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

Yang Ye leafyoung at yahoo.com
Mon Oct 8 18:28:55 CEST 2007

On 10/4/2007 11:50 PM, 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 ?
Make sure that mdrun is compiled with mpi; other, it will result in four 
independent process, with four "different" log files (of course, in such 
case, log files could more or less the same.).
> - 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 can change the nice level by -nice in the mdrun command. So, in 
> principle, there is no need to recompile mdrun ?
You don't need to re-compile mdrun in order to get rid of the "nice" 

Setting nice to 19 for mdrun is alright, but I got a bit inefficiency 
with analysis tools at nice 19. This results in slow execution of the 
analysis tools when there is background jobs, e.g. mdrun.
> Thank you so very much for the inputs,
> -Maria
> -- 
> Maria G.
> Technical University of Denmark
> Copenhagen
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