The MSRI Computing Handbook

Mathematical Software

In General

MSRI has collected many modern mathematical software packages. Ultimately, this is the most important reason for maintaining computers at MSRI. We encourage you to browse and experiment with any or all of these programs. This documentation cannot serve the technical role of thoroughly introducing these complex packages. A brief description is included to guide you to the package which will most interest you. Periodically, MSRI holds classes on various mathematical software packages. Notices will appear on the seminar board and via electronic mail. If there is a package which you have found useful, but which we do not have, please tell us, and we will try to get it. For more information on these programs, please see Rachelle Summers, in room 229.

Really Big Jobs

For intensive mathematical computations, MSRI has two cycle servers, ted and carol. ted is a 200 Mhz, dual processor Hewlett-Packard D250 with 256 MB of RAM and 1GB of virtual memory. carol is a 166 Mhz, dual processor Sun Ultra2 with 128 MB of RAM and 2GB of virtual memory. The command xrsh ted resp. carol will open a window from ted resp. carol on your machine allowing you run applications on a cycle server with their display on your desktop. We are in the process of building an SMP Linux cluster to supplement these older machines.

Please restrict your use of these machines to scientific calculation. While they access your home directory like any other machine at MSRI and have the full complement of compilers and mathematical software, routine user applications like Netscape or TeX are not available. Conversely, please be considerate of other users of the ordinary MSRI machines; while running a calculation which takes a few minutes is OK, if your calculation takes hours, please use a cycle server. If you would like help taking advantage of the power of our cycle servers, please talk to the computing staff.

Really, Really Big Jobs

Through an alliance with Lawrence Berkeley National Laboratory, MSRI members can get accounts at the National Energy Research Scientific Computing Center (NERSC). NERSC has a variety of High Performance Computing resources, including parallel super-computers, a visualization server, and a mathematics server, loaded with commercial mathematics software.

Mathematica

Mathematica is a system for doing symbolic and numeric computation, and two- or three-dimensional graphics. At MSRI we are at version 4.02 of Mathematica.

All documentation for Mathematica is available online within the Notebook front end; bound documentation and further books can be checked out from the library.

To start Mathematica, issue the command: mathematica to get the Notebook front end or math to get a dumb terminal version.

MSRI maintains a large library of third party Mathematica packages beyond those supplied by its publisher. They can be found in the directory /usr/msri/mathsw/MSRImathematica/LocalPackages/ This directory is on Mathematica's default search $Path at MSRI.

Maple

Maple is a system for doing symbolic and numeric computation, and two- or three-dimensional graphics. At MSRI, typing maple gives MapleV, release4. Maple from the Math menu gives release 5.

All documentation for Maple is available online within the graphical front end; bound documentation and further books can be checked out from the library.

To start Maple, issue the command: xmaple to get a graphical front end, or maple to get a dumb terminal version. Releses 3 and 5 are available by appending V3 or V5 to these commands. e.g. mapleV3 or xmapleV5.

Matlab

Matlab's main strengths are linear algebra and numerics.

MSRI has Matlab5.

Documentation on Matlab is available online and can be checked out from the library.

To start Matlab, issue the command: matlab

Geomview

Geomview is a mathematician's 2D and 3D geometry viewer. Geomview comes with a large library of interesting external modules and beautiful mathematical objects. Geomview can be used to view the graphic output of Mathematica, as well as a front end for custom applications.

Geomview is available on all platforms at MSRI. Version 1.7 is installed under Linux.

For more information on Geomview, see Rachelle Summers in room 229. Documentation for Geomview is available locally at MSRI and in the labs. The official site for Geomview is http://www.geomview.org/. Documentation available there is at http://www.geomview.org/docs/

To start Geomview, issue the command: geomview

Gap

Gap is a powerful mathematical program for general algebra, and especially group theory. (GAP stands for ``Groups, Algorithms, and Programming''.)

MSRI no longer has Gap v3. The command gap4 gives you version 4b5. Version 4b4 is still available with the command gap4b4.

The official site for Gap is http://www-groups.dcs.st-and.ac.uk/~gap/

Documentation for Gap is available locally at MSRI, from within gap, or on the internet at http://www-groups.dcs.st-and.ac.uk/~gap/Info4/manual.html.

Magma

Magma is a another group theory and general algebra environment, similar to Gap. In fact, both are descendents of Cayley.

Documentation on Magma is available online, or within magma.

MSRI has version 2.3 installed on the Sun Ultras in room 225, and on our cycle server, carol. Version 2.7 is installed on the Linux machines.

To Magma, issue the command: magma. On Linux machines, you may also choose "magma" from the "Math" menu.

KBMAG

KBMAG is a stands for Knuth-Bendix on Monoids, and Automatic Groups. Aptly enough KBMAG is a suite of programs which implement the Knuth-Bendix algorithm on general monoids, and computing various finite state automata associated with words and cosets in automatic groups. It is best to read the documentation before beginning to use these powerful programs.

Magnus

Magnus is designed to carry out computations and do experiments with infinite groups, especially finitely presented groups.

Documentation on magnus is available within magnus or locally at MSRI.

MSRI has version 3.0.0 installed on the Linux machines.

To magnus, issue the command: magnus.

Macaulay2

Macaulay2's main strength is commutative algebra.

Macaulay2 (0.8.60) is available on our Linux and Solaris machines.

To start Macaulay2, issue the command: M2. Version 0.8.52 is available using the command: M2-52.

Macaulay2's home page is at: http://www.math.uiuc.edu/Macaulay2/

Documentation on Macaulay2 is available locally, or over the internet (with search!) at http://www.math.uiuc.edu/Macaulay2/Manual/.

To use Macaulay2 from within emacs, you need to first edit your .emacs file. Running UseM2InEmacs will make all the necessary changes. You only need to run this script once. From then on, pressing F12 from within emacs will load Macaulay2. For more information about the Macaulay2 emacs mode, see http://www.math.uiuc.edu/Macaulay2/Manual/1372.html or the local text documentation.

Macaulay

The ``Classic'' version of Macaulay has slightly different syntax, but is still quite useful.

Documentation on Macaulay is available online.

Macaulay is available everywhere, by issuing the command: M1. The kernel on our cycle server ted was tuned for this version of Macaulay.

CoCoA

CoCoA is a platform for commutative computer algebra

Documentation is available within CoCoA itself, which is invoked as cocoa or CoCoA. MSRI has version 4.0. [XCoCoA and emacs bindings are not fully functional yet]

Singular

Singular is a system for computation in general polynomial rings.

Singular's homepage is at http://www.singular.uni-kl.de/

Singular 1.2.2 is installed on Linux and Solaris machines here. Documentation is available locally at MSRI, at http://www.singular.uni-kl.de/documentation.html, and mirrored at http://www.bangor.ac.uk/ma/research/comp-alg/singular/singular_toc.html

Invoke Singular via the command: Singular.

Pari-GP

Pari is a collection of libraries for computation in number theory. GP is a calculator built on top of Pari.

To invoke GP (version 2.0.11.beta on Solaris, 2.0.20.beta on Linux), type: gp.

A tutorial, user guide, and reference card are available online.

KASH

KASH is a tool for algebraic number theory calculations in number fields and in global function fields.

A user guide, and reference manual are available locally. Kash's homepage is at http://www.math.tu-berlin.de/~kant/kash.html Documentation is also available over the internet at http://www.math.TU-Berlin.DE/~kant/publications.html#docu

Invoke KASH (version 2.2) with: kash.

Qhull

Qhull is a general dimension code for computing convex hulls, Delaunay triangulations, halfspace intersections, Voronoi diagrams, furthest-site Delaunay triangulations, and furthest-site Voronoi diagrams. It has a nice interface to geomview for visualization.

Documentation is available online. Invoke Qhull as: qhull.

Porta

Porta is a collection of routines for analyzing polytopes and polyhedra. Most of the routines have driver programs. Being specialized, they are small and fast. MSRI has version 1.3.2 installed on our Linux machines. A general introduction to porta, its file formats, and its various driver programs is available by typing man porta.

Last modified by Josh Levenberg on 2000/08/21 11:45:11