Merge pull request #18 from rapidsai/branch-0.19

[RELEASE] v0.19 cucim

.github/CODEOWNERS

@@ -1,13 +1,13 @@
 #cpp code owners
-cpp/               @rapidsai/<repo>-cpp-codeowners
+cpp/               @rapidsai/cucim-cpp-codeowners
+python/pybind11    @rapidsai/cucim-cpp-codeowners
 
 #python code owners
-python/            @rapidsai/<repo>-python-codeowners
-python/dask_cudf/  @rapidsai/<repo>-dask-codeowners
+python/            @rapidsai/cucim-python-codeowners
 
 #cmake code owners
-**/CMakeLists.txt  @rapidsai/<repo>-cmake-codeowners
-**/cmake/          @rapidsai/<repo>-cmake-codeowners
+**/CMakeLists.txt  @rapidsai/cucim-cmake-codeowners
+**/cmake/          @rapidsai/cucim-cmake-codeowners
 
 #build/ops code owners
 .github/           @rapidsai/ops-codeowners 

3rdparty/LICENSE.cuda

@@ -1,6 +1,16 @@
 End User License Agreement
 --------------------------
 
+The CUDA Toolkit End User License Agreement applies to the
+NVIDIA CUDA Toolkit, the NVIDIA CUDA Samples, the NVIDIA
+Display Driver, NVIDIA Nsight tools (Visual Studio Edition),
+and the associated documentation on CUDA APIs, programming
+model and development tools. If you do not agree with the
+terms and conditions of the license agreement, then do not
+download or use the software.
+
+Last updated: Mar 24, 2021.
+
 
 Preface
 -------
@@ -99,10 +109,6 @@ Windows platform:
 ---------------------------------------------------------
 
 
-Release Date: May 21, 2019
---------------------------
-
-
 Important Notice—Read before downloading, installing,
 copying or using the licensed software:
 -------------------------------------------------------
@@ -257,6 +263,11 @@ terms, the terms of this Agreement. Copyright to third party
 software is held by the copyright holders indicated in the
 third-party software or license.
 
+Subject to the other terms of this Agreement, you may use the
+SDK to develop and test applications released under Open
+Source Initiative (OSI) approved open source software
+licenses.
+
 
 1.1.7. Reservation of Rights
 
@@ -304,12 +315,12 @@ SDK:
     application where the use or failure of the system or
     application can reasonably be expected to threaten or
     result in personal injury, death, or catastrophic loss.
-    Examples include use in nuclear, avionics, navigation,
-    military, medical, life support or other life critical
-    applications. NVIDIA does not design, test or manufacture
-    the SDK for these critical uses and NVIDIA shall not be
-    liable to you or any third party, in whole or in part, for
-    any claims or damages arising from such uses.
+    Examples include use in avionics, navigation, military,
+    medical, life support or other life critical applications.
+    NVIDIA does not design, test or manufacture the SDK for
+    these critical uses and NVIDIA shall not be liable to you
+    or any third party, in whole or in part, for any claims or
+    damages arising from such uses.
 
   7. You agree to defend, indemnify and hold harmless NVIDIA
     and its affiliates, and their respective employees,
@@ -328,8 +339,8 @@ SDK:
   1.  NVIDIA or its licensors hold all rights, title and
     interest in and to the SDK and its modifications and
     derivative works, including their respective intellectual
-    property rights, subject to your rights described here .
-    This SDK may include software and materials from
+    property rights, subject to your rights under Section
+    1.3.2. This SDK may include software and materials from
     NVIDIA’s licensors, and these licensors are intended
     third party beneficiaries that may enforce this Agreement
     with respect to their intellectual property rights.
@@ -338,7 +349,7 @@ SDK:
     applications and your derivative works of the sample
     source code delivered in the SDK, including their
     respective intellectual property rights, subject to
-    NVIDIA’s rights described here .
+    NVIDIA’s rights under Section 1.3.1.
 
   3. You may, but don’t have to, provide to NVIDIA
     suggestions, feature requests or other feedback regarding
@@ -519,10 +530,6 @@ parties.
 NVIDIA Software Development Kits
 ------------------------------------------------------------
 
-
-Release date: August 16, 2018
------------------------------
-
 The terms in this supplement govern your use of the NVIDIA
 CUDA Toolkit SDK under the terms of your license agreement
 (“Agreement”) as modified by this supplement. Capitalized
@@ -582,8 +589,12 @@ [email protected].
 
 2.6. Attachment A
 
-The following portions of the SDK are distributable under the
-Agreement:
+The following CUDA Toolkit files may be distributed with
+Licensee Applications developed by you, including certain
+variations of these files that have version number or
+architecture specific information embedded in the file name -
+as an example only, for release version 9.0 of the 64-bit
+Windows software, the file cudart64_90.dll is redistributable.
 
 Component
 
@@ -729,26 +740,6 @@ libcurand.so, libcurand_static.a
 
 Component
 
-CUDA Accelerated Graph Library
-
-Windows
-
-nvgraph.dll, nvgraph.lib
-
-Mac OSX
-
-libnvgraph.dylib, libnvgraph_static.a
-
-Linux
-
-libnvgraph.so, libnvgraph_static.a
-
-Android
-
-libnvgraph.so, libnvgraph_static.a
-
-Component
-
 NVIDIA Performance Primitives Library
 
 Windows
@@ -814,7 +805,11 @@ libculibos.a
 
 Component
 
-NVIDIA Runtime Compilation Library
+NVIDIA Runtime Compilation Library and Header
+
+All
+
+nvrtc.h
 
 Windows
 
@@ -914,8 +909,20 @@ NVIDIA CUDA Driver Libraries
 
 Linux
 
-libcuda.so, libnvidia-fatbinaryloader.so,
-libnvidia-ptxjitcompiler.so
+libcuda.so, libnvidia-ptxjitcompiler.so
+
+Component
+
+NVIDIA CUDA File IO Libraries and Header
+
+All
+
+cufile.h
+
+Linux
+
+libcufile.so, libcufile_rdma.so, libcufile_static.a,
+libcufile_rdma_static.a
 
 The NVIDIA CUDA Driver Libraries are only distributable in
 applications that meet this criteria:
@@ -1062,8 +1069,9 @@ conditions:
     ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
     DEALINGS WITH THE SOFTWARE.
 
-  5. Licensee's use of the PCRE third party component is
-    subject to the following terms and conditions:
+  5. Licensee's use (e.g. nvprof) of the PCRE third party
+    component is subject to the following terms and
+    conditions:
 
     ------------
     PCRE LICENCE

CHANGELOG.md

@@ -1,13 +1,3 @@
-# ___PROJECT___ 0.0.0 (DD Mon YYYY)
+# cuCIM 0.19.0 (15 Apr 2021)
 
-## New Features
-
-- ...
-
-## Improvements
-
-- ...
-
-## Bug Fixes
-
-- ...
+Initial release of cuCIM including cuClaraImage and [cupyimg](https://github.com/mritools/cupyimg).

CMakeLists.txt

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2021, 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
@@ -120,11 +120,9 @@ superbuild_depend(abseil)
 superbuild_depend(rmm) # this imports googletest internally
 #superbuild_depend(googletest)
 superbuild_depend(googlebenchmark)
-#superbuild_depend(gds)
 superbuild_depend(openslide)
 superbuild_depend(catch2)
 superbuild_depend(cli11)
-superbuild_depend(pybind11)
 superbuild_depend(json)
 
 ################################################################################

LICENSE-3rdparty.md

@@ -83,16 +83,11 @@ DLPack
   - https://github.com/dmlc/dlpack/blob/main/LICENSE
 - Copyright: DLPack Contributors
 
-NVIDIA CUDA TOOLKIT
+NVIDIA CUDA TOOLKIT (including libcufile)
 - License: NVIDIA License
   - https://docs.nvidia.com/cuda/pdf/EULA.pdf
 - Copyright: NVIDIA Corporation
 
-NVIDIA cufile (GDS)
-- License: NVIDIA License
-  - TBD
-- Copyright: NVIDIA Corporation
-
 RAPIDS RMM
 - License: Apache-2.0 License
   - https://github.com/rapidsai/rmm/blob/branch-0.17/LICENSE

README.md

@@ -5,17 +5,48 @@
 
 **NOTE:** For the latest stable [README.md](https://github.com/rapidsai/cucim/blob/main/README.md) ensure you are on the `main` branch.
 
+- [GTC 2021 cuCIM: A GPU Image I/O and Processing Toolkit [S32194]](https://www.nvidia.com/en-us/gtc/catalog/?search=cuCIM#/)
+  - [video](https://gtc21.event.nvidia.com/media/cuCIM%3A%20A%20GPU%20Image%20I_O%20and%20Processing%20Toolkit%20%5BS32194%5D/1_fwfxd0iu)
+
 ## Install cuCIM
 
 ### Conda
 
 #### Conda (stable)
 
-> conda create -n cucim -c rapidsai -c conda-forge/label/cupy_rc cucim
+> conda create -n cucim -c rapidsai -c conda-forge/label/cupy_rc -c conda-forge cucim cudatoolkit=`<CUDA version>`
+
+`<CUDA version>` should be 11.0+ (e.g., `11.0`, `11.2`, etc.)
+
+**NOTE:** The first cuCIM conda package (v0.19.0) would be available on 4/19/2021.
 
 #### Conda (nightlies)
 
-> conda create -n cucim -c rapidsai-nightly -c conda-forge/label/cupy_rc cucim
+> conda create -n cucim -c rapidsai-nightly -c conda-forge/label/cupy_rc -c conda-forge cucim cudatoolkit=`<CUDA version>`
+
+`<CUDA version>` should be 11.0+ (e.g., `11.0`, `11.2`, etc)
+
+### Notebooks
+
+Please check out our [Welcome](notebooks/Welcome.ipynb) notebook.
+
+#### Downloading sample images
+
+To download images used in the notebooks, please execute the following commands from the repository root folder to copy sample input images into `notebooks/input` folder:
+
+(You will need [Docker](https://www.docker.com/) installed in your system)
+
+```bash
+./run download_testdata
+```
+or
+
+```bash
+mkdir -p notebooks/input
+tmp_id=$(docker create gigony/svs-testdata:little-big)
+docker cp $tmp_id:/input notebooks
+docker rm -v ${tmp_id}
+```
 
 ## Build/Install from Source
 See build [instructions](CONTRIBUTING.md#setting-up-your-build-environment).

ci/cpu/build.sh

@@ -89,7 +89,10 @@ if [ "$BUILD_LIBCUCIM" == 1 ]; then
 fi
 
 if [ "$BUILD_CUCIM" == 1 ]; then
-  gpuci_conda_retry build -c conda-forge/label/cupy_rc -c conda-forge -c rapidsai-nightly \
+  # Set libcucim conda build folder for CPU build
+  export LIBCUCIM_BLD_PATH=${WORKSPACE}/ci/artifacts/cucim/cpu/.conda-bld
+
+  gpuci_conda_retry build -c ${LIBCUCIM_BLD_PATH} -c conda-forge/label/cupy_rc -c conda-forge -c rapidsai-nightly \
     --python=${PYTHON_VER} \
     --dirty \
     --no-remove-work-dir \

ci/docs/build.sh

@@ -25,10 +25,18 @@ nvidia-smi
 
 gpuci_logger "Activate conda env"
 . /opt/conda/etc/profile.d/conda.sh
-conda activate rapids
-# TODO: Move installs to docs-build-env meta package
-gpuci_conda_retry install -c anaconda markdown beautifulsoup4 jq
-pip install sphinx-markdown-tables
+
+gpuci_logger "Installing cuCIM / Deps / Docs into new env"
+gpuci_conda_retry create -n cucim -y -c conda-forge -c conda-forge/label/cupy_rc -c rapidsai-nightly \
+    rapids-doc-env \
+    python=3.8 \
+    conda-forge/label/cupy_rc::cupy=9 \
+    cudatoolkit=11.2 \
+    scikit-image=0.18.1 \
+    cucim
+
+conda activate cucim
+
 
 gpuci_logger "Check versions"
 python --version

conda/environments/env.yml

@@ -23,3 +23,4 @@ dependencies:
   - gcc_linux-64=9
   - compilers
   - click
+  - yasm # [x86_64]

conda/recipes/libcucim/meta.yaml

@@ -20,6 +20,7 @@ requirements:
   build:
     - cmake >=3.18.0
     - {{ compiler("cxx") }}
+    - yasm # [x86_64]
   host:
     - cudatoolkit {{ cuda_version }}.*
     - openslide

cpp/CMakeLists.txt

@@ -1,5 +1,5 @@
 #
-# Copyright (c) 2020, NVIDIA CORPORATION.
+# Copyright (c) 2020-2021, 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
@@ -28,8 +28,6 @@ if(NOT BUILD_SHARED_LIBS)
     set(BUILD_SHARED_LIBS ON)
 endif()
 
-set(CMAKE_C_FLAGS "-O2")
-
 ################################################################################
 # Set definitions
 ################################################################################
@@ -110,6 +108,7 @@ target_compile_definitions(${CUCIM_PACKAGE_NAME}
         CUCIM_VERSION_PATCH=${PROJECT_VERSION_PATCH}
         CUCIM_VERSION_BUILD=${PROJECT_VERSION_BUILD}
         CUCIM_SUPPORT_GDS=$<BOOL:${CUCIM_SUPPORT_GDS}>
+        CUCIM_STATIC_GDS=$<BOOL:${CUCIM_STATIC_GDS}>
         _GLIBCXX_USE_CXX11_ABI=0  # TODO: create two library, one with CXX11 ABI and one without it.
 )
 
@@ -118,7 +117,6 @@ target_link_libraries(${CUCIM_PACKAGE_NAME}
         PUBLIC
             ${CMAKE_DL_LIBS}
             $<BUILD_INTERFACE:deps::fmt>
-            $<BUILD_INTERFACE:deps::gds>
 #            $<BUILD_INTERFACE:deps::boost>
 #            $<BUILD_INTERFACE:deps::rmm>
 #            $<BUILD_INTERFACE:deps::gds>
@@ -128,6 +126,7 @@ target_link_libraries(${CUCIM_PACKAGE_NAME}
 ##            $<INSTALL_INTERFACE:cucim::gds>
         PRIVATE
             deps::abseil
+            deps::gds
         )
 
 if (CUCIM_STATIC_GDS)
@@ -164,6 +163,7 @@ target_compile_definitions(${CUCIM_PACKAGE_NAME}-header-only
         CUCIM_VERSION_PATCH=${PROJECT_VERSION_PATCH}
         CUCIM_VERSION_BUILD=${PROJECT_VERSION_BUILD}
         CUCIM_SUPPORT_GDS=$<BOOL:${CUCIM_SUPPORT_GDS}>
+        CUCIM_STATIC_GDS=$<BOOL:${CUCIM_STATIC_GDS}>
         CUCIM_HEADER_ONLY=1
         )
 target_compile_features(${CUCIM_PACKAGE_NAME}-header-only INTERFACE ${CUCIM_REQUIRED_FEATURES})