[gmx-developers] problem about Gromacs CVS version 3.3.99_development_200800503 parallel efficiency

Carsten Kutzner ckutzne at gwdg.de
Fri Jun 20 14:22:11 CEST 2008

xuji wrote:
> Hi all
> I have 3 nodes, and there're 8 CPUs in each node. I run a 24 processes 
> mdrun on the three nodes. And I use MPICH2 environment. But the 
> efficiency of the mdrun program is very low. The occupancy of each CPU 
> is only about 10%. I don't know why. Can some one give me some help?

what kind of interconnect do you have? It should be *at least* Gigabit
Ethernet! How big is your system? Are you using PME? Please give more
information, also on what was your command line to start the runs and
what CVS version (date) you are using.


Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics Department
Am Fassberg 11
37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302

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