Backport H5Dchunk_iter to 1.12 branch (#1970)

* Revert "Revert H5Dchunk_iter changes in hdf5_1_12_1 (#733)"

This reverts commit 10abe9a8b4985a18a0c88615686184d233d7b845.

* Apply clang-format

* Reincorporate spelling fix from #1166

* Incorporate H5Dchunk_iter changes from #161

* Backport to 1.12: Adds a quick for for some egregious chunk_info badness (#722)

* Backport to 1.12: Converts testhdf5 macros to h5test macros in chunk_info.c (#1820)

The two macro schemes were not designed to work together. Also
quiets some MSVC warnings about comparing pointers and integers.

* Backport to 1.12: H5Dchunk_iter now passes offsets in units of dataset elements, fix #1419 (#1969)

* H5Dchunk_iter now passes chunk dimension scaled offsets, fix #1419

* Update docs for H5Dchunk_iter, H5Dget_chunk_info*

Modified description for `H5Dchunk_iter`, `H5Dget_chunk_info`, and `H5Dget_chunk_info_by_coord` to the following

 * offset          Logical position of the chunk’s first element in units of dataset elements
 * filter_mask  Bitmask indicating the filters used when the chunk was written
 * size             Chunk size in bytes, 0 if the chunk does not exist

* Sync H5Dchunk_iter documentation with develop

* Remove H5VL_DATASET_WAIT references from 1.12

* Backport to 1.12 #161, #1474, review comments

Co-authored-by: Dana Robinson <43805+derobins@users.noreply.github.com>

1 files changed, 110 insertions, 0 deletions

diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index f58f3ec..e0eaaeb 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -249,6 +249,12 @@ typedef struct H5D_chunk_coll_fill_info_t {
 } H5D_chunk_coll_fill_info_t;
 #endif /* H5_HAVE_PARALLEL */
 
+typedef struct H5D_chunk_iter_ud_t {
+    H5D_chunk_iter_op_t op;      /* User defined callback */
+    void               *op_data; /* User data for user defined callback */
+    H5O_layout_chunk_t *chunk;   /* Chunk layout */
+} H5D_chunk_iter_ud_t;
+
 /********************/
 /* Local Prototypes */
 /********************/
@@ -272,6 +278,7 @@ static herr_t H5D__chunk_dest(H5D_t *dset);
 static int H5D__get_num_chunks_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
 static int H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
 static int H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
+static int H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata);
 
 /* "Nonexistent" layout operation callback */
 static ssize_t H5D__nonexistent_readvv(const H5D_io_info_t *io_info, size_t chunk_max_nseq,
@@ -7649,3 +7656,106 @@ H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned
 done:
     FUNC_LEAVE_NOAPI_TAG(ret_value)
 } /* end H5D__get_chunk_info_by_coord() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5D__chunk_iter_cb
+ *
+ * Purpose:     Call the user-defined function with the chunk data. The iterator continues if
+ *              the user-defined function returns H5_ITER_CONT, and stops if H5_ITER_STOP is
+ *              returned.
+ *
+ * Return:      Success:    H5_ITER_CONT or H5_ITER_STOP
+ *              Failure:    Negative (H5_ITER_ERROR)
+ *
+ * Programmer:  Gaute Hope
+ *              August 2020
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__chunk_iter_cb(const H5D_chunk_rec_t *chunk_rec, void *udata)
+{
+    const H5D_chunk_iter_ud_t *data      = (H5D_chunk_iter_ud_t *)udata;
+    const H5O_layout_chunk_t  *chunk     = data->chunk;
+    int                        ret_value = H5_ITER_CONT;
+    hsize_t                    offset[H5O_LAYOUT_NDIMS];
+    unsigned                   ii; /* Match H5O_layout_chunk_t.ndims */
+
+    /* Similar to H5D__get_chunk_info */
+    for (ii = 0; ii < chunk->ndims; ii++)
+        offset[ii] = chunk_rec->scaled[ii] * chunk->dim[ii];
+
+    FUNC_ENTER_PACKAGE_NOERR
+
+    /* Check for callback failure and pass along return value */
+    if ((ret_value = (data->op)(offset, chunk_rec->filter_mask, chunk_rec->chunk_addr, chunk_rec->nbytes,
+                                data->op_data)) < 0)
+        HERROR(H5E_DATASET, H5E_CANTNEXT, "iteration operator failed");
+
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_iter_cb */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5D__chunk_iter
+ *
+ * Purpose:     Iterate over all the chunks in the dataset with given callback.
+ *
+ * Return:      Success:        Non-negative
+ *              Failure:        Negative
+ *
+ * Programmer:  Gaute Hope
+ *              August 2020
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__chunk_iter(H5D_t *dset, H5D_chunk_iter_op_t op, void *op_data)
+{
+    const H5D_rdcc_t  *rdcc   = NULL;       /* Raw data chunk cache */
+    H5O_layout_t      *layout = NULL;       /* Dataset layout */
+    H5D_rdcc_ent_t    *ent;                 /* Cache entry index */
+    H5D_chk_idx_info_t idx_info;            /* Chunked index info */
+    herr_t             ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
+
+    /* Check args */
+    HDassert(dset);
+    HDassert(dset->shared);
+
+    /* Get dataset layout and raw data chunk cache */
+    layout = &(dset->shared->layout);
+    rdcc   = &(dset->shared->cache.chunk);
+    HDassert(layout);
+    HDassert(rdcc);
+    HDassert(H5D_CHUNKED == layout->type);
+
+    /* Search for cached chunks that haven't been written out */
+    for (ent = rdcc->head; ent; ent = ent->next)
+        /* Flush the chunk out to disk, to make certain the size is correct later */
+        if (H5D__chunk_flush_entry(dset, ent, FALSE) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTFLUSH, FAIL, "cannot flush indexed storage buffer")
+
+    /* Compose chunked index info struct */
+    idx_info.f       = dset->oloc.file;
+    idx_info.pline   = &dset->shared->dcpl_cache.pline;
+    idx_info.layout  = &layout->u.chunk;
+    idx_info.storage = &layout->storage.u.chunk;
+
+    /* If the dataset is not written, return without errors */
+    if (H5F_addr_defined(idx_info.storage->idx_addr)) {
+        H5D_chunk_iter_ud_t ud;
+
+        /* Set up info for iteration callback */
+        ud.op      = op;
+        ud.op_data = op_data;
+        ud.chunk   = &dset->shared->layout.u.chunk;
+
+        /* Iterate over the allocated chunks calling the iterator callback */
+        if ((ret_value = (layout->storage.u.chunk.ops->iterate)(&idx_info, H5D__chunk_iter_cb, &ud)) < 0)
+            HERROR(H5E_DATASET, H5E_CANTNEXT, "chunk iteration failed");
+    } /* end if H5F_addr_defined */
+
+done:
+    FUNC_LEAVE_NOAPI_TAG(ret_value)
+} /* end H5D__chunk_iter() */