VMD-L Mailing List

From: Sam Wallace (sam.wallace_at_adelaide.edu.au)
Date: Sun Aug 26 2012 - 06:52:39 CDT

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"