Sample MPI Batch Script for Fox

Here is a sample batch script that demonstrates usage of various variables and processes for a normal job on Fox. (To run in other job types, please see Fox job scripts.

#!/bin/bash

##############################################
# Script example for a normal MPI job on Fox #
##############################################

## Project: replace XXX with your project ID
#SBATCH --account=ecXXX

## Job name:
#SBATCH --job-name=MyJob
## Number of tasks (aka processes) to start: Pure mpi, one cpu per task
#SBATCH --ntasks=16
## Amount of memory per cpu (= per task, since we get 1 cpu per task):
#SBATCH --mem-per-cpu=4G
## Run for 10 minutes, syntax is d-hh:mm:ss
#SBATCH --time=0-00:10:00 

# you may not place bash commands before the last SBATCH directive
######################################################
## Setting variables and prepare runtime environment:
##----------------------------------------------------
## Recommended safety settings:
set -o errexit # Make bash exit on any error
set -o nounset # Treat unset variables as errors

# Loading Software modules
# Allways be explicit on loading modules and setting run time environment!!!
module --quiet purge            # Restore loaded modules to the default
module load MySoftWare/Versions #nb: Versions is important!

# Type "module avail MySoftware" to find available modules and versions
# It is also recommended to to list loaded modules, for easier debugging:
module list

#######################################################
## Prepare jobs, moving input files and making sure 
# output is copied back and taken care of
##-----------------------------------------------------

# Prepare input files
cp inputfiles $SCRATCH
cd $SCRATCH

# Make sure output is copied back after job finishes
savefile outputfile1 outputfile2

########################################################
# Run the application, and we typically time it:
##------------------------------------------------------

# Run the application  - please add hash in front of srun and remove 
# hash in front of mpirun if using intel-toolchain 

time srun MySoftWare-exec

The actual startup of MPI application differs for different MPI libraries. Since this part is crucial for application performance, please read about running scientific software.

^{CC Attribution: This page is maintained by the University of Oslo IT FFU-BT group. It has either been modified from, or is a derivative of, "Sample MPI Batch Script" by NRIS under CC-BY-4.0. Changes: Small changes to code snippet. Deletion of some text.}