diff --git a/bench/log.1Feb14.chain.fixed.linux.1 b/bench/log.15May15.chain.fixed.icc.1 similarity index 71% rename from bench/log.1Feb14.chain.fixed.linux.1 rename to bench/log.15May15.chain.fixed.icc.1 index 9d35f3fb8..5414c69a9 100644 --- a/bench/log.1Feb14.chain.fixed.linux.1 +++ b/bench/log.15May15.chain.fixed.icc.1 @@ -1,63 +1,67 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # FENE beadspring benchmark units lj atom_style bond special_bonds fene read_data data.chain orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 1 by 1 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 1 = max bonds/atom reading bonds ... 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 = 11.5156 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 1 steps, check yes + master list distance cutoff = 1.52 +Memory usage per processor = 11.5189 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 100 0.9729966 0.4361122 20.507698 22.40326 4.6548819 -Loop time of 1.00129 on 1 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.201344 (20.1083) -Bond time (%) = 0.0870376 (8.69251) -Neigh time (%) = 0.45714 (45.6549) -Comm time (%) = 0.0338521 (3.38083) -Outpt time (%) = 0.000102043 (0.0101911) -Other time (%) = 0.221819 (22.1532) +Loop time of 0.978717 on 1 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.195673 (19.9928) +Bond time (%) = 0.0878832 (8.97943) +Neigh time (%) = 0.448004 (45.7746) +Comm time (%) = 0.0329976 (3.37152) +Outpt time (%) = 0.000105143 (0.0107429) +Other time (%) = 0.214054 (21.8709) Nlocal: 32000 ave 32000 max 32000 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 9493 ave 9493 max 9493 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 155873 ave 155873 max 155873 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 155873 Ave neighs/atom = 4.87103 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.1Feb14.chain.fixed.linux.4 b/bench/log.15May15.chain.fixed.icc.4 similarity index 71% rename from bench/log.1Feb14.chain.fixed.linux.4 rename to bench/log.15May15.chain.fixed.icc.4 index c1622f405..fbc2d8a00 100644 --- a/bench/log.1Feb14.chain.fixed.linux.4 +++ b/bench/log.15May15.chain.fixed.icc.4 @@ -1,63 +1,67 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # FENE beadspring benchmark units lj atom_style bond special_bonds fene read_data data.chain orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 1 = max bonds/atom reading bonds ... 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 = 4.85536 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 1 steps, check yes + master list distance cutoff = 1.52 +Memory usage per processor = 3.91518 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97029772 0.44484087 20.494523 22.394765 4.6721833 100 0.97145835 0.43803883 20.502691 22.397872 4.626988 -Loop time of 0.274804 on 4 procs for 100 steps with 32000 atoms - -Pair time (%) = 0.0507675 (18.4741) -Bond time (%) = 0.0225385 (8.20169) -Neigh time (%) = 0.121537 (44.2269) -Comm time (%) = 0.0207262 (7.54219) -Outpt time (%) = 8.74996e-05 (0.0318408) -Other time (%) = 0.0591468 (21.5233) +Loop time of 0.274371 on 4 procs for 100 steps with 32000 atoms + +Pair time (%) = 0.0504887 (18.4016) +Bond time (%) = 0.0229129 (8.35106) +Neigh time (%) = 0.119957 (43.7206) +Comm time (%) = 0.020835 (7.59373) +Outpt time (%) = 5.74589e-05 (0.0209421) +Other time (%) = 0.0601202 (21.912) Nlocal: 8000 ave 8030 max 7974 min Histogram: 1 0 0 1 0 1 0 0 0 1 Nghost: 4177 ave 4191 max 4160 min Histogram: 1 0 0 0 1 0 0 1 0 1 Neighs: 38995.8 ave 39169 max 38852 min Histogram: 1 0 0 1 1 0 0 0 0 1 Total # of neighbors = 155983 Ave neighs/atom = 4.87447 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.1Feb14.chain.scaled.linux.4 b/bench/log.15May15.chain.scaled.icc.4 similarity index 76% rename from bench/log.1Feb14.chain.scaled.linux.4 rename to bench/log.15May15.chain.scaled.icc.4 index 0b2062bf4..af328d174 100644 --- a/bench/log.1Feb14.chain.scaled.linux.4 +++ b/bench/log.15May15.chain.scaled.icc.4 @@ -1,79 +1,83 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 orthogonal box = (-16.796 -16.796 -16.796) to (16.796 16.796 16.796) 1 by 2 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 1 = max bonds/atom reading bonds ... 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 MPI 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 = 13.4806 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 1 steps, check yes + master list distance cutoff = 1.52 +Memory usage per processor = 12.8735 Mbytes Step Temp E_pair E_mol TotEng Press 0 0.97027498 0.44484087 20.494523 22.394765 4.6721833 100 0.97682955 0.44239968 20.500229 22.407862 4.6527025 -Loop time of 1.16627 on 4 procs for 100 steps with 128000 atoms +Loop time of 1.19919 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 0.224354 (19.2369) -Bond time (%) = 0.0961447 (8.24378) -Neigh time (%) = 0.510646 (43.7846) -Comm time (%) = 0.0876382 (7.5144) -Outpt time (%) = 0.000156462 (0.0134156) -Other time (%) = 0.24733 (21.207) +Pair time (%) = 0.227794 (18.9957) +Bond time (%) = 0.0981662 (8.18606) +Neigh time (%) = 0.527868 (44.0188) +Comm time (%) = 0.0980042 (8.17255) +Outpt time (%) = 0.000200272 (0.0167006) +Other time (%) = 0.247155 (20.6102) Nlocal: 32000 ave 32015 max 31983 min Histogram: 1 0 1 0 0 0 0 0 1 1 Nghost: 9492 ave 9522 max 9432 min Histogram: 1 0 0 0 0 0 1 0 0 2 Neighs: 155837 ave 156079 max 155506 min Histogram: 1 0 0 0 0 1 0 0 1 1 Total # of neighbors = 623349 Ave neighs/atom = 4.86991 Ave special neighs/atom = 1.98 Neighbor list builds = 25 Dangerous builds = 0 diff --git a/bench/log.1Feb14.chute.fixed.linux.1 b/bench/log.15May15.chute.fixed.icc.1 similarity index 73% rename from bench/log.1Feb14.chute.fixed.linux.1 rename to bench/log.15May15.chute.fixed.icc.1 index 6fe0cbe06..0677a933c 100644 --- a/bench/log.1Feb14.chute.fixed.linux.1 +++ b/bench/log.15May15.chute.fixed.icc.1 @@ -1,65 +1,69 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees units lj atom_style sphere boundary p p fs newton off -communicate single vel yes +comm_modify vel yes read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 1 by 1 by 1 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 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 = 21.4184 Mbytes +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + master list distance cutoff = 1.1 +Memory usage per processor = 15.567 Mbytes Step Atoms KinEng 1 Volume 0 32000 784139.13 1601.1263 29833.783 100 32000 784292.08 1571.0968 29834.707 -Loop time of 0.540977 on 1 procs for 100 steps with 32000 atoms +Loop time of 0.539647 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 0.330571 (61.1064) -Neigh time (%) = 0.0416589 (7.70067) -Comm time (%) = 0.018239 (3.3715) -Outpt time (%) = 0.000189066 (0.034949) -Other time (%) = 0.150319 (27.7865) +Pair time (%) = 0.328789 (60.9267) +Neigh time (%) = 0.0401711 (7.44397) +Comm time (%) = 0.0179052 (3.31795) +Outpt time (%) = 0.00019908 (0.0368907) +Other time (%) = 0.152582 (28.2745) 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.1Feb14.chute.fixed.linux.4 b/bench/log.15May15.chute.fixed.icc.4 similarity index 73% rename from bench/log.1Feb14.chute.fixed.linux.4 rename to bench/log.15May15.chute.fixed.icc.4 index 0acf14ded..03b071a7a 100644 --- a/bench/log.1Feb14.chute.fixed.linux.4 +++ b/bench/log.15May15.chute.fixed.icc.4 @@ -1,65 +1,69 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # LAMMPS benchmark of granular flow # chute flow of 32000 atoms with frozen base at 26 degrees units lj atom_style sphere boundary p p fs newton off -communicate single vel yes +comm_modify vel yes read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 2 by 1 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 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 = 10.7034 Mbytes +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + master list distance cutoff = 1.1 +Memory usage per processor = 6.81783 Mbytes Step Atoms KinEng 1 Volume 0 32000 784139.13 1601.1263 29833.783 100 32000 784292.08 1571.0968 29834.707 -Loop time of 0.133553 on 4 procs for 100 steps with 32000 atoms +Loop time of 0.146584 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 0.0669281 (50.1135) -Neigh time (%) = 0.01061 (7.9444) -Comm time (%) = 0.0142241 (10.6505) -Outpt time (%) = 9.28044e-05 (0.0694888) -Other time (%) = 0.041698 (31.2221) +Pair time (%) = 0.0737562 (50.3167) +Neigh time (%) = 0.0105147 (7.17314) +Comm time (%) = 0.0147474 (10.0607) +Outpt time (%) = 0.000131965 (0.0900267) +Other time (%) = 0.0474337 (32.3594) Nlocal: 8000 ave 8008 max 7992 min Histogram: 2 0 0 0 0 0 0 0 0 2 Nghost: 2439 ave 2450 max 2428 min Histogram: 2 0 0 0 0 0 0 0 0 2 Neighs: 29500.5 ave 30488 max 28513 min Histogram: 2 0 0 0 0 0 0 0 0 2 Total # of neighbors = 118002 Ave neighs/atom = 3.68756 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.1Feb14.chute.scaled.linux.4 b/bench/log.15May15.chute.scaled.icc.4 similarity index 73% rename from bench/log.1Feb14.chute.scaled.linux.4 rename to bench/log.15May15.chute.scaled.icc.4 index 804f04128..67926ffa0 100644 --- a/bench/log.1Feb14.chute.scaled.linux.4 +++ b/bench/log.15May15.chute.scaled.icc.4 @@ -1,75 +1,79 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 sphere boundary p p fs newton off -communicate single vel yes +comm_modify vel yes read_data data.chute orthogonal box = (0 0 0) to (40 20 37.2886) 2 by 1 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities replicate $x $y 1 replicate 2 $y 1 replicate 2 2 1 - orthogonal box = (0 0 0) to (80 40 37.2923) + orthogonal box = (0 0 0) to (80 40 37.2922) 2 by 2 by 1 MPI 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 = 22.3334 Mbytes +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + master list distance cutoff = 1.1 +Memory usage per processor = 15.7007 Mbytes Step Atoms KinEng 1 Volume 0 128000 3136556.5 6404.5051 119335.13 100 128000 3137168.3 6284.3873 119338.83 -Loop time of 0.862817 on 4 procs for 100 steps with 128000 atoms +Loop time of 0.899154 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 0.518524 (60.0966) -Neigh time (%) = 0.0441293 (5.11455) -Comm time (%) = 0.057479 (6.66178) -Outpt time (%) = 0.000286222 (0.0331729) -Other time (%) = 0.242399 (28.0939) +Pair time (%) = 0.523338 (58.2033) +Neigh time (%) = 0.0433982 (4.82656) +Comm time (%) = 0.0642623 (7.14697) +Outpt time (%) = 0.000541449 (0.0602175) +Other time (%) = 0.267615 (29.7629) Nlocal: 32000 ave 32000 max 32000 min Histogram: 4 0 0 0 0 0 0 0 0 0 Nghost: 5463 ave 5463 max 5463 min Histogram: 4 0 0 0 0 0 0 0 0 0 Neighs: 115133 ave 115133 max 115133 min Histogram: 4 0 0 0 0 0 0 0 0 0 Total # of neighbors = 460532 Ave neighs/atom = 3.59791 Neighbor list builds = 2 Dangerous builds = 0 diff --git a/bench/log.1Feb14.eam.fixed.linux.1 b/bench/log.15May15.eam.fixed.icc.1 similarity index 75% rename from bench/log.1Feb14.eam.fixed.linux.1 rename to bench/log.15May15.eam.fixed.icc.1 index 98446148b..739bc1126 100644 --- a/bench/log.1Feb14.eam.fixed.linux.1 +++ b/bench/log.15May15.eam.fixed.icc.1 @@ -1,67 +1,71 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 MPI 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 = 15.3727 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + master list distance cutoff = 5.95 +Memory usage per processor = 10.2238 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 5.93175 on 1 procs for 100 steps with 32000 atoms +Loop time of 5.89995 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 5.20741 (87.7887) -Neigh time (%) = 0.618579 (10.4283) -Comm time (%) = 0.0310862 (0.524064) -Outpt time (%) = 0.000214815 (0.00362144) -Other time (%) = 0.0744634 (1.25533) +Pair time (%) = 5.21525 (88.3948) +Neigh time (%) = 0.579447 (9.82122) +Comm time (%) = 0.0302751 (0.513142) +Outpt time (%) = 0.000234127 (0.00396829) +Other time (%) = 0.0747423 (1.26683) 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.1Feb14.eam.fixed.linux.4 b/bench/log.15May15.eam.fixed.icc.4 similarity index 75% rename from bench/log.1Feb14.eam.fixed.linux.4 rename to bench/log.15May15.eam.fixed.icc.4 index 02ea03515..f89a5d5fe 100644 --- a/bench/log.1Feb14.eam.fixed.linux.4 +++ b/bench/log.15May15.eam.fixed.icc.4 @@ -1,67 +1,71 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 MPI 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 = 4.92441 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + master list distance cutoff = 5.95 +Memory usage per processor = 5.09629 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 1.57335 on 4 procs for 100 steps with 32000 atoms +Loop time of 1.57597 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 1.35199 (85.9304) -Neigh time (%) = 0.160176 (10.1806) -Comm time (%) = 0.0413526 (2.62832) -Outpt time (%) = 0.000119448 (0.00759193) -Other time (%) = 0.0197157 (1.2531) +Pair time (%) = 1.36786 (86.7953) +Neigh time (%) = 0.152391 (9.6697) +Comm time (%) = 0.0353726 (2.2445) +Outpt time (%) = 0.000111699 (0.00708766) +Other time (%) = 0.0202255 (1.28337) 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.1Feb14.eam.scaled.linux.4 b/bench/log.15May15.eam.scaled.icc.4 similarity index 75% rename from bench/log.1Feb14.eam.scaled.linux.4 rename to bench/log.15May15.eam.scaled.icc.4 index 350c397a6..e35bbfd71 100644 --- a/bench/log.1Feb14.eam.scaled.linux.4 +++ b/bench/log.15May15.eam.scaled.icc.4 @@ -1,67 +1,71 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 MPI 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 = 15.2891 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + master list distance cutoff = 5.95 +Memory usage per processor = 10.1402 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 6.55459 on 4 procs for 100 steps with 128000 atoms +Loop time of 6.4972 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 5.63064 (85.9037) -Neigh time (%) = 0.698691 (10.6596) -Comm time (%) = 0.123277 (1.88077) -Outpt time (%) = 0.000314116 (0.00479231) -Other time (%) = 0.101672 (1.55115) +Pair time (%) = 5.61297 (86.3906) +Neigh time (%) = 0.655333 (10.0864) +Comm time (%) = 0.130434 (2.00755) +Outpt time (%) = 0.000279069 (0.00429522) +Other time (%) = 0.0981811 (1.51113) 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.1Feb14.lj.fixed.linux.1 b/bench/log.15May15.lj.fixed.icc.1 similarity index 74% rename from bench/log.1Feb14.lj.fixed.linux.1 rename to bench/log.15May15.lj.fixed.icc.1 index d0e616e23..4d5ea9915 100644 --- a/bench/log.1Feb14.lj.fixed.linux.1 +++ b/bench/log.15May15.lj.fixed.icc.1 @@ -1,64 +1,68 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 MPI 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 = 13.2266 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check no + master list distance cutoff = 2.8 +Memory usage per processor = 8.21387 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 2.26599 on 1 procs for 100 steps with 32000 atoms +Loop time of 2.25588 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 1.92891 (85.1244) -Neigh time (%) = 0.252641 (11.1493) -Comm time (%) = 0.0243704 (1.07549) -Outpt time (%) = 0.000110865 (0.00489256) -Other time (%) = 0.059957 (2.64596) +Pair time (%) = 1.93512 (85.7815) +Neigh time (%) = 0.236483 (10.483) +Comm time (%) = 0.0239627 (1.06224) +Outpt time (%) = 0.000118017 (0.00523155) +Other time (%) = 0.0601869 (2.66801) 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.1Feb14.lj.fixed.linux.4 b/bench/log.15May15.lj.fixed.icc.4 similarity index 74% rename from bench/log.1Feb14.lj.fixed.linux.4 rename to bench/log.15May15.lj.fixed.icc.4 index dfcb7e924..d5b8e2420 100644 --- a/bench/log.1Feb14.lj.fixed.linux.4 +++ b/bench/log.15May15.lj.fixed.icc.4 @@ -1,64 +1,68 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 MPI 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 = 4.31282 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check no + master list distance cutoff = 2.8 +Memory usage per processor = 4.09506 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 0.628341 on 4 procs for 100 steps with 32000 atoms +Loop time of 0.623887 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 0.505093 (80.3851) -Neigh time (%) = 0.0659957 (10.5032) -Comm time (%) = 0.0406293 (6.46611) -Outpt time (%) = 8.43406e-05 (0.0134227) -Other time (%) = 0.016539 (2.63216) +Pair time (%) = 0.50691 (81.2504) +Neigh time (%) = 0.0619052 (9.92251) +Comm time (%) = 0.0389298 (6.23989) +Outpt time (%) = 5.85914e-05 (0.00939135) +Other time (%) = 0.0160829 (2.57785) 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.1Feb14.lj.scaled.linux.4 b/bench/log.15May15.lj.scaled.icc.4 similarity index 74% rename from bench/log.1Feb14.lj.scaled.linux.4 rename to bench/log.15May15.lj.scaled.icc.4 index 6fc614af2..4370f63fb 100644 --- a/bench/log.1Feb14.lj.scaled.linux.4 +++ b/bench/log.15May15.lj.scaled.icc.4 @@ -1,64 +1,68 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 MPI 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 = 13.1495 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check no + master list distance cutoff = 2.8 +Memory usage per processor = 8.13678 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 2.54147 on 4 procs for 100 steps with 128000 atoms +Loop time of 2.53011 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 2.08305 (81.9623) -Neigh time (%) = 0.258072 (10.1545) -Comm time (%) = 0.116279 (4.57528) -Outpt time (%) = 0.000139415 (0.00548562) -Other time (%) = 0.0839326 (3.30252) +Pair time (%) = 2.09024 (82.6146) +Neigh time (%) = 0.24414 (9.64939) +Comm time (%) = 0.111739 (4.41638) +Outpt time (%) = 0.000135601 (0.00535947) +Other time (%) = 0.0838551 (3.31428) 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.1Feb14.rhodo.fixed.linux.1 b/bench/log.15May15.rhodo.fixed.icc.1 similarity index 79% rename from bench/log.1Feb14.rhodo.fixed.linux.1 rename to bench/log.15May15.rhodo.fixed.icc.1 index 08af73ac1..4417fb51d 100644 --- a/bench/log.1Feb14.rhodo.fixed.linux.1 +++ b/bench/log.15May15.rhodo.fixed.icc.1 @@ -1,109 +1,110 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 1 by 1 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 8 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 27723 bonds reading angles ... 40467 angles reading dihedrals ... 56829 dihedrals reading impropers ... 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248835 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0355478 estimated relative force accuracy = 0.000107051 using double precision FFTs 3d grid and FFT values/proc = 41070 25600 -Memory usage per processor = 139.238 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + master list distance cutoff = 12 +Memory usage per processor = 91.7487 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035 Volume = 307995.0335 ----------------- Step 50 ----- CPU = 17.8100 (sec) ---------------- +---------------- Step 50 ----- CPU = 17.3751 (sec) ---------------- TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230 PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975 E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754 E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701 Volume = 308031.5639 ----------------- Step 100 ----- CPU = 36.2348 (sec) ---------------- -TotEng = -25290.7592 KinEng = 21592.0117 Temp = 301.0920 +---------------- Step 100 ----- CPU = 35.3771 (sec) ---------------- +TotEng = -25290.7593 KinEng = 21592.0117 Temp = 301.0920 PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408 E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783 -E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960 +E_coul = 206659.2326 E_long = -270404.9733 Press = 6.9960 Volume = 308133.9888 -Loop time of 36.2348 on 1 procs for 100 steps with 32000 atoms +Loop time of 35.3771 on 1 procs for 100 steps with 32000 atoms -Pair time (%) = 26.0418 (71.8696) -Bond time (%) = 1.26644 (3.4951) -Kspce time (%) = 3.24933 (8.96742) -Neigh time (%) = 4.47968 (12.3629) -Comm time (%) = 0.0700378 (0.193289) -Outpt time (%) = 0.000230074 (0.000634953) -Other time (%) = 1.12729 (3.11108) - -FFT time (% of Kspce) = 0.276809 (8.51896) -FFT Gflps 3d (1d only) = 1.87746 3.23903 +Pair time (%) = 25.4765 (72.0139) +Bond time (%) = 1.27905 (3.61547) +Kspce time (%) = 3.22381 (9.11269) +Neigh time (%) = 4.26655 (12.0602) +Comm time (%) = 0.0692198 (0.195663) +Outpt time (%) = 0.000253916 (0.00071774) +Other time (%) = 1.06179 (3.00134) 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 = 12028107 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 diff --git a/bench/log.1Feb14.rhodo.fixed.linux.4 b/bench/log.15May15.rhodo.fixed.icc.4 similarity index 77% rename from bench/log.1Feb14.rhodo.fixed.linux.4 rename to bench/log.15May15.rhodo.fixed.icc.4 index 1cb4138e4..3fa411c70 100644 --- a/bench/log.1Feb14.rhodo.fixed.linux.4 +++ b/bench/log.15May15.rhodo.fixed.icc.4 @@ -1,109 +1,110 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 2 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 8 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 27723 bonds reading angles ... 40467 angles reading dihedrals ... 56829 dihedrals reading impropers ... 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248835 grid = 25 32 32 stencil order = 5 estimated absolute RMS force accuracy = 0.0355478 estimated relative force accuracy = 0.000107051 using double precision FFTs 3d grid and FFT values/proc = 13230 6400 -Memory usage per processor = 54.595 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + master list distance cutoff = 12 +Memory usage per processor = 36.629 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -25356.2064 KinEng = 21444.8313 Temp = 299.0397 PotEng = -46801.0377 E_bond = 2537.9940 E_angle = 10921.3742 E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634 E_coul = 207025.8927 E_long = -270403.7333 Press = -142.6035 Volume = 307995.0335 ----------------- Step 50 ----- CPU = 4.7061 (sec) ---------------- -TotEng = -25330.0829 KinEng = 21501.0029 Temp = 299.8230 +---------------- Step 50 ----- CPU = 4.6438 (sec) ---------------- +TotEng = -25330.0828 KinEng = 21501.0029 Temp = 299.8230 PotEng = -46831.0857 E_bond = 2471.7004 E_angle = 10836.4975 E_dihed = 5239.6299 E_impro = 227.1218 E_vdwl = -1993.2754 E_coul = 206797.6331 E_long = -270410.3930 Press = 237.6701 Volume = 308031.5639 ----------------- Step 100 ----- CPU = 9.5889 (sec) ---------------- -TotEng = -25290.7592 KinEng = 21592.0117 Temp = 301.0920 -PotEng = -46882.7709 E_bond = 2567.9807 E_angle = 10781.9408 +---------------- Step 100 ----- CPU = 9.4301 (sec) ---------------- +TotEng = -25290.7591 KinEng = 21592.0117 Temp = 301.0920 +PotEng = -46882.7708 E_bond = 2567.9807 E_angle = 10781.9408 E_dihed = 5198.7432 E_impro = 216.7834 E_vdwl = -1902.4783 E_coul = 206659.2327 E_long = -270404.9733 Press = 6.9960 Volume = 308133.9888 -Loop time of 9.58898 on 4 procs for 100 steps with 32000 atoms +Loop time of 9.43015 on 4 procs for 100 steps with 32000 atoms -Pair time (%) = 6.62576 (69.0976) -Bond time (%) = 0.317414 (3.31019) -Kspce time (%) = 1.04771 (10.9262) -Neigh time (%) = 1.15891 (12.0859) -Comm time (%) = 0.0844751 (0.88096) -Outpt time (%) = 0.00015074 (0.00157201) -Other time (%) = 0.354558 (3.69756) - -FFT time (% of Kspce) = 0.0967343 (9.23289) -FFT Gflps 3d (1d only) = 5.37243 12.7459 +Pair time (%) = 6.53815 (69.3324) +Bond time (%) = 0.323679 (3.43239) +Kspce time (%) = 1.02664 (10.8868) +Neigh time (%) = 1.11839 (11.8597) +Comm time (%) = 0.0812459 (0.861554) +Outpt time (%) = 0.000150442 (0.00159533) +Other time (%) = 0.341896 (3.62557) 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: 3.00703e+06 ave 3.0975e+06 max 2.96493e+06 min Histogram: 1 2 0 0 0 0 0 0 0 1 Total # of neighbors = 12028107 Ave neighs/atom = 375.878 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0 diff --git a/bench/log.1Feb14.rhodo.scaled.linux.4 b/bench/log.15May15.rhodo.scaled.icc.4 similarity index 78% rename from bench/log.1Feb14.rhodo.scaled.linux.4 rename to bench/log.15May15.rhodo.scaled.icc.4 index d44aa9ced..71a40c6ca 100644 --- a/bench/log.1Feb14.rhodo.scaled.linux.4 +++ b/bench/log.15May15.rhodo.scaled.icc.4 @@ -1,130 +1,131 @@ -LAMMPS (1 Feb 2014) +LAMMPS (30 Apr 2015) # 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 orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 1 by 2 by 2 MPI processor grid reading atoms ... 32000 atoms reading velocities ... 32000 velocities scanning bonds ... 4 = max bonds/atom scanning angles ... 8 = max angles/atom scanning dihedrals ... 18 = max dihedrals/atom scanning impropers ... 2 = max impropers/atom reading bonds ... 27723 bonds reading angles ... 40467 angles reading dihedrals ... 56829 dihedrals reading impropers ... 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 MPI 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 temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 50 thermo_style multi timestep 2.0 run 100 PPPM initialization ... G vector (1/distance) = 0.248593 grid = 48 60 36 stencil order = 5 estimated absolute RMS force accuracy = 0.0359793 estimated relative force accuracy = 0.00010835 using double precision FFTs 3d grid and FFT values/proc = 41615 25920 -Memory usage per processor = 146.358 Mbytes +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + master list distance cutoff = 12 +Memory usage per processor = 95.5339 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -101425.4887 KinEng = 85779.3251 Temp = 299.0304 PotEng = -187204.8138 E_bond = 10151.9760 E_angle = 43685.4968 E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537 E_coul = 827053.5824 E_long = -1080565.6077 Press = -142.3092 Volume = 1231980.1340 ----------------- Step 50 ----- CPU = 18.9852 (sec) ---------------- -TotEng = -101320.2676 KinEng = 86003.4837 Temp = 299.8118 +---------------- Step 50 ----- CPU = 18.5923 (sec) ---------------- +TotEng = -101320.2677 KinEng = 86003.4837 Temp = 299.8118 PotEng = -187323.7514 E_bond = 9887.1072 E_angle = 43346.7922 E_dihed = 20958.7032 E_impro = 908.4715 E_vdwl = -7973.4457 E_coul = 826141.3831 E_long = -1080592.7629 Press = 238.0161 Volume = 1232126.1855 ----------------- Step 100 ----- CPU = 38.9161 (sec) ---------------- -TotEng = -101158.1853 KinEng = 86355.6148 Temp = 301.0393 -PotEng = -187513.8001 E_bond = 10272.0693 E_angle = 43128.6453 +---------------- Step 100 ----- CPU = 38.1551 (sec) ---------------- +TotEng = -101158.1849 KinEng = 86355.6149 Temp = 301.0393 +PotEng = -187513.7998 E_bond = 10272.0693 E_angle = 43128.6454 E_dihed = 20793.9759 E_impro = 867.0826 E_vdwl = -7586.7186 -E_coul = 825583.7120 E_long = -1080572.5667 Press = 15.2151 +E_coul = 825583.7122 E_long = -1080572.5667 Press = 15.2151 Volume = 1232535.8423 -Loop time of 38.9162 on 4 procs for 100 steps with 128000 atoms +Loop time of 38.1551 on 4 procs for 100 steps with 128000 atoms -Pair time (%) = 27.1908 (69.8701) -Bond time (%) = 1.30758 (3.35999) -Kspce time (%) = 3.99359 (10.262) -Neigh time (%) = 4.65272 (11.9557) -Comm time (%) = 0.216829 (0.557168) -Outpt time (%) = 0.000280738 (0.000721391) -Other time (%) = 1.55441 (3.99426) - -FFT time (% of Kspce) = 0.448314 (11.2258) -FFT Gflps 3d (1d only) = 5.34183 11.5795 +Pair time (%) = 26.4472 (69.3149) +Bond time (%) = 1.31402 (3.44388) +Kspce time (%) = 4.23553 (11.1008) +Neigh time (%) = 4.45503 (11.6761) +Comm time (%) = 0.208946 (0.547622) +Outpt time (%) = 0.000290096 (0.000760307) +Other time (%) = 1.49411 (3.91587) 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 = 48112472 Ave neighs/atom = 375.879 Ave special neighs/atom = 7.43187 Neighbor list builds = 11 Dangerous builds = 0