Sync 1.14 branch with develop (#3923)

* Fix build error on freebsd (#3883)

Fixes:

checking for config freebsd12.1... no
checking for config freebsd... found
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpicc' is GNU gcc-9.2.0
compiler '/home/svcpetsc/petsc-hash-pkgs/39f577/bin/mpif90' is GNU gfortran-9.2.0
stdout: .: cannot open ./config/classic-fflags: No such file or directory

* Correct CMake command and example packaging (#3888)

* Feat: Hashpin sensitive dependencies on GitHub Actions and enable Dependabot to update them monthly (#3892)

* feat: hashpin sensitive dependencies on GHAs

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

* feat: enable dependabot for monthly updates on GHA

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

---------

Signed-off-by: Diogo Teles Sant'Anna <diogoteles@google.com>

* Some changes to portal links when they could be found on docs.hdfgroup.org, and changed the helpdesk link to help.hdfgroup.org (#3893)

* Updated some portal links to go directly to docs.hdfgroup. 

* Fixed some portal and help desk links

* Add variable option syncing for examples (#3885)

* Add period(.) at the end of the sentence for consistency. (#3897)

* Remove redundant backslash character from comment. (#3899)

* Disable doxygen as errors for netcdf (#3900)

* disable building doxygen for netcdf test

* Doc versions (#3903)

* Added missing \since tags to H5D.

* Committing clang-format changes

* Fixed H5T version info.

* Committing clang-format changes

* Added missing version info to H5E.

* Committing clang-format changes

* Added version info to H5F public APIs.

* Committing clang-format changes

* Added missing H5Z public API version info.

* Added missing version info to H5G public APIs

* Added missing version info to H5I public API.

* Added missing version info to H5 public APIs

* Committing clang-format changes

* Added missing version info to H5P public APIs

* Added missing version info to H5R public APIs

* Fix comment error.

* Committing clang-format changes

---------

Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>

* Change Trouble Shooting to Troubleshooting (#3905)

* Implement optimized support for vector I/O in Subfiling VFD (#3896)

Vector I/O requests are now processed within a single
set of I/O call batches, rather than each I/O vector
entry (tuple constructed from the types, addrs, sizes
and bufs arrays) being processed individually. This allows I/O to be
more efficiently parallelized among the I/O concentrator processes
during large I/O requests.

* Fixed some calculations and add test cases for issues spotted from review

* Removed a variable that was compensating for previous miscalculations

* Add 'warning density' computation to the warnhist script (#3910)

* Add 'warning density' computation to the warnhist script, along with several
cleanups to it.   Add "--enable-show-all-warnings" configure (and CMake)
option to disable compiler diagnostic suppression (and therefore show all the
otherwise suppressed compiler diagnostics), disabled by default.  Clean up
a buncn of misc. warnings.

Signed-off-by: Quincey Koziol <qkoziol@amazon.com>

* Added H5Fdelete_f with test (#3912)

* New Fortran Examples added (#3916)

* added subfiling example

* Added filtered writes with no selection example

* Version and space corrections.

* Restore H5_VERSION definition in configure.ac.

* renamed defined H5_VERS* to avoid conflicts (#3926)

15 files changed, 82 insertions, 82 deletions

diff --git a/tools/libtest/CMakeLists.txt b/tools/libtest/CMakeLists.txt
index f6d8912..3578560 100644
--- a/tools/libtest/CMakeLists.txt
+++ b/tools/libtest/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_LIBTEST C)
 #-----------------------------------------------------------------------------
 add_executable (h5tools_test_utils ${HDF5_TOOLS_LIBTEST_SOURCE_DIR}/h5tools_test_utils.c)
 target_compile_options(h5tools_test_utils PRIVATE "${HDF5_CMAKE_C_FLAGS}")
-target_include_directories(h5tools_test_utils PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+target_include_directories(h5tools_test_utils PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
 if (BUILD_STATIC_LIBS)
   TARGET_C_PROPERTIES (h5tools_test_utils STATIC)
   target_link_libraries (h5tools_test_utils PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} ${HDF5_TEST_LIB_TARGET})
diff --git a/tools/src/h5copy/CMakeLists.txt b/tools/src/h5copy/CMakeLists.txt
index efd38cd..5b79a85 100644
--- a/tools/src/h5copy/CMakeLists.txt
+++ b/tools/src/h5copy/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5COPY C)
 # --------------------------------------------------------------------
 if (BUILD_STATIC_LIBS)
   add_executable (h5copy ${HDF5_TOOLS_SRC_H5COPY_SOURCE_DIR}/h5copy.c)
-  target_include_directories (h5copy PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5copy PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5copy PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5copy STATIC)
   target_link_libraries (h5copy PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -18,7 +18,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h5copy-shared ${HDF5_TOOLS_SRC_H5COPY_SOURCE_DIR}/h5copy.c)
-  target_include_directories (h5copy-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5copy-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5copy-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5copy-shared SHARED)
   target_link_libraries (h5copy-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
diff --git a/tools/src/h5diff/CMakeLists.txt b/tools/src/h5diff/CMakeLists.txt
index f01d1aa..8de7c61 100644
--- a/tools/src/h5diff/CMakeLists.txt
+++ b/tools/src/h5diff/CMakeLists.txt
@@ -10,7 +10,7 @@ if (BUILD_STATIC_LIBS)
       ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c
       ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.h
   )
-  target_include_directories (h5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5diff PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5diff PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   #target_compile_definitions (h5diff PRIVATE H5_TOOLS_DEBUG)
   TARGET_C_PROPERTIES (h5diff STATIC)
@@ -26,7 +26,7 @@ if (BUILD_SHARED_LIBS)
       ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_main.c
       ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.h
   )
-  target_include_directories (h5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5diff-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5diff-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   #target_compile_definitions (h5diff-shared PRIVATE H5_TOOLS_DEBUG)
   TARGET_C_PROPERTIES (h5diff-shared SHARED)
@@ -54,7 +54,7 @@ if (H5_HAVE_PARALLEL)
         ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c
         ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c
     )
-    target_include_directories (ph5diff PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+    target_include_directories (ph5diff PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
     target_compile_options(ph5diff PRIVATE "${HDF5_CMAKE_C_FLAGS}")
     TARGET_C_PROPERTIES (ph5diff STATIC)
     target_link_libraries (ph5diff PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>")
@@ -67,7 +67,7 @@ if (H5_HAVE_PARALLEL)
         ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/h5diff_common.c
         ${HDF5_TOOLS_SRC_H5DIFF_SOURCE_DIR}/ph5diff_main.c
     )
-    target_include_directories (ph5diff-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+    target_include_directories (ph5diff-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
     target_compile_options(ph5diff-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
     TARGET_C_PROPERTIES (ph5diff-shared SHARED)
     target_link_libraries (ph5diff-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET} "$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:MPI::MPI_C>")
diff --git a/tools/src/h5dump/CMakeLists.txt b/tools/src/h5dump/CMakeLists.txt
index f382020..3284949 100644
--- a/tools/src/h5dump/CMakeLists.txt
+++ b/tools/src/h5dump/CMakeLists.txt
@@ -15,7 +15,7 @@ if (BUILD_STATIC_LIBS)
       ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.h
       ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.h
   )
-  target_include_directories (h5dump PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5dump PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5dump PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5dump STATIC)
   target_link_libraries (h5dump PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -36,7 +36,7 @@ if (BUILD_SHARED_LIBS)
       ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_ddl.h
       ${HDF5_TOOLS_SRC_H5DUMP_SOURCE_DIR}/h5dump_xml.h
   )
-  target_include_directories (h5dump-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5dump-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5dump-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5dump-shared SHARED)
   target_link_libraries (h5dump-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
diff --git a/tools/src/h5format_convert/CMakeLists.txt b/tools/src/h5format_convert/CMakeLists.txt
index d1e2158..2a7e3cb 100644
--- a/tools/src/h5format_convert/CMakeLists.txt
+++ b/tools/src/h5format_convert/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5FC C)
 # --------------------------------------------------------------------
 if (BUILD_STATIC_LIBS)
   add_executable (h5format_convert ${HDF5_TOOLS_SRC_H5FC_SOURCE_DIR}/h5format_convert.c)
-  target_include_directories (h5format_convert PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5format_convert PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5format_convert PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5format_convert STATIC)
   target_link_libraries (h5format_convert PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -17,7 +17,7 @@ if (BUILD_STATIC_LIBS)
 endif ()
 if (BUILD_SHARED_LIBS)
   add_executable (h5format_convert-shared ${HDF5_TOOLS_SRC_H5FC_SOURCE_DIR}/h5format_convert.c)
-  target_include_directories (h5format_convert-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5format_convert-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5format_convert-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5format_convert-shared SHARED)
   target_link_libraries (h5format_convert-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
diff --git a/tools/src/h5import/CMakeLists.txt b/tools/src/h5import/CMakeLists.txt
index b2337cd..f8268a1 100644
--- a/tools/src/h5import/CMakeLists.txt
+++ b/tools/src/h5import/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5IMPORT C)
 # --------------------------------------------------------------------
 if (BUILD_STATIC_LIBS)
   add_executable (h5import ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.h)
-  target_include_directories (h5import PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5import PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5import STATIC)
   target_link_libraries (h5import PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
   #set_target_properties (h5import PROPERTIES COMPILE_DEFINITIONS H5DEBUGIMPORT)
@@ -18,7 +18,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h5import-shared ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.c ${HDF5_TOOLS_SRC_H5IMPORT_SOURCE_DIR}/h5import.h)
-  target_include_directories (h5import-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5import-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5import-shared SHARED)
   target_link_libraries (h5import-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
   #set_target_properties (h5import-shared PROPERTIES COMPILE_DEFINITIONS H5DEBUGIMPORT)
diff --git a/tools/src/h5import/h5import.c b/tools/src/h5import/h5import.c
index 2d3574a..663f68a 100644
--- a/tools/src/h5import/h5import.c
+++ b/tools/src/h5import/h5import.c
@@ -26,48 +26,48 @@
 #endif
 
 /* Local function declarations */
-static int gtoken(char *s);
-static int process(struct Options *opt);
-static int processConfigurationFile(char *infile, struct Input *in);
-static int mapKeywordToIndex(char *key);
-static int parsePathInfo(struct path_info *path, char *strm);
-static int parseDimensions(struct Input *in, char *strm);
-static int getInputSize(struct Input *in, int ival);
-static int getInputClass(struct Input *in, char *strm);
-static int getInputClassType(struct Input *in, char *strm);
-static int getInputByteOrder(struct Input *in, FILE *strm);
-static int InputClassStrToInt(char *temp);
-static int getRank(struct Input *in, FILE *strm);
-static int getDimensionSizes(struct Input *in, FILE *strm);
-static int getOutputSize(struct Input *in, FILE *strm);
-static int getOutputClass(struct Input *in, FILE *strm);
-static int OutputClassStrToInt(char *temp);
-static int getOutputArchitecture(struct Input *in, FILE *strm);
-static int OutputArchStrToInt(const char *temp);
-static int getOutputByteOrder(struct Input *in, FILE *strm);
-static int OutputByteOrderStrToInt(const char *temp);
-static int getChunkedDimensionSizes(struct Input *in, FILE *strm);
-static int getCompressionType(struct Input *in, FILE *strm);
-static int CompressionTypeStrToInt(char *temp);
-static int getCompressionParameter(struct Input *in, FILE *strm);
-static int getExternalFilename(struct Input *in, FILE *strm);
-static int getMaximumDimensionSizes(struct Input *in, FILE *strm);
-static int processDataFile(char *infile, struct Input *in, hid_t file_id);
-static int readIntegerData(FILE *strm, struct Input *in);
-static int readFloatData(FILE *strm, struct Input *in);
-static int allocateIntegerStorage(struct Input *in);
-static int allocateFloatStorage(struct Input *in);
-static int readUIntegerData(FILE *strm, struct Input *in);
-static int allocateUIntegerStorage(struct Input *in);
-static int validateConfigurationParameters(struct Input *in);
-static int processStrData(FILE *strm, struct Input *in, hid_t file_id);
-static int processStrHDFData(FILE *strm, struct Input *in, hid_t file_id);
-uint16_t   swap_uint16(uint16_t val);
-int16_t    swap_int16(int16_t val);
-uint32_t   swap_uint32(uint32_t val);
-int32_t    swap_int32(int32_t val);
-int64_t    swap_int64(int64_t val);
-uint64_t   swap_uint64(uint64_t val);
+static int             gtoken(char *s);
+static int             process(struct Options *opt);
+static int             processConfigurationFile(char *infile, struct Input *in);
+static int             mapKeywordToIndex(char *key);
+static int             parsePathInfo(struct path_info *path, char *strm);
+static int             parseDimensions(struct Input *in, char *strm);
+static int             getInputSize(struct Input *in, int ival);
+static int             getInputClass(struct Input *in, char *strm);
+static int             getInputClassType(struct Input *in, char *strm);
+static int             getInputByteOrder(struct Input *in, FILE *strm);
+static int             InputClassStrToInt(char *temp);
+static int             getRank(struct Input *in, FILE *strm);
+static int             getDimensionSizes(struct Input *in, FILE *strm);
+static int             getOutputSize(struct Input *in, FILE *strm);
+static int             getOutputClass(struct Input *in, FILE *strm);
+static int             OutputClassStrToInt(char *temp);
+static int             getOutputArchitecture(struct Input *in, FILE *strm);
+static int             OutputArchStrToInt(const char *temp);
+static int             getOutputByteOrder(struct Input *in, FILE *strm);
+static int             OutputByteOrderStrToInt(const char *temp);
+static int             getChunkedDimensionSizes(struct Input *in, FILE *strm);
+static int             getCompressionType(struct Input *in, FILE *strm);
+static int             CompressionTypeStrToInt(char *temp);
+static int             getCompressionParameter(struct Input *in, FILE *strm);
+static int             getExternalFilename(struct Input *in, FILE *strm);
+static int             getMaximumDimensionSizes(struct Input *in, FILE *strm);
+static int             processDataFile(char *infile, struct Input *in, hid_t file_id);
+static int             readIntegerData(FILE *strm, struct Input *in);
+static int             readFloatData(FILE *strm, struct Input *in);
+static int             allocateIntegerStorage(struct Input *in);
+static int             allocateFloatStorage(struct Input *in);
+static int             readUIntegerData(FILE *strm, struct Input *in);
+static int             allocateUIntegerStorage(struct Input *in);
+static int             validateConfigurationParameters(struct Input *in);
+static int             processStrData(FILE *strm, struct Input *in, hid_t file_id);
+static int             processStrHDFData(FILE *strm, struct Input *in, hid_t file_id);
+H5_ATTR_CONST uint16_t swap_uint16(uint16_t val);
+H5_ATTR_CONST int16_t  swap_int16(int16_t val);
+H5_ATTR_CONST uint32_t swap_uint32(uint32_t val);
+H5_ATTR_CONST int32_t  swap_int32(int32_t val);
+H5_ATTR_CONST int64_t  swap_int64(int64_t val);
+H5_ATTR_CONST uint64_t swap_uint64(uint64_t val);
 
 int
 main(int argc, char *argv[])
diff --git a/tools/src/h5jam/CMakeLists.txt b/tools/src/h5jam/CMakeLists.txt
index 8642d6f..7efd0d8 100644
--- a/tools/src/h5jam/CMakeLists.txt
+++ b/tools/src/h5jam/CMakeLists.txt
@@ -6,14 +6,14 @@ project (HDF5_TOOLS_SRC_H5JAM C)
 # --------------------------------------------------------------------
 if (BUILD_STATIC_LIBS)
   add_executable (h5jam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c)
-  target_include_directories (h5jam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5jam PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5jam STATIC)
   target_link_libraries (h5jam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
   set_target_properties (h5jam PROPERTIES FOLDER tools)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam")
 
   add_executable (h5unjam ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c)
-  target_include_directories (h5unjam PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5unjam PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5unjam STATIC)
   target_link_libraries (h5unjam PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
   set_target_properties (h5unjam PROPERTIES FOLDER tools)
@@ -27,14 +27,14 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h5jam-shared ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5jam.c)
-  target_include_directories (h5jam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5jam-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5jam-shared SHARED)
   target_link_libraries (h5jam-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
   set_target_properties (h5jam-shared PROPERTIES FOLDER tools)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5jam-shared")
 
   add_executable (h5unjam-shared ${HDF5_TOOLS_SRC_H5JAM_SOURCE_DIR}/h5unjam.c)
-  target_include_directories (h5unjam-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5unjam-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5unjam-shared SHARED)
   target_link_libraries (h5unjam-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
   set_target_properties (h5unjam-shared PROPERTIES FOLDER tools)
diff --git a/tools/src/h5ls/CMakeLists.txt b/tools/src/h5ls/CMakeLists.txt
index 9499253..67122a1 100644
--- a/tools/src/h5ls/CMakeLists.txt
+++ b/tools/src/h5ls/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5LS C)
 #-----------------------------------------------------------------------------
 if (BUILD_STATIC_LIBS)
   add_executable (h5ls ${HDF5_TOOLS_SRC_H5LS_SOURCE_DIR}/h5ls.c)
-  target_include_directories (h5ls PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5ls PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5ls PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   #target_compile_definitions(h5ls PRIVATE H5_TOOLS_DEBUG)
   TARGET_C_PROPERTIES (h5ls STATIC)
@@ -19,7 +19,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h5ls-shared ${HDF5_TOOLS_SRC_H5LS_SOURCE_DIR}/h5ls.c)
-  target_include_directories (h5ls-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5ls-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5ls-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   #target_compile_definitions(h5ls-shared PRIVATE H5_TOOLS_DEBUG)
   TARGET_C_PROPERTIES (h5ls-shared SHARED)
diff --git a/tools/src/h5repack/CMakeLists.txt b/tools/src/h5repack/CMakeLists.txt
index 360fb0f..ea1ee80 100644
--- a/tools/src/h5repack/CMakeLists.txt
+++ b/tools/src/h5repack/CMakeLists.txt
@@ -17,7 +17,7 @@ set (REPACK_COMMON_SOURCES
 
 if (BUILD_STATIC_LIBS)
   add_executable (h5repack ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c)
-  target_include_directories (h5repack PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5repack PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5repack PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5repack STATIC)
   target_link_libraries (h5repack PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -29,7 +29,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h5repack-shared ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR}/h5repack_main.c)
-  target_include_directories (h5repack-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5repack-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5repack-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5repack-shared SHARED)
   target_link_libraries (h5repack-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
diff --git a/tools/src/h5stat/CMakeLists.txt b/tools/src/h5stat/CMakeLists.txt
index c0c0b32..c3aef5f 100644
--- a/tools/src/h5stat/CMakeLists.txt
+++ b/tools/src/h5stat/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_SRC_H5STAT C)
 # --------------------------------------------------------------------
 if (BUILD_STATIC_LIBS)
   add_executable (h5stat ${HDF5_TOOLS_SRC_H5STAT_SOURCE_DIR}/h5stat.c)
-  target_include_directories (h5stat PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5stat PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5stat PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5stat STATIC)
   target_link_libraries (h5stat PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -18,7 +18,7 @@ endif ()
 
 if (BUILD_SHARED_LIBS)
   add_executable (h5stat-shared ${HDF5_TOOLS_SRC_H5STAT_SOURCE_DIR}/h5stat.c)
-  target_include_directories (h5stat-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5stat-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5stat-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5stat-shared SHARED)
   target_link_libraries (h5stat-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
diff --git a/tools/src/misc/CMakeLists.txt b/tools/src/misc/CMakeLists.txt
index d2b1f51..62bd443 100644
--- a/tools/src/misc/CMakeLists.txt
+++ b/tools/src/misc/CMakeLists.txt
@@ -7,7 +7,7 @@ project (HDF5_TOOLS_SRC_MISC C)
 #-- Misc Executables
 if (BUILD_STATIC_LIBS)
   add_executable (h5debug ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5debug.c)
-  target_include_directories (h5debug PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5debug PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5debug PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5debug STATIC)
   target_link_libraries (h5debug PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -15,7 +15,7 @@ if (BUILD_STATIC_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5debug")
 
   add_executable (h5repart ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5repart.c)
-  target_include_directories (h5repart PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5repart PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5repart PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5repart STATIC)
   target_link_libraries (h5repart PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -23,7 +23,7 @@ if (BUILD_STATIC_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repart")
 
   add_executable (h5mkgrp ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5mkgrp.c)
-  target_include_directories (h5mkgrp PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5mkgrp PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5mkgrp PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5mkgrp STATIC)
   target_link_libraries (h5mkgrp PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -31,7 +31,7 @@ if (BUILD_STATIC_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp")
 
   add_executable (h5clear ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5clear.c)
-  target_include_directories (h5clear PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5clear PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5clear PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5clear STATIC)
   target_link_libraries (h5clear PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -39,7 +39,7 @@ if (BUILD_STATIC_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5clear")
 
   add_executable (h5delete ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5delete.c)
-  target_include_directories (h5delete PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5delete PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5delete PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5delete STATIC)
   target_link_libraries (h5delete PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -56,7 +56,7 @@ if (BUILD_STATIC_LIBS)
 endif ()
 if (BUILD_SHARED_LIBS)
   add_executable (h5debug-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5debug.c)
-  target_include_directories (h5debug-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5debug-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5debug-shared SHARED)
   target_compile_options(h5debug-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   target_link_libraries (h5debug-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
@@ -64,7 +64,7 @@ if (BUILD_SHARED_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5debug-shared")
 
   add_executable (h5repart-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5repart.c)
-  target_include_directories (h5repart-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5repart-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5repart-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5repart-shared SHARED)
   target_link_libraries (h5repart-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
@@ -72,7 +72,7 @@ if (BUILD_SHARED_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5repart-shared")
 
   add_executable (h5mkgrp-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5mkgrp.c)
-  target_include_directories (h5mkgrp-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5mkgrp-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5mkgrp-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5mkgrp-shared SHARED)
   target_link_libraries (h5mkgrp-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
@@ -80,7 +80,7 @@ if (BUILD_SHARED_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5mkgrp-shared")
 
   add_executable (h5clear-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5clear.c)
-  target_include_directories (h5clear-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5clear-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5clear-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5clear-shared SHARED)
   target_link_libraries (h5clear-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
@@ -88,7 +88,7 @@ if (BUILD_SHARED_LIBS)
   set_global_variable (HDF5_UTILS_TO_EXPORT "${HDF5_UTILS_TO_EXPORT};h5clear-shared")
 
   add_executable (h5delete-shared ${HDF5_TOOLS_SRC_MISC_SOURCE_DIR}/h5delete.c)
-  target_include_directories (h5delete-shared PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5delete-shared PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   target_compile_options(h5delete-shared PRIVATE "${HDF5_CMAKE_C_FLAGS}")
   TARGET_C_PROPERTIES (h5delete-shared SHARED)
   target_link_libraries (h5delete-shared PRIVATE ${HDF5_TOOLS_LIBSH_TARGET} ${HDF5_LIBSH_TARGET})
diff --git a/tools/test/h5copy/CMakeTests.cmake b/tools/test/h5copy/CMakeTests.cmake
index fb02d81..b4daa87 100644
--- a/tools/test/h5copy/CMakeTests.cmake
+++ b/tools/test/h5copy/CMakeTests.cmake
@@ -163,8 +163,8 @@
         COMMAND ${CMAKE_CROSSCOMPILING_EMULATOR} $<TARGET_FILE:h5copy${tgt_file_ext}> -i ./testfiles/${infile} -o ./testfiles/${testname}.out.h5 -v -s ${psparam} -d ${pdparam}
     )
     set_tests_properties (H5COPY-${testname}-prefill PROPERTIES DEPENDS H5COPY-${testname}-clear-objects)
-    if ("" MATCHES "${HDF5_DISABLE_TESTS_REGEX}")
-      set_tests_properties ( PROPERTIES DISABLED true)
+    if ("H5COPY-${testname}-prefill" MATCHES "${HDF5_DISABLE_TESTS_REGEX}")
+      set_tests_properties (H5COPY-${testname}-prefill PROPERTIES DISABLED true)
     endif ()
 
     add_test (
diff --git a/tools/test/h5jam/CMakeLists.txt b/tools/test/h5jam/CMakeLists.txt
index 160ecdf..e6017fd 100644
--- a/tools/test/h5jam/CMakeLists.txt
+++ b/tools/test/h5jam/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_TEST_H5JAM C)
 # --------------------------------------------------------------------
 if (HDF5_BUILD_GENERATORS AND BUILD_STATIC_LIBS)
   add_executable (h5jamgentest ${HDF5_TOOLS_TEST_H5JAM_SOURCE_DIR}/h5jamgentest.c)
-  target_include_directories (h5jamgentest PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+  target_include_directories (h5jamgentest PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
   TARGET_C_PROPERTIES (h5jamgentest STATIC)
   target_link_libraries (h5jamgentest PRIVATE ${HDF5_LIB_TARGET})
   set_target_properties (h5jamgentest PROPERTIES FOLDER generator/tools)
@@ -22,7 +22,7 @@ if (HDF5_BUILD_GENERATORS AND BUILD_STATIC_LIBS)
 endif ()
 
 add_executable (getub ${HDF5_TOOLS_TEST_H5JAM_SOURCE_DIR}/getub.c)
-target_include_directories (getub PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+target_include_directories (getub PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
 if (BUILD_STATIC_LIBS)
   TARGET_C_PROPERTIES (getub STATIC)
   target_link_libraries (getub PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
@@ -33,7 +33,7 @@ endif ()
 set_target_properties (getub PROPERTIES FOLDER tools)
 
 add_executable (tellub ${HDF5_TOOLS_TEST_H5JAM_SOURCE_DIR}/tellub.c)
-target_include_directories (tellub PRIVATE "${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
+target_include_directories (tellub PRIVATE "${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
 if (BUILD_STATIC_LIBS)
   TARGET_C_PROPERTIES (tellub STATIC)
   target_link_libraries (tellub PRIVATE ${HDF5_TOOLS_LIB_TARGET} ${HDF5_LIB_TARGET})
diff --git a/tools/test/h5repack/CMakeLists.txt b/tools/test/h5repack/CMakeLists.txt
index 3e7c6c2..5c0075c 100644
--- a/tools/test/h5repack/CMakeLists.txt
+++ b/tools/test/h5repack/CMakeLists.txt
@@ -6,7 +6,7 @@ project (HDF5_TOOLS_TEST_H5REPACK C)
 # --------------------------------------------------------------------
 add_executable (testh5repack_detect_szip ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/testh5repack_detect_szip.c)
 target_include_directories (testh5repack_detect_szip
-    PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+    PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
 )
 if (BUILD_STATIC_LIBS)
   TARGET_C_PROPERTIES (testh5repack_detect_szip STATIC)
@@ -29,7 +29,7 @@ set (REPACK_COMMON_SOURCES
 )
 add_executable (h5repacktest ${REPACK_COMMON_SOURCES} ${HDF5_TOOLS_TEST_H5REPACK_SOURCE_DIR}/h5repacktst.c)
 target_include_directories (h5repacktest
-    PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_TEST_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
+    PRIVATE "${HDF5_TOOLS_SRC_H5REPACK_SOURCE_DIR};${HDF5_TOOLS_ROOT_DIR}/lib;${HDF5_SRC_INCLUDE_DIRS};${HDF5_TEST_SRC_DIR};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>"
 )
 if (BUILD_STATIC_LIBS)
   TARGET_C_PROPERTIES (h5repacktest STATIC)