Re: [AMBER] AMBER12 build on Linux x86_64

From: Jason Swails <>
Date: Mon, 23 Apr 2012 15:31:21 -0400

Matthew's comments are accurate. I realize that -xHost is not ideal for a
heterogeneous cluster, but the arguments against canning it were that it
would disable vectorization completely and significantly hurt performance.
 For those that have heterogeneous clusters, I guess the idea is that they
can figure out the vectorization flags they need.

When I compile, I use sed on the config.h file that configure produces: sed
-i "s.-xHost.Replacement Flag(s)@g" config.h

The only deviation from Amber 10 (which is what Matt's system was), is that
there is only one config.h file ($AMBERHOME/config.h) that needs editing.
 (Note there may appear to be config.h files in $AMBERHOME, $AMBERHOME/src,
and $AMBERHOME/AmberTools/src, but they are all the same file referenced
via symlinks).


On Mon, Apr 23, 2012 at 3:16 PM, Matthew Zwier <> wrote:

> Hi Sharon,
> I've not done this with Amber 12, but I have done it with Amber 10 and
> 11. In those versions, it didn't seem to be possible with parameters
> to the configure scripts, but changing both config.h files (one each
> for Amber and AmberTools) was sufficient. I tended to do it with "sed
> -i 's/-xHost/-xSSE3/g' config.h" or whatever (and I rolled it in with
> a few other changes I had to make locally). Those changes had to be
> made every time config.h was regenerated, which in the early days of
> Amber 11 was up to four times if I recall (Amber vs. AmberTools,
> serial vs. parallel). I wound up doing everything (configuration,
> patching the config files, and building each toolset) in a shell
> script to keep it all straight. Your mileage may vary slightly.
> If you're doing this for a single CPU microarchitecture or for
> debugging reasons, that should be enough. If you're trying to get the
> same executable to run on a small number of different CPU
> microarchitectures, you may have better luck (i.e. greater performance
> and/or stability) compiling separate copies of Amber for each,
> particularly if you're targeting both Intel and AMD CPUs.
> Maybe someone else on the list can comment on what needs to change, if
> anything, for Amber 12.
> Cheers,
> Matt Z.
> On Mon, Apr 23, 2012 at 2:41 PM, Shaw, Sharon <> wrote:
> > Hi,
> > I would like to build Amber 12 with the Intel compilers but replace
> "-xHost" with a different
> > "-x" flag everywhere "-xHost" exists. Is there any easy way to do this?
> > If not, could you please supply the filenames that I would need to
> manually edit?
> > It seems I am missing editing a few.
> >
> > thank you,
> > Sharon
> >
> > Sharon Shaw
> > Hewlett-Packard Co.
> > High Performance Computing
> > 972-605-4603
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> >
> >
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Apr 23 2012 - 13:00:02 PDT
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