diff --git a/CMakeLists.txt b/CMakeLists.txt index 4cd7b13472961881d145be297834d22768ccdaa1..d1f4c7a64e63a4cdf51e8b11275bf763c2fb4792 100644 --- a/CMakeLists.txt +++ b/CMakeLists.txt @@ -99,7 +99,7 @@ if("${CMAKE_CXX_COMPILER_ID}" MATCHES "Clang") endif() elseif("${CMAKE_CXX_COMPILER_ID}" STREQUAL "GNU") # 去掉 -DMKL_LP64 -DEIGEN_USE_MKL_ALL -m64 - set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SSE} -pthread -fvisibility=hidden -fvisibility-inlines-hidden") + set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${SSE} -I ../submods/plink-ng/2.0/simde/ -pthread -fvisibility=hidden -fvisibility-inlines-hidden") set(CMAKE_CXX_FLAGS_RELEASE "${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) @@ -148,20 +148,14 @@ if(APPLE) else() if (CMAKE_CXX_COMPILER_ID MATCHES "Clang") # error keeps only - #target_link_libraries(gcta64 ${libs_list} mainV1 z ${KML_LIB - } iomp5 pthread m dl ) - #target_link_libraries(gcta64 mainV1 ${libs_list} z ${KML_LIB - } pthread m dl) + #target_link_libraries(gcta64 ${libs_list} mainV1 z ${KML_LIB} iomp5 pthread m dl ) + #target_link_libraries(gcta64 mainV1 ${libs_list} z ${KML_LIB} pthread m dl) # Dynamic link works - #target_link_libraries(gcta64 mainV1 ${libs_list} -Wl,-Bstatic z -Wl,--start-group ${KML_LIB - } -Wl,--end-group iomp5 -Wl,-Bdynamic pthread m dl) - target_link_libraries(gcta64 mainV1 ${libs_list} Pgenlib -static z sqlite3 zstd -Wl,--start-group ${KML_LIB - } -Wl,--end-group iomp5 -Wl,--whole-archive -lpthread -Wl,--no-whole-archive m dl) + #target_link_libraries(gcta64 mainV1 ${libs_list} -Wl,-Bstatic z -Wl,--start-group ${KML_LIB} -Wl,--end-group iomp5 -Wl,-Bdynamic pthread m dl) + target_link_libraries(gcta64 mainV1 ${libs_list} Pgenlib -static z sqlite3 zstd -Wl,--start-group ${KML_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 ${KML_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 ${KML_LIB - } -Wl,--end-group gomp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive m dl) + #target_link_libraries(gcta64 mainV1 ${libs_list} -Wl,-Bstatic z -Wl,--start-group ${KML_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 ${KML_LIB} -Wl,--end-group gomp -Wl,--whole-archive -lpthread -Wl,--no-whole-archive m dl) endif() endif() diff --git a/include/Matrix.hpp b/include/Matrix.hpp index f31aa83369efd5033ad5c172cd46522aa6a1f96c..8e4b9c205bfcdd77c6e45ff71482ebffc6a6fe01 100644 --- a/include/Matrix.hpp +++ b/include/Matrix.hpp @@ -2,7 +2,7 @@ #define GCTA2_MATRIX_H #include -#include +#include #include #include diff --git a/main/gcta.h b/main/gcta.h index a6049e8453dbf07b7ff122755faa211edc62f6d7..b870df5c0724dfe956a9d2a118e82c106e620a9f 100644 --- a/main/gcta.h +++ b/main/gcta.h @@ -37,8 +37,8 @@ #include #include #include -#include -#include +#include +#include #include "Logger.h" #include "Matrix.hpp" diff --git a/src/GRM.cpp b/src/GRM.cpp index 15cfedc03e99a7f8e82476db8f6497d1fc225d5d..78c7357ef7f1aa2b795741bb487401a2ea56a104 100644 --- a/src/GRM.cpp +++ b/src/GRM.cpp @@ -33,7 +33,7 @@ #include #include #include -#include +#include #include using std::to_string; diff --git a/src/LD.cpp b/src/LD.cpp index d34fa24c6547708fcfe677139bfc3fde3fef68d9..f83134188ace8f9298351020eff5c630a24532fe 100644 --- a/src/LD.cpp +++ b/src/LD.cpp @@ -7,7 +7,7 @@ #include #include #include -#include +#include #include #include diff --git a/src/StatLib.cpp b/src/StatLib.cpp index 4656ed2b02760a1815a8eb127bb5f0172f1c383c..fb2606ade5823ccd55e8f5321153dd5a79b85fbb 100644 --- a/src/StatLib.cpp +++ b/src/StatLib.cpp @@ -18,7 +18,7 @@ #include #include #include -#include +#include using namespace boost::math; diff --git a/test/tests/CMakeLists.txt b/test/tests/CMakeLists.txt index 8637b164c5ba17b422830d58668bc830c06cb15a..5bac532a5716f3599828e3c93e7e2e54c3ac0306 100644 --- a/test/tests/CMakeLists.txt +++ b/test/tests/CMakeLists.txt @@ -15,7 +15,7 @@ function(addTestItem test_name source lib_name run_param) ${lib_name} libgtest libgmock - -Wl,-Bstatic z -Wl,--start-group ${MKL_LIB} -Wl,--end-group gomp -Wl,-Bdynamic pthread m dl + -Wl,-Bstatic z -Wl,--start-group ${KML_LIB} -Wl,--end-group gomp -Wl,-Bdynamic pthread m dl ) add_test(${test_name} ${test_name} "${run_param}")