update log files for USER-SCAFACOS (e01ba84f) · Commits · 郑智淋 / lammps

examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.16

deleted100644 → 0

+0 −99

Original line number	Diff line number	Diff line
		LAMMPS (2 Aug 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task
		units lj
		atom_style charge

		read_data data.cloud_wall
		orthogonal box = (0 0 0) to (10 10 10)
		2 by 2 by 4 MPI processor grid
		reading atoms ...
		300 atoms

		velocity all set 0.0 0.0 0.0 mom no

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify delay 0

		fix 1 all nve


		#pair_style coul/long 3.0
		#pair_coeff * *
		#kspace_style pppm 1.0e-3

		kspace_style scafacos fmm 1.0e-3
		kspace_modify scafacos tolerance energy_rel
		kspace_modify scafacos fmm_tuning 1
		ScaFaCoS setting fmm inhomogen tuning ...

		timestep 0.005

		thermo_style custom step atoms cpu temp pe ke etotal ecoul press

		run_style verlet

		#dump simple all custom 1000 id x y z vx vy vz
		#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
		#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
		#dump_modify dmpvtk pad 7

		thermo 10
		run 100
		Setting up ScaFaCoS with solver fmm ...
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2
		ghost atom cutoff = 2
		binsize = 1, bins = 10 10 10
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair zero, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 3.313 \| 3.501 \| 3.689 Mbytes
		Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
		0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
		10 300 0.023007393 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
		20 300 0.045746088 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
		30 300 0.068123341 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
		40 300 0.090359211 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
		50 300 0.11304998 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
		60 300 0.13585806 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
		70 300 0.15867376 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
		80 300 0.18324137 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
		90 300 0.20960689 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
		100 300 0.23539281 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
		Loop time of 0.235411 on 16 procs for 100 steps with 300 atoms

		Performance: 183509.107 tau/day, 424.790 timesteps/s
		97.9% CPU use with 16 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 3.2425e-05 \| 4.4718e-05 \| 6.1274e-05 \| 0.0 \| 0.02
		Kspace \| 0.23097 \| 0.23143 \| 0.2318 \| 0.1 \| 98.31
		Neigh \| 0.00015116 \| 0.00035347 \| 0.00075746 \| 0.0 \| 0.15
		Comm \| 0.0020316 \| 0.002282 \| 0.0025339 \| 0.3 \| 0.97
		Output \| 0.00034404 \| 0.00037053 \| 0.00042701 \| 0.0 \| 0.16
		Modify \| 9.3937e-05 \| 0.00014532 \| 0.00018811 \| 0.0 \| 0.06
		Other \| \| 0.0007878 \| \| \| 0.33

		Nlocal: 18.75 ave 36 max 6 min
		Histogram: 4 3 1 0 0 1 2 1 2 2
		Nghost: 127 ave 196 max 71 min
		Histogram: 8 0 0 0 0 0 0 1 6 1
		Neighs: 153.688 ave 491 max 10 min
		Histogram: 8 1 1 1 1 1 0 0 0 3

		Total # of neighbors = 2459
		Ave neighs/atom = 8.19667
		Neighbor list builds = 15
		Dangerous builds = 0
		Total wall time: 0:00:01

examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.2

deleted100644 → 0

+0 −99

Original line number	Diff line number	Diff line
		LAMMPS (2 Aug 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task
		units lj
		atom_style charge

		read_data data.cloud_wall
		orthogonal box = (0 0 0) to (10 10 10)
		1 by 1 by 2 MPI processor grid
		reading atoms ...
		300 atoms

		velocity all set 0.0 0.0 0.0 mom no

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify delay 0

		fix 1 all nve


		#pair_style coul/long 3.0
		#pair_coeff * *
		#kspace_style pppm 1.0e-3

		kspace_style scafacos fmm 1.0e-3
		kspace_modify scafacos tolerance energy_rel
		kspace_modify scafacos fmm_tuning 1
		ScaFaCoS setting fmm inhomogen tuning ...

		timestep 0.005

		thermo_style custom step atoms cpu temp pe ke etotal ecoul press

		run_style verlet

		#dump simple all custom 1000 id x y z vx vy vz
		#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
		#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
		#dump_modify dmpvtk pad 7

		thermo 10
		run 100
		Setting up ScaFaCoS with solver fmm ...
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2
		ghost atom cutoff = 2
		binsize = 1, bins = 10 10 10
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair zero, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 3.354 \| 3.354 \| 3.355 Mbytes
		Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
		0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
		10 300 0.038181543 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
		20 300 0.076276302 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
		30 300 0.11437607 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
		40 300 0.15244293 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
		50 300 0.19081283 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
		60 300 0.22923493 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
		70 300 0.26754427 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
		80 300 0.30721259 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
		90 300 0.34865618 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
		100 300 0.39100981 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
		Loop time of 0.391022 on 2 procs for 100 steps with 300 atoms

		Performance: 110479.760 tau/day, 255.740 timesteps/s
		99.6% CPU use with 2 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 8.0109e-05 \| 8.1539e-05 \| 8.297e-05 \| 0.0 \| 0.02
		Kspace \| 0.38534 \| 0.38582 \| 0.3863 \| 0.1 \| 98.67
		Neigh \| 0.0014851 \| 0.0019699 \| 0.0024548 \| 1.1 \| 0.50
		Comm \| 0.0019314 \| 0.0020101 \| 0.0020888 \| 0.2 \| 0.51
		Output \| 0.00014496 \| 0.00017297 \| 0.00020099 \| 0.0 \| 0.04
		Modify \| 0.0005033 \| 0.00052273 \| 0.00054216 \| 0.0 \| 0.13
		Other \| \| 0.0004461 \| \| \| 0.11

		Nlocal: 150 ave 159 max 141 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Nghost: 392 ave 395 max 389 min
		Histogram: 1 0 0 0 0 0 0 0 0 1
		Neighs: 1229.5 ave 1773 max 686 min
		Histogram: 1 0 0 0 0 0 0 0 0 1

		Total # of neighbors = 2459
		Ave neighs/atom = 8.19667
		Neighbor list builds = 15
		Dangerous builds = 0
		Total wall time: 0:00:01

examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.fmm.8

deleted100644 → 0

+0 −99

Original line number	Diff line number	Diff line
		LAMMPS (2 Aug 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task
		units lj
		atom_style charge

		read_data data.cloud_wall
		orthogonal box = (0 0 0) to (10 10 10)
		2 by 2 by 2 MPI processor grid
		reading atoms ...
		300 atoms

		velocity all set 0.0 0.0 0.0 mom no

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify delay 0

		fix 1 all nve


		#pair_style coul/long 3.0
		#pair_coeff * *
		#kspace_style pppm 1.0e-3

		kspace_style scafacos fmm 1.0e-3
		kspace_modify scafacos tolerance energy_rel
		kspace_modify scafacos fmm_tuning 1
		ScaFaCoS setting fmm inhomogen tuning ...

		timestep 0.005

		thermo_style custom step atoms cpu temp pe ke etotal ecoul press

		run_style verlet

		#dump simple all custom 1000 id x y z vx vy vz
		#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
		#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
		#dump_modify dmpvtk pad 7

		thermo 10
		run 100
		Setting up ScaFaCoS with solver fmm ...
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2
		ghost atom cutoff = 2
		binsize = 1, bins = 10 10 10
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair zero, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 3.317 \| 3.317 \| 3.317 Mbytes
		Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
		0 300 0 0 0.49646402 0 0.49646402 0 0.016548801
		10 300 0.026465416 0.015455559 0.47335833 0.02310606 0.49646439 0 0.020399823
		20 300 0.057377338 0.06229069 0.40334177 0.093124582 0.49646635 0 0.032069642
		30 300 0.088356495 0.14310163 0.28254277 0.21393694 0.49647971 0 0.05220548
		40 300 0.11900806 0.52929788 0.089669015 0.79130033 0.88096934 0 0.16124903
		50 300 0.15157914 1.1963022 -0.082792461 1.7884718 1.7056794 0 0.35493462
		60 300 0.18608141 1.3928167 -0.37659239 2.082261 1.7056686 0 0.40389911
		70 300 0.21956491 1.7069009 -0.84571914 2.5518169 1.7060978 0 0.48217274
		80 300 0.24269128 15.358343 -3.368063 22.960722 19.592659 0 4.4798757
		90 300 0.26847005 42.280432 -2.1623864 63.209247 61.04686 0 12.56977
		100 300 0.29283834 41.48079 -0.89904529 62.013782 61.114736 0 12.372788
		Loop time of 0.292855 on 8 procs for 100 steps with 300 atoms

		Performance: 147513.337 tau/day, 341.466 timesteps/s
		98.4% CPU use with 8 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 4.7207e-05 \| 5.5045e-05 \| 6.9618e-05 \| 0.0 \| 0.02
		Kspace \| 0.28739 \| 0.28773 \| 0.2881 \| 0.0 \| 98.25
		Neigh \| 0.00040698 \| 0.00060901 \| 0.00082922 \| 0.0 \| 0.21
		Comm \| 0.0029533 \| 0.0031788 \| 0.0034056 \| 0.3 \| 1.09
		Output \| 0.00029063 \| 0.00030866 \| 0.00035119 \| 0.0 \| 0.11
		Modify \| 0.00018978 \| 0.00022188 \| 0.00026703 \| 0.0 \| 0.08
		Other \| \| 0.0007486 \| \| \| 0.26

		Nlocal: 37.5 ave 45 max 31 min
		Histogram: 1 1 1 1 1 0 1 0 1 1
		Nghost: 200 ave 209 max 189 min
		Histogram: 1 0 0 0 1 4 0 0 0 2
		Neighs: 307.375 ave 514 max 115 min
		Histogram: 2 1 0 1 1 0 0 0 1 2

		Total # of neighbors = 2459
		Ave neighs/atom = 8.19667
		Neighbor list builds = 15
		Dangerous builds = 0
		Total wall time: 0:00:01

examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.16

deleted100644 → 0

+0 −92

Original line number	Diff line number	Diff line
		LAMMPS (2 Aug 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task

		units lj
		atom_style charge

		read_data data.cloud_wall
		orthogonal box = (0 0 0) to (10 10 10)
		2 by 2 by 4 MPI processor grid
		reading atoms ...
		300 atoms

		velocity all set 0.0 0.0 0.0 mom no

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify delay 0

		fix 1 all nve
		kspace_style scafacos p2nfft 0.001
		kspace_modify scafacos tolerance field

		timestep 0.005

		thermo_style custom step atoms cpu temp pe ke etotal ecoul press

		run_style verlet

		#dump simple all custom 1000 id x y z vx vy vz
		#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
		#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
		#dump_modify dmpvtk pad 7

		thermo 10
		run 100
		Setting up ScaFaCoS with solver p2nfft ...
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2
		ghost atom cutoff = 2
		binsize = 1, bins = 10 10 10
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair zero, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 3.313 \| 3.501 \| 3.689 Mbytes
		Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
		0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
		10 300 0.015678644 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
		20 300 0.031283855 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
		30 300 0.046878099 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
		40 300 0.062416077 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
		50 300 0.078029871 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
		60 300 0.093806505 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
		70 300 0.1096344 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
		80 300 0.12532592 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
		90 300 0.14175463 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
		100 300 0.15838337 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
		Loop time of 0.158406 on 16 procs for 100 steps with 300 atoms

		Performance: 272716.448 tau/day, 631.288 timesteps/s
		99.4% CPU use with 16 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 2.718e-05 \| 3.7491e-05 \| 5.6744e-05 \| 0.0 \| 0.02
		Kspace \| 0.15435 \| 0.15482 \| 0.15516 \| 0.1 \| 97.74
		Neigh \| 0.00014806 \| 0.0003508 \| 0.00074744 \| 0.0 \| 0.22
		Comm \| 0.0016866 \| 0.0019967 \| 0.0023787 \| 0.5 \| 1.26
		Output \| 0.00027871 \| 0.00033027 \| 0.00038028 \| 0.0 \| 0.21
		Modify \| 8.0347e-05 \| 0.00011933 \| 0.00016522 \| 0.0 \| 0.08
		Other \| \| 0.0007506 \| \| \| 0.47

		Nlocal: 18.75 ave 33 max 6 min
		Histogram: 2 6 0 0 0 0 2 1 2 3
		Nghost: 128.875 ave 198 max 71 min
		Histogram: 7 1 0 0 0 0 0 1 5 2
		Neighs: 153.812 ave 490 max 14 min
		Histogram: 8 0 3 0 1 1 0 0 1 2

		Total # of neighbors = 2461
		Ave neighs/atom = 8.20333
		Neighbor list builds = 15
		Dangerous builds = 0
		Total wall time: 0:00:00

examples/USER/scafacos/log.08Aug18.scafacos.cw.g++.p2nfft.8

deleted100644 → 0

+0 −92

Original line number	Diff line number	Diff line
		LAMMPS (2 Aug 2018)
		OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
		using 1 OpenMP thread(s) per MPI task

		units lj
		atom_style charge

		read_data data.cloud_wall
		orthogonal box = (0 0 0) to (10 10 10)
		2 by 2 by 2 MPI processor grid
		reading atoms ...
		300 atoms

		velocity all set 0.0 0.0 0.0 mom no

		pair_style zero 1.0
		pair_coeff * *

		neighbor 1.0 bin
		neigh_modify delay 0

		fix 1 all nve
		kspace_style scafacos p2nfft 0.001
		kspace_modify scafacos tolerance field

		timestep 0.005

		thermo_style custom step atoms cpu temp pe ke etotal ecoul press

		run_style verlet

		#dump simple all custom 1000 id x y z vx vy vz
		#dump dmp all custom 1000 part.dump id mol x y z vx vy vz fx fy fz q mass
		#dump dmpvtk all vtk 1000 vtk/part_*.vtk id mol x y z vx vy vz fx fy fz q mass
		#dump_modify dmpvtk pad 7

		thermo 10
		run 100
		Setting up ScaFaCoS with solver p2nfft ...
		Neighbor list info ...
		update every 1 steps, delay 0 steps, check yes
		max neighbors/atom: 2000, page size: 100000
		master list distance cutoff = 2
		ghost atom cutoff = 2
		binsize = 1, bins = 10 10 10
		1 neighbor lists, perpetual/occasional/extra = 1 0 0
		(1) pair zero, perpetual
		attributes: half, newton on
		pair build: half/bin/atomonly/newton
		stencil: half/bin/3d/newton
		bin: standard
		Per MPI rank memory allocation (min/avg/max) = 3.317 \| 3.317 \| 3.317 Mbytes
		Step Atoms CPU Temp PotEng KinEng TotEng E_coul Press
		0 300 0 0 0.49683273 0 0.49683273 0 0.016561091
		10 300 0.01961565 0.015479312 0.47369009 0.023141571 0.49683166 0 0.020417984
		20 300 0.039346695 0.062386358 0.40356181 0.093267605 0.49682941 0 0.032105581
		30 300 0.059037447 0.14331637 0.2825636 0.21425798 0.49682157 0 0.052270382
		40 300 0.078732729 0.53041843 0.089505208 0.79297556 0.88248077 0 0.16157862
		50 300 0.098586798 1.1948397 -0.083317439 1.7862853 1.7029679 0 0.35447982
		60 300 0.11857247 1.3915614 -0.37745551 2.0803842 1.7029287 0 0.40349499
		70 300 0.1385541 1.7061978 -0.84746071 2.5507657 1.703305 0 0.48190445
		80 300 0.15850091 20.692093 -3.32971 30.93468 27.60497 0 6.0759456
		90 300 0.17892075 48.999403 -2.1632167 73.254107 71.090891 0 14.578714
		100 300 0.19964767 51.199785 -0.81127924 76.543678 75.732399 0 15.281693
		Loop time of 0.199664 on 8 procs for 100 steps with 300 atoms

		Performance: 216363.074 tau/day, 500.840 timesteps/s
		99.4% CPU use with 8 MPI tasks x 1 OpenMP threads

		MPI task timing breakdown:
		Section \| min time \| avg time \| max time \|%varavg\| %total
		---------------------------------------------------------------
		Pair \| 4.5061e-05 \| 4.7535e-05 \| 5.3167e-05 \| 0.0 \| 0.02
		Kspace \| 0.19551 \| 0.19584 \| 0.19611 \| 0.0 \| 98.08
		Neigh \| 0.00041366 \| 0.00060952 \| 0.00082064 \| 0.0 \| 0.31
		Comm \| 0.0021496 \| 0.0022282 \| 0.0024025 \| 0.2 \| 1.12
		Output \| 0.0002346 \| 0.00024167 \| 0.00027847 \| 0.0 \| 0.12
		Modify \| 0.00016665 \| 0.00017652 \| 0.0001924 \| 0.0 \| 0.09
		Other \| \| 0.0005245 \| \| \| 0.26

		Nlocal: 37.5 ave 42 max 33 min
		Histogram: 2 1 0 1 0 0 1 0 1 2
		Nghost: 202.25 ave 212 max 194 min
		Histogram: 1 0 2 1 0 2 0 1 0 1
		Neighs: 307.625 ave 505 max 129 min
		Histogram: 3 0 0 1 1 0 0 0 1 2

		Total # of neighbors = 2461
		Ave neighs/atom = 8.20333
		Neighbor list builds = 15
		Dangerous builds = 0
		Total wall time: 0:00:00

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