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

.gitattributes

@@ -573,7 +573,6 @@ tools/h5diff/testfiles/tmpSingleSiteBethe.output.h5 -text
 tools/h5diff/testfiles/tmpSingleSiteBethe.reference.h5 -text
 tools/h5diff/testfiles/tmptest.he5 -text
 tools/h5diff/testfiles/tmptest2.he5 -text
-tools/h5dump/errfiles/non_existing.err -text
 tools/h5format_convert/CMakeLists.txt -text
 tools/h5format_convert/CMakeTests.cmake -text
 tools/h5format_convert/Makefile.am -text

config/cmake/ZLIB/CMakeLists.txt

@@ -129,7 +129,7 @@ endif ()
 # Compiler specific flags : Shouldn't there be compiler tests for these
 #-----------------------------------------------------------------------------
 if (CMAKE_C_COMPILER_ID STREQUAL "GNU")
-  set (CMAKE_C_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_C_FLAGS} -Wno-strict-prototypes")
+  set (CMAKE_C_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_C_FLAGS} -Wno-strict-prototypes -Wno-implicit-function-declaration")
 endif ()
 if (CMAKE_C_COMPILER_ID MATCHES "IntelLLVM" OR CMAKE_C_COMPILER_ID MATCHES "[Cc]lang")
    set (CMAKE_C_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_C_FLAGS} -Wno-implicit-function-declaration")

config/cmake/runTest.cmake

@@ -265,12 +265,22 @@ if (NOT TEST_SKIP_COMPARE)
           endif ()
           math (EXPR _FP_LEN "${len_ref} - 1")
           foreach (line RANGE 0 ${_FP_LEN})
-            list (GET test_act ${line} str_act)
-            list (GET test_ref ${line} str_ref)
-            if (NOT str_act STREQUAL str_ref)
-              if (str_act)
-                set (TEST_COMPARE_RESULT 1)
-                message (STATUS "line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
+            if (line GREATER_EQUAL len_act)
+              message (STATUS "COMPARE FAILED: ran out of lines in ${TEST_FOLDER}/${TEST_OUTPUT}")
+              set (TEST_COMPARE_RESULT 1)
+              break ()
+            elseif (line GREATER_EQUAL len_ref)
+              message (STATUS "COMPARE FAILED: ran out of lines in ${TEST_FOLDER}/${TEST_REFERENCE}")
+              set (TEST_COMPARE_RESULT 1)
+              break ()
+            else ()
+              list (GET test_act ${line} str_act)
+              list (GET test_ref ${line} str_ref)
+              if (NOT str_act STREQUAL str_ref)
+                if (str_act)
+                  set (TEST_COMPARE_RESULT 1)
+                  message (STATUS "line = ${line}\n***ACTUAL: ${str_act}\n****REFER: ${str_ref}\n")
+                endif ()
               endif ()
             endif ()
           endforeach ()

doxygen/dox/APIVersions.dox

@@ -139,7 +139,7 @@
 /**
  * \ingroup H5R
  * \def H5Rget_obj_type
- * \api_vers_3{H5Rget_obj_type,H5Rget_obj_type1,H5Rget_obj_type2,H5R_get_obj_type3}
+ * \api_vers_3{H5Rget_obj_type,H5Rget_obj_type1,H5Rget_obj_type2,H5Rget_obj_type3}
  */
 
 /**

release_docs/RELEASE.txt

@@ -747,20 +747,6 @@ Support for new platforms, languages and compilers
 
 Bug Fixes since HDF5-1.14.0 release
 ===================================
-    Configuration:
-    -------------
-    - Fix Autotools -Werror cleanup
-
-      The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc.
-      so configure checks don't trip over warnings generated by configure
-      check programs. The sed line originally only scrubbed -Werror but not
-      -Werror=something, which would cause errors when the '=something' was
-      left behind in CFLAGS.
-
-      The sed line has been updated to handle -Werror=something lines.
-
-      Fixes one issue raised in #3872
-
     Library
     -------
 
@@ -1672,6 +1658,24 @@ Bug Fixes since HDF5-1.14.0 release
 
     Configuration
     -------------
+    - Fixed a list index out of range issue in the runTest.cmake file
+
+      Fixed an issue in config/cmake/runTest.cmake where the CMake logic
+      would try to access an invalid list index if the number of lines in
+      a test's output and reference files don't match
+
+    - Fix Autotools -Werror cleanup
+
+      The Autotools temporarily scrub -Werror(=whatever) from CFLAGS, etc.
+      so configure checks don't trip over warnings generated by configure
+      check programs. The sed line originally only scrubbed -Werror but not
+      -Werror=something, which would cause errors when the '=something' was
+      left behind in CFLAGS.
+
+      The sed line has been updated to handle -Werror=something lines.
+
+      Fixes one issue raised in #3872
+
     - Changed default of 'Error on HDF5 doxygen warnings' DOXYGEN_WARN_AS_ERROR option.
 
       The default setting of DOXYGEN_WARN_AS_ERROR to 'FAIL_ON_WARNINGS' has been changed
@@ -1785,12 +1789,24 @@ Bug Fixes since HDF5-1.14.0 release
 
     Tools
     -----
+    - Fixed several issues in ph5diff
+
+      The parallel logic for the ph5diff tool inside the shared h5diff code was
+      refactored and cleaned up to fix several issues with the ph5diff tool. This
+      fixed:
+
+        - several concurrency issues in ph5diff that can result in interleaved
+          output
+        - an issue where output can sometimes be dropped when it ends up in
+          ph5diff's output overflow file
+        - an issue where MPI_Init was called after HDF5 had been initialized,
+          preventing the library from setting up an MPI communicator attribute
+          to perform library cleanup on MPI_Finalize
 
     - Renamed h5fuse.sh to h5fuse
 
       Addresses Discussion #3791
 
-
     - Fixed an issue with unmatched MPI messages in ph5diff
 
       The "manager" MPI rank in ph5diff was unintentionally sending "program end"