Addition of two variables in slurm script

Question

I am having slurm scirpt processing fmri data and the maximum value I can give in an array is 999, but the name of my subject ist over 1000.

So I need to to an addition in my slurm script. I tried:

a=${SLURM_ARRAY_TASK_ID} sum=$(($a + 1200))

#!/bin/sh
# 
#SBATCH --job-name psy-stephan_fmriprep_gsp
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=4
#SBATCH --mem=8GB
#SBATCH --output /projects/core-psy/logs/nako/stephan/slurm-%j.log
#SBATCH --error /projects/core-psy/logs/nako/stephan/slurm-%j.err

a=${SLURM_ARRAY_TASK_ID}
sum=$(($a + 1200))

singularity run \
--home /projects/core-psy/tmp3:/home/fmriprep \
--cleanenv \
-B /projects/core-psy/data/nako//swunderl/GSP_new/:/input \
-B /projects/core-psy/data/nako/swunderl/GSP_new/derivatives:/output \
-B //projects/core-psy/data/nako/swunderl/GSP_new_workdir/:/workdir \
-B /projects/core-psy/data/nako/swunderl/license.txt:/license \
/projects/core-psy/images/fmriprep-20.2.2.simg /input/sub-$sum /output participant \
--fs-license-file /license \
--skip-bids-validation \
--use-aroma \
--fs-no-reconall \
-w /workdir/ \
#--output-layout bids \
# sbatch --account=core-psy sbatch-multiple-job.slurm

So i can pass as a command SLURM_ARRAY_TASK_ID as 1. But the addition keeps giving me sub-0+1200 and not the actual sum of both numbers.

Answer 1

Since you do not need to perform math on a, you can perform variable expansion on the string to make a 4 digit subject label for your fmriprep command:

sum="1${SLURM_ARRAY_TASK_ID}"

This way sbatch -a 200 ./your_job_script.sh will run for sub-1200. If you have labels like 1001, you will need to add to the variable expansion since 001 becomes a SLURM_ARRAY_TASK_ID of 1.

Here's an example adapted from my own - albeit not the most succint - code for sbatch scripts

if [ ${#SLURM_ARRAY_TASK_ID} == 1 ];
then

inputNo="100${SLURM_ARRAY_TASK_ID}"
singularity run \
--home /projects/core-psy/tmp3:/home/fmriprep \
--cleanenv \
-B /projects/core-psy/data/nako//swunderl/GSP_new/:/input \
-B /projects/core-psy/data/nako/swunderl/GSP_new/derivatives:/output \
-B //projects/core-psy/data/nako/swunderl/GSP_new_workdir/:/workdir \
-B /projects/core-psy/data/nako/swunderl/license.txt:/license \
/projects/core-psy/images/fmriprep-20.2.2.simg /input/sub-${inputNo} /output participant \
--fs-license-file /license \
--skip-bids-validation \
--use-aroma \
--fs-no-reconall \
-w /workdir/

elif [ ${#SLURM_ARRAY_TASK_ID} == 2 ];
then

inputNo="10${SLURM_ARRAY_TASK_ID}"
singularity run \
--home /projects/core-psy/tmp3:/home/fmriprep \
--cleanenv \
-B /projects/core-psy/data/nako//swunderl/GSP_new/:/input \
-B /projects/core-psy/data/nako/swunderl/GSP_new/derivatives:/output \
-B //projects/core-psy/data/nako/swunderl/GSP_new_workdir/:/workdir \
-B /projects/core-psy/data/nako/swunderl/license.txt:/license \
/projects/core-psy/images/fmriprep-20.2.2.simg /input/sub-${inputNo} /output participant \
--fs-license-file /license \
--skip-bids-validation \
--use-aroma \
--fs-no-reconall \
-w /workdir/

elif [ ${#SLURM_ARRAY_TASK_ID} == 3 ];
then

inputNo="1${SLURM_ARRAY_TASK_ID}"
singularity run \
--home /projects/core-psy/tmp3:/home/fmriprep \
--cleanenv \
-B /projects/core-psy/data/nako//swunderl/GSP_new/:/input \
-B /projects/core-psy/data/nako/swunderl/GSP_new/derivatives:/output \
-B //projects/core-psy/data/nako/swunderl/GSP_new_workdir/:/workdir \
-B /projects/core-psy/data/nako/swunderl/license.txt:/license \
/projects/core-psy/images/fmriprep-20.2.2.simg /input/sub-${inputNo} /output participant \
--fs-license-file /license \
--skip-bids-validation \
--use-aroma \
--fs-no-reconall \
-w /workdir/

fi