VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Aug 28 2006 - 00:59:33 CDT

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