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Update for kim-api beta.3 release

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This commit is contained in:
Ryan S. Elliott
2018-12-12 16:21:54 -06:00
parent 03b1129abd
commit b068690e13
15 changed files with 310 additions and 391 deletions
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6
cmake/CMakeLists.txt
View File

@ -590,8 +590,8 @@ if(PKG_KIM)
enable_language(Fortran)
include(ExternalProject)
ExternalProject_Add(kim_build
URL https://s3.openkim.org/kim-api/kim-api-v2.0.0-beta.2.txz
URL_MD5 1fbdbb734059cf0dc9d807e6dd6cc8ea
URL https://s3.openkim.org/kim-api/kim-api-v2-2.0.0-beta.3.txz
URL_MD5 67c103a00e84865848d004837262c76e
BINARY_DIR build
CMAKE_ARGS -DCMAKE_C_COMPILER=${CMAKE_C_COMPILER}
-DCMAKE_CXX_COMPILER=${CMAKE_CXX_COMPILER}
@ -601,7 +601,7 @@ if(PKG_KIM)
)
ExternalProject_get_property(kim_build INSTALL_DIR)
set(KIM-API-V2_INCLUDE_DIRS ${INSTALL_DIR}/include/kim-api-v2)
set(KIM-API-V2_LIBRARIES ${INSTALL_DIR}/lib/libkim-api-v2.2${CMAKE_SHARED_LIBRARY_SUFFIX})
set(KIM-API-V2_LDFLAGS ${INSTALL_DIR}/lib/libkim-api-v2.2${CMAKE_SHARED_LIBRARY_SUFFIX})
list(APPEND LAMMPS_DEPS kim_build)
else()
find_package(KIM-API-V2)

68
examples/kim/log.11Jul2018.kim.lj.newton-off.ubuntu.1
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@ -1,68 +0,0 @@
--------------------------------------------------------------------------
[[5713,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.00256546 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: half, newton off, cut 8.45
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 21.26 | 21.26 | 21.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.69522 on 1 procs for 100 steps with 32000 atoms
Performance: 3.206 ns/day, 7.487 hours/ns, 37.103 timesteps/s
99.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3655 | 2.3655 | 2.3655 | 0.0 | 87.77
Neigh | 0.28659 | 0.28659 | 0.28659 | 0.0 | 10.63
Comm | 0.0061924 | 0.0061924 | 0.0061924 | 0.0 | 0.23
Output | 0.00034901 | 0.00034901 | 0.00034901 | 0.0 | 0.01
Modify | 0.025061 | 0.025061 | 0.025061 | 0.0 | 0.93
Other | | 0.01157 | | | 0.43
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2370499
Ave neighs/atom = 74.0781
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02

74
examples/kim/log.11Jul2018.kim.lj.newton-off.ubuntu.4
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@ -1,74 +0,0 @@
--------------------------------------------------------------------------
[[5673,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.00215514 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: half, newton off, cut 8.45
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 8.528 | 8.528 | 8.528 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 3.06157 on 4 procs for 100 steps with 32000 atoms
Performance: 2.822 ns/day, 8.504 hours/ns, 32.663 timesteps/s
24.4% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9964 | 2.0369 | 2.084 | 2.5 | 66.53
Neigh | 0.25048 | 0.27467 | 0.29605 | 3.1 | 8.97
Comm | 0.66611 | 0.71603 | 0.74496 | 3.6 | 23.39
Output | 0.00048383 | 0.00070085 | 0.00098836 | 0.0 | 0.02
Modify | 0.0064885 | 0.0065907 | 0.006806 | 0.2 | 0.22
Other | | 0.02664 | | | 0.87
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 630904 ave 632094 max 628209 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 2523614
Ave neighs/atom = 78.8629
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

68
examples/kim/log.11Jul2018.kim.lj.newton-on.ubuntu.1
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@ -1,68 +0,0 @@
--------------------------------------------------------------------------
[[5690,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.00258302 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: half, newton off, cut 8.45
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 20.87 | 20.87 | 20.87 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.7052 on 1 procs for 100 steps with 32000 atoms
Performance: 3.194 ns/day, 7.514 hours/ns, 36.966 timesteps/s
99.6% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.3715 | 2.3715 | 2.3715 | 0.0 | 87.67
Neigh | 0.28386 | 0.28386 | 0.28386 | 0.0 | 10.49
Comm | 0.012808 | 0.012808 | 0.012808 | 0.0 | 0.47
Output | 0.00033716 | 0.00033716 | 0.00033716 | 0.0 | 0.01
Modify | 0.02349 | 0.02349 | 0.02349 | 0.0 | 0.87
Other | | 0.01317 | | | 0.49
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 2.3705e+06 ave 2.3705e+06 max 2.3705e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 2370499
Ave neighs/atom = 74.0781
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02

74
examples/kim/log.11Jul2018.kim.lj.newton-on.ubuntu.4
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@ -1,74 +0,0 @@
--------------------------------------------------------------------------
[[5682,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.00322684 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (../pair_kim.cpp:955)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (../pair_kim.cpp:959)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: half, newton off, cut 8.45
pair build: half/bin/newtoff
stencil: half/bin/3d/newtoff
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 8.263 | 8.263 | 8.263 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 3.1366 on 4 procs for 100 steps with 32000 atoms
Performance: 2.755 ns/day, 8.713 hours/ns, 31.882 timesteps/s
23.7% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3641 | 1.4213 | 1.4783 | 3.5 | 45.31
Neigh | 0.25408 | 0.27714 | 0.29697 | 3.2 | 8.84
Comm | 1.3588 | 1.4045 | 1.4806 | 4.0 | 44.78
Output | 0.00055232 | 0.00072915 | 0.00087484 | 0.0 | 0.02
Modify | 0.0061178 | 0.0062019 | 0.0062811 | 0.1 | 0.20
Other | | 0.02673 | | | 0.85
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 630904 ave 632094 max 628209 min
Histogram: 1 0 0 0 0 0 0 1 0 2
Total # of neighbors = 2523614
Ave neighs/atom = 78.8629
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

37
examples/kim/log.11Jul2018.kim.lj.lmp.newton-off.ubuntu.1 → examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-off.1
View File

@ -1,22 +1,11 @@
--------------------------------------------------------------------------
[[6124,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.00263722 secs
Time spent = 0.00307703 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -37,20 +26,20 @@ Per MPI rank memory allocation (min/avg/max) = 20.37 | 20.37 | 20.37 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.59913 on 1 procs for 100 steps with 32000 atoms
Loop time of 2.58348 on 1 procs for 100 steps with 32000 atoms
Performance: 3.324 ns/day, 7.220 hours/ns, 38.474 timesteps/s
99.4% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 3.344 ns/day, 7.176 hours/ns, 38.707 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2753 | 2.2753 | 2.2753 | 0.0 | 87.54
Neigh | 0.28456 | 0.28456 | 0.28456 | 0.0 | 10.95
Comm | 0.0055908 | 0.0055908 | 0.0055908 | 0.0 | 0.22
Output | 0.00034594 | 0.00034594 | 0.00034594 | 0.0 | 0.01
Modify | 0.023011 | 0.023011 | 0.023011 | 0.0 | 0.89
Other | | 0.01037 | | | 0.40
Pair | 2.2621 | 2.2621 | 2.2621 | 0.0 | 87.56
Neigh | 0.28294 | 0.28294 | 0.28294 | 0.0 | 10.95
Comm | 0.0057185 | 0.0057185 | 0.0057185 | 0.0 | 0.22
Output | 0.00010109 | 0.00010109 | 0.00010109 | 0.0 | 0.00
Modify | 0.023396 | 0.023396 | 0.023396 | 0.0 | 0.91
Other | | 0.009175 | | | 0.36
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

39
examples/kim/log.11Jul2018.kim.lj.lmp.newton-off.ubuntu.4 → examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-off.4
View File

@ -1,22 +1,11 @@
--------------------------------------------------------------------------
[[6116,1],1]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.00125703 secs
Time spent = 0.000934124 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -37,20 +26,20 @@ Per MPI rank memory allocation (min/avg/max) = 8.013 | 8.013 | 8.013 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.99901 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.76167 on 4 procs for 100 steps with 32000 atoms
Performance: 2.881 ns/day, 8.331 hours/ns, 33.344 timesteps/s
24.4% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 11.343 ns/day, 2.116 hours/ns, 131.290 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.3704 | 1.4012 | 1.439 | 2.3 | 46.72
Neigh | 0.252 | 0.27028 | 0.28236 | 2.2 | 9.01
Comm | 0.66355 | 0.73942 | 0.82223 | 6.5 | 24.66
Output | 0.0037821 | 0.0090774 | 0.016142 | 5.1 | 0.30
Modify | 0.0058855 | 0.019317 | 0.044855 | 11.4 | 0.64
Other | | 0.5597 | | | 18.66
Pair | 0.65549 | 0.6589 | 0.66089 | 0.3 | 86.51
Neigh | 0.075691 | 0.075959 | 0.07641 | 0.1 | 9.97
Comm | 0.0073049 | 0.007397 | 0.0074785 | 0.1 | 0.97
Output | 5.6982e-05 | 0.00014746 | 0.00024986 | 0.0 | 0.02
Modify | 0.0068338 | 0.0068703 | 0.0068941 | 0.0 | 0.90
Other | | 0.0124 | | | 1.63
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@ -63,4 +52,4 @@ Total # of neighbors = 2523614
Ave neighs/atom = 78.8629
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03
Total wall time: 0:00:00

37
examples/kim/log.11Jul2018.kim.lj.lmp.newton-on.ubuntu.1 → examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-on.1
View File

@ -1,22 +1,11 @@
--------------------------------------------------------------------------
[[5635,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.00226572 secs
Time spent = 0.00311494 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -37,20 +26,20 @@ Per MPI rank memory allocation (min/avg/max) = 19.23 | 19.23 | 19.23 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.26274 on 1 procs for 100 steps with 32000 atoms
Loop time of 2.22646 on 1 procs for 100 steps with 32000 atoms
Performance: 3.818 ns/day, 6.285 hours/ns, 44.194 timesteps/s
99.0% CPU use with 1 MPI tasks x no OpenMP threads
Performance: 3.881 ns/day, 6.185 hours/ns, 44.914 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.0589 | 2.0589 | 2.0589 | 0.0 | 90.99
Neigh | 0.15362 | 0.15362 | 0.15362 | 0.0 | 6.79
Comm | 0.012277 | 0.012277 | 0.012277 | 0.0 | 0.54
Output | 0.0003387 | 0.0003387 | 0.0003387 | 0.0 | 0.01
Modify | 0.02416 | 0.02416 | 0.02416 | 0.0 | 1.07
Other | | 0.01346 | | | 0.59
Pair | 2.0344 | 2.0344 | 2.0344 | 0.0 | 91.38
Neigh | 0.14575 | 0.14575 | 0.14575 | 0.0 | 6.55
Comm | 0.01127 | 0.01127 | 0.01127 | 0.0 | 0.51
Output | 0.000103 | 0.000103 | 0.000103 | 0.0 | 0.00
Modify | 0.024057 | 0.024057 | 0.024057 | 0.0 | 1.08
Other | | 0.01083 | | | 0.49
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0

39
examples/kim/log.11Jul2018.kim.lj.lmp.newton-on.ubuntu.4 → examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-on.4
View File

@ -1,22 +1,11 @@
--------------------------------------------------------------------------
[[5659,1],0]: A high-performance Open MPI point-to-point messaging module
was unable to find any relevant network interfaces:
Module: OpenFabrics (openib)
Host: ubuntu-artful
Another transport will be used instead, although this may result in
lower performance.
NOTE: You can disable this warning by setting the MCA parameter
btl_base_warn_component_unused to 0.
--------------------------------------------------------------------------
LAMMPS (22 Jun 2018)
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.00213171 secs
Time spent = 0.000946045 secs
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
@ -37,20 +26,20 @@ Per MPI rank memory allocation (min/avg/max) = 7.632 | 7.632 | 7.632 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.44628 on 4 procs for 100 steps with 32000 atoms
Loop time of 0.639437 on 4 procs for 100 steps with 32000 atoms
Performance: 3.532 ns/day, 6.795 hours/ns, 40.878 timesteps/s
24.2% CPU use with 4 MPI tasks x no OpenMP threads
Performance: 13.512 ns/day, 1.776 hours/ns, 156.388 timesteps/s
99.7% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.98717 | 1.0434 | 1.1582 | 6.6 | 42.65
Neigh | 0.10195 | 0.12588 | 0.15258 | 5.2 | 5.15
Comm | 1.1525 | 1.2449 | 1.3061 | 5.1 | 50.89
Output | 0.0005828 | 0.00075188 | 0.00087256 | 0.0 | 0.03
Modify | 0.0057955 | 0.0059132 | 0.006044 | 0.1 | 0.24
Other | | 0.02542 | | | 1.04
Pair | 0.55655 | 0.55752 | 0.55833 | 0.1 | 87.19
Neigh | 0.040557 | 0.040752 | 0.041148 | 0.1 | 6.37
Comm | 0.024693 | 0.025886 | 0.026853 | 0.5 | 4.05
Output | 4.6015e-05 | 5.1558e-05 | 6.0081e-05 | 0.0 | 0.01
Modify | 0.0088108 | 0.0089263 | 0.0090554 | 0.1 | 1.40
Other | | 0.006306 | | | 0.99
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
@ -63,4 +52,4 @@ Total # of neighbors = 2126875
Ave neighs/atom = 66.4648
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:02
Total wall time: 0:00:00

59
examples/kim/log.12Dec2018.in.kim.lj.newton-off.1 Normal file
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@ -0,0 +1,59 @@
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.00450015 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 28.51 | 28.51 | 28.51 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 3.35585 on 1 procs for 100 steps with 32000 atoms
Performance: 2.575 ns/day, 9.322 hours/ns, 29.799 timesteps/s
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.9239 | 2.9239 | 2.9239 | 0.0 | 87.13
Neigh | 0.38492 | 0.38492 | 0.38492 | 0.0 | 11.47
Comm | 0.0072038 | 0.0072038 | 0.0072038 | 0.0 | 0.21
Output | 0.00010204 | 0.00010204 | 0.00010204 | 0.0 | 0.00
Modify | 0.028316 | 0.028316 | 0.028316 | 0.0 | 0.84
Other | | 0.01146 | | | 0.34
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

65
examples/kim/log.12Dec2018.in.kim.lj.newton-off.4 Normal file
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@ -0,0 +1,65 @@
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.00106215 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 10.05 | 10.05 | 10.05 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.930494 on 4 procs for 100 steps with 32000 atoms
Performance: 9.285 ns/day, 2.585 hours/ns, 107.470 timesteps/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.80926 | 0.81195 | 0.81464 | 0.3 | 87.26
Neigh | 0.089949 | 0.092688 | 0.095287 | 0.8 | 9.96
Comm | 0.007302 | 0.0074284 | 0.0075471 | 0.1 | 0.80
Output | 0.00012898 | 0.00014371 | 0.00016093 | 0.0 | 0.02
Modify | 0.011517 | 0.011761 | 0.011959 | 0.2 | 1.26
Other | | 0.006522 | | | 0.70
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

59
examples/kim/log.12Dec2018.in.kim.lj.newton-on.1 Normal file
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@ -0,0 +1,59 @@
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 1 by 1 MPI processor grid
Created 32000 atoms
Time spent = 0.0030508 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 28.12 | 28.12 | 28.12 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 2.97001 on 1 procs for 100 steps with 32000 atoms
Performance: 2.909 ns/day, 8.250 hours/ns, 33.670 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.5982 | 2.5982 | 2.5982 | 0.0 | 87.48
Neigh | 0.32516 | 0.32516 | 0.32516 | 0.0 | 10.95
Comm | 0.012059 | 0.012059 | 0.012059 | 0.0 | 0.41
Output | 0.000103 | 0.000103 | 0.000103 | 0.0 | 0.00
Modify | 0.023878 | 0.023878 | 0.023878 | 0.0 | 0.80
Other | | 0.01058 | | | 0.36
Nlocal: 32000 ave 32000 max 32000 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 19911 ave 19911 max 19911 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 0 ave 0 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 4.25375e+06 ave 4.25375e+06 max 4.25375e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:03

65
examples/kim/log.12Dec2018.in.kim.lj.newton-on.4 Normal file
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@ -0,0 +1,65 @@
LAMMPS (24 Oct 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
using 1 OpenMP thread(s) per MPI task
Lattice spacing in x,y,z = 4.43 4.43 4.43
Created orthogonal box = (0 0 0) to (88.6 88.6 88.6)
1 by 2 by 2 MPI processor grid
Created 32000 atoms
Time spent = 0.000946999 secs
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
WARNING: KIM Model does not provide `partialParticleEnergy'; energy per atom will be zero (src/KIM/pair_kim.cpp:1097)
WARNING: KIM Model does not provide `partialParticleVirial'; virial per atom will be zero (src/KIM/pair_kim.cpp:1102)
Neighbor list info ...
update every 1 steps, delay 0 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 8.45
ghost atom cutoff = 8.45
binsize = 4.225, bins = 21 21 21
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair kim, perpetual
attributes: full, newton off, cut 8.45
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Setting up Verlet run ...
Unit style : metal
Current step : 0
Time step : 0.001
Per MPI rank memory allocation (min/avg/max) = 9.789 | 9.789 | 9.789 Mbytes
Step Temp E_pair E_mol TotEng Press
0 200 6290.8194 0 7118.0584 129712.25
100 95.179725 6718.814 0 7112.496 133346.59
Loop time of 0.891065 on 4 procs for 100 steps with 32000 atoms
Performance: 9.696 ns/day, 2.475 hours/ns, 112.225 timesteps/s
99.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.75777 | 0.75864 | 0.75996 | 0.1 | 85.14
Neigh | 0.088332 | 0.088883 | 0.089737 | 0.2 | 9.97
Comm | 0.027187 | 0.02829 | 0.029602 | 0.6 | 3.17
Output | 4.9114e-05 | 5.4777e-05 | 6.6042e-05 | 0.0 | 0.01
Modify | 0.0088358 | 0.0089488 | 0.0091376 | 0.1 | 1.00
Other | | 0.00625 | | | 0.70
Nlocal: 8000 ave 8018 max 7967 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Nghost: 9131 ave 9164 max 9113 min
Histogram: 2 0 0 1 0 0 0 0 0 1
Neighs: 0 ave 0 max 0 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 1.06344e+06 ave 1.06594e+06 max 1.05881e+06 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 4253750
Ave neighs/atom = 132.93
Neighbor list builds = 3
Dangerous builds = 0
Total wall time: 0:00:00

3
lib/kim/.gitignore vendored
View File

@ -1,3 +1,2 @@
/Makefile.KIM_DIR
/Makefile.KIM_Config
/kim-prefix.txt
/installed-kim-api-*

8
lib/kim/Install.py
View File

@ -21,7 +21,7 @@ Syntax from lib dir: python Install.py -b -v version -a kim-name
specify one or more options, order does not matter
-v = version of KIM API library to use
default = kim-api-v2.0.0-beta.2 (current as of November 2018)
default = kim-api-v2.0.0-beta.3 (current as of December 2018)
-b = download and build base KIM API library with example Models
this will delete any previous installation in the current folder
-n = do NOT download and build base KIM API library.
@ -36,9 +36,9 @@ specify one or more options, order does not matter
Examples:
make lib-kim args="-b" # install KIM API lib with only example models
make lib-kim args="-a Glue_Ercolessi_Adams_Al__MO_324507536345_002" # Ditto plus one model
make lib-kim args="-a EAM_ErcolessiAdams_1994_Al__MO_324507536345_002" # Ditto plus one model
make lib-kim args="-b -a everything" # install KIM API lib with all models
make lib-kim args="-n -a EAM_Dynamo_Ackland_W__MO_141627196590_003" # only add one model or model driver
make lib-kim args="-n -a EAM_Dynamo_Ackland_2003_W__MO_141627196590_005" # only add one model or model driver
See the list of KIM model drivers here:
https://openkim.org/kim-items/model-drivers/alphabetical
@ -109,7 +109,7 @@ nargs = len(args)
if nargs == 0: error()
thisdir = os.environ['PWD']
version = "kim-api-v2.0.0-beta.2"
version = "kim-api-v2-2.0.0-beta.3"
buildflag = False
everythingflag = False