HPC @ Uni.lu

High Performance Computing in Luxembourg

FAQ: How Do I Run a MATLAB Program?

You need to try the following sequence:

  • oarsub -I # you MUST take at least one core on a cluster node
  • module load MATLAB # as of May 2013, default module version is 2013a
  • matlab -nodisplay # add as a parameter with -r whatever .m script you need to run
  • “ver” # use it, if you want to see all the available toolboxes, or another command you want to run

Some very important guidelines:

  • most people would prefer to try first matlab –nosplash –nodesktop –nodisplay –singleCompThread and adjust later on as needed; RTFM.
  • oarsub -I only gets you one core; better reserve more cores if you need such with ‘-l nodes=1” parameter OR, use “-singleCompThread”
  • if you can cope with 200GBs per node, it is wise to set TMPDIR=/tmp on gaia’s SSDs or chaos’ HDDs, especially for generating many small files
  • you may need to do “ssh -X” in order to obtain the graphical environment working (it may be slower over distant network connections)
  • if the X connection gets broken after some time, you will need to log out and reconnect; there is no known remedy to this as of yet
  • Matlab Compiler is a Matlab Toolbox with its own documentation and is available on the cluster
  • use Matlab’s Compiler to compile your code into a standalone executable file; this is important for scalability
  • DISPLAY variable is known to cause issues in various situations; try “unset DISPLAY” as needed.
  • We do provide “Parallel Computing Toolbox” but not “Distributed Computing Server”, as of May 2013.

Helpful pages from Mathworks and other HPC sites using MATLAB: