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authorVailin Choi <vchoi@jam.ad.hdfgroup.org>2017-04-25 23:08:53 (GMT)
committerVailin Choi <vchoi@jam.ad.hdfgroup.org>2017-04-25 23:08:53 (GMT)
commitcb8e82a53d91067b16deba7ebc76307a336b0f02 (patch)
tree88fb7095226155a86b9e8c63c6c621b22b4fe8d5 /src
parent9c30b393163cfaf069aa166ce261034b3010394d (diff)
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Incorporate patch from GE Healthcare (HDFFV-9934)
This is the same patch that had already been integrated to 1.8 branch (pull request #387). Tested on moohan, ostrich, platypus, emu, osx1010test, quail, kituo, mayll.
Diffstat (limited to 'src')
-rw-r--r--src/H5D.c40
-rw-r--r--src/H5Dchunk.c282
-rw-r--r--src/H5Dio.c149
-rw-r--r--src/H5Dpkg.h3
-rw-r--r--src/H5Dpublic.h6
-rw-r--r--src/H5Pdxpl.c28
6 files changed, 438 insertions, 70 deletions
diff --git a/src/H5D.c b/src/H5D.c
index 6f69ee4..a6de952 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -1087,3 +1087,43 @@ done:
FUNC_LEAVE_API(ret_value)
} /* H5Dget_chunk_index_type() */
+
+/*-------------------------------------------------------------------------
+ * Function: H5Dget_chunk_storage_size
+ *
+ * Purpose: Returns the size of an allocated chunk.
+ *
+ * Return: Non-negative on success, negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 20 October 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Dget_chunk_storage_size(hid_t dset_id, const hsize_t *offset, hsize_t *chunk_nbytes)
+{
+ H5D_t *dset = NULL;
+ herr_t ret_value = SUCCEED;
+
+ FUNC_ENTER_API(FAIL)
+ H5TRACE3("e", "i*h*h", dset_id, offset, chunk_nbytes);
+
+ /* Check arguments */
+ if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+ if( NULL == offset )
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
+ if( NULL == chunk_nbytes )
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid argument (null)")
+
+ 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_storage_size(dset, H5P_DATASET_XFER_DEFAULT, offset, chunk_nbytes) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get storage size of chunk")
+
+done:
+ FUNC_LEAVE_API(ret_value);
+}
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index ce684a0..4905a70 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -303,6 +303,9 @@ static herr_t H5D__chunk_collective_fill(const H5D_t *dset, hid_t dxpl_id,
H5D_chunk_coll_info_t *chunk_info, size_t chunk_size, const void *fill_buf);
#endif /* H5_HAVE_PARALLEL */
+static int
+H5D__chunk_dump_index_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
+
/*********************/
/* Package Variables */
/*********************/
@@ -369,8 +372,7 @@ H5FL_EXTERN(H5S_sel_iter_t);
/*-------------------------------------------------------------------------
* Function: H5D__chunk_direct_write
*
- * Purpose: Internal routine to write a chunk
- * directly into the file.
+ * Purpose: Internal routine to write a chunk directly into the file.
*
* Return: Non-negative on success/Negative on failure
*
@@ -408,7 +410,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
/* Allocate dataspace and initialize it if it hasn't been. */
if(!(*layout->ops->is_space_alloc)(&layout->storage)) {
- /* Allocate storage */
+ /* Allocate storage */
if(H5D__alloc_storage(&io_info, H5D_ALLOC_WRITE, FALSE, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize storage")
}
@@ -465,7 +467,7 @@ H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], FALSE) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
} /* end if */
/* Write the data to the file */
@@ -491,6 +493,244 @@ done:
/*-------------------------------------------------------------------------
+ * Function: H5D__chunk_direct_read
+ *
+ * Purpose: Internal routine to read a chunk directly from the file.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 14 February 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__chunk_direct_read(const H5D_t *dset, hid_t dxpl_id, hsize_t *offset,
+ uint32_t* filters, void *buf)
+{
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
+ H5D_chunk_ud_t udata; /* User data for querying chunk info */
+ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */
+ H5D_io_info_t io_info; /* to hold the dset and two dxpls (meta and raw data) */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ hbool_t md_dxpl_generated = FALSE; /* bool to indicate whether we should free the md_dxpl_id at exit */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(offset);
+ HDassert(filters);
+ HDassert(buf);
+
+ io_info.dset = dset;
+ io_info.raw_dxpl_id = dxpl_id;
+ io_info.md_dxpl_id = dxpl_id;
+
+ /* set the dxpl IO type for sanity checking at the FD layer */
+#ifdef H5_DEBUG_BUILD
+ if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls")
+ md_dxpl_generated = TRUE;
+#endif /* H5_DEBUG_BUILD */
+
+ /* Allocate dataspace and initialize it if it hasn't been. */
+ if(!(*layout->ops->is_space_alloc)(&layout->storage))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "storage is not initialized")
+
+ /* Calculate the index of this chunk */
+ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled);
+ scaled[dset->shared->ndims] = 0;
+
+ /* Reset fields about the chunk we are looking for */
+ udata.filter_mask = 0;
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Find out the file address of the chunk */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+
+ /* Sanity check */
+ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) ||
+ (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0));
+
+ /* Check if the requested chunk exists in the chunk cache */
+ if(UINT_MAX != udata.idx_hint) {
+ H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint];
+
+ /* Sanity checks */
+ HDassert(udata.idx_hint < rdcc->nslots);
+ HDassert(rdcc->slot[udata.idx_hint]);
+
+ /* If the cached chunk is dirty, it must be flushed to get accurate size */
+ if( ent->dirty == TRUE ) {
+
+ /* Fill the DXPL cache values for later use */
+ if(H5D__get_dxpl_cache(io_info.raw_dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Flush the chunk to disk and clear the cache entry */
+ if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+
+ /* Reset fields about the chunk we are looking for */
+ udata.filter_mask = 0;
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Get the new file address / chunk size after flushing */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+ }
+ }
+
+ /* Make sure the address of the chunk is returned. */
+ if(!H5F_addr_defined(udata.chunk_block.offset))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
+
+ /* Read the chunk data into the supplied buffer */
+ if(H5F_block_read(dset->oloc.file, H5FD_MEM_DRAW, udata.chunk_block.offset, udata.chunk_block.length, io_info.raw_dxpl_id, buf) < 0)
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk")
+
+ /* Return the filter mask */
+ *filters = udata.filter_mask;
+
+done:
+#ifdef H5_DEBUG_BUILD
+ if(md_dxpl_generated && H5I_dec_ref(io_info.md_dxpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close metadata dxpl")
+#endif /* H5_DEBUG_BUILD */
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5D__chunk_direct_read() */
+
+
+/*-------------------------------------------------------------------------
+ * Function: H5D__get_chunk_storage_size
+ *
+ * Purpose: Internal routine to read the storage size of a chunk on disk.
+ *
+ * Return: Non-negative on success/Negative on failure
+ *
+ * Programmer: Matthew Strong (GE Healthcare)
+ * 20 October 2016
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5D__get_chunk_storage_size(H5D_t *dset, hid_t dxpl_id, const hsize_t *offset, hsize_t *storage_size)
+{
+ const H5O_layout_t *layout = &(dset->shared->layout); /* Dataset layout */
+ const H5D_rdcc_t *rdcc = &(dset->shared->cache.chunk); /* raw data chunk cache */
+ hsize_t scaled[H5S_MAX_RANK]; /* Scaled coordinates for this chunk */
+ H5D_io_info_t io_info; /* to hold the dset and two dxpls (meta and raw data) */
+ H5D_chunk_ud_t udata; /* User data for querying chunk info */
+ H5D_dxpl_cache_t _dxpl_cache; /* Data transfer property cache buffer */
+ H5D_dxpl_cache_t *dxpl_cache = &_dxpl_cache; /* Data transfer property cache */
+ hbool_t md_dxpl_generated = FALSE; /* bool to indicate whether we should free the md_dxpl_id at exit */
+ herr_t ret_value = SUCCEED; /* Return value */
+
+ FUNC_ENTER_STATIC_TAG(dxpl_id, dset->oloc.addr, FAIL)
+
+ /* Check args */
+ HDassert(dset && H5D_CHUNKED == layout->type);
+ HDassert(offset);
+ HDassert(storage_size);
+
+ io_info.dset = dset;
+ io_info.raw_dxpl_id = dxpl_id;
+ io_info.md_dxpl_id = dxpl_id;
+
+ /* set the dxpl IO type for sanity checking at the FD layer */
+#ifdef H5_DEBUG_BUILD
+ if(H5D_set_io_info_dxpls(&io_info, dxpl_id) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOPY, FAIL, "can't set metadata and raw data dxpls")
+ md_dxpl_generated = TRUE;
+#endif /* H5_DEBUG_BUILD */
+
+ /* Allocate dataspace and initialize it if it hasn't been. */
+ if(!(*layout->ops->is_space_alloc)(&layout->storage)) {
+ *storage_size = 0;
+ HGOTO_DONE(SUCCEED)
+ }
+
+ /* Calculate the index of this chunk */
+ H5VM_chunk_scaled(dset->shared->ndims, offset, layout->u.chunk.dim, scaled);
+ scaled[dset->shared->ndims] = 0;
+
+ /* Reset fields about the chunk we are looking for */
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Find out the file address of the chunk */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+
+ /* Sanity check */
+ HDassert((H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length > 0) ||
+ (!H5F_addr_defined(udata.chunk_block.offset) && udata.chunk_block.length == 0));
+
+ /* The requested chunk is not in cache or on disk */
+ if(!H5F_addr_defined(udata.chunk_block.offset) && UINT_MAX == udata.idx_hint)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk storage is not allocated")
+
+ /* Check if there are filters registered to the dataset */
+ if( dset->shared->dcpl_cache.pline.nused > 0 ) {
+ /* Check if the requested chunk exists in the chunk cache */
+ if(UINT_MAX != udata.idx_hint) {
+ /* Sanity checks */
+ HDassert(udata.idx_hint < rdcc->nslots);
+ HDassert(rdcc->slot[udata.idx_hint]);
+ H5D_rdcc_ent_t *ent = rdcc->slot[udata.idx_hint];
+
+ /* If the cached chunk is dirty, it must be flushed to get accurate size */
+ if( ent->dirty == TRUE ) {
+ /* Fill the DXPL cache values for later use */
+ if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+ /* Flush the chunk to disk and clear the cache entry */
+ if(H5D__chunk_cache_evict(dset, io_info.md_dxpl_id, dxpl_cache, rdcc->slot[udata.idx_hint], TRUE) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTREMOVE, FAIL, "unable to evict chunk")
+
+ /* Reset fields about the chunk we are looking for */
+ udata.chunk_block.offset = HADDR_UNDEF;
+ udata.chunk_block.length = 0;
+ udata.idx_hint = UINT_MAX;
+
+ /* Get the new file address / chunk size after flushing */
+ if(H5D__chunk_lookup(dset, io_info.md_dxpl_id, scaled, &udata) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error looking up chunk address")
+ }
+ }
+
+ /* Make sure the address of the chunk is returned. */
+ if(!H5F_addr_defined(udata.chunk_block.offset))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "chunk address isn't defined")
+
+ /* Return the chunk size on disk */
+ *storage_size = udata.chunk_block.length;
+ }
+ /* There are no filters registered, return the chunk size from the storage layout */
+ else
+ *storage_size = dset->shared->layout.u.chunk.size;
+
+done:
+#ifdef H5_DEBUG_BUILD
+ if(md_dxpl_generated && H5I_dec_ref(io_info.md_dxpl_id) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTDEC, FAIL, "can't close metadata dxpl")
+#endif /* H5_DEBUG_BUILD */
+ FUNC_LEAVE_NOAPI(ret_value)
+} /* H5D__get_chunk_storage_size */
+
+
+/*-------------------------------------------------------------------------
* Function: H5D__chunk_set_info_real
*
* Purpose: Internal routine to set the information about chunks for a dataset
@@ -519,22 +759,22 @@ H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims,
/* Compute the # of chunks in dataset dimensions */
for(u = 0, layout->nchunks = 1, layout->max_nchunks = 1; u < ndims; u++) {
/* Round up to the next integer # of chunks, to accomodate partial chunks */
- layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
+ layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
if(H5S_UNLIMITED == max_dims[u])
layout->max_chunks[u] = H5S_UNLIMITED;
else
layout->max_chunks[u] = ((max_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
/* Accumulate the # of chunks */
- layout->nchunks *= layout->chunks[u];
- layout->max_nchunks *= layout->max_chunks[u];
+ layout->nchunks *= layout->chunks[u];
+ layout->max_nchunks *= layout->max_chunks[u];
} /* end for */
/* Get the "down" sizes for each dimension */
if(H5VM_array_down(ndims, layout->chunks, layout->down_chunks) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
if(H5VM_array_down(ndims, layout->max_chunks, layout->max_down_chunks) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't compute 'down' chunk size value")
done:
FUNC_LEAVE_NOAPI(ret_value)
@@ -2383,14 +2623,14 @@ H5D__chunk_dest(H5D_t *dset, hid_t dxpl_id)
/* Flush all the cached chunks */
for(ent = rdcc->head; ent; ent = next) {
- next = ent->next;
- if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
- nerrors++;
+ next = ent->next;
+ if(H5D__chunk_cache_evict(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ nerrors++;
} /* end for */
/* Continue even if there are failures. */
if(nerrors)
- HDONE_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
+ HDONE_ERROR(H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks")
/* Release cache structures */
if(rdcc->slot)
@@ -2997,27 +3237,27 @@ H5D__chunk_cache_evict(const H5D_t *dset, hid_t dxpl_id, const H5D_dxpl_cache_t
HDassert(ent->idx < rdcc->nslots);
if(flush) {
- /* Flush */
- if(H5D__chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
- HDONE_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
+ /* Flush */
+ if(H5D__chunk_flush_entry(dset, dxpl_id, dxpl_cache, ent, TRUE) < 0)
+ HDONE_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "cannot flush indexed storage buffer")
} /* end if */
else {
/* Don't flush, just free chunk */
- if(ent->chunk != NULL)
- ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk,
+ if(ent->chunk != NULL)
+ ent->chunk = (uint8_t *)H5D__chunk_mem_xfree(ent->chunk,
((ent->edge_chunk_state & H5D_RDCC_DISABLE_FILTERS) ? NULL
: &(dset->shared->dcpl_cache.pline)));
} /* end else */
/* Unlink from list */
if(ent->prev)
- ent->prev->next = ent->next;
+ ent->prev->next = ent->next;
else
- rdcc->head = ent->next;
+ rdcc->head = ent->next;
if(ent->next)
- ent->next->prev = ent->prev;
+ ent->next->prev = ent->prev;
else
- rdcc->tail = ent->prev;
+ rdcc->tail = ent->prev;
ent->prev = ent->next = NULL;
/* Unlink from temporary list */
diff --git a/src/H5Dio.c b/src/H5Dio.c
index dfd3f17..572e6cf 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -125,9 +125,13 @@ 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*/)
{
H5D_t *dset = NULL;
- const H5S_t *mem_space = NULL;
- const H5S_t *file_space = NULL;
- herr_t ret_value = SUCCEED; /* Return value */
+ const H5S_t *mem_space = NULL;
+ const H5S_t *file_space = NULL;
+ H5P_genplist_t *plist; /* Property list pointer */
+ hsize_t *direct_offset = NULL;
+ hbool_t direct_read = FALSE;
+ uint32_t direct_filters = 0;
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_API(FAIL)
H5TRACE6("e", "iiiiix", dset_id, mem_type_id, mem_space_id, file_space_id,
@@ -135,28 +139,29 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
/* check arguments */
if(NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(NULL == dset->oloc.file)
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
if(mem_space_id < 0 || file_space_id < 0)
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
if(H5S_ALL != mem_space_id) {
- if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+ if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
- /* Check for valid selection */
- if(H5S_SELECT_VALID(mem_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(mem_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
} /* end if */
+
if(H5S_ALL != file_space_id) {
- if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
+ if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space")
- /* Check for valid selection */
- if(H5S_SELECT_VALID(file_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(file_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
} /* end if */
/* Get the default dataset transfer property list if the user didn't provide one */
@@ -166,9 +171,55 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
if(TRUE != H5P_isa_class(plist_id, H5P_DATASET_XFER))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
- /* read raw data */
- if(H5D__read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
+ /* Get the dataset transfer property list */
+ if(NULL == (plist = (H5P_genplist_t *)H5I_object(plist_id)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
+
+ /* Retrieve the 'direct read' flag */
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &direct_read) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting flag for direct chunk read")
+
+ if(direct_read) {
+ unsigned u;
+ hsize_t dims[H5O_LAYOUT_NDIMS];
+ hsize_t internal_offset[H5O_LAYOUT_NDIMS];
+
+ if(H5D_CHUNKED != dset->shared->layout.type)
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+
+ /* Get the direct chunk offset property */
+ if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &direct_offset) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting direct offset from xfer properties")
+
+ /* The library's chunking code requires the offset terminates with a zero. So transfer the
+ * offset array to an internal offset array */
+ for(u = 0; u < dset->shared->ndims; u++) {
+ /* Make sure the offset doesn't exceed the dataset's dimensions */
+ if(direct_offset[u] > dset->shared->curr_dims[u])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+
+ /* Make sure the offset fall right on a chunk's boundary */
+ if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+
+ internal_offset[u] = direct_offset[u];
+ } /* end for */
+
+ /* Terminate the offset with a zero */
+ internal_offset[dset->shared->ndims] = 0;
+
+ /* Read the raw chunk */
+ if(H5D__chunk_direct_read(dset, plist_id, internal_offset, &direct_filters, buf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read chunk directly")
+ /* Set the chunk filter mask property */
+ if(H5P_set(plist, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, &direct_filters) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error setting filter mask xfer property")
+ }
+ else {
+ /* read raw data */
+ if(H5D__read(dset, mem_type_id, mem_space, file_space, plist_id, buf/*out*/) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
+ }
done:
FUNC_LEAVE_API(ret_value)
@@ -245,28 +296,28 @@ H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
/* Check dataspace selections if this is not a direct write */
if(!direct_write) {
if(mem_space_id < 0 || file_space_id < 0)
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
- if(H5S_ALL != mem_space_id) {
- if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
- /* Check for valid selection */
- if(H5S_SELECT_VALID(mem_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
- } /* end if */
- if(H5S_ALL != file_space_id) {
- if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
-
- /* Check for valid selection */
- if(H5S_SELECT_VALID(file_space) != TRUE)
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
- } /* end if */
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+ if(H5S_ALL != mem_space_id) {
+ if(NULL == (mem_space = (const H5S_t *)H5I_object_verify(mem_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(mem_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "memory selection+offset not within extent")
+ } /* end if */
+ if(H5S_ALL != file_space_id) {
+ if(NULL == (file_space = (const H5S_t *)H5I_object_verify(file_space_id, H5I_DATASPACE)))
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+
+ /* Check for valid selection */
+ if(H5S_SELECT_VALID(file_space) != TRUE)
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "file selection+offset not within extent")
+ } /* end if */
}
if(H5D__pre_write(dset, direct_write, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
done:
FUNC_LEAVE_API(ret_value)
@@ -300,15 +351,15 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
uint32_t direct_filters;
hsize_t *direct_offset;
uint32_t direct_datasize;
- hsize_t internal_offset[H5O_LAYOUT_NDIMS];
- unsigned u; /* Local index variable */
+ hsize_t internal_offset[H5O_LAYOUT_NDIMS];
+ unsigned u; /* Local index variable */
/* Get the dataset transfer property list */
if(NULL == (plist = (H5P_genplist_t *)H5I_object(dxpl_id)))
HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
if(H5D_CHUNKED != dset->shared->layout.type)
- HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
/* Retrieve parameters for direct chunk write */
if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &direct_filters) < 0)
@@ -318,19 +369,19 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
if(H5P_get(plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &direct_datasize) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "error getting data size for direct chunk write")
- /* The library's chunking code requires the offset terminates with a zero. So transfer the
+ /* The library's chunking code requires the offset terminates with a zero. So transfer the
* offset array to an internal offset array */
- for(u = 0; u < dset->shared->ndims; u++) {
- /* Make sure the offset doesn't exceed the dataset's dimensions */
+ for(u = 0; u < dset->shared->ndims; u++) {
+ /* Make sure the offset doesn't exceed the dataset's dimensions */
if(direct_offset[u] > dset->shared->curr_dims[u])
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset exceeds dimensions of dataset")
/* Make sure the offset fall right on a chunk's boundary */
- if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
- HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+ if(direct_offset[u] % dset->shared->layout.u.chunk.dim[u])
+ HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
- internal_offset[u] = direct_offset[u];
- } /* end for */
+ internal_offset[u] = direct_offset[u];
+ } /* end for */
/* Terminate the offset with a zero */
internal_offset[dset->shared->ndims] = 0;
@@ -342,7 +393,7 @@ H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
else { /* Normal write */
/* write raw data */
if(H5D__write(dset, mem_type_id, mem_space, file_space, dxpl_id, buf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
+ HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
} /* end else */
done:
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 8a4711f..b123b81 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -578,6 +578,7 @@ H5_DLL herr_t H5D__get_space_status(H5D_t *dset, H5D_space_status_t *allocation,
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(H5D_t *dset, hid_t dxpl_id, hsize_t *storage_size);
+H5_DLL herr_t H5D__get_chunk_storage_size(H5D_t *dset, hid_t dxpl_id, const hsize_t *offset, hsize_t *storage_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,
@@ -685,6 +686,8 @@ H5_DLL herr_t H5D__chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh,
H5O_storage_t *store);
H5_DLL herr_t H5D__chunk_direct_write(const H5D_t *dset, hid_t dxpl_id, uint32_t filters,
hsize_t *offset, uint32_t data_size, const void *buf);
+H5_DLL herr_t H5D__chunk_direct_read(const H5D_t *dset, hid_t dxpl_id, hsize_t *offset,
+ uint32_t *filters, void *buf);
#ifdef H5D_CHUNK_DEBUG
H5_DLL herr_t H5D__chunk_stats(const H5D_t *dset, hbool_t headers);
#endif /* H5D_CHUNK_DEBUG */
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index fe408b2..baa844a 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -40,6 +40,11 @@
#define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME "direct_chunk_filters"
#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME "direct_chunk_offset"
#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME "direct_chunk_datasize"
+
+/* Property names for H5LTDdirect_chunk_read */
+#define H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME "direct_chunk_read_flag"
+#define H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME "direct_chunk_read_offset"
+#define H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME "direct_chunk_read_filters"
/*******************/
/* Public Typedefs */
@@ -146,6 +151,7 @@ H5_DLL hid_t H5Dget_type(hid_t dset_id);
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 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/H5Pdxpl.c b/src/H5Pdxpl.c
index fdb402f..3c53c15 100644
--- a/src/H5Pdxpl.c
+++ b/src/H5Pdxpl.c
@@ -169,6 +169,13 @@
#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF NULL
#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE sizeof(uint32_t)
#define H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF 0
+/* Definitions for properties of direct chunk read */
+#define H5D_XFER_DIRECT_CHUNK_READ_FLAG_SIZE sizeof(hbool_t)
+#define H5D_XFER_DIRECT_CHUNK_READ_FLAG_DEF FALSE
+#define H5D_XFER_DIRECT_CHUNK_READ_FILTERS_SIZE sizeof(uint32_t)
+#define H5D_XFER_DIRECT_CHUNK_READ_FILTERS_DEF 0
+#define H5D_XFER_DIRECT_CHUNK_READ_OFFSET_SIZE sizeof(hsize_t *)
+#define H5D_XFER_DIRECT_CHUNK_READ_OFFSET_DEF NULL
/* Ring type - private property */
#define H5AC_XFER_RING_SIZE sizeof(unsigned)
#define H5AC_XFER_RING_DEF H5AC_RING_USER
@@ -293,6 +300,9 @@ static const hbool_t H5D_def_direct_chunk_flag_g = H5D_XFER_DIRECT_CHUNK_WRITE_F
static const uint32_t H5D_def_direct_chunk_filters_g = H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF; /* Default value for the filters of direct chunk write */
static const hsize_t *H5D_def_direct_chunk_offset_g = H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_DEF; /* Default value for the offset of direct chunk write */
static const uint32_t H5D_def_direct_chunk_datasize_g = H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_DEF; /* Default value for the datasize of direct chunk write */
+static const hbool_t direct_chunk_read_flag = H5D_XFER_DIRECT_CHUNK_READ_FLAG_DEF; /* Default value for the flag of direct chunk read */
+static const hsize_t *direct_chunk_read_offset = H5D_XFER_DIRECT_CHUNK_READ_OFFSET_DEF; /* Default value for the offset of direct chunk read */
+static const uint32_t direct_chunk_read_filters = H5D_XFER_DIRECT_CHUNK_READ_FILTERS_DEF; /* Default value for the filters of direct chunk read */
static const H5AC_ring_t H5D_ring_g = H5AC_XFER_RING_DEF; /* Default value for the cache entry ring type */
#ifdef H5_DEBUG_BUILD
static const H5FD_dxpl_type_t H5D_dxpl_type_g = H5FD_NOIO_DXPL; /* Default value for the dxpl type */
@@ -497,6 +507,24 @@ H5P__dxfr_reg_prop(H5P_genclass_t *pclass)
NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+ /* Register the property of flag for direct chunk read */
+ /* (Note: this property should not have an encode/decode callback) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, H5D_XFER_DIRECT_CHUNK_READ_FLAG_SIZE, &direct_chunk_read_flag,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+ /* Register the property of filter for direct chunk read */
+ /* (Note: this property should not have an encode/decode callback) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_SIZE, &direct_chunk_read_filters,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+ /* Register the property of offset for direct chunk read */
+ /* (Note: this property should not have an encode/decode callback) */
+ if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_SIZE, &direct_chunk_read_offset,
+ NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
/* Register the ring property (private) */
if(H5P_register_real(pclass, H5AC_RING_NAME, H5AC_XFER_RING_SIZE, &H5D_ring_g,
NULL, NULL, NULL, H5AC_XFER_RING_ENC, H5AC_XFER_RING_DEC,