[svn-r8600] Purpose:

    Code optimization

Description:
    Don't recompute the internal index value for looking up the chunk in the
hash table, just use the value already computed from iterating through the
chunks.

Platforms tested:
    Solaris 2.7 (arabica)
    FreeBSD 4.9 (sleipnir) w/parallel

13 files changed, 426 insertions, 179 deletions

diff --git a/src/H5D.c b/src/H5D.c
index 7b74f8c..f5793b6 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -199,7 +199,7 @@ H5D_init_interface(void)
     H5P_genplist_t *def_dcpl;               /* Default Dataset Creation Property list */
     size_t          nprops;                 /* Number of properties */
     herr_t          ret_value                = SUCCEED;   /* Return value */
-           
+
     FUNC_ENTER_NOAPI_NOINIT(H5D_init_interface)
 
     /* Initialize the atom group for the dataset IDs */
@@ -2048,7 +2048,7 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space
     assert (H5I_GENPROP_LST==H5I_get_type(dxpl_id));
 
     /* Check if the filters in the DCPL can be applied to this dataset */
-    if (H5Z_can_apply(dcpl_id,type_id)<0)
+    if(H5Z_can_apply(dcpl_id,type_id)<0)
         HGOTO_ERROR(H5E_ARGS, H5E_CANTINIT, NULL, "I/O filters can't operate on this dataset")
 
     /* Get the dataset's datatype */
@@ -2056,15 +2056,15 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "not a datatype")
 
     /* Check if the datatype is "sensible" for use in a dataset */
-    if (H5T_is_sensible(type)!=TRUE)
+    if(H5T_is_sensible(type)!=TRUE)
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, NULL, "datatype is not sensible")
 
     /* Check if the datatype is/contains a VL-type */
-    if (H5T_detect_class(type, H5T_VLEN))
+    if(H5T_detect_class(type, H5T_VLEN))
         has_vl_type=TRUE;
 
     /* Initialize the dataset object */
-    if (NULL == (new_dset = H5D_new(dcpl_id,TRUE,has_vl_type)))
+    if(NULL == (new_dset = H5D_new(dcpl_id,TRUE,has_vl_type)))
         HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
 
     /* Make the "set local" filter callbacks for this dataset */
@@ -2072,7 +2072,7 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to set local filter parameters")
 
     /* What file is the dataset being added to? */
-    if (NULL==(file=H5G_insertion_file(loc, name, dxpl_id)))
+    if(NULL==(file=H5G_insertion_file(loc, name, dxpl_id)))
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, NULL, "unable to locate insertion point")
 
     /* Copy datatype for dataset */
@@ -2080,7 +2080,7 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space
         HGOTO_ERROR(H5E_DATATYPE, H5E_CANTCOPY, NULL, "can't copy datatype")
 
     /* Mark any datatypes as being on disk now */
-    if (H5T_set_loc(new_dset->type, file, H5T_LOC_DISK)<0)
+    if(H5T_set_loc(new_dset->type, file, H5T_LOC_DISK)<0)
         HGOTO_ERROR(H5E_DATATYPE, H5E_CANTINIT, NULL, "invalid datatype location")
 
     /* Copy dataspace for dataset */
@@ -2216,7 +2216,7 @@ H5D_create(H5G_entry_t *loc, const char *name, hid_t type_id, const H5S_t *space
                  * Chunked storage allows any type of data space extension, so we
                  * don't even bother checking.
                  */
-                if(chunk_ndims != ndims)
+                if(chunk_ndims != (unsigned)ndims)
                     HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, NULL, "dimensionality of chunks doesn't match the data space")
                 if (new_dset->efl.nused>0)
                     HGOTO_ERROR (H5E_DATASET, H5E_BADVALUE, NULL, "external storage not supported with chunked layout")
@@ -2400,7 +2400,7 @@ H5D_open(H5G_entry_t *ent, hid_t dxpl_id)
 
         /* Clear any errors from H5FO_opened() */
         H5E_clear(NULL);
-        
+
         /* Open the dataset object */
         if ((dataset=H5D_open_oid(ent, dxpl_id)) ==NULL)
             HGOTO_ERROR(H5E_DATASET, H5E_NOTFOUND, FAIL, "not found")
@@ -2802,6 +2802,11 @@ H5D_extend (H5D_t *dataset, const hsize_t *size, hid_t dxpl_id)
 	if (H5S_modify (&(dataset->ent), space, TRUE, dxpl_id)<0)
 	    HGOTO_ERROR (H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace")
 
+        /* Update the index values for the cached chunks for this dataset */
+        if(H5D_CHUNKED == dataset->layout.type)
+            if(H5F_istore_update_cache(dataset->ent.file, dxpl_id, &dataset->layout, space) < 0)
+                HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices")
+
 	/* Allocate space for the new parts of the dataset, if appropriate */
         if(dataset->alloc_time==H5D_ALLOC_TIME_EARLY)
             if (H5D_alloc_storage(dataset->ent.file, dxpl_id, dataset, H5D_ALLOC_EXTEND, TRUE, FALSE)<0)
@@ -3208,7 +3213,6 @@ done:
 static hsize_t
 H5D_get_storage_size(const H5D_t *dset, hid_t dxpl_id)
 {
-    unsigned	u;              /* Index variable */
     hsize_t	ret_value;
     
     FUNC_ENTER_NOAPI(H5D_get_storage_size, 0)
@@ -3218,8 +3222,7 @@ H5D_get_storage_size(const H5D_t *dset, hid_t dxpl_id)
             if(dset->layout.u.chunk.addr == HADDR_UNDEF)
                 ret_value=0;
             else
-                ret_value = H5F_istore_allocated(dset->ent.file, dxpl_id, dset->layout.u.chunk.ndims,
-                                             dset->layout.u.chunk.addr);
+                ret_value = H5F_istore_allocated(dset->ent.file, dxpl_id, &dset->layout);
             break;
 
         case H5D_CONTIGUOUS:
@@ -3419,7 +3422,7 @@ H5Diterate(void *buf, hid_t type_id, hid_t space_id, H5D_operator_t op,
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid datatype")
     if (NULL == (space = H5I_object_verify(space_id, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "invalid dataspace")
-            
+
     ret_value=H5S_select_iterate(buf,type_id,space,op,operator_data);
 
 done:
@@ -3803,6 +3806,11 @@ H5D_set_extent(H5D_t *dset, const hsize_t *size, hid_t dxpl_id)
         if(H5S_modify(&(dset->ent), space, TRUE, dxpl_id) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update file with new dataspace")
 
+        /* Update the index values for the cached chunks for this dataset */
+        if(H5D_CHUNKED == dset->layout.type)
+            if(H5F_istore_update_cache(dset->ent.file, dxpl_id, &dset->layout, space) < 0)
+                HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "unable to update cached chunk indices")
+
 	/* Allocate space for the new parts of the dataset, if appropriate */
         if(expand && dset->alloc_time==H5D_ALLOC_TIME_EARLY)
             if(H5D_alloc_storage(dset->ent.file, dxpl_id, dset, H5D_ALLOC_EXTEND, TRUE, FALSE) < 0)
diff --git a/src/H5Dio.c b/src/H5Dio.c
index a465413..2d6d016 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -64,7 +64,7 @@ typedef struct fm_map {
     unsigned m_ndims;           /* Number of dimensions for memory dataspace */
     hsize_t chunks[H5O_LAYOUT_NDIMS];   /* Number of chunks in each dimension */
     hsize_t chunk_dim[H5O_LAYOUT_NDIMS];    /* Size of chunk in each dimension */
-    hsize_t down_chunks[H5O_LAYOUT_NDIMS];      /* "down" size of number of chunks in each dimension */
+    hsize_t down_chunks[H5O_LAYOUT_NDIMS];   /* "down" size of number of chunks in each dimension */
     H5O_layout_t *layout;       /* Dataset layout information*/
     H5S_sel_type msel_type;     /* Selection type in memory */
 } fm_map;
@@ -130,7 +130,6 @@ H5FL_BLK_DEFINE(type_conv);
 /* Declare a free list to manage the H5D_chunk_info_t struct */
 H5FL_DEFINE_STATIC(H5D_chunk_info_t);
 
-
 
 /*--------------------------------------------------------------------------
  NAME
@@ -175,7 +174,7 @@ H5Dfill(const void *fill, hid_t fill_type_id, void *buf, hid_t buf_type_id, hid_
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype")
     if (NULL == (buf_type=H5I_object_verify(buf_type_id, H5I_DATATYPE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, 0, "not a datatype")
-            
+
     /* Fill the selection in the memory buffer */
     if(H5D_fill(fill,fill_type,buf,buf_type,space, H5AC_dxpl_id)<0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed")
@@ -308,7 +307,7 @@ H5D_get_dxpl_cache_real(hid_t dxpl_id, H5D_dxpl_cache_t *cache)
     /* Get the dataset transfer property list */
     if (NULL == (dx_plist = H5I_object(dxpl_id)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
-    
+
     /* Get maximum temporary buffer size */
     if(H5P_get(dx_plist, H5D_XFER_MAX_TEMP_BUF_NAME, &cache->max_temp_buf)<0)
         HGOTO_ERROR (H5E_PLIST, H5E_CANTGET, FAIL, "Can't retrieve maximum temporary buffer size")
@@ -478,7 +477,7 @@ H5Dread(hid_t dset_id, hid_t mem_type_id, hid_t mem_space_id,
 	if(H5S_SELECT_VALID(file_space)!=TRUE)
 	    HGOTO_ERROR(H5E_DATASPACE, H5E_BADRANGE, FAIL, "selection+offset not within extent")
     }
-    
+
     /* Get the default dataset transfer property list if the user didn't provide one */
     if (H5P_DEFAULT == plist_id)
         plist_id= H5P_DATASET_XFER_DEFAULT;
@@ -1071,14 +1070,13 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
     hsize_t	smine_start;		/*strip mine start loc	*/
     hsize_t	n, smine_nelmts;	/*elements per strip	*/
     herr_t	ret_value = SUCCEED;	/*return value		*/
-       
+
     FUNC_ENTER_NOAPI_NOINIT(H5D_contig_read)
- 
+
     /*
      * If there is no type conversion then read directly into the
      * application's buffer.  This saves at least one mem-to-mem copy.
      */
-                
     if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
 #ifdef H5S_DEBUG
 	H5_timer_begin(&timer);
@@ -1219,7 +1217,6 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
          */
         if (H5T_convert(tpath, src_id, dst_id, smine_nelmts, 0, 0, tconv_buf, bkg_buf, dxpl_id)<0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "data type conversion failed")
-   
 
 	/* Do the data transform after the conversion (since we're using type mem_type) */
         if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
@@ -1229,7 +1226,6 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
 	}
         /* end of LA additions */
 
-
         /*
          * Scatter the data into memory.
          */
@@ -1238,8 +1234,6 @@ H5D_contig_read(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type,
 #endif
         status = H5S_select_mscat(tconv_buf, mem_space,
                           &mem_iter, smine_nelmts, dxpl_cache, buf/*out*/);
-
-
 #ifdef H5S_DEBUG
 	H5_timer_end(&(sconv->stats[1].scat_timer), &timer);
 	sconv->stats[1].scat_nbytes += smine_nelmts * dst_type_size;
@@ -1321,12 +1315,11 @@ H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5
     herr_t	ret_value = SUCCEED;	/*return value		*/
     
     FUNC_ENTER_NOAPI_NOINIT(H5D_contig_write)
- 
+
     /*
      * If there is no type conversion then write directly from the
      * application's buffer.  This saves at least one mem-to-mem copy.
      */
-
     if ( H5Z_xform_noop(dxpl_cache->data_xform_prop) && H5T_path_noop(tpath)) {
 #ifdef H5S_DEBUG
 	H5_timer_begin(&timer);
@@ -1335,7 +1328,6 @@ H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5
         status = (sconv->write)(dataset->ent.file, &(dataset->layout),
                 &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), (size_t)nelmts, H5T_get_size(dataset->type),
                 file_space, mem_space, dxpl_cache, dxpl_id, buf);
-
 #ifdef H5S_DEBUG
         H5_timer_end(&(sconv->stats[0].write_timer), &timer);
         sconv->stats[0].write_nbytes += nelmts * H5T_get_size(mem_type);
@@ -1456,8 +1448,6 @@ H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5
                 HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
         } /* end if */
 	
-	       
-    
 	/*
          * Perform data type conversion.
          */
@@ -1472,19 +1462,15 @@ H5D_contig_write(hsize_t nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5
 	}
         /* End of LA modifications */
 
-
         /*
          * Scatter the data out to the file.
          */
 #ifdef H5S_DEBUG
         H5_timer_begin(&timer);
 #endif
- 
 	status = H5S_select_fscat(dataset->ent.file, &(dataset->layout), 
               &dataset->dcpl_cache, (H5D_storage_t *)&(dataset->efl), file_space, &file_iter,
               smine_nelmts, dxpl_cache, dxpl_id, tconv_buf);
-
-
 #ifdef H5S_DEBUG
         H5_timer_end(&(sconv->stats[0].scat_timer), &timer);
         sconv->stats[0].scat_nbytes += smine_nelmts * dst_type_size;
@@ -1534,7 +1520,6 @@ done:
  *      Leon Arber: 4/20/04
  *      Added support for data transforms.
  *
-
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -1571,7 +1556,7 @@ UNUSED
     uint8_t	*bkg_buf = NULL;	/*background buffer	*/
     H5D_storage_t store;                /*union of EFL and chunk pointer in file space */
     herr_t	ret_value = SUCCEED;	/*return value		*/
-    
+
     FUNC_ENTER_NOAPI_NOINIT(H5D_chunk_read)
     
     /* Map elements between file and memory for each chunk*/
@@ -1602,7 +1587,8 @@ UNUSED
             chunk_info=chunk_node->data;
 
             /* Pass in chunk's coordinates in a union. */
-            store.chunk_coords = chunk_info->coords;
+            store.chunk.offset = chunk_info->coords;
+            store.chunk.index = chunk_info->index;
 
             /* Perform the actual read operation */
             status = (sconv->read)(dataset->ent.file, &(dataset->layout),
@@ -1701,7 +1687,8 @@ UNUSED
         bkg_iter_init=1;	/*file selection iteration info has been initialized */
         
         /* Pass in chunk's coordinates in a union*/
-        store.chunk_coords = chunk_info->coords;
+        store.chunk.offset = chunk_info->coords;
+        store.chunk.index = chunk_info->index;
            
         for (smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) {
             /* Go figure out how many elements to read from the file */
@@ -1756,10 +1743,8 @@ UNUSED
 
            /* Do the data transform after the conversion (since we're using type mem_type) */
             if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
-	    {
 	       if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, mem_type) < 0)
 		      HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
-	    }
 
             /*
              * Scatter the data into memory.
@@ -1804,7 +1789,7 @@ done:
     if(file_iter_init) {
         if(H5S_SELECT_ITER_RELEASE(&file_iter)<0)
             HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
-        } /* end if */
+    } /* end if */
     if(mem_iter_init) {
         if(H5S_SELECT_ITER_RELEASE(&mem_iter)<0)
             HDONE_ERROR (H5E_DATASET, H5E_CANTFREE, FAIL, "Can't release selection iterator")
@@ -1932,7 +1917,8 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
             chunk_info=chunk_node->data;
 
             /* Pass in chunk's coordinates in a union. */
-            store.chunk_coords = chunk_info->coords;
+            store.chunk.offset = chunk_info->coords;
+            store.chunk.index = chunk_info->index;
 
             /* Perform the actual write operation */
             status = (sconv->write)(dataset->ent.file, &(dataset->layout),
@@ -2051,7 +2037,8 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
         bkg_iter_init=1;	/*file selection iteration info has been initialized */
         
         /*pass in chunk's coordinates in a union*/
-        store.chunk_coords = chunk_info->coords;
+        store.chunk.offset = chunk_info->coords;
+        store.chunk.index = chunk_info->index;
        
         for (smine_start=0; smine_start<chunk_info->chunk_points; smine_start+=smine_nelmts) {
             /* Go figure out how many elements to read from the file */
@@ -2093,8 +2080,6 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
                 if (n!=smine_nelmts)
                     HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "file gather failed")
             } /* end if */
-   
-
 
 	    /*
              * Perform data type conversion.
@@ -2105,10 +2090,8 @@ nelmts, H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
 
  	    /* Do the data transform after the type conversion (since we're using dataset->type) */
             if(!H5Z_xform_noop(dxpl_cache->data_xform_prop))
-	    {
 	      if( H5Z_xform_eval(dxpl_cache->data_xform_prop, tconv_buf, smine_nelmts, dataset->type) < 0)
 		     HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Error performing data transform")
-	    }          
 
             /*
              * Scatter the data out to the file.
@@ -2302,7 +2285,6 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
     hbool_t iter_init=0;        /* Selection iteration info has been initialized */
     unsigned f_ndims;           /* The number of dimensions of the file's dataspace */
     int sm_ndims;               /* The number of dimensions of the memory buffer's dataspace (signed) */
-    hsize_t nchunks, last_nchunks;      /* Number of chunks in dataset */
     H5TB_NODE *curr_node;       /* Current node in TBBT */
     H5S_sel_type fsel_type;     /* Selection type on disk */
     char bogus;                 /* "bogus" buffer to pass to selection iterator */
@@ -2358,22 +2340,12 @@ H5D_create_chunk_map(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *file_sp
         HGOTO_ERROR (H5E_DATASPACE, H5E_CANTGET, FAIL, "unable to get dimensionality")
 
     /* Decide the number of chunks in each dimension*/
-    last_nchunks=0;
-    nchunks=1;
     for(u=0; u<f_ndims; u++) {
         /* Keep the size of the chunk dimensions as hsize_t for various routines */
         fm->chunk_dim[u]=fm->layout->u.chunk.dim[u];
 
         /* Round up to the next integer # of chunks, to accomodate partial chunks */
         fm->chunks[u] = ((fm->f_dims[u]+dataset->layout.u.chunk.dim[u])-1) / dataset->layout.u.chunk.dim[u];
-
-        /* Track total number of chunks in dataset */
-        nchunks *= fm->chunks[u];
-
-        /* Check if the chunk indices will overflow */
-        if(nchunks<last_nchunks)
-            HGOTO_ERROR (H5E_DATASET, H5E_OVERFLOW, FAIL, "too many chunks")
-        last_nchunks=nchunks;
     } /* end for */
         
     /* Compute the "down" size of 'chunks' information */
diff --git a/src/H5Distore.c b/src/H5Distore.c
index 2434cc2..a5aeb70 100644
--- a/src/H5Distore.c
+++ b/src/H5Distore.c
@@ -1346,7 +1346,7 @@ static void *
 H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5O_layout_t *layout,
     const H5O_pline_t *pline, const H5O_fill_t *fill, H5D_fill_time_t fill_time,
     H5F_istore_ud1_t *udata,
-    const hssize_t offset[], hbool_t relax,
+    const H5D_storage_t *store, hbool_t relax,
     unsigned *idx_hint/*in,out*/)
 {
     int		idx=0;			/*hash index number	*/
@@ -1369,18 +1369,14 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con
 
     /* Search for the chunk in the cache */
     if (rdcc->nslots>0) {
-        for (u=0, temp_idx=0; u<layout->u.chunk.ndims; u++) {
-            temp_idx += offset[u];
-            temp_idx *= layout->u.chunk.dim[u];
-        }
-        temp_idx += (hsize_t)(layout->u.chunk.addr);
+        temp_idx = store->chunk.index + (hsize_t)(layout->u.chunk.addr);
         idx=H5F_HASH(f,temp_idx);
         ent = rdcc->slot[idx];
         
         if (ent && layout->u.chunk.ndims==ent->layout.u.chunk.ndims &&
                 H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
             for (u=0, found=TRUE; u<ent->layout.u.chunk.ndims; u++) {
-                if (offset[u]!=ent->offset[u]) {
+                if (store->chunk.offset[u]!=ent->offset[u]) {
                     found = FALSE;
                     break;
                 }
@@ -1423,7 +1419,7 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con
              * Not in the cache.  Read it from the file and count this as a miss
              * if it's in the file or an init if it isn't.
              */
-            chunk_addr = H5F_istore_get_addr(f, dxpl_id, layout, offset, udata);
+            chunk_addr = H5F_istore_get_addr(f, dxpl_id, layout, store->chunk.offset, udata);
         } /* end else */
 
         if (H5F_addr_defined(chunk_addr)) {
@@ -1508,7 +1504,7 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con
         H5O_copy(H5O_LAYOUT_ID, layout, &ent->layout);
         H5O_copy(H5O_PLINE_ID, pline, &ent->pline);
         for (u=0; u<layout->u.chunk.ndims; u++)
-            ent->offset[u] = offset[u];
+            ent->offset[u] = store->chunk.offset[u];
         ent->rd_count = chunk_size;
         ent->wr_count = chunk_size;
         ent->chunk = chunk;
@@ -1612,7 +1608,7 @@ done:
 static herr_t
 H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
     const H5O_layout_t *layout, const H5O_pline_t *pline, hbool_t dirty,
-    const hssize_t offset[], unsigned *idx_hint, uint8_t *chunk, size_t naccessed)
+    const H5D_storage_t *store, unsigned idx_hint, uint8_t *chunk, size_t naccessed)
 {
     H5F_rdcc_t		*rdcc = &(f->shared->rdcc);
     H5F_rdcc_ent_t	*ent = NULL;
@@ -1621,13 +1617,13 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
     
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5F_istore_unlock);
 
-    if (UINT_MAX==*idx_hint) {
+    if (UINT_MAX==idx_hint) {
 	/*not in cache*/
     } else {
-	assert(*idx_hint<rdcc->nslots);
-	assert(rdcc->slot[*idx_hint]);
-	assert(rdcc->slot[*idx_hint]->chunk==chunk);
-	found = *idx_hint;
+	assert(idx_hint<rdcc->nslots);
+	assert(rdcc->slot[idx_hint]);
+	assert(rdcc->slot[idx_hint]->chunk==chunk);
+	found = idx_hint;
     }
     
     if (found<0) {
@@ -1645,7 +1641,7 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
             H5O_copy (H5O_LAYOUT_ID, layout, &x.layout);
             H5O_copy (H5O_PLINE_ID, pline, &x.pline);
             for (u=0; u<layout->u.chunk.ndims; u++)
-                x.offset[u] = offset[u];
+                x.offset[u] = store->chunk.offset[u];
             assert(layout->u.chunk.size>0);
             H5_ASSIGN_OVERFLOW(x.chunk_size,layout->u.chunk.size,hsize_t,size_t);
             x.alloc_size = x.chunk_size;
@@ -1692,7 +1688,7 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
  */
 ssize_t
 H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
-    const H5O_layout_t *layout, const struct H5D_dcpl_cache_t *dcpl_cache, hssize_t chunk_coords[],
+    const H5O_layout_t *layout, const struct H5D_dcpl_cache_t *dcpl_cache, const H5D_storage_t *store,
     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)
@@ -1718,7 +1714,7 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp
 
 #ifndef NDEBUG
     for (u=0; u<layout->u.chunk.ndims; u++)
-        assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */
+        assert(store->chunk.offset[u]>=0); /*negative coordinates not supported (yet) */
 #endif
     
     /* Get the address of this chunk on disk */
@@ -1727,7 +1723,7 @@ HDfprintf(stderr,"%s: chunk_coords={",FUNC);
 for(u=0; u<layout->u.chunk.ndims; u++)
     HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n"));
 #endif /* QAK */
-    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata);
+    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, store->chunk.offset, &udata);
 #ifdef QAK
 HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->u.chunk.size);
 HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]);
@@ -1757,7 +1753,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
          * chunk.
          */
         if (NULL==(chunk=H5F_istore_lock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, &dcpl_cache->fill, dcpl_cache->fill_time,
-                     &udata, chunk_coords, FALSE, &idx_hint)))
+                     &udata, store, FALSE, &idx_hint)))
             HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk");
 
         /* Use the vectorized memory copy routine to do actual work */
@@ -1766,7 +1762,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
 
         H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
         if (H5F_istore_unlock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, FALSE,
-                  chunk_coords, &idx_hint, chunk, (size_t)naccessed)<0)
+                  store, idx_hint, chunk, (size_t)naccessed)<0)
             HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk");
 
         /* Set return value */
@@ -1796,7 +1792,7 @@ done:
 ssize_t
 H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
     hid_t dxpl_id, const H5O_layout_t *layout,
-    const struct H5D_dcpl_cache_t *dcpl_cache, hssize_t chunk_coords[],
+    const struct H5D_dcpl_cache_t *dcpl_cache, const H5D_storage_t *store,
     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)
@@ -1822,7 +1818,7 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
 
 #ifndef NDEBUG
     for (u=0; u<layout->u.chunk.ndims; u++)
-        assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */
+        assert(store->chunk.offset[u]>=0); /*negative coordinates not supported (yet) */
 #endif
     
     /* Get the address of this chunk on disk */
@@ -1831,7 +1827,7 @@ HDfprintf(stderr,"%s: chunk_coords={",FUNC);
 for(u=0; u<layout->u.chunk.ndims; u++)
     HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n"));
 #endif /* QAK */
-    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata);
+    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, store->chunk.offset, &udata);
 #ifdef QAK
 HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->u.chunk.size);
 HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]);
@@ -1877,7 +1873,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
             relax = FALSE;
 
         if (NULL==(chunk=H5F_istore_lock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, &dcpl_cache->fill, dcpl_cache->fill_time,
-                 &udata, chunk_coords, relax, &idx_hint)))
+                 &udata, store, 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 */
@@ -1886,7 +1882,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
 
         H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
         if (H5F_istore_unlock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, TRUE,
-                  chunk_coords, &idx_hint, chunk, (size_t)naccessed)<0)
+                  store, idx_hint, chunk, (size_t)naccessed)<0)
             HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk");
 
         /* Set return value */
@@ -1967,16 +1963,33 @@ done:
  *-------------------------------------------------------------------------
  */
 hsize_t
-H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, unsigned ndims, haddr_t addr)
+H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout)
 {
+    H5F_rdcc_t         *rdcc = &(f->shared->rdcc);	/*raw data chunk cache */
+    H5F_rdcc_ent_t     *ent;    /*cache entry  */
+    H5D_dxpl_cache_t    dxpl_cache;     /* Cached data transfer properties */
     H5F_istore_ud1_t	udata;
     hsize_t      ret_value;       /* Return value */
 
     FUNC_ENTER_NOAPI(H5F_istore_allocated, 0);
 
+    /* Fill the DXPL cache values for later use */
+    if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't fill dxpl cache")
+
+    /* Search for cached chunks that haven't been written out */
+    for(ent = rdcc->head; ent; ent = ent->next) {
+        /* Make certain we are dealing with the correct B-tree, etc */
+        if (H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
+            /* Flush the chunk out to disk, to make certain the size is correct later */
+            if (H5F_istore_flush_entry(f, &dxpl_cache, dxpl_id, ent, FALSE)<0)
+                HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, 0, "cannot flush indexed storage buffer");
+        } /* end if */
+    } /* end for */
+
     HDmemset(&udata, 0, sizeof udata);
-    udata.mesg.u.chunk.ndims = ndims;
-    if (H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_iter_allocated, addr, &udata)<0)
+    udata.mesg.u.chunk.ndims = layout->u.chunk.ndims;
+    if (H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_iter_allocated, layout->u.chunk.addr, &udata)<0)
         HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree");
 
     /* Set return value */
@@ -1984,7 +1997,7 @@ H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, unsigned ndims, haddr_t addr)
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
-}
+} /* end H5F_istore_allocated() */
 
 
 /*-------------------------------------------------------------------------
@@ -2487,7 +2500,7 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
     H5F_rdcc_t             *rdcc = &(f->shared->rdcc);	/*raw data chunk cache */
     H5F_rdcc_ent_t         *ent = NULL, *next = NULL;	/*cache entry  */
     unsigned                u;	/*counters  */
-    int                     found = 0;	/*remove this entry  */
+    int                     found;	/*remove this entry  */
     H5F_istore_ud1_t        udata;	/*B-tree pass-through */
     hsize_t                 curr_dims[H5O_LAYOUT_NDIMS];	/*current dataspace dimensions */
     herr_t      ret_value=SUCCEED;       /* Return value */
@@ -2510,13 +2523,12 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
   * and release them from the linked list raw data cache
   *-------------------------------------------------------------------------
   */
+    found = 0;
     for(ent = rdcc->head; ent; ent = next) {
 	next = ent->next;
 
         /* Make certain we are dealing with the correct B-tree, etc */
-        if (layout->u.chunk.ndims==ent->layout.u.chunk.ndims &&
-                H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
-            found = 0;
+        if (H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
             for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) {
                 if((hsize_t)ent->offset[u] > curr_dims[u]) {
                     found = 1;
@@ -2526,17 +2538,18 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
         } /* end if */
 
 	if(found) {
-#if defined (H5F_ISTORE_DEBUG)
-	    HDfputs("cache:remove:[", stdout);
-	    for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) {
-		HDfprintf(stdout, "%s%Hd", u ? ", " : "", ent->offset[u]);
-	    }
-	    HDfputs("]\n", stdout);
+#ifdef H5F_ISTORE_DEBUG
+	    HDfputs("cache:remove:[", stderr);
+	    for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++)
+		HDfprintf(stderr, "%s%Hd", u ? ", " : "", ent->offset[u]);
+	    HDfputs("]\n", stderr);
 #endif
 
 	    /* Preempt the entry from the cache, but do not flush it to disk */
 	    if(H5F_istore_preempt(f, dxpl_cache, dxpl_id, ent, FALSE) < 0)
 		HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to preempt chunk");
+
+            found=0;
 	}
     }
 
@@ -2597,12 +2610,10 @@ H5F_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t UNUSED a
     /* Figure out what chunks are no longer in use for the specified extent and release them */
     for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++)
 	if((hsize_t)lt_key->offset[u] > bt_udata->dims[u]) {
-#if defined (H5F_ISTORE_DEBUG)
+#ifdef H5F_ISTORE_DEBUG
             HDfputs("b-tree:remove:[", bt_udata->stream);
-            for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++) {
-                HDfprintf(bt_udata->stream, "%s%Hd", u ? ", " : "",
-                        lt_key->offset[u]);
-            }
+            for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++)
+                HDfprintf(bt_udata->stream, "%s%Hd", u ? ", " : "", lt_key->offset[u]);
             HDfputs("]\n", bt_udata->stream);
 #endif
 
@@ -2710,6 +2721,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
     H5S_t                  *space_chunk = NULL;	/*dataspace for a chunk */
     hsize_t                 chunk_dims[H5O_LAYOUT_NDIMS];	/*current chunk dimensions */
     hsize_t                 curr_dims[H5O_LAYOUT_NDIMS];	/*current dataspace dimensions */
+    hsize_t                 chunks[H5O_LAYOUT_NDIMS];	        /*current number of chunks in each dimension */
+    hsize_t                 down_chunks[H5O_LAYOUT_NDIMS];   /* "down" size of number of elements in each dimension */
     int                     srank;	/*current # of dimensions (signed) */
     unsigned                rank;	/*current # of dimensions */
     int                     i, carry;	/*counters  */
@@ -2718,6 +2731,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
     H5O_pline_t             pline;      /* I/O pipeline information */
     H5O_fill_t              fill;       /* Fill value information */
     H5D_fill_time_t         fill_time;  /* Fill time information */
+    H5D_storage_t           store;      /* Dataset storage information */
     herr_t	            ret_value=SUCCEED;	/* Return value */
 
     FUNC_ENTER_NOAPI(H5F_istore_initialize_by_extent, FAIL);
@@ -2747,10 +2761,18 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
     H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned);
 
     /* Copy current dimensions */
-    for(u = 0; u < rank; u++)
+    for(u = 0; u < rank; u++) {
 	size[u] = curr_dims[u];
+
+        /* Round up to the next integer # of chunks, to accomodate partial chunks */
+        chunks[u] = ((curr_dims[u]+layout->u.chunk.dim[u])-1) / layout->u.chunk.dim[u];
+    } /* end for */
     size[u] = layout->u.chunk.dim[u];
 
+    /* Get the "down" sizes for each dimension */
+    if(H5V_array_down(rank,chunks,down_chunks)<0)
+        HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
+
     /* Create a data space for a chunk & set the extent */
     for(u = 0; u < rank; u++)
 	chunk_dims[u] = layout->u.chunk.dim[u];
@@ -2792,8 +2814,13 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
 
 	if(found) {
 
+            /* Calculate the index of this chunk */
+            if(H5V_chunk_index(rank,chunk_offset,layout->u.chunk.dim,down_chunks,&store.chunk.index)<0)
+                HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
+
+            store.chunk.offset=chunk_offset;
 	    if(NULL == (chunk = H5F_istore_lock(f, dxpl_cache, dxpl_id, layout, &pline, &fill, fill_time,
-			    NULL, chunk_offset, FALSE, &idx_hint)))
+			    NULL, &store, FALSE, &idx_hint)))
 		HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk");
 
 	    if(H5S_select_all(space_chunk,1) < 0)
@@ -2802,7 +2829,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
 	    for(u = 0; u < rank; u++)
 		count[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u], size[u] - chunk_offset[u]);
 
-#if defined (H5F_ISTORE_DEBUG)
+#ifdef H5F_ISTORE_DEBUG
 	    HDfputs("cache:initialize:offset:[", stdout);
 	    for(u = 0; u < layout->u.chunk.ndims - 1; u++)
 		HDfprintf(stdout, "%s%Hd", u ? ", " : "", chunk_offset[u]);
@@ -2826,7 +2853,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
 		HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed");
 
 	    if(H5F_istore_unlock(f, dxpl_cache, dxpl_id, layout, &pline, TRUE,
-                    chunk_offset, &idx_hint, chunk, (size_t)naccessed) < 0)
+                    &store, idx_hint, chunk, (size_t)naccessed) < 0)
 		HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk");
 	} /*found */
 
@@ -2887,8 +2914,8 @@ H5F_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout)
             /* Is the chunk to be deleted this cache entry? */
             if(layout->u.chunk.addr==ent->layout.u.chunk.addr)
                 /* Remove entry without flushing */
-            if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, ent, FALSE )<0)
-                    HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks");
+                if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, ent, FALSE )<0)
+                        HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks");
         } /* end for */
 
         /* Set up user data for B-tree deletion */
@@ -2906,6 +2933,111 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5F_istore_update_cache
+ *
+ * Purpose:	Update any cached chunks index values after the dataspace
+ *              size has changed
+ *
+ * Return:	Success:	Non-negative
+ *		Failure:	negative
+ *
+ * Programmer:	Quincey Koziol
+ *              Saturday, May 29, 2004
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_istore_update_cache(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const H5S_t * space)
+{
+    H5F_rdcc_t         *rdcc = &(f->shared->rdcc);	/*raw data chunk cache */
+    H5F_rdcc_ent_t     *ent, *next;	/*cache entry  */
+    H5F_rdcc_ent_t     *old_ent;	/* Old cache entry  */
+    H5D_dxpl_cache_t    dxpl_cache;     /* Cached data transfer properties */
+    int                 srank;	/*current # of dimensions (signed) */
+    unsigned            rank;	/*current # of dimensions */
+    hsize_t             curr_dims[H5O_LAYOUT_NDIMS];	/*current dataspace dimensions */
+    hsize_t             chunks[H5O_LAYOUT_NDIMS];	        /*current number of chunks in each dimension */
+    hsize_t             down_chunks[H5O_LAYOUT_NDIMS];   /* "down" size of number of elements in each dimension */
+    hsize_t             idx;    /* Chunk index */
+    hsize_t	        temp_idx;	/* temporary index number	*/
+    unsigned	        old_idx;	/* Previous index number	*/
+    unsigned            u;	/*counters  */
+    herr_t      ret_value=SUCCEED;      /* Return value */
+
+    FUNC_ENTER_NOAPI(H5F_istore_update_cache, FAIL);
+
+    /* Check args */
+    assert(f);
+    assert(layout && H5D_CHUNKED == layout->type);
+    assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
+    assert(space);
+
+    /* Go get the rank & dimensions */
+    if((srank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
+	HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
+    H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned);
+
+    /* Copy current dimensions */
+    for(u = 0; u < rank; u++) {
+        /* Round up to the next integer # of chunks, to accomodate partial chunks */
+        chunks[u] = ((curr_dims[u]+layout->u.chunk.dim[u])-1) / layout->u.chunk.dim[u];
+    } /* end for */
+
+    /* Get the "down" sizes for each dimension */
+    if(H5V_array_down(rank,chunks,down_chunks)<0)
+        HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
+
+    /* Fill the DXPL cache values for later use */
+    if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+    /* Recompute the index for each cached chunk that is in a dataset */
+    for(ent = rdcc->head; ent; ent = next) {
+        next=ent->next;
+
+        /* Make certain we are dealing with the correct B-tree, etc */
+        if (H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
+            /* Calculate the index of this chunk */
+            if(H5V_chunk_index(rank,ent->offset,layout->u.chunk.dim,down_chunks,&idx)<0)
+                HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
+
+            /* Compute the index for the chunk entry */
+            temp_idx = idx + (hsize_t)(layout->u.chunk.addr);
+            old_idx=ent->idx;   /* Save for later */
+            ent->idx=H5F_HASH(f,temp_idx);
+
+            if(old_idx!=ent->idx) {
+                /* Check if there is already a chunk at this chunk's new location */
+                old_ent = rdcc->slot[ent->idx];
+                if(old_ent!=NULL) {
+                    assert(old_ent->locked==0);
+
+                    /* Check if we are removing the entry we would walk to next */
+                    if(old_ent==next)
+                        next=old_ent->next;
+
+                    /* Remove the old entry from the cache */
+                    if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, old_ent, TRUE )<0)
+                        HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks");
+                } /* end if */
+
+                /* Insert this chunk into correct location in hash table */
+                rdcc->slot[ent->idx]=ent;
+
+                /* Null out previous location */
+                rdcc->slot[old_idx]=NULL;
+            } /* end if */
+        } /* end if */
+    } /* end for */
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+} /* end H5F_istore_update_cache() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5F_istore_dump_btree
  *
  * Purpose:	Prints information about the storage B-tree to the specified
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index 985d935..bdbe126 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -164,7 +164,10 @@ typedef struct H5D_t H5D_t;
 /* Typedef for dataset storage information */
 typedef union H5D_storage_t {
     H5O_efl_t   efl;            /* External file list information for dataset */
-    hssize_t    *chunk_coords;  /* chunk's coordinates in file chunks */
+    struct {
+        hsize_t index;          /* "Index" of chunk in dataset (must be first for TBBT routines) */
+        hssize_t *offset;       /* Chunk's coordinates in elements */
+    } chunk;
 } H5D_storage_t;
 
 /* Typedef for cached dataset transfer property list information */
diff --git a/src/H5Dseq.c b/src/H5Dseq.c
index 9bf10e7..f8ecf00 100644
--- a/src/H5Dseq.c
+++ b/src/H5Dseq.c
@@ -237,7 +237,7 @@ H5F_seq_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_i
 
         case H5D_CHUNKED:
             assert(store);
-            if((ret_value=H5F_istore_readvv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store->chunk_coords,
+            if((ret_value=H5F_istore_readvv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store,
                     dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr,
                     mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr,
                     buf))<0)
@@ -346,7 +346,7 @@ H5F_seq_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
 
         case H5D_CHUNKED:
             assert(store);
-            if((ret_value=H5F_istore_writevv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store->chunk_coords,
+            if((ret_value=H5F_istore_writevv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store,
                     dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr,
                     mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr,
                     buf))<0)
diff --git a/src/H5F.c b/src/H5F.c
index 63ebdde..41fb972 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -2148,7 +2148,7 @@ H5Fcreate(const char *filename, unsigned flags, hid_t fcpl_id, hid_t fapl_id)
 
     /* Keep this ID in file object structure */
     new_file->file_id = ret_value;
-            
+
 done:
     if (ret_value<0 && new_file)
         if(H5F_close(new_file)<0)
@@ -2225,7 +2225,7 @@ H5Fopen(const char *filename, unsigned flags, hid_t fapl_id)
     /* Get an atom for the file */
     if ((ret_value = H5I_register(H5I_FILE, new_file))<0)
 	HGOTO_ERROR(H5E_ATOM, H5E_CANTREGISTER, FAIL, "unable to atomize file handle")
-            
+
     /* Keep this ID in file object structure */
     new_file->file_id = ret_value;
 
@@ -3333,7 +3333,7 @@ H5F_close(H5F_t *f)
 
     /* Invalidate file ID */
     f->file_id = -1;
-    
+
     /* Only flush at this point if the file will be closed */
     assert(closing);
     /* Dump debugging info */
diff --git a/src/H5Fistore.c b/src/H5Fistore.c
index 2434cc2..a5aeb70 100644
--- a/src/H5Fistore.c
+++ b/src/H5Fistore.c
@@ -1346,7 +1346,7 @@ static void *
 H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, const H5O_layout_t *layout,
     const H5O_pline_t *pline, const H5O_fill_t *fill, H5D_fill_time_t fill_time,
     H5F_istore_ud1_t *udata,
-    const hssize_t offset[], hbool_t relax,
+    const H5D_storage_t *store, hbool_t relax,
     unsigned *idx_hint/*in,out*/)
 {
     int		idx=0;			/*hash index number	*/
@@ -1369,18 +1369,14 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con
 
     /* Search for the chunk in the cache */
     if (rdcc->nslots>0) {
-        for (u=0, temp_idx=0; u<layout->u.chunk.ndims; u++) {
-            temp_idx += offset[u];
-            temp_idx *= layout->u.chunk.dim[u];
-        }
-        temp_idx += (hsize_t)(layout->u.chunk.addr);
+        temp_idx = store->chunk.index + (hsize_t)(layout->u.chunk.addr);
         idx=H5F_HASH(f,temp_idx);
         ent = rdcc->slot[idx];
         
         if (ent && layout->u.chunk.ndims==ent->layout.u.chunk.ndims &&
                 H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
             for (u=0, found=TRUE; u<ent->layout.u.chunk.ndims; u++) {
-                if (offset[u]!=ent->offset[u]) {
+                if (store->chunk.offset[u]!=ent->offset[u]) {
                     found = FALSE;
                     break;
                 }
@@ -1423,7 +1419,7 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con
              * Not in the cache.  Read it from the file and count this as a miss
              * if it's in the file or an init if it isn't.
              */
-            chunk_addr = H5F_istore_get_addr(f, dxpl_id, layout, offset, udata);
+            chunk_addr = H5F_istore_get_addr(f, dxpl_id, layout, store->chunk.offset, udata);
         } /* end else */
 
         if (H5F_addr_defined(chunk_addr)) {
@@ -1508,7 +1504,7 @@ H5F_istore_lock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id, con
         H5O_copy(H5O_LAYOUT_ID, layout, &ent->layout);
         H5O_copy(H5O_PLINE_ID, pline, &ent->pline);
         for (u=0; u<layout->u.chunk.ndims; u++)
-            ent->offset[u] = offset[u];
+            ent->offset[u] = store->chunk.offset[u];
         ent->rd_count = chunk_size;
         ent->wr_count = chunk_size;
         ent->chunk = chunk;
@@ -1612,7 +1608,7 @@ done:
 static herr_t
 H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
     const H5O_layout_t *layout, const H5O_pline_t *pline, hbool_t dirty,
-    const hssize_t offset[], unsigned *idx_hint, uint8_t *chunk, size_t naccessed)
+    const H5D_storage_t *store, unsigned idx_hint, uint8_t *chunk, size_t naccessed)
 {
     H5F_rdcc_t		*rdcc = &(f->shared->rdcc);
     H5F_rdcc_ent_t	*ent = NULL;
@@ -1621,13 +1617,13 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
     
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5F_istore_unlock);
 
-    if (UINT_MAX==*idx_hint) {
+    if (UINT_MAX==idx_hint) {
 	/*not in cache*/
     } else {
-	assert(*idx_hint<rdcc->nslots);
-	assert(rdcc->slot[*idx_hint]);
-	assert(rdcc->slot[*idx_hint]->chunk==chunk);
-	found = *idx_hint;
+	assert(idx_hint<rdcc->nslots);
+	assert(rdcc->slot[idx_hint]);
+	assert(rdcc->slot[idx_hint]->chunk==chunk);
+	found = idx_hint;
     }
     
     if (found<0) {
@@ -1645,7 +1641,7 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
             H5O_copy (H5O_LAYOUT_ID, layout, &x.layout);
             H5O_copy (H5O_PLINE_ID, pline, &x.pline);
             for (u=0; u<layout->u.chunk.ndims; u++)
-                x.offset[u] = offset[u];
+                x.offset[u] = store->chunk.offset[u];
             assert(layout->u.chunk.size>0);
             H5_ASSIGN_OVERFLOW(x.chunk_size,layout->u.chunk.size,hsize_t,size_t);
             x.alloc_size = x.chunk_size;
@@ -1692,7 +1688,7 @@ H5F_istore_unlock(H5F_t *f, const H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
  */
 ssize_t
 H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_id,
-    const H5O_layout_t *layout, const struct H5D_dcpl_cache_t *dcpl_cache, hssize_t chunk_coords[],
+    const H5O_layout_t *layout, const struct H5D_dcpl_cache_t *dcpl_cache, const H5D_storage_t *store,
     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)
@@ -1718,7 +1714,7 @@ H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxp
 
 #ifndef NDEBUG
     for (u=0; u<layout->u.chunk.ndims; u++)
-        assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */
+        assert(store->chunk.offset[u]>=0); /*negative coordinates not supported (yet) */
 #endif
     
     /* Get the address of this chunk on disk */
@@ -1727,7 +1723,7 @@ HDfprintf(stderr,"%s: chunk_coords={",FUNC);
 for(u=0; u<layout->u.chunk.ndims; u++)
     HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n"));
 #endif /* QAK */
-    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata);
+    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, store->chunk.offset, &udata);
 #ifdef QAK
 HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->u.chunk.size);
 HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]);
@@ -1757,7 +1753,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
          * chunk.
          */
         if (NULL==(chunk=H5F_istore_lock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, &dcpl_cache->fill, dcpl_cache->fill_time,
-                     &udata, chunk_coords, FALSE, &idx_hint)))
+                     &udata, store, FALSE, &idx_hint)))
             HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to read raw data chunk");
 
         /* Use the vectorized memory copy routine to do actual work */
@@ -1766,7 +1762,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
 
         H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
         if (H5F_istore_unlock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, FALSE,
-                  chunk_coords, &idx_hint, chunk, (size_t)naccessed)<0)
+                  store, idx_hint, chunk, (size_t)naccessed)<0)
             HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "unable to unlock raw data chunk");
 
         /* Set return value */
@@ -1796,7 +1792,7 @@ done:
 ssize_t
 H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
     hid_t dxpl_id, const H5O_layout_t *layout,
-    const struct H5D_dcpl_cache_t *dcpl_cache, hssize_t chunk_coords[],
+    const struct H5D_dcpl_cache_t *dcpl_cache, const H5D_storage_t *store,
     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)
@@ -1822,7 +1818,7 @@ H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
 
 #ifndef NDEBUG
     for (u=0; u<layout->u.chunk.ndims; u++)
-        assert(chunk_coords[u]>=0); /*negative coordinates not supported (yet) */
+        assert(store->chunk.offset[u]>=0); /*negative coordinates not supported (yet) */
 #endif
     
     /* Get the address of this chunk on disk */
@@ -1831,7 +1827,7 @@ HDfprintf(stderr,"%s: chunk_coords={",FUNC);
 for(u=0; u<layout->u.chunk.ndims; u++)
     HDfprintf(stderr,"%Hd%s",chunk_coords[u],(u<(layout->u.chunk.ndims-1) ? ", " : "}\n"));
 #endif /* QAK */
-    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, chunk_coords, &udata);
+    chunk_addr=H5F_istore_get_addr(f, dxpl_id, layout, store->chunk.offset, &udata);
 #ifdef QAK
 HDfprintf(stderr,"%s: chunk_addr=%a, chunk_size=%Hu\n",FUNC,chunk_addr,layout->u.chunk.size);
 HDfprintf(stderr,"%s: chunk_len_arr[%Zu]=%Zu\n",FUNC,*chunk_curr_seq,chunk_len_arr[*chunk_curr_seq]);
@@ -1877,7 +1873,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
             relax = FALSE;
 
         if (NULL==(chunk=H5F_istore_lock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, &dcpl_cache->fill, dcpl_cache->fill_time,
-                 &udata, chunk_coords, relax, &idx_hint)))
+                 &udata, store, 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 */
@@ -1886,7 +1882,7 @@ HDfprintf(stderr,"%s: mem_offset_arr[%Zu]=%Hu\n",FUNC,*mem_curr_seq,mem_offset_a
 
         H5_CHECK_OVERFLOW(naccessed,ssize_t,size_t);
         if (H5F_istore_unlock(f, dxpl_cache, dxpl_id, layout, &dcpl_cache->pline, TRUE,
-                  chunk_coords, &idx_hint, chunk, (size_t)naccessed)<0)
+                  store, idx_hint, chunk, (size_t)naccessed)<0)
             HGOTO_ERROR (H5E_IO, H5E_WRITEERROR, FAIL, "uanble to unlock raw data chunk");
 
         /* Set return value */
@@ -1967,16 +1963,33 @@ done:
  *-------------------------------------------------------------------------
  */
 hsize_t
-H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, unsigned ndims, haddr_t addr)
+H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout)
 {
+    H5F_rdcc_t         *rdcc = &(f->shared->rdcc);	/*raw data chunk cache */
+    H5F_rdcc_ent_t     *ent;    /*cache entry  */
+    H5D_dxpl_cache_t    dxpl_cache;     /* Cached data transfer properties */
     H5F_istore_ud1_t	udata;
     hsize_t      ret_value;       /* Return value */
 
     FUNC_ENTER_NOAPI(H5F_istore_allocated, 0);
 
+    /* Fill the DXPL cache values for later use */
+    if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, 0, "can't fill dxpl cache")
+
+    /* Search for cached chunks that haven't been written out */
+    for(ent = rdcc->head; ent; ent = ent->next) {
+        /* Make certain we are dealing with the correct B-tree, etc */
+        if (H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
+            /* Flush the chunk out to disk, to make certain the size is correct later */
+            if (H5F_istore_flush_entry(f, &dxpl_cache, dxpl_id, ent, FALSE)<0)
+                HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, 0, "cannot flush indexed storage buffer");
+        } /* end if */
+    } /* end for */
+
     HDmemset(&udata, 0, sizeof udata);
-    udata.mesg.u.chunk.ndims = ndims;
-    if (H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_iter_allocated, addr, &udata)<0)
+    udata.mesg.u.chunk.ndims = layout->u.chunk.ndims;
+    if (H5B_iterate(f, dxpl_id, H5B_ISTORE, H5F_istore_iter_allocated, layout->u.chunk.addr, &udata)<0)
         HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to iterate over chunk B-tree");
 
     /* Set return value */
@@ -1984,7 +1997,7 @@ H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, unsigned ndims, haddr_t addr)
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
-}
+} /* end H5F_istore_allocated() */
 
 
 /*-------------------------------------------------------------------------
@@ -2487,7 +2500,7 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
     H5F_rdcc_t             *rdcc = &(f->shared->rdcc);	/*raw data chunk cache */
     H5F_rdcc_ent_t         *ent = NULL, *next = NULL;	/*cache entry  */
     unsigned                u;	/*counters  */
-    int                     found = 0;	/*remove this entry  */
+    int                     found;	/*remove this entry  */
     H5F_istore_ud1_t        udata;	/*B-tree pass-through */
     hsize_t                 curr_dims[H5O_LAYOUT_NDIMS];	/*current dataspace dimensions */
     herr_t      ret_value=SUCCEED;       /* Return value */
@@ -2510,13 +2523,12 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
   * and release them from the linked list raw data cache
   *-------------------------------------------------------------------------
   */
+    found = 0;
     for(ent = rdcc->head; ent; ent = next) {
 	next = ent->next;
 
         /* Make certain we are dealing with the correct B-tree, etc */
-        if (layout->u.chunk.ndims==ent->layout.u.chunk.ndims &&
-                H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
-            found = 0;
+        if (H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
             for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) {
                 if((hsize_t)ent->offset[u] > curr_dims[u]) {
                     found = 1;
@@ -2526,17 +2538,18 @@ H5F_istore_prune_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
         } /* end if */
 
 	if(found) {
-#if defined (H5F_ISTORE_DEBUG)
-	    HDfputs("cache:remove:[", stdout);
-	    for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++) {
-		HDfprintf(stdout, "%s%Hd", u ? ", " : "", ent->offset[u]);
-	    }
-	    HDfputs("]\n", stdout);
+#ifdef H5F_ISTORE_DEBUG
+	    HDfputs("cache:remove:[", stderr);
+	    for(u = 0; u < ent->layout.u.chunk.ndims - 1; u++)
+		HDfprintf(stderr, "%s%Hd", u ? ", " : "", ent->offset[u]);
+	    HDfputs("]\n", stderr);
 #endif
 
 	    /* Preempt the entry from the cache, but do not flush it to disk */
 	    if(H5F_istore_preempt(f, dxpl_cache, dxpl_id, ent, FALSE) < 0)
 		HGOTO_ERROR(H5E_IO, H5E_CANTINIT, 0, "unable to preempt chunk");
+
+            found=0;
 	}
     }
 
@@ -2597,12 +2610,10 @@ H5F_istore_prune_extent(H5F_t *f, hid_t dxpl_id, void *_lt_key, haddr_t UNUSED a
     /* Figure out what chunks are no longer in use for the specified extent and release them */
     for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++)
 	if((hsize_t)lt_key->offset[u] > bt_udata->dims[u]) {
-#if defined (H5F_ISTORE_DEBUG)
+#ifdef H5F_ISTORE_DEBUG
             HDfputs("b-tree:remove:[", bt_udata->stream);
-            for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++) {
-                HDfprintf(bt_udata->stream, "%s%Hd", u ? ", " : "",
-                        lt_key->offset[u]);
-            }
+            for(u = 0; u < bt_udata->mesg.u.chunk.ndims - 1; u++)
+                HDfprintf(bt_udata->stream, "%s%Hd", u ? ", " : "", lt_key->offset[u]);
             HDfputs("]\n", bt_udata->stream);
 #endif
 
@@ -2710,6 +2721,8 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
     H5S_t                  *space_chunk = NULL;	/*dataspace for a chunk */
     hsize_t                 chunk_dims[H5O_LAYOUT_NDIMS];	/*current chunk dimensions */
     hsize_t                 curr_dims[H5O_LAYOUT_NDIMS];	/*current dataspace dimensions */
+    hsize_t                 chunks[H5O_LAYOUT_NDIMS];	        /*current number of chunks in each dimension */
+    hsize_t                 down_chunks[H5O_LAYOUT_NDIMS];   /* "down" size of number of elements in each dimension */
     int                     srank;	/*current # of dimensions (signed) */
     unsigned                rank;	/*current # of dimensions */
     int                     i, carry;	/*counters  */
@@ -2718,6 +2731,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
     H5O_pline_t             pline;      /* I/O pipeline information */
     H5O_fill_t              fill;       /* Fill value information */
     H5D_fill_time_t         fill_time;  /* Fill time information */
+    H5D_storage_t           store;      /* Dataset storage information */
     herr_t	            ret_value=SUCCEED;	/* Return value */
 
     FUNC_ENTER_NOAPI(H5F_istore_initialize_by_extent, FAIL);
@@ -2747,10 +2761,18 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
     H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned);
 
     /* Copy current dimensions */
-    for(u = 0; u < rank; u++)
+    for(u = 0; u < rank; u++) {
 	size[u] = curr_dims[u];
+
+        /* Round up to the next integer # of chunks, to accomodate partial chunks */
+        chunks[u] = ((curr_dims[u]+layout->u.chunk.dim[u])-1) / layout->u.chunk.dim[u];
+    } /* end for */
     size[u] = layout->u.chunk.dim[u];
 
+    /* Get the "down" sizes for each dimension */
+    if(H5V_array_down(rank,chunks,down_chunks)<0)
+        HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
+
     /* Create a data space for a chunk & set the extent */
     for(u = 0; u < rank; u++)
 	chunk_dims[u] = layout->u.chunk.dim[u];
@@ -2792,8 +2814,13 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
 
 	if(found) {
 
+            /* Calculate the index of this chunk */
+            if(H5V_chunk_index(rank,chunk_offset,layout->u.chunk.dim,down_chunks,&store.chunk.index)<0)
+                HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
+
+            store.chunk.offset=chunk_offset;
 	    if(NULL == (chunk = H5F_istore_lock(f, dxpl_cache, dxpl_id, layout, &pline, &fill, fill_time,
-			    NULL, chunk_offset, FALSE, &idx_hint)))
+			    NULL, &store, FALSE, &idx_hint)))
 		HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to read raw data chunk");
 
 	    if(H5S_select_all(space_chunk,1) < 0)
@@ -2802,7 +2829,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
 	    for(u = 0; u < rank; u++)
 		count[u] = MIN((idx_cur[u] + 1) * layout->u.chunk.dim[u], size[u] - chunk_offset[u]);
 
-#if defined (H5F_ISTORE_DEBUG)
+#ifdef H5F_ISTORE_DEBUG
 	    HDfputs("cache:initialize:offset:[", stdout);
 	    for(u = 0; u < layout->u.chunk.ndims - 1; u++)
 		HDfprintf(stdout, "%s%Hd", u ? ", " : "", chunk_offset[u]);
@@ -2826,7 +2853,7 @@ H5F_istore_initialize_by_extent(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_ca
 		HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "filling selection failed");
 
 	    if(H5F_istore_unlock(f, dxpl_cache, dxpl_id, layout, &pline, TRUE,
-                    chunk_offset, &idx_hint, chunk, (size_t)naccessed) < 0)
+                    &store, idx_hint, chunk, (size_t)naccessed) < 0)
 		HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "unable to unlock raw data chunk");
 	} /*found */
 
@@ -2887,8 +2914,8 @@ H5F_istore_delete(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout)
             /* Is the chunk to be deleted this cache entry? */
             if(layout->u.chunk.addr==ent->layout.u.chunk.addr)
                 /* Remove entry without flushing */
-            if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, ent, FALSE )<0)
-                    HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks");
+                if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, ent, FALSE )<0)
+                        HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks");
         } /* end for */
 
         /* Set up user data for B-tree deletion */
@@ -2906,6 +2933,111 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5F_istore_update_cache
+ *
+ * Purpose:	Update any cached chunks index values after the dataspace
+ *              size has changed
+ *
+ * Return:	Success:	Non-negative
+ *		Failure:	negative
+ *
+ * Programmer:	Quincey Koziol
+ *              Saturday, May 29, 2004
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F_istore_update_cache(H5F_t *f, hid_t dxpl_id, const H5O_layout_t *layout, const H5S_t * space)
+{
+    H5F_rdcc_t         *rdcc = &(f->shared->rdcc);	/*raw data chunk cache */
+    H5F_rdcc_ent_t     *ent, *next;	/*cache entry  */
+    H5F_rdcc_ent_t     *old_ent;	/* Old cache entry  */
+    H5D_dxpl_cache_t    dxpl_cache;     /* Cached data transfer properties */
+    int                 srank;	/*current # of dimensions (signed) */
+    unsigned            rank;	/*current # of dimensions */
+    hsize_t             curr_dims[H5O_LAYOUT_NDIMS];	/*current dataspace dimensions */
+    hsize_t             chunks[H5O_LAYOUT_NDIMS];	        /*current number of chunks in each dimension */
+    hsize_t             down_chunks[H5O_LAYOUT_NDIMS];   /* "down" size of number of elements in each dimension */
+    hsize_t             idx;    /* Chunk index */
+    hsize_t	        temp_idx;	/* temporary index number	*/
+    unsigned	        old_idx;	/* Previous index number	*/
+    unsigned            u;	/*counters  */
+    herr_t      ret_value=SUCCEED;      /* Return value */
+
+    FUNC_ENTER_NOAPI(H5F_istore_update_cache, FAIL);
+
+    /* Check args */
+    assert(f);
+    assert(layout && H5D_CHUNKED == layout->type);
+    assert(layout->u.chunk.ndims > 0 && layout->u.chunk.ndims <= H5O_LAYOUT_NDIMS);
+    assert(space);
+
+    /* Go get the rank & dimensions */
+    if((srank = H5S_get_simple_extent_dims(space, curr_dims, NULL)) < 0)
+	HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get dataset dimensions");
+    H5_ASSIGN_OVERFLOW(rank,srank,int,unsigned);
+
+    /* Copy current dimensions */
+    for(u = 0; u < rank; u++) {
+        /* Round up to the next integer # of chunks, to accomodate partial chunks */
+        chunks[u] = ((curr_dims[u]+layout->u.chunk.dim[u])-1) / layout->u.chunk.dim[u];
+    } /* end for */
+
+    /* Get the "down" sizes for each dimension */
+    if(H5V_array_down(rank,chunks,down_chunks)<0)
+        HGOTO_ERROR (H5E_INTERNAL, H5E_BADVALUE, FAIL, "can't compute 'down' sizes")
+
+    /* Fill the DXPL cache values for later use */
+    if (H5D_get_dxpl_cache(dxpl_id,&dxpl_cache)<0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
+
+    /* Recompute the index for each cached chunk that is in a dataset */
+    for(ent = rdcc->head; ent; ent = next) {
+        next=ent->next;
+
+        /* Make certain we are dealing with the correct B-tree, etc */
+        if (H5F_addr_eq(layout->u.chunk.addr, ent->layout.u.chunk.addr)) {
+            /* Calculate the index of this chunk */
+            if(H5V_chunk_index(rank,ent->offset,layout->u.chunk.dim,down_chunks,&idx)<0)
+                HGOTO_ERROR (H5E_DATASPACE, H5E_BADRANGE, FAIL, "can't get chunk index")
+
+            /* Compute the index for the chunk entry */
+            temp_idx = idx + (hsize_t)(layout->u.chunk.addr);
+            old_idx=ent->idx;   /* Save for later */
+            ent->idx=H5F_HASH(f,temp_idx);
+
+            if(old_idx!=ent->idx) {
+                /* Check if there is already a chunk at this chunk's new location */
+                old_ent = rdcc->slot[ent->idx];
+                if(old_ent!=NULL) {
+                    assert(old_ent->locked==0);
+
+                    /* Check if we are removing the entry we would walk to next */
+                    if(old_ent==next)
+                        next=old_ent->next;
+
+                    /* Remove the old entry from the cache */
+                    if (H5F_istore_preempt(f, &dxpl_cache, dxpl_id, old_ent, TRUE )<0)
+                        HGOTO_ERROR (H5E_IO, H5E_CANTFLUSH, FAIL, "unable to flush one or more raw data chunks");
+                } /* end if */
+
+                /* Insert this chunk into correct location in hash table */
+                rdcc->slot[ent->idx]=ent;
+
+                /* Null out previous location */
+                rdcc->slot[old_idx]=NULL;
+            } /* end if */
+        } /* end if */
+    } /* end for */
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+} /* end H5F_istore_update_cache() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5F_istore_dump_btree
  *
  * Purpose:	Prints information about the storage B-tree to the specified
diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
index 8160a98..94655f9 100644
--- a/src/H5Fpkg.h
+++ b/src/H5Fpkg.h
@@ -189,6 +189,7 @@ struct H5F_t {
 /* Forward declarations for prototype arguments */
 struct H5D_dxpl_cache_t;
 struct H5D_dcpl_cache_t;
+union H5D_storage_t;
 
 /* Private functions, not part of the publicly documented API */
 #ifdef NOT_YET
@@ -204,14 +205,14 @@ H5_DLL herr_t H5F_istore_dest (H5F_t *f, hid_t dxpl_id);
 H5_DLL ssize_t H5F_istore_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
     hid_t dxpl_id,
     const struct H5O_layout_t *layout, const struct H5D_dcpl_cache_t *dcpl_cache,
-    hssize_t chunk_coords[],
+    const union H5D_storage_t *store,
     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);
 H5_DLL ssize_t H5F_istore_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
     hid_t dxpl_id,
     const struct H5O_layout_t *layout, const struct H5D_dcpl_cache_t *dcpl_cache,
-    hssize_t chunk_coords[],
+    const union H5D_storage_t *store,
     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);
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index addb247..c16c9f1 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -447,7 +447,7 @@ H5_DLL herr_t H5F_istore_create(H5F_t *f, hid_t dxpl_id,
 H5_DLL herr_t H5F_istore_allocate (H5F_t *f, hid_t dxpl_id,
     const struct H5O_layout_t *layout, const hsize_t *space_dim,
     struct H5P_genplist_t *dc_plist, hbool_t full_overwrite);
-H5_DLL hsize_t H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, unsigned ndims, haddr_t addr);
+H5_DLL hsize_t H5F_istore_allocated(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout);
 H5_DLL herr_t H5F_istore_dump_btree(H5F_t *f, hid_t dxpl_id, FILE *stream, unsigned ndims,
         haddr_t addr);
 H5_DLL herr_t H5F_istore_prune_by_extent( H5F_t *f,
@@ -459,6 +459,8 @@ H5_DLL herr_t H5F_istore_initialize_by_extent( H5F_t *f,
         const struct H5S_t *space );
 H5_DLL herr_t H5F_istore_delete(H5F_t *f, hid_t dxpl_id,
         const struct H5O_layout_t *layout);
+H5_DLL herr_t H5F_istore_update_cache(H5F_t *f, hid_t dxpl_id, const struct H5O_layout_t *layout,
+        const struct H5S_t * space);
 
 /* Address-related functions */
 H5_DLL void H5F_addr_encode(const H5F_t *, uint8_t** /*in,out*/, haddr_t);
diff --git a/src/H5Fseq.c b/src/H5Fseq.c
index 9bf10e7..f8ecf00 100644
--- a/src/H5Fseq.c
+++ b/src/H5Fseq.c
@@ -237,7 +237,7 @@ H5F_seq_readvv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache, hid_t dxpl_i
 
         case H5D_CHUNKED:
             assert(store);
-            if((ret_value=H5F_istore_readvv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store->chunk_coords,
+            if((ret_value=H5F_istore_readvv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store,
                     dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr,
                     mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr,
                     buf))<0)
@@ -346,7 +346,7 @@ H5F_seq_writevv(H5F_t *f, const struct H5D_dxpl_cache_t *dxpl_cache,
 
         case H5D_CHUNKED:
             assert(store);
-            if((ret_value=H5F_istore_writevv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store->chunk_coords,
+            if((ret_value=H5F_istore_writevv(f, dxpl_cache, dxpl_id, layout, dcpl_cache, store,
                     dset_max_nseq, dset_curr_seq, dset_len_arr, dset_offset_arr,
                     mem_max_nseq, mem_curr_seq, mem_len_arr, mem_offset_arr,
                     buf))<0)
diff --git a/src/H5Oprivate.h b/src/H5Oprivate.h
index 6520877..63cac3c 100644
--- a/src/H5Oprivate.h
+++ b/src/H5Oprivate.h
@@ -35,10 +35,10 @@
 #include "H5Spublic.h"		/* Dataspace functions			  */
 
 /* Private headers needed by this file */
-#include "H5private.h"          /* Generic functions                    */
-#include "H5HGprivate.h"        /* Global heap functions                */
-#include "H5Tprivate.h"		/* Datatype functions			*/
-#include "H5Zprivate.h"         /* I/O pipeline filters			*/
+#include "H5private.h"          /* Generic functions                      */
+#include "H5HGprivate.h"        /* Global heap functions                  */
+#include "H5Tprivate.h"		/* Datatype functions			  */
+#include "H5Zprivate.h"         /* I/O pipeline filters			  */
 
 /* Object header macros */
 #define H5O_MIN_SIZE	H5O_ALIGN(32)	/*min obj header data size	     */
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index d2b57df..ce2e227 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -747,8 +747,7 @@ H5Pget_filter(hid_t plist_id, unsigned idx, unsigned int *flags/*out*/,
 #endif /* H5_WANT_H5_V1_6_COMPAT */
     
     /* Check args */
-    if (cd_nelmts || cd_values)
-{
+    if (cd_nelmts || cd_values) {
         if (cd_nelmts && *cd_nelmts>256)
             /*
              * It's likely that users forget to initialize this on input, so
@@ -1641,4 +1640,3 @@ H5Premove_filter(hid_t plist_id, H5Z_filter_t filter)
 done:
     FUNC_LEAVE_API(ret_value);
 }
-
diff --git a/src/H5Z.c b/src/H5Z.c
index 9de1966..cc3e3f5 100644
--- a/src/H5Z.c
+++ b/src/H5Z.c
@@ -1159,4 +1159,3 @@ H5Z_delete(H5O_pline_t *pline, H5Z_filter_t filter)
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } 
-