From 77fe3db02c7b0a243e1884dd87cbd48310847b9e Mon Sep 17 00:00:00 2001 From: sjplimp Date: Mon, 15 Feb 2016 17:21:52 +0000 Subject: [PATCH] git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@14608 f3b2605a-c512-4ea7-a41b-209d697bcdaa --- bench/log.15Feb16.chain.fixed.icc.1 | 78 +++++++++++++++ bench/log.15Feb16.chain.fixed.icc.4 | 78 +++++++++++++++ bench/log.15Feb16.chain.scaled.icc.4 | 94 ++++++++++++++++++ bench/log.15Feb16.chute.fixed.icc.1 | 80 +++++++++++++++ bench/log.15Feb16.chute.fixed.icc.4 | 80 +++++++++++++++ bench/log.15Feb16.chute.scaled.icc.4 | 90 +++++++++++++++++ bench/log.15Feb16.eam.fixed.icc.1 | 83 ++++++++++++++++ bench/log.15Feb16.eam.fixed.icc.4 | 83 ++++++++++++++++ bench/log.15Feb16.eam.scaled.icc.4 | 83 ++++++++++++++++ bench/log.15Feb16.lj.fixed.icc.1 | 79 +++++++++++++++ bench/log.15Feb16.lj.fixed.icc.4 | 79 +++++++++++++++ bench/log.15Feb16.lj.scaled.icc.4 | 79 +++++++++++++++ bench/log.15Feb16.rhodo.fixed.icc.1 | 121 +++++++++++++++++++++++ bench/log.15Feb16.rhodo.fixed.icc.4 | 121 +++++++++++++++++++++++ bench/log.15Feb16.rhodo.scaled.icc.4 | 142 +++++++++++++++++++++++++++ 15 files changed, 1370 insertions(+) create mode 100644 bench/log.15Feb16.chain.fixed.icc.1 create mode 100644 bench/log.15Feb16.chain.fixed.icc.4 create mode 100644 bench/log.15Feb16.chain.scaled.icc.4 create mode 100644 bench/log.15Feb16.chute.fixed.icc.1 create mode 100644 bench/log.15Feb16.chute.fixed.icc.4 create mode 100644 bench/log.15Feb16.chute.scaled.icc.4 create mode 100644 bench/log.15Feb16.eam.fixed.icc.1 create mode 100644 bench/log.15Feb16.eam.fixed.icc.4 create mode 100644 bench/log.15Feb16.eam.scaled.icc.4 create mode 100644 bench/log.15Feb16.lj.fixed.icc.1 create mode 100644 bench/log.15Feb16.lj.fixed.icc.4 create mode 100644 bench/log.15Feb16.lj.scaled.icc.4 create mode 100644 bench/log.15Feb16.rhodo.fixed.icc.1 create mode 100644 bench/log.15Feb16.rhodo.fixed.icc.4 create mode 100644 bench/log.15Feb16.rhodo.scaled.icc.4 diff --git a/bench/log.15Feb16.chain.fixed.icc.1 b/bench/log.15Feb16.chain.fixed.icc.1 new file mode 100644 index 0000000000..553241bf22 --- /dev/null +++ b/bench/log.15Feb16.chain.fixed.icc.1 @@ -0,0 +1,78 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.52 + ghost atom cutoff = 1.52 + binsize = 0.76 -> bins = 45 45 45 +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 0.978585 on 1 procs for 100 steps with 32000 atoms + +Performance: 105948.895 tau/day, 102.188 timesteps/s +100.0% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.19562 | 0.19562 | 0.19562 | 0.0 | 19.99 +Bond | 0.087475 | 0.087475 | 0.087475 | 0.0 | 8.94 +Neigh | 0.44861 | 0.44861 | 0.44861 | 0.0 | 45.84 +Comm | 0.032932 | 0.032932 | 0.032932 | 0.0 | 3.37 +Output | 0.00010395 | 0.00010395 | 0.00010395 | 0.0 | 0.01 +Modify | 0.19413 | 0.19413 | 0.19413 | 0.0 | 19.84 +Other | | 0.01972 | | | 2.02 + +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 +Total wall time: 0:00:01 diff --git a/bench/log.15Feb16.chain.fixed.icc.4 b/bench/log.15Feb16.chain.fixed.icc.4 new file mode 100644 index 0000000000..1ff445b27a --- /dev/null +++ b/bench/log.15Feb16.chain.fixed.icc.4 @@ -0,0 +1,78 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.52 + ghost atom cutoff = 1.52 + binsize = 0.76 -> bins = 45 45 45 +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 0.271187 on 4 procs for 100 steps with 32000 atoms + +Performance: 382319.453 tau/day, 368.749 timesteps/s +99.6% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.048621 | 0.050076 | 0.051229 | 0.4 | 18.47 +Bond | 0.022254 | 0.022942 | 0.023567 | 0.3 | 8.46 +Neigh | 0.11873 | 0.11881 | 0.11887 | 0.0 | 43.81 +Comm | 0.019066 | 0.021357 | 0.024297 | 1.3 | 7.88 +Output | 5.0068e-05 | 5.5015e-05 | 6.1035e-05 | 0.1 | 0.02 +Modify | 0.048737 | 0.050198 | 0.051231 | 0.4 | 18.51 +Other | | 0.007751 | | | 2.86 + +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 +Total wall time: 0:00:00 diff --git a/bench/log.15Feb16.chain.scaled.icc.4 b/bench/log.15Feb16.chain.scaled.icc.4 new file mode 100644 index 0000000000..df541d404c --- /dev/null +++ b/bench/log.15Feb16.chain.scaled.icc.4 @@ -0,0 +1,94 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 1 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.52 + ghost atom cutoff = 1.52 + binsize = 0.76 -> bins = 89 89 45 +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 1.20889 on 4 procs for 100 steps with 128000 atoms + +Performance: 85764.410 tau/day, 82.720 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.21738 | 0.23306 | 0.23926 | 1.9 | 19.28 +Bond | 0.094536 | 0.10196 | 0.10534 | 1.4 | 8.43 +Neigh | 0.52311 | 0.52392 | 0.52519 | 0.1 | 43.34 +Comm | 0.090161 | 0.10022 | 0.12557 | 4.7 | 8.29 +Output | 0.00012207 | 0.00017327 | 0.00019598 | 0.2 | 0.01 +Modify | 0.19662 | 0.20262 | 0.20672 | 0.8 | 16.76 +Other | | 0.04694 | | | 3.88 + +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 +Total wall time: 0:00:01 diff --git a/bench/log.15Feb16.chute.fixed.icc.1 b/bench/log.15Feb16.chute.fixed.icc.1 new file mode 100644 index 0000000000..e256524152 --- /dev/null +++ b/bench/log.15Feb16.chute.fixed.icc.1 @@ -0,0 +1,80 @@ +LAMMPS (15 Feb 2016) +# 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 +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 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55 -> bins = 73 37 68 +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 0.550482 on 1 procs for 100 steps with 32000 atoms + +Performance: 1569.534 tau/day, 181.659 timesteps/s +100.1% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.33849 | 0.33849 | 0.33849 | 0.0 | 61.49 +Neigh | 0.040353 | 0.040353 | 0.040353 | 0.0 | 7.33 +Comm | 0.018023 | 0.018023 | 0.018023 | 0.0 | 3.27 +Output | 0.00020385 | 0.00020385 | 0.00020385 | 0.0 | 0.04 +Modify | 0.13155 | 0.13155 | 0.13155 | 0.0 | 23.90 +Other | | 0.02186 | | | 3.97 + +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 +Total wall time: 0:00:00 diff --git a/bench/log.15Feb16.chute.fixed.icc.4 b/bench/log.15Feb16.chute.fixed.icc.4 new file mode 100644 index 0000000000..8252408833 --- /dev/null +++ b/bench/log.15Feb16.chute.fixed.icc.4 @@ -0,0 +1,80 @@ +LAMMPS (15 Feb 2016) +# 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 +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 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55 -> bins = 73 37 68 +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 0.13141 on 4 procs for 100 steps with 32000 atoms + +Performance: 6574.833 tau/day, 760.976 timesteps/s +99.3% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.062505 | 0.067 | 0.07152 | 1.5 | 50.99 +Neigh | 0.010041 | 0.0101 | 0.010178 | 0.1 | 7.69 +Comm | 0.012347 | 0.012895 | 0.013444 | 0.5 | 9.81 +Output | 6.3896e-05 | 0.00010294 | 0.00014091 | 0.3 | 0.08 +Modify | 0.031802 | 0.032348 | 0.032897 | 0.3 | 24.62 +Other | | 0.008965 | | | 6.82 + +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 +Total wall time: 0:00:00 diff --git a/bench/log.15Feb16.chute.scaled.icc.4 b/bench/log.15Feb16.chute.scaled.icc.4 new file mode 100644 index 0000000000..0b9807a447 --- /dev/null +++ b/bench/log.15Feb16.chute.scaled.icc.4 @@ -0,0 +1,90 @@ +LAMMPS (15 Feb 2016) +# 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 +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 37.2922) + 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 +Neighbor list info ... + 2 neighbor list requests + update every 1 steps, delay 0 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 1.1 + ghost atom cutoff = 1.1 + binsize = 0.55 -> bins = 146 73 68 +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 0.906913 on 4 procs for 100 steps with 128000 atoms + +Performance: 952.683 tau/day, 110.264 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.51454 | 0.53094 | 0.55381 | 2.0 | 58.54 +Neigh | 0.042597 | 0.043726 | 0.045801 | 0.6 | 4.82 +Comm | 0.063027 | 0.064657 | 0.067367 | 0.7 | 7.13 +Output | 0.00024891 | 0.00059718 | 0.00086498 | 1.0 | 0.07 +Modify | 0.16508 | 0.17656 | 0.1925 | 2.6 | 19.47 +Other | | 0.09043 | | | 9.97 + +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 +Total wall time: 0:00:01 diff --git a/bench/log.15Feb16.eam.fixed.icc.1 b/bench/log.15Feb16.eam.fixed.icc.1 new file mode 100644 index 0000000000..0408d2c8d7 --- /dev/null +++ b/bench/log.15Feb16.eam.fixed.icc.1 @@ -0,0 +1,83 @@ +LAMMPS (15 Feb 2016) +# 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 +Reading potential file Cu_u3.eam with DATE: 2007-06-11 + +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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.95 + ghost atom cutoff = 5.95 + binsize = 2.975 -> bins = 25 25 25 +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 5.90097 on 1 procs for 100 steps with 32000 atoms + +Performance: 7.321 ns/day, 3.278 hours/ns, 16.946 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.2121 | 5.2121 | 5.2121 | 0.0 | 88.33 +Neigh | 0.58212 | 0.58212 | 0.58212 | 0.0 | 9.86 +Comm | 0.030392 | 0.030392 | 0.030392 | 0.0 | 0.52 +Output | 0.00023389 | 0.00023389 | 0.00023389 | 0.0 | 0.00 +Modify | 0.060871 | 0.060871 | 0.060871 | 0.0 | 1.03 +Other | | 0.01527 | | | 0.26 + +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 +Total wall time: 0:00:06 diff --git a/bench/log.15Feb16.eam.fixed.icc.4 b/bench/log.15Feb16.eam.fixed.icc.4 new file mode 100644 index 0000000000..6a7c47a58b --- /dev/null +++ b/bench/log.15Feb16.eam.fixed.icc.4 @@ -0,0 +1,83 @@ +LAMMPS (15 Feb 2016) +# 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 +Reading potential file Cu_u3.eam with DATE: 2007-06-11 + +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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.95 + ghost atom cutoff = 5.95 + binsize = 2.975 -> bins = 25 25 25 +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 1.58019 on 4 procs for 100 steps with 32000 atoms + +Performance: 27.338 ns/day, 0.878 hours/ns, 63.284 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.3617 | 1.366 | 1.3723 | 0.4 | 86.45 +Neigh | 0.15123 | 0.15232 | 0.15374 | 0.2 | 9.64 +Comm | 0.033429 | 0.041275 | 0.047066 | 2.7 | 2.61 +Output | 0.00011301 | 0.0001573 | 0.000211 | 0.3 | 0.01 +Modify | 0.014694 | 0.015085 | 0.015421 | 0.2 | 0.95 +Other | | 0.005342 | | | 0.34 + +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 +Total wall time: 0:00:01 diff --git a/bench/log.15Feb16.eam.scaled.icc.4 b/bench/log.15Feb16.eam.scaled.icc.4 new file mode 100644 index 0000000000..2c1cd3273e --- /dev/null +++ b/bench/log.15Feb16.eam.scaled.icc.4 @@ -0,0 +1,83 @@ +LAMMPS (15 Feb 2016) +# 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 +Reading potential file Cu_u3.eam with DATE: 2007-06-11 + +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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 5.95 + ghost atom cutoff = 5.95 + binsize = 2.975 -> bins = 49 49 25 +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 6.46849 on 4 procs for 100 steps with 128000 atoms + +Performance: 6.679 ns/day, 3.594 hours/ns, 15.460 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 5.581 | 5.5997 | 5.6265 | 0.8 | 86.57 +Neigh | 0.65287 | 0.658 | 0.66374 | 0.5 | 10.17 +Comm | 0.075706 | 0.11015 | 0.13655 | 7.2 | 1.70 +Output | 0.00026488 | 0.00028312 | 0.00029302 | 0.1 | 0.00 +Modify | 0.069607 | 0.072407 | 0.074555 | 0.7 | 1.12 +Other | | 0.02794 | | | 0.43 + +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 +Total wall time: 0:00:06 diff --git a/bench/log.15Feb16.lj.fixed.icc.1 b/bench/log.15Feb16.lj.fixed.icc.1 new file mode 100644 index 0000000000..e889fba225 --- /dev/null +++ b/bench/log.15Feb16.lj.fixed.icc.1 @@ -0,0 +1,79 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4 -> bins = 24 24 24 +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 2.26309 on 1 procs for 100 steps with 32000 atoms + +Performance: 19088.920 tau/day, 44.187 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 1.9341 | 1.9341 | 1.9341 | 0.0 | 85.46 +Neigh | 0.2442 | 0.2442 | 0.2442 | 0.0 | 10.79 +Comm | 0.024158 | 0.024158 | 0.024158 | 0.0 | 1.07 +Output | 0.00011611 | 0.00011611 | 0.00011611 | 0.0 | 0.01 +Modify | 0.053222 | 0.053222 | 0.053222 | 0.0 | 2.35 +Other | | 0.007258 | | | 0.32 + +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 not checked +Total wall time: 0:00:02 diff --git a/bench/log.15Feb16.lj.fixed.icc.4 b/bench/log.15Feb16.lj.fixed.icc.4 new file mode 100644 index 0000000000..53cdcdbee6 --- /dev/null +++ b/bench/log.15Feb16.lj.fixed.icc.4 @@ -0,0 +1,79 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4 -> bins = 24 24 24 +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 0.640733 on 4 procs for 100 steps with 32000 atoms + +Performance: 67422.779 tau/day, 156.071 timesteps/s +99.7% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 0.49487 | 0.51733 | 0.5322 | 1.9 | 80.74 +Neigh | 0.061131 | 0.063685 | 0.065433 | 0.6 | 9.94 +Comm | 0.02457 | 0.042349 | 0.069598 | 8.1 | 6.61 +Output | 5.9843e-05 | 6.3181e-05 | 6.6996e-05 | 0.0 | 0.01 +Modify | 0.012961 | 0.013863 | 0.014491 | 0.5 | 2.16 +Other | | 0.003448 | | | 0.54 + +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 not checked +Total wall time: 0:00:00 diff --git a/bench/log.15Feb16.lj.scaled.icc.4 b/bench/log.15Feb16.lj.scaled.icc.4 new file mode 100644 index 0000000000..7676040c54 --- /dev/null +++ b/bench/log.15Feb16.lj.scaled.icc.4 @@ -0,0 +1,79 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 20 steps, delay 0 steps, check no + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 2.8 + ghost atom cutoff = 2.8 + binsize = 1.4 -> bins = 48 48 24 +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 2.57914 on 4 procs for 100 steps with 128000 atoms + +Performance: 16749.768 tau/day, 38.773 timesteps/s +99.8% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 2.042 | 2.1092 | 2.1668 | 3.1 | 81.78 +Neigh | 0.23982 | 0.24551 | 0.25233 | 1.0 | 9.52 +Comm | 0.067088 | 0.13887 | 0.22681 | 15.7 | 5.38 +Output | 0.00013185 | 0.00021666 | 0.00027108 | 0.4 | 0.01 +Modify | 0.060348 | 0.071269 | 0.077063 | 2.5 | 2.76 +Other | | 0.01403 | | | 0.54 + +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 not checked +Total wall time: 0:00:02 diff --git a/bench/log.15Feb16.rhodo.fixed.icc.1 b/bench/log.15Feb16.rhodo.fixed.icc.1 new file mode 100644 index 0000000000..994c69e585 --- /dev/null +++ b/bench/log.15Feb16.rhodo.fixed.icc.1 @@ -0,0 +1,121 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6 -> bins = 10 13 13 +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 = 17.6362 (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 = 35.9089 (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 = 206659.2326 E_long = -270404.9733 Press = 6.9960 +Volume = 308133.9888 +Loop time of 35.9089 on 1 procs for 100 steps with 32000 atoms + +Performance: 0.481 ns/day, 49.874 hours/ns, 2.785 timesteps/s +99.9% CPU use with 1 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 25.731 | 25.731 | 25.731 | 0.0 | 71.66 +Bond | 1.2771 | 1.2771 | 1.2771 | 0.0 | 3.56 +Kspace | 3.2094 | 3.2094 | 3.2094 | 0.0 | 8.94 +Neigh | 4.4538 | 4.4538 | 4.4538 | 0.0 | 12.40 +Comm | 0.068507 | 0.068507 | 0.068507 | 0.0 | 0.19 +Output | 0.00025916 | 0.00025916 | 0.00025916 | 0.0 | 0.00 +Modify | 1.1417 | 1.1417 | 1.1417 | 0.0 | 3.18 +Other | | 0.027 | | | 0.08 + +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 +Total wall time: 0:00:37 diff --git a/bench/log.15Feb16.rhodo.fixed.icc.4 b/bench/log.15Feb16.rhodo.fixed.icc.4 new file mode 100644 index 0000000000..dfa5b065f9 --- /dev/null +++ b/bench/log.15Feb16.rhodo.fixed.icc.4 @@ -0,0 +1,121 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6 -> bins = 10 13 13 +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 = 4.7461 (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 = 9.6332 (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 9.63322 on 4 procs for 100 steps with 32000 atoms + +Performance: 1.794 ns/day, 13.379 hours/ns, 10.381 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 6.4364 | 6.5993 | 6.7208 | 4.7 | 68.51 +Bond | 0.30755 | 0.32435 | 0.35704 | 3.4 | 3.37 +Kspace | 0.92248 | 1.0782 | 1.2597 | 13.0 | 11.19 +Neigh | 1.1669 | 1.1672 | 1.1675 | 0.0 | 12.12 +Comm | 0.094674 | 0.098065 | 0.10543 | 1.4 | 1.02 +Output | 0.00015521 | 0.00016224 | 0.00018215 | 0.1 | 0.00 +Modify | 0.32982 | 0.34654 | 0.35365 | 1.6 | 3.60 +Other | | 0.01943 | | | 0.20 + +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 +Total wall time: 0:00:10 diff --git a/bench/log.15Feb16.rhodo.scaled.icc.4 b/bench/log.15Feb16.rhodo.scaled.icc.4 new file mode 100644 index 0000000000..73cdb163b0 --- /dev/null +++ b/bench/log.15Feb16.rhodo.scaled.icc.4 @@ -0,0 +1,142 @@ +LAMMPS (15 Feb 2016) +# 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 +Neighbor list info ... + 1 neighbor list requests + update every 1 steps, delay 5 steps, check yes + max neighbors/atom: 2000, page size: 100000 + master list distance cutoff = 12 + ghost atom cutoff = 12 + binsize = 6 -> bins = 19 26 13 +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 = 18.7806 (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 = 38.3684 (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 = 825583.7122 E_long = -1080572.5667 Press = 15.2151 +Volume = 1232535.8423 +Loop time of 38.3684 on 4 procs for 100 steps with 128000 atoms + +Performance: 0.450 ns/day, 53.289 hours/ns, 2.606 timesteps/s +99.9% CPU use with 4 MPI tasks x no OpenMP threads + +MPI task timing breakdown: +Section | min time | avg time | max time |%varavg| %total +--------------------------------------------------------------- +Pair | 26.205 | 26.538 | 26.911 | 5.0 | 69.17 +Bond | 1.298 | 1.3125 | 1.3277 | 1.0 | 3.42 +Kspace | 3.7099 | 4.0992 | 4.4422 | 13.3 | 10.68 +Neigh | 4.6137 | 4.6144 | 4.615 | 0.0 | 12.03 +Comm | 0.21398 | 0.21992 | 0.22886 | 1.2 | 0.57 +Output | 0.00030518 | 0.00031543 | 0.00033307 | 0.1 | 0.00 +Modify | 1.5066 | 1.5232 | 1.5388 | 1.0 | 3.97 +Other | | 0.06051 | | | 0.16 + +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 +Total wall time: 0:00:39