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.github/workflows/build-test.yml

@@ -18,6 +18,7 @@ jobs:
     name: ${{ matrix.os }}-${{ matrix.cxx-compiler }}-${{ matrix.cmake-build-type }}
     runs-on: ${{ matrix.os }}
     strategy:
+      fail-fast: true
       max-parallel: 3
       matrix:
         name: [ubuntu, windows, macos]
@@ -63,23 +64,41 @@ jobs:
           cd ..
           git clone --branch ${{ env.opencl-icd-loader-git-tag }} https://github.com/KhronosGroup/OpenCL-ICD-Loader
           git clone --branch ${{ env.opencl-headers-git-tag }} https://github.com/KhronosGroup/OpenCL-Headers
-          cmake -D CMAKE_INSTALL_PREFIX="./OpenCL-Headers/install" -S "./OpenCL-Headers" -B "./OpenCL-Headers/build" 
+          cmake -D CMAKE_INSTALL_PREFIX="${{ github.workspace }}/OpenCL-Headers/install" -S "./OpenCL-Headers" -B "./OpenCL-Headers/build" 
           cmake --build "./OpenCL-Headers/build" --parallel 6 --target install
-          cmake -D CMAKE_PREFIX_PATH="./OpenCL-Headers/install" -D OPENCL_ICD_LOADER_HEADERS_DIR="./OpenCL-Headers/install/include" -S "./OpenCL-ICD-Loader" -B "./OpenCL-ICD-Loader/build" -A x64
+          cmake -D CMAKE_PREFIX_PATH="${{ github.workspace }}/OpenCL-Headers/install" -D OPENCL_ICD_LOADER_HEADERS_DIR="./OpenCL-Headers/install/include" -S "./OpenCL-ICD-Loader" -B "./OpenCL-ICD-Loader/build" -A x64
           cmake --build "./OpenCL-ICD-Loader/build" --parallel 6 --target install --config Release
         shell: bash -l {0}
 
+      - name: Install cuda toolkit (windows)
+        if: matrix.os == 'windows-latest'
+        uses: Jimver/cuda-toolkit@v0.2.10
+        id: cuda-toolkit
+        with:
+          cuda: '12.1.0'
+
       - name: Install ocl-icd-loader - linux
         if: matrix.os == 'ubuntu-latest'
         run: |
           cd ..
           git clone --branch ${{ env.opencl-icd-loader-git-tag }} https://github.com/KhronosGroup/OpenCL-ICD-Loader
           git clone --branch ${{ env.opencl-headers-git-tag }} https://github.com/KhronosGroup/OpenCL-Headers
-          cmake -D CMAKE_INSTALL_PREFIX="./OpenCL-Headers/install" -S "./OpenCL-Headers" -B "./OpenCL-Headers/build" 
+          cmake -D CMAKE_INSTALL_PREFIX="${{ github.workspace }}/OpenCL-Headers/install" -S "./OpenCL-Headers" -B "./OpenCL-Headers/build" 
           cmake --build "./OpenCL-Headers/build" --parallel 6 --target install
-          cmake -D CMAKE_PREFIX_PATH="./OpenCL-Headers/install" -D OPENCL_ICD_LOADER_HEADERS_DIR="./OpenCL-Headers/install/include" -S "./OpenCL-ICD-Loader" -B "./OpenCL-ICD-Loader/build"
+          cmake -D CMAKE_PREFIX_PATH="${{ github.workspace }}/OpenCL-Headers/install" -D OPENCL_ICD_LOADER_HEADERS_DIR="./OpenCL-Headers/install/include" -S "./OpenCL-ICD-Loader" -B "./OpenCL-ICD-Loader/build"
           sudo cmake --build "./OpenCL-ICD-Loader/build" --parallel 6 --target install --config Release
         shell: bash -l {0}
+
+      - name: Install cuda toolkit (ubuntu)
+        if: matrix.os == 'ubuntu-latest'
+        run: |
+          wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/x86_64/cuda-ubuntu2204.pin
+          sudo mv cuda-ubuntu2204.pin /etc/apt/preferences.d/cuda-repository-pin-600
+          wget https://developer.download.nvidia.com/compute/cuda/12.1.1/local_installers/cuda-repo-ubuntu2204-12-1-local_12.1.1-530.30.02-1_amd64.deb
+          sudo dpkg -i cuda-repo-ubuntu2204-12-1-local_12.1.1-530.30.02-1_amd64.deb
+          sudo cp /var/cuda-repo-ubuntu2204-12-1-local/cuda-*-keyring.gpg /usr/share/keyrings/
+          sudo apt-get update
+          sudo apt-get -y install cuda
 
       - uses: actions/checkout@v3
         with:
@@ -89,14 +108,14 @@ jobs:
         if: matrix.os == 'ubuntu-latest'
         run : |
           pwd
-          cmake -S "${{ github.workspace }}" -B "${{ runner.workspace }}/build" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DBUILD_BENCHMARK=OFF -DOpenCL_LIBRARY:FILEPATH="/usr/local/lib/libOpenCL.so.1.2"
+          cmake -S "${{ github.workspace }}" -B "${{ runner.workspace }}/build" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DBUILD_BENCHMARK=OFF -DOpenCL_LIBRARIES:FILEPATH="/usr/local/lib/libOpenCL.so" -DOpenCL_INCLUDE_DIRS:PATH="${{ github.workspace }}/OpenCL-Headers/install/include/"
           cmake --build "${{ runner.workspace }}/build" --parallel 10 --config Release
         shell: bash -l {0}    
 
       - name: compile CLIc - windows
         if: matrix.os == 'windows-latest'
         run : |
-          cmake -S "${{ github.workspace }}" -B "${{ runner.workspace }}/build" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DBUILD_BENCHMARK=OFF -DOpenCL_LIBRARY:FILEPATH="C:/Program Files/OpenCL-ICD-Loader/lib/OpenCL.lib"
+          cmake -S "${{ github.workspace }}" -B "${{ runner.workspace }}/build" -DCMAKE_BUILD_TYPE=${{ matrix.cmake-build-type }} -DBUILD_BENCHMARK=OFF -DOpenCL_LIBRARIES:FILEPATH="C:/Program Files/OpenCL-ICD-Loader/lib/OpenCL.lib" -DOpenCL_INCLUDE_DIRS:PATH="${{ github.workspace }}/OpenCL-Headers/install/include/"
           cmake --build "${{ runner.workspace }}/build" --parallel 10 --config Release
         shell: bash -l {0}
 
@@ -107,11 +126,6 @@ jobs:
           cmake --build "${{ runner.workspace }}/build" --parallel 10 --config Release
         shell: bash -l {0}
 
-      - name: run CLIc core test
-        run: |
-          cd "${{ runner.workspace }}/build"
-          ctest -R core_gpu_test -C Release
-        shell: bash -l {0}
 
 
 

.github/workflows/tests_and_coverage.yml

@@ -46,17 +46,23 @@ jobs:
         run: |
           cd ${{ runner.workspace }}/build && ctest -C ${{ matrix.buildtype }} --output-on-failure
 
+      # - name: Format coverage
+      #   shell: bash
+      #   run: |
+      #     cd ${{ runner.workspace }}/build
+      #     lcov --directory . --capture --output-file coverage.info
+      #     lcov --remove coverage.info '/usr/*' "${HOME}"'/.cache/*' --output-file coverage.info
+      #     lcov --list coverage.info
+
       - name: Format coverage
         shell: bash
         run: |
           cd ${{ runner.workspace }}/build
-          lcov --directory . --capture --output-file coverage.info
-          lcov --remove coverage.info '/usr/*' "${HOME}"'/.cache/*' --output-file coverage.info
-          lcov --list coverage.info
+          gcovr --root .. --output coverage.xml
 
       - name: Upload coverage report
         uses: codecov/codecov-action@v3
         with:
           token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-          files: ${{ runner.workspace }}/build/coverage.info
+          files: ${{ runner.workspace }}/build/coverage.xml
           fail_ci_if_error: true # optional (default = false)

CMakeLists.txt

@@ -1,55 +1,73 @@
-# Set minimum version of CMake.
 cmake_minimum_required(VERSION 3.20)
 
-# Set project name and version
-project(CLIc VERSION 0.6.3)
+project(CLIc VERSION 0.7.0)
 
-# Set environment variables
-include(${PROJECT_SOURCE_DIR}/cmake/SetEnv.cmake)
+# set environment variables
+include(${PROJECT_SOURCE_DIR}/cmake/CMakeSetEnv.cmake)
+# find library dependencies
+include(${PROJECT_SOURCE_DIR}/cmake/CMakeDependencies.cmake)
+# managed third party libraries
+add_subdirectory(thirdparty)
 
-# find required package
-if(NOT OpenCL_FOUND AND NOT DEFINED OpenCL_LIBRARY)
-    find_package(OpenCL REQUIRED)
-    # find_package(OpenCLHeaders REQUIRED)
-    # find_package(OpenCLICDLoader REQUIRED)
-endif()
-message(STATUS "OpenCL_LIBRARY : ${OpenCL_LIBRARY}")
+# manage configuration files
+configure_file(
+    "${CMAKE_CURRENT_SOURCE_DIR}/${LIBRARY_NAME_LOWERCASE}/${LIBRARY_NAME_LOWERCASE}.hpp.in"
+    "${CMAKE_CURRENT_BINARY_DIR}/${LIBRARY_NAME_LOWERCASE}/include/${LIBRARY_NAME_LOWERCASE}.hpp"
+    NO_SOURCE_PERMISSIONS @ONLY
+)
+
+# list project source files
+file(GLOB_RECURSE SOURCES "${CMAKE_CURRENT_SOURCE_DIR}/${LIBRARY_NAME_LOWERCASE}/src/*.cpp")
+file(GLOB_RECURSE HEADERS_SRC "${CMAKE_CURRENT_SOURCE_DIR}/${LIBRARY_NAME_LOWERCASE}/include/*.hpp")
+file(GLOB_RECURSE HEADERS_BIN "${CMAKE_CURRENT_BINARY_DIR}/${LIBRARY_NAME_LOWERCASE}/include/*.hpp")
+set(HEADERS ${HEADERS_SRC})
+list(APPEND HEADERS ${HEADERS_BIN})
+
+# target library definition
+add_library(${LIBRARY_NAME} ${SOURCES} ${HEADERS})
+add_library(${PROJECT_NAME}::${LIBRARY_NAME} ALIAS ${LIBRARY_NAME})
+target_include_directories(${LIBRARY_NAME} PUBLIC
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/${LIBRARY_NAME_LOWERCASE}/include>
+    $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/${LIBRARY_NAME_LOWERCASE}/include>
+    $<BUILD_INTERFACE:${KERNELS_HEADER_DIR}>
+    $<INSTALL_INTERFACE:include>
+)
+
+set_target_properties(${LIBRARY_NAME} PROPERTIES LINKER_LANGUAGE CXX)        # force C++ linker
+set_target_properties(${LIBRARY_NAME} PROPERTIES VERSION ${PROJECT_VERSION}) # set version
+add_dependencies(${LIBRARY_NAME} generate_kernels)
 
-if(NOT Python3_Interpreter_FOUND)
-    find_package(Python3 COMPONENTS Interpreter REQUIRED)
+# link GPU framework to the target
+if (OpenCL_FOUND)
+    message (STATUS "OpenCL found")
+    target_include_directories(${LIBRARY_NAME} PUBLIC ${OpenCL_INCLUDE_DIRS})
+    target_link_libraries(${LIBRARY_NAME} PUBLIC ${OpenCL_LIBRARIES})
 endif()
+if (CUDAToolkit_FOUND)
+    message (STATUS "CUDA found")
+    set_target_properties(${LIBRARY_NAME} PROPERTIES CUDA_SEPARABLE_COMPILATION ON)
+    set_target_properties(${LIBRARY_NAME} PROPERTIES POSITION_INDEPENDENT_CODE ON)
+    target_include_directories(${LIBRARY_NAME} PUBLIC ${CUDAToolkit_INCLUDE_DIRS})
+    target_link_libraries(${LIBRARY_NAME} PUBLIC CUDA::cudart CUDA::cuda_driver CUDA::nvrtc CUDA::OpenCL) 
+endif()
+
+# # Set RPATH configuration
+# if(APPLE)
+#     set(CMAKE_BUILD_RPATH "@loader_path")
+#     set(CMAKE_INSTALL_RPATH "@loader_path/../lib")
+# else()
+#     set(CMAKE_BUILD_RPATH "$ORIGIN")
+#     set(CMAKE_INSTALL_RPATH "$ORIGIN/../lib")
+# endif()
 
-# Library sources
-add_subdirectory(${THIRDPARTY_DIR})
-add_subdirectory(${LIBRARY_DIR})
+# library install instructions
+include(${PROJECT_SOURCE_DIR}/cmake/Install.cmake)
 
 # Build and run tests
 if(BUILD_TESTING)
     include(CTest)
     add_subdirectory(${PROJECT_SOURCE_DIR}/tests)
 endif(BUILD_TESTING)
 
-# Build and run benchmark
-if(BUILD_BENCHMARK)
-    add_subdirectory(benchmark)
-endif(BUILD_BENCHMARK)
-
-if(BUILD_DOCUMENTATION)
-    # find_package(Doxygen)
-    # if(DOXYGEN_FOUND)
-    # # set input and output files
-    # set(DOXYGEN_IN ${CMAKE_CURRENT_SOURCE_DIR}/docs/Doxyfile.in)
-    # set(DOXYGEN_OUT ${CMAKE_CURRENT_BINARY_DIR}/Doxyfile)
-    # # request to configure the file
-    # configure_file(${DOXYGEN_IN} ${DOXYGEN_OUT} @ONLY)
-    # message("Doxygen build started")
-    # # note the option ALL which allows to build the docs together with the application
-    # add_custom_target( doc_doxygen ALL
-    # COMMAND ${DOXYGEN_EXECUTABLE} ${DOXYGEN_OUT}
-    # WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
-    # COMMENT "Generating API documentation with Doxygen"
-    # VERBATIM )
-    # else(DOXYGEN_FOUND)
-    # message("Doxygen need to be installed to generate the documentation")
-    # endif(DOXYGEN_FOUND)
-endif(BUILD_DOCUMENTATION)
+
+

LICENSE

@@ -1,5 +1,5 @@
 Copyright 2020 Stéphane Rigaud, Robert Haase,
-Institut Pasteur Paris, Max Planck Institute for Molecular Cell Biology and Genetics Dresden
+Institut Pasteur of Paris, Max Planck Institute for Molecular Cell Biology and Genetics Dresden
 
 Redistribution and use in source and binary forms, with or without 
 modification, are permitted provided that the following conditions are met: