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GNU/Linux in Science and Engineering

 

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GNU/Linux in Science and Engineering

Co-sponsored by the Vancouver Linux Users Group

Please consider joining the IEEE/VanLUG Science and Engineering SIG and participating in both our mailing list and other events that we may schedule from time to time.  In the meantime, we hope that you'll find this list of Frequently Asked Questions about GNU/Linux in Science and Engineering to be useful.  While the target audience for this FAQ are scientists and engineers who are in the process of migrating to Linux, hopefully even those with lots of experience will find a few useful nuggets.

  1.  How do I convince our senior management to let the technical staff run Linux 
       rather than a widely used (but deeply flawed) alternative?
  2.  What is the purpose of the IEEE/VanLUG Science and Engineering SIG?
  3.  How does one join the IEEE/VanLUG Science and Engineering SIG?
  4.  What are some free alternatives to proprietary software?
  5.  Which commercial Science and Engineering software has been ported to GNU/Linux?
  6.  Which commercial Science and Engineering software hasn't yet been ported to GNU/Linux?
  7.  Can I compile and run my existing Fortran code under Linux?
  8.  Is there a good mechanical CAD or drafting package for Linux?
  9.  How can one keep up to date with science and engineering software for GNU/Linux?
       (journals, mailing lists, websites)
10.  How is the Scientific Applications on Linux (SAL) website structured?
11.  What is Scilab?
12.  What is the Intel/ASCI Red Software?
13.  What is IBM techexplorer?
14.  What is Python?
15   What is PERL and why is it of interest to scientific programmers?
16.  What are ten good practices for scientific programming?


FAQ Contributors: Dave Michelson, Petar Knezevich, Andrew Daviel, Xavier Calbet, ...

1.  How do I convince our senior management to let the technical staff run Linux rather than a widely used (but deeply flawed) alternative?   [back to FAQ ToC]

Explain that scientists and engineers tend to use their computers for different types of tasks than do conventional business users.  These tasks may include:
  • technical document processing (equations, complex graphs and diagrams),
  • symbolic mathematics,
  • mathematical modeling and numerical methods,
  • scientific visualization,
  • data acquisition and process control, and.
  • production and maintenance of scientific databases.
For these types of tasks, UNIX-derived operating systems have several advantages.  For example, they:
  • are generally more robust and reliable than the alternatives,
  • provide a flexible and convenient software development environment
  • have an open, modular, and extensible design,
  • have an network-oriented architecture (NFS, X, RPC, etc.), and,
  • are easily ported to high-performance machines.
While several manufacturers have (unsuccessfully) attempted to displace UNIX-derived operating systems in Science and Engineering applications over the years, none have succeeded.  This can undoubtedly be at least partly explained by Henry Spencer's observation that,
"Those who do not understand UNIX are condemned to re-invent it, poorly."

2.  What is the purpose of the IEEE/VanLUG Science and Engineering SIG?   [back to FAQ ToC]

Linux discussions and presentations often tend to focus on system configuration, system administration, network administration, Linux for the Enterprise, Linux in the Small Office/Home Office environment, and related topics.  This falls a bit short of addressing the specialized needs of scientists and engineers. Accordingly, the VanLUG Science and Engineering SIG seeks to fill that gap by:
  • promoting awareness of the GNU Linux in Science and Engineering community,
  • providing a focus for the exchange of information about GNU Linux in Science and Engineering,
  • helping scientists and engineers promote GNU Linux to their employers, and,
  • arranging for tutorials and presentations of interest to scientists and engineers,
    • without boring those who have no interest in these topics :-)

    3.  How does one join the IEEE/VanLUG Science and Engineering SIG?   [back to FAQ ToC]

    Those who subscribe to the IEEE/VanLUG Sci/Eng mailing list are considered to be members of the SIG.  To join, please send a message to <scieng-request@gweep.bc.ca> with the words

        subscribe 

    (and nothing else) in the body of the message.

    The list server will send you an authentication request to which you must respond before it will add you to the list.

    If the list becomes very busy, we'll consider spawning an announcements-only list.  For now, a single list is both practical and appropriate.

    4.  What are some freely available alternatives to proprietary software?   [back to FAQ ToC]

    We're very enthusiastic about the freely available alternatives to proprietary software (especially those which have been released under the GNU GPL) that are available to scientists and engineers who use UNIX-derived operating systems such as Linux.  Some of these, such as Gnuplot, LaTeX, and the GNU programming tools are well known.  Others, such as Scilab, Octave, muPad, Python, and GRASS, are less well-known.  In any case, these packages are all worth your serious consideration.  We discuss Scilab and Python in greater detail in FAQ B8 and B11, respectively.
  • Math: Scilab, Octave, muPad, Gnuplot, Physica, Python
  • Document Processing: TeX, LaTeX, teTeX
  • Spatial or Image Data: GRASS
  • Fortran/C/C++ compilers: g77, gcc, g++
  • Software Development: GNU programming tools

    • 5.  Which proprietary Science and Engineering software has been ported to GNU Linux?   [back to FAQ ToC]

    Many vendors of science and engineering software have ported their software to Linux in recent years.  Here are just a few examples:
    * freely available;  (S) student versions available.

    We don't necessarily promote the use of proprietary software given that the true strength of UNIX as a scientific and engineering platform lies in the great tradition of sharing source code and improvements to same.  However, we recognize that those migrating from other platforms require access to familiar tools and environments.  Also, free versions of some tools simply aren't available.

    6.  Which commercial Science and Engineering software hasn't yet been ported to GNU Linux?   [back to FAQ ToC]

    While many vendors have made a serious effort to port their products to Linux, a few short-sighted organizations have not.  A few packages that we're often asked about include:
    • Math: MathCAD
    • GIS and CAD: MapInfo, ArcInfo, AutoCAD
    • Electronic Design Automation (EDA) Software: EEsof, others.
    MathCAD, MapInfo, AutoCAD are native Windows applications and porting them to UNIX and X would likely be rather time consuming.  However, ArcInfo, FrameMaker, and EEsof are already running under UNIX and X.  If the experience of Sybase, Informix, and others is any guide, porting them to Linux might not require much more than typing "make". 

    If you really need to run any of this software, a possible interim solution is to run them under a Windows Virtual Machine such as VMware and Win4Lin.  A better alternative, where possible, is to migrate to native Linux alternatives.

    7.  Can I compile and run my existing Fortran code under Linux?   [back to FAQ ToC]

    In a word, yes.
    • The GNU Project's g77 compiler works quite well for most purposes.  It is a standard component of Red Hat Linux, Caldera Open Linux, and most other Linux distributions.  Follow the highlighted link for more details.
    • A free Fortran 90 compiler for Linux plus other freely available compiler tools are available for personal use from Pacific-Sierra Research.  F is a subset of Fortran 90 without backward compatibility with Fortran 77.  A Linux version is freely available from Imagine1.
    • UNIX for FORTRAN Programmers by Mike Loukides (O'Reilly & Assoc, 1990; ISBN: 0-937175-51-X) is a very practical and useful reference for Fortran 77 programmers who are migrating to the UNIX/Linux programming environment.  The tools discussed include:
      • The FORTRAN compiler (f77).
      • UNIX interactive command languages, or shells (csh for interactive use, sh for shell programming).
      • vi, the standard UNIX editor.
      • Object library management tools (ar and ranlib).
      • The programming environment (I/O, basic system calls, error handling).
      • The adb and dbx debuggers.
      • prof, gprof, time, profiling tools.
      • make, a tool for automating complex compilations.
      • rcs, a source code management system for large projects.
      • Common porting problems.


      While it is out of print, copies can often be obtained from second-hand book dealers.  Tim O'Reilly also suggests that  "if you're desperate for a copy, try calling our customer service department at 800-998-9938. We will often still have a few copies in stock, or can track one down and sell it to you."

      Much of the material concerning the GNU programming tools is also contained in Programming with GNU Software by Mike Loukides & Andy Oram (O'Reilly & Assoc, 1996; ISBN: 1-56592-112-7) but without any reference to either vi or Fortran.

      If you need to include graphics routines in your Fortan code, we strongly recommend the PGPLOT package by Tim Pearson at Caltech.  See http://astro.caltech.edu/~tjp/pgplot/ for more details.

    8.  Is there a good mechanical CAD or drafting package for Linux?   [back to FAQ ToC]

    This a very frequently asked question.  However, I'm not a user of mechanical CAD or drafting software (xfig satisfies all my drawing requirements quite handily) so I can't offer much personal insight.

    However, there are certainly many CAD packages listed on the Scientific Applications on Linux website.  (They're given in the CAD, Drawing & Painting Tools  and Modelers  sections.)  They include GPL'd packages, ports of commercial packages (such as Bentley Microstation 95 and Varicad), and others.  I have no personal experience with any of them so would be most appreciative of any information that others might care to share.  Having said that, I would recommend one read the review by Thomas Wuest, P.E. before considering LinuxCAD, a product of a company called Software Forge.

    9.  How can one keep up to date with Science and Engineering Software for GNU Linux?   [back to FAQ ToC]

    a.  Two journals which often contain useful information are: IEEE Computing in Science and Engineering is a joint venture of the IEEE Computer Society and the American Institute of Physics in technical cosponsorship with the IEEE Antennas and Propagation Society and the IEEE Signal Processing Society.  It combines IEEE Computational Science & Engineering (1995-1998) and AIP's Computers in Physics (1987-1998).

    Linux Journal occasionally reports case studies of Linux applications in science and engineering in both regular and themed issues throughout the year.  In the past, it has also reviewed packages such as Scilab and Microstation.

    b.  Relevant mailing lists including:

    c. Some useful websites include: d.  A recent conference that was completely concerned with GNU Linux in Science and Engineering:

    10.  How is the Scientific Applications on Linux (SAL) website structured?   [back to FAQ ToC]

    The Scientific Applications on Linux website, http://sal.kachinatech.com/, has almost 2500 entries covering a wide range of applications.  In addition, each section and subsection of the SAL website carries links to specialized collections or information pages on other websites.

    While the SAL website is superbly organized, there is no master index.  The following list corrects that oversight:

    11.  What is Scilab?   [back to FAQ ToC]

    • a MATLAB-like software package for numerical computation
    • developed by INRIA in France
    • freely distributable and includes complete source code
    • features include:
      • Elaborate data structures (polynomial, rational and string matrices, lists, multivariable linear systems,...)
      • A sophisticated interpreter and programming language with MATLAB-like syntax
      • Hundreds of built-in math functions (new primitives can easily be added)
      • Stunning graphics (2d, 3d, animation)
      • Open structure (easy interfacing with Fortran and C modules via online dynamic link)
      • Many built-in libraries:
        • Linear Algebra (including sparse matrices, Kronecker form, ordered Schur,...)
        • Control (Classical, LQG, H-infinity,...)
        • Package for LMI (Linear Matrix Inequalities) optimization
        • Signal processing
        • Simulation (various ode's, dassl,...)
        • Optimization (differentiable and non-differentiable, LQ solver)
        • Scicos, an interactive environment for modeling and simulation of hybrid systems
        • Metanet (network analysis and optimization)
        • Symbolic capabilities through an interface to Maple V
    • for more details and documentation, see the Scilab home page,

    12.  What is the Intel/ASCI Red Software? [back to FAQ ToC]

    • a collection of highly optimized Pentium II math routines for Intel-based Unix systems:
      • ASCI Red Pentium Pro BLAS version 1.2D for Pentium II (10 December 1999)
      • 1D FFT's for single CPU's
      • Linux Hardware Performance Monitoring Utilities
      • Linux Extended Precision Math Primitives
    • jointly developed by Intel and the Accelerated Strategic Computing Initiative (ASCI)
    • for more details, see the Intel/ASCI Red Software for Linux home page

    13.  What is IBM techexplorer? [back to FAQ ToC]

    • a plug-in for Netscape Navigator which enables
      • the display of TeX, LaTeX, and MathML documents, and
      • the publishing of  interactive mathematical and scientific material on the Web
    • for more details, see IBM techexplorer home page,
    • Version 2.5, Preview Release 2 for Linux will be released shortly
    • for more details about MathML, see W3C Math home page,

    14.  What is Python?   [back to FAQ ToC]

    • an object-oriented scripting language (an alternative to Perl)
    • rapidly becoming popular in the science and engineering community
      • for stand-alone computation
      • as a steering language for compiled object modules
    • has native support for complex numbers
    • NumPy extensions support fast, efficient numerical array computations
    • Fortran, C, C++ modules are easily linked
    • for more details, see the Python home page and the LLNL Python page,

    15.  What is PERL and why is it of interest to scientific programmers?   [back to FAQ ToC]

    • Pathetically Eclectic Rubbish Lister?  Practical Extraction and Report Language?
    • a high-level scripting language that draws from C, sh, awk, sed, etc
    • very popular amongst UNIX system administrators
    • ported to MacOS and Windows
    • for more details, see the following pages
    • the PDL (``Perl Data Language'') provides standard perl with the ability to COMPACTLY store and SPEEDILY manipulate the large n-dimensional data arrays which are common in scientific computing.
    • pgperl provides standard perl with the ability to generate PUBLICATION QUALITY graphics using the PGPLOT graphics library

    16.  What are ten good practices for scientific programming?  [back to FAQ ToC]

    (adapted from a list published by Paul F. Dubois of LLNL, and published in IEEE Computing in Science and Engineering, vol. 1, no. 1, pp. 7-11, Jan/Feb 1999)
    • Embrace your inner programmer!
    • Organize for change
    • Don't reinvent the wheel
    • Use a modern source-code management system
    • Steer your compute engine using an interpreted scripting language
    • For small jobs, write a script instead of a compiled program
    • Use "Design by Contract" to ensure that interfaces between modules are clean
    • Mix languages (wisely)
    • Use Fortran 9x rather than Fortran 77
    • Use C++ rather than C
    I've re-organized the list slightly, but the emphasis remains the same: Many scientists and engineers spend much of their time writing code but few will admit to being professional programmers.  Paul Dubois argues that most scientists and engineers would be happier and more productive if they took care to better organize their efforts, employ modern software engineering practices, and generally "embrace their inner programmer".   (As one might suspect, Paul lives in California.)  There are three main themes:
  • Science and engineering software is often used much longer than the original authors ever intended.  The task of updating and maintaining such packages is difficult (to say the least) unless care is taken to modularize, document, and manage the source code.  The urge to re-invent the wheel should be resisted.  Use of reliable and actively maintained software libraries, whether for graphics, numerical computation, or user interface design, is a great way to share the programming load with the rest of the community.
  • User interfaces should be coded using an interpreted scripting languages such as Python, Perl, TCL, Scilab, or MATLAB.  This permits other users to modify the interfaces as required while preserving the integrity and performance of the compiled compute engine.  For small tasks, it is often much more efficient to use a scripting language entirely rather than conventional languages such as C or Fortran.  As Bertrand Meyer pointed out, "The problem with top-down structured design is that real problems have no top."  By replacing that all-too-volatile "top" with an interpreter, one enables significant change without requiring source modifications.
    • Object-oriented methods have attracted considerable interest because they give people an effective way of dealing with change.  Paul Dubois expresses a great deal of enthusiasm for the approach in the article. Even if one doesn't want to jump right in, he encourages scientists and engineers to use C++ and Fortran 9x rather than C and Fortran 77 so that they can start taking advantage of at least some of the new language features.  He also endorses Bertrand Meyer's "Design by Contract" method of realizing robust and reliable interfaces between software modules. Two books on the topic that he recommends are:
      • P.F. Dubois, Object Technology for Scientific Programming.  Prentice-Hall, 1997.
      • B. Meyer, Object-Oriented Software Construction, 2ed.  Prentice-Hall, 1997.
      While several commercial vendors have released Fortran 9x compilers for Linux, there is an urgent need for a GPL'd version as well.  If you can help, please visit the comp.lang.fortran newsgroup and let the powers that be know!
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    Last Updated:  21 Feb 2001 22:38