MBG wiki: Editing SGE script to start a parallel job on the cluster

To run a parallel MPI program on the cluster :

* Create a dedicated directory somewhere in /work
* Place all files needed by your job (and possibly also the executable) in this directory.
* Create a file with a suitable name (like myjob.sh) containing the script that follows.

<source>
#!/bin/csh -f
#

#
# The name of the job (MPI_job) ...
#
#$ -N MPI_job

#
# The parallel environment (mpi_fast) and number of processors (9) ...
# 
#$ -pe mpi_fast 9

#
# For the 'mpi_fast' environment you may want to define a master queue :
#
#$ -masterq server.q

#
# The version of MPICH to use, transport protocol & a trick to delete cleanly
# running MPICH jobs ...
#
#$ -v MPIR_HOME=/usr/local/mpich-ssh
#$ -v P4_RSHCOMMAND=rsh
#$ -v MPICH_PROCESS_GROUP=no

#
# Execute from the current working directory ...
#
#$ -cwd

#
# Standard error and output should go into the current working directory ...
#
#$ -e ./
#$ -o ./

echo "Got $NSLOTS slots."

$MPIR_HOME/bin/mpirun -np $NSLOTS -machinefile $TMPDIR/machines my_MPI_program

</source>

* Edit this file and change the obvious things (like program name, arguments to program, job name, number of processors).
* Submit the job with qsub myjob.sh. 
* Check that it started without problems using qstat.

Summary:

This change is a minor edit.

Username:

Replace this text with a file.