VMD-L Mailing List

From: Sam Wallace (sam.wallace_at_adelaide.edu.au)
Date: Sun Aug 26 2012 - 09:33:24 CDT

In the TkConsole example It doesn't make a difference. Each time the
measure gofr is called. The thread handle count goes up by ((4=number
of cpus) * number of frames). Those thread handles aren't getting
released/removed until VMD is terminated.

Alternatively, even if I try deleting and redefining the selections
after each command, handle thread count goes up.

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
$sel1 delete
$sel2 delete
set sel1 [atomselect top "resname MOL"]
set sel2 [atomselect top "segname G2"]
measure gofr $sel1 $sel2 usepbc 1 first 0 last -1 delta 0.2 rmax 20
$sel1 delete
$sel2 delete

-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 23:52, Cruz-Chu Eduardo Roberto
<eduardo.cruz_at_mavt.ethz.ch> wrote:
> you have to add
>
> $sel1 delete;
> $sel2 delete;
>
> after the measure commands.
>
> On Aug 26, 2012, at 4:02 PM, Sam Wallace wrote:
>
>> 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.
>