MATLAB on the ACCRE Cluster
MATLAB is a commercial programming language and computing environment that is widely popular in many areas of engineering and science. Since 2018, MATLAB has been free to use on the cluster for all ACCRE users.
Versions of MATLAB on the ACCRE Cluster
To see a list of installed versions of MATLAB on the cluster, use Lmod:
[jill@vmps12 ~]$ module avail matlab If you need to request software, please submit your request through the PI Dashboard: https://dashboard.accre.vanderbilt.edu/#/rtticket/create Note: We are unable to install Python or R packages. For guidance on how to install Python or R packages, please refer to https://help.accre.vanderbilt.edu. -------------------------------------------- ACCRE specific Core modules -------------------------------------------- matlab/2020a (t) matlab/2021a (t) matlab/2022a (t) matlab/2023a (t) matlab/2020b (t) matlab/2021b (t) matlab/2022b (t) matlab/2023b (t,D) Where: t: Tools for development D: Default Module If the avail list is too long consider trying: "module --default avail" or "ml -d av" to just list the default modules. "module overview" or "ml ov" to display the number of modules for each name. 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".
Multiple versions of MATLAB are available on the cluster. We encourage users to use the most recent version of MATLAB installed, if possible, as we will not offer support for older versions indefinitely.
To load a particular version of MATLAB, use the module load command:
[jill@vmps12 ~]$ module load matlab/2023b [jill@vmps12 ~]$ which matlab /panfs/accrepfs.vampire/accre/software/easybuild/software/2023/x86-64-v3/Core/matlab/2023b/bin/matlab
In order to run MATLAB interactively, simply type `matlab` from the Linux command line:
[jill@vmps12 ~]$ matlab
MATLAB is selecting SOFTWARE OPENGL rendering.
Picked up JAVA_TOOL_OPTIONS: -Xmx2g
Unable to open file for Java VM logging
< M A T L A B (R) >
Copyright 1984-2023 The MathWorks, Inc.
R2023b Update 3 (23.2.0.2409890) 64-bit (glnxa64)
October 4, 2023
To get started, type doc.
For product information, visit www.mathworks.com.
>>
Note that the MATLAB command prompt may take ~30-60 seconds to completely load, depending on which version you are using and whether you’ve loaded it previously in your current shell session. You can also load the full graphical user interface (GUI) to your local machine by logging into the cluster with X11 forwarding enabled (ssh -X <vunetid>@login.accre.vu). In general, using the MATLAB GUI from the cluster will be very slow, especially if you are outside the Vanderbilt network, so we do not recommend it. Instead, most users develop their MATLAB code locally (from a laptop or desktop environment) for testing and then submit jobs to the cluster for batch (non-interactive) processing. Another option is to run MATLAB through a virtual desktop through the ACCRE Visualization Portal.
To see a list of the available Matlab toolboxes on the cluster, use the ver command from the MATLAB command prompt:
>>>> ver --------------------------------------------------------------------------------------------------------------- MATLAB Version: 23.2.0.2409890 (R2023b) Update 3 MATLAB License Number: 299681 Operating System: Linux 5.14.0-427.35.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Thu Sep 12 18:24:53 UTC 2024 x86_64 Java Version: Java 1.8.0_202-b08 with Oracle Corporation Java HotSpot(TM) 64-Bit Server VM mixed mode --------------------------------------------------------------------------------------------------------------- MATLAB Version 23.2 (R2023b) Simulink Version 23.2 (R2023b) 5G Toolbox Version 23.2 (R2023b) AUTOSAR Blockset Version 23.2 (R2023b) Aerospace Blockset Version 23.2 (R2023b) Aerospace Toolbox Version 23.2 (R2023b) Antenna Toolbox Version 23.2 (R2023b) Audio Toolbox Version 23.2 (R2023b) Automated Driving Toolbox Version 23.2 (R2023b) Bioinformatics Toolbox Version 23.2 (R2023b) Bluetooth Toolbox Version 23.2 (R2023b) C2000 Microcontroller Blockset Version 23.2 (R2023b) Communications Toolbox Version 23.2 (R2023b) Computer Vision Toolbox Version 23.2 (R2023b) Control System Toolbox Version 23.2 (R2023b) Curve Fitting Toolbox Version 23.2 (R2023b) DDS Blockset Version 23.2 (R2023b) DSP HDL Toolbox Version 23.2 (R2023b) DSP System Toolbox Version 23.2 (R2023b) Database Toolbox Version 23.2 (R2023b) Datafeed Toolbox Version 23.2 (R2023b) Deep Learning HDL Toolbox Version 23.2 (R2023b) Deep Learning Toolbox Version 23.2 (R2023b) Econometrics Toolbox Version 23.2 (R2023b) Embedded Coder Version 23.2 (R2023b) Filter Design HDL Coder Version 23.2 (R2023b) Financial Instruments Toolbox Version 23.2 (R2023b) Financial Toolbox Version 23.2 (R2023b) Fixed-Point Designer Version 23.2 (R2023b) Fuzzy Logic Toolbox Version 23.2 (R2023b) GPU Coder Version 23.2 (R2023b) Global Optimization Toolbox Version 23.2 (R2023b) HDL Coder Version 23.2 (R2023b) HDL Verifier Version 23.2 (R2023b) Image Acquisition Toolbox Version 23.2 (R2023b) Image Processing Toolbox Version 23.2 (R2023b) Industrial Communication Toolbox Version 23.2 (R2023b) Instrument Control Toolbox Version 23.2 (R2023b) LTE Toolbox Version 23.2 (R2023b) Lidar Toolbox Version 23.2 (R2023b) MATLAB Coder Version 23.2 (R2023b) MATLAB Compiler Version 23.2 (R2023b) MATLAB Compiler SDK Version 23.2 (R2023b) MATLAB Report Generator Version 23.2 (R2023b) MATLAB Test Version 23.2 (R2023b) Mapping Toolbox Version 23.2 (R2023b) Medical Imaging Toolbox Version 23.2 (R2023b) Mixed-Signal Blockset Version 23.2 (R2023b) Model Predictive Control Toolbox Version 23.2 (R2023b) Motor Control Blockset Version 23.2 (R2023b) Navigation Toolbox Version 23.2 (R2023b) Optimization Toolbox Version 23.2 (R2023b) Parallel Computing Toolbox Version 23.2 (R2023b) Partial Differential Equation Toolbox Version 23.2 (R2023b) Phased Array System Toolbox Version 23.2 (R2023b) Powertrain Blockset Version 23.2 (R2023b) Predictive Maintenance Toolbox Version 23.2 (R2023b) RF Blockset Version 23.2 (R2023b) RF PCB Toolbox Version 23.2 (R2023b) RF Toolbox Version 23.2 (R2023b) ROS Toolbox Version 23.2 (R2023b) Radar Toolbox Version 23.2 (R2023b) Reinforcement Learning Toolbox Version 23.2 (R2023b) Requirements Toolbox Version 23.2 (R2023b) Risk Management Toolbox Version 23.2 (R2023b) Robotics System Toolbox Version 23.2 (R2023b) Robust Control Toolbox Version 23.2 (R2023b) Satellite Communications Toolbox Version 23.2 (R2023b) Sensor Fusion and Tracking Toolbox Version 23.2 (R2023b) SerDes Toolbox Version 23.2 (R2023b) Signal Integrity Toolbox Version 23.2 (R2023b) Signal Processing Toolbox Version 23.2 (R2023b) SimBiology Version 23.2 (R2023b) SimEvents Version 23.2 (R2023b) Simscape Version 23.2 (R2023b) Simscape Battery Version 23.2 (R2023b) Simscape Driveline Version 23.2 (R2023b) Simscape Electrical Version 23.2 (R2023b) Simscape Fluids Version 23.2 (R2023b) Simscape Multibody Version 23.2 (R2023b) Simulink 3D Animation Version 23.2 (R2023b) Simulink Check Version 23.2 (R2023b) Simulink Code Inspector Version 23.2 (R2023b) Simulink Coder Version 23.2 (R2023b) Simulink Compiler Version 23.2 (R2023b) Simulink Control Design Version 23.2 (R2023b) Simulink Coverage Version 23.2 (R2023b) Simulink Design Optimization Version 23.2 (R2023b) Simulink Design Verifier Version 23.2 (R2023b) Simulink Desktop Real-Time Version 23.2 (R2023b) Simulink Fault Analyzer Version 23.2 (R2023b) Simulink PLC Coder Version 23.2 (R2023b) Simulink Real-Time Version 23.2 (R2023b) Simulink Report Generator Version 23.2 (R2023b) Simulink Test Version 23.2 (R2023b) SoC Blockset Version 23.2 (R2023b) Stateflow Version 23.2 (R2023b) Statistics and Machine Learning Toolbox Version 23.2 (R2023b) Symbolic Math Toolbox Version 23.2 (R2023b) System Composer Version 23.2 (R2023b) System Identification Toolbox Version 23.2 (R2023b) Text Analytics Toolbox Version 23.2 (R2023b) UAV Toolbox Version 23.2 (R2023b) Vehicle Dynamics Blockset Version 23.2 (R2023b) Vehicle Network Toolbox Version 23.2 (R2023b) Vision HDL Toolbox Version 23.2 (R2023b) WLAN Toolbox Version 23.2 (R2023b) Wavelet Toolbox Version 23.2 (R2023b) Wireless HDL Toolbox Version 23.2 (R2023b) Wireless Testbench Version 23.2 (R2023b)
Note that ACCRE has a license for the Parallel Computing Toolbox, which allows for processing across multiple CPU cores and/or GPUs, and can therefore enable better performance (faster execution time) depending on the application.
Example Scripts
Running a MATLAB script within a SLURM job is generally straightforward. Unless you are attempting to run across multiple CPU cores using MATLAB’s Parallel Computing Toolbox, you will want to request a single task, load the appropriate version of MATLAB from your SLURM script, and then launch your MATLAB job. The following example runs a simple MATLAB script that demonstrates the utility of writing vectorized Matlab code:
[jill@vmps12 run1]$ ls matlab.slurm vectorization.m [jill@vmps12 run1]$ cat matlab.slurm #!/bin/bash #SBATCH --nodes=1 #SBATCH --ntasks=1 #SBATCH --time=00:10:00 #SBATCH --mem=2G #SBATCH --output=matlab_job_slurm.out module load matlab # load the default version of Matlab matlab -nodisplay -nosplash < vectorization.m
The -nodisplay flag informs MATLAB you are operating in batch mode, while the -nosplash flag will prevent the splash screen from being displayed during startup. Additionally, you might try passing the -nojvm flag, which informs MATLAB that you do not need Java features for processing. Passing this flag often leads to faster MATLAB load-up times, but some I/O operations may depend on Java support so use this flag with caution. More information can be found on MATLAB Documentation.
[jill@vmps12 run1]$ cat vectorization.m % surrounding a block of code with tic and toc % will time its execution % non-vectorized code tic i = 0; for t = 0:.00001:10 i = i + 1; y(i) = sin(t); end toc % vectorized code tic t = 0:.00001:10; y = sin(t); toc
[jill@vmps12 run1]$ sbatch matlab.slurm Submitted batch job 1424671
After waiting a few minutes:
[jill@vmps12 run1]$ ls matlab_job_slurm.out matlab.slurm vectorization.m
[jill@vmps12 run1]$ cat matlab_job_slurm.out
Picked up JAVA_TOOL_OPTIONS: -Xmx2g
Unable to open file for Java VM logging
< M A T L A B (R) >
Copyright 1984-2023 The MathWorks, Inc.
R2023b Update 3 (23.2.0.2409890) 64-bit (glnxa64)
October 4, 2023
To get started, type doc.
For product information, visit www.mathworks.com.
>> >> >> >> >> >> >> >>>>>>>> Elapsed time is 0.287125 seconds.
>> >> >> >> >> >> Elapsed time is 0.049262 seconds.
In this particular example no functions were defined in the vectorization.m file. Often users write scripts with functions, and need to call a function from the Linux command line. This can be accomplished by passing the MATLAB interpreter the -r option. For example:
matlab -nodisplay -nosplash -r "myFunc(1),quit()"
Here we are calling myFunc() and passing a single argument (1) to the function. It’s also necessary to call quit() afterwards to ensure your job ends once MATLAB processing has completed. You may also need to update your MATLAB path to include directories containing .m files and their function definitions. There are a few ways to accomplish this. The first way is to update your MATLABPATH Bash environment variable. Something like the following can be done within a SLURM script before MATLAB is launched:
export MATLABPATH=/home/jill/myDir
Alternatively, the path can be updated at runtime like so:
matlab -nodisplay -nosplash -r "addpath(genpath('/home/jill/myDir')),myFunc(1),quit()"
Contributing New Examples
In order to foster collaboration and develop local MATLAB expertise at Vanderbilt, we encourage users to submit examples of their own to ACCRE’s MATLAB Github repository. Furthermore, ACCRE slack can be used as community help material as well. Please report any inconsistencies to this article via the Helpdesk
