sbatch_submit

This script makes it easier to submit sbatch jobs on Linux computing clusters. It's specifically tailored to use the Bluebear cluster at the University of Birmingham (UK), but could be easily adapted for other systems. Make sure this script is available to the shell by setting it as an executable and ensuring it is in the search path.

Setting up the environment and loading libraries

Set up the shell environment using the '--setup' argument. E.g. ./path/to/setup_script.sh.

Examples

Make sure to preserve all quotes! Anything inside triangle brackets <...> is code that should be replaced with your specific calls.

Matlab

matlab_load='module load apps/matlab/r2017a'
matlab_startup='run <PATH/TO/startup.m>' # Your Matlab startup script
matlab_call="matlab -nodisplay -r \"$matlab_startup, run tests/test.m, quit\" "
sbatch_submit.py -i "$matlab_call" -s "$matlab_load" -t 5:0 -m 10G

Replace run tests/test.m with the code you want to run.

Python

python_load='source <PATH/TO/load_python.sh>'
python_call='python tests/test.py'
sbatch_submit.py -i "$python_call" -s "$python_load" -t 5:0 -m 10G

Replace tests/test.py with the script you want to run.

Options

usage: sbatch_submit.py [-h] -i INPUT [-s SETUP] [-n NTASKS] [-o NODES]
                        [-c CPUS] [-t TIME] [-m MEM] [-q {bbdefault,bbshort}]

Submit code as a Bluebear job

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Shell cmd to run
  -s SETUP, --setup SETUP
                        Shell cmd that sets up the environment
  -n NTASKS, --ntasks NTASKS
                        Number of tasks
  -o NODES, --nodes NODES
                        Number of nodes
  -c CPUS, --cpus CPUS  Number of CPUs per task
  -t TIME, --time TIME  Maximum time to let the job run
  -m MEM, --mem MEM     Memory allocation
  -q {bbdefault,bbshort}, --qos {bbdefault,bbshort}
                        Select a QOS on BlueBear