[gmx-users] parallel gromacs

[Anton Feenstra]

Scott Delinger wrote:
> 
> I then move on to d.dppc, which looks like it's meant for parallel
> work. If I run grompp -np 2 -shuffle -sort and then mdrun -np 2 (from
> the original gromacs SRPM), stdout from the mdrun complains that
> GROMACS was compiled without parallel capabilities (but the stdout
> from grompp shows that the job is prepared to run across two
> processors evenly). Fair enough, --enable-mpi likely wasn't in that
> source RPM. If I run grompp -np 2 -shuffle -sort and then mdrun_mpi
> -np 2, stdout from mdrun_mpi complains that it was expecting an input
> file with np = 1 and found np = 2. (!) If I run grompp -shuffle -sort
> and then mdrun_mpi, it runs on a single processor with no performance
> difference from the standard runs I did yesterday and this morning.

OK, I assume you ran mdrun_mpi under 'mpirun', since otherwise
it won't work anyhow. The quirk with mpirun is that it gobbles up
the first '-np' option on the commandline, even if that is *after*
the executable name, so if you do:
# mpirun /usr/local/gromacs/bin/mdrun_mpi -np 2 -s topol.tpr
mdrun won't 'see' the '-np 2' option. (I think someone mentioned once
that it depends on the mpi flavor and version.) Anyhow, if this is
the problem, the workaround is trivial. Try in stead of the above:
# mpirun -np 2 /usr/local/gromacs/bin/mdrun_mpi -np 2 -s topol.tpr
where mpirun will 'see' the first '-np 2' and mdrun the second.

Hope this helps...

-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
| |----  | De Boelelaan 1083 - 1081 HV Amsterdam - The Netherlands   |
| |----  | Tel: +31 20 44 47608 - Fax: +31 20 44 47610               |
| ' __   | Feenstra at chem.vu.nl - http://www.chem.vu.nl/afdelingen/FAR|
|  /  \  |-----------------------------------------------------------|
| (    ) | Dept. of Biophysical Chemistry - University of Groningen  |
|  \__/  | Nijenborgh 4 - 9747 AG Groningen - The Netherlands        |
|   __   | Tel +31 50 363 4327 - Fax +31 50 363 4800                 |
|  /  \  | K.A.Feenstra at chem.rug.nl - http://md.chem.rug.nl/~anton   |
| (    ) |-----------------------------------------------------------|
|  \__/  | "Engage" (J.L. Picard)                                    |
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