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Submitting Rmpi Jobs With Slurm

This script is an example of launching individual Rmpi jobs on the Kennesaw State VHPC Cluster.

Slurm Shell Script

In our example, we saved the following Slurm script as run_Rmpi.slurm (making sure to change netid@kennesaw.edu and account_name in the script to the correct values for your job):

run_Rmpi.slurm
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#!/usr/bin/bash
#SBATCH --nodes=2
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=48
#SBATCH --time=2-00:00:00
#SBATCH --mail-type="BEGIN,END,FAIL"
#SBATCH --mail-user="netid@kennesaw.edu" (1)
#SBATCH --partition="batch"
#SBATCH --account="account_name" (2)

JOBID=$( echo ${SLURM_JOBID} | cut -f1 -d. )

module load R

cd ${SLURM_SUBMIT_DIR}

mpiexec --quiet R --slave --file=${FILE} > ${FILE}.${JOBID}
  1. 🙋‍♂️ Make sure to change netid@kennesaw.edu on this line to your KSU email address or you won't receive emails when the job starts and stops.
  2. 🙋‍♂️ Make sure to change account_name on this line to the VHPC billing account your job should be charged to.

Usage

Assuming you saved the Slurm script from above as run_Rmpi.slurm, and the name of your Rmpi script is mpi_script.R, you can submit your Rmpi job with the following command:

[barney@vhpc ~]$ sbatch --export=ALL,FILE=${PWD}/mpi_script.R run_Rmpi.slurm