[gmx-users] run gromacs on a single machine with mutiple CPUs

David van der Spoel spoel at xray.bmc.uu.se
Thu Dec 21 09:51:17 CET 2006

Yang Ye wrote:
> normally we use following commands when compiling gromacs
> ./configure ... --program_suffix=_mpi --enable-mpi ...
> So we will have mdrun_mpi in the end.
> The usage of mdrun_mpi is the same as mdrun but -np, -replex and other 
> switches are activated.
> That statement on the user manual is to clarify that you don't need 
> MPI-enabled mdrun to run on a multiprocessor machine. But if you want to 
> tap the capability of the multiprocessor machine, you need to use MPI 
> and use mdrun_mpi
As Erik stated, different MPI implementations have different standards 
for starting jobs. The comment in the manual is probably a remnant from 
an old SGI MPI implementation. I will remove the comment.

Otherwise, a little trial and error and man XXX usually does the job...

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://folding.bmc.uu.se

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