Merge remote-tracking branch 'origin/develop' into threading_updates

qkoziol · Apr 30, 2024 · e46edd6 · e46edd6
2 parents 410602a + b23affc
commit e46edd6
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Showing 19 changed files with 1,110 additions and 155 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -533,6 +533,42 @@ if (BUILD_STATIC_EXECS)
   endif ()
 endif ()
 
+option (HDF5_ENABLE_ANALYZER_TOOLS "enable the use of Clang tools" OFF)
+mark_as_advanced (HDF5_ENABLE_ANALYZER_TOOLS)
+if (HDF5_ENABLE_ANALYZER_TOOLS)
+  include (${HDF5_SOURCE_DIR}/config/sanitizer/tools.cmake)
+endif ()
+option (HDF5_ENABLE_SANITIZERS "execute the Clang sanitizer" OFF)
+mark_as_advanced (HDF5_ENABLE_SANITIZERS)
+if (HDF5_ENABLE_SANITIZERS)
+  include (${HDF5_SOURCE_DIR}/config/sanitizer/sanitizers.cmake)
+endif ()
+option (HDF5_ENABLE_FORMATTERS "format source files" OFF)
+mark_as_advanced (HDF5_ENABLE_FORMATTERS)
+if (HDF5_ENABLE_FORMATTERS)
+  include (${HDF5_SOURCE_DIR}/config/sanitizer/formatting.cmake)
+endif ()
+
+#-----------------------------------------------------------------------------
+# Option to use code coverage
+#-----------------------------------------------------------------------------
+option (HDF5_ENABLE_COVERAGE "Enable code coverage for Libraries and Programs" OFF)
+if (HDF5_ENABLE_COVERAGE)
+  include (${HDF5_SOURCE_DIR}/config/sanitizer/code-coverage.cmake)
+  if(CODE_COVERAGE AND CODE_COVERAGE_ADDED)
+    add_code_coverage () # Adds instrumentation to all targets
+  else ()
+    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -O0 --coverage -fprofile-arcs -ftest-coverage")
+    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g --coverage -O0 -fprofile-arcs -ftest-coverage")
+    if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
+      set (LDFLAGS "${LDFLAGS} -fprofile-arcs -ftest-coverage")
+      link_libraries (gcov)
+    else ()
+      set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage")
+    endif ()
+  endif ()
+endif ()
+
 #-----------------------------------------------------------------------------
 # Option to indicate using a memory checker
 #-----------------------------------------------------------------------------
@@ -1142,40 +1178,4 @@ if (EXISTS "${HDF5_SOURCE_DIR}/HDF5Examples" AND IS_DIRECTORY "${HDF5_SOURCE_DIR
   endif ()
 endif ()
 
-option (HDF5_ENABLE_ANALYZER_TOOLS "enable the use of Clang tools" OFF)
-mark_as_advanced (HDF5_ENABLE_ANALYZER_TOOLS)
-if (HDF5_ENABLE_ANALYZER_TOOLS)
-  include (${HDF5_SOURCE_DIR}/config/sanitizer/tools.cmake)
-endif ()
-option (HDF5_ENABLE_SANITIZERS "execute the Clang sanitizer" OFF)
-mark_as_advanced (HDF5_ENABLE_SANITIZERS)
-if (HDF5_ENABLE_SANITIZERS)
-  include (${HDF5_SOURCE_DIR}/config/sanitizer/sanitizers.cmake)
-endif ()
-option (HDF5_ENABLE_FORMATTERS "format source files" OFF)
-mark_as_advanced (HDF5_ENABLE_FORMATTERS)
-if (HDF5_ENABLE_FORMATTERS)
-  include (${HDF5_SOURCE_DIR}/config/sanitizer/formatting.cmake)
-endif ()
-
-#-----------------------------------------------------------------------------
-# Option to use code coverage
-#-----------------------------------------------------------------------------
-option (HDF5_ENABLE_COVERAGE "Enable code coverage for Libraries and Programs" OFF)
-if (HDF5_ENABLE_COVERAGE)
-  include (${HDF5_SOURCE_DIR}/config/sanitizer/code-coverage.cmake)
-  if(CODE_COVERAGE AND CODE_COVERAGE_ADDED)
-    add_code_coverage () # Adds instrumentation to all targets
-  else ()
-    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -g -O0 --coverage -fprofile-arcs -ftest-coverage")
-    set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -g --coverage -O0 -fprofile-arcs -ftest-coverage")
-    if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
-      set (LDFLAGS "${LDFLAGS} -fprofile-arcs -ftest-coverage")
-      link_libraries (gcov)
-    else ()
-      set (CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} --coverage")
-    endif ()
-  endif ()
-endif ()
-
 include (CMakeInstallation.cmake)
diff --git a/config/sanitizer/sanitizers.cmake b/config/sanitizer/sanitizers.cmake
@@ -51,27 +51,18 @@ function(test_san_flags return_var flags)
 endfunction()
 
 message(STATUS "USE_SANITIZER=${USE_SANITIZER}, CMAKE_C_COMPILER_ID=${CMAKE_C_COMPILER_ID}")
-if(CMAKE_CXX_COMPILER_LOADED)
-  message(STATUS "... CMAKE_CXX_COMPILER_ID=${CMAKE_CXX_COMPILER_ID}")
-endif()
 if(USE_SANITIZER)
   if(CMAKE_C_COMPILER_ID MATCHES "IntelLLVM" OR CMAKE_C_COMPILER_ID MATCHES "[Cc]lang")
     set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
     unset(SANITIZER_SELECTED_FLAGS)
 
     if(UNIX)
-      append("-fno-omit-frame-pointer" CMAKE_C_FLAGS)
-      message(STATUS "Building with sanitize, base flags=${CMAKE_C_SANITIZER_FLAGS}")
-      if (CMAKE_CXX_COMPILER_LOADED)
-        append("-fno-omit-frame-pointer" CMAKE_CXX_FLAGS)
-      endif ()
+      append("-fno-omit-frame-pointer" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
+      message(STATUS "Building with sanitize, base flags=${CMAKE_C_FLAGS}")
 
       if(uppercase_CMAKE_BUILD_TYPE STREQUAL "DEBUG")
-        append("-O1" CMAKE_C_FLAGS)
-        if (CMAKE_CXX_COMPILER_LOADED)
-          append("-O1" CMAKE_CXX_FLAGS)
-        endif ()
+        append("-O1" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
       endif()
 
       if(USE_SANITIZER MATCHES "([Aa]ddress)")
@@ -84,10 +75,7 @@ if(USE_SANITIZER)
           append("${SANITIZER_ADDR_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER)
-            if (CMAKE_CXX_COMPILER_LOADED)
-              append_quoteless(AFL_USE_ASAN=1 CMAKE_CXX_COMPILER_LAUNCHER)
-            endif ()
+            append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
           endif()
         else()
           message(FATAL_ERROR "Address sanitizer not available for ${CMAKE_C_COMPILER}")
@@ -115,10 +103,7 @@ if(USE_SANITIZER)
           append("${SANITIZER_MEM_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_MSAN=1 CMAKE_C_COMPILER_LAUNCHER)
-            if (CMAKE_CXX_COMPILER_LOADED)
-              append_quoteless(AFL_USE_MSAN=1 CMAKE_CXX_COMPILER_LAUNCHER)
-            endif ()
+            append_quoteless(AFL_USE_MSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
           endif()
         else()
           message(FATAL_ERROR "Memory [With Origins] sanitizer not available for ${CMAKE_C_COMPILER}")
@@ -140,16 +125,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_UB_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_UBSAN=1 CMAKE_C_COMPILER_LAUNCHER)
-            if (CMAKE_CXX_COMPILER_LOADED)
-              append_quoteless(AFL_USE_UBSAN=1 CMAKE_CXX_COMPILER_LAUNCHER)
-            endif ()
+            append_quoteless(AFL_USE_UBSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
           endif()
         else()
           message(FATAL_ERROR "Undefined Behaviour sanitizer not available for ${CMAKE_C_COMPILER}")
-          if (CMAKE_CXX_COMPILER_LOADED)
-            message(FATAL_ERROR "Undefined Behaviour sanitizer not available for ${CMAKE_CXX_COMPILER}")
-          endif ()
         endif()
       endif()
 
@@ -162,16 +141,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_THREAD_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_TSAN=1 CMAKE_C_COMPILER_LAUNCHER)
-            if (CMAKE_CXX_COMPILER_LOADED)
-              append_quoteless(AFL_USE_TSAN=1 CMAKE_CXX_COMPILER_LAUNCHER)
-            endif ()
+            append_quoteless(AFL_USE_TSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
           endif()
         else()
           message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_C_COMPILER}")
-          if (CMAKE_CXX_COMPILER_LOADED)
-            message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_CXX_COMPILER}")
-          endif ()
         endif()
       endif()
 
@@ -184,16 +157,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_LEAK_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_LSAN=1 CMAKE_C_COMPILER_LAUNCHER)
-            if (CMAKE_CXX_COMPILER_LOADED)
-              append_quoteless(AFL_USE_LSAN=1 CMAKE_CXX_COMPILER_LAUNCHER)
-            endif ()
+            append_quoteless(AFL_USE_LSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
           endif()
         else()
           message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_C_COMPILER}")
-          if (CMAKE_CXX_COMPILER_LOADED)
-            message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_CXX_COMPILER}")
-          endif ()
         endif()
       endif()
 
@@ -206,43 +173,28 @@ if(USE_SANITIZER)
           append("${SANITIZER_LEAK_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_CFISAN=1 CMAKE_C_COMPILER_LAUNCHER)
-            if (CMAKE_CXX_COMPILER_LOADED)
-              append_quoteless(AFL_USE_CFISAN=1 CMAKE_CXX_COMPILER_LAUNCHER)
-            endif ()
+            append_quoteless(AFL_USE_CFISAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
           endif()
         else()
           message(FATAL_ERROR "Control Flow Integrity(CFI) sanitizer not available for ${CMAKE_C_COMPILER}")
-          if (CMAKE_CXX_COMPILER_LOADED)
-            message(FATAL_ERROR "Control Flow Integrity(CFI) sanitizer not available for ${CMAKE_CXX_COMPILER}")
-          endif ()
         endif()
       endif()
 
       message(STATUS "Sanitizer flags: ${SANITIZER_SELECTED_FLAGS}")
       test_san_flags(SANITIZER_SELECTED_COMPATIBLE ${SANITIZER_SELECTED_FLAGS})
       if(SANITIZER_SELECTED_COMPATIBLE)
         message(STATUS " Building with ${SANITIZER_SELECTED_FLAGS}")
-        append("${SANITIZER_SELECTED_FLAGS}" CMAKE_C_FLAGS)
-        if (CMAKE_CXX_COMPILER_LOADED)
-          append("${SANITIZER_SELECTED_FLAGS}" CMAKE_CXX_FLAGS)
-        endif ()
+        append("${SANITIZER_SELECTED_FLAGS}" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
       else()
         message(FATAL_ERROR "Unsupported value of USE_SANITIZER: ${USE_SANITIZER}")
       endif()
     elseif(MSVC)
       if(USE_SANITIZER MATCHES "([Aa]ddress)")
         message(STATUS "Building with Address sanitizer")
-        append("-fsanitize=address" CMAKE_C_FLAGS)
-        if (CMAKE_CXX_COMPILER_LOADED)
-          append("-fsanitize=address" CMAKE_CXX_FLAGS)
-        endif ()
+        append("-fsanitize=address" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
 
         if(AFL)
-          append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER)
-          if (CMAKE_CXX_COMPILER_LOADED)
-            append_quoteless(AFL_USE_ASAN=1 CMAKE_CXX_COMPILER_LAUNCHER)
-          endif ()
+          append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
         endif()
       else()
         message(FATAL_ERROR "This sanitizer not yet supported in the MSVC environment: ${USE_SANITIZER}")
@@ -253,10 +205,7 @@ if(USE_SANITIZER)
   elseif(MSVC)
     if(USE_SANITIZER MATCHES "([Aa]ddress)")
       message(STATUS "Building with Address sanitizer")
-      append("/fsanitize=address" CMAKE_C_FLAGS)
-      if (CMAKE_CXX_COMPILER_LOADED)
-        append("/fsanitize=address" CMAKE_CXX_FLAGS)
-      endif ()
+      append("/fsanitize=address" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
     else()
       message(FATAL_ERROR "This sanitizer not yet supported in the MSVC environment: ${USE_SANITIZER}")
     endif()

diff --git a/configure.ac b/configure.ac
@@ -1543,7 +1543,7 @@ if test "X$HDF5_DOXYGEN" = "Xyes"; then
   DOXYGEN_OPTIMIZE_OUTPUT_FOR_C=YES
   DOXYGEN_MACRO_EXPANSION=YES
   DOXYGEN_OUTPUT_DIRECTORY=hdf5lib_docs
-  DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/dox/cookbook $(SRCDIR)/doxygen/examples $(SRCDIR)/src $(SRCDIR)/examples $(SRCDIR)/test'
+  DOXYGEN_EXAMPLES_DIRECTORY='$(SRCDIR)/doxygen/dox/cookbook $(SRCDIR)/doxygen/examples $(SRCDIR)/src $(SRCDIR)/release_docs $(SRCDIR)/test'
   DOXYGEN_LAYOUT_FILE='$(SRCDIR)/doxygen/hdf5doxy_layout.xml'
   DOXYGEN_HTML_HEADER='$(SRCDIR)/doxygen/hdf5_header.html'
   DOXYGEN_HTML_FOOTER='$(SRCDIR)/doxygen/hdf5_footer.html'

diff --git a/doxygen/CMakeLists.txt b/doxygen/CMakeLists.txt
@@ -17,7 +17,7 @@ if (DOXYGEN_FOUND)
   set (DOXYGEN_OPTIMIZE_OUTPUT_FOR_C YES)
   set (DOXYGEN_MACRO_EXPANSION YES)
   set (DOXYGEN_OUTPUT_DIRECTORY ${HDF5_BINARY_DIR}/hdf5lib_docs)
-  set (DOXYGEN_EXAMPLES_DIRECTORY "${HDF5_DOXYGEN_DIR}/dox/cookbook ${HDF5_DOXYGEN_DIR}/examples ${HDF5_SRC_DIR} ${HDF5_SOURCE_DIR}/examples ${HDF5_TEST_SRC_DIR}")
+  set (DOXYGEN_EXAMPLES_DIRECTORY "${HDF5_DOXYGEN_DIR}/dox/cookbook ${HDF5_DOXYGEN_DIR}/examples ${HDF5_SRC_DIR} ${HDF5_SOURCE_DIR}/release_docs ${HDF5_TEST_SRC_DIR}")
   set (DOXYGEN_LAYOUT_FILE ${HDF5_DOXYGEN_DIR}/hdf5doxy_layout.xml)
   set (DOXYGEN_HTML_HEADER ${HDF5_DOXYGEN_DIR}/hdf5_header.html)
   set (DOXYGEN_HTML_FOOTER ${HDF5_DOXYGEN_DIR}/hdf5_footer.html)

diff --git a/doxygen/dox/LearnBasics1.dox b/doxygen/dox/LearnBasics1.dox
@@ -21,6 +21,9 @@ directories and files, an HDF5 object in an HDF5 file is often referred to by it
 
 \li <code style="background-color:whitesmoke;">/foo/zoo</code>  signifies a member of the group foo, which in turn is a member of the root group.
 
+<hr>
+Next Chapter \ref LBAPI
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBAPI The HDF5 API
@@ -135,6 +138,9 @@ The APIs are listed below:
 </tr>
 </table>
 
+<hr>
+Previous Chapter \ref LBFileOrg - Next Chapter \ref LBProg
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBProg Programming Issues
@@ -203,6 +209,9 @@ Java:     Add <code>"import hdf.hdf5lib.H5;
 </li>
 </ul>
 
+<hr>
+Previous Chapter \ref LBAPI - Next Chapter \ref LBFileCreate
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBFileCreate Creating an HDF5 File
@@ -395,6 +404,9 @@ The simplified DDL for file definition is as follows:
         <group_member> ::= <group> | <dataset>
 \endcode
 
+<hr>
+Previous Chapter \ref LBProg - Next Chapter \ref LBDsetCreate
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBDsetCreate Creating a Dataset
@@ -712,6 +724,9 @@ The following is the simplified DDL dataset definition:
 \endcode
 
 <hr>
+
+Previous Chapter \ref LBFileCreate - Next Chapter \ref LBDsetRW
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBDsetRW Reading From and Writing To a Dataset
@@ -852,6 +867,8 @@ Shown below is the contents of dsetf.h5 (created by the FORTRAN program).
 \endcode
 
 <hr>
+Previous Chapter \ref LBDsetCreate - Next Chapter \ref LBAttrCreate
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBAttrCreate Creating an Attribute
@@ -1018,6 +1035,8 @@ ATTRIBUTE "attr" {
 \endcode
 
 <hr>
+Previous Chapter \ref LBDsetRW - Next Chapter \ref LBGrpCreate
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 */
diff --git a/doxygen/dox/LearnBasics2.dox b/doxygen/dox/LearnBasics2.dox
@@ -63,6 +63,8 @@ GROUP "/" {
 \endcode
 
 <hr>
+Previous Chapter \ref LBAttrCreate - Next Chapter \ref LBGrpCreateNames
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBGrpCreateNames Creating Groups using Absolute and Relative Names
@@ -189,6 +191,8 @@ GROUP "/" {
 \endcode
 
 <hr>
+Previous Chapter \ref LBGrpCreate - Next Chapter \ref LBGrpDset
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBGrpDset Creating Datasets in Groups
@@ -298,6 +302,8 @@ DATASET "dset1" {
 \endcode
 
 <hr>
+Previous Chapter \ref LBGrpCreateNames - Next Chapter \ref LBDsetSubRW
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBDsetSubRW Reading From or Writing To a Subset of a Dataset
@@ -477,6 +483,8 @@ example code. The memory dataspace was defined as one-dimensional.
 for these parameters, rather than passing in an array for each, and for Fortran 90 you can omit these parameters.
 
 <hr>
+Previous Chapter \ref LBGrpDset - Next Chapter \ref LBDatatypes
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 @page LBDatatypes Datatype Basics
@@ -1159,6 +1167,8 @@ If nested VL datatypes were used to create the buffer, this routine frees them f
 releasing all the memory without creating memory leaks.
 
 <hr>
+Previous Chapter \ref LBDsetSubRW - Next Chapter \ref LBPropsList
+
 Navigate back: \ref index "Main" / \ref GettingStarted / \ref LearnBasics
 
 */