[gmx-users] (no subject)

Carsten Kutzner ckutzne at gwdg.de
Fri Oct 12 13:37:22 CEST 2007

sarbani chattopadhyay wrote:
>   hi,
>     I am using gromacs to run MD simulations using "Intel dual core
> machine OSX (version
> 10.4.10) ".I downloaded the 'already compiled gromacs package'. Is there
> any way to find
> whether the simulation process makes optimum usage of the 2 processors.

Hi Sarbani,

I assume you have the MPI version of Gromacs. You could for example run
a 1000-step simulation on 1 CPU and afterwards on 2 CPUs. Gromacs prints
performance numbers at the end of the md0.log file. You could then
divide the ns/day value of your 2 CPU run by two times that value of the
1 CPU run and receive a measure for the scaling, which should not be
much lower than 1.00 on a dual or quad core machine. Use longer runs for
more reliable numbers. But a 10 minute run or so should suffice.

> Is there any command to direct the 'mdrun' that takes the optimum
> advantage of the
> available processors?

You might want to use the -shuffle and -sort options together with
setting the number of CPUs by -np in the preprocessor grompp.

> We have another machine which has "Xeon Quad Core ,the MAC version being
> 10.4.10.
> How to run gromacs making optimum usage of the 4 processors?

mpirun -np 4 mdrun -s x.tpr

Hope that helps,

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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