[gmx-users] Nicelevel default 0 - mdrun_mpi of Gromacs 4.0.2
João M. Damas
jmdamas at itqb.unl.pt
Fri Feb 6 16:22:54 CET 2009
On Mon, Jan 19, 2009 at 6:09 PM, Berk Hess <gmx3 at hotmail.com> wrote:
> 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
> running an MPI mdrun binary without mpirun will still give nice 19.
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?
> 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
> 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
> Thanks in advance,
> João M. Damas
> PhD Student
> Protein Modelling Group
> ITQB-UNL, Oeiras, Portugal
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João M. Damas
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal
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