[1.12 Merge] Hdf5 1 12 develop merges (#2012)

* Fix invalid comment about character encoding in H5Fint.c (#1845)

* Convert assertion on (possibly corrupt) file contents to normal error check (#1861)

* Convert assertion on (possibly corrupt) file contents to normal error check

* Committing clang-format changes

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

* Avoid allocating chunk map for contiguous and compact dataset I/O (#1927)

* Add documentation for parallel compression feature (#1981)

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

3 files changed, 23 insertions, 8 deletions

diff --git a/src/H5Dio.c b/src/H5Dio.c
index 466cfdf..bd98aa2 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -366,6 +366,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_space
     H5D_chunk_map_t *fm = NULL;                   /* Chunk file<->memory mapping */
     H5D_io_info_t    io_info;                     /* Dataset I/O info     */
     H5D_type_info_t  type_info;                   /* Datatype info for operation */
+    H5D_layout_t     layout_type;                 /* Dataset's layout type (contig, chunked, compact, etc.) */
     hbool_t          type_info_init      = FALSE; /* Whether the datatype info has been initialized */
     H5S_t           *projected_mem_space = NULL;  /* If not NULL, ptr to dataspace containing a     */
                                                   /* projection of the supplied mem_space to a new  */
@@ -397,6 +398,8 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_space
         mem_space = file_space;
     nelmts = H5S_GET_SELECT_NPOINTS(mem_space);
 
+    layout_type = dataset->shared->layout.type;
+
     /* Set up datatype info for operation */
     if (H5D__typeinfo_init(dataset, mem_type_id, FALSE, &type_info) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info")
@@ -521,11 +524,13 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_space
         HDassert((*dataset->shared->layout.ops->is_space_alloc)(&dataset->shared->layout.storage) ||
                  (dataset->shared->layout.ops->is_data_cached &&
                   (*dataset->shared->layout.ops->is_data_cached)(dataset->shared)) ||
-                 dataset->shared->dcpl_cache.efl.nused > 0 || dataset->shared->layout.type == H5D_COMPACT);
+                 dataset->shared->dcpl_cache.efl.nused > 0 || layout_type == H5D_COMPACT);
 
     /* Allocate the chunk map */
-    if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t)))
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map")
+    if (H5D_CONTIGUOUS != layout_type && H5D_COMPACT != layout_type) {
+        if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t)))
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map")
+    }
 
     /* Call storage method's I/O initialization routine */
     if (io_info.layout_ops.io_init &&
@@ -581,6 +586,7 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_spac
     H5D_chunk_map_t *fm = NULL;                   /* Chunk file<->memory mapping */
     H5D_io_info_t    io_info;                     /* Dataset I/O info     */
     H5D_type_info_t  type_info;                   /* Datatype info for operation */
+    H5D_layout_t     layout_type;                 /* Dataset's layout type (contig, chunked, compact, etc.) */
     hbool_t          type_info_init      = FALSE; /* Whether the datatype info has been initialized */
     hbool_t          should_alloc_space  = FALSE; /* Whether or not to initialize dataset's storage */
     H5S_t           *projected_mem_space = NULL;  /* If not NULL, ptr to dataspace containing a     */
@@ -607,6 +613,8 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_spac
     /* check args */
     HDassert(dataset && dataset->oloc.file);
 
+    layout_type = dataset->shared->layout.type;
+
     /* All filters in the DCPL must have encoding enabled. */
     if (!dataset->shared->checked_filters) {
         if (H5Z_can_apply(dataset->shared->dcpl_id, dataset->shared->type_id) < 0)
@@ -753,8 +761,10 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, H5S_t *mem_space, H5S_t *file_spac
     } /* end if */
 
     /* Allocate the chunk map */
-    if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t)))
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map")
+    if (H5D_CONTIGUOUS != layout_type && H5D_COMPACT != layout_type) {
+        if (NULL == (fm = H5FL_CALLOC(H5D_chunk_map_t)))
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "can't allocate chunk map")
+    }
 
     /* Call storage method's I/O initialization routine */
     if (io_info.layout_ops.io_init &&
diff --git a/src/H5Fint.c b/src/H5Fint.c
index 8d2af3d..1da8c01 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -2708,10 +2708,13 @@ H5F__build_actual_name(const H5F_t *f, const H5P_genplist_t *fapl, const char *n
             if (NULL == (new_fapl = (H5P_genplist_t *)H5I_object(new_fapl_id)))
                 HGOTO_ERROR(H5E_FILE, H5E_CANTCREATE, FAIL, "can't get property list")
 
-            /* Set the character encoding on the new property list */
+            /*
+             * Set the private property for retrieving the backing store
+             * POSIX file descriptor from the Core VFD
+             */
             want_posix_fd = TRUE;
             if (H5P_set(new_fapl, H5F_ACS_WANT_POSIX_FD_NAME, &want_posix_fd) < 0)
-                HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set character encoding")
+                HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set property for retrieving file descriptor")
 
             /* Retrieve the file handle */
             if (H5F_get_vfd_handle(f, new_fapl_id, (void **)&fd) < 0)
diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c
index 6f6df96..62d0398 100644
--- a/src/H5Fsuper.c
+++ b/src/H5Fsuper.c
@@ -686,7 +686,9 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read)
         /* Sanity check - superblock extension should only be defined for
          *      superblock version >= 2.
          */
-        HDassert(sblock->super_vers >= HDF5_SUPERBLOCK_VERSION_2);
+        if (sblock->super_vers < HDF5_SUPERBLOCK_VERSION_2)
+            HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, FAIL,
+                        "invalid superblock - extension message should not be defined for version < 2")
 
         /* Check for superblock extension being located "outside" the stored
          *      'eoa' value, which can occur with the split/multi VFD.