[gmx-users] problem with profiling grompp using callgrind
gmx3 at hotmail.com
Tue May 9 09:31:35 CEST 2006
>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.
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