From: L. Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Mon Aug 28 2006 - 01:12:18 CDT

Hi John,
You're right, I was just wondering how well autoionize will perform,
but I see that it is VERY slow, just to share that with you guys :).
I'll definitely prepare my system with the new ionize tool. I'll make
you know what I got.

Thanks!
Michel

2006/8/28, John Stone <johns_at_ks.uiuc.edu>:
>
> Michel,
> Yes, now you see why I suggested using the new tool... ;-)
> The existing autoionize plugin is just a Tcl script, and so it doesn't
> have the ability to use more than one processor (even though VMD itself
> can). The new ionize program we have written is compiled C code,
> and thus it is able to run on multiple processors and runs much faster
> than any scripting language is presently able to. Placing ions on
> multi-million atom systems on a single processor can take _several days_
> of CPU time, even with reasonably written C code. The new ionize tool
> we've written uses both vectorization (use the Intel C/C++ compiler)
> and multithreading in order to run much much faster. The new ionize program
> can use all 48 processors of your Altix to good effect, the script-based
> autoionize plugin cannot.
>
> Thanks,
> John
>
> On Mon, Aug 28, 2006 at 12:44:24AM -0500, L. Michel Espinoza-Fonseca wrote:
> > Hi all,
> >
> > I've been testing the autoionize plugin using VMD 1.8.5 and a 8M atoms
> > system. Even though I haven't tried the ionize program yet, I wanted
> > to see how autoionize behaves with such a big system. I ran autoionize
> > on a 48-processor Altix machine with 96 GB of RAM, and autoionize has
> > been working for more than a day and still doesn't finish! I'm not
> > complaining at all, I'm just sharing what I'm getting. It might be
> > useful to mention that VMD is using only 1 processor out of the 48
> > available, and the memory requirements averages 6 GB.
> >
> > That's all for now, I'll keep testing it and I'll make you know about
> > the results.
> >
> > Enjoy!
> >
> > Michel
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> Email: johns_at_ks.uiuc.edu Phone: 217-244-3349
> WWW: http://www.ks.uiuc.edu/~johns/ Fax: 217-244-6078
>