Older blog entries for RickMuller (starting at number 16)

Played with VTK for a while yesterday, in part inspired by this story. Got all of my old scripts working. Really is a neat library. I continually destroy myself by thinking that I can make a better viz system if I custom write everything, which I never in fact do, which means that I never have any graphics working. VTK gives a very workable set of algorithms and data structures, and if I had used it more often I would have prettier pictures for all of my presentations.

Hopefully will be off to Sequoia for the weekend for a bit of emotional recharging.

etrepum: Thanks for the tip. I'll give this a shot when I sit down with it again.

3 Apr 2003 (updated 3 Apr 2003 at 18:15 UTC) »

Still having problems with the gopenmol port to OS X. I got the following error when compiling:

ld: warning suggest use of -bind_at_load, as lazy binding may result in errors or different symbols being used
symbol _gluErrorString used from dynamic library /usr/X11R6/lib/libGLU.dylib(error.o) not from earlier dynamic library /System/Library/Frameworks/OpenGL.framework/Versions/A/Libraries/libGLU.dylib(error.o)
make[1]: *** [gom_shared] Error 1
make: *** [shared] Error 2
Does anyone know what I should do? I tried the obvious, i.e. adding -bind_at_load to the load line, but I got the same mistake again. Suggestions?

I've spent a little time getting to know the Gnu Scientific Library, after I found it so useful earlier with quasirandom numbers. It's a really impressive piece of work. I'm amazed that it isn't more widely adopted in scientific computing. Maybe it is, and I just didn't know about it, but I know a lot of programmers, and I'm the only person I know who has used it. It would be nice if -lgsl could one day be as common as -lglibc is today -- it would mean that programs would share a common base of functions, and would keep people from reinventing functionality that already exists and is stable.

There is an embryonic effort for Python wrappers for the GSL. Maybe if I can cross off some other items on my todo list I can write some code for them.

I've spent a little time getting to know the Gnu Scientific Library, after I found it so useful earlier with quasirandom numbers. It's a really impressive piece of work. I'm amazed that it isn't more widely adopted in scientific computing. Maybe it is, and I just didn't know about it, but I know a lot of programmers, and I'm the only person I know who has used it. It would be nice if -lgsl could one day be as common as -lglibc is today -- it would mean that programs would share a common base of functions, and would keep people from reinventing functionality that already exists and is stable.

There is an embryonic effort for Python wrappers for the GSL. Maybe if I can cross off some other items on my todo list I can write some code for them.

28 Mar 2003 (updated 28 Mar 2003 at 01:52 UTC) »

It's been a while since I've posted. Spent much of the intervening time at my research center's annual meeting. Gave a talk on some new computational rapid prototyping techniques we have been working on to develop new catalysts. The paper should be coming out soon in Topics in Catalysis. The idea is to develop algorithms where computers can do much of the drudgework involved in finding new catalysts rather than doing time-consuming experiments. The technology is still probably years away, but we wanted to start thinking about what questions we wanted to ask and answer along the way.

Spent most of the rest of the time writing a grant proposal for the DOE, which always makes me feel like I've been in a time warp where I wake up a week later and wonder where I've been.

To escape grant proposal hell, I learned a bit about quasirandom number sequences. There's a great reference here, and a good chapter from Numerical Recipes. Quasirandom sequences can be used when you normally use pseudorandom sequences, e.g. in Monte Carlo simulations, but often converge quicker (1/N rather than 1/sqrt(N)). The Gnu Scientific Library has some good generators. I have a Python implementation of their Sobol' sequence if anyone is looking for one.

21 Mar 2003 (updated 21 Mar 2003 at 21:15 UTC) »
Tutorial or ShortCourse Advice

Over the past 3 years I've taught a Python Short Course twice as an unofficial info course here at Caltech, mostly just to graduate students and post-docs here in the MSC. The first time I taught it I did a 7 lectures (one per week) of about 45 minutes, with some time for questions each week. The second time I taught the course, I crammed the most important info into 3-4 hours and taught a mamoth single-lecture version.

Both courses were well-received. I think the problem with the first format was that, even though I told people the topics were independent, and that they didn't have to go to all of the previous lectures to benefit from some of the subsequent ones, once people missed a lecture, they stopped showing up altogether. The problem with the second format was that 3-4 hours puts a big demand on both the lecturer and the audience.

Surely there must be people who have far more experience than I in teaching these courses. Can anyone give me any input? I've been toying with the idea of turning everything into a self-paced tutorial, but I worry that some of the concepts won't get across.

I would welcome any advice people have...

Still struggling with my gOpenmol port. Autoconf isn't playing nice, so I'm going to have to hack the Makefile and work out autoconf later. Bad nerd, bad nerd.

GWB Democrat? Remember the term Reagan Democrat, which referred to a (generally Southern) Democrat who voted for Reagan? I propose we coin the new term GWB Democrat for a person who was a loyal Republican until GWB. Not that I'm naming any names...

18 Mar 2003 (updated 18 Mar 2003 at 20:09 UTC) »

Have been babysitting all morning, so my mind really isn't on computers...

Terry Pratchett

Have been absolutely addicted to Terry Pratchett's Discworld Series of late. Found him almost by accident, because of the Good Omens book he wrote with Neil Gaiman another one of my recent obsessions. I guess I had associated "humorous fantasy" with writers like Pier Anthony, and wasn't all that thrilled by it, so I'm amazed how enthralled I am by Pratchett's characters and his wit.

I had thought that tearing through paperback books in a single day was something I left behind me long ago in adolescence, and it's a nice surprise to feel that way about an author again.

Netflix

Bought my wife a DVD player for Christmas, and went ahead and signed up for Netflix. Really like the service -- much more convenient than going to Blockbuster, and we've seen a whole lot of great movies. Highly recommended, if you haven't already signed up.

etrepum: thanks for the pointer -- turns out autoconf is bombing out when looking for GLUT, so I'm trying to figure out what's wrong there. The gotchas page looks great!

chalst: thanks for the news tips. Can't believe I forgot about the Economist. I'll check out the others as well.

Quick question for the Advogotroids: I'm currently porting gOpenMol to OS X. During compilation, I get a complaint that the compiler can't find GL/glaux.h. Neither Apple's nor Fink's installation has a glaux.h include file. I did a little web searching and found this note on the OpenGL web site, which makes me believe that I've done something wrong in configuring the program, and that the program should have found what it needed from GLUT. Thoughts?

Found this article interesting: evidently, Americans are flocking to foreign news sites in droves because of the timidity of US News organizations. The article mentions The Guardian. Does anyone have any other faves? I personally find Google News pretty international, since it's put together by a computer without much of an agenda, but maybe that's my provincial American worldview speaking...

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