I’m trying to use GNU parallel to run a set of experiments using MATLAB on our supercomputer which uses SLURM. I have a text file containing combinations of 4 parameters that are read in and passed to a MATLAB function. That text file is called gnu_parameters.txt and and has 4 columns separated by a single space.

fs_method data_name use_vars 1
fs_method1 data_name use_vars 1
fs_method3 data_name use_vars 1 

where parameters in columns 1-3 should be read in as a string, and parameter 4 is a number.

I want to run each combination of parameters in parallel to speed up the process. My SLURM script is below, but when I tell GNU-parallel where to put each parameter using the notation {1} {2} {3} {4}, I get an error that MATLAB doesn’t recognize the variable fs_method. Looking at the log tells me that the error means fs_method isn’t read as a string by MATLAB. To fix that, I tried adding single quotes in the SLURM script like so:

#!/bin/bash -l
#SBATCH --time=4-00:00:00
#SBATCH --ntasks=1
#SBATCH --mem=1200g
#SBATCH --tmp=500g
#SBATCH --cpus-per-task=115
#SBATCH --mail-type=FAIL,END
#SBATCH --mail-user=myemail
#SBATCH -p groupPartition
cd $WRK_DIR
module load matlab
module load parallel
export JOBS_PER_NODE=$(( $SLURM_CPUS_ON_NODE / $SLURM_CPUS_PER_TASK ))
echo $JOBS_PER_NODE
cat gnu_parameters.txt | parallel --jobs $JOBS_PER_NODE --joblog tasklog.log --progress --colsep ' ' 'matlab -nodisplay -r "run_holdout_parallel('{1}', '{2}', '{3}', {4});exit" ' 

But that returns the same error. How can I get these parameters passed as strings to MATLAB? Is there a better way to run these experiments in parallel than the method I’m doing?