Thank you very much for both contributions. I will conduct some tests to assess which approach works best for my system.
Much appreciated, Best regards, João Henriques On Tue, Jun 4, 2013 at 6:30 PM, Szilárd Páll <szilard.p...@cbr.su.se> wrote: > mdrun is not blind, just the current design does report the hardware > of all compute nodes used. Whatever CPU/GPU hardware mdrun reports in > the log/std output is *only* what rank 0, i.e. the first MPI process, > detects. If you have a heterogeneous hardware configuration, in most > cases you should be able to run just fine, but you'll still get only > the hardware the first rank sits on reported. > > Hence, if you want to run on 5 of the nodes you mention, you just do: > mpirun -np 10 mdrun_mpi [-gpu_id 01] > > You may want to try both -ntomp 8 and -ntomp 16 (using HyperThreading > does not always help). > > Also note that if you use GPU sharing among ranks (in order to use <8 > threads/rank), (for some technical reasons) disabling dynamic load > balancing may help - especially if you have a homogenous simulation > system (and hardware setup). > > > Cheers, > -- > Szilárd > > > On Tue, Jun 4, 2013 at 3:31 PM, João Henriques > <joao.henriques.32...@gmail.com> wrote: > > Dear all, > > > > Since gmx-4.6 came out, I've been particularly interested in taking > > advantage of the native GPU acceleration for my simulations. Luckily, I > > have access to a cluster with the following specs PER NODE: > > > > CPU > > 2 E5-2650 (2.0 Ghz, 8-core) > > > > GPU > > 2 Nvidia K20 > > > > I've become quite familiar with the "heterogenous parallelization" and > > "multiple MPI ranks per GPU" schemes on a SINGLE NODE. Everything works > > fine, no problems at all. > > > > Currently, I'm working with a nasty system comprising 608159 tip3p water > > molecules and it would really help to accelerate things up a bit. > > Therefore, I would really like to try to parallelize my system over > > multiple nodes and keep the GPU acceleration. > > > > I've tried many different command combinations, but mdrun seems to be > blind > > towards the GPUs existing on other nodes. It always finds GPUs #0 and #1 > on > > the first node and tries to fit everything into these, completely > > disregarding the existence of the other GPUs on the remaining requested > > nodes. > > > > Once again, note that all nodes have exactly the same specs. > > > > Literature on the official gmx website is not, well... you know... > in-depth > > and I would really appreciate if someone could shed some light into this > > subject. > > > > Thank you, > > Best regards, > > > > -- > > João Henriques > > -- > > 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 > -- João Henriques -- 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