[svn-r1210] Changed parameters for function calls which figure out the buffer size for

H5Dread/H5Dwrite to use to allow the I/O calls to break up a user's buffer into
pieces that are at least as large as the sequence of bytes being written in the
fastest changing dimension.

Also fixed a hard-to-find bug in the hyperslab I/O routines which could cause
data to be corrupted when writing out fields to compound datatype data with
background preservation turned on and hyperslabs which were large enough to
require two I/O passes on a hyperslab block.  A pretty obscure situation, but
it would be worthwhile for users to upgrade to this code in order to be certain
that correct data is being written.

4 files changed, 56 insertions, 37 deletions

diff --git a/src/H5Sall.c b/src/H5Sall.c
index 6ebd241..4deb877 100644
--- a/src/H5Sall.c
+++ b/src/H5Sall.c
@@ -19,7 +19,7 @@
 static intn             interface_initialize_g = 0;
 
 static herr_t H5S_all_init (const struct H5O_layout_t *layout,
-			    const H5S_t *space, H5S_sel_iter_t *iter);
+			    const H5S_t *space, H5S_sel_iter_t *iter, size_t *min_elem_out);
 static size_t H5S_all_favail (const H5S_t *space, const H5S_sel_iter_t *iter,
 			      size_t max);
 static size_t H5S_all_fgath (H5F_t *f, const struct H5O_layout_t *layout,
@@ -76,8 +76,13 @@ const H5S_mconv_t	H5S_ALL_MCONV[1] = {{
  */
 static herr_t
 H5S_all_init (const struct H5O_layout_t UNUSED *layout,
-	       const H5S_t *space, H5S_sel_iter_t *sel_iter)
+	       const H5S_t *space, H5S_sel_iter_t *sel_iter, size_t *min_elem_out)
 {
+    hsize_t	hsize[H5O_LAYOUT_NDIMS];	/*size of hyperslab	*/
+    intn	space_ndims;			/*dimensionality of space*/
+    hsize_t	acc;				    /*accumulator		*/
+    intn	i;				/*counters		*/
+
     FUNC_ENTER (H5S_all_init, FAIL);
 
     /* Check args */
@@ -90,6 +95,19 @@ H5S_all_init (const struct H5O_layout_t UNUSED *layout,
 
     /* Start at the upper left location */
     sel_iter->all.offset=0;
+
+    /* Get the dimensions of the space, to set the min. # of elements */
+    if ((space_ndims=H5S_get_simple_extent_dims (space, hsize, NULL))<0) {
+        HRETURN_ERROR (H5E_DATASPACE, H5E_CANTINIT, FAIL,
+		       "unable to retrieve hyperslab parameters");
+    }
+
+    /* Adjust the slowest varying dimension to account for strip mining */
+    for (i=1, acc=1; i<space_ndims; i++)
+        acc *= hsize[i];
+    
+    /* Set the minimum # of elements to output */
+    *min_elem_out=acc;
     
     FUNC_LEAVE (SUCCEED);
 }
@@ -471,8 +489,9 @@ H5S_all_mscat (const void *_tconv_buf, size_t elmt_size,
         }
 
         /* Adjust the slowest varying dimension to take care of strip mining */
-        for (i=1, acc=1; i<space_ndims; i++)
+        for (i=1, acc=1; i<space_ndims; i++) {
             acc *= hsize[i];
+        }
         assert (0==mem_iter->all.offset % acc);
         assert (0==nelmts % acc);
         mem_offset[0] += mem_iter->all.offset / acc;
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index 2fba497..3e4df79 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -51,7 +51,7 @@ static size_t H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info);
 static size_t H5S_hyper_fwrite (intn dim,
 				H5S_hyper_fhyper_info_t *fhyper_info);
 static herr_t H5S_hyper_init (const struct H5O_layout_t *layout,
-			      const H5S_t *space, H5S_sel_iter_t *iter);
+			      const H5S_t *space, H5S_sel_iter_t *iter, size_t *min_elem_out);
 static size_t H5S_hyper_favail (const H5S_t *space, const H5S_sel_iter_t *iter,
 				size_t max);
 static size_t H5S_hyper_fgath (H5F_t *f, const struct H5O_layout_t *layout,
@@ -114,7 +114,7 @@ static const hssize_t	zero[H5O_LAYOUT_NDIMS]={0};		/* Array of zeros */
  */
 static herr_t
 H5S_hyper_init (const struct H5O_layout_t UNUSED *layout,
-	       const H5S_t *space, H5S_sel_iter_t *sel_iter)
+	       const H5S_t *space, H5S_sel_iter_t *sel_iter, size_t *min_elem_out)
 {
     FUNC_ENTER (H5S_hyper_init, FAIL);
 
@@ -160,7 +160,7 @@ H5S_hyper_favail (const H5S_t UNUSED *space,
     assert (sel_iter);
 
 #ifdef QAK
-    printf("%s: max=%d\n",FUNC,(int)max);
+    printf("%s: max=%u\n",FUNC,(unsigned)max);
 #endif /* QAK */
     FUNC_LEAVE (MIN(sel_iter->hyp.elmt_left,max));
 }   /* H5S_hyper_favail() */
@@ -464,9 +464,9 @@ H5S_hyper_block_cache (H5S_hyper_node_t *node,
 /* keep information for writing block later? */
     } /* end else */
     
-    /* Set up parameters for accessing block */
-    node->cinfo.left=node->cinfo.size;
-    node->cinfo.pos=node->cinfo.block;
+    /* Set up parameters for accessing block (starting the read and write information at the same point) */
+    node->cinfo.wleft=node->cinfo.rleft=node->cinfo.size;
+    node->cinfo.wpos=node->cinfo.rpos=node->cinfo.block;
 
     /* Set cached flag */
     node->cinfo.cached=1;
@@ -502,18 +502,18 @@ H5S_hyper_block_read (H5S_hyper_node_t *node, H5S_hyper_fhyper_info_t *fhyper_in
             permutations from the standard 'C' ordering!
     */
     HDmemcpy(fhyper_info->dst,
-	     node->cinfo.pos,
+	     node->cinfo.rpos,
 	     (size_t)(region_size*fhyper_info->elmt_size));
 
     /*
      * Decrement the number of elements left in block to read & move the
      * offset
      */
-    node->cinfo.pos+=region_size*fhyper_info->elmt_size;
-    node->cinfo.left-=region_size;
+    node->cinfo.rpos+=region_size*fhyper_info->elmt_size;
+    node->cinfo.rleft-=region_size;
 
     /* If we've read in all the elements from the block, throw it away */
-    if(node->cinfo.left==0) {
+    if(node->cinfo.rleft==0 && (node->cinfo.wleft==0 || node->cinfo.wleft==node->cinfo.size)) {
         /* Release the temporary buffer */
         H5TB_release_buf(node->cinfo.block_id);
 
@@ -557,7 +557,7 @@ H5S_hyper_block_write (H5S_hyper_node_t *node,
         !! NOTE !! This will need to be changed for different dimension
             permutations from the standard 'C' ordering!
     */
-    HDmemcpy(node->cinfo.pos,
+    HDmemcpy(node->cinfo.wpos,
 	     fhyper_info->src,
 	     (size_t)(region_size*fhyper_info->elmt_size));
 
@@ -565,11 +565,11 @@ H5S_hyper_block_write (H5S_hyper_node_t *node,
      * Decrement the number of elements left in block to read & move the
      * offset
      */
-    node->cinfo.pos+=region_size*fhyper_info->elmt_size;
-    node->cinfo.left-=region_size;
+    node->cinfo.wpos+=region_size*fhyper_info->elmt_size;
+    node->cinfo.wleft-=region_size;
 
     /* If we've read in all the elements from the block, throw it away */
-    if(node->cinfo.left==0) {
+    if(node->cinfo.wleft==0 && (node->cinfo.rleft==0 || node->cinfo.rleft==node->cinfo.size)) {
         /* Copy the location of the region in the file */
         HDmemcpy(file_offset,
 		 node->start,
@@ -697,7 +697,7 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info)
                     } /* end if */
 
 #ifdef QAK
-            printf("%s: check 2.2, i=%d\n",FUNC,(int)i);
+    printf("%s: check 2.2, i=%d\n",FUNC,(int)i);
 #endif /* QAK */
                     /* Fill in the region specific parts of the I/O request */
                     hsize[fhyper_info->space->extent.u.simple.rank-1]=region_size;
@@ -715,10 +715,9 @@ H5S_hyper_fread (intn dim, H5S_hyper_fhyper_info_t *fhyper_info)
 				       "read error");
                     }
 #ifdef QAK
-		    printf("%s: check 2.3, region #%d\n",FUNC,(int)i);
-		    for(j=0; j<fhyper_info->space->extent.u.simple.rank; j++)
-			printf("%s: %d - pos=%d\n",
-			       FUNC,j,(int)fhyper_info->iter->hyp.pos[j]);
+    printf("%s: check 2.3, region #%d\n",FUNC,(int)i);
+    for(j=0; j<fhyper_info->space->extent.u.simple.rank; j++)
+    printf("%s: %d - pos=%d\n", FUNC,j,(int)fhyper_info->iter->hyp.pos[j]);
 #endif /* QAK */
                 } /* end else */
 
@@ -929,6 +928,11 @@ H5S_hyper_fwrite (intn dim, H5S_hyper_fhyper_info_t *fhyper_info)
         regions=H5TB_buf_ptr(reg_id);
 #ifdef QAK
     printf("%s: check 1.1, regions=%p\n", FUNC,regions);
+	printf("%s: check 1.2, rank=%d\n",
+	       FUNC,(int)fhyper_info->space->extent.u.simple.rank);
+	for(i=0; i<num_regions; i++)
+	    printf("%s: check 2.1, region #%d: start=%d, end=%d\n",
+		   FUNC,i,(int)regions[i].start,(int)regions[i].end);
 #endif /* QAK */
 
         /* Check if this is the second to last dimension in dataset */
@@ -1875,9 +1879,6 @@ H5S_hyper_add (H5S_t *space, const hssize_t *start, const hsize_t *end)
     size_t elem_count;          /* Number of elements in hyperslab selection */
     intn i;     /* Counters */
     herr_t ret_value=SUCCEED;
-#ifdef QAK
-    extern int qak_debug;
-#endif /* QAK */
 
     FUNC_ENTER (H5S_hyper_add, FAIL);
 
@@ -1886,9 +1887,6 @@ H5S_hyper_add (H5S_t *space, const hssize_t *start, const hsize_t *end)
     assert (start);
     assert (end);
 
-#ifdef QAK
-    qak_debug=1;
-#endif /* QAK */
 
 #ifdef QAK
     printf("%s: check 1.0\n",FUNC);
@@ -1918,9 +1916,9 @@ H5S_hyper_add (H5S_t *space, const hssize_t *start, const hsize_t *end)
     /* Initialize caching parameters */
     slab->cinfo.cached=0;
     slab->cinfo.size=elem_count;
-    slab->cinfo.left=0;
+    slab->cinfo.wleft=slab->cinfo.rleft=0;
     slab->cinfo.block_id=(-1);
-    slab->cinfo.block=slab->cinfo.pos=NULL;
+    slab->cinfo.block=slab->cinfo.wpos=slab->cinfo.rpos=NULL;
 
 #ifdef QAK
     printf("%s: check 3.0, lo_bounds=%p, hi_bounds=%p\n",
diff --git a/src/H5Spoint.c b/src/H5Spoint.c
index a58461b..7d8672a 100644
--- a/src/H5Spoint.c
+++ b/src/H5Spoint.c
@@ -20,7 +20,7 @@
 static intn             interface_initialize_g = 0;
 
 static herr_t H5S_point_init (const struct H5O_layout_t *layout,
-			      const H5S_t *space, H5S_sel_iter_t *iter);
+			      const H5S_t *space, H5S_sel_iter_t *iter, size_t *min_elem_out);
 static size_t H5S_point_favail (const H5S_t *space, const H5S_sel_iter_t *iter,
 				size_t max);
 static size_t H5S_point_fgath (H5F_t *f, const struct H5O_layout_t *layout,
@@ -83,7 +83,7 @@ const H5S_mconv_t	H5S_POINT_MCONV[1] = {{
  */
 static herr_t
 H5S_point_init (const struct H5O_layout_t UNUSED *layout,
-		const H5S_t *space, H5S_sel_iter_t *sel_iter)
+		const H5S_t *space, H5S_sel_iter_t *sel_iter, size_t *min_elem_out)
 {
     FUNC_ENTER (H5S_point_init, FAIL);
 
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index ff0a021..b01d9dc 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -78,11 +78,13 @@ typedef struct H5S_hyper_node_tag {
     hssize_t *end;      /* Pointer to a corner of a hyperslab furthest from the origin */
     struct {
         uintn cached;   /* Flag to indicate that the block is cached (during I/O only) */
-        size_t size;     /* Size of cached block (in elements) */
-        uintn left;     /* Elements left to access in block */
+        size_t size;    /* Size of cached block (in elements) */
+        uintn rleft;    /* Read elements left to access in block */
+        uintn wleft;    /* Write elements left to access in block */
         hid_t block_id; /* Temporary buffer ID */
         uint8_t *block; /* Pointer into temporary buffer for cache */
-        uint8_t *pos;   /* Pointer to current location within block */
+        uint8_t *rpos;  /* Pointer to current read location within block */
+        uint8_t *wpos;  /* Pointer to current write location within block */
     } cinfo;
     struct H5S_hyper_node_tag *next;  /* pointer to next hyperslab in list */
 } H5S_hyper_node_t;
@@ -182,7 +184,7 @@ typedef struct H5S_fconv_t {
     
     /* Initialize file element numbering information */
     herr_t (*init)(const struct H5O_layout_t *layout, const H5S_t *space,
-		   H5S_sel_iter_t *iter);
+		   H5S_sel_iter_t *iter, size_t *min_elem_out);
 
     /* Determine optimal number of elements to transfer */
     size_t (*avail)(const H5S_t *file_space, const H5S_sel_iter_t *file_iter,
@@ -214,7 +216,7 @@ typedef struct H5S_mconv_t {
     
     /* Initialize memory element numbering information */
     herr_t (*init)(const struct H5O_layout_t *layout, const H5S_t *space,
-		   H5S_sel_iter_t *iter);
+		   H5S_sel_iter_t *iter, size_t *min_elem_out);
 
     /* Gather elements from app buffer to type conversion buffer */
     size_t (*gath)(const void *buf, size_t elmt_size,