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% add euler

athena% euler &

There is an euler Web page

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

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% add fityk

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

Title and description:

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

To run:

athena% add gnuplot

athena% gnuplot

athena% gnuplot file

(for internal commands, type gnuplot, followed by ? at the gnuplot> prompt; to run demos, copy demo directory to a location where you have write permission, cd to that location and type gnuplot all.dem; see 4.2 README.athena SUPPORT ISSUES -> TRAINING for information on how to access this in release 4.2)

There is also an FAQ, extended tutorial and gnuplot homepage; also 4.2 html and pdf documentation

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

Title and description:

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

To run:

athena% add grace

athena% xmgrace

There is a Grace homepage; local documentation starts here

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

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 local pdf documentation and a jmp page

Support for MIT statistical software packages is available from the Harvard-MIT Data Center (HMDC) Statistical Consulting service

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% add k3dsurf

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

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)

athena% maple.java & (for Java interface)

athena% maple.tty (for text interface)

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

NEW: there is an introductory Web-based interactive tutorial (MIT only)

There are release 12 Getting Started Guide, User Manual, Quick Reference, Introductory Programming Guide, Advanced Programming Guide

There are release 11 online Getting Started Guide, User Manual, Quick Reference; 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

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 [-ver 6.0.2] & (for Notebook/X interface; -ver switch for new 6.0.2 release)

athena% math [-ver 6.0.2] (for text interface)

There is an online information center, an online version of the Mathematica Book and Mathematica 6 demonstrations; also 6.0.2 new features

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

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 &

(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)

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)

There is also a portal to technical and scientific applications

See also: GDL, euler, GNU Scientific Library, 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% add maxima

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)

athena% maximaemacs (for Emacs interface; M-x maxima or M-x maxima-mode invoke maxima modes)

(typing quit(); at the maxima prompt will exit the application; in maxima-mode, C-c C-p starts maxima, C-c C-k stops it)

Local 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% add 5c

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. Now includes octave-forge add-ons

Versions: there is version skew (Sun version is 2.9.9, Linux is 2.9.17)

To run:

athena% add octave

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 local 2.9.9 introduction, library reference and quick reference

There is also local 2.9.17 FAQ, manual, reference card and README.athena with pointers to other information

There is also a portal to technical and scientific applications

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

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% add pari-gp

athena% gp (to run interactive calculator)

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% attach pari-gp_v2.3.1

athena% gcc -o file -I/mit/pari-gp_v2.3.1/include file.c -R,/mit/pari-gp_v2.3.1/lib -lm -L/mit/pari-gp_v2.3.1/lib -lgmp -lpari (to compile file.c and link against libpari.so)

There is local pdf documentation, local gp2c html 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)

Support for MIT statistical software packages such as R is available from the Harvard-MIT Data Center (HMDC) Statistical Consulting service

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% 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

Support for MIT statistical software packages such as sas is available from the Harvard-MIT Data Center (HMDC) Statistical Consulting service

See also: jmp, R, splus, stata

Important:

sas is moving from Sun/Solaris to Linux machines in Summer 2008

Title and description:

scilab
Description: scientific software package for numeric computation. Comparable to, but not an exact clone of matlab. Can support distributed computing through PVM interface and a set of PVM libraries installed in the locker. Also comes with an interface to Maple, and to external C and FORTRAN code

To run:

athena% add scilab

athena% scilab

There is a Scilab home page, links to documentation and a newsgroup. Also a Scilab for Matlab users document

See also the portal to technical and scientific applications

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

Note:

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

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% add singular

athena% Singular (for text interface)

athena% ESingular (for Emacs interface)

(typing exit; at the singular prompt will exit the application; typing help; will start online help)

There is local online documentation, a singular Web page

See also: Mathematica, PARI/GP, SAGE

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, 8.0 Release Notes

Support for MIT statistical software packages such as splus is available from the Harvard-MIT Data Center (HMDC) Statistical Consulting service

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 such as Netscape

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

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

Support for MIT statistical software packages such as stata is available from the Harvard-MIT Data Center (HMDC) Statistical Consulting service

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

athena% tec360 &

There are various pdf manuals and a local Web page

See also: gnuplot, Grace, K3DSurf, ParaView

Title and description:

Applix Spreadsheets
Description: general-purpose spreadsheet

To run:

athena% add applix

athena% applix & (select Applixware Spreadsheets icon from icon bar, or Spreadsheets from * menu)

See also: gnumeric, sc, Star Office Spreadsheet, table, xess

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% add gnumeric

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: Applix Spreadsheets, sc, Star Office Spreadsheet, table, xess

Title and description:

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

To run:

athena% ooffice &

There is 2.x documentation: Getting Started guide, User Guide and entry point to other manuals; also the openoffice.org support page

See also: Applix Spreadsheets, sc, Star Office Spreadsheet, table, xess

Note:

Open Office is derived from Star Office and corresponding releases of both are very similar

Title and description:

sc
Description: spreadsheet calculator based on rectangular tables

To run:

athena% add sipb

athena% sc

See also: Applix Spreadsheets, gnumeric, Star Office Spreadsheet, table, xess

Title and description:

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

To run:

athena% add soffice

athena% soffice &

There is 8.0 "what's new", 8.0 "getting started", Sun's Star Office site, the Star Office User Portal

See also: Applix Spreadsheets, gnumeric, Open Office Spreadsheet, sc, table, xess

Title and description:

table
Description: Andrew utility allowing creation, printing and spreadsheet manipulation of rectangular tables of data

To run:

athena% add andrew

athena% table file.table

See also: ahelp, Applix Spreadsheets, ez, gnumeric, Star 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: Applix Spreadsheets, gnumeric, sc, Star Office Spreadsheet, table