[gmx-users] MD simulations on a remote workstation

[Amjad Farooq]

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 wish some benchmark was available.



*AMJAD FAROOQ PhD DIC | Associate Professor *Dept of Biochemistry, University
of Miami School of Medicine
*Location*:  Gautier Building, Suite 217
*Address*:  1011 NW 15th Street #217, Miami , FL 33136, USA
*Contact*:   amjad at farooqlab.net | 305-243-2429
*Labpage*: farooqlab.net <http://www.farooqlab.net> |
structuropedia.org<http://dalton.med.miami.edu>




On Wed, Apr 2, 2014 at 2:13 PM, Aldo Segura <asegurac666 at yahoo.com.mx>wrote:

> Hi Farooq,
>
> Are the machines working in parallel? I mean,  is the simulation running
> on both machines? or Are you using your PC just to send and monitoring the
> simulation on the workstation? In the former case, you'll see an
> improvement in the communication between both machines and speed of
> simulations (I don't know how much, sorry).  For last case, you'll notice
> the difference when you're transfering files between your PC and the
> workstation.
>
>
> Best,
>
> Aldo
>
>
> =======================================
> Aldo Segura-Cabrera
> Postdoctoral Fellow
> Division of Experimental Hematology and Cancer Biology
> Cancer and Blood Diseases Institute
> Cincinnati Children's Hospital Medical Center
> 3333 Burnet Ave, MLC 7013, Cincinnati OH 45229
>
> =========================================
> El Miércoles, 2 de abril, 2014 13:49:53, Amjad Farooq <amjad at farooqlab.net>
> escribió:
>
> Hi everyone,
>
> I am running Gromacs 5.0-beta on a remote workstation (next door) from my
> PC. The two machines are networked via 1-Gigabit PCI-E ethernet cards (on
> each machine) and a CAT-6 ethernet cable.
>
> My question is:
> Would my MD simulations benefit in terms of speed if I were to use
> 10-Gigabit PCI-E ethernet cards (they are damn expensive)? Is it worth my
> dime and time? How much would I gain in terms of speed? Halve the run time?
> Or even better?
>
> Thank you for any suggestions that you may have.
>
> Amjad Farooq
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