Remove rmm/nvcc dependencies (#175)

Including [rmm](https://github.com/rapidsai/rmm)'s CMakeLists.txt (by using add_subdirectory() method with FetchContent in CMakeList.txt), though it is not used/linked to `libcucim.so`, polluted main libcucim's CMake environment variables (cuCIM was including old `rmm` version whose CMakeLists.txt was not modernized) so PTX code was always included in libcucim.so causing the issue in #170. Since cuCIM currently doesn't use `rmm`, This patch removes rmm dependency completely and makes sure that `libcucim.so` doesn't have PTX code. - Remove `superbuild_depend(rmm)` and add `superbuild_depend(googletest)` - Remove CUDA language in CMakeLists.txt - Fix compilation warnings/errors caused by switching to GCC compiler (instead of nvcc).
rapidsai · Dec 3, 2021 · ab4ed64 · ab4ed64
1 parent 28ac81f
commit ab4ed64
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Showing 18 changed files with 62 additions and 159 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -28,7 +28,7 @@ set(PROJECT_VERSION_BUILD dev)
 
 # Append local cmake module path
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cpp/cmake/modules")
-project(libcucim VERSION ${VERSION} DESCRIPTION "libcucim" LANGUAGES CXX CUDA)
+project(libcucim VERSION ${VERSION} DESCRIPTION "libcucim" LANGUAGES CXX)
 
 ################################################################################
 # Include utilities
@@ -62,19 +62,7 @@ endif ()
 
 find_package(CUDAToolkit REQUIRED)
 set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CUDA_STANDARD 17) # Clion issue: https://youtrack.jetbrains.com/issue/CPP-19165 (fixed)
-set(CMAKE_CUDA_STANDARD_REQUIRED YES)
 set(CMAKE_CXX_STANDARD_REQUIRED YES)
-cucim_define_cuda_architectures(60;70;75;80;86)
-# https://github.com/Kitware/CMake/blob/master/Modules/Compiler/NVIDIA-CUDA.cmake#L11
-# https://gitlab.kitware.com/cmake/cmake/-/issues/19017
-# For CUDA >= 10.2, we cannot use --compiler-options as '-forward-unknown-to-host-compiler' wouldbe added by default to nvcc options.
-# For the reason, we add "${CMAKE_CXX_FLAGS}" instead of "--compiler-options ${CMAKE_CXX_FLAGS}" here.
-# ==> We changed to use "${CMAKE_CUDA_FLAGS}" instead of "${CMAKE_CXX_FLAGS}" ${CMAKE_CXX_FLAGS} can have wrong options such as '-march=nocona'
-set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -use_fast_math -Xptxas=-v")
-set(CMAKE_CUDA_FLAGS_DEBUG "${CMAKE_CUDA_FLAGS_DEBUG} -G")
-set(CMAKE_CUDA_FLAGS_RELEASE "${CMAKE_CUDA_FLAGS_RELEASE} -lineinfo")
-set(CMAKE_CUDA_FLAGS_RELWITHDEBINFO "${CMAKE_CUDA_FLAGS_RELWITHDEBINFO} -lineinfo")
 
 # Include CUDA headers explicitly for VSCode intelli-sense
 include_directories(AFTER SYSTEM ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
@@ -113,14 +101,23 @@ option(CUCIM_SUPPORT_NVTX "Support NVTX" ON)
 #   whether added before or after this command is invoked, and for the ones in sub-directories added after.
 add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0) # TODO: create two library, one with CXX11 ABI and one without it.
 
+################################################################################
+# Define basic dependencies
+################################################################################
+# Include pthread
+# (https://cmake.org/cmake/help/v3.18/module/FindThreads.html)
+set(CMAKE_THREAD_PREFER_PTHREAD TRUE)
+set(THREADS_PREFER_PTHREAD_FLAG TRUE)
+find_package(Threads REQUIRED)
+
 ################################################################################
 # Define dependencies
 ################################################################################
 superbuild_depend(fmt)
 #superbuild_depend(boost)
 superbuild_depend(abseil)
-superbuild_depend(rmm) # this imports googletest internally
-#superbuild_depend(googletest)
+# superbuild_depend(rmm) # this imports googletest internally
+superbuild_depend(googletest)
 superbuild_depend(googlebenchmark)
 superbuild_depend(openslide)
 superbuild_depend(catch2)
@@ -156,13 +153,8 @@ configure_file(${CMAKE_CURRENT_LIST_DIR}/examples/cpp/CMakeLists.txt.examples.re
 ################################################################################
 set(INSTALL_TARGETS
         ${CUCIM_PACKAGE_NAME}
-#        ${CUCIM_PACKAGE_NAME}-header-only
-#        rmm
         fmt-header-only
-#        spdlog_header_only # required by rmm
         cucim_benchmarks
-#        cufile_stub
-#        cucim_tests
         )
 
 install(TARGETS ${INSTALL_TARGETS}

diff --git a/benchmarks/CMakeLists.txt b/benchmarks/CMakeLists.txt
@@ -18,18 +18,12 @@
 ################################################################################
 
 add_executable(cucim_benchmarks main.cpp config.h)
-#set_source_files_properties(main.cpp PROPERTIES LANGUAGE CUDA) # failed with CLI11 library
 
 set_target_properties(cucim_benchmarks
     PROPERTIES
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
 )
 target_compile_features(cucim_benchmarks PRIVATE ${CUCIM_REQUIRED_FEATURES})
 # Use generator expression to avoid `nvcc fatal   : Value '-std=c++17' is not defined for option 'Werror'`
@@ -63,11 +57,6 @@ set_target_properties(cucim_primitives_benchmarks
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
 )
 target_compile_features(cucim_primitives_benchmarks PRIVATE ${CUCIM_REQUIRED_FEATURES})
 # Use generator expression to avoid `nvcc fatal   : Value '-std=c++17' is not defined for option 'Werror'`

diff --git a/cpp/CMakeLists.txt b/cpp/CMakeLists.txt
@@ -100,7 +100,7 @@ add_library(${CUCIM_PACKAGE_NAME}
         src/io/format/image_format.cpp
         src/logger/logger.cpp
         src/logger/timer.cpp
-        src/memory/memory_manager.cu
+        src/memory/memory_manager.cpp
         src/plugin/image_format.cpp
         src/plugin/plugin_config.cpp
         src/profiler/profiler.cpp
@@ -114,17 +114,12 @@ set_target_properties(${CUCIM_PACKAGE_NAME}
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
         SOVERSION ${PROJECT_VERSION_MAJOR}
         VERSION ${PROJECT_VERSION}
 )
 
 # Note: Looks like the following line causes error on CMake 3.18.4 (it is working on 3.18.2). Keeping it for now.
-set(CUCIM_REQUIRED_FEATURES cxx_std_17 cuda_std_17)
+set(CUCIM_REQUIRED_FEATURES cxx_std_17)
 target_compile_features(${CUCIM_PACKAGE_NAME} PRIVATE ${CUCIM_REQUIRED_FEATURES})
 # Use generator expression to avoid `nvcc fatal   : Value '-std=c++17' is not defined for option 'Werror'`
 target_compile_options(${CUCIM_PACKAGE_NAME}
@@ -150,13 +145,7 @@ target_link_libraries(${CUCIM_PACKAGE_NAME}
         PUBLIC
             ${CMAKE_DL_LIBS}
             $<BUILD_INTERFACE:deps::fmt>
-#            $<BUILD_INTERFACE:deps::boost>
-#            $<BUILD_INTERFACE:deps::rmm>
-#            $<BUILD_INTERFACE:deps::gds>
             $<INSTALL_INTERFACE:cucim::fmt-header-only>
-##            $<INSTALL_INTERFACE:cucim::boost>
-            # $<INSTALL_INTERFACE:cucim::rmm>
-##            $<INSTALL_INTERFACE:cucim::gds>
         PRIVATE
             CUDA::cudart
             deps::abseil
@@ -179,8 +168,6 @@ target_include_directories(${CUCIM_PACKAGE_NAME}
         PUBLIC
             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>
             $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include/${CUCIM_PACKAGE_NAME}/3rdparty>
-#            $<BUILD_INTERFACE:${CMAKE_SOURCE_DIR}/gds/lib> # for GDS header
-#            $<BUILD_INTERFACE:${THRUST_INCLUDE_DIR}>
             $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>
             $<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}/${CUCIM_PACKAGE_NAME}/3rdparty> # for 3rdparty libraries such as dlpack, nvtx3, and fmt
         PRIVATE

diff --git a/cpp/cmake/deps/nvtx3.cmake b/cpp/cmake/deps/nvtx3.cmake
@@ -30,6 +30,9 @@ if (NOT TARGET deps::nvtx3)
     # Create shared library
     cucim_set_build_shared_libs(ON) # since nvtx3 is header-only library, this may not needed.
 
+    set(BUILD_TESTS OFF)
+    set(BUILD_BENCHMARKS OFF)
+
     add_subdirectory(${deps-nvtx3_SOURCE_DIR}/cpp ${deps-nvtx3_BINARY_DIR} EXCLUDE_FROM_ALL)
     cucim_restore_build_shared_libs()
 

diff --git a/cpp/include/cucim/io/device.h b/cpp/include/cucim/io/device.h
@@ -38,6 +38,7 @@ class EXPORT_VISIBLE Device
 public:
     explicit Device();
     Device(const Device& device);
+    Device& operator=(const Device& device) = default;
     explicit Device(const std::string& device_name);
     Device(const char* device_name);
     Device(DeviceType type, DeviceIndex index);

diff --git a/cpp/include/cucim/memory/memory_manager.h b/cpp/include/cucim/memory/memory_manager.h
@@ -77,7 +77,7 @@ CUCIM_API void get_pointer_attributes(PointerAttributes& attr, const void* ptr);
  * @param dst_device Destination device of the memory.
  * @return `true` if succeed.
  */
-bool move_raster_from_host(void** target, size_t size, const cucim::io::Device& dst_device);
+CUCIM_API bool move_raster_from_host(void** target, size_t size, const cucim::io::Device& dst_device);
 
 /**
  * @brief Move device memory of `size` bytes to a new memory in `out_device`.
@@ -90,7 +90,7 @@ bool move_raster_from_host(void** target, size_t size, const cucim::io::Device&
  * @param dst_device Destination device of the memory.
  * @return `true` if succeed.
  */
-bool move_raster_from_device(void** target, size_t size, const cucim::io::Device& dst_device);
+CUCIM_API bool move_raster_from_device(void** target, size_t size, const cucim::io::Device& dst_device);
 
 } // namespace cucim::memory
 #endif // CUCIM_MEMORY_MANAGER_H
diff --git a/cpp/plugins/cucim.kit.cumed/CMakeLists.txt b/cpp/plugins/cucim.kit.cumed/CMakeLists.txt
@@ -28,7 +28,7 @@ file(STRINGS ${CMAKE_CURRENT_LIST_DIR}/VERSION VERSION)
 # Append local cmake module path
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake/modules")
 
-project(cumed VERSION ${VERSION} DESCRIPTION "cumed" LANGUAGES CXX CUDA)
+project(cumed VERSION ${VERSION} DESCRIPTION "cumed" LANGUAGES CXX)
 set(CUCIM_PLUGIN_NAME "cucim.kit.cumed")
 
 ################################################################################
@@ -72,19 +72,7 @@ endif()
 find_package(CUDAToolkit REQUIRED)
 
 set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CUDA_STANDARD 17) # Clion issue: https://youtrack.jetbrains.com/issue/CPP-19165 (fixed)
-set(CMAKE_CUDA_STANDARD_REQUIRED YES)
 set(CMAKE_CXX_STANDARD_REQUIRED YES)
-cucim_define_cuda_architectures(60;70;75;80;86)
-# https://github.com/Kitware/CMake/blob/master/Modules/Compiler/NVIDIA-CUDA.cmake#L11
-# https://gitlab.kitware.com/cmake/cmake/-/issues/19017
-# For CUDA >= 10.2, we cannot use --compiler-options as '-forward-unknown-to-host-compiler' would be added by default to nvcc options.
-# For the reason, we add "${CMAKE_CXX_FLAGS}" instead of "--compiler-options ${CMAKE_CXX_FLAGS}" here.
-# ==> We changed to use "${CMAKE_CUDA_FLAGS}" instead of "${CMAKE_CXX_FLAGS}" ${CMAKE_CXX_FLAGS} can have wrong options such as '-march=nocona'
-set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -use_fast_math -Xptxas=-v")
-set(CMAKE_CUDA_FLAGS_DEBUG "${CMAKE_CUDA_FLAGS_DEBUG} -G")
-set(CMAKE_CUDA_FLAGS_RELEASE "${CMAKE_CUDA_FLAGS_RELEASE} -lineinfo")
-set(CMAKE_CUDA_FLAGS_RELWITHDEBINFO "${CMAKE_CUDA_FLAGS_RELWITHDEBINFO} -lineinfo")
 
 # Include CUDA headers explicitly for VSCode intelli-sense
 include_directories(AFTER SYSTEM ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
@@ -169,11 +157,6 @@ set_target_properties(${CUCIM_PLUGIN_NAME}
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
         SOVERSION ${PROJECT_VERSION_MAJOR}
         VERSION ${PROJECT_VERSION}
 )

diff --git a/cpp/plugins/cucim.kit.cumed/benchmarks/CMakeLists.txt b/cpp/plugins/cucim.kit.cumed/benchmarks/CMakeLists.txt
@@ -17,18 +17,12 @@
 # Add executable: cumed_benchmarks
 ################################################################################
 add_executable(cumed_benchmarks main.cpp config.h)
-#set_source_files_properties(main.cpp PROPERTIES LANGUAGE CUDA) # failed with CLI11 library
 
 set_target_properties(cumed_benchmarks
     PROPERTIES
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
 )
 target_compile_features(cumed_benchmarks PRIVATE ${CUCIM_REQUIRED_FEATURES})
 # Use generator expression to avoid `nvcc fatal   : Value '-std=c++17' is not defined for option 'Werror'`

diff --git a/cpp/plugins/cucim.kit.cumed/tests/CMakeLists.txt b/cpp/plugins/cucim.kit.cumed/tests/CMakeLists.txt
@@ -24,18 +24,12 @@ add_executable(cumed_tests
         main.cpp
         test_basic.cpp
         )
-set_source_files_properties(test_basic.cpp PROPERTIES LANGUAGE CUDA) # failed with CLI11 library
 
 set_target_properties(cumed_tests
     PROPERTIES
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
 )
 target_compile_features(cumed_tests PRIVATE ${CUCIM_REQUIRED_FEATURES})
 # Use generator expression to avoid `nvcc fatal   : Value '-std=c++17' is not defined for option 'Werror'`

diff --git a/cpp/plugins/cucim.kit.cuslide/CMakeLists.txt b/cpp/plugins/cucim.kit.cuslide/CMakeLists.txt
@@ -28,7 +28,7 @@ file(STRINGS ${CMAKE_CURRENT_LIST_DIR}/VERSION VERSION)
 # Append local cmake module path
 list(APPEND CMAKE_MODULE_PATH "${CMAKE_CURRENT_LIST_DIR}/cmake/modules")
 
-project(cuslide VERSION ${VERSION} DESCRIPTION "cuslide" LANGUAGES C CXX CUDA)
+project(cuslide VERSION ${VERSION} DESCRIPTION "cuslide" LANGUAGES C CXX)
 set(CUCIM_PLUGIN_NAME "cucim.kit.cuslide")
 
 ################################################################################
@@ -72,19 +72,7 @@ endif()
 find_package(CUDAToolkit REQUIRED)
 
 set(CMAKE_CXX_STANDARD 17)
-set(CMAKE_CUDA_STANDARD 17) # Clion issue: https://youtrack.jetbrains.com/issue/CPP-19165 (fixed)
-set(CMAKE_CUDA_STANDARD_REQUIRED YES)
 set(CMAKE_CXX_STANDARD_REQUIRED YES)
-cucim_define_cuda_architectures(60;70;75;80;86)
-# https://github.com/Kitware/CMake/blob/master/Modules/Compiler/NVIDIA-CUDA.cmake#L11
-# https://gitlab.kitware.com/cmake/cmake/-/issues/19017
-# For CUDA >= 10.2, we cannot use --compiler-options as '-forward-unknown-to-host-compiler' would be added by default to nvcc options.
-# For the reason, we add "${CMAKE_CXX_FLAGS}" instead of "--compiler-options ${CMAKE_CXX_FLAGS}" here.
-# ==> We changed to use "${CMAKE_CUDA_FLAGS}" instead of "${CMAKE_CXX_FLAGS}" ${CMAKE_CXX_FLAGS} can have wrong options such as '-march=nocona'
-set(CMAKE_CUDA_FLAGS "${CMAKE_CUDA_FLAGS} -use_fast_math -Xptxas=-v")
-set(CMAKE_CUDA_FLAGS_DEBUG "${CMAKE_CUDA_FLAGS_DEBUG} -G")
-set(CMAKE_CUDA_FLAGS_RELEASE "${CMAKE_CUDA_FLAGS_RELEASE} -lineinfo")
-set(CMAKE_CUDA_FLAGS_RELWITHDEBINFO "${CMAKE_CUDA_FLAGS_RELWITHDEBINFO} -lineinfo")
 
 # Include CUDA headers explicitly for VSCode intelli-sense
 include_directories(AFTER SYSTEM ${CMAKE_CUDA_TOOLKIT_INCLUDE_DIRECTORIES})
@@ -123,7 +111,6 @@ add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0) # TODO: create two library, one with
 ################################################################################
 # Define dependencies
 ################################################################################
-#superbuild_depend(cucim)
 superbuild_depend(fmt)
 superbuild_depend(libjpeg-turbo) # libjpeg-turbo should be located before libtiff as libtiff depends on libjpeg-turbo
 superbuild_depend(libopenjpeg)
@@ -211,11 +198,6 @@ set_target_properties(${CUCIM_PLUGIN_NAME}
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
         SOVERSION ${PROJECT_VERSION_MAJOR}
         VERSION ${PROJECT_VERSION}
 )
@@ -228,7 +210,6 @@ target_link_libraries(${CUCIM_PLUGIN_NAME}
         PRIVATE
             CUDA::cudart
             deps::fmt
-            #cucim::rmm
             cucim::cucim
             deps::libtiff
             deps::libjpeg-turbo

diff --git a/cpp/plugins/cucim.kit.cuslide/benchmarks/CMakeLists.txt b/cpp/plugins/cucim.kit.cuslide/benchmarks/CMakeLists.txt
@@ -24,11 +24,6 @@ set_target_properties(cuslide_benchmarks
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
 )
 target_compile_features(cuslide_benchmarks PRIVATE ${CUCIM_REQUIRED_FEATURES})
 # Use generator expression to avoid `nvcc fatal   : Value '-std=c++17' is not defined for option 'Werror'`

diff --git a/cpp/plugins/cucim.kit.cuslide/tests/CMakeLists.txt b/cpp/plugins/cucim.kit.cuslide/tests/CMakeLists.txt
@@ -26,18 +26,11 @@ add_executable(cuslide_tests
         test_read_rawtiff.cpp
         test_philips_tiff.cpp
         )
-set_source_files_properties(test_read_rawtiff.cpp PROPERTIES LANGUAGE CUDA) # failed with CLI11 library
-
 set_target_properties(cuslide_tests
     PROPERTIES
         CXX_STANDARD 17
         CXX_STANDARD_REQUIRED YES
         CXX_EXTENSIONS NO
-        CUDA_STANDARD 17
-        CUDA_STANDARD_REQUIRED YES
-        CUDA_EXTENSIONS NO
-        CUDA_SEPARABLE_COMPILATION ON
-        CUDA_RUNTIME_LIBRARY Shared
 )
 target_compile_features(cuslide_tests PRIVATE ${CUCIM_REQUIRED_FEATURES})
 # Use generator expression to avoid `nvcc fatal   : Value '-std=c++17' is not defined for option 'Werror'`
@@ -52,6 +45,7 @@ target_compile_definitions(cuslide_tests
 )
 target_link_libraries(cuslide_tests
         PRIVATE
+            CUDA::cudart
             cucim::cucim
             ${CUCIM_PLUGIN_NAME}
             deps::catch2