VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Dec 02 2015 - 15:52:53 CST

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/biophysikalische-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/