What Runs Where on Athena: Numerical/Math Software

On this page:
Analysis/Plotting Software
Spreadsheets

Analysis/Plotting Software

dc

Description: desk calculator, based on arbitrary precision math package

TO RUN:

athena% dc commandfile

See also: gnome-calculator, nickle, xcalc

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

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

Fiji

Description: image processing package based on Java and Java 3d which incorporates many analysis tool packaged as plugins and used primarily in the Life Sciences. Fiji is a repackaging of the ImageJ image analysis tool with many plugins preinstalled

TO RUN:

athena% add imj-fiji

athena% fiji &

There are Fiji and ImageJ web pages; documentation is online and also available at the Fiji and ImageJ sites

See also: FWTools

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

Gephi

Description: Gephi is an interactive visualization and exploration platform for networks and complex systems, dynamic and hierarchical graphs. It is used for:

Exploratory Data Analysis
Link Analysis
Social Network Analysis
Biological Network analysis
Poster creation

TO RUN:

athena% add gephi

athena% gephi &

There is a Gephi Web page and documentation

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

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

Julia

Description: high level dynamic programming language for technical computing developed at MIT by Professor Alan Edelman, Jeff Bezanson, Stefan Karpinski and Viral Shah. Julia uses syntax that is familiar to users of other technical computing environments. It provides a compiler, distributed parallel execution (though this is not currently supported on Athena), numerical accuracy and a mathematical function library. The library, mostly written in Julia itself, also integrates mature C and Fortran libraries for linear algebra, random number generation, FFTs and string processing.

TO RUN:

athena% add julia

athena% julia (to run interactive interpreter)

athena% julia file.jl (to run julia script file.jl)

There is a local README, Julia page, online documentation and development site. After adding the locker, typing man julialanguage will give extensive documentation

There is also a local pdf manual

Note: Julia is currently under rapid development and the julia Athena locker is updated only twice annually, before the start of each academic term. If you need to run the latest update the best way to proceed is to clone the latest sources and build it yourself:

git clone git://github.com/JuliaLang/julia.git
cd julia
make

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

Note: There is very little documentation and the design is somewhat idiosyncratic, but the application is fairly intuitive; the forums at the author site will also help you get started. This application is no longer installed. You can install it from the k3dsurf Ubuntu package using aptitude or synaptic

maple, mint

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

TO RUN:

From Ubuntu Dash: type maple in Search box

From command line:

athena% add maple

athena% maple & (for traditional GUI; 32 bit only, not available on 64 bit Linux)

athena% maple.java & (for Java GUI)

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 17 User Manual, Programming Guide; also a support site called Maple Primes. You need to register before you can access it; instructions are here

There is 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, matlab, maxima, Reduce, SAGE, TeXmacs

Mathematica

Description: multi-featured symbolic math program

Licenses: we have 1000 floating licenses

TO RUN:

From Ubuntu Dash: type mathematica in Search box

From command line:

athena% add math

athena% mathematica & (for Notebook/X interface)

athena% math (for text interface)

You can also create executable Mathematica scripts using MathematicaScript: create a file script.m contaning Mathematica commands, with first line:

#!/afs/athena/software/math/current/bin/MathematicaScript -script

and make it executable with:

athena% chmod +x script.m (this will use the "current" Mathematica version defined by the current link in the math locker)

There is an online information center, and Mathematica demonstrations; also 9.0 new features, a newsgroup and a revision history

Learning resources:

Mathematica Tutorial Collection

Mathematica Learning Center

Wolfram Education Group (for $ items, mentioning MIT site license qualifies MIT users for 30% discount)

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.

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:

From Ubuntu Dash: type matlab in Search box

From command line:

athena% add matlab

athena% matlab & (for terminal window launch)

athena% matlab -desktop & (for desktop launch)

athena% matlab -tty (for command-line launch)

(typing demo at the >> prompt will run throughexamples)

athena% simulink &

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

To access the Maple Symbolic Toolbox instead of the default Symbolic Toolbox, type one of the following lines in a terminal window and launch matlab from the command prompt (documentation is available from within the help browser):

athena% setenv MATLAB_SYMBOLIC maple (C shell users)

athena% export MATLAB_SYMBOLIC=maple (bash shell users)

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

There is 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

Note: Matlab is 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 IS&T Software Distribution (enter MATLAB in the Title field).

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

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

Documentation is here; there is a maxima Website

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

Note: maxima can be launched from within TeXmacs to author documents containing nicely rendered formulas- see the tutorial; maxima is different from the commercial and now defunct macsyma

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

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/octave3.2-htmldoc/interpreter/index.html and file:///usr/share/doc/octave3.2-htmldoc/liboctave/index.html

There is also a portal to technical and scientific applications

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

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% paraview

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

Note: This application is no longer installed. You can install it from the paraview Ubuntu package using aptitude or synaptic

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

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. RStudio is a GUI for R

TO RUN:

athena% add r

athena% rstudio (GUI graphical interface)

athena% R (command-line interface)

(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. We have added bioconductor to our R installation. RStudio documentation is here

See also: Biopython, BLAST, clustalw, emboss, hmmer, 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; it can also be invoked from Mathematica; look up RLink in the Mathematica help system for details

Reduce

Description: symbolic algebra system with many add-on packages

TO RUN:

athena% add reduce

athena% reduce (for graphical interface)

athena% reduce -w (for text interface)

(typing bye; at the Reduce prompt will exit the application)

A local manual and primer are available; there are development and Web sites with additional documentation

See also: maple, Mathematica, Matlab, maxima

Note: Open Source Reduce is in early development and is likely to contain bugs. In particular, printing is known to not work. Please see the README.athena file for links to support resources and how to report bugs. Reduce uses gnuplot for plotting

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, Julia, maple, Mathematica, matlab, maxima, OpenModelica, PARI/GP, singular, yorick

Note: If you get an error message like localhost:8000 uses an invalid security certificate perform the following steps:

Start SAGE and type notebook() as described above
In firefox, choose Edit -> Preferences
Select the Advanced settings screen (it has a gear icon)
Select the Encryption tab
Choose View Certificates
Click Add Exception...
In the Location box, type https://localhost:8000
Click Get Certificate
ClickConfirm Security Exception
ClickOK
ClickClose

You only need to do this once, not every time you launch SAGE

Note: you may need to install the libssl0.9.8 Ubuntu package using aptitude or synaptic to run this application

sas

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

Licenses: we have 50 licenses

TO RUN:

From Ubuntu Dash: type sas in Search box

From command line:

athena% add sas

athena% sas &

There is free online training for MIT users, a local Web page, local SAS tips, SAS documentation and resources for faculty and students

See also: R, splus, stata

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

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

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 a singular Web page

See also: Mathematica, PARI/GP, SAGE

Note: ESingular is currently broken in the debathena-precise release (singular.el file is missing)

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, 32-bit only)

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, 8.2 Release Notes

See also: 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

stata

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

Licenses: we have 50 licenses

TO RUN:

From Ubuntu Dash: type stata in Search box

From command line:

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, as are recent Stata Journal issues

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

See also: 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

tecplot

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

Licenses: we have 25 floating licenses

TO RUN:

From Ubuntu Dash: type tecplot in Search box

From command line:

athena% add tecplot

athena% tecplot &

There are various 360-13 pdf manuals, a local Web page and vendor site and 360-2013 R1 release notes

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

Note: If you are running Tecplot on a virtual machine or displaying it remotely, you may need to launch it with the -mesa flag to get rendering within the Tecplot window to work

Spreadsheets

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, LibreOffice Spreadsheet, xess

LibreOffice Spreadsheet

Description: spreadsheet component of LibreOffice office suite

TO RUN:

Click on LibreOffice Calc icon on Gnome applet bar

From command line:

athena% libreoffice & (select File -> New -> Spreadsheet)

For documentation look here

See also: gnumeric, sc, xess

sc

Description: spreadsheet calculator based on rectangular tables

TO RUN:

athena% sc

See also: gnumeric, LibreOffice Spreadsheet, xess

xess

Note: (old; not recommended for new work)

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

TO RUN:

From Ubuntu Dash: type xess in Search box

From command line:

athena% add xess

athena% xess &

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

See also: gnumeric, LibreOffice Spreadsheet, sc

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What Runs Where on Athena: Numerical/Math Software

You are here

Analysis/Plotting Software

dc

euler

Fiji

fityk

Gephi

gnuplot

Grace

Julia

K3DSurf

maple, mint

Mathematica

matlab, simulink

maxima

nickle

octave

ParaView

PARI/GP

R

Reduce

SAGE

sas

scilab

singular

splus

stata

tecplot

Spreadsheets

gnumeric

LibreOffice Spreadsheet

sc

xess