[GE users] OpenMPI job on stay on one node

reuti reuti at staff.uni-marburg.de
Mon Sep 7 11:33:39 BST 2009


Hi,

Am 07.09.2009 um 12:04 schrieb sgexav:

> 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

a) you compiled Open MPI with SGE support?

b) what does your PE look like - you followed the Howto for SGE on  
the Open MPI site (http://www.open-mpi.org/faq/?category=running#run- 
n1ge-or-sge)?

-- Reuti

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