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Computer Bulletin Board
Linux and the Chemist
edited by
Steven D. Gammon Western Washington University Bellingham, WA 98225
Jerry F. Moore* and Michael P. McCann Materials Science Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439; *
[email protected] Many people have heard of the operating system Linux (Figure 1). It was created in 1991 by a Finnish student at the University of Helsinki, Linus Torvalds (1). The Linux operating system soon was offered under the General Public License of the Free Software Foundation (2). This means that Linux can be freely traded under specific guidelines designed to protect the integrity of the operating system. There are now many professional and amateur programmers who contribute to the kernel (the heart of the operating system, ref 3), plus many others that contribute applications (4). Linux has evolved into a sophisticated, user-friendly, well-supported operating system worthy of the attention of general computer users. Chemists, in particular, have many good reasons to use Linux. If you are a chemist at an institution with many computers, you may legally download and install as many copies of Linux as you wish. This means that you no longer need to buy a copy of the operating system for each computer running that operating system. There are no licensing fees. For those limited to a modem, Linux is available on CD for a cost as little as $1.98 (5). Again, this CD may be used to legally install as many copies as are needed. Additionally, a number of companies or organizations offer distributions: packages of the Linux operating system with enhancements,
utilities, and even applications. This distribution is similar to what one gets when purchasing Windows or Macintosh OS licenses. The cost of these distributions is typically low ($1–$50), and as before, an unlimited number of copies is allowed, so the cost per computer is very low. Extensive technical support is also available from many of these companies for a charge. Linux was created on a computer with an Intel 80386 microprocessor. Since that time Linux has been ported to many different processors: Intel 80486, 80586, Pentium, Celeron; AMD K5, K6; Cyrix 6×86; Motorola 680×0; Power PC; DEC Alpha (64-bit RISC chip); and Sun SPARC. Essentially any modern desktop computer is capable of running Linux. Linux also works with computers with symmetric multi-processors (SMP). Computers running Linux have been linked together to form Beowulf clusters, essentially groups of PCs linked by a network to perform parallel calculations (6). In some cases, Beowulf clusters have hundreds of computers (or nodes) and their performance rivals a supercomputer. The popularity of Linux use in clustering is due to the ease with which Linux handles networking. Linux is available in many distributions, which include the Linux kernel and a selected number of applications. Various distributions have advantages and disadvantages related
Figure 1. Screenshot of Linux desktop.
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to ease of installation, number of included applications, graphical user interface, et cetera. Distributions are available that are tuned for minimalist computers, Power PC-based computers, general purpose desktop work, and many other configurations. Some of the more popular distributions are listed in ref 7. Typically, a distribution contains a few compilers (C, C++, Fortran), text editing, word processing and publishing software, a Web browser, several server daemons (Web server, e-mail server, ftp server, dns server), X-Windows, graphics software, along with a number of utilities and games. To purchase commercial software comparable to that available in a Linux distribution would cost about $2000–$3000, and copies would have to be purchased for each computer. Software is available that is of particular interest to chemists. The quantum mechanics program Gaussian runs under Linux (8). GNUPlot has been used to display atomic orbitals (9). A Linux version of Mathematica is also available (10). Numerous programs for chemists such as statistical treatment, molecular modeling, NMR spectral processing, DNA sequence evaluation, crystal structure solving, and molecular dynamics are available, many for free. An extensive list may be found on the Web site Scientific Applications on Linux (11). Software for interfacing computers with scientific instruments, LabView for Linux, may also be purchased (12). A number of office suites are available. WordPerfect runs under Linux (13). StarOffice and Applixware are two office suites that contain word processing, spreadsheet, database, and presentation software (14, 15). They are able to import and export Word and Excel files (16). The strengths and weaknesses of each have been compared (17). There are a number of resources for more information on Linux. The University of North Carolina maintains a site where the various Linux distributions may be downloaded (18). Equally useful are their Linux documents, which explain anything from how to use Linux on an Alpha computer to using X-Windows. To keep up on Linux news there is the Web site Slashdot (19), and the Web site Freshmeat provides a source for the latest Linux software (4). The most recent Linux kernel may be downloaded along with the latest version of X-Windows (21, 22). The Free Software Foundation offers software that runs under Linux along with documentation (2). There is also the Linux Journal for those who need a hardcopy of the latest Linux news and information (22). Finally, there are a number of books that have been written about various aspects of Linux, many of them published by O’Reilly & Associates (23). Linux is not for people who choose to treat their computers as a black box. It has been said that what you don’t pay for Linux in money, you pay for with your own time. Linux is generally not as easy to install as other operating systems. Because software is written when someone takes the time to write it, it often takes a while before the latest hardware is supported by Linux. The technical data must be made available before someone can write a Linux driver. So you might have to wait a while before new hardware (like a 3D video card) has a driver that works under Linux. If the company doesn’t release the technical data, your new 3D video card may never work under Linux. Visual programming also isn’t as well developed as in other operating systems. So writing a program with a nice graphical user interface is often more difficult under Linux. 220
The situation with respect to usability and support is improving. Linux is much easier to install than it was a few years ago and should continue to improve. More and more companies are writing Linux drivers for their hardware (printers, video cards, scanners), so more hardware works with Linux, and it works much sooner. Linux is an operating system that lives on the Internet. The most popular Web server is Apache, which runs mostly under Linux (24). There is a huge Net presence of Linux users and developers. Linux is running at a number of universities, colleges, and high schools. Along with the network presence comes concern about security: in particular, virus susceptibility. Although Linux computers passed on the latest e-mail viruses, they were not subjected to their symptoms. Though Linux likely will become the target of viruses as it becomes more popular, it is better able to withstand these attacks. For those concerned about being able to use some familiar programs there is a DOS emulator (25) and a Windows emulator (26). These programs pretend to be DOS or Windows well enough to run some software written for those operating systems. Word and Excel 2000 run under the Windows emulator (16, 26). Running these emulators removes the need for maintaining two operating systems on one computer. The Windows emulator, WINE, should still be considered experimental. It takes some configuring and does not work with all Windows programs. There is also the obvious performance penalty due to Windows commands being translated into Linux commands. Another option for achieving the same effect is a commercial program that allows multiple operating systems to coexist, so that Linux could play ‘host’ to your preferred version of Windows (27). What is the bottom line? If you find your current operating system lacking, you might want to take a look at Linux. It is not going to fade away anytime soon, and is likely to become a major force in computing owing to its powerful Internet strengths. To paraphrase a tune from the 80s: its future’s so bright ... it’s got to wear shades. Literature Cited 1. Welsh, Matt; Kaufman, Lar. Running Linux, 2nd ed; O’Reilly & Associates: Sebastopol, 1995; p 4. 2. The GNU Project and the Free SoftwareFoundation. http:// www.gnu.org (accessed Aug 2002). 3. Richardson, Marjorie. Linux Journal 2000 (June), 74, 85. 4. Freshmeat.net. http://freshmeat.net (accessed Aug 2002). 5. Linuxmall. http://www.linuxmall.com (accessed Aug 2002). 6. Beowulf Project. http://www.beowulf.org (accessed Aug 2002). 7. Wallace, Richard. Linux Journal 2000 (July), 75, 10. 8. The Official Gaussian Web Site. http://www.gaussian.com (accessed Aug 2002). 9. Moore, Brian G. J. Chem. Educ. 2000, 77, 785. 10. Wolfram Research, Inc. http://www.wolfram.com (accessed Aug 2002). 11. Scientific Applications on Linux. http://sal.kachinatech.com/ index.shtml (accessed Aug 2002). 12. National Instruments. http://www.ni.com (accessed Aug 2002). 13. Corel LINUX Community. http://linux.corel.com (accessed Aug 2002). 14. Star Office 6.0 Office Suite. http://www.sun.com/staroffice/ (accessed Aug 2002).
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Information • Textbooks • Media • Resources 15. Anyware RealTime. http://www.vistasource.com (accessed Aug 2002). 16. Microsoft Corp. http://www.microsoft.com (accessed Aug 2002). 17. Kroll, Jason. Linux Journal 2000 (February), 70, 70. 18. ibiblio:Linux! http://www.ibiblio.org/ (accessed Aug 2002). 19. Slashdot: News for nerds, stuff that matters. http:// www.slashdot.com (accessed Aug 2002). 20. Linux Kernel Archives. http://www.kernel.org (accessed Aug 2002). 21. XFree86 Home Page. http://www.xfree86.org (accessed Aug 2002).
22. Linux Journal. http://www.linuxjournal.com (accessed Aug 2002). 23. O’Reilly & Associates Home Page. http://www.oreilly.com (accessed Aug 2002). 24. The Apache Software Foundation. http://www.apache.org (accessed Aug 2002). 25. DOSEMU Home Page. http://www.dosemu.org (accessed Aug 2002). 26. WINE Development HQ. http://www.winehq.com (accessed Aug 2002). 27. Virtual Machine Software. http://www.vmware.com/ (accessed Aug 2002).
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