[gmx-users] parallelization

[Amin Rouy]

I see, thank you.

On Fri, Mar 2, 2018 at 3:09 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> No, GROMACS long pre-dates useful implementations of MPI I/O (which anyway
> don't suit GROMACS needs), and handles its own MPI reduction and does I/O
> from a single rank per simulation.
>
> Mark
>
> On Fri, Mar 2, 2018 at 3:00 PM Amin Rouy <aminrou1986 at gmail.com> wrote:
>
> > sorry Justin, I am familiar with this information in the link. But I do
> not
> > know  * I/O*   and   *MPI-IO*   which is not in the link ?
> > and I was asked from our HPC if I use them in Gromacs.
> >
> >
> >
> > On Fri, Mar 2, 2018 at 2:43 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >
> > >
> > >
> > > On 3/2/18 8:40 AM, Amin Rouy wrote:
> > >
> > >> Hi
> > >>
> > >> I am not so familiar with parallelization. Can some one please tell me
> > if
> > >> Gromacs
> > >> use MPI-parallel I/O (MPI-IO), or one should do it by himself for his
> > MPI
> > >> jobs?
> > >>
> > >
> > > Everything you need to know is in the manual:
> > >
> > > http://manual.gromacs.org/documentation/current/user-guide/m
> > > drun-performance.html
> > >
> > > -Justin
> > >
> > > --
> > > ==================================================
> > >
> > > 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
> > > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html
> > >
> > > ==================================================
> > >
> > > --
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