SciClone Cluster Project Computational Science Cluster
User Info

Name: MATLAB and Simulink

Version: R2006b


MATLAB is a technical computing environment for data analysis, mathematical modeling, visualization, and application development. Simulink is a companion package for multidomain simulation and model-based design for dynamic systems. The MATLAB/Simulink installation on SciClone includes the following components:

Availability: UltraSPARC only

Installation Path:



Usage Notes:

MATLAB should not be run on the SciClone front end node (monsoon) unless you are doing something truly trivial. For operations which use significant amounts of CPU time or memory, use the qlogin command to obtain an interactive shell on a compute node, or else run MATLAB in batch mode from a PBS job script. Note that if you use qlogin to start an interactive PBS job, the MATLAB graphical interface will still work properly assuming that:

  • the system you logged in from is running an X11 server,
  • your local SSH configuration supports X11 forwarding, and
  • your network connection to SciClone is fast enough to support a remote X session.

Additional information about establishing X11 connections to remote workstations can be found in the SciClone User's Guide.

To run MATLAB non-interactively as a PBS batch job, use the "-nojvm" and "-nodisplay" options and read your command script from standard input, e.g.:

qsub -l nodes=1:c7:ppn=1
cd mydir
matlab -nojvm -nodisplay <script.m >results.out

Multiple copies of MATLAB can be invoked independently on different nodes and/or on multiple processors within a single node to exploit coarse-grained parallelism. Because the College has purchased a site license with essentially unlimited usage, the maximum number of simultaneous MATLAB jobs is limited only by the number of processors available in the system and the job queue parameters.

Interactive MATLAB sessions require large amounts of memory (minimum of 1 GB is recommended) and will not run on SciClone's c1, c2, or c6 compute nodes. Non-interactive jobs (without the desktop GUI and Java) use much less memory and will run on any node type, subject to the application's memory requirements.

Despite the fact that Solaris has been 64-bit capable since 1997, MathWorks has yet to release a 64-bit version of MATLAB for Solaris. This means that MATLAB applications on SciClone are currently limited to 2 GB of memory. We have asked MathWorks to rectify this situation, and are hopeful that a 64-bit Solaris version will become available at some point in the future.

MATLAB is not presently available for x86/x64 systems running Solaris, and therefore is not installed on SciClone's tempest subcluster.

MATLAB 7 introduced a capability for distributing computations across multiple processors via the Distributed Computing Toolbox. This feature has not been integrated into SciClone's PBS batch environment, although it is probably possible to do so. If you are interested in using the Distributed Computing Toolbox on SciClone, please contact for more information.