VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Sun Aug 26 2012 - 21:33:39 CDT

Sam,
  I have a small change I can make to the VMD code that I'd like you to test.
It will likely cure the handle count issue you're seeing, but that may
or may not cure the larger symptom you describe. I can probably have a
new Windows test build ready in the next couple of days after I make
sure the change doesn't cause other problems on the older revs of Windows.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Sun, Aug 26, 2012 at 09:22:39PM +0930, Sam Wallace wrote:
> Hi
>
> I wrote a script to analyse my data that calls upon the 'measure
> gofr'. It's measuring a large number of atom pairs and processing
> through a large number of trajectories.
>
> I noticed that performance of my PC dropped significantly as the
> script continued. I checked for any errors in the script I wrote
> that'd cause a leak but couldn't find any.
>
> I used ProcessExplorer
> (http://technet.microsoft.com/en-us/sysinternals/bb896653.aspx) to
> track memory/cpu usage to see what was causing the issue. I noticed
> there was a steady increase in the number of handles as my script ran.
> The system became mostly unresponsive as the number of handles
> approached 3.5 million. Normally, system is at 40000.
>
> Since I couldn't find anything wrong with my own code I suspected it
> might be in the measure gofr command itself.
>
> I tested it by loading VMD, loading up a small trajectory, creating
> two selections in the TkConsole and calling it. Each time the number
> of handles increased and never decreased until VMD was terminated.
>
> I don't know any C, so looking through the source code of the
> functions has not helped me.
>
> Hopefully someone can help
>
> -Sam
> --------------------------------------------------------------
> Sam Wallace, Ph.D Student
> School of Chemistry and Physics, University of Adelaide
> Adelaide, South Australia 5005, Australia
> Phone: +61-(0)8-8303-4332
> Fax: +61-(0)8-8303-4358
> Email: sam.wallace_at_adelaide.edu.au
> "I suppose you wouldn't have a problem with me saying the fermi-dirac
> distribution is a soup kitchen" 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078