AMBER Archive (2005)

Subject: Re: AMBER: maximum number of processors

From: Asim Okur (aokur_at_ic.sunysb.edu)
Date: Thu May 12 2005 - 10:41:25 CDT

Hi,

The number of CPU's you can use depends on the system size and the
communication between nodes. When you use more CPU's communication
increases and the efficiency drops. It is even possible that sometimes
with more CPU's your simulations actually run slower. The easiest way is
to run some benchmark simulations with different number of processors
(~1000 steps should be enough) and determine the number of nodes you need.

I hope this helps,

Asim

MURAT CETINKAYA wrote:

>Hi Amber users,
>
>I normally run sander with 16 nodes (dual processor in each) and I know the
>speed of the run. This time I tried using 32 nodes, but the speed seems just
>the same as 16 node runs. The system I simulate is completely the same as
>before. Is there a limit for the number of nodes that AMBER can use? Or is
>there another point I cannot figure out?
>
>Thanks.
>
>PS: I use amber7 and all nodes are functioning well.
>Murat CETINKAYA
>Biomolecular Materials Lab,
>Dept. of Engr. Science and Mechanics,
>The Pennsylvania State University,
>University Park, PA 16802
>office: (814) 863 9967
>web: www.personal.psu.edu/muc176
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-- 
Asim Okur
Stony Brook University
Chemistry Department
Stony Brook, NY 11794-3400
631 - 632 1560

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