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.

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,