VMD-L Mailing List

From: Ondrej Marsalek (ondrej.marsalek_at_gmail.com)
Date: Tue Dec 02 2008 - 12:40:26 CST

axel,

thanks again, now it seems that i have really encountered what you
described. for reference, my system is ubuntu 8.10 64-bit. vmd was
compiled using g++. i do have intel compilers as well, but did not set
the ICC flag in vmd configuration, so i hope i really got g++.

i still don't understand why it happens only with some data, but i am
not sure i want to understand that. often (in my intended use always)
vmd (or rather the memory system) does not free any memory after
deleting molecules. this memory gets "recycled" for further data
loaded into vmd, so the total memory footprint of vmd is the maximum
use of the given run.

while i agree that this is strictly speaking not a memory leak and
probably not caused by vmd code, it is still something i would like
to get rid of. vmd is not the only thing running on my system :-) i am
not sure it is worth playing with my system libraries, though. any
other options?

regards,
ondrej

On Tue, Dec 2, 2008 at 18:23, Axel Kohlmeyer
<akohlmey_at_cmm.chem.upenn.edu> wrote:
> 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
> =======================================================================
> If you make something idiot-proof, the universe creates a better idiot.
>