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-rw-r--r--src/H5D.c179
-rw-r--r--src/H5Dchunk.c392
-rw-r--r--src/H5Dnone.c57
-rw-r--r--src/H5Dpkg.h3
-rw-r--r--src/H5Dpublic.h3
-rw-r--r--src/H5EA.c14
-rw-r--r--src/H5FA.c14
-rw-r--r--src/H5VLnative.h7
-rw-r--r--src/H5VLnative_dataset.c102
9 files changed, 707 insertions, 64 deletions
diff --git a/src/H5D.c b/src/H5D.c
index a8cefd9..9c3a096 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -457,8 +457,8 @@ done:
*
* Failure: H5I_INVALID_HID
*
- * Programmer: Robb Matzke
- * Tuesday, February 3, 1998
+ * Programmer: Robb Matzke
+ * Tuesday, February 3, 1998
*
*-------------------------------------------------------------------------
*/
@@ -512,8 +512,8 @@ done:
*
* Failure: H5I_INVALID_HID
*
- * Programmer: Neil Fortner
- * Wednesday, October 29, 2008
+ * Programmer: Neil Fortner
+ * Wednesday, October 29, 2008
*
*-------------------------------------------------------------------------
*/
@@ -610,9 +610,9 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5Diterate
+ * Function: H5Diterate
*
- * Purpose: This routine iterates over all the elements selected in a memory
+ * Purpose: This routine iterates over all the elements selected in a memory
* buffer. The callback function is called once for each element selected
* in the dataspace. The selection in the dataspace is modified so
* that any elements already iterated over are removed from the selection
@@ -659,11 +659,11 @@ done:
* indicating failure. The iterator can be restarted at the next
* element.
*
- * Return: Returns the return value of the last operator if it was non-zero,
+ * Return: Returns the return value of the last operator if it was non-zero,
* or zero if all elements were processed. Otherwise returns a
* negative value.
*
- * Programmer: Quincey Koziol
+ * Programmer: Quincey Koziol
* Friday, June 11, 1999
*
*-------------------------------------------------------------------------
@@ -706,16 +706,16 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5Dvlen_reclaim
+ * Function: H5Dvlen_reclaim
*
- * Purpose: Frees the buffers allocated for storing variable-length data
+ * Purpose: Frees the buffers allocated for storing variable-length data
* in memory. Only frees the VL data in the selection defined in the
* dataspace. The dataset transfer property list is required to find the
* correct allocation/free methods for the VL data in the buffer.
*
- * Return: Non-negative on success, negative on failure
+ * Return: Non-negative on success, negative on failure
*
- * Programmer: Quincey Koziol
+ * Programmer: Quincey Koziol
* Thursday, June 10, 1999
*
*-------------------------------------------------------------------------
@@ -756,9 +756,9 @@ done:
/*-------------------------------------------------------------------------
- * Function: H5Dvlen_get_buf_size
+ * Function: H5Dvlen_get_buf_size
*
- * Purpose: This routine checks the number of bytes required to store the VL
+ * Purpose: This routine checks the number of bytes required to store the VL
* data from the dataset, using the space_id for the selection in the
* dataset on disk and the type_id for the memory representation of the
* VL data, in memory. The *size value is modified according to how many
@@ -772,9 +772,9 @@ done:
* Kinda kludgy, but easier than the other method of trying to figure out
* the sizes without actually reading the data in... - QAK
*
- * Return: Non-negative on success, negative on failure
+ * Return: Non-negative on success, negative on failure
*
- * Programmer: Quincey Koziol
+ * Programmer: Quincey Koziol
* Wednesday, August 11, 1999
*
*-------------------------------------------------------------------------
@@ -1095,3 +1095,150 @@ done:
FUNC_LEAVE_API(ret_value);
} /* H5Dget_chunk_storage_size() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5Dget_num_chunks
+ *
+ * Purpose: Retrieves the number of chunks that have non-empty intersection
+ * with a specified selection.
+ *
+ * Note: Currently, this function only gets the number of all written
+ * chunks, regardless the dataspace.
+ *
+ * Parameters:
+ * hid_t dset_id; IN: Chunked dataset ID
+ * hid_t fspace_id; IN: File dataspace ID
+ * hsize_t *nchunks; OUT: Number of non-empty chunks
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Binh-Minh Ribler
+ * May 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Dget_num_chunks(hid_t dset_id, hid_t fspace_id, hsize_t *nchunks)
+{
+ H5VL_object_t *vol_obj = NULL; /* Dataset for this operation */
+ herr_t ret_value = SUCCEED;
+
+ FUNC_ENTER_API(FAIL)
+ H5TRACE3("e", "ii*h", dset_id, fspace_id, nchunks);
+
+ /* Check arguments */
+ if(NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset identifier")
+ if(NULL == nchunks)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
+
+ /* Get the number of written chunks */
+ if(H5VL_dataset_optional(vol_obj, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, H5VL_NATIVE_DATASET_GET_NUM_CHUNKS, fspace_id, nchunks) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't get number of chunks")
+
+done:
+ FUNC_LEAVE_API(ret_value);
+} /* H5Dget_num_chunks() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5Dget_chunk_info
+ *
+ * Purpose: Retrieves information about a chunk specified by its index.
+ *
+ * Parameters:
+ * hid_t dset_id; IN: Chunked dataset ID
+ * hid_t fspace_id; IN: File dataspace ID
+ * hsize_t index; IN: Index of written chunk
+ * hsize_t *offset OUT: Logical position of the chunk’s
+ * first element in the dataspace
+ * unsigned *filter_mask OUT: Mask for identifying the filters in use
+ * haddr_t *addr OUT: Address of the chunk
+ * hsize_t *size OUT: Size of the chunk
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Binh-Minh Ribler
+ * May 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_index, hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size)
+{
+ H5VL_object_t *vol_obj = NULL; /* Dataset for this operation */
+ hsize_t nchunks= 0;
+ herr_t ret_value = SUCCEED;
+
+ FUNC_ENTER_API(FAIL)
+ H5TRACE7("e", "iih*h*Iu*a*h", dset_id, fspace_id, chk_index, offset,
+ filter_mask, addr, size);
+
+ /* Check arguments */
+ if(NULL == offset && NULL == filter_mask && NULL == addr && NULL == size)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid arguments, must have at least one non-null output argument")
+ if(NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset identifier")
+
+ /* Get the number of written chunks to check range */
+ if(H5VL_dataset_optional(vol_obj, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, H5VL_NATIVE_DATASET_GET_NUM_CHUNKS, fspace_id, &nchunks) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't get number of chunks")
+
+ /* Check range for chunk index */
+ if(chk_index >= nchunks)
+ HGOTO_ERROR(H5E_IO, H5E_BADRANGE, FAIL, "chunk index is out of range")
+
+ /* Call private function to get the chunk info given the chunk's index */
+ if(H5VL_dataset_optional(vol_obj, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_IDX, fspace_id, chk_index, offset, filter_mask, addr, size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't get chunk info by index")
+
+done:
+ FUNC_LEAVE_API(ret_value);
+} /* H5Dget_chunk_info() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5Dget_chunk_info_by_coord
+ *
+ * Purpose: Retrieves information about a chunk specified by its logical
+ * coordinates.
+ *
+ * Parameters:
+ * hid_t dset_id; IN: Chunked dataset ID
+ * hsize_t *offset IN: Logical position of the chunk’s
+ * first element in the dataspace
+ * unsigned *filter_mask OUT: Mask for identifying the filters in use
+ * haddr_t *addr OUT: Address of the chunk
+ * hsize_t *size OUT: Size of the chunk
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Binh-Minh Ribler
+ * May 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size)
+{
+ H5VL_object_t *vol_obj = NULL; /* Dataset for this operation */
+ herr_t ret_value = SUCCEED;
+
+ FUNC_ENTER_API(FAIL)
+ H5TRACE5("e", "i*h*Iu*a*h", dset_id, offset, filter_mask, addr, size);
+
+ /* Check arguments */
+ if(NULL == (vol_obj = (H5VL_object_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset identifier")
+ if(NULL == filter_mask && NULL == addr && NULL == size)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid arguments, must have at least one non-null output argument")
+ if(NULL == offset)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
+
+ /* Call private function to get the chunk info given the chunk's index */
+ if(H5VL_dataset_optional(vol_obj, H5P_DATASET_XFER_DEFAULT, H5_REQUEST_NULL, H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR, offset, filter_mask, addr, size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "Can't get chunk info by its logical coordinates")
+
+done:
+ FUNC_LEAVE_API(ret_value)
+} /* end H5Dget_chunk_info_by_coord() */
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 082aac3..4976075 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -216,6 +216,18 @@ typedef struct H5D_chunk_readvv_ud_t {
const H5D_t *dset; /* Dataset to operate on */
} H5D_chunk_readvv_ud_t;
+typedef struct H5D_chunk_info_iter_ud_t {
+ hsize_t scaled[H5O_LAYOUT_NDIMS]; /* Logical offset of the chunk */
+ hsize_t ndims; /* Number of dimensions in the dataset */
+ uint32_t nbytes; /* Size of stored data in the chunk */
+ unsigned filter_mask; /* Excluded filters */
+ haddr_t chunk_addr; /* Address of the chunk in file */
+ hsize_t chunk_idx; /* Chunk index, where the iteration needs to stop */
+ hsize_t curr_idx; /* Current index, where the iteration is */
+ unsigned idx_hint; /* Index of chunk in cache, if present */
+ hbool_t found; /* Whether the chunk was found */
+} H5D_chunk_info_iter_ud_t;
+
/* Callback info for file selection iteration */
typedef struct H5D_chunk_file_iter_ud_t {
H5D_chunk_map_t *fm; /* File->memory chunk mapping info */
@@ -252,6 +264,11 @@ static herr_t H5D__chunk_flush(H5D_t *dset);
static herr_t H5D__chunk_io_term(const H5D_chunk_map_t *fm);
static herr_t H5D__chunk_dest(H5D_t *dset);
+/* Chunk query operation callbacks */
+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);
+
/* "Nonexistent" layout operation callback */
static ssize_t
H5D__nonexistent_readvv(const H5D_io_info_t *io_info,
@@ -6956,3 +6973,378 @@ done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__chunk_format_convert() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_num_chunks_cb
+ *
+ * Purpose: Callback function that increments the number of written
+ * chunks in the dataset.
+ *
+ * Note: Currently, this function only gets the number of all written
+ * chunks, regardless the dataspace.
+ *
+ * Return: H5_ITER_CONT
+ *
+ * Programmer: Binh-Minh Ribler
+ * June 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__get_num_chunks_cb(const H5D_chunk_rec_t H5_ATTR_UNUSED *chunk_rec, void *_udata)
+{
+ hsize_t *num_chunks = (hsize_t *)_udata;
+ int ret_value = H5_ITER_CONT; /* Callback return value */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ HDassert(num_chunks);
+
+ (*num_chunks)++;
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__get_num_chunks_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_num_chunks
+ *
+ * Purpose: Gets the number of written chunks in a dataset.
+ *
+ * Note: Currently, this function only gets the number of all written
+ * chunks, regardless the dataspace.
+ *
+ * Return: Success: Non-negative
+ * Failure: Negative
+ *
+ * Programmer: Binh-Minh Ribler
+ * June 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__get_num_chunks(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_t *nchunks)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ hsize_t num_chunks = 0; /* Number of written chunks */
+ H5D_rdcc_ent_t *ent; /* Cache entry */
+ const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
+ const H5O_layout_t *layout; /* Dataset layout */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
+
+ HDassert(dset);
+ HDassert(dset->shared);
+ HDassert(space);
+ HDassert(nchunks);
+
+ layout = &(dset->shared->layout); /* Dataset layout */
+ rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
+ HDassert(rdcc);
+
+ /* 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_IO, H5E_WRITEERROR, 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 = &dset->shared->layout.u.chunk;
+ idx_info.storage = &dset->shared->layout.storage.u.chunk;
+
+ /* If the dataset is not written, number of chunks will be 0 */
+ if(!H5F_addr_defined(idx_info.storage->idx_addr)) {
+ *nchunks = 0;
+ }
+ else {
+ /* Iterate over the allocated chunks */
+ if((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_num_chunks_cb, &num_chunks) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
+ *nchunks = num_chunks;
+ }
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__get_num_chunks() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_chunk_info_cb
+ *
+ * Purpose: Get the chunk info of the queried chunk, given by its index.
+ *
+ * Return: Success: H5_ITER_CONT or H5_ITER_STOP
+ * H5_ITER_STOP indicates the queried chunk is found
+ * Failure: Negative (H5_ITER_ERROR)
+ *
+ * Programmer: Binh-Minh Ribler
+ * June 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ H5D_chunk_info_iter_ud_t *chunk_info = (H5D_chunk_info_iter_ud_t *)_udata;
+ hsize_t ii = 0; /* Dimension index */
+ int ret_value = H5_ITER_CONT; /* Callback return value */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(chunk_rec);
+ HDassert(chunk_info);
+
+ /* If this is the queried chunk, retrieve its info and stop iterating */
+ if (chunk_info->curr_idx == chunk_info->chunk_idx) {
+ chunk_info->filter_mask = chunk_rec->filter_mask;
+ chunk_info->chunk_addr = chunk_rec->chunk_addr;
+ chunk_info->nbytes = chunk_rec->nbytes;
+ for (ii = 0; ii < chunk_info->ndims; ii++)
+ chunk_info->scaled[ii] = chunk_rec->scaled[ii];
+ chunk_info->found = TRUE;
+
+ /* Stop iterating */
+ ret_value = H5_ITER_STOP;
+ }
+ /* Go to the next chunk */
+ else
+ chunk_info->curr_idx++;
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__get_chunk_info_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_chunk_info
+ *
+ * Purpose: Iterate over the chunks in the dataset to get the info
+ * of the desired chunk.
+ *
+ * Note: Currently, this function only gets the number of all written
+ * chunks, regardless the dataspace.
+ *
+ * Return: Success: SUCCEED
+ * Failure: FAIL
+ *
+ * Programmer: Binh-Minh Ribler
+ * June 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__get_chunk_info(const H5D_t *dset, const H5S_t H5_ATTR_UNUSED *space, hsize_t chk_index, hsize_t *offset, unsigned *filter_mask, haddr_t *addr, hsize_t *size)
+{
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ H5D_chunk_info_iter_ud_t udata; /* User data for callback */
+ const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
+ H5D_rdcc_ent_t *ent; /* Cache entry index */
+ hsize_t ii = 0; /* Dimension index */
+ hsize_t nchunks = 0; /* Number of chunks in this dset */
+ hsize_t scaled[H5S_MAX_RANK];
+ herr_t ret_value = SUCCEED;/* Return value */
+
+ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
+
+ HDassert(dset);
+ HDassert(dset->shared);
+ HDassert(space);
+
+ /* Get the raw data chunk cache */
+ rdcc = &(dset->shared->cache.chunk);
+ HDassert(rdcc);
+
+ /* 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_IO, H5E_WRITEERROR, 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 = &dset->shared->layout.u.chunk;
+ idx_info.storage = &dset->shared->layout.storage.u.chunk;
+
+ /* Set addr & size for when dset is not written or queried chunk is not found */
+ if (addr)
+ *addr = HADDR_UNDEF;
+ if (size)
+ *size = 0;
+
+ /* If the chunk is written, get its info, otherwise, return without error */
+ if(H5F_addr_defined(idx_info.storage->idx_addr)) {
+ /* Initialize before iteration */
+ udata.chunk_idx = chk_index;
+ udata.curr_idx = 0;
+ udata.ndims = dset->shared->ndims;
+ udata.nbytes = 0;
+ udata.filter_mask = 0;
+ udata.chunk_addr = HADDR_UNDEF;
+ udata.found = FALSE;
+
+ /* Iterate over the allocated chunks */
+ if((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_chunk_info_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve allocated chunk information from index")
+
+ /* Obtain requested info if the chunk is found */
+ if(udata.found) {
+ if(filter_mask)
+ *filter_mask = udata.filter_mask;
+ if(addr)
+ *addr = udata.chunk_addr;
+ if(size)
+ *size = udata.nbytes;
+ if(offset)
+ for(ii = 0; ii < udata.ndims; ii++)
+ offset[ii] = udata.scaled[ii] * dset->shared->layout.u.chunk.dim[ii];
+ }
+ } /* end if H5F_addr_defined */
+
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__get_chunk_info() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_chunk_info_by_coord_cb
+ *
+ * Purpose: Get the chunk info of the desired chunk, given its offset
+ * coordinates.
+ *
+ * Return: Success: H5_ITER_CONT or H5_ITER_STOP
+ * Failure: Negative (H5_ITER_ERROR)
+ *
+ * Programmer: Binh-Minh Ribler
+ * June 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+static int
+H5D__get_chunk_info_by_coord_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata)
+{
+ hsize_t ii;
+ H5D_chunk_info_iter_ud_t *chunk_info = (H5D_chunk_info_iter_ud_t *)_udata;
+ hbool_t different = FALSE; /* TRUE when a scaled value pair mismatch */
+ int ret_value = H5_ITER_CONT; /* Callback return value */
+
+ FUNC_ENTER_STATIC_NOERR
+
+ /* Check args */
+ HDassert(chunk_rec);
+ HDassert(chunk_info);
+
+ /* Going through the scaled, stop when a mismatch is found */
+ for (ii = 0; ii < chunk_info->ndims && !different; ii++)
+ if (chunk_info->scaled[ii] != chunk_rec->scaled[ii])
+ different = TRUE;
+
+ /* Same scaled coords means the chunk is found, copy the chunk info */
+ if (!different) {
+ chunk_info->nbytes = chunk_rec->nbytes;
+ chunk_info->filter_mask = chunk_rec->filter_mask;
+ chunk_info->chunk_addr = chunk_rec->chunk_addr;
+ chunk_info->found = TRUE;
+
+ /* Stop iterating */
+ ret_value = H5_ITER_STOP;
+ }
+
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__get_chunk_info_by_coord_cb() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_chunk_info_by_coord
+ *
+ * Purpose: Iterate over the chunks in the dataset to get the info
+ * of the desired chunk, given by its offset coordinates.
+ *
+ * Return: Success: Non-negative
+ * Failure: Negative
+ *
+ * Programmer: Binh-Minh Ribler
+ * June 2019 (HDFFV-10677)
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *offset, unsigned* filter_mask, haddr_t *addr, hsize_t *size)
+{
+ const H5O_layout_t *layout = NULL; /* Dataset layout */
+ const H5D_rdcc_t *rdcc = NULL; /* Raw data chunk cache */
+ H5D_rdcc_ent_t *ent; /* Cache entry index */
+ H5D_chk_idx_info_t idx_info; /* Chunked index info */
+ H5D_chunk_info_iter_ud_t udata; /* User data for callback */
+ H5D_chunk_ud_t udata2;
+ hsize_t scaled[H5S_MAX_RANK];
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_PACKAGE_TAG(dset->oloc.addr)
+
+ /* Check args */
+ HDassert(dset);
+ HDassert(dset->shared);
+ HDassert(offset);
+
+ /* 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);
+
+/* Is this expensive? */
+ /* 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_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+
+ /* Set addr & size for when dset is not written or queried chunk is not found */
+ if (addr)
+ *addr = HADDR_UNDEF;
+ if (size)
+ *size = 0;
+
+ /* Compose chunked index info struct */
+ idx_info.f = dset->oloc.file;
+ idx_info.pline = &dset->shared->dcpl_cache.pline;
+ idx_info.layout = &dset->shared->layout.u.chunk;
+ idx_info.storage = &dset->shared->layout.storage.u.chunk;
+
+ /* If the dataset is not written, return without errors */
+ if(H5F_addr_defined(idx_info.storage->idx_addr)) {
+ /* Calculate the scaled of this chunk */
+ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, udata.scaled);
+ udata.scaled[dset->shared->ndims] = 0;
+
+ /* Initialize before iteration */
+ udata.ndims = dset->shared->ndims;
+ udata.nbytes = 0;
+ udata.filter_mask = 0;
+ udata.chunk_addr = HADDR_UNDEF;
+ udata.found = FALSE;
+
+ /* Iterate over the allocated chunks to find the requested chunk */
+ if((dset->shared->layout.storage.u.chunk.ops->iterate)(&idx_info, H5D__get_chunk_info_by_coord_cb, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to retrieve information of the chunk by its scaled coordinates")
+
+ /* Obtain requested info if the chunk is found */
+ if (udata.found) {
+ if(filter_mask)
+ *filter_mask = udata.filter_mask;
+ if(addr)
+ *addr = udata.chunk_addr;
+ if(size)
+ *size = udata.nbytes;
+ }
+ } /* end if H5F_addr_defined */
+
+done:
+ FUNC_LEAVE_NOAPI_TAG(ret_value)
+} /* end H5D__get_chunk_info_by_coord() */
+
diff --git a/src/H5Dnone.c b/src/H5Dnone.c
index be421b6..9346220 100644
--- a/src/H5Dnone.c
+++ b/src/H5Dnone.c
@@ -242,9 +242,9 @@ H5D__none_idx_iterate(const H5D_chk_idx_info_t *idx_info,
unsigned u; /* Local index variable */
int curr_dim; /* Current rank */
hsize_t idx; /* Array index of chunk */
- int ret_value = -1; /* Return value */
+ int ret_value = H5_ITER_CONT; /* Return value */
- FUNC_ENTER_STATIC_NOERR
+ FUNC_ENTER_STATIC
/* Sanity checks */
HDassert(idx_info);
@@ -266,34 +266,35 @@ H5D__none_idx_iterate(const H5D_chk_idx_info_t *idx_info,
HDassert(ndims > 0);
/* Iterate over all the chunks in the dataset's dataspace */
- for(u = 0; u < idx_info->layout->nchunks; u++) {
- /* Calculate the index of this chunk */
- idx = H5VM_array_offset_pre(ndims, idx_info->layout->max_down_chunks, chunk_rec.scaled);
-
- /* Calculate the address of the chunk */
- chunk_rec.chunk_addr = idx_info->storage->idx_addr + idx * idx_info->layout->size;
-
- /* Make "generic chunk" callback */
- if((ret_value = (*chunk_cb)(&chunk_rec, chunk_udata)) < 0)
- HERROR(H5E_DATASET, H5E_CALLBACK, "failure in generic chunk iterator callback");
-
- /* Update coordinates of chunk in dataset */
- curr_dim = (int)(ndims - 1);
- while(curr_dim >= 0) {
- /* Increment coordinate in current dimension */
- chunk_rec.scaled[curr_dim]++;
-
- /* Check if we went off the end of the current dimension */
- if(chunk_rec.scaled[curr_dim] >= idx_info->layout->chunks[curr_dim]) {
- /* Reset coordinate & move to next faster dimension */
- chunk_rec.scaled[curr_dim] = 0;
- curr_dim--;
- } /* end if */
- else
- break;
- } /* end while */
+ for(u = 0; u < idx_info->layout->nchunks && ret_value == H5_ITER_CONT; u++) {
+ /* Calculate the index of this chunk */
+ idx = H5VM_array_offset_pre(ndims, idx_info->layout->max_down_chunks, chunk_rec.scaled);
+
+ /* Calculate the address of the chunk */
+ chunk_rec.chunk_addr = idx_info->storage->idx_addr + idx * idx_info->layout->size;
+
+ /* Make "generic chunk" callback */
+ if((ret_value = (*chunk_cb)(&chunk_rec, chunk_udata)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CALLBACK, H5_ITER_ERROR, "failure in generic chunk iterator callback")
+
+ /* Update coordinates of chunk in dataset */
+ curr_dim = (int)(ndims - 1);
+ while(curr_dim >= 0) {
+ /* Increment coordinate in current dimension */
+ chunk_rec.scaled[curr_dim]++;
+
+ /* Check if we went off the end of the current dimension */
+ if(chunk_rec.scaled[curr_dim] >= idx_info->layout->chunks[curr_dim]) {
+ /* Reset coordinate & move to next faster dimension */
+ chunk_rec.scaled[curr_dim] = 0;
+ curr_dim--;
+ } /* end if */
+ else
+ break;
+ } /* end while */
} /* end for */
+done:
FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__none_idx_iterate() */
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index ed3bc12..723acf9 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -569,6 +569,9 @@ H5_DLL herr_t H5D__get_space_status(const H5D_t *dset, H5D_space_status_t *alloc
H5_DLL herr_t H5D__alloc_storage(const H5D_io_info_t *io_info, H5D_time_alloc_t time_alloc, hbool_t full_overwrite, hsize_t old_dim[]);
H5_DLL herr_t H5D__get_storage_size(const H5D_t *dset, hsize_t *storage_size);
H5_DLL herr_t H5D__get_chunk_storage_size(H5D_t *dset, const hsize_t *offset, hsize_t *storage_size);
+H5_DLL herr_t H5D__get_num_chunks(const H5D_t *dset, const H5S_t *space, hsize_t *nchunks);
+H5_DLL herr_t H5D__get_chunk_info(const H5D_t *dset, const H5S_t *space, hsize_t chk_idx, hsize_t *coord, unsigned *filter_mask, haddr_t *offset, hsize_t *size);
+H5_DLL herr_t H5D__get_chunk_info_by_coord(const H5D_t *dset, const hsize_t *coord, unsigned *filter_mask, haddr_t *addr, hsize_t *size);
H5_DLL haddr_t H5D__get_offset(const H5D_t *dset);
H5_DLL void *H5D__vlen_get_buf_size_alloc(size_t size, void *info);
H5_DLL herr_t H5D__vlen_get_buf_size(void *elem, hid_t type_id, unsigned ndim, const hsize_t *point, void *op_data);
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 63f1a24..7234d16 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -142,6 +142,9 @@ H5_DLL hid_t H5Dget_create_plist(hid_t dset_id);
H5_DLL hid_t H5Dget_access_plist(hid_t dset_id);
H5_DLL hsize_t H5Dget_storage_size(hid_t dset_id);
H5_DLL herr_t H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_bytes);
+H5_DLL herr_t H5Dget_num_chunks(hid_t dset_id, hid_t fspace_id, hsize_t *nchunks);
+H5_DLL herr_t H5Dget_chunk_info_by_coord(hid_t dset_id, const hsize_t *coord, unsigned *filter_mask, haddr_t *addr, hsize_t *size);
+H5_DLL herr_t H5Dget_chunk_info(hid_t dset_id, hid_t fspace_id, hsize_t chk_idx, hsize_t *coord, unsigned *filter_mask, haddr_t *addr, hsize_t *size);
H5_DLL haddr_t H5Dget_offset(hid_t dset_id);
H5_DLL herr_t H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
hid_t file_space_id, hid_t plist_id, void *buf/*out*/);
diff --git a/src/H5EA.c b/src/H5EA.c
index d0bf474..96eee12 100644
--- a/src/H5EA.c
+++ b/src/H5EA.c
@@ -987,19 +987,25 @@ END_FUNC(PRIV) /* end H5EA_delete() */
* Purpose: Iterate over the elements of an extensible array
* (copied and modified from FA_iterate() in H5FA.c)
*
- * Return: SUCCEED/FAIL
+ * Return: H5_ITER_CONT/H5_ITER_ERROR
*
* Programmer: Vailin Choi; Feb 2015
*
+ * Modification:
+ * Prototype changed (HDFFV-10661)
+ * - herr_t to int
+ * - SUCCEED/FAIL to H5_ITER_CONT/H5_ITER_ERROR
+ * June 6, 2019 -BMR
*-------------------------------------------------------------------------
*/
BEGIN_FUNC(PRIV, ERR,
-herr_t, SUCCEED, FAIL,
+int, H5_ITER_CONT, H5_ITER_ERROR,
H5EA_iterate(H5EA_t *ea, H5EA_operator_t op, void *udata))
/* Local variables */
uint8_t *elmt = NULL;
hsize_t u;
+ int cb_ret = H5_ITER_CONT; /* Return value from callback */
/*
* Check arguments.
@@ -1013,9 +1019,7 @@ H5EA_iterate(H5EA_t *ea, H5EA_operator_t op, void *udata))
H5E_THROW(H5E_CANTALLOC, "memory allocation failed for extensible array element")
/* Iterate over all elements in array */
- for(u = 0; u < ea->hdr->stats.stored.max_idx_set; u++) {
- int cb_ret; /* Return value from callback */
-
+ for(u = 0; u < ea->hdr->stats.stored.max_idx_set && cb_ret == H5_ITER_CONT; u++) {
/* Get array element */
if(H5EA_get(ea, u, elmt) < 0)
H5E_THROW(H5E_CANTGET, "unable to delete fixed array")
diff --git a/src/H5FA.c b/src/H5FA.c
index 8c86193..df53f27 100644
--- a/src/H5FA.c
+++ b/src/H5FA.c
@@ -686,20 +686,26 @@ END_FUNC(PRIV) /* end H5FA_delete() */
* Note: This is not very efficient, we should be iterating directly
* over the fixed array's direct block [pages].
*
- * Return: SUCCEED/FAIL
+ * Return: H5_ITER_CONT/H5_ITER_ERROR
*
* Programmer: Vailin Choi
* Thursday, April 30, 2009
*
+ * Modification:
+ * Prototype changed (HDFFV-10661)
+ * - herr_t to int
+ * - SUCCEED/FAIL to H5_ITER_CONT/H5_ITER_ERROR
+ * June 6, 2019 -BMR
*-------------------------------------------------------------------------
*/
BEGIN_FUNC(PRIV, ERR,
-herr_t, SUCCEED, FAIL,
+int, H5_ITER_CONT, H5_ITER_ERROR,
H5FA_iterate(H5FA_t *fa, H5FA_operator_t op, void *udata))
/* Local variables */
uint8_t *elmt = NULL;
hsize_t u;
+ int cb_ret = H5_ITER_CONT; /* Return value from callback */
/*
* Check arguments.
@@ -713,9 +719,7 @@ H5FA_iterate(H5FA_t *fa, H5FA_operator_t op, void *udata))
H5E_THROW(H5E_CANTALLOC, "memory allocation failed for fixed array element")
/* Iterate over all elements in array */
- for(u = 0; u < fa->hdr->stats.nelmts; u++) {
- int cb_ret; /* Return value from callback */
-
+ for(u = 0; u < fa->hdr->stats.nelmts && cb_ret == H5_ITER_CONT; u++) {
/* Get array element */
if(H5FA_get(fa, u, elmt) < 0)
H5E_THROW(H5E_CANTGET, "unable to delete fixed array")
diff --git a/src/H5VLnative.h b/src/H5VLnative.h
index 1a3007a..73c6189 100644
--- a/src/H5VLnative.h
+++ b/src/H5VLnative.h
@@ -36,8 +36,11 @@ typedef int H5VL_native_dataset_optional_t;
#define H5VL_NATIVE_DATASET_FORMAT_CONVERT 0 /* H5Dformat_convert (internal) */
#define H5VL_NATIVE_DATASET_GET_CHUNK_INDEX_TYPE 1 /* H5Dget_chunk_index_type */
#define H5VL_NATIVE_DATASET_GET_CHUNK_STORAGE_SIZE 2 /* H5Dget_chunk_storage_size */
-#define H5VL_NATIVE_DATASET_CHUNK_READ 3 /* H5Dchunk_read */
-#define H5VL_NATIVE_DATASET_CHUNK_WRITE 4 /* H5Dchunk_write */
+#define H5VL_NATIVE_DATASET_GET_NUM_CHUNKS 3 /* H5Dget_num_chunks */
+#define H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_IDX 4 /* H5Dget_chunk_info */
+#define H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR 5 /* H5Dget_chunk_info_by_coord */
+#define H5VL_NATIVE_DATASET_CHUNK_READ 6 /* H5Dchunk_read */
+#define H5VL_NATIVE_DATASET_CHUNK_WRITE 7 /* H5Dchunk_write */
/* Typedef and values for native VOL connector file optional VOL operations */
typedef int H5VL_native_file_optional_t;
diff --git a/src/H5VLnative_dataset.c b/src/H5VLnative_dataset.c
index 1e3d263..631eb19 100644
--- a/src/H5VLnative_dataset.c
+++ b/src/H5VLnative_dataset.c
@@ -339,7 +339,7 @@ H5VL__native_dataset_specific(void *obj, H5VL_dataset_specific_t specific_type,
switch(specific_type) {
/* H5Dspecific_space */
case H5VL_DATASET_SET_EXTENT:
- {
+ { /* H5Dset_extent (H5Dextend - deprecated) */
const hsize_t *size = HDva_arg(arguments, const hsize_t *);
if(H5D__set_extent(dset, size) < 0)
@@ -348,7 +348,7 @@ H5VL__native_dataset_specific(void *obj, H5VL_dataset_specific_t specific_type,
}
case H5VL_DATASET_FLUSH:
- {
+ { /* H5Dflush */
hid_t dset_id = HDva_arg(arguments, hid_t);
/* Flush the dataset */
@@ -359,7 +359,7 @@ H5VL__native_dataset_specific(void *obj, H5VL_dataset_specific_t specific_type,
}
case H5VL_DATASET_REFRESH:
- {
+ { /* H5Drefresh */
hid_t dset_id = HDva_arg(arguments, hid_t);
/* Refresh the dataset */
@@ -399,7 +399,7 @@ H5VL__native_dataset_optional(void *obj, hid_t H5_ATTR_UNUSED dxpl_id,
switch(optional_type) {
case H5VL_NATIVE_DATASET_FORMAT_CONVERT:
- {
+ { /* H5Dformat_convert */
dset = (H5D_t *)obj;
switch(dset->shared->layout.type) {
@@ -434,7 +434,7 @@ H5VL__native_dataset_optional(void *obj, hid_t H5_ATTR_UNUSED dxpl_id,
}
case H5VL_NATIVE_DATASET_GET_CHUNK_INDEX_TYPE:
- {
+ { /* H5Dget_chunk_index_type */
H5D_chunk_index_t *idx_type = HDva_arg(arguments, H5D_chunk_index_t *);
dset = (H5D_t *)obj;
@@ -450,7 +450,7 @@ H5VL__native_dataset_optional(void *obj, hid_t H5_ATTR_UNUSED dxpl_id,
}
case H5VL_NATIVE_DATASET_GET_CHUNK_STORAGE_SIZE:
- {
+ { /* H5Dget_chunk_storage_size */
hsize_t *offset = HDva_arg(arguments, hsize_t *);
hsize_t *chunk_nbytes = HDva_arg(arguments, hsize_t *);
@@ -467,8 +467,94 @@ H5VL__native_dataset_optional(void *obj, hid_t H5_ATTR_UNUSED dxpl_id,
break;
}
+ case H5VL_NATIVE_DATASET_GET_NUM_CHUNKS:
+ { /* H5Dget_num_chunks */
+ const H5S_t *space = NULL;
+ hid_t space_id = HDva_arg(arguments, hid_t);
+ hsize_t *nchunks = HDva_arg(arguments, hsize_t *);
+
+ dset = (H5D_t *)obj;
+ HDassert(dset);
+ HDassert(dset->shared);
+ HDassert(dset->shared->space);
+
+ /* When default dataspace is given, use the dataset's dataspace */
+ if(space_id == H5S_ALL)
+ space = dset->shared->space;
+ else /* otherwise, use the given space ID */
+ if(NULL == (space = (const H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a valid dataspace ID")
+
+ /* Make sure the dataset is chunked */
+ if(H5D_CHUNKED != dset->shared->layout.type)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+ /* Call private function */
+ if(H5D__get_num_chunks(dset, space, nchunks) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get number of chunks")
+
+ break;
+ }
+
+ case H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_IDX:
+ { /* H5Dget_chunk_info */
+ const H5S_t *space = NULL;
+ hid_t space_id = HDva_arg(arguments, hid_t);
+ hsize_t chk_index = HDva_arg(arguments, hsize_t);
+ hsize_t *offset = HDva_arg(arguments, hsize_t *);
+ unsigned *filter_mask = HDva_arg(arguments, unsigned *);
+ haddr_t *addr = HDva_arg(arguments, haddr_t *);
+ hsize_t *size = HDva_arg(arguments, hsize_t *);
+
+ dset = (H5D_t *)obj;
+ HDassert(dset);
+ HDassert(dset->shared);
+
+ /* When default dataspace is given, use the dataset's dataspace */
+ if(space_id == H5S_ALL)
+ {
+ space = dset->shared->space;
+ if(NULL == space)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "unable to obtain a dataspace")
+ } /* otherwise, use the given space ID */
+ else
+ if(NULL == (space = (const H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a valid dataspace ID")
+
+ /* Make sure the dataset is chunked */
+ if(H5D_CHUNKED != dset->shared->layout.type)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+ /* Call private function */
+ if(H5D__get_chunk_info(dset, space, chk_index, offset, filter_mask, addr, size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info by index")
+ break;
+ }
+
+ case H5VL_NATIVE_DATASET_GET_CHUNK_INFO_BY_COOR:
+ { /* H5Dget_chunk_info_by_coord */
+ hsize_t *offset = HDva_arg(arguments, hsize_t *);
+ unsigned *filter_mask = HDva_arg(arguments, unsigned *);
+ haddr_t *addr = HDva_arg(arguments, haddr_t *);
+ hsize_t *size = HDva_arg(arguments, hsize_t *);
+
+ dset = (H5D_t *)obj;
+ HDassert(dset);
+ HDassert(dset->shared);
+
+ /* Make sure the dataset is chunked */
+ if(H5D_CHUNKED != dset->shared->layout.type)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+ /* Call private function */
+ if(H5D__get_chunk_info_by_coord(dset, offset, filter_mask, addr, size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get chunk info by its logical coordinates")
+
+ break;
+ }
+
case H5VL_NATIVE_DATASET_CHUNK_READ:
- {
+ { /* H5Dread_chunk */
const hsize_t *offset = HDva_arg(arguments, hsize_t *);
uint32_t *filters = HDva_arg(arguments, uint32_t *);
void *buf = HDva_arg(arguments, void *);
@@ -496,7 +582,7 @@ H5VL__native_dataset_optional(void *obj, hid_t H5_ATTR_UNUSED dxpl_id,
}
case H5VL_NATIVE_DATASET_CHUNK_WRITE:
- {
+ { /* H5Dwrite_chunk */
uint32_t filters = HDva_arg(arguments, uint32_t);
const hsize_t *offset = HDva_arg(arguments, const hsize_t *);
uint32_t data_size_32 = HDva_arg(arguments, uint32_t);