VMD-L Mailing List

From: Sam Wallace (sam.wallace_at_adelaide.edu.au)
Date: Tue Aug 28 2012 - 00:54:21 CDT

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