PS: if your compute-nodes are Intel of some recent architecture OpenMP-only parallelization can be considerably more efficient.
For more details see http://www.gromacs.org/Documentation/Acceleration_and_parallelization -- Szilárd On Thu, May 16, 2013 at 7:26 PM, Szilárd Páll <[email protected]> wrote: > 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 <[email protected]> > 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 [email protected] >> 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 [email protected]. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list [email protected] 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 [email protected]. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
