VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Tue Dec 02 2008 - 11:23:28 CST

On 12/2/08, Ondrej Marsalek <ondrej.marsalek_at_gmail.com> wrote:
> hi again,
>
> i have encountered a memory leak in vmd, one that i find pretty
> severe. i am using a cvs version of vmd from 2008-11-21, i can provide
> details of my setup if it's relevant.
>
> as i have mentioned before, i am interested in getting rid of
> volumetric data "on the fly", as it won't fit into memory. it was
> recommended before that i use separate molecules, as volumetric data
> can't be removed from molecules. i have done just that, the only
> problem - the molecules do get removed, but the memory is not released
> until i quit vmd. i would like to ask for a fix of this, as it makes

ondrej,

please note that this is not yet a memory leak if that memory
gets re-used for the next molecule. this is frequently a "feature"
of the malloc(3) functionality of the respective OS and/or c++
compiler and depends on whether the new operator gets memory
from the stack or from the heap. on some operating systems, one
can work around this by compiling the GNU malloc library
(as libgmalloc.a) and link to that instead of the default malloc.
gmalloc also uses mmap(2) to allocate (and re-use, if possible)
larger chunks and those _can_ be given back to the process.

cheers,
    axel.
> my intended use impossible. on a more general level, i consider it a
> clear memory leak and would report it even if it was not an issue for
> me at the moment.
>
> thanks for considering it,
>
> regards,
> ondrej marsalek
>
> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
  Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.