On Fri, Oct 25, 2013 at 11:19 AM, Tiago Gomes <tiagogome...@gmail.com>wrote:
> Hi, > > I am relatively new to the gromacs environment and would like to optimize > performance for my mac pro (osx 10.6.8) > with 8 cores (16 in hyper-theading). I´ve read that one can use > the g_tune_pme, i guess with np = 16. Don´t know if using mpirun or gromacs > compiled mpi > would be faster. Won't be. GROMACS's default built-in thread-MPI is designed for this case. Do check out http://www.gromacs.org/Documentation/Acceleration_and_parallelization > I guess sin gromacs 4,5 mpirun is deprecated and mdrun > automatically distributes the workload through all the cores, i think. > We also have a 40 core condor cluster; would setting it up there increase > performance? Using more than one node for the same simulation is not useful unless you have a high-speed network, e.g. Infiniband. A network over which one would use Condor would generally not be suitable. > I think also that the scaling depends on the number of atoms. > Any info on this? > Depends very much on the hardware, compiler, model physics and simulation composition, also. You should aim for something at least around 500-800 atoms per physical core, though. 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