##################################################################
# IQ-TREE cmake build definition
# Copyright (c) 2012-2015 Bui Quang Minh, Lam-Tung Nguyen
##################################################################

# Windows example usages:
#------------------------
# cmake -G "Visual Studio 12" <source_dir>			(32-bit version, compiled with MSVC)
# cmake -G "Visual Studio 12 Win64" <source_dir>	(64-bit version, compiled with MSVC)
# cmake -G "Visual Studio 12 Win64" -T "Intel C++ Compiler XE 15.0" <source_dir>		(64-bit version, compiled with ICC)
# cmake -G "MinGW Makefiles" <source_dir> (TDM-GCC)
# cmake -G "Unix Makefiles" -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ -DCMAKE_MAKE_PROGRAM=mingw32-make <source_dir> (TDM-GCC and clang)

# Linux example usages:
#----------------------
# cmake <source_dir>						   (sequential version)
# cmake -DIQTREE_FLAGS="omp" <source_dir>      (OpenMP version)
# cmake -DIQTREE_FLAGS="m32" <source_dir>      (32-bit sequential version)
# cmake -DIQTREE_FLAGS="m32 omp" <source_dir>  (32-bit OpenMP version)
#
# To compile with CLANG on Linux:
# export CC=/usr/bin/clang
# export CXX=/usr/bin/clang++
# Best practices for setting up CMAKE for diffrent compiler can be found here:
# http://stackoverflow.com/questions/7031126/switching-between-gcc-and-clang-llvm-using-cmake
#
# Mac OSX example usages:
#------------------------
# cmake -DCMAKE_C_COMPILER=clang -DCMAKE_CXX_COMPILER=clang++ <source_dir>							(sequential version)
#
# To build OpenMP version one needs to download Clang version 3.7 or later (as of November 2015)
# Then assuming clang3.7 and clang++3.7 are the newly built compilers, then:
# cmake -DCMAKE_C_COMPILER=clang3.7 -DCMAKE_CXX_COMPILER=clang++3.7 -DIQTREE_FLAGS="omp" <source_dir>		(OpenMP version)
#


# Compile OpenMP version: cmake -DIQTREE_FLAGS=omp ....
# Compile 32-bit version: cmake -DIQTREE_FLAGS=m32 ....
# Compile static version: cmake -DIQTREE_FLAGS=static ....
# Compile static OpenMP version: cmake -DIQTREE_FLAGS="omp static" ....

#NOTE: Static linking with clang windows: make a symlink libgcc_eh.a to libgcc.a (administrator required)
# C:\TDM-GCC-64\lib\gcc\x86_64-w64-mingw32\5.1.0>mklink libgcc_eh.a libgcc.a

cmake_minimum_required(VERSION 2.8.10 FATAL_ERROR)
set(CMAKE_LEGACY_CYGWIN_WIN32 0)

project(iqtree)
add_definitions(-DIQ_TREE)
# The version number.
set (iqtree_VERSION_MAJOR 1)
set (iqtree_VERSION_MINOR 5)
set (iqtree_VERSION_PATCH "3")

set(BUILD_SHARED_LIBS OFF)

if (CMAKE_C_COMPILER MATCHES "mpi")
    set(IQTREE_FLAGS "${IQTREE_FLAGS} mpi")
endif()

message("IQ-TREE flags : ${IQTREE_FLAGS}")

if (NOT CMAKE_BUILD_TYPE)
	set(CMAKE_BUILD_TYPE "Release")
endif()

if (CMAKE_BUILD_TYPE STREQUAL "Release")
	message("Builde mode   : Release")
endif()

if (CMAKE_GENERATOR MATCHES "Xcode")
    set(CMAKE_XCODE_ATTRIBUTE_DEBUG_INFORMATION_FORMAT "dwarf-with-dsym")
endif()

include_directories("${PROJECT_SOURCE_DIR}")

##################################################################
# Detect target platforms
##################################################################
if (WIN32)
	message("Target OS     : Windows")
	# build as static binary to run on most machines
    if (IQTREE_FLAGS MATCHES "static")
        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
    endif()
    SET(CMAKE_FIND_LIBRARY_SUFFIXES .lib .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
    add_definitions(-DWIN32)
elseif (APPLE)
	message("Target OS     : Mac OS X")
	# to be compatible back to Mac OS X 10.6
	if (IQTREE_FLAGS MATCHES "oldmac")
		add_definitions("-mmacosx-version-min=10.5")
		set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=10.5")
	else()
		add_definitions("-mmacosx-version-min=10.6")
		set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -mmacosx-version-min=10.6")
	endif()
    SET(CMAKE_FIND_LIBRARY_SUFFIXES .a ${CMAKE_FIND_LIBRARY_SUFFIXES})
elseif (UNIX)
	message("Target OS     : Unix")
	# build as static binary to run on most machines
    if (NOT IQTREE_FLAGS MATCHES "static")
        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -rdynamic")
    else()
        set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -static")
    endif()
else()
	# Note that IQ-TREE has NOT been tested on other platforms
	message("Target OS     : Unknown and untested yet")
endif()

##################################################################
# Setup compiler, currently supported GCC, CLANG, MSVC, and ICC
##################################################################

set(GCC "FALSE")   #  GNU compiler
set(CLANG "FALSE") # Clang compiler
set(ICC "FALSE")   # Intel compiler
set(VCC "FALSE")   # MS Visual C Compiler, note that it is different from MSVC variable
# using C++11 standard
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")

if (CMAKE_COMPILER_IS_GNUCXX)
	message("Compiler      : GNU Compiler (gcc)")
	set(GCC "TRUE")
#	set(COMBINED_FLAGS "-Wall -Wno-unused-function -Wno-sign-compare -pedantic -D_GNU_SOURCE -fms-extensions -Wno-deprecated")
	set(CMAKE_CXX_FLAGS_RELEASE "-O3 -g")
	set(CMAKE_C_FLAGS_RELEASE "-O3 -g")
    # require at least gcc 4.8
    if (CMAKE_CXX_COMPILER_VERSION VERSION_LESS 4.8)
        message(FATAL_ERROR "GCC version must be at least 4.8!")
    endif()
    if (WIN32)
        # disable AVX on Windows due to memory alignment
        set(IQTREE_FLAGS "${IQTREE_FLAGS} novx")
        message("WARNING: AVX is disabled on Windows as GCC does not properly suport memory alignment")
    endif()
elseif (CMAKE_CXX_COMPILER_ID MATCHES "Clang")
	message("Compiler      : Clang")
	set(CLANG "TRUE")
#	set(COMBINED_FLAGS "-Wall -Wno-unused-function -Wno-sign-compare -pedantic -D_GNU_SOURCE -Wno-nested-anon-types")
    #if (APPLE AND NOT CMAKE_BUILD_TYPE MATCHES "Debug")
    #    set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -stdlib=libc++")
    #    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -stdlib=libc++")
    #endif()
	set(CMAKE_CXX_FLAGS_RELEASE "-O3")
	set(CMAKE_C_FLAGS_RELEASE "-O3")
elseif (CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
	set(VCC "TRUE")
	message("Compiler      : MS Visual C++ Compiler")
elseif (CMAKE_CXX_COMPILER_ID MATCHES "Intel")
	message("Compiler      : Intel C++ Compiler (icc)")
	set(ICC "TRUE")
    #set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} /Qstd=c99")
else()
	message("Compiler      : Unknown and untested yet")
endif()

set(EXE_SUFFIX "")

if (MSVC)
	# MS Visual Studio environment
	message("Exporting MS Visual Studio projects...")
	add_definitions(/MP) # enable multi-processor compilation
	if (CMAKE_BUILD_TYPE STREQUAL "Release")
		add_definitions(/Ot /Oi)
		if (VCC)
			add_definitions(/O2)
		elseif (ICC)
            #add_definitions(/O3)
			add_definitions(/O3)
		endif()
	endif()
endif()

##################################################################
# configure MPI compilation
##################################################################

if (IQTREE_FLAGS MATCHES "mpi")
    add_definitions(-D_IQTREE_MPI)
    if (NOT CMAKE_CXX_COMPILER MATCHES "mpi")
        # if not using the MPI compiler wrapper, set own options manually 
        find_package(MPI REQUIRED)
        set(CMAKE_CXX_COMPILE_FLAGS "${CMAKE_CXX_COMPILE_FLAGS} ${MPI_CXX_COMPILE_FLAGS}")
        set(CMAKE_C_COMPILE_FLAGS "${CMAKE_C_COMPILE_FLAGS} ${MPI_C_COMPILE_FLAGS}")
        set(CMAKE_CXX_LINK_FLAGS "${CMAKE_CXX_LINK_FLAGS} ${MPI_CXX_LINK_FLAGS}")
        set(CMAKE_C_LINK_FLAGS "${CMAKE_C_LINK_FLAGS} ${MPI_C_LINK_FLAGS}")
        include_directories(${MPI_C_INCLUDE_PATH})
        include_directories(${MPI_CXX_INCLUDE_PATH})
    endif()
endif()


##################################################################
# Configure PLL build
##################################################################
if (IQTREE_FLAGS MATCHES "pll")
	add_definitions(-DUSING_PLL)
	set(EXE_SUFFIX "${EXE_SUFFIX}-pll")
endif()

##################################################################
# detect 32 or 64 bit binary
##################################################################
set (BINARY32 "FALSE")
if(CMAKE_SIZEOF_VOID_P EQUAL 4 OR IQTREE_FLAGS MATCHES "m32")
	set(BINARY32 "TRUE")
	message("Target binary : 32-bit")
	if (CMAKE_GENERATOR MATCHES "Win64")
		error("Both 32-bit and 64-bit mode cannot be specified")
	endif()
	#SET(EXE_SUFFIX "${EXE_SUFFIX}32")
	if (GCC OR CLANG) 
		set(COMBINED_FLAGS "${COMBINED_FLAGS} -m32")
  	endif()
    add_definitions(-DBINARY32)
else()
	message("Target binary : 64-bit")
endif()

if(IQTREE_FLAGS MATCHES "novx")
    add_definitions(-D__NOAVX__)
endif()

##################################################################
# configure OpenMP/PThreads compilation
# change the executable name if compiled for OpenMP parallel version
##################################################################
if (IQTREE_FLAGS MATCHES "omp")
	message("OpenMP        : Yes")
	SET(EXE_SUFFIX "${EXE_SUFFIX}-omp")
	add_definitions(-D_USE_PTHREADS)
	if (MSVC)
		add_definitions(/MT)
	endif()

	if (VCC)
  		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /openmp")
  		include_directories("${PROJECT_SOURCE_DIR}/pll") # for PThreads headers
	elseif (ICC)
  		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Qopenmp")
  		if (WIN32)
  			include_directories("${PROJECT_SOURCE_DIR}/pll") # for PThreads headers
  		endif()
  	elseif (GCC)
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
  		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp -pthread")
  	elseif (CLANG)
		set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -pthread")
  		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp=libomp")
  	endif()
else()
	message("OpenMP        : NONE")
endif()


if (IQTREE_FLAGS MATCHES "mpi")
	message("MPI           : Yes")
	SET(EXE_SUFFIX "${EXE_SUFFIX}-mpi")
else()
	message("MPI           : NONE")
endif()

##################################################################
# configure SSE/AVX/FMA instructions
##################################################################

SET(AVX_FLAGS "-D__SSE3 -D__AVX")
if (VCC) 
	set(AVX_FLAGS "${AVX_FLAGS} /arch:AVX")
elseif (CLANG)
	set(AVX_FLAGS "${AVX_FLAGS} -mavx")
elseif (GCC)
	set(AVX_FLAGS "${AVX_FLAGS} -mavx -fabi-version=0")
elseif (ICC)
	if (WIN32)
		 set(AVX_FLAGS "${AVX_FLAGS} /arch:AVX")
	else()
		 set(AVX_FLAGS "${AVX_FLAGS} -mavx")
	endif()
endif()

SET(SSE_FLAGS "-D__SSE3")
if (VCC)
	set(SSE_FLAGS "${SSE_FLAGS} /arch:SSE2 -D__SSE3__")
elseif (GCC OR CLANG)
	set(SSE_FLAGS "${SSE_FLAGS} -msse3")
elseif (ICC)
	if (WIN32)
		set(SSE_FLAGS "${SSE_FLAGS} /arch:SSE3")
	else()
		set(SSE_FLAGS "${SSE_FLAGS} -msse3")
	endif()
endif()

SET(FMA_FLAGS "-D__SSE3 -D__AVX")
if (VCC) 
	set(FMA_FLAGS "${FMA_FLAGS} /arch:AVX2")
elseif (CLANG)
	set(FMA_FLAGS "${FMA_FLAGS} -mavx -mfma")
elseif (GCC)
	set(FMA_FLAGS "${FMA_FLAGS} -mavx -fabi-version=0 -mfma")
elseif (ICC) 
	if (WIN32)
		 set(FMA_FLAGS "${FMA_FLAGS} /arch:AVX /Qfma")
	else()
		 set(FMA_FLAGS "${FMA_FLAGS} -march=core-avx2")
	endif()
endif()

SET(AVX512_FLAGS "-D__SSE3 -D__AVX")
if (VCC)
    message("AVX512 not available in Visual C++")
	#set(AVX512_FLAGS "${AVX512_FLAGS} /arch:AVX512")
elseif (CLANG)
	set(AVX512_FLAGS "${AVX512_FLAGS} -mavx512f -mfma")
elseif (GCC)
	set(AVX512_FLAGS "${AVX512_FLAGS} -mavx512f -mfma")
elseif (ICC) 
	if (WIN32)
		 set(AVX512_FLAGS "${AVX512_FLAGS} /arch:MIC-AVX512 /Qfma")
	else()
		 set(AVX512_FLAGS "${AVX512_FLAGS} -xMIC-AVX512 -mfma")
	endif()
endif()


# further flag to improve performance

if (IQTREE_FLAGS MATCHES "fma") # AVX+FMA instruction set
 	message("Vectorization : AVX+FMA")
	add_definitions(-D__SSE3 -D__AVX) # define both SSE3 and AVX directive
    set(COMBINED_FLAGS "${COMBINED_FLAGS} ${FMA_FLAGS}")
	#SET(EXE_SUFFIX "${EXE_SUFFIX}-fma")
elseif (IQTREE_FLAGS MATCHES "avx") # AVX instruction set
 	message("Vectorization : AVX")
	add_definitions(-D__SSE3 -D__AVX) # define both SSE3 and AVX directive
	set(COMBINED_FLAGS "${COMBINED_FLAGS} ${AVX_FLAGS}")
	#SET(EXE_SUFFIX "${EXE_SUFFIX}-avx")
elseif (NOT IQTREE_FLAGS MATCHES "nosse") #SSE intruction set
	message("Vectorization : SSE3/AVX/AVX2")
	#add_definitions(-D__SSE3)
    #set(COMBINED_FLAGS "${COMBINED_FLAGS} ${SSE_FLAGS}")
endif()


##################################################################
# Setup compiler flags
##################################################################

set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${COMBINED_FLAGS}")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${COMBINED_FLAGS}")
set(CMAKE_CXX_FLAGS_PROFILE "${CMAKE_CXX_FLAGS} -fno-inline-functions -fno-inline-functions-called-once -fno-optimize-sibling-calls -fno-default-inline -fno-inline -O2 -fno-omit-frame-pointer -g")
set(CMAKE_C_FLAGS_PROFILE "${CMAKE_C_FLAGS} -fno-inline-functions -fno-inline-functions-called-once -fno-optimize-sibling-calls -O2 -fno-omit-frame-pointer -g")

if (CMAKE_BUILD_TYPE STREQUAL "Release")
	message("C flags       : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_RELEASE}")
	message("CXX flags     : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_RELEASE}")
endif()

if (CMAKE_BUILD_TYPE STREQUAL "Debug")
	message("C flags       : ${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_DEBUG}")
	message("CXX flags     : ${CMAKE_CXX_FLAGS} ${CMAKE_CXX_FLAGS_DEBUG}")
endif()

if (CMAKE_BUILD_TYPE STREQUAL "Profile")
	message("C flags       : ${CMAKE_C_FLAGS_PROFILE} ")
	message("CXX flags     : ${CMAKE_CXX_FLAGS_PROFILE} ")
endif()


if (GCC)
	set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g -fno-inline-functions -fno-inline-functions-called-once -fno-default-inline -fno-inline")
	set(CMAKE_C_FLAGS_DEBUG "-O0 -g -fno-inline-functions -fno-inline-functions-called-once -fno-default-inline -fno-inline")
	set(CMAKE_CXX_FLAGS_MEM "-g -O1")
	set(CMAKE_C_FLAGS_MEM "-g -O1")
elseif (CLANG)
	set(CMAKE_CXX_FLAGS_DEBUG "-O0 -g -fno-inline-functions -fno-inline")
	set(CMAKE_C_FLAGS_DEBUG "-O0 -g -fno-inline-functions -fno-inline")
	set(CMAKE_CXX_FLAGS_MEM "-g -O1")
	set(CMAKE_C_FLAGS_MEM "-g -O1")
endif()

##################################################################
# check existence of a few basic functions
##################################################################
include (${CMAKE_ROOT}/Modules/CheckFunctionExists.cmake)
check_function_exists (gettimeofday HAVE_GETTIMEOFDAY)
check_function_exists (getrusage HAVE_GETRUSAGE)
check_function_exists (GlobalMemoryStatusEx HAVE_GLOBALMEMORYSTATUSEX)
check_function_exists (strndup HAVE_STRNDUP)
find_package(Backtrace)

# configure a header file to pass some of the CMake settings
# to the source code
configure_file (
  "${PROJECT_SOURCE_DIR}/iqtree_config.h.in"
  "${PROJECT_BINARY_DIR}/iqtree_config.h"
  )

# add the binary tree to the search path for include files
# so that we will find iqtree_config.h
include_directories("${PROJECT_BINARY_DIR}")

#zlib will be detected for appearance
#include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7")


##################################################################
# subdirectories containing necessary libraries for the build
##################################################################
add_subdirectory(pll)
add_subdirectory(ncl)
add_subdirectory(lbfgsb)
add_subdirectory(whtest)
add_subdirectory(sprng)
#add_subdirectory(zlib-1.2.7)
add_subdirectory(vectorclass)
LIST(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}")
find_package(Eigen3)
if(EIGEN3_FOUND)
  include_directories(${EIGEN3_INCLUDE_DIR})
endif(EIGEN3_FOUND)
add_subdirectory(model)
add_subdirectory(gsl)

##################################################################
# the main executable
##################################################################

add_library(kernelsse phylokernelsse.cpp)

if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
add_library(kernelavx phylotreeavx.cpp)
add_library(kernelfma phylokernelfma.cpp)
if (IQTREE_FLAGS MATCHES "512")
    add_library(kernelavx512 phylokernelavx512.cpp)
    add_definitions(-DINCLUDE_AVX512)
endif()
endif()

if (IQTREE_FLAGS MATCHES "mpi")
	add_library(mympi TreeCollection.cpp ObjectStream.cpp)
endif()

add_executable(iqtree
alignment.cpp alignment.h
alignmentpairwise.cpp alignmentpairwise.h
circularnetwork.cpp circularnetwork.h
eigendecomposition.cpp eigendecomposition.h
greedy.cpp greedy.h
gss.cpp gss.h
gurobiwrapper.cpp gurobiwrapper.h
gzstream.cpp gzstream.h
hashsplitset.cpp hashsplitset.h
iqtree.cpp iqtree.h
maalignment.cpp maalignment.h
matree.cpp matree.h
mexttree.cpp mexttree.h
mpdablock.cpp mpdablock.h
msetsblock.cpp msetsblock.h
msplitsblock.cpp msplitsblock.h
modelsblock.cpp modelsblock.h
mtree.cpp mtree.h
mtreeset.cpp mtreeset.h
ncbitree.cpp ncbitree.h
ngs.cpp ngs.h
node.cpp node.h
optimization.cpp optimization.h
parsmultistate.cpp parsmultistate.h
pattern.cpp pattern.h
pda.cpp
pdnetwork.cpp pdnetwork.h
pdtree.cpp pdtree.h
pdtreeset.cpp pdtreeset.h
phyloanalysis.cpp phyloanalysis.h
phylonode.cpp phylonode.h
phylosupertree.cpp phylosupertree.h
phylotree.cpp phylotree.h
phylotreesse.cpp phylokernelnew.h
phylotreepars.cpp
pruning.cpp pruning.h
quartet.cpp
split.cpp split.h
splitgraph.cpp splitgraph.h
splitset.cpp splitset.h
stoprule.cpp stoprule.h
superalignment.cpp superalignment.h
superalignmentpairwise.cpp superalignmentpairwise.h
supernode.cpp supernode.h
tinatree.cpp tinatree.h
tools.cpp tools.h
whtest_wrapper.cpp whtest_wrapper.h
lpwrapper.c lpwrapper.h
pllnni.cpp pllnni.h
phylosupertreeplen.cpp phylosupertreeplen.h
phylotesting.cpp phylotesting.h
ecopd.cpp ecopd.h
ecopdmtreeset.cpp ecopdmtreeset.h
graph.cpp graph.h
candidateset.cpp candidateset.h
checkpoint.cpp checkpoint.h
constrainttree.cpp constrainttree.h
MPIHelper.cpp MPIHelper.h
memslot.cpp memslot.h
)

if(Backtrace_FOUND)
  include_directories(${Backtrace_INCLUDE_DIR})
  target_link_libraries(iqtree ${Backtrace_LIBRARY})
endif(Backtrace_FOUND)

if (NOT IQTREE_FLAGS MATCHES "nozlib")
    find_package(ZLIB)
endif()

if(ZLIB_FOUND)
  message ("Using system zlib")
  include_directories(${ZLIB_INCLUDE_DIRS})
  target_link_libraries(iqtree ${ZLIB_LIBRARIES})
else(ZLIB_FOUND)
  message ("Using own zlib-1.2.7")
  include_directories("${PROJECT_BINARY_DIR}/zlib-1.2.7" "${PROJECT_SOURCE_DIR}/zlib-1.2.7")
  add_subdirectory(zlib-1.2.7)
  target_link_libraries(iqtree zlibstatic)
endif(ZLIB_FOUND)

if (NOT IQTREE_FLAGS MATCHES "avx" AND NOT IQTREE_FLAGS MATCHES "fma")
    if (NOT IQTREE_FLAGS MATCHES "nosse")
        set_target_properties(iqtree ncl lbfgsb whtest sprng vectorclass model PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
    endif()
    set_target_properties(kernelsse pll PROPERTIES COMPILE_FLAGS "${SSE_FLAGS}")
	if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
		set_target_properties(kernelavx pllavx PROPERTIES COMPILE_FLAGS "${AVX_FLAGS}")
		set_target_properties(kernelfma PROPERTIES COMPILE_FLAGS "${FMA_FLAGS}")
        if (IQTREE_FLAGS MATCHES "512")
            set_target_properties(kernelavx512 PROPERTIES COMPILE_FLAGS "${AVX512_FLAGS}")
        endif()
	endif()
endif()

##################################################################
# setup linking flags
##################################################################

# link special lib for WIN32
if (WIN32)
	set(PLATFORM_LIB "ws2_32")
else()
	set(PLATFORM_LIB "m")
endif()

if(CLANG AND WIN32 AND IQTREE_FLAGS MATCHES "static")
    set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -pthread -Wl,--allow-multiple-definition")
endif()

set(THREAD_LIB "")
if (IQTREE_FLAGS MATCHES "omp")
	link_directories(${PROJECT_SOURCE_DIR}/lib)
	if (MSVC)
		if (BINARY32)
            set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /LIBPATH:${PROJECT_SOURCE_DIR}/lib32")
			set(THREAD_LIB "pthreadVC2")
		else()
            set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} /LIBPATH:${PROJECT_SOURCE_DIR}/lib")
			set(THREAD_LIB "pthreadVC2")
		endif()
	elseif(CLANG AND APPLE)
		set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L${PROJECT_SOURCE_DIR}/libmac -fopenmp=libomp")
	elseif(CLANG AND WIN32)
        if (BINARY32)
            set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L${PROJECT_SOURCE_DIR}/lib32 libiomp5md.dll")
        else()
            set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} -L${PROJECT_SOURCE_DIR}/lib libiomp5md.dll")
        endif()
#        set(THREAD_LIB "ompstatic")
	endif()
endif()

# basic linking librararies
target_link_libraries(iqtree pll ncl lbfgsb whtest sprng vectorclass model gsl ${PLATFORM_LIB} ${STD_LIB} ${THREAD_LIB})

if (NOT IQTREE_FLAGS MATCHES "nosse")
    target_link_libraries(iqtree kernelsse)
endif()

# MPI libraries
if (IQTREE_FLAGS MATCHES "mpi")
    target_link_libraries(iqtree mympi)
    if (NOT CMAKE_CXX_COMPILER MATCHES "mpi")
        target_link_libraries(iqtree ${MPI_CXX_LIBRARIES})
    endif()
endif()

# SSE, AVX etc. libraries
if (NOT BINARY32 AND NOT IQTREE_FLAGS MATCHES "novx")
    target_link_libraries(iqtree pllavx kernelavx kernelfma)
    if (IQTREE_FLAGS MATCHES "512")
        target_link_libraries(iqtree kernelavx512)
    endif()
endif()

# setup the executable name
##################################################################
set_target_properties(iqtree PROPERTIES OUTPUT_NAME "iqtree${EXE_SUFFIX}")

# strip the release build
if (CMAKE_BUILD_TYPE STREQUAL "Release" AND (GCC OR CLANG)) # strip is not necessary for MSVC
	if (WIN32)
		ADD_CUSTOM_COMMAND(TARGET iqtree POST_BUILD COMMAND strip $<TARGET_FILE:iqtree>)
	elseif (NOT APPLE)
		ADD_CUSTOM_COMMAND(TARGET iqtree POST_BUILD COMMAND ${CMAKE_STRIP} $<TARGET_FILE:iqtree>)
	endif()
endif()

if (MSVC)
	set (BINARY_DIR "${PROJECT_BINARY_DIR}/Release")
else()
	set (BINARY_DIR "${PROJECT_BINARY_DIR}")
endif()

if (WIN32)
	if (MSVC)
		ADD_CUSTOM_COMMAND(TARGET iqtree POST_BUILD COMMAND copy "Release\\iqtree${EXE_SUFFIX}.exe" "Release\\iqtree${EXE_SUFFIX}-click.exe")
	else()
		ADD_CUSTOM_COMMAND(TARGET iqtree POST_BUILD COMMAND copy "iqtree${EXE_SUFFIX}.exe" "iqtree${EXE_SUFFIX}-click.exe")
	endif()
endif()

##############################################################
# add the install targets
##############################################################
install (TARGETS iqtree DESTINATION bin)
install (FILES "${PROJECT_SOURCE_DIR}/example/models.nex" DESTINATION .)
install (FILES "${PROJECT_SOURCE_DIR}/example/example.phy" DESTINATION .)
install (FILES "${PROJECT_SOURCE_DIR}/example/example.nex" DESTINATION .)

if (WIN32)
	install (FILES "${BINARY_DIR}/iqtree${EXE_SUFFIX}-click.exe" DESTINATION bin)
	if (EXE_SUFFIX MATCHES "omp" AND MSVC)
        if (BINARY32)
            install(FILES  "${PROJECT_SOURCE_DIR}/lib32/pthreadVC2.dll" DESTINATION bin)
            install(FILES  "${PROJECT_SOURCE_DIR}/lib32/libiomp5md.dll" DESTINATION bin)
        else()
            install(FILES  "${PROJECT_SOURCE_DIR}/lib/pthreadVC2.dll" DESTINATION bin)
            install(FILES  "${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll" DESTINATION bin)
        endif()
#		install(FILES  "${PROJECT_SOURCE_DIR}/lib/pthreadGC2.dll" DESTINATION bin)
#		install(FILES  "${PROJECT_SOURCE_DIR}/lib/pthreadGC2_64.dll" DESTINATION bin)
	endif()

	if (EXE_SUFFIX MATCHES "omp" AND CLANG)
        if (BINARY32)
            install(FILES  "${PROJECT_SOURCE_DIR}/lib32/libiomp5md.dll" DESTINATION bin)
        else()
            install(FILES  "${PROJECT_SOURCE_DIR}/lib/libiomp5md.dll" DESTINATION bin)
        endif()
	endif()

endif()

##############################################################
# build a CPack driven installer package
##############################################################
include (InstallRequiredSystemLibraries)
set (CPACK_RESOURCE_FILE_LICENSE
     "${CMAKE_CURRENT_SOURCE_DIR}/License.txt")
set (CPACK_PACKAGE_VERSION_MAJOR "${iqtree_VERSION_MAJOR}")
set (CPACK_PACKAGE_VERSION_MINOR "${iqtree_VERSION_MINOR}")
set (CPACK_PACKAGE_VERSION_PATCH "${iqtree_VERSION_PATCH}")
if(WIN32 OR APPLE)
  set(CPACK_GENERATOR "ZIP")
  set(CPACK_SOURCE_GENERATOR "ZIP")
else()
  set(CPACK_GENERATOR "TGZ")
  set(CPACK_SOURCE_GENERATOR "TGZ")
endif()

#set(CPACK_SOURCE_PACKAGE_FILE_NAME
#  "${CMAKE_PROJECT_NAME}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}")
set(CPACK_SOURCE_IGNORE_FILES
  "/build.*/;/debug.*/;/examples/;/test_scripts/;/manual/;/.bzr/;~$;/\\\\.svn/;/\\\\.git/;/pllrepo/;${CPACK_SOURCE_IGNORE_FILES}")

set (SYSTEM_NAME "${CMAKE_SYSTEM_NAME}")
if (${CMAKE_SYSTEM_NAME} STREQUAL "Darwin")
	if (IQTREE_FLAGS MATCHES "oldmac")
		set (SYSTEM_NAME "MacOS10.5")
	else()
		set (SYSTEM_NAME "MacOSX")
	endif()
endif()

if (BINARY32) 
    set (SYSTEM_NAME "${SYSTEM_NAME}32")
endif()

set(CPACK_PACKAGE_FILE_NAME 
	"${CMAKE_PROJECT_NAME}${EXE_SUFFIX}-${CPACK_PACKAGE_VERSION_MAJOR}.${CPACK_PACKAGE_VERSION_MINOR}.${CPACK_PACKAGE_VERSION_PATCH}-${SYSTEM_NAME}")

set(CPACK_STRIP_FILES TRUE)

include (CPack)

#add_custom_target(dist COMMAND ${CMAKE_MAKE_PROGRAM} package_source)
