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

From: B. Lachele Foley <>
Date: Tue, 3 Apr 2012 00:28:34 +0000

I can. Same here. Been too overwhelmed to make a nice report.

gcc (Ubuntu/Linaro 4.6.1-9ubuntu3) 4.6.1
Ubuntu 11.10
non-apt-get openmpi-1.4.4 from sources

If I comment out all neb, it runs fine.

:-) Lachele

Dr. B. Lachele Foley
Complex Carbohydrate Research Center
The University of Georgia
Athens, GA USA

From: Jason Swails []
Sent: Monday, April 02, 2012 6:21 PM
To: AMBER Developers Mailing List
Subject: [AMBER-Developers] partial NEB issue with release candidate 3

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

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).


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Mon Apr 02 2012 - 17:30:02 PDT
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