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How to run BASH on taki

Introduction

Now we’ll see how to run a Bash script on the cluster. Before proceeding, make sure you’ve read the How To Run tutorial first.

Simple BASH example

Let’s start with the following script. We initiate a one minute sleep to allow it to run. This is such a simple example, we could have included it directly in the slurm script. In practice though, we’ll usually want to keep our functional code separate from our scripts.


Download: ..code-2018/taki/BASH/pause.bash

Here is the slurm script we will use to launch it.


Download: ..code-2018/taki/BASH/run.slurm

We first make our bash script executable, before submitting the job.

[reetam1@taki-usr1 bashtest]$ ls -l
total 5
-rw-rw---- 1 reetam1 pi_gobbert  80 Apr 28  2011 pause.bash
-rw-rw---- 1 reetam1 pi_gobbert 223 Feb  3 09:24 run.slurm
[reetam1@taki-usr1 bashtest]$ chmod 760 pause.bash
[reetam1@taki-usr1 bashtest]$ ls -l
total 5
-rwxrw---- 1 reetam1 pi_gobbert  80 Apr 28  2011 pause.bash*
-rw-rw---- 1 reetam1 pi_gobbert 223 Feb  3 09:24 run.slurm
[reetam1@taki-usr1 bashtest]$ sbatch run.slurm
Submitted batch job 3544107

After about a minute, we get the following output.

[reetam1@taki-usr1 bashtest]$ ls -l
total 6
-rwxrw---- 1 reetam1 pi_gobbert  80 Apr 28  2011 pause.bash*
-rw-rw---- 1 reetam1 pi_gobbert 223 Feb  3 09:24 run.slurm
-rw-rw---- 1 reetam1 pi_gobbert   0 Feb  3 09:31 slurm.err
-rw-rw---- 1 reetam1 pi_gobbert  90 Feb  3 09:32 slurm.out
[reetam1@taki-usr1 bashtest]$ more slurm.out
Script started at Wed Feb 3 09:31:31 EST 2021
Script ended at Wed Feb 3 09:32:34 EST 2021
[reetam1@taki-usr1 bashtest]$

If we had killed the job during its execution, the scheduler would have been able to stop it cleanly, and no processes would continue to run on the compute node.