LAMMPS (31 Aug 2021) Reading data file ... orthogonal box = (-0.75841574 -0.81445865 -0.73597454) to (31.771384 31.715341 31.793825) 2 by 4 by 7 MPI processor grid reading atoms ... 3216 atoms scanning bonds ... 4 = max bonds/atom scanning angles ... 6 = max angles/atom reading bonds ... 2144 bonds reading angles ... 1216 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 = 0.004 seconds read_data CPU = 0.032 seconds Finding SHAKE clusters ... 0 = # of size 2 clusters 0 = # of size 3 clusters 0 = # of size 4 clusters 1000 = # of frozen angles find clusters CPU = 0.003 seconds Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/cut, 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 : 1 SHAKE stats (type/ave/delta/count) on step 0 1 1.03814 1.93928 3000 1 98.5500 107.289 1000 Per MPI rank memory allocation (min/avg/max) = 9.212 | 9.227 | 9.236 Mbytes Step Temp E_pair E_mol TotEng Press 0 435.44018 -34950.397 2675.3249 -29400.081 26635.63 SHAKE stats (type/ave/delta/count) on step 10 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 20 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 30 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 40 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 50 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 60 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 70 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 80 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 90 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 SHAKE stats (type/ave/delta/count) on step 100 1 1.00001 0.000386456 3000 1 109.468 0.0609568 1000 100 435.44018 -33951.062 2675.3249 -28400.746 27341.272 Loop time of 0.0895699 on 56 procs for 100 steps with 3216 atoms Performance: 96.461 ns/day, 0.249 hours/ns, 1116.447 timesteps/s 100.4% CPU use with 56 MPI tasks x no OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.015334 | 0.028605 | 0.049968 | 4.5 | 31.94 Bond | 1.0967e-05 | 7.0014e-05 | 0.00022316 | 0.0 | 0.08 Neigh | 0.0013478 | 0.0013921 | 0.0014439 | 0.1 | 1.55 Comm | 0.017979 | 0.038737 | 0.051631 | 3.7 | 43.25 Output | 5.6982e-05 | 6.6268e-05 | 7.6056e-05 | 0.0 | 0.07 Modify | 0.013738 | 0.016618 | 0.018358 | 0.7 | 18.55 Other | | 0.004082 | | | 4.56 Nlocal: 57.4286 ave 74 max 36 min Histogram: 2 2 2 7 4 13 8 13 2 3 Nghost: 3442.11 ave 3622 max 3347 min Histogram: 2 14 15 13 4 0 0 0 1 7 Neighs: 19515.7 ave 25961 max 11291 min Histogram: 4 1 4 4 11 6 10 6 5 5 Total # of neighbors = 1092881 Ave neighs/atom = 339.82618 Ave special neighs/atom = 2.0895522 Neighbor list builds = 1 Dangerous builds = 1 System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin stencil: full/bin/3d bin: standard (2) pair lj/cut/coul/cut, perpetual attributes: half, newton on pair build: half/bin/newton stencil: half/bin/3d bin: standard WARNING: Ignoring 'compress yes' for molecular system (../delete_atoms.cpp:126) Deleted 0 atoms, new total = 3216 Deleted 0 bonds, new total = 2144 Deleted 0 angles, new total = 1216 Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 6 6 6 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair lj/cut/coul/cut, 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 : 1 Per MPI rank memory allocation (min/avg/max) = 9.593 | 9.608 | 9.616 Mbytes Step Temp PotEng KinEng TotEng 0 300 -31275.737 2874.9913 -28400.746 1 361.0347 -31456.802 3459.9054 -27996.896 2 538.13671 -32726.855 5157.1278 -27569.727 3 824.30608 -35645.726 7899.576 -27746.15 4 1215.2459 -41436.794 11646.071 -29790.724 5 1718.2922 -46568.462 16466.917 -30101.545 6 2371.9729 -54405.468 22731.338 -31674.13 7 3356.0738 -62598.02 32162.276 -30435.743 8 74292.513 -81950.499 711967.76 630017.26 ERROR on proc 47: Bond atoms 775 777 missing on proc 47 at step 9 (../ntopo_bond_all.cpp:61) srun: Job step aborted: Waiting up to 32 seconds for job step to finish. slurmstepd: error: *** STEP 13895040.0 ON cn1143 CANCELLED AT 2024-11-26T17:18:58 *** application called MPI_Abort(MPI_COMM_WORLD, 1) - process 47 srun: error: cn1143: tasks 0-27: Killed srun: error: cn1144: tasks 28-55: Killed