Re: AMBER: Amber compilation on opteron with PGI compiler

From: Robert Duke <>
Date: Fri, 30 Sep 2005 09:53:58 -0400

PLEASE, if you install pmemd 8 on anything, first pick up the new_configure
package from the website (it is reached through the link
"March 2005 configuration update for pmemd" which is under the big header
"Amber-related links". One should definitely not just hack the config.h
under /amber8/src to install pmemd, and taking what a vendor (like pgi)
provides is also a little risky as they may not have explored the impact of
my various conditionally compiled optimizations. The outer config.h for
amber typically sets lower optimization levels than does pmemd because there
is code out ther in the general amber product that does not compile
correctly at higher optimization levels. Anyway, please download the
package, and enter "./new_configure -help" in the pmemd directory. There is
complete support available there for the opteron using either the pgi,
pathscale, or ifort compilers, and you will get it correctly optimized for
both the cpu and interconnect to boot (it will be faster :-)).
Regards - Bob Duke

----- Original Message -----
From: "Mingfeng Yang" <>
To: <>
Sent: Friday, September 30, 2005 9:15 AM
Subject: AMBER: Amber compilation on opteron with PGI compiler

> Installed both Amber 7 and 8 on our newly purchased cluster (AMD opteron
> CPU) connected by myrinet (MPICH-MX).
> Got many helps from different sites by google. I wrote a short report to
> record something worth to be shared.
> Benchmarks on factor fix system are also included. It seems Intel
> compiler does outperform PGI even on opteron CPU.
> Hope it will be helpful to others.
> Happy simulating!
> Yang

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Received on Fri Sep 30 2005 - 15:53:00 PDT
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