AMBER Archive (2004)

Subject: Re: AMBER: Opteron PMEMD

From: David A. Case (
Date: Thu May 06 2004 - 17:09:47 CDT

On Thu, May 06, 2004, Robert Duke wrote:

> It SHOULD be possible to use the 32 bit emulation libraries, but first you
> have to be sure they are installed on the system. Then, I think you have to
> look at the ld man page and use various incantations to get things linked to
> 32 bit libraries. I DID try all this with pmemd (I am the pmemd author, by
> the way) on RHEL v 3, AMD64, and ifc 7.1.038 (if memory serves). In the
> timeframe I was doing all this, ifc 8 did not work at all. Now, I had an
> absolutely horrible time with machine stability (probably heating), and
> though I got everything linked, it was also clear that all the various
> pieces had some serious misunderstandings with each other (seg faults).
> Maybe it will work now.

Our limited experience is this: we have had good success with an opteron using
the amber8/src/pmemd/config_data/linux_opteron.ifc7.nopar file that Bob
supplies with the Amber 8 distribution (and we did have to make sure that the
proper libraries were installed). So this would be the configuration to try
first, followed by parallel tests.

(This just indicates that the configuration works, i.e. gives correct answers.
It is not meant to indicate that we achieve anything like the optimal
performance that is possible with this cpu.)

Although the current release of ifc8 (ifort) from Intel works fine for us with
pmemd on Pentium IA32 machines, we have not been successful using the above
configuration for an opteron (i.e. just substituting ifort for ifc, with all
other flags the same.) But this was very limited testing: like Bob, we don't
actually have an opteron system, and just borrow time on a friend's machine to
see if things will work.

I'm hoping that someone on the list who actually has and uses opteron systems
can chime in....



================================================================== David A. Case | e-mail: Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896 The Scripps Research Institute | phone: +1-858-784-9768 10550 N. Torrey Pines Rd. | home page: La Jolla CA 92037 USA | ================================================================== ----------------------------------------------------------------------- The AMBER Mail Reflector To post, send mail to To unsubscribe, send "unsubscribe amber" to