Getting started with job submission scripts

A submission script is a shell script that consists of a list of processing tasks that need to be carried out, such as the command, runtime libraries, and input and/or output files for the tasks. If you know the resources that your tasks need to consume, you may also modify the SBATCH script with some of the common directives, e.g.:

Short Format        Long Format             Default         Description
------------        -----------             -------         -----------
-N count    --nodes=count           One             One node will be used.  Used to allocate count nodes to your job.
-A accountID        --account=accountID     One             Enter the account ID for your group. You may check your available account(s) with id command.
-t HH:MM:SS --time=HH:MM:SS         02:00:00        Always specify the maximum wallclock time for your job, max is 7 days.
-p partition        --partition=partition   m3a             Always specify your partition (i.e. m3c, m3d, m3f)
-n count    --ntasks                One             Controls the number of tasks to be created for the job
N/A         --ntasks-per-node       One             Controls the maximum number of tasks per allocated node
-c count    --cpus-per-task         One             Controls the number of CPUs allocated per task
N/A         --mem-per-cpu           4096MB          Memory size per CPU
-m size             --mem=size              4096MB          Total memory size
-J jobname  --job-name=job_name     slurm-{jobid}   Up to 15 printable, non-whitespace characters
N/A         --gres=gpu:1            N/A             Generic consumable resources e.g. GPU
N/A         --no-requeue            --requeue       By default, job will be requeued after a node failure

Running Simple Batch Jobs

Submitting a job to SLURM is performed by running the sbatch command and specifying a job script.

sbatch job.script

You can supply options (e.g. --ntasks=xx) to the sbatch command. If an option is already defined in the job.script file, it will be overridden by the commandline argument.

sbatch [options] job.script

An example Slurm job script

#!/bin/bash
#SBATCH --job-name=MyJob
#SBATCH --account=nq46
#SBATCH --time=01:00:00
#SBATCH --ntasks=1
#SBATCH --mem-per-cpu=4096
#SBATCH --cpus-per-task=1
./helloworld

This script describes the job: it is a serial job with only one process (--ntasks=1). It only needs one CPU core to run the ./helloworld process. The default memory per CPU has been set to 4GB and you should adjust the script based on how much your job needs.

Cancelling jobs

To cancel one job

scancel [JOBID]

To cancel all of your jobs

scancel -u [USERID]