[gmx-users] gmx_mpi -nt

[Mark Abraham]

Hi,

Using -nt is rarely the best approach for anything. If you want to control
the number of ranks (or domains) then that is what

gmx mdrun -ntmpi N

or

mpirun -np N gmx_mpi mdrun

do.

Mark

On Mon, Apr 23, 2018, 23:47 Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 4/23/18 5:45 PM, Alex wrote:
> > Thanks.
> >
> > On Mon, Apr 23, 2018 at 5:38 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> >>
> >> On 4/23/18 4:55 PM, Alex wrote:
> >>
> >>> Dear all,
> >>> My gxm_mpi works fine, however, due to the doman decompistion error of
> a
> >>> system of mine, I want to use the *gmx_mpi mdrun with -nt XXX*, but the
> >>> gromacs states that I can not use -nt as gromacs builds without
> >>> thread-mpi,
> >>> so, I was wondering which flag I should use in compilation of gromacs
> to
> >>> be
> >>> able to use gmx_mpi with -nt option?
> >>>
> >> It's the default behavior. If you want it, don't compile using an
> external
> >> MPI library.
> >>
> > For the one I have I used  something like "cmake .. -DGMX_MPI=ON
> > -DGMX_FFT_LIBRARY=mkl -DREGRESSIONTEST_PATH=ON
> -DCMAKE_INSTALL_PREFIX=/home/
> > alex54/.local/gromacs-2018.1".
> >
> > What change should I do on the above cmake ... ?
> > If you mean I should do -DGMX_MPI=OFF , then can it run in parallel with
> > -nt at the end?
>
> Yes. See the installation instructions where this is discussed.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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> Blacksburg, VA 24061
>
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