De-vendor CMake dependencies and use shared libraries

CMakeLists.txt

@@ -96,10 +96,6 @@ option(CUCIM_STATIC_GDS "Use static cufile library" OFF)
 option(CUCIM_SUPPORT_CUDA "Support CUDA" ON)
 option(CUCIM_SUPPORT_NVTX "Support NVTX" ON)
 
-# Setup CXX11 ABI
-# : Adds CXX11 ABI definition to the compiler command line for targets in the current directory,
-#   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
@@ -122,7 +118,7 @@ superbuild_depend(googlebenchmark)
 superbuild_depend(openslide)
 superbuild_depend(catch2)
 superbuild_depend(cli11)
-superbuild_depend(json)
+superbuild_depend(nlohmann_json)
 superbuild_depend(libcuckoo)
 superbuild_depend(boost-header-only)
 superbuild_depend(nvtx3)
@@ -154,10 +150,10 @@ configure_file(${CMAKE_CURRENT_LIST_DIR}/examples/cpp/CMakeLists.txt.examples.re
 ################################################################################
 set(INSTALL_TARGETS
         ${CUCIM_PACKAGE_NAME}
-        fmt-header-only
         cucim_benchmarks
         )
 
+
 install(TARGETS ${INSTALL_TARGETS}
         EXPORT ${CUCIM_PACKAGE_NAME}-targets
         RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
@@ -207,11 +203,15 @@ install(DIRECTORY
 
 # Copy 3rdparty headers
 install(DIRECTORY
-            ${deps-fmt_SOURCE_DIR}/include/
-            ${deps-nvtx3_SOURCE_DIR}/c/include/
-            ${deps-nvtx3_SOURCE_DIR}/cpp/include/
-        DESTINATION
-            ${CMAKE_INSTALL_INCLUDEDIR}/${CUCIM_PACKAGE_NAME}/3rdparty)
+        ${fmt_INCLUDE_DIR}/fmt/
+    DESTINATION
+        ${CMAKE_INSTALL_INCLUDEDIR}/${CUCIM_PACKAGE_NAME}/3rdparty/fmt
+)
+install(DIRECTORY
+        ${nvtx3_INCLUDE_DIR}/nvtx3/
+    DESTINATION
+        ${CMAKE_INSTALL_INCLUDEDIR}/${CUCIM_PACKAGE_NAME}/3rdparty/nvtx3
+)
 
 set(CMAKE_EXPORT_PACKAGE_REGISTRY ON)
 export(PACKAGE ${CUCIM_PACKAGE_NAME})

CONTRIBUTING.md

@@ -133,9 +133,9 @@ Note that `./conda/environments/all_cuda-118_arch-x86_64.yaml` is currently set
 If you want to change the version of gcc or CUDA toolkit package, please update `./conda/environments/all_cuda-118_arch-x86_64.yaml` before executing the following commands.
 
 ```bash
-conda env create -n cucim -f ./conda/environments/all_cuda-118_arch-x86_64.yaml
+mamba env create -n cucim -f conda/environments/all_cuda-125_arch-x86_64.yaml
 # activate the environment
-conda activate cucim
+mamba activate cucim
 ```
 
 ### Building `libcucim` and install `cucim` (python bindings):

benchmarks/CMakeLists.txt

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2024, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -26,8 +26,6 @@ set_target_properties(cucim_benchmarks
         CXX_EXTENSIONS NO
 )
 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'`
-target_compile_options(cucim_benchmarks PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Werror -Wall -Wextra>)
 target_compile_definitions(cucim_benchmarks
     PUBLIC
         CUCIM_VERSION=${PROJECT_VERSION}
@@ -59,8 +57,6 @@ set_target_properties(cucim_primitives_benchmarks
         CXX_EXTENSIONS NO
 )
 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'`
-target_compile_options(cucim_primitives_benchmarks PRIVATE $<$<COMPILE_LANGUAGE:CXX>:-Werror -Wall -Wextra>)
 target_link_libraries(cucim_primitives_benchmarks
         PRIVATE
             ${CUCIM_PACKAGE_NAME}

conda/environments/all_cuda-118_arch-x86_64.yaml

@@ -6,18 +6,23 @@ channels:
 - conda-forge
 - nvidia
 dependencies:
+- boost-cpp
 - c-compiler
+- catch2
+- cli11
 - click
 - cmake>=3.26.4,!=3.30.0
 - cuda-version=11.8
 - cudatoolkit
 - cupy>=12.0.0
 - cxx-compiler
+- fmt
 - gcc_linux-64=11.*
 - imagecodecs>=2021.6.8
 - ipython
 - jbig
 - lazy_loader>=0.1
+- libabseil
 - libcufile-dev=1.4.0.31
 - libcufile=1.4.0.31
 - libnvjpeg-dev=11.6.0.55
@@ -26,14 +31,18 @@ dependencies:
 - matplotlib-base
 - nbsphinx
 - ninja
+- nlohmann_json
 - numpy>=1.23.4,<3.0a0
 - numpydoc>=1.5
 - nvcc_linux-64=11.8
+- nvtx-c >=3.1.0
 - openslide-python>=1.3.0
 - pip
 - pooch>=1.6.0
 - pre-commit
 - psutil>=5.8.0
+- pybind11
+- pybind11_json
 - pydata-sphinx-theme
 - pytest-cov>=2.12.1
 - pytest-lazy-fixtures>=1.0.0
@@ -46,6 +55,7 @@ dependencies:
 - scipy>=1.6.0
 - sphinx<6
 - sysroot_linux-64==2.17
+- taskflow
 - tifffile>=2022.7.28
 - xz
 - yasm

conda/environments/all_cuda-125_arch-x86_64.yaml

@@ -6,33 +6,42 @@ channels:
 - conda-forge
 - nvidia
 dependencies:
+- boost-cpp
 - c-compiler
+- catch2
+- cli11
 - click
 - cmake>=3.26.4,!=3.30.0
 - cuda-cudart-dev
 - cuda-nvcc
 - cuda-version=12.5
 - cupy>=12.0.0
 - cxx-compiler
+- fmt
 - gcc_linux-64=11.*
 - imagecodecs>=2021.6.8
 - ipython
 - jbig
 - lazy_loader>=0.1
+- libabseil
 - libcufile-dev
 - libnvjpeg-dev
 - libnvjpeg-static
 - libwebp-base
 - matplotlib-base
 - nbsphinx
 - ninja
+- nlohmann_json
 - numpy>=1.23.4,<3.0a0
 - numpydoc>=1.5
+- nvtx-c >=3.1.0
 - openslide-python>=1.3.0
 - pip
 - pooch>=1.6.0
 - pre-commit
 - psutil>=5.8.0
+- pybind11
+- pybind11_json
 - pydata-sphinx-theme
 - pytest-cov>=2.12.1
 - pytest-lazy-fixtures>=1.0.0
@@ -45,6 +54,7 @@ dependencies:
 - scipy>=1.6.0
 - sphinx<6
 - sysroot_linux-64==2.17
+- taskflow
 - tifffile>=2022.7.28
 - xz
 - yasm

conda/recipes/cucim/meta.yaml

@@ -62,7 +62,11 @@ requirements:
     - cuda-cudart-dev
     {% endif %}
     - cupy >=12.0.0
+    - fmt
     - libcucim ={{ version }}
+    - nlohmann_json
+    - pybind11
+    - pybind11_json
     - python
     - rapids-build-backend >=0.3.0,<0.4.0.dev0
     - scikit-image >=0.19.0,<0.25.0a0

conda/recipes/libcucim/meta.yaml

@@ -74,10 +74,19 @@ requirements:
     - libnvjpeg-dev
     - libnvjpeg-static
     {% endif %}
+    - boost-cpp
+    - catch2
+    - cli11
+    - fmt
     - jbig
+    - libabseil
     - libwebp-base
     - nvtx-c >=3.1.0
+    - nlohmann_json
     - openslide
+    - pybind11
+    - pybind11_json
+    - taskflow
     - xz
     - zlib
     - zstd
@@ -92,6 +101,7 @@ requirements:
     - libnvjpeg
     {% endif %}
     - {{ pin_compatible('libwebp-base', max_pin='x.x') }}
+    - libabseil
     - jbig
     - xz
     - zlib

cpp/CMakeLists.txt

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020-2021, NVIDIA CORPORATION.
+# Copyright (c) 2020-2024, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -128,11 +128,6 @@ set_target_properties(${CUCIM_PACKAGE_NAME}
 # Note: Looks like the following line causes error on CMake 3.18.4 (it is working on 3.18.2). Keeping it for now.
 set(CUCIM_REQUIRED_FEATURES cxx_std_17)
 target_compile_features(${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}
-    PRIVATE
-        $<$<COMPILE_LANGUAGE:CXX>:-Werror -Wall -Wextra>
-        )
 target_compile_definitions(${CUCIM_PACKAGE_NAME}
     PUBLIC
         CUCIM_VERSION=${PROJECT_VERSION}
@@ -144,23 +139,21 @@ target_compile_definitions(${CUCIM_PACKAGE_NAME}
         CUCIM_STATIC_GDS=$<BOOL:${CUCIM_STATIC_GDS}>
         CUCIM_SUPPORT_CUDA=$<BOOL:${CUCIM_SUPPORT_CUDA}>
         CUCIM_SUPPORT_NVTX=$<BOOL:${CUCIM_SUPPORT_NVTX}>
-        _GLIBCXX_USE_CXX11_ABI=0  # TODO: create two library, one with CXX11 ABI and one without it.
 )
 
 # Link libraries
 target_link_libraries(${CUCIM_PACKAGE_NAME}
         PUBLIC
             ${CMAKE_DL_LIBS}
             Threads::Threads # -lpthread
-            $<BUILD_INTERFACE:deps::fmt>
-            $<INSTALL_INTERFACE:cucim::fmt-header-only>
+            deps::fmt
         PRIVATE
             CUDA::cudart
             deps::abseil
             deps::gds
             deps::libcuckoo
             deps::boost-header-only
-            deps::json
+            deps::nlohmann_json
             deps::nvtx3
             deps::taskflow
         )

cpp/cmake/deps/abseil.cmake

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2024, NVIDIA CORPORATION.
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -14,31 +14,49 @@
 #
 
 if (NOT TARGET deps::abseil)
-    FetchContent_Declare(
-            deps-abseil
-            GIT_REPOSITORY https://github.com/abseil/abseil-cpp.git
-            GIT_TAG 20200225.2
-            GIT_SHALLOW TRUE
-    )
-    FetchContent_GetProperties(deps-abseil)
-    if (NOT deps-abseil_POPULATED)
-        message(STATUS "Fetching abseil sources")
-        FetchContent_Populate(deps-abseil)
-        message(STATUS "Fetching abseil sources - done")
-    endif ()
+    set(Abseil_VERSION 20240116.2)
 
-    # Create static library
-    cucim_set_build_shared_libs(OFF)
-    set(BUILD_TESTING FALSE) # Disable BUILD_TESTING (cmake-build-debug/_deps/deps-abseil-src/CMakeLists.txt:97)
-    add_subdirectory(${deps-abseil_SOURCE_DIR} ${deps-abseil_BINARY_DIR} EXCLUDE_FROM_ALL)
+    if (DEFINED ENV{CONDA_PREFIX})
+        find_package(absl REQUIRED)
+        if (NOT absl_FOUND)
+            message(FATAL_ERROR "fmt package not found in conda environment")
+        endif()
 
-    # Set PIC to prevent the following error message
-    # : /usr/bin/ld: ../lib/libabsl_strings.a(escaping.cc.o): relocation R_X86_64_PC32 against symbol `_ZN4absl14lts_2020_02_2516numbers_internal8kHexCharE' can not be used when making a shared object; recompile with -fPIC
-    set_target_properties(absl_strings absl_strings_internal absl_int128 absl_raw_logging_internal PROPERTIES POSITION_INDEPENDENT_CODE ON)
-    cucim_restore_build_shared_libs()
+        add_library(deps::abseil ALIAS absl::strings)
+        get_target_property(abseil_INCLUDE_DIR absl::strings INTERFACE_INCLUDE_DIRECTORIES)
 
-    add_library(deps::abseil INTERFACE IMPORTED GLOBAL)
-    target_link_libraries(deps::abseil INTERFACE absl::strings)
-    set(deps-abseil_SOURCE_DIR ${deps-abseil_SOURCE_DIR} CACHE INTERNAL "" FORCE)
-    mark_as_advanced(deps-abseil_SOURCE_DIR)
+        set(abseil_INCLUDE_DIR ${abseil_INCLUDE_DIR} CACHE INTERNAL "" FORCE)
+        mark_as_advanced(abseil_INCLUDE_DIR)
+    else()
+        # Fallback to fetching Abseil sources
+        FetchContent_Declare(
+                deps-abseil
+                GIT_REPOSITORY https://github.com/abseil/abseil-cpp.git
+                GIT_TAG ${Abseil_VERSION}
+                GIT_SHALLOW TRUE
+        )
+        FetchContent_GetProperties(deps-abseil)
+        if (NOT deps-abseil_POPULATED)
+            message(STATUS "Fetching abseil sources")
+            # TODO: use FetchContent_MakeAvailable (with EXCLUDE_FROM_ALL option in FetchContent_Declare) when CMake 3.30 is minimum required
+            #       (https://cmake.org/cmake/help/latest/policy/CMP0169.html#policy:CMP0169)
+            FetchContent_Populate(deps-abseil)
+            message(STATUS "Fetching abseil sources - done")
+        endif ()
+
+        # Create static library
+        cucim_set_build_shared_libs(OFF)
+        set(BUILD_TESTING FALSE) # Disable BUILD_TESTING (cmake-build-debug/_deps/deps-abseil-src/CMakeLists.txt:97)
+        add_subdirectory(${deps-abseil_SOURCE_DIR} ${deps-abseil_BINARY_DIR} EXCLUDE_FROM_ALL)
+
+        # Set PIC to prevent the following error message
+        # : /usr/bin/ld: ../lib/libabsl_strings.a(escaping.cc.o): relocation R_X86_64_PC32 against symbol `_ZN4absl14lts_2020_02_2516numbers_internal8kHexCharE' can not be used when making a shared object; recompile with -fPIC
+        set_target_properties(absl_strings absl_strings_internal absl_int128 absl_raw_logging_internal PROPERTIES POSITION_INDEPENDENT_CODE ON)
+        cucim_restore_build_shared_libs()
+
+        add_library(deps::abseil INTERFACE IMPORTED GLOBAL)
+        target_link_libraries(deps::abseil INTERFACE absl::strings)
+        set(abseil_INCLUDE_DIR ${deps-deps-abseil_SOURCE_DIR} CACHE INTERNAL "" FORCE)
+        mark_as_advanced(abseil_INCLUDE_DIR)
+    endif()
 endif ()