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Matlab

This page will explain how to run Matlab jobs on triton, and introduce important details about Matlab on triton. (Note: We used to have the Matlab Distributed Computing Server (MDCS), but because of low use we no longer have a license. You can still run in parallel on one node, with up to 40 cores.)

Interactive usage

Interactive usage is currently available via the sinteractive tool. Do not use the cluster front-end for this, but connect to a node with sinteractive The login node is only meant for submitting jobs/compiling. To run an interactive session with a user interface run the following commands from a terminal.

ssh -X user@triton.aalto.fi
sinteractive
module load matlab
matlab &

Simple serial script

Running a simple Matlab job is easy through the slurm queue. A sample slurm script is provided below:

#!/bin/bash -l
#SBATCH --time=00:05:00
#SBATCH --mem=100M
#SBATCH -o serial_Matlab.out
module load matlab
n=3
m=2
srun matlab -nojvm -nosplash -r "serial_Matlab($n,$m) ; exit(0)"

The above script can then be saved as a file (e.g. matlab_test.sh) and the job can be submitted with sbatch matlab_test.sh. The actual calculation is done in serial_Matlab.m-file:

function C = serial_Matlab(n,m)
        try
                A=0:(n*m-1);
                A=reshape(A,[2,3]).'

                B=2:(n*m+1);
                B=reshape(B,[2,3]).'

                C=0.5*ones(n,n)
                C=A*(B.') + 2.0*C
        catch error
                disp(getReport(error))
                exit(1)
        end
end

Remember to always set exit into your slurm script so that the program quits once the function serial_Matlab has finished. Using a try-catch-statement will allow your job to finish in case of any error within the program. If you don't do this, Matlab will drop into interactive mode and do nothing while your job wastes time.

NOTE: Starting from version r2019a the launch options -r ...; exit(0) can be easily replaced with the -batch option which automatically exits matlab at the end of the command that is passed (see here for details). So the last command from the slurm script above for Matlab r2019a will look like:

srun matlab -nojvm -nosplash -batch "serial_Matlab($n,$m);"

Running Matlab Array jobs

The most common way to utilize Matlab is to write a single .M-file that can be used to run tasks as a non-interactive batch job. These jobs are then submitted as independent tasks and when the heavy part is done, the results are collected for analysis. For these kinds of jobs the Slurm array jobs is the best choice; For more information on array jobs see Array jobs in the Triton user guide</triton/tut/serial>.

Here is an example of testing multiple mutation rates for a genetic algorithm. First, the matlab code.

/triton/examples/multilang/matlab/serial.m

We run this code with the following slurm script using sbatch

/triton/examples/multilang/matlab/serial.sh

Collecting the results

Finally a wrapper script to read in the .mat files and plots the resulting values

/triton/examples/multilang/matlab/collectResults.m

Seeding the random number generator

Note that by default MATLAB always initializes the random number generator with a constant value. Thus if you launch several matlab instances e.g. to calculate distinct ensembles, then you need to seed the random number generator such that it's distinct for each instance. In order to do this, you can call the rng() function, passing the value of $SLURM_ARRAY_TASK_ID to it.

Parallel matlab in exclusive mode

#!/bin/bash -l
#SBATCH --time=00:15:00
#SBATCH --exclusive
#SBATCH -o parallel_Matlab3.out

export OMP_NUM_THREADS=$(nproc)

module load matlab/r2017b
matlab_multithread -nosplash -r "parallel_Matlab3($OMP_NUM_THREADS) ; exit(0)"

parallel_Matlab3.m:

function parallel_Matlab3(n)
        % Try-catch expression that quits the Matlab session if your code crashes
        try
                % Initialize the parallel pool
                c=parcluster();
                % Ensure that workers don't overlap with other jobs on the cluster
                t=tempname()
                mkdir(t)
                c.JobStorageLocation=t;
                parpool(c,n);
                % The actual program calls from matlab's example.
                % The path for r2017b
                addpath(strcat(matlabroot, '/examples/distcomp/main'));
                % The path for r2016b
                % addpath(strcat(matlabroot, '/examples/distcomp'));
                pctdemo_aux_parforbench(10000,100,n);
        catch error
                getReport(error)
                disp('Error occured');
                exit(0)
        end
end

FAQ / troubleshooting

If things randomly don't work, you can try removing or moving either the ~/.matlab directory or ~/.matlab/Rxxxxy directory to see if it's caused by configuration.

Random error messages about things not loading and/or something (Matlab Live Editor maybe) doesn't work: ls *.m, do you have any unexpected files like pathdef.m in there? Remove them.

Also, check your home quota. Often .matlab gets large and fills up your home directory. Check the answer at the very top of the page, under "Matlab Configuration".