sbatch submits a script to be executed to the slurm controller and returns immediately. The script may be queued for running later if there are currently no resources (cores) available to run it. The script is “detached” from your terminal, so even if you log out it will run, or continue to run.

The working directory for the script will be set to the current working directory when you submit the job.

By default, stdout and stderr of the script are sent to a file named slurm-%j.out where the “%j” is replaced by the SLURM job number. You can change this with the -o option, but you would likely still want to use the “%j” to prevent output from different jobs getting jumbled up.

sbatch -o gwas-test-%j.out run-gwas-test

You can also set sbatch options from within the script itself.

#!/bin/bash
#SBATCH -o gwas-test-%j.out
gwas-program filename1 filename2

The “#SBATCH” lines should appear before any commands in the script.

sbatch will only run scripts (i.e. not object/executable programs), but there is a –wrap option that will automatically wrap your program in a script.

ex1.bash

#!/bin/bash
hostname
echo Arg1 = $1
echo Arg2 = $2

sbatch ex1.bash one two

You can probably do everything you want to do with this sort of command.

sbatch -N4 ex1.bash one two

The “-N4” option says run on 4 nodes. But even in this case we see that sbatch only runs the script once. What it is doing is allocating 4 nodes and running the script on the first one.