VMD-L Mailing List

From: maria goranovic (mariagoranovic_at_gmail.com)
Date: Wed May 25 2011 - 06:05:44 CDT

I will run this with a new vmd version and update the thread in a few days.
I will be out of station for a week.

Thank you again for the help,

Maria

On Wed, May 25, 2011 at 12:57 PM, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com
> 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
>>
>
> 

-- 
Maria G.
Technical University of Denmark
Copenhagen