[gmx-users] MD simulations on a remote workstation

[Mark Abraham]

On Apr 3, 2014 1:46 AM, "Amjad Farooq" <amjad at farooqlab.net> wrote:
>
> Justin,
>
> I am trying to set up a single system image using PC as the master node
and
> two workstations as slave nodes (essentially a supercompuer; more nodes
> will be added later), so that I can have everything together, instead of
> running my simulations individually on each workstation. But, all nodes
> will share the master hard disk. That is where all I/O will take place but
> processing will be split between different nodes.
>
> The problem:
> The slaves nodes are being networked with the master node using 1-Gb
> ethernet cards.
>
> The Question:
> Is it worth upgrading to 10-Gb ethernet cards? How much improvement can I
> expect?

No. Likely zero. Measure the time for a run writing to local disk and to
network disk. 10gb will be between them.

Mark

> Thank you,
> Amjad
>
>
>
> On Wed, Apr 2, 2014 at 4:25 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 4/2/14, 3:28 PM, Amjad Farooq wrote:
> >
> >> Aldo,
> >>
> >> Thank you so very much for your prompt response.
> >>
> >> Well, I have my data files on the PC but MD simulations are running on
the
> >> remote workstation. So, yes, you are right: it is the file
write/transfer
> >> or I/O operation that will be affected.
> >>
> >> But, the question is by how much? How much is this gonna slow down my
> >> simulations? I wonder what the rate-limiting step in Gromacs is? Is it
> >> integrating the Newton's equation or writing data to disk?
> >>
> >>
> > I/O is expensive.  I/O over a network is even worse, but the impact on
the
> > simulation depends on how often you write to disk.  Is there some reason
> > why you aren't writing to the disk on the remote workstation?  That
> > eliminates any dependence on the interconnect completely.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 601
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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