VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Mon Jun 06 2011 - 07:36:35 CDT

As it turns out, the newer version of VMD (1.9) had no errors. my apologies
for using an out of date version.

-Maria

On Wed, May 25, 2011 at 5:18 PM, John Stone <johns_at_ks.uiuc.edu> wrote:

>
> Ajasja, Maria,
> Selections are a fixed size in terms of their memory footprint.
> The only thing that matters in the case of a leak is how many
> such selections are created, not how many atoms they contain...
>
> In older versions of VMD that precede the debugging plugin that
> Axel referred to, one can see how many atom selections exist
> part way through a run like this:
> atomselect list
>
> Cheers,
> John
>
> On Wed, May 25, 2011 at 12:57:10PM +0200, Ajasja Ljubeti?? wrote:
> > 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
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen