NAMD on blue gene BG/P

From: Andrew Emerson (
Date: Thu Jul 10 2008 - 05:46:36 CDT

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

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