Commit cef41644 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
Browse files

update log files for min, msst, nb3b, nemd, and obstacle examples

parent 074a9663

examples/min/log.5Oct16.min.box.g++.1→examples/min/log.27Nov18.min.box.g++.1

+80 −73
Original line number Diff line number Diff line 
LAMMPS (5 Oct 2016)

LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# 2d Lennard-Jones melt and subsequent energy minimization,

# followed by box relaxation to a target stress state

#
@@ -14,6 +15,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) 
  1 by 1 by 1 MPI processor grid

create_atoms	1 box

Created 800 atoms

  Time spent = 0.000453234 secs

mass		1 1.0



velocity	all create 5.0 87287 loop geom
@@ -40,13 +42,18 @@ thermo 100 


run		1000

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4 -> bins = 22 22 1

Memory usage per processor = 2.47843 Mbytes

  binsize = 1.4, bins = 22 22 1

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 3.056 | 3.056 | 3.056 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0            5    -2.461717            0     2.532033    5.0190509 

     100    3.2788864  -0.74311698            0    2.5316708    15.912832
@@ -59,20 +66,20 @@ Step Temp E_pair E_mol TotEng Press 
     800    3.3016275  -0.76569171            0    2.5318087    15.639335 

     900    3.4639203  -0.92788002            0    2.5317104    14.765912 

    1000    3.3256788  -0.79078181            0    2.5307399    15.599298 

Loop time of 0.202646 on 1 procs for 1000 steps with 800 atoms

Loop time of 0.210142 on 1 procs for 1000 steps with 800 atoms



Performance: 2131796.155 tau/day, 4934.713 timesteps/s

99.7% CPU use with 1 MPI tasks x no OpenMP threads

Performance: 2055749.118 tau/day, 4758.679 timesteps/s

98.4% CPU use with 1 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.12926    | 0.12926    | 0.12926    |   0.0 | 63.79

Neigh   | 0.051169   | 0.051169   | 0.051169   |   0.0 | 25.25

Comm    | 0.0044918  | 0.0044918  | 0.0044918  |   0.0 |  2.22

Output  | 9.3222e-05 | 9.3222e-05 | 9.3222e-05 |   0.0 |  0.05

Modify  | 0.011879   | 0.011879   | 0.011879   |   0.0 |  5.86

Other   |            | 0.005755   |            |       |  2.84

Pair    | 0.12951    | 0.12951    | 0.12951    |   0.0 | 61.63

Neigh   | 0.053642   | 0.053642   | 0.053642   |   0.0 | 25.53

Comm    | 0.0062521  | 0.0062521  | 0.0062521  |   0.0 |  2.98

Output  | 0.0001297  | 0.0001297  | 0.0001297  |   0.0 |  0.06

Modify  | 0.0142     | 0.0142     | 0.0142     |   0.0 |  6.76

Other   |            | 0.006405   |            |       |  3.05



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -98,7 +105,7 @@ thermo 50 
# atoms only



minimize	1.0e-6 0.001 1000 10000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp E_pair E_mol TotEng Press 

    1000            0  -0.79078181            0  -0.79078181     12.79527 

    1050            0   -2.8361415            0   -2.8361415   -1.1950285
@@ -111,9 +118,9 @@ Step Temp E_pair E_mol TotEng Press 
    1400            0   -2.9131297            0   -2.9131297   -1.0962069 

    1450            0   -2.9167506            0   -2.9167506   -1.0259809 

    1475            0   -2.9169436            0   -2.9169436   -1.0125744 

Loop time of 0.232023 on 1 procs for 475 steps with 800 atoms

Loop time of 0.234897 on 1 procs for 475 steps with 800 atoms



100.0% CPU use with 1 MPI tasks x no OpenMP threads

99.4% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = energy tolerance
@@ -127,12 +134,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.18865    | 0.18865    | 0.18865    |   0.0 | 81.30

Neigh   | 0.020881   | 0.020881   | 0.020881   |   0.0 |  9.00

Comm    | 0.0028429  | 0.0028429  | 0.0028429  |   0.0 |  1.23

Output  | 7.0095e-05 | 7.0095e-05 | 7.0095e-05 |   0.0 |  0.03

Modify  | 0.0020018  | 0.0020018  | 0.0020018  |   0.0 |  0.86

Other   |            | 0.01758    |            |       |  7.58

Pair    | 0.18533    | 0.18533    | 0.18533    |   0.0 | 78.90

Neigh   | 0.02206    | 0.02206    | 0.02206    |   0.0 |  9.39

Comm    | 0.0041955  | 0.0041955  | 0.0041955  |   0.0 |  1.79

Output  | 0.000108   | 0.000108   | 0.000108   |   0.0 |  0.05

Modify  | 0.002362   | 0.002362   | 0.002362   |   0.0 |  1.01

Other   |            | 0.02084    |            |       |  8.87



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -156,7 +163,7 @@ thermo_style custom step temp pe pxx pyy pxy f_3 v_emin 
# anisotropic volume relaxation to hydrostatic target



minimize	0.0 10.0e0 10000 100000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 

    1475            0   -2.9169436   -1.0208231   -1.0043256  0.042048233            0   -2.9169436 

    1500            0   -2.9112018    1.4420862    1.4721681  0.065929095 -0.087730988   -2.9989327
@@ -164,9 +171,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 
    1600            0    -2.924265    1.4545702    1.5281333  0.053590255  -0.12032598    -3.044591 

    1650            0   -2.9289538    1.4528452    1.5692678  0.038096542  -0.12516914    -3.054123 

    1699            0   -2.9334511    1.4447667    1.5587557  0.044510608  -0.12731783    -3.060769 

Loop time of 0.109303 on 1 procs for 224 steps with 800 atoms

Loop time of 0.112146 on 1 procs for 224 steps with 800 atoms



99.7% CPU use with 1 MPI tasks x no OpenMP threads

97.8% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = force tolerance
@@ -180,12 +187,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.086675   | 0.086675   | 0.086675   |   0.0 | 79.30

Neigh   | 0.0040114  | 0.0040114  | 0.0040114  |   0.0 |  3.67

Comm    | 0.0010419  | 0.0010419  | 0.0010419  |   0.0 |  0.95

Output  | 9.4891e-05 | 9.4891e-05 | 9.4891e-05 |   0.0 |  0.09

Modify  | 0.00085473 | 0.00085473 | 0.00085473 |   0.0 |  0.78

Other   |            | 0.01662    |            |       | 15.21

Pair    | 0.084376   | 0.084376   | 0.084376   |   0.0 | 75.24

Neigh   | 0.0042746  | 0.0042746  | 0.0042746  |   0.0 |  3.81

Comm    | 0.0015385  | 0.0015385  | 0.0015385  |   0.0 |  1.37

Output  | 0.0001235  | 0.0001235  | 0.0001235  |   0.0 |  0.11

Modify  | 0.0011208  | 0.0011208  | 0.0011208  |   0.0 |  1.00

Other   |            | 0.02071    |            |       | 18.47



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -202,13 +209,13 @@ Dangerous builds = 0 
fix             3 all box/relax aniso 1.5 vmax 1.0e-3



minimize	0.0 10.0 10000 100000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 

    1699            0   -2.9334511    1.4447667    1.5587557  0.044510608            0   -2.9334511 

    1700            0   -2.9335996    1.4982915    1.4969508  0.044657372  9.09619e-05   -2.9335086 

Loop time of 0.000785828 on 1 procs for 1 steps with 800 atoms

Loop time of 0.000793934 on 1 procs for 1 steps with 800 atoms



127.3% CPU use with 1 MPI tasks x no OpenMP threads

99.8% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = force tolerance
@@ -222,12 +229,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.00063896 | 0.00063896 | 0.00063896 |   0.0 | 81.31

Pair    | 0.00061846 | 0.00061846 | 0.00061846 |   0.0 | 77.90

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 5.9605e-06 | 5.9605e-06 | 5.9605e-06 |   0.0 |  0.76

Comm    | 1.0014e-05 | 1.0014e-05 | 1.0014e-05 |   0.0 |  1.26

Output  | 0          | 0          | 0          |   0.0 |  0.00

Modify  | 6.1989e-06 | 6.1989e-06 | 6.1989e-06 |   0.0 |  0.79

Other   |            | 0.0001347  |            |       | 17.14

Modify  | 7.6294e-06 | 7.6294e-06 | 7.6294e-06 |   0.0 |  0.96

Other   |            | 0.0001578  |            |       | 19.88



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -246,7 +253,7 @@ Dangerous builds = 0 
fix             3 all box/relax x 1.0 y 2.0 vmax 1.0e-3



minimize	0.0 10.0 10000 100000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 

    1700            0   -2.9335996    1.4982915    1.4969508  0.044657372 -3.5527137e-17   -2.9335996 

    1750            0   -2.9306696   0.95043712     1.984164   0.04474671 -0.014282691   -2.9449523
@@ -254,9 +261,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 
    1850            0    -2.935585   0.98224846    1.9920507  0.047038767 -0.021070874   -2.9566559 

    1900            0   -2.9380757   0.96811097    1.9677247  0.068809483 -0.024274947   -2.9623506 

    1913            0   -2.9391305   0.98238419    1.9782761  0.074400364 -0.025108208   -2.9642387 

Loop time of 0.0971339 on 1 procs for 213 steps with 800 atoms

Loop time of 0.0997889 on 1 procs for 213 steps with 800 atoms



100.9% CPU use with 1 MPI tasks x no OpenMP threads

99.4% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = force tolerance
@@ -270,12 +277,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.076124   | 0.076124   | 0.076124   |   0.0 | 78.37

Neigh   | 0.0027554  | 0.0027554  | 0.0027554  |   0.0 |  2.84

Comm    | 0.00085568 | 0.00085568 | 0.00085568 |   0.0 |  0.88

Output  | 0.00012589 | 0.00012589 | 0.00012589 |   0.0 |  0.13

Modify  | 0.00077486 | 0.00077486 | 0.00077486 |   0.0 |  0.80

Other   |            | 0.0165     |            |       | 16.98

Pair    | 0.074305   | 0.074305   | 0.074305   |   0.0 | 74.46

Neigh   | 0.0028846  | 0.0028846  | 0.0028846  |   0.0 |  2.89

Comm    | 0.0012925  | 0.0012925  | 0.0012925  |   0.0 |  1.30

Output  | 0.00016117 | 0.00016117 | 0.00016117 |   0.0 |  0.16

Modify  | 0.00090647 | 0.00090647 | 0.00090647 |   0.0 |  0.91

Other   |            | 0.02024    |            |       | 20.28



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -290,7 +297,7 @@ Neighbor list builds = 11 
Dangerous builds = 0



minimize	0.0 1.0 10000 100000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 

    1913            0   -2.9391305   0.98238419    1.9782761  0.074400364 7.1054274e-17   -2.9391305 

    1950            0   -2.9397224   0.98880561    2.0105792   0.10042798 -0.0026601558   -2.9423825
@@ -382,9 +389,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 
    6250            0   -3.0378032   0.99964291    1.9971778  0.033045048 -0.037140636   -3.0749439 

    6300            0   -3.0377782    0.9965492    1.9980669  0.032201395 -0.037170252   -3.0749485 

    6314            0   -3.0377854   0.99649081    1.9975871  0.032243768 -0.037163869   -3.0749493 

Loop time of 2.27089 on 1 procs for 4401 steps with 800 atoms

Loop time of 2.33993 on 1 procs for 4401 steps with 800 atoms



99.9% CPU use with 1 MPI tasks x no OpenMP threads

98.8% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = force tolerance
@@ -398,12 +405,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 1.8251     | 1.8251     | 1.8251     |   0.0 | 80.37

Neigh   | 0.027037   | 0.027037   | 0.027037   |   0.0 |  1.19

Comm    | 0.019059   | 0.019059   | 0.019059   |   0.0 |  0.84

Output  | 0.0027676  | 0.0027676  | 0.0027676  |   0.0 |  0.12

Modify  | 0.018233   | 0.018233   | 0.018233   |   0.0 |  0.80

Other   |            | 0.3786     |            |       | 16.67

Pair    | 1.7909     | 1.7909     | 1.7909     |   0.0 | 76.54

Neigh   | 0.028373   | 0.028373   | 0.028373   |   0.0 |  1.21

Comm    | 0.029514   | 0.029514   | 0.029514   |   0.0 |  1.26

Output  | 0.0037448  | 0.0037448  | 0.0037448  |   0.0 |  0.16

Modify  | 0.021746   | 0.021746   | 0.021746   |   0.0 |  0.93

Other   |            | 0.4657     |            |       | 19.90



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -418,7 +425,7 @@ Neighbor list builds = 109 
Dangerous builds = 0



minimize	0.0 1.0e-2 10000 100000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 

    6314            0   -3.0377854   0.99649081    1.9975871  0.032243768 3.5527137e-17   -3.0377854 

    6350            0   -3.0377426    0.9995618    1.9997582  0.032364722 -4.5395813e-05    -3.037788
@@ -454,9 +461,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 
    7850            0   -3.0378352    1.0000397    2.0000524  0.033753896 -7.5318252e-05   -3.0379105 

    7900            0   -3.0378354    1.0000486    2.0000488  0.033742064 -7.5113089e-05   -3.0379105 

    7904            0   -3.0378356    1.0000321    2.0000425  0.033740786 -7.491864e-05   -3.0379105 

Loop time of 0.831561 on 1 procs for 1590 steps with 800 atoms

Loop time of 0.85351 on 1 procs for 1590 steps with 800 atoms



99.9% CPU use with 1 MPI tasks x no OpenMP threads

98.7% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = force tolerance
@@ -470,12 +477,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.67727    | 0.67727    | 0.67727    |   0.0 | 81.45

Neigh   | 0.0004921  | 0.0004921  | 0.0004921  |   0.0 |  0.06

Comm    | 0.0065284  | 0.0065284  | 0.0065284  |   0.0 |  0.79

Output  | 0.0010114  | 0.0010114  | 0.0010114  |   0.0 |  0.12

Modify  | 0.0067346  | 0.0067346  | 0.0067346  |   0.0 |  0.81

Other   |            | 0.1395     |            |       | 16.78

Pair    | 0.66264    | 0.66264    | 0.66264    |   0.0 | 77.64

Neigh   | 0.00052071 | 0.00052071 | 0.00052071 |   0.0 |  0.06

Comm    | 0.010136   | 0.010136   | 0.010136   |   0.0 |  1.19

Output  | 0.0012524  | 0.0012524  | 0.0012524  |   0.0 |  0.15

Modify  | 0.0080862  | 0.0080862  | 0.0080862  |   0.0 |  0.95

Other   |            | 0.1709     |            |       | 20.02



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -494,7 +501,7 @@ Dangerous builds = 0 
fix             3 all box/relax x 1.0 y 2.0 vmax 1.0e-3 nreset 100



minimize	0.0 1.0e-4 10000 100000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 

    7904            0   -3.0378356    1.0000321    2.0000425  0.033740786            0   -3.0378356 

    7950            0   -3.0378364     1.000001    2.0000015   0.03373689 8.3404927e-07   -3.0378356
@@ -515,9 +522,9 @@ Step Temp PotEng Pxx Pyy Pxy f_3 v_emin 
    8700            0   -3.0378364            1    1.9999997  0.033725586 4.9116894e-09   -3.0378364 

    8750            0   -3.0378364   0.99999991            2  0.033725386 7.3634181e-10   -3.0378364 

    8753            0   -3.0378364            1            2  0.033725385 -1.0901182e-09   -3.0378364 

Loop time of 0.445577 on 1 procs for 849 steps with 800 atoms

Loop time of 0.457836 on 1 procs for 849 steps with 800 atoms



99.9% CPU use with 1 MPI tasks x no OpenMP threads

99.2% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = force tolerance
@@ -531,12 +538,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.36325    | 0.36325    | 0.36325    |   0.0 | 81.52

Pair    | 0.3559     | 0.3559     | 0.3559     |   0.0 | 77.74

Neigh   | 0          | 0          | 0          |   0.0 |  0.00

Comm    | 0.0034921  | 0.0034921  | 0.0034921  |   0.0 |  0.78

Output  | 0.00052595 | 0.00052595 | 0.00052595 |   0.0 |  0.12

Modify  | 0.0036132  | 0.0036132  | 0.0036132  |   0.0 |  0.81

Other   |            | 0.07469    |            |       | 16.76

Comm    | 0.0054362  | 0.0054362  | 0.0054362  |   0.0 |  1.19

Output  | 0.00070548 | 0.00070548 | 0.00070548 |   0.0 |  0.15

Modify  | 0.004298   | 0.004298   | 0.004298   |   0.0 |  0.94

Other   |            | 0.09149    |            |       | 19.98



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0

examples/min/log.5Oct16.min.box.g++.4→examples/min/log.27Nov18.min.box.g++.4

+79 −72

File changed and moved.

Preview size limit exceeded, changes collapsed.

examples/min/log.5Oct16.min.g++.1→examples/min/log.27Nov18.min.g++.1

+29 −22
Original line number Diff line number Diff line 
LAMMPS (5 Oct 2016)

LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# 2d Lennard-Jones melt and subsequent energy minimization



units		lj
@@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) 
  1 by 1 by 1 MPI processor grid

create_atoms	1 box

Created 800 atoms

  Time spent = 0.000434637 secs

mass		1 1.0



velocity	all create 5.0 87287 loop geom
@@ -39,13 +41,18 @@ thermo 100 


run		1000

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4 -> bins = 22 22 1

Memory usage per processor = 2.47843 Mbytes

  binsize = 1.4, bins = 22 22 1

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 3.056 | 3.056 | 3.056 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0            5    -2.461717            0     2.532033    5.0190509 

     100    3.2788864  -0.74311698            0    2.5316708    15.912832
@@ -58,20 +65,20 @@ Step Temp E_pair E_mol TotEng Press 
     800    3.3016275  -0.76569171            0    2.5318087    15.639335 

     900    3.4639203  -0.92788002            0    2.5317104    14.765912 

    1000    3.3256788  -0.79078181            0    2.5307399    15.599298 

Loop time of 0.201747 on 1 procs for 1000 steps with 800 atoms

Loop time of 0.206744 on 1 procs for 1000 steps with 800 atoms



Performance: 2141296.412 tau/day, 4956.705 timesteps/s

99.6% CPU use with 1 MPI tasks x no OpenMP threads

Performance: 2089538.727 tau/day, 4836.895 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    | 0.12879    | 0.12879    | 0.12879    |   0.0 | 63.84

Neigh   | 0.051049   | 0.051049   | 0.051049   |   0.0 | 25.30

Comm    | 0.0043695  | 0.0043695  | 0.0043695  |   0.0 |  2.17

Output  | 8.1301e-05 | 8.1301e-05 | 8.1301e-05 |   0.0 |  0.04

Modify  | 0.011838   | 0.011838   | 0.011838   |   0.0 |  5.87

Other   |            | 0.005622   |            |       |  2.79

Pair    | 0.12643    | 0.12643    | 0.12643    |   0.0 | 61.15

Neigh   | 0.053694   | 0.053694   | 0.053694   |   0.0 | 25.97

Comm    | 0.0061328  | 0.0061328  | 0.0061328  |   0.0 |  2.97

Output  | 0.00011373 | 0.00011373 | 0.00011373 |   0.0 |  0.06

Modify  | 0.014107   | 0.014107   | 0.014107   |   0.0 |  6.82

Other   |            | 0.006263   |            |       |  3.03



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0
@@ -91,7 +98,7 @@ neigh_modify delay 0 every 1 check yes 


thermo		50

minimize	1.0e-6 0.001 1000 10000

Memory usage per processor = 3.60343 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.182 | 4.182 | 4.182 Mbytes

Step Temp E_pair E_mol TotEng Press 

    1000    3.3256788  -0.79078181            0    2.5307399    15.599298 

    1050    3.3256788   -2.8361415            0   0.48538014    1.6090001
@@ -104,9 +111,9 @@ Step Temp E_pair E_mol TotEng Press 
    1400    3.3256788   -2.9131297            0   0.40839199    1.7078217 

    1450    3.3256788   -2.9167506            0   0.40477104    1.7780477 

    1475    3.3256788   -2.9169436            0    0.4045781    1.7914542 

Loop time of 0.231352 on 1 procs for 475 steps with 800 atoms

Loop time of 0.233542 on 1 procs for 475 steps with 800 atoms



99.8% CPU use with 1 MPI tasks x no OpenMP threads

99.3% CPU use with 1 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = energy tolerance
@@ -120,12 +127,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.18807    | 0.18807    | 0.18807    |   0.0 | 81.29

Neigh   | 0.02088    | 0.02088    | 0.02088    |   0.0 |  9.03

Comm    | 0.0028048  | 0.0028048  | 0.0028048  |   0.0 |  1.21

Output  | 6.9618e-05 | 6.9618e-05 | 6.9618e-05 |   0.0 |  0.03

Modify  | 0.0020773  | 0.0020773  | 0.0020773  |   0.0 |  0.90

Other   |            | 0.01745    |            |       |  7.54

Pair    | 0.18404    | 0.18404    | 0.18404    |   0.0 | 78.80

Neigh   | 0.02204    | 0.02204    | 0.02204    |   0.0 |  9.44

Comm    | 0.0040922  | 0.0040922  | 0.0040922  |   0.0 |  1.75

Output  | 0.00010443 | 0.00010443 | 0.00010443 |   0.0 |  0.04

Modify  | 0.0023651  | 0.0023651  | 0.0023651  |   0.0 |  1.01

Other   |            | 0.0209     |            |       |  8.95



Nlocal:    800 ave 800 max 800 min

Histogram: 1 0 0 0 0 0 0 0 0 0

examples/min/log.5Oct16.min.g++.4→examples/min/log.27Nov18.min.g++.4

+29 −22
Original line number Diff line number Diff line 
LAMMPS (5 Oct 2016)

LAMMPS (27 Nov 2018)

  using 1 OpenMP thread(s) per MPI task

# 2d Lennard-Jones melt and subsequent energy minimization



units		lj
@@ -13,6 +14,7 @@ Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919) 
  2 by 2 by 1 MPI processor grid

create_atoms	1 box

Created 800 atoms

  Time spent = 0.000340223 secs

mass		1 1.0



velocity	all create 5.0 87287 loop geom
@@ -39,13 +41,18 @@ thermo 100 


run		1000

Neighbor list info ...

  1 neighbor list requests

  update every 1 steps, delay 0 steps, check yes

  max neighbors/atom: 2000, page size: 100000

  master list distance cutoff = 2.8

  ghost atom cutoff = 2.8

  binsize = 1.4 -> bins = 22 22 1

Memory usage per processor = 2.47676 Mbytes

  binsize = 1.4, bins = 22 22 1

  1 neighbor lists, perpetual/occasional/extra = 1 0 0

  (1) pair lj/cut, perpetual

      attributes: half, newton on

      pair build: half/bin/atomonly/newton

      stencil: half/bin/2d/newton

      bin: standard

Per MPI rank memory allocation (min/avg/max) = 3.049 | 3.049 | 3.049 Mbytes

Step Temp E_pair E_mol TotEng Press 

       0            5    -2.461717            0     2.532033    5.0190509 

     100    3.2788864  -0.74311698            0    2.5316708    15.912832
@@ -58,20 +65,20 @@ Step Temp E_pair E_mol TotEng Press 
     800    3.3016408  -0.76570603            0    2.5318077    15.639259 

     900    3.4621697  -0.92610292            0    2.5317391    14.773473 

    1000    3.3058424  -0.77076863            0    2.5309414    15.708171 

Loop time of 0.162444 on 4 procs for 1000 steps with 800 atoms

Loop time of 0.0730537 on 4 procs for 1000 steps with 800 atoms



Performance: 2659379.051 tau/day, 6155.970 timesteps/s

78.3% CPU use with 4 MPI tasks x no OpenMP threads

Performance: 5913456.756 tau/day, 13688.557 timesteps/s

95.7% CPU use with 4 MPI tasks x 1 OpenMP threads



MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.032602   | 0.033969   | 0.034999   |   0.5 | 20.91

Neigh   | 0.013433   | 0.013719   | 0.013862   |   0.1 |  8.45

Comm    | 0.08291    | 0.088224   | 0.099287   |   2.2 | 54.31

Output  | 0.00084209 | 0.00093055 | 0.00097394 |   0.2 |  0.57

Modify  | 0.0030942  | 0.0033001  | 0.0035179  |   0.3 |  2.03

Other   |            | 0.0223     |            |       | 13.73

Pair    | 0.031481   | 0.031893   | 0.032234   |   0.2 | 43.66

Neigh   | 0.014234   | 0.014466   | 0.014672   |   0.1 | 19.80

Comm    | 0.017078   | 0.01775    | 0.018055   |   0.3 | 24.30

Output  | 0.00017548 | 0.00027454 | 0.00056386 |   0.0 |  0.38

Modify  | 0.0038447  | 0.0038754  | 0.0038893  |   0.0 |  5.30

Other   |            | 0.004795   |            |       |  6.56



Nlocal:    200 ave 202 max 196 min

Histogram: 1 0 0 0 0 0 0 0 2 1
@@ -91,7 +98,7 @@ neigh_modify delay 0 every 1 check yes 


thermo		50

minimize	1.0e-6 0.001 1000 10000

Memory usage per processor = 3.60176 Mbytes

Per MPI rank memory allocation (min/avg/max) = 4.174 | 4.174 | 4.174 Mbytes

Step Temp E_pair E_mol TotEng Press 

    1000    3.3058424  -0.77076863            0    2.5309414    15.708171 

    1050    3.3058424   -2.8318266            0   0.46988351    1.5980106
@@ -100,9 +107,9 @@ Step Temp E_pair E_mol TotEng Press 
    1200    3.3058424   -2.8831122            0   0.41859789    1.6869035 

    1250    3.3058424   -2.8877971            0     0.413913    1.7276622 

    1300    3.3058424   -2.8887969            0   0.41291311    1.7424655 

Loop time of 0.048058 on 4 procs for 300 steps with 800 atoms

Loop time of 0.055995 on 4 procs for 300 steps with 800 atoms



98.8% CPU use with 4 MPI tasks x no OpenMP threads

96.0% CPU use with 4 MPI tasks x 1 OpenMP threads



Minimization stats:

  Stopping criterion = energy tolerance
@@ -116,12 +123,12 @@ Minimization stats: 
MPI task timing breakdown:

Section |  min time  |  avg time  |  max time  |%varavg| %total

---------------------------------------------------------------

Pair    | 0.03076    | 0.031581   | 0.032226   |   0.3 | 65.71

Neigh   | 0.0037913  | 0.0038914  | 0.0039353  |   0.1 |  8.10

Comm    | 0.004194   | 0.0049016  | 0.0058777  |   1.0 | 10.20

Output  | 6.3181e-05 | 6.6817e-05 | 7.7009e-05 |   0.1 |  0.14

Modify  | 0.00035    | 0.00036556 | 0.0003829  |   0.1 |  0.76

Other   |            | 0.007252   |            |       | 15.09

Pair    | 0.029709   | 0.030492   | 0.031057   |   0.3 | 54.45

Neigh   | 0.0040245  | 0.0042111  | 0.0046084  |   0.4 |  7.52

Comm    | 0.010827   | 0.011703   | 0.012587   |   0.6 | 20.90

Output  | 9.8228e-05 | 0.00024104 | 0.00066733 |   0.0 |  0.43

Modify  | 0.0004456  | 0.00045222 | 0.00045633 |   0.0 |  0.81

Other   |            | 0.008895   |            |       | 15.89



Nlocal:    200 ave 202 max 196 min

Histogram: 1 0 0 0 0 0 1 0 0 2

examples/msst/log.5Oct16.msst.g++.1→examples/msst/log.27Nov18.msst.g++.1

+31 −24

File changed and moved.

Preview size limit exceeded, changes collapsed.

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