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
lfoley.uga.edu
http://glycam.ccrc.uga.edu
________________________________________
From: Jason Swails [jason.swails.gmail.com]
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
./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 - 17:30:02 PDT
