matlab
Table of Content
Versions and Availability
▶ Display Module Names for matlab on all clusters.
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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/$U
SER/.matlab/R2020a_licenses.
Usage
Licensing
Matlab is installed on most of the HPC clusters. It is, however, license software, which means that it is only availabe to users or user groups who have access to a license, purchased either individually or by the users' institution.
If you do have lots of similar jobs, we recommend you to compile your Mablab scripts using the Matlab compiler, and the jobs using the compiled executable will not take license seats, If you need help in this regard, please contact us at sys-help@loni.org.
If you are not enrolled at LSU, you are not allowed to use Matlab on our LSU HPC clusters according to the current terms of our Matlab license agreement and the program offering guide.
Note: For LSU and ULL users on QB2, a license file has been created, so the steps described below are not necessary for them.
For LONI users who want to use Matlab on QB2, you need to provide your own license file. The license file should have a .lic extension and be located under the "/home/$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 sys-help@loni.org.
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'); parallel.defaultClusterProfile(profile_master);
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:
parpool('SuperMIC',80)
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'); parallel.defaultClusterProfile(profile_master); primeNumbers = primes(uint64(2^21)); compositeNumbers = primeNumbers.*primeNumbers(randperm(numel(primeNumbers))); factors = zeros(numel(primeNumbers),2); parpool('SuperMike2',64); numWorkers = [1 2 4 6 16 32 64]; tCluster = zeros(size(numWorkers)); for w = 1:numel(numWorkers) tic; parfor (idx = 1:numel(compositeNumbers), numWorkers(w)) factors(idx,:) = factor(compositeNumbers(idx)); end tCluster(w) = toc; end f = figure; speedup = tCluster(1)./tCluster; plot(numWorkers, speedup); title('Speedup with the number of workers'); xlabel('Number of workers'); xticks(numWorkers(2:end)); ylabel('Speedup'); saveas(gcf, 'composite_speedup.png'); delete(gcf); delete(gcp);
Content of the job script:
$ cat mps.pbs #!/bin/bash #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 cd $PBS_O_WORKDIR 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?
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?
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?
Note: Clusters supported by HPC@LSU do not have parallel Matlab installed due to license issues.
Resources
- Extensive on-line documentation is available at Mathworks TechDocs.
Last modified: September 10 2020 11:58:50.