On Jun 8, 2010, at 3:06 PM, Jeff Squyres wrote:
> I know nothing about Gromacs, but you might want to ensure that your Gromacs was compiled with Open MPI. A common symptom of "mpirun -np 4 my_mpi_application" running 4 1-process MPI jobs (instead of 1 4-process MPI job) is that you compiled my_mpi_application with one MPI implementation, but then used the mpirun from a different MPI implementation.
this can be checked by looking at the Gromacs output file md.log. The second line should
read something like
Host: <somename> pid: <somepid> nodeid: 0 nnodes: 4
Lauren, you will want to ensure that nnodes is 4 in your case, and not 1.
You can also easily test that without any input file by typing
mpirun -np 4 mdrun -h
and then should see
NNODES=4, MYRANK=1, HOSTNAME=<...>
NNODES=4, MYRANK=2, HOSTNAME=<...>
NNODES=4, MYRANK=3, HOSTNAME=<...>
NNODES=4, MYRANK=4, HOSTNAME=<...>
> On Jun 8, 2010, at 8:59 AM, lauren wrote:
>> The version of Gromacs is 4.0.7.
>> This is the first time that I using Gromacs, then excuse me if I'm nonsense.
>> Wich part of md.log output should I post?
>> after or before the input description?
>> thanks for all,
>> and sorry
>> De: Carsten Kutzner <ckutzne_at_[hidden]>
>> Para: Open MPI Users <users_at_[hidden]>
>> Enviadas: Domingo, 6 de Junho de 2010 9:51:26
>> Assunto: Re: [OMPI users] Gromacs run in parallel
>> which version of Gromacs is this? Could you post the first lines of
>> the md.log output file?
>> On Jun 5, 2010, at 10:23 PM, lauren wrote:
>>> sorry my english..
>>> I want to know how can I run Gromancs in parallel!
>>> Because when I used
>>> mdrun &
>>> mpiexec -np 4 mdrun_mpi -v -deffnm em
>>> to run the minimization in 4 cores > all cores make the same job, again!
>>> They don't run together.
>>> I want all in parallel make the job faster.
>>> what could be wrong?
>>> thank's a lot!
>>> users mailing list
>> users mailing list
> Jeff Squyres
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Theoretical and Computational Biophysics
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