[gmx-users] run gromacs on a single machine with mutiple CPUs
oceanclear at gmail.com
Thu Dec 21 09:20:16 CET 2006
On 12/20/06, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Seaclear Theory wrote:
> > On 12/20/06, *Mark Abraham* <Mark.Abraham at anu.edu.au
> > <mailto:Mark.Abraham at anu.edu.au>> wrote:
> > Seaclear Theory wrote:
> > > Hi! All,
> > >
> > > I have a linux server with 4 CPUs. How can I run gromacs on all
> > > The gromacs manual has very limit information. And it does not
> > So which part of the manual section entitled "Running GROMACS in
> > parallel" doesn't work?
> > What I want is to run gromacs on a signle machine with multiple
> > processors.
> > In "A.5 Running GROMACS in parallel"
> > "If you have a single machine with multiple processors you don't have to
> > use the mpirun command,
> > but you can do with an extra option to mdrun:
> > % mdrun -np 8 -s topol -v -N 8
> > In this example MPI reads the first option from the command line. Since
> > mdrun also wants to
> > know the number of processes you have to type it twice."
> So what does it say? Should you be using mdrun_mpi? How about using a
> mpirun command anyway...
> If you want meaningful feedback you need to describe your setup
> thoroughly, say what you've tried and why that didn't work and why the
> error messages didn't help you. Otherwise, you need to pay someone for a
> support contract :-) I'll help solve problems, but I won't help if you
> don't give the impression you're helping yourself too!
I do not understand why you are so upset. Are you the author of the user
manual :-) Any way, let's go back for the issue, not person.
The user manual said that "you don't have to use the mpirun command" if you
want to run gromacs on a single machine with multiple processors. How should
I understand this? By the way, the manual (v.3.3) and the reference does not
have information about "mdrun_mpi". Thanks.
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