AMBER Archive (2006)

Subject: Re: AMBER: ACML and MASS/MASSV for sander and pmemd

From: Robert Duke (
Date: Tue Sep 19 2006 - 15:03:00 CDT

Hi Nick -
There are basically two reasons I have not used ACML:
1) until the introduction of generalized Born code to pmemd, there were no
code paths that were significantly impacted by math libraries - ie., math
libraries did not help much for pretty much all of the pme functionality. I
introduced generalized Born code pretty late in the last release cycle.
2) The ACML libraries have not had particularly high visibility on the
machines that I commonly use. They are probably there in some places like
NERSC, but folks have not been making a big deal about it. I actually got
the MASSV libs in for GB very very late (I had used MASSV before, but due to
changing optimizations in the pme direct force code, it was actually no
longer the fastest compile option for the sp4/5).
Especially if people using GB on opterons complain, I'll probably take an
afternoon off and do this for the next release. I don't recollect this
stuff being anywhere in the rest of amber 9, but maybe I missed it.
Regards - Bob Duke

----- Original Message -----
From: "Nicolas Lux Fawzi" <>
To: <>
Sent: Tuesday, September 19, 2006 3:36 PM
Subject: AMBER: ACML and MASS/MASSV for sander and pmemd

> Hi Bob (and others who might be able to help),
> I noticed your timings ( were
> on NERSC's new infiniband opteron and power5 machines. I am starting to
> run sander and pmemd on these machines. I also noticed that you did not
> use the ACML math library on the operton, but did use the MASSV lib on the
> power5. Here come the questions: Is there a reason you (or anyone else)
> skipped the opteron math library -- is it no faster? And second, clearly
> I could test this myself, but I need to figure out how to get the ACML and
> MASSV libraries to be used instead of the built in functions. I have seen
> this page from Pathscale regarding amber8
> ( from which I suppose
> I can put together how to use the math libraries for sander and pmemd, but
> I was wondering if there were instructions out there somewhere. I checked
> through the Amber9 manual, but didn't find anything.
> Thanks for helping out a new person!
> -Nick
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