How to run Parallel Batch jobs

On Shamu we have three (3) parallel Grid Engine environments but you only need to use one.

First you need to load the "sge" module on the login node so qsub will open
[abc123@login-0-0 abc123]$ module load sge

In your submit file add a line to use the parallel environment

#$ -pe openmpi #

Change "#" to the number of cores you wish to use. Also use the same # for your mpirun command. Below is a sample submit script using the mpi hello world test binary.

#$ -cwd
#$ -pe openmpi 4

module load openmpi/gcc/64/1.10.1

mpirun -np 4 $PWD/mpi-helloworld

Now submit your job using qsub:

[abc123@login-0-0 abc123]$ qsub mpi-helloworld.qsub

-- AdminUser - 18 Aug 2016
Topic revision: r1 - 18 Aug 2016, AdminUser
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