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Created October 18, 2022 07:10
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/MBX-0.7/plugins/lammps/examples/ch4/20atm/125K
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gistfile1.txt
(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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