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boegel/dorado-0.7.0-foss-2023a-CUDA-12.1.1_partial.log

Created May 22, 2024 17:39
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(partial) EasyBuild log for failed build of /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb (PR(s) #20596)
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dorado-0.7.0-foss-2023a-CUDA-12.1.1_partial.log
== 2024-05-22 19:39:24,314 easyblock.py:313 INFO This is EasyBuild 4.9.1.dev0 (framework: 4.9.1.dev0, easyblocks: 4.9.1.dev0) on host node3304.joltik.os.
== 2024-05-22 19:39:24,314 easyblock.py:319 INFO This is easyblock CMakeMake from module easybuild.easyblocks.generic.cmakemake (/data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyblocks-4.9.1.dev0-py3.6.egg/easybuild/easyblocks/generic/cmakemake.py)
== 2024-05-22 19:39:24,314 easyblock.py:1056 INFO Build dir set to /tmp/vsc40023/easybuild_build/dorado/0.7.0/foss-2023a-CUDA-12.1.1
== 2024-05-22 19:39:24,314 config.py:696 DEBUG software install path as specified by 'installpath' and 'subdir_software': /tmp/vsc40023/software
== 2024-05-22 19:39:24,314 easyconfig.py:2653 DEBUG Determining software installation subdir for dorado EasyConfig @ /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-22 19:39:24,314 easyconfig.py:2656 DEBUG Using fixed naming software installation subdir: dorado/0.7.0-foss-2023a-CUDA-12.1.1
== 2024-05-22 19:39:24,315 easyblock.py:1113 INFO Software install dir set to /tmp/vsc40023/software/dorado/0.7.0-foss-2023a-CUDA-12.1.1
== 2024-05-22 19:39:24,315 config.py:696 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /tmp/vsc40023/modules
== 2024-05-22 19:39:24,315 easyblock.py:1118 INFO Module install dir set to /tmp/vsc40023/modules/all
== 2024-05-22 19:39:24,315 easyblock.py:288 INFO Init completed for application name dorado version 0.7.0
== 2024-05-22 19:39:24,315 easyblock.py:4234 INFO Obtained application instance of for dorado (easyblock: CMakeMake)
== 2024-05-22 19:39:24,315 easyblock.py:4247 DEBUG Skip set to False
== 2024-05-22 19:39:24,315 easyconfig.py:1702 INFO Generating template values...
== 2024-05-22 19:39:24,315 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-22 19:39:24,315 templates.py:231 DEBUG version found in easyconfig is 0.7.0
== 2024-05-22 19:39:24,315 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-05-22 19:39:24,315 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-05-22 19:39:24,315 templates.py:333 DEBUG name: name, config: dorado
== 2024-05-22 19:39:24,315 templates.py:333 DEBUG name: parallel, config: None
== 2024-05-22 19:39:24,316 templates.py:333 DEBUG name: version, config: 0.7.0
== 2024-05-22 19:39:24,316 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-05-22 19:39:24,316 templates.py:333 DEBUG name: versionprefix, config:
== 2024-05-22 19:39:24,316 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-05-22 19:39:24,316 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-05-22 19:39:24,316 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', cuda_cc_cmake='70', cuda_cc_semicolon_sep='7.0', cuda_cc_space_sep='7.0', cuda_compute_capabilities='7.0', cuda_sm_comma_sep='sm_70', cuda_sm_space_sep='sm_70', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', module_name='dorado/0.7.0-foss-2023a-CUDA-12.1.1', mpi_cmd_prefix='mpirun -n 1', name='dorado', nameletter='d', nameletterlower='d', namelower='dorado', sysroot='', toolchain_name='foss', toolchain_version='2023a', version='0.7.0', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-05-22 19:39:24,316 one.py:150 DEBUG Not copying '__builtins__' variable from parsed easyconfig
== 2024-05-22 19:39:24,317 one.py:529 DEBUG Extracted comments:
{'above': {'preconfigopts': ["# don't link to OpenSSL static libraries",
'# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL '
'libraries are available)']},
'header': [],
'inline': {},
'iterabove': {'configopts': {'configopts += \'-DCMAKE_C_FLAGS="$CFLAGS -pthread" \'': ['# add -pthread flag (in '
'addition to -lpthread) to '
'avoid linking error:',
'# in function '
"`_GLOBAL__sub_I_mutex.cc': "
'mutex.cc:(.text.startup+0x17): '
'undefined reference to '
"`pthread_atfork'"]},
'preconfigopts': {'preconfigopts += "rm -r ../dorado/dorado/3rdparty/htslib/ && "': ["# don't use "
'vendored HTSlib, '
'use provided '
'HTSlib '
'dependency'],
'preconfigopts += "sed -i \'s/-Werror//g\' ../dorado/cmake/Warnings.cmake && "': ['# '
'disable '
'treating '
'warnings '
'like '
'errors '
'by '
'stripping '
'out '
'-Werror',
'# '
'cfr. '
'https://github.com/nanoporetech/dorado/issues/779'],
'preconfigopts += "sed -i \'s/OpenSSL::SSL/ssl\\\\n crypto/g\' ../dorado/dorado/utils/CMakeLists.txt && "': ['# '
'link '
'in '
'the '
'ssl '
'and '
'crypto '
'libs, '
'to '
'fix:',
'# '
'undefined '
'reference '
'to '
'symbol '
"'SSL_get_peer_certificate@@OPENSSL_1_1_0'"],
'preconfigopts += "sed -i \'s/htslib/hts/g\' ../dorado/CMakeLists.txt && "': ['# link '
'with '
'-lhts, '
'not '
'-lhtslib']}},
'iterinline': {},
'tail': []}
== 2024-05-22 19:39:24,317 one.py:180 INFO Skipping reformatting value for parameter 'toolchain'
== 2024-05-22 19:39:24,317 one.py:180 INFO Skipping reformatting value for parameter 'toolchainopts'
== 2024-05-22 19:39:24,319 easyconfig.py:1265 DEBUG Dumped easyconfig: easyblock = 'CMakeMake'
name = 'dorado'
version = '0.7.0'
versionsuffix = '-CUDA-%(cudaver)s'
homepage = 'https://github.com/nanoporetech/dorado'
description = "Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads."
toolchain = {'name': 'foss', 'version': '2023a'}
toolchainopts = {'usempi': True}
source_urls = ['https://github.com/nanoporetech/%(name)s/archive/']
sources = [
{'git_config': {'url': 'https://github.com/nanoporetech', 'repo_name': '%(name)s', 'tag': 'v%(version)s', 'recursive': True}, 'filename': SOURCE_TAR_GZ},
]
patches = ['%(name)s-0.6.1_include-fstream.patch']
checksums = [
None,
'a7692a2d67422d808b3b81f3a297b7b89299ab0091e5d01f0b8a9aee9b942377',
]
builddependencies = [
('binutils', '2.40', '', ('GCCcore', '12.3.0')),
('CMake', '3.26.3', '', ('GCCcore', '12.3.0')),
]
dependencies = [
('CUDA', '12.1.1', '', SYSTEM),
('OpenSSL', '1.1', '', SYSTEM),
('PyTorch', '2.1.2', '-CUDA-%(cudaver)s'),
('HDF5', '1.14.0', '', ('gompi', '2023a')),
('zstd', '1.5.5', '', ('GCCcore', '12.3.0')),
('HTSlib', '1.18', '', ('GCC', '12.3.0')),
('kineto', '0.4.0', '', ('GCC', '12.3.0')),
('libaec', '1.0.6', '', ('GCCcore', '12.3.0')),
]
# don't link to OpenSSL static libraries
# fix for CMake Error "missing: OPENSSL_CRYPTO_LIBRARY" (if only shared OpenSSL libraries are available)
preconfigopts = "sed -i '/OPENSSL_USE_STATIC_LIBS TRUE/d' ../%(name)s/cmake/OpenSSL.cmake && export OPENSSL_ROOT_DIR=$EBROOTOPENSSL && sed -i 's/OpenSSL::SSL/ssl\\n crypto/g' ../%(name)s/%(name)s/utils/CMakeLists.txt && rm -r ../%(name)s/%(name)s/3rdparty/htslib/ && sed -i '/add_dependencies.*htslib_project/d' ../%(name)s/CMakeLists.txt && sed -i '/add_dependencies.*htslib_project/d' ../%(name)s/%(name)s/utils/CMakeLists.txt && sed -i '/Htslib.cmake/d' ../%(name)s/CMakeLists.txt && sed -i 's/htslib/hts/g' ../%(name)s/CMakeLists.txt && sed -i 's/htslib/hts/g' ../%(name)s/%(name)s/utils/CMakeLists.txt && sed -i 's/-Werror//g' ../%(name)s/cmake/Warnings.cmake && "
configopts = '-DDORADO_INSTALL_PATH=%(installdir)s -DCUDA_TOOLKIT_ROOT_DIR=$EBROOTCUDA -DCMAKE_CUDA_COMPILER=$EBROOTCUDA/bin/nvcc -DDORADO_LIBTORCH_DIR=$EBROOTPYTORCH/lib -DCMAKE_C_FLAGS="$CFLAGS -pthread" '
sanity_check_paths = {
'files': ['bin/%(name)s'],
'dirs': [],
}
sanity_check_commands = ['%(name)s basecaller --help']
moduleclass = 'bio'
== 2024-05-22 19:39:24,319 filetools.py:1911 INFO Creating directory /tmp/eb-3yv25ait/reprod_20240522193924_2494183 (parents: True, set_gid: False, sticky: False)
== 2024-05-22 19:39:24,319 easyblock.py:4488 INFO Dumped easyconfig instance to /tmp/eb-3yv25ait/reprod_20240522193924_2494183/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-22 19:39:24,321 filetools.py:1911 INFO Creating directory /tmp/eb-3yv25ait/reprod_20240522193924_2494183/easyblocks (parents: True, set_gid: False, sticky: False)
== 2024-05-22 19:39:24,334 filetools.py:2424 INFO /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyblocks-4.9.1.dev0-py3.6.egg/easybuild/easyblocks/generic/configuremake.py copied to /tmp/eb-3yv25ait/reprod_20240522193924_2494183/easyblocks/configuremake.py
== 2024-05-22 19:39:24,334 easyblock.py:4468 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-3yv25ait/reprod_20240522193924_2494183/easyblocks
== 2024-05-22 19:39:24,334 filetools.py:1930 DEBUG Not creating existing path /tmp/eb-3yv25ait/reprod_20240522193924_2494183/easyblocks
== 2024-05-22 19:39:24,345 filetools.py:2424 INFO /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyblocks-4.9.1.dev0-py3.6.egg/easybuild/easyblocks/generic/cmakemake.py copied to /tmp/eb-3yv25ait/reprod_20240522193924_2494183/easyblocks/cmakemake.py
== 2024-05-22 19:39:24,345 easyblock.py:4468 INFO Dumped easyblock cmakemake.py required for reproduction to /tmp/eb-3yv25ait/reprod_20240522193924_2494183/easyblocks
== 2024-05-22 19:39:24,348 filetools.py:1911 INFO Creating directory /tmp/eb-3yv25ait/reprod_20240522193924_2494183/hooks (parents: True, set_gid: False, sticky: False)
== 2024-05-22 19:39:24,363 filetools.py:2424 INFO /data/gent/400/vsc40023/eb_hooks.py copied to /tmp/eb-3yv25ait/reprod_20240522193924_2494183/hooks/eb_hooks.py
== 2024-05-22 19:39:24,363 easyblock.py:4500 INFO Dumped hooks file /data/gent/400/vsc40023/eb_hooks.py which is (potentially) required for reproduction to /tmp/eb-3yv25ait/reprod_20240522193924_2494183/hooks/eb_hooks.py
== 2024-05-22 19:39:24,363 easyblock.py:2239 INFO Number of iterations to perform for central part of installation procedure: 1
== 2024-05-22 19:39:24,363 build_log.py:267 INFO building and installing dorado/0.7.0-foss-2023a-CUDA-12.1.1...
== 2024-05-22 19:39:24,367 config.py:696 DEBUG software install path as specified by 'installpath' and 'subdir_software': /tmp/vsc40023/software
== 2024-05-22 19:39:24,368 filetools.py:2004 INFO Lock /tmp/vsc40023/software/.locks/_tmp_vsc40023_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock does not exist
== 2024-05-22 19:39:24,368 config.py:696 DEBUG software install path as specified by 'installpath' and 'subdir_software': /tmp/vsc40023/software
== 2024-05-22 19:39:24,368 filetools.py:1945 INFO Creating lock at /tmp/vsc40023/software/.locks/_tmp_vsc40023_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock...
== 2024-05-22 19:39:24,368 filetools.py:1911 INFO Creating directory /tmp/vsc40023/software/.locks/_tmp_vsc40023_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock (parents: True, set_gid: False, sticky: False)
== 2024-05-22 19:39:24,368 filetools.py:1954 INFO Lock created: /tmp/vsc40023/software/.locks/_tmp_vsc40023_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock
== 2024-05-22 19:39:24,368 easyblock.py:3948 DEBUG Not skipping fetch step (skippable: False, skip: None, skipsteps: [], module_only: False, force: True, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-05-22 19:39:24,368 build_log.py:267 INFO fetching files...
== 2024-05-22 19:39:24,370 easyblock.py:3956 INFO Starting fetch step
== 2024-05-22 19:39:24,370 easyconfig.py:1702 INFO Generating template values...
== 2024-05-22 19:39:24,370 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-22 19:39:24,370 templates.py:231 DEBUG version found in easyconfig is 0.7.0
== 2024-05-22 19:39:24,370 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-05-22 19:39:24,370 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-05-22 19:39:24,370 templates.py:333 DEBUG name: name, config: dorado
== 2024-05-22 19:39:24,371 templates.py:333 DEBUG name: parallel, config: None
== 2024-05-22 19:39:24,371 templates.py:333 DEBUG name: version, config: 0.7.0
== 2024-05-22 19:39:24,371 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-05-22 19:39:24,371 templates.py:333 DEBUG name: versionprefix, config:
== 2024-05-22 19:39:24,371 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-05-22 19:39:24,371 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-05-22 19:39:24,371 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/tmp/vsc40023/easybuild_build/dorado/0.7.0/foss-2023a-CUDA-12.1.1', cuda_cc_cmake='70', cuda_cc_semicolon_sep='7.0', cuda_cc_space_sep='7.0', cuda_compute_capabilities='7.0', cuda_sm_comma_sep='sm_70', cuda_sm_space_sep='sm_70', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', installdir='/tmp/vsc40023/software/dorado/0.7.0-foss-2023a-CUDA-12.1.1', module_name='dorado/0.7.0-foss-2023a-CUDA-12.1.1', mpi_cmd_prefix='mpirun -n 1', name='dorado', nameletter='d', nameletterlower='d', namelower='dorado', start_dir='None', sysroot='', toolchain_name='foss', toolchain_version='2023a', version='0.7.0', version_major='0', version_major_minor='0.7', version_minor='7', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-05-22 19:39:24,371 easyblock.py:3964 INFO Running method fetch_step part of step fetch
== 2024-05-22 19:39:24,371 easyblock.py:2361 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2024-05-22 19:39:24,371 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /tmp/eb-3yv25ait/files_pr20596/d/dorado
== 2024-05-22 19:39:24,372 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /data/gent/400/vsc40023/easybuild_easy_installed/bin/eb
== 2024-05-22 19:39:24,372 tools.py:289 INFO Not considering /data/gent/400/vsc40023/easybuild_easy_installed (no easybuild/easyconfigs subdir found)
== 2024-05-22 19:39:24,372 tools.py:297 INFO Also considering installation prefix /kyukon/data/gent/vo/000/gvo00002/vsc40023/easybuild_easy_installed (via resolved path to 'eb')...
== 2024-05-22 19:39:24,372 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-22 19:39:24,372 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-3yv25ait/files_pr20596/easybuild/easyconfigs
== 2024-05-22 19:39:24,373 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-3yv25ait/fake_vsc_jt_ltmy8/easybuild/easyconfigs
== 2024-05-22 19:39:24,373 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-05-22 19:39:24,374 tools.py:302 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-05-22 19:39:24,376 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,376 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/python-dateutil/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,377 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/keyring/lib/python2.7/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,377 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,377 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /kyukon/home/gent/400/vsc40023/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/keyring/lib/python2.7/site-packages/pep8-1.7.1-py2.7.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/pip-20.2b1-py2.7.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_framework-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyblocks-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:306 DEBUG Added /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/lib-dynload/easybuild/easyconfigs
== 2024-05-22 19:39:24,378 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,379 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,379 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/python-dateutil/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,379 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-05-22 19:39:24,379 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /kyukon/data/gent/vo/000/gvo00002/vsc40023/easybuild_easy_installed/easybuild/easyconfigs
== 2024-05-22 19:39:24,387 easyblock.py:881 WARNING Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /tmp/eb-3yv25ait/files_pr20596/d/dorado/d/dorado/checksums.json, /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado/checksums.json, /tmp/eb-3yv25ait/files_pr20596/d/dorado/checksums.json, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/d/dorado/checksums.json, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/dorado/checksums.json, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/checksums.json, /tmp/eb-3yv25ait/files_pr20596/d/dorado/checksums.json, /tmp/eb-3yv25ait/files_pr20596/dorado/checksums.json, /tmp/eb-3yv25ait/files_pr20596/checksums.json, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/d/dorado/checksums.json, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/dorado/checksums.json, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/checksums.json, /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/checksums.json, /data/gent/400/vsc40023/EasyBuild/sources/dorado/checksums.json, /data/gent/400/vsc40023/EasyBuild/sources/checksums.json, /apps/gent/source/d/dorado/checksums.json, /apps/gent/source/dorado/checksums.json, /apps/gent/source/checksums.json
== 2024-05-22 19:39:24,387 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for dorado-0.7.0.tar.gz: /tmp/eb-3yv25ait/files_pr20596/d/dorado
== 2024-05-22 19:39:24,387 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /data/gent/400/vsc40023/easybuild_easy_installed/bin/eb
== 2024-05-22 19:39:24,387 tools.py:289 INFO Not considering /data/gent/400/vsc40023/easybuild_easy_installed (no easybuild/easyconfigs subdir found)
== 2024-05-22 19:39:24,387 tools.py:297 INFO Also considering installation prefix /kyukon/data/gent/vo/000/gvo00002/vsc40023/easybuild_easy_installed (via resolved path to 'eb')...
== 2024-05-22 19:39:24,387 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-22 19:39:24,387 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-3yv25ait/files_pr20596/easybuild/easyconfigs
== 2024-05-22 19:39:24,387 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-3yv25ait/fake_vsc_jt_ltmy8/easybuild/easyconfigs
== 2024-05-22 19:39:24,387 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/python-dateutil/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/keyring/lib/python2.7/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /kyukon/home/gent/400/vsc40023/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/keyring/lib/python2.7/site-packages/pep8-1.7.1-py2.7.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/pip-20.2b1-py2.7.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_framework-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyblocks-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:306 DEBUG Added /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
== 2024-05-22 19:39:24,388 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/lib-dynload/easybuild/easyconfigs
== 2024-05-22 19:39:24,389 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,389 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,389 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/python-dateutil/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,389 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-05-22 19:39:24,389 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /kyukon/data/gent/vo/000/gvo00002/vsc40023/easybuild_easy_installed/easybuild/easyconfigs
== 2024-05-22 19:39:24,389 easyblock.py:851 INFO Found file dorado-0.7.0.tar.gz at /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.7.0.tar.gz
== 2024-05-22 19:39:24,389 easyblock.py:452 DEBUG File /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.7.0.tar.gz found for source dorado-0.7.0.tar.gz
== 2024-05-22 19:39:24,389 easyblock.py:496 INFO Added sources: [{'name': 'dorado-0.7.0.tar.gz', 'path': '/data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.7.0.tar.gz', 'cmd': None, 'checksum': None, 'finalpath': '/tmp/vsc40023/easybuild_build/dorado/0.7.0/foss-2023a-CUDA-12.1.1'}]
== 2024-05-22 19:39:24,390 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for dorado-0.6.1_include-fstream.patch: /tmp/eb-3yv25ait/files_pr20596/d/dorado
== 2024-05-22 19:39:24,390 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /data/gent/400/vsc40023/easybuild_easy_installed/bin/eb
== 2024-05-22 19:39:24,390 tools.py:289 INFO Not considering /data/gent/400/vsc40023/easybuild_easy_installed (no easybuild/easyconfigs subdir found)
== 2024-05-22 19:39:24,390 tools.py:297 INFO Also considering installation prefix /kyukon/data/gent/vo/000/gvo00002/vsc40023/easybuild_easy_installed (via resolved path to 'eb')...
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-3yv25ait/files_pr20596/easybuild/easyconfigs
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-3yv25ait/fake_vsc_jt_ltmy8/easybuild/easyconfigs
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/python-dateutil/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,390 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/keyring/lib/python2.7/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /kyukon/home/gent/400/vsc40023/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/keyring/lib/python2.7/site-packages/pep8-1.7.1-py2.7.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/pip-20.2b1-py2.7.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_framework-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyblocks-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:306 DEBUG Added /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/lib-dynload/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/.local/python-dateutil/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /user/gent/400/vsc40023/py3/lib/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-05-22 19:39:24,391 tools.py:302 DEBUG Checking for easybuild/easyconfigs at /kyukon/data/gent/vo/000/gvo00002/vsc40023/easybuild_easy_installed/easybuild/easyconfigs
== 2024-05-22 19:39:24,392 filetools.py:1930 DEBUG Not creating existing path /data/gent/400/vsc40023/EasyBuild/sources/d/dorado
== 2024-05-22 19:39:24,392 easyblock.py:938 DEBUG Trying to download file dorado-0.6.1_include-fstream.patch from https://github.com/nanoporetech/dorado/archive/dorado-0.6.1_include-fstream.patch to /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.6.1_include-fstream.patch ...
== 2024-05-22 19:39:24,392 filetools.py:752 DEBUG Trying to download dorado-0.6.1_include-fstream.patch from https://github.com/nanoporetech/dorado/archive/dorado-0.6.1_include-fstream.patch to /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.6.1_include-fstream.patch
== 2024-05-22 19:39:24,392 filetools.py:755 DEBUG Using timeout of 10 seconds for initiating download
== 2024-05-22 19:39:24,392 filetools.py:1930 DEBUG Not creating existing path /data/gent/400/vsc40023/EasyBuild/sources/d/dorado
== 2024-05-22 19:39:24,558 filetools.py:832 WARNING URL https://github.com/nanoporetech/dorado/archive/dorado-0.6.1_include-fstream.patch was not found (HTTP response code 404), not trying again
== 2024-05-22 19:39:24,559 filetools.py:859 WARNING Download of https://github.com/nanoporetech/dorado/archive/dorado-0.6.1_include-fstream.patch to /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.6.1_include-fstream.patch failed, done trying
== 2024-05-22 19:39:24,565 easyblock.py:938 DEBUG Trying to download file dorado-0.6.1_include-fstream.patch from https://sources.easybuild.io/d/dorado/dorado-0.6.1_include-fstream.patch to /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.6.1_include-fstream.patch ...
== 2024-05-22 19:39:24,565 filetools.py:752 DEBUG Trying to download dorado-0.6.1_include-fstream.patch from https://sources.easybuild.io/d/dorado/dorado-0.6.1_include-fstream.patch to /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.6.1_include-fstream.patch
== 2024-05-22 19:39:24,565 filetools.py:755 DEBUG Using timeout of 10 seconds for initiating download
== 2024-05-22 19:39:24,565 filetools.py:1930 DEBUG Not creating existing path /data/gent/400/vsc40023/EasyBuild/sources/d/dorado
== 2024-05-22 19:39:24,639 filetools.py:832 WARNING URL https://sources.easybuild.io/d/dorado/dorado-0.6.1_include-fstream.patch was not found (HTTP response code 404), not trying again
== 2024-05-22 19:39:24,640 filetools.py:859 WARNING Download of https://sources.easybuild.io/d/dorado/dorado-0.6.1_include-fstream.patch to /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.6.1_include-fstream.patch failed, done trying
== 2024-05-22 19:39:24,919 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): Couldn't find file dorado-0.6.1_include-fstream.patch anywhere, and downloading it didn't work either... Paths attempted (in order): /tmp/eb-3yv25ait/files_pr20596/d/dorado/d/dorado/dorado-0.6.1_include-fstream.patch, /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado/dorado-0.6.1_include-fstream.patch, /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/dorado/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/dorado-0.6.1_include-fstream.patch, /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado-0.6.1_include-fstream.patch, /tmp/eb-3yv25ait/files_pr20596/dorado/dorado-0.6.1_include-fstream.patch, /tmp/eb-3yv25ait/files_pr20596/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/d/dorado/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/dorado/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/easybuild_easy_installed/lib/python3.6/site-packages/easybuild_easyconfigs-4.9.1.dev0-py3.6.egg/easybuild/easyconfigs/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/EasyBuild/sources/d/dorado/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/EasyBuild/sources/dorado/dorado-0.6.1_include-fstream.patch, /data/gent/400/vsc40023/EasyBuild/sources/dorado-0.6.1_include-fstream.patch, /apps/gent/source/d/dorado/dorado-0.6.1_include-fstream.patch, /apps/gent/source/dorado/dorado-0.6.1_include-fstream.patch, /apps/gent/source/dorado-0.6.1_include-fstream.patch, https://github.com/nanoporetech/dorado/archive/dorado-0.6.1_include-fstream.patch, https://sources.easybuild.io/d/dorado/dorado-0.6.1_include-fstream.patch (at easybuild/framework/easyblock.py:975 in obtain_file)
== 2024-05-22 19:39:24,919 build_log.py:267 INFO ... (took < 1 sec)
== 2024-05-22 19:39:24,922 config.py:696 DEBUG software install path as specified by 'installpath' and 'subdir_software': /tmp/vsc40023/software
== 2024-05-22 19:39:24,922 filetools.py:2012 INFO Removing lock /tmp/vsc40023/software/.locks/_tmp_vsc40023_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock...
== 2024-05-22 19:39:24,922 filetools.py:383 INFO Path /tmp/vsc40023/software/.locks/_tmp_vsc40023_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock successfully removed.
== 2024-05-22 19:39:24,922 filetools.py:2016 INFO Lock removed: /tmp/vsc40023/software/.locks/_tmp_vsc40023_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock
== 2024-05-22 19:39:24,923 easyblock.py:4291 WARNING build failed (first 300 chars): Couldn't find file dorado-0.6.1_include-fstream.patch anywhere, and downloading it didn't work either... Paths attempted (in order): /tmp/eb-3yv25ait/files_pr20596/d/dorado/d/dorado/dorado-0.6.1_include-fstream.patch, /tmp/eb-3yv25ait/files_pr20596/d/dorado/dorado/dorado-0.6.1_include-fstream.patch,
== 2024-05-22 19:39:24,923 easyblock.py:328 INFO Closing log for application name dorado version 0.7.0
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