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lammps/bench-nsf/sds/log.omp-2m-2t
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log.omp-2m-2t
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LAMMPS (22 Jul 2013-ICMS)
using 2 OpenMP thread(s) per MPI task
using multi-threaded neighbor list subroutines
prefer double precision OpenMP force kernels
1 = max bonds/atom
1 = max angles/atom
0 = max impropers/atom
orthogonal box = (-27.713 -27.713 -200) to (27.713 27.713 200)
2 by 1 by 1 MPI processor grid
3910 atoms
512 bonds
384 angles
0 impropers
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
2 = max # of 1-4 neighbors
4 = max # of special neighbors
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
orthogonal box = (-27.713 -27.713 -200) to (193.991 193.991 200)
2 by 1 by 1 MPI processor grid
62560 atoms
8192 bonds
6144 angles
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of special neighbors
4096 atoms in group charged
PPPM initialization ...
G vector (1/distance) = 0.0800658
grid = 15 15 25
stencil order = 3
estimated absolute RMS force accuracy = 0.00264607
estimated relative force accuracy = 7.96856e-06
using double precision FFTs
3d grid and FFT values/proc = 5544 3000
Hybrid pair style last /omp style coul/long
Last active /omp style is kspace_style pppm/cg/omp
PPPM/cg optimization cutoff: 1e-05
Total charged atoms: 6.5%
Min/max charged atoms/proc: 6.5% 6.5%
Memory usage per processor = 39.5629 Mbytes
Step PotEng Temp E_vdwl E_coul S/CPU
0 -495659.47 325 -499273.8 -814.32954 0
100 -492323.78 309.45572 -496520.89 -844.64057 23.580572
200 -491827.03 310.65917 -495823.64 -828.59781 22.981416
300 -490499.7 310.13258 -494545.66 -815.31392 22.850218
400 -489685.55 308.35252 -493810.3 -810.17578 22.858156
500 -489024.64 310.8087 -493074.41 -820.28223 22.088313
600 -487765.36 309.25466 -491940.26 -801.65391 22.811078
700 -486753.1 309.19411 -490923.56 -800.38237 22.84173
800 -486337.63 309.28257 -490430.51 -813.57908 22.836348
900 -485991.8 310.81634 -490063.43 -811.3228 22.368838
1000 -485721.97 310.91914 -489860.66 -810.2604 22.529901
Loop time of 43.9204 on 4 procs (2 MPI x 2 OpenMP) for 1000 steps with 62560 atoms
Performance: 19.672 ns/day 1.220 hours/ns 22.768 timesteps/s
MPI task wallclock breakdown
Section | min time | avg time | max time |%total | %CPU
---------------------------------------------------------------
Pair | 30.976 | 30.992 | 31.008 | 70.56 | 197.1
Bond | 0.21908 | 0.22035 | 0.22162 | 0.50 | 200.0
Kspace | 1.5007 | 1.5327 | 1.5646 | 3.49 | 189.1
Neigh | 9.7155 | 9.7411 | 9.7666 | 22.18 | 197.6
Comm | 0.5531 | 0.56007 | 0.56705 | 1.28 | 191.4
Output | 0.0013666 | 0.0014318 | 0.001497 | 0.00 | 100.0
Modify | 0.76798 | 0.7837 | 0.79942 | 1.78 | 197.1
Other | | 0.0892 | | 0.20 |
Thread activity (MPI rank 0 only): Total time 40.73 / 92.7%
Section | min time | avg time | max time |%total |var/avg
---------------------------------------------------------------
Pair | 30.737 | 30.752 | 30.767 | 75.25 | 0.3%
Bond | 0.21164 | 0.21342 | 0.2152 | 0.52 | 0.4%
Kspace | 0.26158 | 0.2663 | 0.27101 | 0.65 | 0.9%
Neigh | 9.3537 | 9.4801 | 9.6065 | 23.20 | 4.1%
Reduce | 0.15493 | 0.15644 | 0.15795 | 0.38 | 0.4%
Modify | 0 | 0 | 0 | 0.00 | 0.0%
Nlocal: 31280 ave 31342 max 31218 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Nghost: 15887 ave 15901 max 15873 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Neighs: 3.32828e+06 ave 3.33382e+06 max 3.32275e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 1
Total # of neighbors = 6656569
Ave neighs/atom = 106.403
Ave special neighs/atom = 0.458312
Neighbor list builds = 100
Dangerous builds = 0
------------------------------------------------------------------------
This simulation made use of algorithms and methodologies described
in the following references:
The LAMMPS Molecular Dynamics Simulator, Version 22 Jul 2013
http://lammps.sandia.gov
S.J. Plimpton,
Fast Parallel Algorithms for Short-Range Molecular Dynamics,
J. Comp. Phys., 117, 1-19 (1995)
S.J. Plimpton, R. Pollock, M. Stevens,
Particle-Mesh Ewald and r-RESPA for Parallel Molecular Dynamics Simulations,
Proc. of the 8th SIAM Conference on Parallel Processing for Scientific Computing,
Minneapolis, MN (March 1997).
P.J. in 't Veld, S.J. Plimpton, G.S. Grest,
Accurate and Efficient Methods for Modeling Colloidal Mixtures in an
Explicit Solvent using Molecular Dynamics,
Comp. Phys. Comm., 179, 320-329 (2008).
A.P. Thompson, S.J. Plimpton, W. Mattson,
General formulation of pressure and stress tensor for arbitrary many-body
interaction potentials under periodic boundary conditions,
J. Chem. Phys., 131, 154107 (2009)
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