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[lammps-users] mprun error


From: bahman daneshian <bahmanpbamp@...24...>
Date: Mon, 21 May 2018 12:39:58 +0200

Dear LAMMPS and HPC experts, 

I am trying to run lammps on HPC. We installed LAMMPS (16 Mar 2018). So, lammps correctly works for small models. However, it seems that when the model becomes large(in order of 100 nm), computation cannot start and we face with this error:

mpirun noticed that process rank 56 with PID 0 on node node03 exited on signal 9 (Killed).

 please let me know whether you have any idea to solve this issue or not.

the output is listed below:

LAMMPS (16 Mar 2018)
Created orthogonal box = (0 0 0) to (1893 1893 2288.06)
  4 by 6 by 6 MPI processor grid
Lattice spacing in x,y,z = 3.786 3.786 9.514
Created 46073888 atoms
  Time spent = 5.00858 secs
46073888 atoms in group particle
Setting atom values ...
  15357926 settings made for charge
Setting atom values ...
  30715962 settings made for charge
Created 6000000 atoms
  Time spent = 0.403862 secs
6000000 atoms in group substrate
Setting atom values ...
  17357926 settings made for charge
Setting atom values ...
  34715962 settings made for charge
Created 3000000 atoms
  Time spent = 0.485369 secs
3000000 atoms in group lower_substrate
Setting atom values ...
  18357926 settings made for charge
Setting atom values ...
  36715962 settings made for charge
52073888 atoms in group model
WARNING: New thermo_style command, previous thermo_modify settings will be lost (/builddir/build/BUILD/lammps-stable_16Mar2018/src/output.cpp:705)
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -120.78 (/builddir/build/BUILD/lammps-stable_16Mar2018/src/kspace.cpp:302)
  using 12-bit tables for long-range coulomb (/builddir/build/BUILD/lammps-stable_16Mar2018/src/kspace.cpp:321)
  G vector (1/distance) = 0.176612
  grid = 675 675 768
  stencil order = 5
  estimated absolute RMS force accuracy = 0.0429126
  estimated relative force accuracy = 0.00012923
  using double precision FFTs
  3d grid and FFT values/proc = 2746450 2733750
Neighbor list info ...
  update every 1 steps, delay 5 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 17
  ghost atom cutoff = 17
  binsize = 8.5, bins = 223 223 270
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair buck/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/atomonly/newton
      stencil: half/bin/3d/newton
      bin: standard
Setting up Verlet run ...
  Unit style    : real
  Current step  : 0
  Time step     : 1
--------------------------------------------------------------------------
mpirun noticed that process rank 56 with PID 0 on node node03 exited on signal 9 (Killed).


Yours Sincerey,
Bahman Daneshian