[gmx-users] MPI tips

David Mobley dmobley at gmail.com
Mon Jan 30 17:39:42 CET 2006

I am pretty sure that normally what you would want to do is only use mpi for
mdrun (which DOES behave differently with mpi). Perhaps you might
occasionally want MPI for some of the analysis tools (g_*) and I haven't the
foggiest idea whether they support it or not. But usually running things
like pdb2gmx is so fast there is really no reason to parallelize.

I haven't, however, use MPI that much myself. But I do know it works with
mdrun, and that's ordinarily the part you want to run in parallel.


On 1/30/06, David Mathog <mathog at caltech.edu> wrote:
> 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.
> Thanks,
> David Mathog
> mathog at caltech.edu
> Manager, Sequence Analysis Facility, Biology Division, Caltech
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