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). There is a –wrap option that will automatically wrap your program in a script but it seems a little awkward to use. Write your own.

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.

ex2.bash

#!/bin/bash
#SBATCH -o ex2-%j.out
/bin/hostname
pwd
echo Arg1 is $1
echo Arg2 is $2

sbatch -N4 ex1.bash one two

The “-N4” option requests an allocation of 4 nodes for this job. sbatch only runs the script once. What it is doing is allocating 4 nodes and running the script on the first one. Tasks can be run on the allocated nodes by using srun from within your script.

This does not reserve all 4 nodes for you exclusively: just one core per node.

(Not yet available on the BRC Cluster.)

sbatch --array 1-22 one_chromo.bash

ex3.bash

#!/bin/bash
echo Array job id = $SLURM_ARRAY_JOB_ID
echo Array task id = $SLURM_ARRAY_TASK_ID

sbatch --array 1-3 ex3.bash

This produces 3 output files by default: slurm_NNNN_1.out, slurm_NNNN_2.out, and slurm_NNNN_3.out, where NNNN is the SLURM job number.