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CMakeLists.txt
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CMakeLists.txt
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cmake_minimum_required(VERSION 3.12)
project(HyPhy)
#cmake_policy(VERSION 3.0.0)
enable_testing()
#enable_language(Fortran)
set(CMAKE_CONFIGURATION_TYPES Release)
#-------------------------------------------------------------------------------
# OPTIONS
#-------------------------------------------------------------------------------
option(NOAVX OFF)
option(NOSSE4 OFF)
option(NONEON OFF)
option(NOZLIB OFF)
option(NOBLAS OFF)
if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
set(NOAVX ON)
#set(NOSSE4 ON)
set(NONEON ON)
set(NOZLIB ON)
set(LIBRARY_PATH "/hyphy")
#set(CMAKE_EXECUTABLE_SUFFIX ".html")
add_definitions (-D_USE_EMSCRIPTEN_)
endif()
#-------------------------------------------------------------------------------
# SSE MACROS
#-------------------------------------------------------------------------------
macro(PCL_CHECK_FOR_SSE4)
include(CheckCXXSourceRuns)
set(CMAKE_REQUIRED_FLAGS)
#if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
set(CMAKE_REQUIRED_FLAGS "-msse4.1")
#endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
check_cxx_source_runs("
#include <smmintrin.h>
#include <stdio.h>
int main ()
{
__m128d a, b;
double vals[2] = {0};
a = _mm_loadu_pd (vals);
b = _mm_hadd_pd (a,a);
_mm_storeu_pd (vals, _mm_blend_pd (a,b,2));
printf (\"%g\", vals[0]);
return (0);
}"
HAVE_SSE4_EXTENSIONS)
endmacro(PCL_CHECK_FOR_SSE4)
#-------------------------------------------------------------------------------
# NEON MACROS
#-------------------------------------------------------------------------------
macro(PCL_CHECK_FOR_NEON)
include(CheckCXXSourceRuns)
set(CMAKE_REQUIRED_FLAGS)
check_cxx_source_runs("
#include <stdio.h>
#include <arm_neon.h>
int main() {
double array[4] = {4.,2.,3.,4};
float64x2_t a1 = vld1q_f64 (array),
a2 = vld1q_f64 (array+2);
a1 = vmulq_f64 (a1,a2);
vst1q_lane_f64 (array, a1, 0);
printf (\"%g\", array[0]);
return 0;
}"
HAVE_NEON_EXTENSIONS)
endmacro(PCL_CHECK_FOR_NEON)
#-------------------------------------------------------------------------------
# SSE MACROS
#-------------------------------------------------------------------------------
macro(PCL_CHECK_FOR_AVX)
include(CheckCXXSourceRuns)
set(CMAKE_REQUIRED_FLAGS)
#if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
set(CMAKE_REQUIRED_FLAGS "-mavx2")
#endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
check_cxx_source_runs("
#include <immintrin.h>
#include <stdio.h>
int main ()
{
__m256d a, b;
double vals[4] = {0.};
a = _mm256_loadu2_m128d (vals, vals+2);
b = _mm256_permute4x64_pd (_mm256_hadd_pd (a,a), 2);
_mm256_storeu_pd (vals, b);
printf (\"%g\", vals[0]);
return (0);
}"
HAVE_AVX_EXTENSIONS)
endmacro(PCL_CHECK_FOR_AVX)
#-------------------------------------------------------------------------------
# FMA3 MACROS
#-------------------------------------------------------------------------------
macro(PCL_CHECK_FOR_FMA3)
include(CheckCXXSourceRuns)
set(CMAKE_REQUIRED_FLAGS)
#if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
set(CMAKE_REQUIRED_FLAGS "-mavx2 -mfma ")
#endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX OR CMAKE_COMPILER_IS_CLANG)
check_cxx_source_runs("
#include <immintrin.h>
#include <stdio.h>
int main ()
{
__m256d a, b, c;
double vals[4] = {2.};
a = _mm256_loadu_pd (vals);
b = _mm256_loadu_pd (vals);
c = _mm256_loadu_pd (vals);
a = _mm256_fmadd_pd (a, b, c);
_mm256_storeu_pd (vals, a);
printf (\"%g\", vals[0]);
return 0;
}"
HAVE_FMA3)
endmacro(PCL_CHECK_FOR_FMA3)
#-------------------------------------------------------------------------------
# set the CMAKE_MODULE_PATH so we can import OpenCL
#-------------------------------------------------------------------------------
set(CMAKE_MODULE_PATH cmake)
set(HYPHY_VERSION 2.1)
#-------------------------------------------------------------------------------
# setup the files we'll be using
#-------------------------------------------------------------------------------
file(GLOB SRC_CORE src/core/*.cpp)
file(GLOB SRC_NEW src/new/*.cpp)
file(GLOB SRC_CONTRIB src/contrib/*.cpp)
set(SRC_LINK src/lib/link/THyPhy.cpp)
set(SRC_SQLITE3 contrib/SQLite-3.8.2/sqlite3.c)
set(SRC_UNIXMAIN src/mains/unix.cpp)
set(SRC_UTILS src/utils/hyphyunixutils.cpp)
set(SRC_COMMON ${SRC_CORE} ${SRC_NEW} ${SRC_SQLITE3} ${SRC_UTILS} ${SRC_CONTRIB})
set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")
#-------------------------------------------------------------------------------
# make it fast, scotty
#-------------------------------------------------------------------------------
set(DEFAULT_WARNING_FLAGS " -w -Weffc++ -Wextra -Wall ")
set(DEFAULT_DEBUG_WARNING_FLAGS "-Wall -Wno-int-to-pointer-cast -Wno-conversion-null -Wno-sign-compare")
set(ADDITIONAL_FLAGS "-g")
if (DEBUGFLAGS)
set(ADDITIONAL_FLAGS "-g")
endif()
#include_directories("/Library/Developer/CommandLineTools/SDKs/MacOSX15.2.sdk/usr/include/c++/v1")
if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
execute_process(
COMMAND ${CMAKE_CXX_COMPILER} -dumpversion
OUTPUT_VARIABLE GCC_VERSION
)
if (${GCC_VERSION} VERSION_LESS 4.9)
message(FATAL_ERROR "Require at least gcc-4.9")
endif()
if(${GCC_VERSION} VERSION_LESS 6.0)
set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=gnu++14")
else(${GCC_VERSION} VERSION_LESS 6.0)
set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -Wall -std=c++14")
endif(${GCC_VERSION} VERSION_LESS 6.0)
#set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fopt-info")
if(NOAVX)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-avx")
if(NOSSE4)
if(NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-sse3")
endif()
else(NOSSE4)
PCL_CHECK_FOR_SSE4()
if(${HAVE_SSE4_EXTENSIONS})
add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msimd128 ")
endif()
endif(${HAVE_SSE4_EXTENSIONS})
endif(NOSSE4)
else(NOAVX)
PCL_CHECK_FOR_AVX()
if(${HAVE_AVX_EXTENSIONS})
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx2")
add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
PCL_CHECK_FOR_FMA3()
if (${HAVE_FMA3})
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mfma")
add_definitions (-D_SLKP_USE_FMA3_INTRINSICS)
endif (${HAVE_FMA3})
else(${HAVE_AVX_EXTENSIONS})
PCL_CHECK_FOR_SSE4()
if(${HAVE_SSE4_EXTENSIONS})
add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
endif(${HAVE_SSE4_EXTENSIONS})
endif(${HAVE_AVX_EXTENSIONS})
endif(NOAVX)
if(NOT NONEON)
PCL_CHECK_FOR_NEON()
if(${HAVE_NEON_EXTENSIONS})
add_definitions (-D_SLKP_USE_ARM_NEON)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mcpu=native -mtune=native ")
endif(${HAVE_NEON_EXTENSIONS})
endif(NOT NONEON)
set(DEFAULT_LINK_FLAGS "${DEFAULT_COMPILE_FLAGS}")
endif(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
if (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
#set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -fsave-optimization-record=yaml ")
set(DEFAULT_COMPILE_FLAGS "-fsigned-char -O3 -D_FORTIFY_SOURCE=2 -std=c++14 -Wall")
if(NOAVX)
if(NOSSE4)
if(NOT CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mno-sse3")
endif()
else(NOSSE4)
PCL_CHECK_FOR_SSE4()
if("${HAVE_SSE4_EXTENSIONS}" OR ${CMAKE_SYSTEM_NAME} STREQUAL "Emscripten")
add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msimd128 ")
endif()
endif()
endif(NOSSE4)
else(NOAVX)
PCL_CHECK_FOR_AVX()
if(${HAVE_AVX_EXTENSIONS})
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -march=native -mtune=native -mavx2")
add_definitions (-D_SLKP_USE_AVX_INTRINSICS)
PCL_CHECK_FOR_FMA3()
if (${HAVE_FMA3})
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mfma")
add_definitions (-D_SLKP_USE_FMA3_INTRINSICS)
endif (${HAVE_FMA3})
else(${HAVE_AVX_EXTENSIONS})
PCL_CHECK_FOR_SSE4()
if(${HAVE_SSE4_EXTENSIONS})
add_definitions (-D_SLKP_USE_SSE_INTRINSICS)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -msse4.1 ")
endif(${HAVE_SSE4_EXTENSIONS})
endif (${HAVE_AVX_EXTENSIONS})
endif(NOAVX)
if(NOT NONEON)
PCL_CHECK_FOR_NEON()
if(${HAVE_NEON_EXTENSIONS})
add_definitions (-D_SLKP_USE_ARM_NEON)
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -mcpu=native -mtune=native ")
endif(${HAVE_NEON_EXTENSIONS})
endif(NOT NONEON)
set_property(
SOURCE ${SRC_CORE} ${SRC_NEW} ${SRC_UTILS} ${SRC_UNIXMAIN}
APPEND_STRING PROPERTY COMPILE_FLAGS " -std=c++14 "
)
endif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
#set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fopt-info -fopt-info-vec-missed")
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${ADDITIONAL_FLAGS}")
if(NOT DEFINED DEFAULT_COMPILE_FLAGS)
set(DEFAULT_COMPILE_FLAGS "")
endif(NOT DEFINED DEFAULT_COMPILE_FLAGS)
if(NOT DEFINED DEFAULT_LINK_FLAGS)
set(DEFAULT_LINK_FLAGS "")
endif(NOT DEFINED DEFAULT_LINK_FLAGS)
set(DEFAULT_LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${ADDITIONAL_FLAGS}")
if(NOT DEFINED DEFAULT_WARNING_FLAGS)
set(DEFAULT_WARNING_FLAGS "")
endif(NOT DEFINED DEFAULT_WARNING_FLAGS)
if(CMAKE_SYSTEM_NAME STREQUAL "Emscripten")
set(DEFAULT_COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -fwasm-exceptions ")
endif()
MESSAGE ("Set compiler flags to ${DEFAULT_COMPILE_FLAGS}")
MESSAGE ("Set linker flags to ${DEFAULT_LINK_FLAGS}")
set(BLA_VENDOR Apple)
find_package(BLAS)
#-------------------------------------------------------------------------------
# OpenMP support
#-------------------------------------------------------------------------------
find_package(OpenMP)
# emulate missing OpenMP for testing
#set (OPENMP_FOUND FALSE)
#set (OpenMP_CXX_FLAGS "")
#-------------------------------------------------------------------------------
# default installation prefix
#-------------------------------------------------------------------------------
if(NOT DEFINED CMAKE_INSTALL_PREFIX)
set(CMAKE_INSTALL_PREFIX "/usr/local" CACHE PATH "Installation prefix")
endif()
if(NOT DEFINED INSTALL_PREFIX)
set(INSTALL_PREFIX ${CMAKE_INSTALL_PREFIX} CACHE INTERNAL "Installation prefix" FORCE)
endif()
if(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
set(DEFAULT_LIBRARIES )
else(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
set(DEFAULT_LIBRARIES dl)
endif(CMAKE_SYSTEM_NAME MATCHES "FreeBSD")
#-------------------------------------------------------------------------------
# LIBCurl support
#-------------------------------------------------------------------------------
find_package(CURL)
if(${CURL_FOUND})
message(${CURL_LIBRARIES})
list(APPEND DEFAULT_LIBRARIES ${CURL_LIBRARIES})
add_definitions (-D__HYPHYCURL__)
endif(${CURL_FOUND})
if(NOT NOZLIB)
find_package(ZLIB 1.2.9)
if(${ZLIB_FOUND})
list(APPEND DEFAULT_LIBRARIES ${ZLIB_LIBRARIES})
include_directories(${ZLIB_INCLUDE_DIRS})
add_definitions (-D__ZLIB__)
endif(${ZLIB_FOUND})
endif(NOT NOZLIB)
#-------------------------------------------------------------------------------
# uninstall target
#-------------------------------------------------------------------------------
configure_file(
"${CMAKE_CURRENT_SOURCE_DIR}/cmake/cmake_uninstall.cmake.in"
"${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake"
IMMEDIATE @ONLY
)
add_custom_target(uninstall
COMMAND ${CMAKE_COMMAND} -P ${CMAKE_CURRENT_BINARY_DIR}/cmake_uninstall.cmake
)
find_program(NODE npm)
if(NOT NODE)
message("Node not installed; API documentation will not be generated")
else(NOT NODE)
add_custom_target(
docs
rm -rf ./docs && npm install -g documentation@4 && documentation build --polyglot -f md ./res/TemplateBatchFiles/libv3/**/*.bf -o ./docs.md
)
endif(NOT NODE)
#-------------------------------------------------------------------------------
# setup some source properties so that we don't spam stdout
#-------------------------------------------------------------------------------
set_property(
SOURCE ${SRC_CORE}
APPEND_STRING PROPERTY COMPILE_FLAGS "${DEFAULT_WARNING_FLAGS}"
)
set_property(
SOURCE ${SRC_SQLITE3}
APPEND_STRING PROPERTY COMPILE_FLAGS " -Wno-int-to-pointer-cast -Wno-pointer-to-int-cast -std=c99"
)
set_property(
SOURCE src/core/calcnode2.cpp
APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"
)
set_property(
SOURCE ${SRC_CORE}
APPEND_STRING PROPERTY COMPILE_FLAGS " -Wno-int-to-pointer-cast"
)
#-------------------------------------------------------------------------------
# shared compilation definitions and header includes
#-------------------------------------------------------------------------------
add_definitions(-D_SLKP_LFENGINE_REWRITE_ -D__AFYP_REWRITE_BGM__)
include_directories(
src/core/include
src/contrib
src/lib/Link src/new/include
contrib/SQLite-3.8.2 # SQLite
)
if (${BLAS_FOUND} AND NOT NOBLAS)
add_definitions (-D_SLKP_USE_APPLE_BLAS)
set(DEFAULT_LIBRARIES "${DEFAULT_LIBRARIES}")
endif()
#-------------------------------------------------------------------------------
# shared hyphy hbl stdlib target
#-------------------------------------------------------------------------------
install(DIRECTORY res/ DESTINATION share/hyphy)
#-------------------------------------------------------------------------------
# HYPHYMP target
#-------------------------------------------------------------------------------
add_executable(
hyphy
${SRC_COMMON} ${SRC_UNIXMAIN}
)
if(${OPENMP_FOUND})
target_link_libraries(hyphy PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
else(${OPENMP_FOUND})
target_link_libraries(hyphy PRIVATE ${DEFAULT_LIBRARIES})
endif(${OPENMP_FOUND})
if(${BLAS_FOUND} AND NOT NOBLAS)
target_link_libraries(hyphy PRIVATE ${BLAS_LIBRARIES})
endif ()
add_custom_target(MP DEPENDS hyphy)
install(
TARGETS hyphy
RUNTIME DESTINATION bin
OPTIONAL
)
if (NOT DEFINED LIBRARY_PATH)
set(LIBRARY_PATH "${CMAKE_INSTALL_PREFIX}/share/hyphy")
endif()
MESSAGE (${LIBRARY_PATH})
#-------------------------------------------------------------------------------
# hyphy mpi target
#-------------------------------------------------------------------------------
find_package(MPI)
if(${MPI_FOUND})
add_executable(
HYPHYMPI
EXCLUDE_FROM_ALL
${SRC_COMMON} ${SRC_UNIXMAIN}
)
include_directories(${MPI_INCLUDE_PATH})
if(${OPENMP_FOUND})
target_link_libraries(HYPHYMPI ${DEFAULT_LIBRARIES} ${MPI_LIBRARIES} OpenMP::OpenMP_CXX)
else(${OPENMP_FOUND})
target_link_libraries(HYPHYMPI ${DEFAULT_LIBRARIES} ${MPI_LIBRARIES})
endif(${OPENMP_FOUND})
if(${BLAS_FOUND} AND NOT NOBLAS)
target_link_libraries(HYPHYMPI ${BLAS_LIBRARIES})
endif ()
install(
TARGETS HYPHYMPI
RUNTIME DESTINATION bin
OPTIONAL
)
add_custom_target(MPI DEPENDS HYPHYMPI)
# set definitions here 'cause "s_t_p" below doesn't like lists
set_property(
TARGET HYPHYMPI
APPEND PROPERTY COMPILE_DEFINITIONS __HYPHYMPI__ __UNIX__ _HYPHY_LIBDIRECTORY_="${LIBRARY_PATH}"
)
message ("${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS}")
set_target_properties(
HYPHYMPI
PROPERTIES
if(${OPENMP_FOUND})
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS}"
LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
else(${OPENMP_FOUND})
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${MPI_COMPILE_FLAGS}"
LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${MPI_LINK_FLAGS}"
endif(${OPENMP_FOUND})
)
endif(${MPI_FOUND})
#-------------------------------------------------------------------------------
# hyphy profile target
#-------------------------------------------------------------------------------
add_executable(
HYPHYPROFILE
EXCLUDE_FROM_ALL
${SRC_COMMON} ${SRC_UNIXMAIN}
)
if(${OPENMP_FOUND})
target_link_libraries(HYPHYPROFILE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
else(${OPENMP_FOUND})
target_link_libraries(HYPHYPROFILE ${DEFAULT_LIBRARIES})
endif(${OPENMP_FOUND})
add_custom_target(PROFILE DEPENDS HYPHYPROFILE)
set_target_properties(
HYPHYPROFILE
PROPERTIES
if(${OPENMP_FOUND})
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-generate -fanalyzer "
LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} -g -fprofile-generate -fanalyzer "
else(${OPENMP_FOUND})
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS}-g -fprofile-generate -fanalyzer "
LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} -g -fprofile-generate -fanalyzer "
endif(${OPENMP_FOUND})
)
#-------------------------------------------------------------------------------
# hyphy profile target
#-------------------------------------------------------------------------------
add_executable(
HYPHYGPERF
EXCLUDE_FROM_ALL
${SRC_COMMON} ${SRC_UNIXMAIN}
)
if(${OPENMP_FOUND})
target_link_libraries(HYPHYGPERF PRIVATE ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
else(${OPENMP_FOUND})
target_link_libraries(HYPHYGPERF PRIVATE ${DEFAULT_LIBRARIES})
endif(${OPENMP_FOUND})
add_custom_target(GPERF DEPENDS HYPHYGPERF)
set_target_properties(
HYPHYGPERF
PROPERTIES
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} -g"
LINK_FLAGS "${DEFAULT_LINK_FLAGS} -g -lprofiler -ltcmalloc"
endif(${OPENMP_FOUND})
)
#-------------------------------------------------------------------------------
# hyphy debug target
#-------------------------------------------------------------------------------
add_executable(
HYPHYDEBUG
EXCLUDE_FROM_ALL
${SRC_COMMON} ${SRC_UNIXMAIN}
)
if(${OPENMP_FOUND})
target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES} OpenMP::OpenMP_CXX)
else(${OPENMP_FOUND})
target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES})
endif(${OPENMP_FOUND})
target_link_libraries(HYPHYDEBUG ${DEFAULT_LIBRARIES})
add_custom_target(DEBUG DEPENDS HYPHYDEBUG)
if(${BLAS_FOUND})
target_link_libraries(HYPHYDEBUG ${BLAS_LIBRARIES})
endif ()
set_target_properties(
HYPHYDEBUG
PROPERTIES
if(${OPENMP_FOUND})
#COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} ${MPI_COMPILE_FLAGS} -g -fsanitize=address -O0 "
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} ${OpenMP_CXX_FLAGS} ${MPI_COMPILE_FLAGS} -g -fsanitize=address -O0 "
LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} ${OpenMP_CXX_FLAGS} ${MPI_LINK_FLAGS} -g -fsanitize=address -O0 "
else(${OPENMP_FOUND})
#COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -g -fsanitize=address -O0 "
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_DEBUG_WARNING_FLAGS} -g -fsanitize=address -O0 "
LINK_FLAGS "${DEFAULT_COMPILE_FLAGS} -g -fsanitize=address -O0 "
endif(${OPENMP_FOUND})
)
#-------------------------------------------------------------------------------
# target-specific and occasionally-shared properties
#-------------------------------------------------------------------------------
if(UNIX)
set_property(
TARGET hyphy HYPHYDEBUG HYPHYPROFILE HYPHYGPERF
APPEND PROPERTY COMPILE_DEFINITIONS __UNIX__
)
if(${SWIG_FOUND})
set_property(
TARGET LIBRARY
APPEND PROPERTY COMPILE_DEFINITIONS __UNIX__ __HEADLESS__
)
endif(${SWIG_FOUND})
endif(UNIX)
set_property(
TARGET hyphy
APPEND PROPERTY COMPILE_DEFINITIONS __MP__ __MP2__
)
set_property(
TARGET hyphy HYPHYDEBUG HYPHYPROFILE
APPEND PROPERTY COMPILE_DEFINITIONS _HYPHY_LIBDIRECTORY_="${LIBRARY_PATH}"
)
set_property(
TARGET HYPHYDEBUG
APPEND PROPERTY COMPILE_DEFINITIONS __HYPHYDEBUG__
)
set_target_properties(
hyphy
PROPERTIES
if(${OPENMP_FOUND})
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS} ${OpenMP_CXX_FLAGS}"
LINK_FLAGS "${DEFAULT_LINK_FLAGS} ${OpenMP_CXX_FLAGS}"
else(${OPENMP_FOUND})
COMPILE_FLAGS "${DEFAULT_COMPILE_FLAGS} ${DEFAULT_WARNING_FLAGS}"
LINK_FLAGS "${DEFAULT_LINK_FLAGS}"
endif(${OPENMP_FOUND})
)
macro(makeLink src dest target)
add_custom_command(TARGET ${target} POST_BUILD
COMMAND ln -sf ${dest} ${src} DEPENDS ${dest} COMMENT "mklink ${src} -> ${dest}")
endmacro()
makeLink(HYPHYMP hyphy hyphy)
#-------------------------------------------------------------------------------
# TESTS
#-------------------------------------------------------------------------------
add_test (NAME UNIT-TESTS COMMAND bash run_unit_tests.sh)
add_test (CODON HYPHYMP tests/hbltests/SimpleOptimizations/SmallCodon.bf)
add_test (PROTEIN HYPHYMP tests/hbltests/SimpleOptimizations/IntermediateProtein.bf)
add_test (MTCODON HYPHYMP tests/hbltests/libv3/mtDNA-code.wbf)
add_test (ALGAE HYPHYMP tests/hbltests/libv3/algae-mtDNA.wbf)
add_test (CILIATES HYPHYMP tests/hbltests/libv3/ciliate-code.wbf)
add_test (NAME SLAC COMMAND HYPHYMP tests/hbltests/libv3/SLAC.wbf)
add_test (NAME SLAC-PARTITIONED COMMAND HYPHYMP tests/hbltests/libv3/SLAC-partitioned.wbf)
add_test (NAME FEL COMMAND HYPHYMP tests/hbltests/libv3/FEL.wbf)
add_test (MEME HYPHYMP tests/hbltests/libv3/MEME.wbf)
#add_test (MEME_MPI mpirun -np 4 HYPHYMPI tests/hbltests/libv3/MEME.wbf)
add_test (MEME-PARTITIONED HYPHYMP tests/hbltests/libv3/MEME-partitioned.wbf)
add_test (BUSTED HYPHYMP tests/hbltests/libv3/BUSTED.wbf)
add_test (BUSTED-SRV HYPHYMP tests/hbltests/libv3/BUSTED-SRV.wbf)
add_test (RELAX HYPHYMP tests/hbltests/libv3/RELAX.wbf)
add_test (FUBAR HYPHYMP tests/hbltests/libv3/FUBAR.wbf)
add_test (BGM HYPHYMP tests/hbltests/libv3/BGM.wbf)
add_test (CONTRAST-FEL HYPHYMP tests/hbltests/libv3/CFEL.wbf)
add_test (GARD HYPHYMP tests/hbltests/libv3/GARD.wbf ENV="TOLERATE_NUMERICAL_ERRORS=1;")
add_test (FADE HYPHYMP tests/hbltests/libv3/FADE.wbf)
add_test (ABSREL HYPHYMP tests/hbltests/libv3/ABSREL.wbf)
#add_test (FMM HYPHYMP tests/hbltests/libv3/FMM.wbf)
#add_test (NAME ABSREL-MH COMMAND HYPHYMP tests/hbltests/libv3/ABSREL-MH.wbf)