Yes, documentation and output is not optimal. Resources are limited, sorry. Some of these issues are discussed in http://bugzilla.gromacs.org/issues/1135. The good news is that it sounds like you are having a non-problem. The output tacitly assumes heterogeneity. If your performance results are linear over small numbers of nodes, then you're doing fine.
Mark 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
