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Merge pull request #165 from rapidsai/branch-21.12
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[RELEASE] cucim v21.12
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218 changes: 218 additions & 0 deletions 3rdparty/LICENSE.NVTX
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26 changes: 24 additions & 2 deletions CHANGELOG.md
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@@ -1,6 +1,28 @@
# cuCIM 21.10.00 (Date TBD)
# cuCIM 21.12.00 (Date TBD)

Please see https://github.com/rapidsai/cucim/releases/tag/v21.10.00a for the latest changes to this development branch.
Please see https://github.com/rapidsai/cucim/releases/tag/v21.12.00a for the latest changes to this development branch.

# cuCIM 21.10.00 (7 Oct 2021)

## 🐛 Bug Fixes

- fix failing regionprops test cases ([#110](https://github.com/rapidsai/cucim/pull/110)) [@grlee77](https://github.com/grlee77)

## 📖 Documentation

- Forward-merge branch-21.08 to branch-21.10 ([#88](https://github.com/rapidsai/cucim/pull/88)) [@jakirkham](https://github.com/jakirkham)
- Update PyPI cuCIM v21.08.01 README.md and CHANGELOG.md ([#87](https://github.com/rapidsai/cucim/pull/87)) [@gigony](https://github.com/gigony)

## 🚀 New Features

- Support raw RGB tiled TIFF ([#108](https://github.com/rapidsai/cucim/pull/108)) [@gigony](https://github.com/gigony)
- Add a mechanism for user to know the availability of cucim.CuImage ([#107](https://github.com/rapidsai/cucim/pull/107)) [@gigony](https://github.com/gigony)
- Enable GDS and Support Runtime Context (__enter__, __exit__) for CuFileDriver and CuImage ([#106](https://github.com/rapidsai/cucim/pull/106)) [@gigony](https://github.com/gigony)
- Add transforms for Digital Pathology ([#100](https://github.com/rapidsai/cucim/pull/100)) [@shekhardw](https://github.com/shekhardw)

## 🛠️ Improvements

- ENH Replace gpuci_conda_retry with gpuci_mamba_retry ([#69](https://github.com/rapidsai/cucim/pull/69)) [@dillon-cullinan](https://github.com/dillon-cullinan)

# cuCIM 21.08.00 (4 Aug 2021)

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36 changes: 16 additions & 20 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand Down Expand Up @@ -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})
Expand Down Expand Up @@ -106,27 +94,38 @@ include(ExternalProject)
option(CUCIM_SUPPORT_GDS "Support cufile library" ON)
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
################################################################################
# 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)
superbuild_depend(cli11)
superbuild_depend(json)
superbuild_depend(libcuckoo)
superbuild_depend(boost-header-only)
superbuild_depend(nvtx3)

################################################################################
# Define some names
Expand Down Expand Up @@ -154,13 +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}
Expand Down Expand Up @@ -213,6 +207,8 @@ 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)

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6 changes: 4 additions & 2 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
Expand Up @@ -144,11 +144,13 @@ The build command will create the following files:
- `./install/lib/libcucim*`
- `./python/install/lib/_cucim.cpython-*-x86_64-linux-gnu.so`
- `./cpp/plugins/cucim.kit.cuslide/install/lib/cucim.kit.cuslide@*.so`
- `./cpp/plugins/cucim.kit.cumed/install/lib/cucim.kit.cumed@*.so`

And, it will copy the built library files to `python/cucim/src/cucim/clara/` folder:
- `libcucim.so.*`
- `_cucim.cpython-*-x86_64-linux-gnu.so`
- `cucim.kit.cuslide@*.so`
- `cucim.kit.cumed@*.so`


**Building `cucim`(python bindings)**
Expand All @@ -173,14 +175,14 @@ Once it is built, the subsequent build doesn't take much time.

However, if a build option or dependent packages are updated, the build can be failed (due to CMakeCache.txt or existing build files). In that case, you can remove use the following commands to remove CMakeCache.txt or build folder, then build it again.

1) Remove CMakeCache.txt for libcucim, cuslide plugin, and the python wrapper (pybind11).
1) Remove CMakeCache.txt for libcucim, cuslide/cumed plugin, and the python wrapper (pybind11).

```bash
# this command wouldn't remove already downloaded dependency so faster than `clean` subcommand
./run build_local clean_cache
```

2) Remove `build-*` and `install` folder for libcucim, cuslide plugin, and the python wrapper (pybind11).
2) Remove `build-*` and `install` folder for libcucim, cuslide/cumed plugin, and the python wrapper (pybind11).

```bash
# this command is for clean build
Expand Down
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