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.
________________________________________________________________________
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
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