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"
effect.
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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