Annotated SLURM Script

HiPerGator 2.0 documentation

This is a walk-through for a basic SLURM scheduler job script. Annotations are marked with bullet points. You can click on the link below to download the raw job script file without the annotation. Values in brackets are placeholders. You need to replace them with your own values. E.g. Change '<job name>' to something like 'blast_proj22'.

Download raw source of the [{{#fileLink: scratch_local.PBS}} scratch_local.PBS] file.

• Set the shell to use

{{#fileAnchor: slurm_job.sh}}

#!/bin/bash

Common arguments

• Name the job to make it easier to see in the job queue

{{#fileAnchor: slurm_job.sh}}

#SBATCH --job-name=<JOBNAME>

Email

Your email address to use for all batch system communications

{{#fileAnchor: slurm_job.sh}}

##SBATCH --mail-user=<EMAIL>

What emails to send

NONE - no emails

ALL - all emails

END,FAIL - only email if the job fails and email the summary at the end of the job

{{#fileAnchor: slurm_job.sh}}

#SBATCH --mail-type=FAIL,END

Standard Output and Error log files

Use file patterns

%j - job id

%A-$a - Array job id (A) and task id (a)

{{#fileAnchor: slurm_job.sh}}

#SBATCH --output <my_job-%j.out>
#SBATCH --error <my_job-%j.err>

Number of tasks (usually translate to processor cores) to use

{{#fileAnchor: slurm_job.sh}}

#SBATCH --ntasks=1

Memory per cpu core in MB

For example, 2gb ~ 2000mb

{{#fileAnchor: slurm_job.sh}}

#SBATCH --mem-per-cpu=2000

Job run time in [DAYS]

HOURS:MINUTES:SECONDS

[DAYS] are optional, use when it is convenient

{{#fileAnchor: slurm_job.sh}}

#SBATCH --time=72:00:00

Optional

A group to use if you belong to multiple groups. Otherwise, do not use.

{{#fileAnchor: slurm_job.sh}}

#SBATCH --account=<GROUP>

A job array, which will create many jobs (called array tasks) different only in the '$SLURM_ARRAY_TASK_ID' variable, similar to Torque_Job_Arrays on HiPerGator 1

{{#fileAnchor: slurm_job.sh}}

#SBATCH --array=<BEGIN-END>

Example of five tasks

#SBATCH --array=1-5

END OF PBS SETTINGS

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Recommended convenient shell code to put into your job script

• If we're inside a job change to this directory instead of /home/$USER.

{{#fileAnchor: slurm_job.sh}}

[[ -d $SLURM_SUBMIT_DIR ]] && cd $SLURM_SUBMIT_DIR

• Add host, time, and directory name for later troubleshooting

{{#fileAnchor: slurm_job.sh}}

date;hostname;pwd

Below is the shell script part - the commands you will run to analyze your data. The following is an example.

• Load the software you need

{{#fileAnchor: slurm_job.sh}}

module load ncbi_blast

• Run the program

{{#fileAnchor: slurm_job.sh}}

blastn -db nt -query input.fa -outfmt 6 -out results.xml

date