On Mon, Jan 21, 2013 at 11:50 PM, Brad Van Oosten <bv0...@brocku.ca> wrote:
> I have been lost in the sea of terminology for installing gromacs with > multi-processors. The plan is to upgrade from 4.5.5 to the 4.6 and i want > the optimal install for my system. There is a a nice explanaion at > http://www.gromacs.org/**Documentation/Acceleration_**and_parallelization<http://www.gromacs.org/Documentation/Acceleration_and_parallelization>but > the number of different options and terminology has confused me. > That's life, unfortunately. Nomenclature is poorly standardized and gets re-used by different vendors to mean different things, or in different contexts. I currently have one computer with 2 processor sockets each with 4 cores > each with 2 threads. A mouthful which in the end allows for 16 processes > at once(2*4*2). > Your sockets don't require a network to talk to each other, so thread-mpi suffices. Probably your "threads" are hyper-threads, which may or may not be useful for GROMACS. But you will need to read actual documentation and look up chip set descriptions to really know what you have. > The way i read the documentation is that MPI is needed for the talk > between the 2 physical processors, OpenMP does the talk between the 4 cores > in each processor and thread-MPI does the treading? or does thread-MPI do > everything? > > What would be the Parallelization scheme is required? Probably, use ThreadMPI and forget about everything else :-) This question cannot be answered in the abstract (you'd need to know full hardware characteristics and simulation system characteristics). It is best assessed by trying a few options and comparing the throughput you observe on the systems you care about. Mark -- 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
