VMD-L Mailing List

From: Irene Newhouse (einew_at_hotmail.com)
Date: Mon Feb 08 2010 - 16:51:23 CST

Thanks! I'll scroll through the various messages looking for frame numbers.

 

Irene
 
> From: jan.saam_at_gmail.com
> Date: Mon, 8 Feb 2010 22:31:29 +0100
> Subject: Re: vmd-l: how long do ILS runs take?
> To: einew_at_hotmail.com
> CC: johns_at_ks.uiuc.edu; vmd-l_at_ks.uiuc.edu; dhardy_at_ks.uiuc.edu
>
> Irene,
>
> take a look at your VMD console. ILS should print it's output there.
> You should find one or several lines for each frame, including a frame
> count and a timer. This should give you a good idea how far your
> calculation has progressed and how long it wil take to finish.
>
> Jan
>
> On Mon, Feb 8, 2010 at 9:56 PM, Irene Newhouse <einew_at_hotmail.com> wrote:
> > 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
> >> >
> >> > ----------------------------------------------------------------------
> >> >
> >> > Hotmail: Free, trusted and rich email service. Get it now.
> >>
> >> --
> >> 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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