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

IMOD-4.11.5-foss-2020b_partial.log

== 2021-07-13 16:45:02,962 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 16:45:02,962 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 16:45:02,963 easyblock.py:927 INFO Build dir set to /tmp/eb-build/IMOD/4.11.5/foss-2020b
== 2021-07-13 16:45:02,963 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 16:45:02,963 easyconfig.py:2586 DEBUG Determining software installation subdir for <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f34e1e9da10>
== 2021-07-13 16:45:02,963 easyconfig.py:2589 DEBUG Using fixed naming software installation subdir: IMOD/4.11.5-foss-2020b
== 2021-07-13 16:45:02,963 easyblock.py:987 INFO Software install dir set to /g/easybuild/x86_64/CentOS/7/rome/software/IMOD/4.11.5-foss-2020b
== 2021-07-13 16:45:02,963 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 16:45:02,963 easyblock.py:992 INFO Module install dir set to /g/easybuild/x86_64/CentOS/7/rome/modules/all
== 2021-07-13 16:45:02,963 easyblock.py:270 INFO Init completed for application name IMOD version 4.11.5
== 2021-07-13 16:45:02,963 easyblock.py:3600 INFO Obtained application instance of for IMOD (easyblock: ConfigureMake)
== 2021-07-13 16:45:02,963 easyblock.py:3613 DEBUG Skip set to False
== 2021-07-13 16:45:02,963 easyconfig.py:1654 INFO Generating template values...
== 2021-07-13 16:45:02,963 templates.py:189 DEBUG config: <easybuild.framework.easyconfig.easyconfig.EasyConfig object at 0x7f34e1e9da10>
== 2021-07-13 16:45:02,963 templates.py:216 DEBUG version found in easyconfig is 4.11.5
== 2021-07-13 16:45:02,964 systemtools.py:1061 DEBUG Version is already a string ('11'), OK
== 2021-07-13 16:45:02,964 systemtools.py:1061 DEBUG Version is already a string ('3.8.6'), OK
== 2021-07-13 16:45:02,964 templates.py:318 DEBUG name: bitbucket_account, config: %(namelower)s
== 2021-07-13 16:45:02,964 templates.py:318 DEBUG name: github_account, config: %(namelower)s
== 2021-07-13 16:45:02,964 templates.py:318 DEBUG name: name, config: IMOD
== 2021-07-13 16:45:02,964 templates.py:318 DEBUG name: parallel, config: None
== 2021-07-13 16:45:02,964 templates.py:318 DEBUG name: version, config: 4.11.5
== 2021-07-13 16:45:02,964 templates.py:318 DEBUG name: versionsuffix, config: 
== 2021-07-13 16:45:02,964 templates.py:318 DEBUG name: versionprefix, config: 
== 2021-07-13 16:45:02,964 mpi.py:119 INFO Using template MPI command 'mpirun -n %(nr_ranks)s %(cmd)s' for MPI family 'OpenMPI'
== 2021-07-13 16:45:02,964 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 16:45:02,964 easyconfig.py:1673 INFO Template values: arch='x86_64', bitbucket_account='imod', github_account='imod', javamajver='11', javashortver='11', javaver='11', module_name='IMOD/4.11.5-foss-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='foss', toolchain_version='2020b', version='4.11.5', version_major='4', version_major_minor='4.11', version_minor='11', versionprefix='', versionsuffix=''
== 2021-07-13 16:45:02,968 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.'],
           '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_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 16:45:02,968 one.py:169 INFO Skipping reformatting value for parameter 'toolchain'
== 2021-07-13 16:45:02,968 one.py:169 INFO Skipping reformatting value for parameter 'toolchainopts'
== 2021-07-13 16:45:02,970 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': 'foss', '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', '', ('gompi', '2020b')),
    ('Python', '3.8.6', '', ('GCCcore', '10.2.0')),
]

preconfigopts = """export QTDIR=$EBROOTQT5 &&export HDF5_DIR=$EBROOTHDF5 &&export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&export CFLAGS="$CFLAGS -fallow-argument-mismatch" &&find -name *.pro -exec sed -i -e '$aQMAKE_CXXFLAGS += $$(CFLAGS)' {} \\; &&"""

prebuildopts = 'export QTDIR=$EBROOTQT5 &&export HDF5_DIR=$EBROOTHDF5 &&export QMAKESPEC=$EBROOTQT5/mkspecs/`qmake -query QMAKE_SPEC` &&export CFLAGS="$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 $IMOD_CALIB_DIR if appropriate."
# IMOD's configure script is named setup and does not know the parameter --prefix, but -i. 
# CFLAGs are passed with -flags.
configure_cmd = './setup -flags "$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 16:45:02,970 filetools.py:1775 INFO Creating directory /tmp/eb-LPzPbR/reprod_20210713164502_43095 (parents: True, set_gid: False, sticky: False)
== 2021-07-13 16:45:02,970 easyblock.py:3821 INFO Dumped easyconfig instance to /tmp/eb-LPzPbR/reprod_20210713164502_43095/IMOD-4.11.5-foss-2020b.eb
== 2021-07-13 16:45:02,970 filetools.py:1775 INFO Creating directory /tmp/eb-LPzPbR/reprod_20210713164502_43095/easyblocks (parents: True, set_gid: False, sticky: False)
== 2021-07-13 16:45:02,983 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_20210713164502_43095/easyblocks/configuremake.py
== 2021-07-13 16:45:02,983 easyblock.py:3801 INFO Dumped easyblock configuremake.py required for reproduction to /tmp/eb-LPzPbR/reprod_20210713164502_43095/easyblocks
== 2021-07-13 16:45:03,007 easyblock.py:1771 INFO Number of iterations to perform for central part of installation procedure: 1
== 2021-07-13 16:45:03,007 build_log.py:265 INFO building and installing IMOD/4.11.5-foss-2020b...
== 2021-07-13 16:45:03,008 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 16:45:03,044 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-foss-2020b.lock does not exist
== 2021-07-13 16:45:03,044 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 16:45:03,044 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-foss-2020b.lock...
== 2021-07-13 16:45:03,045 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-foss-2020b.lock (parents: True, set_gid: False, sticky: False)
== 2021-07-13 16:45:03,212 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-foss-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-foss-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 16:45:03,212 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-foss-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-foss-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 16:45:03,212 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-foss-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-foss-2020b.lock
== 2021-07-13 16:45:03,213 easyblock.py:300 INFO Closing log for application name IMOD version 4.11.5