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

[David van der Spoel]

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.
________________________________________________________________________
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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