Load and Run MATLAB¶

Check all available MATLAB versions with:

module avail matlab

---------------------------- /sw/mf/rackham/applications ----------------------------
   matlab/R2014a    matlab/R2018a    matlab/R2022b          matlab/7.10
   matlab/R2015a    matlab/R2018b    matlab/R2023a          matlab/7.13
   matlab/R2015b    matlab/R2019a    matlab/R2023b (L,D)    matlab/8.0
   matlab/R2016a    matlab/R2020b    matlab/7.4             matlab/8.1
   matlab/R2017a    matlab/R2022a    matlab/7.8

  Where:
   L:  Module is loaded
   D:  Default Module

Use "module spider" to find all possible modules and extensions.
Use "module keyword key1 key2 ..." to search for all possible modules matching any
of the "keys".

Output on Tetralith as of 27 Feb 2025:

--------------------- /software/sse2/tetralith_el9/modules ---------------------
   MATLAB/recommendation (D)    MATLAB/2023b-bdist
   MATLAB/2023a-bdist           MATLAB/2024a-hpc1-bdist

  Where:
   D:  Default Module

Check all available MATLAB versions with:

module spider MATLAB

As of 26 Sep 2024, the above outputs the following on Kebnekaise:

----------------------------------------------------------------------------
  MATLAB:
----------------------------------------------------------------------------
    Description:
      MATLAB is a high-level language and interactive environment that
      enables you to perform computationally intensive tasks faster than
      with traditional programming languages such as C, C++, and Fortran.

     Versions:
        MATLAB/2019b.Update2
        MATLAB/2021a
        MATLAB/2021b
        MATLAB/2022b.Update3
        MATLAB/2023a.Update4
     Other possible modules matches:
        MATLAB-parallel-support

----------------------------------------------------------------------------

Note that it is case-sensitive and must be in ALL-CAPS. There will be results if you type matlab, but they won’t be the ones you want. To see how to load a specific version of MATLAB, including the prerequisites, do

module spider MATLAB/<version>

Example for MATLAB 2023a.Update4

module spider MATLAB/2023a.Update4

See all available MATLAB versions at the command line with:

ml spider matlab

Or, if on Desktop On-Demand, select Applications in the top left corner and hover over Applications - Matlab (see also GUI section below).

As of 27 Feb 2025, ml spider matlab on COSMOS outputs the following:

----------------------------------------------------------------------------
matlab:
----------------------------------------------------------------------------
    Versions:
        matlab/2022a
        matlab/2023a
        matlab/2023b
        matlab/2024b

----------------------------------------------------------------------------
For detailed information about a specific "matlab" package (including how to
load the modules) use the module's full name. Note that names that have a
trailing (E) are extensions provided by other modules.
For example:

module spider matlab/2023b
----------------------------------------------------------------------------

See all available MATLAB versions at the command line with:

ml spider matlab

As of 17 Mar 2025, the above command outputs the following on Dardel:

Versions:
  matlab/r2020b
  matlab/r2021b
  matlab/r2022b
  matlab/r2023a
  matlab/r2024a-ps
  matlab/r2024a
  matlab/r2024b

On Dardel, all MATLAB versions have a prerequisite that needs to be loaded (it will called something like PDC/xx.xx or PDCOLD/xx.xx). To view the prerequisites for a specific version of MATLAB, do

module spider matlab/<version>

For example, module spider matlab/r2024b outputs the following:

matlab: matlab/r2024b
  You will need to load all module(s) on any one of the lines below before the "matlab/r2024b" module is available to load.
    PDC/23.12
  Help:
    For more information, visit:
       https://www.mathworks.com

To load version 2023b, do:

module load matlab/R2023b

Note: all lowercase except the R. For short, you can also use:

ml matlab/R2023b

To load version 2023b, do:

module load MATLAB/2023b

Note: all Uppercase except for the letter after the year. For short, you can also use:

ml MATLAB/2023b

To load version 2024b, do:

module load matlab/2024b

Note: all lowercase. For short, you can also use:

ml matlab/2024b

To load version 2023b, do:

module load MATLAB/2023b-bdist

Note: all Uppercase except for the letter after the year. For short, you can also use:

ml MATLAB/2023b

If you check with ml which version is loaded, you will see the -bdist suffix was added automatically. Versions without -bdist at the end only appear with ml spider matlab and they do not appear to be loadable.

Go back and check which MATLAB modules were available, and what their prerequisites are. To load version 2024b, do:

module load PDC/23.12
module load matlab/r2024b

Notes: the module name is all lowercase including the r before the year. For short, you can also use:

ml PDC/23.12 matlab/r2024b

Once you’ve loaded your preferred version of MATLAB, type:

matlab -nodisplay

to start MATLAB in the terminal. The maximum number of computational threads will be set to 1 automatically if you are on a log-in node.

The GUI can be started in a ThinLinc session by going to “Application” → “HPC2N Applications” → “Applications” → “Matlab ” and clicking the desired version.

To start MATLAB in the terminal, load matlab/2023b or your preferred version, and then type:

matlab -singleCompThread -nodisplay

to start MATLAB in the terminal. The -singleCompThread is important to prevent MATLAB from hogging a whole node, and the -nodisplay flag prevents the GUI from launching.

It is recommended that GUI be started in ThinLinc at the LUNARC HPC Desktop On-Demand.

To start MATLAB in the terminal, you must first choose the correct terminal. There are several: two in Applications → Applications - General, which can safely launch either the MATLAB GUI or MATLAB command line on a compute node, one in Applications → Visualization, which should be reserved for very graphics-heavy jobs, and one in Applications → Favorites → Terminal, which runs on a login node and should be avoided. Starting any of the other three will open the GfxLauncher and prompt you for your account and resource selections. Even users who have been awarded GPU time are encouraged to use the CPU-only terminal whenever possible, as they are abundant and less resource intensive.

Once you’ve opened a terminal session and loaded your preferred version type:

matlab -singleCompThread -nodisplay

Starting a MATLAB session on Dardel looks different depending on whether or not you are affiliated KTH or have been added to the MATLAB user group by PDC support (e.g. as part of this course, if you signed up in time). If you are a KTH affiliate or another PDC-approved academic user, you are covered by KTH’s university license. Otherwise, you will need to have a MathWorks account and be logged into it in your browser before getting started, because MATLAB on Dardel will ask you provide the email associated with your MathWorks account and a one-time password (OTP) sent to that account online (which you will have to copy from your browser).

Either way, you will first need to load the corresponding PDC, PDCOLD, or PDCTEST prerequisite. The current default is PDC/23.12, and that makes available any MATLAB version from 2024. The only version that reliably works for non-KTH users without asking for credentials is r2024-ps.

If you, for example, wanted to start matlab/r2024a-ps in the terminal, the sequence would look as follows:

ml PDC/23.12  matlab/r2024a-ps
matlab -singleCompThread -nosplash -nodesktop -nodisplay

If you are an academic user who has been vetted by PDC staff, the above should be enough to eventually take you to the MATLAB command prompt. Otherwise, you will see the following:

Please enter your MathWorks Account email address and press Enter: <your.email@your.institute.se>
   You need a one-time password to sign in. To get a one-time password, follow these steps:
     1. Go to https://www.mathworks.com/mwa/otp
     2. Enter your MathWorks Account email address.
     3. Copy the generated one-time password.
     4. Return here and enter the password.
   Enter the one-time password:

If you are a student or staff member at KTH and you see these credential requests, that means PDC support did not receive your request for MATLAB access.

PDC users also have the option to go through ThinLinc and open MATLAB from the On-Demand Applications menu, but this is not recommended as only 30 users are allowed to interface with Dardel via ThinLinc at any one time.

For HPC2N, once logged into the remote desktop, the procedure for starting the MATLAB GUI is the same as what was shown above to start it at the command line, except that the -nodisplay flag is omitted (as are -nodesktop -nosplash if applicable). You should still include -singleCompThread!

It is possible to start the MATLAB GUI on a compute node on Kebnekaise (HPC2N). The procedure uses salloc and srun to achieve what other facilities often do with the interactive command (edit time, resources, project ID, and MATLAB version as needed):

salloc -N 1 -t 00:30:00 -A hpc2n20YY-XXX
module load MATLAB/2023b
srun matlab

For UPPMAX users, once logged into the remote desktop, the procedure for starting the MATLAB GUI is the same as what was shown above to start it at the command line, except that the -nodisplay flag is omitted (as are -nodesktop -nosplash if applicable). You should still include -singleCompThread!

It is also possible to start the MATLAB GUI on the login node, but even if you are already logged into Rackham, you must use Snowy for any interactive work. Fortunately, the interactive command takes care of this for you without requiring SSH, as long as you specify -M snowy. A MATLAB GUI session can be run with the following commands (again, edit time, resources, project ID, and MATLAB version as needed):

interactive -M snowy -n 4 -t 00:30:00 -A uppmax20YY-X-XXX
module load matlab/R2023b
matlab

In the above example, -n 4 means the job will run on 4 cores. Snowy nodes have 16 cores. The default partition, core, is for jobs requiring up to 15 cores, and they cannot be exclusive. If you need a full node, or more cores than one node contains, you should change the partition with -p node. Please refer to this link <https://docs.uppmax.uu.se/cluster_guides/snowy/#using-the-batch-system>_ for allowed combinations of interactive parameters.

The best way to start the MATLAB GUI on Tetralith depends on how intensively you plan to use the GUI. Most of the time, it is recommended to use the interactive command first to get an allocation on a compute node. The commands you will need to enter look like the following (change the MATLAB version and interactive job specifications as needed):

interactive -N 1 --exclusive -t 4:00:00
module load MATLAB/2024a-hpc1-bdist
matlab -softwareopengl

For short (<<1 hour) tasks requiring few resources, once you’ve loaded your preferred version of MATLAB, you can use the following command to start MATLAB on a login node:

vglrun matlab -nosoftwareopengl

You do not need to include -singleCompThread because maxNumCompThreads will be set to 1 automatically to account for starting on a login node.

The LUNARC HPC Desktop, available via ThinLinc, uses Desktop On-Demand and GfxLauncher to run certain interactive apps without going through a terminal interface. Click the Applications menu at the top left, hover the cursor over Applications-Matlab to see the versions available, and click your preferred version. That will open a GfxLauncher popup where you can set the resources needed to run the MATLAB GUI (note that batch jobs submitted from within the GUI are not bound by the same settings as the GUI).

There are 3 versions per MATLAB release in the Apps menu—regular, (CPU), and (HEP,CPU)—and your resource choices in the GfxLauncher partly depend on which of those you select.

MATLAB GUI, COSMOS

The (HEP,CPU) nodes are private. The regular versions run on Intel 32-core nodes because they have built-in GPU partitions, but you may choose other nodes. If you don’t plan to do any intensive graphical work inside the GUI, you can choose the (CPU) version of your preferred release to access an AMD 48-core node, which also allows you to run for up to 7 days (168:00:00) instead of the usual 2-day limit.

There are 2 ways to run MATLAB interactively on Dardel: via SSH with X-forwarding (recommended), or via Desktop On-Demand in a ThinLinc window. ThinLinc access to Dardel is limited to 30 users total, and even if you do get through, interactive jobs are likely to be stuck in queues for a long time.

SSH with X-forwarding. When you first ssh into Dardel, you will need to have added the -X flag between ssh and your username. Once you are logged in, you need to book a compute node with salloc, and then SSH (again with the -X flag) into whichever node you are assigned to by salloc. The salloc step and its output will look something like this:

salloc -N 1 -t 00:30:00 -A naiss2025-22-262 -p main

if you request a full node, or

salloc -c 16 -t 00:30:00 -A naiss2025-22-262 -p shared

if you request, for example, 16 cores on a shared node. Adjust the time, resources, and account number as needed. salloc will then print a handful of lines about the progress of allocating and queuing your job. The last line of output, something like salloc: Nodes nid00xxxx are ready for job, will contain the ID of the node you booked. Copy that, and then run the following lines (after the :~> prompt; adjust the node ID as needed):

<user>@login1:~> ssh -X nid001756
<user>@nid001756:~> ml PDC/23.12
<user>@nid001756:~> ml matlab/r2024a-ps
<user>@nid001756:~> matlab

The GUI will take a few minutes to load.

If you are lucky enough to get into Dardel via ThinLinc, the process looks very similar to LUNARC because Dardel’s Desktop On-Demand apps also go through GfxLauncher, except that the MATLAB versions in the app menu are not separated by the types of nodes to run on. You choose the partition in the resources section of the GfxLauncher.