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Created May 24, 2024 15:01
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(partial) EasyBuild log for failed build of /tmp/eb-y8dej94k/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
== 2024-05-24 15:00:28,962 easyblock.py:313 INFO This is EasyBuild 4.9.1 (framework: 4.9.1, easyblocks: 4.9.1) on host easybuild-c7.novalocal.
== 2024-05-24 15:00:28,962 easyblock.py:319 INFO This is easyblock CMakeMake from module easybuild.easyblocks.generic.cmakemake (/eb/maint/software/EasyBuild/4.9.1/lib/python3.6/site-packages/easybuild/easyblocks/generic/cmakemake.py)
== 2024-05-24 15:00:28,962 easyblock.py:1056 INFO Build dir set to /dev/shm/dorado/0.7.0/foss-2023a-CUDA-12.1.1
== 2024-05-24 15:00:28,962 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 15:00:28,963 easyconfig.py:2653 DEBUG Determining software installation subdir for dorado EasyConfig @ /tmp/eb-y8dej94k/files_pr20596/d/dorado/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 15:00:28,963 easyconfig.py:2656 DEBUG Using fixed naming software installation subdir: dorado/0.7.0-foss-2023a-CUDA-12.1.1
== 2024-05-24 15:00:28,963 easyblock.py:1113 INFO Software install dir set to /eb/maint/software/dorado/0.7.0-foss-2023a-CUDA-12.1.1
== 2024-05-24 15:00:28,963 config.py:699 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /eb/maint/modules
== 2024-05-24 15:00:28,963 easyblock.py:1118 INFO Module install dir set to /eb/maint/modules/all
== 2024-05-24 15:00:28,963 easyblock.py:288 INFO Init completed for application name dorado version 0.7.0
== 2024-05-24 15:00:28,963 easyblock.py:4234 INFO Obtained application instance of for dorado (easyblock: CMakeMake)
== 2024-05-24 15:00:28,963 easyblock.py:4247 DEBUG Skip set to False
== 2024-05-24 15:00:28,963 easyconfig.py:1702 INFO Generating template values...
== 2024-05-24 15:00:28,963 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-y8dej94k/files_pr20596/d/dorado/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 15:00:28,963 templates.py:231 DEBUG version found in easyconfig is 0.7.0
== 2024-05-24 15:00:28,963 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-05-24 15:00:28,964 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-05-24 15:00:28,964 templates.py:333 DEBUG name: name, config: dorado
== 2024-05-24 15:00:28,964 templates.py:333 DEBUG name: parallel, config: None
== 2024-05-24 15:00:28,964 templates.py:333 DEBUG name: version, config: 0.7.0
== 2024-05-24 15:00:28,964 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-05-24 15:00:28,964 templates.py:333 DEBUG name: versionprefix, config:
== 2024-05-24 15:00:28,964 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-05-24 15:00:28,964 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-05-24 15:00:28,964 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', 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'
== 2024-05-24 15:00:28,964 one.py:150 DEBUG Not copying '__builtins__' variable from parsed easyconfig
== 2024-05-24 15:00:28,965 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': []}
== 2024-05-24 15:00:28,966 one.py:180 INFO Skipping reformatting value for parameter 'toolchain'
== 2024-05-24 15:00:28,966 one.py:180 INFO Skipping reformatting value for parameter 'toolchainopts'
== 2024-05-24 15:00:28,967 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'
== 2024-05-24 15:00:28,967 filetools.py:1912 INFO Creating directory /tmp/eb-y8dej94k/reprod_20240524150028_9046 (parents: True, set_gid: False, sticky: False)
== 2024-05-24 15:00:28,967 easyblock.py:4488 INFO Dumped easyconfig instance to /tmp/eb-y8dej94k/reprod_20240524150028_9046/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 15:00:28,967 filetools.py:1912 INFO Creating directory /tmp/eb-y8dej94k/reprod_20240524150028_9046/easyblocks (parents: True, set_gid: False, sticky: False)
== 2024-05-24 15:00:28,968 filetools.py:2425 INFO /eb/maint/software/EasyBuild/4.9.1/lib/python3.6/site-packages/easybuild/easyblocks/generic/configuremake.py copied to /tmp/eb-y8dej94k/reprod_20240524150028_9046/easyblocks/configuremake.py
== 2024-05-24 15:00:28,968 easyblock.py:4468 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-y8dej94k/reprod_20240524150028_9046/easyblocks
== 2024-05-24 15:00:28,968 filetools.py:1931 DEBUG Not creating existing path /tmp/eb-y8dej94k/reprod_20240524150028_9046/easyblocks
== 2024-05-24 15:00:28,969 filetools.py:2425 INFO /eb/maint/software/EasyBuild/4.9.1/lib/python3.6/site-packages/easybuild/easyblocks/generic/cmakemake.py copied to /tmp/eb-y8dej94k/reprod_20240524150028_9046/easyblocks/cmakemake.py
== 2024-05-24 15:00:28,969 easyblock.py:4468 INFO Dumped easyblock cmakemake.py required for reproduction to /tmp/eb-y8dej94k/reprod_20240524150028_9046/easyblocks
== 2024-05-24 15:00:28,969 easyblock.py:2239 INFO Number of iterations to perform for central part of installation procedure: 1
== 2024-05-24 15:00:28,969 build_log.py:267 INFO building and installing dorado/0.7.0-foss-2023a-CUDA-12.1.1...
== 2024-05-24 15:00:28,974 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 15:00:28,974 filetools.py:2005 INFO Lock /eb/maint/software/.locks/_eb_maint_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock does not exist
== 2024-05-24 15:00:28,974 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 15:00:28,974 filetools.py:1946 INFO Creating lock at /eb/maint/software/.locks/_eb_maint_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock...
== 2024-05-24 15:00:28,974 filetools.py:1912 INFO Creating directory /eb/maint/software/.locks/_eb_maint_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock (parents: True, set_gid: False, sticky: False)
== 2024-05-24 15:00:28,974 filetools.py:1955 INFO Lock created: /eb/maint/software/.locks/_eb_maint_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock
== 2024-05-24 15:00:28,975 easyblock.py:3948 DEBUG Not skipping fetch step (skippable: False, skip: None, skipsteps: [], module_only: False, force: False, sanity_check_only: False, skip_extensions: False, skip_test_step: False)
== 2024-05-24 15:00:28,975 build_log.py:267 INFO fetching files...
== 2024-05-24 15:00:28,977 easyblock.py:3956 INFO Starting fetch step
== 2024-05-24 15:00:28,977 easyconfig.py:1702 INFO Generating template values...
== 2024-05-24 15:00:28,977 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-y8dej94k/files_pr20596/d/dorado/dorado-0.7.0-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 15:00:28,977 templates.py:231 DEBUG version found in easyconfig is 0.7.0
== 2024-05-24 15:00:28,977 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-05-24 15:00:28,977 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-05-24 15:00:28,977 templates.py:333 DEBUG name: name, config: dorado
== 2024-05-24 15:00:28,977 templates.py:333 DEBUG name: parallel, config: None
== 2024-05-24 15:00:28,977 templates.py:333 DEBUG name: version, config: 0.7.0
== 2024-05-24 15:00:28,977 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-05-24 15:00:28,977 templates.py:333 DEBUG name: versionprefix, config:
== 2024-05-24 15:00:28,977 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-05-24 15:00:28,977 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'})
== 2024-05-24 15:00:28,977 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/dev/shm/dorado/0.7.0/foss-2023a-CUDA-12.1.1', cudamajver='12', cudaminver='1', cudashortver='12.1', cudaver='12.1.1', github_account='dorado', installdir='/eb/maint/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'
== 2024-05-24 15:00:28,978 easyblock.py:3964 INFO Running method fetch_step part of step fetch
== 2024-05-24 15:00:28,978 easyblock.py:2361 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2024-05-24 15:00:28,978 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /tmp/eb-y8dej94k/files_pr20596/d/dorado
== 2024-05-24 15:00:28,978 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /eb/maint/software/EasyBuild/4.9.1/bin/eb
== 2024-05-24 15:00:28,978 tools.py:288 INFO Also considering installation prefix /eb/maint/software/EasyBuild/4.9.1 (determined via path to 'eb' script)...
== 2024-05-24 15:00:28,978 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/easybuild/local/easybuild/easyconfigs
== 2024-05-24 15:00:28,978 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/local/easybuild/easyconfigs
== 2024-05-24 15:00:28,978 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 15:00:28,978 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 15:00:28,978 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-y8dej94k/files_pr20596/easybuild/easyconfigs
== 2024-05-24 15:00:28,978 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-y8dej94k/fake_vsc_6n21j78x/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/lib-dynload/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/.local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs
== 2024-05-24 15:00:28,979 tools.py:307 DEBUG Added /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-05-24 15:00:28,980 easyblock.py:881 WARNING Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /tmp/eb-y8dej94k/files_pr20596/d/dorado/d/dorado/checksums.json, /tmp/eb-y8dej94k/files_pr20596/d/dorado/dorado/checksums.json, /tmp/eb-y8dej94k/files_pr20596/d/dorado/checksums.json, /home/software/src/easybuild/local/d/dorado/checksums.json, /home/software/src/easybuild/local/dorado/checksums.json, /home/software/src/easybuild/local/checksums.json, /eb/maint/local/d/dorado/checksums.json, /eb/maint/local/dorado/checksums.json, /eb/maint/local/checksums.json, /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/d/dorado/checksums.json, /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/dorado/checksums.json, /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/checksums.json, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/d/dorado/checksums.json, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/dorado/checksums.json, /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /tmp/eb-y8dej94k/files_pr20596/d/dorado/checksums.json, /tmp/eb-y8dej94k/files_pr20596/dorado/checksums.json, /tmp/eb-y8dej94k/files_pr20596/checksums.json, /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/d/dorado/checksums.json, /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/dorado/checksums.json, /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/checksums.json, /eb/maint/sources/d/dorado/checksums.json, /eb/maint/sources/dorado/checksums.json, /eb/maint/sources/checksums.json
== 2024-05-24 15:00:28,980 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for dorado-0.7.0.tar.gz: /tmp/eb-y8dej94k/files_pr20596/d/dorado
== 2024-05-24 15:00:28,980 tools.py:274 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /eb/maint/software/EasyBuild/4.9.1/bin/eb
== 2024-05-24 15:00:28,980 tools.py:288 INFO Also considering installation prefix /eb/maint/software/EasyBuild/4.9.1 (determined via path to 'eb' script)...
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/easybuild/local/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/local/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-y8dej94k/files_pr20596/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-y8dej94k/fake_vsc_6n21j78x/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-05-24 15:00:28,980 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/lib-dynload/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/.local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs
== 2024-05-24 15:00:28,981 tools.py:307 DEBUG Added /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-05-24 15:00:28,981 filetools.py:1931 DEBUG Not creating existing path /eb/maint/sources/d/dorado
== 2024-05-24 15:00:28,982 run.py:180 DEBUG run_cmd: Output of "git clone --depth 1 --branch v0.7.0 --recursive https://github.com/nanoporetech/dorado.git" will be logged to /tmp/eb-y8dej94k/easybuild-run_cmd-nwwz7wxj.log
== 2024-05-24 15:00:28,985 run.py:221 DEBUG run_cmd: running cmd git clone --depth 1 --branch v0.7.0 --recursive https://github.com/nanoporetech/dorado.git (in /tmp/eb-y8dej94k/tmpgi2c8o8p)
== 2024-05-24 15:00:28,985 run.py:247 INFO running cmd: git clone --depth 1 --branch v0.7.0 --recursive https://github.com/nanoporetech/dorado.git
== 2024-05-24 15:01:07,875 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): cmd "git clone --depth 1 --branch v0.7.0 --recursive https://github.com/nanoporetech/dorado.git" exited with exit code 1 and output:
Cloning into 'dorado'...
Note: checking out '71cc74429f0daa43f1ca32b203b2af569b1e6386'.
You are in 'detached HEAD' state. You can look around, make experimental
changes and commit them, and you can discard any commits you make in this
state without impacting any branches by performing another checkout.
If you want to create a new branch to retain commits you create, you may
do so (now or later) by using -b with the checkout command again. Example:
git checkout -b new_branch_name
Submodule 'cmake/ios-cmake' (https://github.com/leetal/ios-cmake.git) registered for path 'cmake/ios-cmake'
Submodule 'dorado/3rdparty/HighFive' (https://github.com/BlueBrain/HighFive.git) registered for path 'dorado/3rdparty/HighFive'
Submodule 'dorado/3rdparty/NVTX' (https://github.com/NVIDIA/NVTX.git) registered for path 'dorado/3rdparty/NVTX'
Submodule 'dorado/3rdparty/cpp-httplib' (https://github.com/yhirose/cpp-httplib.git) registered for path 'dorado/3rdparty/cpp-httplib'
Submodule 'dorado/3rdparty/cxxpool' (https://github.com/bloomen/cxxpool.git) registered for path 'dorado/3rdparty/cxxpool'
Submodule 'dorado/3rdparty/date' (https://github.com/HowardHinnant/date.git) registered for path 'dorado/3rdparty/date'
Submodule 'dorado/3rdparty/edlib' (https://github.com/martinsos/edlib) registered for path 'dorado/3rdparty/edlib'
Submodule 'dorado/3rdparty/11Zip' (https://github.com/Sygmei/11Zip.git) registered for path 'dorado/3rdparty/elzip'
Submodule 'dorado/3rdparty/hdf_plugins' (https://github.com/nanoporetech/vbz_compression.git) registered for path 'dorado/3rdparty/hdf_plugins'
Submodule 'dorado/3rdparty/htslib' (https://github.com/samtools/htslib.git) registered for path 'dorado/3rdparty/htslib'
Submodule 'dorado/3rdparty/indicators' (https://github.com/p-ranav/indicators.git) registered for path 'dorado/3rdparty/indicators'
Submodule 'dorado/3rdparty/ont-minimap2' (https://github.com/nanoporetech/ont-minimap2.git) registered for path 'dorado/3rdparty/ont-minimap2'
Submodule 'dorado/3rdparty/spdlog' (https://github.com/gabime/spdlog) registered for path 'dorado/3rdparty/spdlog'
Submodule 'dorado/3rdparty/toml11' (https://github.com/ToruNiina/toml11.git) registered for path 'dorado/3rdparty/toml11'
Submodule 'dorado/3rdparty/zstd' (https://github.com/facebook/zstd.git) registered for path 'dorado/3rdparty/zstd'
Cloning into 'cmake/ios-cmake'...
Submodule path 'cmake/ios-cmake': checked out '04d91f6675dabb3c97df346a32f6184b0a7ef845'
Cloning into 'dorado/3rdparty/HighFive'...
Submodule path 'dorado/3rdparty/HighFive': checked out 'c59464737afb8cc8d0042d2d9e495967860797d1'
Submodule 'deps/catch2' (https://github.com/catchorg/Catch2.git) registered for path 'deps/catch2'
Cloning into 'deps/catch2'...
Submodule path 'dorado/3rdparty/HighFive/deps/catch2': checked out '216713a4066b79d9803d374f261ccb30c0fb451f'
Cloning into 'dorado/3rdparty/NVTX'...
Submodule path 'dorado/3rdparty/NVTX': checked out '61372b7a4cf1da41e9df4a1cb5a7a6e2c62113a8'
Cloning into 'dorado/3rdparty/cpp-httplib'...
Submodule path 'dorado/3rdparty/cpp-httplib': checked out 'c7ed1796a778592ae5a122287a16b1dd4770858a'
Cloning into 'dorado/3rdparty/cxxpool'...
Submodule path 'dorado/3rdparty/cxxpool': checked out '4d8526e93771c4728cbdcd238369e434bad58d32'
Cloning into 'dorado/3rdparty/date'...
Submodule path 'dorado/3rdparty/date': checked out 'cc4685a21e4a4fdae707ad1233c61bbaff241f93'
Cloning into 'dorado/3rdparty/edlib'...
Submodule path 'dorado/3rdparty/edlib': checked out '18794ae1e74b64ff13975239a96417dfba63997b'
Cloning into 'dorado/3rdparty/elzip'...
Submodule path 'dorado/3rdparty/elzip': checked out '516e161d5c96aa8f2603fb30b10b7770a87332c2'
Submodule 'extlibs/minizip' (https://github.com/zlib-ng/minizip-ng.git) registered for path 'extlibs/minizip'
Cloning into 'extlibs/minizip'...
Submodule path 'dorado/3rdparty/elzip/extlibs/minizip': checked out 'cee6d8cbd4da70c48e9df1426607ff95b4f24fa6'
Cloning into 'dorado/3rdparty/hdf_plugins'...
Submodule path 'dorado/3rdparty/hdf_plugins': checked out '02fb8f50b93921ffa3c040106e809aaf8adbe5c5'
Submodule 'third_party/streamvbyte' (https://github.com/lemire/streamvbyte.git) registered for path 'third_party/streamvbyte'
Cloning into 'third_party/streamvbyte'...
Submodule path 'dorado/3rdparty/hdf_plugins/third_party/streamvbyte': checked out '1813d4ec3d732f3f615821fd8d1f725204c15ecc'
Cloning into 'dorado/3rdparty/htslib'...
Submodule path 'dorado/3rdparty/htslib': checked out '3c6f83f11e6e99cdcbed3541ae7d8d5f7786578d'
Submodule 'htscodecs' (https://github.com/samtools/htscodecs.git) registered for path 'htscodecs'
Cloning into 'htscodecs'...
Submodule path 'dorado/3rdparty/htslib/htscodecs': checked out '3ef17f6fb5b8b6b0ad2d4c1c562165664f0703f8'
Cloning into 'dorado/3rdparty/indicators'...
fatal: reference is not a tree: 88544847c51397004a31cf2817c334624c6350cf
Cloning into 'dorado/3rdparty/ont-minimap2'...
Submodule path 'dorado/3rdparty/ont-minimap2': checked out '41b2c01bba3b1a89304f8220694385fcdbe9ed67'
Submodule 'minimap2' (https://github.com/lh3/minimap2.git) registered for path 'src/3rdparty/minimap2'
Submodule 'pthread-win32' (https://github.com/GerHobbelt/pthread-win32.git) registered for path 'src/3rdparty/pthread-win32'
Submodule 'zlib-ng' (https://github.com/zlib-ng/zlib-ng.git) registered for path 'src/3rdparty/zlib-ng'
Cloning into 'src/3rdparty/minimap2'...
Submodule path 'dorado/3rdparty/ont-minimap2/src/3rdparty/minimap2': checked out '5279377544a36f690e8aa34fec856c6106d259e5'
Submodule 'lib/simde' (https://github.com/nemequ/simde.git) registered for path 'lib/simde'
Cloning into 'lib/simde'...
Submodule path 'dorado/3rdparty/ont-minimap2/src/3rdparty/minimap2/lib/simde': checked out 'b30129b3b48a6823013da2b309c50a081177b6b8'
Submodule 'munit' (https://github.com/nemequ/munit.git) registered for path 'test/munit'
Cloning into 'test/munit'...
Submodule path 'dorado/3rdparty/ont-minimap2/src/3rdparty/minimap2/lib/simde/test/munit': checked out 'da8f73412998e4f1adf1100dc187533a51af77fd'
Cloning into 'src/3rdparty/pthread-win32'...
Submodule path 'dorado/3rdparty/ont-minimap2/src/3rdparty/pthread-win32': checked out 'a89bf2154a28113a7373e25fe2729dee4e004385'
Cloning into 'src/3rdparty/zlib-ng'...
Submodule path 'dorado/3rdparty/ont-minimap2/src/3rdparty/zlib-ng': checked out 'c255e58dd5e0ec3b2febb29c0905e89032419bcd'
Cloning into 'dorado/3rdparty/spdlog'...
Submodule path 'dorado/3rdparty/spdlog': checked out '7e635fca68d014934b4af8a1cf874f63989352b7'
Cloning into 'dorado/3rdparty/toml11'...
Submodule path 'dorado/3rdparty/toml11': checked out '59243256528d4133321e845c3193db2d2725e6ee'
Cloning into 'dorado/3rdparty/zstd'...
Submodule path 'dorado/3rdparty/zstd': checked out '97a3da1df009d4dc67251de0c4b1c9d7fe286fc1'
Unable to checkout '88544847c51397004a31cf2817c334624c6350cf' in submodule path 'dorado/3rdparty/indicators'
(at easybuild/tools/run.py:682 in parse_cmd_output)
== 2024-05-24 15:01:07,877 build_log.py:267 INFO ... (took 38 secs)
== 2024-05-24 15:01:07,880 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 15:01:07,880 filetools.py:2013 INFO Removing lock /eb/maint/software/.locks/_eb_maint_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock...
== 2024-05-24 15:01:07,880 filetools.py:383 INFO Path /eb/maint/software/.locks/_eb_maint_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock successfully removed.
== 2024-05-24 15:01:07,880 filetools.py:2017 INFO Lock removed: /eb/maint/software/.locks/_eb_maint_software_dorado_0.7.0-foss-2023a-CUDA-12.1.1.lock
== 2024-05-24 15:01:07,880 easyblock.py:4291 WARNING build failed (first 300 chars): cmd "git clone --depth 1 --branch v0.7.0 --recursive https://github.com/nanoporetech/dorado.git" exited with exit code 1 and output:
Cloning into 'dorado'...
Note: checking out '71cc74429f0daa43f1ca32b203b2af569b1e6386'.
You are in 'detached HEAD' state. You can look around, make experimental
chang
== 2024-05-24 15:01:07,880 easyblock.py:328 INFO Closing log for application name dorado version 0.7.0
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