VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Wed May 25 2011 - 05:57:10 CDT

Well, I would first try to VMD 1.9 and see if it works better.
(And if I understand correctly the new verson has a debugger plugin that can
be very useful in exactly this situation).

It is strange that the less waters you try to find the earlier the analysis
crashes. If it were a memory leak one would expect just the opposite?

Best regards,
Ajasja

On Wed, May 25, 2011 at 11:51, 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
> 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
>