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

[Mark Abraham]

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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