Use Bash variable within SLURM sbatch script

Slurm stops processing #SBATCH directives on the first line of executable code in a script. For users whose #SBATCH directives are not dependent on the code they're trying to run above those directives, just put the #SBATCH lines at the top.

See the other answer for a workaround/solution if, as with OP, your sbatch options are dependent on the commands you've placed above them.

The batch script may contain options preceded with "#SBATCH" before any executable commands in the script. sbatch will stop processing further #SBATCH directives once the first non-comment non-whitespace line has been reached in the script.

From the sbatch docs, my emphasis.

This won't work. What happens when you run

sbatch myscript.sh

is that slurm parses the script for those special #SBATCH lines, generates a job record, stores the batch script somewhere. The batch script is executed only later when the job runs.

So you need to structure you workflow in a slightly different way, and first calculate the number of procs you need before submitting the job. Note that you can use something like

sbatch -n $numProcs myscript.sh

, you don't need to autogenerate the script (also, mpirun should be able to get the number of procs in your allocation automatically, no need to use "-np").