Re: NAMD on blue gene BG/P

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Thu Jul 10 2008 - 17:00:50 CDT

Hi Andrew,

from my experience with BG/L and BG/P machines you get better
performance when recompiling from the source.

also, we get better performance running in virtual mode.

our systems are ~40-60000 atoms and scaling goes very well up 512
processors in virtual mode (128 nodes).

I hope this helps,

george

On Thu, 2008-07-10 at 12:46 +0200, Andrew Emerson wrote:
> Dear All
>
> I want to use NAMD 2.6 on a Blue Gene/P machine. I have tried the
> downloadable executable but the performance and scaling are very poor,
> even with the twoAway options in the configuration file and setting
> BG_MAPPING=TXYZ (the system is also a bit small, 33000 atoms but I cant
> change that).
> Are there any other "simple" fixes which might help ?
>
> Assuming that the only solution is to compile it myself any suggestions
> before I dive in ?
>
> many thanks
> Andy Emerson
>

-- 
________________________________________________________________________
George Madalin Giambasu                        PhD Student
University of Minnesota                        Phone : (612) 625-6317
Department of Chemistry                        Fax   : (612) 626-7541
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Minneapolis, MN USA 55455-0431                 GeorgeMGiambasu_at_umn.edu
York Research Group                            giambasu_at_gmail.com
http://theory.chem.umn.edu/
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