Sync develop branch changes March 4 - 6 to hdf5_1_14 branch (#4121)

* Do not enable szip for sanitizer runs (#4057)

* Add note to H5Tset_fields about needing to set datatype precision first (#4059)

* Offset of a floating-point type also needs to be accounted for

* Clarify ordering of H5Tset_precision and H5Tset_fields

* Fix issue where H5Tset_fields does not account for datatype offsets (#4061)

H5Tset_fields did not account for any offset in a floating-point datatype,
causing it to fail when a datatype's precision is correctly set such that
it doesn't include the offset bits.

* Ignore UserPresets and Use only C compiler for sanitizers (#4066)

* Remove user presets file

* Only use C compiler for sanitzers

* Rename incorrectly named option (#4067)

* Rename incorrectly named option

* Restore the correct uses of USING_MEMCHECKER

* Update release note

* Fix a memory leak in the cmpd_dset test (#4071)

This was due to not freeing a test buffer. It was not a core
library memory leak.

* Fix uninitialized bytes in cmpd_dset test (#4072)

Compound fill values were set to the integer -1, causing valgrind
to flag 'uninitialized bytes' errors.

This is just a problem with the cmpd_dset test and not a core
library problem.

* Update INSTALL files (#4052)

* Add NEWSLETTER and merge abi reports and add sha256sums (#4055)

* Fix uninitialized bytes in selection I/O test (#4073)

This was due to a complex type fill value being set to -1 instead
of a proper complex value. This was a test problem and not a core
library issue.

* fix path for S3 build path in CI (#4076)

* Correct paths for 1.14 and add lines missing from release_docs/INSTALL_CMake.txt.

---------

Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: jhendersonHDF <jhenderson@hdfgroup.org>
Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

5 files changed, 41 insertions, 38 deletions

diff --git a/config/cmake-presets/hidden-presets.json b/config/cmake-presets/hidden-presets.json
index 64ccfb9..98a42b7 100644
--- a/config/cmake-presets/hidden-presets.json
+++ b/config/cmake-presets/hidden-presets.json
@@ -540,7 +540,7 @@
       "name": "ci-x64-Release-Intel",
       "configurePreset": "ci-x64-Release-Intel",
       "hidden": true,
-      "inherits": "ci-base",
+      "inherits": "ci-base"
     }
   ]
 }
diff --git a/config/cmake/HDFMacros.cmake b/config/cmake/HDFMacros.cmake
index 64e77c0..1533827 100644
--- a/config/cmake/HDFMacros.cmake
+++ b/config/cmake/HDFMacros.cmake
@@ -279,6 +279,7 @@ macro (HDF_README_PROPERTIES target_fortran)
   if (WIN32)
     set (BINARY_EXAMPLE_ENDING "zip")
     set (BINARY_INSTALL_ENDING "msi")
+    set (BINARY_COMPRESS_ENDING "zip")
     if (CMAKE_CL_64)
       set (BINARY_SYSTEM_NAME "win64")
     else ()
@@ -330,12 +331,14 @@ macro (HDF_README_PROPERTIES target_fortran)
     endif ()
   elseif (APPLE)
     set (BINARY_EXAMPLE_ENDING "tar.gz")
+    set (BINARY_COMPRESS_ENDING "tar.gz")
     set (BINARY_INSTALL_ENDING "sh") # if packaging changes - use dmg
     set (BINARY_PLATFORM "${BINARY_PLATFORM} ${CMAKE_SYSTEM_VERSION} ${CMAKE_SYSTEM_PROCESSOR}")
     set (BINARY_PLATFORM "${BINARY_PLATFORM}, using ${CMAKE_C_COMPILER_ID} C ${CMAKE_C_COMPILER_VERSION}")
   else ()
     set (BINARY_EXAMPLE_ENDING "tar.gz")
-    set (BINARY_INSTALL_ENDING "sh")
+    set (BINARY_COMPRESS_ENDING "tar.gz")
+    set (BINARY_INSTALL_ENDING "sh/deb/rpm")
     set (BINARY_PLATFORM "${BINARY_PLATFORM} ${CMAKE_SYSTEM_VERSION} ${CMAKE_SYSTEM_PROCESSOR}")
     set (BINARY_PLATFORM "${BINARY_PLATFORM}, using ${CMAKE_C_COMPILER_ID} C ${CMAKE_C_COMPILER_VERSION}")
   endif ()
diff --git a/config/cmake/README.md.cmake.in b/config/cmake/README.md.cmake.in
index d7e4bc4..5ba93f3 100644
--- a/config/cmake/README.md.cmake.in
+++ b/config/cmake/README.md.cmake.in
@@ -2,13 +2,13 @@
 ------------------------------------------------------------------------------
 
 This directory contains the binary (release) distribution of
-@HDF5_PACKAGE_NAME@ @HDF5_PACKAGE_VERSION_MAJOR@ that was compiled on;
+@HDF5_PACKAGE_NAME@ @HDF5_PACKAGE_VERSION_MAJOR@.@HDF5_PACKAGE_VERSION_MINOR@ that was compiled on;
     @BINARY_PLATFORM@.
 
 It was built with the following options:
     -- @LIB_TYPE@ C/C++/Fortran libraries
     -- SZIP (encoder enabled) and ZLIB
-    -- @LIB_TYPE@ HDF5 tools
+    -- HDF5 tools
     -- Java @Java_VERSION@
 
 The contents of this directory are:
@@ -16,17 +16,12 @@ The contents of this directory are:
     COPYING                 - Copyright notice
     README.md               - This file
     @HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@-@BINARY_SYSTEM_NAME@.@BINARY_INSTALL_ENDING@    - HDF5 Install Package
+    OR
+    @HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@-@BINARY_SYSTEM_NAME@.@BINARY_COMPRESS_ENDING@    - HDF5 Compressed Package
 
 This binary was built with the ZLIB and SZIP/Libaec external libraries and are
 included for convenience.  Libaec is an unrestricted open-source replacement for SZIP
-(version 1.0.4, Encoder ENABLED).
-
-The official ZLIB and SZIP/Libaec pages are at:
-
-    ZLIB: https://git.savannah.gnu.org/cgit/gzip.git/
-        https://git.savannah.gnu.org/cgit/gzip.git/tree/COPYING
-    SZIP/Libaec: https://github.com/MathisRosenhauer/libaec
-        https://github.com/MathisRosenhauer/libaec/blob/master/LICENSE.txt
+(Encoder ENABLED).
 
 
 Installation
@@ -35,6 +30,11 @@ Installation
 2. Follow prompts
 ===========================================================================
 
+Uncompress
+===========================================================================
+1. Extract @HDF5_PACKAGE_NAME@-@HDF5_PACKAGE_VERSION@-@BINARY_SYSTEM_NAME@.@BINARY_COMPRESS_ENDING@
+===========================================================================
+
 After Installation
 ===========================================================================
 The examples folder, HDF5Examples, located in the
@@ -75,6 +75,6 @@ For more information see USING_CMake_Examples.txt in the install folder.
 ===========================================================================
 
 Documentation for this release can be found at the following URL:
-     https://portal.hdfgroup.org/display/HDF5/HDF5
+    https://portal.hdfgroup.org/documentation/index.html#hdf5
 
 Bugs should be reported to help@hdfgroup.org.
diff --git a/config/cmake/mccacheinit.cmake b/config/cmake/mccacheinit.cmake
index 5b41167..9e4d581 100644
--- a/config/cmake/mccacheinit.cmake
+++ b/config/cmake/mccacheinit.cmake
@@ -33,13 +33,13 @@ set (HDF5_BUILD_EXAMPLES ON CACHE BOOL "Build HDF5 Library Examples" FORCE)
 
 set (HDF5_ENABLE_Z_LIB_SUPPORT ON CACHE BOOL "Enable Zlib Filters" FORCE)
 
-set (HDF5_ENABLE_SZIP_SUPPORT ON CACHE BOOL "Use SZip Filter" FORCE)
+set (HDF5_ENABLE_SZIP_SUPPORT OFF CACHE BOOL "Use SZip Filter" FORCE)
 
-set (HDF5_ENABLE_SZIP_ENCODING ON CACHE BOOL "Use SZip Encoding" FORCE)
+set (HDF5_ENABLE_SZIP_ENCODING OFF CACHE BOOL "Use SZip Encoding" FORCE)
 
 set (MPIEXEC_MAX_NUMPROCS "4" CACHE STRING "Minimum number of processes for HDF parallel tests" FORCE)
 
-set (HDF5_ENABLE_USING_MEMCHECKER ON CACHE BOOL "Indicate that a memory checker is used" FORCE)
+set (HDF5_USING_ANALYSIS_TOOL ON CACHE BOOL "Indicate that an analysis checker is used" FORCE)
 
 set (HDF5_NO_PACKAGES ON CACHE BOOL "CPACK - Disable packaging" FORCE)
 
diff --git a/config/sanitizer/sanitizers.cmake b/config/sanitizer/sanitizers.cmake
index 53591d2..bf2aad2 100644
--- a/config/sanitizer/sanitizers.cmake
+++ b/config/sanitizer/sanitizers.cmake
@@ -13,8 +13,6 @@
 # License for the specific language governing permissions and limitations under
 # the License.
 
-include(CheckCXXSourceCompiles)
-
 set(USE_SANITIZER
     ""
     CACHE
@@ -44,11 +42,12 @@ function(test_san_flags return_var flags)
   unset(${return_var} CACHE)
   set(FLAGS_BACKUP ${CMAKE_REQUIRED_FLAGS})
   set(CMAKE_REQUIRED_FLAGS "${flags}")
-  check_cxx_source_compiles("int main() { return 0; }" ${return_var})
+  check_c_source_compiles("int main() { return 0; }" ${return_var})
   set(CMAKE_REQUIRED_FLAGS "${FLAGS_BACKUP}")
   set(CMAKE_REQUIRED_QUIET "${QUIET_BACKUP}")
 endfunction()
 
+message(STATUS "USE_SANITIZER=${USE_SANITIZER}, CMAKE_C_COMPILER_ID=${CMAKE_C_COMPILER_ID}")
 if(USE_SANITIZER)
   if(CMAKE_C_COMPILER_ID MATCHES "IntelLLVM" OR CMAKE_C_COMPILER_ID MATCHES "[Cc]lang")
     set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
@@ -56,10 +55,11 @@ if(USE_SANITIZER)
     unset(SANITIZER_SELECTED_FLAGS)
 
     if(UNIX)
-      append("-fno-omit-frame-pointer" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
+      append("-fno-omit-frame-pointer" CMAKE_C_FLAGS)
+      message(STATUS "Building with sanitize, base flags=${CMAKE_C_SANITIZER_FLAGS}")
 
       if(uppercase_CMAKE_BUILD_TYPE STREQUAL "DEBUG")
-        append("-O1" CMAKE_C_FLAGS CMAKE_CXX_FLAGS)
+        append("-O1" CMAKE_C_FLAGS)
       endif()
 
       if(USE_SANITIZER MATCHES "([Aa]ddress)")
@@ -72,10 +72,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_ADDR_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
+            append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER)
           endif()
         else()
-          message(FATAL_ERROR "Address sanitizer not available for ${CMAKE_CXX_COMPILER}")
+          message(FATAL_ERROR "Address sanitizer not available for ${CMAKE_C_COMPILER}")
         endif()
       endif()
 
@@ -98,10 +98,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_MEM_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_MSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
+            append_quoteless(AFL_USE_MSAN=1 CMAKE_C_COMPILER_LAUNCHER)
           endif()
         else()
-          message(FATAL_ERROR "Memory [With Origins] sanitizer not available for ${CMAKE_CXX_COMPILER}")
+          message(FATAL_ERROR "Memory [With Origins] sanitizer not available for ${CMAKE_C_COMPILER}")
         endif()
       endif()
 
@@ -117,10 +117,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_UB_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_UBSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
+            append_quoteless(AFL_USE_UBSAN=1 CMAKE_C_COMPILER_LAUNCHER)
           endif()
         else()
-          message(FATAL_ERROR "Undefined Behaviour sanitizer not available for ${CMAKE_CXX_COMPILER}")
+          message(FATAL_ERROR "Undefined Behaviour sanitizer not available for ${CMAKE_C_COMPILER}")
         endif()
       endif()
 
@@ -133,10 +133,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_THREAD_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_TSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
+            append_quoteless(AFL_USE_TSAN=1 CMAKE_C_COMPILER_LAUNCHER)
           endif()
         else()
-          message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_CXX_COMPILER}")
+          message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_C_COMPILER}")
         endif()
       endif()
 
@@ -149,10 +149,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_LEAK_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_LSAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
+            append_quoteless(AFL_USE_LSAN=1 CMAKE_C_COMPILER_LAUNCHER)
           endif()
         else()
-          message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_CXX_COMPILER}")
+          message(FATAL_ERROR "Thread sanitizer not available for ${CMAKE_C_COMPILER}")
         endif()
       endif()
 
@@ -165,10 +165,10 @@ if(USE_SANITIZER)
           append("${SANITIZER_LEAK_FLAG}" SANITIZER_SELECTED_FLAGS)
 
           if(AFL)
-            append_quoteless(AFL_USE_CFISAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
+            append_quoteless(AFL_USE_CFISAN=1 CMAKE_C_COMPILER_LAUNCHER)
           endif()
         else()
-          message(FATAL_ERROR "Control Flow Integrity(CFI) sanitizer not available for ${CMAKE_CXX_COMPILER}")
+          message(FATAL_ERROR "Control Flow Integrity(CFI) sanitizer not available for ${CMAKE_C_COMPILER}")
         endif()
       endif()
 
@@ -176,17 +176,17 @@ if(USE_SANITIZER)
       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 CMAKE_CXX_FLAGS)
+        append("${SANITIZER_SELECTED_FLAGS}" CMAKE_C_FLAGS)
       else()
-        message(FATAL_ERROR " Sanitizer flags ${SANITIZER_SELECTED_FLAGS} are not compatible.")
+        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 CMAKE_CXX_FLAGS)
+        append("-fsanitize=address" CMAKE_C_FLAGS)
 
         if(AFL)
-          append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER CMAKE_CXX_COMPILER_LAUNCHER)
+          append_quoteless(AFL_USE_ASAN=1 CMAKE_C_COMPILER_LAUNCHER)
         endif()
       else()
         message(FATAL_ERROR "This sanitizer not yet supported in the MSVC environment: ${USE_SANITIZER}")
@@ -197,7 +197,7 @@ 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)
+      append("/fsanitize=address" CMAKE_C_FLAGS)
     else()
       message(FATAL_ERROR "This sanitizer not yet supported in the MSVC environment: ${USE_SANITIZER}")
     endif()