[gmx-users] gromacs-4.0.5 parallel run in 8 cpu: slow speed

Mark Abraham Mark.Abraham at anu.edu.au
Thu Jun 11 08:43:54 CEST 2009

Thamu wrote:
>     Hi
>     Recently I successfully installed the gromacs-4.0.5 mpi version.


>     I could run in 8 cpu. but the speed is very slow.
>     Total number of atoms in the system is 78424.
>     while running all 8 cpu showing 95-100% CPU.
>     How to speed up the calculation.

You haven't given us any diagnostic information. The problem could be 
that you're not running an MPI GROMACS (show us your configure line, 
your mdrun command line and the top 50 lines of your .log file).


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