[gmx-users] slow gmx
mark.j.abraham at gmail.com
Wed Feb 6 15:20:08 CET 2019
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.
And only gmx mdrun makes any use of any kind of MPI, too.
On Wed, 6 Feb 2019 at 14:53 Albert <mailmd2011 at gmail.com> wrote:
> I've installed Gromacs 2018v4 in my Linux X64 OS. When I try to run
> command line:
> gmx_mpi -h
> 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
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * 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-request at gromacs.org.
More information about the gromacs.org_gmx-users