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MATLAB#

Note

To run a MATLAB program on the HPC-UGent infrastructure you must compile it first, because the MATLAB license server is not accessible from cluster workernodes (except for the interactive debug cluster).

Compiling MATLAB programs is only possible on the interactive debug cluster, not on the HPC-UGent login nodes where resource limits w.r.t. memory and max. number of progress are too strict.

Why is the MATLAB compiler required?#

The main reason behind this alternative way of using MATLAB is licensing: only a limited number of MATLAB sessions can be active at the same time. However, once the MATLAB program is compiled using the MATLAB compiler, the resulting stand-alone executable can be run without needing to contact the license server.

Note that a license is required for the MATLAB Compiler, see https://nl.mathworks.com/help/compiler/index.html. If the mcc command is provided by the MATLAB installation you are using, the MATLAB compiler can be used as explained below.

Only a limited amount of MATLAB sessions can be active at the same time because there are only a limited amount of MATLAB research licenses available on the UGent MATLAB license server. If each job would need a license, licenses would quickly run out.

How to compile MATLAB code#

Compiling MATLAB code can only be done from the login nodes, because only login nodes can access the MATLAB license server, workernodes on clusters cannot.

To access the MATLAB compiler, the MATLAB module should be loaded first. Make sure you are using the same MATLAB version to compile and to run the compiled MATLAB program.

$ module avail MATLAB/
----------------------/apps/gent/RHEL8/zen2-ib/modules/all----------------------
   MATLAB/2021b    MATLAB/2022b-r5 (D)
$ module load MATLAB/2021b

After loading the MATLAB module, the mcc command can be used. To get help on mcc, you can run mcc -?.

To compile a standalone application, the -m flag is used (the -v flag means verbose output). To show how mcc can be used, we use the magicsquare example that comes with MATLAB.

First, we copy the magicsquare.m example that comes with MATLAB to example.m:

cp $EBROOTMATLAB/extern/examples/compiler/magicsquare.m example.m

To compile a MATLAB program, use mcc -mv:

mcc -mv example.m
Opening log file:  /user/home/gent/vsc400/vsc40000/java.log.34090
Compiler version: 8.3 (R2021b)
Dependency analysis by REQUIREMENTS.
Parsing file "/user/home/gent/vsc400/vsc40000/example.m"
    (Referenced from: "Compiler Command Line").
Deleting 0 temporary MEX authorization files.
Generating file "/user/home/gent/vsc400/vsc40000/readme.txt".
Generating file "run\_example.sh".

Libraries#

To compile a MATLAB program that needs a library, you can use the -I library_path flag. This will tell the compiler to also look for files in library_path.

It's also possible to use the -a path flag. That will result in all files under the path getting added to the final executable.

For example, the command mcc -mv example.m -I examplelib -a datafiles will compile example.m with the MATLAB files in examplelib, and will include all files in the datafiles directory in the binary it produces.

Memory issues during compilation#

If you are seeing Java memory issues during the compilation of your MATLAB program on the login nodes, consider tweaking the default maximum heap size (128M) of Java using the _JAVA_OPTIONS environment variable with:

export _JAVA_OPTIONS="-Xmx64M"

The MATLAB compiler spawns multiple Java processes. Because of the default memory limits that are in effect on the login nodes, this might lead to a crash of the compiler if it's trying to create to many Java processes. If we lower the heap size, more Java processes will be able to fit in memory.

Another possible issue is that the heap size is too small. This could result in errors like:

Error: Out of memory

A possible solution to this is by setting the maximum heap size to be bigger:

export _JAVA_OPTIONS="-Xmx512M"

Multithreading#

MATLAB can only use the cores in a single workernode (unless the Distributed Computing toolbox is used, see https://nl.mathworks.com/products/distriben.html).

The amount of workers used by MATLAB for the parallel toolbox can be controlled via the parpool function: parpool(16) will use 16 workers. It's best to specify the amount of workers, because otherwise you might not harness the full compute power available (if you have too few workers), or you might negatively impact performance (if you have too many workers). By default, MATLAB uses a fixed number of workers (12).

You should use a number of workers that is equal to the number of cores you requested when submitting your job script (the ppn value, see Generic resource requirements). You can determine the right number of workers to use via the following code snippet in your MATLAB program:

parpool.m
% specify the right number of workers (as many as there are cores available in the job) when creating the parpool
c = parcluster('local')
pool = parpool(c.NumWorkers)

See also the parpool documentation.

Java output logs#

Each time MATLAB is executed, it generates a Java log file in the users home directory. The output log directory can be changed using:

MATLAB_LOG_DIR=<OUTPUT_DIR>

where <OUTPUT_DIR> is the name of the desired output directory. To create and use a temporary directory for these logs:

# create unique temporary directory in $TMPDIR (or /tmp/$USER if
$TMPDIR is not defined)
# instruct MATLAB to use this directory for log files by setting $MATLAB_LOG_DIR
$  export MATLAB_LOG_DIR=$ (mktemp -d -p $TMPDIR:-/tmp/$USER)

You should remove the directory at the end of your job script:

rm -rf $MATLAB_LOG_DIR

Cache location#

When running, MATLAB will use a cache for performance reasons. This location and size of this cache can be changed through the MCR_CACHE_ROOT and MCR_CACHE_SIZE environment variables.

The snippet below would set the maximum cache size to 1024MB and the location to /tmp/testdirectory.

export MATLAB_CACHE_ROOT=/tmp/testdirectory 
export MATLAB_CACHE_SIZE=1024M

So when MATLAB is running, it can fill up to 1024MB of cache in /tmp/testdirectory.

MATLAB job script#

All of the tweaks needed to get MATLAB working have been implemented in an example job script. This job script is also available on the HPC.

jobscript.sh
#!/bin/bash
#PBS -l nodes=1:ppn=1
#PBS -l walltime=1:0:0
#
# Example (single-core) MATLAB job script
#

# make sure the MATLAB version matches with the one used to compile the MATLAB program!
module load MATLAB/2021b

# use temporary directory (not $HOME) for (mostly useless) MATLAB log files
# subdir in $TMPDIR (if defined, or /tmp otherwise)
export MATLAB_LOG_DIR=$(mktemp -d -p  ${TMPDIR:-/tmp})

# configure MATLAB Compiler Runtime cache location & size (1GB)
# use a temporary directory in /dev/shm (i.e. in memory) for performance reasons
export MCR_CACHE_ROOT=$(mktemp -d -p /dev/shm)
export MCR_CACHE_SIZE=1024MB

# change to directory where job script was submitted from
cd $PBS_O_WORKDIR

# run compiled example MATLAB program 'example', provide '5' as input argument to the program
# $EBROOTMATLAB points to MATLAB installation directory
./run_example.sh $EBROOTMATLAB 5