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Re: [lammps-users] Problem with create_bonds and MPI
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Re: [lammps-users] Problem with create_bonds and MPI

From: Axel Kohlmeyer <akohlmey@...24...>
Date: Wed, 02 May 2018 17:09:15 +0000

Please report this as an issue on GitHub and include a suitable input deck to reproduce it. 

Thanks, Axel. 

Dr. Axel Kohlmeyer  akohlmey@...24...
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.

On Wed, May 2, 2018, 12:03 Robert Meißner <robert.meissner@...4427...> wrote:
Dear lammps-users,

I'm using the new create_bonds single/... commands to create on the fly
new bonds, angles and dihedrals in a loop and continue the simulation.
If I'm running the simulation on only one CPU everything works fine.
Running it on multiple cores it creates an error message that some of
the atoms don't exist. I've checked the source code and found that
sometimes the allcount variable (in line 331) is 4 (and should be 2)
since some atoms may be found on multiple processes and
MPI_Allreduce(...,MPI_SUM,...) sums thus up to more than two atoms.
However, this happens only if I place the create_bonds command after a
previous run command. I've attached a small (quite random script) which
reproduces this behavior. It runs for simulations with one core and
crashes for simulations with more than one core giving the previously
mentioned error.

I was not able to track down the error, maybe you know a solution for this?



Prof Dr.-Ing Robert Horst Meißner

Institute of Polymer and Composites
Denickestr. 15
D-21073 Hamburg
Tel.:  +49 (0)40 42878 2580
E-mail: robert.meissner@...4427...

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