MIT Athena Computing Environment: What Runs Where: Numerical/Math Software Detail
Keywords: athena, what runs where, athena help, numerical, math, software

What Runs Where
| Major Applications |
### Full Table:
| Help/Information Screen Accessories Communication Text Software Graphics Software Audio Software Numerical/Math Soft Languages/Debuggers Programming Libraries Simulation & Modeling Courseware Miscellaneous Utilities |
Help
| What's new? Tips for Using Athena Software Academic Computing locker configuration Web browser Java plugin issues Note on changing window managers |
| # What Runs Where on Athena: Numerical/Math Software
| Analysis/Plotting 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, J, 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 Versions: there is version skew (Athena 9.4 version is 7.0.1, Athena 10 version is 8.0.1) To run: athena% add sasjmp athena% jmp & There is local 7.0 pdf documentation, 8.0 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; 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 & (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% 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, and newsgroup 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, IMSL Numerical Libraries, 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). There is also an R search engine 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 Versions: there is version skew (Sun is 4.0, Linux is 5.0.3) 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 and local pdf manual (5.0 scilab release) 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
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, 8.1 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 360-09 pdf manuals, a local Web page and vendor site See also: gnuplot, Grace, K3DSurf, 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
| Spreadsheets |
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 Note: Applixware will no longer be available on Athena as of 8/1/09. More information is here
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% add -f ooffice (for new 3.1 release on Athena 10; not necessary on Athena 9.4) athena% ooffice [-ver 3.1] & (-ver switch for new 3.1 release) There is 2.x documentation: Getting Started guide, User Guide and entry point to other manuals; also the openoffice.org support page and a 3.x User Guide 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

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