[gmx-users] Optimizing a parallel simulation

Mark Abraham Mark.Abraham at anu.edu.au
Thu Oct 8 08:03:36 CEST 2009

vivek sharma wrote:
> Hi There,
> While running a parallel MD simulation, I got following message while 
> playing with parameters:
> NOTE 3 [file aminoacids.dat, line 1]:
>   The optimal PME mesh load for parallel simulations is below 0.5
>   and for highly parallel simulations between 0.25 and 0.33,
>   for higher performance, increase the cut-off and the PME grid spacing
> ---------------------------
> I don't have any idea when a run should be called a highly parallel 
> simulation?

Well below 224 :-)

> Is it depend on problem-size or the number of processor we are using?


> I am trying to optimize my simulation to run on 224 processors and 
> system consist of:
> Total atom count = 54640
> where water molecules = 17074

You will want to tweak rcoulomb and fourier_space like the above message 
says. Even so, with less than 500 atoms per particle-particle processor 
you may find yourself spending more time communicating than processing. 
I suspect your system may be too small to get value from so many 
processors, even if you have good network (e.g. Infiniband). You will 
wish to read 3.17 of the manual to start understand the issues involved 

> Also, I am getting following message while running grompp
> ---------------------------------
> NOTE 1 [file md.mdp, line unknown]:
>   The Berendsen thermostat does not generate the correct kinetic energy
>   distribution. You might want to consider using the V-rescale thermostat.
> ------------------------------------
> Any insight in the above message will be highly appreciated.

Seems self-explanatory to me - you're using Berendsen and that might not 
be the right choice. Read the manual sections about the different 


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