[gmx-users] run gromacs on a single machine with mutiple CPUs
oceanclear at gmail.com
Thu Dec 21 10:04:47 CET 2006
I believed the case that single machine with multiple processors (like Dell
server with 2 due core CPUs) should be very popular for end user. Because
not everyone can offer a 32 nodes cluster or has access to supercomputer
Could we have detail tutorial for "run gromacs on single machine with
multiple processors" Thanks.
On 12/21/06, David van der Spoel <spoel at xray.bmc.uu.se> wrote:
> 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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