How to Run a List of Commands as a Slurm Array Job

If you’re working with high-performance computing (HPC) clusters, Slurm (Simple Linux Utility for Resource Management) is one of the most commonly used job scheduling systems. A Slurm array job allows you to execute multiple tasks in parallel, making it an efficient way to process large datasets or automate workflows.

What is a Slurm Array Job?

A Slurm array job enables users to submit multiple similar jobs simultaneously using a single job script. This is particularly useful when you have a list of independent tasks that need to be executed in parallel.

Steps to Run a List of Commands as a Slurm Array Job

1. Create a File with Commands

Prepare a text file that contains the list of commands you want to execute. Each line should be a separate command.

commands.txt
python script1.py
python script2.py
data_processing.sh

2. Create a Slurm Job Script

Write a Slurm batch script to execute each command using the SLURM_ARRAY_TASK_ID variable.

#!/bin/bash
#SBATCH --job-name=array_job
#SBATCH --output=output_%A_%a.txt
#SBATCH --array=1-3

COMMAND=$(sed -n "${SLURM_ARRAY_TASK_ID}p" commands.txt)
eval $COMMAND

3. Submit the Slurm Job

Use the sbatch command to submit your job script:

sbatch slurm_script.sh

Conclusion

Using Slurm array jobs is an efficient way to manage and execute multiple independent tasks in parallel. By following the steps above, you can easily process large datasets and automate workflows efficiently.