[gmx-users] Vagrant 2-node slurm cluster with gromacs, mpi

[Victor Rosas Garcia]

OK, thanks.

2016-12-08 10:57 GMT-06:00 Mark Abraham <mark.j.abraham at gmail.com>:

> Hi,
>
> I literally have no idea, but I have heard from Szilard Pall that it can be
> done and runs reasonably :-)
>
> Mark
>
> On Fri, Dec 9, 2016 at 3:49 AM Victor Rosas Garcia <rosas.victor at gmail.com
> >
> wrote:
>
> > Interesting.
> >
> > Mark, would you mind pointing out a few resources on how to configure
> for a
> > Gigabit network? So far I have found J Comput Chem 28: 2075–2084, 2007,
> but
> > there must be something else out there.
> >
> > Victor
> >
> > 2016-12-08 10:08 GMT-06:00 Mark Abraham <mark.j.abraham at gmail.com>:
> >
> > > Hi,
> > >
> > > Thanks for the tip. I would further suggest that people consider the
> > > attributes of their network before attempting such a setup. It is
> > possible
> > > to get reasonable performance from multi-node GROMACS using Gigabit
> > > ethernet, but I would expect to have to do a lot of work configuring
> it.
> > > GROMACS performance is extremely sensitive to communication latency,
> and
> > > every extra layer of middleware hurts that.
> > >
> > > Mark
> > >
> > > On Tue, Dec 6, 2016 at 1:16 AM Jan Domanski <jandom at gmail.com> wrote:
> > >
> > > > Hi guys,
> > > >
> > > > While not exactly related to gromacs per-se, this may be useful to
> > folks
> > > > who want to try running gromacs with slurm out on their laptops,
> rather
> > > > than deploying on a slice of a hardware cluster.
> > > >
> > > > https://github.com/jandom/gromacs-slurm-openmpi-vagrant
> > > >
> > > > - Jan
> > > > --
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