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 _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
