[gmx-users] problem with profiling grompp using callgrind

Berk Hess 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.


More information about the gromacs.org_gmx-users mailing list