LAMMPS using 2 OpenMP thread(s) per MPI task package intel 1 package intel 0 # Rhodopsin model variable N index on # Newton Setting variable w index 10 # Warmup Timesteps variable t index 520 # Main Run Timesteps variable m index 1 # Main Run Timestep Multiplier variable n index 0 # Use NUMA Mapping for Multi-Node variable p index 0 # Use Power Measurement variable c index 0 # 1 to use collectives for PPPM variable d index 1 # 1 to use 'diff ad' for PPPM variable x index 4 variable y index 2 variable z index 2 variable rr equal floor($t*$m) variable rr equal floor(520*$m) variable rr equal floor(520*1) variable root getenv LMP_ROOT newton $N newton on if "$n > 0" then "processors * * * grid numa" 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 if "$c > 0" then "kspace_modify collective yes" if "$d > 0" then "kspace_modify diff ad" kspace_modify diff ad read_data ${root}/bench/data.rhodo read_data ../../..//bench/data.rhodo orthogonal box = (-27.5 -38.5 -36.3646) to (27.5 38.5 36.3615) 3 by 4 by 3 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 4 $y $z replicate 4 2 $z replicate 4 2 2 orthogonal box = (-27.5 -38.5 -36.3646) to (192.5 115.5 109.088) 4 by 3 by 3 MPI processor grid 512000 atoms 443568 bonds 647472 angles 909264 dihedrals 16544 impropers 4 = max # of 1-2 neighbors 12 = max # of 1-3 neighbors 24 = max # of 1-4 neighbors 26 = max # of special neighbors Time spent = 0.0871329 secs fix 1 all shake 0.0001 5 0 m 1.0 a 232 25872 = # of size 2 clusters 58128 = # of size 3 clusters 11952 = # of size 4 clusters 67728 = # of frozen angles fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1 special_bonds charmm thermo 100 thermo_style multi timestep 2.0 if "$p > 0" then "run_style verlet/power" if "$w > 0" then "run $w" run $w run 10 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.249155 grid = 90 60 60 stencil order = 7 estimated absolute RMS force accuracy = 0.0349853 estimated relative force accuracy = 0.000105357 using single precision FFTs 3d grid and FFT values/proc = 21870 10800 Neighbor list info ... 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 = 37 26 25 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/charmm/coul/long/intel, perpetual attributes: half, newton on, intel pair build: half/bin/newton/intel stencil: half/bin/3d/newton bin: intel Per MPI rank memory allocation (min/avg/max) = 182.3 | 183.8 | 185.6 Mbytes ---------------- Step 0 ----- CPU = 0.0000 (sec) ---------------- TotEng = -405720.8400 KinEng = 343117.3005 Temp = 299.0280 PotEng = -748838.1405 E_bond = 40607.8729 E_angle = 174741.9568 E_dihed = 83388.5824 E_impro = 3416.2178 E_vdwl = -36925.8156 E_coul = 3317970.3207 E_long = -4332037.2757 Press = -148.1694 Volume = 4927920.5360 ---------------- Step 10 ----- CPU = 0.4775 (sec) ---------------- TotEng = -405708.2342 KinEng = 343174.1863 Temp = 299.0776 PotEng = -748882.4205 E_bond = 41012.3205 E_angle = 172778.1923 E_dihed = 83352.1155 E_impro = 3406.2613 E_vdwl = -35703.6203 E_coul = 3318392.6414 E_long = -4332120.3313 Press = 102.3485 Volume = 4927870.5704 Loop time of 0.47756 on 72 procs for 10 steps with 512000 atoms Performance: 3.618 ns/day, 6.633 hours/ns, 20.940 timesteps/s 173.7% CPU use with 36 MPI tasks x 2 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.28806 | 0.29896 | 0.31225 | 1.3 | 62.60 Bond | 0.011414 | 0.016546 | 0.019757 | 2.5 | 3.46 Kspace | 0.050602 | 0.059088 | 0.068696 | 2.3 | 12.37 Neigh | 0.024261 | 0.02459 | 0.024842 | 0.1 | 5.15 Comm | 0.019909 | 0.021748 | 0.02458 | 0.9 | 4.55 Output | 8.4877e-05 | 8.7347e-05 | 0.00012398 | 0.0 | 0.02 Modify | 0.050676 | 0.052938 | 0.054692 | 0.6 | 11.09 Other | | 0.003602 | | | 0.75 Nlocal: 14222.2 ave 14455 max 14048 min Histogram: 8 4 8 0 4 0 0 4 4 4 Nghost: 30658.1 ave 30843 max 30410 min Histogram: 4 4 0 4 0 4 0 12 4 4 Neighs: 5.3472e+06 ave 5.51614e+06 max 5.22584e+06 min Histogram: 4 12 4 0 4 0 4 0 4 4 Total # of neighbors = 192499054 Ave neighs/atom = 375.975 Ave special neighs/atom = 7.43187 Neighbor list builds = 1 Dangerous builds = 0 run ${rr} run 520 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) G vector (1/distance) = 0.249156 grid = 90 60 60 stencil order = 7 estimated absolute RMS force accuracy = 0.0349851 estimated relative force accuracy = 0.000105357 using single precision FFTs 3d grid and FFT values/proc = 21870 10800 Per MPI rank memory allocation (min/avg/max) = 182.3 | 183.8 | 185.6 Mbytes ---------------- Step 10 ----- CPU = 0.0000 (sec) ---------------- TotEng = -405708.6017 KinEng = 343174.1863 Temp = 299.0776 PotEng = -748882.7880 E_bond = 41012.3205 E_angle = 172778.1923 E_dihed = 83352.1155 E_impro = 3406.2613 E_vdwl = -35703.6203 E_coul = 3318395.9698 E_long = -4332124.0272 Press = 101.3029 Volume = 4927870.5704 ---------------- Step 100 ----- CPU = 4.3274 (sec) ---------------- TotEng = -404651.3821 KinEng = 345420.2728 Temp = 301.0351 PotEng = -750071.6549 E_bond = 41089.2213 E_angle = 172509.3250 E_dihed = 83176.0023 E_impro = 3467.0933 E_vdwl = -30388.5027 E_coul = 3312145.3591 E_long = -4332070.1533 Press = 12.7870 Volume = 4930151.5437 ---------------- Step 200 ----- CPU = 9.1503 (sec) ---------------- TotEng = -401302.2586 KinEng = 344138.3861 Temp = 299.9179 PotEng = -745440.6447 E_bond = 39844.8753 E_angle = 177222.5954 E_dihed = 83545.4624 E_impro = 3720.4898 E_vdwl = -34128.6903 E_coul = 3316279.3441 E_long = -4331924.7215 Press = 72.1763 Volume = 4943913.8729 ---------------- Step 300 ----- CPU = 13.9227 (sec) ---------------- TotEng = -399280.2915 KinEng = 344189.1224 Temp = 299.9621 PotEng = -743469.4139 E_bond = 41101.4095 E_angle = 174931.6149 E_dihed = 83581.3527 E_impro = 3540.7035 E_vdwl = -36289.5898 E_coul = 3321553.6021 E_long = -4331888.5068 Press = -421.2760 Volume = 4954650.7140 ---------------- Step 400 ----- CPU = 18.7409 (sec) ---------------- TotEng = -401676.1197 KinEng = 343086.0113 Temp = 299.0008 PotEng = -744762.1310 E_bond = 40512.0198 E_angle = 175582.6474 E_dihed = 83826.1731 E_impro = 3561.7636 E_vdwl = -34433.9361 E_coul = 3318197.2297 E_long = -4332008.0285 Press = 178.4098 Volume = 4956634.4343 ---------------- Step 500 ----- CPU = 23.5403 (sec) ---------------- TotEng = -400954.5593 KinEng = 343510.6744 Temp = 299.3708 PotEng = -744465.2337 E_bond = 41500.1247 E_angle = 174744.6073 E_dihed = 84083.4351 E_impro = 3479.2921 E_vdwl = -32866.1003 E_coul = 3316475.3650 E_long = -4331881.9577 Press = -148.6823 Volume = 4955606.5914 ---------------- Step 530 ----- CPU = 24.9927 (sec) ---------------- TotEng = -399415.0559 KinEng = 345096.1599 Temp = 300.7526 PotEng = -744511.2158 E_bond = 41171.7353 E_angle = 175498.3655 E_dihed = 83857.4471 E_impro = 3648.8287 E_vdwl = -31753.9073 E_coul = 3314923.0421 E_long = -4331856.7270 Press = 349.5057 Volume = 4954711.0444 Loop time of 24.9928 on 72 procs for 520 steps with 512000 atoms Performance: 3.595 ns/day, 6.675 hours/ns, 20.806 timesteps/s 173.3% CPU use with 36 MPI tasks x 2 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 14.806 | 15.374 | 16.075 | 8.8 | 61.51 Bond | 0.59759 | 0.86328 | 1.0325 | 17.5 | 3.45 Kspace | 2.6158 | 3.0711 | 3.5833 | 15.4 | 12.29 Neigh | 1.4803 | 1.4926 | 1.5065 | 0.7 | 5.97 Comm | 1.1467 | 1.227 | 1.3673 | 6.0 | 4.91 Output | 0.00055122 | 0.00056601 | 0.00057197 | 0.0 | 0.00 Modify | 2.6713 | 2.7877 | 2.8766 | 4.4 | 11.15 Other | | 0.1767 | | | 0.71 Nlocal: 14222.2 ave 14415 max 14033 min Histogram: 3 4 6 7 4 0 0 0 1 11 Nghost: 30534.8 ave 30766 max 30344 min Histogram: 9 3 0 0 4 6 7 5 1 1 Neighs: 5.31908e+06 ave 5.4539e+06 max 5.2233e+06 min Histogram: 8 8 3 5 0 0 0 2 2 8 Total # of neighbors = 191487021 Ave neighs/atom = 373.998 Ave special neighs/atom = 7.43187 Neighbor list builds = 61 Dangerous builds = 0 Total wall time: 0:00:27