[gmx-users] Computational efficiency

[Diego Enry]

Ethernet has very high latency, it wasn't made for this kind of thing.
Gmx 4 will be much much better, check the paper gromacs website.


On 3/6/08, Ricardo Soares <rsoares at fcfrp.usp.br> wrote:
>
>  Diego Enry wrote:
>  On Thu, Mar 6, 2008 at 1:26 PM, Ricardo Soares <rsoares at fcfrp.usp.br>
> wrote:
>
>
>  Hello everyone,
>
>  I have 3 available computers for my simulations; two of them are dual
>  core. Which is better for me: run one simulation each independently or
>  parallelize them all?
>
>
>  In theory, if the simulations are independent it would be faster to
> run them independently, but you actually doubles the speed if you run
> in parallel in a SINGLE dual core machine.
> I would not recommend you to parallelize it to more than one machine
> if your network fabric is Gigabit Ethernet... unless you are really in
> a hurry to finish a single simulation.
>
> have fun !
>
>
>
>  Thanks!
>
>  Ricardo.
>
>  --
> ___________________________________________________________
>
>  Ricardo Oliveira dos Santos Soares
>  Post-graduation Student in Biological Physics
>  University of Sao Paulo - USP
>  Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
>  Phone: 55 (16) 3602-4840
>  Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
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>
>
>
>  Hello Diego,
>
>  Thanks for the tips. Just one more thing, what is the deal with the Gigabit
> Ethernet concerning this topic?
>
>  Regards,
>
>  Ricardo.
>
>  --
> ___________________________________________________________
>
> Ricardo Oliveira dos Santos Soares
> Post-graduation Student in Biological Physics
> University of Sao Paulo - USP
> Faculty of Farmaceutical Sciences of Ribeirao Preto - FCFRP
> Phone: 55 (16) 3602-4840
> Curriculum Lattes - http://lattes.cnpq.br/0777038258459931
> ___________________________________________________________
>
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-- 
Diego Enry B. Gomes
Laboratório de Modelagem e Dinamica Molecular
Universidade Federal do Rio de Janeiro - Brasil.