[gmx-users] problem with profiling grompp using callgrind

David van der Spoel spoel at xray.bmc.uu.se
Tue May 9 09:36:36 CEST 2006

Berk Hess wrote:
>> this seems more like a bug that is dependent on memory allocation. I'm 
>> no aware of any known bug in grompp. Maybe you can recompile all of 
>> grompp with the -g flag and retry. For memory debugging simpler tools 
>> like Electric Fence usually work. For profiling, you'd probably want 
>> to profile mdrun, although there is a bugzilla about grompp being 
>> excessively slow for large systems with OPLS and dummies.
> grompp with OPLS is excessively slow in general, because it generates
> LJ parameters for all ~1000^2 atom type combinations.
> If you have little memory it will start swapping to disk.

the real problem is in the dummy code, I've done some profiling and 
there are quite a few nested loops there. It's a low priority bug as far 
as I'm concerned, but it's in bugzilla so it will get fixed some time.

> Berk.
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David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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