Re: NAMD on blue gene BG/P

From: Andrew Emerson (a.emerson_at_cineca.it)
Date: Fri Jul 11 2008 - 05:44:16 CDT

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
>>

-- 
Dr Andrew Emerson
CINECA (High Performance Systems)
via Magnanelli, 6/3
40033 Casalecchio di Reno (BO)-ITALY
tel: +39-051-6171653, fax: +39-051-6137273
e-mail: a.emerson_at_cineca.it

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