Sync with 43a2421 (#22)

Co-authored-by: Jérémie Dumas <jeremie.dumas@ens-lyon.org>

.github/workflows/wheel.yaml

@@ -25,7 +25,7 @@ jobs:
           python-version: '3.8'
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.12.1
+        uses: pypa/cibuildwheel@v2.16.2
         env:
           CIBW_ARCHS_LINUX: auto64
           CIBW_ARCHS_WINDOWS: auto64

.gitignore

@@ -46,7 +46,9 @@ __pycache__
 *.vtk
 
 # Openvdb files
-*.vdb
+tensor_*.json
+tensor_*.vdb
+func_*.json
 
 # Extra directories
 /.vscode

CMakeLists.txt

@@ -129,26 +129,27 @@ else()
 endif()
 
 # Python defaults
-if(SKBUILD)
-    if(LINUX)
-        # MKL doesn't support building Python modules with individual shared libraries. On Linux dlopen()
-        # would fail with the following error:
-        #
-        #   INTEL MKL ERROR: <...>/libmkl_def.so.1: undefined symbol: mkl_sparse_optimize_bsr_trsm_i8.
-        #   Intel MKL FATAL ERROR: Cannot load libmkl_def.so.1.
-        #
-        # The reason is that the three libraries libmkl_core, libmkl_intel and libmkl_thread need to be
-        # dlopened with RTLD_GLOBAL first. One needs to link against libmkl_rt instead. See this issue for
-        # more details:
-        #
-        # https://gitlab.kitware.com/cmake/cmake/-/issues/20491
-        #
-        # Note: We should probably enable this on macOS as well, but our Jenkins nodes don't have a
-        # Fortran compiler (and our pre-built Arpack doesn't link against mkl_rt).
-        #
-        set(MKL_LINKING "sdl" CACHE STRING "Linking strategy to use with MKL (static, dynamic or sdl)")
-        option(ARPACK_BUILD_FROM_SOURCE "Build arpack from source using a Fortran compiler" ON)
-    endif()
+if(SKBUILD AND LINUX)
+    # MKL doesn't support building Python modules with individual shared libraries. On Linux dlopen()
+    # would fail with the following error:
+    #
+    #   INTEL MKL ERROR: <...>/libmkl_def.so.1: undefined symbol: mkl_sparse_optimize_bsr_trsm_i8.
+    #   Intel MKL FATAL ERROR: Cannot load libmkl_def.so.1.
+    #
+    # The reason is that the three libraries libmkl_core, libmkl_intel and libmkl_thread need to be
+    # dlopened with RTLD_GLOBAL first. One needs to link against libmkl_rt instead. See this issue for
+    # more details:
+    #
+    # https://gitlab.kitware.com/cmake/cmake/-/issues/20491
+    #
+    # Note: We should probably enable this on macOS as well, but our Jenkins nodes don't have a
+    # Fortran compiler (and our pre-built Arpack doesn't link against mkl_rt).
+    #
+    set(MKL_LINKING "sdl" CACHE STRING "Linking strategy to use with MKL (static, dynamic or sdl)")
+    option(ARPACK_BUILD_FROM_SOURCE "Build arpack from source using a Fortran compiler" ON)
+
+    # Set RPATH to $ORIGIN on Linux
+    set(CMAKE_INSTALL_RPATH $ORIGIN)
 endif()
 
 # Meta target: ALL includes all optional modules and UI.
@@ -177,6 +178,7 @@ option(LAGRANGE_PERFORMANCE_TESTS       "Build all performance tests"
 option(LAGRANGE_UNIT_TESTS              "Build all unit tests"                                 ${LAGRANGE_TOPLEVEL_PROJECT})
 option(LAGRANGE_USE_PCH                 "Enable precompiled headers"                           OFF)
 option(LAGRANGE_USE_WASM_EXCEPTIONS     "Use -fwasm-exception flag with Emscripten"            OFF)
+option(LAGRANGE_USE_WASM_THREADS        "Enable threads (-pthread) with Emscripten"            ON)
 option(LAGRANGE_WITH_ONETBB             "Build Lagrange with OneTBB 2021 rather than TBB 2020" ON)
 option(LAGRANGE_WITH_TRACY              "Build tracy client with Lagrange"                     OFF)
 
@@ -294,6 +296,7 @@ include(lagrange_include_modules)
 include(lagrange_install)
 include(lagrange_limit_parallelism)
 include(lagrange_warnings)
+include(lagrange_xcode_check)
 include(sanitizers)
 
 if(LAGRANGE_TOPLEVEL_PROJECT)
@@ -308,7 +311,15 @@ if(LAGRANGE_LIMIT_PARALLELISM)
     lagrange_limit_parallelism()
 endif()
 
-find_package(Threads REQUIRED)
+set(TBB_ENABLE_WASM_THREADS ${LAGRANGE_USE_WASM_THREADS})
+
+# Force -pthread during compilation for Emscripten
+if(EMSCRIPTEN AND LAGRANGE_USE_WASM_THREADS)
+    set(THREADS_HAVE_PTHREAD_ARG TRUE)
+endif()
+
+set(THREADS_PREFER_PTHREAD_FLAG TRUE)
+find_package(Threads REQUIRED GLOBAL)
 
 # Include OneTBB early to provide TBB::tbb target
 if(LAGRANGE_WITH_ONETBB)

LagrangeOptions.cmake.sample

@@ -50,6 +50,8 @@
 # Optional modules in alphabetical order.
 # option(LAGRANGE_MODULE_BVH          "Build module lagrange::bvh"          ON)
 # option(LAGRANGE_MODULE_FS           "Build module lagrange::fs"           ON)
+# option(LAGRANGE_MODULE_IMAGE        "Build module lagrange::image"        ON)
+# option(LAGRANGE_MODULE_IMAGE_IO     "Build module lagrange::image_io"     ON)
 # option(LAGRANGE_MODULE_IO           "Build module lagrange::io"           ON)
 # option(LAGRANGE_MODULE_PARTITIONING "Build module lagrange::partitioning" ON)
 # option(LAGRANGE_MODULE_PYTHON       "Build module lagrange::python"       ON)

VERSION

@@ -1 +1 @@
-6.17.0
+6.18.0

cmake/lagrange/lagrange_add_test.cmake

@@ -47,6 +47,7 @@ function(lagrange_add_test)
     # TSan suppression file to be passed to catch_discover_tests
     set(LAGRANGE_TESTS_ENVIRONMENT
         "TSAN_OPTIONS=suppressions=${PROJECT_SOURCE_DIR}/.github/tsan.suppressions.ini"
+        "ASAN_SAVE_DUMPS=${module_name}.dmp"
     )
 
     # Output directory

cmake/lagrange/lagrange_download_data.cmake

@@ -29,7 +29,7 @@ function(lagrange_download_data)
             PREFIX "${FETCHCONTENT_BASE_DIR}/lagrange-test-data"
             SOURCE_DIR ${LAGRANGE_DATA_FOLDER}
             GIT_REPOSITORY https://github.com/adobe/lagrange-test-data.git
-            GIT_TAG 3b2de026c4b96a85f1a40b2d412586dc071c8761
+            GIT_TAG c9a65d430c74bb8a30c3b556682cfaf88024ddf6
             CONFIGURE_COMMAND ""
             BUILD_COMMAND ""
             INSTALL_COMMAND ""

cmake/lagrange/lagrange_global_flags.cmake

@@ -73,6 +73,12 @@ if(EMSCRIPTEN)
         set(EMSCRIPTEN_EXCEPTION_HANDLER_FLAG "-fexceptions")
     endif()
 
-    add_compile_options(${EMSCRIPTEN_EXCEPTION_HANDLER_FLAG} -pthread)
-    add_link_options(${EMSCRIPTEN_EXCEPTION_HANDLER_FLAG} -pthread)
+    if(LAGRANGE_USE_WASM_THREADS)
+        set(EMSCRIPTEN_THREAD_FLAG "-pthread")
+    else()
+        set(EMSCRIPTEN_THREAD_FLAG "")
+    endif()
+
+    add_compile_options(${EMSCRIPTEN_EXCEPTION_HANDLER_FLAG} ${EMSCRIPTEN_THREAD_FLAG})
+    add_link_options(${EMSCRIPTEN_EXCEPTION_HANDLER_FLAG} ${EMSCRIPTEN_THREAD_FLAG})
 endif()

cmake/lagrange/lagrange_xcode_check.cmake

@@ -0,0 +1,59 @@
+#
+# Copyright 2023 Adobe. All rights reserved.
+# This file is licensed to you 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 http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software distributed under
+# the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR REPRESENTATIONS
+# OF ANY KIND, either express or implied. See the License for the specific language
+# governing permissions and limitations under the License.
+#
+if(NOT CMAKE_CXX_COMPILER_ID STREQUAL "AppleClang")
+    return()
+endif()
+
+# Xcode 15's new linker will crash. We suggest either using the classical linker, or upgrading to Xcode 15.1.
+if(CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 15.0 AND CMAKE_CXX_COMPILER_VERSION VERSION_LESS 15.1)
+    # First let's check if we are using the classical linker
+    set(is_using_classical_linker FALSE)
+    foreach(type IN ITEMS EXE SHARED MODULE)
+        set(suffix_types "none")
+        if(DEFINED CMAKE_CONFIGURATION_TYPES)
+            list(APPEND suffix_types ${CMAKE_CONFIGURATION_TYPES})
+        endif()
+        foreach(config IN LISTS suffix_types)
+            if(config STREQUAL "none")
+                set(config "")
+            else()
+                set(config "_${config}")
+            endif()
+            if(NOT DEFINED CMAKE_${type}_LINKER_FLAGS${config}_INIT)
+                continue()
+            endif()
+            if(CMAKE_${type}_LINKER_FLAGS${config}_INIT MATCHES "-Wl,-ld_classic")
+                set(is_using_classical_linker TRUE)
+                break()
+            endif()
+        endforeach()
+    endforeach()
+
+    # If not, display an error message
+    if(NOT is_using_classical_linker)
+        option(LAGRANGE_IGNORE_XCODE_15_LINKER_ERROR "Turn Xcode 15 linker check from an error into a warning" OFF)
+        if(LAGRANGE_IGNORE_XCODE_15_LINKER_ERROR)
+            set(mode WARNING)
+            set(postfix "")
+        else()
+            set(mode FATAL_ERROR)
+            set(postfix "You can also ignore this error by calling CMake with -DLAGRANGE_IGNORE_XCODE_15_LINKER_ERROR=ON\n")
+        endif()
+        message(${mode}
+            "Xcode 15.0 has a new linker that will cause a crash when linking weak symbols in C++. "
+            "We suggest either:\n1. Upgrading to Xcode >= 15.1, or\n2. Using the classical linker by deleting "
+            "your <build>/CMakeCache.txt and re-running CMake configure with \n"
+            "    LDFLAGS=\"$LDFLAGS -Wl,-ld_classic\" cmake ..\n"
+            ${postfix}
+        )
+    endif()
+endif()

cmake/recipes/external/assimp.cmake

@@ -42,7 +42,7 @@ include(CPM)
 CPMAddPackage(
     NAME assimp
     GITHUB_REPOSITORY assimp/assimp
-    GIT_TAG 0fdae2879d78864693ee730610dcf8ee10707875
+    GIT_TAG c1deb808faadd85a7a007447b62ae238a4be2337
 )
 
 set_target_properties(assimp PROPERTIES FOLDER third_party//assimp)

cmake/recipes/external/boost.cmake

@@ -81,6 +81,11 @@ option(BOOST_IOSTREAMS_ENABLE_ZSTD "Boost.Iostreams: Enable Zstd support" OFF)
 add_library(boost_numeric_ublas INTERFACE)
 add_library(Boost::numeric_ublas ALIAS boost_numeric_ublas)
 
+if(SKBUILD)
+    set(OLD_BUILD_SHARED_LIBS ${BUILD_SHARED_LIBS})
+    set(BUILD_SHARED_LIBS ON)
+endif()
+
 # Boost 1.82.0 is the min version we can use that supports upstream modern
 # CMake targets (Boost::boost, Boost::headers, etc.)
 include(CPM)
@@ -92,6 +97,10 @@ CPMAddPackage(
     EXCLUDE_FROM_ALL ON
 )
 
+if(SKBUILD)
+    set(BUILD_SHARED_LIBS ${OLD_BUILD_SHARED_LIBS})
+endif()
+
 target_include_directories(boost_numeric_ublas INTERFACE
     "${Boost_SOURCE_DIR}/libs/numeric/ublas/include"
 )
@@ -125,7 +134,6 @@ target_compile_features(boost_numeric_ublas INTERFACE cxx_std_11)
 # spoof the <auto_link.hpp> header with a blank one and remove the problematic error message.
 if(TARGET Boost::random)
     set(boost_dummy_autolink_dir "${Boost_BINARY_DIR}/dummy/boost/config/")
-    message("Creating dummy <auto_link.hpp> in ${boost_dummy_autolink_dir}")
     file(WRITE "${boost_dummy_autolink_dir}/auto_link.hpp.in" "")
     configure_file(${boost_dummy_autolink_dir}/auto_link.hpp.in ${boost_dummy_autolink_dir}/auto_link.hpp COPYONLY)
     target_include_directories(boost_random PRIVATE "${Boost_BINARY_DIR}/dummy")

cmake/recipes/external/embree.cmake

@@ -115,6 +115,7 @@ function(embree_import_target)
     set(unix_compilers "AppleClang;Clang;GNU")
     if(CMAKE_CXX_COMPILER_ID IN_LIST unix_compilers) # IN_LIST wants the second arg to be a var
         target_compile_options(embree PRIVATE "-Wno-unused-private-field")
+        target_compile_options(embree PRIVATE "-Wno-unused-but-set-variable")
     endif()
 
     # Now we need to do some juggling to propagate the include directory properties

cmake/recipes/external/miniz.cmake

@@ -32,6 +32,7 @@ target_include_directories(miniz PUBLIC
 )
 
 set_target_properties(miniz PROPERTIES FOLDER third_party)
+set_target_properties(miniz PROPERTIES POSITION_INDEPENDENT_CODE ON)
 
 target_include_directories(miniz PUBLIC
     $<BUILD_INTERFACE:${miniz_BINARY_DIR}>

cmake/recipes/external/nanobind.cmake

@@ -19,7 +19,7 @@ include(CPM)
 CPMAddPackage(
     NAME nanobind
     GITHUB_REPOSITORY wjakob/nanobind
-    GIT_TAG v1.0.0
+    GIT_TAG v1.8.0
     DOWNLOAD_ONLY ON
 )
 

cmake/recipes/external/nlohmann_json.cmake

@@ -33,6 +33,7 @@ target_include_directories(nlohmann_json INTERFACE
     "$<BUILD_INTERFACE:${nlohmann_json_SOURCE_DIR}>/include"
     "$<INSTALL_INTERFACE:${CMAKE_INSTALL_INCLUDEDIR}>"
 )
+target_compile_features(nlohmann_json INTERFACE cxx_std_11)
 
 # Install rules
 set(CMAKE_INSTALL_DEFAULT_COMPONENT_NAME nlohmann_json)

cmake/recipes/external/onetbb.cmake

@@ -25,6 +25,7 @@ option(TBB_TEST "Enable testing" OFF)
 option(TBB_EXAMPLES "Enable examples" OFF)
 option(TBB_STRICT "Treat compiler warnings as errors" OFF)
 option(TBB_PREFER_STATIC "Use the static version of TBB for the alias target" ON)
+option(TBB_ENABLE_WASM_THREADS "Use wasm threads" ON)
 unset(TBB_DIR CACHE)
 
 function(onetbb_import_target)
@@ -62,12 +63,18 @@ function(onetbb_import_target)
 
     set(CMAKE_INSTALL_DEFAULT_COMPONENT_NAME tbb)
     include(CPM)
+
     CPMAddPackage(
         NAME tbb
         GITHUB_REPOSITORY oneapi-src/oneTBB
-        GIT_TAG v2021.10.0
+        GIT_TAG v2021.11.0
     )
 
+    # TODO: This might break with future versions of onetbb. Onetbb should eventually add a proper cmake option to turn wasm threads on/off.
+    if (EMSCRIPTEN AND NOT TBB_ENABLE_WASM_THREADS)
+        set_property(TARGET Threads::Threads PROPERTY INTERFACE_LINK_LIBRARIES "")
+    endif()
+
     pop_variable(BUILD_SHARED_LIBS)
 endfunction()
 

cmake/recipes/external/openvdb.cmake

@@ -119,7 +119,7 @@ function(openvdb_import_target)
     CPMAddPackage(
         NAME openvdb
         GITHUB_REPOSITORY AcademySoftwareFoundation/openvdb
-        GIT_TAG v10.1.0
+        GIT_TAG v11.0.0
     )
 
     unignore_package(TBB)

cmake/recipes/external/python.cmake

@@ -14,4 +14,4 @@ if(TARGET Python::Module)
 endif()
 
 set(Python_FIND_VIRTUALENV FIRST)
-find_package(Python 3.8 COMPONENTS Interpreter Development.Module REQUIRED)
+find_package(Python 3.9 COMPONENTS Interpreter Development.Module REQUIRED)

cmake/recipes/external/sanitizers.cmake

@@ -35,9 +35,9 @@ function(append value)
 endfunction()
 
 if(USE_SANITIZER)
-  append("-fno-omit-frame-pointer" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
-
   if(UNIX)
+    append("-fno-omit-frame-pointer" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
+
     if(uppercase_CMAKE_BUILD_TYPE STREQUAL "DEBUG")
       append("-O1" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
     endif()
@@ -79,7 +79,27 @@ if(USE_SANITIZER)
   elseif(MSVC)
     if(USE_SANITIZER MATCHES "([Aa]ddress)")
       message(STATUS "Building with Address sanitizer")
-      append("-fsanitize=address" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
+      # Do use AddressSanitizer you need to disable incompatible options. See details here:
+      # https://learn.microsoft.com/en-us/cpp/sanitizers/asan?view=msvc-170#ide-msbuild
+      #
+      # Please note that there are some issues with using it directly from the IDE, it may work better to
+      # run the code from the command-line (and through `ctest` which enables the ASAN_SAVE_DUMPS env variable):
+      # https://stackoverflow.com/questions/76781556/visual-studio-22-asan-failed-to-use-and-restart-external-symbolizer
+      # https://developercommunity.visualstudio.com/t/Fail-to-use-and-restart-external-symbol/10222443?q=+Failed+to+use+and+restart+external+symbolizer
+      append("/fsanitize=address" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
+
+      # Disable incremental linking
+      add_link_options(/INCREMENTAL:NO)
+
+      # Disable RTC flag
+      foreach(flag_var
+        CMAKE_CXX_FLAGS CMAKE_CXX_FLAGS_DEBUG CMAKE_CXX_FLAGS_RELEASE
+        CMAKE_CXX_FLAGS_MINSIZEREL CMAKE_CXX_FLAGS_RELWITHDEBINFO)
+        string(REGEX REPLACE "/RTC[^ ]*" "" ${flag_var} "${${flag_var}}")
+      endforeach(flag_var)
+
+      # Do not use program database for debug builds (since it requires incremental linking).
+      set(CMAKE_MSVC_DEBUG_INFORMATION_FORMAT "$<$<CONFIG:Debug,RelWithDebInfo>:Embedded>")
     else()
       message(
         FATAL_ERROR

cmake/recipes/external/stackwalker.cmake

@@ -0,0 +1,33 @@
+#
+# Copyright 2023 Adobe. All rights reserved.
+# This file is licensed to you 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 http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software distributed under
+# the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR REPRESENTATIONS
+# OF ANY KIND, either express or implied. See the License for the specific language
+# governing permissions and limitations under the License.
+#
+if(TARGET StackWalker::StackWalker)
+    return()
+endif()
+
+message(STATUS "Third-party (external): creating target 'StackWalker::StackWalker'")
+
+option(StackWalker_DISABLE_TESTS  "Disable tests" ON)
+
+include(CPM)
+CPMAddPackage(
+    NAME StackWalker
+    GITHUB_REPOSITORY JochenKalmbach/StackWalker
+    GIT_TAG 5b0df7a4db8896f6b6dc45d36e383c52577e3c6b
+    DOWNLOAD_ONLY YES
+)
+
+add_library(StackWalker STATIC ${StackWalker_SOURCE_DIR}/Main/StackWalker/StackWalker.cpp)
+add_library(StackWalker::StackWalker ALIAS StackWalker)
+
+target_include_directories(StackWalker PUBLIC ${StackWalker_SOURCE_DIR}/Main/StackWalker)
+
+set_target_properties(StackWalker PROPERTIES FOLDER third_party)