AMBER Archive (2009)

Subject: Re: [AMBER] What is the parallel efficiency of amber10

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Mon Jun 08 2009 - 08:44:26 CDT

Just to complement on the answers you have already received. In our
experience with large numbers of processors, it is usually a good idea
to leave some cores idle during the calculation. With 8-core nodes,
for example, we get better throughput by allocating the whole node and
only using 1-2 MPI processes per node. Still, the best thing is for
you to run some test calculations with your own system.

Gustavo Seabra
Postdoctoral Associate
Quantum Theory Project - University of Florida
Gainesville - Florida - USA
-------------------------------------------------------------------------------------------
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On Sun, Jun 7, 2009 at 11:19 PM, Catein Catherine<askamber23_at_hotmail.com> wrote:
>
> Dear Sir/Madam,
>
>
>
> Could you mind to share your experience with me about the parallel efficiency of amber10.  It seems to me  that we can run AMBER10 efficiently in 8 processors on the same node.
>
>
>
> However, the jobs may have problem to run on 2 nodes with 8 processors each.
>
>
>
> Is it better to do the sander within the same node?  Could you pls kindly share your experiences with me?
>
>
>
> Best regards,
>
>
>
> Cat
>
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