Depending on the level of parallelization (number of nodes and number of particles/core) you may want to try:
- 2 ranks/node: 8 cores + 1 GPU, no separate PME (default): mpirun -np 2*Nnodes mdrun_mpi [-gpu_id 01 -npme 0] - 4 ranks per node: 4 cores + 1 GPU (shared between two ranks), no separate PME mpirun -np 4*Nnodes mdrun_mpi -gpu_id 0011 [-npme 0] - 4 ranks per node, 2 PP/2PME: 4 cores + 1 GPU (not shared), separate PME mpirun -np 4*Nnodes mdrun_mpi [-gpu_id 01] -npme 2*Nnodes - at high parallelization you may want to try (especially with homogeneous systems) 8 ranks per node Cheers, -- Szilárd On Fri, Jul 19, 2013 at 4:35 AM, Éric Germaneau <german...@sjtu.edu.cn> wrote: > Dear all, > > I'm note a gromacs user, I've installed gromacs 4.6.3 on our cluster and > making some test. > Each node of our machine has 16 cores and 2 GPU. > I'm trying to figure how to submit efficient multiple nodes LSF jobs using > the maximum of resources. > After reading the documentation > <http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores> > on "Acceleration and parallelization" I got confused and inquire some help. > I'm just wondering whether someone with some experiences on this matter. > I thank you in advance, > > Éric. > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm> > > Shanghai Jiao Tong University > Network & Information Center > room 205 > Minhang Campus > 800 Dongchuan Road > Shanghai 200240 > China > > View Éric Germaneau's profile on LinkedIn > <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986> > > /Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ > > -- > 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 -- 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
