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Re: [lammps-users] NEB EXAMPLE
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Re: [lammps-users] NEB EXAMPLE


From: Alexandra Davila <davila@...6924...>
Date: Tue, 15 Aug 2017 10:16:48 +0200

thanks!

I did make ubuntu, and now the neb examples are working.


On 14.08.2017 18:40, Axel Kohlmeyer wrote:


On Mon, Aug 14, 2017 at 12:35 PM, Alexandra Davila <davila@...6924...> wrote:

if I do:

$ mpirun -np 4 lmp_mpi -partition 4x1 -in in.neb.hop1
ERROR: Processor partitions do not match number of allocated processors (../lammps.cpp:260)
ERROR: Processor partitions do not match number of allocated processors (../lammps.cpp:260)

​this doesn't make sense. it would be either one line or four lines.​

-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[51470,1],0]
  Exit code:    1
--------------------------------------------------------------------------

my mpi version is

$ mpirun --version
mpirun (Open MPI) 1.10.2                                                                                                                                                                 Report bugs to http://www.open-mpi.org/community/help/

I thought, if I used OpenMPI, i didnt need to specify the MPI variables.

​what MPI variables and where are you talking about.​
 
What do you recommend me ?

​i can only repeat what i had said before. either you have inconsistent mpi libraries or your executable was compiled for MPI stubs.

i cannot read minds of people nor those of computers, so i cannot know what you have done exactly and what is going wrong on your computer.
all i can say from my (remote) position, that the command line works for me, and that what you are seeing is not a LAMMPS error, but due to some form of inconsistent usage.

axel.

 

thanks,

On 14.08.2017 18:10, Axel Kohlmeyer wrote:


On Mon, Aug 14, 2017 at 12:01 PM, Alexandra Davila <davila@...7062...de> wrote:
Hi Lammps-users,

I am trying to run the neb example, but i become this ERROR message:

mpirun -np 2 lmp_mpi -partition 2x1 -in in.diffusion

##

ERROR: Processor partitions do not match number of allocated processors (../lammps.cpp:260)
ERROR: Processor partitions do not match number of allocated processors (../lammps.cpp:260)
-------------------------------------------------------
Primary job  terminated normally, but 1 process returned
a non-zero exit code.. Per user-direction, the job has been aborted.
-------------------------------------------------------
--------------------------------------------------------------------------
mpirun detected that one or more processes exited with non-zero status, thus causing
the job to be terminated. The first process to do so was:

  Process name: [[51984,1],0]
  Exit code:    1
##

what am i doing wrong?

​the fact you you get two error messages is worrisome. there should be only one. do you get four, if you use mpirun -np 4?
if yes, it means, that either your lmp_mpi executable is not compiled for use with MPI, or that your mpirun command belongs to a different MPI library than what lmp_mpi was compiled with (e.g. MPICH vs. OpenMPI vs. IntelMPI vs. MVAPICH)​.

axel.


 

thanks,


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--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.


------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, Slashdot.org! http://sdm.link/slashdot
_______________________________________________
lammps-users mailing list
lammps-users@...396...sourceforge.net
https://lists.sourceforge.net/lists/listinfo/lammps-users




--
Dr. Axel Kohlmeyer  akohlmey@...24...  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.