On Wed, Mar 4, 2015 at 5:24 PM, Federico Padua <pa...@uni-mainz.de> wrote: > Dear Gromacs team, > > I am interested in the following information about Gromacs since I'm > writing part of a publication so will be few lines and I would like to > get the right info directly from the people closer to the code (I read > the paper). We are using Gromacs version 5.0.4 and we > would like to know without going too much into details: > > - how Gromacs distribute the data to be processed among processors?
Neutral-territory domain decomposition using MPI + OpenMP multi-threading within a rank. > - how Gromacs distribute the work among the processors involved in the > calculation? Work = ? Nitpick, but this second question more or less includes the first. Anyway, I assume here you meant task-decomposition and the answer is: MPMD task decompostion with MPI (separate PME ranks) and non-bonded offload to GPUs. For a fairly detailed overview, you can check our last paper in LNCS (DOI: 10.1007/978-3-319-15976-8_1), and the wiki's parallelization page is quite fairly comprehensive too (with a more practical touch to it). To understand details of the data-/task-decomposition and the different parallelization levels, i.e. intra-core: SIMD, intra-node:threading & accelerators, inter-node: MPI, you may want to dig up the original papers that describe the various algorithms (DOIs: 10.1002/jcc.20703, 10.1021/ct700301q, doi:10.1016/j.cpc.2013.06.003, to name a few). Cheers, -- Szilárd > > Thank you very much in advance for your answer and for your time. > > > Best Regards, > > Federico Padua > > > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
