VMD-L Mailing List

From: Sam Wallace (sam.wallace_at_adelaide.edu.au)
Date: Fri Sep 21 2012 - 19:14:00 CDT

Hi John

I've just tested the build now. It works fine, no leaking of thread handles.

Thanks very much

-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 22 September 2012 07:23, John Stone <johns_at_ks.uiuc.edu> wrote:
> 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