VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed May 25 2011 - 04:51:02 CDT

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