Re: NAMD on blue gene BG/P

From: George Madalin Giambasu (giambasu_at_gmail.com)
Date: Fri Jul 11 2008 - 10:17:27 CDT

Hi!

for BG/L the distributed 2.6 source code works.

for BG/P I compiled the latest CVS version - the developers have
included the machine specific options in there.

all the best,

George

On Fri, 2008-07-11 at 12:44 +0200, Andrew Emerson wrote:
> Hi George
>
> Thanks for the advice.
>
> Is the standard NAMD 2.6 distribution sufficient ? Or do I need a later
> version?
>
> Andrew
>
> George Madalin Giambasu wrote:
> > 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
207 Pleasant St. SE                            e-mail:
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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