Running MATLAB in Batch Mode
Learn how to run MATLAB software in batch mode
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:
Note
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, the standard output is saved in a file called
slurm-<JobID>.out
, standard error to slurm-<JobID>.out
, 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
# 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