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CMakeLists.txt
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CMAKE_MINIMUM_REQUIRED(VERSION 3.1)
SET(CMAKE_EXPORT_COMPILE_COMMANDS ON)
SET(PROJECT_NAME_STR GCTA2)
PROJECT(${PROJECT_NAME_STR} C CXX)
SET(CMAKE_INCLUDE_CURRENT_DIR ON)
SET(CMAKE_CXX_STANDARD 11)
SET(CMAKE_C_STANDARD 11)
# get system architecture
EXECUTE_PROCESS(COMMAND uname -m COMMAND tr -d '\n' OUTPUT_VARIABLE ARCHITECTURE)
set(CMAKE_LIBRARY_ARCHITECTURE ${ARCHITECTURE})
# fix win stack size issue
if(WIN32)
SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wl,--stack,10000000")
MESSAGE(FATAL_ERROR "Use the Visual Studio project file which located in gcta_win64 directory")
endif()
if("${CMAKE_SYSTEM_NAME}" MATCHES "Linux" OR "${CMAKE_SYSTEM_NAME}" MATCHES "Darwin")
MESSAGE("Linux and Mac are supported.")
else()
MESSAGE("Your system: ${CMAKE_SYSTEM_NAME}")
MESSAGE(FATAL_ERROR "Only Linux and Mac are currently supported.")
endif()
if (CMAKE_COMPILER_IS_GNUCC)
MESSAGE("Compiling by GCC${CMAKE_CXX_COMPILER_VERSION}")
if (NOT (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 6.0))
MESSAGE(FATAL_ERROR "GCTA can't build without GCC version >= 6.1")
endif()
elseif ("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
MESSAGE("Compiling by Clang${CMAKE_CXX_COMPILER_VERSION}")
if (NOT (CMAKE_CXX_COMPILER_VERSION VERSION_GREATER 8.0))
MESSAGE(FATAL_ERROR "GCTA can't build without Clang version >= 8.0")
endif()
else()
MESSAGE(FATAL_ERROR "GCTA can only compile with GCC or Clang")
endif()
SET(EIGEN3_INCLUDE_DIR "$ENV{EIGEN3_INCLUDE_DIR}")
IF(NOT EIGEN3_INCLUDE_DIR)
MESSAGE(FATAL_ERROR "Specify environment variable EIGEN3_INCLUDE_DIR to the location of Eigen3 package")
ENDIF()
INCLUDE_DIRECTORIES("${EIGEN3_INCLUDE_DIR}")
SET(SPECTRA_LIB "$ENV{SPECTRA_LIB}")
IF(NOT SPECTRA_LIB)
MESSAGE(FATAL_ERROR "Specify environment variable SPECTRA_LIB to the location of Spectra package")
ENDIF()
INCLUDE_DIRECTORIES("${SPECTRA_LIB}")
SET(BOOST_LIB "$ENV{BOOST_LIB}")
IF(NOT BOOST_LIB)
MESSAGE(FATAL_ERROR "Specify environment variable BOOST_LIB to the location of BOOST library")
ENDIF()
INCLUDE_DIRECTORIES("${BOOST_LIB}")
# PLINK2.0 pgen library;
INCLUDE_DIRECTORIES("submods/plink-ng/2.0")
INCLUDE_DIRECTORIES("submods/plink-ng/2.0/simde")
message(STATUS "ARCHITECTURE:${CMAKE_LIBRARY_ARCHITECTURE}")
if(CMAKE_LIBRARY_ARCHITECTURE STREQUAL "aarch64")
SET(OPENBLAS "$ENV{OPENBLAS}")
IF(NOT OPENBLAS)
MESSAGE(FATAL_ERROR "Specify environment variable OPENBLAS to the location of OPENBLAS package")
ENDIF()
INCLUDE_DIRECTORIES("${OPENBLAS}/include")
find_library(lib_openblas NAMES openblas PATHS "${OPENBLAS}" "${OPENBLAS}/lib")
set(BLAS_LIB ${lib_openblas})
if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -pthread")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g")
add_compile_options(-openmp)
set(CMAKE_EXE_LINKER_FLAGS "-Wl,-no_implicit_dylibs")
if(NOT APPLE)
# don't delete this it will result in _implibs
set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native -pthread -fvisibility=hidden -fvisibility-inlines-hidden")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG") #-flto
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -fno-inline -fno-implicit-inline-templates -g3")
add_compile_options(-fopenmp)
set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -openmp -pthread")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -ipo -DNDEBUG")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g")
endif()
else()
SET(MKLROOT "$ENV{MKLROOT}")
IF(NOT MKLROOT)
MESSAGE(FATAL_ERROR "Specify environment variable MKLROOT to the location of Intel MKL package")
ENDIF()
INCLUDE_DIRECTORIES("${MKLROOT}/include")
find_library(lib_lp64 NAMES mkl_intel_lp64 PATHS "${MKLROOT}/lib/intel64" "${MKLROOT}/lib")
if(CMAKE_CXX_COMPILER_ID MATCHES "Clang" OR APPLE)
find_library(lib_thread NAMES mkl_intel_thread PATHS "${MKLROOT}/lib/intel64" "${MKLROOT}/lib")
else()
find_library(lib_thread NAMES mkl_gnu_thread PATHS "${MKLROOT}/lib/intel64" "${MKLROOT}/lib")
endif()
find_library(lib_core NAMES mkl_core PATHS "${MKLROOT}/lib/intel64" "${MKLROOT}/lib")
set(BLAS_LIB ${lib_lp64} ${lib_thread} ${lib_core})
IF(NOT SSE)
set(SSE "-msse2")
message("SSE build")
ENDIF()
if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 ${SSE} -DMKL_LP64 -pthread")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g")
add_compile_options(-openmp)
set(CMAKE_EXE_LINKER_FLAGS "-Wl,-no_implicit_dylibs")
if(NOT APPLE)
# don't delete this it will result in _implibs
set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
endif()
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -m64 ${SSE} -pthread -DMKL_LP64 -fvisibility=hidden -fvisibility-inlines-hidden")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -DNDEBUG") #-flto
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -fno-inline -fno-implicit-inline-templates -g3")
add_compile_options(-fopenmp)
set(CMAKE_EXE_LINKER_FLAGS "-static-libgcc -static-libstdc++")
elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "Intel")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -openmp -axAVX2 -pthread")
set(CMAKE_CXX_FLAGS_RELEASE "${CMAKE_CXX_FLAGS_RELEASE} -O3 -ipo -DNDEBUG")
set(CMAKE_CXX_FLAGS_DEBUG "${CMAKE_CXX_FLAGS_DEBUG} -O0 -g")
elseif ("${CMAKE_CXX_COMPILER_ID}" STREQUAL "MSVC")
message(FALTAL_ERROR "GCTA can not compile by Microsft C++ compiler in CMake currently, please use gcta_win64 folder to build")
endif()
endif()
IF(NOT CMAKE_BUILD_TYPE)
set(CMAKE_BUILD_TYPE RELEASE)
message("Setting to release build")
ENDIF()
set(COMMON_INCLUDES ${PROJECT_SOURCE_DIR}/include)
set(MAIN_SOURCE "${PROJECT_SOURCE_DIR}/src/main.cpp")
include_directories(${COMMON_INCLUDES})
file(GLOB SRCS "${PROJECT_SOURCE_DIR}/src/*.cpp")
list(REMOVE_ITEM SRCS "${MAIN_SOURCE}")
list(APPEND SRCS "${PROJECT_SOURCE_DIR}/src/acat.c")
set(libs_list "")
foreach(_lib ${SRCS})
get_filename_component(file_name "${_lib}" NAME_WE)
string(TOLOWER ${file_name} lib_name)
add_library(${lib_name} STATIC "${_lib}")
list(APPEND libs_list ${lib_name})
endforeach(_lib)
add_subdirectory(main)
add_subdirectory(submods)
if(APPLE)
link_directories(${MKLROOT}/lib)
link_directories(/usr/local/lib)
else(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
#linux
link_directories(${MKLROOT}/../../../lib/intel64)
endif()
add_executable(gcta64 ${MAIN_SOURCE})
if(APPLE)
# iomp5
target_link_libraries(gcta64 ${libs_list} Pgenlib mainV1 z ${BLAS_LIB} sqlite3 zstd omp pthread m dl gsl gslcblas)
else()
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
# error keeps only
#target_link_libraries(gcta64 ${libs_list} mainV1 z ${MKL_LIB} iomp5 pthread m dl )
#target_link_libraries(gcta64 mainV1 ${libs_list} z ${MKL_LIB} pthread m dl)
# Dynamic link works
#target_link_libraries(gcta64 mainV1 ${libs_list} -Wl,-Bstatic z -Wl,--start-group ${MKL_LIB} -Wl,--end-group iomp5 -Wl,-Bdynamic pthread m dl)
target_link_libraries(gcta64 mainV1 ${libs_list} Pgenlib z sqlite3 zstd -Wl,--start-group ${BLAS_LIB} -Wl,--end-group iomp5 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive m dl)
else()
#target_link_libraries(gcta64 mainV1 ${libs_list} -Wl,-Bstatic z -Wl,--start-group ${MKL_LIB} -Wl,--end-group gomp -Wl,-Bdynamic pthread m dl)
#target_link_libraries(gcta64 mainV1 ${libs_list} Pgenlib -static z sqlite3 zstd -Wl,--start-group ${MKL_LIB} -Wl,--end-group gomp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive m dl)
target_link_libraries(gcta64 mainV1 -static ${libs_list} Pgenlib z sqlite3 zstd gsl gslcblas m -Wl,--start-group ${BLAS_LIB} -Wl,--end-group gomp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive m dl)
endif()
endif()
# Testing has some problems currently
#enable_testing()
#ADD_SUBDIRECTORY(test)
IF(EXISTS "${CMAKE_CURRENT_BINARY_DIR}/compile_commands.json")
EXECUTE_PROCESS( COMMAND ${CMAKE_COMMAND} -E copy_if_different
${CMAKE_CURRENT_BINARY_DIR}/compile_commands.json
${CMAKE_CURRENT_SOURCE_DIR}/compile_commands.json
)
ENDIF()