I'm not sure what you mean by "threads". In GROMACS this can refer to either thread-MPI or OpenMP multi-threading. To run within a single compute node a default GROMACS installation using either of the two aforementioned parallelization methods (or a combination of the two) can be used.
-- Szilárd On Thu, May 16, 2013 at 6:57 PM, Thomas Schlesier <schl...@uni-mainz.de> wrote: > Dear all, > if one performs a parallel calculation on a single node / computer with more > than 1 core, is there a speed difference between MPI and Threads? > > Problem is for gromacs 4.6.1 i'm facing problems to link it to OpenMpi. A > serial version (without threads) worked, so i think i should be able to > compile a version which supports threads. > Since we only run calculations on a single node on our cluster (no > infini-band), i'm wondering if the programm with threads would be sufficient > in our case. > > Greetings > Thomas > -- > 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
