Re: [AMBER-Developers] need suggestions about Amber12 build/test procedure

From: David A Case <>
Date: Wed, 15 Feb 2012 10:36:11 -0500

On Wed, Feb 15, 2012, Daniel Roe wrote:
> I recently created a new build target, 'openmp' for use when '-openmp'
> is passed to configure. Right now this valid for AmberTools only and
> just builds cpptraj and NAB.

Thanks for doing that. (Actually, what you did builds everything that nab
needs as well, which includes sff.)

As far as I know the only parts of Amber
> that use openMP are:
> cpptraj
> sff
> sqm
> nab (via sff)
> sander (via sqm)

Are we ready to support the openmp versions of sqm and sander/sqm? These
would never have been built or tested in Amber11. My feeling is that it is
way too late in the release cycle to add support for this, and that we should
just limit the openmp stuff to nab/sff/cpptraj.

Or: is someone using and testing the openmp sqm and can vouch for it?
[Aside: it looks the the stand-alone sqm is configured to use MPI if
requested, but there is no target in the Makefile to create sqm.MPI. Has
anyone ever tried this?]

> INSTALLTYPE could be set to 'openmp' in config.h and a top-level 'make
> install' from $AMBERHOME would take care of everything.
> Similarly for tests a 'test.openmp' target can be created that only
> tests the openmp-dependent parts of the code...
> and ensures that DO_PARALLEL is not set.

Above sounds correct to me. The documentation needs to inform people that
compiling with openmp creates new versions of nab and cpptraj that are now
openmp-aware (i.e. depend on OMP_NUM_THREADS), but the executable
names are not changed.

Aside: is there (or is there going to be) an MPI version of cpptraj?


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Received on Wed Feb 15 2012 - 08:00:03 PST
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