Running MATLAB in Batch Mode on the Eagle System

Learn how to run MATLAB software in batch mode on the Eagle system.

Below is an example MATLAB script, matlabTest.m, that creates and populates a vector using a simple for-loop and writes the result to a binary file, x.dat. The shell script matlabTest.sb can be passed to the scheduler to run the job in batch (non-interactive) mode.

To try the example out, create both matlabTest.sb and matlabTest.m files in an appropriate directory,  cd to that directory, and call sbatch:

$ sbatch matlabTest.sb

Note: MATLAB comprises many independently licensed components, and in your work it might be necessary to wait for multiple components to become available. Currently, the scheduler does not handle this automatically. Because of this, we strongly recommend using compiled MATLAB code for batch processing.

Calling squeue should show that your job is queued: 

JOBID       PARTITION       NAME       USER       ST       TIME       NODES       NODELIST(REASON)
<JobID>     <partition>     matlabTe   username   PD       0:00       1           (<reason>)

Once the job has finished:

JOBID       PARTITION       NAME       USER       ST       TIME       NODES       NODELIST(REASON)
<JobID>     <partition>     matlabTe   username   CD       0:01       1           (<reason>)

The standard output is saved in a file called test_matlab.o<JobID>, standard error to test_matlab.e<JobID>, and the binary file x.dat contains the result of the MATLAB script.

Notes on matlabTest.sb File

  • Setting a low walltime increases the chances that the job will be scheduled sooner due to backfill. 
  • The --account=<account_string> flag must include a valid account string or the job will encounter a permanent hold (it will appear in the queue but will never run).  For more information, see user accounts.
  • The environment variable $SLURM_SUBMIT_DIR is set by the scheduler to the directory from which the sbatch command was executed, e.g., /scratch/$USER. In this example, it is also the directory into which MATLAB will write the output file x.dat.

matlabTest.sb

#!/bin/bash  --login
#SBATCH --time=05:00          # Maximum time requested for job (5 min.)
#SBATCH --nodes=1                # Number of nodes
#SBATCH --job-name=matlabTest              # Name of job
#SBATCH --account=<account_string>        # Program-based WCID (account string associated with job)

module purge                    
module load matlab/R2018b 
  
# execute code  
cd $SLURM_SUBMIT_DIR                        # Change directories (output will save here)
matlab -nodisplay -r matlabTest          # Run the MATLAB script  

matlabTest.m

format long
xmin = 2;
xmax = 10;
x = zeros(xmax-xmin+1,1);
for i = xmin:xmax
    display(i);
    x(i-xmin+1) = i
end
savefile = 'x.dat';
save(savefile,'x','-ASCII')
exit

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