Yes, I'm using all cores. All nodes are connected by Ethernet. Now I see that when I change number of processes or number of threads per node I can change mdrun performance. But I think it is still too slow. Is there a way to speed up mdrun on cluster? Some specific settongs or so? Sorry for my questions, but I'm quite novice in running gromacs on cluster.
2013/5/21 Justin Lemkul <jalem...@vt.edu> > > > On 5/21/13 1:15 PM, Андрей Гончар wrote: > >> Hello. I have a cluster (12 nodes, 24 cores on each). Also I've compiled >> mdrun with MPI. >> Now when I try to run a MD on this cluster, it takes near 20 hours to >> complete. But when I try the same simulation on a PC with 8 cores, it >> takes >> near 10 hours to complete. I thought that it will take less on cluster but >> I see the opposite. What I'm doing wrong? >> >> > Are you trying to use all available cores on the cluster? No system is > infinitely parallelizable, so if you're exceeding the limit of scaling > efficiency, you're going to see degradation in performance. Do you get > similar performance using 8 cores of the cluster? What type of network do > you have between the nodes? > > Note that the end of the .log file will have a breakdown of where your run > spent time doing what. That information can be informative in determining > where performance is being lost. > > -Justin > > -- > ==============================**========== > > Justin A. Lemkul, Ph.D. > Research Scientist > Department of Biochemistry > Virginia Tech > Blacksburg, VA > jalemkul[at]vt.edu | (540) 231-9080 > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > * Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > * Please don't post (un)subscribe requests to the list. Use the www > interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> > -- Andrew Gonchar Андрей Гончар -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
