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.

2 files changed, 42 insertions, 194 deletions

diff --git a/hl/src/H5DO.c b/hl/src/H5DO.c
index 99cf2f7..20d5a4a 100644
--- a/hl/src/H5DO.c
+++ b/hl/src/H5DO.c
@@ -22,163 +22,20 @@
 /* public LT prototypes			*/
 #include "H5DOpublic.h"
 
-
 
 /*-------------------------------------------------------------------------
- * Function:	H5DOwrite_chunk
- *
- * Purpose:     Writes an entire chunk to the file directly.	
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Raymond Lu
- *		        30 July 2012
+ * Function:    H5DOappend()
  *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, const hsize_t *offset, 
-         size_t data_size, const void *buf)
-{
-    hbool_t created_dxpl = FALSE;       /* Whether we created a DXPL */
-    hbool_t do_direct_write = TRUE;     /* Flag for direct writes */
-    uint32_t data_size_32;              /* Chunk data size (limited to 32-bits currently) */
-    herr_t  ret_value = FAIL;           /* Return value */
-    
-    /* Check arguments */
-    if(dset_id < 0)
-        goto done;
-    if(!buf)
-        goto done;
-    if(!offset)
-        goto done;
-    if(!data_size)
-        goto done;
-    data_size_32 = (uint32_t)data_size;
-    if(data_size != (size_t)data_size_32)
-        goto done;
-
-    /* If the user passed in a default DXPL, create one to pass to H5Dwrite() */
-    if(H5P_DEFAULT == dxpl_id) {
-        if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
-            goto done;
-        created_dxpl = TRUE;
-    } /* end if */
-
-    /* Set direct write parameters */
-    if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0)
-        goto done;
-    if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FILTERS_NAME, &filters) < 0)
-        goto done;
-    if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_OFFSET_NAME, &offset) < 0)
-        goto done;
-    if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_DATASIZE_NAME, &data_size_32) < 0)
-        goto done;
-
-    /* Write chunk */
-    if(H5Dwrite(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0)
-        goto done;
-
-    /* Indicate success */
-    ret_value = SUCCEED;
-
-done:
-    if(created_dxpl) {
-        if(H5Pclose(dxpl_id) < 0)
-            ret_value = FAIL;
-    } /* end if */
-    else {
-        /* Reset the direct write flag on user DXPL */
-        do_direct_write = FALSE;
-        if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_WRITE_FLAG_NAME, &do_direct_write) < 0)
-            ret_value = FAIL;
-    }
-
-    return ret_value;
-} /* end H5DOwrite_chunk() */
-
-
-/*-------------------------------------------------------------------------
- * Function:    H5DOread_chunk
+ * Purpose:     To append elements to a dataset.
  *
- * Purpose:     Reads an entire chunk from the file directly.
+ *      axis:       the dataset dimension (zero-based) for the append
+ *      extension:  the # of elements to append for the axis-th dimension
+ *      memtype:    the datatype
+ *      buf:        buffer with data for the append
  *
  * Return:      Non-negative on success/Negative on failure
  *
- * Programmer:  Matthew Strong (GE Healthcare)
- *              14 February 2016
- *
- *---------------------------------------------------------------------------
- */
-herr_t
-H5DOread_chunk(hid_t dset_id, hid_t dxpl_id, const hsize_t *offset, uint32_t *filters,
-         void *buf)
-{
-    hbool_t created_dxpl = FALSE;       /* Whether we created a DXPL */
-    hbool_t do_direct_read = TRUE;     /* Flag for direct writes */
-    herr_t  ret_value = FAIL;           /* Return value */
-
-    /* Check arguments */
-    if(dset_id < 0)
-        goto done;
-    if(!buf)
-        goto done;
-    if(!offset)
-        goto done;
-    if(!filters)
-        goto done;
-
-    /* If the user passed in a default DXPL, create one to pass to H5Dwrite() */
-    if(H5P_DEFAULT == dxpl_id) {
-        if((dxpl_id = H5Pcreate(H5P_DATASET_XFER)) < 0)
-            goto done;
-        created_dxpl = TRUE;
-    } /* end if */
-
-    /* Set direct write parameters */
-    if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &do_direct_read) < 0)
-        goto done;
-    if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_OFFSET_NAME, &offset) < 0)
-        goto done;
-
-    /* Read chunk */
-    if(H5Dread(dset_id, 0, H5S_ALL, H5S_ALL, dxpl_id, buf) < 0)
-        goto done;
-    /* Get the filter mask */
-    if(H5Pget(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_FILTERS_NAME, filters) < 0)
-        goto done;
-
-    /* Indicate success */
-    ret_value = SUCCEED;
-
-done:
-    if(created_dxpl) {
-        if(H5Pclose(dxpl_id) < 0)
-            ret_value = FAIL;
-    } /* end if */
-    else {
-        /* Reset the direct read flag on user DXPL */
-        do_direct_read = FALSE;
-        if(H5Pset(dxpl_id, H5D_XFER_DIRECT_CHUNK_READ_FLAG_NAME, &do_direct_read) < 0)
-            ret_value = FAIL;
-    }
-
-    return ret_value;
-} /* end H5DOread_chunk() */
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5DOappend()
- *
- * Purpose:     To append elements to a dataset.
- *		axis: the dataset dimension (zero-based) for the append
- *		extension: the # of elements to append for the axis-th dimension
- *		memtype: the datatype
- *		buf: buffer with data for the append
- *
- * Return:	Non-negative on success/Negative on failure
- *
- * Programmer:	Vailin Choi; Jan 2014
+ * Programmer:  Vailin Choi; Jan 2014
  *
  * Note:
  * 	This routine is copied from the fast forward feature branch: features/hdf5_ff
@@ -227,7 +84,7 @@ H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension,
 
     /* check arguments */
     if(H5I_DATASET != H5Iget_type(dset_id))
-	goto done;
+        goto done;
 
     /* If the user passed in a default DXPL, create one to pass to H5Dwrite() */
     if(H5P_DEFAULT == dxpl_id) {
@@ -236,35 +93,35 @@ H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension,
         created_dxpl = TRUE;
     } /* end if */
     else if(TRUE != H5Pisa_class(dxpl_id, H5P_DATASET_XFER))
-	goto done;
+        goto done;
 
     /* Get the dataspace of the dataset */
     if(FAIL == (space_id = H5Dget_space(dset_id)))
-	goto done;
+        goto done;
 
     /* Get the rank of this dataspace */
     if((sndims = H5Sget_simple_extent_ndims(space_id)) < 0)
-	goto done;
+        goto done;
     ndims = (unsigned)sndims;
 
     /* Verify correct axis */
     if(axis >= ndims)
-	goto done;
+        goto done;
 
     /* Get the dimensions sizes of the dataspace */
     if(H5Sget_simple_extent_dims(space_id, size, NULL) < 0)
-	goto done;
+        goto done;
 
     /* Adjust the dimension size of the requested dimension, 
        but first record the old dimension size */
     old_size = size[axis];
     size[axis] += extension;
     if(size[axis] < old_size)
-	goto done;
+        goto done;
 
     /* Set the extent of the dataset to the new dimension */
     if(H5Dset_extent(dset_id, size) < 0)
-	goto done;
+        goto done;
 
     /* Get the new dataspace of the dataset */
     if(FAIL == (new_space_id = H5Dget_space(dset_id)))
@@ -282,51 +139,51 @@ H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis, size_t extension,
         } /* end if */
     } /* end for */
     if(FAIL == H5Sselect_hyperslab(new_space_id, H5S_SELECT_SET, start, stride, count, block))
-	goto done;
+        goto done;
 
     /* The # of elemnts in the new extended dataspace */
     if((snelmts = H5Sget_select_npoints(new_space_id)) < 0)
-	goto done;
+        goto done;
     nelmts = (hsize_t)snelmts;
 
     /* create a memory space */
     if(FAIL == (mem_space_id = H5Screate_simple(1, &nelmts, NULL)))
-	goto done;
+        goto done;
 
     /* Write the data */
     if(H5Dwrite(dset_id, memtype, mem_space_id, new_space_id, dxpl_id, buf) < 0)
-	goto done;
+        goto done;
 
     /* Obtain the dataset's access property list */
     if((dapl = H5Dget_access_plist(dset_id)) < 0)
-	goto done;
+        goto done;
 
     /* Allocate the boundary array */
     boundary = (hsize_t *)HDmalloc(ndims * sizeof(hsize_t));
 
     /* Retrieve the append flush property */
     if(H5Pget_append_flush(dapl, ndims, boundary, &append_cb, &udata) < 0)
-	goto done;
+        goto done;
 
     /* No boundary for this axis */
     if(boundary[axis] != 0) {
 
-	/* Determine whether a boundary is hit or not */
-	for(k = start[axis]; k < size[axis]; k++)
-	    if(!((k + 1) % boundary[axis])) {
-		hit = TRUE;
-		break;
-	    }
-
-	if(hit) { /* Hit the boundary */
-	    /* Invoke callback if there is one */
-	    if(append_cb && append_cb(dset_id, size, udata) < 0)
-		goto done;
-
-	    /* Do a dataset flush */
-	    if(H5Dflush(dset_id) < 0)
-		goto done;
-	} /* end if */
+        /* Determine whether a boundary is hit or not */
+        for(k = start[axis]; k < size[axis]; k++)
+            if(!((k + 1) % boundary[axis])) {
+                hit = TRUE;
+                break;
+            }
+
+        if(hit) { /* Hit the boundary */
+            /* Invoke callback if there is one */
+            if(append_cb && append_cb(dset_id, size, udata) < 0)
+                goto done;
+
+	        /* Do a dataset flush */
+	        if(H5Dflush(dset_id) < 0)
+                goto done;
+        } /* end if */
     } /* end if */
 
     /* Indicate success */
@@ -341,22 +198,22 @@ done:
 
     /* Close old dataspace */
     if(space_id != FAIL && H5Sclose(space_id) < 0)
-	ret_value = FAIL;
+        ret_value = FAIL;
 
     /* Close new dataspace */
     if(new_space_id != FAIL && H5Sclose(new_space_id) < 0)
-	ret_value = FAIL;
+        ret_value = FAIL;
 
     /* Close memory dataspace */
     if(mem_space_id != FAIL && H5Sclose(mem_space_id) < 0)
-	ret_value = FAIL;
+        ret_value = FAIL;
 
     /* Close the dataset access property list */
     if(dapl != FAIL && H5Pclose(dapl) < 0)
-	ret_value = FAIL;
+        ret_value = FAIL;
 
     if(boundary)
-	HDfree(boundary);
+        HDfree(boundary);
 
     return ret_value;
 } /* H5DOappend() */
diff --git a/hl/src/H5DOpublic.h b/hl/src/H5DOpublic.h
index d5c8de4..7f83a7f 100644
--- a/hl/src/H5DOpublic.h
+++ b/hl/src/H5DOpublic.h
@@ -25,15 +25,6 @@ extern "C" {
  *-------------------------------------------------------------------------
  */
 
-H5_HLDLL herr_t H5DOwrite_chunk(hid_t dset_id, hid_t dxpl_id, uint32_t filters, 
-    const hsize_t *offset, size_t data_size, const void *buf);
-
-H5_HLDLL herr_t H5DOread_chunk(hid_t dset_id, /*in*/
-            hid_t dxpl_id,         /*in*/
-            const hsize_t *offset, /*in*/
-            uint32_t *filters,     /*out*/
-            void *buf);            /*out*/
-
 H5_HLDLL herr_t H5DOappend(hid_t dset_id, hid_t dxpl_id, unsigned axis,
     size_t extension, hid_t memtype, const void *buf);