Mathematica

Contents

1. Summary and Version Information
2. Running Mathematica
   1. With the GUI
   2. Commandline/Without the GUI

Summary and Version Information

Notes:
^*: Packages labelled as "available" on an HPC cluster means that it can be used on the compute nodes of that cluster. Even software not listed as available on an HPC cluster is generally available on the login nodes of the cluster (assuming it is available for the appropriate OS version; e.g. RedHat Linux 6 for the two Deepthought clusters). This is due to the fact that the compute nodes do not use AFS and so have copies of the AFS software tree, and so we only install packages as requested. Contact us if you need a version listed as not available on one of the clusters.

In general, you need to prepare your Unix environment to be able to use this software. To do this, either:

• tap TAPFOO

• module load MODFOO

where TAPFOO and MODFOO are one of the tags in the tap and module columns above, respectively. The tap command will print a short usage text (use -q to supress this, this is needed in startup dot files); you can get a similar text with module help MODFOO. For more information on the tap and module commands.

For packages which are libraries which other codes get built against, see the section on compiling codes for more help.

Tap/module commands listed with a version of current will set up for what we considered the most current stable and tested version of the package installed on the system. The exact version is subject to change with little if any notice, and might be platform dependent. Versions labelled new would represent a newer version of the package which is still being tested by users; if stability is not a primary concern you are encouraged to use it. Those with versions listed as old set up for an older version of the package; you should only use this if the newer versions are causing issues. Old versions may be dropped after a while. Again, the exact versions are subject to change with little if any notice.

In general, you can abbreviate the module tags. If no version is given, the default current version is used. For packages with compiler/MPI/etc dependencies, if a compiler module or MPI library was previously loaded, it will try to load the correct build of the package for those packages. If you specify the compiler/MPI dependency, it will attempt to load the compiler/MPI library for you if needed.

Running Mathematica

This section provides a little help on running Mathematica.

Running Mathematica with the GUI

This is generally fairly simple. Just type mathematica and the Mathematica notebook should open. This assumes you have an X11 server running on your desktop.

NOTE: Mathematica uses specialized fonts to display the mathematical and other symbols it uses. These fonts must be installed on the system the X11 server is running on, e.g. your desktop. If you are receiving graphics errors, or the fonts are screwed up, you probably need to install the fonts on your desktop system. See this knowledge base article for Macs, or the Wolfram site for the official Wolfram solution.

Running Mathematica from the Commandline/Without the GUI

There are times when you wish to run a mathematica script non-interactively. E.g., submit it from the command line to run as a batch job, for instance on an HPC cluster.

In this case, you should place your mathematica commands into a file using a text editor. For this example, we will assume the commands are in the file my-math-script.m. You should then run the script file with the command math -noprompt -script my-math-script.m. The math command runs the command line version of Mathematica, the -noprompt argument suppresses the display of the command prompt, and the -script argument tells it to take input from the following file name.