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|
LAMMPS (30 Aug 2013)
Reading data file ...
orthogonal box = (-37.835 -16.215 -16.215) to (37.835 16.215 16.215)
4 by 1 by 1 MPI processor grid
1288 atoms
1288 velocities
Lattice spacing in x,y,z = 5.405 5.405 5.405
1000 atoms in group internal
288 atoms in group ghost
Lattice spacing in x,y,z = 5.405 5.405 5.405
ATC: constructing thermal coupling with parameter file Ar_thermal.mat
ATC: version 2.0
ATC: peratom PE compute created with ID: 3
ATC: 1 materials defined from Ar_thermal.mat
ATC: created uniform mesh with 28 nodes, 7 unique nodes, and 6 elements
ATC: created nodeset lbc with 1 nodes
ATC: created nodeset rbc with 1 nodes
Setting up run ...
Memory usage per processor = 18.9868 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -994.32071 -1292.1036 1073.0916 99.9 100
200 0.79 -1039.0541 -1337.1351 1073.0916 100 100
400 1.6 -1063.5946 -1361.6756 1073.0916 100 100
600 2.4 -1074.9626 -1373.0436 1073.0916 100 100
800 3.1 -1081.7626 -1379.8436 1073.0916 100 100
1000 3.9 -1078.0299 -1376.1109 1073.0916 100 100
1200 4.7 -1084.8934 -1382.9744 1073.0916 100 100
1400 5.5 -1082.8007 -1380.8817 1073.0916 100 100
1600 6.3 -1091.2229 -1389.3039 1073.0916 100 100
1800 7 -1089.9946 -1388.0756 1073.0916 100 100
2000 7.8 -1090.382 -1388.463 1073.0916 100 100
Loop time of 7.8121 on 4 procs for 2000 steps with 1288 atoms
Pair time (%) = 4.29234 (54.9447)
Neigh time (%) = 1.82193 (23.3219)
Comm time (%) = 0.717004 (9.17812)
Outpt time (%) = 0.00291193 (0.0372746)
Other time (%) = 0.977916 (12.518)
Nlocal: 322 ave 348 max 291 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 3287.5 ave 4022 max 2578 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 59795.5 ave 61368 max 56848 min
Histogram: 1 0 0 0 0 0 0 1 1 1
FullNghs: 119591 ave 122807 max 113769 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Total # of neighbors = 478364
Ave neighs/atom = 371.401
Neighbor list builds = 200
Dangerous builds = 0
ATC: Warning : text output can create _LARGE_ files
ATC: output custom names:
Setting up run ...
Memory usage per processor = 25.6115 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
0 0 -1090.382 -1388.463 1073.0916 100 100
100 0.43 -1087.5927 -1390.2846 1075.454 101.54684 100.25977
200 0.87 -1081.8609 -1380.2432 1075.0766 100.10105 100.30105
300 1.3 -1076.5286 -1384.5736 1077.5462 103.3427 100.56974
400 1.8 -1078.3503 -1388.7033 1083.8991 104.11699 101.14862
500 2.2 -1074.2004 -1390.3057 1091.383 106.04678 101.81783
600 2.6 -1072.5105 -1390.2059 1098.5161 106.58021 102.45902
700 3.1 -1065.5654 -1373.1988 1105.2316 103.20464 103.06686
800 3.5 -1062.4651 -1386.6034 1110.624 108.74168 103.56901
900 4 -1054.767 -1378.04 1119.5121 108.45141 104.35038
1000 4.4 -1048.6471 -1376.1878 1129.6369 109.88311 105.23054
1100 4.8 -1049.0911 -1378.9232 1137.6524 110.65183 105.94222
1200 5.3 -1048.3472 -1381.7201 1147.7652 111.83972 106.82141
1300 5.7 -1051.0343 -1380.5791 1156.3021 110.55547 107.57474
1400 6.2 -1047.5028 -1377.2009 1162.231 110.60686 108.11974
1500 6.6 -1049.3227 -1379.9459 1168.2617 110.91724 108.67288
1600 7.1 -1044.2411 -1376.4008 1172.3108 111.43272 109.06773
1700 7.5 -1041.3107 -1376.9092 1178.0968 112.58635 109.60132
1800 8 -1041.7106 -1387.1043 1185.6231 115.87242 110.27393
1900 8.4 -1032.7907 -1374.3649 1193.8935 114.59107 111.00596
2000 8.9 -1026.8551 -1378.0117 1201.8627 117.80577 111.71394
Loop time of 8.85518 on 4 procs for 2000 steps with 1288 atoms
Pair time (%) = 4.25851 (48.0906)
Neigh time (%) = 1.84167 (20.7977)
Comm time (%) = 0.61528 (6.94825)
Outpt time (%) = 0.0105819 (0.119499)
Other time (%) = 2.12913 (24.0439)
Nlocal: 322 ave 342 max 299 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Nghost: 3298.25 ave 4012 max 2561 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 59867 ave 62381 max 58653 min
Histogram: 2 0 1 0 0 0 0 0 0 1
FullNghs: 119734 ave 124715 max 117251 min
Histogram: 1 1 1 0 0 0 0 0 0 1
Total # of neighbors = 478936
Ave neighs/atom = 371.845
Neighbor list builds = 200
Dangerous builds = 0
Setting up run ...
Memory usage per processor = 25.6115 Mbytes
Step CPU TotEng PotEng AtC[1] Temp AtC[2]
2000 0 -1026.8551 -1378.0117 1201.8627 117.80577 111.71394
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 3.61161e-11
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 3.61161e-11
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 3.61161e-11
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 3.61161e-11
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.71428e-06
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 9.13519e-14
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 9.13519e-14
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 9.13519e-14
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 9.13519e-14
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.59202e-07
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.59202e-07
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.59202e-07
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 1.59202e-07
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 0.0532513
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 0.0532513
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 0.0532513
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 0.0532513
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
ATC: P3, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
ATC: P1, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
ATC: P2, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
ATC: P0, Iterative solve for lambda failed to converge after 50 iterations, final tolerance was 2.79083
terminate called after throwing an instance of 'ATC::ATC_Error'
[pharsalus:02292] *** Process received signal ***
[pharsalus:02292] Signal: Aborted (6)
[pharsalus:02292] Signal code: (-6)
terminate called after throwing an instance of 'ATC::ATC_Error'
[pharsalus:02293] *** Process received signal ***
[pharsalus:02293] Signal: Aborted (6)
[pharsalus:02293] Signal code: (-6)
terminate called after throwing an instance of 'ATC::ATC_Error'
[pharsalus:02294] *** Process received signal ***
[pharsalus:02294] Signal: Aborted (6)
[pharsalus:02294] Signal code: (-6)
terminate called after throwing an instance of 'ATC::ATC_Error'
[pharsalus:02295] *** Process received signal ***
[pharsalus:02295] Signal: Aborted (6)
[pharsalus:02295] Signal code: (-6)
ATC: P2, ERROR: CG solve did not converge, iterations: 4 residual: -nan
ATC: P3, ERROR: CG solve did not converge, iterations: 4 residual: -nan
ATC: P1, ERROR: CG solve did not converge, iterations: 4 residual: -nan
ATC: P0, ERROR: CG solve did not converge, iterations: 4 residual: -nan
[pharsalus:02295] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:02295] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:02295] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:02295] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:02295] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:02295] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:02295] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:02295] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC11end_of_stepEv+0xb0) [0x696b60]
[pharsalus:02295] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Modify11end_of_stepEv+0x79) [0x7ce489]
[pharsalus:02295] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Verlet3runEi+0x37e) [0xa756de]
[pharsalus:02295] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0x296) [0xa445b6]
[pharsalus:02295] [11] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15command_creatorINS_3RunEEEvPNS_6LAMMPSEiPPc+0x33) [0x7a1ec3]
[pharsalus:02295] [12] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0x7a7) [0x79f987]
[pharsalus:02295] [13] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
[pharsalus:02295] [14] ../../../lmp_openmpi(main+0x49) [0x7af929]
[pharsalus:02295] [15] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:02295] [16] ../../../lmp_openmpi() [0x53b429]
[pharsalus:02295] *** End of error message ***
[pharsalus:02292] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:02292] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:02292] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:02292] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:02292] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:02292] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:02292] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:02292] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC11end_of_stepEv+0xb0) [0x696b60]
[pharsalus:02292] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Modify11end_of_stepEv+0x79) [0x7ce489]
[pharsalus:02292] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Verlet3runEi+0x37e) [0xa756de]
[pharsalus:02292] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0x296) [0xa445b6]
[pharsalus:02292] [11] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15command_creatorINS_3RunEEEvPNS_6LAMMPSEiPPc+0x33) [0x7a1ec3]
[pharsalus:02292] [12] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0x7a7) [0x79f987]
[pharsalus:02292] [13] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
[pharsalus:02292] [14] ../../../lmp_openmpi(main+0x49) [0x7af929]
[pharsalus:02292] [15] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:02292] [16] ../../../lmp_openmpi() [0x53b429]
[pharsalus:02292] *** End of error message ***
[pharsalus:02293] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:02293] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:02293] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:02293] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:02293] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:02293] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:02293] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:02293] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC11end_of_stepEv+0xb0) [0x696b60]
[pharsalus:02293] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Modify11end_of_stepEv+0x79) [0x7ce489]
[pharsalus:02293] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Verlet3runEi+0x37e) [0xa756de]
[pharsalus:02293] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0x296) [0xa445b6]
[pharsalus:02293] [11] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15command_creatorINS_3RunEEEvPNS_6LAMMPSEiPPc+0x33) [0x7a1ec3]
[pharsalus:02293] [12] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0x7a7) [0x79f987]
[pharsalus:02293] [13] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
[pharsalus:02293] [14] ../../../lmp_openmpi(main+0x49) [0x7af929]
[pharsalus:02293] [15] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:02293] [16] ../../../lmp_openmpi() [0x53b429]
[pharsalus:02293] *** End of error message ***
[pharsalus:02294] [ 0] /lib64/libpthread.so.0() [0x3e7ce0f500]
[pharsalus:02294] [ 1] /lib64/libc.so.6(gsignal+0x35) [0x3e7c2328a5]
[pharsalus:02294] [ 2] /lib64/libc.so.6(abort+0x175) [0x3e7c234085]
[pharsalus:02294] [ 3] /usr/lib64/libstdc++.so.6(_ZN9__gnu_cxx27__verbose_terminate_handlerEv+0x12d) [0x3e83ebea5d]
[pharsalus:02294] [ 4] /usr/lib64/libstdc++.so.6() [0x3e83ebcbe6]
[pharsalus:02294] [ 5] /usr/lib64/libstdc++.so.6() [0x3e83ebcc13]
[pharsalus:02294] [ 6] /usr/lib64/libstdc++.so.6(__cxa_rethrow+0x46) [0x3e83ebcc96]
[pharsalus:02294] [ 7] ../../../lmp_openmpi(_ZN9LAMMPS_NS6FixATC11end_of_stepEv+0xb0) [0x696b60]
[pharsalus:02294] [ 8] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Modify11end_of_stepEv+0x79) [0x7ce489]
[pharsalus:02294] [ 9] ../../../lmp_openmpi(_ZN9LAMMPS_NS6Verlet3runEi+0x37e) [0xa756de]
[pharsalus:02294] [10] ../../../lmp_openmpi(_ZN9LAMMPS_NS3Run7commandEiPPc+0x296) [0xa445b6]
[pharsalus:02294] [11] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15command_creatorINS_3RunEEEvPNS_6LAMMPSEiPPc+0x33) [0x7a1ec3]
[pharsalus:02294] [12] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input15execute_commandEv+0x7a7) [0x79f987]
[pharsalus:02294] [13] ../../../lmp_openmpi(_ZN9LAMMPS_NS5Input4fileEv+0x63c) [0x7a196c]
[pharsalus:02294] [14] ../../../lmp_openmpi(main+0x49) [0x7af929]
[pharsalus:02294] [15] /lib64/libc.so.6(__libc_start_main+0xfd) [0x3e7c21ecdd]
[pharsalus:02294] [16] ../../../lmp_openmpi() [0x53b429]
[pharsalus:02294] *** End of error message ***
--------------------------------------------------------------------------
mpirun noticed that process rank 2 with PID 2294 on node pharsalus exited on signal 6 (Aborted).
--------------------------------------------------------------------------
|
