Re: [AMBER] Building distributable executable

From: Jason Swails <>
Date: Wed, 17 May 2017 13:40:08 -0400

One possible concern is that configure actually runs some other configure
files as well (fftw, netcdf, cpptraj, etc.), so even if you change config.h
to remove -xHost after running configure, you may still wind up with some
binaries that cannot easily run on multiple CPU architectures. I don't
remember if this was a problem or not.

In the rare cases that I needed to build for a heterogeneous cluster, I'd
just remove all instances of "-xHost" from the configure2 file
(AmberTools/src/configure2) and run configure after I do that (a helpful
hint is to back up configure2 first lest you lose the original). In most
cases, -xHost is the right thing to do, though.


On Wed, May 17, 2017 at 12:21 PM, Scott Brozell <>

> On Wed, May 17, 2017 at 08:52:30AM -0400, David Case wrote:
> > On Tue, May 16, 2017, D'Auria, Raffaella wrote:
> > >
> > > While trying to build Amber 16 with the intel compiler I realized
> > > that the xHost flag is now sprinkled in many configure files and
> > > makefiles. Since I need to build an executable that will run across
> > > different processors (on a heterogeneous cluster) the xHost flag is a
> > > problem (since it will generate a processor-specific executable). Is
> > > there any option that will allow me to get rid of it without having to
> > > edit any config/makefile where xHost may be?
> >
> > Can you be more specific? The xHost flag should only be in the single
> > config.h created by the configure script (which actually calls
> > AmberTools/src/configure2 to do the real work.) Note that a couple of
> > other "config.h" scripts are just links to the master one, so that
> editing
> > the config.h in $AMBERHOME changes all of them.
> >
> > Bottom line: you *should* be able to just hand-edit $AMBERHOME/config.h
> to
> > remove the xHost invocations after the ./configure step but before the
> > "make install" step. It's certainly worth a try.
> >
> > You mention that xHost shows up in Makefiles as well, but I don't
> readily see
> > that, but I haven't examined every one. Try the suggestion above, and
> let us
> > know details of what (if anything) goes wrong.
> In the repo amber tree, I grepped all 368 Makefiles and all 701 *akefile*
> files - no xhost, ignoring case, in any of them.
> One file that is not used in most (all?) situations has an -march:
> ./AmberTools/src/gleap/freelib/gtkglext/examples/Makefile.mingw:15:OPTIMIZE
> = -march=pentium -O2
> There are 11 config.h files. But as Dave indicated ./config.h
> is the only one that should matter.
> There is 1 that hard codes xhost,
> but that file is not used and probably should be removed:
> ./AmberTools/src/cphstats/config.h
> scott
> ps
> A Unix operating system is an awesome tool.
> When it comes to finding things in textual files, some of the greatest
> programmers of all time (several of them Turing award winners), have
> created softwares (and textbooks) that are still the best tools.
> Learn find and grep.
> _______________________________________________
> AMBER mailing list

Jason M. Swails
AMBER mailing list
Received on Wed May 17 2017 - 11:00:03 PDT
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