[GE users] OpenMPI job on stay on one node

l_heck lydia.heck at durham.ac.uk
Mon Sep 7 11:19:58 BST 2009


Hi Xav,

with your all.q and your parallel environment you have already
told SGE which hosts to use.

so your command should be

/path-to-your-mpirun/mpriun  -np ${NSLOTS}
-nooversubscribe your-executable


No hosts file is required as the system decides on the best use of
hosts from the pool provided by the hosts allocated to all.q and
the mpi parallel environment.

if you also use -nooversubscribe then the system will use atmost
the amount of slots allocated to each host.

Lydia

On Mon, 7 Sep 2009, sgexav wrote:

> Hi,
> I am running a parallel code with openmpi.
> the code needs 12 proc and nodes have 8.
>
> With the classicam mpirun -np 12 ........; it works prefectly
>
> But with SGE the 12 process stay on one node.
>
> qsub script.sh
> Here is may submission script,
>  #!/bin/sh
> #
> # job name
> #$ -N ROMS_TEST
> #
> # Use current working directory
> #$ -cwd
> #
> # Join stdout and stderr
> #$ -j y
>
> # define queue
> #$ -q all.q
>
> #$ -pe mpi 12
>
> # Run job through bash shell
> #$ -S /bin/bash
> #
> echo "Got $NSLOTS processors."
> echo "Machines:"
> cat $TMPDIR/machines
>
> export PATH=/opt/openmpi-1.3.3/bin/:$PATH
> export
> LD_LIBRARY_PATH=/opt/openmpi-1.3.3/lib:/opt/intel/Compiler/11.1/046/lib/intel64:$LD_LIBRARY_PATH
> #export OMPI_MCA_pls_rsh_agent=rsh
>
> mpirun -np $NSLOTS  -hostfile $TMPDIR/machines ./roms roms.in
>
> thanks
> Xav
>
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------------------------------------------
Dr E L  Heck

University of Durham
Institute for Computational Cosmology
Ogden Centre
Department of Physics
South Road

DURHAM, DH1 3LE
United Kingdom

e-mail: lydia.heck at durham.ac.uk

Tel.: + 44 191 - 334 3628
Fax.: + 44 191 - 334 3645
___________________________________________

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