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more changes to insure each triplet IJK computed exactly once

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This commit is contained in:
Steven J. Plimpton
2018-08-27 17:09:59 -06:00
parent c01fb5f701
commit 31ed3f7178
3 changed files with 53 additions and 65 deletions
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32
examples/atm/log.23Aug18.atm.g++.1 → examples/atm/log.27Aug18.g++.1
View File

@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 1 by 1 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.00126314 secs
Time spent = 0.00139618 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.47 | 11.47 | 11.47 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.033 -4.8899813 0 -3.3408686 -4.2298176
5 1.0337853 -4.8928208 0 -3.3425304 -4.2233154
10 1.0358056 -4.8953304 0 -3.3420104 -4.1897183
15 1.0380938 -4.8990457 0 -3.3422942 -4.1310148
20 1.0389566 -4.9014345 0 -3.3433892 -4.0406616
25 1.0358313 -4.8989663 0 -3.3456079 -3.9093019
Loop time of 12.2062 on 1 procs for 25 steps with 4000 atoms
0 1.033 -4.8404387 0 -3.291326 -4.1332095
5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
Loop time of 15.95 on 1 procs for 25 steps with 4000 atoms
Performance: 353.920 tau/day, 2.048 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 270.846 tau/day, 1.567 timesteps/s
100.0% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.202 | 12.202 | 12.202 | 0.0 | 99.96
Pair | 15.946 | 15.946 | 15.946 | 0.0 | 99.97
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.0015621 | 0.0015621 | 0.0015621 | 0.0 | 0.01
Output | 0.00020814 | 0.00020814 | 0.00020814 | 0.0 | 0.00
Modify | 0.0019698 | 0.0019698 | 0.0019698 | 0.0 | 0.02
Other | | 0.0007734 | | | 0.01
Comm | 0.0015042 | 0.0015042 | 0.0015042 | 0.0 | 0.01
Output | 0.00013781 | 0.00013781 | 0.00013781 | 0.0 | 0.00
Modify | 0.0017776 | 0.0017776 | 0.0017776 | 0.0 | 0.01
Other | | 0.0006771 | | | 0.00
Nlocal: 4000 ave 4000 max 4000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:13
Total wall time: 0:00:16

32
examples/atm/log.23Aug18.atm.g++.4 → examples/atm/log.27Aug18.g++.4
View File

@ -26,7 +26,7 @@ Created orthogonal box = (0 0 0) to (18.3252 18.3252 18.3252)
1 by 2 by 2 MPI processor grid
create_atoms 1 box
Created 4000 atoms
Time spent = 0.000785112 secs
Time spent = 0.000900984 secs
pair_style hybrid/overlay lj/cut 4.5 atm 4.5 2.5
pair_coeff * * lj/cut 1.0 1.0
@ -60,26 +60,26 @@ Neighbor list info ...
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.532 | 5.532 | 5.532 Mbytes
Step Temp E_pair E_mol TotEng Press
0 1.033 -4.8921547 0 -3.343042 -4.2340557
5 1.0337949 -4.8947881 0 -3.3444835 -4.2271456
10 1.0358286 -4.8973178 0 -3.3439632 -4.1935779
15 1.0381322 -4.9010593 0 -3.3442503 -4.134913
20 1.0390107 -4.9034854 0 -3.3453589 -4.0446162
25 1.0358988 -4.9010506 0 -3.3475908 -3.9133006
Loop time of 3.20632 on 4 procs for 25 steps with 4000 atoms
0 1.033 -4.8404387 0 -3.291326 -4.1332095
5 1.0337247 -4.8402263 0 -3.290027 -4.1207962
10 1.0355935 -4.8425889 0 -3.2895869 -4.0870158
15 1.0376519 -4.84599 0 -3.2899013 -4.0278711
20 1.0382257 -4.8478854 0 -3.2909361 -3.9368052
25 1.0347886 -4.84473 0 -3.2929351 -3.8044469
Loop time of 4.34636 on 4 procs for 25 steps with 4000 atoms
Performance: 1347.340 tau/day, 7.797 timesteps/s
100.0% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 993.935 tau/day, 5.752 timesteps/s
99.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.1207 | 3.1553 | 3.1859 | 1.5 | 98.41
Pair | 3.9977 | 4.1036 | 4.209 | 4.9 | 94.41
Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.019466 | 0.05009 | 0.084602 | 12.0 | 1.56
Output | 7.1049e-05 | 8.2076e-05 | 0.00011325 | 0.0 | 0.00
Modify | 0.00056338 | 0.00057292 | 0.00058413 | 0.0 | 0.02
Other | | 0.0003092 | | | 0.01
Comm | 0.13588 | 0.24134 | 0.34722 | 20.4 | 5.55
Output | 0.00013757 | 0.00015104 | 0.00016761 | 0.0 | 0.00
Modify | 0.00087953 | 0.00091547 | 0.00095582 | 0.0 | 0.02
Other | | 0.0003656 | | | 0.01
Nlocal: 1000 ave 1000 max 1000 min
Histogram: 4 0 0 0 0 0 0 0 0 0
@ -97,4 +97,4 @@ Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03
Total wall time: 0:00:04