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/MBX-0.7/plugins/lammps/examples/ch4/20atm/125K
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| (work) 125K > mpirun -np 2 lmp_mpi_mbx -in lammps.in | |
| -------------------------------------------------------------------------- | |
| By default, for Open MPI 4.0 and later, infiniband ports on a device | |
| are not used by default. The intent is to use UCX for these devices. | |
| You can override this policy by setting the btl_openib_allow_ib MCA parameter | |
| to true. | |
| Local host: login-0-0 | |
| Local adapter: mlx4_0 | |
| Local port: 1 | |
| -------------------------------------------------------------------------- | |
| -------------------------------------------------------------------------- | |
| WARNING: There was an error initializing an OpenFabrics device. | |
| Local host: login-0-0 | |
| Local device: mlx4_0 | |
| -------------------------------------------------------------------------- | |
| LAMMPS (29 Sep 2021 - Update 3) | |
| OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:98) | |
| using 1 OpenMP thread(s) per MPI task | |
| Reading data file ... | |
| orthogonal box = (-12.019398 -12.019398 -12.019398) to (12.019398 12.019398 12.019398) | |
| 1 by 1 by 2 MPI processor grid | |
| reading atoms ... | |
| 1280 atoms | |
| reading velocities ... | |
| 1280 velocities | |
| scanning bonds ... | |
| 4 = max bonds/atom | |
| scanning angles ... | |
| 6 = max angles/atom | |
| reading bonds ... | |
| 1024 bonds | |
| reading angles ... | |
| 1536 angles | |
| Finding 1-2 1-3 1-4 neighbors ... | |
| special bond factors lj: 0 0 0 | |
| special bond factors coul: 0 0 0 | |
| 4 = max # of 1-2 neighbors | |
| 3 = max # of 1-3 neighbors | |
| 3 = max # of 1-4 neighbors | |
| 4 = max # of special neighbors | |
| special bonds CPU = 0.000 seconds | |
| read_data CPU = 0.023 seconds | |
| [MBX] Using json_file= mbx.json | |
| [MBX] # molecule types= 1 | |
| [MBX] # molecules= 256 | |
| [MBX] i= 0 # of molecules= 256 name= ' ch4' offset= 0 | |
| [0] json_settings= { | |
| "Note" : "json file for MB-nrg CH4", | |
| "MBX" : { | |
| "box" : [], | |
| "twobody_cutoff" : 9.0, | |
| "threebody_cutoff" : 4.5, | |
| "max_n_eval_1b" : 500, | |
| "max_n_eval_2b" : 500, | |
| "max_n_eval_3b" : 500, | |
| "dipole_tolerance" : 1E-8, | |
| "dipole_max_it" : 100, | |
| "dipole_method" : "cg", | |
| "alpha_ewald_elec" : 0.60, | |
| "grid_density_elec" : 2.5, | |
| "spline_order_elec" : 6, | |
| "alpha_ewald_disp" : 0.60, | |
| "grid_density_disp" : 2.5, | |
| "spline_order_disp" : 6, | |
| "ttm_pairs" : [], | |
| "ignore_2b_poly" : [], | |
| "ignore_3b_poly" : [["h2o","h2o","ch4"]] | |
| } | |
| } | |
| CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE | |
| Your simulation uses code contributions which should be cited: | |
| - fix mbx command: | |
| The log file lists these citations in BibTeX format. | |
| CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE | |
| WARNING: Bonds are defined but no bond style is set (../force.cpp:191) | |
| WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:193) | |
| WARNING: Angles are defined but no angle style is set (../force.cpp:196) | |
| WARNING: Likewise 1-3 special neighbor interactions != 1.0 (../force.cpp:198) | |
| Neighbor list info ... | |
| update every 1 steps, delay 10 steps, check yes | |
| max neighbors/atom: 2000, page size: 100000 | |
| master list distance cutoff = 11 | |
| ghost atom cutoff = 11 | |
| binsize = 5.5, bins = 5 5 5 | |
| 1 neighbor lists, perpetual/occasional/extra = 1 0 0 | |
| (1) pair mbx, perpetual | |
| attributes: half, newton on | |
| pair build: half/bin/newton | |
| stencil: half/bin/3d | |
| bin: standard | |
| Setting up Verlet run ... | |
| Unit style : real | |
| Current step : 0 | |
| Time step : 0.5 | |
| Per MPI rank memory allocation (min/avg/max) = 11.22 | 11.22 | 11.22 Mbytes | |
| Step Time Temp TotEng KinEng PotEng Enthalpy Density Lx Ly Lz Volume Pxx Pyy Pzz Press | |
| 0 0 125 124.33099 476.55701 -352.22602 455.96278 0.49059107 24.038796 24.038796 24.038796 13891.148 141.06512 1933.8308 2836.0301 1636.9753 | |
| [login-0-0.um.edu.mo:268848] 1 more process has sent help message help-mpi-btl-openib.txt / ib port not selected | |
| [login-0-0.um.edu.mo:268848] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages | |
| [login-0-0.um.edu.mo:268848] 1 more process has sent help message help-mpi-btl-openib.txt / error in device init | |
| 1 0.5 123.79772 124.39678 471.97338 -347.5766 459.02758 0.49059102 24.038797 24.038797 24.038797 13891.149 446.68505 1825.3769 2683.2741 1651.7787 | |
| 2 1 118.82382 124.72349 453.01058 -328.28709 478.86776 0.49059088 24.038799 24.038799 24.038799 13891.153 925.32913 1829.1948 2489.7731 1748.099 | |
| 3 1.5 111.396 125.20323 424.69234 -299.48911 508.98048 0.49059064 24.038803 24.038803 24.038803 13891.16 1517.0487 1922.9514 2243.1102 1894.3701 | |
| 4 2 103.45336 125.68435 394.41138 -268.72703 539.5761 0.49059028 24.038809 24.038809 24.038809 13891.17 2137.861 2062.6959 1928.4951 2043.0173 | |
| 5 2.5 96.944814 126.02173 369.59784 -243.57611 560.90758 0.49058981 24.038816 24.038816 24.038816 13891.183 2699.4306 2198.9309 1541.5722 2146.6446 | |
| 6 3 93.238767 126.11954 355.4687 -229.34916 566.54615 0.49058921 24.038826 24.038826 24.038826 13891.2 3129.8289 2293.3809 1098.7654 2173.9917 | |
| 7 3.5 92.733921 125.95951 353.544 -227.58449 555.51847 0.49058849 24.038838 24.038838 24.038838 13891.221 3389.3754 2330.7525 640.90634 2120.3447 | |
| 8 4 94.786331 125.60718 361.36872 -235.76155 532.61063 0.49058764 24.038852 24.038852 24.038852 13891.245 3477.0696 2321.7246 228.2211 2009.0051 | |
| 9 4.5 97.976006 125.19192 373.52922 -248.33729 506.74366 0.49058668 24.038868 24.038868 24.038868 13891.272 3425.771 2296.6072 -72.269716 1883.3695 | |
| 10 5 100.62912 124.86357 383.64412 -258.78055 487.94402 0.49058561 24.038885 24.038885 24.038885 13891.302 3287.8214 2292.1094 -203.36141 1792.1898 | |
| Loop time of 40.0099 on 2 procs for 10 steps with 1280 atoms | |
| Performance: 0.011 ns/day, 2222.771 hours/ns, 0.250 timesteps/s | |
| 99.3% CPU use with 2 MPI tasks x 1 OpenMP threads | |
| MPI task timing breakdown: | |
| Section | min time | avg time | max time |%varavg| %total | |
| --------------------------------------------------------------- | |
| Pair | 39.748 | 39.748 | 39.748 | 0.0 | 99.34 | |
| Bond | 9.138e-06 | 1.2341e-05 | 1.5543e-05 | 0.0 | 0.00 | |
| Neigh | 0.013062 | 0.013158 | 0.013255 | 0.1 | 0.03 | |
| Comm | 0.003327 | 0.0033309 | 0.0033348 | 0.0 | 0.01 | |
| Output | 0.19372 | 0.19383 | 0.19394 | 0.0 | 0.48 | |
| Modify | 0.051717 | 0.051718 | 0.051718 | 0.0 | 0.13 | |
| Other | | 0.0002553 | | | 0.00 | |
| Nlocal: 640.000 ave 641 max 639 min | |
| Histogram: 1 0 0 0 0 0 0 0 0 1 | |
| Nghost: 6023.00 ave 6023 max 6023 min | |
| Histogram: 2 0 0 0 0 0 0 0 0 0 | |
| Neighs: 162678.0 ave 163489 max 161867 min | |
| Histogram: 1 0 0 0 0 0 0 0 0 1 | |
| Total # of neighbors = 325356 | |
| Ave neighs/atom = 254.18437 | |
| Ave special neighs/atom = 4.0000000 | |
| Neighbor list builds = 2 | |
| Dangerous builds = 0 | |
| System init for write_data ... | |
| WARNING: Bonds are defined but no bond style is set (../force.cpp:191) | |
| WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:193) | |
| WARNING: Angles are defined but no angle style is set (../force.cpp:196) | |
| WARNING: Likewise 1-3 special neighbor interactions != 1.0 (../force.cpp:198) | |
| System init for write_restart ... | |
| WARNING: Bonds are defined but no bond style is set (../force.cpp:191) | |
| WARNING: Likewise 1-2 special neighbor interactions != 1.0 (../force.cpp:193) | |
| WARNING: Angles are defined but no angle style is set (../force.cpp:196) | |
| WARNING: Likewise 1-3 special neighbor interactions != 1.0 (../force.cpp:198) | |
| [MBX] Total MBX fix/pair time= 43.475743 seconds | |
| [MBX] Timing Summary | |
| [MBX] kernel tmin tavg tmax count %total | |
| [MBX] ----------------------------------------------------------------------------------- | |
| [MBX] INIT : 0.049096 0.049201 0.049307 3 0.11% | |
| [MBX] UPDATE_XYZ : 0.008133 0.0081422 0.0081514 11 0.02% | |
| [MBX] ACCUMULATE_F : 0.015519 0.015644 0.01577 55 0.04% | |
| [MBX] E1B : 0.017978 0.019076 0.020174 11 0.05% | |
| [MBX] E2B_LOCAL : 0 0 0 0 0.00% | |
| [MBX] E2B_GHOST : 13.67 14.157 14.644 11 33.68% | |
| [MBX] E3B_LOCAL : 0 0 0 0 0.00% | |
| [MBX] E3B_GHOST : 0.19005 0.191 0.19194 11 0.44% | |
| [MBX] DISP : 7.5055 7.5444 7.5833 11 17.44% | |
| [MBX] DISP_PME : 0.42091 0.87218 1.3235 11 3.04% | |
| [MBX] BUCK : 0.0036354 0.0038522 0.004069 11 0.01% | |
| [MBX] ELE : 20.295 20.296 20.298 11 46.69% | |
| [MBX] INIT_FULL : 0 0 0 0 0.00% | |
| [MBX] UPDATE_XYZ_FULL : 0 0 0 0 0.00% | |
| [MBX] ACCUMULATE_F_FULL : 0 0 0 0 0.00% | |
| [MBX] INIT_LOCAL : 0.03443 0.034568 0.034705 3 0.08% | |
| [MBX] UPDATE_XYZ_LOCAL : 0.0017275 0.0017323 0.0017371 11 0.00% | |
| [MBX] ACCUMULATE_F_LOCAL : 0.004715 0.0048215 0.0049279 22 0.01% | |
| [MBX] Electrostatics Summary | |
| [MBX] kernel tmin tavg tmax count %total | |
| [MBX] ----------------------------------------------------------------------------------- | |
| [MBX] ELE_PERMDIP_REAL : 5.5022 5.5927 5.6832 11 13.07% | |
| [MBX] ELE_PERMDIP_PME : 0.20422 0.29326 0.38229 11 0.88% | |
| [MBX] ELE_DIPFIELD_REAL : 7.9181 8.005 8.092 83 18.61% | |
| [MBX] ELE_DIPFIELD_PME : 1.4568 1.5444 1.6321 83 3.75% | |
| [MBX] ELE_GRAD_REAL : 3.9495 3.9844 4.0193 11 9.24% | |
| [MBX] ELE_GRAD_PME : 0.78713 0.82223 0.85734 11 1.97% | |
| [MBX] ELE_GRAD_FIN : 0.0010997 0.0011686 0.0012375 11 0.00% | |
| [MBX] ELE_PME_SETUP : 0.20979 0.41948 0.62918 105 1.45% | |
| [MBX] ELE_PME_C : 0.39782 0.39849 0.39917 22 0.92% | |
| [MBX] ELE_PME_D : 1.552 1.5531 1.5542 94 3.57% | |
| [MBX] ELE_PME_E : 0.27388 0.27444 0.275 11 0.63% | |
| [MBX] DISP_PME_SETUP : 0.022627 0.47295 0.92327 11 2.12% | |
| [MBX] DISP_PME_E : 0.38952 0.38987 0.39022 11 0.90% | |
| [MBX] ELE_COMM_REVFOR : 0.039841 0.040682 0.041524 94 0.10% | |
| [MBX] ELE_COMM_REVSET : 0.012568 0.012642 0.012716 3 0.03% | |
| [MBX] ELE_COMM_REV : 0.0038425 0.0046611 0.0054797 91 0.01% | |
| [MBX] ELE_COMM_FORSET : 0.018843 0.018952 0.019061 3 0.04% | |
| [MBX] ELE_COMM_FOR : 0.0036985 0.0037107 0.003723 91 0.01% | |
| Total wall time: 0:00:43 |
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