AMBER Archive (2005)

Subject: Re: AMBER: amber8 parallel sander

From: MURAT CETINKAYA (cetinkayam_at_psu.edu)
Date: Mon Oct 03 2005 - 21:04:04 CDT

Hi Kathleen,

I genereally use 16nodes (dual processor) for the optimum speed. I tried 32
nodes, but there was no change in the computation speed, however I used twice
as much resources. In my opinion you should find the optimum node# by trial.
After a point I think, your system's speed will be counterbalanced with the
time spent during the communication between nodes.
I am not an expert in parallel computing, but this is the situation I had in my
case.

hope this helps.

On Mon, 03 Oct 2005 14:37:47 +0000, "Kathleen Erickson" wrote:

> Hi Carlos:
>
> If you don't mind my asking, is scaling efficiency a concern? I'm curious
> to know what % of n# of nodes/processors you are able to scale to in order
> to identify the satisfactory level of scaling efficiency. In other words,
> if you are getting only 20% scaling efficiency out of 160 nodes, is that
> sufficient for your needs or do you need more efficiency out of your
> existing nodes/processors?
>
> Anyone else have an opinion?- Kathleen
>
>
>
>
>
> Hi
> Carlos:
>  
> If you
> don't mind my asking,  is scaling efficiency a concern?  I'm
> curious to know what % of n# of nodes/processors you are able to scale to in
> order to identify the satisfactory level of scaling efficiency.  In
> other words, if you are getting only 20% scaling efficiency out of 160 nodes,
is
> that sufficient for your needs or do you need more efficiency out of your
> existing nodes/processors? 
>  
> Anyone
> else have an opinion?- Kathleen

Murat CETINKAYA, M.Sc.
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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