Skip to main content


Versions and Availability


Module Names for matlab on qb2
Machine Version Module Name
qb2 r2013a matlab/r2013a
qb2 r2015b matlab/r2015b
qb2 r2017a matlab/r2017a
qb2 r2020a matlab/r2020a

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.



A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.


System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

  1. ~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
  2. ~/.bashrc (interactive login only)
  3. ~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.


The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.


Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

▶ Did not find the version you want to use??

If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.


Types of request

Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:

  • The user's home directory
    • Software packages installed here will be accessible only to the user.
    • It is suitable for software packages that will be used by a single user.
    • Python, Perl and R modules should be installed here.
  • /project
    • Software packages installed in /project can be accessed by a group of users.
    • It is suitable for software packages that
      • Need to be shared by users from the same research group, or
      • are bigger than the quota on the home file syste.
    • This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.
  • /usr/local/packages
    • Software packages installed under /usr/local/packages can be accessed by all users.
    • It is suitable for software packages that will be used by users from multiple research groups.
    • This type of request must be sent by the PI of a research group.


How to request

Please send an email to with the following information:

  • Your user name
  • The name of cluster where you want to use the requested software
  • The name, version and download link of the software
  • Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
  • Why the software is needed
  • Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.

Please note that, once the software is installed, testing and validation are users' responsibility.

About the Software

MATLAB is a high-level language and interactive environment developed by Mathworks. It is widely u sed in science and engineering across industry and academia. Users need to provide their own license file, which should have a .lic extension and be located under /home/$U SER/.matlab/R2020a_licenses.



Matlab is installed on most of the HPC clusters. It is, however, license software, which means that it is only availabe to users or user groups who have access to a license, purchased either individually or by the users' institution.

If you do have lots of similar jobs, we recommend you to compile your Mablab scripts using the Matlab compiler, and the jobs using the compiled executable will not take license seats, If you need help in this regard, please contact us at

If you are not enrolled at LSU, you are not allowed to use Matlab on our LSU HPC clusters according to the current terms of our Matlab license agreement and the program offering guide.

Note: For LSU and ULL users on QB2, a license file has been created, so the steps described below are not necessary for them.

For LONI users who want to use Matlab on QB2, you need to provide your own license file. The license file should have a .lic extension and be located under the "/home/$USER/.matlab/R<matlab version>_licenses" directory. For example, in order to user Matlab R2013a, you need to create the directory ".matlab/R2013a_licenses" under your home directory and put the license file there.

Users should note that most Matlab license servers are restrictive about the IP addresses from which licenses can be checked out. In another word, a user will not be able to run Matlab on QB2 until the IP addresses of QB2 nodes are added to the allowed list of the license server specified in the license file. In most cases, users need to contact the admistrator of their license server and request the IP addresses of QB2 nodes to be added. If you need help in this regard, please contact us at

Running Matalb

Matlab can be run interactively, but requires use of X-windows for any graphical capability.

Running Matlab Parallel Server

Note: The content of this section applies to LSU HPC users only.

Matlab Parallel Server (MPS) allows users to run their Matlab codes on multiple nodes, potentially accelerating the execution significantly. To use MPS on Super Mike 2 or SuperMIC, follow the steps below:

Step 1: Make sure the module "matlab/r2019b" is loaded. MPS will not work with other versions of Matlab.

Step 2: Import the cluster profile in your Matlab code:

    profile_master = parallel.importProfile('/usr/local/packages/license/matlab/r2019b/lsuhpcparserver/SuperMike2.mlsettings');


For SuperMIC, change the "SuperMike2.mlsettings" to "SuperMIC.mlsettings";

Step 3: Create a pool of workers before any other parallel functions:

    parpool(<name of cluster>,<number of workers>)

, where the <name of cluster> should be 'SuperMike2' on Super Mike 2 and 'SuperMIC' on SuperMIC, and the <number of workeres> should be equal to the number of cores available to your job. For instance, for 4 nodes on SuperMIC, the line should look like:


Step 4: Now all implicitly parallel functions such as parfor can launch workers on multiple hosts.

MPS Example

The example below is based on the one described on this web page.

It runs integer factorization on 1 to 64 cores on 4 Super Mike 2 nodes, records the timing information and plots the speedup (as compared to running on 1 core).

Content of the code:

$ cat composite.m

profile_master = parallel.importProfile('/usr/local/packages/license/matlab/r2019b/lsuhpcparserver/SuperMike2.mlsettings');

primeNumbers = primes(uint64(2^21));
compositeNumbers = primeNumbers.*primeNumbers(randperm(numel(primeNumbers)));
factors = zeros(numel(primeNumbers),2);


numWorkers = [1 2 4 6 16 32 64];
tCluster = zeros(size(numWorkers));
for w = 1:numel(numWorkers)
    parfor (idx = 1:numel(compositeNumbers), numWorkers(w))
        factors(idx,:) = factor(compositeNumbers(idx));
    tCluster(w) = toc;
f = figure;
speedup = tCluster(1)./tCluster;
plot(numWorkers, speedup);
title('Speedup with the number of workers');
xlabel('Number of workers');
saveas(gcf, 'composite_speedup.png');

Content of the job script:

$ cat mps.pbs


#PBS -l nodes=4:ppn=16
#PBS -l walltime=4:00:00
#PBS -j oe
#PBS -N matlab.parallel.server
#PBS -A hpc_my_allocation
#PBS -q checkpt

matlab -nodesktop -r "try; run composite; catch; end; quit"

A user can submit this job script as any other jobs:

$ qsub mps.pbs

▶ X11 FAQ?

From *nix

Since ssh and X11 are already on most client machines running some sort of unix (Linux, FreeBSD, etc), one would simply use the following command:

% ssh -X -Y

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, email us.

From Mac OS X

An X11 service is not installed by default, but one is available for installation on the OS distribution disks as an add-on. An alternative would be to install the XQuartz version. Make sure the X11 application is running and connect to the cluster using:

% ssh -X -Y

From Windows

Microsoft Windows does not provide an X11 server, but there are both open source and commercial versions available. You also need to install an SSH client. Recommended applications are:

  • MobaXterm - a Windows ssh client with X11 server integrated (recommended)
  • Xming - a Windows X11 server
  • PuTTY - a Windows ssh client

When a PuTTY session is created, make sure the "X11 Forwarding Enabled" option is set, and that the X11 server is running before starting the session.


Once Xming and puTTY have been set up and in stalled, the following will provide a simple test for success:

  1. start Xming
  2. start puTTY
  3. connect to the remote host (make sure puTTY knows about Xming for this host)

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, refer to "Trouble with Xming?" or email us.

Note About Cygwin

Cygwin is still a useful environment, but is too complicated and contains too many unnecessary parts when all one wants is to interface with remote X11 sessions.

Advanced Usage

The most important connection that is made is from the user's client machine to the first remote host. One may "nest" X11 forwarding by using the ssh -XY command to jump to other remote hosts.

For example:

1. on client PC (*nix or Windows), ssh to remotehost1

2. on remotehost1 (presumably a *nix machine), ssh -XY to remotehost2

3. on remotehost2 (presumably a *nix machine), ssh -XY to remotehost3


8. on remotehost8 (presumably a *nix machine), ssh -XY to remotehost9

9. on remotehost9, running an X11 application like xterm should propagate the remote window back to the initial client PC through all of the additional remote connects.

Matlab can also be run in batch mode using a PBS script (say matlab.pbs). The execution command line would look like:

matlab -nodisplay -nojvm -nosplash -r matlab_cmd

▶ Open Example?

#PBS -q single 
#PBS -l nodes=1:ppn=4 
#PBS -l walltime=HH:MM:SS 
#PBS -o myoutput
#PBS -j oe 

cd /path/to/your/matlab/files
matlab -nodisplay -nojvm -nosplash -r matlab_cmd

matlab_cmd can be the name of a Matlab function, or a command string, exactly as you would type interactively. For instance you could add a path name to Matlab's internal path and run fname.m like so:

matlab -nodisplay -nojvm -nosplash -r "addpath /my/custom/path; fname"

The script would then be submitted to PBS via qsub:

$ qsub matlab.pbs

▶ QSub FAQ?

Portable Batch System: qsub


All HPC@LSU clusters use the Portable Batch System (PBS) for production processing. Jobs are submitted to PBS using the qsub command. A PBS job file is basically a shell script which also contains directives for PBS.

$ qsub job_script

Where job_script is the name of the file containing the script.

PBS Directives

PBS directives take the form:

#PBS -X value

Where X is one of many single letter options, and value is the desired setting. All PBS directives must appear before any active shell statement.

Example Job Script
 # Use "workq" as the job queue, and specify the allocation code.
 #PBS -q workq
 #PBS -A your_allocation_code
 # Assuming you want to run 16 processes, and each node supports 4 processes, 
 # you need to ask for a total of 4 nodes. The number of processes per node 
 # will vary from machine to machine, so double-check that your have the right 
 # values before submitting the job.
 #PBS -l nodes=4:ppn=4
 # Set the maximum wall-clock time. In this case, 10 minutes.
 #PBS -l walltime=00:10:00
 # Specify the name of a file which will receive all standard output,
 # and merge standard error with standard output.
 #PBS -o /scratch/myName/parallel/output
 #PBS -j oe
 # Give the job a name so it can be easily tracked with qstat.
 #PBS -N MyParJob
 # That is it for PBS instructions. The rest of the file is a shell script.
 #   1. Copy the necessary files from your home directory to your scratch directory.
 #   2. Execute in your scratch directory.
 #   3. Copy any necessary files back to your home directory.

 # Let's mark the time things get started.


 # Set some handy environment variables.

 export HOME_DIR=/home/$USER/parallel
 export WORK_DIR=/scratch/myName/parallel
 # Set a variable that will be used to tell MPI how many processes will be run.
 # This makes sure MPI gets the same information provided to PBS above.

 export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`

 # Copy the files, jump to WORK_DIR, and execute! The program is named "hydro".

 cp $HOME_DIR/hydro $WORK_DIR
 mpirun -machinefile $PBS_NODEFILE -np $NPROCS $WORK_DIR/hydro

 # Mark the time processing ends.

 # And we're out'a here!

 exit 0

Note: Clusters supported by HPC@LSU do not have parallel Matlab installed due to license issues.


Last modified: September 10 2020 11:58:50.