(partial) EasyBuild log for failed build of /tmp/eb-LPzPbR/files_pr12499/i/IMOD/IMOD-4.11.5-fosscuda-2020b.eb (PR #12499)

IMOD-4.11.5-fosscuda-2020b_partial.log

== 2021-07-13 16:45:03,218 easyblock.py:285 INFO This is EasyBuild 4.4.0 (framework: 4.4.0, easyblocks: 4.4.0) on host srv-eustermann-01.
== 2021-07-13 16:45:03,218 easyblock.py:291 INFO This is easyblock ConfigureMake from module easybuild.easyblocks.generic.configuremake (/g/easybuild/x86_64/CentOS/7/rome/software/EasyBuild/4.4.0/lib/python2.7/site-packages/easybuild/easyblocks/generic/configuremake.pyo)
== 2021-07-13 16:45:03,219 easyblock.py:927 INFO Build dir set to /tmp/eb-build/IMOD/4.11.5/fosscuda-2020b
== 2021-07-13 16:45:03,219 config.py:616 DEBUG software install path as specified by 'installpath' and 'subdir_software': /g/easybuild/x86_64/CentOS/7/rome/software
== 2021-07-13 16:45:03,219 easyconfig.py:2586 DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f34e1933fd0>
== 2021-07-13 16:45:03,219 easyconfig.py:2589 DEBUG Using fixed naming software installation subdir: IMOD/4.11.5-fosscuda-2020b
== 2021-07-13 16:45:03,219 easyblock.py:987 INFO Software install dir set to /g/easybuild/x86_64/CentOS/7/rome/software/IMOD/4.11.5-fosscuda-2020b
== 2021-07-13 16:45:03,219 config.py:616 DEBUG modules install path as specified by 'installpath' and 'subdir_modules': /g/easybuild/x86_64/CentOS/7/rome/modules
== 2021-07-13 16:45:03,219 easyblock.py:992 INFO Module install dir set to /g/easybuild/x86_64/CentOS/7/rome/modules/all
== 2021-07-13 16:45:03,219 easyblock.py:270 INFO Init completed for application name IMOD version 4.11.5
== 2021-07-13 16:45:03,219 easyblock.py:3600 INFO Obtained application instance of for IMOD (easyblock: ConfigureMake)
== 2021-07-13 16:45:03,219 easyblock.py:3613 DEBUG Skip set to False
== 2021-07-13 16:45:03,219 easyconfig.py:1654 INFO Generating template values...
== 2021-07-13 16:45:03,219 templates.py:189 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f34e1933fd0>
== 2021-07-13 16:45:03,219 templates.py:216 DEBUG version found in easyconfig is 4.11.5
== 2021-07-13 16:45:03,220 systemtools.py:1061 DEBUG Version is already a string ('11'), OK
== 2021-07-13 16:45:03,220 systemtools.py:1061 DEBUG Version is already a string ('3.8.6'), OK
== 2021-07-13 16:45:03,220 systemtools.py:1061 DEBUG Version is already a string ('11.1.1'), OK
== 2021-07-13 16:45:03,220 templates.py:318 DEBUG name: bitbucket_account, config: %(namelower)s
== 2021-07-13 16:45:03,220 templates.py:318 DEBUG name: github_account, config: %(namelower)s
== 2021-07-13 16:45:03,220 templates.py:318 DEBUG name: name, config: IMOD
== 2021-07-13 16:45:03,220 templates.py:318 DEBUG name: parallel, config: None
== 2021-07-13 16:45:03,220 templates.py:318 DEBUG name: version, config: 4.11.5
== 2021-07-13 16:45:03,220 templates.py:318 DEBUG name: versionsuffix, config: 
== 2021-07-13 16:45:03,220 templates.py:318 DEBUG name: versionprefix, config: 
== 2021-07-13 16:45:03,220 mpi.py:119 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2021-07-13 16:45:03,220 mpi.py:304 INFO Using MPI command template 'mpirun -n %(nr_ranks)s %(cmd)s' (params: {'cmd': 'xxx_command_xxx', 'nr_ranks': 1})
== 2021-07-13 16:45:03,220 easyconfig.py:1673 INFO Template values: arch='x86_64', bitbucket_account='imod', cuda_cc_semicolon_sep='3.5;5.0;6.0;7.0;7.5;8.0;8.6', cuda_cc_space_sep='3.5 5.0 6.0 7.0 7.5 8.0 8.6', cuda_compute_capabilities='3.5,5.0,6.0,7.0,7.5,8.0,8.6', cuda_sm_comma_sep='sm_35,sm_50,sm_60,sm_70,sm_75,sm_80,sm_86', cuda_sm_space_sep='sm_35 sm_50 sm_60 sm_70 sm_75 sm_80 sm_86', cudamajver='11', cudaminver='1', cudashortver='11.1', cudaver='11.1.1', github_account='imod', javamajver='11', javashortver='11', javaver='11', module_name='IMOD/4.11.5-fosscuda-2020b', mpi_cmd_prefix='mpirun -n 1', name='IMOD', nameletter='I', nameletterlower='i', namelower='imod', pymajver='3', pyminver='8', pyshortver='3.8', pyver='3.8.6', toolchain_name='fosscuda', toolchain_version='2020b', version='4.11.5', version_major='4', version_major_minor='4.11', version_minor='11', versionprefix='', versionsuffix=''
== 2021-07-13 16:45:03,224 one.py:518 DEBUG Extracted comments:
{'above': {'configure_cmd': ["# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. ",
                             '# CFLAGs are passed with -flags.'],
           'cuda_compute_capabilities': ['# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)'],
           'dependencies': ['# mercurial repository',
                            '# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD',
                            '# get lunch',
                            '# cd IMOD',
                            '# hg update -r IMOD_4-11-5',
                            '# cd ..',
                            '# tar czf IMOD-4.11.5.tar.gz IMOD',
                            '',
                            ''],
           'local_cuda_replace': ['# replace hardcoded CUDA compute capabilitites in machines/rhlinux. '],
           'local_exports': ['# exports required for configure and build'],
           'local_qmake_pass_cflags': ['# modify all qmake pro files in order to pass CFLAGS'],
           'preinstallopts': ['# create some missing directories required for installation process:'],
           'sanity_check_paths': ['# Observed problems with alias on a tcl based module system. Use bin/subm python script instead.',
                                  '# modaliases = {',
                                  "# 'subm': 'submfg $* &'",
                                  '# }']},
 'header': ['# Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04'],
 'inline': {},
 'iterabove': {'local_exports': {'local_exports += \'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&\'': ['#  readw_or_imod.f and others with gfortran10: ',
                                                                                                               '# Error: Type mismatch between actual argument at (1) and actual argument at (2) (INTEGER(4)/INTEGER(2))',
                                                                                                               '# => set -fallow-argument-mismatch. Runs through without this option with GCC 8.3.0.']}},
 'iterinline': {'configure_cmd': {"configure_cmd += ' #'": '  # avoid passing unknown arg --prefix',
                                  'configure_cmd += \'-flags "$CFLAGS" \'': '  # inject CFLAGS',
                                  "configure_cmd += '-i %(installdir)s '": '  # set installdir'},
                'local_exports': {'local_exports += \'export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&\'': '  # required for gfortran10'}},
 'tail': []}
== 2021-07-13 16:45:03,224 one.py:169 INFO Skipping reformatting value for parameter 'toolchain'
== 2021-07-13 16:45:03,224 one.py:169 INFO Skipping reformatting value for parameter 'toolchainopts'
== 2021-07-13 16:45:03,225 easyconfig.py:1220 DEBUG Dumped easyconfig: # Thomas Hoffmann, EMBL Heidelberg, structures-it@embl.de, 2021/04
easyblock = 'ConfigureMake'

name = 'IMOD'
version = '4.11.5'

homepage = 'https://bio3d.colorado.edu/imod/'
description = """IMOD is a set of image processing, modeling and display
programs used for tomographic reconstruction and for 3D reconstruction of EM
serial sections and optical sections. The package contains tools for assembling
and aligning data within multiple types and sizes of image stacks, viewing 3-D
data from any orientation, and modeling and display of the image files. IMOD
was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim
Kremer, Quanren Xiong, and John Heumann at the University of Colorado."""

toolchain = {'name': 'fosscuda', 'version': '2020b'}
toolchainopts = {'openmp': True, 'pic': True}

sources = [SOURCE_TAR_GZ]
checksums = ['5c50f1457134fe5113b95e0939d3181b948d211f25d9a05ad2b4ec0f23251c79']

# mercurial repository
# hg clone --debug http://bio3d.colorado.edu/imod/nightlyBuilds/IMOD
# get lunch
# cd IMOD
# hg update -r IMOD_4-11-5
# cd ..
# tar czf IMOD-4.11.5.tar.gz IMOD


dependencies = [
    ('LibTIFF', '4.1.0', '', ('GCCcore', '10.2.0')),
    ('Qt5', '5.14.2', '', ('GCCcore', '10.2.0')),
    ('Java', '11', '', True),
    ('HDF5', '1.10.7', '', ('gompic', '2020b')),
    ('Python', '3.8.6', '', ('GCCcore', '10.2.0')),
]

preconfigopts = """export QTDIR=$EBROOTQT5 &&export HDF5_DIR=$EBROOTHDF5 &&export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&export CUDA_DIR=$CUDA_HOME &&export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&sed -i "s/-arch sm_35/`echo %(cuda_cc_space_sep)s|sed "s/\\.//g"|   awk '{          printf "-arch sm_"$1;           for (i=1;i<=NF; i++){printf(" -gencode=arch=compute_%s,code=sm_%s",$i,$i) }    }'`/g" machines/rhlinux &&find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&"""

prebuildopts = 'export QTDIR=$EBROOTQT5 &&export HDF5_DIR=$EBROOTHDF5 &&export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&export CUDA_DIR=$CUDA_HOME &&export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&'

# create some missing directories required for installation process:
preinstallopts = "mkdir %(installdir)s/{man/cat1,bin,autodoc,SystemTemplate,lib/imodplug,com,html,Plugins} -p &&"

modloadmsg = "Please set the environment variable $IMOD_CALIB_DIR if appropriate."
# default CUDA compute capabilities to use (override via --cuda-compute-capabilities)
cuda_compute_capabilities = [
    '3.5',
    '5.0',
    '6.0',
    '7.0',
    '7.5',
    '8.0',
    '8.6',
]
# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. 
# CFLAGs are passed with -flags.
configure_cmd = './setup -flags "$CFLAGS" -i %(installdir)s  #'

# Observed problems with alias on a tcl based module system. Use bin/subm python script instead.
# modaliases = {
# 'subm': 'submfg $* &'
# }
sanity_check_paths = {
    'files': ['VERSION', 'bin/subm'],
    'dirs': ['bin', 'lib', 'com', 'autodoc', 'pylib', 'Plugins', 'man', 'SystemTemplate'],
}

modextravars = {
    'FOR_DISABLE_STACK_TRACE': '1',
    'IMOD_DIR': '%(installdir)s',
    'IMOD_JAVADIR': '$JAVA_HOME',
    'IMOD_PLUGIN_DIR': '%(installdir)s/lib/imodplug',
}

moduleclass = 'vis'

== 2021-07-13 16:45:03,225 filetools.py:1775 INFO Creating directory /tmp/eb-LPzPbR/reprod_20210713164503_43095 (parents: True, set_gid: False, sticky: False)
== 2021-07-13 16:45:03,225 easyblock.py:3821 INFO Dumped easyconfig instance to /tmp/eb-LPzPbR/reprod_20210713164503_43095/IMOD-4.11.5-fosscuda-2020b.eb
== 2021-07-13 16:45:03,226 filetools.py:1775 INFO Creating directory /tmp/eb-LPzPbR/reprod_20210713164503_43095/easyblocks (parents: True, set_gid: False, sticky: False)
== 2021-07-13 16:45:03,227 filetools.py:2286 INFO /g/easybuild/x86_64/CentOS/7/rome/software/EasyBuild/4.4.0/lib/python2.7/site-packages/easybuild/easyblocks/generic/configuremake.py copied to /tmp/eb-LPzPbR/reprod_20210713164503_43095/easyblocks/configuremake.py
== 2021-07-13 16:45:03,227 easyblock.py:3801 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-LPzPbR/reprod_20210713164503_43095/easyblocks
== 2021-07-13 16:45:03,227 easyblock.py:1771 INFO Number of iterations to perform for central part of installation procedure: 1
== 2021-07-13 16:45:03,227 build_log.py:265 INFO building and installing IMOD/4.11.5-fosscuda-2020b...
== 2021-07-13 16:45:03,227 config.py:616 DEBUG software install path as specified by 'installpath' and 'subdir_software': /g/easybuild/x86_64/CentOS/7/rome/software
== 2021-07-13 16:45:03,227 filetools.py:1868 INFO Lock /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock does not exist
== 2021-07-13 16:45:03,227 config.py:616 DEBUG software install path as specified by 'installpath' and 'subdir_software': /g/easybuild/x86_64/CentOS/7/rome/software
== 2021-07-13 16:45:03,228 filetools.py:1809 INFO Creating lock at /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock...
== 2021-07-13 16:45:03,228 filetools.py:1775 INFO Creating directory /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock (parents: True, set_gid: False, sticky: False)
== 2021-07-13 16:45:03,228 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/x86_64/CentOS/7/rome/software/EasyBuild/4.4.0/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 in __init__): Failed to create directory /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock: [Errno 13] Permission denied: '/g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock' (at easybuild/x86_64/CentOS/7/rome/software/EasyBuild/4.4.0/lib/python2.7/site-packages/easybuild/tools/filetools.py:1787 in mkdir)
== 2021-07-13 16:45:03,229 build_log.py:169 ERROR EasyBuild crashed with an error (at easybuild/x86_64/CentOS/7/rome/software/EasyBuild/4.4.0/lib/python2.7/site-packages/easybuild/base/exceptions.py:124 in __init__): Failed to create lock /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock: [Errno 13] Permission denied: /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock (at easybuild/x86_64/CentOS/7/rome/software/EasyBuild/4.4.0/lib/python2.7/site-packages/easybuild/tools/filetools.py:1817 in create_lock)
== 2021-07-13 16:45:03,229 easyblock.py:3643 WARNING build failed (first 300 chars): Failed to create lock /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lock: [Errno 13] Permission denied: /g/easybuild/x86_64/CentOS/7/rome/software/.locks/_g_easybuild_x86_64_CentOS_7_rome_software_IMOD_4.11.5-fosscuda-2020b.lo
== 2021-07-13 16:45:03,229 easyblock.py:300 INFO Closing log for application name IMOD version 4.11.5