Scientific Computing with Free software on GNU/Linux HOWTO
Contents
1. essere enne enne enne nent enne 6 4 Matheinatics AAA O 7 5 Numerical Methods and Librariesisssscccckscocscccccsvccovenss ssseeeiavecsesedecoceedecgscesecceeedosusecceseseocsseeaceossveeveseceescessssses 9 REPOSO rt A DERE 9 5 2 Other topic specific numerical libraries sse esee eee enne 9 6 Graphics And VisualiZatlOMsssisiccsscissersscensssscessessessoscssecdesvncseudes earn sar epo aee ae eee pase eva Ee poco eese tuo eue eoa Lu aene pa sesi seot 11 7 Programming systems for GNU LinUx eee eese eee eee eee eee en aestas etta setae etae seen set en sesso conse s eaae seen eS 13 7 1 The GNU Linux Workstation cccccccccsssssescsssccccescssseavsesccccesecsssenssesscsscectecssssvsscceccsescesenevssscees 13 7 2 Parallel Processing and Symmetric Multiprocessing Supercomputing sssssss 13 7 2 1 Parallel computing document links essere enne enne 13 7 2 2 Parallel processing software for Linux eese 14 8 Word Processing and Poster presenting tools on LinUx eee eee ee eee ee eren eee enne tete etna etta ae enas 15 8 1 Word Processing TOMS 2 ioiii rettet e eei Save Venet ds ee Rente 15 3 2 Poster presentation tools rtr ede PR e LOW GRUT URN iaa 15 9 Free Database Management Systems for Linux ccce ecce eee ee ee eren ette seen aestas seen setate sene2. 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 3 Code Development Tools 5 Scientific Computing with Free software on GNU Linux HOWTO on the latest developments in PRCS can be found e Gbuild gbuild is a seript 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 1s 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 e 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 integrat
3. 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 e The Parallel Processing on Linux HOWTO e The Symmetric Multiprocessing HOWTO 7 Programming systems for GNU Linux 13 Scientific Computing with Free software on GNU Linux 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 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 mpich is also available at that site There are a lot of documents for Learning to use MPI e Local Area Multicomputer LAM LAM Local Area Multicomputer is an MPI programming environment and development system for heterogeneous computers on a network With LAM
4. 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_here A host of MPI tutorial links and also a getting started with LAM tutorial is available here e 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 e 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 7 Programming systems for GNU Linux 14 8 Word
5. 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 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 e 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 Gentoo Linux Documentation and a free CVS book is available_here e 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
6. Processing and Poster presenting tools on Linux Those of you who do not use_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 e 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 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 LyX This is a front end for latex It isn t as powerful as latex proper but helps with a good WYSIWIG e 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 e 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 e 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 Wh
7. 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 e 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 5 Numerical Methods and Libraries 9 Scientific Computing with Free software on GNU Linux HOWTO Its written in C and is callable from either C or Fortran e 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 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 5 Numerical Methods and Libraries 10 6 Graphics and Visualization 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 a
8. 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 2 Introduction 3 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 The GCC online documentation 77 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
9. 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 gt 1 6 Translations No translations yet 1 Preamble 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 exa
10. 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 e 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_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 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
11. 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 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 e The Beowulf Project home page and e 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 e The Beowulf Howto
12. workstations onto Linux systems The g77 manual is available at The Gcc Online documentation site 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 95 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 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 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 Scientific Python You may want to explore Python for your scientific computing needs Python is an interpreted interactive
13. 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 MuPAD a good symbolic math package since is not really free Check out if their most_free license suits you 4 Mathematics Packages 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 here You can get a GNOME based front end for it_here It is distributed under the GNU Public License 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 free license 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 packa
14. Management Systems for Linux 16 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 e 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 e 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 10 Linux in the laboratory 17
15. Scientific Computing with Free software on GNU Linux HOWTO Manoj Warrier m war at users sourceforge net gt Shishir Deshpande lt shishir at ipr res in gt V S Ashoka lt 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 Scientific Computing with Free software on GNU Linux HOWTO Table of Contents A A 1 Ls Copyright and LICEO A das 1 1 2 DISCla mE oet arto beer bete dalt 1 173 I VIOLEVAtL OD 1560 A NTE 1 TA Credits COntrIDUtOES orte eere eee e eee Reeve Ete aea Pe eee e veas 1 1 5 Feedback oe ee ec ie e tere da ma dele peo 2 126 Translations li x ASEN E eadixsbes 2 PAM E HE CO 0 AEAEE DT TIONEM 3 3 COdE Development ToO0ls eor eeo O 4 3 1 Programming Languages uer etit bene eter Certe eee ee eet teca ee e eie ete veniae v 4 3 2 Debugging Tools ewe qe E ERI FOTO ERE ERE Re 5 3 3 Version Control Tools ie diuo ut te ct A ss 5 3 4 Integrated Development Environments
16. ail 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 e 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 e 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 1 Preamble 1 Scientific Computing with Free software on GNU Linux HOWTO Shishir and Ashoka are co authors of this
17. c 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 e 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 6 Graphics and Visualization 12 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 the Linux Documentation project s home page is a priceless source You might first want to read_The Linux Installation HOWTO For those who want to install Linux along with Windows might want to browse through 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
18. et of manuals dealing with installation introduction writing extensions etc is available here It is distributed under the GNU General Public License e 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 manual It is distributed under the GNU General Public License 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 bc bc is an arbitrary precision numeric processing language It supports interactive execution of statements Click here for a Manual in a variety of formats It is GNU software and is distributed under the GNU General Public License 4 Mathematics Packages 8 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_GSL It however has source code only in C and pe
19. ether 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 koffice suite 8 2 Poster presentation tools e 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 e 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 p
20. ge 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 here Yorick is open source software copyright of the Regents of the University of California 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 here It is distributed under the GNU General Public License 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 here It is distributed under the GNU General Public License RLAB The above link describes it thus Rlab is an interactive interpreted scientific programming envi
21. ing 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 e 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 3 Code Development Tools 6 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
22. ly added by writing a small number of device dependent routines To download click here 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 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 6 Graphics and Visualization 11 Scientific Computing with Free software on GNU Linux HOWTO export graphics e 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 e ImLib3D ImLib3D is an open source C library for 3D volumetric image processing It contains most basi
23. ly available libraries OO of course and freely available tools for object oriented scientific computing 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 e 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 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 e 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
24. mple 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 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 The Science and Engineering section at Freshmeat net The software links provided are classified into Code development tools e Mathematics packages e Numerical subroutines and libraries e Graphics and visualization e GNU Linux Systems e Publishing tools e Databases e 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 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 Quantian which probably is the first GNU Linux distribution tailored for Scientists I
25. nd 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 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 here for going to the documentation of all its various components 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 Gri It is a language for scientific graphics programming The claim that Gri is similar to LaTeX in the sense that both provide extensi
26. 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 4 Scientific Python A collection of modules for scientific computing on Python All the 3 Code Development Tools 4 Scientific Computing with Free software on GNU Linux HOWTO 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 Scientific Computing in Python 4 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
27. ople 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_Netlib and_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 Object Oriented Numerics GSL and_GiNaC which are exciting developments 5 1 Repositories e 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 Parallel Tools Library and a search by subject 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 e Object Oriented Numerics A site devoted to object oriented numerics It has a Mailing list Extensive Links to free
28. oster 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 8 Word Processing and Poster presenting tools on Linux 15 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 e Free database list e ACM SIGMOD Index of publicly available database software e MySQL A relational Database management system e 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 9 Free Database
29. ronment 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 The Linux Journal titled An Introduction to Rlab which as he reminds us is a bit dated and a Reference Manual is also available 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 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 Scientific Computing with Free software on GNU Linux HOWTO 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 s
30. s tease eaa 16 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 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 det
31. ve power as a reward for tolerating a learning curve seems exciting and I for one want to check this out Check out the following 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 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 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 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 easi
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