Slurm Job Scripts

This page describes how to create SLURM job scripts.

SLURM job scripts look as follows. On the top you have lines starting with #SBATCH. These appear as comments to bash scripts. These lines are interpreted by sbatch in the same way as command line arguments. That is, when later submitting the script with sbatch my-job.sh you can either have the parameter to the sbatch call or in the file.

Multi-Node Allocation in Slurm

Classically, jobs on HPC systems are written in a way that they can run on multiple nodes at once, using the network to communicate. Slurm comes from this world and when allocating more than one CPU/core, it might allocate them on different nodes. Please use --nodes=1 to force Slurm to allocate them on a single node.

Creating the Script

host:example$ cat >my-job.sh <<"EOF"
#!/bin/bash
#
#SBATCH --job-name=this-is-my-job
#SBATCH --output=output.txt
#
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --time=10:00
#SBATCH --mem-per-cpu=100M

date

hostname
>&2 echo "Hello World"

sleep 1m

date
EOF

Also see the SLURM Rosetta Stone for more options.

Submit, Look at Queue & Result

host:example$ sbatch script.sh 
Submitted batch job 315
host:example$ squeue  -u holtgrem_c
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
               315     debug this-is- holtgrem  R       0:40      1 med0127 
host:example$ sleep 2m
host:example$ squeue  -u holtgrem_c
             JOBID PARTITION     NAME     USER ST       TIME  NODES NODELIST(REASON) 
host:example$ cat output.txt 
Wed Mar 25 13:30:56 CET 2020
med0127
Hello World
Wed Mar 25 13:31:56 CET 2020