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Subject: Re: [OMPI users] Res: Gromacs run in parallel
From: Carsten Kutzner (ckutzne_at_[hidden])
Date: 2010-06-08 09:20:05


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.
>
Hi,

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=<...>
...

Carsten

>
> 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
>>
>> Hi,
>>
>> which version of Gromacs is this? Could you post the first lines of
>> the md.log output file?
>>
>> Carsten
>>
>>
>> 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_at_[hidden]
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>>
>> _______________________________________________
>> users mailing list
>> users_at_[hidden]
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquyres_at_[hidden]
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
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> http://www.open-mpi.org/mailman/listinfo.cgi/users

--
Dr. Carsten Kutzner
Max Planck Institute for Biophysical Chemistry
Theoretical and Computational Biophysics
Am Fassberg 11, 37077 Goettingen, Germany
Tel. +49-551-2012313, Fax: +49-551-2012302
http://www.mpibpc.mpg.de/home/grubmueller/ihp/ckutzne