Commit 68ec8822 authored by Ryan S. Elliott's avatar Ryan S. Elliott
Browse files

Update example/kim/log.*

parent 955fe583

examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.1

deleted100644 → 0
+0 −33
Original line number Diff line number Diff line 
LAMMPS (15 May 2015)

Lattice spacing in x,y,z = 4.43 4.43 4.43

Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)

  1 by 1 by 1 MPI processor grid

Created 32000 atoms

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  master list distance cutoff = 8.45

Setting up run ...

Memory usage per processor = 9.18789 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          200   -741.55469            0    85.684388   -34.939092 

     100    108.37517   -362.56658            0    85.694308    3963.7892 

Loop time of 2.95205 on 1 procs for 100 steps with 32000 atoms



Pair  time (%) = 2.52074 (85.3894)

Neigh time (%) = 0.347949 (11.7867)

Comm  time (%) = 0.0228171 (0.772925)

Outpt time (%) = 0.000188828 (0.00639649)

Other time (%) = 0.0603588 (2.04464)



Nlocal:    32000 ave 32000 max 32000 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    20131 ave 20131 max 20131 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    1.88909e+06 ave 1.88909e+06 max 1.88909e+06 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 1889091

Ave neighs/atom = 59.0341

Neighbor list builds = 5

Dangerous builds = 0

examples/kim/log.28Jun15.kim.lj.lmp.ubuntu.4

deleted100644 → 0
+0 −33
Original line number Diff line number Diff line 
LAMMPS (15 May 2015)

Lattice spacing in x,y,z = 4.43 4.43 4.43

Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)

  1 by 2 by 2 MPI processor grid

Created 32000 atoms

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  master list distance cutoff = 8.45

Setting up run ...

Memory usage per processor = 4.58461 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          200   -741.55469            0    85.684388   -34.939092 

     100    108.37517   -362.56658            0    85.694308    3963.7892 

Loop time of 6.15911 on 4 procs for 100 steps with 32000 atoms



Pair  time (%) = 1.76201 (28.6083)

Neigh time (%) = 0.265002 (4.30261)

Comm  time (%) = 3.64452 (59.1729)

Outpt time (%) = 0.0169877 (0.275815)

Other time (%) = 0.470582 (7.64042)



Nlocal:    8000 ave 8010 max 7989 min

Histogram: 1 0 0 0 0 2 0 0 0 1

Nghost:    9240.25 ave 9249 max 9228 min

Histogram: 1 0 0 0 1 0 0 0 0 2

Neighs:    472273 ave 473390 max 471652 min

Histogram: 2 0 0 1 0 0 0 0 0 1



Total # of neighbors = 1889091

Ave neighs/atom = 59.0341

Neighbor list builds = 5

Dangerous builds = 0

examples/kim/log.28Jun15.kim.lj.ubuntu.1

deleted100644 → 0
+0 −33
Original line number Diff line number Diff line 
LAMMPS (15 May 2015)

Lattice spacing in x,y,z = 4.43 4.43 4.43

Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)

  1 by 1 by 1 MPI processor grid

Created 32000 atoms

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  master list distance cutoff = 8.45

Setting up run ...

Memory usage per processor = 9.43789 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          200   -741.55469            0    85.684388   -34.939092 

     100    108.37517   -362.56658            0    85.694308    3963.7892 

Loop time of 3.79746 on 1 procs for 100 steps with 32000 atoms



Pair  time (%) = 3.18686 (83.9207)

Neigh time (%) = 0.524724 (13.8178)

Comm  time (%) = 0.0244031 (0.642616)

Outpt time (%) = 0.000174046 (0.00458321)

Other time (%) = 0.061305 (1.61437)



Nlocal:    32000 ave 32000 max 32000 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    20131 ave 20131 max 20131 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    2.09236e+06 ave 2.09236e+06 max 2.09236e+06 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 2092355

Ave neighs/atom = 65.3861

Neighbor list builds = 5

Dangerous builds = 0

examples/kim/log.28Jun15.kim.lj.ubuntu.4

deleted100644 → 0
+0 −33
Original line number Diff line number Diff line 
LAMMPS (15 May 2015)

Lattice spacing in x,y,z = 4.43 4.43 4.43

Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)

  1 by 2 by 2 MPI processor grid

Created 32000 atoms

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  master list distance cutoff = 8.45

Setting up run ...

Memory usage per processor = 4.70961 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          200   -741.55469            0    85.684388   -34.939092 

     100    108.37517   -362.56658            0    85.694308    3963.7892 

Loop time of 7.25305 on 4 procs for 100 steps with 32000 atoms



Pair  time (%) = 2.52571 (34.8227)

Neigh time (%) = 0.500287 (6.8976)

Comm  time (%) = 3.70236 (51.0456)

Outpt time (%) = 0.00146681 (0.0202234)

Other time (%) = 0.523229 (7.21391)



Nlocal:    8000 ave 8010 max 7989 min

Histogram: 1 0 0 0 0 2 0 0 0 1

Nghost:    9240.25 ave 9249 max 9228 min

Histogram: 1 0 0 0 1 0 0 0 0 2

Neighs:    555266 ave 555920 max 554805 min

Histogram: 2 0 0 0 0 1 0 0 0 1



Total # of neighbors = 2221065

Ave neighs/atom = 69.4083

Neighbor list builds = 5

Dangerous builds = 0

examples/kim/log.29Jun18.kim.lj.lmp.ubuntu.1

0 → 100644
+66 −0
Original line number Diff line number Diff line 
--------------------------------------------------------------------------

[[30970,1],0]: A high-performance Open MPI point-to-point messaging module

was unable to find any relevant network interfaces:



Module: OpenFabrics (openib)

  Host: ubuntu-artful



Another transport will be used instead, although this may result in

lower performance.



NOTE: You can disable this warning by setting the MCA parameter

btl_base_warn_component_unused to 0.

--------------------------------------------------------------------------

LAMMPS (22 Jun 2018)

Lattice spacing in x,y,z = 4.43 4.43 4.43

Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)

  1 by 1 by 1 MPI processor grid

Created 32000 atoms

  Time spent = 0.0031676 secs

Neighbor list info ...

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 7.85482

  ghost atom cutoff = 7.85482

  binsize = 3.92741, bins = 23 23 23

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/3d/newton

      bin: standard

Setting up Verlet run ...

  Unit style    : metal

  Current step  : 0

  Time step     : 0.001

Per MPI rank memory allocation (min/avg/max) = 16.58 | 16.58 | 16.58 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0          200   -495.29247            0    331.94661   -978.84224 

     100    212.66365   -547.67175            0    331.94665   -1054.2086 

Loop time of 1.40245 on 1 procs for 100 steps with 32000 atoms



Performance: 6.161 ns/day, 3.896 hours/ns, 71.304 timesteps/s

100.0% CPU use with 1 MPI tasks x no OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 1.2556     | 1.2556     | 1.2556     |   0.0 | 89.53

Neigh   | 0.098976   | 0.098976   | 0.098976   |   0.0 |  7.06

Comm    | 0.011525   | 0.011525   | 0.011525   |   0.0 |  0.82

Output  | 0.00021903 | 0.00021903 | 0.00021903 |   0.0 |  0.02

Modify  | 0.023739   | 0.023739   | 0.023739   |   0.0 |  1.69

Other   |            | 0.01244    |            |       |  0.89



Nlocal:    32000 ave 32000 max 32000 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Nghost:    19911 ave 19911 max 19911 min

Histogram: 1 0 0 0 0 0 0 0 0 0

Neighs:    1.36493e+06 ave 1.36493e+06 max 1.36493e+06 min

Histogram: 1 0 0 0 0 0 0 0 0 0



Total # of neighbors = 1364931

Ave neighs/atom = 42.6541

Neighbor list builds = 3

Dangerous builds = 0

Total wall time: 0:00:01

CRA Git | Maintained and supported by SUSTech CRA and CCSE