Hi everyone,
I'm new here. I'll try to introduce my issue.
I'm trying to run multiple jobs on my PC cluster which works with linux shell (bash).
I usually submit one single job at time. Now, I'm struggling so much to make the submission automatic.
I have the project files stored in nested folders. I have successfully created the directories and imported the files correctly in each folder, but the jobs still don't run. I report the error files I get:
*> [compute-0-2.local:15366] Warning: could not find environment variable "LSTC_LICENSE_SERVER"*
*> [compute-0-2.local:15366] Warning: could not find environment variable "LSTC_LICENSE"*
*> /var/spool/torque/mom_priv/jobs/16308.archimede.pcmgroup.dmti.unifi.it.SC: line 35: l2a_r712: command not found*
I share here my script. Any help will be very appreciated.
#!/bin/bash
NUMBERS=$(seq 3 3)
for NUM in ${NUMBERS}
do
NAME=run__0000${NUM}
echo "Submitting: ${NAME}"
PSB="#!/bin/bash\n\
#PBS -N ${NAME}\n\
#PBS -l nodes=compute-0-2:ppn=8\n\
#PBS -l walltime=50:00:00\n\
#PBS -r n\n\
cd \$PBS_O_WORKDIR\n\
. /opt/torque/etc/openmpi-setup.sh\ # set the enviroment vars needed to make OpenMPI work with torque
"
MODEL=tensile_test_results
APPROACH=basic_1/${NAME}/m_1
WORKDIR=/scratch/$USER/$APPROACH
RESULTS=$HOME/Analisi/$APPROACH
NODI=$(awk '!x[$0]++' $PBS_NODEFILE) # reads compute nodes and eliminates duplicates
rocks run host $NODI "mkdir -p $WORKDIR" # crea sul cluster le directory che ho nella $HOME
# stage in
cp $RESULTS/* $WORKDIR # copia i file in $RESULTS nella $WORKDIR
# run
cd $WORKDIR
/usr/lib64/openmpi/bin/mpirun -x LSTC_LICENSE_SERVER -x LSTC_LICENSE -np 8 mpp971s_r712 MEMORY=800000000 MEMORY2=80000000 i=$MODEL.k
l2a_r712 binout**
# stage out
cp -p $WORKDIR/runrsf* $RESULTS
cp -p $WORKDIR/d3dump* $RESULTS
cp -p $WORKDIR/nodout $RESULTS
cp -p $WORKDIR/glstat $RESULTS
cp -p $WORKDIR/sbtout $RESULTS
cp -p $WORKDIR/matsum $RESULTS
cp -p $WORKDIR/deforc $RESULTS
cp -p $WORKDIR/abstat $RESULTS
cp -p $WORKDIR/elout $RESULTS
cp -p $WORKDIR/jntforc $RESULTS
cp -p $WORKDIR/rwforc $RESULTS
cp -p $WORKDIR/rcforc $RESULTS
cp -p $WORKDIR/sbtout $RESULTS
cp -p $WORKDIR/secforc $RESULTS
cp -p $WORKDIR/spc* $RESULTS
cp -p $WORKDIR/sleout $RESULTS
cp -p $WORKDIR/d3p* $RESULTS
cp -p $WORKDIR/d3hsp $RESULTS
rocks run host $NODI "cp -p $WORKDIR/binout* $RESULTS"
rocks run host $NODI "cp -p $WORKDIR/mes* $RESULTS"
echo -e ${PSB} | qsub
done
Many thanks
.