42f704a3504d35367964a171d51e2d9350266f passed. | |
| == 2020-04-08 19:53:08,661 easyblock.py:2863 INFO Running method extract_step part of step source | |
| == 2020-04-08 19:53:08,661 easyblock.py:1883 INFO Unpacking source 3.7.0.tar.gz | |
| == 2020-04-08 19:53:08,662 run.py:219 INFO running cmd: tar xzf /opt/apps/sources/a/arpack-ng/3.7.0.tar.gz | |
| == 2020-04-08 19:53:08,738 build_log.py:265 INFO patching... | |
| == 2020-04-08 19:53:08,738 easyblock.py:2857 INFO Starting patch step | |
| == 2020-04-08 19:53:08,739 easyblock.py:2863 INFO Running method patch_step part of step patch | |
| == 2020-04-08 19:53:08,739 easyblock.py:1895 INFO Applying patch arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch | |
| == 2020-04-08 19:53:08,740 run.py:219 INFO running cmd: patch -b -p1 -i /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch | |
| == 2020-04-08 19:53:08,755 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:124 in __init__): Couldn't apply patch file /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch. Process exited with code 2: patching file CMakeLists.txt | |
| patch: **** malformed patch at line 8: set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib) | |
| (at easybuild/tools/filetools.py:1073 in apply_patch) | |
| == 2020-04-08 19:53:08,758 easyblock.py:3109 WARNING build failed (first 300 chars): Couldn't apply patch file /tmp/eb-cmgp6bsg/files_pr10346/a/arpack-ng/arpack-ng-3.7.0-add_include_CheckSymbolExists_CMakeLists_txt.patch. Process exited with code 2: patching file CMakeLists.txt | |
| patch: **** malformed patch at line 8: set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib) | |
| == 2020-04-08 19:53:08,758 easyblock.py:295 INFO Closing log for application name arpack-ng version 3.7.0 |
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