On Tue, Jun 25, 2013 at 5:46 PM, Pedro Lacerda <kanvuanza+...@gmail.com> wrote: > On Tue, Jun 25, 2013 at 8:53 AM, Mark Abraham <mark.j.abra...@gmail.com>wrote: > >> You're using a real-MPI process per core, and you have six cores per >> processor. The recommended procedure is to map cores to OpenMP >> threads, and choose the number of MPI processes per processor (and >> thus the number of OpenMP threads per MPI process) to maximize >> performance. See >> >> http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Multi-level_parallelization.3a_MPI.2fthread-MPI_.2b_OpenMP > > > The page says: > >> at the moment, the multi-level parallelization will surpass the >> (thread-)MPI-only parallelization only in case of highly parallel runs >> and/or with a slow network. > > > What "highly parallel runs" mean? I'm sure it works for Djurre as he has 72 > nodes, but how many six-core nodes are considered highly parallel?
Not sure, perhaps Szilard can contribute some ballpark estimates. I'd guess fewer than 200 atoms/core would generally be highly parallel (OP has around 300 atoms/core), but it would depend on the number of nodes, socket structure and network quality also. The total cost of doing MPI communication grows with the number of ranks N, and the number of PME-only nodes will grow likewise, and the PME cost will grow probably as N log(N) from the global communication cost... It does boil down to "if you really care about maximum performance, test the available possibilities." But remember to factor that human time into whether it's worth your trouble ;-) Mark -- 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
