1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
|
cmake_minimum_required(VERSION 3.5...3.27)
project(VeryFastTree)
set(CMAKE_CXX_STANDARD 11)
option(USE_SHARED "enable/disable linking of system shared libraries" OFF)
option(USE_NATIVE "enable/disable system's processor architecture optimization (linux)" ON)
option(USE_SEE2 "enable/disable SSE2 in windows (linux default)" ON)
option(USE_SEE4 "enable/disable SSE4.1" OFF)
option(USE_AVX "enable/disable AVX" OFF)
option(USE_AVX2 "enable/disable AVX2" OFF)
option(USE_AVX512 "enable/disable AVX512" OFF)
option(USE_CUDA "enable/disable CUDA" OFF)
set(CUDA_ARCH "80" CACHE STRING "change CUDA Architecture")
add_definitions(-DCLI11_BOOST_OPTIONAL=0)
add_definitions(-DNDEBUG)
ADD_SUBDIRECTORY("libs/CLI11")
ADD_SUBDIRECTORY("libs/bxzstr")
if (USE_SHARED AND NOT MSVC)
set(LIBRARIES z bz2)
else ()
ADD_SUBDIRECTORY("libs/boost-align")
ADD_SUBDIRECTORY("libs/boost-core")
ADD_SUBDIRECTORY("libs/boost-sort")
ADD_SUBDIRECTORY("libs/bzip2")
ADD_SUBDIRECTORY("libs/zlib")
ADD_SUBDIRECTORY("libs/robin-map")
ADD_SUBDIRECTORY("libs/xxhash")
set(LIBRARIES boost-core boost-sort boost-align robin_map xxhash zlibstatic bzip2static)
endif ()
set(LIBRARIES CLI11 bxzstr ${LIBRARIES} )
set(SOURCE_FILES
src/operations/BasicOperations.tcc
src/operations/BasicOperations.h
src/operations/SSE128Operations.tcc
src/operations/SSE128Operations.h
src/operations/AVX256Operations.tcc
src/operations/AVX256Operations.h
src/operations/AVX512Operations.tcc
src/operations/AVX512Operations.h
src/impl/VeryFastTreeDouble.cpp
src/impl/VeryFastTreeDoubleAVX256.cpp
src/impl/VeryFastTreeDoubleAVX512.cpp
src/impl/VeryFastTreeDoubleCuda.cpp
src/impl/VeryFastTreeDoubleSSE128.cpp
src/impl/VeryFastTreeFloat.cpp
src/impl/VeryFastTreeFloatAVX256.cpp
src/impl/VeryFastTreeFloatAVX512.cpp
src/impl/VeryFastTreeFloatCuda.cpp
src/impl/VeryFastTreeFloatSSE128.cpp
src/Knuth.cpp
src/Knuth.h
src/Options.h
src/Constants.h
src/Debug.h
src/DiskMemory.cpp
src/DiskMemory.h
src/Utils.h
src/HashTable.h
src/DistanceMatrix.tcc
src/DistanceMatrix.h
src/TransitionMatrix.tcc
src/TransitionMatrix.h
src/NeighbourJoining.tcc
src/NeighbourJoining.h
src/Alignment.cpp
src/Alignment.h
src/VeryFastTreeImpl.tcc
src/VeryFastTree.cpp
src/VeryFastTree.h
main.cpp
)
if (USE_CUDA)
message("WARNING!! CUDA is only a experimental feature")
set(CMAKE_CUDA_ARCHITECTURES ${CUDA_ARCH})
set(USE_CUDA 1)
enable_language(CUDA)
find_package(CUDAToolkit)
set(SOURCE_FILES
${SOURCE_FILES}
src/operations/CudaOperations.h
src/operations/CudaOperations.cu
)
set(LIBRARIES ${LIBRARIES} CUDA::cublas)
else ()
set(USE_CUDA 0)
endif ()
if (MSVC)
ADD_SUBDIRECTORY("libs/mman-win32")
set(LIBRARIES ${LIBRARIES} mman-win32)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /W2 /O2 /EHsc /bigobj /DUSE_CUDA=${USE_CUDA}")
if (USE_AVX512)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:AVX512 /D__AVX512F__=1 /D__AVX2__=1 /D__AVX__=1")
elseif (USE_AVX2)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:AVX2 /D__AVX2__=1 /D__AVX__=1")
elseif (USE_AVX)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:AVX /D__AVX__=1")
elseif (USE_SEE4)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:SSE2 /D__SSE4_1__=1 /D__SSE2__=1")
elseif (USE_SEE2)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /arch:SSE2 /D__SSE2__=1")
endif ()
else ()
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -O3 -DUSE_CUDA=${USE_CUDA}")
if (USE_AVX512)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mavx512f")
elseif (USE_AVX2)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mavx2")
elseif (USE_AVX)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -mavx")
elseif (USE_SEE4)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -msse4.1")
endif ()
if (USE_NATIVE)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -march=native")
endif ()
endif ()
find_package(OpenMP)
if(NOT TARGET OpenMP::OpenMP_CXX)
find_package(Threads REQUIRED)
add_library(OpenMP::OpenMP_CXX IMPORTED INTERFACE)
set_property(TARGET OpenMP::OpenMP_CXX PROPERTY INTERFACE_COMPILE_OPTIONS ${OpenMP_CXX_FLAGS})
set_property(TARGET OpenMP::OpenMP_CXX PROPERTY INTERFACE_LINK_LIBRARIES ${OpenMP_CXX_FLAGS} Threads::Threads)
endif()
add_executable(${PROJECT_NAME} ${SOURCE_FILES})
target_link_libraries(${PROJECT_NAME} OpenMP::OpenMP_CXX ${LIBRARIES})
install(TARGETS ${PROJECT_NAME} DESTINATION bin)
|
