Loading examples/USER/plumed/log.24Oct18.peptide-plumed.g++.1→examples/USER/plumed/log.27Nov18.peptide-plumed.g++.1 +14 −15 Original line number Diff line number Diff line LAMMPS (24 Oct 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading Loading @@ -78,7 +77,7 @@ variable pe equal pe run 101 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading Loading @@ -107,7 +106,7 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.74 | 18.74 | 18.74 Mbytes Step Temp TotEng PotEng KinEng E_pair E_bond f_2 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0 10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504 Loading @@ -130,22 +129,22 @@ SHAKE stats (type/ave/delta) on step 100 31 104.52 0.000760401 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372 101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332 Loop time of 2.12948 on 1 procs for 101 steps with 2004 atoms Loop time of 2.73445 on 1 procs for 101 steps with 2004 atoms Performance: 8.196 ns/day, 2.928 hours/ns, 47.429 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 6.383 ns/day, 3.760 hours/ns, 36.936 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.757 | 1.757 | 1.757 | 0.0 | 82.51 Bond | 0.0052233 | 0.0052233 | 0.0052233 | 0.0 | 0.25 Kspace | 0.14772 | 0.14772 | 0.14772 | 0.0 | 6.94 Neigh | 0.16455 | 0.16455 | 0.16455 | 0.0 | 7.73 Comm | 0.0083704 | 0.0083704 | 0.0083704 | 0.0 | 0.39 Output | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.01 Modify | 0.044411 | 0.044411 | 0.044411 | 0.0 | 2.09 Other | | 0.001851 | | | 0.09 Pair | 2.2617 | 2.2617 | 2.2617 | 0.0 | 82.71 Bond | 0.0044148 | 0.0044148 | 0.0044148 | 0.0 | 0.16 Kspace | 0.17883 | 0.17883 | 0.17883 | 0.0 | 6.54 Neigh | 0.23945 | 0.23945 | 0.23945 | 0.0 | 8.76 Comm | 0.011672 | 0.011672 | 0.011672 | 0.0 | 0.43 Output | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.01 Modify | 0.0365 | 0.0365 | 0.0365 | 0.0 | 1.33 Other | | 0.001611 | | | 0.06 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading examples/USER/plumed/log.24Oct18.peptide-plumed.g++.4→examples/USER/plumed/log.27Nov18.peptide-plumed.g++.4 +17 −18 Original line number Diff line number Diff line LAMMPS (24 Oct 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading Loading @@ -78,7 +77,7 @@ variable pe equal pe run 101 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading Loading @@ -107,7 +106,7 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.87 | 16.06 Mbytes Step Temp TotEng PotEng KinEng E_pair E_bond f_2 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0 10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504 Loading @@ -118,7 +117,7 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2 60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815 70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896 80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348 90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3466 21.124789 0.5468014 90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014 SHAKE stats (type/ave/delta) on step 100 4 1.111 2.06868e-06 6 0.996999 2.09521e-06 Loading @@ -128,24 +127,24 @@ SHAKE stats (type/ave/delta) on step 100 14 0.959999 0 18 0.9572 9.14098e-06 31 104.52 0.000760401 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.009478437 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372 101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332 Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms Loop time of 0.812799 on 4 procs for 101 steps with 2004 atoms Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s 97.8% CPU use with 4 MPI tasks x 1 OpenMP threads Performance: 21.472 ns/day, 1.118 hours/ns, 124.262 timesteps/s 97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84633 | 0.86651 | 0.88617 | 1.6 | 74.21 Bond | 0.0010614 | 0.0027132 | 0.004288 | 3.0 | 0.23 Kspace | 0.095008 | 0.1162 | 0.13491 | 4.3 | 9.95 Neigh | 0.07834 | 0.078424 | 0.078516 | 0.0 | 6.72 Comm | 0.03314 | 0.033299 | 0.033426 | 0.1 | 2.85 Output | 0.00036979 | 0.00076199 | 0.0019338 | 0.0 | 0.07 Modify | 0.063471 | 0.064011 | 0.065312 | 0.3 | 5.48 Other | | 0.005751 | | | 0.49 Pair | 0.57957 | 0.59988 | 0.62504 | 2.6 | 73.80 Bond | 0.00080013 | 0.0017412 | 0.0028315 | 2.1 | 0.21 Kspace | 0.075724 | 0.10008 | 0.12023 | 6.4 | 12.31 Neigh | 0.067733 | 0.067947 | 0.068168 | 0.1 | 8.36 Comm | 0.01375 | 0.014175 | 0.014681 | 0.3 | 1.74 Output | 0.00025511 | 0.00051183 | 0.001277 | 0.0 | 0.06 Modify | 0.026406 | 0.026436 | 0.026462 | 0.0 | 3.25 Other | | 0.002027 | | | 0.25 Nlocal: 501 ave 512 max 492 min Histogram: 1 0 0 1 0 1 0 0 0 1 Loading @@ -159,4 +158,4 @@ Ave neighs/atom = 353.274 Ave special neighs/atom = 2.34032 Neighbor list builds = 8 Dangerous builds = 0 Total wall time: 0:00:01 Total wall time: 0:00:00 Loading
examples/USER/plumed/log.24Oct18.peptide-plumed.g++.1→examples/USER/plumed/log.27Nov18.peptide-plumed.g++.1 +14 −15 Original line number Diff line number Diff line LAMMPS (24 Oct 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading Loading @@ -78,7 +77,7 @@ variable pe equal pe run 101 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading Loading @@ -107,7 +106,7 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Per MPI rank memory allocation (min/avg/max) = 18.7 | 18.7 | 18.7 Mbytes Per MPI rank memory allocation (min/avg/max) = 18.74 | 18.74 | 18.74 Mbytes Step Temp TotEng PotEng KinEng E_pair E_bond f_2 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0 10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504 Loading @@ -130,22 +129,22 @@ SHAKE stats (type/ave/delta) on step 100 31 104.52 0.000760401 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372 101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332 Loop time of 2.12948 on 1 procs for 101 steps with 2004 atoms Loop time of 2.73445 on 1 procs for 101 steps with 2004 atoms Performance: 8.196 ns/day, 2.928 hours/ns, 47.429 timesteps/s 99.8% CPU use with 1 MPI tasks x 1 OpenMP threads Performance: 6.383 ns/day, 3.760 hours/ns, 36.936 timesteps/s 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 1.757 | 1.757 | 1.757 | 0.0 | 82.51 Bond | 0.0052233 | 0.0052233 | 0.0052233 | 0.0 | 0.25 Kspace | 0.14772 | 0.14772 | 0.14772 | 0.0 | 6.94 Neigh | 0.16455 | 0.16455 | 0.16455 | 0.0 | 7.73 Comm | 0.0083704 | 0.0083704 | 0.0083704 | 0.0 | 0.39 Output | 0.00031424 | 0.00031424 | 0.00031424 | 0.0 | 0.01 Modify | 0.044411 | 0.044411 | 0.044411 | 0.0 | 2.09 Other | | 0.001851 | | | 0.09 Pair | 2.2617 | 2.2617 | 2.2617 | 0.0 | 82.71 Bond | 0.0044148 | 0.0044148 | 0.0044148 | 0.0 | 0.16 Kspace | 0.17883 | 0.17883 | 0.17883 | 0.0 | 6.54 Neigh | 0.23945 | 0.23945 | 0.23945 | 0.0 | 8.76 Comm | 0.011672 | 0.011672 | 0.011672 | 0.0 | 0.43 Output | 0.00028348 | 0.00028348 | 0.00028348 | 0.0 | 0.01 Modify | 0.0365 | 0.0365 | 0.0365 | 0.0 | 1.33 Other | | 0.001611 | | | 0.06 Nlocal: 2004 ave 2004 max 2004 min Histogram: 1 0 0 0 0 0 0 0 0 0 Loading
examples/USER/plumed/log.24Oct18.peptide-plumed.g++.4→examples/USER/plumed/log.27Nov18.peptide-plumed.g++.4 +17 −18 Original line number Diff line number Diff line LAMMPS (24 Oct 2018) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:87) LAMMPS (27 Nov 2018) using 1 OpenMP thread(s) per MPI task # Solvated 5-mer peptide Loading Loading @@ -78,7 +77,7 @@ variable pe equal pe run 101 PPPM initialization ... using 12-bit tables for long-range coulomb (../kspace.cpp:321) using 12-bit tables for long-range coulomb (src/kspace.cpp:321) G vector (1/distance) = 0.268725 grid = 15 15 15 stencil order = 5 Loading Loading @@ -107,7 +106,7 @@ SHAKE stats (type/ave/delta) on step 0 14 0.96 0 18 0.957206 4.37979e-05 31 104.519 0.00396029 Per MPI rank memory allocation (min/avg/max) = 15.65 | 15.86 | 16.05 Mbytes Per MPI rank memory allocation (min/avg/max) = 15.66 | 15.87 | 16.06 Mbytes Step Temp TotEng PotEng KinEng E_pair E_bond f_2 0 282.10052 -5237.458 -6372.3766 1134.9186 -6442.768 16.557152 0 10 276.9783 -5234.3057 -6348.6171 1114.3114 -6421.6171 17.024361 0.47785504 Loading @@ -118,7 +117,7 @@ Step Temp TotEng PotEng KinEng E_pair E_bond f_2 60 273.01449 -5217.7381 -6316.1026 1098.3646 -6406.4709 21.800931 0.92327815 70 274.67549 -5221.0246 -6326.0716 1105.047 -6409.7721 19.41235 0.0016975896 80 273.74824 -5224.7613 -6326.0778 1101.3165 -6418.5055 19.206793 0.48550348 90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3466 21.124789 0.5468014 90 284.32594 -5229.195 -6373.0667 1143.8717 -6461.3467 21.124789 0.5468014 SHAKE stats (type/ave/delta) on step 100 4 1.111 2.06868e-06 6 0.996999 2.09521e-06 Loading @@ -128,24 +127,24 @@ SHAKE stats (type/ave/delta) on step 100 14 0.959999 0 18 0.9572 9.14098e-06 31 104.52 0.000760401 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.009478437 100 270.40648 -5234.9604 -6322.8327 1087.8723 -6417.73 19.666404 0.0094784372 101 270.99811 -5235.8295 -6326.082 1090.2525 -6418.8974 17.285816 0.086681332 Loop time of 1.16767 on 4 procs for 101 steps with 2004 atoms Loop time of 0.812799 on 4 procs for 101 steps with 2004 atoms Performance: 14.947 ns/day, 1.606 hours/ns, 86.497 timesteps/s 97.8% CPU use with 4 MPI tasks x 1 OpenMP threads Performance: 21.472 ns/day, 1.118 hours/ns, 124.262 timesteps/s 97.5% CPU use with 4 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.84633 | 0.86651 | 0.88617 | 1.6 | 74.21 Bond | 0.0010614 | 0.0027132 | 0.004288 | 3.0 | 0.23 Kspace | 0.095008 | 0.1162 | 0.13491 | 4.3 | 9.95 Neigh | 0.07834 | 0.078424 | 0.078516 | 0.0 | 6.72 Comm | 0.03314 | 0.033299 | 0.033426 | 0.1 | 2.85 Output | 0.00036979 | 0.00076199 | 0.0019338 | 0.0 | 0.07 Modify | 0.063471 | 0.064011 | 0.065312 | 0.3 | 5.48 Other | | 0.005751 | | | 0.49 Pair | 0.57957 | 0.59988 | 0.62504 | 2.6 | 73.80 Bond | 0.00080013 | 0.0017412 | 0.0028315 | 2.1 | 0.21 Kspace | 0.075724 | 0.10008 | 0.12023 | 6.4 | 12.31 Neigh | 0.067733 | 0.067947 | 0.068168 | 0.1 | 8.36 Comm | 0.01375 | 0.014175 | 0.014681 | 0.3 | 1.74 Output | 0.00025511 | 0.00051183 | 0.001277 | 0.0 | 0.06 Modify | 0.026406 | 0.026436 | 0.026462 | 0.0 | 3.25 Other | | 0.002027 | | | 0.25 Nlocal: 501 ave 512 max 492 min Histogram: 1 0 0 1 0 1 0 0 0 1 Loading @@ -159,4 +158,4 @@ Ave neighs/atom = 353.274 Ave special neighs/atom = 2.34032 Neighbor list builds = 8 Dangerous builds = 0 Total wall time: 0:00:01 Total wall time: 0:00:00
