On Mon, Apr 2, 2012 at 8:28 PM, B. Lachele Foley <lfoley.uga.edu> wrote:
> 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.
>
Sweet -- did the patch fix it?
>
> :-) 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
>
>
> _______________________________________________
> AMBER-Developers mailing list
> AMBER-Developers.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber-developers
>
--
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 - 18:00:03 PDT
