[gmx-users] running gromacs in parallel, and with nice levels

[Carsten Kutzner]

Hi Maria,

maria goranovic wrote:
> Dear All,
> 
> - So I "think" I succeeded in running gromacs on a 4-core node. How does
> one confirm this without looking at the speed. i.e, where is it
> mentioned in the log file what the number of processors is ? I do get 4
> different log files for 4 processors, is that the final evidence ?
You will get 4 log files at the top of which you will find an entry like
this

Host: lee  pid: 20002  nodeid: 0  nnodes:  4

Obviously this is CPU number 0 of total 4 CPUs. Also in the standard
output (which is usually redirected to some file) you will see on which
node each of the mdrun processes resides (here all 4 were started on
host 'lee'):

NNODES=4, MYRANK=0, HOSTNAME=lee
NNODES=4, MYRANK=1, HOSTNAME=lee
NNODES=4, MYRANK=2, HOSTNAME=lee
NNODES=4, MYRANK=3, HOSTNAME=lee

> 
> - The nice level by default is too high (19). One can change this by
> compiling mdrun with a nonice option. However, does it really matter if
> one is running gromacs on a dedicated supercomputing node ? Also, one

No.

> can change the nice level by -nice in the mdrun command. So, in
> principle, there is no need to recompile mdrun ?

There is no need to recompile or to set the nice level on dedicated
nodes, it will not affect the performance.

Hope that helps, regards,
  Carsten


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