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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required(VERSION 3.10)
project(Sparc-MPI VERSION 0.1.0 LANGUAGES CXX)
#specify the C++ standard
set(CMAKE_STANDARD 11)
set(CMAKE_STANDARD_REQUIRED True)
set(CMAKE_CXX_STANDARD 11)
set(CMAKE_CXX_STANDARD_REQUIRED True)
if(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE Release)
endif()
set(CMAKE_CXX_FLAGS "-Wall -Wextra")
set(CMAKE_CXX_FLAGS_DEBUG "-g -ggdb -DDEBUG")
set(CMAKE_CXX_FLAGS_RELEASE "-O3 -s")
option(BUILD_SPARC_MIMIR "build Mimir version of Sparc" OFF)
option(BUILD_SPARC_MRMPI "build MR-MPI version of Sparc" OFF)
option(BUILD_SPARC_MPI "build pure MPI version of Sparc" OFF)
option(BUILD_SPARC_UPCXX "build UPCXX version of Sparc" OFF)
option(BUILD_SPARC_BCL "build bcl version of Sparc" OFF)
option(BUILD_WITH_LEVELDB "build MPI version of Sparc with leveldb support" OFF)
option(BUILD_WITH_MPIClient "build MPI version of Sparc with mpi client" OFF)
if(NOT DEFINED BCL_BACKEND)
set(BCL_BACKEND gasnet_ex) #mpi, shmem, gasnet_ex
endif()
set(LOCAL_EXT_PREFIX_DIR ${PROJECT_SOURCE_DIR}/extlib/local)
add_custom_target(sparc_mimir)
add_custom_target(sparc_mrmpi)
add_custom_target(sparc_mpi)
add_custom_target(sparc_upcxx)
add_custom_target(sparc_bcl)
include(cmake/CMakefile.external)
######### sparc mpi ##########################
configure_file(src/SparcConfig.h.in src/SparcConfig.h)
add_executable(test_utils src/test_utils.cpp src/sparc/utils.cpp)
add_executable(test_kmer src/test_kmer.cpp src/kmer.cpp src/sparc/utils.cpp)
target_include_directories(test_utils PUBLIC
"${PROJECT_BINARY_DIR}"
)
target_include_directories(test_kmer PUBLIC
"${PROJECT_BINARY_DIR}"
)
############## MRMPI programs ###########################
if(BUILD_SPARC_MRMPI)
#find_package(Boost 1.52 REQUIRED)
find_package(MPI 3.0 REQUIRED)
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib" )
add_executable(kmer_counting_mrmpi src/kmer_counting_mrmpi.cpp src/kmer.cpp src/sparc/utils.cpp)
add_executable(kmer_read_mapping_mrmpi src/kmer_read_mapping_mrmpi.cpp src/kmer.cpp src/sparc/utils.cpp)
add_executable(edge_generating_mrmpi src/edge_generating_mrmpi.cpp src/kmer.cpp src/sparc/utils.cpp)
foreach(EXEC kmer_counting_mrmpi kmer_read_mapping_mrmpi edge_generating_mrmpi)
add_dependencies(${EXEC} mrmpilib)
target_include_directories(${EXEC} PUBLIC "${LOCAL_EXT_PREFIX_DIR}/include/mrmpi" )
target_link_libraries(${EXEC} PUBLIC mrmpi)
target_include_directories(${EXEC} PUBLIC "${MPI_CXX_INCLUDE_DIRS}" )
target_link_libraries(${EXEC} PUBLIC ${MPI_CXX_LIBRARIES})
set_target_properties(${EXEC} PROPERTIES EXCLUDE_FROM_ALL TRUE)
add_dependencies(sparc_mrmpi ${EXEC})
endforeach(EXEC)
endif()
############## MIMIR programs ###########################
if(BUILD_SPARC_MIMIR)
find_package(MPI 3.0 REQUIRED)
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib" )
add_executable(kmer_counting_mimir src/kmer_counting_mimir.cpp src/kmer.cpp src/sparc/utils.cpp)
add_executable(kmer_read_mapping_mimir src/kmer_read_mapping_mimir.cpp src/kmer.cpp src/sparc/utils.cpp)
add_executable(edge_generating_mimir src/edge_generating_mimir.cpp src/kmer.cpp src/sparc/utils.cpp)
foreach(EXEC kmer_counting_mimir kmer_read_mapping_mimir edge_generating_mimir)
add_dependencies(${EXEC} mimirlib)
target_include_directories(${EXEC} PUBLIC "${LOCAL_EXT_PREFIX_DIR}/include" )
target_link_libraries(${EXEC} PUBLIC mimir)
target_include_directories(${EXEC} PUBLIC "${MPI_CXX_INCLUDE_DIRS}" )
target_link_libraries(${EXEC} PUBLIC ${MPI_CXX_LIBRARIES})
set_target_properties(${EXEC} PROPERTIES EXCLUDE_FROM_ALL TRUE)
add_dependencies(sparc_mimir ${EXEC})
endforeach(EXEC)
endif()
############# mpi programs ###########################
if(BUILD_SPARC_MPI)
find_package(MPI 3.0 REQUIRED)
find_package(ZLIB REQUIRED)
find_package(Threads REQUIRED)
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib" )
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib64" )
add_executable(test_lz4string src/test_lz4string.cpp src/sparc/LZ4String.cpp src/sparc/Message.cpp)
target_include_directories(test_lz4string PUBLIC "${LOCAL_EXT_PREFIX_DIR}/include" )
target_link_libraries(test_lz4string PUBLIC lz4 zmqpp zmq Threads::Threads)
add_executable(test_check_input_files src/test_check_input_files.cpp src/sparc/utils.cpp src/kmer.cpp src/sparc/log.cpp)
target_include_directories(test_check_input_files PUBLIC "${MPI_CXX_INCLUDE_DIRS}" )
target_include_directories(test_check_input_files PUBLIC "${LOCAL_EXT_PREFIX_DIR}/include" )
target_link_libraries(test_check_input_files PUBLIC spdlog ${MPI_CXX_LIBRARIES})
add_executable(kmer_counting_mpi
src/kmer_counting_mpi.cpp
src/kmer.cpp src/sparc/log.cpp
src/sparc/KmerCountingListener.cpp
src/sparc/KmerCountingClient.cpp
src/sparc/AbstractClient.cpp
src/sparc/AbstractListener.cpp
src/sparc/Message.cpp
src/sparc/DBHelper.cpp
src/sparc/LZ4String.cpp
src/sparc/utils.cpp
)
add_executable(kmer_read_mapping_mpi
src/kmer_read_mapping_mpi.cpp
src/kmer.cpp src/sparc/log.cpp
src/sparc/KmerCountingListener.cpp
src/sparc/KmerCountingClient.cpp
src/sparc/AbstractClient.cpp
src/sparc/AbstractListener.cpp
src/sparc/DBHelper.cpp
src/sparc/Message.cpp
src/sparc/LZ4String.cpp
src/sparc/utils.cpp
)
add_executable(edge_generating_mpi
src/edge_generating_mpi.cpp
src/kmer.cpp src/sparc/log.cpp
src/sparc/EdgeGeneratingListener.cpp
src/sparc/EdgeGeneratingClient.cpp
src/sparc/AbstractClient.cpp
src/sparc/AbstractListener.cpp
src/sparc/DBHelper.cpp
src/sparc/LZ4String.cpp
src/sparc/Message.cpp
src/sparc/utils.cpp
)
add_executable(merge_intrmed_mpi
src/merge_intrmed_mpi.cpp
src/sparc/MergeClient.cpp
src/sparc/MergeListener.cpp
src/sparc/KmerCountingListener.cpp
src/sparc/KmerCountingClient.cpp
src/sparc/AbstractListener.cpp
src/sparc/AbstractClient.cpp
src/sparc/DBHelper.cpp
src/sparc/LZ4String.cpp
src/sparc/Message.cpp
src/sparc/utils.cpp
src/kmer.cpp src/sparc/log.cpp
)
add_executable(lpav1_mpi
src/lpav1_mpi.cpp
src/sparc/LPAState.cpp
src/sparc/LPAClient.cpp
src/sparc/AbstractClient.cpp
src/sparc/AbstractListener.cpp
src/sparc/LPAListener.cpp
src/sparc/DBHelper.cpp
src/sparc/Message.cpp
src/sparc/LZ4String.cpp
src/sparc/utils.cpp
src/kmer.cpp src/sparc/log.cpp
)
foreach(EXEC kmer_counting_mpi kmer_read_mapping_mpi edge_generating_mpi merge_intrmed_mpi lpav1_mpi)
if(BUILD_WITH_MPIClient)
target_sources(${EXEC} PRIVATE src/sparc/MPIClient.cpp src/sparc/MPIListener.cpp)
target_compile_definitions(${EXEC} PUBLIC "-DUSE_MPICLIENT")
else()
target_sources( ${EXEC} PRIVATE src/sparc/ZMQClient.cpp src/sparc/ZMQListener.cpp )
endif()
if(BUILD_WITH_LEVELDB)
target_sources( ${EXEC} src/sparc/LevelDBHelper.cpp)
add_dependencies(${EXEC} leveldblib)
target_link_libraries(${EXEC} PUBLIC leveldb snappy)
set_target_properties(${EXEC} PROPERTIES COMPILE_FLAGS "-DBUILD_WITH_LEVELDB")
endif()
add_dependencies(${EXEC} lz4lib zmqpplib spdloglib gzstreamlib)
target_include_directories(${EXEC} PUBLIC "${LOCAL_EXT_PREFIX_DIR}/include" )
target_include_directories(${EXEC} PUBLIC "${MPI_CXX_INCLUDE_DIRS}" )
target_link_libraries(${EXEC} PUBLIC zmqpp zmq lz4 spdlog gzstream ZLIB::ZLIB Threads::Threads dl)
target_link_libraries(${EXEC} PUBLIC ${MPI_CXX_LIBRARIES})
set_target_properties(${EXEC} PROPERTIES EXCLUDE_FROM_ALL TRUE)
add_dependencies(sparc_mpi ${EXEC})
endforeach(EXEC)
#some specials
#set_target_properties(merge_intrmed_mpi PROPERTIES COMPILE_OPTIONS -DUSE_TSL_ROBIN_MAP )
target_compile_definitions(merge_intrmed_mpi PUBLIC "-DUSE_TSL_ROBIN_MAP")
add_dependencies(merge_intrmed_mpi tsl_robin_map_lib)
endif()
############# upcxx programs ###########################
if(BUILD_SPARC_UPCXX)
############# check UPCXX ##############################
set (UPCXX_VERBOSE ON)
include(cmake/UPCXXConfig.cmake)
if (NOT EXISTS "${UPCXX_META_EXECUTABLE}")
message( FATAL_ERROR "cannot find upcxx" )
endif()
############# end check UPCXX ##############################
find_package(MPI 3.0 REQUIRED)
find_package(ZLIB REQUIRED)
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib" )
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib64" )
add_executable(edge_generating_upcxx
src/edge_generating_upcxx.cpp
src/kmer.cpp src/sparc/log.cpp src/sparc/utils.cpp
)
add_executable(kmer_counting_upcxx
src/kmer_counting_upcxx.cpp
src/kmer.cpp src/sparc/log.cpp src/sparc/utils.cpp
)
add_executable(kmer_read_mapping_upcxx
src/kmer_read_mapping_upcxx.cpp
src/kmer.cpp src/sparc/log.cpp src/sparc/utils.cpp
)
add_executable(lpav1_upcxx
src/lpav1_upcxx.cpp
src/kmer.cpp src/sparc/log.cpp src/sparc/utils.cpp
)
foreach(EXEC edge_generating_upcxx kmer_counting_upcxx kmer_read_mapping_upcxx lpav1_upcxx)
add_dependencies(${EXEC} spdloglib gzstreamlib)
target_include_directories(${EXEC} PUBLIC ${UPCXX_INCLUDE_DIRS} "${LOCAL_EXT_PREFIX_DIR}/include" )
target_compile_definitions(${EXEC} PUBLIC ${UPCXX_DEFINITIONS})
target_compile_definitions(${EXEC} PUBLIC "-DUSE_UPCXXCLIENT")
target_link_libraries(${EXEC} PUBLIC ${MPI_CXX_LIBRARIES})
target_link_libraries(${EXEC} PUBLIC spdlog gzstream ZLIB::ZLIB ${UPCXX_LIBRARIES})
set_target_properties(${EXEC} PROPERTIES EXCLUDE_FROM_ALL TRUE)
add_dependencies(sparc_upcxx ${EXEC})
endforeach(EXEC)
endif()
############# bcl programs ###########################
if(BUILD_SPARC_BCL)
string( TOLOWER "${BCL_BACKEND}" BCL_BACKEND )
message("using backend ${BCL_BACKEND}")
find_package(Threads REQUIRED)
set(BCL_DEPENDIES bcllib)
set (UPCXX_VERBOSE ON)
include(cmake/UPCXXConfig.cmake)
if (NOT EXISTS "${UPCXX_META_EXECUTABLE}")
message( FATAL_ERROR "cannot find upcxx" )
endif()
if(BCL_BACKEND STREQUAL "shmem")
set(BCL_DEFINITIONS ${BCL_DEFINITIONS} -DGASNET_EX -DGASNET_SEQ)
set(BCL_LIBRARIES shmem shcoll shmemc-ucx shmemt shmemu pmix ucp)
link_directories(${EXEC} PUBLIC "$ENV{HOME}/local2/lib" )
include_directories(${EXEC} PUBLIC "$ENV{HOME}/local2/include" )
set(BCL_DEFINITIONS ${BCL_DEFINITIONS} -DSHMEM)
elseif(BCL_BACKEND STREQUAL "gasnet_ex")
set(BCL_INCLUDED_DIR ${UPCXX_INCLUDE_DIRS})
set(BCL_DEFINITIONS ${BCL_DEFINITIONS} -DGASNET_EX -DGASNET_SEQ)
set(BCL_LIBRARIES ${UPCXX_LIBRARIES})
elseif(BCL_BACKEND STREQUAL "mpi")
set(BCL_INCLUDED_DIR ${MPI_CXX_INCLUDE_DIRS})
else()
message( FATAL_ERROR "unknown backend ${BCL_BACKEND}" )
endif()
find_package(MPI 3.0 REQUIRED)
find_package(ZLIB REQUIRED)
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib" )
link_directories( "${LOCAL_EXT_PREFIX_DIR}/lib64" )
set(NAME "kmer_counting_bcl_${BCL_BACKEND}")
add_executable( ${NAME}
src/kmer_counting_bcl.cpp
src/kmer.cpp src/sparc/log.cpp src/sparc/utils.cpp
)
foreach(EXEC ${NAME} )
target_compile_features(${EXEC} PRIVATE cxx_std_17)
add_dependencies(${EXEC} spdloglib gzstreamlib ${BCL_DEPENDIES})
target_include_directories(${EXEC} PUBLIC ${BCL_INCLUDED_DIR} "${LOCAL_EXT_PREFIX_DIR}/include" )
target_compile_definitions(${EXEC} PUBLIC ${BCL_DEFINITIONS})
target_compile_definitions(${EXEC} PUBLIC "-DUSE_BCLCLIENT")
target_link_libraries(${EXEC} PUBLIC ${MPI_CXX_LIBRARIES})
target_link_libraries(${EXEC} PUBLIC spdlog gzstream ZLIB::ZLIB ${BCL_LIBRARIES})
set_target_properties(${EXEC} PROPERTIES EXCLUDE_FROM_ALL TRUE)
add_dependencies(sparc_bcl ${EXEC})
endforeach(EXEC)
endif()