Merge pull request #1043 in HDFFV/hdf5 from ~DEROBINS/hdf5_der:h5do_direct_chunk_hl_to_src to develop

* commit '1da9c5545c013ebc540ba3044810889d4acfa5be':
  Restored some unused #defines to the deprecated section of H5Dpublic.h.
  Added deprecated symbol wrappers for the H5DOwrite/read_chunk wrappers.
  Updated commenting in the H5DO compat test.
  Stripped out most of the duplicated functionality in the H5DO compat test.
  * Added H5DO compatibility functions. * Changed the offset copy to use an array on the stack. * Yanked some unused #defines.
  * Fixed the error tests * Moved common functionality into helper functions
  Normalize with trunk prior to update merge
  Fixed a warning.
  Finished move of H5DOread/write_chunk calls to H5D.
  First stage of moving H5DOread/write_chunk() to src/ and making them H5D calls. * Moved H5DOread/write_chunk() to H5Dio.c and renamed to H5D*. * Moved the hl/test/test_dset_opt test to test/ and renamed to   direct_chunk. * Moved the hl/test/dectris_hl_perf test to tools/test/perform   and renamed to direct_write_perf. * Updated autotools and CMake files.

8 files changed, 318 insertions, 584 deletions

diff --git a/src/H5CX.c b/src/H5CX.c
index deaf1a1..f809d1c 100644
--- a/src/H5CX.c
+++ b/src/H5CX.c
@@ -233,24 +233,10 @@ typedef struct H5CX_t {
     hbool_t data_transform_valid; /* Whether data transform info is valid */
     H5T_vlen_alloc_info_t vl_alloc_info; /* VL datatype alloc info (H5D_XFER_VLEN_*_NAME) */
     hbool_t vl_alloc_info_valid; /* Whether VL datatype alloc info is valid */
-    hbool_t dcr_flag;           /* Direct chunk read flag (H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME) */
-    hbool_t dcr_flag_valid;     /* Whether direct chunk read flag is valid */
-    hsize_t *dcr_offset;        /* Direct chunk read offset (H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME) */
-    hbool_t dcr_offset_valid;   /* Whether direct chunk read offset is valid */
-    hbool_t dcw_flag;           /* Direct chunk write flag (H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME) */
-    hbool_t dcw_flag_valid;     /* Whether direct chunk write flag is valid */
-    uint32_t dcw_filters;       /* Direct chunk write filter flags (H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME) */
-    hbool_t dcw_filters_valid;  /* Whether direct chunk write filter flags is valid */
-    hsize_t *dcw_offset;        /* Direct chunk write offset (H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME) */
-    hbool_t dcw_offset_valid;   /* Whether direct chunk write offset is valid */
-    uint32_t dcw_datasize;      /* Direct chunk write data size (H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME) */
-    hbool_t dcw_datasize_valid; /* Whether direct chunk write data size is valid */
     H5T_conv_cb_t dt_conv_cb;   /* Datatype conversion struct (H5D_XFER_CONV_CB_NAME) */
     hbool_t dt_conv_cb_valid;   /* Whether datatype conversion struct is valid */
 
     /* Return-only DXPL properties to return to application */
-    uint32_t dcr_filters;       /* Direct chunk read filter flags (H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME) */
-    hbool_t dcr_filters_set;    /* Whether direct chunk read filter flags are set */
 #ifdef H5_HAVE_PARALLEL
     H5D_mpio_actual_chunk_opt_mode_t mpio_actual_chunk_opt; /* Chunk optimization mode used for parallel I/O (H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME) */
     hbool_t mpio_actual_chunk_opt_set; /* Whether chunk optimization mode used for parallel I/O is set */
@@ -321,12 +307,6 @@ typedef struct H5CX_dxpl_cache_t {
     H5Z_cb_t filter_cb;             /* Filter callback function (H5D_XFER_FILTER_CB_NAME) */
     H5Z_data_xform_t *data_transform; /* Data transform info (H5D_XFER_XFORM_NAME) */
     H5T_vlen_alloc_info_t vl_alloc_info; /* VL datatype alloc info (H5D_XFER_VLEN_*_NAME) */
-    hbool_t dcr_flag;               /* Direct chunk read flag (H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME) */
-    hsize_t *dcr_offset;            /* Direct chunk read offset (H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME) */
-    hbool_t dcw_flag;               /* Direct chunk write flag (H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME) */
-    uint32_t dcw_datasize;          /* Direct chunk write data size (H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME) */
-    hsize_t *dcw_offset;            /* Direct chunk write offset (H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME) */
-    uint32_t dcw_filters;           /* Direct chunk write filter flags (H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME) */
     H5T_conv_cb_t dt_conv_cb;       /* Datatype conversion struct (H5D_XFER_CONV_CB_NAME) */
 } H5CX_dxpl_cache_t;
 
@@ -469,27 +449,10 @@ H5CX__init_package(void)
     if(H5P_get(dx_plist, H5D_XFER_VLEN_FREE_INFO_NAME, &H5CX_def_dxpl_cache.vl_alloc_info.free_info) < 0)
         HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve VL datatype alloc info")
 
-    /* Get direct chunk read info */
-    if(H5P_get(dx_plist, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &H5CX_def_dxpl_cache.dcr_flag) < 0)
-        HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve direct chunk read flag")
-    if(H5P_get(dx_plist, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &H5CX_def_dxpl_cache.dcr_offset) < 0)
-        HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve direct chunk read offset")
-
-    /* Get direct chunk write info */
-    if(H5P_get(dx_plist, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &H5CX_def_dxpl_cache.dcw_flag) < 0)
-        HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve direct chunk write flag")
-    if(H5P_get(dx_plist, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &H5CX_def_dxpl_cache.dcw_filters) < 0)
-        HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve direct chunk write filter mask")
-    if(H5P_get(dx_plist, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &H5CX_def_dxpl_cache.dcw_offset) < 0)
-        HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve direct chunk write offset")
-    if(H5P_get(dx_plist, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &H5CX_def_dxpl_cache.dcw_datasize) < 0)
-        HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve direct chunk write data size")
-
     /* Get datatype conversion struct */
     if(H5P_get(dx_plist, H5D_XFER_CONV_CB_NAME, &H5CX_def_dxpl_cache.dt_conv_cb) < 0)
         HGOTO_ERROR(H5E_CONTEXT, H5E_CANTGET, FAIL, "Can't retrieve datatype conversion exception callback")
 
-
     /* Reset the "default LAPL cache" information */
     HDmemset(&H5CX_def_lapl_cache, 0, sizeof(H5CX_lapl_cache_t));
 
@@ -1791,216 +1754,6 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:    H5CX_get_dcr_flag
- *
- * Purpose:     Retrieves the direct chunk read flag for the current API call context.
- *
- * Return:      Non-negative on success / Negative on failure
- *
- * Programmer:  Quincey Koziol
- *              March 6, 2018
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5CX_get_dcr_flag(hbool_t *dcr_flag)
-{
-    H5CX_node_t **head = H5CX_get_my_context();  /* Get the pointer to the head of the API context, for this thread */
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity check */
-    HDassert(dcr_flag);
-    HDassert(head && *head);
-    HDassert(H5P_DEFAULT != (*head)->ctx.dxpl_id);
-
-    H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, dcr_flag)
-
-    /* Get the value */
-    *dcr_flag = (*head)->ctx.dcr_flag;
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5CX_get_dcr_flag() */
-
-
-/*-------------------------------------------------------------------------
- * Function:    H5CX_get_dcr_offset
- *
- * Purpose:     Retrieves the direct chunk read offset for the current API call context.
- *
- * Return:      Non-negative on success / Negative on failure
- *
- * Programmer:  Quincey Koziol
- *              March 6, 2018
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5CX_get_dcr_offset(hsize_t **dcr_offset)
-{
-    H5CX_node_t **head = H5CX_get_my_context();  /* Get the pointer to the head of the API context, for this thread */
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity check */
-    HDassert(dcr_offset);
-    HDassert(head && *head);
-    HDassert(H5P_DEFAULT != (*head)->ctx.dxpl_id);
-
-    H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, dcr_offset)
-
-    /* Get the value */
-    *dcr_offset = (*head)->ctx.dcr_offset;
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5CX_get_dcr_offset() */
-
-
-/*-------------------------------------------------------------------------
- * Function:    H5CX_get_dcw_flag
- *
- * Purpose:     Retrieves the direct chunk write flag for the current API call context.
- *
- * Return:      Non-negative on success / Negative on failure
- *
- * Programmer:  Quincey Koziol
- *              March 6, 2018
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5CX_get_dcw_flag(hbool_t *dcw_flag)
-{
-    H5CX_node_t **head = H5CX_get_my_context();  /* Get the pointer to the head of the API context, for this thread */
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity check */
-    HDassert(dcw_flag);
-    HDassert(head && *head);
-    HDassert(H5P_DEFAULT != (*head)->ctx.dxpl_id);
-
-    H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, dcw_flag)
-
-    /* Get the value */
-    *dcw_flag = (*head)->ctx.dcw_flag;
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5CX_get_dcw_flag() */
-
-
-/*-------------------------------------------------------------------------
- * Function:    H5CX_get_dcw_filters
- *
- * Purpose:     Retrieves the direct chunk write filter mask for the current API call context.
- *
- * Return:      Non-negative on success / Negative on failure
- *
- * Programmer:  Quincey Koziol
- *              March 6, 2018
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5CX_get_dcw_filters(uint32_t *dcw_filters)
-{
-    H5CX_node_t **head = H5CX_get_my_context();  /* Get the pointer to the head of the API context, for this thread */
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity check */
-    HDassert(dcw_filters);
-    HDassert(head && *head);
-    HDassert(H5P_DEFAULT != (*head)->ctx.dxpl_id);
-
-    H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, dcw_filters)
-
-    /* Get the value */
-    *dcw_filters = (*head)->ctx.dcw_filters;
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5CX_get_dcw_filters() */
-
-
-/*-------------------------------------------------------------------------
- * Function:    H5CX_get_dcw_offset
- *
- * Purpose:     Retrieves the direct chunk write offset for the current API call context.
- *
- * Return:      Non-negative on success / Negative on failure
- *
- * Programmer:  Quincey Koziol
- *              March 6, 2018
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5CX_get_dcw_offset(hsize_t **dcw_offset)
-{
-    H5CX_node_t **head = H5CX_get_my_context();  /* Get the pointer to the head of the API context, for this thread */
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity check */
-    HDassert(dcw_offset);
-    HDassert(head && *head);
-    HDassert(H5P_DEFAULT != (*head)->ctx.dxpl_id);
-
-    H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, dcw_offset)
-
-    /* Get the value */
-    *dcw_offset = (*head)->ctx.dcw_offset;
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5CX_get_dcw_offset() */
-
-
-/*-------------------------------------------------------------------------
- * Function:    H5CX_get_dcw_datasize
- *
- * Purpose:     Retrieves the direct chunk write data size for the current API call context.
- *
- * Return:      Non-negative on success / Negative on failure
- *
- * Programmer:  Quincey Koziol
- *              March 6, 2018
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5CX_get_dcw_datasize(uint32_t *dcw_datasize)
-{
-    H5CX_node_t **head = H5CX_get_my_context();  /* Get the pointer to the head of the API context, for this thread */
-    herr_t ret_value = SUCCEED;         /* Return value */
-
-    FUNC_ENTER_NOAPI(FAIL)
-
-    /* Sanity check */
-    HDassert(dcw_datasize);
-    HDassert(head && *head);
-    HDassert(H5P_DEFAULT != (*head)->ctx.dxpl_id);
-
-    H5CX_RETRIEVE_PROP_VALID(dxpl, H5P_DATASET_XFER_DEFAULT, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, dcw_datasize)
-
-    /* Get the value */
-    *dcw_datasize = (*head)->ctx.dcw_datasize;
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value)
-} /* end H5CX_get_dcw_datasize() */
-
-
-/*-------------------------------------------------------------------------
  * Function:    H5CX_get_dt_conv_cb
  *
  * Purpose:     Retrieves the datatype conversion exception callback for the current API call context.
@@ -2358,38 +2111,6 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5CX_set_nlinks() */
 
-
-/*-------------------------------------------------------------------------
- * Function:    H5CX_set_dcr_filters
- *
- * Purpose:     Sets the direct chunk read filter flags for the current API call context.
- *
- * Return:      <none>
- *
- * Programmer:  Quincey Koziol
- *              March 6, 2018
- *
- *-------------------------------------------------------------------------
- */
-void
-H5CX_set_dcr_filters(uint32_t direct_filters)
-{
-    H5CX_node_t **head = H5CX_get_my_context();  /* Get the pointer to the head of the API context, for this thread */
-
-    FUNC_ENTER_NOAPI_NOINIT_NOERR
-
-    /* Sanity checks */
-    HDassert(head && *head);
-    HDassert(!((*head)->ctx.dxpl_id == H5P_DEFAULT || 
-            (*head)->ctx.dxpl_id == H5P_DATASET_XFER_DEFAULT));
-
-    /* Cache the filter mask for later, marking it to set in DXPL when context popped */
-    (*head)->ctx.dcr_filters = direct_filters;
-    (*head)->ctx.dcr_filters_set = TRUE;
-
-    FUNC_LEAVE_NOAPI_VOID
-} /* end H5CX_set_dcr_filters() */
-
 #ifdef H5_HAVE_PARALLEL
 
 /*-------------------------------------------------------------------------
@@ -2755,7 +2476,6 @@ H5CX__pop_common(void)
     HDassert(head && *head);
 
     /* Check for cached DXPL properties to return to application */
-    H5CX_SET_PROP(H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, dcr_filters)
 #ifdef H5_HAVE_PARALLEL
     H5CX_SET_PROP(H5D_MPIO_ACTUAL_CHUNK_OPT_MODE_NAME, mpio_actual_chunk_opt)
     H5CX_SET_PROP(H5D_MPIO_ACTUAL_IO_MODE_NAME, mpio_actual_io_mode)
diff --git a/src/H5CXprivate.h b/src/H5CXprivate.h
index 3566f11..44a4067 100644
--- a/src/H5CXprivate.h
+++ b/src/H5CXprivate.h
@@ -95,12 +95,6 @@ H5_DLL herr_t H5CX_get_err_detect(H5Z_EDC_t *err_detect);
 H5_DLL herr_t H5CX_get_filter_cb(H5Z_cb_t *filter_cb);
 H5_DLL herr_t H5CX_get_data_transform(H5Z_data_xform_t **data_transform);
 H5_DLL herr_t H5CX_get_vlen_alloc_info(H5T_vlen_alloc_info_t *vl_alloc_info);
-H5_DLL herr_t H5CX_get_dcr_flag(hbool_t *direct_read);
-H5_DLL herr_t H5CX_get_dcr_offset(hsize_t **direct_offset);
-H5_DLL herr_t H5CX_get_dcw_flag(hbool_t *direct_write);
-H5_DLL herr_t H5CX_get_dcw_filters(uint32_t *direct_filters);
-H5_DLL herr_t H5CX_get_dcw_offset(hsize_t **direct_offset);
-H5_DLL herr_t H5CX_get_dcw_datasize(uint32_t *direct_datasize);
 H5_DLL herr_t H5CX_get_dt_conv_cb(H5T_conv_cb_t *cb_struct);
 
 /* "Getter" routines for LAPL properties cached in API context */
@@ -127,7 +121,6 @@ H5_DLL herr_t H5CX_set_vlen_alloc_info(H5MM_allocate_t alloc_func,
 H5_DLL herr_t H5CX_set_nlinks(size_t nlinks);
 
 /* "Setter" routines for cached DXPL properties that must be returned to application */
-H5_DLL void H5CX_set_dcr_filters(uint32_t direct_filters);
 #ifdef H5_HAVE_PARALLEL
 H5_DLL void H5CX_set_mpio_actual_chunk_opt(H5D_mpio_actual_chunk_opt_mode_t chunk_opt);
 H5_DLL void H5CX_set_mpio_actual_io_mode(H5D_mpio_actual_io_mode_t actual_io_mode);
diff --git a/src/H5Dio.c b/src/H5Dio.c
index 1566b5e..452105e 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -50,7 +50,8 @@
 /* Local Prototypes */
 /********************/
 
-/* Setup/teardown routines */
+static herr_t H5D__get_offset_copy(const H5D_t *dset, const hsize_t *offset,
+        hsize_t *offset_copy/*out*/);
 static herr_t H5D__ioinfo_init(H5D_t *dset, const H5D_type_info_t *type_info,
     H5D_storage_t *store, H5D_io_info_t *io_info);
 static herr_t H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id,
@@ -80,32 +81,81 @@ H5FL_DEFINE(H5D_chunk_map_t);
 
 
 /*-------------------------------------------------------------------------
+ * Function:    H5D__get_offset_copy
+ *
+ * Purpose:     Gets a copy of the user's offset array that is guaraneteed
+ *              to be suitable for use by the library.
+ *
+ * Return:      SUCCEED/FAIL
+ *
+ *-------------------------------------------------------------------------
+ */
+static herr_t
+H5D__get_offset_copy(const H5D_t *dset, const hsize_t *offset, hsize_t *offset_copy)
+{
+    unsigned u;
+    herr_t ret_value = SUCCEED;     /* Return value */
+
+    FUNC_ENTER_NOAPI(FAIL)
+
+    HDassert(dset);
+    HDassert(offset);
+    HDassert(offset_copy);
+
+
+    /* The library's chunking code requires the offset to terminate with a zero.
+     * So transfer the offset array to an internal offset array that we
+     * can properly terminate (handled via the calloc call).
+     */
+
+    HDmemset(offset_copy, 0, H5O_LAYOUT_NDIMS * sizeof(hsize_t));
+
+    for (u = 0; u < dset->shared->ndims; u++) {
+        /* Make sure the offset doesn't exceed the dataset's dimensions */
+        if (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 (offset[u] % dset->shared->layout.u.chunk.dim[u])
+            HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL, "offset doesn't fall on chunks's boundary")
+
+        offset_copy[u] = offset[u];
+    }
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+
+} /* end H5D__get_offset_copy() */
+
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5Dread
  *
- * Purpose:	Reads (part of) a DSET from the file into application
- *		memory BUF. The part of the dataset to read is defined with
- *		MEM_SPACE_ID and FILE_SPACE_ID.	 The data points are
- *		converted from their file type to the MEM_TYPE_ID specified.
- *		Additional miscellaneous data transfer properties can be
- *		passed to this function with the PLIST_ID argument.
+ * Purpose:     Reads (part of) a DSET from the file into application
+ *              memory BUF. The part of the dataset to read is defined with
+ *              MEM_SPACE_ID and FILE_SPACE_ID.	 The data points are
+ *              converted from their file type to the MEM_TYPE_ID specified.
+ *              Additional miscellaneous data transfer properties can be
+ *              passed to this function with the PLIST_ID argument.
  *
- *		The FILE_SPACE_ID can be the constant H5S_ALL which indicates
- *		that the entire file dataspace is to be referenced.
+ *              The FILE_SPACE_ID can be the constant H5S_ALL which indicates
+ *              that the entire file dataspace is to be referenced.
  *
- *		The MEM_SPACE_ID can be the constant H5S_ALL in which case
- *		the memory dataspace is the same as the file dataspace
- *		defined when the dataset was created.
+ *              The MEM_SPACE_ID can be the constant H5S_ALL in which case
+ *              the memory dataspace is the same as the file dataspace
+ *              defined when the dataset was created.
  *
- *		The number of elements in the memory dataspace must match
- *		the number of elements in the file dataspace.
+ *              The number of elements in the memory dataspace must match
+ *              the number of elements in the file dataspace.
  *
- *		The PLIST_ID can be the constant H5P_DEFAULT in which
- *		case the default data transfer properties are used.
+ *              The PLIST_ID can be the constant H5P_DEFAULT in which
+ *              case the default data transfer properties are used.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Robb Matzke
- *		Thursday, December  4, 1997
+ * Programmer:  Robb Matzke
+ *              Thursday, December 4, 1997
  *
  *-------------------------------------------------------------------------
  */
@@ -113,135 +163,136 @@ herr_t
 H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
     hid_t file_space_id, hid_t dxpl_id, void *buf/*out*/)
 {
-    H5D_t	    *dset = NULL;
-    const H5S_t	    *mem_space = NULL;
-    const H5S_t	    *file_space = NULL;
-    hbool_t         direct_read = FALSE;
-    herr_t          ret_value = SUCCEED;    /* Return value */
+    H5D_t	       *dset        = NULL;
+    const H5S_t	   *mem_space   = NULL;
+    const H5S_t	   *file_space  = NULL;
+    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,
              dxpl_id, buf);
 
-    /* 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 == dset->oloc.file)
-        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset")
+    /* Get dataset pointer */
+    if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID")
+    if (NULL == dset->oloc.file)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
 
-    if(mem_space_id < 0 || file_space_id < 0)
-        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataspace")
+    /* Get validated dataspace pointers */
+    if (H5S_get_validated_dataspace(mem_space_id, &mem_space) < 0)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from mem_space_id")
+    if (H5S_get_validated_dataspace(file_space_id, &file_space) < 0)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from file_space_id")
 
-    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")
+    /* Get the default dataset transfer property list if the user didn't provide one */
+    if (H5P_DEFAULT == dxpl_id)
+        dxpl_id = H5P_DATASET_XFER_DEFAULT;
+    else
+        if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
 
-        /* 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 */
+    /* Set DXPL for operation */
+    H5CX_set_dxpl(dxpl_id);
 
-    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")
+    /* Read raw data */
+    if (H5D__read(dset, mem_type_id, mem_space, file_space, buf/*out*/) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
 
-        /* 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 */
+done:
+    FUNC_LEAVE_API(ret_value)
+} /* end H5Dread() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5Dread_chunk
+ *
+ * Purpose:     Reads an entire chunk from the file directly.
+ *
+ * Return:      Non-negative on success/Negative on failure
+ *
+ * Programmer:  Matthew Strong (GE Healthcare)
+ *              14 February 2016
+ *
+ *---------------------------------------------------------------------------
+ */
+herr_t
+H5Dread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters,
+         void *buf)
+{
+    H5D_t      *dset = NULL;
+    hsize_t     offset_copy[H5O_LAYOUT_NDIMS];  /* Internal copy of chunk offset */
+    herr_t      ret_value = SUCCEED;            /* Return value */
+
+    FUNC_ENTER_API(FAIL)
+    H5TRACE5("e", "ii*h*Iu*x", dset_id, dxpl_id, offset, filters, buf);
+
+    /* Check arguments */
+    if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID")
+    if (NULL == dset->oloc.file)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
+    if (H5D_CHUNKED != dset->shared->layout.type)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+    if (!buf)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "buf cannot be NULL")
+    if (!offset)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "offset cannot be NULL")
+    if (!filters)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "filters cannot be NULL")
 
     /* Get the default dataset transfer property list if the user didn't provide one */
-    if(H5P_DEFAULT == dxpl_id)
+    if (H5P_DEFAULT == dxpl_id)
         dxpl_id = H5P_DATASET_XFER_DEFAULT;
     else
-        if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
-            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
+        if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID")
 
     /* Set DXPL for operation */
     H5CX_set_dxpl(dxpl_id);
 
-    /* Retrieve the 'direct read' flag */
-    if(H5CX_get_dcr_flag(&direct_read) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error getting flag for direct chunk read")
-
-    /* Set up for direct read of chunk, bypassing filters, etc. */
-    if(direct_read) {
-        hsize_t *direct_offset;         /* Chunk offset from calling routine */
-        hsize_t internal_offset[H5O_LAYOUT_NDIMS];      /* Internal copy of chunk offset */
-        uint32_t direct_filters = 0;    /* Filters for chunk */
-        unsigned u;                     /* Local index variable */
-
-        /* Sanity check */
-        if(H5D_CHUNKED != dset->shared->layout.type)
-            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
-
-        /* Get the direct chunk offset */
-        if(H5CX_get_dcr_offset(&direct_offset) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error getting offset for direct chunk read")
-        HDassert(direct_offset);
-
-        /* 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, internal_offset, &direct_filters, buf) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read chunk directly")
-
-        /* Set the chunk filter mask for application */
-        H5CX_set_dcr_filters(direct_filters);
-    } /* end if */
-    else
-        /* Read raw data */
-        if(H5D__read(dset, mem_type_id, mem_space, file_space, buf/*out*/) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read data")
+    /* Copy the user's offset array so we can be sure it's terminated properly.
+     * (we don't want to mess with the user's buffer).
+     */
+    if (H5D__get_offset_copy(dset, offset, offset_copy) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failure to copy offset array")
+
+    /* Read the raw chunk */
+    if (H5D__chunk_direct_read(dset, offset_copy, filters, buf) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "can't read unprocessed chunk data")
 
 done:
     FUNC_LEAVE_API(ret_value)
-} /* end H5Dread() */
+} /* end H5Dread_chunk() */
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5Dwrite
+ * Function:    H5Dwrite
  *
- * Purpose:	Writes (part of) a DSET from application memory BUF to the
- *		file.  The part of the dataset to write is defined with the
- *		MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
- *		are converted from their current type (MEM_TYPE_ID) to their
- *		file datatype.	 Additional miscellaneous data transfer
- *		properties can be passed to this function with the
- *		PLIST_ID argument.
+ * Purpose:     Writes (part of) a DSET from application memory BUF to the
+ *              file. The part of the dataset to write is defined with the
+ *              MEM_SPACE_ID and FILE_SPACE_ID arguments. The data points
+ *              are converted from their current type (MEM_TYPE_ID) to their
+ *              file datatype. Additional miscellaneous data transfer
+ *              properties can be passed to this function with the
+ *              PLIST_ID argument.
  *
- *		The FILE_SPACE_ID can be the constant H5S_ALL which indicates
- *		that the entire file dataspace is to be referenced.
+ *              The FILE_SPACE_ID can be the constant H5S_ALL which indicates
+ *              that the entire file dataspace is to be referenced.
  *
- *		The MEM_SPACE_ID can be the constant H5S_ALL in which case
- *		the memory dataspace is the same as the file dataspace
- *		defined when the dataset was created.
+ *              The MEM_SPACE_ID can be the constant H5S_ALL in which case
+ *              the memory dataspace is the same as the file dataspace
+ *              defined when the dataset was created.
  *
- *		The number of elements in the memory dataspace must match
- *		the number of elements in the file dataspace.
+ *              The number of elements in the memory dataspace must match
+ *              the number of elements in the file dataspace.
  *
- *		The PLIST_ID can be the constant H5P_DEFAULT in which
- *		case the default data transfer properties are used.
+ *              The PLIST_ID can be the constant H5P_DEFAULT in which
+ *              case the default data transfer properties are used.
  *
- * Return:	Non-negative on success/Negative on failure
+ * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:	Robb Matzke
- *		Thursday, December  4, 1997
+ * Programmer:  Robb Matzke
+ *              Thursday, December 4, 1997
  *
  *-------------------------------------------------------------------------
  */
@@ -249,61 +300,40 @@ herr_t
 H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
     hid_t file_space_id, hid_t dxpl_id, const void *buf)
 {
-    H5D_t		   *dset = NULL;
+    H5D_t                  *dset = NULL;
     const H5S_t            *mem_space = NULL;
     const H5S_t            *file_space = NULL;
-    hbool_t                 direct_write = FALSE;
     herr_t                  ret_value = SUCCEED;  /* Return value */
 
     FUNC_ENTER_API(FAIL)
     H5TRACE6("e", "iiiii*x", dset_id, mem_type_id, mem_space_id, file_space_id,
              dxpl_id, buf);
 
-    /* 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 == dset->oloc.file)
-	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a file")
+    /* Get dataset pointer and ensure it's associated with a file */
+    if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dset_id is not a dataset ID")
+    if (NULL == dset->oloc.file)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
+
+    /* Get validated dataspace pointers */
+    if (H5S_get_validated_dataspace(mem_space_id, &mem_space) < 0)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from mem_space_id")
+    if (H5S_get_validated_dataspace(file_space_id, &file_space) < 0)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "could not get a validated dataspace from file_space_id")
 
     /* Get the default dataset transfer property list if the user didn't provide one */
-    if(H5P_DEFAULT == dxpl_id)
+    if (H5P_DEFAULT == dxpl_id)
         dxpl_id = H5P_DATASET_XFER_DEFAULT;
     else
-        if(TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
+        if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not xfer parms")
 
     /* Set DXPL for operation */
     H5CX_set_dxpl(dxpl_id);
 
-    /* Retrieve the 'direct write' flag */
-    if(H5CX_get_dcw_flag(&direct_write) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error getting flag for direct chunk read")
-
-    /* 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 */
-    } /* end if */
-
-    if(H5D__pre_write(dset, direct_write, mem_type_id, mem_space, file_space, buf) < 0) 
-        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't prepare for writing data")
+    /* Write the data */
+    if (H5D__write(dset, mem_type_id, mem_space, file_space, buf) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
 
 done:
     FUNC_LEAVE_API(ret_value)
@@ -311,70 +341,71 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:    H5D__pre_write
+ * Function:    H5Dwrite_chunk
  *
- * Purpose:     Preparation for writing data.
+ * Purpose:     Writes an entire chunk to the file directly.	
  *
- * Return:      SUCCEED/FAIL
+ * Return:      Non-negative on success/Negative on failure
+ *
+ * Programmer:	Raymond Lu
+ *		        30 July 2012
  *
  *-------------------------------------------------------------------------
  */
 herr_t
-H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id, 
-    const H5S_t *mem_space, const H5S_t *file_space, const void *buf)
+H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, 
+         size_t data_size, const void *buf)
 {
-    herr_t                  ret_value = SUCCEED;  /* Return value */
+    H5D_t      *dset = NULL;
+    hsize_t     offset_copy[H5O_LAYOUT_NDIMS];  /* Internal copy of chunk offset */
+    uint32_t    data_size_32;                   /* Chunk data size (limited to 32-bits currently) */
+    herr_t      ret_value = SUCCEED;            /* Return value */
+    
+    FUNC_ENTER_API(FAIL)
+    H5TRACE6("e", "iiIu*hz*x", dset_id, dxpl_id, filters, offset, data_size, buf);
+
+    /* Check arguments */
+    if (NULL == (dset = (H5D_t *)H5I_object_verify(dset_id, H5I_DATASET)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataset ID")
+    if (NULL == dset->oloc.file)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dataset is not associated with a file")
+    if (H5D_CHUNKED != dset->shared->layout.type)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
+    if (!buf)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "buf cannot be NULL")
+    if (!offset)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "offset cannot be NULL")
+    if (0 == data_size)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "data_size cannot be zero")
+
+    /* Make sure data size is less than 4 GiB */
+    data_size_32 = (uint32_t)data_size;
+    if (data_size != (size_t)data_size_32)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "invalid data_size - chunks cannot be > 4 GiB")
 
-    FUNC_ENTER_PACKAGE_VOL
-
-    /* Direct chunk write */
-    if(direct_write) {
-        uint32_t direct_filters;
-        hsize_t *direct_offset;
-        uint32_t direct_datasize;
-        hsize_t  internal_offset[H5O_LAYOUT_NDIMS];
-        unsigned u;                 /* Local index variable */
-
-        if(H5D_CHUNKED != dset->shared->layout.type)
-            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a chunked dataset")
-
-        /* Retrieve parameters for direct chunk write */
-        if(H5CX_get_dcw_filters(&direct_filters) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error getting filter info for direct chunk write")
-        if(H5CX_get_dcw_offset(&direct_offset) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "error getting offset info for direct chunk write")
-        if(H5CX_get_dcw_datasize(&direct_datasize) < 0)
-            HGOTO_ERROR(H5E_DATASET, 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 
-         * 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;
-
-	/* write raw data */
-	if(H5D__chunk_direct_write(dset, direct_filters, internal_offset, direct_datasize, buf) < 0)
-	    HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write chunk directly")
-    } /* end if */
+    /* Get the default dataset transfer property list if the user didn't provide one */
+    if (H5P_DEFAULT == dxpl_id)
+        dxpl_id = H5P_DATASET_XFER_DEFAULT;
     else
-        /* Normal write of raw data */
-        if(H5D__write(dset, mem_type_id, mem_space, file_space, buf) < 0)
-            HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write data")
+        if (TRUE != H5P_isa_class(dxpl_id, H5P_DATASET_XFER))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "dxpl_id is not a dataset transfer property list ID")
+
+    /* Set DXPL for operation */
+    H5CX_set_dxpl(dxpl_id);
+
+    /* Copy the user's offset array so we can be sure it's terminated properly.
+     * (we don't want to mess with the user's buffer).
+     */
+    if (H5D__get_offset_copy(dset, offset, offset_copy) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "failure to copy offset array")
+
+    /* Write chunk */
+    if (H5D__chunk_direct_write(dset, filters, offset_copy, data_size_32, buf) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "can't write unprocessed chunk data")
 
 done:
-    FUNC_LEAVE_NOAPI_VOL(ret_value)
-} /* end H5D__pre_write() */
+    FUNC_LEAVE_API(ret_value)
+} /* end H5Dwrite_chunk() */
 
 
 /*-------------------------------------------------------------------------
@@ -400,7 +431,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
     hbool_t type_info_init = FALSE;     /* Whether the datatype info has been initialized */
     H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a     */
                                         /* projection of the supplied mem_space to a new  */
-                                        /* dataspace with rank equal to that of          */
+                                        /* dataspace with rank equal to that of           */
                                         /* file_space.                                    */
                                         /*                                                */
                                         /* This field is only used if                     */
@@ -428,7 +459,7 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
     if(!mem_space)
         mem_space = file_space;
     if((snelmts = H5S_GET_SELECT_NPOINTS(mem_space)) < 0)
-	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dst dataspace has invalid selection")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "dst dataspace has invalid selection")
     H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t);
 
     /* Set up datatype info for operation */
@@ -612,7 +643,7 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
     hbool_t type_info_init = FALSE;     /* Whether the datatype info has been initialized */
     H5S_t * projected_mem_space = NULL; /* If not NULL, ptr to dataspace containing a     */
                                         /* projection of the supplied mem_space to a new  */
-                                        /* dataspace with rank equal to that of          */
+                                        /* dataspace with rank equal to that of           */
                                         /* file_space.                                    */
                                         /*                                                */
                                         /* This field is only used if                     */
@@ -645,7 +676,7 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
 
     /* Check if we are allowed to write to this file */
     if(0 == (H5F_INTENT(dataset->oloc.file) & H5F_ACC_RDWR))
-	HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file")
+        HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "no write intent on file")
 
     /* Set up datatype info for operation */
     if(H5D__typeinfo_init(dataset, mem_type_id, TRUE, &type_info) < 0)
@@ -691,12 +722,12 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
         mem_space = file_space;
 
     if((snelmts = H5S_GET_SELECT_NPOINTS(mem_space)) < 0)
-	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src dataspace has invalid selection")
     H5_CHECKED_ASSIGN(nelmts, hsize_t, snelmts, hssize_t);
 
     /* Make certain that the number of elements in each selection is the same */
     if(nelmts != (hsize_t)H5S_GET_SELECT_NPOINTS(file_space))
-	HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest dataspaces have different number of elements selected")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "src and dest dataspaces have different number of elements selected")
 
     /* Check for a NULL buffer, after the H5S_ALL dataspace selection has been handled */
     if(NULL == buf) {
@@ -934,7 +965,7 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write,
 
     /* Get the memory & dataset datatypes */
     if(NULL == (type_info->mem_type = (const H5T_t *)H5I_object_verify(mem_type_id, H5I_DATATYPE)))
-	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
     type_info->dset_type = dset->shared->type;
 
     if(do_write) {
@@ -959,11 +990,11 @@ H5D__typeinfo_init(const H5D_t *dset, hid_t mem_type_id, hbool_t do_write,
      * turns off background preservation.
      */
     if(NULL == (type_info->tpath = H5T_path_find(src_type, dst_type)))
-	HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype")
+        HGOTO_ERROR(H5E_DATASET, H5E_UNSUPPORTED, FAIL, "unable to convert between src and dest datatype")
 
     /* Retrieve info from API context */
     if(H5CX_get_data_transform(&data_transform) < 0)
-	HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info")
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data transform info")
 
     /* Precompute some useful information */
     type_info->src_type_size = H5T_get_size(src_type);
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 126a3c0..b887b87 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -583,8 +583,6 @@ H5_DLL herr_t H5D__refresh(hid_t dset_id, H5D_t *dataset);
 H5_DLL herr_t H5D__format_convert(H5D_t *dataset);
 
 /* Internal I/O routines */
-H5_DLL herr_t H5D__pre_write(H5D_t *dset, hbool_t direct_write, hid_t mem_type_id,
-    const H5S_t *mem_space, const H5S_t *file_space, const void *buf);
 H5_DLL herr_t H5D__read(H5D_t *dataset, hid_t mem_type_id,
     const H5S_t *mem_space, const H5S_t *file_space, void *buf/*out*/);
 H5_DLL herr_t H5D__write(H5D_t *dataset, hid_t mem_type_id,
diff --git a/src/H5Dpublic.h b/src/H5Dpublic.h
index 790674a..a1ccda0 100644
--- a/src/H5Dpublic.h
+++ b/src/H5Dpublic.h
@@ -35,17 +35,6 @@
 /* Bit flags for the H5Pset_chunk_opts() and H5Pget_chunk_opts() */
 #define H5D_CHUNK_DONT_FILTER_PARTIAL_CHUNKS      (0x0002u)
 
-/* Property names for H5DOwrite_chunk */   
-#define H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME	        "direct_chunk_flag"
-#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 H5DOread_chunk */
-#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 */
 /*******************/
@@ -157,6 +146,10 @@ 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*/);
 H5_DLL herr_t H5Dwrite(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
 			 hid_t file_space_id, hid_t plist_id, const void *buf);
+H5_DLL herr_t H5Dwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, 
+            const hsize_t *offset, size_t data_size, const void *buf);
+H5_DLL herr_t H5Dread_chunk(hid_t dset_id, hid_t dxpl_id,
+            const hsize_t *offset, uint32_t *filters, void *buf);
 H5_DLL herr_t H5Diterate(void *buf, hid_t type_id, hid_t space_id,
             H5D_operator_t op, void *operator_data);
 H5_DLL herr_t H5Dvlen_reclaim(hid_t type_id, hid_t space_id, hid_t plist_id, void *buf);
@@ -185,7 +178,19 @@ H5_DLL herr_t H5Dget_chunk_index_type(hid_t did, H5D_chunk_index_t *idx_type);
 /* Macros */
 #define H5D_CHUNK_BTREE H5D_CHUNK_IDX_BTREE
 
-
+/* Formerly used to support the H5DOread/write_chunk() API calls.
+ * These symbols are no longer used in the library.
+ */
+/* Property names for H5DOwrite_chunk */
+#define H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME       "direct_chunk_flag"
+#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 H5DOread_chunk */
+#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"
+ 
 /* Typedefs */
 
 
diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c
index e33e762..b56c137 100644
--- a/src/H5Pdxpl.c
+++ b/src/H5Pdxpl.c
@@ -152,22 +152,6 @@
 #define H5D_XFER_XFORM_COPY         H5P__dxfr_xform_copy
 #define H5D_XFER_XFORM_CMP          H5P__dxfr_xform_cmp
 #define H5D_XFER_XFORM_CLOSE        H5P__dxfr_xform_close
-/* Definitions for properties of direct chunk write */
-#define H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_SIZE		sizeof(hbool_t)
-#define H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_DEF		FALSE
-#define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_SIZE	sizeof(uint32_t)
-#define H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_DEF		0
-#define H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_SIZE		sizeof(hsize_t *)
-#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
 
 
 /******************/
@@ -266,13 +250,6 @@ static const H5Z_EDC_t H5D_def_enable_edc_g = H5D_XFER_EDC_DEF;            /* De
 static const H5Z_cb_t H5D_def_filter_cb_g = H5D_XFER_FILTER_CB_DEF;        /* Default value for filter callback */
 static const H5T_conv_cb_t H5D_def_conv_cb_g = H5D_XFER_CONV_CB_DEF;       /* Default value for datatype conversion callback */
 static const void *H5D_def_xfer_xform_g = H5D_XFER_XFORM_DEF;          /* Default value for data transform */
-static const hbool_t H5D_def_direct_chunk_flag_g = H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_DEF; 	/* Default value for the flag of direct chunk write */
-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 */
 
 
 /*-------------------------------------------------------------------------
@@ -423,48 +400,6 @@ H5P__dxfr_reg_prop(H5P_genclass_t *pclass)
             H5D_XFER_XFORM_DEL, H5D_XFER_XFORM_COPY, H5D_XFER_XFORM_CMP, H5D_XFER_XFORM_CLOSE) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
 
-    /* Register the property of flag for direct chunk write */
-    /* (Note: this property should not have an encode/decode callback -QAK) */
-    if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_SIZE, &H5D_def_direct_chunk_flag_g,
-            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 write */
-    /* (Note: this property should not have an encode/decode callback -QAK) */
-    if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_SIZE, &H5D_def_direct_chunk_filters_g,
-            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 write */
-    /* (Note: this property should not have an encode/decode callback -QAK) */
-    if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_SIZE, &H5D_def_direct_chunk_offset_g,
-            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 datasize for direct chunk write */
-    /* (Note: this property should not have an encode/decode callback -QAK) */
-    if(H5P_register_real(pclass, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_SIZE, &H5D_def_direct_chunk_datasize_g,
-            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")
-
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5P__dxfr_reg_prop() */
diff --git a/src/H5S.c b/src/H5S.c
index 3d09fa0..88c2f72 100644
--- a/src/H5S.c
+++ b/src/H5S.c
@@ -26,7 +26,6 @@
 #include "H5Fprivate.h"		/* Files				*/
 #include "H5FLprivate.h"	/* Free lists                           */
 #include "H5Iprivate.h"		/* IDs			  		*/
-#include "H5MMprivate.h"	/* Memory management			*/
 #include "H5Oprivate.h"		/* Object headers		  	*/
 #include "H5Spkg.h"		/* Dataspaces 				*/
 
@@ -208,6 +207,58 @@ H5S_term_package(void)
     FUNC_LEAVE_NOAPI(n)
 } /* end H5S_term_package() */
 
+
+
+/*--------------------------------------------------------------------------
+ NAME
+    H5S_get_validiated_dataspace
+ PURPOSE
+    Get a pointer to a validated H5S_t pointer
+ USAGE
+   H5S_t *H5S_get_validated_space(dataspace_id, space)
+    hid_t           space_id;       IN: The ID of the dataspace
+    const H5S_t *   space;          OUT: A pointer to the dataspace
+ RETURNS
+    SUCCEED/FAIL
+ DESCRIPTION
+    Gets a pointer to a dataspace struct after validating it. The pointer
+    can be NULL (if the ID is H5S_ALL, for example).
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5S_get_validated_dataspace(hid_t space_id, const H5S_t **space)
+{
+    herr_t ret_value = SUCCEED;     /* Return value */
+
+    FUNC_ENTER_NOAPI(FAIL)
+
+    HDassert(space);
+
+    if (space_id < 0)
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid space_id (ID cannot be a negative number)")
+ 
+    if (H5S_ALL == space_id) {
+        /* No special dataspace struct for H5S_ALL */
+        *space = NULL;
+    }
+    else {
+        /* Get the dataspace pointer */
+        if (NULL == (*space = (const H5S_t *)H5I_object_verify(space_id, H5I_DATASPACE)))
+            HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "space_id is not a dataspace ID")
+
+        /* Check for valid selection */
+        if (H5S_SELECT_VALID(*space) != TRUE)
+            HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection + offset not within extent")
+    }
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+
+} /* end H5S_get_validated_dataspace() */
+
 
 /*--------------------------------------------------------------------------
  NAME
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index b4ae1ff..15ce75d 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -215,6 +215,7 @@ H5_DLL herr_t H5S_set_extent_real(H5S_t *space, const hsize_t *size);
 H5_DLL herr_t H5S_set_extent_simple(H5S_t *space, unsigned rank,
     const hsize_t *dims, const hsize_t *max);
 H5_DLL H5S_t *H5S_create(H5S_class_t type);
+H5_DLL herr_t H5S_get_validated_dataspace(hid_t space_id, const H5S_t **space/*out*/);
 H5_DLL H5S_t *H5S_create_simple(unsigned rank, const hsize_t dims[/*rank*/],
     const hsize_t maxdims[/*rank*/]);
 H5_DLL herr_t H5S_set_version(H5F_t *f, H5S_t *ds);