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Created May 24, 2024 14:34
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(partial) EasyBuild log for failed build of /tmp/eb-6pmj6r2w/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb (PR(s) #20444)
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dorado-0.6.1-foss-2023a-CUDA-12.1.1_partial.log
== 2024-05-24 14:34:08,565 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 14:34:08,566 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 14:34:08,566 easyblock.py:1056 INFO Build dir set to /dev/shm/dorado/0.6.1/foss-2023a-CUDA-12.1.1
== 2024-05-24 14:34:08,566 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 14:34:08,566 easyconfig.py:2653 DEBUG Determining software installation subdir for dorado EasyConfig @ /tmp/eb-6pmj6r2w/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 14:34:08,566 easyconfig.py:2656 DEBUG Using fixed naming software installation subdir: dorado/0.6.1-foss-2023a-CUDA-12.1.1
== 2024-05-24 14:34:08,566 easyblock.py:1113 INFO Software install dir set to /eb/maint/software/dorado/0.6.1-foss-2023a-CUDA-12.1.1
== 2024-05-24 14:34:08,566 config.py:699 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /eb/maint/modules
== 2024-05-24 14:34:08,566 easyblock.py:1118 INFO Module install dir set to /eb/maint/modules/all
== 2024-05-24 14:34:08,566 easyblock.py:288 INFO Init completed for application name dorado version 0.6.1
== 2024-05-24 14:34:08,566 easyblock.py:4234 INFO Obtained application instance of for dorado (easyblock: CMakeMake)
== 2024-05-24 14:34:08,566 easyblock.py:4247 DEBUG Skip set to True
== 2024-05-24 14:34:08,567 easyconfig.py:1702 INFO Generating template values...
== 2024-05-24 14:34:08,567 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-6pmj6r2w/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 14:34:08,567 templates.py:231 DEBUG version found in easyconfig is 0.6.1
== 2024-05-24 14:34:08,567 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-05-24 14:34:08,567 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-05-24 14:34:08,567 templates.py:333 DEBUG name: name, config: dorado
== 2024-05-24 14:34:08,567 templates.py:333 DEBUG name: parallel, config: None
== 2024-05-24 14:34:08,567 templates.py:333 DEBUG name: version, config: 0.6.1
== 2024-05-24 14:34:08,567 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-05-24 14:34:08,567 templates.py:333 DEBUG name: versionprefix, config:
== 2024-05-24 14:34:08,567 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-05-24 14:34:08,567 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 14:34:08,568 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/0.6.1-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='0.6.1', version_major='0', version_major_minor='0.6', version_minor='6', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-05-24 14:34:08,568 one.py:150 DEBUG Not copying '__builtins__' variable from parsed easyconfig
== 2024-05-24 14:34:08,569 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 14:34:08,569 one.py:180 INFO Skipping reformatting value for parameter 'toolchain'
== 2024-05-24 14:34:08,569 one.py:180 INFO Skipping reformatting value for parameter 'toolchainopts'
== 2024-05-24 14:34:08,571 easyconfig.py:1265 DEBUG Dumped easyconfig: easyblock = 'CMakeMake'
name = 'dorado'
version = '0.6.1'
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-%(version_major_minor)s.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" '
skip = True
sanity_check_paths = {
'files': ['bin/%(name)s'],
'dirs': [],
}
sanity_check_commands = ['%(name)s basecaller --help']
moduleclass = 'bio'
== 2024-05-24 14:34:08,571 filetools.py:1912 INFO Creating directory /tmp/eb-6pmj6r2w/reprod_20240524143408_1369 (parents: True, set_gid: False, sticky: False)
== 2024-05-24 14:34:08,571 easyblock.py:4488 INFO Dumped easyconfig instance to /tmp/eb-6pmj6r2w/reprod_20240524143408_1369/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 14:34:08,571 filetools.py:1912 INFO Creating directory /tmp/eb-6pmj6r2w/reprod_20240524143408_1369/easyblocks (parents: True, set_gid: False, sticky: False)
== 2024-05-24 14:34:08,571 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-6pmj6r2w/reprod_20240524143408_1369/easyblocks/configuremake.py
== 2024-05-24 14:34:08,572 easyblock.py:4468 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-6pmj6r2w/reprod_20240524143408_1369/easyblocks
== 2024-05-24 14:34:08,572 filetools.py:1931 DEBUG Not creating existing path /tmp/eb-6pmj6r2w/reprod_20240524143408_1369/easyblocks
== 2024-05-24 14:34:08,572 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-6pmj6r2w/reprod_20240524143408_1369/easyblocks/cmakemake.py
== 2024-05-24 14:34:08,572 easyblock.py:4468 INFO Dumped easyblock cmakemake.py required for reproduction to /tmp/eb-6pmj6r2w/reprod_20240524143408_1369/easyblocks
== 2024-05-24 14:34:08,574 easyblock.py:2239 INFO Number of iterations to perform for central part of installation procedure: 1
== 2024-05-24 14:34:08,574 build_log.py:267 INFO building and installing dorado/0.6.1-foss-2023a-CUDA-12.1.1...
== 2024-05-24 14:34:08,579 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 14:34:08,579 filetools.py:2005 INFO Lock /eb/maint/software/.locks/_eb_maint_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock does not exist
== 2024-05-24 14:34:08,579 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 14:34:08,579 filetools.py:1946 INFO Creating lock at /eb/maint/software/.locks/_eb_maint_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock...
== 2024-05-24 14:34:08,579 filetools.py:1912 INFO Creating directory /eb/maint/software/.locks/_eb_maint_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock (parents: True, set_gid: False, sticky: False)
== 2024-05-24 14:34:08,579 filetools.py:1955 INFO Lock created: /eb/maint/software/.locks/_eb_maint_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock
== 2024-05-24 14:34:08,579 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 14:34:08,579 build_log.py:267 INFO fetching files...
== 2024-05-24 14:34:08,582 easyblock.py:3956 INFO Starting fetch step
== 2024-05-24 14:34:08,582 easyconfig.py:1702 INFO Generating template values...
== 2024-05-24 14:34:08,582 templates.py:201 DEBUG config: dorado EasyConfig @ /tmp/eb-6pmj6r2w/files_pr20444/d/dorado/dorado-0.6.1-foss-2023a-CUDA-12.1.1.eb
== 2024-05-24 14:34:08,582 templates.py:231 DEBUG version found in easyconfig is 0.6.1
== 2024-05-24 14:34:08,582 templates.py:333 DEBUG name: bitbucket_account, config: %(namelower)s
== 2024-05-24 14:34:08,582 templates.py:333 DEBUG name: github_account, config: %(namelower)s
== 2024-05-24 14:34:08,582 templates.py:333 DEBUG name: name, config: dorado
== 2024-05-24 14:34:08,582 templates.py:333 DEBUG name: parallel, config: None
== 2024-05-24 14:34:08,582 templates.py:333 DEBUG name: version, config: 0.6.1
== 2024-05-24 14:34:08,582 templates.py:333 DEBUG name: versionsuffix, config: -CUDA-%(cudaver)s
== 2024-05-24 14:34:08,582 templates.py:333 DEBUG name: versionprefix, config:
== 2024-05-24 14:34:08,582 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2024-05-24 14:34:08,583 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 14:34:08,583 easyconfig.py:1721 INFO Template values: arch='x86_64', bitbucket_account='dorado', builddir='/dev/shm/dorado/0.6.1/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/0.6.1-foss-2023a-CUDA-12.1.1', module_name='dorado/0.6.1-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='0.6.1', version_major='0', version_major_minor='0.6', version_minor='6', versionprefix='', versionsuffix='-CUDA-12.1.1'
== 2024-05-24 14:34:08,583 easyblock.py:3964 INFO Running method fetch_step part of step fetch
== 2024-05-24 14:34:08,583 easyblock.py:2361 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version
== 2024-05-24 14:34:08,583 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /tmp/eb-6pmj6r2w/files_pr20444/d/dorado
== 2024-05-24 14:34:08,583 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 14:34:08,583 tools.py:288 INFO Also considering installation prefix /eb/maint/software/EasyBuild/4.9.1 (determined via path to 'eb' script)...
== 2024-05-24 14:34:08,583 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/easybuild/local/easybuild/easyconfigs
== 2024-05-24 14:34:08,583 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/local/easybuild/easyconfigs
== 2024-05-24 14:34:08,583 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 14:34:08,583 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-6pmj6r2w/files_pr20444/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-6pmj6r2w/fake_vsc_bw6kq3yb/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-05-24 14:34:08,584 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 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/lib-dynload/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/.local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs
== 2024-05-24 14:34:08,584 tools.py:307 DEBUG Added /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-05-24 14:34:08,586 easyblock.py:881 WARNING Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /tmp/eb-6pmj6r2w/files_pr20444/d/dorado/d/dorado/checksums.json, /tmp/eb-6pmj6r2w/files_pr20444/d/dorado/dorado/checksums.json, /tmp/eb-6pmj6r2w/files_pr20444/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-6pmj6r2w/files_pr20444/d/dorado/checksums.json, /tmp/eb-6pmj6r2w/files_pr20444/dorado/checksums.json, /tmp/eb-6pmj6r2w/files_pr20444/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 14:34:08,586 easyblock.py:810 INFO Considering directory in which easyconfig file is located when searching for dorado-0.6.1.tar.gz: /tmp/eb-6pmj6r2w/files_pr20444/d/dorado
== 2024-05-24 14:34:08,586 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 14:34:08,586 tools.py:288 INFO Also considering installation prefix /eb/maint/software/EasyBuild/4.9.1 (determined via path to 'eb' script)...
== 2024-05-24 14:34:08,586 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/easybuild/local/easybuild/easyconfigs
== 2024-05-24 14:34:08,586 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/local/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/src/github/easybuild-easyconfigs/easybuild/easyconfigs/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-6pmj6r2w/files_pr20444/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /tmp/eb-6pmj6r2w/fake_vsc_bw6kq3yb/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/git/ext/gitdb/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at easybuild/easyconfigs
== 2024-05-24 14:34:08,587 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 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python36.zip/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/lib-dynload/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /home/software/.local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/local/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib/python3.6/site-packages/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /usr/lib64/python3.6/site-packages/gitdb/ext/smmap/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:303 DEBUG Checking for easybuild/easyconfigs at /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs
== 2024-05-24 14:34:08,587 tools.py:307 DEBUG Added /eb/maint/software/EasyBuild/4.9.1/easybuild/easyconfigs to list of paths for easybuild/easyconfigs
== 2024-05-24 14:34:08,588 filetools.py:1931 DEBUG Not creating existing path /eb/maint/sources/d/dorado
== 2024-05-24 14:34:08,588 run.py:180 DEBUG run_cmd: Output of "git clone --depth 1 --branch v0.6.1 --recursive https://github.com/nanoporetech/dorado.git" will be logged to /tmp/eb-6pmj6r2w/easybuild-run_cmd-l7zaxfi2.log
== 2024-05-24 14:34:08,593 run.py:221 DEBUG run_cmd: running cmd git clone --depth 1 --branch v0.6.1 --recursive https://github.com/nanoporetech/dorado.git (in /tmp/eb-6pmj6r2w/tmp4jaad7z8)
== 2024-05-24 14:34:08,593 run.py:247 INFO running cmd: git clone --depth 1 --branch v0.6.1 --recursive https://github.com/nanoporetech/dorado.git
== 2024-05-24 14:34:48,796 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/base/exceptions.py:126 in __init__): cmd "git clone --depth 1 --branch v0.6.1 --recursive https://github.com/nanoporetech/dorado.git" exited with exit code 1 and output:
Cloning into 'dorado'...
Note: checking out '79b5da50f86cdd59f24aedfeb48fd97fd9149233'.
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 14:34:48,798 build_log.py:267 INFO ... (took 40 secs)
== 2024-05-24 14:34:48,801 config.py:699 DEBUG software install path as specified by 'installpath' and 'subdir_software': /eb/maint/software
== 2024-05-24 14:34:48,801 filetools.py:2013 INFO Removing lock /eb/maint/software/.locks/_eb_maint_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock...
== 2024-05-24 14:34:48,801 filetools.py:383 INFO Path /eb/maint/software/.locks/_eb_maint_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock successfully removed.
== 2024-05-24 14:34:48,801 filetools.py:2017 INFO Lock removed: /eb/maint/software/.locks/_eb_maint_software_dorado_0.6.1-foss-2023a-CUDA-12.1.1.lock
== 2024-05-24 14:34:48,802 easyblock.py:4291 WARNING build failed (first 300 chars): cmd "git clone --depth 1 --branch v0.6.1 --recursive https://github.com/nanoporetech/dorado.git" exited with exit code 1 and output:
Cloning into 'dorado'...
Note: checking out '79b5da50f86cdd59f24aedfeb48fd97fd9149233'.
You are in 'detached HEAD' state. You can look around, make experimental
chang
== 2024-05-24 14:34:48,802 easyblock.py:328 INFO Closing log for application name dorado version 0.6.1
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