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Subject: Re: [OMPI users] Res: Gromacs run in parallel
From: Jeff Squyres (jsquyres_at_[hidden])
Date: 2010-06-08 09:06:25


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.

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
>
>
>
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-- 
Jeff Squyres
jsquyres_at_[hidden]
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