What Runs Where on Athena: Programming Libraries

Title and Description:

OpenDX
Description: 3d data visualization and exploration system. Supports generation of standalone binaries and Java applets that can be run from a Web server

TO RUN:

athena% dx &

Online documentation starts at file:///usr/share/doc/dx/html/index.html

See also: ac3d, blender, geomview, ParaView, Open Inventor, Visualization Toolkit

Title and Description:

Visualization Toolkit
Description: graphics library for 3d image visualization - can generate stand-alone binaries or interface with Tcl/Tk, Java and Python

TO RUN:

Please see documentation at file:///usr/share/doc/vtk-doc/README.html, file:///usr/share/doc/vtk-doc/html/index.html and file:///usr/share/doc/vtk-examples/README.examples

To run with Tcl:

athena% vtk myfile.tcl (Tcl demos are in various Tcl example directories like /usr/share/vtk/Modelling/Tcl)

To run with Python:

athena% vtkpython myfile.py (Python demos are in various Python example directories like /usr/share/vtk/Modelling/Python)

To run C++ applications, see README.examples above; see documentation for use with Java

See book "The Visualization Toolkit", 3d Ed. (Kitware, Inc.), and other documentation starting from here. Author Web site is here

See also: ac3d, blender, K3DSurf, geomview, Maya, OpenDX, Qt, ParaView, Open Inventor, Tcl/Tk

Title and Description:

GNU Scientific Library
Description: collection of routines for numerical computing, meant to present a modern API for C programmers while allowing wrappers to be written for very high level languages (C source code available)

TO RUN:

To link against it:

athena% gcc -O2 -o file `gsl-config --libs --cflags` file.c

and add include lines such as the following in your program:

#include <gsl/gsl_routine.h> (where routine identifies the name of the routine being used- see documentation for details)

documentation is at file:///usr/share/doc/gsl-ref-html/index.html; see also the GSL home page

For more background see the Numerical Analysis FAQ

There is also a portal to technical and scientific applications

See also: boost, IMSL Numerical Libraries, IT++, LAPACK, matlab, Netlib, Numerical Recipes, NumPy, octave, scilab

Title and Description:

IMSL Numerical Libraries
Description: collection of numeric and statistical routines for scientific computation in various languages. The versions currently on Athena are FORTRAN 6.0.0 (Linux), C 7.0.0 (Sun, Linux) and Java 5.0.1 (Sun, Linux). However, for FORTRAN the Intel ifort compiler, version 10 or later, is required. This compiler is not available on Athena (for licensing reasons), and users will need to provide their own locally installed copy

TO RUN:

athena% attach imsl

FORTRAN version (requires user-supplied Intel ifort compiler):

athena% source /mit/imsl/fnlsetup.csh (C shell)

athena% . /mit/imsl/fnlsetup.sh (Bourne/bash shell)

To link against it:

athena% $FC $F90FLAGS -o file file.f90 $LINK_FNL (dynamic link)

athena% $FC $F90FLAGS -o file file.f90 $LINK_FNL_STATIC (static link)

C version (uses gcc):

athena% source /mit/imsl/cnlsetup.csh (C shell)

athena% . /mit/imsl/cnlsetup.sh (Bourne/bash shell)

To link against it:

athena% $CC $CFLAGS -o file file.c $LINK_CNL (dynamic link)

athena% $CC $CFLAGS -o file file.c $LINK_CNL_STATIC (static link)

Java version (uses Java in /afs/athena/software/java/current/distrib/home):

athena% source /mit/imsl/jmslsetup.csh (C shell)

athena% . /mit/imsl/jmslsetup.sh (Bourne/bash shell)

athena% javac file.java (compile to bytecode)

athena% java $LIC file (run)

Local FORTRAN documentation: math, special functions, statistics

Local C documentation: entry point

Local Java documentation: entry point, quickstart

There is also a local README.athena, a Vendor documentation site, an IMSL home page

For more background see the Numerical Analysis FAQ

There is also a portal to technical and scientific applications

See also: boost, GNU Scientific Library, IT++, LAPACK, matlab, Netlib, Numerical Recipes, NumPy, octave, scilab

Note:

Contains a timeout key that expires on 1/6/12- this affects both the ability to create new binaries and the ability to run existing ones. We don't have renewal information at this time

Title and Description:

IT++
Description: C++ library of mathematical, signal processing, speech processing and communications classes and functions. The kernel of the IT++ library consists of templated vector and matrix classes, and many functions for vectors and matrices; this makes the library functionality similar to that of matlab

TO RUN:

To link against it:

athena% g++ -O2 `itpp-config --cflags` -o file file.cpp `itpp-config --libs`

and add include lines such as the following in your program:

#include <itpp/file.h> (where file identifies the include file required by the function(s) you are using- see documentation for details)

See also the IT++ home page and the IT++ documentation page

See also the Numerical Analysis FAQ and the portal to technical and scientific applications

See also: boost, GNU Scientific Library, IMSL Numerical Libraries, LAPACK, matlab, Netlib, Numerical Recipes, NumPy, octave, scilab

Title and Description:

LAPACK
Description: library of FORTRAN 77 and C subroutines for solving many problems in numerical linear algebra and matrix applications

TO RUN:

To link against it:

FORTRAN version:

athena% gfortran -O2 -o file file.f -llapack

C version:

athena% gcc -O2 -o file file.c -llapack -lcblas

and add the following include line to your program:

#include <f2c.h>

Some code may also require:

#include <clapack.h>

See the User's Guide: file:///usr/share/doc/liblapack-doc/lug/index.html, release notes: file:///usr/share/doc/liblapack-doc/release_notes.html and FAQ: file:///usr/share/doc/liblapack-doc/faq.html

For more background see the Numerical Analysis FAQ

There is also a portal to technical and scientific applications

See also: GNU Scientific Library, IMSL Numerical Libraries, IT++, Numerical Recipes, Netlib

Title and Description:

Netlib
Description: Netlib is an archive containing code for Lapack, Blas and other related public-domain numerical computation routines. It is currently accessed by forms on the Web

TO RUN:

Go to the Netlib Web page

For more general information see the Guide to Available Mathematical Software and the IML++ Iterative Methods Library

For more background see the Numerical Analysis FAQ

There is also a portal to technical and scientific applications

See also: LAPACK, GNU Scientific Library, IMSL Numerical Libraries, IT++

Title and Description:

Numerical Recipes (old: second edition; the newer third edition is not available on Athena)
Description: library of many numerical analysis routines (FORTRAN and C source available)

TO RUN:

athena% add recipes

See books "Numerical Recipes in C" or "Numerical Recipes in FORTRAN" that go with the software available online

To link against it:

C code:

add the following include lines to you program:

#include "nr.h"

#include "nrutil.h"

athena% gcc -O2 -I/mit/recipes/include -o file file.c -L/mit/recipes/lib -lrecipes_c -lm

FORTRAN code:

athena% gfortran -O2 -o file file.f -L/mit/recipes/lib -lrecipes_f

For more general information see the Guide to Available Mathematical Software and the IML++ Iterative Methods Library

For more background see the Numerical Analysis FAQ Numerical Analysis FAQ

There is also a portal to technical and scientific applications

See also: GNU Scientific Library, IT++, IMSL Numerical Libraries, LAPACK, matlab, Netlib, octave, scilab

Note:

Numerical Recipes on Athena are now at release level 2.1.0

Title and Description:

boost
Description: extensive set of general-purpose and specialized C++ programming libraries that significantly extend the functionality of the C++ Standard Library

TO RUN:

To compile and link C++ code against the boost libraries, include the appropriate headers in your code; possible formats include:

#include <boost/test/test_tools.hpp>

#include <vector>

To link against it:

athena% g++ -O2 -o file file.cpp (simplest case, for code that doesn't require linkage against boost libraries)

athena% g++ -O2 -o file file.cpp -lboostlibrary (where boostlibrary is one (or more) required libraries, like boost_regex)

There is a boost Web site with documentation; local documentation is at file:///usr/share/doc/libboost1.37-doc/HTML/index.html

boost is very complex and you will most likely need to consult the documentation to use it effectively; this may help you get started

See also: g++, GNU Scientific Library, IMSL Numerical Libraries, IT++, NumPy, Qt

Note:

Selecting the appropriate name for one (or more) libraries to link against can be complicated, and you must consult the documentation to understand how this works

Title and Description:

FLTK
Description: cross-platform C++ GUI toolkit. FLTK provides modern GUI functionality and supports 3d graphics via OpenGL and its built-in GLUT emulation. fluid is a GUI designer for FLTK

TO RUN:

athena % fluid options (to run fluid GUI designer)

To link against it:

athena% g++ -O2 -o file `fltk-config --cxxflags --ldflags` file.cxx

and add include lines such as the following in your program:

#include <FL/FL_Component.H> (where Component identifies the name of the component being used- see documentation for details)

Local documentation is at file:///usr/share/doc/fltk1.1-doc/HTML/index.html; see also the FLTK home page

See also: Motif, PerlQt, Qt

Title and Description:

guile
Description: implementation of the Scheme programming language, also made available as a library that allows interfacing the interpreter with code from other programming languages (such as C)

TO RUN:

athena% guile (to start an interactive session)

To compile and link C code against the guile library put the following #include in your code:

#include <guile/gh.h>

and run the following from the command line:

athena% gcc -O2 `guile-config compile` -o file file.c `guile-config link`

where file.c is the file you are compiling (you may need to link against additional libraries)

There is a guile documentation page and code samples to clarify the details.

See also: Clojure, drscheme, newLISP, scheme, SCM

Title and Description:

Motif
Description: software suite from Open Group incorporating the mwm Window Manager and a library of Widgets for building GUI applications with a "Motif look and feel". The instructions below describe how to build your own Motif applications by linking against the Motif library

Linux now comes with various versions of Motif libraries and associated header files (dynamic linking is the default). Linux formerly used Lesstif, a Motif clone, but now generally uses Motif released under Open Source license (OpenMotif).

To compile and link C code against the Motif library, put whatever include files your code requires at the top of your source file file.c, typically including:

#include <Xm/Xm.h>

#include <Xm/Label.h>

and compile as follows from the command line:

athena% gcc -o file file.c -lXm -lXt -lX11

You may run into further complications, such as the need to link against additional libraries or supply additional directories for header files, that are beyond the scope of this document

See also: FLTK, Qt, Xaw, Wcl

Title and Description:

PerlQt
Description: Perl interface to Qt GUI Toolkit

TO RUN:

athena% puic options uifile (to run Perl User Interface Compiler)

athena% pqtapi (to run API-listing utility)

athena% pqtsh (to run PerlQt shell)

to run executable PerlQt scripts, add the following lines to the top of your scripts:

#!/usr/bin/env perl

use Qt; (you may need additional use directives depending on your code)

There is a Web page with documentation

See also: FLTK, Perl, Qt

Please read the file /mit/perlqt_v3.009/README.athena for additional important information

Title and Description:

Qt
Description: Object-oriented framework for developing graphical user interface (GUI) applications using C++. Used as basis for Linux KDE interface; both Qt 4 and Qt 3 are available, but headers are only installed for Qt 4

TO RUN:

athena% designer & (to run Qt 4 GUI interface builder)

athena% assistant-qt4 & (to run Qt 4 GUI help browser)

athena% assistant-qt3 & (to run Qt 4 GUI help browser)

For command-line builds, in a directory where you put your Qt C++ source code:

athena% qmake -project (to build Qt 4 .pro project file)

athena% qmake (to build UNIX Makefile from .pro file)

athena% make (to compile and build your code)

Qt is complex and has changed significantly in the 4.0 release; you will need to study the documentation to build non-trivial code projects; there is online documentation; see also the Independent Qt Tutorial and the Qt home page

See also: boost, FLTK, Motif, PerlQt, Tcl, Tk, Visualization Toolkit

Title and Description:

Tcl, Tk
Description: Programming environment for creating GUI interfaces under X windows

TO RUN:

athena% tclsh (for an interactive Tcl interpreter)

or executable script in Tcl with first line:

#!/usr/bin/wish -f (to run executable scripts with a windowing interpreter)

To compile applications that link against Tcl/Tk libraries:

Add include lines like the following in your code:

#include <tcl8.4/tcl.h>

#include <tcl8.4/tk.h>

link against libtcl8.4.so.0 and libtk8.4.so.0

See also: lua, newLISP, perl, Qt, Visualization Toolkit

Note:

Title and Description:

Xaw, Xt, Xlib
Description: Xaw is a set of X widgets called the Athena Toolkit. Xt is a set of X routines called X Toolkit Intrinsics, upon which widgets are built. Xlib is the lowest level of X routines. These are all low-level routines. Most graphical applications are now developed with one of the many more modern, high-level widget sets

To use:

To link against the Xlib libraries:

athena% gcc -o file file.c -lX11

To link against the Xt libraries:

athena% gcc -o file file.c -lXt -lX11

To link against the Athena widget libraries:

athena% gcc -o file file.c -lXaw -lXt -lX11

See also: Motif