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Created September 19, 2018 09:59
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EasyBuild test report for easyconfigs PR #6712
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easybuild_test_report_easyconfigs_pr6712_20185919-UTC-09-59-18.md

Test report for easybuilders/easybuild-easyconfigs#6712

Test result

Build succeeded for 5 out of 5 (5 easyconfigs in this PR)

Overview of tested easyconfigs (in order)

  • SUCCESS Java-1.8.eb
  • SUCCESS R-3.5.1-foss-2018b.eb
  • SUCCESS Bazel-0.16.0-GCCcore-7.3.0.eb
  • SUCCESS GATK-4.0.8.1-foss-2018b-Python-2.7.15.eb
  • SUCCESS GATK-4.0.8.1-foss-2018b-Python-3.6.6.eb

Time info

  • start: Wed, 19 Sep 2018 09:58:33 +0000 (UTC)
  • end: Wed, 19 Sep 2018 09:59:18 +0000 (UTC)

EasyBuild info

  • easybuild-framework version: 3.7.0.dev0
  • easybuild-easyblocks version: 3.7.0.dev0
  • command line:
eb --from-pr 6712 -dr --module-only --upload-test-report
  • full configuration (includes defaults):
--allow-loaded-modules='EasyBuild'
--backup-modules
--buildpath='/tmp/vsc40023/easybuild_build'
--check-ebroot-env-vars='warn'
--cleanup-builddir
--cleanup-easyconfigs
--cleanup-tmpdir
--color='auto'
--container-type='singularity'
--containerpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/containers'
--debug
--default-opt-level='defaultopt'
--detect-loaded-modules='error'
--disable-add-dummy-to-minimal-toolchains
--disable-allow-modules-tool-mismatch
--disable-allow-use-as-root-and-accept-consequences
--disable-avail-cfgfile-constants
--disable-avail-easyconfig-constants
--disable-avail-easyconfig-licenses
--disable-avail-easyconfig-params
--disable-avail-easyconfig-templates
--disable-avail-hooks
--disable-avail-module-naming-schemes
--disable-avail-modules-tools
--disable-avail-repositories
--disable-check-conflicts
--disable-check-contrib
--disable-check-github
--disable-check-style
--disable-consider-archived-easyconfigs
--disable-container-build-image
--disable-containerize
--disable-debug-lmod
--disable-devel
--disable-dry-run
--disable-dry-run-short
--disable-dump-autopep8
--disable-dump-env-script
--disable-enforce-checksums
--disable-experimental
--disable-extended-dry-run
--disable-fetch
--disable-fixed-installdir-naming-scheme
--disable-force
--disable-group-writable-installdir
--disable-hidden
--disable-ignore-checksums
--disable-ignore-osdeps
--disable-info
--disable-install-github-token
--disable-install-latest-eb-release
--disable-job
--disable-last-log
--disable-list-toolchains
--disable-logtostdout
--disable-minimal-toolchains
--disable-module-depends-on
--disable-new-pr
--disable-package
--disable-pretend
--disable-preview-pr
--disable-quiet
--disable-read-only-installdir
--disable-rebuild
--disable-recursive-module-unload
--disable-regtest
--disable-rpath
--disable-sequential
--disable-set-default-module
--disable-set-gid-bit
--disable-show-config
--disable-show-default-configfiles
--disable-show-default-moduleclasses
--disable-show-full-config
--disable-skip
--disable-skip-test-cases
--disable-sticky-bit
--disable-terse
--disable-update-modules-tool-cache
--disable-use-existing-modules
--disable-verify-easyconfig-filenames
--extended-dry-run-ignore-errors
--from-pr='6712'
--github-user='boegel'
--ignore-dirs='.git,.svn'
--include-easyblocks=''
--include-module-naming-schemes=''
--include-toolchains=''
--installpath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib'
--job-backend='PbsPython'
--job-max-jobs='0'
--job-max-walltime='24'
--job-output-dir='/kyukon/data/gent/gvo000/gvo00002/vsc40023'
--job-polling-interval='30.0'
--lib64-fallback-sanity-check
--logfile-format='easybuild,easybuild-%(name)s-%(version)s-%(date)s.%(time)s.log'
--max-fail-ratio-adjust-permissions='0.5'
--module-naming-scheme='EasyBuildMNS'
--module-only
--module-syntax='Lua'
--moduleclasses='base,bio,cae,chem,compiler,data,debugger,devel,geo,ide,lang,lib,math,mpi,numlib,perf,phys,system,toolchain,tools,vis'
--modules-tool='Lmod'
--mpi-tests
--output-format='txt'
--package-naming-scheme='EasyBuildPNS'
--package-release='1'
--package-tool-options=''
--package-tool='fpm'
--package-type='rpm'
--packagepath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/packages'
--pr-target-account='easybuilders'
--pr-target-branch='develop'
--pr-target-repo='easybuild-easyconfigs'
--prefix='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib'
--repository='FileRepository'
--repositorypath='/user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/ebfiles_repo'
--robot-paths=''
--robot='/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages/easybuild_easyconfigs-3.7.0.dev0-py2.7.egg/easybuild/easyconfigs'
--sourcepath='/user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/'
--strict='warn'
--subdir-modules='modules'
--subdir-software='software'
--suffix-modules-path='all'
--trace
--upload-test-report
--use-ccache='False'
--use-f90cache='False'

System info

  • core count: 9
  • cpu model: Intel(R) Xeon(R) Gold 6140 CPU @ 2.30GHz
  • cpu speed: 2300.0
  • cpu vendor: Intel
  • gcc version: Using built-in specs.; COLLECT_GCC=gcc; COLLECT_LTO_WRAPPER=/usr/libexec/gcc/x86_64-redhat-linux/4.8.5/lto-wrapper; Target: x86_64-redhat-linux; Configured with: ../configure --prefix=/usr --mandir=/usr/share/man --infodir=/usr/share/info --with-bugurl=http://bugzilla.redhat.com/bugzilla --enable-bootstrap --enable-shared --enable-threads=posix --enable-checking=release --with-system-zlib --enable-__cxa_atexit --disable-libunwind-exceptions --enable-gnu-unique-object --enable-linker-build-id --with-linker-hash-style=gnu --enable-languages=c,c++,objc,obj-c++,java,fortran,ada,go,lto --enable-plugin --enable-initfini-array --disable-libgcj --with-isl=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/isl-install --with-cloog=/builddir/build/BUILD/gcc-4.8.5-20150702/obj-x86_64-redhat-linux/cloog-install --enable-gnu-indirect-function --with-tune=generic --with-arch_32=x86-64 --build=x86_64-redhat-linux; Thread model: posix; gcc version 4.8.5 20150623 (Red Hat 4.8.5-28) (GCC) ;
  • glibc version: 2.17
  • hostname: node3140.skitty.os
  • os name: centos linux
  • os type: Linux
  • os version: 7.5.1804
  • platform name: x86_64-unknown-linux
  • python version: 2.7.5 (default, Jul 13 2018, 13:06:57) ; [GCC 4.8.5 20150623 (Red Hat 4.8.5-28)]
  • system gcc path: /usr/bin/gcc
  • system python path: /usr/bin/python
  • total memory: 191943

List of loaded modules

  • cluster/skitty

Environment

BASH_FUNC_ml() = () {  eval $($LMOD_DIR/ml_cmd "$@")
}
BASH_FUNC_module() = () {  eval $($LMOD_CMD bash "$@") && eval $(${LMOD_SETTARG_CMD:-:} -s sh)
}
CARGO_HOME = /user/scratch/gent/vsc400/vsc40023/.cargo
CCACHE_COMPILERCHECK = echo %compiler%; %compiler% -v; %compiler% -dumpmachine
CCACHE_COMPRESS = true
CCACHE_MAXFILES = 1000000
CCACHE_MAXSIZE = 0
CCACHE_NLEVELS = 4
EASYBUILD_BUILDPATH = /tmp/vsc40023/easybuild_build
EASYBUILD_DEBUG = 1
EASYBUILD_DETECT_LOADED_MODULES = error
EASYBUILD_GITHUB_USER = boegel
EASYBUILD_JOB_BACKEND = PbsPython
EASYBUILD_PREFIX = /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib
EASYBUILD_SOURCEPATH = /user/data/gent/vsc400/vsc40023/EasyBuild/sources:/apps/gent/source:/nfsmuk/apps/gent/source/
EASYBUILD_TRACE = 1
F90CACHE_NLEVELS = 4
FANCYLOGGER_IGNORE_MPI4PY = 1
HISTCONTROL = ignoredups
HISTSIZE = 1000
HOME = /user/home/gent/vsc400/vsc40023
HOSTNAME = node3140.skitty.os
HPCUGENT_FAMILY_CLUSTER = cluster
HPCUGENT_FAMILY_CLUSTER_VERSION = skitty
LANG = en_US.utf8
LC_ALL = en_US.utf8
LESSOPEN = ||/usr/bin/lesspipe.sh %s
LMOD_ANCIENT_TIME = 604800
LMOD_CMD = /usr/share/lmod/lmod/libexec/lmod
LMOD_DIR = /usr/share/lmod/lmod/libexec
LMOD_FAMILY_CLUSTER = cluster
LMOD_FAMILY_CLUSTER_VERSION = skitty
LMOD_PKG = /usr/share/lmod/lmod
LMOD_SETTARG_FULL_SUPPORT = no
LMOD_SHORT_TIME = 86400
LMOD_SYSTEM_NAME = CO7-skylake
LMOD_VERSION = 7.7.26
LOADEDMODULES = cluster/skitty
LOGNAME = vsc40023
LS_COLORS = 
MAIL = /var/spool/mail/vsc40023
MANPATH = :
MODULEPATH = /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:/etc/modulefiles/vsc
MODULESHOME = /usr/share/lmod/lmod
PATH = /user/data/gent/gvo000/gvo00002/JUBE/bin:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/bin:/user/home/gent/vsc400/vsc40023/bin:/usr/libexec/slurm/wrapper:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin
PBS_DEFAULT = SLURM_NOT_TORQUE_PBS
PBS_JOBDIR = /kyukon/home/gent/vsc400/vsc40023
PBS_JOBID = 55200
PBS_JOBNAME = INTERACTIVE
PBS_NODEFILE = /tmp/IH9pyyvzH_
PBS_NODENUM = 0
PBS_NP = 9
PBS_NUM_NODES = 1
PBS_NUM_PPN = 9
PBS_O_HOME = /user/home/gent/vsc400/vsc40023
PBS_O_WORKDIR = /kyukon/home/gent/vsc400/vsc40023
PBS_TASKNUM = 1
PWD = /user/home/gent/vsc400/vsc40023/data
PYTHONOPTIMIZE = 1
PYTHONPATH = /user/data/gent/gvo000/gvo00002/JUBE:/user/home/gent/vsc400/vsc40023/.local/python-dateutil/lib/python2.7/site-packages/:/user/home/gent/vsc400/vsc40023/.local/keyring/lib/python2.7/site-packages/keyring-3.8:/user/data/gent/vsc400/vsc40023/easybuild_easy_installed/lib/python2.7/site-packages:
PYTHON_EGG_CACHE = /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/python-eggs
QT_GRAPHICSSYSTEM_CHECKED = 1
SHLVL = 2
SLURMD_NODENAME = node3140.skitty.os
SLURM_CHECKPOINT_IMAGE_DIR = /var/spool/slurm/checkpoint
SLURM_CLUSTERS = skitty
SLURM_CLUSTER_NAME = skitty
SLURM_CONF = /etc/slurm/slurm.conf_skitty
SLURM_CPUS_ON_NODE = 9
SLURM_CPU_BIND = verbose,mask_cpu:0x111010199
SLURM_CPU_BIND_LIST = 0x111010199
SLURM_CPU_BIND_TYPE = mask_cpu:
SLURM_CPU_BIND_VERBOSE = verbose
SLURM_DISTRIBUTION = block
SLURM_GTIDS = 0,1,2,3,4,5,6,7,8
SLURM_JOBID = 55200
SLURM_JOB_CPUS_PER_NODE = 9
SLURM_JOB_GID = 2540023
SLURM_JOB_ID = 55200
SLURM_JOB_NAME = INTERACTIVE
SLURM_JOB_NODELIST = node3140.skitty.os
SLURM_JOB_NUM_NODES = 1
SLURM_JOB_PARTITION = skitty
SLURM_JOB_UID = 2540023
SLURM_JOB_USER = vsc40023
SLURM_LAUNCH_NODE_IPADDR = 10.141.13.3
SLURM_LOCALID = 0
SLURM_MEM_PER_CPU = 5120
SLURM_NNODES = 1
SLURM_NODEID = 0
SLURM_NODELIST = node3140.skitty.os
SLURM_NPROCS = 9
SLURM_NTASKS = 9
SLURM_NTASKS_PER_NODE = 9
SLURM_PRIO_PROCESS = 0
SLURM_PROCID = 0
SLURM_PTY_PORT = 30820
SLURM_PTY_WIN_COL = 204
SLURM_PTY_WIN_ROW = 48
SLURM_SRUN_COMM_HOST = 10.141.13.3
SLURM_SRUN_COMM_PORT = 30821
SLURM_STEPID = 0
SLURM_STEP_ID = 0
SLURM_STEP_LAUNCHER_PORT = 30821
SLURM_STEP_NODELIST = node3140.skitty.os
SLURM_STEP_NUM_NODES = 1
SLURM_STEP_NUM_TASKS = 9
SLURM_STEP_TASKS_PER_NODE = 9
SLURM_SUBMIT_DIR = /kyukon/home/gent/vsc400/vsc40023
SLURM_SUBMIT_HOST = gligar03.gligar.os
SLURM_TASKS_PER_NODE = 9
SLURM_TASK_PID = 220112
SLURM_TOPOLOGY_ADDR = node3140.skitty.os
SLURM_TOPOLOGY_ADDR_PATTERN = node
SLURM_UMASK = 0002
SLURM_WORKING_CLUSTER = skitty:master27.skitty.os:6817:8192
TERM = screen
TMPDIR = /tmp
USER = vsc40023
VSCPROFILELOADED = 1
VSC_ARCH_LOCAL = skylake
VSC_ARCH_SUFFIX = -ib
VSC_DATA = /user/data/gent/vsc400/vsc40023
VSC_DATA_VO = /user/data/gent/gvo000/gvo00002
VSC_DATA_VO_USER = /user/data/gent/gvo000/gvo00002/vsc40023
VSC_DEFAULT_CLUSTER_MODULE = skitty
VSC_HOME = /user/home/gent/vsc400/vsc40023
VSC_INSTITUTE = gent
VSC_INSTITUTE_CLUSTER = skitty
VSC_INSTITUTE_LOCAL = gent
VSC_OS_LOCAL = CO7
VSC_SCRATCH = /user/scratch/gent/vsc400/vsc40023
VSC_SCRATCH_CLUSTER = /local
VSC_SCRATCH_KYUKON = /user/scratchkyukon/gent/vsc400/vsc40023
VSC_SCRATCH_KYUKON_VO = /user/scratchkyukon/gent/gvo000/gvo00002
VSC_SCRATCH_KYUKON_VO_USER = /user/scratchkyukon/gent/gvo000/gvo00002/vsc40023
VSC_SCRATCH_NODE = /local
VSC_SCRATCH_PHANPY = /user/scratchphanpy/gent/vsc400/vsc40023
VSC_SCRATCH_PHANPY_VO = /user/scratchphanpy/gent/gvo000/gvo00002
VSC_SCRATCH_PHANPY_VO_USER = /user/scratchphanpy/gent/gvo000/gvo00002/vsc40023
VSC_SCRATCH_SITE = /user/scratch/gent/vsc400/vsc40023
VSC_SCRATCH_VO = /user/scratch/gent/gvo000/gvo00002
VSC_SCRATCH_VO_USER = /user/scratch/gent/gvo000/gvo00002/vsc40023
VSC_VO = gvo00002
_ = /usr/bin/python2
_LMFILES_ = /etc/modulefiles/vsc/cluster/skitty.lua
_ModuleTable001_ = 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
_ModuleTable002_ = YW5weXNjcmF0Y2gvQ083L3NreWxha2UtaWIvbW9kdWxlcy9hbGwiLCIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfSxbInN5c3RlbUJhc2VNUEFUSCJdPSIvZXRjL21vZHVsZWZpbGVzL3ZzYyIsfQ==
_ModuleTable_Sz_ = 2
__LMOD_REF_COUNT_LOADEDMODULES = cluster/skitty:1
__LMOD_REF_COUNT_MODULEPATH = /user/home/gent/vsc400/vsc40023/eb_phanpyscratch/CO7/skylake-ib/modules/all:1;/etc/modulefiles/vsc:1
__LMOD_REF_COUNT_PATH = /usr/libexec/slurm/wrapper:1;/usr/local/bin:1;/usr/bin:1;/usr/local/sbin:1;/usr/sbin:1;/opt/ibutils/bin:1
__LMOD_REF_COUNT__LMFILES_ = /etc/modulefiles/vsc/cluster/skitty.lua:1
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