Syntax error near unexpected token '(' from export of BASH_FUNC_module() #61

edickie · 2016-03-23T18:51:52Z

Hey guys,

My jobs finish with the following error message:

/var/spool/torque/mom_priv/jobs/35134401-1.gpc-sched-ib0.SC: line 102: syntax error near unexpected token `('
/var/spool/torque/mom_priv/jobs/35134401-1.gpc-sched-ib0.SC: line 102: `export BASH_FUNC_module()="() {  if [ \"$$1\" = load ]; then'

Here is what the .array script looked like...

#!/bin/bash
#PBS -l nodes=1:ppn=8
#PBS -j oe
#PBS -o /bg01/homescinet/a/arisvoin/edickie/myscripts/abide/logs
#PBS -d /bg01/homescinet/a/arisvoin/edickie/myscripts/abide
#PBS -N Caltech
#PBS 
#PBS -t 1-7
#PBS -l walltime=2:00:00
#PBS 
#PBS 
# -- start copied env
export scratch="/scratch/a/arisvoin/edickie"
export MODULESHOME="/scinet/gpc/Modules6/Modules/3.2.9"
export MKLPATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/lib/intel64"
export HCP_DATA="/scratch/a/arisvoin/edickie/ABIDE/hcp"
export SHELL="/bin/bash"
export HISTSIZE="1000"
export HCPPIPEDIR_tfMRIAnalysis="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//TaskfMRIAnalysis/scripts"
export MANPATH="/scinet/gpc/mpi/openmpi/1.4.4-intel-v12.1/share/man:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/man/en_US:/scinet/gpc/tools/editors/nano/nano-2.2.4/share/man:/scinet/gpc/x11/6/man:/usr/local/share/man:/usr/share/man:/scinet/gpc/man:/scinet/gpc/Modules6/Modules/3.2.9/man:/scinet/gpc/man/:/usr/local/share/man:/usr/share/man:/scinet/gpc/man:/scinet/gpc/toolbin/x11/man:/scinet/gpc/man/:/scinet/gpc/Modules6/Modules/3.2.9/man:/scinet/gpc/man/:/scinet/gpc/share/man:/scinet/gpc/tools/gnuparallel/20140622/share/man"
export HCPPIPEDIR_Global="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//global/scripts"
export MKL_F95_MOD_ROOT="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/include/intel64"
export FSLOUTPUTTYPE="NIFTI_GZ"
export PYTHONPATH="/scinet/gpc/mpi/mpi4py/centos6/python2.7/openmpi-intel-1.4.x/lib/python2.7/site-packages/:/home/a/arisvoin/edickie/code/epitome/:/home/a/arisvoin/edickie/code/epitome/"
export FPATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/include"
export MIC_LIBRARY_PATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb/lib/mic"
export GS_LIB="/scinet/gpc/x11/6/share/ghostscript/8.70/Resource/Init:/scinet/gpc/x11/6/share/ghostscript/8.70/Resource/Font:/scinet/gpc/x11/6/share/ghostscript/8.70/lib:/scinet/gpc/x11/6/fonts/default/ghostscript"
export PARALLEL="--workdir . --env PATH --env LD_LIBRARY_PATH --env LOADEDMODULES --env _LMFILES_ --env MODULE_VERSION --env MODULEPATH --env MODULEVERSION_STACK --env MODULESHOME --env OMP_DYNAMICS --env OMP_MAX_ACTIVE_LEVELS --env OMP_NESTED --env OMP_NUM_THREADS --env OMP_SCHEDULE --env OMP_STACKSIZE --env OMP_THREAD_LIMIT --env OMP_WAIT_POLICY"
export SCREENDIR="/scratch/a/arisvoin/edickie/.screen_run/"
export SCINET_X11_INC="/scinet/gpc/x11/6/include"
export HCPPIPEDIR_fMRIVol="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//fMRIVolume/scripts"
export VOLUME_CACHE_THRESHOLD="-1"
export MKLROOT="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/lib/intel64"
export CXX="icpc"
export FSLGECUDAQ="cuda.q"
export HOSTNAME="gpc-f103n084-ib0"
export HCPPIPEDIR_PreFS="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//PreFreeSurfer/scripts"
export MNI_DATAPATH="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/data"
export MNI_DIR="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni"
export MAIL="/var/spool/mail/edickie"
export HCPPIPEDIR_PostFS="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//PostFreeSurfer/scripts"
export OS="Linux"
export FS_OVERRIDE="0"
export SCINET_MPI_LIB="/scinet/gpc/mpi/openmpi/1.4.4-intel-v12.1/lib"
export GROUP="arisvoin"
export LESSOPEN="|/usr/bin/lesspipe.sh %s"
export FSLTCLSH="/home/a/arisvoin/edickie/quarantine//FSL/5.0.9/build/bin/fsltclsh"
export CPATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb/include:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/include"
export USER="edickie"
export FSL_BIN="/home/a/arisvoin/edickie/quarantine//FSL/5.0.9/build/bin"
export MODULE_VERSION_STACK="3.2.9"
export FMRI_ANALYSIS_DIR="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/fsfast"
export SCINET_TBB_INC="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb/include"
export HCPPIPEDIR_Templates="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//global/templates"
export SHLVL="1"
export SCINET_INTERACTIVE="1"
export EPITOME_DATA="/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain"
export MIC_LD_LIBRARY_PATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb/lib/mic:/opt/intel/mic/coi/device-linux-release/lib:/opt/intel/mic/myo/lib:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/compiler/lib/mic:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mpirt/lib/mic:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/lib/mic"
export FREESURFER_HOME="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer"
export SCINET_X11_LIB="/scinet/gpc/x11/6/lib"
export CVSROOT="/usr/local/cvsroot"
export SCINET_NANO_BASE="/scinet/gpc/tools/editors/nano/nano-2.2.4"
export ENV="/home/a/arisvoin/edickie/.bashrc"
export BASH_ENV="/home/a/arisvoin/edickie/.bashrc"
export _="/home/a/arisvoin/edickie/code/qbatch/bin/qbatch"
export MODULEPATH="/scinet/gpc/Modules6/Modules/versions:/scinet/gpc/Modules6/Modules/$$MODULE_VERSION/modulefiles:/scinet/gpc/Modules6/Modules/modulefiles:/home/t/tpaus/tpaus/privatemodules:/home/a/arisvoin/edickie/quarantine/modules:/home/a/arisvoin/edickie/quarantine//modules"
export PERL5LIB="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/lib/perl5/5.8.5:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/lib/perl5/5.8.5:/home/t/tpaus/tpaus/opt/minc/perl/lib/perl5/site_perl/5.8.8:"
export SCINET_FONTPATH="/scinet/gpc/x11/6/fonts/largerset"
export SSH_CONNECTION="172.20.82.14 38764 172.20.250.251 22"
export FSLMULTIFILEQUIT="TRUE"
export FIX_VERTEX_AREA=""
export HCPPIPEDIR_FS="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//FreeSurfer/scripts"
export PBS_DEFAULT="gpc-sched-ib0"
export HCPPIPEDIR_fMRISurf="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//fMRISurface/scripts"
export SUBJECTS_DIR="/scratch/a/arisvoin/edickie/ABIDE/FSout"
export _LMFILES_="/scinet/gpc/Modules6/Modules/modulefiles/extras/64_6.4:/scinet/gpc/Modules6/Modules/modulefiles/Xlibraries/X11-64:/scinet/gpc/Modules6/Modules/modulefiles/ImageMagick/6.6.7:/scinet/gpc/Modules6/Modules/modulefiles/nano/2.2.4:/scinet/gpc/Modules6/Modules/modulefiles/intel/14.0.1:/scinet/gpc/Modules6/Modules/modulefiles/openmpi/1.4.4-intel-v12.1:/scinet/gpc/Modules6/Modules/modulefiles/gnu-parallel/20140622:/home/a/arisvoin/edickie/quarantine/modules/edickie_quarantine:/home/a/arisvoin/edickie/quarantine/modules/FSL/5.0.9:/home/a/arisvoin/edickie/quarantine/modules/AFNI/2015.12.15:/home/a/arisvoin/edickie/quarantine/modules/FIX/1.06:/home/a/arisvoin/edickie/quarantine/modules/connectome-workbench/1.1.1:/home/a/arisvoin/edickie/quarantine/modules/hcp-pipelines/3.13.1:/home/a/arisvoin/edickie/quarantine/modules/python/2.7.11-Anaconda2-2.5.0"
export HCPPIPEDIR_dMRITract="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//DiffusionTractography/scripts"
export MKL_HOME="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl"
export MODULE_VERSION="3.2.9"
export FSLDISPLAY="/usr/bin/display"
export INTEL_LICENSE_FILE="/scinet/gpc/intel/licenses"
export HCPPIPEDIR_dMRI="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//DiffusionPreprocessing/scripts"
export SCINET_VIZ="0"
export FC="ifort"
export HOME="/home/a/arisvoin/edickie"
export HCPPIPEDIR_Config="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//global/config"
export LD_LIBRARY_PATH="/scinet/gpc/mpi/openmpi/1.4.4-intel-v12.1/lib/openmpi:/scinet/gpc/mpi/openmpi/1.4.4-intel-v12.1/lib:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb/lib/intel64:/scinet/gpc/x11/6/lib:/scinet/gpc/toolbin/x11/lib:/scinet/gpc/lib64_6.4:/scinet/gpc/lib64_6.4/mysql:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/compiler/lib/intel64:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/debugger/lib/intel64:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/lib/intel64:/opt/intel/mic/coi/host-linux-release/lib:/opt/intel/mic/myo/lib"
export LANG="C"
export LIBRARY_PATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb/lib/intel64:/scinet/gpc/lib64_6.4:/scinet/gpc/lib64_6.4/mysql:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/compiler/lib/intel64:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/debugger/lib/intel64:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/lib/intel64"
export FSF_OUTPUT_FORMAT="nii.gz"
export SCINET_OTPO_BASE="/scinet/gpc/mpi/openmpi/otpo/1.0.0/"
export NLSPATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/compiler/lib/intel64/locale/en_US"
export G_BROKEN_FILENAMES="1"
export SCINET_EXTRAS_INC="/scinet/gpc/include6"
export SCINET_JOBID=""
export SCINET_INTEL_BASE="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/"
export MSMBin="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//MSMBinaries"
export CC="icc"
export SINK_LD_LIBRARY_PATH="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/compiler/lib/mic:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/lib/mic:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mpirt/lib/mic"
export SCINET_TBB_LIB="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb/lib/intel64"
export TBBROOT="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/tbb"
export BASH_FUNC_module()="() {  if [ \"$$1\" = load ]; then
 shift;
 for each_module in $$*;
 do
 eval `/scinet/gpc/Modules6/Modules/3.2.9/bin/modulecmd bash load $$each_module`;
 done;
 unset each_module;
 else
 if [ \"$$1\" = advice ]; then
 shift;
 /scinet/gpc/bin6/moduleadvice $$*;
 else
 if [ \"$$1\" = find ]; then
 shift;
 /scinet/gpc/bin6/modulefind $$*;
 else
 eval `/scinet/gpc/Modules6/Modules/3.2.9/bin/modulecmd bash $$*`;
 fi;
 fi;
 fi
}"
export SCINETVIZDONE="1"
export F77="ifort"
export SSH_TTY="/dev/pts/19"
export QUARANTINE_ENV="scinet"
export SCINET_X11_BIN="/scinet/gpc/x11/6/bin"
export GDB_CROSS="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/debugger/gdb/intel64_mic/py26/bin/gdb-mic"
export CVS_RSH="ssh"
export SCINET_INTEL_INC="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/compiler/include"
export LOCAL_DIR="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/local"
export CARET7DIR="/home/a/arisvoin/edickie/quarantine//connectome-workbench/1.1.1/build/bin_rh_linux64"
export FSLCONVERT="/usr/bin/convert"
export FSLDIR="/home/a/arisvoin/edickie/quarantine//FSL/5.0.9/build"
export MKL="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/mkl/"
export SCINET_EXTRAS_LIB="/scinet/gpc/lib64_6.4"
export SSH_CLIENT="172.20.82.14 38764 22"
export LOGNAME="edickie"
export PATH="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/bin:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/fsfast/bin:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/tktools:/home/a/arisvoin/edickie/quarantine//FSL/5.0.9/build/bin:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/bin:/home/a/arisvoin/edickie/quarantine//python/2.7.11-Anaconda2-2.5.0/build/bin:/home/a/arisvoin/edickie/quarantine//connectome-workbench/1.1.1/build/bin_rh_linux64:/home/a/arisvoin/edickie/quarantine//FIX/1.06/build:/home/a/arisvoin/edickie/quarantine//AFNI/2015.12.10/build:/home/a/arisvoin/edickie/quarantine//FSL/5.0.9/build/bin:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/bin:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/fsfast/bin:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/tktools:/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/bin:/scinet/gpc/mpi/openmpi/otpo/1.0.0//bin:/scinet/gpc/mpi/openmpi/1.4.4-intel-v12.1/bin:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/bin/intel64:/scinet/gpc/graphics/ffmpeg-0.8.2-centos6/bin:/scinet/gpc/graphics/ImageMagick-6.6.7-7-centos6/bin:/scinet/gpc/x11/6/bin:/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/sbin:/scinet/gpc/toolbin:/scinet/gpc/toolbin/vnc:/scinet/gpc/toolbin/x11/bin:/usr/lpp/mmfs/bin:/opt/torque/bin:/opt/torque/sbin:/scinet/gpc/bin6:/scinet/gpc/x11/6/bin/old:/scinet/gpc/tools/editors/nano/nano-2.2.4/bin:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/bin/intel64_mic:/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/debugger/gdb/intel64_mic/py26/bin:/opt/intel/mic/bin:/scinet/gpc/tools/gnuparallel/20140622/bin:/home/a/arisvoin/edickie/code/epitome/bin:/home/a/arisvoin/edickie/code/epitome/bin"
export SCINET_INTEL_LIB="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/compiler/lib/intel64"
export TERM="xterm"
export FSL_DIR="/home/a/arisvoin/edickie/quarantine//FSL/5.0.9/build"
export MNI_PERL5LIB="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/lib/perl5/5.8.5"
export EPITOME_CLONE="/home/a/arisvoin/edickie/epi-clone"
export FSLWISH="/home/a/arisvoin/edickie/quarantine//FSL/5.0.9/build/bin/fslwish"
export HCPPIPEDIR_Bin="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//global/binaries"
export SCINET_MPI_BASE="/scinet/gpc/mpi/openmpi/1.4.4-intel-v12.1"
export MINC_BIN_DIR="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/bin"
export SCINET_MPI_INC="/scinet/gpc/mpi/openmpi/1.4.4-intel-v12.1/include"
export FSFAST_HOME="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/fsfast"
export PROJECT="/project/a/arisvoin/edickie"
export SCINET_USE_LMOD="false"
export MINC_LIB_DIR="/scratch/project/t/tpaus/tpaus/FREESURFER/freesurfer/mni/lib"
export edickie_QUARANTINE_PATH="/home/a/arisvoin/edickie/quarantine/"
export HCPPIPEDIR="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build/"
export HCPPIPEDIR_tfMRI="/home/a/arisvoin/edickie/quarantine//hcp-pipelines/3.13.1/build//tfMRI/scripts"
export GDBSERVER_MIC="/scinet/gpc/intel/ics/composer_xe_2013_sp1.1.106/debugger/gdb/target/mic/bin/gdbserver"
export SCRATCH="/scratch/a/arisvoin/edickie"
export OLDPWD="/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Yale"
export LOADEDMODULES="extras/64_6.4:Xlibraries/X11-64:ImageMagick/6.6.7:nano/2.2.4:intel/14.0.1:openmpi/1.4.4-intel-v12.1:gnu-parallel/20140622:edickie_quarantine:FSL/5.0.9:AFNI/2015.12.15:FIX/1.06:connectome-workbench/1.1.1:hcp-pipelines/3.13.1:python/2.7.11-Anaconda2-2.5.0"
export HISTCONTROL="ignoredups"
export SCINET_LOGIN="0"
# -- end copied env

ARRAY_IND=PBS_ARRAYID
CHUNK_SIZE=4
CORES=8
sed -n "$(( (${ARRAY_IND} - 1) * ${CHUNK_SIZE} + 1 )),+$(( ${CHUNK_SIZE} - 1 ))p" << EOF | parallel -j${CORES}
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51456/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51458/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51461/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51462/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51463/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51466/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51470/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51471/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51472/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51475/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51476/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51477/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51478/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51479/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51480/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51481/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51482/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51483/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51484/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51485/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51487/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51489/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51491/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51492/cmd_160319_104903_20160319.sh
/scratch/a/arisvoin/edickie/ABIDE/epi-fixtrain/Caltech/Caltech_51493/cmd_160319_104903_20160319.sh

The text was updated successfully, but these errors were encountered:

gdevenyi · 2016-03-23T19:14:06Z

Jobs and the module system are a recurring issue

Questions:

Did the jobs finish successfully?
What is the contents of your .bashrc and .bash_profile?

edickie · 2016-03-23T21:20:13Z

My .bashrc and bash_profiles are below...
There's not mush in it but i do load a lot of modules right before running
qbatch

##################################################
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi

commands which work for both GPC and TCS can go here

#setting $scratch
export scratch=$SCRATCH

setting alias to the camh scc

alias scc='edickie@192.197.205.74'

#adding this to PATH
#export PATH=$PATH:/home/t/tpaus/tpaus/opt/pipelines
#export PATH=/home/t/tpaus/tpaus/opt/lib/X11:$PATH

#other enviroment stuff
export
PERL5LIB=/home/t/tpaus/tpaus/opt/minc/perl/lib/perl5/site_perl/5.8.8:$PeRL5LIB
export VOLUME_CACHE_THRESHOLD=-1
export CVSROOT=/usr/local/cvsroot

#export LD_LIBRARY_PATH=/home/t/tpaus/tpaus/opt/minc_prereq/lib

HOST=$(uname)

if [ "${HOST}" == "AIX" ]; then
# do things for the TCS machine
# user environment for all shells goes here
# replace colon with your own commands
:
else
# do things for the GPC machine

module load Xlibraries extras ImageMagick nano
module unload intel openmpi
module load intel/14.0.1 openmpi
module use --append /home/t/tpaus/tpaus/privatemodules

### for fsl/fix to work
##module load R/3.0.1 hdf5/187-v18-serial-intel octave/3.8.1
#module purge
#module load extras intel/14.0.1 openmpi/intel/1.6.4 R/3.1.1

hdf5/187-v18-serial-intel octave/3.8.1

# user environment for all shells goes here
# replace colon with your own commands
:

fi

####################################################
if [ -f /etc/profile ]; then
. /etc/profile
fi

commands which work for both GPC and TCS can go here

alias passwd='echo "Please use the SciNet portal to change password:
https://portal.scinet.utoronto.ca/change_password"'

HOST=$(uname)

if [ "${HOST}" == "AIX" ]
then
# do things for the TCS machine
alias llq1='/xcat/tools/tcs-scripts/LL/jobState.sh'
alias llstat='/xcat/tools/tcs-scripts/LL/jobSummary.sh'

if [ "${TERM}" = "xterm-color" ]; then
    export TERM=xterm
fi

# user environment for login shells goes here
# replace colon with your own commands
:

else
# do things for the GPC machine
# user environment for login shells goes here
# replace colon with your own commands
:

fi

PS1="\h-$ "

if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi

FSL Setup

#FSLDIR=/home/j/jlerch/edickie/fsl5/fsl
#PATH=${FSLDIR}/bin:${PATH}
#export FSLDIR PATH
#. ${FSLDIR}/etc/fslconf/fsl.sh

On Wed, Mar 23, 2016 at 3:14 PM, Gabriel A. Devenyi <
notifications@github.com> wrote:

Jobs and the module system are a recurring issue

Questions:

Did the jobs finish successfully?

What is the contents of your .bashrc and .bash_profile?

—
You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub
#61 (comment)

gdevenyi · 2016-03-23T21:21:04Z

Did the jobs work?

gdevenyi · 2016-03-23T21:22:52Z

You are loading modules in your .bashrc/.bash_profile

From what I recall, those are the origin of the modules errors you posted. Please remove those and try again.

pipitone · 2016-03-25T20:01:40Z

We could add BASH_FUNC_module() to our list of environment vars to exclude from export... Or perhaps just exclude all vars matching [()] :-)

gdevenyi · 2016-03-25T22:38:29Z

We should test of excluding that breaks module loading in the job script preamble

pipitone · 2016-04-04T16:07:22Z

FYI, just tested this on scinet and I am also seeing this same error. I am investigating.

pipitone · 2016-04-04T17:09:45Z

Okay, if I remove the export, the jobs run fine. Question is, why aren't you seeing this error on scinet?

If I run a job script modified to not have the module() export and to contain a module load statement, then I do get an error when trying to load modules as expected:

$ env -i PBS_ARRAYID=1 .scripts/qbatch.test.array                                                                                     
.scripts/qbatch.test.array: line 94: module: command not found

Oh environment-modules... what a mess.

This is a fix for issue #61

pipitone · 2016-04-04T17:59:42Z

Okay, I've submitted a fix to ignore the BASH_FUNC_module() environment variable. @gdevenyi, what do you think of this?

gdevenyi · 2016-04-04T19:11:25Z

Does this allow modules to be loaded in the job? Or is that now broken?

pipitone · 2016-04-04T19:35:34Z

Does this allow modules to be loaded in the job? Or is that now broken?

It's broken on scinet now (unless we switch back to using bash -l). I don't yet understand it, but bash on Ubuntu (and the same version of Bash on Centos here at CAMH) doesn't export the BASH_FUNC_modules() variable so isn't broken by this change.

pipitone · 2016-04-04T19:35:39Z

I'd still like to know more about how you have things configured on Scinet such that you aren't seeing this error. What does your .bashrc look like?

gdevenyi · 2016-04-04T19:38:15Z

I actually didn't say anywhere than I don't see those errors... I haven't tested the latest version with module saving directly on scinet.

Furthermore, on SGE here at the CIC, I get that error with the latest qbatch.

pipitone · 2016-04-04T19:45:44Z

I haven't tested the latest version with module saving directly on scinet.

What do you mean by "module saving"?

Furthermore, on SGE here at the CIC, I get that error with the latest qbatch.

Latest, as in, including the fix to ignore "BASH_FUNC_module()"?

gdevenyi · 2016-04-04T19:48:09Z

** environment saving intrinsic to qbatch, rather than using the scheduler system to handle it.

Latest as in immediately prior to the "fix"

gdevenyi · 2016-04-04T20:27:51Z

Fun fact, this isn't an SGE issue, this in an importing bash environment issue.

Running python tests for an (unrelated change):

======================================================================
FAIL: test_qbatch.test_run_qbatch_local_piped_commands
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
    self.test(*self.arg)
  File "/data/chamal/projects/gabriel/src/qbatch/test/test_qbatch.py", line 106, in test_run_qbatch_local_piped_commands
    assert out == expected, out
AssertionError: cmdTrace.c(713):ERROR:104: '5857*' is an unrecognized subcommand
cmdModule.c(411):ERROR:104: '5857*' is an unrecognized subcommand
/data/chamal/projects/gabriel/src/qbatch/tmp1Ic79Y/STDIN.0: line 34: export: `BASH_FUNC_module%%=() {  eval
}': not a valid identifier
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello
hello

This is of course, without the "fix"

gdevenyi · 2016-04-04T21:04:57Z

See PR #68 for a broader fix to ignore function exports.

gdevenyi · 2016-04-05T18:51:29Z

Fixed by #68

pipitone mentioned this issue Mar 23, 2016

ARRAY_IND should be set with the value of the job array index #62

Closed

pipitone changed the title ~~Error message~~ Syntax error near unexpected token '(' from export of BASH_FUNC_module() Mar 25, 2016

pipitone added a commit that referenced this issue Apr 4, 2016

Ignore environment var BASH_FUNC_module()

a836638

This is a fix for issue #61

gdevenyi closed this as completed Apr 5, 2016

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Syntax error near unexpected token '(' from export of BASH_FUNC_module() #61

Syntax error near unexpected token '(' from export of BASH_FUNC_module() #61

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Syntax error near unexpected token '(' from export of BASH_FUNC_module() #61

Syntax error near unexpected token '(' from export of BASH_FUNC_module() #61

Comments

edickie commented Mar 23, 2016

gdevenyi commented Mar 23, 2016

edickie commented Mar 23, 2016

commands which work for both GPC and TCS can go here

setting alias to the camh scc

commands which work for both GPC and TCS can go here

FSL Setup

gdevenyi commented Mar 23, 2016

gdevenyi commented Mar 23, 2016

pipitone commented Mar 25, 2016

gdevenyi commented Mar 25, 2016

pipitone commented Apr 4, 2016

pipitone commented Apr 4, 2016

pipitone commented Apr 4, 2016

gdevenyi commented Apr 4, 2016

pipitone commented Apr 4, 2016 via email

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