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-rw-r--r--src/H5Dchunk.c387
1 files changed, 387 insertions, 0 deletions
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 082aac3..e3bbd59 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 +6973,373 @@ 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, the domain of the index in this function is of all
+ * the 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 */
+ 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 */
+ 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);
+
+ /* 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() */
+