RE: AMBER: Blue Gene, compile Amber9?

From: Ross Walker <>
Date: Fri, 6 Apr 2007 14:23:33 -0700

Dear Mike,
There is little point trying to run the rest of Amber on Blue Gene. The
scaling of sander is not sufficient to be efficient on Blue Gene and the
memory requirements will likely stop you running any decent size systems.
PMEMD scales much better than sander and requires less memory. The memory
usage also goes down with the cpu count making it more suitable for Blue
Gene. Note PMEMD 9 supports both PME simulations and implicit solvent GB
I attach the config.h I used to build pmemd 9 on SDSC's Blue Gene. Try the
one on the Amber website first though since this may have been optimized by
Bob Duke and give better performance. Benchmarks and job submission scripts
are here:
Note: Blue Gene is not a machine that was actively targetted by the Amber
developers during the Amber 9 development and so the code has not had any
specific optimizations for Blue Gene. Amber 10's PMEMD may contain some Blue
Gene tweaks that will improve the performance but this won't be released
until next year. Bob Duke may be able to comment more.
All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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From: [] On Behalf Of
Mike Hanby
Sent: Friday, April 06, 2007 10:23
Subject: AMBER: Blue Gene, compile Amber9?



Has anyone compiled Amber9 for use on an IBM Blue Gene/L (bgl) system that
wouldn't mind sharing the steps they used to cross compile the code using
the blrts_xl compilers?


I found one section on the Amber site that provides a config.h file for
compiling pmemd but nothing to do with the rest of Amber.


Thanks, Mike

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Received on Sun Apr 08 2007 - 06:07:41 PDT
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