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
Regards,
Yang Ye
On 12/21/2006 4:20 PM, Seaclear Theory wrote:
On 12/20/06, *Mark Abraham* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>> wrote:
Seaclear Theory wrote:
>
>
> On 12/20/06, *Mark Abraham* <[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>
> <mailto:[EMAIL PROTECTED]
<mailto:[EMAIL PROTECTED]>>> wrote:
>
> Seaclear Theory wrote:
> > Hi! All,
> >
> > I have a linux server with 4 CPUs. How can I run gromacs
on all CPUs?
> > The gromacs manual has very limit information. And it
does not works.
>
> 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!
Mark
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.
Ocean
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