[svn-r19413] Description:

	Bring r19349:19411 from trunk to revise_chunks branch.

Tested on:
        FreeBSD/32 6.3 (duty) in debug mode
        FreeBSD/64 6.3 (liberty) w/C++ & FORTRAN, in debug mode
        Linux/32 2.6 (jam) w/PGI compilers, w/default API=1.8.x,
                w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-amd64 2.6 (amani) w/Intel compilers, w/default API=1.6.x,
                w/C++ & FORTRAN, in production mode
        Solaris/32 2.10 (linew) w/deprecated symbols disabled, w/C++ & FORTRAN,
                w/szip filter, w/threadsafe, in production mode
        Linux/PPC 2.6 (heiwa) w/C++ & FORTRAN, w/threadsafe, in debug mode
        Linux/64-ia64 2.6 (cobalt) w/Intel compilers, w/C++ & FORTRAN,
                in production mode
        Linux/64-amd64 2.6 (abe) w/parallel, w/FORTRAN, in debug mode
        Mac OS X/32 10.6.4 (amazon) in debug mode
        Mac OS X/32 10.6.4 (amazon) w/C++ & FORTRAN, w/threadsafe,
                in production mode
        Mac OS X/32 10.6.4 (amazon) w/parallel, in debug mode

5 files changed, 157 insertions, 17 deletions

diff --git a/config/cmake/CTestCustom.ctest b/config/cmake/CTestCustom.ctest
index c1538c0..acb1918 100755
--- a/config/cmake/CTestCustom.ctest
+++ b/config/cmake/CTestCustom.ctest
@@ -4,6 +4,7 @@ SET (CTEST_CUSTOM_WARNING_EXCEPTION
     ${CTEST_CUSTOM_WARNING_EXCEPTION}
     "H5detect.c.[0-9]+.[ ]*: warning C4090:"
     "testhdf5.h.[0-9]+.[ ]*: warning C4005:"
+    "POSIX name for this item is deprecated"
     "disabling jobserver mode"
 )
  
diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake
index 1318e90..b5b1170 100644
--- a/config/cmake/ConfigureChecks.cmake
+++ b/config/cmake/ConfigureChecks.cmake
@@ -35,6 +35,7 @@ OPTION (HDF5_Enable_Clear_File_Buffers "Securely clear file buffers before writi
 IF (HDF5_Enable_Clear_File_Buffers)
   SET (H5_CLEAR_MEMORY 1)
 ENDIF (HDF5_Enable_Clear_File_Buffers)
+MARK_AS_ADVANCED (HDF5_Enable_Clear_File_Buffers)
 
 #-----------------------------------------------------------------------------
 # Option for --enable-instrument
@@ -46,6 +47,7 @@ OPTION (HDF5_Enable_Instrument "Instrument The library" HDF5_Enable_Instrument)
 IF (HDF5_Enable_Instrument)
   SET (H5_HAVE_INSTRUMENTED_LIBRARY 1)
 ENDIF (HDF5_Enable_Instrument)
+MARK_AS_ADVANCED (HDF5_Enable_Instrument)
 
 #-----------------------------------------------------------------------------
 # Option for --enable-strict-format-checks
@@ -54,6 +56,7 @@ OPTION (HDF5_STRICT_FORMAT_CHECKS "Whether to perform strict file format checks"
 IF (HDF5_STRICT_FORMAT_CHECKS)
   SET (H5_STRICT_FORMAT_CHECKS 1)
 ENDIF (HDF5_STRICT_FORMAT_CHECKS)
+MARK_AS_ADVANCED (HDF5_STRICT_FORMAT_CHECKS)
 
 #-----------------------------------------------------------------------------
 # Option for --enable-metadata-trace-file
@@ -62,6 +65,7 @@ OPTION (HDF5_METADATA_TRACE_FILE "Enable metadata trace file collection" OFF)
 IF (HDF5_METADATA_TRACE_FILE)
   SET (H5_METADATA_TRACE_FILE 1)
 ENDIF (HDF5_METADATA_TRACE_FILE)
+MARK_AS_ADVANCED (HDF5_METADATA_TRACE_FILE)
 
 # ----------------------------------------------------------------------
 # Decide whether the data accuracy has higher priority during data
@@ -73,6 +77,7 @@ OPTION (HDF5_WANT_DATA_ACCURACY "IF data accuracy is guaranteed during data conv
 IF (HDF5_WANT_DATA_ACCURACY)
   SET (H5_WANT_DATA_ACCURACY 1)
 ENDIF(HDF5_WANT_DATA_ACCURACY)
+MARK_AS_ADVANCED (HDF5_WANT_DATA_ACCURACY)
 
 # ----------------------------------------------------------------------
 # Decide whether the presence of user's exception handling functions is
@@ -84,24 +89,16 @@ OPTION (HDF5_WANT_DCONV_EXCEPTION "exception handling functions is checked durin
 IF (HDF5_WANT_DCONV_EXCEPTION)
   SET (H5_WANT_DCONV_EXCEPTION 1)
 ENDIF (HDF5_WANT_DCONV_EXCEPTION)
+MARK_AS_ADVANCED (HDF5_WANT_DCONV_EXCEPTION)
 
-SET (LINUX_LFS 0)
-SET (HDF5_EXTRA_FLAGS)
-IF (CMAKE_SYSTEM MATCHES "Linux-([3-9]\\.[0-9]|2\\.[4-9])\\.")
-  # Linux Specific flags
-  ADD_DEFINITIONS (-D_POSIX_SOURCE -D_BSD_SOURCE)
-  OPTION (HDF5_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON)
-  IF (HDF5_ENABLE_LARGE_FILE)
-    SET (LARGEFILE 1)
-    SET (HDF5_EXTRA_FLAGS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE)
-    SET (CMAKE_REQUIRED_DEFINITIONS ${HDF5_EXTRA_FLAGS})
-  ENDIF (HDF5_ENABLE_LARGE_FILE)
-ENDIF (CMAKE_SYSTEM MATCHES "Linux-([3-9]\\.[0-9]|2\\.[4-9])\\.")
-IF (LINUX_LFS)
-  SET (HDF5_EXTRA_FLAGS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE)
-  SET (CMAKE_REQUIRED_DEFINITIONS ${HDF5_EXTRA_FLAGS})
-ENDIF (LINUX_LFS)
-ADD_DEFINITIONS (${HDF5_EXTRA_FLAGS})
+# ----------------------------------------------------------------------
+# Check if they would like the function stack support compiled in
+#
+OPTION (HDF5_ENABLE_CODESTACK "Enable the function stack tracing (for developer debugging)." OFF)
+IF (HDF5_ENABLE_CODESTACK)
+  SET (H5_HAVE_CODESTACK 1)
+ENDIF (HDF5_ENABLE_CODESTACK)
+MARK_AS_ADVANCED (HDF5_ENABLE_CODESTACK)
 
 #IF (WIN32)
 #  SET (DEFAULT_STREAM_VFD OFF)
@@ -253,6 +250,28 @@ IF (H5_HAVE_STDINT_H AND CMAKE_CXX_COMPILER_LOADED)
 ENDIF (H5_HAVE_STDINT_H AND CMAKE_CXX_COMPILER_LOADED)
 
 #-----------------------------------------------------------------------------
+#  Check for large file support
+#-----------------------------------------------------------------------------
+
+SET (LINUX_LFS 0)
+SET (HDF5_EXTRA_FLAGS)
+IF (CMAKE_SYSTEM MATCHES "Linux-([3-9]\\.[0-9]|2\\.[4-9])\\.")
+  # Linux Specific flags
+  ADD_DEFINITIONS (-D_POSIX_SOURCE -D_BSD_SOURCE)
+  OPTION (HDF5_ENABLE_LARGE_FILE "Enable support for large (64-bit) files on Linux." ON)
+  IF (HDF5_ENABLE_LARGE_FILE)
+    SET (LARGEFILE 1)
+    SET (HDF5_EXTRA_FLAGS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE)
+    SET (CMAKE_REQUIRED_DEFINITIONS ${HDF5_EXTRA_FLAGS})
+  ENDIF (HDF5_ENABLE_LARGE_FILE)
+ENDIF (CMAKE_SYSTEM MATCHES "Linux-([3-9]\\.[0-9]|2\\.[4-9])\\.")
+IF (LINUX_LFS)
+  SET (HDF5_EXTRA_FLAGS -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_LARGEFILE_SOURCE)
+  SET (CMAKE_REQUIRED_DEFINITIONS ${HDF5_EXTRA_FLAGS})
+ENDIF (LINUX_LFS)
+ADD_DEFINITIONS (${HDF5_EXTRA_FLAGS})
+
+#-----------------------------------------------------------------------------
 #  Check the size in bytes of all the int and float types
 #-----------------------------------------------------------------------------
 MACRO (H5_CHECK_TYPE_SIZE type var)
@@ -531,6 +550,18 @@ ELSE (WINDOWS)
 ENDIF (WINDOWS)
 
 #-----------------------------------------------------------------------------
+# Option to see if GPFS is available on this filesystem --enable-gpfs
+#-----------------------------------------------------------------------------
+OPTION (HDF5_ENABLE_GPFS "Enable GPFS hints for the MPI/POSIX file driver" OFF)
+IF (HDF5_ENABLE_GPFS)
+  CHECK_INCLUDE_FILE_CONCAT ("gpfs.h"        HAVE_GPFS)
+  IF (HAVE_GPFS)
+    HDF5_FUNCTION_TEST (HAVE_GPFS)  
+  ENDIF (HAVE_GPFS)
+ENDIF (HDF5_ENABLE_GPFS)
+MARK_AS_ADVANCED (HDF5_ENABLE_GPFS)
+
+#-----------------------------------------------------------------------------
 # Look for 64 bit file stream capability
 #-----------------------------------------------------------------------------
 IF (HAVE_OFF64_T)
diff --git a/config/cmake/HDF5Macros.cmake b/config/cmake/HDF5Macros.cmake
index 8b30fbf..99fbea1 100644
--- a/config/cmake/HDF5Macros.cmake
+++ b/config/cmake/HDF5Macros.cmake
@@ -120,3 +120,39 @@ MACRO (H5_SET_LIB_OPTIONS libtarget libname libtype)
 
 ENDMACRO (H5_SET_LIB_OPTIONS)
 
+#-------------------------------------------------------------------------------
+MACRO (TARGET_WIN_PROPERTIES target)
+  IF (WIN32)
+    IF (MSVC)
+      IF (NOT BUILD_SHARED_LIBS)
+        SET_TARGET_PROPERTIES (${target}
+            PROPERTIES
+                LINK_FLAGS "/NODEFAULTLIB:MSVCRT"
+        ) 
+      ENDIF (NOT BUILD_SHARED_LIBS)
+    ENDIF (MSVC)
+  ENDIF (WIN32)
+ENDMACRO (TARGET_WIN_PROPERTIES)
+
+#-------------------------------------------------------------------------------
+MACRO (TARGET_FORTRAN_WIN_PROPERTIES target)
+  IF (WIN32)
+    IF (BUILD_SHARED_LIBS)
+      IF (MSVC)
+        SET_TARGET_PROPERTIES (${target}
+            PROPERTIES
+                COMPILE_FLAGS "/dll"
+                LINK_FLAGS "/SUBSYSTEM:CONSOLE"
+        ) 
+      ENDIF (MSVC)
+    ELSE (BUILD_SHARED_LIBS)
+      IF (MSVC)
+        SET_TARGET_PROPERTIES (${target}
+            PROPERTIES
+                LINK_FLAGS "/NODEFAULTLIB:MSVCRT"
+        ) 
+      ENDIF (MSVC)
+    ENDIF (BUILD_SHARED_LIBS)
+  ENDIF (WIN32)
+ENDMACRO (TARGET_FORTRAN_WIN_PROPERTIES)
+
diff --git a/config/cmake/HDF5Tests.c b/config/cmake/HDF5Tests.c
index f909ed9..7fb5756 100644
--- a/config/cmake/HDF5Tests.c
+++ b/config/cmake/HDF5Tests.c
@@ -371,4 +371,15 @@ int main(int argc, char * argv)
 }
 #endif
 
+#ifdef HAVE_GPFS
+
+#include <gpfs.h>
+int main ()
+{
+    int fd = 0; 
+    gpfs_fcntl(fd, (void *)0);
+}
+
+#endif /* HAVE_GPFS */
+
 
diff --git a/config/cmake/grepTest.cmake b/config/cmake/grepTest.cmake
new file mode 100644
index 0000000..cc3a9b4
--- /dev/null
+++ b/config/cmake/grepTest.cmake
@@ -0,0 +1,61 @@
+# runTest.cmake executes a command and captures the output in a file. File is then compared
+# against a reference file. Exit status of command can also be compared.
+
+# arguments checking
+IF (NOT TEST_PROGRAM)
+  MESSAGE (FATAL_ERROR "Require TEST_PROGRAM to be defined")
+ENDIF (NOT TEST_PROGRAM)
+#IF (NOT TEST_ARGS)
+#  MESSAGE (STATUS "Require TEST_ARGS to be defined")
+#ENDIF (NOT TEST_ARGS)
+IF (NOT TEST_FOLDER)
+  MESSAGE ( FATAL_ERROR "Require TEST_FOLDER to be defined")
+ENDIF (NOT TEST_FOLDER)
+IF (NOT TEST_OUTPUT)
+  MESSAGE (FATAL_ERROR "Require TEST_OUTPUT to be defined")
+ENDIF (NOT TEST_OUTPUT)
+#IF (NOT TEST_EXPECT)
+#  MESSAGE (STATUS "Require TEST_EXPECT to be defined")
+#ENDIF (NOT TEST_EXPECT)
+IF (NOT TEST_FILTER)
+  MESSAGE (STATUS "Require TEST_FILTER to be defined")
+ENDIF (NOT TEST_FILTER)
+IF (NOT TEST_REFERENCE)
+  MESSAGE (FATAL_ERROR "Require TEST_REFERENCE to be defined")
+ENDIF (NOT TEST_REFERENCE)
+
+MESSAGE (STATUS "COMMAND: ${TEST_PROGRAM} ${TEST_ARGS}")
+
+# run the test program, capture the stdout/stderr and the result var
+EXECUTE_PROCESS (
+    COMMAND ${TEST_PROGRAM} ${TEST_ARGS}
+    WORKING_DIRECTORY ${TEST_FOLDER}
+    RESULT_VARIABLE TEST_RESULT
+    OUTPUT_FILE ${TEST_OUTPUT}
+    ERROR_FILE ${TEST_OUTPUT}.err
+    OUTPUT_VARIABLE TEST_ERROR
+    ERROR_VARIABLE TEST_ERROR
+)
+
+MESSAGE (STATUS "COMMAND Result: ${TEST_RESULT}")
+MESSAGE (STATUS "COMMAND Error: ${TEST_ERROR}")
+
+# now grep the output with the reference
+FILE (READ ${TEST_FOLDER}/${TEST_OUTPUT} TEST_STREAM)
+
+STRING(REGEX MATCH "${TEST_FILTER}" TEST_MATCH ${TEST_STREAM}) 
+IF (${TEST_EXPECT})
+  STRING(LENGTH "${TEST_MATCH}" TEST_RESULT) 
+  IF (NOT ${TEST_RESULT} STREQUAL "0")
+    MESSAGE (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did contain ${TEST_REFERENCE}")
+  ENDIF (NOT ${TEST_RESULT} STREQUAL "0")
+ELSE (${TEST_EXPECT})
+  STRING(COMPARE EQUAL "${TEST_REFERENCE}" "${TEST_MATCH}" TEST_RESULT) 
+  IF (${TEST_RESULT} STREQUAL "0")
+    MESSAGE (FATAL_ERROR "Failed: The output of ${TEST_PROGRAM} did not contain ${TEST_REFERENCE}")
+  ENDIF (${TEST_RESULT} STREQUAL "0")
+ENDIF (${TEST_EXPECT})
+
+# everything went fine...
+MESSAGE ("Passed: The output of ${TEST_PROGRAM} matched")
+