diff --git a/bench/log.9Jan09.chain.fixed.linux.1 b/bench/log.9Jan09.chain.fixed.linux.1 index e2bdc407c..d0b9c9e5c 100644 --- a/bench/log.9Jan09.chain.fixed.linux.1 +++ b/bench/log.9Jan09.chain.fixed.linux.1 @@ -1,59 +1,59 @@ LAMMPS (9 Jan 2009) # FENE beadspring benchmark units lj atom_style bond special_bonds fene read_data data.chain 1 = max bonds/atom orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 1 by 1 processor grid 32000 atoms 32000 velocities 31680 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors neighbor 0.4 bin neigh_modify every 1 delay 1 bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 pair_style lj/cut 1.12 pair_modify shift yes pair_coeff 1 1 1.0 1.0 1.12 fix 1 all nve fix 2 all langevin 1.0 1.0 10.0 904297 thermo 100 timestep 0.012 run 100 Memory usage per processor = 8.37288 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 100 0.97434451 0.439712 20.499596 22.400779 4.6558589 -Loop time of 2.03092 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.530133 (26.1031) -Bond time (%) = 0.248769 (12.2491) -Neigh time (%) = 0.773854 (38.1036) -Comm time (%) = 0.0591824 (2.91407) -Outpt time (%) = 0.000180006 (0.00886327) -Other time (%) = 0.418803 (20.6213) +Loop time of 1.94308 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.484938 (24.9571) +Bond time (%) = 0.247065 (12.7151) +Neigh time (%) = 0.739737 (38.0702) +Comm time (%) = 0.0544686 (2.8032) +Outpt time (%) = 0.000195026 (0.0100369) +Other time (%) = 0.416682 (21.4443) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9537 ave 9537 max 9537 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155877 ave 155877 max 155877 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155877 Ave neighs/atom = 4.87116 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.9Jan09.chain.fixed.linux.4 b/bench/log.9Jan09.chain.fixed.linux.4 index 54f308651..c3afdfd2c 100644 --- a/bench/log.9Jan09.chain.fixed.linux.4 +++ b/bench/log.9Jan09.chain.fixed.linux.4 @@ -1,59 +1,59 @@ LAMMPS (9 Jan 2009) # FENE beadspring benchmark units lj atom_style bond special_bonds fene read_data data.chain 1 = max bonds/atom orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 2 by 2 processor grid 32000 atoms 32000 velocities 31680 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors neighbor 0.4 bin neigh_modify every 1 delay 1 bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 pair_style lj/cut 1.12 pair_modify shift yes pair_coeff 1 1 1.0 1.0 1.12 fix 1 all nve fix 2 all langevin 1.0 1.0 10.0 904297 thermo 100 timestep 0.012 run 100 Memory usage per processor = 3.56846 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 100 0.96717514 0.4422441 20.503712 22.396674 4.6686541 -Loop time of 0.533736 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.0891582 (16.7046) -Bond time (%) = 0.0588746 (11.0307) -Neigh time (%) = 0.168715 (31.6102) -Comm time (%) = 0.112924 (21.1572) -Outpt time (%) = 0.000586271 (0.109843) -Other time (%) = 0.103478 (19.3875) +Loop time of 0.511235 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.0860159 (16.8251) +Bond time (%) = 0.0585467 (11.452) +Neigh time (%) = 0.165503 (32.3732) +Comm time (%) = 0.0969891 (18.9715) +Outpt time (%) = 0.000457227 (0.0894357) +Other time (%) = 0.103723 (20.2887) Nlocal: 8000 ave 8024 max 7973 min Histogram: 1 0 0 1 0 0 0 1 0 1 Nghost: 4169 ave 4212 max 4141 min Histogram: 1 0 1 1 0 0 0 0 0 1 Neighs: 38936.2 ave 39212 max 38690 min Histogram: 1 0 0 1 0 1 0 0 0 1 Total # of neighbors = 155745 Ave neighs/atom = 4.86703 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.9Jan09.chain.scaled.linux.4 b/bench/log.9Jan09.chain.scaled.linux.4 index c42433251..f92b364b1 100644 --- a/bench/log.9Jan09.chain.scaled.linux.4 +++ b/bench/log.9Jan09.chain.scaled.linux.4 @@ -1,75 +1,75 @@ LAMMPS (9 Jan 2009) # FENE beadspring benchmark variable x index 1 variable y index 1 variable z index 1 units lj atom_style bond atom_modify map hash special_bonds fene read_data data.chain 1 = max bonds/atom orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 2 by 2 processor grid 32000 atoms 32000 velocities 31680 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors replicate $x $y $z replicate 2 $y $z replicate 2 2 $z replicate 2 2 1 orthogonal box = (-16.796 -16.796 -16.796) to (50.388 50.388 16.796) 2 by 2 by 1 processor grid 128000 atoms 126720 bonds 2 = max # of 1-2 neighbors 2 = max # of special neighbors neighbor 0.4 bin neigh_modify every 1 delay 1 bond_style fene bond_coeff 1 30.0 1.5 1.0 1.0 pair_style lj/cut 1.12 pair_modify shift yes pair_coeff 1 1 1.0 1.0 1.12 fix 1 all nve fix 2 all langevin 1.0 1.0 10.0 904297 thermo 100 timestep 0.012 run 100 Memory usage per processor = 10.0339 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97027498 0.44484087 20.494523 22.394765 4.6721833 100 0.97400897 0.44134715 20.501052 22.403401 4.6879813 -Loop time of 2.50981 on 4 procs for 100 steps with 128000 atoms +Loop time of 2.49274 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 0.530044 (21.1189) -Bond time (%) = 0.267865 (10.6727) -Neigh time (%) = 0.786584 (31.3403) -Comm time (%) = 0.288274 (11.4859) -Outpt time (%) = 0.000725567 (0.0289092) -Other time (%) = 0.636322 (25.3534) +Pair time (%) = 0.522603 (20.965) +Bond time (%) = 0.266725 (10.7001) +Neigh time (%) = 0.782715 (31.3999) +Comm time (%) = 0.285618 (11.458) +Outpt time (%) = 0.000653207 (0.0262044) +Other time (%) = 0.634421 (25.4508) Nlocal: 32000 ave 32015 max 31986 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 9499 ave 9524 max 9446 min Histogram: 1 0 0 0 0 0 0 1 0 2 Neighs: 155798 ave 156103 max 155422 min Histogram: 1 0 0 0 1 0 0 0 1 1 Total # of neighbors = 623193 Ave neighs/atom = 4.8687 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.9Jan09.chute.fixed.linux.1 b/bench/log.9Jan09.chute.fixed.linux.1 index 1dba5d766..90bb4f276 100644 --- a/bench/log.9Jan09.chute.fixed.linux.1 +++ b/bench/log.9Jan09.chute.fixed.linux.1 @@ -1,62 +1,62 @@ LAMMPS (9 Jan 2009) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees units lj atom_style granular boundary p p fs newton off read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 1 by 1 by 1 processor grid 32000 atoms 32000 velocities pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 pair_coeff * * neighbor 0.1 bin neigh_modify every 1 delay 0 timestep 0.0001 group bottom type 2 912 atoms in group bottom group active subtract all bottom 31088 atoms in group active neigh_modify exclude group bottom bottom fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/sphere compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo_modify norm no thermo 100 run 100 Memory usage per processor = 33.1524 Mbytes Step Atoms KinEng 1 Volume 0 32000 784139.13 1601.1263 29830.88 100 32000 784289.99 1571.0137 29831.804 -Loop time of 1.82843 on 1 procs for 100 steps with 32000 atoms +Loop time of 1.85041 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 1.08846 (59.5297) -Neigh time (%) = 0.0839028 (4.58879) -Comm time (%) = 0.0980868 (5.36454) -Outpt time (%) = 0.000559092 (0.0305777) -Other time (%) = 0.557422 (30.4864) +Pair time (%) = 1.08948 (58.8777) +Neigh time (%) = 0.085561 (4.6239) +Comm time (%) = 0.0984347 (5.31962) +Outpt time (%) = 0.000525951 (0.0284236) +Other time (%) = 0.576409 (31.1504) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 5463 ave 5463 max 5463 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 115133 ave 115133 max 115133 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 115133 Ave neighs/atom = 3.59791 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.9Jan09.chute.fixed.linux.4 b/bench/log.9Jan09.chute.fixed.linux.4 index 59a71f5fe..bd320aa3c 100644 --- a/bench/log.9Jan09.chute.fixed.linux.4 +++ b/bench/log.9Jan09.chute.fixed.linux.4 @@ -1,62 +1,62 @@ LAMMPS (9 Jan 2009) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees units lj atom_style granular boundary p p fs newton off read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 2 by 1 by 2 processor grid 32000 atoms 32000 velocities pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 pair_coeff * * neighbor 0.1 bin neigh_modify every 1 delay 0 timestep 0.0001 group bottom type 2 912 atoms in group bottom group active subtract all bottom 31088 atoms in group active neigh_modify exclude group bottom bottom fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/sphere compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo_modify norm no thermo 100 run 100 Memory usage per processor = 14.5608 Mbytes Step Atoms KinEng 1 Volume 0 32000 784139.13 1601.1263 29830.88 100 32000 784289.99 1571.0137 29831.804 -Loop time of 0.380444 on 4 procs for 100 steps with 32000 atoms +Loop time of 0.351977 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 0.179283 (47.1246) -Neigh time (%) = 0.0191138 (5.02407) -Comm time (%) = 0.0715591 (18.8093) -Outpt time (%) = 0.00048852 (0.128408) -Other time (%) = 0.11 (28.9136) +Pair time (%) = 0.163966 (46.5842) +Neigh time (%) = 0.0196812 (5.59162) +Comm time (%) = 0.0661123 (18.7831) +Outpt time (%) = 0.000420809 (0.119556) +Other time (%) = 0.101797 (28.9215) Nlocal: 8000 ave 8010 max 7990 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 2439 ave 2452 max 2426 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 29503.5 ave 30500 max 28507 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 118014 Ave neighs/atom = 3.68794 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.9Jan09.chute.scaled.linux.4 b/bench/log.9Jan09.chute.scaled.linux.4 index f0d857375..7f76f932e 100644 --- a/bench/log.9Jan09.chute.scaled.linux.4 +++ b/bench/log.9Jan09.chute.scaled.linux.4 @@ -1,72 +1,72 @@ LAMMPS (9 Jan 2009) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees variable x index 1 variable y index 1 units lj atom_style granular boundary p p fs newton off read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 2 by 1 by 2 processor grid 32000 atoms 32000 velocities replicate $x $y 1 replicate 2 $y 1 replicate 2 2 1 orthogonal box = (0 0 0) to (80 40 37.2887) 4 by 1 by 1 processor grid 128000 atoms pair_style gran/hooke/history 200000.0 NULL 50.0 NULL 0.5 0 pair_coeff * * neighbor 0.1 bin neigh_modify every 1 delay 0 timestep 0.0001 group bottom type 2 3648 atoms in group bottom group active subtract all bottom 124352 atoms in group active neigh_modify exclude group bottom bottom fix 1 all gravity 1.0 chute 26.0 fix 2 bottom freeze fix 3 active nve/sphere compute 1 all erotate/sphere thermo_style custom step atoms ke c_1 vol thermo_modify norm no thermo 100 run 100 Memory usage per processor = 35.1222 Mbytes Step Atoms KinEng 1 Volume 0 128000 3136556.5 6404.5051 119323.52 100 128000 3137160 6284.0549 119327.22 -Loop time of 3.37589 on 4 procs for 100 steps with 128000 atoms +Loop time of 3.33365 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 1.62026 (47.995) -Neigh time (%) = 0.0885705 (2.62362) -Comm time (%) = 0.308013 (9.1239) -Outpt time (%) = 0.002312 (0.0684858) -Other time (%) = 1.35674 (40.189) +Pair time (%) = 1.55602 (46.6762) +Neigh time (%) = 0.0902495 (2.70723) +Comm time (%) = 0.307178 (9.21448) +Outpt time (%) = 0.00193202 (0.0579552) +Other time (%) = 1.37827 (41.3441) Nlocal: 32000 ave 32000 max 32000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 5456 ave 5456 max 5456 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 115135 ave 115135 max 115135 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460540 Ave neighs/atom = 3.59797 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.9Jan09.eam.fixed.linux.1 b/bench/log.9Jan09.eam.fixed.linux.1 index ee173a5bf..3ef3136d8 100644 --- a/bench/log.9Jan09.eam.fixed.linux.1 +++ b/bench/log.9Jan09.eam.fixed.linux.1 @@ -1,67 +1,67 @@ LAMMPS (9 Jan 2009) # bulk Cu lattice variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units metal atom_style atomic lattice fcc 3.615 Lattice spacing in x,y,z = 3.615 3.615 3.615 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) 1 by 1 by 1 processor grid create_atoms 1 box Created 32000 atoms pair_style eam pair_coeff 1 1 Cu_u3.eam velocity all create 1600.0 376847 loop geom neighbor 1.0 bin neigh_modify every 1 delay 5 check yes fix 1 all nve timestep 0.005 thermo 50 run 100 Memory usage per processor = 13.3815 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -113280 0 -106662.09 18703.573 50 781.69049 -109873.35 0 -106640.13 52273.088 100 801.832 -109957.3 0 -106640.77 51322.821 -Loop time of 11.5642 on 1 procs for 100 steps with 32000 atoms +Loop time of 11.5404 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 10.3929 (89.8717) -Neigh time (%) = 0.881366 (7.62153) -Comm time (%) = 0.0753665 (0.651725) -Outpt time (%) = 0.000486135 (0.00420381) -Other time (%) = 0.214035 (1.85085) +Pair time (%) = 10.3766 (89.9153) +Neigh time (%) = 0.887614 (7.69138) +Comm time (%) = 0.0720561 (0.624382) +Outpt time (%) = 0.000415087 (0.00359682) +Other time (%) = 0.203732 (1.76538) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19909 ave 19909 max 19909 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20778e+06 ave 1.20778e+06 max 1.20778e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1207784 Ave neighs/atom = 37.7433 Neighbor list builds = 13 Dangerous builds = 0 diff --git a/bench/log.9Jan09.eam.fixed.linux.4 b/bench/log.9Jan09.eam.fixed.linux.4 index 7b1840c4d..1254449e2 100644 --- a/bench/log.9Jan09.eam.fixed.linux.4 +++ b/bench/log.9Jan09.eam.fixed.linux.4 @@ -1,67 +1,67 @@ LAMMPS (9 Jan 2009) # bulk Cu lattice variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units metal atom_style atomic lattice fcc 3.615 Lattice spacing in x,y,z = 3.615 3.615 3.615 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (72.3 72.3 72.3) 1 by 2 by 2 processor grid create_atoms 1 box Created 32000 atoms pair_style eam pair_coeff 1 1 Cu_u3.eam velocity all create 1600.0 376847 loop geom neighbor 1.0 bin neigh_modify every 1 delay 5 check yes fix 1 all nve timestep 0.005 thermo 50 run 100 Memory usage per processor = 4.30641 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -113280 0 -106662.09 18703.573 50 781.69049 -109873.35 0 -106640.13 52273.088 100 801.832 -109957.3 0 -106640.77 51322.821 -Loop time of 3.00127 on 4 procs for 100 steps with 32000 atoms +Loop time of 2.96272 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 2.56049 (85.3135) -Neigh time (%) = 0.220936 (7.36143) -Comm time (%) = 0.161708 (5.38798) -Outpt time (%) = 0.000860035 (0.0286557) -Other time (%) = 0.0572762 (1.9084) +Pair time (%) = 2.53518 (85.5692) +Neigh time (%) = 0.221443 (7.4743) +Comm time (%) = 0.152706 (5.15424) +Outpt time (%) = 0.000851989 (0.028757) +Other time (%) = 0.0525432 (1.77348) Nlocal: 8000 ave 8008 max 7993 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 9130.25 ave 9138 max 9122 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 301946 ave 302392 max 301360 min Histogram: 1 0 0 0 1 0 0 0 1 1 Total # of neighbors = 1207784 Ave neighs/atom = 37.7433 Neighbor list builds = 13 Dangerous builds = 0 diff --git a/bench/log.9Jan09.eam.scaled.linux.4 b/bench/log.9Jan09.eam.scaled.linux.4 index a20738e6f..281889cbb 100644 --- a/bench/log.9Jan09.eam.scaled.linux.4 +++ b/bench/log.9Jan09.eam.scaled.linux.4 @@ -1,67 +1,67 @@ LAMMPS (9 Jan 2009) # bulk Cu lattice variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*2 variable yy equal 20*$y variable yy equal 20*2 variable zz equal 20*$z variable zz equal 20*1 units metal atom_style atomic lattice fcc 3.615 Lattice spacing in x,y,z = 3.615 3.615 3.615 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 40 0 ${yy} 0 ${zz} region box block 0 40 0 40 0 ${zz} region box block 0 40 0 40 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (144.6 144.6 72.3) 2 by 2 by 1 processor grid create_atoms 1 box Created 128000 atoms pair_style eam pair_coeff 1 1 Cu_u3.eam velocity all create 1600.0 376847 loop geom neighbor 1.0 bin neigh_modify every 1 delay 5 check yes fix 1 all nve timestep 0.005 thermo 50 run 100 Memory usage per processor = 13.2978 Mbytes Step Temp E_pair E_mol TotEng Press 0 1600 -453120 0 -426647.73 18704.012 50 779.50001 -439457.02 0 -426560.06 52355.276 100 797.97828 -439764.76 0 -426562.07 51474.74 -Loop time of 12.41 on 4 procs for 100 steps with 128000 atoms +Loop time of 12.4126 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 10.5682 (85.1589) -Neigh time (%) = 0.972487 (7.83633) -Comm time (%) = 0.387733 (3.12436) -Outpt time (%) = 0.00146055 (0.0117692) -Other time (%) = 0.480096 (3.86862) +Pair time (%) = 10.5795 (85.2322) +Neigh time (%) = 0.98051 (7.89934) +Comm time (%) = 0.377976 (3.04511) +Outpt time (%) = 0.0014239 (0.0114714) +Other time (%) = 0.47315 (3.81187) Nlocal: 32000 ave 32092 max 31914 min Histogram: 1 0 0 1 0 1 0 0 0 1 Nghost: 19910 ave 19997 max 19818 min Histogram: 1 0 0 0 1 0 1 0 0 1 Neighs: 1.20728e+06 ave 1.21142e+06 max 1.2036e+06 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 4829126 Ave neighs/atom = 37.7275 Neighbor list builds = 14 Dangerous builds = 0 diff --git a/bench/log.9Jan09.lj.fixed.linux.1 b/bench/log.9Jan09.lj.fixed.linux.1 index d9d51555e..136f4760b 100644 --- a/bench/log.9Jan09.lj.fixed.linux.1 +++ b/bench/log.9Jan09.lj.fixed.linux.1 @@ -1,64 +1,64 @@ LAMMPS (9 Jan 2009) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 1 by 1 processor grid create_atoms 1 box Created 32000 atoms mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve run 100 Memory usage per processor = 11.5405 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 -Loop time of 4.28707 on 1 procs for 100 steps with 32000 atoms +Loop time of 4.26341 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 3.6872 (86.0075) -Neigh time (%) = 0.363374 (8.47604) -Comm time (%) = 0.0615745 (1.43628) -Outpt time (%) = 0.000239849 (0.00559471) -Other time (%) = 0.17468 (4.07457) +Pair time (%) = 3.6779 (86.2667) +Neigh time (%) = 0.366276 (8.59114) +Comm time (%) = 0.0579388 (1.35898) +Outpt time (%) = 0.000221968 (0.00520634) +Other time (%) = 0.161072 (3.77802) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 19657 ave 19657 max 19657 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20283e+06 ave 1.20283e+06 max 1.20283e+06 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 1202833 Ave neighs/atom = 37.5885 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.9Jan09.lj.fixed.linux.4 b/bench/log.9Jan09.lj.fixed.linux.4 index 55fee16b1..a40ed0205 100644 --- a/bench/log.9Jan09.lj.fixed.linux.4 +++ b/bench/log.9Jan09.lj.fixed.linux.4 @@ -1,64 +1,64 @@ LAMMPS (9 Jan 2009) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*1 variable yy equal 20*$y variable yy equal 20*1 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 20 0 ${yy} 0 ${zz} region box block 0 20 0 20 0 ${zz} region box block 0 20 0 20 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (33.5919 33.5919 33.5919) 1 by 2 by 2 processor grid create_atoms 1 box Created 32000 atoms mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve run 100 Memory usage per processor = 3.77112 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6134356 -5.0197073 100 0.7574531 -5.7585055 0 -4.6223613 0.20726105 -Loop time of 1.15946 on 4 procs for 100 steps with 32000 atoms +Loop time of 1.13233 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 0.878825 (75.7963) -Neigh time (%) = 0.0893251 (7.70404) -Comm time (%) = 0.151175 (13.0384) -Outpt time (%) = 0.000439286 (0.0378872) -Other time (%) = 0.0396926 (3.42338) +Pair time (%) = 0.863788 (76.2842) +Neigh time (%) = 0.0899835 (7.94676) +Comm time (%) = 0.146824 (12.9666) +Outpt time (%) = 0.000514269 (0.0454169) +Other time (%) = 0.0312189 (2.75706) Nlocal: 8000 ave 8037 max 7964 min Histogram: 2 0 0 0 0 0 0 0 1 1 Nghost: 9007.5 ave 9050 max 8968 min Histogram: 1 1 0 0 0 0 0 1 0 1 Neighs: 300708 ave 305113 max 297203 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 1202833 Ave neighs/atom = 37.5885 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.9Jan09.lj.scaled.linux.4 b/bench/log.9Jan09.lj.scaled.linux.4 index 770a1bbca..2a3725eef 100644 --- a/bench/log.9Jan09.lj.scaled.linux.4 +++ b/bench/log.9Jan09.lj.scaled.linux.4 @@ -1,64 +1,64 @@ LAMMPS (9 Jan 2009) # 3d Lennard-Jones melt variable x index 1 variable y index 1 variable z index 1 variable xx equal 20*$x variable xx equal 20*2 variable yy equal 20*$y variable yy equal 20*2 variable zz equal 20*$z variable zz equal 20*1 units lj atom_style atomic lattice fcc 0.8442 Lattice spacing in x,y,z = 1.6796 1.6796 1.6796 region box block 0 ${xx} 0 ${yy} 0 ${zz} region box block 0 40 0 ${yy} 0 ${zz} region box block 0 40 0 40 0 ${zz} region box block 0 40 0 40 0 20 create_box 1 box Created orthogonal box = (0 0 0) to (67.1838 67.1838 33.5919) 2 by 2 by 1 processor grid create_atoms 1 box Created 128000 atoms mass 1 1.0 velocity all create 1.44 87287 loop geom pair_style lj/cut 2.5 pair_coeff 1 1 1.0 1.0 2.5 neighbor 0.3 bin neigh_modify delay 0 every 20 check no fix 1 all nve run 100 Memory usage per processor = 11.4634 Mbytes Step Temp E_pair E_mol TotEng Press 0 1.44 -6.7733681 0 -4.6133849 -5.0196788 100 0.75841891 -5.759957 0 -4.6223375 0.20008866 -Loop time of 4.87984 on 4 procs for 100 steps with 128000 atoms +Loop time of 4.83113 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 3.73 (76.4369) -Neigh time (%) = 0.355545 (7.28599) -Comm time (%) = 0.398626 (8.16882) -Outpt time (%) = 0.000897169 (0.0183852) -Other time (%) = 0.394776 (8.08993) +Pair time (%) = 3.72908 (77.1885) +Neigh time (%) = 0.357173 (7.39314) +Comm time (%) = 0.342958 (7.09891) +Outpt time (%) = 0.000697494 (0.0144375) +Other time (%) = 0.401227 (8.30502) Nlocal: 32000 ave 32060 max 31939 min Histogram: 1 0 1 0 0 0 0 1 0 1 Nghost: 19630.8 ave 19681 max 19562 min Histogram: 1 0 0 0 1 0 0 0 1 1 Neighs: 1.20195e+06 ave 1.20354e+06 max 1.19931e+06 min Histogram: 1 0 0 0 0 0 0 2 0 1 Total # of neighbors = 4807797 Ave neighs/atom = 37.5609 Neighbor list builds = 5 Dangerous builds = 0 diff --git a/bench/log.9Jan09.rhodo.fixed.linux.1 b/bench/log.9Jan09.rhodo.fixed.linux.1 index a3a2ff91e..30b2ad432 100644 --- a/bench/log.9Jan09.rhodo.fixed.linux.1 +++ b/bench/log.9Jan09.rhodo.fixed.linux.1 @@ -1,97 +1,97 @@ LAMMPS (9 Jan 2009) # Rhodopsin model units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo 4 = max bonds/atom 8 = max angles/atom 18 = max dihedrals/atom 2 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 1 by 1 processor grid 32000 atoms 32000 velocities 27723 bonds 40467 angles 56829 dihedrals 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors fix 1 all shake 0.0001 5 0 m 1.0 a 232 1617 = # of size 2 clusters 3633 = # of size 3 clusters 747 = # of size 4 clusters 4233 = # of frozen angles fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector = 0.248831 grid = 25 32 32 stencil order = 5 RMS precision = 7.57143e-05 brick FFT buffer size/proc = 41070 25600 12321 Memory usage per processor = 124.369 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055 Volume = 307995.0335 ----------------- Step 50 ----- CPU = 38.3140 (sec) ---------------- +---------------- Step 50 ----- CPU = 37.1470 (sec) ---------------- TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229 PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978 E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861 E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633 Volume = 308031.6776 ----------------- Step 100 ----- CPU = 77.4579 (sec) ---------------- +---------------- Step 100 ----- CPU = 75.1354 (sec) ---------------- TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920 PotEng = -46882.7493 E_bond = 2567.9820 E_angle = 10781.9426 E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962 E_coul = 206655.0353 E_long = -270400.7390 Press = 6.9485 Volume = 308134.2307 -Loop time of 77.458 on 1 procs for 100 steps with 32000 atoms +Loop time of 75.1355 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 57.5481 (74.2959) -Bond time (%) = 2.74544 (3.54442) -Kspce time (%) = 6.23445 (8.04882) -Neigh time (%) = 8.52504 (11.006) -Comm time (%) = 0.216151 (0.279056) -Outpt time (%) = 0.000380754 (0.000491562) -Other time (%) = 2.18842 (2.8253) +Pair time (%) = 55.5501 (73.9332) +Bond time (%) = 2.72528 (3.62716) +Kspce time (%) = 6.11772 (8.14225) +Neigh time (%) = 8.37398 (11.1452) +Comm time (%) = 0.206403 (0.274708) +Outpt time (%) = 0.000414848 (0.000552134) +Other time (%) = 2.1616 (2.87694) -FFT time (% of Kspce) = 0.443897 (7.12007) -FFT Gflps 3d (1d only) = 1.17076 1.72232 +FFT time (% of Kspce) = 0.43406 (7.09513) +FFT Gflps 3d (1d only) = 1.19729 1.73014 Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 47958 ave 47958 max 47958 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 12028097 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 diff --git a/bench/log.9Jan09.rhodo.fixed.linux.4 b/bench/log.9Jan09.rhodo.fixed.linux.4 index b8108afb4..8ea52d596 100644 --- a/bench/log.9Jan09.rhodo.fixed.linux.4 +++ b/bench/log.9Jan09.rhodo.fixed.linux.4 @@ -1,97 +1,97 @@ LAMMPS (9 Jan 2009) # Rhodopsin model units real neigh_modify delay 5 every 1 atom_style full bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo 4 = max bonds/atom 8 = max angles/atom 18 = max dihedrals/atom 2 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 2 by 2 processor grid 32000 atoms 32000 velocities 27723 bonds 40467 angles 56829 dihedrals 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors fix 1 all shake 0.0001 5 0 m 1.0 a 232 1617 = # of size 2 clusters 3633 = # of size 3 clusters 747 = # of size 4 clusters 4233 = # of frozen angles fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector = 0.248831 grid = 25 32 32 stencil order = 5 RMS precision = 7.57143e-05 brick FFT buffer size/proc = 13230 6400 5670 Memory usage per processor = 47.7552 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055 Volume = 307995.0335 ----------------- Step 50 ----- CPU = 9.2803 (sec) ---------------- +---------------- Step 50 ----- CPU = 9.3752 (sec) ---------------- TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229 PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978 E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861 E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633 Volume = 308031.6776 ----------------- Step 100 ----- CPU = 18.8670 (sec) ---------------- +---------------- Step 100 ----- CPU = 19.0189 (sec) ---------------- TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920 PotEng = -46882.7494 E_bond = 2567.9820 E_angle = 10781.9426 E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962 E_coul = 206655.0352 E_long = -270400.7391 Press = 6.9485 Volume = 308134.2307 -Loop time of 18.8674 on 4 procs for 100 steps with 32000 atoms +Loop time of 19.0195 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 12.5283 (66.4019) -Bond time (%) = 0.674376 (3.57429) -Kspce time (%) = 2.40336 (12.7381) -Neigh time (%) = 1.93746 (10.2688) -Comm time (%) = 0.45106 (2.39068) -Outpt time (%) = 0.00137442 (0.00728463) -Other time (%) = 0.871471 (4.61891) +Pair time (%) = 12.4864 (65.6503) +Bond time (%) = 0.675608 (3.55218) +Kspce time (%) = 2.5226 (13.2632) +Neigh time (%) = 1.92456 (10.1188) +Comm time (%) = 0.488407 (2.56793) +Outpt time (%) = 0.00168824 (0.00887637) +Other time (%) = 0.920283 (4.83862) -FFT time (% of Kspce) = 0.367566 (15.2939) -FFT Gflps 3d (1d only) = 1.41389 6.65193 +FFT time (% of Kspce) = 0.394826 (15.6516) +FFT Gflps 3d (1d only) = 1.31627 6.72146 Nlocal: 8000 ave 8143 max 7933 min Histogram: 1 2 0 0 0 0 0 0 0 1 Nghost: 22733.5 ave 22769 max 22693 min Histogram: 1 0 0 0 0 2 0 0 0 1 Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96493e+06 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 12028097 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 diff --git a/bench/log.9Jan09.rhodo.scaled.linux.4 b/bench/log.9Jan09.rhodo.scaled.linux.4 index 6fc0a7d8c..5b99f5813 100644 --- a/bench/log.9Jan09.rhodo.scaled.linux.4 +++ b/bench/log.9Jan09.rhodo.scaled.linux.4 @@ -1,118 +1,118 @@ LAMMPS (9 Jan 2009) # Rhodopsin model variable x index 1 variable y index 1 variable z index 1 units real neigh_modify delay 5 every 1 atom_style full atom_modify map hash bond_style harmonic angle_style charmm dihedral_style charmm improper_style harmonic pair_style lj/charmm/coul/long 8.0 10.0 pair_modify mix arithmetic kspace_style pppm 1e-4 read_data data.rhodo 4 = max bonds/atom 8 = max angles/atom 18 = max dihedrals/atom 2 = max impropers/atom orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 2 by 2 processor grid 32000 atoms 32000 velocities 27723 bonds 40467 angles 56829 dihedrals 1034 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors replicate $x $y $z replicate 2 $y $z replicate 2 2 $z replicate 2 2 1 orthogonal box = (-27.5 -38.5 -36.3646) to (82.5 115.5 36.3615) 2 by 2 by 1 processor grid 128000 atoms 110892 bonds 161868 angles 227316 dihedrals 4136 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors fix 1 all shake 0.0001 5 0 m 1.0 a 232 6468 = # of size 2 clusters 14532 = # of size 3 clusters 2988 = # of size 4 clusters 16932 = # of frozen angles fix 2 all npt 300.0 300.0 100.0 aniso NULL NULL NULL NULL 0.0 0.0 1000.0 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector = 0.248586 grid = 48 60 36 stencil order = 5 RMS precision = 7.66425e-05 brick FFT buffer size/proc = 41615 25920 12915 Memory usage per processor = 130.497 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -101425.4928 KinEng = 85779.3251 Temp = 299.0304 PotEng = -187204.8179 E_bond = 10151.9760 E_angle = 43685.4968 E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538 E_coul = 827025.3455 E_long = -1080537.3748 Press = -142.3110 Volume = 1231980.1340 ----------------- Step 50 ----- CPU = 36.8473 (sec) ---------------- +---------------- Step 50 ----- CPU = 36.7780 (sec) ---------------- TotEng = -101320.2392 KinEng = 86003.4766 Temp = 299.8118 PotEng = -187323.7158 E_bond = 9887.1093 E_angle = 43346.7930 E_dihed = 20958.7048 E_impro = 908.4715 E_vdwl = -7973.4918 E_coul = 826113.2245 E_long = -1080564.5270 Press = 237.9865 Volume = 1232126.6400 ----------------- Step 100 ----- CPU = 75.3270 (sec) ---------------- +---------------- Step 100 ----- CPU = 75.0375 (sec) ---------------- TotEng = -101158.0378 KinEng = 86355.6419 Temp = 301.0394 PotEng = -187513.6797 E_bond = 10272.0762 E_angle = 43128.6553 E_dihed = 20793.9769 E_impro = 867.0831 E_vdwl = -7586.7842 E_coul = 825555.6424 E_long = -1080544.3294 Press = 15.1826 Volume = 1232536.8037 -Loop time of 75.3276 on 4 procs for 100 steps with 128000 atoms +Loop time of 75.038 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 52.0978 (69.1617) -Bond time (%) = 2.7286 (3.62232) -Kspce time (%) = 8.03362 (10.6649) -Neigh time (%) = 8.05846 (10.6979) -Comm time (%) = 0.959758 (1.27411) -Outpt time (%) = 0.00157326 (0.00208856) -Other time (%) = 3.44773 (4.57698) +Pair time (%) = 51.8107 (69.0459) +Bond time (%) = 2.73268 (3.64172) +Kspce time (%) = 8.13185 (10.837) +Neigh time (%) = 7.95464 (10.6008) +Comm time (%) = 0.946348 (1.26116) +Outpt time (%) = 0.00172728 (0.00230188) +Other time (%) = 3.46009 (4.61111) -FFT time (% of Kspce) = 1.5589 (19.4047) -FFT Gflps 3d (1d only) = 1.53622 6.10821 +FFT time (% of Kspce) = 1.69206 (20.8078) +FFT Gflps 3d (1d only) = 1.41532 6.11725 Nlocal: 32000 ave 32000 max 32000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 47957 ave 47957 max 47957 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 48112464 Ave neighs/atom = 375.879 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0