VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Feb 23 2016 - 14:45:50 CST

Daniel,
  I finally had a chance to run a thorough memory leak test on the
Amber plugin that you were using for your files, and on machine, I see
no leaks after going through a loop loading/analyzing and deleting your
test molecule 600 times. My "analysis" test was just doing an atom
selection and querying the number of selected atoms, but given the
original problem description this seemed adequate to try and reproduce
the problem. This makes me wonder if there leaks in the shared libraries
on your particular Linux machine or something similar. I ran my tests
using the latest test builds of VMD 1.9.3.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Fri, Dec 04, 2015 at 11:23:09AM +0100, Daniel Möller wrote:
> Hi,
>
> I get this problem even without any analysis.
> The leak rate is same with the used memory. So if an analysis loads extra
> data into a molecule (like stride), this will be stay occupied too.
>
> As attachment is a parm7 file, I use.
>
>
> Sincerely
>
> Daniel Möller
>
>
> -----Ursprüngliche Nachricht-----
> Von: John Stone [mailto:johns_at_ks.uiuc.edu]
> Gesendet: Mittwoch, 2. Dezember 2015 22:53
> An: Daniel Möller
> Cc: vmd-l_at_ks.uiuc.edu
> Betreff: Re: vmd-l: Possible memory leak with adding and deleting molecules
> frequently
>
> Daniel,
> Can you zip up send me an example of one of the parm7 files that produces
> the behavior you have observed? It might also be helpful to know what your
> analysis involves, as the leak might be in any of the steps you described,
> but without knowing what they are, it would be very difficult to find a
> leak. If the leak happens without the analysis, then I would ask whether
> the leak rate is the same or different...
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Nov 27, 2015 at 11:33:06AM +0100, Daniel Möller wrote:
> > Hi,
> >
> >
> >
> > seems I discovered a memory leak in V1.9.2 while running an analyse
> > script. The script simply performs the following steps:
> >
> > 1. Load a new molecule with structure (amber7 parm) and
> trajectory
> > (NAMD dcd)
> >
> > 2. Carry out some analysis
> >
> > 3. Delete molecule to free RAM
> >
> > 4. Goto 1
> >
> >
> >
> > Example code:
> >
> > mol new {mol1.top} type {parm7} first 0 last -1 step 1 waitfor 1
> >
> > mol addfile {mol1.dcd} type {dcd} first 0 last -1 step 25 waitfor
> > -1 0
> >
> > # some analyse scripts, which are clean (also happens without)
> >
> > mol delete 0
> >
> >
> >
> > mol new {mol2.top} type {parm7} first 0 last -1 step 1 waitfor 1
> >
> > mol addfile {mol2.dcd} type {dcd} first 0 last -1 step 25 waitfor
> > -1 1
> >
> > # some analyse scripts, which are clean (also happens without)
> >
> > mol delete 1
> >
> > and so on.
> >
> >
> >
> > But after deleting the molecule VMD doesn't reuse the memory, but uses
> new
> > free memory which adds to the previously used memory.
> >
> > This shows up on GUI or TEXTMODE.
> >
> >
> >
> >
> >
> > Sincerely
> >
> >
> >
> > Daniel Moeller
> >
> >
> >
> > --
> >
> > ------------------------
> >
> > Dipl. Biochem. Daniel Moeller
> >
> >
> >
> > Biophysical Chemistry
> >
> > Institut of Biochemistry
> >
> > Unversity of Greifswald
> >
> > Felix-Hausdorff-Strasse 4
> >
> > 17489 Greifswald - Germany
> >
> >
> >
> > Tel +49 3834 86 4406
> >
> >
> >
> >
> > http://www.mnf.uni-greifswald.de/institute/institut-fuer-biochemie/bio
> > physikalische-chemie.html
> >
> >
> >
> >
>
> --
> NIH Center 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/ 

-- 
NIH Center 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/