[gmx-users] MD simulations on a remote workstation

[Mark Abraham]

On Apr 3, 2014 3:14 AM, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>
> On 4/2/14, 6:29 PM, Amjad Farooq 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.
>>
>
> OK, that's a very different situation than what you originally described,
which basically was "computer 1 needs to talk to computer 2."  It's much
more complicated than that :)

Sorry, I missed this change of topic when I read last night!

>> 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.  If you want decent performance out of a cluster of any size,
Infiniband is the way to go.  Gb ethernet is generally not up to the task
here.

Correct. For parallelizing between nodes, GROMACS is likely to pay off any
money you can spend on network hardware. For writing to disk, network
hardware is likely irrelevant.

Mark

> -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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