VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Wed May 25 2011 - 05:35:42 CDT

On Wed, May 25, 2011 at 5:51 AM, maria goranovic
<mariagoranovic_at_gmail.com> wrote:
> Hi All
> This is vmd version 1.8.6. there is only one selection that I make using

nobody will help to debug some thing on a VMD version "from
the stone ages". there have been a huge number of bugs fixed
in the code since. please upgrade first.

axel.

> atomselect, and am deleting it immediately after. The number of frames after
> which i see the segmentation fault depends on the number of closest waters I
> try to find.
> If I try to find 50 closest waters, the seg fault appears after 51 frames.
> Other numbers are :
> # waters      # frames before segfault
> 50            51
> 100          51
> 1000          51
> 2000          51
> 3000          603
> 4000
> On Tue, May 24, 2011 at 9:08 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:
>>
>> hi
>>
>> i totally forgot to insert a plug (pun intended) here for the vmd debug
>> plugin.
>>
>> (sidenode: john, i just noticed that there is no working URL for the
>> vmddebug plugin documentation.)
>>
>>
>>
>> On Tue, May 24, 2011 at 1:13 PM, John Stone <johns_at_ks.uiuc.edu> wrote:
>> >
>> > Maria,
>> >  This is most likely an "atom selection leak", where your script is
>> > creating a large number of atom selections but not deleting them as
>> > it no longer needs them.  Make sure that you delete any atom selections
>> > that are being created as each frame is loaded, before the script moves
>> > on to process the next frame.
>>
>> as of VMD 1.9 there is a plugin that can help tracking how many atom
>> selections
>> you make and thus show you whether you have a "selection leak". it can
>> even
>> help with narrowing down where the leak is. this makes use of some
>> advanced
>> Tcl scripting features so i would love to hear, if this works for
>> everybody or if not
>> and where and how not.
>>
>> the usage of the plugin is very simple.
>>
>> package require vmddebug
>> debug atomselect on
>>
>> and then run your code and with:
>>
>> debug atomselect stats
>>
>> you can get an update of how many selections have been
>> allocated. if you want to track individual atomselect invocations
>> and uses of the selection functions, you can do:
>>
>> debug atomselect verbose
>>
>>
>> good luck,
>>     axel.
>>
>>
>>
>>
>>
>> >
>> > Cheers,
>> >  John Stone
>> >  vmd_at_ks.uiuc.edu
>> --
>> Dr. Axel Kohlmeyer
>> akohlmey_at_gmail.com  http://goo.gl/1wk0
>>
>> Institute for Computational Molecular Science
>> Temple University, Philadelphia PA, USA.
>
>
>
> --
> Maria G.
> Technical University of Denmark
> Copenhagen
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.