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lammps/bench-nsf/wat/log.wat-gpu-longhorn
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LAMMPS (19 Nov 2010-ICMS)
# TIPS water from charmm.
boundary p p p
units real
atom_style full
special_bonds lj/coul 0.0 0.0 1.0
newton off
read_data data.wat
2 = max bonds/atom
1 = max angles/atom
orthogonal box = (-5.2675 -4.985 -4.9345) to (4.7325 5.015 5.0655)
2 by 4 by 4 processor grid
84 atoms
56 bonds
28 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
replicate ${num} ${num} ${num}
replicate 10 ${num} ${num}
replicate 10 10 ${num}
replicate 10 10 10
orthogonal box = (-5.2675 -4.985 -4.9345) to (94.7325 95.015 95.0655)
2 by 4 by 4 processor grid
84000 atoms
56000 bonds
28000 angles
2 = max # of 1-2 neighbors
1 = max # of 1-3 neighbors
2 = max # of special neighbors
pair_style lj/cut/coul/long/gpu 14.0
pair_modify mix arithmetic
pair_coeff 2 2 0.1521000000 3.15057
pair_coeff 1 1 0.046 0.400014
# 100x larger for minimize
angle_style harmonic
angle_coeff 1 5500 104.52
# 100x larger constant for minimize
bond_style harmonic
bond_coeff 1 45000 0.9572
kspace_style pppm 1.0e-4
velocity all create 300 234324 dist gaussian
neighbor 1.5 bin
neigh_modify delay 2 every 1 check yes
thermo 10
thermo_style custom step pe temp evdwl ecoul vol press spcpu
thermo_modify norm yes
fix 0 all gpu force/neigh 0 1 1.0
minimize 1.0e-4 1.0e-6 100 1000
WARNING: Resetting reneighboring criteria during minimization
PPPM initialization ...
G vector = 0.186884
grid = 36 36 36
stencil order = 5
RMS precision = 5.73697e-05
using single precision FFTs
brick FFT buffer size/proc = 4508 2592 2898
Memory usage per processor = 10.4855 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 656.38475 300 623.47661 10.791304 1000000 13051859 0
10 2.1108392 300 3.7712846 10.33965 1000000 159125.18 47.391766
20 -0.84971121 300 0.84196099 10.204882 1000000 -61673.652 34.85633
30 -1.2796824 300 0.69236674 10.165245 1000000 48523.08 17.841209
40 -1.8895207 300 0.34600987 9.9084457 1000000 47949.196 26.757715
50 -1.9656233 300 0.32957597 9.8608067 1000000 7094.5985 15.592747
60 -2.2151401 300 0.27472652 9.6674725 1000000 1846.6812 24.203051
68 -2.374605 300 0.25896003 9.5302182 1000000 3939.7045 16.243755
Loop time of 2.97929 on 32 procs for 68 steps with 84000 atoms
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
656.384750745 -2.37444162079 -2.37460497991
Force two-norm initial, final = 2.24422e+07 1471.21
Force max component initial, final = 305693 19.7007
Final line search alpha, max atom move = 6.60889e-06 0.000130199
Iterations, force evaluations = 68 324
Pair time (%) = 0.0841061 (2.82303)
Bond time (%) = 0.076263 (2.55978)
Kspce time (%) = 2.45945 (82.5517)
Neigh time (%) = 9.17539e-05 (0.00307973)
Comm time (%) = 0.219994 (7.38412)
Outpt time (%) = 0.00308741 (0.103629)
Other time (%) = 0.136293 (4.5747)
FFT time (% of Kspce) = 0.074782 (3.0406)
FFT Gflps 3d (1d only) = 9.12179 41.2433
Nlocal: 2625 ave 2665 max 2585 min
Histogram: 16 0 0 0 0 0 0 0 0 16
Nghost: 18714.2 ave 19043 max 18381 min
Histogram: 8 0 0 0 0 16 0 0 0 8
Neighs: 0 ave 0 max 0 min
Histogram: 32 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 2
Neighbor list builds = 1
Dangerous builds = 0
reset_timestep 0
thermo 500
fix 1 all shake 0.0001 20 2000 b 1 a 1
0 = # of size 2 clusters
0 = # of size 3 clusters
0 = # of size 4 clusters
28000 = # of frozen angles
fix 2 all npt temp 300.0 300.0 100.0 iso 0.0 0.0 1000.0
timestep 2.0
run 10000
PPPM initialization ...
G vector = 0.186884
grid = 36 36 36
stencil order = 5
RMS precision = 5.73697e-05
using single precision FFTs
brick FFT buffer size/proc = 4508 2592 2898
SHAKE stats (type/ave/delta) on step 0
1 0.957318 0.000397322
1 104.491 0.109203
Memory usage per processor = 10.1326 Mbytes
Step PotEng Temp E_vdwl E_coul Volume Press S/CPU
0 -2.3759313 450.00268 0.25896003 9.5302182 1000000 3033.3929 0
500 -3.1001014 307.13881 0.31499359 8.7569709 958510.7 -1250.1039 52.179702
1000 -3.2034402 299.48171 0.33458457 8.6343893 908455.99 -1021.2187 48.708713
1500 -3.2292483 301.66003 0.34359644 8.5995522 873597.11 -486.01811 50.944599
SHAKE stats (type/ave/delta) on step 2000
1 0.957186 4.45425e-06
1 104.52 0.000616725
2000 -3.2488685 299.76947 0.34094058 8.5828506 851269.44 -346.60125 47.74261
2500 -3.2604084 298.56413 0.34282021 8.5696557 837269.67 -88.749774 45.756455
3000 -3.2660697 300.57561 0.34188167 8.5649838 833865.36 -98.172497 45.097784
3500 -3.2651091 298.40524 0.34012645 8.5676568 832398.88 -134.2966 46.780803
SHAKE stats (type/ave/delta) on step 4000
1 0.957201 4.05532e-06
1 104.52 0.000466336
4000 -3.2715124 298.96109 0.34512507 8.5560735 829253.82 31.378278 47.217657
4500 -3.2690833 301.13258 0.34336204 8.560337 829910.93 -22.863571 47.219329
5000 -3.2674971 301.56764 0.34740997 8.5578399 828977.5 100.43085 46.281165
5500 -3.2692654 301.65619 0.34549817 8.5579246 828426.49 63.345609 46.485375
SHAKE stats (type/ave/delta) on step 6000
1 0.957206 4.14909e-06
1 104.52 0.000442579
6000 -3.2666558 300.44171 0.35052833 8.5555989 830626.75 155.16213 46.738883
6500 -3.2640425 300.95653 0.34373486 8.5650652 829636.51 28.84625 46.631264
7000 -3.2680286 298.82456 0.34477455 8.5599737 828595.9 17.742764 46.552031
7500 -3.262383 298.13328 0.33879383 8.5715374 831048.25 -108.91379 47.975737
SHAKE stats (type/ave/delta) on step 8000
1 0.957206 4.02236e-06
1 104.52 0.000441662
8000 -3.2625702 298.85921 0.34635274 8.5640491 832251.89 30.705882 47.617691
8500 -3.264569 299.23274 0.34474001 8.5636749 831209.09 12.920161 48.051031
9000 -3.2656093 299.21102 0.33808153 8.5689993 829630.41 -126.0656 46.421863
9500 -3.2655805 300.15112 0.3425093 8.5646057 830329.91 -40.820358 47.830129
SHAKE stats (type/ave/delta) on step 10000
1 0.957197 4.3978e-06
1 104.52 0.000514105
10000 -3.2636438 297.40676 0.34122064 8.5679722 830011.48 -49.548074 46.359444
Loop time of 211.074 on 32 procs for 10000 steps with 84000 atoms
Pair time (%) = 73.5808 (34.8602)
Bond time (%) = 0.00829104 (0.00392803)
Kspce time (%) = 93.01 (44.0652)
Neigh time (%) = 0.127719 (0.060509)
Comm time (%) = 10.072 (4.7718)
Outpt time (%) = 0.0103079 (0.00488353)
Other time (%) = 34.2646 (16.2335)
FFT time (% of Kspce) = 12.4859 (13.4243)
FFT Gflps 3d (1d only) = 8.03431 41.1591
Nlocal: 2625 ave 2672 max 2576 min
Histogram: 2 2 5 4 3 2 5 3 3 3
Nghost: 20817.5 ave 20933 max 20682 min
Histogram: 1 0 5 2 3 8 6 4 1 2
Neighs: 0 ave 0 max 0 min
Histogram: 32 0 0 0 0 0 0 0 0 0
Total # of neighbors = 0
Ave neighs/atom = 0
Ave special neighs/atom = 2
Neighbor list builds = 1638
Dangerous builds = 0
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