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

[Seaclear Theory]

Thanks for the guideline. I installed the lam/mpi 7.0.6 and compile the
gromance with "--enable-mpi" option.
When I run mdrun, I got message that lamboot is not start. Then I start the
lamboot and try to run mdrun witn "-np 4 -v N 4" (gromacs user guide
example). However, the gromacs still run on single CPU. It does not take the
advantage of other three CPUs on the server. Do I miss anything? Or I
misunderstand the parallel computing/MPI concept? Thanks.

Best,

Ocean

On 12/20/06, Erik Lindahl <lindahl at cbr.su.se> wrote:
>
> Hi,
>
> On Dec 21, 2006, at 3:12 AM, 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.
> > I installed Lam/mpi and compile gromacs with mpi. Thanks lot!
> >
>
> The problem is that there is no standard for how you start MPI
> programs - that is entirely up to the MPI implementation.
>
> Essentially, add "-np 4" to grompp to get a parallel input file, boot
> your "virtual" parallel computer with "lamboot <hostfile>", and then
> start a parallel run as "mpirun -np 4 mdrun <normal args>".
>
> Most MPI libraries use mpirun is some form, but they differ in how
> you specify the machines to run on.
>
> Cheers,
>
> Erik
>
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