Loading cmake/CMakeLists.txt +3 −3 Original line number Diff line number Diff line Loading @@ -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} Loading @@ -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) Loading examples/kim/log.11Jul2018.kim.lj.lmp.newton-off.ubuntu.1→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-off.1 +13 −24 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading examples/kim/log.11Jul2018.kim.lj.lmp.newton-off.ubuntu.4→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-off.4 +14 −25 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading @@ -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 examples/kim/log.11Jul2018.kim.lj.lmp.newton-on.ubuntu.1→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-on.1 +13 −24 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading examples/kim/log.11Jul2018.kim.lj.lmp.newton-on.ubuntu.4→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-on.4 +14 −25 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading @@ -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 Loading
cmake/CMakeLists.txt +3 −3 Original line number Diff line number Diff line Loading @@ -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} Loading @@ -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) Loading
examples/kim/log.11Jul2018.kim.lj.lmp.newton-off.ubuntu.1→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-off.1 +13 −24 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading
examples/kim/log.11Jul2018.kim.lj.lmp.newton-off.ubuntu.4→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-off.4 +14 −25 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading @@ -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
examples/kim/log.11Jul2018.kim.lj.lmp.newton-on.ubuntu.1→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-on.1 +13 −24 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading
examples/kim/log.11Jul2018.kim.lj.lmp.newton-on.ubuntu.4→examples/kim/log.12Dec2018.in.kim.lj.lmp.newton-on.4 +14 −25 Original line number Diff line number Diff line -------------------------------------------------------------------------- [[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 Loading @@ -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 Loading @@ -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
