[gmx-users] Parallel message passing

[Nathan Moore]

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.

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?

NT Moore