What Runs Where on Athena: Numerical/Math Software

Title and Description:

dc
Description: desk calculator, based on arbitrary precision math package

TO RUN:

athena% dc commandfile

See also: gnome-calculator, nickle, xcalc

Title and Description:

euler
Description: interpreted, interactive programming language for real and complex numerical analysis. Can handle matrices in ways similar to matlab and octave, and comes with 2d and 3d plotting capabilities. Supplied with extensive libraries of numeric, statistical and graphics routines. Supports notebooks, similar to but less sophisticated than Mathematica notebooks

TO RUN:

athena% euler &

There is an euler Web page

See also: gnuplot, J, K3DSurf, Mathematica, matlab, nickle, octave, PARI/GP, SAGE, scilab, yorick

Note:

this application is no longer installed. You can install it from the euler Ubuntu package using aptitude or synaptic

Title and Description:

fityk
Description: peak fitting application for experimental data. It can do nonlinear fits with analytic functions (Gaussian, Lorentzian, Voigt, Pearson VII, bifurcated Gaussian, EMG, Doniach-Sunjic and more). It also supports user-defined functions, a graphical user interface and a variety of optimization methods (standard Marquardt least-square, Genetic Algorithms, Nelder-Mead simplex), equality constraints, correcting for data baseline shift, dataset handling and automation of common tasks via scripts

TO RUN:

athena% fityk & (for GUI interface)

athena% cfityk (for text interface)

There is a fityk Web page; documentation is online in the GUI version

See also: g3data

Note:

this application is no longer installed. You can install it from the fityk Ubuntu package using aptitude or synaptic

Title and Description:

gnuplot
Description: command-driven interactive function plotting program with scriptable command language

TO RUN:

athena% gnuplot

athena% gnuplot file

(for internal commands, type gnuplot, followed by ? at the gnuplot> prompt; to run demos, copy /usr/share/doc/gnuplot-doc/examples directory to a location where you have write permission, cd to that location and type gnuplot any.dem

There is also an FAQ, extended tutorial and gnuplot homepage

See also: euler, GLE, GNU plot utilities, Grace, K3DSurf, matplotlib, ParaView, SAGE, tecplot, TeXmacs

Title and Description:

Grace
Description: GUI 2D mathematical plotting tool with internal plot description language

TO RUN:

athena% xmgrace

There is a Grace homepage and User's Guide

See also: gnuplot, GNU plot utilities, tecplot , tgif

Note:

this application is no longer installed. You can install it from the grace or grace6 Ubuntu packages using aptitude or synaptic

Title and Description:

jmp
Description: graphics-based data exploration and discovery application that incorporates many statistical tests and analyses

TO RUN:

athena% add sasjmp

athena% jmp &

There is 8.0 documentation and a jmp page; also 8.0.2 release notes

See also: R, sas, splus, stata

Title and Description:

K3DSurf
Description: application for visualizing and manipulating mathematical surfaces described by equations in 3, 4, 5 and 6 dimensions. Supports parametric equations and isosurfaces

TO RUN:

athena% k3dsurf &

There is a K3DSurf Web page

See also: ac3d, euler, geomview, gnuplot, maple, Mathematica, matlab, Open Inventor, POV-Ray, tecplot, Visualization Toolkit, yorick

Note:

There is very little documentation and the design is somewhat idiosyncratic, but the application is fairly intuitive and the sample.k3ds files at the top level of the k3dsurf_v0.6.2 locker illustrate the syntax for save files; the forums at the author site will also help you get started

Note:

this application is no longer installed. You can install it from the k3dsurf Ubuntu package using aptitude or synaptic

Title and Description:

maple, mint
Description: multi-featured symbolic math program. mint is a debugger for Maple script files similar to lint for C programs

TO RUN:

athena% add maple

athena% maple & (for traditional GUI X interface; not available on 64 bit Linux)

athena% maple.java & (for Java interface)

athena% maple.tty (for text interface)

athena% mint scriptfile (to debug a a maple script)

There is an introductory Web-based interactive tutorial (MIT only)

There are release 13 User Manual, Quick Reference, Introductory Programming Guide, Advanced Programming Guide; also a new support site called Maple Primes. You need to register before you can access it; instructions are here

There is online introductory documentation, a local Web page and What's New. For application examples, see the Maple Application Center. See also the Maple Advisor Database and newsgroup

Maple is available to members of the MIT community under our site license. Information is here

See also: K3DSurf, Mathematica, maxima, SAGE, TeXmacs

Title and Description:

Mathematica
Description: multi-featured symbolic math program

Licenses: we have 1000 floating licenses

TO RUN:

athena% add math

athena% mathematica & (for Notebook/X interface)

athena% math (for text interface)

There is an online information center, an online version of the Mathematica Book (old) and Mathematica demonstrations; also 7.0 new features and screencast, and a newsgroup

The IMTEK Mathematica Supplement add-on is a collection of extra packages that offers enhanced functionality in a variety of domain areas, notably in partial differential equations representing physical systems and finite-element analysis. Examples in the supplement use the mesh generators EasyMesh, tetgen and triangle which have been installed on Athena. This is currently accessible only within Mathematica 5.2

To access the IMTEK Mathematica Supplement (5.2 only) , launch the help browser: Help -> Help Browser, and, from within the browser, search for IMTEK (you may need to run Help -> Rebuild Help Index first). There is extensive documentation and many examples

Mathematica is available to members of the MIT community under our site license. Information is here

See also: CalculiX, EasyMesh, Elmer, euler, FreeFem++, K3DSurf, maple, maxima, OpenFOAM, PARI/GP, SAGE, singular, TeXmacs, tetgen, triangle

Title and Description:

matlab, simulink
Description: interactive "matrix lab" for data analysis tasks involving matrices, graphics and numerical computation. Includes specialized-subject "toolbox" extensions for many topics, including Control, Robust Control, Signal Processing and others

simulink is a modular package for analyzing dynamic digital signal processing systems

TO RUN:

athena% add matlab

athena% matlab [-ver 7.9] & (-ver switch for new 7.9 release)

(typing demo at the >> prompt will run through examples)

athena% simulink &

(typing helpdesk at the >> prompt will launch the help system)

There is an introductory Web-based interactive tutorial (MIT only); release notes; what's new

There is a Mathematical Tools at MIT Web page, latest version documentation at the MathWorks, 6.5.1/R13SP1 local online docs (MIT only) (to use search feature, access through matlabdoc), documentation for using lpsolve add-on (Mixed Integer Linear Programming Solver), documentation for using snopt add-on (Constrained Linear or Nonlinear Optimization Solver) and newsgroup

There is also a portal to technical and scientific applications and FAQ

See also: GDL, euler, GNU Scientific Library, IMSL Numerical Libraries, IT++, K3DSurf, lpsolve, Meep, Numerical Recipes, NumPy, octave, SAGE, scilab, snopt, TeXmacs

Note:

Matlab is now available for installation on student machines. Information is here (MIT certificate and student status required)

Matlab on non-Athena Linux machines may be run over OpenAFS only by students (undergraduate and graduate). All other users must purchase licenses from VSLS Software Distribution

Title and Description:

maxima
Description: Maxima is a version of the MIT-developed MACSYMA symbolic algebra system, modified to run under SBCL. Written in LISP, it allows differentiation, integration, solution of linear or polynomial equations, factoring of polynomials, expansion of functions in Laurent or Taylor series, computation of Poisson series, matrix and tensor manipulations, and two- and three-dimensional graphics

TO RUN:

athena% maxima (for text interface)

athena% rmaxima (for text interface, command-line editing enabled)

athena% xmaxima (for GUI interface, incorporating live examples and online help)

(typing quit(); at the maxima prompt will exit the applicationt)

Documentation is here; there is a maxima Web site

See also: maple, Mathematica, maxima, PARI/GP, SAGE, TeXmacs

Note:

maxima can be run from within TeXmacs to produce nicely rendered formulas- see the tutorial; maxima is different from the commercial and now defunct macsyma

Title and Description:

nickle
Description: desk calculator language with powerful programming and scripting capabilities. Nickle supports a variety of datatypes, especially arbitrary precision numbers. The input language vaguely resembles C

TO RUN:

athena% nickle

There is an author Web page

See also: dc, euler, gnome-calculator, xcalc, yorick

Title and Description:

octave
Description: high-level language intended primarily for numerical computations; can solve linear and non-linear problems in a variety of application areas; easily extensible using its internal programming language, or by running dynamically loaded modules in C++ and C. Mostly compatible with matlab

TO RUN:

athena% octave (to run octave)

athena% mkoctfile file.cc (to compile a C++ source file in octave syntax to file.oct binary, which can be run in octave)

There is an Octave home page, also an online manual and newsgroup; local documentation is at file:///usr/share/doc/octave3.0-htmldoc/interpreter/index.html and file:///usr/share/doc/octave3.0-htmldoc/liboctave/index.html

There is also a portal to technical and scientific applications

See also: GDL, euler, GNU Scientific Library, IMSL Numerical Libraries, IT++, matlab, Numerical Recipes, scilab, TeXmacs

Note:

octave comes with a large number of optional add-ons that are mostly part of the octave-forge project. There are too many for it to be practical to install them all; users should search for the desired ones in the Ubuntu Packages Search page (names start with octave-) and install the desired ones themselves

Title and Description:

ParaView
Description: data visualization and modeling application that can run in a variety of modes. Single-machine standalone mode is the only one currently supported on Athena. Uses Tcl/Tk as scripting language, is extensible and can read input data in a variety of formats. The underlying data processing and rendering engine is based on the Visualization Toolkit

TO RUN:

athena% add paraview

athena% paraview

There is a ParaView home page and links to documentation and tutorials

See also: ac3d, blender, geomview, gnuplot, Maya, OpenDX, Open Inventor, tecplot, Visualization Toolkit

Title and Description:

PARI/GP
Description: Computer Algebra system designed for fast computation in number theory (factorizations, algebraic number theory, elliptic curves...). It also contains a large variety of utility functions for computing with matrices, polynomials, power series, algebraic functions etc.. and standard numeric functions. It supports graphics output and can be linked as a C library (libpari.so). The interactive shell (gp) supports an embedded scripting language (GP)

gp2c is an add-on for translating GP routines into C code that can be compiled and used within the PARI system or the gp calculator

TO RUN:

athena% gp (to run interactive calculator)

athena% gphelp (to get manual)

athena% gp2c-run options file.gp (to compile/run code in file.gp)

athena% gp2c file.gp > file.gp.c (to generate commented C code from file.gp)

athena% gcc -O2 -o file -lm -lgmp -lpari (to compile file.c and link against libpari.so)

There is documentation and a PARI/GP Web page

See also: euler, Mathematica, maxima, SAGE, singular, yorick

Title and Description:

R
Description: system for statistical computation and graphics, with an internal programming language. It bears a passing resemblance to the S language developed at AT&T Bell Laboratories, and to the subsequent commercial splus application

TO RUN:

athena% add r

athena% R

(typing help.start() will start the html help system in your Web browser)

There is an Introduction, Language Definition, Data Import/Export Guide, Reference Manual and FAQ; also a guide to the Emacs modes (ESS). There is also an R search engine

See also: jmp, sas, splus, stata

Note:

R can be run from within Emacs; see the README.athena for information on how to set this up and use it

Title and Description:

SAGE
Description: pure and applied mathematics system based on Python and incorporating notebooks and interfaces to many other non-commercial and commercial mathematics applications

TO RUN:

athena% add sage

athena% /mit/sage/arch/i386_linux3/bin/sage

(typing notebook() at the sage: prompt will open a notebook within your Web browser; the latter has links to online documentation and a tutorial)

There is a SAGE home page

See also: euler, gnuplot, maple, Mathematica, matlab, maxima, PARI/GP, singular, yorick

Title and Description:

sas
Description: comprehensive statistics package, incorporating many capabilities and features for data visualization, display and extraction

TO RUN:

athena% add sas

Licenses: we have 50 licenses

athena% sas &

There is a local Web page, local SAS tips, SAS 9.2 documentation and resources for faculty and students

See also: jmp, R, splus, stata

Title and Description:

scilab
Description: scientific software package for numeric computation. Comparable to, but not an exact clone of matlab

TO RUN:

athena% scilab

There is a Scilab home page, links to documentation and a newsgroup

See also the portal to technical and scientific applications

See also: euler, GNU Scientific Library, IMSL Numerical Libraries, IT++, matlab, Numerical Recipes, octave, TeXmacs

Note:

scilab can be run from within TeXmacs to produce nicely rendered formulas

this application is no longer installed. You can install it from the scilab Ubuntu package using aptitude or synaptic

Title and Description:

singular
Description: Computer Algebra system for polynomial computations with emphasis on the special needs of commutative algebra, algebraic geometry and singularity theory

TO RUN:

athena% Singular (for text interface)

athena% ESingular (for Emacs interface)

(typing exit; at the singular prompt will exit the application)

There is local online documentation, a singular Web page

See also: Mathematica, PARI/GP, SAGE

Note:

the built-in documentation browser appears to be broken

Title and Description:

splus
Description: statistical data analysis and plotting package. Incorporates an internal programming language, with many built-in functions

TO RUN:

athena% add splus

athena% splus

athena% splus -g & (for Java-based GUI)

athena% splus -w & (for Eclipse-based Workbench)

athena% splus -bigdata (to run with Bigdata library)

athena% splus -j (for text interface with Java enabled for Java calls, graphics and help system)

(typing help() at the > prompt will give a help summary; typing help.start() will start a Java-based help system)

There is a local Web page; also: Getting Started, Programming Guide, Statistics Manual (part 1), Statistics Manual (part 2), User's Guide, 8.1 Release Notes

See also: jmp, R, sas, stata

Note:

the Java GUI uses a large amount of memory- it may fail to launch properly or at all if you are running on a machine with less than 256 meg of memory, or if you have any other memory-intensive applications open

Title and Description:

stata
Description: statistical analysis package incorporating many tests, simpler to use than sas or splus

Licenses: we have 50 licenses

TO RUN:

athena% add stata

athena% xstata (GUI interface)

athena% stata (text interface)

athena% xstata-se (GUI interface, enhanced version)

athena% stata-se (text interface, enhanced version)

athena% stata -b do mybatchfile (to run batch file mybatchfile.do in batch mode)

There is a great deal of online help. Type help at the Stata . prompt, or pull down Help in xstata to get started; see also the Stata resources page. Selecting Help -> What's New? in xstata will describe new features in latest release

Online pdf manuals are now locally accessible

stata is now available to members of the MIT community for institute or personal purchase at discounted pricing. Information is here

See also: jmp, R, sas, splus

Note:

copies of the Stata Technical Bulletin, with software on diskette, are available. This publication provides a variety of customized statistical procedures in various application areas. Contact <3partysw@mit.edu> for details

Title and Description:

tecplot
Description: Advanced data plotting package that can do many types of 2d and 3d plots

Licenses: we have 25 floating licenses

TO RUN:

athena% add tecplot [-ver 360-09r2] (-ver switch for new 360-2009 R2 release)

athena% tec360 &

There are various 360-09 pdf manuals, a local Web page and vendor site and 360-2009 R2 release notes

See also: gnuplot, Grace, K3DSurf, matplotlib, ParaView

Note:

if you are running Tecplot on a virtual machine or on Ubuntu Jaunty, you may need to launch it with the -mesa or -sgiopengl flag to get rendering within the Tecplot window to work

Title and Description:

gnumeric
Description: multi-function spreadsheet, with the ability to import and export files in native formats of other leading spreadsheets

TO RUN:

athena% gnumeric &

athena% ssconvert options (to use spreadsheet format conversion utility --help switch gives usage info)

There is a developer page and current documentation

See also: sc, Open Office Spreadsheet, xess

Title and Description:

Open Office Spreadsheet
Description: spreadsheet component of Open Office office suite- select File -> New -> Spreadsheet

TO RUN:

athena% add -f ooffice (to access new 3.1.1 release; not necessary to access default version)

athena% ooffice [-ver 3.1.1] & (-ver switch for new 3.1.1 release)

For documentation look here

See also: sc, xess

Note:

In the future, the only version available will be the default one installed in the debathena release

Title and Description:

sc
Description: spreadsheet calculator based on rectangular tables

TO RUN:

athena% sc

See also: gnumeric, Open Office Spreadsheet, xess

Title and Description:

xess
Description: scientific spreadsheet for UNIX. Includes many internal functions and a C based API that allows full access to the spreadsheet capabilities

TO RUN:

athena% add xess

athena% xess &

There is online documentation, a local Web page, 5.0 HTML online help, 6.0 HTML online help

xess is available for installation on Institute-owned computers on a variety of UNIX platforms. Contact (3partysw@mit.edu), x3-8613 for information

See also: gnumeric, sc, Open Office Spreadsheet