[gmx-users] GROMACS in parallel on a multicore PC?

Carsten Kutzner ckutzne at gwdg.de
Wed Nov 21 12:50:21 CET 2007

Hi Vasilii,

Vasilii Artyukhov wrote:
> Hi everybody,
> Sorry for a somewhat technical question, but I'd like to know which is
> the best way to run GROMACS on a SMP machine (in particular, a multicore
> PC). The (known) points of interest are:
> - Does GROMACS support multithreaded execution & how efficient is it?
As far as I know this is planned, but not supported yet.

> - Should I rather use some kind of MPI & which (LAM/Open/MPICH) is
> better & why?
Yes. This is the way to go. On an SMP box you will probably not see
large differences between the different MPI implementations, but why not
try a few? My own experience is that LAM tends to be the fastest, partly
due to the memory mangager it uses.


> Surely, there's always the option to run two serial jobs instead with a
> greater efficiency, but having some means to boost the single job
> performance by something like 1.9x would be very useful...
> Thanks in advance,
> Vasilii
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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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