Job Scripts

Serial Single Threaded

This example illustrates a job script designed to run a simple single-threaded processes on a single compute node:

#SBATCH --job-name=mySerialjob
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=1
#SBATCH --time=0-00:20:00
#SBATCH --mem=3102

module load someApp
someApp

Explanation

A single process run only requires 1 node, as well as 1 cpu and a single task. These are reflected in the example script. We change to the same directory from where we submitted the job ( ${SLURM_SUBMIT_DIR} to produce our output. Then we load the module "someApp" and execute it.

Multi-Threaded Single Node

In this example we are running an application capable of utilizing multiple process threads on a single node (BLAST):

#SBATCH --job-name=myBLASTjob
#SBATCH --nodes=1
#SBATCH --ntasks-per-node=1
#SBATCH --cpus-per-task=8
#SBATCH --time=0-01:00:00
#SBATCH --mem=3102

cd ${SLURM_SUBMIT_DIR}

module load BLAST
blastn --num_threads 8 <...>

Explanation

In this case we still have a single task (our blastn run) but we require 8 cpu cores to accommodate the 8 threads we've specified on the command line. The ellipses between the angle brackets represents the balance of our command line arguments.

Multiple Serial Jobs

Here we demonstrate it is possible to run multiple copies of the same application, and leverage SLURM's "srun" command to distribute tasks on multiple nodes:

#SBATCH --nodes=2
#SBATCH --ntasks-per-node=2
#SBATCH --cpus-per-task=1
#SBATCH --time=0-01:00:00
#SBATCH --mem=3102

module load someApp
srun -n 2 python myScript.py &
srun -n 2 someApp &
wait

Explanation

command


CategoryHPC