single-cell-data · jp-dark · Oct 14, 2024 · Aug 22, 2024 · Oct 8, 2024 · Oct 8, 2024
diff --git a/.github/workflows/python-ci-packaging.yml b/.github/workflows/python-ci-packaging.yml
@@ -94,7 +94,7 @@ jobs:
             -D TILEDB_REMOVE_DEPRECATIONS=ON \
             -D TILEDBSOMA_ENABLE_WERROR=ON \
             -D FORCE_BUILD_TILEDB=OFF
-          cmake --build build-libtiledbsoma -j $(nproc)
+          cmake --build build-libtiledbsoma -j $(nproc) --verbose
           cmake --build build-libtiledbsoma --target install-libtiledbsoma
           ls external/lib/
           echo "TILEDBSOMA_PATH=$(pwd)/external" >> $GITHUB_ENV

diff --git a/libtiledbsoma/CMakeLists.txt b/libtiledbsoma/CMakeLists.txt
@@ -71,6 +71,7 @@ option(TILEDB_VERBOSE "If true, sets default logging to verbose for TileDB" OFF)
 option(OVERRIDE_INSTALL_PREFIX "Ignores the setting of CMAKE_INSTALL_PREFIX and sets a default prefix" ON)
 option(ENABLE_ARROW_EXPORT "Installs an extra header for exporting in-memory results with Apache Arrow" ON)
 option(TILEDB_LOG_OUTPUT_ON_FAILURE "If true, print error logs if dependency sub-project build fails" ON)
+option(TILEDB_SANITIZER "Sanitizer to use in TILEDB. ")
 
 # Enable compiler cache to speed up recompilation
 find_program(CCACHE_FOUND ccache)
@@ -88,9 +89,24 @@ set(CMAKE_CXX_EXTENSIONS OFF) # Don't use GNU extensions
 # Build with fPIC
 set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 
-# Release builds by default.
-if(NOT CMAKE_BUILD_TYPE)
-  set(CMAKE_BUILD_TYPE RELEASE)
+# Set default builds/configuration to be Release.
+get_property(is_multi_config GLOBAL PROPERTY GENERATOR_IS_MULTI_CONFIG)
+if (is_multi_config)
+  set(CMAKE_CONFIGURATION_TYPES
+      "Release;Debug;RelWithDebInfo;ASAN;TSAN;LSAN;UBSAN;MSAN"
+      CACHE
+      STRING
+      "Semi-colon separate list of build types for multi-configuration generators."
+  )
+  set(CMAKE_MAP_IMPORTED_CONFIG_ASAN Debug)
+  set(CMAKE_MAP_IMPORTED_CONFIG_TSAN Debug)
+  set(CMAKE_MAP_IMPORTED_CONFIG_LSAN Debug)
+  set(CMAKE_MAP_IMPORTED_CONFIG_UBSAN Debug)
+  set(CMAKE_MAP_IMPORTED_CONFIG_MSAN Debug)
+else()
+    set(CMAKE_BUILD_TYPE
+      "Release" CACHE STRING "Build type for single-configuration generators."
+    )
 endif()
 
 # Use @rpath on macOS for building shared libraries.
@@ -214,54 +230,45 @@ else()
   # build generators that set the config type at build time.
   list(APPEND
     TILEDBSOMA_COMPILE_OPTIONS
-    $<$<STREQUAL:${CMAKE_BUILD_TYPE},Debug>: -DDEBUG -O0 -g3 -ggdb3 -gdwarf-3>
+    $<$<CONFIG:Debug>: -DDEBUG -O0 -g3 -ggdb3 -gdwarf-3>
   )
   list(APPEND
     TILEDBSOMA_COMPILE_OPTIONS
-    $<$<STREQUAL:${CMAKE_BUILD_TYPE},Release>: -DNDEBUG -O3>
+    $<$<CONFIG:Release>: -DNDEBUG -O3>
   )
   list(APPEND
     TILEDBSOMA_COMPILE_OPTIONS
-    $<$<STREQUAL:${CMAKE_BUILD_TYPE},RelWithDebInfo>: -DNDEBUG -O3 -g3 -ggdb3 -gdwarf-3>
+    $<$<CONFIG:RelWithDebInfo>: -DNDEBUG -O3 -g3 -ggdb3 -gdwarf-3>
   )
   list(APPEND
     TILEDBSOMA_COMPILE_OPTIONS
-    $<$<STREQUAL:${CMAKE_BUILD_TYPE},>: -DDEBUG -g3 -gdwarf-3 --coverage>
+    $<$<CONFIG:ASAN,TSAN,LSAN,UBSAN,MSAN>: -DDEBUG -O1 -g -fno-omit-frame-pointer  -fno-optimize-sibling-calls>
   )
 
-  # Use -Wno-literal-suffix on Linux for C++ libtiledbsoma target.
-  if(NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-    list(APPEND TILEDBSOMA_COMPILE_OPTIONS -Wno-literal-suffix)
-  endif()
-endif()
-
-# ###########################################################
-# Compile options/definitions
-# ###########################################################
-if(SANITIZER)
-  string(TOLOWER "${CMAKE_BUILD_TYPE}" CMAKE_BUILD_TYPE_LOWER)
 
-  if(NOT CMAKE_BUILD_TYPE_LOWER MATCHES "debug")
-    message(FATAL_ERROR "Sanitizers only enabled for Debug build")
-  endif()
+  # TODO: There is a bug in CMake 3.22.1 but not 3.27.6 where nested generators
+  # are not fully evaluated in the `target_link_library` commands. The GENEX_EVAL
+  # commands are not multi-configuration friendly and should be removed after we
+  # update CMake.
+  # See https://www.reddit.com/r/cmake/comments/17d70h6/why_arent_generator_expressions_evaluated_for/
+  # for this placeholder solution.
+  set(TILEDBSOMA_SANITIZER_FLAG "")
+  list(APPEND TILEDBSOMA_SANITIZER_FLAG "\$<GENEX_EVAL:$<$<CONFIG:ASAN>:-fsanitize=address>>")
+  list(APPEND TILEDBSOMA_SANITIZER_FLAG "\$<GENEX_EVAL:$<$<CONFIG:LSAN>:-fsanitize=leak>>")
+  list(APPEND TILEDBSOMA_SANITIZER_FLAG "\$<GENEX_EVAL:$<$<CONFIG:TSAN>:-fsanitize=thread>>")
+  list(APPEND TILEDBSOMA_SANITIZER_FLAG "\$<GENEX_EVAL:$<$<CONFIG:UBSAN>:-fsanitize=undefined>>")
+  list(APPEND TILEDBSOMA_SANITIZER_FLAG "\$<GENEX_EVAL:$<$<CONFIG:MSAN>:-fsanitize=memory>>")
 
-  string(TOLOWER ${SANITIZER} SANITIZER)
 
-  if(NOT SANITIZER MATCHES "^(address|memory|leak|thread|undefined)$")
-    message(FATAL_ERROR "Unknown clang sanitizer: ${SANITIZER})")
-  else()
-    message(STATUS "The TileDB-SOMA library is compiled with sanitizer ${SANITIZER} enabled")
+  # Compiler specific additions:
+  if(NOT CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+    # Use -Wno-literal-suffix on Linux for C++ libtiledbsoma target.
+    list(APPEND TILEDBSOMA_COMPILE_OPTIONS -Wno-literal-suffix)
   endif()
 
-  set(TILEDBSOMA_SANITIZER_OPTIONS
-    -g -fno-omit-frame-pointer -fno-optimize-sibling-calls -fsanitize=${SANITIZER}
-  )
-else()
- set(TILEDBSOMA_SANITIZER_OPTIONS "")
 endif()
 
 
-
 # Definitions for all targets
 add_definitions(-D_FILE_OFFSET_BITS=64)
 

diff --git a/libtiledbsoma/cmake/Superbuild.cmake b/libtiledbsoma/cmake/Superbuild.cmake
@@ -63,8 +63,8 @@ set(INHERITED_CMAKE_ARGS
   -DTILEDB_SERIALIZATION=${TILEDB_SERIALIZATION}
   -DTILEDB_WERROR=${TILEDB_WERROR}
   -DTILEDB_VERBOSE=${TILEDB_VERBOSE}
+  -DTILEDB_SANITIZER=${TILEDB_SANITIZER}
   -DTileDB_DIR=${TileDB_DIR}
-  -DSANITIZER=${SANITIZER}
   -DENABLE_ARROW_EXPORT=${ENABLE_ARROW_EXPORT}
   -DOVERRIDE_INSTALL_PREFIX=${OVERRIDE_INSTALL_PREFIX}
   -DTILEDBSOMA_BUILD_STATIC=${TILEDBSOMA_BUILD_STATIC}

diff --git a/libtiledbsoma/src/CMakeLists.txt b/libtiledbsoma/src/CMakeLists.txt
@@ -9,10 +9,14 @@ set_source_files_properties(
 add_library(TILEDBSOMA_NANOARROW_OBJECT OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/external/src/nanoarrow/nanoarrow.c
 )
+target_link_options(TILEDBSOMA_NANOARROW_OBJECT
+  PRIVATE
+    ${TILEDBSOMA_SANITIZER_FLAG}
+)
 target_compile_options(TILEDBSOMA_NANOARROW_OBJECT
   PRIVATE
     ${TILEDBSOMA_COMPILE_OPTIONS}
-    ${TILEDBSOMA_SANITIZER_OPTIONS}
+    ${TILEDBSOMA_SANITIZER_FLAG}
 )
 target_include_directories(TILEDBSOMA_NANOARROW_OBJECT
   PUBLIC
@@ -52,15 +56,20 @@ add_library(TILEDB_SOMA_OBJECTS OBJECT
 
 target_compile_definitions(TILEDB_SOMA_OBJECTS
   PRIVATE
-  -DTILEDB_NO_API_DEPRECATION_WARNINGS
+    -DTILEDB_NO_API_DEPRECATION_WARNINGS
 )
 
 target_compile_options(TILEDB_SOMA_OBJECTS
   PRIVATE
-  ${TILEDBSOMA_COMPILE_OPTIONS}
-  ${TILEDBSOMA_WERROR_OPTION}
-  ${TILEDBSOMA_SANITIZER_OPTIONS}
+    ${TILEDBSOMA_COMPILE_OPTIONS}
+    ${TILEDBSOMA_WERROR_OPTION}
+    ${TILEDBSOMA_SANITIZER_FLAG}
 )
+target_link_options(TILEDB_SOMA_OBJECTS
+  PRIVATE
+    ${TILEDBSOMA_SANITIZER_FLAG}
+)
+
 
 set_property(TARGET TILEDB_SOMA_OBJECTS PROPERTY POSITION_INDEPENDENT_CODE ON)
 target_include_directories(TILEDB_SOMA_OBJECTS
@@ -91,6 +100,11 @@ add_library(TILEDB_SOMA_GEOMETRY_OBJECTS OBJECT
   ${CMAKE_CURRENT_SOURCE_DIR}/geometry/operators/io/write.cc
 )
 
+target_link_options(TILEDB_SOMA_GEOMETRY_OBJECTS
+  PRIVATE
+    ${TILEDBSOMA_SANITIZER_FLAG}
+)
+
 target_compile_definitions(TILEDB_SOMA_GEOMETRY_OBJECTS
   PRIVATE
   -DTILEDB_NO_API_DEPRECATION_WARNINGS
@@ -141,12 +155,9 @@ if(TILEDBSOMA_BUILD_STATIC)
       OUTPUT_NAME "tiledbsoma"
     )
   endif()
-  if(SANITIZER)
-    target_link_libraries(tiledbsoma_static
-      INTERFACE
-      -fsanitize=${SANITIZER}
-    )
-  endif()
+  target_link_libraries(tiledbsoma_static
+    PRIVATE
+  )
 else()
   add_library(tiledbsoma SHARED
     $<TARGET_OBJECTS:TILEDB_SOMA_OBJECTS>
@@ -156,15 +167,13 @@ else()
   list(APPEND TILEDBSOMA_INSTALL_TARGETS tiledbsoma)
   target_link_libraries(tiledbsoma
     PUBLIC
-    TileDB::tiledb_shared
-    spdlog::spdlog
+      TileDB::tiledb_shared
+      spdlog::spdlog
+  )
+  target_link_options(tiledbsoma
+    PRIVATE
+      ${TILEDBSOMA_SANITIZER_FLAG}
   )
-  if(SANITIZER)
-    target_link_libraries(tiledbsoma
-      INTERFACE
-      -fsanitize=${SANITIZER}
-    )
-  endif()
 endif()
 
 # Install header files
@@ -297,20 +306,16 @@ if(TILEDBSOMA_BUILD_CLI)
 
   target_link_libraries(tiledbsoma-cli
     PUBLIC
-
-    # CLI11::CLI11
-    # spdlog::spdlog
-    tiledbsoma
-    TileDB::tiledb_shared
+      # CLI11::CLI11
+      # spdlog::spdlog
+      tiledbsoma
+      TileDB::tiledb_shared
+  )
+  target_link_options(tiledbsoma-cli
+    PRIVATE
+      ${TILEDBSOMA_SANITIZER_FLAG}
   )
 
-  # Sanitizer linker flags
-  if(SANITIZER)
-    target_link_libraries(tiledbsoma-cli
-      INTERFACE
-      -fsanitize=${SANITIZER}
-    )
-  endif()
 
   if(NOT APPLE AND NOT WIN32)
     target_link_libraries(tiledbsoma-cli PRIVATE pthread)

diff --git a/libtiledbsoma/test/CMakeLists.txt b/libtiledbsoma/test/CMakeLists.txt
@@ -42,6 +42,10 @@ target_link_libraries(unit_soma
     Catch2::Catch2WithMain
     TileDB::tiledb_shared
 )
+target_link_options(unit_soma
+  PRIVATE
+    ${TILEDBSOMA_SANITIZER_FLAG}
+)
 
 target_include_directories(unit_soma
   PRIVATE
@@ -59,6 +63,7 @@ target_compile_definitions(unit_soma
 target_compile_options(unit_soma
   PRIVATE
     ${TILEDBSOMA_COMPILE_OPTIONS}
+    ${TILEDBSOMA_SANITIZER_FLAG}
     ${TILEDBSOMA_WERROR_OPTION}
 )
 
@@ -105,6 +110,11 @@ target_link_libraries(unit_geometry
     TileDB::tiledb_shared
 )
 
+target_link_options(unit_geometry
+  PRIVATE
+    ${TILEDBSOMA_SANITIZER_FLAG}
+)
+
 target_include_directories(unit_geometry
   PRIVATE
     ${CMAKE_CURRENT_SOURCE_DIR}/../src