[AMBER-Developers] partial NEB issue with release candidate 3

From: Jason Swails <jason.swails.gmail.com>
Date: Mon, 2 Apr 2012 18:21:55 -0400

Hello everyone,

I was wondering if anybody could corroborate an issue I've observed on 2
machines with the NEB tests. My system configurations that cause this
issue are:

GNU 4.5.3 + OpenMPI 1.4.5
GNU 4.6.1 + OpenMPI 1.4.3
(It did NOT happen with GNU 4.1.2 + OpenMPI 1.4.5)

(I believe it also happened with OpenMPI 1.5.4). The issue does not crop
up with those compilers using mpich2-1.4.1p1, so it is strictly the GNU 4.5
(maybe 4.4?) or GNU 4.6 compilers combined with OpenMPI 1.4+. (The issue
is 100% reproducible on these systems, though). The NEB tests require 4+
processors to run, so you should be able to test this by going to

$AMBERHOME/test/neb-testcases/neb_gb_partial/ and doing the following:

export TESTsander=$AMBERHOME/bin/sander.MPI
export DO_PARALLEL='mpirun -np 4' # or 8
./Run.neb_gb_partial

The test should pass almost instantly. I've attached a patch that fixes
the issue for me (which was checked into the master branch recently), but I
do not understand why the patch is necessary in the first place. (apply
the patch from $AMBERHOME using 'patch -p0 -N < neb.patch')

Any indication that I'm not going crazy is appreciated (or even better, if
you can shed light on the actual origin of the problem).

Thanks!
Jason

-- 
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032



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Received on Mon Apr 02 2012 - 15:30:09 PDT
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