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lammps/bench-nsf/sds/log.cpu-1m-4t
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LAMMPS (22 Jul 2013-ICMS)
using 4 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)
1 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)
1 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
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 = 9072 5625
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 = 74.9849 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 19.947729
200 -491827.03 310.65917 -495823.64 -828.59781 19.299449
300 -490499.7 310.13258 -494545.66 -815.31392 19.723866
400 -489685.55 308.35252 -493810.3 -810.17578 19.574306
500 -489024.64 310.8087 -493074.41 -820.28223 19.312054
600 -487765.36 309.25466 -491940.26 -801.65391 19.529724
700 -486753.1 309.19411 -490923.56 -800.38237 18.132669
800 -486337.63 309.28257 -490430.51 -813.57908 19.699814
900 -485991.79 310.81633 -490063.43 -811.32283 18.537815
1000 -485721.93 310.91936 -489860.62 -810.26047 19.276905
Loop time of 51.8449 on 4 procs (1 MPI x 4 OpenMP) for 1000 steps with 62560 atoms
Performance: 16.665 ns/day 1.440 hours/ns 19.288 timesteps/s
MPI task wallclock breakdown
Section | min time | avg time | max time |%total | %CPU
---------------------------------------------------------------
Pair | 40.853 | 40.853 | 40.853 | 78.80 | 392.5
Bond | 0.31153 | 0.31153 | 0.31153 | 0.60 | 368.8
Kspace | 1.7674 | 1.7674 | 1.7674 | 3.41 | 394.4
Neigh | 7.0787 | 7.0787 | 7.0787 | 13.65 | 392.0
Comm | 0.51281 | 0.51281 | 0.51281 | 0.99 | 386.6
Output | 0.002598 | 0.002598 | 0.002598 | 0.01 | 100.0
Modify | 1.1843 | 1.1843 | 1.1843 | 2.28 | 396.1
Other | | 0.1348 | | 0.26 |
Thread activity (MPI rank 0 only): Total time 47.33 / 91.3%
Section | min time | avg time | max time |%total |var/avg
---------------------------------------------------------------
Pair | 31.718 | 37.636 | 39.711 | 83.98 | 55.7%
Bond | 0.22345 | 0.23243 | 0.244 | 0.52 | 1.5%
Kspace | 0.15708 | 0.28926 | 0.42208 | 0.65 | 24.0%
Neigh | 4.8998 | 6.2574 | 6.8495 | 13.96 | 31.5%
Reduce | 0.36275 | 0.39782 | 0.48379 | 0.89 | 7.9%
Modify | 0 | 0 | 0 | 0.00 | 0.0%
Nlocal: 62560 ave 62560 max 62560 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 20685 ave 20685 max 20685 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.65657e+06 ave 6.65657e+06 max 6.65657e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6656573
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).
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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