Sync 1.14 branch with develop (#3887)

* Preserve MPI-I/O file hints when fapl is closed (#3755)

* Fix for issue #3025: Save the MPI info in the file struct so H5Fget_access_plist() can retrieve it from there.

* Add compression tests for subfiling (#3769)

* Fix typo in comment (#3775)

* Fixed a file handle leak in the core VFD (#3779)

When opening a file with the core VFD and a file image, if the file
already exists, the file check would leak the POSIX file handle.

Fixes GitHub issue #635

* Fix a format string warning in the C++ examples (#3776)

* Cancel running GitHub workflows on push to same PR (#3772)

* Cancel running GitHub workflows on push to same PR

* Remove github.sha from workflow concurrency groups

* Print some messages in parallel tests on MPI rank 0 only (#3785)

Avoids overly verbose output from all processes emitting progress, etc. info.

* Avoid attempted use of NULL pointer in parallel compression code (#3786)

The parallel compression test code tests for the case where all MPI ranks have no selection in a dataset when writing to it. Add an early exit to the code to avoid attempting to use a NULL pointer due to there being no work to do.

* Don't install h5tools_test_utils test program on system (#3793)

* Add Doxygen to H5FDsplitter.h (#3794)

* H5FD_CURR_SPLITTER_VFD_CONFIG_VERSION
* H5FD_SPLITTER_PATH_MAX
* H5FD_SPLITTER_MAGIC
* H5FD_splitter_vfd_config_t
* H5Pset_fapl_splitter()
* H5Pget_fapl_splitter()

* Update Doxygen initializers & identifiers in VFDs (#3795)

* Add Doxygen for all H5FD_<VFD> initializers
* Add Doxygen for all H5FD_<VFD>_VALUE values
* Mark H5FD_<vfd>_init() calls private in Doxygen

* Fix memory corruption in 'MPI I/O FAPL preserve' test (#3806)

* Fix usage of h5_clean_files in t_pflush2.c (#3807)

* Fix parallel driver check in h5_fixname_real (#3808)

* Fix a couple usages of MPI_Info_get (#3809)

* Remove H5system.c warning on Windows oneAPI. (#3812)

* Add processing of NVHPC flags in linux-gnulibc1 file (#3804)

* Disable testing as tests are failing the same as in CMake

* Use the current toolchain for examples as default (#3810)

* Fix misc. warnings from GCC when compiling with -fsanitize=undefined (#3787)

* Set NVHPC maximum optimization level to -O1 for now (#3800)

* Set NVHPC maximum optimization level to -O1 for now

Compiling HDF5 with NVHPC 23.5 - 23.9 results in test failures in
4 different test files that need to be resolved. Since those tests
pass with an optimization level of -O1 (and -O0) and it is currently
unclear whether the test failures are due to issues in HDF5 or issues
in the 'nvc' compiler, set the maximum optimization level for NVHPC
to -O1 until the test failures are resolved.

* Disable nvhpc Java testing in CMake and amend known issues

* Re-enable testing of Autotools nvhpc

* Update some doxygen links to local refs (#3814)

* Rework MPI Info FAPL preserve PR to use VFD 'ctl' operations (#3782)

* Removed the use of C wrappers from H5P APIs. (#3824)

* fix seg fault on frontier/cray

* fix seg fault on frontier/cray

* fix seg fault on frontier/cray

* removed the use of h5pclose_c

* removed the use of h5pclose_c

* Fortran Wrappers H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f (#3801)

* Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f

* Added H5VLnative_addr_to_token_f and H5VLnative_token_to_address_f tests

* Create test for H5Pget_dxpl_mpio (#3825)

* Create test and add to testphdf5

* Renamed h5fuse.sh to h5fuse (#3834)

* provide an alternative to mapfile for older bash

* Disable FP exceptions in H5T init code (#3837)

The H5T floating-point datatype initialization code can raise exceptions when handling signaling NaNs. This change disables FE_INVALID exceptions during initialization.

Also removes the -ieee=full change for NAG Fortran as that shouldn't be necessary anymore.

Fixes #3831

* Add intel oneapi windows build to CI CMake (#3836)

* Remove printf format warning on Windows oneAPI. (#3838)

* Correct ENV variables (#3841)

* Remove Autotools sed hack (#3848)

configure.ac contains a sed line that cleans up incorrect library
flags which was added to paper over some bugs in earlier versions
of the Autotools. These issues are not a problem with the current
versions of the Autootols.

The sed line causes problems on MacOS, so it has been removed.

Fixes #3843

* Make filter unregister callbacks safe for VOL connectors (#3629)

* Make filter callbacks use top-level API functions

When using VOL connectors, H5I_iterate may not provide
valid object pointers to its callback. This change keeps
existing functionality in H5Zunregister() without using
potentially unsafe pointers.

* Filter callbacks use internal API

* Skip MPI work on non-native VOL

* Add extra space in comments for consistency (#3852)

* Add extra space in comments for consistency

* uncomment tfloatsattrs test

* Update Actions badges to link to relevant workflow (#3850)

* Add CMake long double cross-compile defaults (#3683)

HDF5 performs a couple of checks at build time to see if long double
values can be converted correctly (IBM's Power architecture uses a
special format for long doubles). These checks were performed using
TRY_RUN, which is a problem when cross-compiling.

These checks now use default values appropriate for most non-Power
systems when cross-compiling. The cache values can be pre-set if
necessary, which will preempt both the TRY_RUN and the default.

Affected values:
    H5_LDOUBLE_TO_LONG_SPECIAL      (default no)
    H5_LONG_TO_LDOUBLE_SPECIAL      (default no)
    H5_LDOUBLE_TO_LLONG_ACCURATE    (default yes)
    H5_LLONG_TO_LDOUBLE_CORRECT     (default yes)
    H5_DISABLE_SOME_LDOUBLE_CONV    (default no)

Fixes GitHub #3585

* Updates for building and testing VOL connectors

* Fix issue with HDF5_VOL_ALLOW_EXTERNAL CMake variable

* Initialize parallel testing with MPI_THREAD_MULTIPLE when testing API

* Add CMake variable to allow specifying a VOL connector's package name

* Remove call to MPI_Init in serial API tests

While previously necessary, it now interferes with VOL connectors that
may need to be initialized with MPI_THREAD_MULTIPLE

* Fixes for CI and presets (#3853)

* Change dest for doxygen (#3856)

* Implement selection vector I/O with collective chunk filling (#3826)

* Changes for ECP-344: Implement selection vector I/O with collective chunk filling.
Also fix a bug in H5FD__mpio_write_vector() to account for fixed size optimization
when computing max address.

* Fixes based on PR review comments:
For H5Dchunk.c: fix H5MM_xfree()
For H5FDmpio.c:
1) Revert the fix to H5FD__mpio_write_vector()
2) Apply the patch from Neil on the proper length of s_sizes reported by H5FD__mpio_vector_build_types()

* Put back the logic of dividing up the work among all the mpi ranks similar to the
original H5D__chunk_collective_fill() routine.

* Add a test to verify the fix for the illegal reference problem in H5FD__mpio_write_vector().

* Do not publish compression headers or docs (#3865)

* Fix typo: look -> loop (#3866)

* Moved the README to markdown and expanded its overview of the files, file generation, and other Fortran wrapper development practices as mentioned in the HDF5 architectural document. I added a new figure and included the SVG file and the original xfig file it was generated from. (#3862)

* Add HDF5_DISABLE_TESTS_REGEX option to skip tests (#3859)

* Fix typo in error message for `MPI_Type_dup`. (#3867)

* Complete the `if command line option` sentence. (#3868)

* Fix h5dump segmentation fault when --vfd-value option is used (#3873)

* Updated URL in funding.yml (#3882)

Using new shortened URL, might look better.

* Remove unused variable from unmerged changes

* Update src/H5Tinit_float.c

4 files changed, 14 insertions, 19 deletions

diff --git a/utils/Makefile.am b/utils/Makefile.am
index 229712e..740f5c3 100644
--- a/utils/Makefile.am
+++ b/utils/Makefile.am
@@ -41,6 +41,6 @@ endif
 # All subdirectories
 SUBDIRS=$(MIRROR_VFD_DIR) $(TESTUTIL_DIR) $(TOOLS_DIR)
 
-bin_SCRIPTS = subfiling_vfd/h5fuse.sh
+bin_SCRIPTS = subfiling_vfd/h5fuse
 
 include $(top_srcdir)/config/conclude.am
diff --git a/utils/mirror_vfd/CMakeLists.txt b/utils/mirror_vfd/CMakeLists.txt
index 51d4694..a123c02 100644
--- a/utils/mirror_vfd/CMakeLists.txt
+++ b/utils/mirror_vfd/CMakeLists.txt
@@ -6,10 +6,10 @@ project (HDF5_UTILS_MIRRORVFD C)
 #-----------------------------------------------------------------------------
 
 set (mirror_server_SOURCES
-        ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_remote.c
-        ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_server.c
-        ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_writer.c
-        ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_remote.h
+    ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_remote.c
+    ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_server.c
+    ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_writer.c
+    ${HDF5_UTILS_MIRRORVFD_SOURCE_DIR}/mirror_remote.h
 )
 add_executable (mirror_server ${mirror_server_SOURCES})
 target_include_directories (mirror_server PRIVATE "${HDF5_UTILS_DIR};${HDF5_SRC_INCLUDE_DIRS};${HDF5_SRC_BINARY_DIR};$<$<BOOL:${HDF5_ENABLE_PARALLEL}>:${MPI_C_INCLUDE_DIRS}>")
@@ -71,10 +71,8 @@ if (HDF5_EXPORTED_TARGETS)
   endforeach ()
 
   install (
-      TARGETS
-          ${H5_DEP_EXECUTABLES}
-      EXPORT
-          ${HDF5_EXPORTED_TARGETS}
+      TARGETS ${H5_DEP_EXECUTABLES}
+      EXPORT ${HDF5_EXPORTED_TARGETS}
       RUNTIME DESTINATION ${HDF5_INSTALL_BIN_DIR} COMPONENT utilsapplications
   )
 endif ()
diff --git a/utils/subfiling_vfd/CMakeLists.txt b/utils/subfiling_vfd/CMakeLists.txt
index 3acdc6b..db59710 100644
--- a/utils/subfiling_vfd/CMakeLists.txt
+++ b/utils/subfiling_vfd/CMakeLists.txt
@@ -1,20 +1,17 @@
 cmake_minimum_required (VERSION 3.18)
 project (HDF5_UTILS_SUBFILINGVFD C)
 
-configure_file (${HDF5_UTILS_SUBFILINGVFD_SOURCE_DIR}/h5fuse.sh.in ${HDF5_UTILS_SUBFILINGVFD_BINARY_DIR}/h5fuse.sh @ONLY)
+configure_file (${HDF5_UTILS_SUBFILINGVFD_SOURCE_DIR}/h5fuse.in ${HDF5_UTILS_SUBFILINGVFD_BINARY_DIR}/h5fuse @ONLY)
 
-# Copy h5fuse.sh to testpar directory for subfiling tests
+# Copy h5fuse to testpar directory for subfiling tests
 if (HDF5_ENABLE_PARALLEL AND HDF5_TEST_PARALLEL)
-  file (
-    COPY
-    ${HDF5_UTILS_SUBFILINGVFD_BINARY_DIR}/h5fuse.sh
-    DESTINATION
-    ${HDF5_TEST_PAR_BINARY_DIR}
+  file (COPY ${HDF5_UTILS_SUBFILINGVFD_BINARY_DIR}/h5fuse
+        DESTINATION ${HDF5_TEST_PAR_BINARY_DIR}
   )
 endif ()
 
 install (
-    FILES ${HDF5_UTILS_SUBFILINGVFD_BINARY_DIR}/h5fuse.sh
+    FILES ${HDF5_UTILS_SUBFILINGVFD_BINARY_DIR}/h5fuse
     DESTINATION ${HDF5_INSTALL_BIN_DIR}
     PERMISSIONS OWNER_READ OWNER_WRITE OWNER_EXECUTE GROUP_READ GROUP_EXECUTE WORLD_READ WORLD_EXECUTE
     COMPONENT utilsapplications
diff --git a/utils/subfiling_vfd/h5fuse.sh.in b/utils/subfiling_vfd/h5fuse.in
index 6f4bf61..a4c6a05 100755
--- a/utils/subfiling_vfd/h5fuse.sh.in
+++ b/utils/subfiling_vfd/h5fuse.in
@@ -26,11 +26,11 @@ function usage {
          configuration file either as a command-line argument or the script will
          search for the *.config file in the current directory."
    echo ""
-   echo "usage: h5fuse.sh [-f filename] [-h] [-p] [-q] [-r] [-v] "
+   echo "usage: h5fuse [-f filename] [-h] [-p] [-q] [-r] [-v] "
    echo "-f filename  Subfile configuration file."
    echo "-h           Print this help."
    echo "-q           Quiet all output. [no]"
-   echo "-p           h5fuse.sh is being run in parallel, with more than one rank. [no]"
+   echo "-p           h5fuse is being run in parallel, with more than one rank. [no]"
    echo "-r           Remove subfiles after being processed. [no]"
    echo "-v           Verbose output. [no]"
    echo ""