Re: [AMBER] AMBER12 build on Linux x86_64

From: Shaw, Sharon <sharon.shaw.hp.com>
Date: Mon, 23 Apr 2012 20:51:14 +0000

Hi Matthew and Jason,
Thank you for your suggestions.

I edited $AMBERHOME/config.h after configure ran,
and then did a "make install". I have attached the gzip'd output.
You will see that -xHost is somehow still in the compiles.
If you can figure out where it is coming from, I would appreciate it.
My goal is to make one build for multiple architectures or to at least
give it a try!

I normally do make a build script after I get it all figured out
and use sed. I just was hoping there was an ARCH_FLAG or something
similar where one could set the architecture code generation flags like -x, -ax
for the entire application. No biggie.

thanks
Sharon


-----Original Message-----
From: Jason Swails [mailto:jason.swails.gmail.com]
Sent: Monday, April 23, 2012 2:31 PM
To: AMBER Mailing List
Subject: Re: [AMBER] AMBER12 build on Linux x86_64

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).

HTH,
Jason

On Mon, Apr 23, 2012 at 3:16 PM, Matthew Zwier <mczwier.gmail.com> 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 <sharon.shaw.hp.com> 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
> > sharon.shaw.hp.com
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
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>



-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Apr 23 2012 - 14:00:02 PDT
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