Sample MPI Batch Script
Here is a sample batch script that demonstrates usage of various variables and processes for a normal job on Saga. (To run in other job types, please read Job Scripts on Saga.
#!/bin/bash
###############################################
# Script example for a normal MPI job on Saga #
###############################################
## Project: replace XXXX with your project ID
#SBATCH --account=nnXXXXk
## 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
# For OpenMPI (foss and iomkl toolchains), srun is recommended:
time srun MySoftWare-exec
## For IntelMPI (intel toolchain), mpirun is recommended:
#time mpirun MySoftWare-exec
#########################################################
# That was about all this time; lets call it a day...
##-------------------------------------------------------
# Finish the script
exit 0
Download the script:
The actual startup of MPI application differs for different MPI libraries. Since this part is crucial for application performance, please read about Running MPI Applications.