Merge branch 'develop' of https://bitbucket.hdfgroup.org/scm/~bmribler/hdf5_bmr_CppAPI into develop

13 files changed, 415 insertions, 117 deletions

diff --git a/CTestConfig.cmake b/CTestConfig.cmake
index 45fa7d5..849d218 100644
--- a/CTestConfig.cmake
+++ b/CTestConfig.cmake
@@ -17,7 +17,7 @@ else (CDASH_LOCAL)
 endif (CDASH_LOCAL)
 set (CTEST_DROP_SITE_CDASH TRUE)
 
-set (UPDATE_TYPE svn)
+set (UPDATE_TYPE git)
 set (VALGRIND_COMMAND "/usr/bin/valgrind")
 set (VALGRIND_COMMAND_OPTIONS "-v --tool=memcheck --leak-check=full --track-fds=yes --num-callers=50 --show-reachable=yes --track-origins=yes --malloc-fill=0xff --free-fill=0xfe")
 set (CTEST_MEMORYCHECK_COMMAND "/usr/bin/valgrind")
diff --git a/config/cmake/FindJNI.cmake b/config/cmake/FindJNI.cmake
index 440a9889..9105f3d 100644
--- a/config/cmake/FindJNI.cmake
+++ b/config/cmake/FindJNI.cmake
@@ -63,7 +63,7 @@ macro(java_append_library_directories _var)
     elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(powerpc|ppc)64")
         set(_java_libarch "ppc64" "ppc")
     elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^(powerpc|ppc)")
-        set(_java_libarch "ppc")
+        set(_java_libarch "ppc" "ppc64")
     elseif(CMAKE_SYSTEM_PROCESSOR MATCHES "^sparc")
         # Both flavours can run on the same processor
         set(_java_libarch "${CMAKE_SYSTEM_PROCESSOR}" "sparc" "sparcv9")
@@ -92,10 +92,14 @@ macro(java_append_library_directories _var)
         if(_path MATCHES "{libarch}")
             foreach(_libarch ${_java_libarch})
                 string(REPLACE "{libarch}" "${_libarch}" _newpath "${_path}")
-                list(APPEND ${_var} "${_newpath}")
+                if(EXISTS ${_newpath})
+                    list(APPEND ${_var} "${_newpath}")
+                endif()
             endforeach()
         else()
-            list(APPEND ${_var} "${_path}")
+            if(EXISTS ${_path})
+                list(APPEND ${_var} "${_path}")
+            endif()
         endif()
     endforeach()
 endmacro()
@@ -161,6 +165,10 @@ JAVA_APPEND_LIBRARY_DIRECTORIES(JAVA_AWT_LIBRARY_DIRECTORIES
   /usr/lib/jvm/default-java/jre/lib/{libarch}
   /usr/lib/jvm/default-java/jre/lib
   /usr/lib/jvm/default-java/lib
+  # Ubuntu specific paths for default JVM
+  /usr/lib/jvm/java-8-openjdk-{libarch}/jre/lib/{libarch}     # Ubuntu 15.10
+  /usr/lib/jvm/java-7-openjdk-{libarch}/jre/lib/{libarch}     # Ubuntu 15.10
+  /usr/lib/jvm/java-6-openjdk-{libarch}/jre/lib/{libarch}     # Ubuntu 15.10
   # OpenBSD specific paths for default JVM
   /usr/local/jdk-1.7.0/jre/lib/{libarch}
   /usr/local/jre-1.7.0/lib/{libarch}
@@ -191,6 +199,9 @@ list(APPEND JAVA_AWT_INCLUDE_DIRECTORIES
   "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.4;JavaHome]/include"
   "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\1.3;JavaHome]/include"
   "[HKEY_LOCAL_MACHINE\\SOFTWARE\\JavaSoft\\Java Development Kit\\${java_install_version};JavaHome]/include"
+)
+
+JAVA_APPEND_LIBRARY_DIRECTORIES(JAVA_AWT_INCLUDE_DIRECTORIES
   ${_JAVA_HOME}/include
   /usr/include
   /usr/java/include
@@ -209,6 +220,9 @@ list(APPEND JAVA_AWT_INCLUDE_DIRECTORIES
   /usr/lib/jvm/java-7-openjdk-amd64/include
   /usr/lib64/jvm/java-7-openjdk/include
   /usr/lib64/jvm/java-7-openjdk-amd64/include
+  /usr/lib/jvm/java-8-openjdk-{libarch}/include  # ubuntu 15.10
+  /usr/lib/jvm/java-7-openjdk-{libarch}/include  # ubuntu 15.10
+  /usr/lib/jvm/java-6-openjdk-{libarch}/include  # ubuntu 15.10
   /usr/local/share/java/include
   /usr/lib/j2sdk1.4-sun/include
   /usr/lib/j2sdk1.5-sun/include
@@ -290,7 +304,8 @@ find_path(JAVA_INCLUDE_PATH jni.h
   ${JAVA_AWT_INCLUDE_DIRECTORIES}
 )
 
-find_path(JAVA_INCLUDE_PATH2 jni_md.h
+find_path(JAVA_INCLUDE_PATH2 NAMES jni_md.h jniport.h
+  PATHS
   ${JAVA_INCLUDE_PATH}
   ${JAVA_INCLUDE_PATH}/darwin
   ${JAVA_INCLUDE_PATH}/win32
@@ -300,6 +315,7 @@ find_path(JAVA_INCLUDE_PATH2 jni_md.h
   ${JAVA_INCLUDE_PATH}/solaris
   ${JAVA_INCLUDE_PATH}/hp-ux
   ${JAVA_INCLUDE_PATH}/alpha
+  ${JAVA_INCLUDE_PATH}/aix
 )
 
 find_path(JAVA_AWT_INCLUDE_PATH jawt.h
@@ -316,8 +332,11 @@ endif()
 
 #include(${CMAKE_CURRENT_LIST_DIR}/FindPackageHandleStandardArgs.cmake)
 INCLUDE (FindPackageHandleStandardArgs)
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(JNI  DEFAULT_MSG  JAVA_AWT_LIBRARY JAVA_JVM_LIBRARY
-                                                    JAVA_INCLUDE_PATH  JAVA_INCLUDE_PATH2 JAVA_AWT_INCLUDE_PATH)
+FIND_PACKAGE_HANDLE_STANDARD_ARGS(JNI  DEFAULT_MSG  JAVA_AWT_LIBRARY
+                                                    JAVA_JVM_LIBRARY
+                                                    JAVA_INCLUDE_PATH
+                                                    JAVA_INCLUDE_PATH2
+                                                    JAVA_AWT_INCLUDE_PATH)
 
 mark_as_advanced(
   JAVA_AWT_LIBRARY
diff --git a/config/cmake/HDF518_Examples.cmake.in b/config/cmake/HDF518_Examples.cmake.in
index 561bdb7..efabbe6 100644
--- a/config/cmake/HDF518_Examples.cmake.in
+++ b/config/cmake/HDF518_Examples.cmake.in
@@ -45,6 +45,18 @@ if(NOT DEFINED FORTRAN_LIBRARIES)
 else(NOT DEFINED FORTRAN_LIBRARIES)
     set(FORTRANLIBRARIES "YES")
 endif()
+if(NOT DEFINED HDF_LOCAL)
+    set(CDASH_LOCAL "NO")
+else(NOT HDF_LOCAL)
+    set(CDASH_LOCAL "YES")
+endif()
+if(NOT DEFINED CTEST_SITE)
+    set(CTEST_SITE "local")
+endif()
+if(NOT DEFINED CTEST_BUILD_NAME)
+    set(CTEST_BUILD_NAME "examples")
+endif()
+set(BUILD_OPTIONS "${BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDNAME:STRING=${CTEST_BUILD_NAME}")
 
 #TAR_SOURCE - name of tarfile
 #if(NOT DEFINED TAR_SOURCE)
@@ -77,6 +89,9 @@ if(${FORTRANLIBRARIES})
 else()
   set(ADD_BUILD_OPTIONS "${ADD_BUILD_OPTIONS} -DHDF_BUILD_FORTRAN:BOOL=OFF")
 endif()
+if(${CDASH_LOCAL})
+  set(BUILD_OPTIONS "${BUILD_OPTIONS} -DCDASH_LOCAL:BOOL=ON")
+endif()
 set(BUILD_OPTIONS "${BUILD_OPTIONS} -DHDF5_PACKAGE_NAME:STRING=@HDF5_PACKAGE@@HDF_PACKAGE_EXT@")
 
 ###############################################################################################################
diff --git a/config/cmake/HDF5_Examples.cmake.in b/config/cmake/HDF5_Examples.cmake.in
index d7e2591..8ea6d18 100644
--- a/config/cmake/HDF5_Examples.cmake.in
+++ b/config/cmake/HDF5_Examples.cmake.in
@@ -51,6 +51,18 @@ if(NOT DEFINED JAVA_LIBRARIES)
 else(NOT DEFINED JAVA_LIBRARIES)
     set(JAVALIBRARIES "YES")
 endif()
+if(NOT DEFINED HDF_LOCAL)
+    set(CDASH_LOCAL "NO")
+else(NOT HDF_LOCAL)
+    set(CDASH_LOCAL "YES")
+endif()
+if(NOT DEFINED CTEST_SITE)
+    set(CTEST_SITE "local")
+endif()
+if(NOT DEFINED CTEST_BUILD_NAME)
+    set(CTEST_BUILD_NAME "examples")
+endif()
+set(BUILD_OPTIONS "${BUILD_OPTIONS} -DSITE:STRING=${CTEST_SITE} -DBUILDNAME:STRING=${CTEST_BUILD_NAME}")
 
 #TAR_SOURCE - name of tarfile
 #if(NOT DEFINED TAR_SOURCE)
@@ -88,6 +100,9 @@ if(${JAVALIBRARIES})
 else()
   set(BUILD_OPTIONS "${BUILD_OPTIONS} -DHDF_BUILD_JAVA:BOOL=OFF")
 endif()
+if(${CDASH_LOCAL})
+  set(BUILD_OPTIONS "${BUILD_OPTIONS} -DCDASH_LOCAL:BOOL=ON")
+endif()
 set(BUILD_OPTIONS "${BUILD_OPTIONS} -DHDF5_PACKAGE_NAME:STRING=@HDF5_PACKAGE@@HDF_PACKAGE_EXT@")
 
 ###############################################################################################################
diff --git a/config/cmake/UseJava.cmake b/config/cmake/UseJava.cmake
index 9b2b1e0..4f8e4c8 100644
--- a/config/cmake/UseJava.cmake
+++ b/config/cmake/UseJava.cmake
@@ -169,7 +169,7 @@
 #
 # ::
 #
-#    The add_jar() functions sets some target properties. You can get these
+#    The add_jar() function sets some target properties. You can get these
 #    properties with the
 #       get_property(TARGET <target_name> PROPERTY <propery_name>)
 #    command.
@@ -217,6 +217,19 @@
 # This command installs the TARGET_NAME files to the given DESTINATION.
 # It should be called in the same scope as add_jar() or it will fail.
 #
+# Target Properties:
+#
+# ::
+#
+#    The install_jar() function sets the INSTALL_DESTINATION target property
+#    on jars so installed. This property holds the DESTINATION as described
+#    above, and is used by install_jar_exports(). You can get this property
+#    with the
+#       get_property(TARGET <target_name> PROPERTY INSTALL_DESTINATION)
+#    command.
+#
+#
+#
 # ::
 #
 #  install_jni_symlink(target_name destination)
@@ -228,6 +241,24 @@
 #
 # ::
 #
+#  install_jar_exports(TARGETS jar1 [jar2 ...]
+#                      FILE export_filename
+#                      DESTINATION destination [COMPONENT component])
+#
+# This command installs a target export file export_filename for the named jar
+# targets to the given DESTINATION. Its function is similar to that of
+# install(EXPORTS).
+#
+# ::
+#
+#  export_jars(TARGETS jar1 [jar2 ...]
+#              FILE export_filename)
+#
+# This command writes a target export file export_filename for the named jar
+# targets. Its function is similar to that of export().
+#
+# ::
+#
 #  create_javadoc(<VAR>
 #                 PACKAGES pkg1 [pkg2 ...]
 #                 [SOURCEPATH <sourcepath>]
@@ -324,7 +355,7 @@
 # that allow your Java and C code to interact.
 #
 # There are two main signatures for create_javah.  The first signature
-# returns generated files throught variable specified by GENERATED_FILES option:
+# returns generated files through variable specified by GENERATED_FILES option:
 #
 # ::
 #
@@ -389,14 +420,36 @@ include(CMakeParseArguments)
 function (__java_copy_file src dest comment)
     add_custom_command(
         OUTPUT  ${dest}
-        COMMAND cmake -E copy_if_different
+        COMMAND ${CMAKE_COMMAND} -E copy_if_different
         ARGS    ${src}
                 ${dest}
         DEPENDS ${src}
         COMMENT ${comment})
 endfunction ()
 
+function(__java_lcat VAR)
+    foreach(_line ${ARGN})
+        set(${VAR} "${${VAR}}${_line}\n")
+    endforeach()
+
+    set(${VAR} "${${VAR}}" PARENT_SCOPE)
+endfunction()
+
+function(__java_export_jar VAR TARGET PATH)
+    get_target_property(_jarpath ${TARGET} JAR_FILE)
+    get_filename_component(_jarname ${_jarpath} NAME)
+    __java_lcat(${VAR}
+      "# Create imported target ${TARGET}"
+      "add_custom_target(${TARGET})"
+      "set_target_properties(${TARGET} PROPERTIES"
+      "  JAR_FILE \"${PATH}/${_jarname}\")"
+      ""
+    )
+    set(${VAR} "${${VAR}}" PARENT_SCOPE)
+endfunction()
+
 # define helper scripts
+set(_JAVA_EXPORT_TARGETS_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/javaTargets.cmake.in)
 set(_JAVA_CLASS_FILELIST_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/UseJavaClassFilelist.cmake)
 set(_JAVA_SYMLINK_SCRIPT ${CMAKE_CURRENT_LIST_DIR}/UseJavaSymlinks.cmake)
 
@@ -435,6 +488,8 @@ function(add_jar _TARGET_NAME)
 
     if (NOT DEFINED _add_jar_OUTPUT_DIR)
         set(_add_jar_OUTPUT_DIR ${CMAKE_CURRENT_BINARY_DIR})
+    else()
+        get_filename_component(_add_jar_OUTPUT_DIR ${_add_jar_OUTPUT_DIR} ABSOLUTE)
     endif()
 
     if (_add_jar_ENTRY_POINT)
@@ -554,11 +609,6 @@ function(add_jar _TARGET_NAME)
         endif ()
     endforeach()
 
-    # create an empty java_class_filelist
-    if (NOT EXISTS ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist)
-        file(WRITE ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist "")
-    endif()
-
     if (_JAVA_COMPILE_FILES OR _JAVA_COMPILE_FILELISTS)
         set (_JAVA_SOURCES_FILELISTS)
 
@@ -598,6 +648,11 @@ function(add_jar _TARGET_NAME)
             DEPENDS ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_compiled_${_TARGET_NAME}
             WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
         )
+    else ()
+        # create an empty java_class_filelist
+        if (NOT EXISTS ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist)
+            file(WRITE ${CMAKE_JAVA_CLASS_OUTPUT_PATH}/java_class_filelist "")
+        endif()
     endif ()
 
     # create the jar file
@@ -716,6 +771,13 @@ function(INSTALL_JAR _TARGET_NAME)
         PROPERTY
             INSTALL_FILES
     )
+    set_property(
+        TARGET
+            ${_TARGET_NAME}
+        PROPERTY
+            INSTALL_DESTINATION
+            ${_DESTINATION}
+    )
 
     if (__FILES)
         install(
@@ -1348,3 +1410,94 @@ function (create_javah)
       set (${_create_javah_GENERATED_FILES} ${_output_files} PARENT_SCOPE)
     endif()
 endfunction()
+
+function(export_jars)
+    # Parse and validate arguments
+    cmake_parse_arguments(_export_jars
+      ""
+      "FILE"
+      "TARGETS"
+      ${ARGN}
+    )
+    if (NOT _export_jars_FILE)
+      message(SEND_ERROR "export_jars: FILE must be specified.")
+    endif()
+    if (NOT _export_jars_TARGETS)
+      message(SEND_ERROR "export_jars: TARGETS must be specified.")
+    endif()
+
+    # Set content of generated exports file
+    string(REPLACE ";" " " __targets__ "${_export_jars_TARGETS}")
+    set(__targetdefs__ "")
+    foreach(_target ${_export_jars_TARGETS})
+        get_target_property(_jarpath ${_target} JAR_FILE)
+        get_filename_component(_jarpath ${_jarpath} PATH)
+        __java_export_jar(__targetdefs__ ${_target} "${_jarpath}")
+    endforeach()
+
+    # Generate exports file
+    configure_file(
+      ${_JAVA_EXPORT_TARGETS_SCRIPT}
+      ${_export_jars_FILE}
+      @ONLY
+    )
+endfunction()
+
+function(install_jar_exports)
+    # Parse and validate arguments
+    cmake_parse_arguments(_install_jar_exports
+      ""
+      "FILE;DESTINATION;COMPONENT"
+      "TARGETS"
+      ${ARGN}
+    )
+    if (NOT _install_jar_exports_FILE)
+      message(SEND_ERROR "install_jar_exports: FILE must be specified.")
+    endif()
+    if (NOT _install_jar_exports_DESTINATION)
+      message(SEND_ERROR "install_jar_exports: DESTINATION must be specified.")
+    endif()
+    if (NOT _install_jar_exports_TARGETS)
+      message(SEND_ERROR "install_jar_exports: TARGETS must be specified.")
+    endif()
+
+    if (_install_jar_exports_COMPONENT)
+      set (_COMPONENT COMPONENT ${_install_jar_exports_COMPONENT})
+    endif()
+
+    # Determine relative path from installed export file to install prefix
+    if(IS_ABSOLUTE ${_install_jar_exports_DESTINATION})
+      file(RELATIVE_PATH _relpath
+        ${_install_jar_exports_DESTINATION}
+        ${CMAKE_INSTALL_PREFIX}
+      )
+    else()
+      file(RELATIVE_PATH _relpath
+        ${CMAKE_INSTALL_PREFIX}/${_install_jar_exports_DESTINATION}
+        ${CMAKE_INSTALL_PREFIX}
+      )
+    endif()
+
+    # Set up unique location for generated exports file
+    string(SHA256 _hash "${_install_jar_exports_DESTINATION}")
+    set(_tmpdir ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/JavaExports/${_hash})
+
+    # Set content of generated exports file
+    string(REPLACE ";" " " __targets__ "${_install_jar_exports_TARGETS}")
+    set(__targetdefs__ "set(_prefix \${CMAKE_CURRENT_LIST_DIR}/${_relpath})\n\n")
+    foreach(_target ${_install_jar_exports_TARGETS})
+        get_target_property(_dir ${_target} INSTALL_DESTINATION)
+        __java_export_jar(__targetdefs__ ${_target} "\${_prefix}/${_dir}")
+    endforeach()
+    __java_lcat(__targetdefs__ "\nunset(_prefix)")
+
+    # Generate and install exports file
+    configure_file(
+      ${_JAVA_EXPORT_TARGETS_SCRIPT}
+      ${_tmpdir}/${_install_jar_exports_FILE}
+      @ONLY
+    )
+    install(FILES ${_tmpdir}/${_install_jar_exports_FILE}
+            DESTINATION ${_install_jar_exports_DESTINATION}
+            ${_COMPONENT})
+endfunction()
diff --git a/config/cmake_ext_mod/FindMPI.cmake b/config/cmake_ext_mod/FindMPI.cmake
index 1c9a2e3..80d8511 100644
--- a/config/cmake_ext_mod/FindMPI.cmake
+++ b/config/cmake_ext_mod/FindMPI.cmake
@@ -11,7 +11,8 @@
 # of them have somewhat different include paths, libraries to link
 # against, etc., and this module tries to smooth out those differences.
 #
-# === Variables ===
+# Variables
+# ^^^^^^^^^
 #
 # This module will set the following variables per language in your
 # project, where <lang> is one of C, CXX, or Fortran:
@@ -37,11 +38,12 @@
 #                               before the executable to run.
 #    MPIEXEC_POSTFLAGS          Flags to pass to MPIEXEC after other flags
 #
-# === Usage ===
+# Usage
+# ^^^^^
 #
 # To use this module, simply call FindMPI from a CMakeLists.txt file, or
-# run find_package(MPI), then run CMake.  If you are happy with the
-# auto- detected configuration for your language, then you're done.  If
+# run ``find_package(MPI)``, then run CMake.  If you are happy with the
+# auto-detected configuration for your language, then you're done.  If
 # not, you have two options:
 #
 # ::
@@ -55,24 +57,25 @@
 #       listed above, but these two are required.  This will circumvent
 #       autodetection entirely.
 #
-# When configuration is successful, MPI_<lang>_COMPILER will be set to
-# the compiler wrapper for <lang>, if it was found.  MPI_<lang>_FOUND
+# When configuration is successful, ``MPI_<lang>_COMPILER`` will be set to
+# the compiler wrapper for <lang>, if it was found.  ``MPI_<lang>_FOUND``
 # and other variables above will be set if any MPI implementation was
 # found for <lang>, regardless of whether a compiler was found.
 #
-# When using MPIEXEC to execute MPI applications, you should typically
-# use all of the MPIEXEC flags as follows:
+# When using ``MPIEXEC`` to execute MPI applications, you should typically
+# use all of the ``MPIEXEC`` flags as follows:
 #
 # ::
 #
 #    ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} PROCS
 #      ${MPIEXEC_PREFLAGS} EXECUTABLE ${MPIEXEC_POSTFLAGS} ARGS
 #
-# where PROCS is the number of processors on which to execute the
-# program, EXECUTABLE is the MPI program, and ARGS are the arguments to
+# where ``PROCS`` is the number of processors on which to execute the
+# program, ``EXECUTABLE`` is the MPI program, and ``ARGS`` are the arguments to
 # pass to the MPI program.
 #
-# === Backward Compatibility ===
+# Backward Compatibility
+# ^^^^^^^^^^^^^^^^^^^^^^
 #
 # For backward compatibility with older versions of FindMPI, these
 # variables are set, but deprecated:
@@ -83,7 +86,7 @@
 #    MPI_COMPILE_FLAGS   MPI_INCLUDE_PATH    MPI_EXTRA_LIBRARY
 #    MPI_LINK_FLAGS      MPI_LIBRARIES
 #
-# In new projects, please use the MPI_<lang>_XXX equivalents.
+# In new projects, please use the ``MPI_<lang>_XXX`` equivalents.
 
 #=============================================================================
 # Copyright 2001-2011 Kitware, Inc.
@@ -204,7 +207,7 @@ function (_mpi_check_compiler compiler options cmdvar resvar)
   # Intel MPI 5.0.1 will return a zero return code even when the
   # argument to the MPI compiler wrapper is unknown.  Attempt to
   # catch this case.
-  if("${cmdline}" MATCHES "undefined reference")
+  if(cmdline MATCHES "undefined reference" OR cmdline MATCHES "unrecognized")
     set(success 255 )
   endif()
   set(${cmdvar} "${cmdline}" PARENT_SCOPE)
@@ -325,7 +328,7 @@ function (interrogate_mpi_compiler lang try_libs)
 
         foreach(FLAG ${MPI_ALL_COMPILE_FLAGS})
           if (MPI_COMPILE_FLAGS_WORK)
-            set(MPI_COMPILE_FLAGS_WORK "${MPI_COMPILE_FLAGS_WORK} ${FLAG}")
+            string(APPEND MPI_COMPILE_FLAGS_WORK " ${FLAG}")
           else()
             set(MPI_COMPILE_FLAGS_WORK ${FLAG})
           endif()
@@ -355,10 +358,10 @@ function (interrogate_mpi_compiler lang try_libs)
         endif()
 
         # Extract linker paths from the link command line
-        string(REGEX MATCHALL "(^| |-Wl,)-L([^\" ]+|\"[^\"]+\")" MPI_ALL_LINK_PATHS "${MPI_LINK_CMDLINE}")
+        string(REGEX MATCHALL "(^| |-Wl,)(-L|/LIBPATH:)([^\" ]+|\"[^\"]+\")" MPI_ALL_LINK_PATHS "${MPI_LINK_CMDLINE}")
         set(MPI_LINK_PATH)
         foreach(LPATH ${MPI_ALL_LINK_PATHS})
-          string(REGEX REPLACE "^(| |-Wl,)-L" "" LPATH ${LPATH})
+          string(REGEX REPLACE "^(| |-Wl,)(-L|/LIBPATH:)" "" LPATH ${LPATH})
           string(REPLACE "//" "/" LPATH ${LPATH})
           list(APPEND MPI_LINK_PATH ${LPATH})
         endforeach()
@@ -374,7 +377,7 @@ function (interrogate_mpi_compiler lang try_libs)
         set(MPI_LINK_FLAGS_WORK)
         foreach(FLAG ${MPI_ALL_LINK_FLAGS})
           if (MPI_LINK_FLAGS_WORK)
-            set(MPI_LINK_FLAGS_WORK "${MPI_LINK_FLAGS_WORK} ${FLAG}")
+            string(APPEND MPI_LINK_FLAGS_WORK " ${FLAG}")
           else()
             set(MPI_LINK_FLAGS_WORK ${FLAG})
           endif()
@@ -383,20 +386,31 @@ function (interrogate_mpi_compiler lang try_libs)
         # Extract the set of libraries to link against from the link command
         # line
         string(REGEX MATCHALL "(^| )-l([^\" ]+|\"[^\"]+\")" MPI_LIBNAMES "${MPI_LINK_CMDLINE}")
+        if(WIN32)
+          # The intel wrappers on windows link against static versions of the MPI libraries.
+          # The static libraries are simply listed on the command line without -l.
+          # For instance: " icl ... impi.lib "
+          string(REGEX MATCHALL "(^| )([^\" ]+)\\.lib" tmp "${MPI_LINK_CMDLINE}")
+          list(APPEND MPI_LIBNAMES ${tmp})
+        endif()
 
         # add the compiler implicit directories because some compilers
         # such as the intel compiler have libraries that show up
         # in the showme list that can only be found in the implicit
         # link directories of the compiler.
         if (DEFINED CMAKE_${lang}_IMPLICIT_LINK_DIRECTORIES)
-          set(MPI_LINK_PATH
-            "${MPI_LINK_PATH};${CMAKE_${lang}_IMPLICIT_LINK_DIRECTORIES}")
+          string(APPEND MPI_LINK_PATH
+            ";${CMAKE_${lang}_IMPLICIT_LINK_DIRECTORIES}")
         endif ()
 
         # Determine full path names for all of the libraries that one needs
         # to link against in an MPI program
         foreach(LIB ${MPI_LIBNAMES})
           string(REGEX REPLACE "^ ?-l" "" LIB ${LIB})
+          if(WIN32)
+            string(REGEX REPLACE "\\.lib$" "" LIB ${LIB})
+          endif()
+          string(STRIP ${LIB} LIB)
           # MPI_LIB is cached by find_library, but we don't want that.  Clear it first.
           set(MPI_LIB "MPI_LIB-NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
           find_library(MPI_LIB NAMES ${LIB} HINTS ${MPI_LINK_PATH})
@@ -597,14 +611,13 @@ foreach (lang C CXX Fortran)
   if (CMAKE_${lang}_COMPILER_WORKS)
     # If the user supplies a compiler *name* instead of an absolute path, assume that we need to find THAT compiler.
     if (MPI_${lang}_COMPILER)
-      is_file_executable(MPI_${lang}_COMPILER MPI_COMPILER_IS_EXECUTABLE)
-      if (NOT MPI_COMPILER_IS_EXECUTABLE)
+      if (NOT IS_ABSOLUTE "${MPI_${lang}_COMPILER}")
         # Get rid of our default list of names and just search for the name the user wants.
         set(_MPI_${lang}_COMPILER_NAMES ${MPI_${lang}_COMPILER})
         set(MPI_${lang}_COMPILER "MPI_${lang}_COMPILER-NOTFOUND" CACHE FILEPATH "Cleared" FORCE)
-        # If the user specifies a compiler, we don't want to try to search libraries either.
-        set(try_libs FALSE)
       endif()
+      # If the user specifies a compiler, we don't want to try to search libraries either.
+      set(try_libs FALSE)
     else()
       set(try_libs TRUE)
     endif()
diff --git a/fortran/src/CMakeLists.txt b/fortran/src/CMakeLists.txt
index ea38c58..d4ca791 100644
--- a/fortran/src/CMakeLists.txt
+++ b/fortran/src/CMakeLists.txt
@@ -65,6 +65,7 @@ set_target_properties (H5_buildiface PROPERTIES
 )
 
 if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  file (MAKE_DIRECTORY "${HDF5_F90_BINARY_DIR}/shared")
   if (WIN32)
     set (MODSH_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/shared/\${BUILD_TYPE})
   else (WIN32)
@@ -92,6 +93,8 @@ add_custom_command (
     WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}
     DEPENDS H5match_types
 )
+set_source_files_properties (${HDF5_F90_BINARY_DIR}/H5f90i_gen.h PROPERTIES GENERATED TRUE)
+set_source_files_properties (${HDF5_F90_BINARY_DIR}/H5fortran_types.F90 PROPERTIES GENERATED TRUE)
 
 #-----------------------------------------------------------------------------
 # f90CStub lib
@@ -114,7 +117,6 @@ set (f90CStub_C_SOURCES
     ${HDF5_F90_SRC_SOURCE_DIR}/H5Tf.c
     ${HDF5_F90_SRC_SOURCE_DIR}/H5Zf.c
 )
-
 set_source_files_properties (${f90CStub_C_SOURCES} PROPERTIES LANGUAGE C)
 
 set (f90CStub_C_HDRS
@@ -150,15 +152,43 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
   set (install_targets ${install_targets} ${HDF5_F90_C_LIBSH_TARGET})
 endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
-set_source_files_properties (${HDF5_F90_BINARY_DIR}/H5_gen.F90 PROPERTIES GENERATED TRUE)
-
 #-----------------------------------------------------------------------------
 # Fortran Modules
 #-----------------------------------------------------------------------------
-set (f90_F_BASE_SOURCES
-    # generated files
-    ${HDF5_F90_BINARY_DIR}/H5fortran_types.F90
+set (f90_F_GEN_SOURCES
+    ${HDF5_F90_SRC_SOURCE_DIR}/H5Aff.F90
+    ${HDF5_F90_SRC_SOURCE_DIR}/H5Dff.F90
+    ${HDF5_F90_SRC_SOURCE_DIR}/H5Pff.F90
+)
+set (CMD $<TARGET_FILE:H5_buildiface>)
+add_custom_command (
+    OUTPUT ${HDF5_F90_BINARY_DIR}/H5_gen.F90
+    COMMAND ${CMD}
+    WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}
+    DEPENDS ${f90_F_GEN_SOURCES}
+    COMMENT "Generating the H5_gen.F90 file"
+)
+add_custom_target (H5gen ALL
+    DEPENDS ${HDF5_F90_BINARY_DIR}/H5_gen.F90
+)
+set_source_files_properties (${HDF5_F90_BINARY_DIR}/H5_gen.F90 PROPERTIES GENERATED TRUE)
 
+if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  set (CMDSH $<TARGET_FILE:H5_buildiface>)
+  add_custom_command (
+      OUTPUT ${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90
+      COMMAND ${CMDSH}
+      WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}/shared
+      DEPENDS ${f90_F_GEN_SOURCES}
+      COMMENT "Generating the H5_gen.F90 shared file"
+  )
+  add_custom_target (H5genSH ALL
+      DEPENDS ${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90
+  )
+  set_source_files_properties (${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90 PROPERTIES GENERATED TRUE)
+endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+
+set (f90_F_BASE_SOURCES
     # normal distribution
     ${HDF5_F90_SRC_SOURCE_DIR}/H5f90global.F90
     ${HDF5_F90_SRC_SOURCE_DIR}/H5fortkit.F90
@@ -179,6 +209,9 @@ set (f90_F_BASE_SOURCES
 )
 
 set (f90_F_SOURCES
+    # generated file
+    ${HDF5_F90_BINARY_DIR}/H5fortran_types.F90
+
     ${f90_F_BASE_SOURCES}
 
     # generated file
@@ -187,16 +220,20 @@ set (f90_F_SOURCES
     # normal distribution
     ${HDF5_F90_SRC_SOURCE_DIR}/HDF5.F90
 )
+if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  set (f90_F_SOURCES_SHARED
+      # generated file
+      ${HDF5_F90_BINARY_DIR}/H5fortran_types.F90
 
-set (CMD $<TARGET_FILE:H5_buildiface>)
-add_custom_target (H5gen ALL
-    COMMAND ${CMD}
-#v3.2    BYPRODUCT ${HDF5_F90_BINARY_DIR}/H5_gen.F90
-    WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}
-    DEPENDS ${f90_F_BASE_SOURCES}
-)
+      ${f90_F_BASE_SOURCES}
+
+     # generated file
+      ${HDF5_F90_BINARY_DIR}/shared/H5_gen.F90
 
-set_source_files_properties (${f90_F_SOURCES} PROPERTIES LANGUAGE Fortran)
+      # normal distribution
+      ${HDF5_F90_SRC_SOURCE_DIR}/HDF5.F90
+  )
+endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
 #-----------------------------------------------------------------------------
 # Add Main fortran library
@@ -222,9 +259,10 @@ if (WIN32)
   )
 endif (WIN32)
 set (install_targets ${install_targets} ${HDF5_F90_LIB_TARGET})
+add_dependencies(${HDF5_F90_LIB_TARGET} H5gen)
 
 if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
-  add_library (${HDF5_F90_LIBSH_TARGET} SHARED ${f90_F_SOURCES})
+  add_library (${HDF5_F90_LIBSH_TARGET} SHARED ${f90_F_SOURCES_SHARED})
   set (SHARED_LINK_FLAGS " ")
   if (WIN32 AND MSVC)
     set (SHARED_LINK_FLAGS "/DLL /DEF:${HDF5_F90_SRC_BINARY_DIR}/hdf5_fortrandll.def")
@@ -250,6 +288,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
     )
   endif (WIN32)
   set (install_targets ${install_targets} ${HDF5_F90_LIBSH_TARGET})
+  add_dependencies(${HDF5_F90_LIBSH_TARGET} H5genSH)
 endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
 #-----------------------------------------------------------------------------
diff --git a/fortran/test/CMakeLists.txt b/fortran/test/CMakeLists.txt
index d1ca6e8..219f937 100644
--- a/fortran/test/CMakeLists.txt
+++ b/fortran/test/CMakeLists.txt
@@ -32,13 +32,19 @@ set_target_properties (H5_test_buildiface PROPERTIES
     Fortran_MODULE_DIRECTORY ${CMAKE_Fortran_MODULE_DIRECTORY}
 )
 
-if (NOT SKIP_HDF5_FORTRAN_SHARED)
+if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  file (MAKE_DIRECTORY "${HDF5_F90_BINARY_DIR}/shared")
   if (WIN32)
-    set (MOD_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/static/\${BUILD_TYPE})
+    set (MODSH_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/shared/\${BUILD_TYPE})
   else (WIN32)
-    set (MOD_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/static)
+    set (MODSH_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/shared)
   endif (WIN32)
-endif (NOT SKIP_HDF5_FORTRAN_SHARED)
+endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+if (WIN32)
+  set (MOD_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/static/\${BUILD_TYPE})
+else (WIN32)
+  set (MOD_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/static)
+endif (WIN32)
 
 INCLUDE_DIRECTORIES (${CMAKE_Fortran_MODULE_DIRECTORY} ${MOD_BUILD_DIR})
 
@@ -75,29 +81,54 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
   )
 endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
-set (HDF5_F90_TF_SOURCES
-     # generated files
-     ${HDF5_F90_BINARY_DIR}/tf_gen.F90
-)
-set_source_files_properties (
-    ${HDF5_F90_BINARY_DIR}/tf_gen.F90
-    PROPERTIES GENERATED TRUE
-)
-set_source_files_properties (tf.F90 ${HDF5_F90_BINARY_DIR}/${HDF5_F90_TF_SOURCES} PROPERTIES LANGUAGE Fortran)
-
 set (CMD $<TARGET_FILE:H5_test_buildiface>)
-add_custom_target (H5testgen ALL
+add_custom_command (
+    OUTPUT ${HDF5_F90_BINARY_DIR}/tf_gen.F90
     COMMAND ${CMD}
-#v3.2    BYPRODUCT ${HDF5_F90_BINARY_DIR}/tf_gen.F90
     WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}
     DEPENDS H5_test_buildiface
+    COMMENT "Generating the tf_gen.F90 file"
 )
+add_custom_target (H5testgen ALL
+    DEPENDS ${HDF5_F90_BINARY_DIR}/tf_gen.F90
+)
+set_source_files_properties (${HDF5_F90_BINARY_DIR}/tf_gen.F90 PROPERTIES GENERATED TRUE)
 
-add_library (${HDF5_F90_TEST_LIB_TARGET} STATIC tf.F90 ${HDF5_F90_TF_SOURCES})
 if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
-   add_library (${HDF5_F90_TEST_LIBSH_TARGET} SHARED tf.F90 ${HDF5_F90_TF_SOURCES})
+  set (CMDSH $<TARGET_FILE:H5_test_buildiface>)
+  add_custom_command (
+      OUTPUT ${HDF5_F90_BINARY_DIR}/shared/tf_gen.F90
+      COMMAND ${CMDSH}
+      WORKING_DIRECTORY ${HDF5_F90_BINARY_DIR}/shared
+      DEPENDS H5_test_buildiface
+      COMMENT "Generating the tf_gen.F90 shared file"
+  )
+  add_custom_target (H5testgenSH ALL
+      DEPENDS ${HDF5_F90_BINARY_DIR}/shared/tf_gen.F90
+  )
+  set_source_files_properties (${HDF5_F90_BINARY_DIR}/shared/tf_gen.F90 PROPERTIES GENERATED TRUE)
+endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+
+set (HDF5_F90_TF_SOURCES
+    # generated files
+    ${HDF5_F90_BINARY_DIR}/tf_gen.F90
+
+    # normal distribution
+    tf.F90
+)
+set_source_files_properties (${HDF5_F90_TF_SOURCES} PROPERTIES LANGUAGE Fortran)
+if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  set (HDF5_F90_TF_SOURCES_SHARED
+      # generated file
+      ${HDF5_F90_BINARY_DIR}/shared/tf_gen.F90
+
+      # normal distribution
+      tf.F90
+  )
+  set_source_files_properties (${HDF5_F90_TF_SOURCES_SHARED} PROPERTIES LANGUAGE Fortran)
 endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
+add_library (${HDF5_F90_TEST_LIB_TARGET} STATIC ${HDF5_F90_TF_SOURCES})
 TARGET_FORTRAN_PROPERTIES (${HDF5_F90_TEST_LIB_TARGET} STATIC " " " ")
 target_link_libraries (${HDF5_F90_TEST_LIB_TARGET}
     ${HDF5_F90_C_TEST_LIB_TARGET}
@@ -117,7 +148,10 @@ if (WIN32)
         COMPILE_DEFINITIONS "HDF5F90_WINDOWS"
     )
 endif (WIN32)
+add_dependencies(${HDF5_F90_TEST_LIB_TARGET} H5testgen)
+
 if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  add_library (${HDF5_F90_TEST_LIBSH_TARGET} SHARED ${HDF5_F90_TF_SOURCES_SHARED})
   set (SHARED_LINK_FLAGS " ")
   if (WIN32 AND MSVC)
     set (SHARED_LINK_FLAGS "/DLL")
@@ -143,6 +177,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
         COMPILE_DEFINITIONS "BUILD_HDF5_TEST_DLL;HDF5F90_WINDOWS"
     )
   endif (WIN32)
+  add_dependencies(${HDF5_F90_TEST_LIBSH_TARGET} H5testgenSH)
 endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
 #-----------------------------------------------------------------------------
@@ -327,6 +362,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
   if (WIN32 AND MSVC)
     target_link_libraries (fortranlib_test_F03-shared "ws2_32.lib")
   endif (WIN32 AND MSVC)
+
   target_include_directories (fortranlib_test_F03-shared PRIVATE ${CMAKE_Fortran_MODULE_DIRECTORY}/shared)
   set_target_properties (fortranlib_test_F03-shared PROPERTIES
       LINKER_LANGUAGE Fortran
diff --git a/hl/fortran/src/CMakeLists.txt b/hl/fortran/src/CMakeLists.txt
index 6419ab8..774aa7c 100644
--- a/hl/fortran/src/CMakeLists.txt
+++ b/hl/fortran/src/CMakeLists.txt
@@ -37,6 +37,7 @@ set_target_properties (H5HL_buildiface PROPERTIES
 )
 
 if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  file (MAKE_DIRECTORY "${HDF5_HL_F90_SRC_BINARY_DIR}/shared")
   if (WIN32)
     set (MODSH_BUILD_DIR ${CMAKE_Fortran_MODULE_DIRECTORY}/shared/\${BUILD_TYPE})
   else (WIN32)
@@ -111,30 +112,61 @@ set (HDF5_HL_F90_F_BASE_SOURCES
     ${HDF5_HL_F90_SRC_SOURCE_DIR}/H5LTff.F90
     ${HDF5_HL_F90_SRC_SOURCE_DIR}/H5IMff.F90
 )
-set (HDF5_HL_F90_F_SOURCES
-     ${HDF5_HL_F90_F_BASE_SOURCES}
 
-     # generated files
-     ${HDF5_HL_F90_SRC_BINARY_DIR}/H5LTff_gen.F90
-     ${HDF5_HL_F90_SRC_BINARY_DIR}/H5TBff_gen.F90
+set (CMD $<TARGET_FILE:H5HL_buildiface>)
+add_custom_command (
+    OUTPUT ${HDF5_HL_F90_SRC_BINARY_DIR}/H5LTff_gen.F90 ${HDF5_HL_F90_SRC_BINARY_DIR}/H5TBff_gen.F90
+    COMMAND ${CMD}
+    WORKING_DIRECTORY ${HDF5_HL_F90_SRC_BINARY_DIR}
+    DEPENDS ${HDF5_HL_F90_F_BASE_SOURCES}
+    COMMENT "Generating the H5LTff_gen.F90, H5TBff_gen.F90 files"
+)
+add_custom_target (H5HLgen ALL
+    DEPENDS ${HDF5_HL_F90_SRC_BINARY_DIR}/H5LTff_gen.F90 ${HDF5_HL_F90_SRC_BINARY_DIR}/H5TBff_gen.F90
 )
-
-set_source_files_properties (${HDF5_HL_F90_F_SOURCES} PROPERTIES LANGUAGE Fortran)
-
 set_source_files_properties (
     ${HDF5_HL_F90_SRC_BINARY_DIR}/H5LTff_gen.F90
     ${HDF5_HL_F90_SRC_BINARY_DIR}/H5TBff_gen.F90
     PROPERTIES GENERATED TRUE
 )
+if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  set (CMDSH $<TARGET_FILE:H5HL_buildiface>)
+  add_custom_command (
+      OUTPUT ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5LTff_gen.F90 ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5TBff_gen.F90
+      COMMAND ${CMD}
+      WORKING_DIRECTORY ${HDF5_HL_F90_SRC_BINARY_DIR}/shared
+      DEPENDS ${HDF5_HL_F90_F_BASE_SOURCES}
+      COMMENT "Generating the H5LTff_gen.F90, H5TBff_gen.F90 shared files"
+  )
+  add_custom_target (H5HLgenSH ALL
+      DEPENDS ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5LTff_gen.F90 ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5TBff_gen.F90
+  )
+  set_source_files_properties (
+      ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5LTff_gen.F90
+      ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5TBff_gen.F90
+      PROPERTIES GENERATED TRUE
+  )
+endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
-set (CMD $<TARGET_FILE:H5HL_buildiface>)
-add_custom_target (H5HLgen ALL
-    COMMAND ${CMD}
-#v3.2    BYPRODUCT ${HDF5_HL_F90_SRC_BINARY_DIR}/H5LTff_gen.F90
-#v3.2              ${HDF5_HL_F90_SRC_BINARY_DIR}/H5TBff_gen.F90
-    WORKING_DIRECTORY ${HDF5_HL_F90_SRC_BINARY_DIR}
-    DEPENDS ${HDF5_HL_F90_F_BASE_SOURCES}
+set (HDF5_HL_F90_F_SOURCES
+    ${HDF5_HL_F90_F_BASE_SOURCES}
+
+    # generated files
+    ${HDF5_HL_F90_SRC_BINARY_DIR}/H5LTff_gen.F90
+    ${HDF5_HL_F90_SRC_BINARY_DIR}/H5TBff_gen.F90
 )
+set_source_files_properties (${HDF5_HL_F90_F_SOURCES} PROPERTIES LANGUAGE Fortran)
+
+if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
+  set (HDF5_HL_F90_F_SOURCES_SHARED
+      ${HDF5_HL_F90_F_BASE_SOURCES}
+
+      # generated files
+      ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5LTff_gen.F90
+      ${HDF5_HL_F90_SRC_BINARY_DIR}/shared/H5TBff_gen.F90
+  )
+  set_source_files_properties (${HDF5_HL_F90_F_SOURCES_SHARED} PROPERTIES LANGUAGE Fortran)
+endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
 add_library (${HDF5_HL_F90_LIB_TARGET} STATIC ${HDF5_HL_F90_F_SOURCES})
 TARGET_FORTRAN_PROPERTIES (${HDF5_HL_F90_LIB_TARGET} STATIC " " " ")
@@ -153,9 +185,10 @@ if (WIN32)
   )
 endif (WIN32)
 set (install_targets ${install_targets} ${HDF5_HL_F90_LIB_TARGET})
+add_dependencies(${HDF5_HL_F90_LIB_TARGET} H5HLgen)
 
 if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
-  add_library (${HDF5_HL_F90_LIBSH_TARGET} SHARED ${HDF5_HL_F90_F_SOURCES})
+  add_library (${HDF5_HL_F90_LIBSH_TARGET} SHARED ${HDF5_HL_F90_F_SOURCES_SHARED})
   set (SHARED_LINK_FLAGS " ")
   if (WIN32 AND MSVC)
     set (SHARED_LINK_FLAGS "/DLL /DEF:${HDF5_HL_F90_SRC_BINARY_DIR}/hdf5_hl_fortrandll.def")
@@ -177,6 +210,7 @@ if (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
     )
   endif (WIN32)
   set (install_targets ${install_targets} ${HDF5_HL_F90_LIBSH_TARGET})
+  add_dependencies(${HDF5_HL_F90_LIBSH_TARGET} H5HLgenSH)
 endif (BUILD_SHARED_LIBS AND NOT SKIP_HDF5_FORTRAN_SHARED)
 
 #-----------------------------------------------------------------------------
diff --git a/java/src/jni/h5pImp.c b/java/src/jni/h5pImp.c
index ad79733..7c71da1 100644
--- a/java/src/jni/h5pImp.c
+++ b/java/src/jni/h5pImp.c
@@ -4947,7 +4947,6 @@ H5P_cls_create_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
         cls = CBENVPTR->GetObjectClass(CBENVPAR create_callback);
@@ -4972,7 +4971,6 @@ H5P_cls_copy_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
         cls = CBENVPTR->GetObjectClass(CBENVPAR copy_callback);
@@ -4995,7 +4993,6 @@ H5P_cls_close_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
         cls = CBENVPTR->GetObjectClass(CBENVPAR close_callback);
@@ -5019,7 +5016,6 @@ H5D_append_cb
     jclass     cls;
     jmethodID  mid;
     jlongArray cur_dimsArray;
-    jsize      size;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
         JVMPTR->DetachCurrentThread(JVMPAR);
@@ -5135,7 +5131,6 @@ H5P_prp_create_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
     jstring    str;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
@@ -5160,7 +5155,6 @@ H5P_prp_copy_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
     jstring    str;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
@@ -5185,7 +5179,6 @@ H5P_prp_close_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
     jstring    str;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
@@ -5210,7 +5203,6 @@ H5P_prp_compare_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
         cls = CBENVPTR->GetObjectClass(CBENVPAR compare_callback);
@@ -5233,7 +5225,6 @@ H5P_prp_get_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
     jstring    str;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
@@ -5258,7 +5249,6 @@ H5P_prp_set_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
     jstring    str;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
@@ -5283,7 +5273,6 @@ H5P_prp_delete_cb
     jint       status = -1;
     jclass     cls;
     jmethodID  mid;
-    jmethodID  constructor;
     jstring    str;
 
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) == 0) {
@@ -5472,7 +5461,6 @@ H5P_iterate_cb
     jclass     cls;
     jmethodID  mid;
     jstring    str;
-    jmethodID  constructor;
 
     /* fprintf(stderr, "\nJNI H5P_iterate_cb entered\n"); fflush(stderr); */
     if(JVMPTR->AttachCurrentThread(JVMPAR2 (void**)&cbenv, NULL) != 0) {
diff --git a/java/src/jni/h5util.c b/java/src/jni/h5util.c
index acf57c8..0d2999a 100644
--- a/java/src/jni/h5util.c
+++ b/java/src/jni/h5util.c
@@ -181,7 +181,6 @@ h5str_sprintf
     char           *this_str;
     size_t          this_strlen;
     int             n;
-    int             len;
     hvl_t          *vlptr;
     char           *cptr = (char*) ptr;
     unsigned char  *ucptr = (unsigned char*) ptr;
@@ -522,7 +521,6 @@ h5str_print_region_data_blocks
     hsize_t     *count = NULL;
     hsize_t      blkndx;
     hsize_t      total_size[H5S_MAX_RANK];
-    unsigned int region_flags; /* buffer extent flags */
     hsize_t      numelem;
     hsize_t      numindex;
     size_t       jndx;
@@ -622,7 +620,6 @@ h5str_dump_region_blocks_data
     hsize_t   *ptdata;
     hid_t      dtype = -1;
     hid_t      type_id = -1;
-    char       tmp_str[256];
     int        ndims = H5Sget_simple_extent_ndims(region);
 
     /*
@@ -634,8 +631,6 @@ h5str_dump_region_blocks_data
 
     /* Print block information */
     if (nblocks > 0) {
-        int i;
-
         alloc_size = (hsize_t)nblocks * (hsize_t)ndims * 2 * (hsize_t)sizeof(ptdata[0]);
         if (alloc_size == (hsize_t)((size_t) alloc_size)) {
             ptdata = (hsize_t *)HDmalloc((size_t) alloc_size);
@@ -745,13 +740,10 @@ h5str_print_region_data_points
     hsize_t        *dims1 = NULL;
     hsize_t         total_size[H5S_MAX_RANK];
     size_t          jndx;
-    unsigned        indx;
     size_t          type_size;
     int             ret_value = SUCCEED;
-    unsigned int    region_flags; /* buffer extent flags */
     hid_t           mem_space = -1;
     void           *region_buf = NULL;
-    char            tmp_str[256];
 
     /* Allocate space for the dimension array */
     if((dims1 = (hsize_t *)HDmalloc(sizeof(hsize_t) * (size_t)ndims)) != NULL) {
@@ -810,7 +802,6 @@ h5str_dump_region_points_data
     hssize_t   npoints;
     hsize_t    alloc_size;
     hsize_t   *ptdata;
-    char       tmp_str[256];
     hid_t      dtype = -1;
     hid_t      type_id = -1;
     int        ndims = H5Sget_simple_extent_ndims(region);
@@ -824,8 +815,6 @@ h5str_dump_region_points_data
 
     /* Print point information */
     if (npoints > 0) {
-        int i;
-
         alloc_size = (hsize_t)npoints * (hsize_t)ndims * (hsize_t)sizeof(ptdata[0]);
         if (alloc_size == (hsize_t)((size_t) alloc_size)) {
             ptdata = (hsize_t *)HDmalloc((size_t) alloc_size);
@@ -1297,7 +1286,7 @@ h5str_render_bin_output
                 case H5T_ARRAY:
                 {
                     int     k, ndims;
-                    hsize_t i, dims[H5S_MAX_RANK], temp_nelmts, nelmts;
+                    hsize_t dims[H5S_MAX_RANK], temp_nelmts, nelmts;
                     hid_t   memb;
 
                     /* get the array's base datatype for each element */
@@ -1325,7 +1314,6 @@ h5str_render_bin_output
                 break;
                 case H5T_VLEN:
                 {
-                    unsigned int i;
                     hsize_t      nelmts;
                     hid_t        memb;
 
@@ -1416,7 +1404,6 @@ render_bin_output_region_data_blocks
     hsize_t     *start = NULL;
     hsize_t     *count = NULL;
     hsize_t      numelem;
-    hsize_t      numindex;
     hsize_t      total_size[H5S_MAX_RANK];
     int          jndx;
     size_t       type_size;
@@ -1587,7 +1574,6 @@ render_bin_output_region_data_points
         hid_t container, int ndims, hid_t type_id, hssize_t npoints, hsize_t *ptdata)
 {
     hsize_t *dims1 = NULL;
-    int      jndx;
     size_t   type_size;
     hid_t    mem_space = -1;
     void    *region_buf = NULL;
@@ -1705,7 +1691,6 @@ h5str_dump_simple_dset
     int                 ndims;
     int                 carry;                    /* counter carry value */
     hsize_t             zero[8];                  /* vector of zeros */
-    unsigned int        flags;                    /* buffer extent flags */
     hsize_t             total_size[H5S_MAX_RANK]; /* total size of dataset*/
 
     /* Print info */
@@ -1862,7 +1847,6 @@ h5tools_dump_simple_data
     int                line_count;
     unsigned char     *mem  = (unsigned char*)_mem;
     size_t             size;   /* datum size */
-    H5T_class_t        type_class;
     hsize_t            i;         /*element counter  */
     h5str_t            buffer;    /*string into which to render */
 
diff --git a/tools/h5ls/CMakeTests.cmake b/tools/h5ls/CMakeTests.cmake
index 009ea79..2367df8 100644
--- a/tools/h5ls/CMakeTests.cmake
+++ b/tools/h5ls/CMakeTests.cmake
@@ -258,6 +258,7 @@
           tvldtypes2be.out
           tvldtypes2be.out.err
     )
+    set_tests_properties (H5LS-clearall-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles")
     if (NOT "${last_test}" STREQUAL "")
       set_tests_properties (H5LS-clearall-objects PROPERTIES DEPENDS ${last_test})
     endif (NOT "${last_test}" STREQUAL "")
diff --git a/tools/h5ls/CMakeTestsVDS.cmake b/tools/h5ls/CMakeTestsVDS.cmake
index 0d08774..e6c216d 100644
--- a/tools/h5ls/CMakeTestsVDS.cmake
+++ b/tools/h5ls/CMakeTestsVDS.cmake
@@ -73,7 +73,7 @@
       add_test (
           NAME H5LS-${resultfile}-clear-objects
           COMMAND    ${CMAKE_COMMAND}
-              -E remove ./testfiles/${resultfile}.out ./testfiles/vds/${resultfile}.out.err
+              -E remove ./testfiles/vds/${resultfile}.out ./testfiles/vds/${resultfile}.out.err
       )
       add_test (
           NAME H5LS-${resultfile}
@@ -127,6 +127,7 @@
           tvds_layout-5.out
           tvds_layout-5.out.err
     )
+    set_tests_properties (H5LS_VDS-clearall-objects PROPERTIES WORKING_DIRECTORY "${PROJECT_BINARY_DIR}/testfiles/vds")
     if (NOT "${last_test}" STREQUAL "")
       set_tests_properties (H5LS_VDS-clearall-objects PROPERTIES DEPENDS ${last_test})
     endif (NOT "${last_test}" STREQUAL "")