VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Sun Aug 26 2012 - 08:05:00 CDT

On Sun, Aug 26, 2012 at 1:52 PM, Sam Wallace
<sam.wallace_at_adelaide.edu.au> 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.

what kind of handles?

> 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 disagree. it is most likely that your script is the problem.
those kind of issues happen a lot with analysis scripts.

> I don't know any C, so looking through the source code of the
> functions has not helped me.

a lot of people have been using the measure gofr command
since it was added to VMD. some did a lot and very large
analysis with it. thus i would consider it unlikely. however,
it is quite common that people without a lot of experience
in programming write Tcl scripts with memory leaks.

so let us get that one sorted out first.
please provide your script and let us have a look.

axel.

>
> 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" 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.