Merge pull request #1447 in HDFFV/hdf5 from ~BYRN/hdf5_adb:hdf5_1_10 to hdf5_1_10

* commit 'f7d530dd275e176e59b26c1b7363ba16b3ab6c9c':
  HDFFV-10674, 10664, 10674

9 files changed, 102 insertions, 78 deletions

diff --git a/config/cmake/HDF5UseFortran.cmake b/config/cmake/HDF5UseFortran.cmake
index 157befd..14774c7 100644
--- a/config/cmake/HDF5UseFortran.cmake
+++ b/config/cmake/HDF5UseFortran.cmake
@@ -40,7 +40,7 @@ macro (FORTRAN_RUN FUNCTION_NAME SOURCE_CODE RUN_RESULT_VAR1 COMPILE_RESULT_VAR1
     TRY_RUN (RUN_RESULT_VAR COMPILE_RESULT_VAR
         ${CMAKE_BINARY_DIR}
         ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/testFortranCompiler1.f90
-        LINK_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}"
+        LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
     )
 
     if (${COMPILE_RESULT_VAR})
@@ -367,9 +367,9 @@ ENABLE_LANGUAGE (C)
 #-----------------------------------------------------------------------------
 macro (C_RUN FUNCTION_NAME SOURCE_CODE RETURN_VAR)
     message (STATUS "Detecting C ${FUNCTION_NAME}")
-    if (CMAKE_REQUIRED_LIBRARIES)
+    if (HDF5_REQUIRED_LIBRARIES)
       set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES
-          "-DLINK_LIBRARIES:STRING=${CMAKE_REQUIRED_LIBRARIES}")
+          "-DLINK_LIBRARIES:STRING=${HDF5_REQUIRED_LIBRARIES}")
     else ()
       set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES)
     endif ()
diff --git a/config/cmake/HDFCompilerFlags.cmake b/config/cmake/HDFCompilerFlags.cmake
index 93ebc3c..0a39568 100644
--- a/config/cmake/HDFCompilerFlags.cmake
+++ b/config/cmake/HDFCompilerFlags.cmake
@@ -9,16 +9,16 @@
 # If you do not have access to either file, you may request a copy from
 # help@hdfgroup.org.
 #
+set(CMAKE_C_STANDARD 99)
+set(CMAKE_C_STANDARD_REQUIRED TRUE)
 
 message (STATUS "Warnings Configuration:")
+set (CMAKE_C_FLAGS "${CMAKE_C99_STANDARD_COMPILE_OPTION} ${CMAKE_C_FLAGS}")
 #-----------------------------------------------------------------------------
 # Compiler specific flags : Shouldn't there be compiler tests for these
 #-----------------------------------------------------------------------------
 if (CMAKE_COMPILER_IS_GNUCC)
   set (CMAKE_C_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_C_FLAGS}")
-  if (NOT CYGWIN)
-    set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -std=c99")
-  endif ()
   if (${HDF_CFG_NAME} MATCHES "Debug")
     if (NOT CMAKE_C_COMPILER_VERSION VERSION_LESS 5.0)
       set (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -Og -ftrapv -fno-common")
diff --git a/config/cmake_ext_mod/ConfigureChecks.cmake b/config/cmake_ext_mod/ConfigureChecks.cmake
index 40f1440..0424ed6 100644
--- a/config/cmake_ext_mod/ConfigureChecks.cmake
+++ b/config/cmake_ext_mod/ConfigureChecks.cmake
@@ -70,7 +70,7 @@ if (WIN32)
     set (CMAKE_REQUIRED_FLAGS "-DWIN32_LEAN_AND_MEAN=1 -DNOGDI=1")
   endif ()
   set (${HDF_PREFIX}_HAVE_WIN32_API 1)
-  set (CMAKE_REQUIRED_LIBRARIES "ws2_32.lib;wsock32.lib")
+  set (HDF5_REQUIRED_LIBRARIES "ws2_32.lib;wsock32.lib")
   if (NOT UNIX AND NOT MINGW)
     set (WINDOWS 1)
     set (CMAKE_REQUIRED_FLAGS "/DWIN32_LEAN_AND_MEAN=1 /DNOGDI=1")
@@ -109,6 +109,78 @@ endif ()
 # END of WINDOWS Hard code Values
 # ----------------------------------------------------------------------
 
+if (NOT WINDOWS)
+  TEST_BIG_ENDIAN (${HDF_PREFIX}_WORDS_BIGENDIAN)
+endif ()
+
+#-----------------------------------------------------------------------------
+# Check IF header file exists and add it to the list.
+#-----------------------------------------------------------------------------
+macro (CHECK_INCLUDE_FILE_CONCAT FILE VARIABLE)
+  CHECK_INCLUDE_FILES ("${USE_INCLUDES};${FILE}" ${VARIABLE})
+  if (${VARIABLE})
+    set (USE_INCLUDES ${USE_INCLUDES} ${FILE})
+  endif ()
+endmacro ()
+
+#-----------------------------------------------------------------------------
+#  Check for the existence of certain header files
+#-----------------------------------------------------------------------------
+CHECK_INCLUDE_FILE_CONCAT ("sys/file.h"      ${HDF_PREFIX}_HAVE_SYS_FILE_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/ioctl.h"     ${HDF_PREFIX}_HAVE_SYS_IOCTL_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/resource.h"  ${HDF_PREFIX}_HAVE_SYS_RESOURCE_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/socket.h"    ${HDF_PREFIX}_HAVE_SYS_SOCKET_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/stat.h"      ${HDF_PREFIX}_HAVE_SYS_STAT_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/time.h"      ${HDF_PREFIX}_HAVE_SYS_TIME_H)
+CHECK_INCLUDE_FILE_CONCAT ("sys/types.h"     ${HDF_PREFIX}_HAVE_SYS_TYPES_H)
+CHECK_INCLUDE_FILE_CONCAT ("features.h"      ${HDF_PREFIX}_HAVE_FEATURES_H)
+CHECK_INCLUDE_FILE_CONCAT ("dirent.h"        ${HDF_PREFIX}_HAVE_DIRENT_H)
+CHECK_INCLUDE_FILE_CONCAT ("setjmp.h"        ${HDF_PREFIX}_HAVE_SETJMP_H)
+CHECK_INCLUDE_FILE_CONCAT ("stddef.h"        ${HDF_PREFIX}_HAVE_STDDEF_H)
+CHECK_INCLUDE_FILE_CONCAT ("stdint.h"        ${HDF_PREFIX}_HAVE_STDINT_H)
+CHECK_INCLUDE_FILE_CONCAT ("unistd.h"        ${HDF_PREFIX}_HAVE_UNISTD_H)
+
+# Darwin
+CHECK_INCLUDE_FILE_CONCAT ("mach/mach_time.h" ${HDF_PREFIX}_HAVE_MACH_MACH_TIME_H)
+
+# Windows
+CHECK_INCLUDE_FILE_CONCAT ("io.h"            ${HDF_PREFIX}_HAVE_IO_H)
+if (NOT CYGWIN)
+  CHECK_INCLUDE_FILE_CONCAT ("winsock2.h"      ${HDF_PREFIX}_HAVE_WINSOCK2_H)
+endif ()
+CHECK_INCLUDE_FILE_CONCAT ("sys/timeb.h"     ${HDF_PREFIX}_HAVE_SYS_TIMEB_H)
+
+if (CMAKE_SYSTEM_NAME MATCHES "OSF")
+  CHECK_INCLUDE_FILE_CONCAT ("sys/sysinfo.h" ${HDF_PREFIX}_HAVE_SYS_SYSINFO_H)
+  CHECK_INCLUDE_FILE_CONCAT ("sys/proc.h"    ${HDF_PREFIX}_HAVE_SYS_PROC_H)
+else ()
+  set (${HDF_PREFIX}_HAVE_SYS_SYSINFO_H "" CACHE INTERNAL "" FORCE)
+  set (${HDF_PREFIX}_HAVE_SYS_PROC_H    "" CACHE INTERNAL "" FORCE)
+endif ()
+
+CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
+CHECK_INCLUDE_FILE_CONCAT ("pdb.h"           ${HDF_PREFIX}_HAVE_PDB_H)
+CHECK_INCLUDE_FILE_CONCAT ("pthread.h"       ${HDF_PREFIX}_HAVE_PTHREAD_H)
+CHECK_INCLUDE_FILE_CONCAT ("srbclient.h"     ${HDF_PREFIX}_HAVE_SRBCLIENT_H)
+CHECK_INCLUDE_FILE_CONCAT ("string.h"        ${HDF_PREFIX}_HAVE_STRING_H)
+CHECK_INCLUDE_FILE_CONCAT ("strings.h"       ${HDF_PREFIX}_HAVE_STRINGS_H)
+CHECK_INCLUDE_FILE_CONCAT ("stdlib.h"        ${HDF_PREFIX}_HAVE_STDLIB_H)
+CHECK_INCLUDE_FILE_CONCAT ("memory.h"        ${HDF_PREFIX}_HAVE_MEMORY_H)
+CHECK_INCLUDE_FILE_CONCAT ("dlfcn.h"         ${HDF_PREFIX}_HAVE_DLFCN_H)
+CHECK_INCLUDE_FILE_CONCAT ("inttypes.h"      ${HDF_PREFIX}_HAVE_INTTYPES_H)
+CHECK_INCLUDE_FILE_CONCAT ("netinet/in.h"    ${HDF_PREFIX}_HAVE_NETINET_IN_H)
+# _Bool type support
+CHECK_INCLUDE_FILE_CONCAT (stdbool.h    ${HDF_PREFIX}_HAVE_STDBOOL_H)
+
+## Check for non-standard extenstion quadmath.h
+
+CHECK_INCLUDE_FILES(quadmath.h C_HAVE_QUADMATH)
+if (${C_HAVE_QUADMATH})
+  set(${HDF_PREFIX}_HAVE_QUADMATH_H 1)
+else ()
+  set(${HDF_PREFIX}_HAVE_QUADMATH_H 0)
+endif ()
+
 if (CYGWIN)
   set (${HDF_PREFIX}_HAVE_LSEEK64 0)
 endif ()
@@ -127,17 +199,13 @@ endif ()
 CHECK_LIBRARY_EXISTS_CONCAT ("ucb"    gethostname  ${HDF_PREFIX}_HAVE_LIBUCB)
 
 # For other tests to use the same libraries
-set (CMAKE_REQUIRED_LIBRARIES ${CMAKE_REQUIRED_LIBRARIES} ${LINK_LIBS})
+set (HDF5_REQUIRED_LIBRARIES ${HDF5_REQUIRED_LIBRARIES} ${LINK_LIBS})
 
 set (USE_INCLUDES "")
 if (WINDOWS)
   set (USE_INCLUDES ${USE_INCLUDES} "windows.h")
 endif ()
 
-if (NOT WINDOWS)
-  TEST_BIG_ENDIAN (${HDF_PREFIX}_WORDS_BIGENDIAN)
-endif ()
-
 # For other specific tests, use this MACRO.
 macro (HDF_FUNCTION_TEST OTHER_TEST)
   if (NOT DEFINED ${HDF_PREFIX}_${OTHER_TEST})
@@ -165,7 +233,7 @@ macro (HDF_FUNCTION_TEST OTHER_TEST)
         ${CMAKE_BINARY_DIR}
         ${HDF_RESOURCES_EXT_DIR}/HDFTests.c
         COMPILE_DEFINITIONS "${MACRO_CHECK_FUNCTION_DEFINITIONS}"
-        LINK_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}"
+        LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
         OUTPUT_VARIABLE OUTPUT
     )
     if (${OTHER_TEST})
@@ -188,63 +256,6 @@ endmacro ()
 HDF_FUNCTION_TEST (STDC_HEADERS)
 
 #-----------------------------------------------------------------------------
-# Check IF header file exists and add it to the list.
-#-----------------------------------------------------------------------------
-macro (CHECK_INCLUDE_FILE_CONCAT FILE VARIABLE)
-  CHECK_INCLUDE_FILES ("${USE_INCLUDES};${FILE}" ${VARIABLE})
-  if (${VARIABLE})
-    set (USE_INCLUDES ${USE_INCLUDES} ${FILE})
-  endif ()
-endmacro ()
-
-#-----------------------------------------------------------------------------
-#  Check for the existence of certain header files
-#-----------------------------------------------------------------------------
-CHECK_INCLUDE_FILE_CONCAT ("sys/file.h"      ${HDF_PREFIX}_HAVE_SYS_FILE_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/ioctl.h"     ${HDF_PREFIX}_HAVE_SYS_IOCTL_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/resource.h"  ${HDF_PREFIX}_HAVE_SYS_RESOURCE_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/socket.h"    ${HDF_PREFIX}_HAVE_SYS_SOCKET_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/stat.h"      ${HDF_PREFIX}_HAVE_SYS_STAT_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/time.h"      ${HDF_PREFIX}_HAVE_SYS_TIME_H)
-CHECK_INCLUDE_FILE_CONCAT ("sys/types.h"     ${HDF_PREFIX}_HAVE_SYS_TYPES_H)
-CHECK_INCLUDE_FILE_CONCAT ("features.h"      ${HDF_PREFIX}_HAVE_FEATURES_H)
-CHECK_INCLUDE_FILE_CONCAT ("dirent.h"        ${HDF_PREFIX}_HAVE_DIRENT_H)
-CHECK_INCLUDE_FILE_CONCAT ("setjmp.h"        ${HDF_PREFIX}_HAVE_SETJMP_H)
-CHECK_INCLUDE_FILE_CONCAT ("stddef.h"        ${HDF_PREFIX}_HAVE_STDDEF_H)
-CHECK_INCLUDE_FILE_CONCAT ("stdint.h"        ${HDF_PREFIX}_HAVE_STDINT_H)
-CHECK_INCLUDE_FILE_CONCAT ("unistd.h"        ${HDF_PREFIX}_HAVE_UNISTD_H)
-
-# Darwin
-CHECK_INCLUDE_FILE_CONCAT ("mach/mach_time.h" ${HDF_PREFIX}_HAVE_MACH_MACH_TIME_H)
-
-# Windows
-CHECK_INCLUDE_FILE_CONCAT ("io.h"            ${HDF_PREFIX}_HAVE_IO_H)
-if (NOT CYGWIN)
-  CHECK_INCLUDE_FILE_CONCAT ("winsock2.h"      ${HDF_PREFIX}_HAVE_WINSOCK2_H)
-endif ()
-CHECK_INCLUDE_FILE_CONCAT ("sys/timeb.h"     ${HDF_PREFIX}_HAVE_SYS_TIMEB_H)
-
-if (CMAKE_SYSTEM_NAME MATCHES "OSF")
-  CHECK_INCLUDE_FILE_CONCAT ("sys/sysinfo.h" ${HDF_PREFIX}_HAVE_SYS_SYSINFO_H)
-  CHECK_INCLUDE_FILE_CONCAT ("sys/proc.h"    ${HDF_PREFIX}_HAVE_SYS_PROC_H)
-else ()
-  set (${HDF_PREFIX}_HAVE_SYS_SYSINFO_H "" CACHE INTERNAL "" FORCE)
-  set (${HDF_PREFIX}_HAVE_SYS_PROC_H    "" CACHE INTERNAL "" FORCE)
-endif ()
-
-CHECK_INCLUDE_FILE_CONCAT ("globus/common.h" ${HDF_PREFIX}_HAVE_GLOBUS_COMMON_H)
-CHECK_INCLUDE_FILE_CONCAT ("pdb.h"           ${HDF_PREFIX}_HAVE_PDB_H)
-CHECK_INCLUDE_FILE_CONCAT ("pthread.h"       ${HDF_PREFIX}_HAVE_PTHREAD_H)
-CHECK_INCLUDE_FILE_CONCAT ("srbclient.h"     ${HDF_PREFIX}_HAVE_SRBCLIENT_H)
-CHECK_INCLUDE_FILE_CONCAT ("string.h"        ${HDF_PREFIX}_HAVE_STRING_H)
-CHECK_INCLUDE_FILE_CONCAT ("strings.h"       ${HDF_PREFIX}_HAVE_STRINGS_H)
-CHECK_INCLUDE_FILE_CONCAT ("stdlib.h"        ${HDF_PREFIX}_HAVE_STDLIB_H)
-CHECK_INCLUDE_FILE_CONCAT ("memory.h"        ${HDF_PREFIX}_HAVE_MEMORY_H)
-CHECK_INCLUDE_FILE_CONCAT ("dlfcn.h"         ${HDF_PREFIX}_HAVE_DLFCN_H)
-CHECK_INCLUDE_FILE_CONCAT ("inttypes.h"      ${HDF_PREFIX}_HAVE_INTTYPES_H)
-CHECK_INCLUDE_FILE_CONCAT ("netinet/in.h"    ${HDF_PREFIX}_HAVE_NETINET_IN_H)
-
-#-----------------------------------------------------------------------------
 #  Check for large file support
 #-----------------------------------------------------------------------------
 
@@ -408,7 +419,6 @@ endif ()
 #-----------------------------------------------------------------------------
 
 # _Bool type support
-CHECK_INCLUDE_FILE_CONCAT (stdbool.h    ${HDF_PREFIX}_HAVE_STDBOOL_H)
 if (HAVE_STDBOOL_H)
   set (CMAKE_EXTRA_INCLUDE_FILES stdbool.h)
   HDF_CHECK_TYPE_SIZE (bool         ${HDF_PREFIX}_SIZEOF_BOOL)
@@ -580,7 +590,7 @@ if (WINDOWS)
         ${CMAKE_BINARY_DIR}
         ${HDF_RESOURCES_EXT_DIR}/HDFTests.c
         COMPILE_DEFINITIONS "${CMAKE_REQUIRED_DEFINITIONS} ${MACRO_CHECK_FUNCTION_DEFINITIONS}"
-        LINK_LIBRARIES "${CMAKE_REQUIRED_LIBRARIES}"
+        LINK_LIBRARIES "${HDF5_REQUIRED_LIBRARIES}"
         CMAKE_FLAGS "${CHECK_C_SOURCE_COMPILES_ADD_INCLUDES} -DCMAKE_SKIP_RPATH:BOOL=${CMAKE_SKIP_RPATH}"
         COMPILE_OUTPUT_VARIABLE OUTPUT
     )
diff --git a/config/cmake_ext_mod/HDFUseCXX.cmake b/config/cmake_ext_mod/HDFUseCXX.cmake
index f293ec5..efaa556 100644
--- a/config/cmake_ext_mod/HDFUseCXX.cmake
+++ b/config/cmake_ext_mod/HDFUseCXX.cmake
@@ -48,8 +48,8 @@ macro (HDF_CXX_FUNCTION_TEST OTHER_TEST)
   if (NOT DEFINED ${OTHER_TEST})
     set (MACRO_CHECK_FUNCTION_DEFINITIONS "-D${OTHER_TEST} ${CMAKE_REQUIRED_FLAGS}")
     set (OTHER_TEST_ADD_LIBRARIES)
-    if (CMAKE_REQUIRED_LIBRARIES)
-      set (OTHER_TEST_ADD_LIBRARIES "-DLINK_LIBRARIES:STRING=${CMAKE_REQUIRED_LIBRARIES}")
+    if (HDF5_REQUIRED_LIBRARIES)
+      set (OTHER_TEST_ADD_LIBRARIES "-DLINK_LIBRARIES:STRING=${HDF5_REQUIRED_LIBRARIES}")
     endif ()
 
     foreach (def
diff --git a/config/cmake_ext_mod/HDFUseFortran.cmake b/config/cmake_ext_mod/HDFUseFortran.cmake
index f8f3cea..c68c921 100644
--- a/config/cmake_ext_mod/HDFUseFortran.cmake
+++ b/config/cmake_ext_mod/HDFUseFortran.cmake
@@ -48,9 +48,9 @@ set (H5_FC_FUNC_ "H5_FC_FUNC_(name,NAME) ${CMAKE_MATCH_1}")
 #-----------------------------------------------------------------------------
 macro (CHECK_FORTRAN_FEATURE FUNCTION CODE VARIABLE)
     message (STATUS "Testing Fortran ${FUNCTION}")
-    if (CMAKE_REQUIRED_LIBRARIES)
+    if (HDF5_REQUIRED_LIBRARIES)
       set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES
-          "-DLINK_LIBRARIES:STRING=${CMAKE_REQUIRED_LIBRARIES}")
+          "-DLINK_LIBRARIES:STRING=${HDF5_REQUIRED_LIBRARIES}")
     else ()
       set (CHECK_FUNCTION_EXISTS_ADD_LIBRARIES)
     endif ()
diff --git a/config/toolchain/GCC.cmake b/config/toolchain/GCC.cmake
index ddb1641..c41d0ca 100644
--- a/config/toolchain/GCC.cmake
+++ b/config/toolchain/GCC.cmake
@@ -1,5 +1,6 @@
-# Uncomment the following to use cross-compiling
+# Uncomment the following line and the correct system name to use cross-compiling
 #set(CMAKE_SYSTEM_NAME Linux)
+
 set(CMAKE_COMPILER_VENDOR "GCC")
 
 set(CMAKE_C_COMPILER cc)
diff --git a/config/toolchain/PGI.cmake b/config/toolchain/PGI.cmake
new file mode 100644
index 0000000..ec58cbb
--- /dev/null
+++ b/config/toolchain/PGI.cmake
@@ -0,0 +1,11 @@
+# Uncomment the following to use cross-compiling
+#set(CMAKE_SYSTEM_NAME Linux)
+
+set(CMAKE_COMPILER_VENDOR "PGI")
+
+set(CMAKE_C_COMPILER pgcc)
+set(CMAKE_CXX_COMPILER pgc++)
+set(CMAKE_Fortran_COMPILER pgf90)
+
+# the following is used if cross-compiling
+set(CMAKE_CROSSCOMPILING_EMULATOR "")
diff --git a/config/toolchain/crayle.cmake b/config/toolchain/crayle.cmake
index a83147b..47d8afc 100644
--- a/config/toolchain/crayle.cmake
+++ b/config/toolchain/crayle.cmake
@@ -1,5 +1,6 @@
-# Uncomment the following to use cross-compiling
+# The following line will use cross-compiling
 set(CMAKE_SYSTEM_NAME Linux)
+
 set(CMAKE_COMPILER_VENDOR "CrayLinuxEnvironment")
 
 set(CMAKE_C_COMPILER cc)
diff --git a/config/toolchain/intel.cmake b/config/toolchain/intel.cmake
index f1a5734..97f6a64 100644
--- a/config/toolchain/intel.cmake
+++ b/config/toolchain/intel.cmake
@@ -1,5 +1,6 @@
 # Uncomment the following to use cross-compiling
 #set(CMAKE_SYSTEM_NAME Linux)
+
 set(CMAKE_COMPILER_VENDOR "intel")
 
 set(CMAKE_C_COMPILER icc)