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A basic job

Introduction

Here you will learn about how to run jobs on LUNARC nodes. It is assumed that you know the basics of SLURM, which you can learn in our beginner course on HPC use, or from (http://slurm.schedmd.com/).

To run a job you need to have the following prepared:

  • Research data
  • An application to use
  • Your login information
  • A text editor can be helpful (nano is a good choice for new users)

Make sure you are logged in before continuing.

The job script and sbatch

You register your program with SLURM for execution using the `sbatch command. This is easiest accomplished using a job description file. The job description file is also known as a job script.

A very simple job script looks as follows:

#!/bin/bash
#SBATCH -t 00:05:00

echo "hello"

Write this into a file. In the following, we assume the file is named echo_script.sh, but in principle, any name will do. You can now send the script for execution using the sbatch command. This command will execute the “program” on the backend compute servers in the cluster.

sbatch echo_script.sh

This should deliver a screen output similar to

[fred@aurora Serial]$ sbatch echo_script.sh
Submitted batch job 7185

Where 7185 is the job number assigned by SLURM. Once your job has been executed, you will find a file, slurm-7185.out, in your directory, containing the program output and error messages.

The three parts of a job script

The example echo_script.sh shows the three parts every job script requires

  1. Shell specification
  2. Resource statement
  3. Body containing a UNIX script

In our example, each part consists of a single line. The first line of our example contains the shell specification, in most cases the sh-shell as used here is just fine. The second line starting with #SBATCH specifies the resources needed. In our case, it asks for 5 minutes of computer time. If the job hasn’t finished after that time, SLURM will terminate it. Job scripts typically contain more than one of these statements, specifying e.g. more than one processor or more memory.

The most commonly used resource statements at LUNARC will be explained below. The resource statements are followed by a list of programs and UNIX commands to be executed on the system. A job script is a normal UNIX script; everything you can do in a UNIX script can also be done here. In our example, the script consists of the UNIX echo command.

Author: (LUNARC)

Last Updated: 2022-10-05