[GE users] OpenMPI job on stay on one node

sgexav xaviercouvelard at gmail.com
Mon Sep 7 11:04:41 BST 2009


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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