[gmx-users] Parallel message passing

[David]

On Wed, 2005-06-08 at 15:25 -0500, Nathan Moore wrote:
> I have a parallel version of gromacs running on a commercial ppc machine
> with many nodes available.  Whn I look at parallel scaling (only the
> villin benchmark so far) I see linear speedup only up to about 10
> processors.  Is villin (~9000 atoms) too small to show proper speedup?  I
> mean to look at the parallel benchmark in a few days.
Scaling Villin to 10 processors is great. I haven't heard of that
anywhere else.
> 
> In reading through the manual it sounds like GROMACS only passes messages
> to it's nearest neighbors (node_i only talks to node_{i+1} and node_{i-1})
>  Is this really how things are set up?  I have a full-featured MPI network
> available that I'd like to utilize fully - is an alternate communications
> protocol set up?
The PME algorithm uses full all-to-all communication. However in general
you want to reduce communication to a minimum (by using clever
algorithms). What kind of network do you have?

> 
> NT Moore
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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