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change input and log files for new example to give consistent results in serial and parallel.

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the remaining files and logs are updated in PR #2162
This commit is contained in:
Axel Kohlmeyer
2020-06-16 21:11:34 -04:00
parent a2f78e7cda
commit b97cd78e80
3 changed files with 54 additions and 52 deletions
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2
examples/snap/in.snap.InP.JCPA2020
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@ -40,7 +40,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD # Run MD
velocity all create 300.0 4928459 velocity all create 300.0 4928459 loop geom
fix 1 all nve fix 1 all nve
run ${nsteps} run ${nsteps}

51
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.1 → examples/snap/log.15Jun20.snap.InP.JCPA2020.g++.1
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@ -1,4 +1,5 @@
LAMMPS (2 Jun 2020) LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP InP potential # Demonstrate SNAP InP potential
# Initialize simulation # Initialize simulation
@ -43,10 +44,10 @@ include InP_JCPA2020.snap
# Definition of SNAP+ZBL potential. # Definition of SNAP+ZBL potential.
variable zblcutinner equal 4 variable zblcutinner index 4
variable zblcutouter equal 4.2 variable zblcutouter index 4.2
variable zblz1 equal 49 variable zblz1 index 49
variable zblz2 equal 15 variable zblz2 index 15
# Specify hybrid with SNAP and ZBL # Specify hybrid with SNAP and ZBL
@ -90,7 +91,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD # Run MD
velocity all create 300.0 4928459 velocity all create 300.0 4928459 loop geom
fix 1 all nve fix 1 all nve
run ${nsteps} run ${nsteps}
run 100 run 100
@ -114,30 +115,30 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes Per MPI rank memory allocation (min/avg/max) = 6.027 | 6.027 | 6.027 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 300 -3.4805794 0 -3.4418771 1353.5968 0 300 -3.4805794 0 -3.4418771 1353.5968
10 286.42264 -3.4788274 0 -3.4418767 1586.4881 10 285.84677 -3.4787531 0 -3.4418766 1611.7131
20 250.14148 -3.4741459 0 -3.4418757 2219.0344 20 248.14649 -3.4738884 0 -3.4418756 2312.0308
30 202.52417 -3.4680017 0 -3.4418745 2982.7272 30 198.94136 -3.4675394 0 -3.4418744 3168.1543
40 157.39113 -3.4621782 0 -3.4418735 3631.0936 40 152.74831 -3.4615791 0 -3.4418734 3903.5749
50 126.7004 -3.4582183 0 -3.441873 4053.7725 50 121.9796 -3.4576091 0 -3.4418728 4387.1254
60 117.00722 -3.4569679 0 -3.441873 4204.9542 60 113.27555 -3.4564863 0 -3.4418729 4556.3003
70 127.65968 -3.4583427 0 -3.4418736 4106.3112 70 125.68089 -3.4580873 0 -3.4418735 4431.2083
80 151.50217 -3.4614195 0 -3.4418745 3840.7205 80 151.47475 -3.4614159 0 -3.4418745 4107.2369
90 177.67607 -3.464797 0 -3.4418754 3527.9794 90 179.18708 -3.4649919 0 -3.4418754 3739.5881
100 195.30359 -3.4670717 0 -3.4418761 3300.3795 100 197.50662 -3.4673559 0 -3.441876 3492.7778
Loop time of 18.0803 on 1 procs for 100 steps with 512 atoms Loop time of 13.3103 on 1 procs for 100 steps with 512 atoms
Performance: 0.239 ns/day, 100.446 hours/ns, 5.531 timesteps/s Performance: 0.325 ns/day, 73.946 hours/ns, 7.513 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads 99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 18.078 | 18.078 | 18.078 | 0.0 | 99.99 Pair | 13.309 | 13.309 | 13.309 | 0.0 | 99.99
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.000979 | 0.000979 | 0.000979 | 0.0 | 0.01 Comm | 0.00068474 | 0.00068474 | 0.00068474 | 0.0 | 0.01
Output | 0.000243 | 0.000243 | 0.000243 | 0.0 | 0.00 Output | 0.00020504 | 0.00020504 | 0.00020504 | 0.0 | 0.00
Modify | 0.000591 | 0.000591 | 0.000591 | 0.0 | 0.00 Modify | 0.0003829 | 0.0003829 | 0.0003829 | 0.0 | 0.00
Other | | 0.000469 | | | 0.00 Other | | 0.0004075 | | | 0.00
Nlocal: 512 ave 512 max 512 min Nlocal: 512 ave 512 max 512 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0
@ -153,4 +154,4 @@ Ave neighs/atom = 122
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:18 Total wall time: 0:00:13

53
examples/snap/log.01Jun20.snap.InP_JCPA2020.g++.4 → examples/snap/log.15Jun20.snap.InP.JCPA2020.g++.4
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@ -1,4 +1,5 @@
LAMMPS (2 Jun 2020) LAMMPS (15 Jun 2020)
using 1 OpenMP thread(s) per MPI task
# Demonstrate SNAP InP potential # Demonstrate SNAP InP potential
# Initialize simulation # Initialize simulation
@ -31,7 +32,7 @@ Created orthogonal box = (0.0 0.0 0.0) to (23.32 23.32 23.32)
1 by 2 by 2 MPI processor grid 1 by 2 by 2 MPI processor grid
create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2 create_atoms 1 box basis 5 2 basis 6 2 basis 7 2 basis 8 2
Created 512 atoms Created 512 atoms
create_atoms CPU = 0.001 seconds create_atoms CPU = 0.000 seconds
mass 1 114.76 mass 1 114.76
mass 2 30.98 mass 2 30.98
@ -43,10 +44,10 @@ include InP_JCPA2020.snap
# Definition of SNAP+ZBL potential. # Definition of SNAP+ZBL potential.
variable zblcutinner equal 4 variable zblcutinner index 4
variable zblcutouter equal 4.2 variable zblcutouter index 4.2
variable zblz1 equal 49 variable zblz1 index 49
variable zblz2 equal 15 variable zblz2 index 15
# Specify hybrid with SNAP and ZBL # Specify hybrid with SNAP and ZBL
@ -90,7 +91,7 @@ neigh_modify once no every 1 delay 0 check yes
# Run MD # Run MD
velocity all create 300.0 4928459 velocity all create 300.0 4928459 loop geom
fix 1 all nve fix 1 all nve
run ${nsteps} run ${nsteps}
run 100 run 100
@ -114,30 +115,30 @@ Neighbor list info ...
Per MPI rank memory allocation (min/avg/max) = 4.587 | 4.587 | 4.587 Mbytes Per MPI rank memory allocation (min/avg/max) = 4.587 | 4.587 | 4.587 Mbytes
Step Temp E_pair E_mol TotEng Press Step Temp E_pair E_mol TotEng Press
0 300 -3.4805794 0 -3.4418771 1353.5968 0 300 -3.4805794 0 -3.4418771 1353.5968
10 286.58246 -3.478848 0 -3.4418767 1582.995 10 285.84677 -3.4787531 0 -3.4418766 1611.7131
20 250.70996 -3.4742192 0 -3.4418757 2207.7507 20 248.14649 -3.4738884 0 -3.4418756 2312.0308
30 203.58199 -3.4681382 0 -3.4418746 2968.5206 30 198.94136 -3.4675394 0 -3.4418744 3168.1543
40 158.84622 -3.462366 0 -3.4418736 3619.0285 40 152.74831 -3.4615791 0 -3.4418734 3903.5749
50 128.30488 -3.4584254 0 -3.4418731 4047.173 50 121.9796 -3.4576091 0 -3.4418728 4387.1254
60 118.40349 -3.4571481 0 -3.4418731 4203.3421 60 113.27555 -3.4564863 0 -3.4418729 4556.3003
70 128.48973 -3.4584499 0 -3.4418737 4109.0296 70 125.68089 -3.4580873 0 -3.4418735 4431.2083
80 151.54241 -3.4614247 0 -3.4418746 3847.4617 80 151.47475 -3.4614159 0 -3.4418745 4107.2369
90 176.92084 -3.4646996 0 -3.4418755 3548.7811 90 179.18708 -3.4649919 0 -3.4418754 3739.5881
100 193.9555 -3.4668978 0 -3.4418761 3342.8083 100 197.50662 -3.4673559 0 -3.441876 3492.7778
Loop time of 4.99339 on 4 procs for 100 steps with 512 atoms Loop time of 3.73974 on 4 procs for 100 steps with 512 atoms
Performance: 0.865 ns/day, 27.741 hours/ns, 20.026 timesteps/s Performance: 1.155 ns/day, 20.776 hours/ns, 26.740 timesteps/s
99.5% CPU use with 4 MPI tasks x no OpenMP threads 98.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 4.8898 | 4.907 | 4.9329 | 0.8 | 98.27 Pair | 3.4687 | 3.5182 | 3.5985 | 2.7 | 94.07
Neigh | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00
Comm | 0.058815 | 0.084739 | 0.1019 | 6.1 | 1.70 Comm | 0.13897 | 0.21952 | 0.26888 | 10.7 | 5.87
Output | 0.000252 | 0.00038775 | 0.000777 | 0.0 | 0.01 Output | 0.00018191 | 0.00047094 | 0.0012944 | 0.0 | 0.01
Modify | 0.000262 | 0.00026675 | 0.000272 | 0.0 | 0.01 Modify | 0.00013065 | 0.00013524 | 0.00014186 | 0.0 | 0.00
Other | | 0.001039 | | | 0.02 Other | | 0.001456 | | | 0.04
Nlocal: 128 ave 128 max 128 min Nlocal: 128 ave 128 max 128 min
Histogram: 4 0 0 0 0 0 0 0 0 0 Histogram: 4 0 0 0 0 0 0 0 0 0
@ -153,4 +154,4 @@ Ave neighs/atom = 122
Neighbor list builds = 0 Neighbor list builds = 0
Dangerous builds = 0 Dangerous builds = 0
Total wall time: 0:00:05 Total wall time: 0:00:03