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Merge branch 'checkpoint-benchmarkIII' into 'master'
Checkpoint and Resilient execution benchmark additions See merge request kokkos-resilience/minimd!1
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| cmake_minimum_required(VERSION 3.12) | ||
| project(minimd) | ||
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| add_executable(minimd) | ||
| # Require C++14 | ||
| if (CMAKE_CXX_COMPILER MATCHES ".*nvcc_wrapper" ) | ||
| message("nvcc wrapper requires that CXX standard by set in kokkos build") | ||
| else() | ||
| target_compile_features(minimd PUBLIC cxx_std_14) | ||
| endif() | ||
|
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||
| # Options | ||
| option(MINIMD_SINGLE_PRECISION, "Use single precision" OFF) | ||
| if (MINIMD_SINGLE_PRECISION) | ||
| target_compile_definitions(minimd PRIVATE PRECISION=1) | ||
| else() | ||
| target_compile_definitions(minimd PRIVATE PRECISION=2) | ||
| endif() | ||
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| option(MINIMD_AUTOMATIC_CHECKPOINT "Use resilience automatic checkpointing" OFF) | ||
| option(MINIMD_MANUAL_CHECKPOINT "Use resilience manual checkpointing" OFF) | ||
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| target_compile_definitions(minimd PRIVATE PREC_TIMER) | ||
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| # Dependencies | ||
| if (MINIMD_USE_MPISTUB) | ||
| find_library( mpi_stub_ NAMES libmpi_stubs.a libmpi_stubs mpi_stubs HINTS ${PROJECT_SOURCE_DIR}/kokkos/MPI-Stubs ) | ||
| #add_library(mpi_stubs) | ||
| #target_link_libraries(minimd PRIVATE mpi_stubs) | ||
| target_link_libraries(minimd PRIVATE ${mpi_stub_}) | ||
| target_include_directories(minimd PUBLIC | ||
| ${PROJECT_SOURCE_DIR}/kokkos/MPI-Stubs | ||
| ) | ||
| else() | ||
| find_package(MPI REQUIRED) | ||
| target_link_libraries(minimd PRIVATE MPI::MPI_CXX) | ||
| endif() | ||
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||
| find_package(Kokkos REQUIRED NO_CMAKE_PACKAGE_REGISTRY) | ||
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| # Optional resilience | ||
| if(MINIMD_AUTOMATIC_CHECKPOINT OR MINIMD_MANUAL_CHECKPOINT OR MINIMD_RESILIENT_EXECUTION) | ||
| find_package(resilience REQUIRED) | ||
| target_link_libraries(minimd PRIVATE Kokkos::resilience) | ||
| target_compile_definitions(minimd PRIVATE MINIMD_RESILIENCE) | ||
| if(MINIMD_AUTOMATIC_CHECKPOINT) | ||
| target_compile_definitions(minimd PRIVATE KOKKOS_ENABLE_AUTOMATIC_CHECKPOINT) | ||
| endif() | ||
| if(MINIMD_MANUAL_CHECKPOINT) | ||
| target_compile_definitions(minimd PRIVATE KOKKOS_ENABLE_MANUAL_CHECKPOINT) | ||
| endif() | ||
| if(MINIMD_RESILIENT_EXECUTION) | ||
| target_compile_definitions(minimd PRIVATE KOKKOS_ENABLE_RESILIENT_EXECUTION) | ||
| endif() | ||
| endif() | ||
|
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| TARGET_LINK_KOKKOS(minimd PRIVATE) | ||
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| target_link_libraries(minimd PRIVATE "-L${resilience_LINK_DIRECTORIES}") | ||
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| # VeloC config | ||
| add_custom_command(TARGET minimd PRE_BUILD | ||
| COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/minimd.cfg ${CMAKE_CURRENT_BINARY_DIR}/minimd.cfg) | ||
|
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| # Other inputs | ||
|
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| add_custom_command(TARGET minimd PRE_BUILD | ||
| COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/kokkos/in.lj.miniMD ${CMAKE_CURRENT_BINARY_DIR}/in.lj.miniMD) | ||
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| add_custom_command(TARGET minimd PRE_BUILD | ||
| COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_CURRENT_SOURCE_DIR}/kokkos/Cu_u6.eam ${CMAKE_CURRENT_BINARY_DIR}/Cu_u6.eam) | ||
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| add_subdirectory(kokkos) | ||
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| ##get_cmake_property(_variableNames VARIABLES) | ||
| ##list (SORT _variableNames) | ||
| ##foreach (_variableName ${_variableNames}) | ||
| ## message(STATUS "${_variableName}=${${_variableName}}") | ||
| ##endforeach() | ||
|
|
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,14 @@ | ||
| target_sources(minimd PRIVATE | ||
| ${PROJECT_SOURCE_DIR}/kokkos/atom.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/comm.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/force_eam.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/force_lj.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/input.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/integrate.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/ljs.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/neighbor.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/output.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/setup.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/thermo.cpp | ||
| ${PROJECT_SOURCE_DIR}/kokkos/timer.cpp | ||
| ) |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,59 @@ | ||
| [ | ||
| { | ||
| "name":"atom", | ||
| "Layout_Config":{ | ||
| "data_set":"atom_dataset", | ||
| "rank":2, | ||
| "layout":"REGULAR", | ||
| "data_extents":["{DATA_SIZE}","{MPI_SIZE}"], | ||
| "local_extents":["{DATA_SIZE}","1"], | ||
| "offset":["0","{MPI_RANK}"], | ||
| "stride":["1","{MPI_SIZE}"], | ||
| "count":["1","1","1","1"], | ||
| "block":["{DATA_SIZE}","1"], | ||
| "local_offset":["0","0","0","0"], | ||
| "local_stride":["1","1","1","1"], | ||
| "local_count":["1","1","1","1"], | ||
| "local_block":["{DATA_SIZE}","1","1","1"], | ||
| "view_offset":["0","0"] | ||
| } | ||
| }, | ||
| { | ||
| "name":"velocity", | ||
| "Layout_Config":{ | ||
| "data_set":"velocity_dataset", | ||
| "rank":2, | ||
| "layout":"REGULAR", | ||
| "data_extents":["{DATA_SIZE}","{MPI_SIZE}"], | ||
| "local_extents":["{DATA_SIZE}","1"], | ||
| "offset":["0","{MPI_RANK}"], | ||
| "stride":["1","{MPI_SIZE}"], | ||
| "count":["1","1","1","1"], | ||
| "block":["{DATA_SIZE}","1"], | ||
| "local_offset":["0","0","0","0"], | ||
| "local_stride":["1","1","1","1"], | ||
| "local_count":["1","1","1","1"], | ||
| "local_block":["{DATA_SIZE}","1","1","1"], | ||
| "view_offset":["0","0"] | ||
| } | ||
| }, | ||
| { | ||
| "name":"force", | ||
| "Layout_Config":{ | ||
| "data_set":"force_dataset", | ||
| "rank":2, | ||
| "layout":"REGULAR", | ||
| "data_extents":["{DATA_SIZE}","{MPI_SIZE}"], | ||
| "local_extents":["{DATA_SIZE}","1"], | ||
| "offset":["0","{MPI_RANK}"], | ||
| "stride":["1","{MPI_SIZE}"], | ||
| "count":["1","1","1","1"], | ||
| "block":["{DATA_SIZE}","1"], | ||
| "local_offset":["0","0","0","0"], | ||
| "local_stride":["1","1","1","1"], | ||
| "local_count":["1","1","1","1"], | ||
| "local_block":["{DATA_SIZE}","1","1","1"], | ||
| "view_offset":["0","0"] | ||
| } | ||
| } | ||
| ] |
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