VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Feb 08 2010 - 14:56:53 CST

Thanks for the lightning response. The system has 2.5K non-waters & 23K atoms in all. We're a low-budget op here & don't have a machine with cuda available:-( As this is my first time ever trying this, I left the default settings as they are in the ILS plugin. I told it to do all 5K frames of a 5nsec traj. I'm open to suggestions that will improve speed w/out losing accuracy terminally, such as if I use every nth value instead of all frames, what would a reasonable value be? And any other setting alterations. Thanks again!

 

Irene
 
> Date: Mon, 8 Feb 2010 14:48:16 -0600
> From: johns_at_ks.uiuc.edu
> To: einew_at_hotmail.com
> CC: vmd-l_at_ks.uiuc.edu; saam_at_ks.uiuc.edu; dhardy_at_ks.uiuc.edu
> Subject: Re: vmd-l: how long do ILS runs take?
>
> 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
                                               
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