[gmx-users] slow gmx

[Mark Abraham]

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 <mailmd2011 at gmail.com> 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
>
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