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CMakeLists.txt
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cmake_minimum_required (VERSION 3.8)
# Enable Hot Reload for MSVC compilers if supported.
if (POLICY CMP0141)
cmake_policy(SET CMP0141 NEW)
set(CMAKE_MSVC_DEBUG_INFORMATION_FORMAT "$<IF:$<AND:$<C_COMPILER_ID:MSVC>,$<CXX_COMPILER_ID:MSVC>>,$<$<CONFIG:Debug,RelWithDebInfo>:EditAndContinue>,$<$<CONFIG:Debug,RelWithDebInfo>:ProgramDatabase>>")
endif()
project ("DP-HLS")
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -O0 -g -fsanitize=address -fno-inline -DCMAKE_BUILD_TYPE=Debug")
# "-fsanitize=address" flag was used to check the stack smashing with Google Address Sanitizer. Use this flag with CLang and
# run the program to check.
set(CMAKE_VERBOSE_MAKEFILE ON)
set(EXECUTABLE_TARGETS
test_csim_global_linear
test_csim_banding_global_linear
test_csim_global_affine
test_csim_local_linear
test_csim_local_linear_notb
test_csim_local_affine
test_csim_dtw
test_csim_profile_alignment
test_csim_profile_alignment_real_data
test_csim_viterbi
test_csim_semi_global_linear_long_short
test_csim_semi_global_linear_short_long
test_csim_overlap_linear_prefix_suffix
test_csim_overlap_linear_suffix_prefix
test_csim_local_two_piece_affine
test_csim_global_two_piece_affine
test_csim_banding_global_two_piece_affine
test_csim_banding_local_affine
test_csim_banding_local_affine_scored
test_global_affine_real_data
test_csim_sdtw
test_csim_protein_local_affine
)
add_compile_definitions(PUBLIC CMAKEDEBUG)
add_compile_definitions(PUBLIC VPP_CLI)
set(COMMON_SRCS
"src/seq_align_multiple.cpp"
"src/align.cpp"
"src/pe.cpp"
"src/traceback.cpp"
"src/utils.cpp"
"src/debug.cpp"
"src/host_utils.cpp")
add_executable(test_csim_global_linear
"testbench/test_csim_global_linear.cpp"
"kernels/global_linear/kernel_global_linear.cpp"
${COMMON_SRCS})
add_executable(test_csim_local_linear_notb
"testbench/test_csim_local_linear_notb.cpp"
"kernels/local_linear_notb/kernel_local_linear.cpp"
${COMMON_SRCS})
add_executable(test_csim_banding_global_linear
"testbench/test_csim_banding_global_linear.cpp"
"kernels/banding_global_linear/kernel_banding_global_linear.cpp"
${COMMON_SRCS})
add_executable(test_csim_banding_local_affine
"kernels/banding_local_affine/kernel_banding_local_affine.cpp"
"testbench/test_csim_local_affine.cpp"
${COMMON_SRCS}
)
add_executable(test_csim_local_linear
"testbench/test_csim_local_linear.cpp"
"kernels/local_linear/kernel_local_linear.cpp"
${COMMON_SRCS})
add_executable(test_csim_global_affine
"testbench/test_csim_global_affine.cpp"
"kernels/global_affine/kernel_global_affine.cpp"
${COMMON_SRCS})
# BSW in Darwin-WGA
add_executable(test_csim_banding_local_affine_scored
"kernels/banding_local_affine_scored/banding_local_affine_scored.cpp"
"testbench/test_csim_banding_local_affine_scored.cpp"
${COMMON_SRCS})
add_executable(test_csim_local_affine
"testbench/test_csim_local_affine.cpp"
"kernels/local_affine/kernel_local_affine.cpp"
${COMMON_SRCS})
add_executable(test_csim_profile_alignment
"testbench/test_csim_profile_alignment.cpp"
"kernels/profile_alignment/kernel_profile_alignment.cpp"
${COMMON_SRCS})
add_executable(test_csim_profile_alignment_real_data
"testbench/test_csim_profile_alignment_real_data.cpp"
"kernels/profile_alignment/kernel_profile_alignment.cpp"
${COMMON_SRCS})
add_executable(test_csim_dtw
"testbench/test_csim_dtw.cpp"
"kernels/dtw/kernel_dtw.cpp"
${COMMON_SRCS})
add_executable(test_csim_viterbi
"testbench/test_csim_viterbi.cpp"
"kernels/viterbi/kernel_viterbi.cpp"
${COMMON_SRCS})
add_executable(test_csim_sdtw
"testbench/test_csim_sdtw.cpp"
"kernels/sdtw/kernel_sdtw.cpp"
${COMMON_SRCS})
add_executable(test_csim_semi_global_linear_long_short
"testbench/test_csim_semi_global_linear_long_short.cpp"
"kernels/semi_global_linear_long_short/kernel_semi_global_linear_long_short.cpp"
${COMMON_SRCS})
add_executable(test_csim_semi_global_linear_short_long
"testbench/test_csim_semi_global_linear_short_long.cpp"
"kernels/semi_global_linear_short_long/kernel_semi_global_linear_short_long.cpp"
${COMMON_SRCS})
add_executable(test_csim_overlap_linear_prefix_suffix
"testbench/test_csim_overlap_linear_prefix_suffix.cpp"
"kernels/overlap_linear_prefix_suffix/kernel_overlap_linear_prefix_suffix.cpp"
${COMMON_SRCS})
add_executable(test_csim_overlap_linear_suffix_prefix
"testbench/test_csim_overlap_linear_suffix_prefix.cpp"
"kernels/overlap_linear_suffix_prefix/kernel_overlap_linear_suffix_prefix.cpp"
${COMMON_SRCS})
add_executable(test_csim_global_two_piece_affine
"testbench/test_csim_global_two_piece_affine.cpp"
"kernels/global_two_piece_affine/kernel_global_two_piece_affine.cpp"
${COMMON_SRCS})
add_executable(test_csim_banding_global_two_piece_affine
"kernels/banding_global_two_piece_affine/kernel_banding_global_two_piece_affine.cpp"
"testbench/test_csim_global_two_piece_affine.cpp"
${COMMON_SRCS})
add_executable(test_csim_local_two_piece_affine
"testbench/test_csim_local_two_piece_affine.cpp"
"kernels/local_two_piece_affine/kernel_local_two_piece_affine.cpp"
${COMMON_SRCS})
add_executable(test_global_affine_real_data
"testbench/test_csim_global_affine_real_data.cpp"
"kernels/global_affine/kernel_global_affine.cpp"
${COMMON_SRCS}
)
add_executable(test_csim_protein_local_affine
"testbench/test_csim_protein_local_affine.cpp"
"kernels/protein_local_affine/kernel_protein_local_affine.cpp"
${COMMON_SRCS}
)
target_include_directories(test_csim_global_affine PRIVATE "./kernels/global_affine")
target_include_directories(test_csim_global_linear PRIVATE "./kernels/global_linear")
target_include_directories(test_csim_banding_global_linear PRIVATE "./kernels/banding_global_linear")
target_include_directories(test_csim_local_linear PRIVATE "./kernels/local_linear")
target_include_directories(test_csim_local_linear_notb PRIVATE "./kernels/local_linear_notb")
target_include_directories(test_csim_local_affine PRIVATE "./kernels/local_affine")
target_include_directories(test_csim_profile_alignment PRIVATE "./kernels/profile_alignment")
target_include_directories(test_csim_profile_alignment_real_data PRIVATE "./kernels/profile_alignment")
target_include_directories(test_csim_dtw PRIVATE "./kernels/dtw")
target_include_directories(test_csim_viterbi PRIVATE "./kernels/viterbi")
target_include_directories(test_csim_overlap_linear_suffix_prefix PRIVATE "./kernels/overlap_linear_suffix_prefix")
target_include_directories(test_csim_overlap_linear_prefix_suffix PRIVATE "./kernels/overlap_linear_prefix_suffix")
target_include_directories(test_csim_semi_global_linear_long_short PRIVATE "./kernels/semi_global_linear_long_short")
target_include_directories(test_csim_semi_global_linear_short_long PRIVATE "./kernels/semi_global_linear_short_long")
target_include_directories(test_csim_local_two_piece_affine PRIVATE "./kernels/local_two_piece_affine")
target_include_directories(test_csim_global_two_piece_affine PRIVATE "./kernels/global_two_piece_affine")
target_include_directories(test_global_affine_real_data PRIVATE "./kernels/global_affine")
target_include_directories(test_csim_banding_global_two_piece_affine PRIVATE "./kernels/banding_global_two_piece_affine")
target_include_directories(test_csim_banding_local_affine PRIVATE "./kernels/banding_local_affine")
target_include_directories(test_csim_banding_local_affine_scored PRIVATE "./kernels/banding_local_affine_scored")
target_include_directories(test_csim_sdtw PRIVATE "./kernels/sdtw")
target_include_directories(test_csim_protein_local_affine PRIVATE "./kernels/protein_local_affine")
# >>> Add CMake Compile Vitis header and library path >>>
set(HLS_HOME "/opt/Xilinx/Vitis_HLS/2021.2/") # Default HLS_HOME if using FPGA Developer AMI
include_directories(${EXECUTABLE_TARGETS} PUBLIC "${HLS_HOME}/include")
include_directories(${EXECUTABLE_TARGETS} PUBLIC "./include")
include_directories(${EXECUTABLE_TARGETS} PUBLIC "./common/includes")
link_directories(${EXECUTABLE_TARGETS} PUBLIC "${HLS_HOME}/lib")
link_directories(${EXECUTABLE_TARGETS} PUBLIC "/usr/lib64")
link_directories(${EXECUTABLE_TARGETS} PUBLIC "/usr/lib/x86_64-linux-gnu" "/usr/lib32" "/usr/libx32")
link_libraries(${EXECUTABLE_TARGETS} PUBLIC xrt_coreutil)
target_link_libraries(test_csim_dtw PUBLIC OpenCL)
target_link_libraries(test_csim_profile_alignment_real_data PUBLIC OpenCL)
target_link_libraries(test_csim_global_linear PUBLIC OpenCL)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
# <<< Add CMake Compile Vitis header and library path <<<
if (CMAKE_VERSION VERSION_GREATER 3.12)
set_property(TARGET ${EXECUTABLE_TARGETS} PROPERTY CXX_STANDARD 17)
endif()