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

Berk Hess gmx3 at hotmail.com
Mon Jan 19 19:09:04 CET 2009


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.


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 anything.

Thanks in advance,
João M. Damas
PhD Student
Protein Modelling Group
ITQB-UNL, Oeiras, Portugal

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