Submit a simple MPI job

INCD uses soSGE for job submission and schedulling. We currently planning a migration to a new batch system slurm

Quick syntax guide

Command	Comments
qstat	Standard queue status command (see man qstat for details )
qdel	Delete your jobs from the queues. The jobid is returned by qsub at job submission time
qsub	Submit jobs to the queues. (see man qsub for details)

Examples

Submit a simple MPI job

• On this example we run a small MPI application doing the following steps:

  • Create a submission file
  • Submit the job to the default queue
  • Load the correct software
  • Execute a simple MPI code

• Create a submission file

vi my_first_job_submit.sh

• Edit the file

#!/bin/bash

# Call the MPI environment, selecting two cores 
#$ -pe mpi 2

# Choose the queue hpc (OPTIONAL). If you leave this option empty system will assume the default queue
#$ -q hpc

# Load software modules (Open MPI 2.1.0 and GCC compiler 7.3). Please check session software for the details
source /etc/profile.d/modules.sh
module load openmpi-2.1.0 
module load gcc-7.3


# Compile application 
echo "=== Compiling ===" 
mpicc -o cpi cpi.c

# Run application. Please note that the number of cores used by MPI must be same as the ones requested.
echo "=== Running ==="
mpirun -np $NSLOTS cpi

• Submit the job

qsub my_first_job_submit.sh


Your job 5076311 ("my_first_job_submit.sh") has been submitted