TWILIGHT/CMakeLists.txt at main · TurakhiaLab/TWILIGHT · GitHub

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
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
cmake_minimum_required(VERSION 3.10)

project(twilight LANGUAGES CXX)

option(USE_CUDA "Build with CUDA" OFF)
option(USE_HIP "Build with HIP" OFF)

include(CheckLanguage)

# Configure TWILIGHT version
set(twilight_VERSION "?.?.?")
execute_process(COMMAND head -n1 ${CMAKE_SOURCE_DIR}/version.txt OUTPUT_VARIABLE VERSION)
string(REGEX REPLACE "^v([0-9]+)\\..*" "\\1" VERSION_MAJOR "${VERSION}")
string(REGEX REPLACE "^v[0-9]+\\.([0-9]+).*" "\\1" VERSION_MINOR "${VERSION}")
string(REGEX REPLACE "^v[0-9]+\\.[0-9]+\\.([0-9]+).*" "\\1" VERSION_PATCH "${VERSION}")
if ("${VERSION_PATCH}" MATCHES "[0-9]+")
    set(twilight_VERSION "${VERSION_MAJOR}.${VERSION_MINOR}.${VERSION_PATCH}")
endif()
message(STATUS "TWILIGHT version ${twilight_VERSION}")
configure_file(src/version.hpp.in ${CMAKE_SOURCE_DIR}/src/version.hpp)

set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_SOURCE_DIR}/bin)

if(CMAKE_SYSTEM_PROCESSOR MATCHES "x86_64|AMD64")
    message(STATUS "Building TALCO with x86 SIMD")
    add_compile_definitions(TALCO_SIMD)
endif()

if(USE_CUDA)
	message(STATUS "Build with CUDA")
	check_language(CUDA)
	if(CMAKE_CUDA_COMPILER)
		enable_language(CUDA)
		message(STATUS "CUDA compiler detected at: ${CMAKE_CUDA_COMPILER}")
		TRY_RUN(
			FIND_GPU_RESULT
			FIND_GPU_COMPILE_RESULT
			${CMAKE_CURRENT_BINARY_DIR}/
			${CMAKE_CURRENT_BINARY_DIR}/../src/cuda/findgpu.cu
			RUN_OUTPUT_VARIABLE GPU_ARCH_OUTPUT
		)
		if("${FIND_GPU_COMPILE_RESULT}" AND ("${FIND_GPU_RESULT}" EQUAL 0))
			message(STATUS "CUDA-capable GPU found. GPU architecture: ${GPU_ARCH_OUTPUT}")
			if(${CMAKE_VERSION} VERSION_LESS "3.18")
			    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -arch=sm_${GPU_ARCH_OUTPUT}")
			else()
			    set(CMAKE_CUDA_ARCHITECTURES ${GPU_ARCH_OUTPUT})
			endif()
			set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -lineinfo")
		else()
			message(STATUS "No CUDA-capable GPU found. Generating binary to support multiple GPU generations.")
			set(CMAKE_CUDA_ARCHITECTURES 70 75 80 86 89 90)
			set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -lineinfo")
		endif()
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O4 -std=c++17 -Wall -g -Wno-sign-compare -Wno-unused-variable -march=native")
		set(SRC_FILES src/cuda/twilight-main.cu
					  src/cuda/gpu-info.cu
				      src/cuda/alignment-gpu.cu
				      src/cuda/device-function.cu
					  src/phylogeny.cpp
					  src/tree.cpp
					  src/partitionInfo.cpp
					  src/node.cpp
					  src/scoring-matrix.cpp
					  src/io.cpp
					  src/option.cpp
					  src/sequencedb.cpp
					  src/progressive.cpp
					  src/alignment-cpu.cpp
					  src/alignment-helper.cpp
					  src/TALCO-XDrop.cpp

		)
	else()
	    message(FATAL_ERROR "No CUDA found")
	endif()
elseif(USE_HIP)
	message(STATUS "Build with HIP")
	find_package(HIP QUIET)
	if(HIP_FOUND)
		enable_language(HIP)
	    message(STATUS "HIP found: ${HIP_VERSION}")
		add_definitions(-D__HIP_PLATFORM_AMD__)
		set(CMAKE_CXX_COMPILER "/opt/rocm-${HIP_COMPILE_VERSION}/bin/hipcc")
		include_directories("/opt/rocm-${HIP_COMPILE_VERSION}/include/")
		set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O4 -std=c++17 -Wall -g -Wno-sign-compare -Wno-unused-variable -Wno-unused-result -Wno-unused-but-set-variable -Wno-self-assign -Wno-deprecated -march=native")
		set(SRC_FILES src/hip/twilight-main.hip.cpp
					  src/hip/gpu-info.hip.cpp
				      src/hip/alignment-gpu.hip.cpp
				      src/hip/device-function.hip.cpp
			  		  src/phylogeny.cpp
					  src/tree.cpp
					  src/partitionInfo.cpp
					  src/node.cpp
					  src/scoring-matrix.cpp
					  src/io.cpp
					  src/option.cpp
					  src/sequencedb.cpp
					  src/progressive.cpp
					  src/alignment-cpu.cpp
					  src/alignment-helper.cpp
					  src/TALCO-XDrop.cpp
	    )
	else()
	    message(FATAL_ERROR "No HIP found")
	endif()
else()
	message(STATUS "Auto-detecting hardware and selecting compute backend.")
	find_package(HIP QUIET)
	check_language(CUDA)
	if(CMAKE_CUDA_COMPILER)
		message(STATUS "CUDA compiler detected at: ${CMAKE_CUDA_COMPILER}")
		enable_language(CUDA)
		TRY_RUN(
    		FIND_GPU_RESULT
			FIND_GPU_COMPILE_RESULT
			${CMAKE_CURRENT_BINARY_DIR}/
			${CMAKE_CURRENT_BINARY_DIR}/../src/cuda/findgpu.cu
			RUN_OUTPUT_VARIABLE GPU_ARCH_OUTPUT
		)
		if("${FIND_GPU_COMPILE_RESULT}" AND ("${FIND_GPU_RESULT}" EQUAL 0))
			message(STATUS "CUDA-capable GPU found. GPU architecture: ${GPU_ARCH_OUTPUT}")
			if(${CMAKE_VERSION} VERSION_LESS "3.18")
			    set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -arch=sm_${GPU_ARCH_OUTPUT}")
			else()
			    set(CMAKE_CUDA_ARCHITECTURES ${GPU_ARCH_OUTPUT})
			endif()
			set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -lineinfo")
			set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O4 -std=c++17 -Wall -g -Wno-sign-compare -Wno-unused-variable -march=native")
			set(SRC_FILES src/cuda/twilight-main.cu
					      src/cuda/gpu-info.cu
				          src/cuda/alignment-gpu.cu
				          src/cuda/device-function.cu
					      src/phylogeny.cpp
					      src/tree.cpp
					      src/partitionInfo.cpp
					      src/node.cpp
					      src/scoring-matrix.cpp
					      src/io.cpp
					      src/option.cpp
					      src/sequencedb.cpp
					      src/progressive.cpp
					      src/alignment-cpu.cpp
					      src/alignment-helper.cpp
					      src/TALCO-XDrop.cpp
			)
		else()
			message(STATUS "No CUDA-capable GPU found.")
		endif()
	endif()
	if(NOT DEFINED SRC_FILES OR NOT SRC_FILES)
		if (HIP_FOUND)
			enable_language(HIP)
	    	message(STATUS "HIP found: ${HIP_VERSION}")
			add_definitions(-D__HIP_PLATFORM_AMD__)
			set(CMAKE_CXX_COMPILER "/opt/rocm-${HIP_COMPILE_VERSION}/bin/hipcc")
			include_directories("/opt/rocm-${HIP_COMPILE_VERSION}/include/")
			set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O4 -std=c++17 -Wall -g -Wno-sign-compare -Wno-unused-variable -Wno-unused-result -Wno-unused-but-set-variable -Wno-self-assign -Wno-deprecated -march=native")
			set(SRC_FILES src/hip/twilight-main.hip.cpp
					      src/hip/gpu-info.hip.cpp
				          src/hip/alignment-gpu.hip.cpp
				          src/hip/device-function.hip.cpp
			  		      src/phylogeny.cpp
					      src/tree.cpp
					      src/partitionInfo.cpp
					      src/node.cpp
					      src/scoring-matrix.cpp
					      src/io.cpp
					      src/option.cpp
					      src/sequencedb.cpp
					      src/progressive.cpp
					      src/alignment-cpu.cpp
					      src/alignment-helper.cpp
					      src/TALCO-XDrop.cpp
	    	)
		else()
			message(STATUS "No CUDA or HIP detected — building CPU version.")
			set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O4 -std=c++17 -Wall -g -Wno-sign-compare -Wno-unused-variable -Wno-unused-result -Wno-unused-but-set-variable -Wno-self-assign -Wno-deprecated -march=native")
			set(SRC_FILES src/twilight-main.cpp
					      src/phylogeny.cpp
					      src/tree.cpp
					      src/partitionInfo.cpp
					      src/node.cpp
					      src/scoring-matrix.cpp
					      src/io.cpp
					      src/option.cpp
					      src/sequencedb.cpp
					      src/progressive.cpp
					      src/alignment-cpu.cpp
					      src/alignment-helper.cpp
					      src/TALCO-XDrop.cpp
		    )
		endif()
	endif()
endif()

find_package(Boost COMPONENTS program_options system filesystem REQUIRED)
find_package(ZLIB REQUIRED)
include_directories(${ZLIB_INCLUDE_DIR})
find_package(TBB REQUIRED CONFIG)
add_executable (twilight ${SRC_FILES})
target_link_libraries(twilight PRIVATE ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} TBB::tbb)