Hi, Bartosz,
We've moved our Comsol submission to use a web portal we wrote:
https://redmine.rc.usf.edu/projects/2012-jobman
I had planned on sending out a list announcement at some point, but wanted
to get it further stabilized and feature-rich before doing so. Our submit
script basically looks like this:
#$ -l h_rt=%%TIME_LIMIT%%,mps=%%MEMORY%%,nodes=%%NODES%%,ppn=%%CPUS%%
#$ -j y
#$ -o %%JOB_NAME%%_log.txt
#$ -wd %%WORK_DIR%%
module purge
module add compilers/intel/2013_cluster_xe apps/comsol/4.3b
outputfile=$(echo %%MPH_FILE%% | sed 's/\.mph$/_solved\.mph/g')
if [ %%NODES%% == 1 ]; then
time comsol batch -np %%CPUS%% -inputfile %%MPH_FILE%% -outputfile
$outputfile -tmpdir $TMPDIR
else
time comsol batch -nn %%NODES%% -np %%CPUS%% \
-mpibootstrap sge \
-mpiroot /apps/intel/2013/impi/4.1.0.024 \
-blaspath /apps/intel/2013/mkl/lib/intel64/libmkl_blas95_lp64.so \
-scalapackpath
/apps/intel/2013/mkl/lib/intel64/libmkl_scalapack_lp64.so \
-inputfile %%MPH_FILE%% -outputfile $outputfile \
-tmpdir $TMPDIR -mpidebug 5
fi
You should be able to substitute out the %%MACROS%% for appropriate values.
You can probably also remove the blas/scalapack/mpiroot options and use
the stock settings. This runs with MPI and multiple threads. I use our
other project, gepetools (https://github.com/brlindblom/gepetools), in
order to do the 'nodes=,ppn=' request strings.
Obviously, we're doing some fairly custom stuff w/ GE, so it may not
directly apply. The script above should work with 4.3a as well. The big
change hsould probably be
#$ -l h_rt=%%TIME_LIMIT%%
#$ -pe comsol.4 4
will get you 4 threads per node, 4 nodes, if you have PE's set up called
'comsol'.
-Brian
On Fri, Oct 11, 2013 at 9:36 AM, Bartosz Biegun - EN
<[email protected]>wrote:
> Dear Brian,
>
> On old "GE users" mail list you mentioned that you have a script to run
> jobs straight from comsol gui. Unfortunately I cannot send job this way.
>
>
> 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.
>
> Have you a magic fix for comsol?
>
>
> --
> 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
>
>
--
Brian Lindblom (Smith)
Assistant Director
Research Computing, University of South Florida
4202 E. Fowler Ave. SVC4010
Office Phone: +1 813 974-1467
Organization URL: http://rc.usf.edu
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