diff --git a/169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb b/169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb new file mode 100644 index 00000000..9fd7258a --- /dev/null +++ b/169_Bonito/Bonito-0.4.0-fosscuda-2020b.eb @@ -0,0 +1,129 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.7.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.1', '-CUDA-%(cudaver)s'), + ('h5py', '3.7.0'), + ('Mako', '1.2.0'), + ('PyYAML', '6.0'), + ('python-parasail', '1.3.3'), + ('tqdm', '4.64.0'), + ('apex', '20230702', '-CUDA-%(cudaver)s'), + ('minimap2', '2.24'), + ('CuPy', '12.1.0', '-CUDA-%(cudaver)s'), + ('GenomeWorks', '2021.02.2'), + ('pyspoa', '0.0.9'), + ('ont-fast5-api', '3.3.0'), + ('ont-remora', '2.1.2'), + ('Pysam', '0.20.0'), + ('pod5-file-format', '0.1.8'), +] + +use_pip = True + +# strip out too strict version requirements for dependencies +local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " +# fix requirements for stuff we include as a proper dependency +local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && " +local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && " + +exts_list = [ + ('python-editor', '1.0.4', { + 'modulename': 'editor', + 'checksums': ['51fda6bcc5ddbbb7063b2af7509e43bd84bfc32a4ff71349ec7847713882327b'], + }), + ('alembic', '1.6.4', { + 'checksums': ['becb572c6701c90ca249f97fc1ae231468cc9516df367a350901eeb9310a8d43'], + }), + ('cmd2', '1.5.0', { + 'checksums': ['701a8c9975c4abc45e5d13906ab149f959f812869106347323a3f89ac0e82a62'], + }), + ('prettytable', '2.1.0', { + 'checksums': ['5882ed9092b391bb8f6e91f59bcdbd748924ff556bb7c634089d5519be87baa0'], + }), + ('cliff', '3.7.0', { + 'preinstallopts': "sed -i'' 's/cmd2.*/cmd2/g' requirements.txt && ", + 'checksums': ['389c81960de13f05daf1cbd546f33199e86c518ba4266c79ec7a153a280980ea'], + }), + ('colorlog', '5.0.1', { + 'checksums': ['f17c013a06962b02f4449ee07cfdbe6b287df29efc2c9a1515b4a376f4e588ea'], + }), + ('greenlet', '1.1.0', { + 'checksums': ['c87df8ae3f01ffb4483c796fe1b15232ce2b219f0b18126948616224d3f658ee'], + }), + ('SQLAlchemy', '1.4.15', { + 'checksums': ['0ff100c75cd175f35f4d24375a0b3d82461f5b1af5fc8d112ef0e5ceea8049e6'], + }), + ('cmaes', '0.8.2', { + 'checksums': ['1c04ba23ded925ef13b96f42cfbd667a905ea5b80754c750e6448b9fcda96a5d'], + }), + ('optuna', '2.7.0', { + 'checksums': ['eb1595108ec444e840deb0037351074144fecb7a4eff6870fc11569ab782cfc6'], + }), + ('colorama', '0.4.4', { + 'checksums': ['5941b2b48a20143d2267e95b1c2a7603ce057ee39fd88e7329b0c292aa16869b'], + }), + ('pyperclip', '1.8.2', { + 'checksums': ['105254a8b04934f0bc84e9c24eb360a591aaf6535c9def5f29d92af107a9bf57'], + }), + ('importlib_metadata', '4.0.1', { + 'checksums': ['8c501196e49fb9df5df43833bdb1e4328f64847763ec8a50703148b73784d581'], + }), + ('stevedore', '3.3.0', { + 'checksums': ['3a5bbd0652bf552748871eaa73a4a8dc2899786bc497a2aa1fcb4dcdb0debeee'], + }), + ('fast-ctc-decode', '0.3.5', { + 'source_tmpl': 'fast_ctc_decode-%(version)s-cp38-cp38-manylinux2010_x86_64.whl', + 'unpack_sources': False, + }), + ('mappy', '2.24', { + }), + ('seqdist', '0.0.3', { + 'preinstallopts': "sed -i 's/cupy-cuda102//g' settings.ini && sed -i 's/[<>=]=[0-9].*//g' settings.ini && ", + 'checksums': ['bdbbea6ebba1c6dd6698d46e23ba7858f93a7cdf0c7cbc2ea66660291acb044f'], + }), + ('crf-beam', '0.0.1a0', { + 'modulename': 'kbeam', + 'sources': ['crf_beam-%(version)s-cp38-cp38-manylinux1_x86_64.whl'], + 'unpack_sources': False, + 'checksums': ['0cba80ff4d7f90595f498921cf904736e3bce558dba80de5611874d89e72312e'], + }), + ('networkx', '2.5.1', { + 'checksums': ['109cd585cac41297f71103c3c42ac6ef7379f29788eb54cb751be5a663bb235a'], + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': local_bonito_preinstallopts, + 'checksums': ['429310d56e2d7dabd91a9a9c972504a0aa2b6d6469563b14d4aae30adfe9a87e'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/169_Bonito/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb b/169_Bonito/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb new file mode 100644 index 00000000..b7ef5f9b --- /dev/null +++ b/169_Bonito/CuPy/CuPy-11.4.0-foss-2021b-CUDA-11.4.1.eb @@ -0,0 +1,68 @@ +easyblock = 'PythonBundle' + +name = 'CuPy' +version = '12.1.0' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://cupy.dev' +description = "CuPy is an open-source array library accelerated with NVIDIA CUDA." + +toolchain = {'name': 'foss', 'version': '2022a'} + +builddependencies = [ + ('pytest', '7.3.2'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('CUDA', '11.7.0', '', SYSTEM), + ('cuDNN', '8.4.1.50', versionsuffix, SYSTEM), + ('NCCL', '2.12.12', versionsuffix), + ('cuTENSOR', '1.6.1.5', versionsuffix, SYSTEM), + # Adding cuSPARSELt currently makes the build fail. Keeping it around for later versions to pick up. + # ('cuSPARSELt', '0.3.0.3', versionsuffix, SYSTEM), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# A bunch of the tests are failing or are just having problems. +_skip_tests = [ + 'tests/cupyx_tests/scipy_tests', + 'tests/cupyx_tests/distributed_tests', + 'tests/cupyx_tests/tools_tests', + 'tests/example_tests', + 'tests/cupy_tests/testing_tests/test_parameterized.py', + 'tests/cupy_tests/fft_tests/test_fft.py', +] +_ignore_list = ' --ignore='.join(_skip_tests) + +_deselect_tests = [ + 'tests/cupy_tests/core_tests/test_carray.py::TestCArray32BitBoundary_param_', + # float16 has too low precision for these tests as they are written + # See https://github.com/easybuilders/easybuild-easyconfigs/pull/17526#issuecomment-1470843170 for details. + 'tests/cupy_tests/linalg_tests/test_product.py::TestProduct', +] +_deselect_list = ' --deselect='.join(_deselect_tests) + +exts_list = [ + ('fastrlock', '0.8.1', { + }), + ('cupy', version, { + # Must run tests here since the required version of pytest is a builddep + # Note! test_cudnn and some others will likely fail on T4 GPUs due to out of memory. + 'runtest': 'export CUPY_TEST_GPU_LIMIT=1 CUPY_CACHE_DIR="%%(builddir)s" && ' + 'pytest --ignore=%s --deselect=%s tests' % (_ignore_list, _deselect_list), + 'testinstall': True, + }), +] + +sanity_check_commands = [ + "python -c 'import cupy'", +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/169_Bonito/CuPy/pytest-7.2.2-GCCcore-11.2.0.eb b/169_Bonito/CuPy/pytest-7.2.2-GCCcore-11.2.0.eb new file mode 100644 index 00000000..45e71042 --- /dev/null +++ b/169_Bonito/CuPy/pytest-7.2.2-GCCcore-11.2.0.eb @@ -0,0 +1,71 @@ +easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.3.2' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' diff --git a/169_Bonito/GenomeWorks-2021.02.2-fosscuda-2020b.eb b/169_Bonito/GenomeWorks-2021.02.2-fosscuda-2020b.eb new file mode 100644 index 00000000..1b1b694b --- /dev/null +++ b/169_Bonito/GenomeWorks-2021.02.2-fosscuda-2020b.eb @@ -0,0 +1,99 @@ +# author: Denis Kristak (INUITS) +easyblock = 'CMakePythonPackage' + +name = 'GenomeWorks' +version = '2021.02.2' +local_commit = '691380d' # corresponds to 2021.02.2 tag +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/clara-parabricks/GenomeWorks' +description = "SDK for GPU accelerated genome assembly and analysis" + +toolchain = {'name': 'foss', 'version': '2022a'} +toolchainopts = {'pic': True} + +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'git_config': { + 'url': 'https://github.com/clara-parabricks', + 'repo_name': name, + 'commit': local_commit, + 'recursive': True, + }, +}] +# no checksum for source tarball because it's created locally via 'git clone' +checksums = [None] + +builddependencies = [ + ('CMake', '3.24.3'), + ('Doxygen', '1.9.4'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('Autoconf', '2.71'), + ('matplotlib', '3.5.2'), + ('SciPy-bundle', '2022.05'), + ('networkx', '2.8.4'), + ('tqdm', '4.64.0'), +] + +# add missing include to a file +preconfigopts = "sed -i'' 's/#include /#include \\n#include /g'" +preconfigopts += " %(builddir)s/GenomeWorks/3rdparty/spoa/src/alignment_engine.cpp && """ + +preconfigopts += "sed -i 's/==/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && " +preconfigopts += "sed -i 's/~=/>=/g' %(builddir)s/GenomeWorks/pygenomeworks/requirements.txt && " + +# instruction from GenomeWorks' readme +configopts = "-Dgw_cuda_gen_all_arch=OFF " +configopts += " -Dgw_build_shared=ON " + +# no test targets +skipsteps = ['test'] + +exts_defaultclass = 'PythonPackage' + +exts_default_options = { + 'download_dep_fail': True, + 'use_pip': True, + 'sanity_pip_check': True, +} + +local_genomeworks_preinstallopts = "sed -i 's/[=~]=/>=/g' requirements.txt && " +local_genomeworks_preinstallopts += "export GW_INSTALL_DIR=%(installdir)s && " +local_genomeworks_preinstallopts += "export GW_VERSION=%(version)s && " +local_genomeworks_preinstallopts += "export GW_ROOT_DIR=%(builddir)s/GenomeWorks && " + +exts_list = [ + ('sortedcollections', '2.1.0', { + 'source_urls': [PYPI_SOURCE], + 'checksums': ['d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd'], + }), + ('genomeworks', version, { + 'sources': ['GenomeWorks-%(version)s.tar.gz'], + # no checksum for source tarball because it's created locally via 'git clone' + 'checksums': [None], + 'start_dir': 'pygenomeworks', + 'preinstallopts': local_genomeworks_preinstallopts, + }), +] + +sanity_check_paths = { + 'files': ['bin/cudamapper', 'bin/cudapoa', 'bin/genome_simulator', + 'lib/libgwbase.%s' % SHLIB_EXT, 'lib/libgwio.%s' % SHLIB_EXT], + 'dirs': ['benchmarks', 'docs', 'include/claraparabricks/genomeworks', + 'lib/python%(pyshortver)s/site-packages', 'samples', 'tests'], +} + +sanity_check_commands = [ + "cudamapper --help", + "cudapoa --help", + "genome_simulator --help", + "python -c 'import genomeworks'", +] + +modextrapaths = {'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages'} + +moduleclass = 'bio' diff --git a/169_Bonito/apex-20210420-fosscuda-2020b.eb b/169_Bonito/apex-20210420-fosscuda-2020b.eb new file mode 100644 index 00000000..27614950 --- /dev/null +++ b/169_Bonito/apex-20210420-fosscuda-2020b.eb @@ -0,0 +1,34 @@ +easyblock = 'PythonPackage' + +name = 'apex' +local_commit = '8ffc901' +version = '20230702' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nvidia/apex' +description = "A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch" + +toolchain = {'name': 'foss', 'version': '2022a'} + +source_urls = ['https://github.com/NVIDIA/apex/archive/'] +sources = [{ + 'filename': SOURCE_TAR_GZ, + 'download_filename': '%s.tar.gz' % local_commit, +}] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('PyTorch', '1.12.1', '-CUDA-11.7.0'), +] + +download_dep_fail = True +use_pip = True + +installopts = "--no-cache-dir --global-option='--cpp_ext' --global-option='--cuda_ext' --global-option='--pyprof'" + +sanity_pip_check = True + +sanity_check_commands = ["python -c 'from apex import amp'"] + +moduleclass = 'tools' diff --git a/169_Bonito/bonito_test.eb b/169_Bonito/bonito_test.eb new file mode 100644 index 00000000..f860d1f4 --- /dev/null +++ b/169_Bonito/bonito_test.eb @@ -0,0 +1,59 @@ +# author: Denis Kristak (INUITS) +easyblock = 'PythonBundle' + +name = 'Bonito' +version = '0.7.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/bonito' +description = "Convolution Basecaller for Oxford Nanopore Reads" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('CUDA', '11.7.0', '', SYSTEM), + ('SciPy-bundle', '2022.05'), + ('PyTorch', '1.12.1', '-CUDA-%(cudaver)s'), + ('edlib', '1.3.9'), + ('ont-fast5-api', '4.1.1'), +] + +use_pip = True + +# strip out too strict version requirements for dependencies +local_bonito_preinstallopts = "sed -i 's/[><=]=.*//g' requirements.txt && " +# fix requirements for stuff we include as a proper dependency +local_bonito_preinstallopts += "sed -i 's/genomeworks-cuda-10-2/genomeworks/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/cupy-cuda102/cupy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/numpy~=[0-9.]*/numpy/g' requirements.txt && " +local_bonito_preinstallopts += "sed -i 's/torch~=[0-9.]*/torch/g' requirements.txt && " +local_bonito_preinstallopts += "export PATH=%(installdir)s/bin/:$PATH && " + +exts_list = [ + ('fast-ctc-decode', '0.3.2', { + 'source_tmpl': 'fast_ctc_decode-0.3.5-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl', + 'unpack_sources': False, + }), + ('mappy', '2.24', { + }), + ('ont-bonito', version, { + 'modulename': 'bonito', + 'preinstallopts': local_bonito_preinstallopts, + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/bonito'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + "bonito --help", + "bonito convert --help", + "bonito download --help", +] + +moduleclass = 'bio' diff --git a/169_Bonito/easybuild-GenomeWorks-2021.02.2-20230704.140359.tOjpj.log b/169_Bonito/easybuild-GenomeWorks-2021.02.2-20230704.140359.tOjpj.log new file mode 100644 index 00000000..45c50bfc --- /dev/null +++ b/169_Bonito/easybuild-GenomeWorks-2021.02.2-20230704.140359.tOjpj.log @@ -0,0 +1,1129 @@ +== 2023-07-04 14:03:59,469 easyblock.py:313 INFO This is EasyBuild 4.7.3.dev0-r366e71d77260adc73e8976bffeccb83b1b289c5d (framework: 4.7.3.dev0-r366e71d77260adc73e8976bffeccb83b1b289c5d, easyblocks: 4.7.3.dev0-r8a7ffbad49ed3c9a4bf658f6a76c663792342e09) on host node4004.donphan.os. +== 2023-07-04 14:03:59,469 easyblock.py:319 INFO This is easyblock CMakePythonPackage from module easybuild.easyblocks.generic.cmakepythonpackage (/user/gent/445/vsc44588/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/cmakepythonpackage.py) +== 2023-07-04 14:03:59,469 easyblock.py:1040 INFO Build dir set to /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0 +== 2023-07-04 14:03:59,469 easyblock.py:1097 INFO Software install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0 +== 2023-07-04 14:03:59,469 easyblock.py:1102 INFO Module install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 14:03:59,470 easyblock.py:288 INFO Init completed for application name GenomeWorks version 2021.02.2 +== 2023-07-04 14:03:59,470 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'genomeworks' +== 2023-07-04 14:03:59,470 pythonpackage.py:371 INFO Using '%(python)s setup.py %(install_target)s --prefix=%(prefix)s %(installopts)s' as install command +== 2023-07-04 14:03:59,470 easyblock.py:4200 INFO Obtained application instance of for GenomeWorks (easyblock: CMakePythonPackage) +== 2023-07-04 14:03:59,470 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:03:59,470 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:03:59,470 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:03:59,471 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:03:59,472 one.py:180 INFO Skipping reformatting value for parameter 'toolchain' +== 2023-07-04 14:03:59,472 one.py:180 INFO Skipping reformatting value for parameter 'toolchainopts' +== 2023-07-04 14:03:59,473 filetools.py:1913 INFO Creating directory /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127 (parents: True, set_gid: False, sticky: False) +== 2023-07-04 14:03:59,473 easyblock.py:4454 INFO Dumped easyconfig instance to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/GenomeWorks-2021.02.2-foss-2022a-CUDA-11.7.0.eb +== 2023-07-04 14:03:59,476 filetools.py:1913 INFO Creating directory /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks (parents: True, set_gid: False, sticky: False) +== 2023-07-04 14:03:59,506 filetools.py:2426 INFO /user/gent/445/vsc44588/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/cmakemake.py copied to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks/cmakemake.py +== 2023-07-04 14:03:59,506 easyblock.py:4434 INFO Dumped easyblock cmakemake.py required for reproduction to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks +== 2023-07-04 14:03:59,506 filetools.py:2426 INFO /user/gent/445/vsc44588/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/cmakepythonpackage.py copied to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks/cmakepythonpackage.py +== 2023-07-04 14:03:59,506 easyblock.py:4434 INFO Dumped easyblock cmakepythonpackage.py required for reproduction to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks +== 2023-07-04 14:03:59,527 filetools.py:2426 INFO /user/gent/445/vsc44588/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/configuremake.py copied to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks/configuremake.py +== 2023-07-04 14:03:59,527 easyblock.py:4434 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks +== 2023-07-04 14:03:59,554 filetools.py:2426 INFO /user/gent/445/vsc44588/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/pythonpackage.py copied to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks/pythonpackage.py +== 2023-07-04 14:03:59,554 easyblock.py:4434 INFO Dumped easyblock pythonpackage.py required for reproduction to /tmp/vsc44588/eb-26zvow2j/reprod_20230704140359_3505127/easyblocks +== 2023-07-04 14:03:59,555 easyblock.py:2209 INFO Number of iterations to perform for central part of installation procedure: 1 +== 2023-07-04 14:03:59,555 build_log.py:267 INFO building and installing GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0... +== 2023-07-04 14:03:59,560 filetools.py:2006 INFO Lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_GenomeWorks_2021.02.2-foss-2022a-CUDA-11.7.0.lock does not exist +== 2023-07-04 14:03:59,560 filetools.py:1947 INFO Creating lock at /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_GenomeWorks_2021.02.2-foss-2022a-CUDA-11.7.0.lock... +== 2023-07-04 14:03:59,560 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_GenomeWorks_2021.02.2-foss-2022a-CUDA-11.7.0.lock (parents: True, set_gid: False, sticky: False) +== 2023-07-04 14:03:59,589 filetools.py:1956 INFO Lock created: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_GenomeWorks_2021.02.2-foss-2022a-CUDA-11.7.0.lock +== 2023-07-04 14:03:59,589 build_log.py:267 INFO fetching files... +== 2023-07-04 14:03:59,591 easyblock.py:3926 INFO Starting fetch step +== 2023-07-04 14:03:59,591 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:03:59,591 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:03:59,591 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:03:59,592 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:03:59,592 easyblock.py:3934 INFO Running method fetch_step part of step fetch +== 2023-07-04 14:03:59,592 easyblock.py:2331 WARNING Easyconfig does not specify an EasyBuild-version (key 'easybuild_version')! Assuming the latest version +== 2023-07-04 14:03:59,592 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito +== 2023-07-04 14:03:59,592 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/445/vsc44588/easybuild/easybuild-framework/eb +== 2023-07-04 14:03:59,593 tools.py:289 INFO Not considering /user/gent/445/vsc44588/easybuild (no easybuild/easyconfigs subdir found) +== 2023-07-04 14:03:59,593 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/445/vsc44588/easybuild (via resolved path to 'eb')... +== 2023-07-04 14:03:59,864 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/g/GenomeWorks/checksums.json, /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/GenomeWorks/checksums.json, /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/g/GenomeWorks/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/GenomeWorks/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/g/GenomeWorks/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/GenomeWorks/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/g/GenomeWorks/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/GenomeWorks/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/checksums.json, /apps/gent/sources/g/GenomeWorks/checksums.json, /apps/gent/sources/GenomeWorks/checksums.json, /apps/gent/sources/checksums.json (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:870 in obtain_file) +== 2023-07-04 14:03:59,864 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for GenomeWorks-2021.02.2.tar.gz: /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito +== 2023-07-04 14:03:59,864 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/445/vsc44588/easybuild/easybuild-framework/eb +== 2023-07-04 14:03:59,864 tools.py:289 INFO Not considering /user/gent/445/vsc44588/easybuild (no easybuild/easyconfigs subdir found) +== 2023-07-04 14:03:59,864 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/445/vsc44588/easybuild (via resolved path to 'eb')... +== 2023-07-04 14:03:59,865 easyblock.py:844 INFO Found file GenomeWorks-2021.02.2.tar.gz at /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz +== 2023-07-04 14:03:59,865 easyblock.py:496 INFO Added sources: [{'name': 'GenomeWorks-2021.02.2.tar.gz', 'path': '/apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz', 'cmd': None, 'checksum': None, 'finalpath': '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0'}] +== 2023-07-04 14:03:59,865 easyblock.py:2374 INFO no patches provided +== 2023-07-04 14:03:59,955 easyblock.py:2384 INFO md5 checksum for /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz: 2189e57225f67e13e3d51aa3293b0b57 +== 2023-07-04 14:04:00,007 easyblock.py:2384 INFO sha256 checksum for /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz: 6cb53ba08f23e791a018d3a97ad0714ddb1bd5f4efdb01b5fede2a6bdc548a3e +== 2023-07-04 14:04:00,013 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for sortedcollections-2.1.0.tar.gz: /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito +== 2023-07-04 14:04:00,013 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/445/vsc44588/easybuild/easybuild-framework/eb +== 2023-07-04 14:04:00,013 tools.py:289 INFO Not considering /user/gent/445/vsc44588/easybuild (no easybuild/easyconfigs subdir found) +== 2023-07-04 14:04:00,013 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/445/vsc44588/easybuild (via resolved path to 'eb')... +== 2023-07-04 14:04:00,025 easyblock.py:844 INFO Found file sortedcollections-2.1.0.tar.gz at /data/gent/vo/001/gvo00117/easybuild/sources/g/GenomeWorks/extensions/sortedcollections-2.1.0.tar.gz +== 2023-07-04 14:04:00,048 easyblock.py:679 INFO md5 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/g/GenomeWorks/extensions/sortedcollections-2.1.0.tar.gz: 00dfa42bfd6e2e89572dc655403233c6 +== 2023-07-04 14:04:00,049 easyblock.py:679 INFO sha256 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/g/GenomeWorks/extensions/sortedcollections-2.1.0.tar.gz: d8e9609d6c580a16a1224a3dc8965789e03ebc4c3e5ffd05ada54a2fed5dcacd +== 2023-07-04 14:04:00,049 easyblock.py:685 INFO Checksum for extension source sortedcollections-2.1.0.tar.gz verified +== 2023-07-04 14:04:00,049 easyblock.py:532 INFO Fetched extension patches: [] +== 2023-07-04 14:04:00,049 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for GenomeWorks-2021.02.2.tar.gz: /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito +== 2023-07-04 14:04:00,049 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/445/vsc44588/easybuild/easybuild-framework/eb +== 2023-07-04 14:04:00,049 tools.py:289 INFO Not considering /user/gent/445/vsc44588/easybuild (no easybuild/easyconfigs subdir found) +== 2023-07-04 14:04:00,049 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/445/vsc44588/easybuild (via resolved path to 'eb')... +== 2023-07-04 14:04:00,050 easyblock.py:844 INFO Found file GenomeWorks-2021.02.2.tar.gz at /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz +== 2023-07-04 14:04:00,087 easyblock.py:679 INFO md5 checksum for /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz: 2189e57225f67e13e3d51aa3293b0b57 +== 2023-07-04 14:04:00,138 easyblock.py:679 INFO sha256 checksum for /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz: 6cb53ba08f23e791a018d3a97ad0714ddb1bd5f4efdb01b5fede2a6bdc548a3e +== 2023-07-04 14:04:00,139 easyblock.py:685 INFO Checksum for extension source GenomeWorks-2021.02.2.tar.gz verified +== 2023-07-04 14:04:00,139 easyblock.py:532 INFO Fetched extension patches: [] +== 2023-07-04 14:04:00,139 easyblock.py:2419 INFO Checking dirs that need to be created: ['/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/GenomeWorks', '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/bio/GenomeWorks'] +== 2023-07-04 14:04:00,139 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0 (parents: True, set_gid: False, sticky: False) +== 2023-07-04 14:04:00,170 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/GenomeWorks (parents: True, set_gid: False, sticky: False) +== 2023-07-04 14:04:00,190 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/bio/GenomeWorks (parents: True, set_gid: False, sticky: False) +== 2023-07-04 14:04:00,233 configuremake.py:95 INFO config.guess version: 2018-08-29 (last updated: 2023-06-15T10:46:35.192122, SHA256 checksum: c02eb9cc55c86cfd1e9a794e548d25db5c9539e7b2154beb649bc6e2cbffc74c) +== 2023-07-04 14:04:00,233 configuremake.py:150 INFO Found config.guess at /data/gent/vo/001/gvo00117/easybuild/sources/generic/eb_v4.7.3.dev0/ConfigureMake/config.guess +== 2023-07-04 14:04:00,233 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 14:04:00,235 build_log.py:267 INFO creating build dir, resetting environment... +== 2023-07-04 14:04:00,237 easyblock.py:3926 INFO Starting ready step +== 2023-07-04 14:04:00,237 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:04:00,237 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:04:00,237 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:04:00,237 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:04:00,237 easyblock.py:3934 INFO Running method check_readiness_step part of step ready +== 2023-07-04 14:04:00,242 run.py:236 INFO running cmd: ulimit -u +== 2023-07-04 14:04:00,245 easyblock.py:2228 INFO Setting parallelism: 8 +== 2023-07-04 14:04:00,288 easyblock.py:2280 WARNING Loaded modules detected: ['env/vsc/donphan', 'env/slurm/donphan', 'env/software/donphan', 'cluster/donphan'] +== 2023-07-04 14:04:00,289 easyblock.py:3934 INFO Running method make_builddir part of step ready +== 2023-07-04 14:04:00,289 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0 (parents: True, set_gid: False, sticky: False) +== 2023-07-04 14:04:00,291 easyblock.py:3934 INFO Running method reset_env part of step ready +== 2023-07-04 14:04:00,292 easyblock.py:3934 INFO Running method handle_iterate_opts part of step ready +== 2023-07-04 14:04:00,292 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:04:00,292 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:04:00,292 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:04:00,292 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:04:00,292 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 14:04:00,294 build_log.py:267 INFO unpacking... +== 2023-07-04 14:04:00,296 easyblock.py:3926 INFO Starting source step +== 2023-07-04 14:04:00,296 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:04:00,297 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:04:00,297 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:04:00,297 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:04:00,297 easyblock.py:3934 INFO Running method checksum_step part of step source +== 2023-07-04 14:04:00,297 easyblock.py:2437 INFO Checksum verification for /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz using None passed. +== 2023-07-04 14:04:00,297 easyblock.py:3934 INFO Running method extract_step part of step source +== 2023-07-04 14:04:00,297 easyblock.py:2549 INFO Unpacking source GenomeWorks-2021.02.2.tar.gz +== 2023-07-04 14:04:00,301 run.py:236 INFO running cmd: tar xzf /apps/gent/sources/g/GenomeWorks/GenomeWorks-2021.02.2.tar.gz +== 2023-07-04 14:04:00,912 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 14:04:00,914 build_log.py:267 INFO patching... +== 2023-07-04 14:04:00,916 easyblock.py:3926 INFO Starting patch step +== 2023-07-04 14:04:00,916 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:04:00,916 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:04:00,916 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:04:00,917 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:04:00,917 easyblock.py:3934 INFO Running method patch_step part of step patch +== 2023-07-04 14:04:00,917 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 14:04:00,919 build_log.py:267 INFO preparing... +== 2023-07-04 14:04:00,921 easyblock.py:3926 INFO Starting prepare step +== 2023-07-04 14:04:00,921 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:04:00,921 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:04:00,921 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:04:00,921 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:04:00,921 easyblock.py:3934 INFO Running method prepare_step part of step prepare +== 2023-07-04 14:04:00,922 modules.py:626 INFO Checking whether CMake/3.24.3-GCCcore-11.3.0 exists... +== 2023-07-04 14:04:00,922 modules.py:631 INFO Module CMake/3.24.3-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-07-04 14:04:00,923 modules.py:654 INFO Result for existence check of CMake/3.24.3-GCCcore-11.3.0 module: True +== 2023-07-04 14:04:00,923 modules.py:626 INFO Checking whether Doxygen/1.9.4-GCCcore-11.3.0 exists... +== 2023-07-04 14:04:00,923 modules.py:631 INFO Module Doxygen/1.9.4-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-07-04 14:04:00,923 modules.py:654 INFO Result for existence check of Doxygen/1.9.4-GCCcore-11.3.0 module: True +== 2023-07-04 14:04:00,923 modules.py:626 INFO Checking whether Python/3.10.4-GCCcore-11.3.0 exists... +== 2023-07-04 14:04:00,923 modules.py:631 INFO Module Python/3.10.4-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-07-04 14:04:00,923 modules.py:654 INFO Result for existence check of Python/3.10.4-GCCcore-11.3.0 module: True +== 2023-07-04 14:04:00,923 modules.py:626 INFO Checking whether CUDA/11.7.0 exists... +== 2023-07-04 14:04:00,923 modules.py:631 INFO Module CUDA/11.7.0 exists (found in list of available modules) +== 2023-07-04 14:04:00,923 modules.py:654 INFO Result for existence check of CUDA/11.7.0 module: True +== 2023-07-04 14:04:00,923 modules.py:626 INFO Checking whether Autoconf/2.71-GCCcore-11.3.0 exists... +== 2023-07-04 14:04:00,923 modules.py:631 INFO Module Autoconf/2.71-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-07-04 14:04:00,923 modules.py:654 INFO Result for existence check of Autoconf/2.71-GCCcore-11.3.0 module: True +== 2023-07-04 14:04:00,923 modules.py:626 INFO Checking whether matplotlib/3.5.2-foss-2022a exists... +== 2023-07-04 14:04:00,923 modules.py:631 INFO Module matplotlib/3.5.2-foss-2022a exists (found in list of available modules) +== 2023-07-04 14:04:00,923 modules.py:654 INFO Result for existence check of matplotlib/3.5.2-foss-2022a module: True +== 2023-07-04 14:04:00,924 modules.py:626 INFO Checking whether SciPy-bundle/2022.05-foss-2022a exists... +== 2023-07-04 14:04:00,924 modules.py:631 INFO Module SciPy-bundle/2022.05-foss-2022a exists (found in list of available modules) +== 2023-07-04 14:04:00,924 modules.py:654 INFO Result for existence check of SciPy-bundle/2022.05-foss-2022a module: True +== 2023-07-04 14:04:00,924 modules.py:626 INFO Checking whether networkx/2.8.4-foss-2022a exists... +== 2023-07-04 14:04:00,924 modules.py:631 INFO Module networkx/2.8.4-foss-2022a exists (found in list of available modules) +== 2023-07-04 14:04:00,924 modules.py:654 INFO Result for existence check of networkx/2.8.4-foss-2022a module: True +== 2023-07-04 14:04:00,924 modules.py:626 INFO Checking whether tqdm/4.64.0-GCCcore-11.3.0 exists... +== 2023-07-04 14:04:00,924 modules.py:631 INFO Module tqdm/4.64.0-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-07-04 14:04:00,924 modules.py:654 INFO Result for existence check of tqdm/4.64.0-GCCcore-11.3.0 module: True +== 2023-07-04 14:04:00,924 modules.py:626 INFO Checking whether foss/2022a exists... +== 2023-07-04 14:04:00,924 modules.py:634 INFO Module foss/2022a not found in list of available modules, checking via 'module show'... +== 2023-07-04 14:04:03,227 modules.py:654 INFO Result for existence check of foss/2022a module: True +== 2023-07-04 14:04:07,994 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib') +== 2023-07-04 14:04:09,937 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/lib') +== 2023-07-04 14:04:12,075 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib') +== 2023-07-04 14:04:13,939 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/nvvm/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/extras/CUPTI/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/nvvm/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/extras/CUPTI/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib') +== 2023-07-04 14:04:16,309 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/nvvm/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/extras/CUPTI/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib') +== 2023-07-04 14:04:19,735 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Qhull/2020.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LibTIFF/4.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/jbigkit/2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tk/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/X11/20220504-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/fontconfig/2.14.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/util-linux/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/freetype/2.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Brotli/1.0.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/nvvm/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/extras/CUPTI/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Qhull/2020.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LibTIFF/4.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/jbigkit/2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tk/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/X11/20220504-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/fontconfig/2.14.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/util-linux/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/freetype/2.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Brotli/1.0.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib') +== 2023-07-04 14:04:22,398 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to 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14:04:28,031 environment.py:93 INFO Environment variable BLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,031 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,031 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable EBVARBLAS_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,032 environment.py:93 INFO Environment variable BLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARBLAS_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable CC set to gcc (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARCC set to gcc (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable CPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable CXX set to g++ (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,033 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable FFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable EBVARFFTW_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable FFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable EBVARFFTW_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-07-04 14:04:28,034 environment.py:93 INFO Environment variable FFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFTW_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable FFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFTW_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable FFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFT_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable FFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFT_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable FFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS set to libfftw3.so (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable FFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFT_SHARED_LIBS_MT set to libfftw3.so,libpthread.so (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable FFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-07-04 14:04:28,035 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS set to libfftw3.a (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable FFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARFFT_STATIC_LIBS_MT set to libfftw3.a,libpthread.a (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable LAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARLAPACK_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable LAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARLAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable LAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARLAPACK_MT_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable LAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARLAPACK_MT_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable LAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARLAPACK_SHARED_LIBS set to libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable LAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,036 environment.py:93 INFO Environment variable EBVARLAPACK_STATIC_LIBS set to libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable LIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable EBVARLIBBLAS set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable LIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable EBVARLIBBLAS_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable LIBFFT set to -lfftw3 (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable EBVARLIBFFT set to -lfftw3 (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable LIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable EBVARLIBFFT_MT set to -lfftw3 -lpthread (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable LIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable EBVARLIBLAPACK set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable LIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,037 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable LIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARLIBLAPACK_MT_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable LIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARLIBLAPACK_ONLY set to -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable LIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK set to -lscalapack -lflexiblas -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable LIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT set to -lscalapack -lflexiblas -lpthread -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable LIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_MT_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable LIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARLIBSCALAPACK_ONLY set to -lscalapack -lgfortran (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable MPICC set to mpicc (previously undefined) +== 2023-07-04 14:04:28,038 environment.py:93 INFO Environment variable EBVARMPICC set to mpicc (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPICXX set to mpicxx (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable EBVARMPICXX set to mpicxx (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPIF77 set to mpifort (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable EBVARMPIF77 set to mpifort (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPIF90 set to mpifort (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable EBVARMPIF90 set to mpifort (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPIFC set to mpifort (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable EBVARMPIFC set to mpifort (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable EBVARMPI_INC_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable EBVARMPI_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64 (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable EBVARMPI_LIB_SHARED set to /apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib64/libmpi.so (previously undefined) +== 2023-07-04 14:04:28,039 environment.py:93 INFO Environment variable MPI_LIB_STATIC set to (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVARMPI_LIB_STATIC set to (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable OMPI_CC set to gcc (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVAROMPI_CC set to gcc (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable OMPI_CXX set to g++ (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVAROMPI_CXX set to g++ (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable OMPI_F77 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVAROMPI_F77 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable OMPI_F90 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVAROMPI_F90 set to gfortran (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable OMPI_FC set to gfortran (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVAROMPI_FC set to gfortran (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 14:04:28,040 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable SCALAPACK_INC_DIR set to (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable EBVARSCALAPACK_INC_DIR set to (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable SCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable EBVARSCALAPACK_LIB_DIR set to /apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable SCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so,libpthread.so (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable SCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable EBVARSCALAPACK_MT_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a,libpthread.a (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable SCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable EBVARSCALAPACK_SHARED_LIBS set to libscalapack.so,libflexiblas.so,libgfortran.so (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable SCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,041 environment.py:93 INFO Environment variable EBVARSCALAPACK_STATIC_LIBS set to libscalapack.a,libflexiblas.a,libgfortran.a (previously undefined) +== 2023-07-04 14:04:28,041 easyblock.py:1165 INFO Enabling CUDA PTX cache of size 1024 MiB at /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/eb-cuda-cache +== 2023-07-04 14:04:28,042 environment.py:93 INFO Environment variable CUDA_CACHE_DISABLE set to 0 (previously undefined) +== 2023-07-04 14:04:28,042 environment.py:93 INFO Environment variable CUDA_CACHE_PATH set to /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/eb-cuda-cache (previously undefined) +== 2023-07-04 14:04:28,042 environment.py:93 INFO Environment variable CUDA_CACHE_MAXSIZE set to 1073741824 (previously undefined) +== 2023-07-04 14:04:28,042 easyblock.py:2112 INFO Using /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/ as start dir +== 2023-07-04 14:04:28,043 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 14:04:28,043 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 14:04:28,043 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 14:04:31,896 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 14:04:32,159 build_log.py:267 INFO ... (took 31 secs) +== 2023-07-04 14:04:32,161 build_log.py:267 INFO configuring... +== 2023-07-04 14:04:32,163 easyblock.py:3926 INFO Starting configure step +== 2023-07-04 14:04:32,163 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:04:32,163 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:04:32,163 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:04:32,164 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:04:32,164 easyblock.py:3934 INFO Running method configure_step part of step configure +== 2023-07-04 14:04:32,164 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) +== 2023-07-04 14:04:32,164 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 14:04:32,210 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 14:04:32,210 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 14:04:32,210 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 14:04:32,267 environment.py:93 INFO Environment variable CMAKE_INCLUDE_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/include/flexiblas:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/include:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/include:/apps/gent/RHEL8/cascadelake-ib/software/Qhull/2020.2-GCCcore-11.3.0/qhull/include:/apps/gent/RHEL8/cascadelake-ib/software/Qhull/2020.2-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/LibTIFF/4.3.0-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/jbigkit/2.1-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/Tk/8.6.12-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/X11/20220504-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/fontconfig/2.14.0-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/util-linux/2.38-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/freetype/2.12.1-GCCcore-11.3.0/include/freetype2:/apps/gent/RHEL8/cascadelake-ib/software/Brotli/1.0.9-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/pybind11/2.9.2-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/nvvm/include:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/extras/CUPTI/include:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/include:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/include:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/include:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/include/libxml2:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/include:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/include (previously undefined) +== 2023-07-04 14:04:32,268 environment.py:93 INFO Environment variable CMAKE_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64:/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib64:/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib64:/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Qhull/2020.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/LibTIFF/4.3.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libdeflate/1.10-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zstd/1.5.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/lz4/1.9.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/jbigkit/2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libjpeg-turbo/2.1.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tk/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/X11/20220504-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/fontconfig/2.14.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/util-linux/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/freetype/2.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Brotli/1.0.9-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpng/1.6.37-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib/python3.10/site-packages/numpy/core/lib:/apps/gent/RHEL8/cascadelake-ib/software/DB/18.1.40-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/expat/2.4.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/nvvm/lib64:/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/extras/CUPTI/lib64:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libiconv/1.17-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libarchive/3.6.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/cURL/7.83.0-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/FFTW.MPI/3.3.10-gompi-2022a/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenBLAS/0.3.20-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenMPI/4.1.4-GCC-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCC/1.0.0-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/PMIx/4.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libfabric/1.15.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/UCX/1.12.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libevent/2.1.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/hwloc/2.7.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libpciaccess/0.16-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libxml2/2.9.13-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/numactl/2.0.14-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64') +== 2023-07-04 14:04:32,268 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 14:04:32,271 run.py:236 INFO running cmd: sed -i'' 's/#include /#include \n#include /g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/spoa/src/alignment_engine.cpp && sed -i 's/==/>=/g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/pygenomeworks/requirements.txt && sed -i 's/~=/>=/g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/pygenomeworks/requirements.txt && cmake -DCMAKE_INSTALL_PREFIX=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -Dgw_cuda_gen_all_arch=OFF -Dgw_build_shared=ON /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/ +== 2023-07-04 14:04:52,665 run.py:648 INFO cmd "sed -i'' 's/#include /#include \n#include /g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/spoa/src/alignment_engine.cpp && sed -i 's/==/>=/g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/pygenomeworks/requirements.txt && sed -i 's/~=/>=/g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/pygenomeworks/requirements.txt && cmake -DCMAKE_INSTALL_PREFIX=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -Dgw_cuda_gen_all_arch=OFF -Dgw_build_shared=ON /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/" exited with exit code 0 and output: +-- The C compiler identification is GNU 11.3.0 +-- The CXX compiler identification is GNU 11.3.0 +-- Detecting C compiler ABI info +-- Detecting C compiler ABI info - done +-- Check for working C compiler: /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/gcc - skipped +-- Detecting C compile features +-- Detecting C compile features - done +-- Detecting CXX compiler ABI info +-- Detecting CXX compiler ABI info - done +-- Check for working CXX compiler: /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ - skipped +-- Detecting CXX compile features +-- Detecting CXX compile features - done +-- Enabling GenomeWorks unit tests +-- Enabling GenomeWorks benchmarks +-- Building GenomeWorks libraries as shared objects +CMake Warning (dev) at cmake/CUDA.cmake:20 (find_package): + Policy CMP0074 is not set: find_package uses _ROOT variables. + Run "cmake --help-policy CMP0074" for policy details. Use the cmake_policy + command to set the policy and suppress this warning. + + Environment variable CUDA_ROOT is set to: + + /apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0 + + For compatibility, CMake is ignoring the variable. +Call Stack (most recent call first): + CMakeLists.txt:71 (include) +This warning is for project developers. Use -Wno-dev to suppress it. + +-- Performing Test CMAKE_HAVE_LIBC_PTHREAD +-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed +-- Looking for pthread_create in pthreads +-- Looking for pthread_create in pthreads - not found +-- Looking for pthread_create in pthread +-- Looking for pthread_create in pthread - found +-- Found Threads: TRUE +-- Found CUDA: /apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0 (found suitable version "11.7", minimum required is "10.0") +-- Using CUDA 11.7 from /apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0 +CMake Deprecation Warning at 3rdparty/googletest/CMakeLists.txt:1 (cmake_minimum_required): + Compatibility with CMake < 2.8.12 will be removed from a future version of + CMake. + + Update the VERSION argument value or use a ... suffix to tell + CMake that the project does not need compatibility with older versions. + + +CMake Deprecation Warning at 3rdparty/googletest/googlemock/CMakeLists.txt:42 (cmake_minimum_required): + Compatibility with CMake < 2.8.12 will be removed from a future version of + CMake. + + Update the VERSION argument value or use a ... suffix to tell + CMake that the project does not need compatibility with older versions. + + +CMake Deprecation Warning at 3rdparty/googletest/googletest/CMakeLists.txt:53 (cmake_minimum_required): + Compatibility with CMake < 2.8.12 will be removed from a future version of + CMake. + + Update the VERSION argument value or use a ... suffix to tell + CMake that the project does not need compatibility with older versions. + + +-- Found PythonInterp: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python (found version "3.10.4") +CMake Warning (dev) at 3rdparty/benchmark/CMakeLists.txt:17 (option): + Policy CMP0077 is not set: option() honors normal variables. Run "cmake + --help-policy CMP0077" for policy details. Use the cmake_policy command to + set the policy and suppress this warning. + + For compatibility with older versions of CMake, option is clearing the + normal variable 'BENCHMARK_ENABLE_TESTING'. +This warning is for project developers. Use -Wno-dev to suppress it. + +CMake Warning (dev) at 3rdparty/benchmark/CMakeLists.txt:34 (option): + Policy CMP0077 is not set: option() honors normal variables. Run "cmake + --help-policy CMP0077" for policy details. Use the cmake_policy command to + set the policy and suppress this warning. + + For compatibility with older versions of CMake, option is clearing the + normal variable 'BENCHMARK_ENABLE_GTEST_TESTS'. +This warning is for project developers. Use -Wno-dev to suppress it. + +-- Failed to find LLVM FileCheck +-- Found Git: /usr/bin/git (found version "2.31.1") +-- git Version: v0.0.0 +-- Version: 0.0.0 +-- Performing Test HAVE_CXX_FLAG_STD_CXX11 +-- Performing Test HAVE_CXX_FLAG_STD_CXX11 - Success +-- Performing Test HAVE_CXX_FLAG_WALL +-- Performing Test HAVE_CXX_FLAG_WALL - Success +-- Performing Test HAVE_CXX_FLAG_WEXTRA +-- Performing Test HAVE_CXX_FLAG_WEXTRA - Success +-- Performing Test HAVE_CXX_FLAG_WSHADOW +-- Performing Test HAVE_CXX_FLAG_WSHADOW - Success +-- Performing Test HAVE_CXX_FLAG_WERROR +-- Performing Test HAVE_CXX_FLAG_WERROR - Success +-- Performing Test HAVE_CXX_FLAG_PEDANTIC +-- Performing Test HAVE_CXX_FLAG_PEDANTIC - Success +-- Performing Test HAVE_CXX_FLAG_PEDANTIC_ERRORS +-- Performing Test HAVE_CXX_FLAG_PEDANTIC_ERRORS - Success +-- Performing Test HAVE_CXX_FLAG_WSHORTEN_64_TO_32 +-- Performing Test HAVE_CXX_FLAG_WSHORTEN_64_TO_32 - Failed +-- Performing Test HAVE_CXX_FLAG_FSTRICT_ALIASING +-- Performing Test HAVE_CXX_FLAG_FSTRICT_ALIASING - Success +-- Performing Test HAVE_CXX_FLAG_WNO_DEPRECATED_DECLARATIONS +-- Performing Test HAVE_CXX_FLAG_WNO_DEPRECATED_DECLARATIONS - Success +-- Performing Test HAVE_CXX_FLAG_WNO_DEPRECATED +-- Performing Test HAVE_CXX_FLAG_WNO_DEPRECATED - Success +-- Performing Test HAVE_CXX_FLAG_WSTRICT_ALIASING +-- Performing Test HAVE_CXX_FLAG_WSTRICT_ALIASING - Success +-- Performing Test HAVE_CXX_FLAG_WD654 +-- Performing Test HAVE_CXX_FLAG_WD654 - Failed +-- Performing Test HAVE_CXX_FLAG_WTHREAD_SAFETY +-- Performing Test HAVE_CXX_FLAG_WTHREAD_SAFETY - Failed +-- Performing Test HAVE_CXX_FLAG_COVERAGE +-- Performing Test HAVE_CXX_FLAG_COVERAGE - Success +-- Performing Test HAVE_STD_REGEX +-- Performing Test HAVE_STD_REGEX +-- Performing Test HAVE_STD_REGEX -- success +-- Performing Test HAVE_GNU_POSIX_REGEX +-- Performing Test HAVE_GNU_POSIX_REGEX +-- Performing Test HAVE_GNU_POSIX_REGEX -- failed to compile +-- Performing Test HAVE_POSIX_REGEX +-- Performing Test HAVE_POSIX_REGEX +-- Performing Test HAVE_POSIX_REGEX -- success +-- Performing Test HAVE_STEADY_CLOCK +-- Performing Test HAVE_STEADY_CLOCK +-- Performing Test HAVE_STEADY_CLOCK -- success +-- Check if compiler accepts -pthread +-- Check if compiler accepts -pthread - yes +-- Performing Test BENCHMARK_HAS_O3_FLAG +-- Performing Test BENCHMARK_HAS_O3_FLAG - Success +-- Performing Test BENCHMARK_HAS_CXX03_FLAG +-- Performing Test BENCHMARK_HAS_CXX03_FLAG - Success +-- Performing Test BENCHMARK_HAS_WNO_ODR +-- Performing Test BENCHMARK_HAS_WNO_ODR - Success +-- Building htslib +-- Unrecognized Linux distribution - "Red Hat Enterprise Linux" +. Disabling packaging. +-- nvcc flags for gwbase: -lineinfo -use_fast_math -Xcompiler -Wall,-Wno-pedantic -std=c++14 +fatal: not a git repository (or any parent up to mount point /) +Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). +-- nvcc flags for cudapoa: -lineinfo -use_fast_math -Xcompiler -Wall,-Wno-pedantic -std=c++14 -arch=compute_60 --expt-relaxed-constexpr +fatal: not a git repository (or any parent up to mount point /) +Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). +-- Using CUDA 11.7 from /apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0 +-- Autodetected CUDA architecture(s): 8.6 +-- nvcc flags for cudamapper: -lineinfo -use_fast_math -Xcompiler -Wall,-Wno-pedantic -lineinfo --expt-extended-lambda -use_fast_math -Xcompiler -Wall,-Wno-pedantic -std=c++14 -gencode;arch=compute_86,code=sm_86 +-- nvcc flags for cudaaligner: -lineinfo -use_fast_math -Xcompiler -Wall,-Wno-pedantic -std=c++14 -arch=compute_60 --expt-relaxed-constexpr +fatal: not a git repository (or any parent up to mount point /) +Stopping at filesystem boundary (GIT_DISCOVERY_ACROSS_FILESYSTEM not set). +-- Autodetected CUDA architecture(s): 8.6 +-- nvcc flags for GenomeWorks: -lineinfo -use_fast_math -Xcompiler -Wall,-Wno-pedantic -std=c++14 --expt-relaxed-constexpr -gencode;arch=compute_86,code=sm_86 +-- Enabling Doxygen documentation generation +-- Found Doxygen: /apps/gent/RHEL8/cascadelake-ib/software/Doxygen/1.9.4-GCCcore-11.3.0/bin/doxygen (found version "1.9.4") found components: doxygen dot +-- clang-format not found. Auto-formatting disabled. +-- Configuring done +-- Generating done +-- Build files have been written to: /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj + +== 2023-07-04 14:04:52,666 run.py:662 WARNING Found 6 potential errors (some may be harmless) in output of sed -i'' 's/#include /#include \n#include /g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/spoa/src/alignment_engine.cpp && sed -i 's/==/>=/g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/pygenomeworks/requirements.txt && sed -i 's/~=/>=/g' /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/pygenomeworks/requirements.txt && cmake -DCMAKE_INSTALL_PREFIX=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0 -DCMAKE_BUILD_TYPE=Release -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -Dgw_cuda_gen_all_arch=OFF -Dgw_build_shared=ON /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/: + -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed + -- Failed to find LLVM FileCheck + -- Performing Test HAVE_CXX_FLAG_WSHORTEN_64_TO_32 - Failed + -- Performing Test HAVE_CXX_FLAG_WD654 - Failed + -- Performing Test HAVE_CXX_FLAG_WTHREAD_SAFETY - Failed + -- Performing Test HAVE_GNU_POSIX_REGEX -- failed to compile +== 2023-07-04 14:04:52,666 build_log.py:267 INFO ... (took 20 secs) +== 2023-07-04 14:04:52,668 build_log.py:267 INFO building... +== 2023-07-04 14:04:52,670 easyblock.py:3926 INFO Starting build step +== 2023-07-04 14:04:52,671 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 14:04:52,671 mpi.py:122 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI' +== 2023-07-04 14:04:52,671 mpi.py:307 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'nr_ranks': 1, 'cmd': 'xxx_command_xxx'}) +== 2023-07-04 14:04:52,671 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='genomeworks', builddir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0', cudamajver='11', cudaminver='7', cudashortver='11.7', cudaver='11.7.0', github_account='genomeworks', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', module_name='GenomeWorks/2021.02.2-foss-2022a-CUDA-11.7.0', mpi_cmd_prefix='mpirun -n 1', name='GenomeWorks', nameletter='G', nameletterlower='g', namelower='genomeworks', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/', toolchain_name='foss', toolchain_version='2022a', version='2021.02.2', version_major='2021', version_major_minor='2021.02', version_minor='02', versionprefix='', versionsuffix='-CUDA-11.7.0' +== 2023-07-04 14:04:52,671 easyblock.py:3934 INFO Running method build_step part of step build +== 2023-07-04 14:04:52,671 configuremake.py:350 INFO Building target '' +== 2023-07-04 14:04:52,674 run.py:236 INFO running cmd: make -j 8 +== 2023-07-04 14:05:01,761 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): cmd " make -j 8 " exited with exit code 2 and output: +/kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -S/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks -B/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj --check-build-system CMakeFiles/Makefile.cmake 0 +/kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_progress_start /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/CMakeFiles /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj//CMakeFiles/progress.marks +make -f CMakeFiles/Makefile2 all +make[1]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make -f CMakeFiles/htslib_project.dir/build.make CMakeFiles/htslib_project.dir/depend +make -f CMakeFiles/docs.dir/build.make CMakeFiles/docs.dir/depend +make -f common/base/CMakeFiles/gwbase.dir/build.make common/base/CMakeFiles/gwbase.dir/depend +make -f 3rdparty/googletest/googletest/CMakeFiles/gtest.dir/build.make 3rdparty/googletest/googletest/CMakeFiles/gtest.dir/depend +make -f 3rdparty/spoa/CMakeFiles/spoa.dir/build.make 3rdparty/spoa/CMakeFiles/spoa.dir/depend +make -f 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/build.make 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/depend +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/CMakeFiles/htslib_project.dir/DependInfo.cmake --color= +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/spoa /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/spoa /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/spoa/CMakeFiles/spoa.dir/DependInfo.cmake --color= +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/CMakeFiles/docs.dir/DependInfo.cmake --color= +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/googletest/googletest /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/googletest/googletest /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/googletest/googletest/CMakeFiles/gtest.dir/DependInfo.cmake --color= +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/common/base /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/common/base/CMakeFiles/gwbase.dir/DependInfo.cmake --color= +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_depends "Unix Makefiles" /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src/CMakeFiles/benchmark.dir/DependInfo.cmake --color= +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make -f CMakeFiles/htslib_project.dir/build.make CMakeFiles/htslib_project.dir/build +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make -f 3rdparty/spoa/CMakeFiles/spoa.dir/build.make 3rdparty/spoa/CMakeFiles/spoa.dir/build +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make -f CMakeFiles/docs.dir/build.make CMakeFiles/docs.dir/build +make -f common/base/CMakeFiles/gwbase.dir/build.make common/base/CMakeFiles/gwbase.dir/build +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make -f 3rdparty/googletest/googletest/CMakeFiles/gtest.dir/build.make 3rdparty/googletest/googletest/CMakeFiles/gtest.dir/build +make -f 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/build.make 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/build +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[2]: Entering directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +[ 0%] Creating directories for 'htslib_project' +/kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -Dcfgdir= -P /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/htslib/tmp/htslib_project-mkdirs.cmake +[ 1%] Building CXX object 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/benchmark.cc.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DHAVE_POSIX_REGEX -DHAVE_STD_REGEX -DHAVE_STEADY_CLOCK -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/include 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/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/include/claraparabricks/genomeworks/utils/threadsafe_containers.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/include/claraparabricks/genomeworks/utils/threadsafe_containers.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/include/claraparabricks/genomeworks/version.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/include/claraparabricks/genomeworks/version.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/io/include/claraparabricks/genomeworks/io/fasta_parser.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/io/include/claraparabricks/genomeworks/io/fasta_parser.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudapoa/include/claraparabricks/genomeworks/cudapoa/batch.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudapoa/include/claraparabricks/genomeworks/cudapoa/batch.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudapoa/include/claraparabricks/genomeworks/cudapoa/cudapoa.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudapoa/include/claraparabricks/genomeworks/cudapoa/cudapoa.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudapoa/include/claraparabricks/genomeworks/cudapoa/utils.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudapoa/include/claraparabricks/genomeworks/cudapoa/utils.hpp... +Reading /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudapoa/README.md... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/cudamapper.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/cudamapper.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/index.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/index.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/matcher.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/matcher.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/overlapper.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/overlapper.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/sketch_element.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/sketch_element.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/types.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/types.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/utils.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/include/claraparabricks/genomeworks/cudamapper/utils.hpp... +Reading /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudamapper/README.md... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/aligner.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/aligner.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/alignment.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/alignment.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/cudaaligner.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/cudaaligner.hpp... +Reading /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaaligner/README.md... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaextender/include/claraparabricks/genomeworks/cudaextender/cudaextender.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaextender/include/claraparabricks/genomeworks/cudaextender/cudaextender.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaextender/include/claraparabricks/genomeworks/cudaextender/extender.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaextender/include/claraparabricks/genomeworks/cudaextender/extender.hpp... +Preprocessing /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaextender/include/claraparabricks/genomeworks/cudaextender/utils.hpp... +Parsing file /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaextender/include/claraparabricks/genomeworks/cudaextender/utils.hpp... +Reading /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/cudaextender/README.md... +Reading /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md... +Building macro definition list... +Building group list... +Building directory list... +Building namespace list... +Building file list... +Building class list... +Building concept list... +Computing nesting relations for classes... +Associating documentation with classes... +Associating documentation with concepts... +Building example list... +Searching for enumerations... +Searching for documented typedefs... +Searching for members imported via using declarations... +Searching for included using directives... +Searching for documented variables... +Building interface member list... +Building member list... +Searching for friends... +Searching for documented defines... +Computing class inheritance relations... +Computing class usage relations... +Flushing cached template relations that have become invalid... +Computing class relations... +Add enum values to enums... +Searching[ 7%] No update step for 'htslib_project' +/kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E echo_append + for member function documentation... +Creating members for template instances... +Building page list... +Search for main page... +Computing page relations... +Determining the scope of groups... +Sorting lists... +Determining which enums are documented +Computing member relations... +Building full member lists recursively... +Adding members to member groups. +Computing member references... +Inheriting documentation... +Generating disk names... +Adding source references... +Adding xrefitems... +Sorting member lists... +Setting anonymous enum type... +Computing dependencies between directories... +Generating citations page... +Counting members... +Counting data structures... +Resolving user defined references... +Finding anchors and sections in the documentation... +Transferring function references... +Combining using relations... +Adding members to index pages... +Correcting members for VHDL... +Computing tooltip texts... +Generating style sheet... +Generating search indices... +Generating example documentation... +Generating file sources... +Generating code for file common/base/include/claraparabricks/genomeworks/gw_config.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/logging/logging.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/types.hpp... +Generating code for file cudamapper/include/claraparabricks/genomeworks/cudamapper/types.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/allocator.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/cudautils.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/device_buffer.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/exceptions.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/genomeutils.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/graph.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/mathutils.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/signed_integer_utils.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/stringutils.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/utils/threadsafe_containers.hpp... +Generating code for file common/base/include/claraparabricks/genomeworks/version.hpp... +Generating code for file common/io/include/claraparabricks/genomeworks/io/fasta_parser.hpp... +Generating code for file cudaaligner/include/claraparabricks/genomeworks/cudaaligner/aligner.hpp... +Generating code for file cudaaligner/include/claraparabricks/genomeworks/cudaaligner/alignment.hpp... +Generating code for file cudaaligner/include/claraparabricks/genomeworks/cudaaligner/cudaaligner.hpp... +Generating code for file cudaextender/include/claraparabricks/genomeworks/cudaextender/cudaextender.hpp... +Generating code for file cudaextender/include/claraparabricks/genomeworks/cudaextender/extender.hpp... +Generating code for file cudamapper/include/claraparabricks/genomeworks/cudamapper/cudamapper.hpp... +Generating code for file cudamapper/include/claraparabricks/genomeworks/cudamapper/index.hpp... +Generating code for file cudamapper/include/claraparabricks/genomeworks/cudamapper/matcher.hpp... +Generating code for file cudamapper/include/claraparabricks/genomeworks/cudamapper/overlapper.hpp... +Generating code for file cudamapper/include/claraparabricks/genomeworks/cudamapper/sketch_element.hpp... +Generating code for file cudapoa/include/claraparabricks/genomeworks/cudapoa/batch.hpp... +Generating code for file cudapoa/include/claraparabricks/genomeworks/cudapoa/cudapoa.hpp... +Generating code for file cudaextender/include/claraparabricks/genomeworks/cudaextender/utils.hpp... +Generating code for file cudamapper/include/claraparabricks/genomeworks/cudamapper/utils.hpp... +Generating code for file cudapoa//kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E touch /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/htslib/src/htslib_project-stamp/htslib_project-update +include/claraparabricks/genomeworks/cudapoa/utils.hpp... +Generating file documentation... +Generating docs for file common/base/include/claraparabricks/genomeworks/logging/logging.hpp... +Generating docs for file common/base/include/claraparabricks/genomeworks/utils/cudautils.hpp... +Generating page documentation... +Generating docs for page md_cudapoa_README... +Generating docs for page md_cudamapper_README... +Generating docs for page md_cudaaligner_README... +Generating docs for page md_cudaextender_README... +Generating group documentation... +Generating dependency graph for group logging +Generating dependency graph for group cudamapper +Generating class documentation... +Generating concept documentation... +Generating namespace index... +Generating docs for compound claraparabricks::genomeworks::CachingDeviceAllocator... +Generating docs for compound claraparabricks::genomeworks::CudaMallocAllocator... +Generating docs for compound claraparabricks::genomeworks::device_memory_allocation_exception... +Generating docs for compound claraparabricks::genomeworks::DirectedGraph... +Generating docs for compound claraparabricks::genomeworks::Graph... +Generating docs for compound claraparabricks::genomeworks::PairHash... +Generating docs for compound claraparabricks::genomeworks::scoped_device_switch... +Generating docs for compound claraparabricks::genomeworks::ThreadsafeDataProvider... +Generating docs for compound claraparabricks::genomeworks::ThreadsafeProducerConsumer... +Generating docs for compound claraparabricks::genomeworks::UndirectedGraph... +Generating docs for compound claraparabricks::genomeworks::cudaaligner::Aligner... +Generating docs for compound claraparabricks::genomeworks::cudaaligner::Alignment... +Generating docs for compound claraparabricks::genomeworks::cudaaligner::FormattedAlignment... +Generating docs for compound claraparabricks::genomeworks::cudaextender::Extender... +Generating docs for compound claraparabricks::genomeworks::cudaextender::ScoredSegmentPair... +Generating docs for compound claraparabricks::genomeworks::cudaextender::SeedPair... +Generating docs for compound claraparabricks::genomeworks::cudamapper::Anchor... +Generating docs for compound claraparabricks::genomeworks::cudamapper::ArrayBlock... +Generating docs for compound claraparabricks::genomeworks::cudamapper::Index... +Generating docs for compound claraparabricks::genomeworks::cudamapper::IndexDescriptor... +Generating docs for compound claraparabricks::genomeworks::cudamapper::IndexDescriptorHash... +Generating docs for compound claraparabricks::genomeworks::cudamapper::IndexHostCopyBase... +Generating docs for nested compound claraparabricks::genomeworks::cudamapper::IndexHostCopyBase::Span... +Generating docs for compound claraparabricks::genomeworks::cudamapper::IndexNotReadyException... +Generating docs for compound claraparabricks::genomeworks::cudamapper::Matcher... +Generating docs for compound claraparabricks::genomeworks::cudamapper::Overlap... +Generating docs for compound claraparabricks::genomeworks::cudamapper::Overlapper... +Generating docs for compound claraparabricks::genomeworks::cudamapper::SketchElement... +Generating docs for compound claraparabricks::genomeworks::cudapoa::Batch... +Generating docs for compound claraparabricks::genomeworks::cudapoa::BatchConfig... +Generating docs for compound claraparabricks::genomeworks::cudapoa::Entry... +Generating docs for compound claraparabricks::genomeworks::detail::CudaStreamDeleter... +Generating docs for compound claraparabricks::genomeworks::details::buffer... +Generating docs for compound claraparabricks::genomeworks::io::FastaParser... +Generating docs for compound claraparabricks::genomeworks::io::FastaSequence... +Generating graph info page... +Generating directory documentation... +Generating dependency graph for directory common/base +Generating dependency graph for directory common/base/include/claraparabricks +Generating dependency graph for directory common/io/include/claraparabricks +Generating dependency graph for directory cudaaligner/include/claraparabricks +Generating dependency graph for director/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md:6: warning: unable to resolve reference to 'enable-doc-generation' for \ref command +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md:14: warning: unable to resolve reference to 'clone-genomeworks' for \ref command +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md:15: warning: unable to resolve reference to 'system-requirements' for \ref command +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md:16: warning: unable to resolve reference to 'genomeworks-setup' for \ref command +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md:17: warning: unable to resolve reference to 'genomeworks-python-api' for \ref command +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md:18: warning: unable to resolve reference to 'development-support' for \ref command +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/README.md:124: warning: unable to resolve reference to 'build' for \ref command +[ 8%] No patch step for 'htslib_project' +/kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E echo_append +/kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E touch /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/htslib/src/htslib_project-stamp/htslib_project-patch +[ 10%] Performing configure step for 'htslib_project' +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/htslib && autoheader && autoconf && /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/htslib/configure --disable-bz2 --disable-lzma --disable-libcurl --disable-s3 --disable-gcs +[ 10%] Building CXX object common/base/CMakeFiles/gwbase.dir/src/logging.cpp.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/common/base && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DGW_ENABLE_CACHING_ALLOCATOR -Dgwbase_EXPORTS -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/htslib/include/htslib -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/include -I/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/include -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fopenmp -Werror -Wall -Wextra -O3 -DNDEBUG -fPIC -std=gnu++17 -MD -MT common/base/CMakeFiles/gwbase.dir/src/logging.cpp.o -MF CMakeFiles/gwbase.dir/src/logging.cpp.o.d -o CMakeFiles/gwbase.dir/src/logging.cpp.o -c /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/src/logging.cpp +[ 11%] Building CXX object common/base/CMakeFiles/gwbase.dir/src/graph.cpp.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/common/base && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DGW_ENABLE_CACHING_ALLOCATOR -Dgwbase_EXPORTS -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/htslib/include/htslib -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/include -I/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/include -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fopenmp -Werror -Wall -Wextra -O3 -DNDEBUG -fPIC -std=gnu++17 -MD -MT common/base/CMakeFiles/gwbase.dir/src/graph.cpp.o -MF CMakeFiles/gwbase.dir/src/graph.cpp.o.d -o CMakeFiles/gwbase.dir/src/graph.cpp.o -c /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/common/base/src/graph.cpp +y cudaextender/include/claraparabricks +Generating dependency graph for directory cudamapper/include/claraparabricks +Generating dependency graph for directory cudapoa/include/claraparabricks +Generating dependency graph for directory common +Generating dependency graph for directory cudaaligner/include/claraparabricks/genomeworks/cudaaligner +Generating dependency graph for directory cudaextender/include/claraparabricks/genomeworks/cudaextender +Generating dependency graph for directory cudamapper/include/claraparabricks/genomeworks/cudamapper +Generating dependency graph for directory cudapoa +Generating dependency graph for directory cudapoa/include/claraparabricks/genomeworks/cudapoa +Generating dependency graph for directory common/base/include/claraparabricks/genomeworks +Generating dependency graph for directory common/io/include/claraparabricks/genomeworks +Generating dependency graph for directory cudaaligner/include/claraparabricks/genomeworks +Generating dependency graph for directory cudaextender/include/claraparabricks/genomeworks +Generating dependency graph for directory cudamapper/include/claraparabricks/genomeworks +Generating dependency graph for directory cudapoa/include/claraparabricks/genomeworks +Generating dependency graph for directory common/base/include +Generating dependency graph for directory common/io/include +Generating dependency graph for directory cudaaligner/include +Generating dependency graph for directory cudaextender/include +Generating dependency graph for directory cudamapper/include +Generating dependency graph for directory cudapoa/include +Generating dependency graph for directory common/io +Generating dependency graph for directory common/io/include/claraparabricks/genomeworks/io +Generating dependency graph for directory common/base/include/claraparabricks/genomeworks/logging +Generating dependency graph for directory common/base/include/claraparabricks/genomeworks/utils +Generating index page... +Generating page index... +Generating module index... +Generating namespace index... +Generating namespace member index... +Generating concept index... +Generating annotated compound index... +Generating alphabetical compound index... +Generating hierarchical class index... +Generating graphical class hierarchy... +Generating member index... +Generating file index... +Generating file member index... 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3rdparty/benchmark/src/CMakeFiles/benchmark.dir/colorprint.cc.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DHAVE_POSIX_REGEX -DHAVE_STD_REGEX -DHAVE_STEADY_CLOCK -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/include -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/../include -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -std=c++11 -Wall -Wextra -Wshadow -pedantic -pedantic-errors -fstrict-aliasing -Wno-deprecated-declarations -Wstrict-aliasing -O3 -DNDEBUG -Werror -Wno-deprecated -fPIC -MD -MT 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/colorprint.cc.o -MF CMakeFiles/benchmark.dir/colorprint.cc.o.d -o CMakeFiles/benchmark.dir/colorprint.cc.o -c /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/colorprint.cc +In file included from /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/benchmark_register.cc:15: +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/benchmark_register.h: In function typename std::vector::iterator benchmark::internal::AddPowers(std::vector*, T, T, int): +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/benchmark_register.h:22:30: error: numeric_limits is not a member of std + 22 | static const T kmax = std::numeric_limits::max(); + | ^~~~~~~~~~~~~~ +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/benchmark_register.h:22:46: error: expected primary-expression before > token + 22 | static const T kmax = std::numeric_limits::max(); + | ^ +/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/benchmark_register.h:22:49: error: ::max has not been declared; did you mean std::max? + 22 | static const T kmax = std::numeric_limits::max(); + | ^~~ + | std::max +In file included from /kyukon/home/apps/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/include/c++/11.3.0/algorithm:62, + from /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/include/benchmark/benchmark.h:172, + from /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/internal_macros.h:4, + from /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/check.h:8, + from /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/benchmark_register.h:6, + from /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/benchmark_register.cc:15: +/kyukon/home/apps/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/include/c++/11.3.0/bits/stl_algo.h:3467:5: note: std::max declared here + 3467 | max(initializer_list<_Tp> __l, _Compare __comp) + | ^~~ +[ 17%] Building CXX object 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/commandlineflags.cc.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DHAVE_POSIX_REGEX -DHAVE_STD_REGEX -DHAVE_STEADY_CLOCK -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/include -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/../include -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -std=c++11 -Wall -Wextra -Wshadow -pedantic -pedantic-errors -fstrict-aliasing -Wno-deprecated-declarations -Wstrict-aliasing -O3 -DNDEBUG -Werror -Wno-deprecated -fPIC -MD -MT 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/commandlineflags.cc.o -MF CMakeFiles/benchmark.dir/commandlineflags.cc.o.d -o CMakeFiles/benchmark.dir/commandlineflags.cc.o -c /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/commandlineflags.cc +configure: error: cannot find required auxiliary files: config.guess config.sub +make[2]: *** [CMakeFiles/htslib_project.dir/build.make:95: 3rdparty/htslib/src/htslib_project-stamp/htslib_project-configure] Error 1 +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[1]: *** [CMakeFiles/Makefile2:622: CMakeFiles/htslib_project.dir/all] Error 2 +make[1]: *** Waiting for unfinished jobs.... +[ 17%] Building CXX object 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/complexity.cc.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DHAVE_POSIX_REGEX -DHAVE_STD_REGEX -DHAVE_STEADY_CLOCK -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/include -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/../include -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -std=c++11 -Wall -Wextra -Wshadow -pedantic -pedantic-errors -fstrict-aliasing -Wno-deprecated-declarations -Wstrict-aliasing -O3 -DNDEBUG -Werror -Wno-deprecated -fPIC -MD -MT 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/complexity.cc.o -MF CMakeFiles/benchmark.dir/complexity.cc.o.d -o CMakeFiles/benchmark.dir/complexity.cc.o -c /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/complexity.cc +[ 18%] Building CXX object 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/console_reporter.cc.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DHAVE_POSIX_REGEX -DHAVE_STD_REGEX -DHAVE_STEADY_CLOCK -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/include -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/../include -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -std=c++11 -Wall -Wextra -Wshadow -pedantic -pedantic-errors -fstrict-aliasing -Wno-deprecated-declarations -Wstrict-aliasing -O3 -DNDEBUG -Werror -Wno-deprecated -fPIC -MD -MT 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/console_reporter.cc.o -MF CMakeFiles/benchmark.dir/console_reporter.cc.o.d -o CMakeFiles/benchmark.dir/console_reporter.cc.o -c /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/console_reporter.cc +[ 18%] Building CXX object 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/counter.cc.o +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/benchmark/src && /apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -DHAVE_POSIX_REGEX -DHAVE_STD_REGEX -DHAVE_STEADY_CLOCK -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/include -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src -I/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/../include -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -std=c++11 -Wall -Wextra -Wshadow -pedantic -pedantic-errors -fstrict-aliasing -Wno-deprecated-declarations -Wstrict-aliasing -O3 -DNDEBUG -Werror -Wno-deprecated -fPIC -MD -MT 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/counter.cc.o -MF CMakeFiles/benchmark.dir/counter.cc.o.d -o CMakeFiles/benchmark.dir/counter.cc.o -c /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks/3rdparty/benchmark/src/counter.cc +make[2]: *** [3rdparty/benchmark/src/CMakeFiles/benchmark.dir/build.make:121: 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/benchmark_register.cc.o] Error 1 +make[2]: *** Waiting for unfinished jobs.... +[ 18%] Linking CXX shared library libgwio.so +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/common/io && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_link_script CMakeFiles/gwio.dir/link.txt --verbose=1 +/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin/g++ -fPIC -O2 -ftree-vectorize -march=native -fno-math-errno -fPIC -fopenmp -Werror -Wall -Wextra -O3 -DNDEBUG -L/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/tqdm/4.64.0-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/networkx/2.8.4-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/SciPy-bundle/2022.05-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/matplotlib/3.5.2-foss-2022a/lib -L/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FFTW/3.3.10-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/ScaLAPACK/2.2.0-gompi-2022a-fb/lib -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/FlexiBLAS/3.2.0-GCC-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib -shared -Wl,-soname,libgwio.so -o libgwio.so CMakeFiles/gwio.dir/src/fasta_parser.cpp.o CMakeFiles/gwio.dir/src/kseqpp_fasta_parser.cpp.o -Wl,-rpath,/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/common/base: ../base/libgwbase.so -lz /apps/gent/RHEL8/cascadelake-ib/software/CUDA/11.7.0/lib64/libcudart_static.a -lpthread -ldl /usr/lib64/librt.so +[ 20%] Linking CXX static library lib/libspoa.a +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/spoa && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -P CMakeFiles/spoa.dir/cmake_clean_target.cmake +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/spoa && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_link_script CMakeFiles/spoa.dir/link.txt --verbose=1 +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ar qc lib/libspoa.a CMakeFiles/spoa.dir/src/alignment_engine.cpp.o CMakeFiles/spoa.dir/src/graph.cpp.o CMakeFiles/spoa.dir/src/simd_alignment_engine.cpp.o CMakeFiles/spoa.dir/src/sisd_alignment_engine.cpp.o +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +[ 20%] Built target gwio +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ranlib lib/libspoa.a +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +[ 20%] Built target spoa +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make[1]: *** [CMakeFiles/Makefile2:779: 3rdparty/benchmark/src/CMakeFiles/benchmark.dir/all] Error 2 +[ 21%] Linking CXX static library ../../../lib/libgtest.a +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/googletest/googletest && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -P CMakeFiles/gtest.dir/cmake_clean_target.cmake +cd /tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj/3rdparty/googletest/googletest && /kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -E cmake_link_script CMakeFiles/gtest.dir/link.txt --verbose=1 +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ar qc ../../../lib/libgtest.a "CMakeFiles/gtest.dir/src/gtest-all.cc.o" +/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin/ranlib ../../../lib/libgtest.a +make[2]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +[ 21%] Built target gtest +make[1]: Leaving directory '/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/easybuild_obj' +make: *** [Makefile:149: all] Error 2 + (at easybuild/easybuild-framework/easybuild/tools/run.py:643 in parse_cmd_output) +== 2023-07-04 14:05:01,761 build_log.py:267 INFO ... (took 9 secs) +== 2023-07-04 14:05:01,763 filetools.py:2014 INFO Removing lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_GenomeWorks_2021.02.2-foss-2022a-CUDA-11.7.0.lock... +== 2023-07-04 14:05:01,765 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_GenomeWorks_2021.02.2-foss-2022a-CUDA-11.7.0.lock successfully removed. +== 2023-07-04 14:05:01,765 filetools.py:2018 INFO Lock removed: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_GenomeWorks_2021.02.2-foss-2022a-CUDA-11.7.0.lock +== 2023-07-04 14:05:01,765 easyblock.py:4257 WARNING build failed (first 300 chars): cmd " make -j 8 " exited with exit code 2 and output: +/kyukon/home/apps/RHEL8/cascadelake-ib/software/CMake/3.24.3-GCCcore-11.3.0/bin/cmake -S/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA-11.7.0/GenomeWorks -B/tmp/vsc44588/easybuild/build/GenomeWorks/2021.02.2/foss-2022a-CUDA- +== 2023-07-04 14:05:01,766 easyblock.py:328 INFO Closing log for application name GenomeWorks version 2021.02.2 diff --git a/169_Bonito/easybuild-pytest-7.4.0-20230704.024519.HqUDb.log b/169_Bonito/easybuild-pytest-7.4.0-20230704.024519.HqUDb.log new file mode 100644 index 00000000..04ef5dab --- /dev/null +++ b/169_Bonito/easybuild-pytest-7.4.0-20230704.024519.HqUDb.log @@ -0,0 +1,2493 @@ +== 2023-07-04 02:45:19,679 easyblock.py:313 INFO This is EasyBuild 4.7.3.dev0-r366e71d77260adc73e8976bffeccb83b1b289c5d (framework: 4.7.3.dev0-r366e71d77260adc73e8976bffeccb83b1b289c5d, easyblocks: 4.7.3.dev0-r8a7ffbad49ed3c9a4bf658f6a76c663792342e09) on host node4006.donphan.os. +== 2023-07-04 02:45:19,679 easyblock.py:319 INFO This is easyblock PythonBundle from module easybuild.easyblocks.generic.pythonbundle (/user/gent/445/vsc44588/easybuild/easybuild-easyblocks/easybuild/easyblocks/generic/pythonbundle.py) +== 2023-07-04 02:45:19,679 easyblock.py:1040 INFO Build dir set to /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0 +== 2023-07-04 02:45:19,679 easyblock.py:1097 INFO Software install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 +== 2023-07-04 02:45:19,679 easyblock.py:1102 INFO Module install dir set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:19,679 easyblock.py:288 INFO Init completed for application name pytest version 7.4.0 +== 2023-07-04 02:45:19,679 pythonbundle.py:73 INFO Detection of downloaded extension dependencies is enabled +== 2023-07-04 02:45:19,679 pythonbundle.py:75 INFO exts_default_options: {'source_urls': 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easyblock.py:679 INFO md5 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/flit_core-3.9.0.tar.gz: 3bc52f1952b9a78361114147da63c35b +== 2023-07-04 02:45:20,679 easyblock.py:679 INFO sha256 checksum for /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/flit_core-3.9.0.tar.gz: 72ad266176c4a3fcfab5f2930d76896059851240570ce9a98733b658cb786eba +== 2023-07-04 02:45:20,679 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for checksums.json: /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/CuPy +== 2023-07-04 02:45:20,679 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/445/vsc44588/easybuild/easybuild-framework/eb +== 2023-07-04 02:45:20,679 tools.py:289 INFO Not considering /user/gent/445/vsc44588/easybuild (no easybuild/easyconfigs subdir found) +== 2023-07-04 02:45:20,680 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/445/vsc44588/easybuild (via resolved path to 'eb')... +== 2023-07-04 02:45:20,823 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Couldn't find file checksums.json anywhere, and downloading it is disabled... Paths attempted (in order): /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/CuPy/p/pytest/checksums.json, /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/CuPy/pytest/checksums.json, /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/CuPy/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/p/pytest/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/pytest/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/p/pytest/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/pytest/checksums.json, /user/gent/445/vsc44588/easybuild/easybuild-easyconfigs/easybuild/easyconfigs/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/pytest/checksums.json, /data/gent/vo/001/gvo00117/easybuild/sources/checksums.json, /apps/gent/sources/p/pytest/checksums.json, /apps/gent/sources/pytest/checksums.json, /apps/gent/sources/checksums.json (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:870 in obtain_file) +== 2023-07-04 02:45:20,823 easyblock.py:685 INFO Checksum for extension source flit_core-3.9.0.tar.gz verified +== 2023-07-04 02:45:20,823 easyblock.py:532 INFO Fetched extension patches: [] +== 2023-07-04 02:45:20,824 easyblock.py:803 INFO Considering directory in which easyconfig file is located when searching for flit_scm-1.7.0.tar.gz: /kyukon/home/gent/445/vsc44588/inuits/vsc-software-stack/169_Bonito/CuPy +== 2023-07-04 02:45:20,824 tools.py:273 INFO Found location to 'eb' script via $EB_SCRIPT_PATH: /user/gent/445/vsc44588/easybuild/easybuild-framework/eb +== 2023-07-04 02:45:20,824 tools.py:289 INFO Not considering /user/gent/445/vsc44588/easybuild (no easybuild/easyconfigs subdir found) +== 2023-07-04 02:45:20,824 tools.py:297 INFO Also considering installation prefix /kyukon/home/gent/445/vsc44588/easybuild (via resolved path to 'eb')... +== 2023-07-04 02:45:21,182 filetools.py:816 INFO File size for https://pypi.python.org/simple/flit-scm: 5582 +== 2023-07-04 02:45:21,182 filetools.py:270 INFO Not showing progress bar for downloading small file (size 5582) +== 2023-07-04 02:45:21,183 filetools.py:823 INFO Downloaded file flit-scm_urls.html from url https://pypi.python.org/simple/flit-scm to /tmp/vsc44588/eb-gjrihs7a/tmp10qan3hd/flit-scm_urls.html +== 2023-07-04 02:45:21,183 filetools.py:855 INFO Successful download of file flit-scm_urls.html from url https://pypi.python.org/simple/flit-scm to path /tmp/vsc44588/eb-gjrihs7a/tmp10qan3hd/flit-scm_urls.html +== 2023-07-04 02:45:21,415 filetools.py:816 INFO File size for 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(took < 1 sec) +== 2023-07-04 02:45:24,294 build_log.py:267 INFO unpacking... +== 2023-07-04 02:45:24,296 easyblock.py:3926 INFO Starting source step +== 2023-07-04 02:45:24,296 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:24,296 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:24,296 easyblock.py:3934 INFO Running method checksum_step part of step source +== 2023-07-04 02:45:24,296 easyblock.py:3934 INFO Running method extract_step part of step source +== 2023-07-04 02:45:24,296 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:45:24,298 build_log.py:267 INFO patching... +== 2023-07-04 02:45:24,300 easyblock.py:3926 INFO Starting patch step +== 2023-07-04 02:45:24,300 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:24,300 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:24,300 easyblock.py:3934 INFO Running method patch_step part of step patch +== 2023-07-04 02:45:24,301 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:45:24,302 build_log.py:267 INFO preparing... +== 2023-07-04 02:45:24,304 easyblock.py:3926 INFO Starting prepare step +== 2023-07-04 02:45:24,304 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:24,305 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='None', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:24,305 easyblock.py:3934 INFO Running method prepare_step part of step prepare +== 2023-07-04 02:45:24,306 modules.py:626 INFO Checking whether binutils/2.38-GCCcore-11.3.0 exists... +== 2023-07-04 02:45:24,306 modules.py:631 INFO Module binutils/2.38-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-07-04 02:45:24,306 modules.py:654 INFO Result for existence check of binutils/2.38-GCCcore-11.3.0 module: True +== 2023-07-04 02:45:24,306 modules.py:626 INFO Checking whether Python/3.10.4-GCCcore-11.3.0 exists... +== 2023-07-04 02:45:24,306 modules.py:631 INFO Module Python/3.10.4-GCCcore-11.3.0 exists (found in list of available modules) +== 2023-07-04 02:45:24,306 modules.py:654 INFO Result for existence check of Python/3.10.4-GCCcore-11.3.0 module: True +== 2023-07-04 02:45:24,306 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:45:24,306 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:45:27,849 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:45:34,610 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib') +== 2023-07-04 02:45:37,738 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib') +== 2023-07-04 02:45:37,748 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:45:37,748 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:45:37,748 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:45:37,749 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:45:37,751 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:45:37,755 environment.py:93 INFO Environment variable CC set to gcc (previously undefined) +== 2023-07-04 02:45:37,755 environment.py:93 INFO Environment variable EBVARCC set to gcc (previously undefined) +== 2023-07-04 02:45:37,755 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable CPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/include (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/include (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable CXX set to g++ (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-07-04 02:45:37,756 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,757 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 02:45:37,757 easyblock.py:2112 INFO Using /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/ as start dir +== 2023-07-04 02:45:37,758 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:45:37,758 run.py:236 INFO running cmd: python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:45:41,921 run.py:236 INFO running cmd: python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:45:42,144 build_log.py:267 INFO ... (took 17 secs) +== 2023-07-04 02:45:42,146 build_log.py:267 INFO configuring... +== 2023-07-04 02:45:42,148 easyblock.py:3926 INFO Starting configure step +== 2023-07-04 02:45:42,148 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:42,148 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:42,148 easyblock.py:3934 INFO Running method configure_step part of step configure +== 2023-07-04 02:45:42,149 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:45:42,150 build_log.py:267 INFO building... +== 2023-07-04 02:45:42,152 easyblock.py:3926 INFO Starting build step +== 2023-07-04 02:45:42,152 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:42,153 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:42,153 easyblock.py:3934 INFO Running method build_step part of step build +== 2023-07-04 02:45:42,153 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:45:42,155 build_log.py:267 INFO testing... +== 2023-07-04 02:45:42,156 easyblock.py:3926 INFO Starting test step +== 2023-07-04 02:45:42,156 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:42,157 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:42,157 easyblock.py:3934 INFO Running method test_step part of step test +== 2023-07-04 02:45:42,157 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:45:42,159 build_log.py:267 INFO installing... +== 2023-07-04 02:45:42,160 easyblock.py:3926 INFO Starting install step +== 2023-07-04 02:45:42,161 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:42,161 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:42,161 easyblock.py:3934 INFO Running method stage_install_step part of step install +== 2023-07-04 02:45:42,161 easyblock.py:3934 INFO Running method make_installdir part of step install +== 2023-07-04 02:45:42,162 easyblock.py:1122 INFO Found old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 +== 2023-07-04 02:45:42,162 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 successfully removed. +== 2023-07-04 02:45:42,162 easyblock.py:1130 INFO Removed old directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 +== 2023-07-04 02:45:42,162 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:45:42,163 easyblock.py:3934 INFO Running method install_step part of step install +== 2023-07-04 02:45:42,163 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:45:42,165 build_log.py:267 INFO taking care of extensions... +== 2023-07-04 02:45:42,166 easyblock.py:3926 INFO Starting extensions step +== 2023-07-04 02:45:42,167 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:42,167 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:42,167 easyblock.py:3934 INFO Running method extensions_step part of step extensions +== 2023-07-04 02:45:42,167 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) +== 2023-07-04 02:45:42,167 easyblock.py:1678 INFO Loading fake module (pytest/7.4.0-GCCcore-11.3.0) +== 2023-07-04 02:45:42,246 easyblock.py:1595 INFO Only retaining paths for CMAKE_PREFIX_PATH that contain at least one file: [''] -> [] +== 2023-07-04 02:45:42,247 filetools.py:1913 INFO Creating directory /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all/pytest (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:45:42,247 easyblock.py:3742 INFO Module file /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all/pytest/7.4.0-GCCcore-11.3.0.lua written: help([==[ + +Description +=========== +The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. + + +More information +================ + - Homepage: https://docs.pytest.org/en/latest/ + + +Included extensions +=================== +elementpath-4.1.4, exceptiongroup-1.1.2, flit-core-3.9.0, flit-scm-1.7.0, +hypothesis-6.80.0, pytest-7.4.0, setuptools-scm-7.1.0, xmlschema-2.3.1 +]==]) + +whatis([==[Description: The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.]==]) +whatis([==[Homepage: https://docs.pytest.org/en/latest/]==]) +whatis([==[URL: https://docs.pytest.org/en/latest/]==]) +whatis([==[Extensions: elementpath-4.1.4, exceptiongroup-1.1.2, flit-core-3.9.0, flit-scm-1.7.0, hypothesis-6.80.0, pytest-7.4.0, setuptools-scm-7.1.0, xmlschema-2.3.1]==]) + +local root = "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0" + +conflict("pytest") + +if not ( isloaded("GCCcore/11.3.0") ) then + load("GCCcore/11.3.0") +end + +if not ( isloaded("Python/3.10.4-GCCcore-11.3.0") ) then + load("Python/3.10.4-GCCcore-11.3.0") +end + +setenv("EBROOTPYTEST", root) +setenv("EBVERSIONPYTEST", "7.4.0") +setenv("EBDEVELPYTEST", pathJoin(root, "easybuild/pytest-7.4.0-GCCcore-11.3.0-easybuild-devel")) + +prepend_path("PYTHONPATH", pathJoin(root, "lib/python3.10/site-packages")) +-- Built with EasyBuild version 4.7.3.dev0-r366e71d77260adc73e8976bffeccb83b1b289c5d +setenv("EBEXTSLISTPYTEST", "setuptools-scm-7.1.0,flit-core-3.9.0,flit-scm-1.7.0,exceptiongroup-1.1.2,hypothesis-6.80.0,elementpath-4.1.4,xmlschema-2.3.1,pytest-7.4.0") + +== 2023-07-04 02:45:42,249 filetools.py:1913 INFO Creating directory /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/lib/pytest (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:45:42,249 easyblock.py:3773 INFO Skipping devel module... +== 2023-07-04 02:45:42,249 filetools.py:338 INFO Symlinked 7.4.0-GCCcore-11.3.0.lua to /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all/pytest/default +== 2023-07-04 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'/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/man:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/share/man:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/man:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/share/man::') +== 2023-07-04 02:45:46,266 environment.py:93 INFO Environment variable MODULEPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc (previous value: '/tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc') +== 2023-07-04 02:45:46,266 environment.py:93 INFO Environment variable PATH set to /user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:45:46,266 environment.py:93 INFO Environment variable _LMFILES_ set to /etc/modulefiles/vsc/env/vsc/donphan.lua:/etc/modulefiles/vsc/env/slurm/donphan.lua:/etc/modulefiles/vsc/env/software/donphan.lua:/etc/modulefiles/vsc/cluster/donphan.lua (previous value: '/etc/modulefiles/vsc/env/vsc/donphan.lua:/etc/modulefiles/vsc/env/slurm/donphan.lua:/etc/modulefiles/vsc/env/software/donphan.lua:/etc/modulefiles/vsc/cluster/donphan.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/GCCcore/11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/zlib/1.2.12-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/binutils/2.38-GCCcore-11.3.0.lua:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/bzip2/1.0.8-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/ncurses/6.3-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libreadline/8.1.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/Tcl/8.6.12-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/SQLite/3.38.3-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/XZ/5.2.5-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/GMP/6.2.1-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libffi/3.4.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/OpenSSL/1.1.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/Python/3.10.4-GCCcore-11.3.0.lua') +== 2023-07-04 02:45:46,268 modules.py:472 INFO $MODULEPATH set via list of module paths (w/ 'module use'): /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc +== 2023-07-04 02:45:51,328 environment.py:93 INFO Environment variable LD_LIBRARY_PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/lib:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/lib64:/apps/gent/RHEL8/cascadelake-ib/software/GMP/6.2.1-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/lib:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/lib:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/lib') +== 2023-07-04 02:45:51,328 easyblock.py:2870 INFO Installing extensions +== 2023-07-04 02:45:51,336 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:51,337 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:51,337 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:51,337 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:51,337 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:51,338 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:51,339 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:51,339 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:51,340 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:51,340 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:51,340 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:51,340 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:51,341 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:51,342 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:51,342 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:51,342 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:51,345 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,046 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,047 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,049 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'setuptools_scm' +== 2023-07-04 02:45:54,049 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,049 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previously undefined) +== 2023-07-04 02:45:54,049 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,049 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,057 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:54,058 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:54,058 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:54,058 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:54,059 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:54,059 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:54,061 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:54,061 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:54,061 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:54,062 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:54,062 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:54,062 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:54,062 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:54,062 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:54,063 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:54,063 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:54,065 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,066 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,067 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,068 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'flit_core' +== 2023-07-04 02:45:54,069 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,069 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previous value: '/tmp/vsc44588/eb-gjrihs7a') +== 2023-07-04 02:45:54,069 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,069 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,070 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:54,071 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:54,071 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:54,071 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:54,071 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:54,071 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:54,071 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:54,071 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:54,072 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:54,072 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:54,072 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:54,073 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:54,073 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:54,074 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:54,074 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:54,074 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:54,074 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:54,074 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:54,074 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:54,074 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:54,075 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,076 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,076 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,078 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'flit_scm' +== 2023-07-04 02:45:54,078 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,078 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previous value: '/tmp/vsc44588/eb-gjrihs7a') +== 2023-07-04 02:45:54,078 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,078 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,079 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:54,080 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:54,080 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:54,080 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:54,080 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:54,080 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:54,080 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:54,081 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:54,081 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:54,081 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:54,082 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:54,082 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:54,082 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:54,082 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:54,082 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:54,082 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:54,083 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:54,083 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:54,084 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,085 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,086 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,087 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'exceptiongroup' +== 2023-07-04 02:45:54,087 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,087 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previous value: '/tmp/vsc44588/eb-gjrihs7a') +== 2023-07-04 02:45:54,087 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,087 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,088 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:54,089 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:54,089 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:54,089 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:54,089 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:54,089 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:54,090 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:54,090 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:54,090 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:54,091 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:54,091 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:54,091 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:54,091 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:54,091 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:54,091 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:54,092 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:54,092 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:54,093 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,094 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,095 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,096 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'hypothesis' +== 2023-07-04 02:45:54,096 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,096 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previous value: '/tmp/vsc44588/eb-gjrihs7a') +== 2023-07-04 02:45:54,096 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,096 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,097 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:54,098 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:54,098 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:54,098 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:54,098 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:54,098 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:54,099 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:54,099 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:54,100 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:54,100 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:54,100 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:54,100 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:54,101 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:54,102 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:54,102 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,103 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,104 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,105 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'elementpath' +== 2023-07-04 02:45:54,105 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,105 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previous value: '/tmp/vsc44588/eb-gjrihs7a') +== 2023-07-04 02:45:54,106 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,106 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,107 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:54,107 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:54,107 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:54,107 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:54,107 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:54,108 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:54,108 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:54,108 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:54,109 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:54,109 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:54,109 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:54,109 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:54,110 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:54,111 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:54,111 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:54,111 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,112 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,113 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,114 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'xmlschema' +== 2023-07-04 02:45:54,114 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,115 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previous value: '/tmp/vsc44588/eb-gjrihs7a') +== 2023-07-04 02:45:54,115 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,115 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,116 easyconfig.py:464 INFO Performing quick parse to check for valid easyconfig file... +== 2023-07-04 02:45:54,116 environment.py:93 INFO Environment variable LMOD_QUIET set to 1 (previous value: '1') +== 2023-07-04 02:45:54,116 environment.py:93 INFO Environment variable LMOD_IGNORE_CACHE set to 1 (previous value: '1') +== 2023-07-04 02:45:54,117 environment.py:93 INFO Environment variable LMOD_REDIRECT set to no (previous value: 'no') +== 2023-07-04 02:45:54,117 environment.py:93 INFO Environment variable LMOD_EXTENDED_DEFAULT set to no (previous value: 'no') +== 2023-07-04 02:45:54,117 modules.py:299 INFO Full path for Lmod command is /usr/share/lmod/lmod/libexec/lmod, so using it +== 2023-07-04 02:45:54,117 modules.py:455 INFO Prepended list of module paths with path used by EasyBuild: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all +== 2023-07-04 02:45:54,117 easyconfig.py:473 INFO Obtained list of valid module classes: ['base', 'ai', 'astro', 'bio', 'cae', 'chem', 'compiler', 'data', 'debugger', 'devel', 'geo', 'ide', 'lang', 'lib', 'math', 'mpi', 'numlib', 'perf', 'quantum', 'phys', 'system', 'toolchain', 'tools', 'vis'] +== 2023-07-04 02:45:54,118 easyconfig.py:1896 INFO Derived full easyblock module path for PythonBundle: easybuild.easyblocks.generic.pythonbundle +== 2023-07-04 02:45:54,118 easyconfig.py:1943 INFO Successfully obtained class 'PythonBundle' for easyblock 'PythonBundle' (software name 'pytest') +== 2023-07-04 02:45:54,118 easyconfig.py:705 INFO Parsing easyconfig file None with rawcontent: easyblock = 'PythonBundle' + +name = 'pytest' +version = '7.4.0' + +homepage = 'https://docs.pytest.org/en/latest/' +description = """The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.""" + +toolchain = {'name': 'GCCcore', 'version': '11.3.0'} + +builddependencies = [ + ('binutils', '2.38'), +] + +dependencies = [ + ('Python', '3.10.4'), +] + +use_pip = True + +exts_default_options = {'source_urls': [PYPI_LOWER_SOURCE]} + +# Note! Some of the file system related tests may fail on shared file systems. +# Notably TestPOSIXLocalPath.test_copy_stat_file, TestPOSIXLocalPath.test_copy_stat_dir +# and test_source_mtime_long_long are known to fail on GPFS +# Build with buildpath and tmpdir set to a local file system to avoid this +# or use --ignore-test-failures +_skip_tests = [ + 'testing/io/test_terminalwriter.py', + 'testing/test_terminal.py', + 'testing/test_debugging.py', + 'testing/test_config.py', + 'testing/test_helpconfig.py', +] +_ignore_tests = ' --ignore='.join(_skip_tests) + +exts_list = [ + ('setuptools-scm', '7.1.0', { + 'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', + 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27'], + }), + ('flit-core', '3.9.0', { + 'source_tmpl': 'flit_core-%(version)s.tar.gz', + }), + ('flit-scm', '1.7.0', { + 'source_tmpl': 'flit_scm-%(version)s.tar.gz', + 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2'], + }), + ('exceptiongroup', '1.1.2', { + }), + ('hypothesis', '6.80.0', { + }), + ('elementpath', '4.1.4', { + }), + ('xmlschema', '2.3.1', { + }), + (name, version, { + }), +] + +sanity_check_commands = [ + "python -c 'import pytest'", + 'cd %%(builddir)s/%%(name)s/%%(name)s-%%(version)s && %%(installdir)s/bin/pytest --ignore=%s testing' + % _ignore_tests, +] + +sanity_pip_check = True + +moduleclass = 'lib' + +== 2023-07-04 02:45:54,119 parser.py:139 INFO Type checking of easyconfig parameter values passed! +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter builddependencies: value [('binutils', '2.38')] (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter dependencies: value [('Python', '3.10.4')] (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter description: value The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter easyblock: value PythonBundle (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter exts_default_options: value {'source_urls': ['https://pypi.python.org/packages/source/%(nameletterlower)s/%(namelower)s']} (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter exts_list: value [('setuptools-scm', '7.1.0', {'source_tmpl': 'setuptools_scm-%(version)s.tar.gz', 'checksums': ['6c508345a771aad7d56ebff0e70628bf2b0ec7573762be9960214730de278f27']}), ('flit-core', '3.9.0', {'source_tmpl': 'flit_core-%(version)s.tar.gz'}), ('flit-scm', '1.7.0', {'source_tmpl': 'flit_scm-%(version)s.tar.gz', 'checksums': ['961bd6fb24f31bba75333c234145fff88e6de0a90fc0f7e5e7c79deca69f6bb2']}), ('exceptiongroup', '1.1.2', {}), ('hypothesis', '6.80.0', {}), ('elementpath', '4.1.4', {}), ('xmlschema', '2.3.1', {}), ('pytest', '7.4.0', {})] (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter homepage: value https://docs.pytest.org/en/latest/ (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter moduleclass: value lib (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter name: value pytest (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter sanity_check_commands: value ["python -c 'import pytest'", 'cd %(builddir)s/%(name)s/%(name)s-%(version)s && %(installdir)s/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter sanity_pip_check: value True (type: ) +== 2023-07-04 02:45:54,119 easyconfig.py:686 INFO setting easyconfig parameter toolchain: value {'name': 'GCCcore', 'version': '11.3.0'} (type: ) +== 2023-07-04 02:45:54,120 easyconfig.py:686 INFO setting easyconfig parameter use_pip: value True (type: ) +== 2023-07-04 02:45:54,120 easyconfig.py:686 INFO setting easyconfig parameter version: value 7.4.0 (type: ) +== 2023-07-04 02:45:54,120 easyconfig.py:747 INFO Parsing dependency specifications... +== 2023-07-04 02:45:54,120 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:45:54,121 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', github_account='pytest', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:45:54,121 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'binutils', 'version': '2.38', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': True, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,122 easyconfig.py:2357 INFO Minimally resolving dependency {'full_mod_name': None, 'short_mod_name': None, 'name': 'Python', 'version': '3.10.4', 'versionsuffix': '', 'toolchain': {'name': 'GCCcore', 'version': '11.3.0'}, 'toolchain_inherited': True, 'system': False, 'hidden': False, 'build_only': False, 'external_module': False, 'external_module_metadata': {}} using toolchain {'name': 'GCCcore', 'version': '11.3.0'} +== 2023-07-04 02:45:54,124 pythonpackage.py:307 INFO Using default value for expected module name (lowercase software name): 'pytest' +== 2023-07-04 02:45:54,124 pythonpackage.py:339 INFO Using pip with --no-deps option +== 2023-07-04 02:45:54,124 environment.py:93 INFO Environment variable XDG_CACHE_HOME set to /tmp/vsc44588/eb-gjrihs7a (previous value: '/tmp/vsc44588/eb-gjrihs7a') +== 2023-07-04 02:45:54,124 pythonpackage.py:356 INFO Using /tmp/vsc44588/eb-gjrihs7a as pip cache directory +== 2023-07-04 02:45:54,124 pythonpackage.py:371 INFO Using '%(python)s -m pip install --prefix=%(prefix)s %(installopts)s %(loc)s' as install command +== 2023-07-04 02:45:54,205 easyblock.py:1874 INFO Installing extensions sequentially... +== 2023-07-04 02:45:54,205 easyblock.py:1880 INFO Starting extension setuptools-scm +== 2023-07-04 02:45:54,205 build_log.py:267 INFO installing extension setuptools-scm 7.1.0 (1/8)... +== 2023-07-04 02:45:54,290 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:45:54,291 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:45:57,536 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:45:57,537 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:45:57,540 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:45:57,541 environment.py:93 INFO Environment variable CC set to gcc (previously undefined) +== 2023-07-04 02:45:57,541 environment.py:93 INFO Environment variable EBVARCC set to gcc (previously undefined) +== 2023-07-04 02:45:57,541 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable CXX set to g++ (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-07-04 02:45:57,542 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,543 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 02:45:57,544 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:45:57,545 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:45:57,545 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:01,788 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:02,027 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/setuptoolsscm (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:02,033 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/setuptools_scm-7.1.0.tar.gz +== 2023-07-04 02:46:02,105 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:02,107 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) +== 2023-07-04 02:46:02,108 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:02,137 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:02,137 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:02,137 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:02,170 build_log.py:267 INFO building... +== 2023-07-04 02:46:02,173 build_log.py:267 INFO testing... +== 2023-07-04 02:46:02,175 build_log.py:267 INFO installing... +== 2023-07-04 02:46:02,178 filetools.py:1913 INFO Creating directory /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:02,178 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:02,178 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:02,179 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:02,179 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:06,734 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:06,735 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:06,738 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:13,243 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/setuptoolsscm/setuptools_scm-7.1.0 + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' +Building wheels for collected packages: setuptools-scm + Building wheel for setuptools-scm (pyproject.toml): started + Building wheel for setuptools-scm (pyproject.toml): finished with status 'done' + Created wheel for setuptools-scm: filename=setuptools_scm-7.1.0-py3-none-any.whl size=43846 sha256=f6547bb332fb5bfc7ab64a56eb46ee3217325a96183ae35e32ca5db05cb14883 + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/c4/e0/68/33540f4155d79fb222f90895f99df47cc206400454f93d0a21 +Successfully built setuptools-scm +Installing collected packages: setuptools-scm +Successfully installed setuptools-scm-7.1.0 + +== 2023-07-04 02:46:13,243 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:13,244 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:13,244 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:13,244 build_log.py:267 INFO ... (took 19 secs) +== 2023-07-04 02:46:13,246 easyblock.py:1880 INFO Starting extension flit-core +== 2023-07-04 02:46:13,247 build_log.py:267 INFO installing extension flit-core 3.9.0 (2/8)... +== 2023-07-04 02:46:13,334 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:46:13,334 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:46:13,334 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:46:13,335 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:46:13,336 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable CC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable CXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable F77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:13,338 environment.py:93 INFO Environment variable F90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:13,339 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:13,340 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:13,340 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:13,340 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:13,340 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:13,340 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:13,340 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:13,568 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:13,802 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/flitcore (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:13,805 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/flit_core-3.9.0.tar.gz +== 2023-07-04 02:46:13,830 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:13,833 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:46:13,833 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:13,862 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:13,862 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:13,862 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:13,895 build_log.py:267 INFO building... +== 2023-07-04 02:46:13,898 build_log.py:267 INFO testing... +== 2023-07-04 02:46:13,900 build_log.py:267 INFO installing... +== 2023-07-04 02:46:13,902 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:13,903 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:13,903 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:13,903 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:14,276 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:14,277 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:14,280 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:15,173 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/flitcore/flit_core-3.9.0 + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' +Building wheels for collected packages: flit_core + Building wheel for flit_core (pyproject.toml): started + Building wheel for flit_core (pyproject.toml): finished with status 'done' + Created wheel for flit_core: filename=flit_core-3.9.0-py3-none-any.whl size=63141 sha256=5a6505b7c8a8e611b1845ebf45884cb63cf5e6d57ffc0bebe59046f08d65a20e + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/0b/24/bf/ae5005b83d68c97ca2e3b9847ede9b73123c29e476f72d24e2 +Successfully built flit_core +Installing collected packages: flit_core +Successfully installed flit_core-3.9.0 + +== 2023-07-04 02:46:15,173 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:15,173 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:15,173 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:15,173 build_log.py:267 INFO ... (took 1 secs) +== 2023-07-04 02:46:15,176 easyblock.py:1880 INFO Starting extension flit-scm +== 2023-07-04 02:46:15,176 build_log.py:267 INFO installing extension flit-scm 1.7.0 (3/8)... +== 2023-07-04 02:46:15,263 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:46:15,263 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:46:15,263 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:46:15,263 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:46:15,264 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:46:15,266 environment.py:93 INFO Environment variable CC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:15,266 environment.py:93 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:15,266 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,266 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,266 environment.py:93 INFO Environment variable CXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:15,266 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable F77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable F90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:15,267 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:15,268 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:15,268 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:15,268 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:15,268 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:15,501 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:15,730 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/flitscm (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:15,734 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/flit_scm-1.7.0.tar.gz +== 2023-07-04 02:46:15,749 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:15,751 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:46:15,751 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:15,780 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:15,781 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:15,781 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:15,813 build_log.py:267 INFO building... +== 2023-07-04 02:46:15,816 build_log.py:267 INFO testing... +== 2023-07-04 02:46:15,819 build_log.py:267 INFO installing... +== 2023-07-04 02:46:15,821 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:15,821 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:15,821 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:15,821 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:16,181 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:16,182 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:16,185 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:17,030 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/flitscm/flit_scm-1.7.0 + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' +Building wheels for collected packages: flit_scm + Building wheel for flit_scm (pyproject.toml): started + Building wheel for flit_scm (pyproject.toml): finished with status 'done' + Created wheel for flit_scm: filename=flit_scm-1.7.0-py3-none-any.whl size=3017 sha256=15f22eead9c1745c8b1d1141d04be9d857007100e451ac208d2c42e0747c94b6 + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/9f/3f/58/f89ec9b182ffbb51ff2994aafae84c82840fc4435b844fbb87 +Successfully built flit_scm +Installing collected packages: flit_scm +Successfully installed flit_scm-1.7.0 + +== 2023-07-04 02:46:17,030 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:17,031 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:17,031 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:17,031 build_log.py:267 INFO ... (took 1 secs) +== 2023-07-04 02:46:17,033 easyblock.py:1880 INFO Starting extension exceptiongroup +== 2023-07-04 02:46:17,033 build_log.py:267 INFO installing extension exceptiongroup 1.1.2 (4/8)... +== 2023-07-04 02:46:17,120 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:46:17,120 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:46:17,120 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:46:17,121 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:46:17,122 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable CC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable CXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable F77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable F90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,124 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:17,125 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:17,126 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:17,126 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:17,126 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:17,355 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:17,589 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/exceptiongroup (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:17,592 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/exceptiongroup-1.1.2.tar.gz +== 2023-07-04 02:46:17,626 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:17,628 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:46:17,629 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:17,658 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:17,658 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:17,658 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:17,691 build_log.py:267 INFO building... +== 2023-07-04 02:46:17,693 build_log.py:267 INFO testing... +== 2023-07-04 02:46:17,696 build_log.py:267 INFO installing... +== 2023-07-04 02:46:17,698 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:17,698 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:17,698 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:17,698 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:18,061 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:18,061 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:18,065 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:18,898 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/exceptiongroup/exceptiongroup-1.1.2 + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' +Building wheels for collected packages: exceptiongroup + Building wheel for exceptiongroup (pyproject.toml): started + Building wheel for exceptiongroup (pyproject.toml): finished with status 'done' + Created wheel for exceptiongroup: filename=exceptiongroup-1.1.2-py3-none-any.whl size=14446 sha256=d2bcb809f4f731748dec50d5c6b47e34b24f8a9266d61ac32432d67931a966a1 + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/8d/f2/78/ce5c584f005eebce2da5881d610c50424224250b44efdc668e +Successfully built exceptiongroup +Installing collected packages: exceptiongroup +Successfully installed exceptiongroup-1.1.2 + +== 2023-07-04 02:46:18,899 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:18,899 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:18,899 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:18,899 build_log.py:267 INFO ... (took 1 secs) +== 2023-07-04 02:46:18,901 easyblock.py:1880 INFO Starting extension hypothesis +== 2023-07-04 02:46:18,902 build_log.py:267 INFO installing extension hypothesis 6.80.0 (5/8)... +== 2023-07-04 02:46:18,988 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:46:18,989 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:46:18,989 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:46:18,989 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:46:18,990 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable CC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable CXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable F77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable F90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:18,992 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:18,993 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:18,994 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:18,994 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:18,994 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:18,994 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:18,994 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:18,994 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:19,220 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:19,446 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/hypothesis (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:19,450 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/hypothesis-6.80.0.tar.gz +== 2023-07-04 02:46:19,491 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:19,493 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:46:19,493 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:19,522 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:19,522 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:19,522 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:19,555 build_log.py:267 INFO building... +== 2023-07-04 02:46:19,558 build_log.py:267 INFO testing... +== 2023-07-04 02:46:19,561 build_log.py:267 INFO installing... +== 2023-07-04 02:46:19,563 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:19,563 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:19,564 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:19,564 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:19,924 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:19,925 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:19,928 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:24,111 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/hypothesis/hypothesis-6.80.0 + Preparing metadata (setup.py): started + Preparing metadata (setup.py): finished with status 'done' +Building wheels for collected packages: hypothesis + Building wheel for hypothesis (setup.py): started + Building wheel for hypothesis (setup.py): finished with status 'done' + Created wheel for hypothesis: filename=hypothesis-6.80.0-py3-none-any.whl size=414837 sha256=f569ab4ba38b90829d0087ae3b6742157372459f3a5a3194a44e7193e57b812b + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/3a/84/ea/d1d650900419e65fdb4325034f773a184d4c46361b1899d99c +Successfully built hypothesis +Installing collected packages: hypothesis +Successfully installed hypothesis-6.80.0 + +== 2023-07-04 02:46:24,112 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:24,112 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:24,112 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:24,112 build_log.py:267 INFO ... (took 5 secs) +== 2023-07-04 02:46:24,115 easyblock.py:1880 INFO Starting extension elementpath +== 2023-07-04 02:46:24,115 build_log.py:267 INFO installing extension elementpath 4.1.4 (6/8)... +== 2023-07-04 02:46:24,202 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:46:24,202 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:46:24,202 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:46:24,203 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:46:24,204 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:46:24,205 environment.py:93 INFO Environment variable CC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:24,205 environment.py:93 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:24,205 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,205 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable CXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable F77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable F90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,206 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:24,207 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:24,207 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:24,207 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:24,207 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:24,448 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:24,679 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/elementpath (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:24,682 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/elementpath-4.1.4.tar.gz +== 2023-07-04 02:46:24,753 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:24,755 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:46:24,755 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:24,784 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:24,784 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:24,785 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:24,817 build_log.py:267 INFO building... +== 2023-07-04 02:46:24,820 build_log.py:267 INFO testing... +== 2023-07-04 02:46:24,822 build_log.py:267 INFO installing... +== 2023-07-04 02:46:24,825 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:24,825 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:24,825 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:24,825 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:25,183 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:25,183 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:25,186 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:28,780 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/elementpath/elementpath-4.1.4 + Preparing metadata (setup.py): started + Preparing metadata (setup.py): finished with status 'done' +Building wheels for collected packages: elementpath + Building wheel for elementpath (setup.py): started + Building wheel for elementpath (setup.py): finished with status 'done' + Created wheel for elementpath: filename=elementpath-4.1.4-py3-none-any.whl size=216380 sha256=da8e51eb24f326159cf41efead0054bd47edb99ed048822264f6218c9b1c149e + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/02/de/ee/a258842a8b667acd507fc6f54e47e67150f6134f70b5769ccf +Successfully built elementpath +Installing collected packages: elementpath +Successfully installed elementpath-4.1.4 + +== 2023-07-04 02:46:28,780 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:28,780 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:28,781 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:28,781 build_log.py:267 INFO ... (took 4 secs) +== 2023-07-04 02:46:28,783 easyblock.py:1880 INFO Starting extension xmlschema +== 2023-07-04 02:46:28,786 build_log.py:267 INFO installing extension xmlschema 2.3.1 (7/8)... +== 2023-07-04 02:46:28,873 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:46:28,873 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:46:28,873 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:46:28,873 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:46:28,874 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:46:28,876 environment.py:93 INFO Environment variable CC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:28,876 environment.py:93 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:28,876 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,876 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,876 environment.py:93 INFO Environment variable CXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:28,876 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:28,876 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable F77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable F90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:28,877 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:28,878 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:28,878 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:28,878 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:28,878 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:28,878 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:28,878 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:28,878 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:28,878 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:28,878 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:28,878 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:29,109 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:29,340 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/xmlschema (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:29,343 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/xmlschema-2.3.1.tar.gz +== 2023-07-04 02:46:29,396 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:29,398 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:46:29,398 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:29,427 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:29,427 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:29,427 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:29,460 build_log.py:267 INFO building... +== 2023-07-04 02:46:29,463 build_log.py:267 INFO testing... +== 2023-07-04 02:46:29,465 build_log.py:267 INFO installing... +== 2023-07-04 02:46:29,468 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:29,468 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:29,468 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:29,468 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:29,826 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:29,826 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:29,830 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:33,669 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/xmlschema/xmlschema-2.3.1 + Preparing metadata (setup.py): started + Preparing metadata (setup.py): finished with status 'done' +Building wheels for collected packages: xmlschema + Building wheel for xmlschema (setup.py): started + Building wheel for xmlschema (setup.py): finished with status 'done' + Created wheel for xmlschema: filename=xmlschema-2.3.1-py3-none-any.whl size=275680 sha256=b322eaba81328d91a3b62fed7621911dfeee32ac98b84a1bf1c67a860305a161 + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/a9/e7/6e/1a1f962ff752ad1d2f2ddf291f08f1a65c671fc755e743aad9 +Successfully built xmlschema +Installing collected packages: xmlschema +Successfully installed xmlschema-2.3.1 + +== 2023-07-04 02:46:33,670 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:33,670 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:33,670 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:33,670 build_log.py:267 INFO ... (took 4 secs) +== 2023-07-04 02:46:33,672 easyblock.py:1880 INFO Starting extension pytest +== 2023-07-04 02:46:33,673 build_log.py:267 INFO installing extension pytest 7.4.0 (8/8)... +== 2023-07-04 02:46:33,760 modules.py:626 INFO Checking whether GCCcore/11.3.0 exists... +== 2023-07-04 02:46:33,760 modules.py:634 INFO Module GCCcore/11.3.0 not found in list of available modules, checking via 'module show'... +== 2023-07-04 02:46:33,761 modules.py:654 INFO Result for existence check of GCCcore/11.3.0 module: True +== 2023-07-04 02:46:33,761 toolchain.py:762 INFO List of toolchain dependency modules and toolchain definition match! +== 2023-07-04 02:46:33,762 compiler.py:363 INFO _set_optimal_architecture: using march=native as optarch for x86_64. +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable CC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable EBVARCC set to gcc (previous value: 'gcc') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable CFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable EBVARCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable CXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previous value: 'g++') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable F77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable F90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:33,764 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable FC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previous value: 'gfortran') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previous value: '-O2 -ftree-vectorize -march=native -fno-math-errno') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previous value: '-lgfortran') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previous value: '-lm -lpthread') +== 2023-07-04 02:46:33,765 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:33,766 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previous value: '-O2 -ftree-vectorize -march=native') +== 2023-07-04 02:46:33,766 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:33,766 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previous value: '-fno-math-errno') +== 2023-07-04 02:46:33,766 filetools.py:526 INFO Command python found at /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:33,766 pythonpackage.py:409 INFO Python command being used: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python +== 2023-07-04 02:46:33,766 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=False, prefix="/tmp/"))' +== 2023-07-04 02:46:34,002 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import distutils.sysconfig; print(distutils.sysconfig.get_python_lib(plat_specific=True, prefix="/tmp/"))' +== 2023-07-04 02:46:34,232 filetools.py:1913 INFO Creating directory /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:34,236 run.py:236 INFO running cmd: tar xzf /data/gent/vo/001/gvo00117/easybuild/sources/p/pytest/extensions/pytest-7.4.0.tar.gz +== 2023-07-04 02:46:34,288 build_log.py:267 INFO configuring... +== 2023-07-04 02:46:34,291 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:46:34,291 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print("%s.%s.%s" % sys.version_info[:3])' +== 2023-07-04 02:46:34,320 pythonpackage.py:596 INFO Checking of $LDSHARED auto-enabled for sufficiently recent Python version 3.10.4 +== 2023-07-04 02:46:34,320 pythonpackage.py:608 INFO Python's value for $LDSHARED ('gcc -pthread -shared -Wl,-z,relro -Wl,-z,now -g -Wl,-z,relro -Wl,-z,now -g') uses current $CC value ('gcc'), not touching it +== 2023-07-04 02:46:34,320 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -V; /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -c 'import sys; print(sys.executable, sys.path)' +== 2023-07-04 02:46:34,352 build_log.py:267 INFO building... +== 2023-07-04 02:46:34,355 build_log.py:267 INFO testing... +== 2023-07-04 02:46:34,357 build_log.py:267 INFO installing... +== 2023-07-04 02:46:34,360 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:34,360 environment.py:93 INFO Environment variable PATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:34,360 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:46:34,360 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:46:34,719 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:46:34,720 pythonpackage.py:482 INFO Found pip version 22.0.4, OK +== 2023-07-04 02:46:34,723 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation . +== 2023-07-04 02:46:38,203 run.py:648 INFO cmd " /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip install --prefix=/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0 --no-deps --ignore-installed --no-index --no-build-isolation ." exited with exit code 0 and output: +Processing /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 + Preparing metadata (pyproject.toml): started + Preparing metadata (pyproject.toml): finished with status 'done' +Building wheels for collected packages: pytest + Building wheel for pytest (pyproject.toml): started + Building wheel for pytest (pyproject.toml): finished with status 'done' + Created wheel for pytest: filename=pytest-7.4.0-py3-none-any.whl size=323580 sha256=db3c0d4c737306e355fe9f3af75d8458a612d50e51508415d709f9990c2440c6 + Stored in directory: /tmp/vsc44588/eb-gjrihs7a/pip/wheels/f6/f8/74/a946e9e509848601f1ab7d10a09f8558f95dc2659fd3021054 +Successfully built pytest +Installing collected packages: pytest +Successfully installed pytest-7.4.0 + +== 2023-07-04 02:46:38,203 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:38,203 environment.py:93 INFO Environment variable PYTHONPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python (previous value: '/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages:/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/easybuild/python') +== 2023-07-04 02:46:38,203 environment.py:93 INFO Environment variable PATH set to /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: 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2023-07-04 02:46:38,203 build_log.py:267 INFO ... 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LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:42,501 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previous value: '-L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib') +== 2023-07-04 02:46:42,502 build_log.py:267 INFO ... (took 1 min 0 secs) +== 2023-07-04 02:46:42,504 build_log.py:267 INFO restore after iterating... +== 2023-07-04 02:46:42,506 easyblock.py:3926 INFO Starting postiter step +== 2023-07-04 02:46:42,506 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:46:42,507 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:46:42,507 easyblock.py:3934 INFO Running method post_iter_step part of step postiter +== 2023-07-04 02:46:42,507 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:46:42,509 build_log.py:267 INFO postprocessing... +== 2023-07-04 02:46:42,511 easyblock.py:3926 INFO Starting postproc step +== 2023-07-04 02:46:42,511 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:46:42,511 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:46:42,511 easyblock.py:3934 INFO Running method post_install_step part of step postproc +== 2023-07-04 02:46:42,511 easyblock.py:2923 INFO Path to 'env' command to use in patched shebang lines: /usr/bin/env +== 2023-07-04 02:46:42,513 filetools.py:338 INFO Symlinked lib to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib64 +== 2023-07-04 02:46:42,514 build_log.py:267 INFO ... (took < 1 sec) +== 2023-07-04 02:46:42,515 build_log.py:267 INFO sanity checking... +== 2023-07-04 02:46:42,517 easyblock.py:3926 INFO Starting sanitycheck step +== 2023-07-04 02:46:42,517 easyconfig.py:1690 INFO Generating template values... +== 2023-07-04 02:46:42,518 easyconfig.py:1709 INFO Template values: arch='x86_64', bitbucket_account='pytest', builddir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0', github_account='pytest', installdir='/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0', module_name='pytest/7.4.0-GCCcore-11.3.0', name='pytest', nameletter='p', nameletterlower='p', namelower='pytest', parallel='8', pymajver='3', pyminver='10', pyshortver='3.10', pyver='3.10.4', start_dir='/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/', toolchain_name='GCCcore', toolchain_version='11.3.0', version='7.4.0', version_major='7', version_major_minor='7.4', version_minor='4', versionprefix='', versionsuffix='' +== 2023-07-04 02:46:42,518 easyblock.py:3934 INFO Running method sanity_check_step part of step sanitycheck +== 2023-07-04 02:46:42,518 easyblock.py:3326 INFO Using (only) sanity check paths specified by easyconfig file: {'files': [], 'dirs': ['lib/python3.10/site-packages']} +== 2023-07-04 02:46:42,518 easyblock.py:3379 INFO Using (only) sanity check commands specified by easyconfig file: ["python -c 'import pytest'", 'cd /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 && /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing'] +== 2023-07-04 02:46:42,521 easyblock.py:1678 INFO Loading fake module (pytest/7.4.0-GCCcore-11.3.0) +== 2023-07-04 02:46:42,611 easyblock.py:1581 INFO Fixed symlink lib64 in paths for CMAKE_LIBRARY_PATH: ['lib64'] -> [] +== 2023-07-04 02:46:42,612 easyblock.py:1581 INFO Fixed symlink lib64 in paths for LD_LIBRARY_PATH: ['lib', 'lib64'] -> ['lib', 'lib'] +== 2023-07-04 02:46:42,612 easyblock.py:1595 INFO Only retaining paths for LD_LIBRARY_PATH that contain at least one file: ['lib'] -> [] +== 2023-07-04 02:46:42,612 easyblock.py:1581 INFO Fixed symlink lib64 in paths for LIBRARY_PATH: ['lib', 'lib64'] -> ['lib', 'lib'] +== 2023-07-04 02:46:42,613 filetools.py:1913 INFO Creating directory /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all/pytest (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:42,614 easyblock.py:3742 INFO Module file /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all/pytest/7.4.0-GCCcore-11.3.0.lua written: help([==[ + +Description +=========== +The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries. + + +More information +================ + - Homepage: https://docs.pytest.org/en/latest/ + + +Included extensions +=================== +elementpath-4.1.4, exceptiongroup-1.1.2, flit-core-3.9.0, flit-scm-1.7.0, +hypothesis-6.80.0, pytest-7.4.0, setuptools-scm-7.1.0, xmlschema-2.3.1 +]==]) + +whatis([==[Description: The pytest framework makes it easy to write small, +readable tests, and can scale to support complex functional testing for +applications and libraries.]==]) +whatis([==[Homepage: https://docs.pytest.org/en/latest/]==]) +whatis([==[URL: https://docs.pytest.org/en/latest/]==]) +whatis([==[Extensions: elementpath-4.1.4, exceptiongroup-1.1.2, flit-core-3.9.0, flit-scm-1.7.0, hypothesis-6.80.0, pytest-7.4.0, setuptools-scm-7.1.0, xmlschema-2.3.1]==]) + +local root = "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0" + +conflict("pytest") + +if not ( isloaded("GCCcore/11.3.0") ) then + load("GCCcore/11.3.0") +end + +if not ( isloaded("Python/3.10.4-GCCcore-11.3.0") ) then + load("Python/3.10.4-GCCcore-11.3.0") +end + +prepend_path("CMAKE_PREFIX_PATH", root) +prepend_path("LIBRARY_PATH", pathJoin(root, "lib")) +prepend_path("PATH", pathJoin(root, "bin")) +setenv("EBROOTPYTEST", root) +setenv("EBVERSIONPYTEST", "7.4.0") +setenv("EBDEVELPYTEST", pathJoin(root, "easybuild/pytest-7.4.0-GCCcore-11.3.0-easybuild-devel")) + +prepend_path("PYTHONPATH", pathJoin(root, "lib/python3.10/site-packages")) +-- Built with EasyBuild version 4.7.3.dev0-r366e71d77260adc73e8976bffeccb83b1b289c5d +setenv("EBEXTSLISTPYTEST", "setuptools-scm-7.1.0,flit-core-3.9.0,flit-scm-1.7.0,exceptiongroup-1.1.2,hypothesis-6.80.0,elementpath-4.1.4,xmlschema-2.3.1,pytest-7.4.0") + +== 2023-07-04 02:46:42,614 filetools.py:1913 INFO Creating directory /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/lib/pytest (parents: True, set_gid: False, sticky: False) +== 2023-07-04 02:46:42,614 easyblock.py:3773 INFO Skipping devel module... +== 2023-07-04 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'/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/libffi/3.4.2-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/man:/apps/gent/RHEL8/cascadelake-ib/software/libreadline/8.1.2-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/share/man:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/man:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/zlib/1.2.12-GCCcore-11.3.0/share/man:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/share/man::') +== 2023-07-04 02:46:45,810 environment.py:93 INFO Environment variable MODULEPATH set to /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc (previous value: '/tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc') +== 2023-07-04 02:46:45,810 environment.py:93 INFO Environment variable PATH set to /user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools (previous value: '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/OpenSSL/1.1/bin:/apps/gent/RHEL8/cascadelake-ib/software/XZ/5.2.5-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/SQLite/3.38.3-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/Tcl/8.6.12-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/ncurses/6.3-GCCcore-11.3.0/bin:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/bzip2/1.0.8-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/bin:/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/bin:/user/gent/445/vsc44588/.local/bin:/user/gent/445/vsc44588/easybuild/easybuild-framework:/usr/libexec/jobcli:/opt/VirtualGL/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/user/gent/445/vsc44588/.dotnet/tools') +== 2023-07-04 02:46:45,810 environment.py:93 INFO Environment variable _LMFILES_ set to /etc/modulefiles/vsc/env/vsc/donphan.lua:/etc/modulefiles/vsc/env/slurm/donphan.lua:/etc/modulefiles/vsc/env/software/donphan.lua:/etc/modulefiles/vsc/cluster/donphan.lua (previous value: '/etc/modulefiles/vsc/env/vsc/donphan.lua:/etc/modulefiles/vsc/env/slurm/donphan.lua:/etc/modulefiles/vsc/env/software/donphan.lua:/etc/modulefiles/vsc/cluster/donphan.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/GCCcore/11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/zlib/1.2.12-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/binutils/2.38-GCCcore-11.3.0.lua:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all/bzip2/1.0.8-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/ncurses/6.3-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libreadline/8.1.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/Tcl/8.6.12-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/SQLite/3.38.3-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/XZ/5.2.5-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/GMP/6.2.1-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/libffi/3.4.2-GCCcore-11.3.0.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/OpenSSL/1.1.lua:/apps/gent/RHEL8/cascadelake-ib/modules/all/Python/3.10.4-GCCcore-11.3.0.lua') +== 2023-07-04 02:46:45,812 modules.py:472 INFO $MODULEPATH set via list of module paths (w/ 'module use'): /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w/all:/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ampere-ib/modules/all:/apps/gent/RHEL8/cascadelake-ib/modules/all:/etc/modulefiles/vsc +== 2023-07-04 02:46:48,833 run.py:236 INFO running cmd: python -c 'import pytest' +== 2023-07-04 02:46:51,467 easyblock.py:3610 INFO sanity check command python -c 'import pytest' ran successfully! (output: ) +== 2023-07-04 02:46:51,472 run.py:236 INFO running cmd: cd /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 && /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing +== 2023-07-04 02:49:12,465 run.py:662 WARNING Found 1 potential error (some may be harmless) in output of cd /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 && /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing: + FAILED testing/_py/test_local.py::TestLocalPath::test_make_numbered_dir_multiprocess_safe - py.error.ENOENT: [No such file or directory]: open('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588... +== 2023-07-04 02:49:12,465 easyblock.py:3608 WARNING Sanity check: sanity check command cd /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 && /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing exited with code 1 (output: ===================================================================================== test session starts ===================================================================================== +platform linux -- Python 3.10.4, pytest-7.4.0, pluggy-1.0.0 +rootdir: /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 +configfile: pyproject.toml +plugins: hypothesis-6.80.0 +collected 2999 items + +testing/acceptance_test.py ..... [ 0%] +testing/deprecated_test.py ....... [ 0%] +testing/test_argcomplete.py .. [ 0%] +testing/test_assertion.py ..................................................................... [ 2%] +testing/test_assertrewrite.py ............................................ [ 4%] +testing/test_capture.py .............................................................s.. [ 6%] +testing/test_collection.py . [ 6%] +testing/test_compat.py ........... [ 6%] +testing/test_conftest.py ........... [ 7%] +testing/test_doctest.py ............. [ 7%] +testing/test_entry_points.py . [ 7%] +testing/test_faulthandler.py ... [ 7%] +testing/test_findpaths.py ..............s... [ 8%] +testing/test_junitxml.py .... [ 8%] +testing/test_legacypath.py .... [ 8%] +testing/test_main.py ..... [ 8%] +testing/test_mark.py .............. [ 9%] +testing/test_mark_expression.py .................................................................................... [ 12%] +testing/test_monkeypatch.py ............................... [ 13%] +testing/test_nodes.py .............. [ 13%] +testing/test_nose.py ss [ 13%] +testing/test_parseopt.py ............................ [ 14%] +testing/test_pastebin.py .... [ 14%] +testing/test_pathlib.py .............................................s..... [ 16%] +testing/test_pluginmanager.py ......... [ 16%] +testing/test_pytester.py ..................... [ 17%] +testing/test_recwarn.py ........................................ [ 18%] +testing/test_runner.py .............. [ 19%] +testing/test_scope.py .... [ 19%] +testing/test_skipping.py . [ 19%] +testing/test_stash.py . [ 19%] +testing/test_tmpdir.py ...s............... [ 19%] +testing/test_warning_types.py .............. [ 20%] +testing/test_warnings.py . [ 20%] +testing/_py/test_local.py .................................................................ss..............s.................x.....Fs.....................................sssssss...... [ 25%] +......................x... [ 26%] +testing/code/test_code.py ................. [ 27%] +testing/code/test_excinfo.py ................................................................................................................................. [ 31%] +testing/code/test_source.py ....................................................... [ 33%] +testing/freeze/tests/test_trivial.py .. [ 33%] +testing/io/test_saferepr.py .............. [ 33%] +testing/io/test_wcwidth.py ................. [ 34%] +testing/logging/test_fixture.py .................. [ 34%] +testing/logging/test_formatter.py .... [ 35%] +testing/logging/test_reporting.py .. [ 35%] +testing/python/approx.py .sss..sssss......................................ssssss................ss........ [ 37%] +testing/python/collect.py .. [ 37%] +testing/python/fixtures.py .......... [ 38%] +testing/python/integration.py .... [ 38%] +testing/python/metafunc.py ......................................... [ 39%] +testing/python/raises.py ....................... [ 40%] +testing/freeze/tests/test_doctest.txt . [ 40%] +testing/acceptance_test.py ..................................................x.................... [ 42%] +testing/deprecated_test.py ...........ss [ 43%] +testing/test_assertion.py ................................... [ 44%] +testing/test_assertrewrite.py .............................................................. [ 46%] +testing/test_cacheprovider.py ....................................................... [ 48%] +testing/test_capture.py ......x.................................... [ 49%] +testing/test_collection.py ...........................x........................................s................. [ 52%] +testing/test_compat.py .. [ 52%] +testing/test_conftest.py .............s............................. [ 54%] +testing/test_doctest.py ..............................................................x.......................................................... [ 58%] +testing/test_error_diffs.py ............ [ 58%] +testing/test_faulthandler.py ... [ 58%] +testing/test_junitxml.py .................................................................................................s...s....................... [ 62%] +testing/test_legacypath.py .......... [ 63%] +testing/test_link_resolve.py . [ 63%] +testing/test_main.py ............. [ 63%] +testing/test_mark.py ...........................................................x................ [ 66%] +testing/test_monkeypatch.py .... [ 66%] +testing/test_nodes.py .... [ 66%] +testing/test_nose.py ssssssssssssssssssssss [ 67%] +testing/test_parseopt.py s [ 67%] +testing/test_pastebin.py ... [ 67%] +testing/test_pluginmanager.py ................ [ 67%] +testing/test_pytester.py x......................... [ 68%] +testing/test_python_path.py ..... [ 68%] +testing/test_recwarn.py .. [ 69%] +testing/test_reports.py .................. [ 69%] +testing/test_runner.py .......................x..................... [ 71%] +testing/test_runner_xunit.py ............. [ 71%] +testing/test_session.py ........................ [ 72%] +testing/test_setuponly.py .......................... [ 73%] +testing/test_setupplan.py ... [ 73%] +testing/test_skipping.py ............................................................................................ [ 76%] +testing/test_stepwise.py .............. [ 76%] +testing/test_threadexception.py .... [ 77%] +testing/test_tmpdir.py .................... [ 77%] +testing/test_unittest.py ......................sssssss.................................s........ [ 80%] +testing/test_unraisableexception.py .... [ 80%] +testing/test_warning_types.py . [ 80%] +testing/test_warnings.py ...................sss.......... [ 81%] +testing/code/test_excinfo.py ....sssssssss............... [ 82%] +testing/examples/test_issue519.py . [ 82%] +testing/logging/test_fixture.py ........ [ 82%] +testing/logging/test_reporting.py ............................................. [ 84%] +testing/python/approx.py . [ 84%] +testing/python/collect.py ........................................................................... [ 86%] +testing/python/fixtures.py .......................................................................x.................................................................................... [ 91%] +...............s.. [ 92%] +testing/python/integration.py ............... [ 92%] +testing/python/metafunc.py ............................................................ [ 94%] +testing/python/raises.py ... [ 94%] +testing/python/show_fixtures_per_test.py ........ [ 95%] +testing/acceptance_test.py .... [ 95%] +testing/test_assertion.py ............ [ 95%] +testing/test_assertrewrite.py ......... [ 96%] +testing/test_capture.py ........................ [ 96%] +testing/test_collection.py . [ 96%] +testing/test_compat.py . [ 96%] +testing/test_faulthandler.py ..s. [ 97%] +testing/test_legacypath.py . [ 97%] +testing/test_meta.py ................................................................... [ 99%] +testing/test_pytester.py ..... [ 99%] +testing/test_reports.py . [ 99%] +testing/test_unittest.py s. [ 99%] +testing/test_warnings.py ......... [ 99%] +testing/python/collect.py . [ 99%] +testing/python/fixtures.py .. [100%] + +========================================================================================== FAILURES =========================================================================================== +___________________________________________________________________ TestLocalPath.test_make_numbered_dir_multiprocess_safe ____________________________________________________________________ +multiprocessing.pool.RemoteTraceback: +""" +Traceback (most recent call last): + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/error.py", line 85, in checked_call + return func(*args, **kwargs) +FileNotFoundError: [Errno 2] No such file or directory: '/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0/repro-1545/foo' + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/multiprocessing/pool.py", line 125, in worker + result = (True, func(*args, **kwds)) + File "/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0/testing/_py/test_local.py", line 552, in batch_make_numbered_dirs + file_.write_text("%s" % i, encoding="utf-8") + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/path.py", line 905, in write_text + with self.open("w", encoding=encoding) as f: + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/path.py", line 760, in open + return error.checked_call(io.open, self.strpath, mode, encoding=encoding) + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/error.py", line 101, in checked_call + raise cls(f"{func.__name__}{args!r}") +py.error.ENOENT: [No such file or directory]: open('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0/repro-1545/foo', 'w') +""" + +The above exception was the direct cause of the following exception: + +self = , tmpdir = local('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0') + + def test_make_numbered_dir_multiprocess_safe(self, tmpdir): + # https://github.com/pytest-dev/py/issues/30 + with multiprocessing.Pool() as pool: + results = [ + pool.apply_async(batch_make_numbered_dirs, [tmpdir, 100]) + for _ in range(20) + ] + for r in results: +> assert r.get() + +/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0/testing/_py/test_local.py:879: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = , timeout = None + + def get(self, timeout=None): + self.wait(timeout) + if not self.ready(): + raise TimeoutError + if self._success: + return self._value + else: +> raise self._value +E py.error.ENOENT: [No such file or directory]: open('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0/repro-1545/foo', 'w') + +/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/multiprocessing/pool.py:771: ENOENT +=================================================================================== short test summary info =================================================================================== +FAILED testing/_py/test_local.py::TestLocalPath::test_make_numbered_dir_multiprocess_safe - py.error.ENOENT: [No such file or directory]: open('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588... +============================================================= 1 failed, 2903 passed, 85 skipped, 10 xfailed in 140.05s (0:02:20) ============================================================== +) +== 2023-07-04 02:49:12,467 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previously undefined) +== 2023-07-04 02:49:12,468 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:12,468 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:12,468 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:16,569 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:16,572 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:20,495 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:20,496 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:21,478 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:21,481 run.py:236 INFO running cmd: python -c "import setuptools_scm" +== 2023-07-04 02:49:21,684 extensioneasyblock.py:204 INFO Sanity check for setuptools-scm successful! +== 2023-07-04 02:49:21,684 easyblock.py:3487 INFO Sanity check for 'setuptools-scm' extension passed! +== 2023-07-04 02:49:21,684 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:49:21,684 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:21,684 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:21,684 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:22,044 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:22,047 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:23,025 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:23,025 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:23,574 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:23,577 run.py:236 INFO running cmd: python -c "import flit_core" +== 2023-07-04 02:49:23,611 extensioneasyblock.py:204 INFO Sanity check for flit-core successful! +== 2023-07-04 02:49:23,611 easyblock.py:3487 INFO Sanity check for 'flit-core' extension passed! +== 2023-07-04 02:49:23,611 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:49:23,611 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:23,611 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:23,612 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:23,970 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:23,973 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:24,979 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:24,979 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:25,535 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:25,538 run.py:236 INFO running cmd: python -c "import flit_scm" +== 2023-07-04 02:49:25,800 extensioneasyblock.py:204 INFO Sanity check for flit-scm successful! +== 2023-07-04 02:49:25,800 easyblock.py:3487 INFO Sanity check for 'flit-scm' extension passed! +== 2023-07-04 02:49:25,800 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:49:25,800 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:25,801 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:25,801 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:26,158 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:26,161 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:27,139 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:27,139 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:27,694 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:27,697 run.py:236 INFO running cmd: python -c "import exceptiongroup" +== 2023-07-04 02:49:27,746 extensioneasyblock.py:204 INFO Sanity check for exceptiongroup successful! +== 2023-07-04 02:49:27,747 easyblock.py:3487 INFO Sanity check for 'exceptiongroup' extension passed! +== 2023-07-04 02:49:27,747 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:49:27,747 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:27,747 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:27,747 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:28,104 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:28,107 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:29,081 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:29,081 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:29,630 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:29,633 run.py:236 INFO running cmd: python -c "import hypothesis" +== 2023-07-04 02:49:30,468 extensioneasyblock.py:204 INFO Sanity check for hypothesis successful! +== 2023-07-04 02:49:30,468 easyblock.py:3487 INFO Sanity check for 'hypothesis' extension passed! +== 2023-07-04 02:49:30,468 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:49:30,468 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:30,468 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:30,468 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:30,828 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:30,831 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:31,815 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:31,815 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:32,371 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:32,374 run.py:236 INFO running cmd: python -c "import elementpath" +== 2023-07-04 02:49:32,507 extensioneasyblock.py:204 INFO Sanity check for elementpath successful! +== 2023-07-04 02:49:32,507 easyblock.py:3487 INFO Sanity check for 'elementpath' extension passed! +== 2023-07-04 02:49:32,507 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:49:32,507 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:32,507 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:32,507 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:32,863 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:32,866 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:33,844 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:33,845 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:34,399 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:34,402 run.py:236 INFO running cmd: python -c "import xmlschema" +== 2023-07-04 02:49:34,693 extensioneasyblock.py:204 INFO Sanity check for xmlschema successful! +== 2023-07-04 02:49:34,694 easyblock.py:3487 INFO Sanity check for 'xmlschema' extension passed! +== 2023-07-04 02:49:34,694 environment.py:93 INFO Environment variable PYTHONNOUSERSITE set to 1 (previous value: '1') +== 2023-07-04 02:49:34,694 pythonpackage.py:811 INFO Detection of downloaded depenencies enabled, checking output of installation command... +== 2023-07-04 02:49:34,694 pythonpackage.py:212 INFO Determining pip version... +== 2023-07-04 02:49:34,694 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip --version +== 2023-07-04 02:49:35,051 pythonpackage.py:220 INFO Found pip version: 22.0.4 +== 2023-07-04 02:49:35,054 run.py:236 INFO running cmd: /apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check +== 2023-07-04 02:49:36,022 pythonpackage.py:879 INFO `/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip check` completed successfully +== 2023-07-04 02:49:36,022 pythonpackage.py:456 INFO Running command '/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/bin/python -m pip list --isolated --disable-pip-version-check --format json' +== 2023-07-04 02:49:36,568 pythonpackage.py:905 INFO Found 0 invalid packages out of 134 packages +== 2023-07-04 02:49:36,571 run.py:236 INFO running cmd: python -c "import pytest" +== 2023-07-04 02:49:36,795 extensioneasyblock.py:204 INFO Sanity check for pytest successful! +== 2023-07-04 02:49:36,796 easyblock.py:3487 INFO Sanity check for 'pytest' extension passed! +== 2023-07-04 02:49:36,796 easyblock.py:3204 INFO Checking for banned/required linked shared libraries... +== 2023-07-04 02:49:36,796 easyblock.py:3222 INFO No banned/required libraries specified +== 2023-07-04 02:49:40,920 filetools.py:383 INFO Path /tmp/vsc44588/eb-gjrihs7a/tmpwr51fl7w successfully removed. +== 2023-07-04 02:49:40,921 environment.py:93 INFO Environment variable _ModuleTable002_ set to 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CXX set to g++ (previously undefined) +== 2023-07-04 02:49:40,923 environment.py:93 INFO Environment variable EBVARCXX set to g++ (previously undefined) +== 2023-07-04 02:49:40,923 environment.py:93 INFO Environment variable CXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,923 environment.py:93 INFO Environment variable EBVARCXXFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable F77 set to gfortran (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable EBVARF77 set to gfortran (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable F90 set to gfortran (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable EBVARF90 set to gfortran (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable F90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable EBVARF90FLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable FC set to gfortran (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable EBVARFC set to gfortran (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable FCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable EBVARFCFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable FFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable EBVARFFLAGS set to -O2 -ftree-vectorize -march=native -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable FLIBS set to -lgfortran (previously undefined) +== 2023-07-04 02:49:40,924 environment.py:93 INFO Environment variable EBVARFLIBS set to -lgfortran (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable LDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable EBVARLDFLAGS set to -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/lib -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib64 -L/apps/gent/RHEL8/cascadelake-ib/software/GCCcore/11.3.0/lib (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable LIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable EBVARLIBS set to -lm -lpthread (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable OPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable EBVAROPTFLAGS set to -O2 -ftree-vectorize -march=native (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable PRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable EBVARPRECFLAGS set to -fno-math-errno (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable CPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/include (previously undefined) +== 2023-07-04 02:49:40,925 environment.py:93 INFO Environment variable EBVARCPPFLAGS set to -I/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/include -I/apps/gent/RHEL8/cascadelake-ib/software/binutils/2.38-GCCcore-11.3.0/include (previously undefined) +== 2023-07-04 02:49:40,963 build_log.py:171 ERROR EasyBuild crashed with an error (at easybuild/easybuild-framework/easybuild/base/exceptions.py:126 in __init__): Sanity check failed: sanity check command cd /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 && /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testing/test_terminal.py --ignore=testing/test_debugging.py --ignore=testing/test_config.py --ignore=testing/test_helpconfig.py testing exited with code 1 (output: ===================================================================================== test session starts ===================================================================================== +platform linux -- Python 3.10.4, pytest-7.4.0, pluggy-1.0.0 +rootdir: /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 +configfile: pyproject.toml +plugins: hypothesis-6.80.0 +collected 2999 items + +testing/acceptance_test.py ..... [ 0%] +testing/deprecated_test.py ....... [ 0%] +testing/test_argcomplete.py .. [ 0%] +testing/test_assertion.py ..................................................................... [ 2%] +testing/test_assertrewrite.py ............................................ [ 4%] +testing/test_capture.py .............................................................s.. [ 6%] +testing/test_collection.py . [ 6%] +testing/test_compat.py ........... [ 6%] +testing/test_conftest.py ........... [ 7%] +testing/test_doctest.py ............. [ 7%] +testing/test_entry_points.py . [ 7%] +testing/test_faulthandler.py ... [ 7%] +testing/test_findpaths.py ..............s... [ 8%] +testing/test_junitxml.py .... [ 8%] +testing/test_legacypath.py .... [ 8%] +testing/test_main.py ..... [ 8%] +testing/test_mark.py .............. [ 9%] +testing/test_mark_expression.py .................................................................................... [ 12%] +testing/test_monkeypatch.py ............................... [ 13%] +testing/test_nodes.py .............. [ 13%] +testing/test_nose.py ss [ 13%] +testing/test_parseopt.py ............................ [ 14%] +testing/test_pastebin.py .... [ 14%] +testing/test_pathlib.py .............................................s..... [ 16%] +testing/test_pluginmanager.py ......... [ 16%] +testing/test_pytester.py ..................... [ 17%] +testing/test_recwarn.py ........................................ [ 18%] +testing/test_runner.py .............. [ 19%] +testing/test_scope.py .... [ 19%] +testing/test_skipping.py . [ 19%] +testing/test_stash.py . [ 19%] +testing/test_tmpdir.py ...s............... [ 19%] +testing/test_warning_types.py .............. [ 20%] +testing/test_warnings.py . [ 20%] +testing/_py/test_local.py .................................................................ss..............s.................x.....Fs.....................................sssssss...... [ 25%] +......................x... [ 26%] +testing/code/test_code.py ................. [ 27%] +testing/code/test_excinfo.py ................................................................................................................................. [ 31%] +testing/code/test_source.py ....................................................... [ 33%] +testing/freeze/tests/test_trivial.py .. [ 33%] +testing/io/test_saferepr.py .............. [ 33%] +testing/io/test_wcwidth.py ................. [ 34%] +testing/logging/test_fixture.py .................. [ 34%] +testing/logging/test_formatter.py .... [ 35%] +testing/logging/test_reporting.py .. [ 35%] +testing/python/approx.py .sss..sssss......................................ssssss................ss........ [ 37%] +testing/python/collect.py .. [ 37%] +testing/python/fixtures.py .......... [ 38%] +testing/python/integration.py .... [ 38%] +testing/python/metafunc.py ......................................... [ 39%] +testing/python/raises.py ....................... [ 40%] +testing/freeze/tests/test_doctest.txt . [ 40%] +testing/acceptance_test.py ..................................................x.................... [ 42%] +testing/deprecated_test.py ...........ss [ 43%] +testing/test_assertion.py ................................... [ 44%] +testing/test_assertrewrite.py .............................................................. [ 46%] +testing/test_cacheprovider.py ....................................................... [ 48%] +testing/test_capture.py ......x.................................... [ 49%] +testing/test_collection.py ...........................x........................................s................. [ 52%] +testing/test_compat.py .. [ 52%] +testing/test_conftest.py .............s............................. [ 54%] +testing/test_doctest.py ..............................................................x.......................................................... [ 58%] +testing/test_error_diffs.py ............ [ 58%] +testing/test_faulthandler.py ... [ 58%] +testing/test_junitxml.py .................................................................................................s...s....................... [ 62%] +testing/test_legacypath.py .......... [ 63%] +testing/test_link_resolve.py . [ 63%] +testing/test_main.py ............. [ 63%] +testing/test_mark.py ...........................................................x................ [ 66%] +testing/test_monkeypatch.py .... [ 66%] +testing/test_nodes.py .... [ 66%] +testing/test_nose.py ssssssssssssssssssssss [ 67%] +testing/test_parseopt.py s [ 67%] +testing/test_pastebin.py ... [ 67%] +testing/test_pluginmanager.py ................ [ 67%] +testing/test_pytester.py x......................... [ 68%] +testing/test_python_path.py ..... [ 68%] +testing/test_recwarn.py .. [ 69%] +testing/test_reports.py .................. [ 69%] +testing/test_runner.py .......................x..................... [ 71%] +testing/test_runner_xunit.py ............. [ 71%] +testing/test_session.py ........................ [ 72%] +testing/test_setuponly.py .......................... [ 73%] +testing/test_setupplan.py ... [ 73%] +testing/test_skipping.py ............................................................................................ [ 76%] +testing/test_stepwise.py .............. [ 76%] +testing/test_threadexception.py .... [ 77%] +testing/test_tmpdir.py .................... [ 77%] +testing/test_unittest.py ......................sssssss.................................s........ [ 80%] +testing/test_unraisableexception.py .... [ 80%] +testing/test_warning_types.py . [ 80%] +testing/test_warnings.py ...................sss.......... [ 81%] +testing/code/test_excinfo.py ....sssssssss............... [ 82%] +testing/examples/test_issue519.py . [ 82%] +testing/logging/test_fixture.py ........ [ 82%] +testing/logging/test_reporting.py ............................................. [ 84%] +testing/python/approx.py . [ 84%] +testing/python/collect.py ........................................................................... [ 86%] +testing/python/fixtures.py .......................................................................x.................................................................................... [ 91%] +...............s.. [ 92%] +testing/python/integration.py ............... [ 92%] +testing/python/metafunc.py ............................................................ [ 94%] +testing/python/raises.py ... [ 94%] +testing/python/show_fixtures_per_test.py ........ [ 95%] +testing/acceptance_test.py .... [ 95%] +testing/test_assertion.py ............ [ 95%] +testing/test_assertrewrite.py ......... [ 96%] +testing/test_capture.py ........................ [ 96%] +testing/test_collection.py . [ 96%] +testing/test_compat.py . [ 96%] +testing/test_faulthandler.py ..s. [ 97%] +testing/test_legacypath.py . [ 97%] +testing/test_meta.py ................................................................... [ 99%] +testing/test_pytester.py ..... [ 99%] +testing/test_reports.py . [ 99%] +testing/test_unittest.py s. [ 99%] +testing/test_warnings.py ......... [ 99%] +testing/python/collect.py . [ 99%] +testing/python/fixtures.py .. [100%] + +========================================================================================== FAILURES =========================================================================================== +___________________________________________________________________ TestLocalPath.test_make_numbered_dir_multiprocess_safe ____________________________________________________________________ +multiprocessing.pool.RemoteTraceback: +""" +Traceback (most recent call last): + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/error.py", line 85, in checked_call + return func(*args, **kwargs) +FileNotFoundError: [Errno 2] No such file or directory: '/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0/repro-1545/foo' + +During handling of the above exception, another exception occurred: + +Traceback (most recent call last): + File "/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/multiprocessing/pool.py", line 125, in worker + result = (True, func(*args, **kwds)) + File "/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0/testing/_py/test_local.py", line 552, in batch_make_numbered_dirs + file_.write_text("%s" % i, encoding="utf-8") + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/path.py", line 905, in write_text + with self.open("w", encoding=encoding) as f: + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/path.py", line 760, in open + return error.checked_call(io.open, self.strpath, mode, encoding=encoding) + File "/scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/lib/python3.10/site-packages/_pytest/_py/error.py", line 101, in checked_call + raise cls(f"{func.__name__}{args!r}") +py.error.ENOENT: [No such file or directory]: open('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0/repro-1545/foo', 'w') +""" + +The above exception was the direct cause of the following exception: + +self = , tmpdir = local('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0') + + def test_make_numbered_dir_multiprocess_safe(self, tmpdir): + # https://github.com/pytest-dev/py/issues/30 + with multiprocessing.Pool() as pool: + results = [ + pool.apply_async(batch_make_numbered_dirs, [tmpdir, 100]) + for _ in range(20) + ] + for r in results: +> assert r.get() + +/tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0/testing/_py/test_local.py:879: +_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ + +self = , timeout = None + + def get(self, timeout=None): + self.wait(timeout) + if not self.ready(): + raise TimeoutError + if self._success: + return self._value + else: +> raise self._value +E py.error.ENOENT: [No such file or directory]: open('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588/pytest-0/test_make_numbered_dir_multipr0/repro-1545/foo', 'w') + +/apps/gent/RHEL8/cascadelake-ib/software/Python/3.10.4-GCCcore-11.3.0/lib/python3.10/multiprocessing/pool.py:771: ENOENT +=================================================================================== short test summary info =================================================================================== +FAILED testing/_py/test_local.py::TestLocalPath::test_make_numbered_dir_multiprocess_safe - py.error.ENOENT: [No such file or directory]: open('/tmp/vsc44588/eb-gjrihs7a/pytest-of-vsc44588... +============================================================= 1 failed, 2903 passed, 85 skipped, 10 xfailed in 140.05s (0:02:20) ============================================================== +) (at easybuild/easybuild-framework/easybuild/framework/easyblock.py:3639 in _sanity_check_step) +== 2023-07-04 02:49:40,963 build_log.py:267 INFO ... (took 2 mins 58 secs) +== 2023-07-04 02:49:40,965 filetools.py:2014 INFO Removing lock /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pytest_7.4.0-GCCcore-11.3.0.lock... +== 2023-07-04 02:49:40,967 filetools.py:383 INFO Path /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pytest_7.4.0-GCCcore-11.3.0.lock successfully removed. +== 2023-07-04 02:49:40,967 filetools.py:2018 INFO Lock removed: /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/.locks/_scratch_gent_vo_001_gvo00117_easybuild_RHEL8_cascadelake-ampere-ib_software_pytest_7.4.0-GCCcore-11.3.0.lock +== 2023-07-04 02:49:40,967 easyblock.py:4257 WARNING build failed (first 300 chars): Sanity check failed: sanity check command cd /tmp/vsc44588/easybuild/build/pytest/7.4.0/GCCcore-11.3.0/pytest/pytest-7.4.0 && /scratch/gent/vo/001/gvo00117/easybuild/RHEL8/cascadelake-ampere-ib/software/pytest/7.4.0-GCCcore-11.3.0/bin/pytest --ignore=testing/io/test_terminalwriter.py --ignore=testin +== 2023-07-04 02:49:40,968 easyblock.py:328 INFO Closing log for application name pytest version 7.4.0 diff --git a/169_Bonito/ont-fast5-api-4.1.1-foss-2022b.eb b/169_Bonito/ont-fast5-api-4.1.1-foss-2022b.eb new file mode 100644 index 00000000..8398ccc0 --- /dev/null +++ b/169_Bonito/ont-fast5-api-4.1.1-foss-2022b.eb @@ -0,0 +1,43 @@ +easyblock = 'PythonBundle' + +name = 'ont-fast5-api' +version = '4.1.1' + +homepage = 'https://github.com/nanoporetech/ont_fast5_api' +description = "ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format." + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('h5py', '3.7.0'), +] + +use_pip = True + +exts_list = [ + ('progressbar33', '2.4', { + 'modulename': 'progressbar', + 'checksums': ['51fe0d9b3b4023db2f983eeccdfc8c9846b84db8443b9bee002c7f58f4376eff'], + }), + (name, version, { + 'checksums': ['71ea44087f310a2792d1a6c2ffbf5bc194367e769ce96a15961787f90ec7707b'], + }), +] + +sanity_check_paths = { + 'files': ['bin/compress_fast5', 'bin/fast5_subset', 'bin/multi_to_single_fast5', 'bin/single_to_multi_fast5'], + 'dirs': [''], +} + +sanity_check_commands = [ + "compress_fast5 --help", + "fast5_subset --help", + "multi_to_single_fast5 --help", + "single_to_multi_fast5 --help", +] + +sanity_pip_check = True + +moduleclass = 'bio' diff --git a/169_Bonito/ont-remora/ONNX-1.11.0-foss-2021a.eb b/169_Bonito/ont-remora/ONNX-1.11.0-foss-2021a.eb new file mode 100644 index 00000000..193f4f8b --- /dev/null +++ b/169_Bonito/ont-remora/ONNX-1.11.0-foss-2021a.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonPackage' + +name = 'ONNX' +version = '1.14.0' + +homepage = 'https://onnx.ai/' +description = """ +Open Neural Network Exchange (ONNX) is an open ecosystem that empowers AI +developers to choose the right tools as their project evolves. ONNX provides an +open source format for AI models, both deep learning and traditional ML. It +defines an extensible computation graph model, as well as definitions of +built-in operators and standard data types. Currently we focus on the +capabilities needed for inferencing (scoring).""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +sources = [SOURCELOWER_TAR_GZ] + +builddependencies = [ + ('CMake', '3.24.3'), +] + +dependencies = [ + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('protobuf-python', '3.19.4'), + ('typing-extensions', '4.3.0'), +] + +use_pip = True +download_dep_fail = True + +preinstallopts = 'env MAX_JOBS="%(parallel)s"' + +sanity_check_paths = { + 'files': ['bin/check-model', 'bin/check-node', 'bin/backend-test-tools'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('check-model', '-h'), + ('check-node', '-h'), + ('backend-test-tools', '-h'), +] + +sanity_pip_check = True + +moduleclass = 'devel' diff --git a/169_Bonito/ont-remora/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb b/169_Bonito/ont-remora/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000..65d25812 --- /dev/null +++ b/169_Bonito/ont-remora/ONNX-Runtime-1.10.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,58 @@ +easyblock = 'PythonPackage' + +name = 'ONNX-Runtime' +version = '1.15.1' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://onnxruntime.ai/' +description = """ONNX Runtime inference can enable faster customer experiences and lower costs, +supporting models from deep learning frameworks such as PyTorch and +TensorFlow/Keras as well as classical machine learning libraries such as +scikit-learn, LightGBM, XGBoost, etc. ONNX Runtime is compatible with different +hardware, drivers, and operating systems, and provides optimal performance by +leveraging hardware accelerators where applicable alongside graph optimizations +and transforms.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +# ONNX Runtime with support for GPUs is distributed under the name 'onnxruntime-gpu' in PyPI +source_urls = ['http://pypi.python.org/packages/source/o/onnxruntime-gpu'] +local_whl_tmpl = 'onnxruntime_gpu-%%(version)s-cp39-cp39-manylinux_2_17_%s.manylinux2014_%s.whl' +sources = [local_whl_tmpl % ('%(arch)s', '%(arch)s')] +# checksums = [ +# { +# local_whl_tmpl % ('x86_64', 'x86_64'): +# '2ffe8009eef07307a836e654a8449c177c0ef84ef29c4619d464d5ad8ab2d01b', +# } +# ] + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('ONNX', '1.14.0'), + ('flatbuffers-python', '2.0'), +] + +use_pip = True +download_dep_fail = True + +# Due to its name 'onnxruntime-gpu', this package does not fullfil requirements on 'onnxruntime' although it provides +# the 'onnxruntime' python module. Fix this dependency issue in pip by creating a stub 'onnxruntime' dist-info folder +_py_sitepkgs = '%(installdir)s/lib/python%(pyshortver)s/site-packages' +postinstallcmds = [ + "cp -r %s/onnxruntime{_gpu,}-%%(version)s.dist-info" % _py_sitepkgs, + "sed -i 's/onnxruntime.gpu/onnxruntime/g' %s/onnxruntime-%%(version)s.dist-info/{METADATA,RECORD}" % _py_sitepkgs, +] + +sanity_pip_check = True + +_py_sitepkgs_dirs = ['onnxruntime', 'onnxruntime-%(version)s.dist-info', 'onnxruntime_gpu-%(version)s.dist-info'] + +sanity_check_paths = { + 'files': [], + 'dirs': ['lib/python%%(pyshortver)s/site-packages/%s' % x for x in _py_sitepkgs_dirs], +} + +options = {'modulename': 'onnxruntime'} + +moduleclass = 'devel' diff --git a/169_Bonito/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb b/169_Bonito/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb new file mode 100644 index 00000000..349e67e3 --- /dev/null +++ b/169_Bonito/ont-remora/ont-remora-1.0.0-foss-2021a-CUDA-11.3.1.eb @@ -0,0 +1,48 @@ +easyblock = 'PythonBundle' + +name = 'ont-remora' +version = '2.1.2' +versionsuffix = '-CUDA-%(cudaver)s' + +homepage = 'https://github.com/nanoporetech/remora' +description = """Methylation/modified base calling separated from basecalling. Remora primarily +provides an API to call modified bases for basecaller programs such as Bonito. +Remora also provides the tools to prepare datasets, train modified base models +and run simple inference.""" + +toolchain = {'name': 'foss', 'version': '2022a'} + +dependencies = [ + ('CUDA', '11.7.0', '', SYSTEM), + ('Python', '3.10.4'), + ('SciPy-bundle', '2022.05'), + ('ONNX-Runtime', '1.10.0', versionsuffix), + ('PyTorch', '1.12.1', versionsuffix), + ('scikit-learn', '1.1.2'), + ('tqdm', '4.64.0'), +] + +use_pip = True + +exts_list = [ + ('thop', '0.1.1-post2209072238', { + 'source_tmpl': '%(name)s-%(version)s-py3-none-any.whl', + }), + (name, version, { + 'modulename': 'remora', + 'checksums': ['594c7f1d4cc757c0b1d42b1af5203903df10ea11cfc6af3288d60c3df8e37d4a'], + }), +] + +sanity_pip_check = True + +sanity_check_paths = { + 'files': ['bin/remora'], + 'dirs': ['lib/python%(pyshortver)s/site-packages'], +} + +sanity_check_commands = [ + ('remora', '--help'), +] + +moduleclass = 'bio' diff --git a/16_Yambo/Yambo-5.1.2-intel-2021b.eb b/16_Yambo/Yambo-5.1.2-intel-2021b.eb index 3d7cba72..e29b903d 100644 --- a/16_Yambo/Yambo-5.1.2-intel-2021b.eb +++ b/16_Yambo/Yambo-5.1.2-intel-2021b.eb @@ -10,7 +10,7 @@ description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid s Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" toolchain = {'name': 'intel', 'version': '2021b'} -toolchainopts = {'usempi': True, 'openmp': True} +toolchainopts = {'usempi': True} local_yambo_ext_cmd = 'mkdir yambo-%(version)s && ' local_yambo_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s' @@ -37,10 +37,12 @@ sources = [ 'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/', }, ] +patches = ['yambo_slepc_fix.patch'] checksums = [ {'yambo-5.1.2.tar.gz': '9625d8a96bd9a3ff3713ebe53228d5ac9be0a98adecbe2a2bad67234c0e26a2e'}, {'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, + {'yambo_slepc_fix.patch': 'e44a0f85ec5eb55da7c7d42937b4c452bde2ed2c6d2f98fffca15696c82b7df6'}, ] dependencies = [ @@ -57,18 +59,20 @@ with_configure = True configopts = 'FC=mpiifort CC=mpiicc --enable-msgs-comps ' configopts += '--prefix=%(builddir)s/%(namelower)s-%(version)s/ ' configopts += '--enable-open-mp --enable-hdf5-par-io ' -configopts += '--with-blas-libs="$LIBBLAS" ' -configopts += '--with-lapack-libs="$LIBLAPACK" --with-blacs-libs=mkl ' -configopts += '--with-scalapack-libs=mkl ' -configopts += '--with-fft-libs="-mkl" --with-fft-includedir="$FFT_INC_DIR" ' -configopts += '--with-netcdf-lib=$EBROOTNETCDF/lib --with-netcdf-include="$EBROOTNETCDF/include" ' +configopts += '--with-blas-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-lapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-blacs-libs=mkl ' +configopts += '--with-scalapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-fft-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-fft-includedir="${MKLROOT}/include" ' +configopts += '--with-netcdf-path=$EBROOTNETCDF ' configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" ' configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" ' configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" ' configopts += '--enable-par-linalg --enable-slepc-linalg ' -prebuildopts = "export FPATH=$EBROOTPETSC/include:$EBROOTSLEPC/include:$FPATH && " - prebuildopts = "export SHELL='sh -x' && " buildopts = 'all' diff --git a/16_Yambo/Yambo-5.1.2-intel-2021b.eb.bak_20230724150235_3140197 b/16_Yambo/Yambo-5.1.2-intel-2021b.eb.bak_20230724150235_3140197 new file mode 100644 index 00000000..ca10bb43 --- /dev/null +++ b/16_Yambo/Yambo-5.1.2-intel-2021b.eb.bak_20230724150235_3140197 @@ -0,0 +1,93 @@ +easyblock = 'MakeCp' + +name = 'Yambo' +# see https://github.com/yambo-code/yambo/wiki/Releases-%28tar.gz-format%29 +version = '5.1.2' +local_yambo_libs_ver = '1.0' + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +local_yambo_ext_cmd = 'mkdir yambo-%(version)s && ' +local_yambo_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s' +local_yambo_lib_ext_cmd = 'mkdir -p yambo-%(version)s/lib/yambo/ && ' +local_yambo_lib_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/' + +source_urls = ['https://github.com/yambo-code/yambo/archive/'] +sources = [ + { + 'download_filename': '%(version)s.tar.gz', + 'filename': 'yambo-%(version)s.tar.gz', + 'extract_cmd': local_yambo_ext_cmd, + }, + { + 'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'], + 'download_filename': '%s.tar.gz' % local_yambo_libs_ver, + 'filename': 'yambo-libraries-%s.tar.gz' % local_yambo_libs_ver, + 'extract_cmd': local_yambo_lib_ext_cmd, + }, + { + # see https://github.com/yambo-code/yambo/wiki/Libraries#external-libraries + 'source_urls': ['https://github.com/yambo-code/yambo/files/962173/'], + 'filename': 'iotk-y1.2.2.tar.gz', + 'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/', + }, +] +patches = ['yambo_slepc_fix.patch'] +checksums = [ + {'yambo-5.1.2.tar.gz': '9625d8a96bd9a3ff3713ebe53228d5ac9be0a98adecbe2a2bad67234c0e26a2e'}, + {'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, + {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PETSc', '3.18.4'), + ('SLEPc', '3.18.2'), + ('libxc', '5.1.6'), +] + +with_configure = True + +configopts = 'FC=mpiifort CC=mpiicc --enable-msgs-comps ' +configopts += '--prefix=%(builddir)s/%(namelower)s-%(version)s/ ' +configopts += '--enable-open-mp --enable-hdf5-par-io ' +configopts += '--with-blas-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-lapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-blacs-libs=mkl ' +configopts += '--with-scalapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-fft-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-fft-includedir="${MKLROOT}/include" ' +configopts += '--with-netcdf-path=$EBROOTNETCDF ' +configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" ' +configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" ' +configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" ' +configopts += '--enable-par-linalg --enable-slepc-linalg ' + +prebuildopts = "export FPATH=$EBROOTPETSC/include:$EBROOTSLEPC/include:$FPATH && " + +prebuildopts = "export SHELL='sh -x' && " +buildopts = 'all' + +files_to_copy = [ + (['bin/*'], 'bin'), + (['%(builddir)s/%(namelower)s-%(version)s/lib/external/intel/mpiifort/bin/*'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['a2y', 'p2y', 'yambo', 'yambo_ph', 'ypp', 'ypp_ph', + 'iotk', 'iotk.x']], + 'dirs': [] +} + +sanity_check_commands = ["yambo -h"] + +moduleclass = 'phys' diff --git a/16_Yambo/Yambo-5.1.2-intel-2021b.eb.bak_20230724151150_3141664 b/16_Yambo/Yambo-5.1.2-intel-2021b.eb.bak_20230724151150_3141664 new file mode 100644 index 00000000..66f0b200 --- /dev/null +++ b/16_Yambo/Yambo-5.1.2-intel-2021b.eb.bak_20230724151150_3141664 @@ -0,0 +1,94 @@ +easyblock = 'MakeCp' + +name = 'Yambo' +# see https://github.com/yambo-code/yambo/wiki/Releases-%28tar.gz-format%29 +version = '5.1.2' +local_yambo_libs_ver = '1.0' + +homepage = 'http://www.yambo-code.org' +description = """Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. + Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf.""" + +toolchain = {'name': 'intel', 'version': '2021b'} +toolchainopts = {'usempi': True} + +local_yambo_ext_cmd = 'mkdir yambo-%(version)s && ' +local_yambo_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s' +local_yambo_lib_ext_cmd = 'mkdir -p yambo-%(version)s/lib/yambo/ && ' +local_yambo_lib_ext_cmd += 'tar --strip-components=1 -xzf %s -C yambo-%(version)s/lib/yambo/' + +source_urls = ['https://github.com/yambo-code/yambo/archive/'] +sources = [ + { + 'download_filename': '%(version)s.tar.gz', + 'filename': 'yambo-%(version)s.tar.gz', + 'extract_cmd': local_yambo_ext_cmd, + }, + { + 'source_urls': ['https://github.com/yambo-code/yambo-libraries/archive/'], + 'download_filename': '%s.tar.gz' % local_yambo_libs_ver, + 'filename': 'yambo-libraries-%s.tar.gz' % local_yambo_libs_ver, + 'extract_cmd': local_yambo_lib_ext_cmd, + }, + { + # see https://github.com/yambo-code/yambo/wiki/Libraries#external-libraries + 'source_urls': ['https://github.com/yambo-code/yambo/files/962173/'], + 'filename': 'iotk-y1.2.2.tar.gz', + 'extract_cmd': 'cp %s yambo-%(version)s/lib/archive/', + }, +] +patches = ['yambo_slepc_fix.patch'] +checksums = [ + {'yambo-5.1.2.tar.gz': '9625d8a96bd9a3ff3713ebe53228d5ac9be0a98adecbe2a2bad67234c0e26a2e'}, + {'yambo-libraries-1.0.tar.gz': 'f25d86101cc9cead9f64f05181aab1f06eac8528fea5ba5c586b2b9512cb8492'}, + {'iotk-y1.2.2.tar.gz': 'c0a4eb19f3e885d83d7afa52eb90658fba7cb1cb6e66049866a98dcc980de543'}, + {'yambo_slepc_fix.patch': '2653aeecb887c3919204da575d65e9d985b0b23608d5780dc8aa1bba02dc12c5'}, +] + +dependencies = [ + ('HDF5', '1.12.1'), + ('netCDF', '4.8.1'), + ('netCDF-Fortran', '4.5.3'), + ('PETSc', '3.18.4'), + ('SLEPc', '3.18.2'), + ('libxc', '5.1.6'), +] + +with_configure = True + +configopts = 'FC=mpiifort CC=mpiicc --enable-msgs-comps ' +configopts += '--prefix=%(builddir)s/%(namelower)s-%(version)s/ ' +configopts += '--enable-open-mp --enable-hdf5-par-io ' +configopts += '--with-blas-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-lapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-blacs-libs=mkl ' +configopts += '--with-scalapack-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" ' +configopts += '--with-fft-libs="-L${MKLROOT}/lib/intel64 -Wl,--no-as-needed -lmkl_gf_lp64 -lmkl_gnu_thread ' +configopts += '-lmkl_core -lgomp -lpthread -lm -ldl" --with-fft-includedir="${MKLROOT}/include" ' +configopts += '--with-netcdf-path=$EBROOTNETCDF ' +configopts += '--with-netcdff-path="$EBROOTNETCDFMINFORTRAN" ' +configopts += '--with-hdf5-path="$EBROOTHDF5" --with-petsc-path="$EBROOTPETSC" ' +configopts += '--with-slepc-path="$EBROOTSLEPC" --with-libxc-path="$EBROOTLIBXC" ' +configopts += '--enable-par-linalg --enable-slepc-linalg ' + +prebuildopts = "export FPATH=$EBROOTPETSC/include:$EBROOTSLEPC/include:$FPATH && " + +prebuildopts = "export SHELL='sh -x' && " +buildopts = 'all' + +files_to_copy = [ + (['bin/*'], 'bin'), + (['%(builddir)s/%(namelower)s-%(version)s/lib/external/intel/mpiifort/bin/*'], 'bin') +] + +sanity_check_paths = { + 'files': ['bin/' + x for x in ['a2y', 'p2y', 'yambo', 'yambo_ph', 'ypp', 'ypp_ph', + 'iotk', 'iotk.x']], + 'dirs': [] +} + +sanity_check_commands = ["yambo -h"] + +moduleclass = 'phys' diff --git a/16_Yambo/matrix.patch b/16_Yambo/matrix.patch new file mode 100644 index 00000000..6cd48b5b --- /dev/null +++ b/16_Yambo/matrix.patch @@ -0,0 +1,232 @@ +--- orig_matrix 2023-07-24 14:10:37.038073000 +0200 ++++ matrix.F 2023-07-24 14:12:26.588378000 +0200 +@@ -1,8 +1,8 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! +-! Authors (see AUTHORS file for details): HM DS IMA ++! Authors (see AUTHORS file for details): HM DS + ! + ! This file is distributed under the terms of the GNU + ! General Public License. You can redistribute it and/or +@@ -21,15 +21,19 @@ + ! Software Foundation, Inc., 59 Temple Place - Suite 330,Boston, + ! MA 02111-1307, USA or visit http://www.gnu.org/copyleft/gpl.txt. + ! +-subroutine K_multiply_by_V_transpose_slepc(slepc_mat,vi,vo,ierr) ++subroutine K_stored_in_a_slepc_matrix(i_BS_mat,slepc_mat) + ! +- ! Interface with the K_multiply_by_V from the Haydock method +- ! This function has to take the same arguments as MatMult from PETSC ++ ! Here I fill the kernel (coupling not yet included) in a slepc matrix to be ++ ! used for diagonalization and/or invertion + ! +- use pars, ONLY : SP +- use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp +- use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim +- use parallel_m, ONLY : PAR_IND_T_Haydock ++ ! | (K_r) (cI*K_c) | ++ ! K = | | ++ ! | (-cI*K_c^*) (-K_r^*) | ++ ! ++ use pars, ONLY:cI,cONE ++ use BS, ONLY:BS_K_dim,BS_H_dim,BS_blk,n_BS_blks,BS_K_coupling,& ++ & BS_res_ares_n_mat,l_BS_ares_from_res ++ use BS_solvers, ONLY:BSS_eh_E,BSS_eh_W,BSS_perturbative_width + ! + #include + #include +@@ -39,87 +43,114 @@ + #include + ! + use petscmat +- use slepcsys ++ use slepceps ++ use slepcepsdef + use petscmatdef +- use slepcsysdef + ! + implicit none + ! +- PetscScalar :: tmp_value(1) +- PetscInt :: H_pos(1), pet_one +- PetscErrorCode :: ierr ++ integer, intent(in) :: i_BS_mat ++ Mat, intent(out) :: slepc_mat + ! +- VecScatter :: ctx +- PetscScalar, pointer :: xx(:) +- Vec :: vi,vo,x +- Mat :: slepc_mat +- ! +- integer :: fac +- integer :: n, i_g, i_g_start, i_c, start_index, start_index_dg +- ! +- ! create scattering context vi (distributed) -> x (local) +- ! +- pet_one = 1 +- ! +- call VecScatterCreateToAll(vi,ctx,x,ierr); +- ! +- ! scatter from vi (distributed) -> x (local) +- ! +- call VecScatterBegin(ctx,vi,x,INSERT_VALUES,SCATTER_FORWARD,ierr); +- call VecScatterEnd(ctx,vi,x,INSERT_VALUES,SCATTER_FORWARD,ierr); +- ! +- ! from x (local) build Slepc%Vi +- ! +- do i_g=1,BS_nT_grps +- if (.not.PAR_IND_T_Haydock%element_1D(i_g)) cycle +- i_g_start=BS_T_grp(i_g)%i_T_ref +- start_index = sum(BS_T_grp(i_g_start:i_g-1)%size)-1+(BS_T_grp(i_g)%i_res_ares-1)*BS_K_dim(1) +- do i_c=1,BS_T_grp(i_g)%size +- H_pos=start_index+i_c +- !SLEPC funcitons expect C indexes both in Fortran and C +- call VecGetValues( x, pet_one, H_pos, tmp_value, ierr ) +- Slepc_v%Vi(i_g)%fragment(i_c,1)=cmplx(tmp_value(1),kind=SP) +- enddo +- enddo +- ! +- ! destroy scatter context and local vector when no longer needed +- ! +- call VecScatterDestroy(ctx,ierr); +- call VecDestroy(x,ierr); +- ! +- ! fac needed for K_multiply_by_v +- fac=1 +- if(BSS_Slepc_double_grp) fac=(-1)**(Slepc_v%it(2)+1) +- ! use the haydock routine to calculate the BSE auxiliaxy hamiltonian matrix-vector product +- ! Slepc_v%Vo = H Slepc_v%Vi +- call K_multiply_by_V_transpose( Slepc_v%Vi, Slepc_v%Vo,fac ) +- ! +- ! copy output vector Vo -> vo (distributed) +- ! +- ! fac needed for expanding vo to anti-resonant block +- if(BSS_Slepc_double_grp) then +- Slepc_v%it(2)=Slepc_v%it(2)+1 +- fac=(-1)**(Slepc_v%it(2)+1) +- endif +- do i_g=1,BS_nT_grps +- if (.not.PAR_IND_T_Haydock%element_1D(i_g)) cycle +- i_g_start=BS_T_grp(i_g)%i_T_ref +- start_index = sum(BS_T_grp(i_g_start:i_g-1)%size)-1+(BS_T_grp(i_g)%i_res_ares-1)*BS_K_dim(1) +- if(BSS_slepc_double_grp) start_index_dg = sum(BS_T_grp(i_g_start:i_g-1)%size)-1+BS_K_dim(1) +- do i_c=1,BS_T_grp(i_g)%size +- H_pos=start_index+i_c +- tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1)) +- !SLEPC funcitons expect C indexes both in Fortran and C +- call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr ) +- if(BSS_slepc_double_grp) then +- ! Expand vo to anti-resonant block +- H_pos=start_index_dg+i_c +- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr ) +- endif ++ integer :: i_c,i_r,i_Tk,i_Tp,i_B,H_shift(2) ++ PetscScalar :: Mij,Mij_star ++ PetscInt :: H_pos(2),SL_K_dim(2),SL_H_dim ++ PetscErrorCode :: ierr ++ ! ++ if( BS_K_coupling) SL_H_dim=BS_H_dim ++ if(.not.BS_K_coupling) SL_H_dim=BS_K_dim(i_BS_mat) ++ SL_K_dim=BS_K_dim ++ ! ++ ! Allocate the slepc Matrix ++ ! ++ call MatCreate(PETSC_COMM_WORLD,slepc_mat,ierr) ++ call MatSetSizes(slepc_mat,PETSC_DECIDE,PETSC_DECIDE,SL_H_dim,SL_H_dim,ierr) ++ call MatSetType(slepc_mat, MATMPIDENSE,ierr) ++ call MatSetUp(slepc_mat,ierr) ++ ! ++ ! filling of the slepc_mat ++ ! ++ ! ++ do i_B=1,n_BS_blks ++ ! ++ i_Tk =BS_blk(i_B)%iT_k ++ i_Tp =BS_blk(i_B)%iT_p ++ ! ++ if (i_BS_mat/=BS_blk(i_B)%ira_k .and. BS_res_ares_n_mat==2) cycle ++ ! ++ H_shift=0 ++ if(BS_blk(i_B)%mode=="C") H_shift(2)=BS_K_dim(1) ++ if(BS_blk(i_B)%mode=="A") H_shift(:)=BS_K_dim(1) ++ ! ++ do i_r=1,BS_blk(i_B)%size(1) ++ ! ++ H_pos(1)=BS_blk(i_B)%coordinate(1)+i_r-2 ++ ! ++ do i_c=1,BS_blk(i_B)%size(2) ++ ! ++ H_pos(2)=BS_blk(i_B)%coordinate(2)+i_c-2 ++ ! ++ ! Then the upper triangle of each block and direct symmetrization ++ ! ++ if (H_pos(1)+H_shift(1)>H_pos(2)+H_shift(2)) cycle ++ if (l_BS_ares_from_res.and.H_pos(1)>H_pos(2)) cycle ++ ! ++ Mij = BS_blk(i_B)%mat(i_r,i_c) ++ Mij_star= real(BS_blk(i_B)%mat(i_r,i_c))-cI*aimag(BS_blk(i_B)%mat(i_r,i_c)) ++ ! ++ ! Add energies to the diagonal ++ ! ++ if(H_pos(1)+H_shift(1)==H_pos(2)+H_shift(2)) then ++ Mij =real(Mij) +BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE ++ Mij_star=real(Mij_star)+BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE ++ if (allocated(BSS_eh_W).and..not.BSS_perturbative_width) then ++ Mij =Mij +cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) ++ Mij_star=Mij_star -cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) ++ endif ++ endif ++ ! ++ select case(BS_blk(i_B)%mode) ++ case("R") ++ call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr ) ++ ! The resonant block is hermitial ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star, INSERT_VALUES, ierr ) ++ if (l_BS_ares_from_res.and.BS_K_coupling) then ++ ! The anti-resonant block is A=-R* ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), -Mij_star, INSERT_VALUES, ierr ) ++ ! The anti-resonant block is hermitian ++ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), -Mij, INSERT_VALUES, ierr ) ++ endif ++ case("C") ++ call MatSetValue( slepc_mat, H_pos(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) ++ ! Anti-coupling from coupling: the whole BSE matrix is Pseudo-HErmitian ++ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1), -Mij_star , INSERT_VALUES, ierr ) ++ if (l_BS_ares_from_res) then ++ ! The coupling block and the anti-coupling block are symmetric ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), -Mij_star , INSERT_VALUES, ierr ) ++ endif ++ case("A") ++ ! The anti-resonant block is hermitial ++ if(BS_res_ares_n_mat==1) then ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), Mij_star , INSERT_VALUES, ierr ) ++ else ++ call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star , INSERT_VALUES, ierr ) ++ endif ++ case("Q") ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), Mij , INSERT_VALUES, ierr ) ++ ! Coupling from anti-coupling: the whole BSE matrix is Pseudo-HErmitian ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), -Mij_star , INSERT_VALUES, ierr ) ++ end select ++ ! ++ enddo ++ ! + enddo ++ ! + enddo + ! +- call VecAssemblyBegin(vo,ierr) +- call VecAssemblyEnd(vo,ierr) ++ call MatAssemblyBegin(slepc_mat,MAT_FINAL_ASSEMBLY,ierr) ++ call MatAssemblyEnd(slepc_mat,MAT_FINAL_ASSEMBLY,ierr) + ! +-end subroutine K_multiply_by_V_transpose_slepc +\ No newline at end of file ++end subroutine K_stored_in_a_slepc_matrix +\ No newline at end of file diff --git a/16_Yambo/multiply.patch b/16_Yambo/multiply.patch new file mode 100644 index 00000000..4631db1f --- /dev/null +++ b/16_Yambo/multiply.patch @@ -0,0 +1,70 @@ +--- orig_multiply 2023-07-24 13:12:35.459799000 +0200 ++++ test.F 2023-07-24 13:13:28.242373000 +0200 +@@ -3,22 +3,22 @@ + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS IMA +-! +-! This file is distributed under the terms of the GNU +-! General Public License. You can redistribute it and/or +-! modify it under the terms of the GNU General Public +-! License as published by the Free Software Foundation; ++! ++! This file is distributed under the terms of the GNU ++! General Public License. You can redistribute it and/or ++! modify it under the terms of the GNU General Public ++! License as published by the Free Software Foundation; + ! either version 2, or (at your option) any later version. + ! +-! This program is distributed in the hope that it will +-! be useful, but WITHOUT ANY WARRANTY; without even the +-! implied warranty of MERCHANTABILITY or FITNESS FOR A +-! PARTICULAR PURPOSE. See the GNU General Public License ++! This program is distributed in the hope that it will ++! be useful, but WITHOUT ANY WARRANTY; without even the ++! implied warranty of MERCHANTABILITY or FITNESS FOR A ++! PARTICULAR PURPOSE. See the GNU General Public License + ! for more details. + ! +-! You should have received a copy of the GNU General Public +-! License along with this program; if not, write to the Free +-! Software Foundation, Inc., 59 Temple Place - Suite 330,Boston, ++! You should have received a copy of the GNU General Public ++! License along with this program; if not, write to the Free ++! Software Foundation, Inc., 59 Temple Place - Suite 330,Boston, + ! MA 02111-1307, USA or visit http://www.gnu.org/copyleft/gpl.txt. + ! + subroutine K_multiply_by_V_slepc(slepc_mat,vi,vo,ierr) +@@ -26,7 +26,7 @@ + ! Interface with the K_multiply_by_V from the Haydock method + ! This function has to take the same arguments as MatMult from PETSC + ! +- use pars, ONLY : SP ++ use pars, ONLY : SP,cI + use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp + use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim + use parallel_m, ONLY : PAR_IND_T_Haydock +@@ -45,7 +45,7 @@ + ! + implicit none + ! +- PetscScalar :: tmp_value(1) ++ PetscScalar :: tmp_value(1),tmp_value_star(1) + PetscInt :: H_pos(1), pet_one + PetscErrorCode :: ierr + ! +@@ -108,12 +108,13 @@ + do i_c=1,BS_T_grp(i_g)%size + H_pos=start_index+i_c + tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1)) ++ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1)) + !SLEPC funcitons expect C indexes both in Fortran and C + call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr ) + if(BSS_slepc_double_grp) then + ! Expand vo to anti-resonant block + H_pos=start_index_dg+i_c +- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr ) ++ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr ) + endif + enddo + enddo diff --git a/16_Yambo/transpose.patch b/16_Yambo/transpose.patch new file mode 100644 index 00000000..1043a175 --- /dev/null +++ b/16_Yambo/transpose.patch @@ -0,0 +1,42 @@ +--- orig_transpose 2023-07-24 14:10:37.038073000 +0200 ++++ transpose.F 2023-07-24 14:10:04.173729000 +0200 +@@ -1,5 +1,5 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS IMA +@@ -26,7 +26,7 @@ + ! Interface with the K_multiply_by_V from the Haydock method + ! This function has to take the same arguments as MatMult from PETSC + ! +- use pars, ONLY : SP ++ use pars, ONLY : SP,cI + use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp + use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim + use parallel_m, ONLY : PAR_IND_T_Haydock +@@ -45,7 +45,7 @@ + ! + implicit none + ! +- PetscScalar :: tmp_value(1) ++ PetscScalar :: tmp_value(1),tmp_value_star(1) + PetscInt :: H_pos(1), pet_one + PetscErrorCode :: ierr + ! +@@ -109,12 +109,13 @@ + do i_c=1,BS_T_grp(i_g)%size + H_pos=start_index+i_c + tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1)) ++ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1)) + !SLEPC funcitons expect C indexes both in Fortran and C + call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr ) + if(BSS_slepc_double_grp) then + ! Expand vo to anti-resonant block + H_pos=start_index_dg+i_c +- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr ) ++ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr ) + endif + enddo + enddo diff --git a/16_Yambo/yambo_slepc_fix.patch b/16_Yambo/yambo_slepc_fix.patch new file mode 100644 index 00000000..8f2810b4 --- /dev/null +++ b/16_Yambo/yambo_slepc_fix.patch @@ -0,0 +1,172 @@ +Fixes a bug with some parts of Yambo that use SLEPc +Applies most of this commit to this version +https://github.com/yambo-code/yambo/commit/1846c85fdd08ec80ecf90082821cf957a0c93747 +diff -ruN yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F +--- yambo-5.1.2.orig/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:31:48.203323300 +0200 ++++ yambo-5.1.2/src/bse/K_multiply_by_V_slepc.F 2023-07-24 14:35:13.933323300 +0200 +@@ -1,5 +1,5 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS IMA +@@ -26,7 +26,7 @@ + ! Interface with the K_multiply_by_V from the Haydock method + ! This function has to take the same arguments as MatMult from PETSC + ! +- use pars, ONLY : SP ++ use pars, ONLY : SP,cI + use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp + use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim + use parallel_m, ONLY : PAR_IND_T_Haydock +@@ -45,7 +45,7 @@ + ! + implicit none + ! +- PetscScalar :: tmp_value(1) ++ PetscScalar :: tmp_value(1),tmp_value_star(1) + PetscInt :: H_pos(1), pet_one + PetscErrorCode :: ierr + ! +@@ -108,12 +108,13 @@ + do i_c=1,BS_T_grp(i_g)%size + H_pos=start_index+i_c + tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1)) ++ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1)) + !SLEPC funcitons expect C indexes both in Fortran and C + call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr ) + if(BSS_slepc_double_grp) then + ! Expand vo to anti-resonant block + H_pos=start_index_dg+i_c +- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr ) ++ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr ) + endif + enddo + enddo +diff -ruN yambo-5.1.2.orig/src/bse/K_multiply_by_V_transpose_slepc.F yambo-5.1.2/src/bse/K_multiply_by_V_transpose_slepc.F +--- yambo-5.1.2.orig/src/bse/K_multiply_by_V_transpose_slepc.F 2023-07-24 14:31:48.203323300 +0200 ++++ yambo-5.1.2/src/bse/K_multiply_by_V_transpose_slepc.F 2023-07-24 14:34:40.413323300 +0200 +@@ -1,5 +1,5 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS IMA +@@ -26,7 +26,7 @@ + ! Interface with the K_multiply_by_V from the Haydock method + ! This function has to take the same arguments as MatMult from PETSC + ! +- use pars, ONLY : SP ++ use pars, ONLY : SP,cI + use BS_solvers, ONLY : Slepc_v,BSS_Slepc_double_grp + use BS, ONLY : BS_T_grp,BS_nT_grps,BS_K_dim + use parallel_m, ONLY : PAR_IND_T_Haydock +@@ -45,7 +45,7 @@ + ! + implicit none + ! +- PetscScalar :: tmp_value(1) ++ PetscScalar :: tmp_value(1),tmp_value_star(1) + PetscInt :: H_pos(1), pet_one + PetscErrorCode :: ierr + ! +@@ -109,12 +109,13 @@ + do i_c=1,BS_T_grp(i_g)%size + H_pos=start_index+i_c + tmp_value=cmplx(Slepc_v%Vo(i_g)%fragment(i_c,1)) ++ tmp_value_star=real(Slepc_v%Vo(i_g)%fragment(i_c,1))-cI*aimag(Slepc_v%Vo(i_g)%fragment(i_c,1)) + !SLEPC funcitons expect C indexes both in Fortran and C + call VecSetValues( vo, pet_one, H_pos, tmp_value, INSERT_VALUES, ierr ) + if(BSS_slepc_double_grp) then + ! Expand vo to anti-resonant block + H_pos=start_index_dg+i_c +- call VecSetValues( vo, pet_one, H_pos, fac*conjg(tmp_value), INSERT_VALUES, ierr ) ++ call VecSetValues( vo, pet_one, H_pos, fac*tmp_value_star, INSERT_VALUES, ierr ) + endif + enddo + enddo +diff -ruN yambo-5.1.2.orig/src/bse/K_stored_in_a_slepc_matrix.F yambo-5.1.2/src/bse/K_stored_in_a_slepc_matrix.F +--- yambo-5.1.2.orig/src/bse/K_stored_in_a_slepc_matrix.F 2023-07-24 14:31:48.203323300 +0200 ++++ yambo-5.1.2/src/bse/K_stored_in_a_slepc_matrix.F 2023-07-24 14:35:46.923323300 +0200 +@@ -1,5 +1,5 @@ + ! +-! Copyright (C) 2000-2023 the YAMBO team ++! Copyright (C) 2000-2022 the YAMBO team + ! http://www.yambo-code.org + ! + ! Authors (see AUTHORS file for details): HM DS +@@ -53,7 +53,7 @@ + Mat, intent(out) :: slepc_mat + ! + integer :: i_c,i_r,i_Tk,i_Tp,i_B,H_shift(2) +- PetscScalar :: Mij ++ PetscScalar :: Mij,Mij_star + PetscInt :: H_pos(2),SL_K_dim(2),SL_H_dim + PetscErrorCode :: ierr + ! +@@ -95,14 +95,17 @@ + if (H_pos(1)+H_shift(1)>H_pos(2)+H_shift(2)) cycle + if (l_BS_ares_from_res.and.H_pos(1)>H_pos(2)) cycle + ! +- Mij=BS_blk(i_B)%mat(i_r,i_c) ++ Mij = BS_blk(i_B)%mat(i_r,i_c) ++ Mij_star= real(BS_blk(i_B)%mat(i_r,i_c))-cI*aimag(BS_blk(i_B)%mat(i_r,i_c)) + ! + ! Add energies to the diagonal + ! + if(H_pos(1)+H_shift(1)==H_pos(2)+H_shift(2)) then +- Mij=real(Mij)+BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE ++ Mij =real(Mij) +BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE ++ Mij_star=real(Mij_star)+BSS_eh_E(H_pos(1)+H_shift(1)+1)*cONE + if (allocated(BSS_eh_W).and..not.BSS_perturbative_width) then +- Mij=Mij+cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) ++ Mij =Mij +cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) ++ Mij_star=Mij_star -cI*BSS_eh_W(H_pos(1)+H_shift(1)+1) + endif + endif + ! +@@ -110,35 +113,35 @@ + case("R") + call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr ) + ! The resonant block is hermitial +- call MatSetValue( slepc_mat, H_pos(2), H_pos(1), conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star, INSERT_VALUES, ierr ) + if (l_BS_ares_from_res.and.BS_K_coupling) then + ! The anti-resonant block is A=-R* +- call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), -Mij_star, INSERT_VALUES, ierr ) + ! The anti-resonant block is hermitian + call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), -Mij, INSERT_VALUES, ierr ) + endif + case("C") + call MatSetValue( slepc_mat, H_pos(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) + ! Anti-coupling from coupling: the whole BSE matrix is Pseudo-HErmitian +- call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1), -Mij_star , INSERT_VALUES, ierr ) + if (l_BS_ares_from_res) then + ! The coupling block and the anti-coupling block are symmetric + call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) +- call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), -Mij_star , INSERT_VALUES, ierr ) + endif + case("A") + ! The anti-resonant block is hermitial + if(BS_res_ares_n_mat==1) then + call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2)+SL_K_dim(1), Mij , INSERT_VALUES, ierr ) +- call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2)+SL_K_dim(1), H_pos(1)+SL_K_dim(1), Mij_star , INSERT_VALUES, ierr ) + else + call MatSetValue( slepc_mat, H_pos(1), H_pos(2), Mij , INSERT_VALUES, ierr ) +- call MatSetValue( slepc_mat, H_pos(2), H_pos(1), conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1), Mij_star , INSERT_VALUES, ierr ) + endif + case("Q") + call MatSetValue( slepc_mat, H_pos(1)+SL_K_dim(1), H_pos(2), Mij , INSERT_VALUES, ierr ) + ! Coupling from anti-coupling: the whole BSE matrix is Pseudo-HErmitian +- call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1),-conjg(Mij), INSERT_VALUES, ierr ) ++ call MatSetValue( slepc_mat, H_pos(2), H_pos(1)+SL_K_dim(1), -Mij_star , INSERT_VALUES, ierr ) + end select + ! + enddo diff --git a/29_ResistanceGA/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb b/29_ResistanceGA/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb new file mode 100644 index 00000000..c92bd435 --- /dev/null +++ b/29_ResistanceGA/Circuitscape/Circuitscape-5.12.3-Julia-1.7.2.eb @@ -0,0 +1,408 @@ +easyblock = 'JuliaBundle' + +name = 'Circuitscape' +version = '5.12.3' +_julia_ver = '1.9.2' +versionsuffix = "-Julia-%s" % _julia_ver + +homepage = 'https://github.com/Circuitscape/Circuitscape.jl' +description = "Algorithms from circuit theory to predict connectivity in heterogeneous landscapes" + +toolchain = SYSTEM + +dependencies = [ + ('Julia', _julia_ver, '-linux-%s' % ARCH, True), +] + +exts_list = [ + 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('libgeotiff_jll', '100.700.100+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/libgeotiff_jll.jl/archive/'], + 'sources': ['libgeotiff-v%(version)s.tar.gz'], + 'checksums': ['5181a2f0efc07938768644560c80674122e91011ad9e169aaf62d369dd8730df'], + }), + ('GDAL_jll', '301.600.100+0', { + 'source_urls': ['https://github.com/JuliaBinaryWrappers/GDAL_jll.jl/archive/'], + 'sources': ['GDAL-v%(version)s.tar.gz'], + 'checksums': ['7e10b59b3375da11db936fd7f0669e4f0d3490a90fc2dca465c6e07e9670482e'], + }), + ('GDAL', '1.5.0', { + 'source_urls': ['https://github.com/JuliaGeo/GDAL.jl/archive/'], + 'checksums': ['0ef1553577b11a14d7e8e9bc7d139754ccccd6d5def6a9a6de728e5a6b433f1b'], + }), + ('IteratorInterfaceExtensions', '1.0.0', { + 'source_urls': ['https://github.com/queryverse/IteratorInterfaceExtensions.jl/archive/'], + 'checksums': ['c43dc43fc29c0c7aa738793c5a847ce29491c5fca1a0f0e434fff1bb1c5c7994'], + }), + ('TableTraits', '1.0.1', { + 'source_urls': 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['58abf90b037c618daeed89940c77ac129b5155b26429ac77643cc9c5db453363'], + }), + ('ImageCore', '0.9.4', { + 'source_urls': ['https://github.com/JuliaImages/ImageCore.jl/archive/'], + 'checksums': ['de5d244989891f47edc4f27bf8bf6557a6982e907f0874a62ad3480c9c333983'], + }), + ('ArchGDAL', '0.8.5', { + 'source_urls': ['https://github.com/yeesian/ArchGDAL.jl/archive/'], + 'checksums': ['e24ec57d88a3a07feac7db5b2501b8f06a1047c42a8eadcde9500e3601984065'], + }), + ('DelimitedFiles', '1.9.0', { + 'sources': 'v%(version)s.tar.gz', + 'source_urls': ['https://github.com/JuliaData/DelimitedFiles.jl/archive/'], + }), + (name, version, { + 'source_urls': ['https://github.com/Circuitscape/Circuitscape.jl/archive/'], + 'checksums': ['1eb5b6f5711865792204677359c1b9d9247ae3f34af42f58dfe2ec4ad3dd2177'], + }), +] + +sanity_check_commands = ["julia -e 'using Pkg;Pkg.test(\"Circuitscape\")'"] + +moduleclass = 'lib' diff --git a/29_ResistanceGA/ResistanceGA.eb b/29_ResistanceGA/ResistanceGA.eb index 1c398467..171fe234 100644 --- a/29_ResistanceGA/ResistanceGA.eb +++ b/29_ResistanceGA/ResistanceGA.eb @@ -3,7 +3,8 @@ easyblock = 'Bundle' name = 'ResistanceGA' version = '4.2-5' local_commit = '04326a8' -versionsuffix = '-R-%(rver)s' +_julia_ver = '1.9.2' +versionsuffix = '-R-%%(rver)s-Julia-%s' % _julia_ver homepage = 'https://github.com/wpeterman/ResistanceGA' description = "An R package to optimize resistance surfaces using Genetic Algorithms." @@ -12,7 +13,8 @@ toolchain = {'name': 'foss', 'version': '2022a'} dependencies = [ ('R', '4.2.1'), - ('Circuitscape', '5.12.3', "-Julia-1.7.2", SYSTEM), + ('Julia', _julia_ver, '-linux-%s' % ARCH, SYSTEM), + ('Circuitscape', '5.12.3', '-Julia-%s' % _julia_ver, SYSTEM), ] exts_defaultclass = 'RPackage' @@ -28,12 +30,12 @@ exts_default_options = { } exts_list = [ - ('Suppressor', '0.2.0', { + ('Suppressor', '0.2.4', { 'easyblock': 'JuliaPackage', 'source_urls': ['https://github.com/JuliaIO/Suppressor.jl/archive/'], 'sources': ['v%(version)s.tar.gz'], }), - ('RCall', '0.13.13', { + ('RCall', '0.13.15', { 'easyblock': 'JuliaPackage', 'source_urls': ['https://github.com/JuliaInterop/RCall.jl/archive/'], 'sources': ['v%(version)s.tar.gz'], diff --git a/2_CLEAR/CIRCexplorer2/MariaDB-10.6.4-GCC-11.2.0.eb b/2_CLEAR/CIRCexplorer2/MariaDB-10.6.4-GCC-11.2.0.eb index 1eb91a7f..4ca72f2b 100644 --- a/2_CLEAR/CIRCexplorer2/MariaDB-10.6.4-GCC-11.2.0.eb +++ b/2_CLEAR/CIRCexplorer2/MariaDB-10.6.4-GCC-11.2.0.eb @@ -10,17 +10,22 @@ Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.""" toolchain = {'name': 'GCC', 'version': '11.2.0'} -source_urls = ['http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source'] -sources = [SOURCELOWER_TAR_GZ] -patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] -checksums = [ - '75bf9b147a95d38160d01a73b098d50a1960563b46d16a235971fff64d99643c', # mariadb-10.6.4.tar.gz - '8295837e623f6c782e1d64b00e0877ea98cce4bf8846755bb86c8a7732797c19', # MariaDB-10.1.13-link-rt-for-jemalloc.patch +local_pcre2_ver = '10.37' +source_urls = [ + 'https://archive.mariadb.org/mariadb-%(version)s/source/', + 'http://ftp.hosteurope.de/mirror/archive.mariadb.org/mariadb-%(version)s/source', + 'https://downloads.sourceforge.net/project/pcre/pcre2/%s/' % local_pcre2_ver, +] +sources = [ + SOURCELOWER_TAR_GZ, + {'filename': 'pcre2-%s.zip' % local_pcre2_ver, 'extract_cmd': "cp %s %(builddir)s/"}, ] +patches = ['MariaDB-10.1.13-link-rt-for-jemalloc.patch'] builddependencies = [ ('CMake', '3.21.1'), ('libaio', '0.3.112'), + ('Boost', '1.75.0'), # needed by OQGraph ] dependencies = [ @@ -32,13 +37,12 @@ dependencies = [ ('jemalloc', '5.2.1'), # optional ('snappy', '1.1.9'), # needed by RocksDB; optional for InnoDB ('libxml2', '2.9.10'), # needed by Connect XML - ('Boost', '1.75.0'), # needed by OQGraph ('Judy', '1.0.5'), # needed by OQGraph - ('PCRE2', '10.37'), ('OpenSSL', '1.1', '', True), # runtime dep for mysql and PCRE2 for mysqltest ] -separate_build_dir = True +local_pcre2_path = '%%(builddir)s/pcre2-%s.zip' % local_pcre2_ver +preconfigopts = "sed -i 's@http://.*.zip@file://%s@g' ../mariadb-%%(version)s/cmake/pcre.cmake && " % local_pcre2_path configopts = "-DCMAKE_BUILD_TYPE=Release " configopts += "-DCMAKE_SHARED_LINKER_FLAGS='-fuse-ld=bfd' " # Linking fails with default gold linker @@ -47,6 +51,7 @@ configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we bui configopts += "-DWITH_ZLIB=system " configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc +configopts += "-DBoost_USE_STATIC_LIBS=ON" sanity_check_commands = ["mysql --help", "mysqltest --help"] diff --git a/2_CLEAR/CLEAR_clean_run/MariaDB.eb b/2_CLEAR/CLEAR_clean_run/MariaDB.eb index 82fe57b4..e1261776 100644 --- a/2_CLEAR/CLEAR_clean_run/MariaDB.eb +++ b/2_CLEAR/CLEAR_clean_run/MariaDB.eb @@ -53,6 +53,7 @@ configopts += "-DWITH_PCRE=auto " # External download sometimes fails so we bui configopts += "-DWITH_ZLIB=system " configopts += "-DWITH_EMBEDDED_SERVER=ON " # for libmysqld.so & co configopts += "-DWITH_SAFEMALLOC=OFF " # Disable memory debugger with jemalloc +configopts += "-DBoost_USE_STATIC_LIBS=ON" sanity_check_commands = ["mysql --help", "mysqltest --help"]