Merge yuhsiang-dev to main

.vscode/settings.json

@@ -0,0 +1,87 @@
+{
+    "files.associations": {
+        "queue": "cpp",
+        "cctype": "cpp",
+        "clocale": "cpp",
+        "cmath": "cpp",
+        "csetjmp": "cpp",
+        "csignal": "cpp",
+        "cstdarg": "cpp",
+        "cstddef": "cpp",
+        "cstdio": "cpp",
+        "cstdlib": "cpp",
+        "cstring": "cpp",
+        "ctime": "cpp",
+        "cwchar": "cpp",
+        "cwctype": "cpp",
+        "any": "cpp",
+        "array": "cpp",
+        "atomic": "cpp",
+        "strstream": "cpp",
+        "bit": "cpp",
+        "bitset": "cpp",
+        "cfenv": "cpp",
+        "charconv": "cpp",
+        "chrono": "cpp",
+        "cinttypes": "cpp",
+        "codecvt": "cpp",
+        "compare": "cpp",
+        "complex": "cpp",
+        "concepts": "cpp",
+        "condition_variable": "cpp",
+        "coroutine": "cpp",
+        "cstdint": "cpp",
+        "cuchar": "cpp",
+        "deque": "cpp",
+        "forward_list": "cpp",
+        "list": "cpp",
+        "map": "cpp",
+        "set": "cpp",
+        "unordered_map": "cpp",
+        "unordered_set": "cpp",
+        "vector": "cpp",
+        "exception": "cpp",
+        "algorithm": "cpp",
+        "functional": "cpp",
+        "iterator": "cpp",
+        "memory": "cpp",
+        "memory_resource": "cpp",
+        "numeric": "cpp",
+        "optional": "cpp",
+        "random": "cpp",
+        "ratio": "cpp",
+        "string": "cpp",
+        "string_view": "cpp",
+        "system_error": "cpp",
+        "tuple": "cpp",
+        "type_traits": "cpp",
+        "utility": "cpp",
+        "fstream": "cpp",
+        "future": "cpp",
+        "initializer_list": "cpp",
+        "iomanip": "cpp",
+        "iosfwd": "cpp",
+        "iostream": "cpp",
+        "istream": "cpp",
+        "limits": "cpp",
+        "mutex": "cpp",
+        "new": "cpp",
+        "numbers": "cpp",
+        "ostream": "cpp",
+        "ranges": "cpp",
+        "regex": "cpp",
+        "scoped_allocator": "cpp",
+        "shared_mutex": "cpp",
+        "span": "cpp",
+        "sstream": "cpp",
+        "stdexcept": "cpp",
+        "stop_token": "cpp",
+        "streambuf": "cpp",
+        "thread": "cpp",
+        "typeindex": "cpp",
+        "typeinfo": "cpp",
+        "valarray": "cpp",
+        "variant": "cpp",
+        "semaphore": "cpp"
+    }
+}

CMakeLists.txt

@@ -108,22 +108,23 @@ elseif(USE_HIP)
 else()
         message(FATAL_ERROR "Either USE_CUDA or USE_HIP must be enabled. e.g. cmake -DUSE_CUDA=ON ..")
 endif()
-# add_executable (dipper_cpu
-#         src/tree_generation.cu
-#         src/placement.cu
-#         cpu/mash.cu
-#         src/twoBitCompressor.cpp
-#         src/fourBitCompressor.cpp
-#         cpu/matrix_reader.cu
-#         src/MSA.cu
-#         src/tree.cpp
-#         src/neighborJoining.cu
-#         cpu/placement_close_k.cu
-#         src/divide_and_conquer/mash.cu
-#         src/divide_and_conquer/mash.cpp
-#         src/divide_and_conquer/msa.cu
-#         src/divide_and_conquer/placement_close_k.cpp
-#         src/divide_and_conquer/placement_close_k.cu)
+
+add_executable (dipper_cpu
+                cpu/tree_generation.cpp
+                cpu/placement.cpp
+                cpu/mash.cpp
+                src/twoBitCompressor.cpp
+                src/fourBitCompressor.cpp
+                cpu/matrix_reader.cpp
+                cpu/MSA.cpp
+                src/tree.cpp
+                cpu/neighborJoining.cpp
+                cpu/placement_close_k.cpp
+                cpu/divide_and_conquer/mash_cu.cpp
+                cpu/divide_and_conquer/mash.cpp
+                cpu/divide_and_conquer/msa.cpp
+                cpu/divide_and_conquer/placement_close_k.cpp
+                cpu/divide_and_conquer/placement_close_k_cu.cpp)
 
 add_compile_options(-w)
 find_package(Boost COMPONENTS program_options REQUIRED)
@@ -141,4 +142,8 @@ if (STDCXXFS)
 endif()
 target_link_libraries(dipper PRIVATE ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} TBB::tbb) # target_link_libraries(dipper_cpu PRIVATE ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} TBB::tbb)
 
+set_target_properties(dipper_cpu PROPERTIES CUDA_SEPARABLE_COMPILATION ON)
+target_link_libraries(dipper_cpu PRIVATE ${Boost_LIBRARIES} ${ZLIB_LIBRARIES} TBB::tbb)
+
+
 install(TARGETS dipper RUNTIME DESTINATION bin)