Preface to Version 2.0

It has been nearly 5 years since the last major modification to this manual, during which time development on GENPLOT has certainly not ceased. Version 2.0 has been in `beta' test for nearly the same period of time serving a number of research groups very efficiently. As I've told many users, development will never be finished as long as I remain active in research because I will always need the program to do something new - indeed the major driving force behind continued development have been my own requirements. Most of the beta users are well aware that the fastest way to get a new feature enabled is to either (1) get me involved in their problem or (2) challenge my abilities as a programmer.

So why, after 5 years, should I undertake now to finally edit an update the manual for version 2.0. Well, it is in fact for the very same reasons that the first manual was written. First, I find that I can no longer myself remember all of the features and commands and I find myself going back to the code itself too many times to ascertain exactly how a particular feature or command worked. Second, I'm beginning to answer the same questions over and over from other users; do it once right and the number of questions drop rapidly. And finally, there are enough new features in the program that a large number of users do not know about - and cannot know about unless I document them. So with these thoughts in mind, I finally made the effort to again tackle the daunting effort of revising and updating the manual.

The beginnings of GENPLOT in its current form can be traced to at least 1982 in the days of the PC-AT when 640 kB of RAM memory was as much as anyone could possibly imagine using, much less affording, hard disks were still measured in 10's of MB, and processor speeds had not yet exceeded even the 10 MHz speed limits. But it was an exciting time from the scientific computing world - finally a chance to have a computer for working with data in the lab with relatively high speed graphics and ones own control of the machine.

Much has changed since those days. Processors now approach 300 MHz clock speeds with pipelined architectures and embedded co-processors, RAM memory of 16 MB is the minimum with 1 GB not unheard of in scientific circles, and any hard disk not measured in gigabytes is no disk at all. These hardware changes have brought about paradigm shifts striking at the very core of our interaction with computers. The raw computational power of today's desktop machines makes the GUI (graphical user interface) responsive enough even for those of us with absolutely no patience. No longer is the computer the reserved privilege of the computer geeks. Even a computer phobe and neophytes can sit down today to a GUI word processor and very effectively compose letters, draw figures, even make movies. For the creative arts, the age of the GUI has allowed artists to be artists, just on computers.

Reading the old manual, I note with humor my comments concerning the Macintosh. In some sense, I regret my comments because I have always admired the vision of Apple especially in user aesthetics -- their interface and the uniformity of applications in particular. But for serious scientific work, the computation power simply did not exist to support the complexity of the GUI and handle our needs. Today, with the computation power now available, the Mac faces a serious challenges from the markedly inferior imitation of Microsoft Windows (be it 3.1 or 95, 96, ...). (Unfortunately, the Mac still harbors its own grudges toward me and is sure to hang at my briefest of attempts at serious use.)

However, while the paradigm for computer interfaces has markedly changed over the past decade, the task facing scientists and engineers has not (though some may argue the current emphasis on relevant research is as much a revolutionary paradigm shift as the command line interface to a GUI). We are still faced primarily with trying to discern nature around us - trying to identify trends in data, extracting features from data, fitting data to models, critically testing models, building intuition on behavior of mathematical functions, and only then generating pretty pictures for inclusion in papers.

Unfortunately, the advent of the GUI has, in many cases, actively reduced the quality of the work we do. Watching students in my own university, I see them spend enormous amounts of time generating viewgraphs to show data that was collected in less than 10 minutes. At the next scientific meeting, note the inverse correlation between the actual scientific content of a talk and the quality of the viewgraphs. Why? Because it looks really neat to have a blue background with yellow bulleted letters and a 3D border. Manuscripts are the same way - I've gone so far now as to give extra credit for simple typed reports.

So what does this tirade about the failing qualities of modern students have to do with the revisions to GENPLOT? Well, nothing with the changes, but much to do with what remains the same. GENPLOT began as a simple command line driven program, albeit very flexible, and it will probably end its life in the same way (possibly in proof that I am wrong). As a scientist, I am still very much a linear thinker - consider one model and if it fails, try another. Change parameters to see how they change, smooth the data and look again, compare the data to a previous experiment. Understanding and fore-knowledge of what is being done is a critical requirement to quality research.

The GUI in modern programs has also eliminated power and flexibility for the ease of learning. This is not always such a great tradeoff - and putting back in the complexity bloats programs in a way that only Microsoft can love (aka Word 6.0). The GUI learning curve is rapid, but levels out quickly with no further productivity enhancements in time. A powerful command driven program, like UNIX, on the other hand has a long learning curve but the curve never saturates - as one gains experience with the commands the productivity continues to increase seemingly without end. It is toward this latter model that GENPLOT continues to evolve.

There are other problems I have with GUI based programs that try to dumb down the effort of data analysis. There is an advertisement in my `competition' folder for a commercial program that touts its ability to fit your data to 1200 different functional forms, returning a list of those that match most closely. What absolute crap - the old paradigm that if you give me enough parameters I can fit an elephant immediately comes to mind. If you don't have any idea what form the data should take, stop and do a little thinking first. Similarly almost every graphing will do a linear fit and return that horrid correlation coefficient that less than 5% of the scientific population can properly interpret. Computers have brought us fortunately and unfortunately to the point that data can be too easily analyzed - and many critical steps in the scientific process have been lost. Much more careful thought must have been required in the past when comparing a model to experimental data meant several hours of painful calculations with a slide rule (no I never did it and no I don't really wish to return to such days).

I believe GENPLOT 2.0 remains a premiere program for testing and critically evaluating models against data. The expression evaluator has been extensively upgraded and is now almost unlimited in the complexity which can be handled, including complex number expressions. The non-linear least squares fitting has similarly been extended to handle arbitrary expressions and can even call external programs to run complex simulations. Limitations posed by the old DOS architecture have disappeared and curves with millions of points can be routinely handled. But it remains impossible to mold intuitive investigations and scientific examination of data into point and click sets of dialog boxes - I cannot possibly foresee all the twists and convolutions that will be necessary for you to perform to analyze your data. And so GENPLOT remains a command driven environment at version 2.0, flying in the face of modern wisdom.

But there is value in the GUI - if not for more than helping remind one of the proper command syntax. The FFT command has so many options and parameters that there is no feasible way to remember them. A simple dialog box however puts all them in place (albeit very busy and considered anathema to modern GUI design - design rules that specify no more than 3 or 4 topics per dialog box and require one to dig down 4 or 5 levels to get to the single parameter that is to be changed) and when executed, gives the command line version for future reference. Or the dialog box to set all the strange parameters of the axis control. The GUI can complement the command line interface, but it can never replace it.

But what about the graphics? Well, here I have to admit that there is great value in the GUI and I've tried to begin incorporating more control based on the GUI. The absence of a unified graphical environment (covering UNIX, OS/2, Mac, and perhaps even Windoze) has slowed me considerably since the effort is large and the payback only marginal (in terms of the science that can be done). Users of OS/2 will notice much better integration than UNIX, but both will see substantial improvements in the presentation of graphics on postscript printers. But certainly GENPLOT remains behind, in ease of use, programs which emphasis the presentation of data over the analysis. However, though not as easy to use, I still claim that the final graphics produced by GENPLOT are equivalent or superior to almost every other drawing application.

The change from version 1.0 to 2.0 required considerable work since the entire package had to be ported from a FORTRAN 77 and assembly language base to a pure C base. In the days of DOS, memory and speed were critical issues and the Ryan-McFarland FORTRAN compiler was the only high level, robust, compiler that existed (originally sold also as the IBM Professional Fortran). Slow operations were translated to assembly language both for speed and for code size. The 640 kB barrier was rigid and self managed dynamic linking had to be developed. Indeed, the complexity of the code and the dearth of tools to support development amazes me still today. Once memory dropped in price, EMS, XMS and similar contortions began being used to shoe horn the new power in hardware into an already obsolete DOS.

IBM and Microsoft released OS/2 in the later 80's, the first PC based operating system to maintain some compatibility with DOS applications (necessary in the lab) but bypassing the 640 kB memory barrier and running in true preemptive, protected, multitasking mode. We jumped to OS/2 at version 1.2, recognizing that for scientific work the 640 kB barrier would remain a nightmare, and have never looked back again (though the students sometimes would like to!). FORTRAN compilers did not exist for OS/2 and the mix of assembly and FORTRAN was becoming a challenge to support as the complexity grew. C was a more suitable language anyway and the ANSI standard made it feasible to write one version that ran on a variety of hardware. Every line of code had to be translated and converted - and not by automatic programs but manually to take advantage of the features of the language.

A few commands never made it across the translation - they were so seldom used that it was not worth the effort. Similarly, with the new OS there was no need to write device drivers for every device since the operating system provided much of the interface. Unfortunately, UNIX did not provide the same services in the area of device drivers, but X-windows and the common Postscript printers made their absence less noticeable.

The bottom line is that GENPLOT is now almost 100% ANSI standard C with very few extensions. Porting from OS/2 to most flavors of UNIX can be handled in a day given a compliant compiler. If the POSIX subsystem of Windows NT weren't such a joke, even Windows NT would be a viable platform (actually a native NT version does now exist, but it isn't based on the POSIX subsystem). Extensions can be easily written in C for new functions, for control of instruments, or for stand alone applications.

Someone always asks me how big GENPLOT is now. The honest answer is that I do not know. In UNIX or OS/2, only the necessary components of the code are loaded into memory at any time and so size is nearly irrelevant. However, the bloat that marks Microsoft is certainly not present. The actual executable code is on the order of one megabyte and the entire package compressed can still fits on only two diskettes. The kitchen sink is not included and I don't think 35 MB of additional fonts and pictures would do much to enhance the usefulness (though some more example macros will probably make it in the final distributions).

Finally, I looked to see how the average user of GENPLOT has changed over the past half decade; the answer I find is little. Perhaps even more than before, I think the users of GENPLOT are self-selected individuals unafraid of the computer and keyboard, confident in their ability to understand written manuals, sticklers for small details, and demanding in their expectations of the computer. Like me, when someone says that computer cannot do this or that, the first response is bull - it's only that no one has yet programmed the computer for that task. For serious GENPLOT users, the computer is a slave and they demand that it perform for them as they desire, not as some short sighted and idiotic programmer thought it should perform. Flexibility is the key to all things.

This preface would not be complete without recognizing, acknowledging, and thanking those users who have tested the program over these past years, challenged me to incorporate new features, and made so many suggestions that it challenges my talents to incorporate them all. I would especially like to thank Roger de Reus, David Brunco, Anthony Dai, Sjoord Rooda, Larry Doolittle, Jon Custer, Pat Smith, William Boyer and Mike Uttormark. Larry Doolittle and Mike Uttormark also assisted in various pieces of the code, with Larry in particular heavily involved in the early conversion of the RUMP portion of the program to C. And through it all, this effort would have been unsuccessful without my business partner Patricia Ober, and my former partners Mike and Nancy Heisler. And certainly, nothing is possible without the support and encouragement of my wife Lisa and son Ian!

I also recognize the support of the users who have bought GENPLOT and RUMP. It's not the day job, but GENPLOT does provide enough income to keep me supplied with a reasonably powerful computer at home and so supports my programming habit. This eliminates the tricky questions concerning conflict of interest since development of GENPLOT can be nearly independent of the day job, although both GENPLOT and my research certainly benefit from each other significantly.

And so, with humble apologies for all those I've insulted, let's get on with the real problem at hand. How do you tame the beast called GENPLOT?

Michael Thompson - June 21, 1996

Last modified: November 3, 1996
Michael O. Thompson (