[gmx-users] gmx_mpi -nt
mark.j.abraham at gmail.com
Tue Apr 24 00:38:59 CEST 2018
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
mpirun -np N gmx_mpi mdrun
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
> >>> 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
> >>> be
> >>> able to use gmx_mpi with -nt option?
> >> It's the default behavior. If you want it, don't compile using an
> >> MPI library.
> > For the one I have I used something like "cmake .. -DGMX_MPI=ON
> > -DGMX_FFT_LIBRARY=mkl -DREGRESSIONTEST_PATH=ON
> > 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 A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
> 303 Engel Hall
> 340 West Campus Dr.
> Blacksburg, VA 24061
> jalemkul at vt.edu | (540) 231-3129
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