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

Mark Abraham Mark.Abraham at anu.edu.au
Thu Dec 21 08:44:30 CET 2006

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 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!


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