VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Mon Feb 08 2010 - 14:48:16 CST

Irene,
  CPU-only ILS runs can take quite a while depending on the
number of atoms in the simulation, the number of frames,
and the resolution of the occupancy map you are generating.
Scientists in our group have occasionally run CPU-based
ILS jobs for multiple weeks at a time. I can't say for sure
how long your job will run without knowing more details about
the exact atom count in your system and the parameters you
selected when you ran the calculation, but I wouldn't be surprised
if you were still running for another week or so on the type of
machine you're using.

If you've got access to a machine with a CUDA capable GPU,
you would get speed boost likely around 20x compared to the CPU
calculation you're doing now, assuming a somewhat typical
usage scenario. Again, it's hard to estimate without more details.

Cheers,
  John Stone
  johns_at_ks.uiuc.edu

On Mon, Feb 08, 2010 at 10:05:30AM -1000, Irene Newhouse wrote:
> I kicked off an ILS run on my PC on Feb 4. It's Feb 8, & it's still going.
> I'm having it do 5K frames of a 133-residue protein on a 4-processor Xeon
> machine [no cuda] running at 2.33GHz. Can anyone give me a clue how long a
> job like this should run?
>
> Thanks!
> Irene Newhouse
>
> ----------------------------------------------------------------------
>
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-- 
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