VMD-L Mailing List

From: Sam Wallace (sam.wallace_at_adelaide.edu.au)
Date: Sun Aug 26 2012 - 09:02:36 CDT

Hi Axel

Thanks for the reply.

I'm confident it's not the script I wrote, because I'm reproducing the
leaking handle behaviour simply by entering the commands in the
TkConsole
I load up a psf & trajectory

set sel1 [atomselect top "resname MOL"]
set sel2 [atomselect top "segname G3"]
measure gofr $sel1 $sel2 usepbc 1 first 0 last -1 delta 0.1 rmax 20
measure gofr $sel1 $sel2 usepbc 1 first 0 last -1 delta 0.2 rmax 20
measure gofr $sel1 $sel2 usepbc 1 first 0 last -1 delta 0.1 rmax 30
measure gofr $sel1 $sel2 usepbc 1 first 0 last -1 delta 0.1 rmax 30

each time I run the measure command, the number of handles used increases.
I checked what type they are using this handle tool
(http://technet.microsoft.com/en-us/sysinternals/bb896655)
It's adding to thread handles count each time.

I have installed tcllib
(http://sourceforge.net/projects/tcllib/files/tcllib/1.14/) to add
some functions to the TkConsole. To eliminate that as a cause I tried
a clean install of VMD 1.9.1 (no cuda) on a different system running
windows 7. I loaded the same psf and trajectory file and performed the
same steps in the console. I monitored the handle count using
ProcessExplorer and found it increased each time I ran 'measure gofr'.
I've also tried different trajectory files. Each time the measure gofr
command increases the handle count.

It seems the number of thread handles used is 4 * number of frames
specified in measure command.

-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 26 August 2012 22:35, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
> 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.