On Tue, Jan 29, 2013 at 4:39 PM, Susan Chacko <[email protected]> wrote:
> > Sorry for a newbie question -- I've built several versions of Gromacs in > the > past but am not very familiar with the new cmake build system. > > In older versions, the procedure was: > - build the single-threaded version > FYI there is really no point in compiling GROMACS with all parallelization disabled, and by default you get (thread-)MPI and OpenMP which work just fine within a node (and mdrun as well as a few tools support multi-threading). > - then build the MPI version of mdrun only. No need to build the other > executables with MPI. > > Is this still how it should be done, or should one just build everything > once with MPI? > That is how I usually do it so that I have tools and a multi-threaded mdrun without without MPI dependency, then configure again with MPI and install to the same location mdrun only (make install-mdrun) - which by deafult will have the _mpi suffix. > Likewise, if I want a separate GPU version (only a few nodes on our > cluster have GPUs), do I build the whole tree separately with -DGMX_GPU=ON, > or just a GPU-enabled version of mdrun? > You only need to build separate GPU-enabled version of mdrun if you can not have CUDA available on the non-GPU nodes (as mdrun links against the CUDA libraries). Otherwise, a GPU-acceleration enabled mdrun on a node without GPUs works just fine. Cheers, -- Szilard > Thanks for any suggestions, > Susan. > > > > > > > -- > 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
