I have a separate version for DMP, but it doesn't scale well in DMP for my
problems yet. Here's how I do it. I submit a script like this:
qsub -v VER=$VER,NUMCPU=$CPU,MPH=$FILE.mph $FILE.que
Where the .que file looks like:
#!/bin/bash
#$ -V
#$ -S /bin/bash
#$ -N pipe_flow
#$ -m beas
#$ -M user@domain
#$ -j y -o pipe_flow.qlog
#$ -l COMSOL=1 <------------------- This and the following two lines are
complexes I track with flex-grid
#$ -l ACDC=1
#$ -l HEATTRANSFER=1
#$ -pe smp 4
# Assume the data file is located in the directory whence the qsub
# command was issued.
#
dat="$SGE_O_WORKDIR/$MPH"
#
jobdat=${dat##*/}
jobout=${jobdat%.*}
outdir=${dat%/*}
exechost=`hostname`
#
# Change the working directory to the scratch directory.
#
TMPDIR=/PROJECT/$USER/$jobout$RANDOM
/usr/bin/rsh $SGE_O_HOST "echo Your job is running on $exechost >
$outdir/$jobout.log"
/usr/bin/rsh $SGE_O_HOST "echo in directory $TMPDIR >> $outdir/$jobout.log"
/usr/bin/rsh $SGE_O_HOST "echo Job files will be copied back here upon
completion >> $outdir/$jobout.log"
mkdir -p $TMPDIR
cd $TMPDIR
#
# Pull the bulk data file over.
#
/usr/bin/scp $SGE_O_HOST:$dat .
#
# Execute
#
/usr/local/comsol/comsol$VER/bin/comsol -autosave off -np $NUMCPU batch
-inputfile $jobout -outputfile ${jobout}_results -batchlog $jobout.log
#
#
#
# Push the files back to the submitting host and remove.
#
/usr/bin/scp -p $jobout.log $SGE_O_HOST:$outdir
/usr/bin/scp -p ${jobout}_results.mph $SGE_O_HOST:$outdir
rm $jobout.mph
rm $jobout.log
rm ${jobout}_results.mph
rm ${jobout}_results.status
rmdir $TMPDIR
#
# END
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Bartosz Biegun - EN
Sent: Friday, October 11, 2013 9:31 AM
To: [email protected]
Subject: [gridengine users] Comsol integration
Hi all,
I'm trying to integrate comsol 4.3a GUI with my ge2011.11 installation.
GUI of comsol have a pretty form to send job on cluster.
Comsol send job via command:
qsub -b y -pe comsol 1 -wd /opt/comsol/43a/bin -o
/home/bbiegun/batchmodel.mph.log -e /home/bbiegun/batchmodel.mph.log
/opt/comsol/43a/bin/comsol batch -nn ${NHOSTS} -nnhost 1 -clustersimple
-mpibootstrap mavo -mpirsh ssh -job b1 -alivetime 15 -inputfile
/home/bbiegun/batchmodel.mph -batchlog /home/bbiegun/batchmodel.mph.log
But comsol exits with error:
Error: ${NHOSTS} is not an allowed value for the switch -nn.
What is apperent from the "-b y" option.
Has anyone of you have expirience with comsol-ge integration?
--
Regards,
Bartosz Biegun
IT specialist
Computing Techniques Laboratory
Jerzy Haber Institute of Catalysis and Surface Chemistry Polish Academy of
Sciences, ul. Niezapominajek 8, 30 239 Cracow, Poland tel. +48 12 639 51 56,
+48 12 639 52 08, fax. +48 12 425 19 23
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