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Software Applications Available in the CSCS Lab

CSCS strives to offer usable, cost-free software for the purpose of general and scientific computing. Unless otherwise noted, CSCS provides the software listed below only on the CSCS machines running the Linux operating system. A few items are provided on CSCS machines running Windows OS, and a few may be provided under Linux and Windows.

New Applications (updated October, 2006)

Repast Simphony Developer's alpha 1, extends the Repast portoflio by offering a new approach to simulation development and execution. See http://repast.sourceforge.net for more information.
Start command: repastsimphony
Application Directory: /appl/repastsimphony

NetLogo 3.0 Beta 3, a multi-agent programmable modeling environment. See http://ccl.northwestern.edu/netlogo/ for more information.
Start command: netlogo3.0b
Application Directory: /appl/netlogo3.0beta3

Sun's Java 2 JDK SE 5.0, Sun's JDK for Linux http://java.sun.com/j2se/1.5.0/index.jsp
Start Command: /appl/jdk1.5.0_04/bin/java
Application directory: /appl/jdk1.5.0_04
Click here for instructions on upgrading to this newer java release.

DrScheme, an interactive, integrated programming environment designed specifically with the needs of beginners in mind.
http://www.drscheme.org/
Start command: /common/scripts/drscheme
Application directory: /appl/drscheme299.100

EJP, the Extensible Java Profiler, an open-source profiling tool for Java
http://ejp.sourceforge.net/
Application directory: /appl/ejp-r2_2b1
Documentation directory: /appl/ejp-r2_2b1/doc

Mathematica 5.0, symbolic math program www.wolfram.com (tutorial1)
Start Command: /common/scripts/mathematica
Application directory: /appl/mathematica5.0

NetLogo 3D Preview 1, agent-based parallel modeling and simulation environment. See http://ccl.northwestern.edu/netlogo/ for more information.
Start command: netlogo3dp1
Application Directory: /appl/netlogo3dp1

Java Web Start, an application to launch java programs through the web. Check out the complete description and other info (including demos) at http://java.sun.com/products/javawebstart/
The Java Web Start executable is: /appl/jdk1.5.0/bin/javaws

Repast 3.0, latest release of The Recursive Porous Agent Simulation Toolkit. Check out more information at http://repast.sourceforge.net
Repast 3.0 is located under: /appl/repast/repast3.0
Check out the CSCS local Repast docs

PerlGP, Provides the ability to do "strongly typed Genetic Programming in a high level language" Check out more information at http://perlgp.org/
PerlGP is located under: /appl/perlgp1.0.1

Commons-Math: The Jakarta Mathematics Library, " Commons Math is a library of lightweight, self-contained mathematics and statistics components addressing the most common problems not available in the Java programming language or Commons Lang." Check out more information at http://jakarta.apache.org/commons/math/
Commons-Math is located under: /appl/java/commons-math-1.0-RC1

ECJ, ECJ is a research EC system written in Java. It was designed to be highly flexib le, with nearly all classes (and all of their settings) dynamically determined at runtime by a user-provided parameter file. Check out more information at http://cs.gmu.edu/~eclab/projects/ecj/
ECJ is locatd under: /appl/ecj12

Jung, the Java Universal Network/Graph Framework--is a software library that provides a common and extendible language for the modeling, analysis, and visualization of data that can be represented as a graph or network. Check out more information at http://jung.sourceforge.net/index.html
Jung is locatd under: /appl/java/jung1.1.1

MASON, a fast discrete-event multiagent simulation library core in Java. Check out more information at http://cs.gmu.edu/~eclab/projects/mason/
MASON is locatd under: /appl/mason7

Breve 2.2, a 3d simulation environment designed for the simulation of decentralized systems and artificial life. Check out the full documentation at http://www.spiderland.org/breve/index.php
breve is located under: /appl/breve1.8b/

BlueJ integrated Java environment specifically designed for introductory teaching. Check out the full documentation at http://www.bluej.org/doc/documentation.html
bluej is located under: /appl/bluej1.3.0
Start command: /appl/bluej1.3.0/bluej/bluej

graphviz, open source graph drawing software. Check out the full documentation at http://www.research.att.com/sw/tools/graphviz/
graphviz is located under: /appl/graphviz1.10

ArgoUML, a java based UML design tool. Check out the full documentation at http://argouml.tigris.org/documentation/
ArgoUML is located under: /appl/ArgoUML0.12/
Start command (must run in the ArgoUML dir): java -jar argouml.jar

GNUstep, an object-oriented development environment for use with Objective C that is meant to provide generalized visual interface design. Check out the documentation at http://www.gnustep.org/experience/documentation.html

Operating System

The Operating Systems employed at CSCS are Red Hat Enterprise Linux v.3 and Windows 2000.

Red Hat Enterprise Linux - www.redhat.com

Microsoft Windows - www.microsoft.com

For help learning Unix/Linux, please see our general documentation page for assistance.

Desktop Environment

The primary desktop deployed at CSCS is GNOME. KDE is also be available.

The Gnome Project - www.gnome.org

The K Desktop Environment - www.kde.org

Core Scientific Apps

DDL, Discrete Dynamics Lab, provides tools for researching discrete dynamical networks - from Cellular Automata to Random Boolean Networks and beyond. http://www.ddlab.com
Start Command: /common/scripts/ddlab2.3
Application directory: /appl/ddlab2.3

Swarm, agent based simulation www.swarm.org (swarm at UofM, drone-info)
Start Command: n/a
Application directory:
/appl/swarm2.1.1/opt -- optimized SWARMHOME libraries and binaries
/appl/swarm2.1.1/debug -- SWARMHOME for debugging with gdb, ddd, etc.
/appl/swarm2.1.1-um/swarm-2.1.1 -- source for swarm libs
/appl/swarm2.1.1-um/swarmapps-2.1.1 -- source for swarm demos from SDG
/appl/swarm2.1.1-um -- additional demos and libs at UM

Repast, agent based simulation repast.sourceforge.net
Start Command: n/a
Application directory: /appl/repast
Repast at CSCS

NetLogo 2.1, agent-based parallel modeling and simulation environment. See http://ccl.northwestern.edu/netlogo/ for more information.
Click here to read the local documentation.
Start command: /common/scripts/netlogo
Application Directory: /appl/netlogo2.1

Mathematica, symbolic math program www.wolfram.com (tutorial1)
Start Command: /common/scripts/mathematica
Application directory: /appl/mathematica5.0

Matlab 6.5, numerical math program www.mathworks.com
Start Command: /common/scripts/matlab
Application directory: /appl/matlab6.5

Octave, matlab clone for numerical computing www.octave.org
Start Command: octave
Application directory: n/a - installed locally

Stella, a systems dynamics modeling package (available only under Windows)
NOTE: For additional documentation, or for links to programming tutorials/help, please take a look at our main documentation page

Special Purpose Complex Systems Programs

xlife, a very nice 2D cellular automata simulator, including Conway's Game of Life.

xising, a two dimensional Ising model simulator.
Start Command: /appl/xtoys/xising
Application directory: /appl/xtoys

xpotts, for the two dimensional Potts model.
Start Command: /appl/xtoys/xpotts
Application directory: /appl/xtoys

xautomalab, a totalistic cellular automaton simulator.
Start Command: /appl/xtoys/xautomalab
Application directory: /appl/xtoys

xsand, for the Bak, Tang, Wiesenfeld sandpile model.
Start Command: /appl/xtoys/xsand
Application directory: /appl/xtoys/

xfires, a simple forest fire automaton.
Start Command: /appl/xtoys/xfires
Application directory: /appl/xtoys/

schrodinger, a schrodinger equation simulator.

xwaves, shows three different wave equations.

Analysis and Graphing Apps

VisAD http://www.ssec.wisc.edu/~billh/visad.html, a Java library for creating graphs and analyzing numerical data
Application directory: /appl/java/visad2.0
VisAD Online Tutorial
The VisAD Java Component Library Developers Guide

Scientific Graphics Toolkit (SGT) http://www.epic.noaa.gov/java/sgt/index.html, a scientific graphics Java library
Application directory: /appl/java/sgt2.1

Graph3d, a very simple 3D surface plot generator.
Start Command: /common/scripts/graph3d.pl
Application Directory: /appl/java/CSCS/graph3d
To see the documentation simply type:

/common/scripts/graph3d.pl

with no arguments and it will print all of the documentation to the screen.
Click here to see a screenshot of Graph3d in action!

R, statistical clone of S-plus www.r-project.org
Start Command: R
Application directory: /appl/r2.1.0

Grace, graphing program plasma-gate.weizmann.ac.il/Grace (user guide @UofM)
Start Command: /common/scripts/xmgrace
Application directory: /appl/grace5.1.5

Java Related Apps

Sun's Java 2 JDK SE 5.0, Sun's JDK for Linux http://java.sun.com/j2se/1.5.0/index.jsp
Start Command: /appl/jdk1.5.0_04/bin/java
Application directory: /appl/jdk1.5.0_04

MASON, a fast discrete-event multiagent simulation library core in Java. Check out more information at http://cs.gmu.edu/~eclab/projects/mason/
MASON is locatd under: /appl/mason7

breve, a 3d simulation environment designed for the simulation of decentralized systems and artificial life. Check out the full documentation at http://www.spiderland.org/breve/index.php
breve is located under: /appl/breve1.7/

StarLogo - programmable modeling environment for exploring the workings of decentralized systems. See http://education.mit.edu/starlogo/ for more information. StarLogo is accessible under /appl/starlogo2 and can be run with the script /common/scripts/starlogo-unix

SimBuilder, a rapid application development environment for RePast simulations.
The online documentation can be found at http://repast.sourceforge.net/docs/index.html
Start Command: /common/scripts/simbuilder
Application Directory: /appl/SimBuilder-1.0
Documentation Directory: /appl/SimBuilder-1.0/docs

EJP, the Extensible Java Profiler, an open-source profiling tool for Java
http://ejp.sourceforge.net/
Application directory: /appl/ejp-r2_2b1
Documentation Directory: /appl/ejp-r2_2b1/doc

OptimizeIt Suite, a set of tools for profiling and debugging java programs.
http://www.borland.com/optimizeit/
The OptimizeIt suite is installed on the 'optimizeit' account on the CSCS linux machines. For access to the account talk to one of the CSCS Admins in the lab or e-mail cscs.admins@umich.edu.

JFreeChart, a java library for generating charts.
http://www.object-refinery.com/jfreechart/
JavaDoc: http://www.object-refinery.com/jfreechart/javadoc/index.html
Start Command (Demo): /common/scripts/jfreechart-demo
Application directory: /appl/jfreechart-0.9.6

Eclipse, a java interactive development environment (IDE). See http://www.eclipse.org for more information. Eclipse be run with the script /usr/bin/eclipse

Henrik Bengtsson's Java printf (beta version). See http://www.braju.com/beta/ for details and examples of use. hbbeta2-printf.jar is accessable under /appl/java/CSCS/hbbeta2-printf.jar

Jikes http://www.research.ibm.com/jikes/, A compiler that translates Java source files as defined in The Java Language Specification into the bytecoded instruction set and binary format defined in The Java Virtual Machine Specification.
Start Command: /common/scripts/jikes
Application directory: /appl/jikes1.16

Java colt library http://tilde-hoschek.home.cern.ch/~hoschek/colt/index.htm, A library containing useful data structures and algorithms for Java
Application directory: /appl/java/colt1.0.2

Ant http://jakarta.apache.org/ant/manual/index.html, A Java-based build tool.
Start Command: /common/scripts/ant
Application directory: /appl/ant1.6.0

Netbeans, IDE written in Java www.netbeans.org.
Start Command: /common/scripts/netbeans
Application directory: /appl/netbeans3.3

Evolutionary Computation applications

PerlGP, Provides the ability to do "strongly typed Genetic Programming in a high level language" Check out more information at http://perlgp.org/
PerlGP is located under: /appl/perlgp1.0.1

Special Purpose Linux Apps

Valgrind, a memory management debugging tool. See http://developer.kde.org/~sewardj/docs/index.html for full documentation. Valgrind can be run in a terminal window with the command: valgrind.

Mozilla, an open source web browser.
Start Command: mozilla or click on the web browser icon at the bottom of the screen (globe wrapped by a mouse.)

Evolution, a personal and workgroup management program that integrates integrates email, calendaring, meeting scheduling, contact management, and task lists. See http://www.novell.com/products/evolution/ for more information.
Start Command: evolution

Ch, a C/C++ interpreter for learning programming in C/C++, 2D/3D plotting, numerical computing and cross-platform shell programming. See http://www.softintegration.com/docs/ for more information.
Start command: /appl/ch3.0/bin/ch
Application directory: /appl/ch3.0

CLisp 2.30, Common Lisp is a high-level, all-purpose, object-oriented, dynamic, functional programming language. CLISP is a free Common Lisp implementation. To run the interpretor, type "clisp" into a terminal window. Clisp is installed in /appl/clisp2.30

rdesktop, a terminal services client that allows you to connect to open a session on our windows 2000 server.
http://www.rdesktop.org/
For information about connecting to the CSCS's Terminal Services go to http://www.cscs.umich.edu/lab/terminal-services.html
Start command: /common/scripts/rdesktop

Swiki, a web interface that allows visitors to edit the pages. http://minnow.cc.gatech.edu/swiki
CSCS is currently running a swiki server that can be viewed at http://mercato.physics.lsa.umich.edu:8000/
If you would like to host a CSCS related swiki, send an e-mail to cscs.admins@fiore.physics.lsa.umich.edu and we will set one up for you if it seems to be an appropriate use for CSCS resources.

The Gimp, image manipulation program similar to adobe photoshop www.gimp.org. (tutorial)
Start Command: gimp
Application directory: n/a - installed locally

Xemacs, text editor www.xemacs.org (tutorial1, tutorial2, tutorial3)
Start Command: xemacs
Application directory: n/a - installed locally

Source Navigator, Source code editor and project manager sources.redhat.com/sourcenav (tutorial, user guide)
Start Command: snavigator
Application directory: n/a - installed locally

DDD, graphical debugger http://www.gnu.org/software/ddd/ddd.html ( manual and tutorial )
Start Command: ddd
Application directory: n/a - installed locally

Adobe Acrobat, view for PDF files www.adobe.com
Start Command: acroread
Application directory: n/a - installed locally

Real Player, plays .ra and .ram files www.real.com
Start Command: realplay
Application directory: n/a - installed locally

OpenOffice, office productivity suite www.openoffice.org
Start Command: ooffice
Application directory: n/a - installed locally

Document Conversion/Viewing Apps

This group of tools is all available on the CSCS machines and is very useful if you need to convert between PDF, PostScript, HTML, or TeX files. Also included in this list are some X-Windows viewers for the different file types. Most of these document conversion programs are executed by typing:

(program name) (input file) (output file)

Where (program name) is one of the names below(ps2pdf, dvips, etc), (input file) is the file you want to convert, and (output file) is the file name that you want the converted file to be called.

ps2pdf - Convert PostScript to PDF using ghostscript

ps2pdf12 - Convert PostScript to PDF 1.2 (Acrobat 3-and-later compatible) using ghostscript

ps2pdf13 - Convert PostScript to PDF 1.3 (Acrobat 4-and-later compatible) using ghostscript

netscape - If you open up an HTML file in netscape and go to the file menu and click print and click "Print to File" you can convert an HTML document to a PostScript document.
- Also with netscape, you can save an HTML file into ascii text. All you need to do is go to the file menu, choose "Save as" and click save to save the file.

dvips - Convert a TeX DVI file to PostScript

dvipdf - Convert a TeX DVI file to PDF using ghostscript and dvips

pdf2ps - Convert PDF to PostScript using ghostscript

pdftotext - Convert PDF to plain text

a2ps - Format files for printing on a PostScript printer

xpdf - PDF viewer for X-Windows

xdvi - DVI viewer for X-Windows

ggv - Gnome Ghostview is a PostScript and PDF viewer for X-Windows

Windows Apps

Adobe Acrobat, view for PDF files www.adobe.com

Real Player, plays .ra and .ram files www.real.com

Stella, a systems dynamics modeling package

Microsoft Office

emacs

Windows Terminal Services, a windows service that enables a user to open a windows session remotely. For information about connecting to the CSCS's Terminal Services go to http://www.cscs.umich.edu/lab/terminal-services.html

NOTE: To access the application from Linux, go to Programs -> Applications -> CSCS.
To access Windows applications, please contact the CSCS lab staff in the lab, or via email to cscslab@umich.edu.

Updated September 1, 2005