Merge branch 'develop' into H5Rs

brtnfld · Apr 30, 2024 · 078350f · 078350f
2 parents 2eb91a7 + b23affc
commit 078350f
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diff --git a/.github/workflows/h5py.yml b/.github/workflows/h5py.yml
@@ -24,7 +24,7 @@ jobs:
 
     - name: Run a multi-line script
       run: |
-        sed -i 's/hdf5@1.8.4:1.14/hdf5@1.8.4:/g' \
+        sed -i 's/hdf5@1.10.4:1.14/hdf5@1.10.4:/g' \
         ./spack/var/spack/repos/builtin/packages/py-h5py/package.py
         . ./spack/share/spack/setup-env.sh
         ./spack/bin/spack spec py-h5py@master+mpi ^[email protected]

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
 #-----------------------------------------------------------------------------
@@ -1147,40 +1183,4 @@ 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/bin/make_err b/bin/make_err
@@ -223,6 +223,8 @@ sub create_init ($) {
     my $desc;                   # Description of error message
     my $sect_name;              # Section of minor error messages
     my $sect_desc;              # Description of section
+    my $first_major = 0;        # Whether the first major error code was saved
+    my $first_minor = 0;        # Whether the first minor error code was saved
 
     # Rename previous file
 #    rename "${prefix}${file}", "${prefix}${file}~" or die "unable to make backup";
@@ -241,12 +243,22 @@ sub create_init ($) {
     print HEADER   "/* Major error codes */\n";
     print HEADER   "/*********************/\n\n";
     foreach $name (keys %major) {
-        print HEADER " "x(0*$indent),"assert(${name}_g==(-1));\n";
+        print HEADER " "x(0*$indent),"assert(${name}_g==H5I_INVALID_HID);\n";
         print HEADER " "x(0*$indent),"if((msg = H5E__create_msg(cls, H5E_MAJOR, \"${major{$name}}\"))==NULL)\n";
         print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, \"error message initialization failed\");\n";
         print HEADER " "x(0*$indent),"if((${name}_g = H5I_register(H5I_ERROR_MSG, msg, false))<0)\n";
         print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, \"can't register error message\");\n";
+        if ($first_major == 0) {
+            print HEADER " "x(0*$indent),"\n/* Remember first major error code ID */\n";
+            print HEADER " "x(0*$indent),"assert(H5E_first_maj_id_g==H5I_INVALID_HID);\n";
+            print HEADER " "x(0*$indent),"H5E_first_maj_id_g = ${name}_g;\n\n";
+            $first_major = 1;
     }
+        $last_name = $name;
+    }
+    print HEADER " "x(0*$indent),"\n/* Remember last major error code ID */\n";
+    print HEADER " "x(0*$indent),"assert(H5E_last_maj_id_g==H5I_INVALID_HID);\n";
+    print HEADER " "x(0*$indent),"H5E_last_maj_id_g = ${last_name}_g;\n\n";
 
     # Iterate over all the minor error sections
     print HEADER "\n/*********************/\n";
@@ -257,13 +269,24 @@ sub create_init ($) {
 
         # Iterate over all the minor errors in each section
         for $name ( @{$section_list{$sect_name}}) {
-            print HEADER " "x(0*$indent),"assert(${name}_g==(-1));\n";
+            print HEADER " "x(0*$indent),"assert(${name}_g==H5I_INVALID_HID);\n";
             print HEADER " "x(0*$indent),"if((msg = H5E__create_msg(cls, H5E_MINOR, \"${minor{$name}}\"))==NULL)\n";
             print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTINIT, FAIL, \"error message initialization failed\");\n";
             print HEADER " "x(0*$indent),"if((${name}_g = H5I_register(H5I_ERROR_MSG, msg, true))<0)\n";
             print HEADER " "x(1*$indent),"HGOTO_ERROR(H5E_ERROR, H5E_CANTREGISTER, FAIL, \"can't register error message\");\n";
+
+            if ($first_minor == 0) {
+                print HEADER " "x(0*$indent),"\n/* Remember first minor error code ID */\n";
+                print HEADER " "x(0*$indent),"assert(H5E_first_min_id_g==H5I_INVALID_HID);\n";
+                print HEADER " "x(0*$indent),"H5E_first_min_id_g = ${name}_g;\n\n";
+                $first_minor = 1;
+            }
+            $last_name = $name;
         }
     }
+    print HEADER " "x(0*$indent),"\n/* Remember last minor error code ID */\n";
+    print HEADER " "x(0*$indent),"assert(H5E_last_min_id_g==H5I_INVALID_HID);\n";
+    print HEADER " "x(0*$indent),"H5E_last_min_id_g = ${last_name}_g;\n";
 
     print_endprotect(*HEADER, $file);
 
@@ -299,7 +322,9 @@ sub create_term ($) {
     foreach $name (keys %major) {
         print HEADER " "x($indent),"\n${name}_g=";
     }
-    print HEADER " (-1);\n";
+    print HEADER " H5I_INVALID_HID;\n";
+    print HEADER " "x(0*$indent),"H5E_first_maj_id_g = H5I_INVALID_HID;\n\n";
+    print HEADER " "x(0*$indent),"H5E_last_maj_id_g = H5I_INVALID_HID;\n\n";
 
     # Iterate over all the minor error sections
     print HEADER "\n/* Reset minor error IDs */\n";
@@ -311,7 +336,9 @@ sub create_term ($) {
             print HEADER " "x($indent),"\n${name}_g=";
         }
     }
-    print HEADER " (-1);\n";
+    print HEADER " H5I_INVALID_HID;\n";
+    print HEADER " "x(0*$indent),"H5E_first_min_id_g = H5I_INVALID_HID;\n\n";
+    print HEADER " "x(0*$indent),"H5E_last_min_id_g = H5I_INVALID_HID;\n\n";
 
     print_endprotect(*HEADER, $file);
 

diff --git a/bin/release b/bin/release
@@ -455,7 +455,7 @@ cp -p Makefile.dist Makefile
 
 # Update README.md and release_docs/RELEASE.txt with release information in
 # line 1.
-for f in README.md release_docs/RELEASE.txt; do
+for f in README.md release_docs/RELEASE.txt release_docs/NEWSLETTER.txt; do
     echo "HDF5 version $VERS released on $release_date" >$f.x
     sed -e 1d $f >>$f.x
     mv $f.x $f

diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake
@@ -434,6 +434,7 @@ endif ()
 if (MINGW OR NOT WINDOWS)
   foreach (other_test
       HAVE_ATTRIBUTE
+      HAVE_BUILTIN_EXPECT
       SYSTEM_SCOPE_THREADS
       HAVE_SOCKLEN_T
   )

diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
@@ -328,6 +328,9 @@
 /* Define to 1 if you have the <szlib.h> header file. */
 #cmakedefine H5_HAVE_SZLIB_H @H5_HAVE_SZLIB_H@
 
+/* Define to 1 if the compiler supports the __builtin_expect() extension */
+#cmakedefine H5_HAVE_BUILTIN_EXPECT @H5_HAVE_BUILTIN_EXPECT@
+
 #if defined(_WIN32) && !defined(H5_BUILT_AS_DYNAMIC_LIB)
 /* Not supported on WIN32 platforms with static linking */
 /* #undef H5_HAVE_THREADSAFE */

diff --git a/config/cmake/HDFTests.c b/config/cmake/HDFTests.c
@@ -15,6 +15,21 @@
 #define SIMPLE_TEST(x) int main(void){ x; return 0; }
 
 
+#ifdef HAVE_BUILTIN_EXPECT
+
+int
+main ()
+{
+    void *ptr = (void*) 0;
+
+    if (__builtin_expect (ptr != (void*) 0, 1))
+        return 0;
+
+    return 0;
+}
+
+#endif /* HAVE_BUILTIN_EXPECT */
+
 #ifdef HAVE_ATTRIBUTE
 
 int

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()