[gmx-users] MPI tips

David Mathog mathog at caltech.edu
Mon Jan 30 16:59:31 CET 2006

I'm trying to figure out how to use MPI with gromacs.  A few examples
would go a long, long way.  Where are the MPI examples???? 

Which programs support MPI???

When I built gromacs two versions of (all) the programs ended up in
.../gromacs/bin, a "regular" one and ones with an _mpi suffix. The two
versions for each program are about the same size, with the _mpi one
being either 32 bytes bigger or smaller (go figure).  That could just
be compiler noise.

The "regular" ones work (at least those run from gmxdemo/demo.sh
which is my translation to bash of the original csh script.)

Now I'm trying to work through demo_mpi.  The demo_mpi that
gromacs built is IDENTICAL to demo, and even with lam-mpi running
(yes, I tested that MPI works with other programs) it only runs
on the head node.   The man page says that mdrun has an -np
parameter if built with MPI.  I couldn't find any other useful
info on whether or not there were actually MPI versions of the
other programs, _mpi suffix or not.

I'm stuck at the very first program which is pdb2gmx.  The man page
for that doesn't indicate any -np parameter for it. I tried running
pdb2gmx_mpi and it just ran on the head node with no activity on the
compute nodes.


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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