Onion VFD: Sync with develop (#1685)

* Removes unused definitions from module headers (#1624)

* Fix these Doxygen warnings #1581 (#1589)

* Fixes a typo in H5.c (#1639)

* free MPI_Group/MPI_Comm/MPI_Datatype objects (#1638)

* free MPI_Group/MPI_Comm/MPI_Datatype objects

* fix clang-format style

* Adds build and license shields to README.md (#1641)

* First stab at a Github status bar

* Adds a .tokeignore file for counting lines of code accurately

* Yanks lines of code calculation since it wildly overcounts

* not depend on doIO to free an MPI_Comm object (#1642)

* free MPI datatypes previously created (#1637)

* Retrieve MPI-IO hints used by MPI library after file open (#1636)

H5Pget_fapl_mpio() should return an MPI info object containing all the
MPI-IO hints used by the MPI library underneath, after the file is
opened. Some hints, such as cb_nodes (number of I/O aggregators), are
useful for HDF5 applications and I/O libraries built on top of HDF5.

* OESS-168: Remove clang warnings. (#1309)

* OESS-168: Remove clang warnings.

* OESS-168: Address @lrknox review.

* OESS-168: Remove clang warnings. (#1376)

* Remove H5_NO_ALIGNMENT_RESTRICTIONS (#1426)

* Do not conditionally compile code that uses a pointer dereference
and assignment to copy a potentially unaligned variable to aligned
automatic storage, or vice versa.  Instead, always use naked `memcpy(3)`s.
Disassembling the generated code reveals that the `memcpy(3)`s optimize
(`-O3`) to a single `mov` instruction for x86_64, which is not strict
about alignment.

This change reduces the size of code and scripts by 143 lines, eases
our way to cross-compilation, and avoids invoking undefined behavior.

* Committing clang-format changes

* Per discussion, use HD and add comments.

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

* Cleans up some HL library code that inappropriately returns htri_t values cast to herr_t (#1651)

* Cleans up some HL library code that inappropriately returns
htri_t values cast to herr_t

* Committing clang-format changes

* Formatted source

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

* Mirror vfd test fixes (#1629)

* Use the FAPL that was created earlier in the test (and delete an unused
variable).   This allows 'make check-vfd' to pass with --enable-mirror-vfd.

* Check for testing directory before creating, to avoid warning from bash.
Clean out .libs directory before re-using it (after a failed test), to
remove any files generated by libtool.

* Committing clang-format changes

* Increment error count on failed file open and skip tests for VFDs that need
modified filenames.

* Skip the mirror VFD for 'make check-vfd' - the mirror VFD requires networking
configuration parameters and can't be provided for an automated test that
is configured with an environment variable.

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

* Removes HDF Group paths, adds shellcheck fixes (#1656)

For more information:
  https://www.shellcheck.net/wiki/SC2086 -- Double quote to prevent globbing ...
  https://www.shellcheck.net/wiki/SC2230 -- which is non-standard. Use builti...
  https://www.shellcheck.net/wiki/SC2006 -- Use $(...) notation instead of le...

* HDFFV-11306 Fixed (#1657)

* HDFFV-11306,
 * Fixed it so both h5open_f and h5close_f can be called multiple times.
 * Fixed an issue with open objects remaining after h5close_f was called.
 * Added additional tests.

* comments clean-up

* Develop clang format java (#1653)

* added HDFFV-11306 entry (#1662)

* Adds the -q flag to all swmr test programs, quieting noisy output (#1665)

* Adds paths-ignore to the Github pull request workflow (#1663)

* Changes Github action `hdf5 dev CI` to `PR hdf5 dev CI` (#1666)

So the PR action name is not the same as the one in main.yml

* Replace H5detect's build-time detection of C99 integer properties with a (#1400)

* Replace H5detect's build-time detection of C99 integer properties with a
table-driven routine, `H5T__init_native_int()`, that is run at library
initialization time.

* Improve handling of copying of dynamic libraries and clean them up after (#1681)

test finishes.

Co-authored-by: Allen Byrne <50328838+byrnHDF@users.noreply.github.com>
Co-authored-by: Wei-keng Liao <wkliao@users.noreply.github.com>
Co-authored-by: H. Joe Lee <hyoklee@hdfgroup.org>
Co-authored-by: David Young <dyoung@hdfgroup.org>
Co-authored-by: github-actions <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Quincey Koziol <koziol@lbl.gov>
Co-authored-by: Scot Breitenfeld <brtnfld@hdfgroup.org>

4 files changed, 3 insertions, 61 deletions

diff --git a/config/cmake/ConfigureChecks.cmake b/config/cmake/ConfigureChecks.cmake
index 43aa243..9c91d34 100644
--- a/config/cmake/ConfigureChecks.cmake
+++ b/config/cmake/ConfigureChecks.cmake
@@ -416,7 +416,3 @@ H5ConversionTests (${HDF_PREFIX}_LLONG_TO_LDOUBLE_CORRECT "Checking IF correctly
 # some long double values
 #-----------------------------------------------------------------------------
 H5ConversionTests (${HDF_PREFIX}_DISABLE_SOME_LDOUBLE_CONV "Checking IF the cpu is power9 and cannot correctly converting long double values")
-# ----------------------------------------------------------------------
-# Check if pointer alignments are enforced
-#-----------------------------------------------------------------------------
-H5ConversionTests (${HDF_PREFIX}_NO_ALIGNMENT_RESTRICTIONS "Checking IF alignment restrictions are strictly enforced")
diff --git a/config/cmake/ConversionTests.c b/config/cmake/ConversionTests.c
index f80959f..f100dd8 100644
--- a/config/cmake/ConversionTests.c
+++ b/config/cmake/ConversionTests.c
@@ -234,59 +234,6 @@ done:
 }
 #endif
 
-#ifdef H5_NO_ALIGNMENT_RESTRICTIONS_TEST
-
-#include <stdlib.h>
-#include <string.h>
-
-typedef struct {
-    size_t len;
-    void *p;
-} hvl_t;
-
-#ifdef FC_DUMMY_MAIN
-#ifndef FC_DUMMY_MAIN_EQ_F77
-#  ifdef __cplusplus
-extern "C"
-#  endif
-int FC_DUMMY_MAIN()
-{ return 1;}
-#endif
-#endif
-int HDF_NO_UBSAN
-main ()
-{
-
-    char *chp = "beefs";
-    char **chpp = malloc (2 * sizeof (char *));
-    char **chpp2;
-    hvl_t vl = { 12345, (void *) chp };
-    hvl_t *vlp;
-    hvl_t *vlp2;
-
-    memcpy ((void *) ((char *) chpp + 1), &chp, sizeof (char *));
-    chpp2 = (char **) ((char *) chpp + 1);
-    if (strcmp (*chpp2, chp)) {
-        free (chpp);
-        return 1;
-    }
-    free (chpp);
-
-    vlp = malloc (2 * sizeof (hvl_t));
-    memcpy ((void *) ((char *) vlp + 1), &vl, sizeof (hvl_t));
-    vlp2 = (hvl_t *) ((char *) vlp + 1);
-    if (vlp2->len != vl.len || vlp2->p != vl.p) {
-        free (vlp);
-        return 1;
-    }
-    free (vlp);
-
-  ;
-  return 0;
-}
-
-#endif
-
 #ifdef H5_DISABLE_SOME_LDOUBLE_CONV_TEST
 
 #include <stdio.h>
diff --git a/config/cmake/H5pubconf.h.in b/config/cmake/H5pubconf.h.in
index 4956c97..9a581cb 100644
--- a/config/cmake/H5pubconf.h.in
+++ b/config/cmake/H5pubconf.h.in
@@ -434,9 +434,6 @@
 /* Define to enable internal memory allocation sanity checking. */
 #cmakedefine H5_MEMORY_ALLOC_SANITY_CHECK @H5_MEMORY_ALLOC_SANITY_CHECK@
 
-/* Define if we can violate pointer alignment restrictions */
-#cmakedefine H5_NO_ALIGNMENT_RESTRICTIONS @H5_NO_ALIGNMENT_RESTRICTIONS@
-
 /* Define if deprecated public API symbols are disabled */
 #cmakedefine H5_NO_DEPRECATED_SYMBOLS @H5_NO_DEPRECATED_SYMBOLS@
 
diff --git a/config/conclude.am b/config/conclude.am
index e798d8d..bfbe1ec 100644
--- a/config/conclude.am
+++ b/config/conclude.am
@@ -283,7 +283,9 @@ if BUILD_PARALLEL_CONDITIONAL
   # VFD_LIST += mpio
 endif
 if MIRROR_VFD_CONDITIONAL
-  VFD_LIST += mirror
+  # Mirror VFD needs network configuration, etc. and isn't easy to set
+  # reasonable defaults for that info.
+  # VFD_LIST += mirror
 endif
 if ROS3_VFD_CONDITIONAL
   VFD_LIST += ros3