Hi, For use on a single workstation, rely on the built-in thread-MPI. Your library MPI system is clearly configured to expect various devices and that is slow. See e.g. http://manual.gromacs.org/documentation/current/install-guide/index.html#mpi-support
And only gmx mdrun makes any use of any kind of MPI, too. Mark On Wed, 6 Feb 2019 at 14:53 Albert <[email protected]> wrote: > Hello, > > I've installed Gromacs 2018v4 in my Linux X64 OS. When I try to run > command line: > > gmx_mpi -h > > or > > gmx_mpi pdb2gmx -f input.pdb -o gmx.gro > > it is very slow. I always obtained the following information: > > localhost.14713hfi_wait_for_device: The /dev/hfi1_0 device failed to > appear after 15.0 seconds: Connection timed out > > Does anybody know hot to resolve this problem? > > Thanks a lot > > Albert > > -- > 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 [email protected]. > -- 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 [email protected].
