[gmx-users] MD simulations on a remote workstation

[Amjad Farooq]

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?

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
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> University of Maryland, Baltimore
> 20 Penn St.
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>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
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