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git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@3693 f3b2605a-c512-4ea7-a41b-209d697bcdaa

This commit is contained in:
sjplimp 2010-01-14 23:36:49 +00:00
parent 6e8ccfb7f9
commit b69ece12b2
17 changed files with 196 additions and 191 deletions
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1
bench/in.chute
View File

@ -5,6 +5,7 @@ units lj
atom_style granular
boundary p p fs
newton off
communicate single vel yes
read_data data.chute

1
bench/in.chute.scaled
View File

@ -8,6 +8,7 @@ units lj
atom_style granular
boundary p p fs
newton off
communicate single vel yes
read_data data.chute

26
bench/log.7Jul09.chain.fixed.linux.1 → bench/log.15Jan10.chain.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# FENE beadspring benchmark
units lj
@ -35,25 +35,25 @@ run 100
Memory usage per processor = 8.37288 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.97434451 0.439712 20.499596 22.400779 4.6558589
Loop time of 1.95257 on 1 procs for 100 steps with 32000 atoms
100 0.9729966 0.4361122 20.507698 22.40326 4.6548819
Loop time of 1.90831 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 0.495523 (25.3779)
Bond time (%) = 0.247278 (12.6642)
Neigh time (%) = 0.74267 (38.0354)
Comm time (%) = 0.0562346 (2.88002)
Outpt time (%) = 0.000204802 (0.0104888)
Other time (%) = 0.410665 (21.0319)
Pair time (%) = 0.441165 (23.118)
Bond time (%) = 0.289828 (15.1876)
Neigh time (%) = 0.70849 (37.1265)
Comm time (%) = 0.057091 (2.9917)
Outpt time (%) = 0.000185966 (0.00974507)
Other time (%) = 0.411554 (21.5664)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 9537 ave 9537 max 9537 min
Nghost: 9493 ave 9493 max 9493 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 155877 ave 155877 max 155877 min
Neighs: 155873 ave 155873 max 155873 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 155877
Ave neighs/atom = 4.87116
Total # of neighbors = 155873
Ave neighs/atom = 4.87103
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0

32
bench/log.7Jul09.chain.fixed.linux.4 → bench/log.15Jan10.chain.fixed.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# FENE beadspring benchmark
units lj
@ -35,25 +35,25 @@ run 100
Memory usage per processor = 3.56846 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97029772 0.44484087 20.494523 22.394765 4.6721833
100 0.96717514 0.4422441 20.503712 22.396674 4.6686541
Loop time of 0.512345 on 4 procs for 100 steps with 32000 atoms
100 0.97145835 0.43803883 20.502691 22.397872 4.626988
Loop time of 0.503127 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.086697 (16.9216)
Bond time (%) = 0.0585724 (11.4322)
Neigh time (%) = 0.164889 (32.1832)
Comm time (%) = 0.0972116 (18.9739)
Outpt time (%) = 0.000659764 (0.128773)
Other time (%) = 0.104315 (20.3603)
Pair time (%) = 0.0849311 (16.8807)
Bond time (%) = 0.0588253 (11.6919)
Neigh time (%) = 0.164552 (32.7059)
Comm time (%) = 0.0952742 (18.9364)
Outpt time (%) = 0.000495017 (0.098388)
Other time (%) = 0.0990493 (19.6867)
Nlocal: 8000 ave 8024 max 7973 min
Histogram: 1 0 0 1 0 0 0 1 0 1
Nghost: 4169 ave 4212 max 4141 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Neighs: 38936.2 ave 39212 max 38690 min
Nlocal: 8000 ave 8030 max 7974 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 4177 ave 4191 max 4160 min
Histogram: 1 0 0 0 1 0 0 1 0 1
Neighs: 38995.8 ave 39169 max 38852 min
Histogram: 1 0 0 1 1 0 0 0 0 1
Total # of neighbors = 155745
Ave neighs/atom = 4.86703
Total # of neighbors = 155983
Ave neighs/atom = 4.87447
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0

34
bench/log.7Jul09.chain.scaled.linux.4 → bench/log.15Jan10.chain.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# FENE beadspring benchmark
variable x index 1
@ -51,25 +51,25 @@ run 100
Memory usage per processor = 10.0339 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0.97027498 0.44484087 20.494523 22.394765 4.6721833
100 0.97400897 0.44134715 20.501052 22.403401 4.6879813
Loop time of 2.50467 on 4 procs for 100 steps with 128000 atoms
100 0.97682955 0.44239968 20.500229 22.407862 4.6527025
Loop time of 2.54416 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 0.519511 (20.7417)
Bond time (%) = 0.265748 (10.6101)
Neigh time (%) = 0.7827 (31.2497)
Comm time (%) = 0.310183 (12.3842)
Outpt time (%) = 0.000760198 (0.0303512)
Other time (%) = 0.625765 (24.984)
Pair time (%) = 0.515168 (20.2491)
Bond time (%) = 0.346376 (13.6146)
Neigh time (%) = 0.768115 (30.1914)
Comm time (%) = 0.288478 (11.3388)
Outpt time (%) = 0.000588775 (0.0231422)
Other time (%) = 0.62543 (24.583)
Nlocal: 32000 ave 32015 max 31986 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Nghost: 9499 ave 9524 max 9446 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Neighs: 155798 ave 156103 max 155422 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Nlocal: 32000 ave 32015 max 31983 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 9492 ave 9522 max 9432 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Neighs: 155837 ave 156079 max 155506 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 623193
Ave neighs/atom = 4.8687
Total # of neighbors = 623349
Ave neighs/atom = 4.86991
Ave special neighs/atom = 1.98
Neighbor list builds = 25
Dangerous builds = 0

15
bench/log.7Jul09.chute.fixed.linux.1 → bench/log.15Jan10.chute.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -6,6 +6,7 @@ units lj
atom_style granular
boundary p p fs
newton off
communicate single vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
@ -41,13 +42,13 @@ Memory usage per processor = 33.1524 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 1.83466 on 1 procs for 100 steps with 32000 atoms
Loop time of 1.64068 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 1.07154 (58.4054)
Neigh time (%) = 0.0848379 (4.62418)
Comm time (%) = 0.0990076 (5.39652)
Outpt time (%) = 0.000552893 (0.030136)
Other time (%) = 0.578721 (31.5438)
Pair time (%) = 0.911779 (55.5732)
Neigh time (%) = 0.0715709 (4.36227)
Comm time (%) = 0.0714557 (4.35525)
Outpt time (%) = 0.00057888 (0.0352829)
Other time (%) = 0.585296 (35.674)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

15
bench/log.7Jul09.chute.fixed.linux.4 → bench/log.15Jan10.chute.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -6,6 +6,7 @@ units lj
atom_style granular
boundary p p fs
newton off
communicate single vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
@ -41,13 +42,13 @@ Memory usage per processor = 14.5608 Mbytes
Step Atoms KinEng 1 Volume
0 32000 784139.13 1601.1263 29830.88
100 32000 784289.99 1571.0137 29831.804
Loop time of 0.35031 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.325478 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.163634 (46.7111)
Neigh time (%) = 0.0193962 (5.53688)
Comm time (%) = 0.0654779 (18.6914)
Outpt time (%) = 0.000428259 (0.122251)
Other time (%) = 0.101374 (28.9383)
Pair time (%) = 0.14207 (43.6497)
Neigh time (%) = 0.0174815 (5.37102)
Comm time (%) = 0.0710311 (21.8236)
Outpt time (%) = 0.000512004 (0.157308)
Other time (%) = 0.0943834 (28.9984)
Nlocal: 8000 ave 8010 max 7990 min
Histogram: 2 0 0 0 0 0 0 0 0 2

15
bench/log.7Jul09.chute.scaled.linux.4 → bench/log.15Jan10.chute.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# LAMMPS benchmark of granular flow
# chute flow of 32000 atoms with frozen base at 26 degrees
@ -9,6 +9,7 @@ units lj
atom_style granular
boundary p p fs
newton off
communicate single vel yes
read_data data.chute
orthogonal box = (0 0 0) to (40 20 37.2886)
@ -51,13 +52,13 @@ Memory usage per processor = 35.1222 Mbytes
Step Atoms KinEng 1 Volume
0 128000 3136556.5 6404.5051 119323.52
100 128000 3137160 6284.0549 119327.22
Loop time of 3.28694 on 4 procs for 100 steps with 128000 atoms
Loop time of 2.84721 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 1.53495 (46.6984)
Neigh time (%) = 0.0888193 (2.70219)
Comm time (%) = 0.299754 (9.11955)
Outpt time (%) = 0.00184703 (0.056193)
Other time (%) = 1.36157 (41.4237)
Pair time (%) = 1.14766 (40.3083)
Neigh time (%) = 0.0711539 (2.49907)
Comm time (%) = 0.270077 (9.48566)
Outpt time (%) = 0.00183529 (0.0644591)
Other time (%) = 1.35648 (47.6425)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0

14
bench/log.7Jul09.eam.fixed.linux.1 → bench/log.15Jan10.eam.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# bulk Cu lattice
variable x index 1
@ -46,13 +46,13 @@ Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 11.5745 on 1 procs for 100 steps with 32000 atoms
Loop time of 11.3292 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 10.4086 (89.9269)
Neigh time (%) = 0.889291 (7.68321)
Comm time (%) = 0.0718732 (0.620963)
Outpt time (%) = 0.000457048 (0.00394876)
Other time (%) = 0.204283 (1.76494)
Pair time (%) = 10.1802 (89.8578)
Neigh time (%) = 0.86976 (7.67717)
Comm time (%) = 0.0717678 (0.633477)
Outpt time (%) = 0.00044179 (0.00389957)
Other time (%) = 0.207053 (1.82761)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

14
bench/log.7Jul09.eam.fixed.linux.4 → bench/log.15Jan10.eam.fixed.linux.4
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# bulk Cu lattice
variable x index 1
@ -46,13 +46,13 @@ Step Temp E_pair E_mol TotEng Press
0 1600 -113280 0 -106662.09 18703.573
50 781.69049 -109873.35 0 -106640.13 52273.088
100 801.832 -109957.3 0 -106640.77 51322.821
Loop time of 2.96338 on 4 procs for 100 steps with 32000 atoms
Loop time of 2.93381 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 2.53685 (85.6066)
Neigh time (%) = 0.219971 (7.42296)
Comm time (%) = 0.154123 (5.20092)
Outpt time (%) = 0.000876784 (0.0295873)
Other time (%) = 0.0515609 (1.73993)
Pair time (%) = 2.51382 (85.6844)
Neigh time (%) = 0.215437 (7.34327)
Comm time (%) = 0.150149 (5.1179)
Outpt time (%) = 0.000872076 (0.029725)
Other time (%) = 0.053533 (1.82469)
Nlocal: 8000 ave 8008 max 7993 min
Histogram: 2 0 0 0 0 0 0 0 1 1

14
bench/log.7Jul09.eam.scaled.linux.4 → bench/log.15Jan10.eam.scaled.linux.4
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# bulk Cu lattice
variable x index 1
@ -46,13 +46,13 @@ Step Temp E_pair E_mol TotEng Press
0 1600 -453120 0 -426647.73 18704.012
50 779.50001 -439457.02 0 -426560.06 52355.276
100 797.97828 -439764.76 0 -426562.07 51474.74
Loop time of 12.4247 on 4 procs for 100 steps with 128000 atoms
Loop time of 12.2389 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 10.5913 (85.2435)
Neigh time (%) = 0.973452 (7.83479)
Comm time (%) = 0.387031 (3.11501)
Outpt time (%) = 0.00141603 (0.0113968)
Other time (%) = 0.471551 (3.79526)
Pair time (%) = 10.4368 (85.2756)
Neigh time (%) = 0.957641 (7.82459)
Comm time (%) = 0.379168 (3.09807)
Outpt time (%) = 0.00148249 (0.0121129)
Other time (%) = 0.463806 (3.78962)
Nlocal: 32000 ave 32092 max 31914 min
Histogram: 1 0 0 1 0 1 0 0 0 1

14
bench/log.7Jul09.lj.fixed.linux.1 → bench/log.15Jan10.lj.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# 3d Lennard-Jones melt
variable x index 1
@ -43,13 +43,13 @@ Memory usage per processor = 11.5405 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 4.30574 on 1 procs for 100 steps with 32000 atoms
Loop time of 4.23086 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 3.70556 (86.0608)
Neigh time (%) = 0.367506 (8.53526)
Comm time (%) = 0.0611093 (1.41925)
Outpt time (%) = 0.00022912 (0.00532127)
Other time (%) = 0.17134 (3.97933)
Pair time (%) = 3.6458 (86.1715)
Neigh time (%) = 0.356836 (8.43412)
Comm time (%) = 0.0593712 (1.40329)
Outpt time (%) = 0.000228167 (0.00539291)
Other time (%) = 0.16863 (3.98571)
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

14
bench/log.7Jul09.lj.fixed.linux.4 → bench/log.15Jan10.lj.fixed.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# 3d Lennard-Jones melt
variable x index 1
@ -43,13 +43,13 @@ Memory usage per processor = 3.77112 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6134356 -5.0197073
100 0.7574531 -5.7585055 0 -4.6223613 0.20726105
Loop time of 1.12725 on 4 procs for 100 steps with 32000 atoms
Loop time of 1.12234 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 0.86119 (76.3972)
Neigh time (%) = 0.0883378 (7.83655)
Comm time (%) = 0.144409 (12.8106)
Outpt time (%) = 0.000439525 (0.0389907)
Other time (%) = 0.0328775 (2.9166)
Pair time (%) = 0.862278 (76.8285)
Neigh time (%) = 0.0890406 (7.93347)
Comm time (%) = 0.138258 (12.3187)
Outpt time (%) = 0.000519693 (0.0463043)
Other time (%) = 0.0322458 (2.87308)
Nlocal: 8000 ave 8037 max 7964 min
Histogram: 2 0 0 0 0 0 0 0 1 1

14
bench/log.7Jul09.lj.scaled.linux.4 → bench/log.15Jan10.lj.scaled.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# 3d Lennard-Jones melt
variable x index 1
@ -43,13 +43,13 @@ Memory usage per processor = 11.4634 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.44 -6.7733681 0 -4.6133849 -5.0196788
100 0.75841891 -5.759957 0 -4.6223375 0.20008866
Loop time of 4.81151 on 4 procs for 100 steps with 128000 atoms
Loop time of 4.80026 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 3.71749 (77.2624)
Neigh time (%) = 0.35352 (7.34738)
Comm time (%) = 0.339438 (7.0547)
Outpt time (%) = 0.000727534 (0.0151207)
Other time (%) = 0.400338 (8.32042)
Pair time (%) = 3.70192 (77.1193)
Neigh time (%) = 0.349664 (7.28428)
Comm time (%) = 0.353153 (7.35695)
Outpt time (%) = 0.000678301 (0.0141305)
Other time (%) = 0.394836 (8.2253)
Nlocal: 32000 ave 32060 max 31939 min
Histogram: 1 0 1 0 0 0 0 1 0 1

54
bench/log.7Jul09.rhodo.fixed.linux.1 → bench/log.15Jan10.rhodo.fixed.linux.1
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@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# Rhodopsin model
units real
@ -53,35 +53,35 @@ PPPM initialization ...
brick FFT buffer size/proc = 41070 25600 12321
Memory usage per processor = 124.369 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742
TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
Volume = 307995.0335
---------------- Step 50 ----- CPU = 37.3203 (sec) ----------------
TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229
PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978
E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861
E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633
Volume = 308031.6776
---------------- Step 100 ----- CPU = 75.2014 (sec) ----------------
TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920
PotEng = -46882.7493 E_bond = 2567.9820 E_angle = 10781.9426
E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962
E_coul = 206655.0353 E_long = -270400.7390 Press = 6.9485
Volume = 308134.2307
Loop time of 75.2015 on 1 procs for 100 steps with 32000 atoms
---------------- Step 50 ----- CPU = 32.0339 (sec) ----------------
TotEng = -25330.0568 KinEng = 21501.0002 Temp = 299.8229
PotEng = -46831.0570 E_bond = 2471.7010 E_angle = 10836.4976
E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2862
E_coul = 206793.4381 E_long = -270406.1593 Press = 237.6631
Volume = 308031.6773
---------------- Step 100 ----- CPU = 64.9190 (sec) ----------------
TotEng = -25290.7397 KinEng = 21592.0095 Temp = 301.0920
PotEng = -46882.7492 E_bond = 2567.9819 E_angle = 10781.9426
E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4966
E_coul = 206655.0358 E_long = -270400.7390 Press = 6.9488
Volume = 308134.2294
Loop time of 64.9191 on 1 procs for 100 steps with 32000 atoms
Pair time (%) = 55.4142 (73.6876)
Bond time (%) = 2.75074 (3.65783)
Kspce time (%) = 6.20111 (8.24599)
Neigh time (%) = 8.45892 (11.2483)
Comm time (%) = 0.203681 (0.270847)
Outpt time (%) = 0.000455141 (0.000605229)
Other time (%) = 2.1724 (2.88878)
Pair time (%) = 46.2857 (71.2975)
Bond time (%) = 2.89318 (4.45659)
Kspce time (%) = 6.096 (9.39015)
Neigh time (%) = 7.11072 (10.9532)
Comm time (%) = 0.187559 (0.288912)
Outpt time (%) = 0.000407934 (0.000628373)
Other time (%) = 2.34552 (3.61298)
FFT time (% of Kspce) = 0.432577 (6.9758)
FFT Gflps 3d (1d only) = 1.2014 1.71982
FFT time (% of Kspce) = 0.435581 (7.14536)
FFT Gflps 3d (1d only) = 1.19311 1.73673
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -90,7 +90,7 @@ Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20281e+07 max 1.20281e+07 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 12028097
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11

54
bench/log.7Jul09.rhodo.fixed.linux.4 → bench/log.15Jan10.rhodo.fixed.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# Rhodopsin model
units real
@ -53,35 +53,35 @@ PPPM initialization ...
brick FFT buffer size/proc = 13230 6400 5670
Memory usage per processor = 47.7552 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -25356.2081 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0393 E_bond = 2537.9940 E_angle = 10921.3742
TotEng = -25356.2055 KinEng = 21444.8313 Temp = 299.0397
PotEng = -46801.0368 E_bond = 2537.9940 E_angle = 10921.3742
E_dihed = 5211.7865 E_impro = 213.5116 E_vdwl = -2307.8634
E_coul = 207021.6578 E_long = -270399.5000 Press = -142.6055
E_coul = 207021.6603 E_long = -270399.5000 Press = -142.6030
Volume = 307995.0335
---------------- Step 50 ----- CPU = 9.3409 (sec) ----------------
TotEng = -25330.0565 KinEng = 21501.0002 Temp = 299.8229
PotEng = -46831.0567 E_bond = 2471.7010 E_angle = 10836.4978
E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2861
E_coul = 206793.4380 E_long = -270406.1593 Press = 237.6633
Volume = 308031.6776
---------------- Step 100 ----- CPU = 18.9741 (sec) ----------------
TotEng = -25290.7382 KinEng = 21592.0112 Temp = 301.0920
PotEng = -46882.7494 E_bond = 2567.9820 E_angle = 10781.9426
E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4962
E_coul = 206655.0352 E_long = -270400.7391 Press = 6.9485
Volume = 308134.2307
Loop time of 18.9748 on 4 procs for 100 steps with 32000 atoms
---------------- Step 50 ----- CPU = 8.4471 (sec) ----------------
TotEng = -25330.0567 KinEng = 21501.0002 Temp = 299.8229
PotEng = -46831.0569 E_bond = 2471.7010 E_angle = 10836.4976
E_dihed = 5239.6302 E_impro = 227.1217 E_vdwl = -1993.2862
E_coul = 206793.4381 E_long = -270406.1593 Press = 237.6631
Volume = 308031.6773
---------------- Step 100 ----- CPU = 17.2158 (sec) ----------------
TotEng = -25290.7397 KinEng = 21592.0095 Temp = 301.0920
PotEng = -46882.7492 E_bond = 2567.9819 E_angle = 10781.9426
E_dihed = 5198.7430 E_impro = 216.7831 E_vdwl = -1902.4966
E_coul = 206655.0358 E_long = -270400.7390 Press = 6.9488
Volume = 308134.2294
Loop time of 17.2163 on 4 procs for 100 steps with 32000 atoms
Pair time (%) = 12.4679 (65.7076)
Bond time (%) = 0.674445 (3.55442)
Kspce time (%) = 2.50158 (13.1837)
Neigh time (%) = 1.93391 (10.192)
Comm time (%) = 0.488374 (2.5738)
Outpt time (%) = 0.0020867 (0.0109972)
Other time (%) = 0.906525 (4.77751)
Pair time (%) = 11.2337 (65.2502)
Bond time (%) = 0.689357 (4.0041)
Kspce time (%) = 2.22834 (12.9432)
Neigh time (%) = 1.72487 (10.0188)
Comm time (%) = 0.439415 (2.55233)
Outpt time (%) = 0.00139344 (0.00809373)
Other time (%) = 0.899235 (5.22318)
FFT time (% of Kspce) = 0.475504 (19.0082)
FFT Gflps 3d (1d only) = 1.09294 6.72748
FFT time (% of Kspce) = 0.290461 (13.0348)
FFT Gflps 3d (1d only) = 1.78922 6.55107
Nlocal: 8000 ave 8143 max 7933 min
Histogram: 1 2 0 0 0 0 0 0 0 1
@ -90,7 +90,7 @@ Histogram: 1 0 0 0 0 2 0 0 0 1
Neighs: 3.00702e+06 ave 3.0975e+06 max 2.96493e+06 min
Histogram: 1 2 0 0 0 0 0 0 0 1
Total # of neighbors = 12028097
Total # of neighbors = 12028098
Ave neighs/atom = 375.878
Ave special neighs/atom = 7.43187
Neighbor list builds = 11

56
bench/log.7Jul09.rhodo.scaled.linux.4 → bench/log.15Jan10.rhodo.scaled.linux.4
View File

@ -1,4 +1,4 @@
LAMMPS (7 Jul 2009)
LAMMPS (15 Jan 2010)
# Rhodopsin model
variable x index 1
@ -74,35 +74,35 @@ PPPM initialization ...
brick FFT buffer size/proc = 41615 25920 12915
Memory usage per processor = 130.497 Mbytes
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
TotEng = -101425.4928 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8179 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4538
E_coul = 827025.3455 E_long = -1080537.3748 Press = -142.3110
TotEng = -101425.4825 KinEng = 85779.3251 Temp = 299.0304
PotEng = -187204.8077 E_bond = 10151.9760 E_angle = 43685.4968
E_dihed = 20847.1460 E_impro = 854.0463 E_vdwl = -9231.4537
E_coul = 827025.3556 E_long = -1080537.3748 Press = -142.3084
Volume = 1231980.1340
---------------- Step 50 ----- CPU = 36.7640 (sec) ----------------
TotEng = -101320.2392 KinEng = 86003.4766 Temp = 299.8118
PotEng = -187323.7158 E_bond = 9887.1093 E_angle = 43346.7930
E_dihed = 20958.7048 E_impro = 908.4715 E_vdwl = -7973.4918
E_coul = 826113.2245 E_long = -1080564.5270 Press = 237.9865
Volume = 1232126.6400
---------------- Step 100 ----- CPU = 75.1275 (sec) ----------------
TotEng = -101158.0378 KinEng = 86355.6419 Temp = 301.0394
PotEng = -187513.6797 E_bond = 10272.0762 E_angle = 43128.6553
E_dihed = 20793.9769 E_impro = 867.0831 E_vdwl = -7586.7842
E_coul = 825555.6424 E_long = -1080544.3294 Press = 15.1826
Volume = 1232536.8037
Loop time of 75.1281 on 4 procs for 100 steps with 128000 atoms
---------------- Step 50 ----- CPU = 33.7697 (sec) ----------------
TotEng = -101320.2398 KinEng = 86003.4785 Temp = 299.8118
PotEng = -187323.7183 E_bond = 9887.1094 E_angle = 43346.7937
E_dihed = 20958.7044 E_impro = 908.4714 E_vdwl = -7973.4916
E_coul = 826113.2215 E_long = -1080564.5271 Press = 237.9863
Volume = 1232126.6405
---------------- Step 100 ----- CPU = 68.8905 (sec) ----------------
TotEng = -101158.0547 KinEng = 86355.6350 Temp = 301.0394
PotEng = -187513.6897 E_bond = 10272.0754 E_angle = 43128.6542
E_dihed = 20793.9772 E_impro = 867.0829 E_vdwl = -7586.7862
E_coul = 825555.6359 E_long = -1080544.3291 Press = 15.1782
Volume = 1232536.8059
Loop time of 68.8909 on 4 procs for 100 steps with 128000 atoms
Pair time (%) = 51.8045 (68.9549)
Bond time (%) = 2.72669 (3.62939)
Kspce time (%) = 8.1336 (10.8263)
Neigh time (%) = 8.00985 (10.6616)
Comm time (%) = 1.00661 (1.33985)
Outpt time (%) = 0.00222611 (0.00296309)
Other time (%) = 3.44461 (4.58499)
Pair time (%) = 46.1299 (66.9607)
Bond time (%) = 2.90114 (4.21121)
Kspce time (%) = 8.32531 (12.0848)
Neigh time (%) = 7.06748 (10.2589)
Comm time (%) = 0.899294 (1.30539)
Outpt time (%) = 0.00150454 (0.00218395)
Other time (%) = 3.56634 (5.1768)
FFT time (% of Kspce) = 1.77978 (21.8818)
FFT Gflps 3d (1d only) = 1.34557 6.00095
FFT time (% of Kspce) = 1.47549 (17.7229)
FFT Gflps 3d (1d only) = 1.62306 6.12053
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -111,7 +111,7 @@ Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 1.20281e+07 ave 1.20572e+07 max 1.1999e+07 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 48112464
Total # of neighbors = 48112460
Ave neighs/atom = 375.879
Ave special neighs/atom = 7.43187
Neighbor list builds = 11