Re: [AMBER-Developers] Status of the "cray" targets in AmberTools/src/Makefile?

From: Daniel Roe <>
Date: Mon, 16 Jan 2017 19:01:46 -0500

On Mon, Jan 16, 2017 at 12:41 PM, David Case <> wrote:
> Is anyone up on the status of the cray_serial, cray_parallel and
> cray_openmp targets in AmberTools/src/Makefile?

I created these in response to complaints Tom and I got from the Blue
Waters people that the 'cray' compiler option for configure did not
actually work. The problem ended up being certain programs within
Amber (specifically AmberTools) would not compile with cray compilers
since these tend to be a lot less forgiving than other compilers. So I
created the cray_X targets to compile those programs within Amber
which could compile with cray compilers; pmemd, cpptraj, etc.

> The cray_serial target has a comment "does not work...". The parallel
> and openmp targets look (nearly?) identical to their non-cray counterparts.

I think the comment you're referring to is "Not working: pbsa, gbnsr6,
sander, nmr_aux, nss, etc, mmpbsa, amberlite, quick", right? This was
just meant to list the programs which will not (or at least would not
at the time) compile with cray compilers. I think the only problem
with sander is that libpbsa won't compile. The openmp and MPI targets
are almost identical because most (not all) of the programs in the
original targets compile with cray compilers (e.g. RISM doesn't
compile I think).

> So: is anyone using these? Can we simplify or remove them? Do we know
> they still work?

Not sure. I invested a lot of time and effort into making sure that
the 'cray' compiler target built for serial, OpenMP, and MPI (at least
on Blue Waters). It was working as of last summer but I haven't had a
chance to test it recently. This solution was the easiest one I could
think of without rewriting the entire configure/build process. If you
want to get rid of them that's fine, but then we should probably
either remove the 'cray' compiler option or list it as "experimental"
or something. I can try to make sure it works this week if I get a

> Also ripe for documentation: what does "cray" mean in this context? How
> is it different from the "cray_xt5" options in configure? (And: are the
> latter options ever used or tested?)

Jason's explanation of these is spot on.


Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
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Received on Mon Jan 16 2017 - 16:30:02 PST
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