[gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2

[Berk Hess]

Hi,

I always compile Gromacs with --enable_mpi --enable-mpi-environment=...
such that you can run a serial mdrun without using mpirun.

Berk

Date: Fri, 6 Feb 2009 15:22:54 +0000
Subject: Re: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2
From: jmdamas at itqb.unl.pt
To: gmx-users at gromacs.org

On Mon, Jan 19, 2009 at 6:09 PM, Berk Hess <gmx3 at hotmail.com> wrote:






Hi,

When running in parallel on a cluster through a queuing system
one usually does not (or can not) see or check the nice level
of the mdrun processes. But the nice level can have a significant
impact on performance, especially when running in parallel,

since all processes have to wait for the slowest one.
Therefore I set the nicelevel to 0 when running in parallel.

Note that if you configure mdrun with --enable_mpi --enable-mpi-environment,
running an MPI mdrun binary without mpirun will still give nice 19.

Hi Berk,

Thanks for the answer and for the tip. It worked out
fine. But still, I was intrigued when you said "running an MPI mdrun
binary without mpirun". What do you mean with that? Do you mean that
you don't need to launch the mpirun before the MPI mdrun?


Regards,
João 



Berk

Date: Mon, 19 Jan 2009 16:29:16 +0000

From: jmdamas at itqb.unl.pt
To: gmx-users at gromacs.org
Subject: [gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2


Hello,

I would like to know if there is any reason for mdrun_mpi to have a nicelevel default of zero in Gromacs 4.0.2 instead of the default 19 of mdrun of every version or mdrun_mpi of the other versions. I searched the mailing list for any discussion related to this but I haven't found anything.



Thanks in advance,
João
-- 
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

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-- 
João M. Damas
PhD Student

Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
Tel:+351-214469613

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