openMP and PBS

General OpenMP discussion

openMP and PBS

Postby yuanhb » Wed Jan 23, 2008 5:18 am

Hi,
I am new to openMP. I want to run a openMP program on the SGI Altix 330 system. It has 8 nodes, each nodes has two processors and 8 Gb memory. I would like to know how to run my program using 8 cpus with PBS.
Thanks.
yuanhb
 
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Re: openMP and PBS

Postby lfm » Wed Jan 23, 2008 1:03 pm

You need to tell PBS that you want to use 8 threads or something like that. That should be in the PBS documentation for your system. Then you need to tell OpenMP to use 8 threads, with OMP_NUM_THREADS. This is beyond the scope of the OpenMP standard itself but your system administrators should be able to help.

I'm assuming you mean 8 system boards with hardware shared memory between the boards. You can run OpenMP programs only on shared memory systems.
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Re: openMP and PBS

Postby hb » Wed Feb 06, 2008 10:36 am

Thanks.
It is a distributed shared memory system.
hb
 

Re: openMP and PBS

Postby ciccio » Fri Feb 08, 2008 9:25 am

If you mean you are using torque or openPBS, then you should submit your job to a node and define the amount of cores you want to use.

qsub -l nodes=x:ppn=y jobname

this should do the trick.
x is the amount of nodes you want to use, y is the amount of cores you want to use on those nodes.

If you only intend to use OpenMP and no cluster openmp of intel or MPI or things of that sort, you should only do

qsub -l nodes=1:ppn=y jobname
ciccio
 
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Re: openMP and PBS

Postby gonski » Fri Feb 08, 2008 12:53 pm

#!/bin/ksh
#PBS -N case6
#PBS -l walltime=100:00:00
#PBS -l mem=700MB
#PBS -l vmem=900MB
#PBS -l ncpus=2
#PBS -l jobfs=1GB
#PBS -wd

wdir=$PBS_O_WORKDIR
echo $wdir

export OMP_NUM_THREADS=2

$wdir/nspff >>output

if [ ! -e jobfinished ]; then
sleep 10
qsub ./casem
fi

exit 0

here is my pbs_script.
gonski
 
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