VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Fri Sep 21 2012 - 16:53:06 CDT

Sam,
  I have posted a new win32 build of VMD for testing, which includes
the updates I made to the thread code in the hope that it fixes the
handle leak you encountered previously. The build I have posted so
far is a non-CUDA version, but I expect to have the CUDA version compiled
and posted shortly.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Aug 28, 2012 at 03:24:21PM +0930, Sam Wallace wrote:
> Thanks John
>
> That would be appreciated. Let me know when you'd like me to test it.
>
> -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"
>
>
> On 27 August 2012 12:03, John Stone <johns_at_ks.uiuc.edu> wrote:
> > 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 

-- 
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