Update run script for local builds

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 @@ nvidia-compute-license-questions@nvidia.com.
 
 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

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

@@ -18,7 +18,7 @@
 
 `<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 4/15/2021.
+**NOTE:** The first cuCIM conda package (v0.19.0) would be available on 4/19/2021.
 
 #### Conda (nightlies)
 

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})

cpp/include/cucim/filesystem/cufile_driver.h

@@ -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.
@@ -31,6 +31,14 @@ using ScopedLock = std::scoped_lock<Mutex>;
 // Forward declaration.
 class CuFileDriver;
 
+
+/**
+ * @brief Check if the GDS is available in the system.
+ *
+ * @return true if libcufile.so is loaded and cuFileDriverOpen() API call succeeds.
+ */
+bool EXPORT_VISIBLE is_gds_available();
+
 /**
  * Open file with specific flags and mode.
  *
@@ -116,11 +124,11 @@ class CuFileDriverInitializer
     {
         return is_available_;
     }
-    inline uint64_t max_device_cache_size()
+    inline uint64_t max_device_cache_size() const
     {
         return max_device_cache_size_;
     }
-    inline uint64_t max_host_cache_size()
+    inline uint64_t max_host_cache_size() const
     {
         return max_host_cache_size_;
     }

cpp/plugins/cucim.kit.cuslide/CMakeLists.txt

@@ -1,5 +1,5 @@
 # Apache License, Version 2.0
-# Copyright 2020 NVIDIA Corporation
+# Copyright 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.
@@ -127,7 +127,6 @@ add_definitions(-D_GLIBCXX_USE_CXX11_ABI=0) # TODO: create two library, one with
 superbuild_depend(fmt)
 superbuild_depend(libjpeg-turbo) # libjpeg-turbo should be located before libtiff as libtiff depends on libjpeg-turbo
 superbuild_depend(libtiff)
-superbuild_depend(gds)
 superbuild_depend(catch2)
 superbuild_depend(openslide)
 superbuild_depend(googletest)