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