[svn-r6825] Purpose:

    New feature/enhancement

Description:
    Chunked datasets are handled poorly in several circumstances involving
certain selections and chunks that are too large for the chunk cache and/or
chunks with filters, causing the chunk to be read from disk multiple times.

Solution:
    Rearrange raw data I/O infrastructure to handle chunked datasets in a much
more friendly way by creating a selection in memory and on disk for each chunk
in a chunked dataset and performing all of the I/O on that chunk at one time.

    There are still some scalability (the current code attempts to
create a selection for all the chunks in the dataset, instead of just the
chunks that are accessed, requiring portions of the istore.c and fillval.c
tests to be commented out) and performance issues, but checking this in will
allow the changes to be tested by a much wider audience while I address the
remaining issues.


Platforms tested:
    h5committested, FreeBSD 4.8 (sleipnir) serial & parallel, Linux 2.4 (eirene)

1 files changed, 151 insertions, 280 deletions

diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index 7f8d7e1..9629963 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -1685,246 +1685,154 @@ H5F_istore_unlock(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5F_istore_read
+ * Function:	H5F_istore_readvv
  *
  * Purpose:	Reads a multi-dimensional buffer from (part of) an indexed raw
  *		storage array.
  *
  * Return:	Non-negative on success/Negative on failure
  *
- * Programmer:	Robb Matzke
- *		Wednesday, October 15, 1997
+ * Programmer:	Quincey Koziol
+ *		Wednesday, May  7, 2003
  *
  * Modifications:
- *		Robb Matzke, 1999-08-02
- *		The data transfer property list is passed as an object ID
- *		since that's how the virtual file layer wants it.
  *
- *              Quincey Koziol, 2002-04-02
- *              Enable hyperslab I/O into memory buffer
  *-------------------------------------------------------------------------
  */
-herr_t
-H5F_istore_read(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
-                H5P_genplist_t *dc_plist,
-                const hsize_t size_m[], const hssize_t offset_m[],
-		const hssize_t offset_f[], const hsize_t size[], void *buf)
+ssize_t
+H5F_istore_readvv(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
+    H5P_genplist_t *dc_plist, hssize_t chunk_coords[],
+    size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
+    size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
+    void *buf)
 {
-    hsize_t		idx_cur[H5O_LAYOUT_NDIMS];
-    hsize_t		idx_min[H5O_LAYOUT_NDIMS];
-    hsize_t		idx_max[H5O_LAYOUT_NDIMS];
-    hsize_t		sub_size[H5O_LAYOUT_NDIMS];
-    hssize_t		offset_wrt_chunk[H5O_LAYOUT_NDIMS];
-    hssize_t		sub_offset_m[H5O_LAYOUT_NDIMS];
-    hssize_t		chunk_offset[H5O_LAYOUT_NDIMS];
-    int		i, carry;
-    unsigned		u;
-    hsize_t		naccessed;		/*bytes accessed in chnk*/
-    uint8_t		*chunk=NULL;		/*ptr to a chunk buffer	*/
-    unsigned		idx_hint=0;		/*cache index hint	*/
-    hsize_t		chunk_size;     /* Bytes in chunk */
+    hsize_t		chunk_size;     /* Chunk size, in bytes */
     haddr_t	        chunk_addr;     /* Chunk address on disk */
+    hssize_t	        chunk_coords_in_elmts[H5O_LAYOUT_NDIMS];
     H5O_pline_t         pline;          /* I/O pipeline information */
-    H5O_fill_t          fill;           /* Fill value information */
-    herr_t              ret_value = SUCCEED;            /* Return value */
-
-    FUNC_ENTER_NOAPI(H5F_istore_read, FAIL);
+    size_t		u;              /* Local index variables */
+    ssize_t             ret_value;      /* Return value */
+    
+    FUNC_ENTER_NOAPI(H5F_istore_readvv, FAIL);
 
     /* Check args */
     assert(f);
     assert(layout && H5D_CHUNKED==layout->type);
     assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
-    assert(H5F_addr_defined(layout->addr));
-    assert(size_m);
-    assert(offset_m);
-    assert(offset_f);
-    assert(size);
+    assert(chunk_len_arr);
+    assert(chunk_offset_arr);
+    assert(mem_len_arr);
+    assert(mem_offset_arr);
     assert(buf);
 
     /* Get necessary properties from property list */
-    if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value");
     if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data pipeline");
 
     /* Compute chunk size */
     for (u=0, chunk_size=1; u<layout->ndims; u++)
         chunk_size *= layout->dim[u];
-    
+
 #ifndef NDEBUG
-    for (u=0; u<layout->ndims; u++) {
-        assert(offset_f[u]>=0); /*negative offsets not supported*/
-        assert(offset_m[u]>=0); /*negative offsets not supported*/
-        assert(size[u]<SIZET_MAX);
-        assert(offset_m[u]+(hssize_t)size[u]<=(hssize_t)size_m[u]);
-        assert(layout->dim[u]>0);
-    }
+    for (u=0; u<layout->ndims; u++)
+        assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */
 #endif
+    
+    for (u=0; u<layout->ndims; u++)
+        chunk_coords_in_elmts[u] = chunk_coords[u] * (hssize_t)(layout->dim[u]);
+
+    /* Get the address of this chunk on disk */
+    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords_in_elmts);
 
     /*
-     * Set up multi-dimensional counters (idx_min, idx_max, and idx_cur) and
-     * loop through the chunks copying each to its final destination in the
-     * application buffer.
+     * If the chunk is too large to load into the cache and it has no
+     * filters in the pipeline (i.e. not compressed) and if the address
+     * for the chunk has been defined, then don't load the chunk into the
+     * cache, just write the data to it directly.
      */
-    for (u=0; u<layout->ndims; u++) {
-        idx_min[u] = offset_f[u] / layout->dim[u];
-        idx_max[u] = (offset_f[u]+size[u]-1) / layout->dim[u] + 1;
-        idx_cur[u] = idx_min[u];
-    }
-
-    /* Loop over all chunks */
-    carry=0;
-    while (carry==0) {
-        for (u=0, naccessed=1; u<layout->ndims; u++) {
-            /* The location and size of the chunk being accessed */
-            assert(layout->dim[u] < HSSIZET_MAX);
-            chunk_offset[u] = idx_cur[u] * (hssize_t)(layout->dim[u]);
-
-            /* The offset and size wrt the chunk */
-            offset_wrt_chunk[u] = MAX(offset_f[u], chunk_offset[u]) -
-                      chunk_offset[u];
-            sub_size[u] = MIN((idx_cur[u]+1)*layout->dim[u],
-                      offset_f[u]+size[u]) -
-                  (chunk_offset[u] + offset_wrt_chunk[u]);
-            naccessed *= sub_size[u];
-            
-            /* Offset into mem buffer */
-            sub_offset_m[u] = chunk_offset[u] + offset_wrt_chunk[u] +
-                      offset_m[u] - offset_f[u];
-        }
+    if (chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
+            chunk_addr!=HADDR_UNDEF) {
+        if ((ret_value=H5F_contig_readvv(f, chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0)
+            HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data to file");
+    } /* end if */
+    else {
+        uint8_t         *chunk;         /* Pointer to cached chunk in memory */
+        H5O_fill_t      fill;           /* Fill value information */
+        unsigned        idx_hint=0;     /* Cache index hint      */
+        ssize_t         naccessed;      /* Number of bytes accessed in chunk */
 
-        /* Get the address of this chunk on disk */
-        chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_offset);
+        /* Get necessary properties from property list */
+        if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value");
 
         /*
-         * If the chunk is too large to load into the cache and it has no
-         * filters in the pipeline (i.e. not compressed) and if the address
-         * for the chunk has been defined, then don't load the chunk into the
-         * cache, just read the data from it directly.
+         * Lock the chunk, copy from application to chunk, then unlock the
+         * chunk.
          */
-        if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
-                chunk_addr!=HADDR_UNDEF)
+        if (NULL==(chunk=H5F_istore_lock(f, dxpl_id, layout, &pline, &fill,
+                     chunk_coords_in_elmts, FALSE, &idx_hint)))
+            HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk");
 
-        /*
-         * If MPIO, MPIPOSIX, or FPHDF5 is used and file can be written
-         * to, we must bypass the chunk-cache scheme because other MPI
-         * processes could be writing to other elements in the same
-         * chunk.  Do a direct write-through of only the elements
-         * requested.
-         */
-            || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f) || IS_H5FD_FPHDF5(f)) && (H5F_ACC_RDWR & f->shared->flags))
-            ) {
-            H5O_layout_t	l;	/* temporary layout */
+        /* Use the vectorized memory copy routine to do actual work */
+        if((naccessed=H5V_memcpyvv(buf,mem_max_nseq,mem_curr_seq,mem_len_arr,mem_offset_arr,chunk,chunk_max_nseq,chunk_curr_seq,chunk_len_arr,chunk_offset_arr))<0)
+            HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "vectorized memcpy failed");
 
-#ifdef H5_HAVE_PARALLEL
-            /* Additional sanity checks when operating in parallel */
-            if (chunk_addr==HADDR_UNDEF || pline.nfilters>0)
-                HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk");
-#endif /* H5_HAVE_PARALLEL */
-            
-            /*
-             * use default transfer mode as we do not support collective
-             * transfer mode since each data write could decompose into
-             * multiple chunk writes and we are not doing the calculation yet.
-             */
-            l.type = H5D_CONTIGUOUS;
-            l.ndims = layout->ndims;
-            for (u=l.ndims; u-- > 0; /*void*/)
-                l.dim[u] = layout->dim[u];
-            l.addr = chunk_addr;
-            if (H5F_arr_read(f, dxpl_id, &l, dc_plist, sub_size, size_m, sub_offset_m, offset_wrt_chunk, buf)<0)
-                HGOTO_ERROR (H5E_IO, H5E_READERROR, FAIL, "unable to read raw data from file");
-        } /* end if */
-        else {
-            /*
-             * Lock the chunk, transfer data to the application, then unlock
-             * the chunk.
-             */
-            if (NULL==(chunk=H5F_istore_lock(f, dxpl_id, layout, &pline, &fill,
-                         chunk_offset, FALSE, &idx_hint)))
-                HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk");
-            H5V_hyper_copy(layout->ndims, sub_size, size_m, sub_offset_m,
-                   (void*)buf, layout->dim, offset_wrt_chunk, chunk);
-            H5_CHECK_OVERFLOW(naccessed,hsize_t,size_t);
-            if (H5F_istore_unlock(f, dxpl_id, layout, &pline, FALSE,
-                      chunk_offset, &idx_hint, chunk, (size_t)naccessed)<0)
-                HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk");
-        } /* end else */
-
-        /* Increment indices */
-        for (i=(int)(layout->ndims-1), carry=1; i>=0 && carry; --i) {
-            if (++idx_cur[i]>=idx_max[i])
-                idx_cur[i] = idx_min[i];
-            else
-                carry = 0;
-        }
-    }
+        H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
+        if (H5F_istore_unlock(f, dxpl_id, layout, &pline, FALSE,
+                  chunk_coords_in_elmts, &idx_hint, chunk, (size_t)naccessed)<0)
+            HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk");
 
+        /* Set return value */
+        ret_value=naccessed;
+    } /* end else */
+        
 done:
     FUNC_LEAVE_NOAPI(ret_value);
-}
+} /* H5F_istore_readvv() */
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5F_istore_write
+ * Function:	H5F_istore_writevv
  *
  * Purpose:	Writes a multi-dimensional buffer to (part of) an indexed raw
  *		storage array.
  *
  * Return:	Non-negative on success/Negative on failure
  *
- * Programmer:	Robb Matzke
- *		Wednesday, October 15, 1997
+ * Programmer:	Quincey Koziol
+ *		Friday, May  2, 2003
  *
  * Modifications:
- *		Robb Matzke, 1999-08-02
- *		The data transfer property list is passed as an object ID
- *		since that's how the virtual file layer wants it.
  *
- *              Quincey Koziol, 2002-04-02
- *              Enable hyperslab I/O into memory buffer
  *-------------------------------------------------------------------------
  */
-herr_t
-H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
-                 H5P_genplist_t *dc_plist,
-                 const hsize_t size_m[], const hssize_t offset_m[],
-		 const hssize_t offset_f[], const hsize_t size[],
-		 const void *buf)
+ssize_t
+H5F_istore_writevv(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
+    H5P_genplist_t *dc_plist, hssize_t chunk_coords[],
+    size_t chunk_max_nseq, size_t *chunk_curr_seq, size_t chunk_len_arr[], hsize_t chunk_offset_arr[],
+    size_t mem_max_nseq, size_t *mem_curr_seq, size_t mem_len_arr[], hsize_t mem_offset_arr[],
+    const void *buf)
 {
-    int		i, carry;
-    unsigned		u;
-    hsize_t		idx_cur[H5O_LAYOUT_NDIMS];
-    hsize_t		idx_min[H5O_LAYOUT_NDIMS];
-    hsize_t		idx_max[H5O_LAYOUT_NDIMS];
-    hsize_t		sub_size[H5O_LAYOUT_NDIMS];
-    hssize_t	chunk_offset[H5O_LAYOUT_NDIMS];
-    hssize_t	offset_wrt_chunk[H5O_LAYOUT_NDIMS];
-    hssize_t	sub_offset_m[H5O_LAYOUT_NDIMS];
-    uint8_t		*chunk=NULL;
-    unsigned		idx_hint=0;
-    hsize_t		chunk_size, naccessed;
+    hsize_t		chunk_size;     /* Chunk size, in bytes */
     haddr_t	        chunk_addr;     /* Chunk address on disk */
+    hssize_t	        chunk_coords_in_elmts[H5O_LAYOUT_NDIMS];
     H5O_pline_t         pline;          /* I/O pipeline information */
-    H5O_fill_t          fill;           /* Fill value information */
-    herr_t              ret_value = SUCCEED;            /* Return value */
+    size_t		u;              /* Local index variables */
+    ssize_t             ret_value;      /* Return value */
     
-    FUNC_ENTER_NOAPI(H5F_istore_write, FAIL);
+    FUNC_ENTER_NOAPI(H5F_istore_writevv, FAIL);
 
     /* Check args */
     assert(f);
     assert(layout && H5D_CHUNKED==layout->type);
     assert(layout->ndims>0 && layout->ndims<=H5O_LAYOUT_NDIMS);
-    assert(H5F_addr_defined(layout->addr));
-    assert(size_m);
-    assert(offset_m);
-    assert(offset_f);
-    assert(size);
+    assert(chunk_len_arr);
+    assert(chunk_offset_arr);
+    assert(mem_len_arr);
+    assert(mem_offset_arr);
     assert(buf);
 
     /* Get necessary properties from property list */
-    if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value");
     if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get data pipeline");
 
@@ -1933,118 +1841,79 @@ H5F_istore_write(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout,
         chunk_size *= layout->dim[u];
 
 #ifndef NDEBUG
-    for (u=0; u<layout->ndims; u++) {
-        assert(offset_f[u]>=0); /*negative offsets not supported*/
-        assert(offset_m[u]>=0); /*negative offsets not supported*/
-        assert(size[u]<SIZET_MAX);
-        assert(offset_m[u]+(hssize_t)size[u]<=(hssize_t)size_m[u]);
-        assert(layout->dim[u]>0);
-    }
+    for (u=0; u<layout->ndims; u++)
+        assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */
 #endif
+    
+    for (u=0; u<layout->ndims; u++)
+        chunk_coords_in_elmts[u] = chunk_coords[u] * (hssize_t)(layout->dim[u]);
+
+    /* Get the address of this chunk on disk */
+    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords_in_elmts);
 
     /*
-     * Set up multi-dimensional counters (idx_min, idx_max, and idx_cur) and
-     * loop through the chunks copying each chunk from the application to the
-     * chunk cache.
+     * If the chunk is too large to load into the cache and it has no
+     * filters in the pipeline (i.e. not compressed) and if the address
+     * for the chunk has been defined, then don't load the chunk into the
+     * cache, just write the data to it directly.
+     *
+     * If MPIO, MPIPOSIX, or FPHDF5 is used, must bypass the
+     * chunk-cache scheme because other MPI processes could be
+     * writing to other elements in the same chunk.  Do a direct
+     * write-through of only the elements requested.
      */
-    for (u=0; u<layout->ndims; u++) {
-        idx_min[u] = offset_f[u] / layout->dim[u];
-        idx_max[u] = (offset_f[u]+size[u]-1) / layout->dim[u] + 1;
-        idx_cur[u] = idx_min[u];
-    }
-
-
-    /* Loop over all chunks */
-    carry=0;
-    while (carry==0) {
-        for (u=0, naccessed=1; u<layout->ndims; u++) {
-            /* The location and size of the chunk being accessed */
-            assert(layout->dim[u] < HSSIZET_MAX);
-            chunk_offset[u] = idx_cur[u] * (hssize_t)(layout->dim[u]);
-
-            /* The offset and size wrt the chunk */
-            offset_wrt_chunk[u] = MAX(offset_f[u], chunk_offset[u]) -
-                      chunk_offset[u];
-            sub_size[u] = MIN((idx_cur[u]+1)*layout->dim[u],
-                      offset_f[u]+size[u]) -
-                  (chunk_offset[u] + offset_wrt_chunk[u]);
-            naccessed *= sub_size[u];
-
-            /* Offset into mem buffer */
-            sub_offset_m[u] = chunk_offset[u] + offset_wrt_chunk[u] +
-                      offset_m[u] - offset_f[u];
-        }
-
-        /* Get the address of this chunk on disk */
-        chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_offset);
+    if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
+            chunk_addr!=HADDR_UNDEF)
+        || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f) || IS_H5FD_FPHDF5(f)) &&
+            (H5F_ACC_RDWR & f->shared->flags))) {
+#ifdef H5_HAVE_PARALLEL
+        /* Additional sanity check when operating in parallel */
+        if (chunk_addr==HADDR_UNDEF || pline.nfilters>0)
+            HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk");
+#endif /* H5_HAVE_PARALLEL */
+        if ((ret_value=H5F_contig_writevv(f, chunk_size, chunk_addr, chunk_max_nseq, chunk_curr_seq, chunk_len_arr, chunk_offset_arr, mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr, dxpl_id, buf))<0)
+            HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file");
+    } /* end if */
+    else {
+        uint8_t         *chunk;         /* Pointer to cached chunk in memory */
+        H5O_fill_t      fill;           /* Fill value information */
+        unsigned        idx_hint=0;     /* Cache index hint      */
+        ssize_t         naccessed;      /* Number of bytes accessed in chunk */
+        hbool_t         relax;          /* Whether whole chunk is selected */
 
-        /*
-         * If the chunk is too large to load into the cache and it has no
-         * filters in the pipeline (i.e. not compressed) and if the address
-         * for the chunk has been defined, then don't load the chunk into the
-         * cache, just write the data to it directly.
-         */
-        if ((chunk_size>f->shared->rdcc_nbytes && pline.nfilters==0 &&
-                chunk_addr!=HADDR_UNDEF)
+        /* Get necessary properties from property list */
+        if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get fill value");
 
         /*
-         * If MPIO, MPIPOSIX, or FPHDF5 is used, must bypass the
-         * chunk-cache scheme because other MPI processes could be
-         * writing to other elements in the same chunk.  Do a direct
-         * write-through of only the elements requested.
+         * Lock the chunk, copy from application to chunk, then unlock the
+         * chunk.
          */
-            || ((IS_H5FD_MPIO(f) ||IS_H5FD_MPIPOSIX(f) || IS_H5FD_FPHDF5(f)) && (H5F_ACC_RDWR & f->shared->flags))
-            ) {
-            H5O_layout_t	l;	/* temporary layout */
-
-#ifdef H5_HAVE_PARALLEL
-            /* Additional sanity check when operating in parallel */
-            if (chunk_addr==HADDR_UNDEF || pline.nfilters>0) {
-                HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to locate raw data chunk");
-            }
-#endif /* H5_HAVE_PARALLEL */
-            
-            /*
-             * use default transfer mode as we do not support collective
-             * transfer mode since each data write could decompose into
-             * multiple chunk writes and we are not doing the calculation yet.
-             */
-            l.type = H5D_CONTIGUOUS;
-            l.ndims = layout->ndims;
-            for (u=l.ndims; u-- > 0; /*void*/)
-                l.dim[u] = layout->dim[u];
-            l.addr = chunk_addr;
-            if (H5F_arr_write(f, dxpl_id, &l, dc_plist, sub_size, size_m, sub_offset_m, offset_wrt_chunk, buf)<0)
-                HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to write raw data to file");
-        } /* end if */
-        else {
-            /*
-             * Lock the chunk, copy from application to chunk, then unlock the
-             * chunk.
-             */
-            if (NULL==(chunk=H5F_istore_lock(f, dxpl_id, layout, &pline, &fill,
-                     chunk_offset, (hbool_t)(naccessed==chunk_size), &idx_hint)))
-                HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk");
-            H5V_hyper_copy(layout->ndims, sub_size,
-               layout->dim, offset_wrt_chunk, chunk, size_m, sub_offset_m, buf);
-            H5_CHECK_OVERFLOW(naccessed,hsize_t,size_t);
-            if (H5F_istore_unlock(f, dxpl_id, layout, &pline, TRUE,
-                      chunk_offset, &idx_hint, chunk, (size_t)naccessed)<0)
-                HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk");
-        } /* end else */
+        if(chunk_max_nseq==1 && chunk_len_arr[0] == chunk_size)
+            relax = TRUE;
+        else
+            relax = FALSE;
+
+        if (NULL==(chunk=H5F_istore_lock(f, dxpl_id, layout, &pline, &fill,
+                 chunk_coords_in_elmts, relax, &idx_hint)))
+            HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk");
+
+        /* Use the vectorized memory copy routine to do actual work */
+        if((naccessed=H5V_memcpyvv(chunk,chunk_max_nseq,chunk_curr_seq,chunk_len_arr,chunk_offset_arr,buf,mem_max_nseq,mem_curr_seq,mem_len_arr,mem_offset_arr))<0)
+            HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "vectorized memcpy failed");
+
+        H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
+        if (H5F_istore_unlock(f, dxpl_id, layout, &pline, TRUE,
+                  chunk_coords_in_elmts, &idx_hint, chunk, (size_t)naccessed)<0)
+            HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk");
+
+        /* Set return value */
+        ret_value=naccessed;
+    } /* end else */
         
-        /* Increment indices */
-        for (i=layout->ndims-1, carry=1; i>=0 && carry; --i) {
-            if (++idx_cur[i]>=idx_max[i])
-                idx_cur[i] = idx_min[i];
-            else
-                carry = 0;
-        }
-    } /* end while */
-
 done:
     FUNC_LEAVE_NOAPI(ret_value);
-}
+} /* H5F_istore_writevv() */
 
 
 /*-------------------------------------------------------------------------
@@ -2808,7 +2677,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *lay
     hsize_t                 size[H5O_LAYOUT_NDIMS];	/*current size of dimensions */
     H5S_t                  *space_chunk = NULL;	/*dataspace for a chunk */
     hsize_t                 curr_dims[H5O_LAYOUT_NDIMS];	/*current dataspace dimensions */
-    int                     rank;	/*current # of dimensions */
+    int                     srank;	/*current # of dimensions (signed) */
+    unsigned                rank;	/*current # of dimensions */
     int                     i, carry;	/*counters  */
     unsigned                u;
     int                     found = 0;	/*initialize this entry  */
@@ -2836,13 +2706,14 @@ H5F_istore_initialize_by_extent(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *lay
     HDmemset(count, 0, sizeof(count));
 
     /* Go get the rank & dimensions */
-    if((rank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
+    if((srank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
 	HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
+    rank=srank;
 
     /* Copy current dimensions */
-    for(i = 0; i < rank; i++)
-	size[i] = curr_dims[i];
-    size[i] = layout->dim[i];
+    for(u = 0; u < rank; u++)
+	size[u] = curr_dims[u];
+    size[u] = layout->dim[u];
 
     /* Create a data space for a chunk & set the extent */
     if(NULL == (space_chunk = H5S_create_simple(rank,layout->dim,NULL)))
@@ -2891,8 +2762,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *lay
 	    if(H5S_select_all(space_chunk,1) < 0)
 		HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to select space");
 
-	    for(i = 0; i < rank; i++)
-		count[i] = MIN((idx_cur[i] + 1) * layout->dim[i], size[i] - chunk_offset[i]);
+	    for(u = 0; u < rank; u++)
+		count[u] = MIN((idx_cur[u] + 1) * layout->dim[u], size[u] - chunk_offset[u]);
 
 #if defined (H5F_ISTORE_DEBUG)
 	    HDfputs("cache:initialize:offset:[", stdout);