Scientific Computing with Free software on GNU/Linux HOWTO
Manoj Warrier
<m_war (at) users.sourceforge.net>
Shishir Deshpande
<shishir (at) ipr.res.in>
V. S. Ashoka
<ashok (at) rri.res.in>
2003-10-03
Revision History
Revision 1.2 2004-10-19 Revised by: M. W
1 Correction and new additional links
Revision 1.1 2004-06-21 Revised by: M. W
Updates and evaluated distros
Revision 1.0 2003-11-18 Revised by: JP
Document Reviewed by LDP.
Revision 0.0 2003-10-01 Revised by: M. W
first draft proposed
This document aims to show how a PC running GNU/Linux can be used for
scientific computing. It lists the various available free software and also
links on the world wide web to tutorials on getting started with the tools.
-----------------------------------------------------------------------------
Table of Contents
1. Preamble
1.1. Copyright and License
1.2. Disclaimer
1.3. Motivation
1.4. Credits / Contributors
1.5. Feedback
1.6. Translations
2. Introduction
3. Code Development Tools
3.1. Programming Languages
3.2. Debugging Tools
3.3. Version Control Tools
3.4. Integrated Development Environments
4. Mathematics Packages
5. Numerical Methods and Libraries
5.1. Repositories
5.2. Other topic specific numerical libraries
6. Graphics and Visualization
7. Programming systems for GNU/Linux
7.1. The GNU/Linux Workstation
7.2. Parallel Processing and Symmetric Multiprocessing: Supercomputing
8. Word-Processing and Poster presenting tools on Linux
8.1. Word Processing Tools
8.2. Poster presentation tools
9. Free Database Management Systems for Linux
10. Linux in the laboratory
1. Preamble
1.1. Copyright and License
This document, Scientific Computing with free software on GNU/Linux HOWTO,
is copyrighted (c) 2002 by Manoj Warrier. Permission is granted to copy,
distribute and/or modify this document under the terms of the GNU Free
Documentation License, Version 1.1 or any later version published by the Free
Software Foundation; with no Invariant Sections, with no Front-Cover Texts,
and with no Back-Cover Texts. A copy of the license is available [http://
www.gnu.org/licenses/licenses.html#FDL] here
-----------------------------------------------------------------------------
1.2. Disclaimer
No liability for the contents of this document is accepted. Use of the
concepts, examples, links and information is entirely at your own risk. There
may be errors and inaccuracies, that could damage your system, waste your
time, etc... Proceed with caution, and although this is unlikely, the author
takes no responsibility whatsoever.
All copyrights are held by their respective owners, unless specifically
noted otherwise. Use of a term in this document should not be regarded as
affecting the validity of any trademark or service mark. Naming of particular
products, software or brands should not be seen as endorsements
I have not used many of the software applications to which links are
provided. There are simply too many applications that do the same thing, that
one cannot be expected to have used all of them. In a book on Scientific
Computing using GNU/Linux, one would mention ones favorite tool to carry out
a task and describe it in detail. However this is a howto providing links to
various available free tools for scientific computing and may contain links
to some software that promises much but delivers little and vice versa.
-----------------------------------------------------------------------------
1.3. Motivation
This howto mainly consists of the links provided at http://
Scilinux.sourceforge.net which has to be disbanded due to a name conflict.
The best alternative seems to be to make it a Linux document and host it at
the LDP site. Another reason is that there seems to be many free software
applications doing the same things. We hope to provide links to the available
software thereby making it easy for the scientific community to make a choice
without spending much time.
-----------------------------------------------------------------------------
1.4. Credits / Contributors
In this document, I have the pleasure of acknowledging:
* Linus Trovalds, Richard M. Stallman and their merry men for Linux, GNU
and also for indirectly broadening various perspectives which were not
really obvious.
* A host of colleagues and friends from the Institute for Plasma
Research, India for discussions at various times.
* Marcel Bose, Ivan Lamouret, K. Scott Hunziker, Livine Christin, W.
Herbert, Simon Pinches and many others for suggesting various links
mentioned in this document.
* Vasudha my wife for letting me do what I wish and egging me on with
comments like "let us hope that you will finish at least this project"
Shishir and Ashoka are co-authors of this document because such a
collection of links was Shishir's idea and Ashoka is always contributing by
providing links, suggestions and a second point of view. They will be helping
me maintain this HOWTO too.
-----------------------------------------------------------------------------
1.5. Feedback
Feedback is most certainly welcome for this document. Send your additions,
comments and criticisms to the following email address : <m_war at
users.sourceforge.net>.
-----------------------------------------------------------------------------
1.6. Translations
No translations yet.
-----------------------------------------------------------------------------
2. Introduction
GNU/Linux is probably the platform of choice for scientific computing.
There exists a wide variety of high level languages, debugging tools and
other code development tools for programming, numerical subroutines for
solving various types of equations, plotting and visualization packages, word
processing software which can display equations and figures and in fact
parallel programming software to construct a supercomputer with off the shelf
PC parts and some hardware. This document aims to provide a list of free
software for carrying out the above tasks and links to tutorials and other
documents on how to setup and use these software applications.
This document does not aim to provide links to subject specific free
software available for GNU/Linux systems. It aims to show how GNU/Linux can
be used best to handle scientific computing tasks. It is hoped that people or
institutions with interest in a specific subject list, compile a list of the
free software available for that subject ... for example see Linux for
Astronomy, Linux for Biotechnology and Linux for Chemistry at The Random
Factory . Another site with a lot of links (to commercial and free)
scientific software is Scientific Applications on Linux. The [http://
www.gnu.org/directory/science/] GNU Software Directory also has links to
many of the links provided in this howto plus many more topic specific
software. You may also want to check out [http://freshmeat.net/browse/97/]
The Science and Engineering section at Freshmeat.net.
The software links provided are classified into
* [./devtools.html] Code development tools
* [./mathpack.html] Mathematics packages
* [./numlib.html] Numerical subroutines and libraries
* [./graphvis.html] Graphics and visualization
* [./systems.html] GNU/Linux Systems
* [./publish.html] Publishing tools
* [./database.html] Databases
* [./lablinux.html] Linux in the Laboratory
Just installing GNU/Linux on your PC makes it a powerful workstation. The
various popular distributions however do not have all the tools needed to
make it the ideal scientific computing machine. This HOWTO aims to fill in
this gap by creating a list of free software useful for scientific computing.
It is assumed that people reading this document already have a PC with Linux
and the GNU utilities installed. For those who do not have such a setup and
want to install GNU-Linux can check out [./GNULinuxWS.html] GNU/Linux Systems
for links to documents on installing GNU/Linux, and also on how to get
started using GNU/Linux. Recently there has been an effort by Dirk
Eddelbuettel to create a scientific computing environment [http://
dirk.eddelbuettel.com/quantian.html] Quantian which probably is the first
GNU-Linux distribution tailored for Scientists. I checked out the latest
release and it has almost all the packages mentioned in this document and
many packages not mentioned. It is fair to say that if you have any linux
distribution in which the packages are managed by rpms or any debian based
system, you will find pre-compiled binaries of these packages and will not
have to waste much time installing them.
-----------------------------------------------------------------------------
3. Code Development Tools
Code development consists of mainly Programming languages, Debugging tools,
Version Management tools, Compiling tools, and Integrated Development
Environments (IDEs) where all the above are coupled as a single software
application.
-----------------------------------------------------------------------------
3.1. Programming Languages
Links are provided to various compilers used in Scientific Computing like
FORTRAN, C, C++, Java and more recently Python.
* GNU Compiler Collection : GNU's project to produce a world class
optimizing compiler. It works on multiple architectures and diverse
environments. Currently GCC contains front ends for C, C++, Objective C,
GNU Fortran-95, Java, and Ada, as well as libraries for these languages
(libstdc++, libgcj,..).
For manuals on using the various GCC compilers check out [http://
www.gnu.org/software/gcc/onlinedocs/] The GCC online documentation
* g77 : The GCC front end for FORTRAN 77. It is a very good FORTRAN77
compiler. It however does not have the -r8 option which compiles a
program as double precision. This could be a good compiler design
philosophy but in many cases gives problems when porting a code from SUN
/ DEC / HP workstations onto Linux systems. The g77 manual is available
at The Gcc Online documentation site.
* [http://gcc.gnu.org/fortran/] gfortran. I was happy to receive this
link by mail. It was 3 years since I had migrated to using the GNU C
compiler for scientific computing because there was no "truly free"
FORTRAN-95 compiler available then. I thank Paul Thomas for this link.
* [http://g95.sourceforge.net] g95. gfortran above and g95 are reportedly
offshoots from the same CVS tree. Has an impressive list of programs that
compiles and runs using this compiler.
* [http://www.llnl.gov/casc/Overture/henshaw/install/node6.html] fort77
and f2c: fort77 is a perl program which invokes the f2c command (a
Fortran to C translator) transparently, so it can be used just like a
real Fortran compiler. Fort77 can be used to compile Fortran, C and
assembler code and can link the code with f2c libraries. If you install
fort77, you'll also need to install the f2c package. This does not have
the "-r8" problem. You can download fort77 and f2c from the above link.
* [http://lush.sourceforge.net] lush: An object-oriented programming
language, which combines the flexibility of an interpretive language,
with the efficiency of a compiled language. It has full interfaces to
numerical libraries (GSL, LAPACK, BLAS), graphics libraries (OpenGL),
which allows creation of graphics and 3D animations and many other
features that sound too good to be true. I have not yet tried this out,
but it sounds very promising.
* [http://www.python.org/topics/scicomp/] Scientific Python: You may want
to explore [http://www.python.org] Python for your scientific computing
needs. Python is an interpreted, interactive, object-oriented programming
language. It has a number of extensions for numerics, plotting, data
storage and combined with Tk lets you develop very good GUIs for your
codes. The most exciting aspect is that it simplifies programming because
it has modules for almost anything (vectors, tensors, transformations,
derivatives, linear algebra, Fourier transforms, statistics, etc ...) are
available. You can also wrap C and Fortran libraries from Python. Finally
if you want to write a numerical scheme of your own you may find that it
is simpler in Python. There are also interfaces to netCDF (portable
binary files), MPI and BSPlib (parallel programming).
You can further explore Python for Scientific computing here:
+ [http://starship.python.net/crew/hinsen/scientific.html]
Scientific-Python: A collection of modules for scientific computing
on Python. All the necessary modules can be downloaded as either a
tar file or an RPM file from here. The maintainer Konrad HINSEN also
has a nice tutorial on [http://starship.python.net/crew/hinsen/
tutorial.ps] Scientific Computing in Python.
+ [http://www.scipy.org] SciPy An open source library of scientific
tools for Python. It includes modules for graphics and plotting,
optimization, integration, special functions, signal and image
processing, genetic algorithms, ODE solvers, etc.
-----------------------------------------------------------------------------
3.2. Debugging Tools
In this section links are given to mainly debugging tools for GCC and
FORTRAN. I understand that python has a debugging module built in though I
have not used it. The purpose of a debugger is to allow you to see what is
going on inside a program while it executes or what the program was doing
when/if it crashed.
* [http://www.dsm.fordham.edu/~ftnchek] Ftnchek: A FORTRAN checker designed
to detect errors in a Fortran program that a compiler usually does not.
Therefore it is best to run ftnchek on your FORTRAN programs after it has
compiled without errors. Its purpose is to assist the user in finding
semantic errors. Semantic errors are legal in the Fortran language but
are wasteful or may cause incorrect operation. An on-line [http://
www.dsm.fordham.edu/~ftnchek/html/] manual is available. This project
is looking for volunteers to bringing ftnchek up to the Fortran 90
standard.
* gdb : All programs written in the languages supported by GCC can be
debugged using gdb, an excellent interactive, command line debugger. You
can compile your programs using a -g option which then compiles your code
with debugging information inserted into the executable. It can start
your programs, stop your programs on specified conditions and at
specified locations, examine what happened when your program stops. In a
large code with multiple cascading calls to various functions it can back
trace the function calls. You can also Download the document Debugging
with GDB and a quick reference card.
* [ftp://ftp.x.org/contrib/utilities/] xxgdb: It is a front end to the gdb
debugger. Useful for beginners to gdb as it lists out the whole gdb
commands as buttons with a area for viewing source on which one can
include break points, etc by a click of the mouse, and another area for
viewing the debugging results.
* DDD: The GNU Data Display Debugger, GNU DDD, is a graphical front-end for
command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl
debugger, or the Python debugger. Besides ``usual'' front-end features
such as viewing source texts it also has a good interactive graphical
data display, where data structures are displayed as graphs. Follow this
link for a [http://www.gnu.org/manual/ddd/] DDD manual in postscript /
HTML / PDF format.
-----------------------------------------------------------------------------
3.3. Version Control Tools
It will be worth your while investing some time in learning to use one of
the version control tools below (cvs is what I use ..) if you are into any
serious code development.
* [http://www.cvshome.org/dev/codelinux.html] Concurrent Versions System
: CVS is one of the most popular version control systems running on the
Linux operating system. Popular Linux projects like Apache, EGCS, GIMP,
and others are using CVS to coordinate their efforts ... This is how the
URL linked above describes their effort.
A tutorial on CVS is available at [http://www.gentoo.org/doc/
cvs-tutorial.html] Gentoo Linux Documentation and a free CVS book is
available [http://cvsbook.red-bean.com/] here
* [http://www.xcf.berkeley.edu/~jmacd/prcs.html] Project Revision Control
System : PRCS, the Project Revision Control System, is the front end to a
set of tools that (like CVS) provide a way to deal with sets of files and
directories as an entity, preserving coherent versions of the entire set.
PRCS was designed primarily by Paul N. Hilfinger, with input and
modifications by Luigi Semenzato and Josh MacDonald. PRCS is written and
maintained by Josh MacDonald. Its purpose is similar to that of SCCS,
RCS, and CVS, but (according to its authors, at least), it is much
simpler than any of those systems. This page is where information on the
latest developments in PRCS can be found.
* [http://www.cryon.com/gbuild/] Gbuild : gbuild is a script written in the
Bourne shell language to simplify package maintenance by allowing you to
automate code update from CVS, compilation, building tar/rpms/srpms of
your package. some external scripts which certain functions of gbuild
depend on are written in Perl. gbuild is released under the GPL.
-----------------------------------------------------------------------------
3.4. Integrated Development Environments
Integrated development environments (IDEs) can be very useful for building
code and ideally come with all the above tools (i.e a compiler, a debugger
and a version control tool). In addition to that IDEs also usually provide a
makefile generator, documenting help, online help manuals, etc.
* [http://www.kdevelop.org/] Kdeveloper : A easy to use C/C++ IDE
(Integrated Development Environment) for Linux. It supports KDE/Qt,
GNOME, plain C and C++ projects. This site has a lot of documentation
..... a highly browsable site for software developers. Specifically,
KDevelop manages or provides:
All development tools needed for C++ programming like Compiler, Linker,
automake and autoconf; KAppWizard, which generates complete, ready-to-go
sample applications; Class generator, for creating new classes and
integrating them into the current project; File management for sources,
headers, documentation etc. to be included in the project; The creation
of User-Handbooks written with SGML and the automatic generation of
HTML-output with the KDE look and feel; Automatic HTML-based
API-documentation for your project's classes with cross-references to the
used libraries; Internationalization support for your application,
allowing translators to easily add their target language to a project;
KDevelop also includes WYSIWYG (What you see is what you get)-creation of
user interfaces with a built-in dialog editor; Debugging your application
by integrating KDbg; Editing of project-specific pixmaps with KIconEdit;
The inclusion of any other program you need for development by adding it
to the "Tools"-menu according to your individual needs.
* [http://vdkbuilder.sourceforge.net/] VDKbuilder: VDKbuilder is a tool
that helps programmers in constructing GUI interfaces, editing,
compiling, linking, and debugging within an integrated environment. Using
VDKBuilder dramatically reduces developing time since all code related to
GUI construction and signal processing is automatically generated,
maintained and updated. It is distributed under the GNU Public License.
Visit the site for downloading the software.
-----------------------------------------------------------------------------
4. Mathematics Packages
All the links below are free high level languages and Mathematics Packages
for Scientific Computation on Linux. These packages are usually like a
Mathematical Laboratory in which numerical computations can be done and
usually have their own interpreted language. They either link to a popular
(free) plotting package or have their own graphics and plotting capability.
They also provide capability to I/O files and interface with other
programming languages like C, C++, Fortran, etc ... Now a days some of them
have parallel programming capabilities. I have not included [http://
www.mupad.de/] MuPAD, a good symbolic math package, since is not really free.
Check out if their most [http://www.sciface.com/personal.shtml] free license
suits you.
* [http://www.octave.org/] Octave: An excellent package for numerical
computations. It uses gnuplot for plotting and has a online help. It is
also easily extensible (i.e. new functions, procedures can be written)
either using its own language or by using dynamically loadable modules
written in C, C++, Fortran or other languages. An extensive manual is
available [http://www.octave.org/doc/octave_toc.html] here. You can get a
GNOME based front end for it [http://freshmeat.net/projects/goctave/]
here. It is distributed under the GNU Public License.
* [http://www-rocq.inria.fr/scilab/] Scilab: Another superb package
numerical computations having a good user interface and a very good
online click-able help. Its plotting and graphic capabilities are also
very impressive. It also provides for easy interfacing with Fortran and
C. It has its own [http://www-rocq.inria.fr/scilab/license.txt] free
license.
* [http://wuarchive.wustl.edu/languages/yorick/doc/index.html] Yorick:
Yorick is a fast, interpreted language, designed for scientific computing
and numerical analysis. The syntax is similar to C, but the variables
need not be declared. It offers an interactive graphics package based on
X windows. X-Y plots, quadrilateral meshes, filled meshes, cell arrays,
and contours are supported. You can embed compiled routines in Yorick to
solve problems for which the interpreter is too slow. It is also useful
as a pre and post processor for large physical simulation programs. A
tutorial like manual is available [http://wuarchive.wustl.edu/languages/
yorick/doc/manual/yorick.html] here. Yorick is open source software,
[http://wuarchive.wustl.edu/languages/yorick/doc/copyright.html]
copyright of the Regents of the University of California.
* [http://algae.sourceforge.net/] Algae: As the above link describes it,
Algae is a interpreted language for numerical analysis. It was developed
as a fast and versatile tool, capable of handling large problems. Algae
consists of the programming language Algae, and algae, the interpreter.
Its features include speed (generally much faster than octave, RLaB and
Scilab), storage of sparse arrays and a code profiling capability (to
check where your code spends its time). A user manual is available [http:
//algae.sourceforge.net/algae.html] here. It is distributed under the GNU
General Public License.
* [http://yacas.sourceforge.net/] YACAS: As the above link describes it,
"YACAS is an easy to use, general purpose Computer Algebra System, a
program for symbolic manipulation of mathematical expressions. It uses
its own programming language designed for symbolic as well as
arbitrary-precision numerical computations". Links to documentation (user
manual, tutorial, etc ..) is available [http://yacas.sourceforge.net/
manindex.html] here. It is distributed under the GNU General Public
License.
* [http://rlab.sourceforge.net/] RLAB: The above link describes it thus,
"Rlab is an interactive, interpreted scientific programming environment.
Rlab is a very high level language intended to provide fast prototyping
and program development, as well as easy data-visualization, and
processing". It is distributed under the GNU General Public License. The
author Ian Searle has written an article in [http://www.linuxjournal.com
/] The Linux Journal titled An Introduction to Rlab which as he reminds
us, is a bit dated, and a [http://rlab.sourceforge.net/html/
rlab-ref.html] Reference Manual is also available.
* [http://maxima.sourceforge.net] Maxima: Maxima is a symbolic
computation program. The above link describes it as follows, "Maxima is a
descendant of DOE Macsyma, which had its origins in the late 1960s at
MIT. It is the only system based on that effort still publicly available
and with an active user community, thanks to its open source nature.
Macsyma was the first of a new breed of computer algebra systems, leading
the way for programs such as Maple and Mathematica. This particular
variant of Macsyma was maintained by William Schelter from 1982 until he
passed away in 2001. In 1998 he obtained permission to release the source
code under GPL".
* [http://www.r-project.org/] The R-Project for Statistical Computing: R
is a language and environment for statistical computing and graphics. It
provides a large collection of tools for statistical analysis of large
arrays of data and also graphical facilities. R is also a complete
effective programming language. For computationally intensive tasks, C,
C++ and Fortran code can be linked and called at run time. A
comprehensive set of manuals dealing with installation, introduction,
writing extensions, etc ... is available [http://cran.r-project.org/
manuals.html] here. It is distributed under the GNU General Public
License.
* [http://www.fis.unipr.it/%7Estefanw/gtybalt.html] gTybalt: gTybalt is a
step towards a free computer algebra system. It is object oriented,
allowing symbolic calculations within C++. It is efficient, in the sense
that solutions developed with gTybalt can be compiled with a C++ compiler
and executed independently of gTybalt. The mathematical formulae are
visualized using TeX fonts and can easily be converted to LaTeX. I did
not realize that it has good graphic capabilities till I checked out the
gTybalt [http://www.fis.unipr.it/%7Estefanw/gtybalt/gtybalt.html] manual.
It is distributed under the GNU General Public License.
* [http://www-swiss.ai.mit.edu/%7Ejaffer/JACAL.html] JACAL: As the link
above describes it, " JACAL is an interactive symbolic mathematics
program. JACAL can manipulate and simplify equations, scalars, vectors,
and matrices of single and multiple valued algebraic expressions
containing numbers, variables, radicals, and algebraic differential, and
holonomic functions".
* [http://www.gnu.org/software/bc/bc.html] bc: bc is an arbitrary
precision numeric processing language. It supports interactive execution
of statements. Click here for a [http://www.gnu.org/manual/bc/index.html]
Manual in a variety of formats. It is GNU software and is distributed
under the GNU General Public License.
-----------------------------------------------------------------------------
5. Numerical Methods and Libraries
The best thing that could happen for scientific computing with free
software on GNU/Linux is the GNU Scientific Library [http://
sources.redhat.com/gsl] GSL. It however has source code only in C and people
who use FORTRAN will find that a let down. Pouncing on this opportunity it is
recommended that GSL is another reason (in addition to the GCC C compiler,
coupled with the advantages of C programming) for starting to learn to use C.
In addition to this, the two best source code repositories for Numerical
Methods and libraries are [http://www.netlib.org] Netlib and [http://
math.nist.gov/] GAMS. There are new numerical packages being developed
outside the usual "write a FORTRAN program, get a numerical subroutine from
INTERNET for solving the numerics" concepts. The merits and demerits of this
approach are debatable, but there exist more options like [http://
oonumerics.org/oon] Object Oriented Numerics GSL and [http://www.ginac.de/]
GiNaC which are exciting developments.
-----------------------------------------------------------------------------
5.1. Repositories
* [http://www.netlib.org/] Netlib: An amazing amount of free source code
for Numerical Methods. Netlib is THE source code repository which
contains an innumerable amount of source code for Numerical Methods. It
also has an active discussion forum wherein you can submit your queries
and stay posted for help. Netlib also has a [http://www.nhse.org/ptlib]
Parallel Tools Library and a search by subject.
* [http://math.nist.gov/] GAMS: Guide to Available Mathematical
Software GAMS has a very useful search using which one can search for
keywords (example: ``diffusion'' to search for a diffusion equation
solver). However the browse by package at GAMS reveals that a lot of the
software they provide is a link to the netlib repository.
* [http://oonumerics.org/oon] Object Oriented Numerics A site devoted to
object oriented numerics. It has a Mailing list, Extensive Links to
freely available libraries (OO of course) and freely available tools for
object oriented scientific computing.
* [http://sources.redhat.com/gsl] GNU Scientific Library The GNU
Scientific Library (GSL) is a collection of numerical routines written
from scratch in C. It provides an Applications Programming Interface
(API) for C programmers and also allows wrappers to be written for very
high level languages. It covers a wide range of numerical computing
topics, has a good manual, is widely portable and is distributed under
the GNU General Public License.
* [http://www.ginac.de/] GiNaC GiNaC is designed to allow the creation of
software which need symbolic manipulations embedded in them. It extends
C++ by a set of algebraic capabilities and is recursively named for GiNaC
is not a Computer Algebra system. It is distributed under the terms and
conditions of the GNU general public license (GPL).
-----------------------------------------------------------------------------
5.2. Other topic specific numerical libraries
* [http://www.fftw.org/] FFTW FFTW is a collection of fast C routines for
computing the Discrete Fourier Transform in one or more dimensions. It
includes complex, real, and parallel transforms, and can handle arbitrary
array sizes efficiently. This package includes both the double- and
single-precision FFTW uniprocessors and the threads libraries.
* [http://www.netlib.org/lapack] LAPACK LAPACK (Linear Algebra PACKage)
is a standard library for numerical linear algebra. LAPACK provides
routines for solving systems of simultaneous linear equations,
least-squares solutions of linear systems of equations, eigenvalue
problems, and singular value problems. LAPACK is coded in Fortran77 and
is built with egcs. It is well documented and widely used (and therefore
widely tested).
* [http://www.nersc.gov/~xiaoye/SuperLU] SuperLU SuperLU is a general
purpose library which performs an LU decomposition for the direct
solution of large, sparse, non-symmetric systems of linear equations on
high performance machines. Its written in C and is callable from either C
or Fortran.
* ARPACK ARPACK is a set of Fortran77 subroutines designed to solve large
scale eigenvalue problems. A Users Guide is available. The above link
also gives information about a parallel version of ARPACK - PARPACK and a
object oriented version ARPACK++.
* [http://icemcfd.com/cfd/CFD_codes.html] Computational Fluid Dynamics
codes This link contains a comprehensive listing of public domain,
shareware and freeware Computational Fluid Dynamics codes links with a
description of each CFD code.
-----------------------------------------------------------------------------
6. Graphics and Visualization
* [http://www.gnuplot.info] Gnuplot Gnuplot is a command-line driven
interactive function plotting utility. It handles both curves (2
dimensions) and surfaces (3 dimensions). Surfaces can be floating in the
3-d coordinate space, or as a contour plot. For 2-d plots, there are also
many plot styles, including lines, points, lines with points, error bars,
and impulses. Graphs may be labeled with arbitrary labels and arrows,
axes labels, a title, date and time, and a key. It has multiple plotting
capabilities too. It allows saving the graphs in various formats which
can be included in word processors. It can be used to generate
publication quality plots.
* [http://ngwww.ucar.edu] NCAR Graphics A very popular graphics package
which is very well documented and widely used. It provides basic
ingredients for creating complex plots as functions / routines that can
be called from Fortran and C. There is a contributed programming
interface to the NCAR Graphics package: NCL (NCAR Command Language). The
programming interfaces provide access to complex graphics utilities like
contouring, world map projections, and velocity vectors. For the most
part, the C interface is built on top of the Fortran interface... It is
distributed under the GNU public license. Click [http://ngwww.ucar.edu/
ngdoc/ng4.2] here for going to the documentation of all its various
components.
* [http://www.opendx.org] OpenDX A very good Open Source Data eXplorer.
It can handle large amounts of data and creates great visualizations. It
was the tool I stumbled upon when I wanted a free graphics routine to
make 3-D plots and zoom-in, rotate, and really eXplore the output Data
from my codes. The downside is that compiling from source is really
challenging and getting started is a difficult. However it has excellent
documentation distributed with it and once I started off it was the best
tool I have ever used.
* [http://gri.sourceforge.net] Gri: It is a language for scientific
graphics programming. The claim that Gri is similar to LaTeX in the sense
that both provide extensive power as a reward for tolerating a learning
curve seems exciting and I for one want to check this out!! Check out the
following [http://www.linuxjournal.com/article.php?sid=3743] article in
The Linux Journal. Go to the gri home page if you are now impressed by it
and check out download info and manuals.
* [http://mayavi.sf.net] MayaVi: A scientific data visualizer written in
Python. It is distributed under the BSD license. The screenshots look
promising. Check out the above link for more details.
* [http://www.astro.caltech.edu/~tjp/pgplot] PGPLOT: PGPLOT is a Fortran
77 or C callable subroutine package for drawing scientific 2D and Simple
3D plots. One can call these routines during runtime and redirect the
output to a variety of devices at run time. It is well documented and the
full documentation is available at the above site. It is Free for
Non-Commercial Use. A user manual is available online at PGPLOT Users
Manual
* [http://plplot.sourceforge.net/] PLplot: This is a library of
scientific plotting functions that can be called from C, C++, FORTRAN,
TCL, PYTHON. PLplot features as described in the above link are, "It can
be used to create standard x-y plots, semilog plots, log-log plots,
contour plots, 3D plots, mesh plots, bar charts and pie charts. Multiple
graphs (of the same or different sizes) may be placed on a single page
with multiple lines in each graph. There are almost 2000 characters in
the extended character set. This includes four different fonts, the Greek
alphabet and a host of mathematical, musical, and other symbols. A
variety of output devices are supported and new devices can be easily
added by writing a small number of device dependent routines". To
download click [http://sourceforge.net/project/showfiles.php?group_id=
2915] here .
* [http://plasma-gate.weizmann.ac.il/Grace/] Grace Grace is a WYSIWYG 2D
plotting tool for the X Window System and Motif. Grace runs on
practically any version of Unix. Grace is a descendant of ACE/gr, also
known as Xmgr. It is lisenced under the GNU public license. This link
also has a tutorial and download information.
* SciGraphica SciGraphica is a application for data analysis and
technical graphics. It fully supplies plotting features for 2D, 3D and
polar charts. The aim is to obtain a fully-featured, cross-platform,
user-friendly, self-growing scientific application. It is free and
open-source, released under the GPL license.
* [http://www.gnu.org/software/plotutils/plotutils.html] Plotutils: The
GNU plotutils package contains software for both programmers and
technical users. Its centerpiece is libplot.a powerful C/C++ function
library for exporting 2-D vector graphics in many file formats, both
vector and raster. It can also do vector graphics animations. Besides
libplot, the package contains command-line programs for plotting
scientific data. Many of them use libplot to export graphics.
* [http://www.dislin.de] DISLIN DISLIN is a high-level plotting library
for displaying data as curves, polar plots, bar graphs, pie charts,
3D-color plots, surfaces, contours and maps.
* [http://ImLib3d.sourceforge.net] ImLib3D ImLib3D is an open source C++
library for 3D (volumetric) image processing. It contains most basic
image processing algorithms, and some more sophisticated ones. It comes
with an optional viewer that features multi-planar views, animations,
vector field views and 3D (OpenGL) multi-planar.
* [http://ptolemy.eecs.berkeley.edu/java/ptplot] Ptplot: Ptplot is a 2D
data plotter and histogram tool implemented in Java. Ptplot can be used
as a standalone applet or application, or it can be embedded in your own
applet or application.
-----------------------------------------------------------------------------
7. Programming systems for GNU/Linux
This section deals with links to tutorials and documents for installing
Linux on a PC, getting started with Linux, and then going a step further --
to optimize your PC for processing power, using multiple processors
(Symmetric Muliti Processing - SMP); making a cheap, upgradeable
Supercomputing Linux cluster and finally links to software to do parallel
programming on Linux.
-----------------------------------------------------------------------------
7.1. The GNU/Linux Workstation
As with most documentation related to GNU/Linux, [http://tldp.org] the
Linux Documentation project's home page is a priceless source. You might
first want to read [http://tldp.org/HOWTO/Installation-HOWTO/index.html]
The Linux Installation HOWTO. For those who want to install Linux along with
Windows might want to browse through [http://www.tldp.org/HOWTO/
Linux+Windows-HOWTO/index.html] The Linux + Windows HOWTO. When installing
Linux make sure that you choose to install all documentation. After
installing Linux, a good, comprehensive document to getting started with
using Linux is The Rute Users Tutorial and Exposition which is a beginners
guide to Linux and UNIX like systems. I'd like to give a less intimidating
(size-wise) link to a small beginners guide, but U will find this useful
after taking the plunge. You might also want to go through The Linux System
Administrator's Guide and to check out [http://www.tldp.org/LDP/lame/LAME/
linux-admin-made-easy/index.html] The Linux Administration Made Easy (LAME)
guide It attempts to describe day-to-day administration and maintenance
issues commonly faced by Linux system administrators.
-----------------------------------------------------------------------------
7.2. Parallel Processing and Symmetric Multiprocessing: Supercomputing
It is possible to get large volume number crunching without spending
millions of rupees on a supercomputer. You only need to link together (by
some high speed network) the requisite number of CPUs, with GNU/LINUX as the
underlying OS. Add some freely available message passing software and a
effective parallel processing number crunching machine is made. Such clusters
are called "Beowulf clusters". The other advantages of such a cluster other
than building costs is, up-gradation costs are minimal. The two best
resources for Linux cluster builders are
* The Beowulf Project home page and
* The Extreme Linux Project
These sites are upgraded frequently with useful information for cluster
builders.
-----------------------------------------------------------------------------
7.2.1. Parallel computing document links
You will also want to read this excellent article on Linux Clustering
Software (and the large variety of links it provides) by Joe Greenseid. I
hope to go through the links and include them subsequently in this HOWTO.
Other free document links for parallel processing are:
* [http://www.ibiblio.org/pub/Linux/docs/HOWTO/Beowulf-HOWTO] The
Beowulf Howto : This document introduces the Beowulf Supercomputer
architecture and provides background information on parallel programming,
including links to other more specific documents, and web pages. But,
before that for an understanding of parallel processing and Symmetric
multiprocessing on Linux, check out the following:
* [http://www.ibiblio.org/pub/Linux/docs/HOWTO/Parallel-Processing-HOWTO]
The Parallel Processing on Linux HOWTO
* [http://www.ibiblio.org/pub/Linux/docs/HOWTO/SMP-HOWTO] The Symmetric
Multiprocessing HOWTO
-----------------------------------------------------------------------------
7.2.2. Parallel processing software for Linux
Now after reading the above documents, you have an idea of parallel
processing. Parallel program libraries are the core of parallel processing on
a Linux cluster. There are various free implementations of parallel
processing libraries. Since parallel processing is all about performance,
these libraries have some very nice functional tools to analyze your parallel
program performance. Given below is a set of links to these parallel program
libraries and tools.
* [http://www-unix.mcs.anl.gov/mpi] Message Passing Interface: MPI is a
standard specification of message passing libraries. The above document
gives a lot of links to documents on the standard, etc.. A MPI
implementation for Linux [http://www-unix.mcs.anl.gov/mpi/mpich] mpich is
also available at that site. There are a lot of documents for Learning to
use MPI .
* Local Area Multicomputer - LAM: LAM (Local Area Multicomputer) is an
MPI programming environment and development system for heterogeneous
computers on a network. With LAM, a dedicated cluster or an existing
network computing infrastructure can act as one parallel computer solving
one problem. LAM features extensive debugging support in the application
development cycle and peak performance for production applications. LAM
features a full implementation of the MPI communication standard. You can
download the sources (tar-zipped, rpm) or binaries from [http://
www.lam-mpi.org/download/] here A host of MPI tutorial links and also a
`getting started with LAM' tutorial is available [http://www.lam-mpi.org/
tutorials/] here
* [http://www.epm.ornl.gov/pvm/pvm_home.html] Parallel Virtual Machine
: As the PVM home page describes, it is a software package that permits a
heterogeneous collection of Unix and/or NT computers hooked together by a
network to be used as a single large parallel computer. Thus large
computational problems can be solved more cost effectively by using the
aggregate power and memory of many computers. The software is very
portable. The source, which is available free thru netlib, has been
compiled on everything from laptops to CRAYs.
* [http://ganglia.sourceforge.net] Ganglia: Ganglia is an open source
cluster monitoring and execution environment developed at the University
of California, Berkeley Computer Science Division. As the above link
describes it, "Ganglia is as simple to install and use on a 16-node
cluster as it is to use on a 512-node cluster as has been proven by its
use on multiple 500+ node clusters". It not only can link nodes in a
cluster, but also link clusters to other clusters.
-----------------------------------------------------------------------------
8. Word-Processing and Poster presenting tools on Linux
Those of you who do not use [http://www.latex-project.org] LaTeX and find
it challenging and want a WYSIWYG word processor, keep your ears tuned to
OpenOffice which has released version 1.2 of its openoffice software. Its
tools may compare well with the best in the market.
-----------------------------------------------------------------------------
8.1. Word Processing Tools
* [http://www.latex-project.org] Latex: LaTeX is a high-quality
typesetting system, with features designed for the production of
technical and scientific documentation. LaTeX is the de facto standard
for the communication and publication of scientific documents. [http://
www.maths.tcd.ie/~dwilkins/LaTeXPrimer/] David R.Wilkin's primer
"Getting Started with LaTeX" is a good tutorial to getting started with
LaTeX. For those who have to live with a WYSIWYG documenting tool, check
[http://www.lyx.org] LyX. This is a front-end for latex. It isn't as
powerful as latex proper, but helps with a good WYSIWIG.
* [http://lout.sourceforge.net] Lout: A document formatting system
similar to latex. Good features, documentation and history. Light weight
and outputs postscript. Thanks to Emiliano Gavilan for this link.
* [http://www.abisource.com] Abiword: As the AbiWord home page says,
"AbiWord is suitable for typing papers, letters, reports, memos, and so
forth". It has won many awards and seems to be the best open source
WYSIWYG word processor. Check out the above link to know more about it
and download it.
* [http://www.koffice.org/kword] kword: As the kword home page says,
"KWord is a FrameMaker-like word-processing and desktop publishing
application. KWord is capable of creating demanding and professional
looking documents. Whether you are a corporate or home user, production
artist or student, KWord will prove a valuable and easy to use tool for
all your word processing and layout needs". Check out the above link to
know more about it and download it. (you might want to know more about
the whole [http://www.koffice.org] koffice suite).
-----------------------------------------------------------------------------
8.2. Poster presentation tools
* [http://www.koffice.org/kpresenter/] KPresenter: KPresenter is the
presentation tool of the KOffice suite of office utilities. It allows
screen presentations with all the trappings one is used to seeing in
costly presentation tools. It also allows honest, real scientific
presentations where one does not have to impress the audience with non
subject specific stuff :-). The best thing about it is the possibility of
saving the presentation as a html file. It makes portable network
graphics files with each presentation slide. With a smattering of
knowledge of html files one could put in a animated image as a image link
thereby allowing one to show movies too when necessary.
* [http://www-epb.lbl.gov/xfig/] Xfig : Though the man page claims that
it is a facility for the interactive generation of figures ...., It in
fact much more than that. Other than generating figures for elucidating
what you want to say in a poster, it helps you import and export figures
in a variety of formats, write text in various fonts and sizes, generate
Greek symbols and color text, Save as latex picture file or any other
format supported by your word processor for inclusion in your
publications, generate GIFs of each page of the poster to put on your web
site, and finally it generates *.fig files which are small in size. The
only thing on my wish list for xfig is the capability to edit the
imported pictures which are not in *.fig format. Therefore for a computer
screen projected poster presentation you need a frames capable browser
with contents in one frame and the xfig generated posters (exported as
*.png or *.jpg from Xfig) on the other.
-----------------------------------------------------------------------------
9. Free Database Management Systems for Linux
Scientific computing has two parallel data needs, one the physical values
of the data itself, and the other is Database systems to manage the data. In
this document links are provided only to database resources on the net and
free Database systems. I personally do not use databases to manipulate the
data generated by my codes. gawk, sed, and other basic Unix commands like
grep, head and tail seem sufficient to manipulate any data I generate. I
thought I should include this section for the large data generators.
Hopefully a person with experience in databases will make this section
better.
* [http://www.iam.unibe.ch/~scg/Archive/Software/FreeDB/ ] Free
database list
* [http://www.acm.org/sigmod/databaseSoftware/ ] ACM SIGMOD: Index of
publicly available database software.
* [http://www.mysql.com] MySQL: A relational Database management system.
* [http://www.postgresql.org] PostgreSQL As the link above describes it
...PostgreSQL is a sophisticated Object-Relational DBMS, supporting
almost all SQL constructs, including subselects, transactions, and
user-defined types
-----------------------------------------------------------------------------
10. Linux in the laboratory
Again this is a section where I have zero experience and hope someone will
with experience will contribute towards making this document better. However,
I provide below links suggested by Sambaran Pahari and Deepak Gupta. These
links seem to be very good from my inexperienced viewpoint.
* [http://www.llp.fu-berlin.de] The Linux Lab Project A site for "Linux
Lab Project."..everything to do with laboratory process, process control,
automation and data acquisition on Linux. As the above link says, "The
Linux lab project is intended to help people with development of data
collection and process control software for LINUX. It is planned to
provide a standardized development environment for a wide variety of
applications from hardware support to application development".
* [http://www.torque.net/linux-pp.html] Linux Parallel port drivers:
The above link says, "If you have a parallel port device and would like
to know if there is a Linux driver available for it --then this is the
place to look". Sounds like a confident claim.
