[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, 99 insertions, 23 deletions

diff --git a/src/H5Sall.c b/src/H5Sall.c
index f5b92b7..08dc8d3 100644
--- a/src/H5Sall.c
+++ b/src/H5Sall.c
@@ -21,11 +21,11 @@
 
 #define H5S_PACKAGE		/*suppress error about including H5Spkg	  */
 
-#include "H5private.h"		/* Generic Functions			  */
-#include "H5Eprivate.h"		/* Error handling		  */
-#include "H5Iprivate.h"		/* ID Functions		  */
-#include "H5Spkg.h"		/* Dataspace functions			  */
-#include "H5Vprivate.h"         /* Vector functions */
+#include "H5private.h"		/* Generic Functions			*/
+#include "H5Eprivate.h"		/* Error handling		        */
+#include "H5Iprivate.h"		/* ID Functions		                */
+#include "H5Spkg.h"		/* Dataspace functions			*/
+#include "H5Vprivate.h"         /* Vector functions                     */
 
 /* Interface initialization */
 #define PABLO_MASK      H5Sall_mask
@@ -48,7 +48,7 @@ static int             interface_initialize_g = 0;
  *-------------------------------------------------------------------------
  */
 herr_t
-H5S_all_iter_init (const H5S_t *space, size_t UNUSED elmt_size, H5S_sel_iter_t *sel_iter)
+H5S_all_iter_init (H5S_sel_iter_t *iter, const H5S_t *space, size_t UNUSED elmt_size)
 {
     herr_t ret_value=SUCCEED;   /* Return value */
 
@@ -56,13 +56,19 @@ H5S_all_iter_init (const H5S_t *space, size_t UNUSED elmt_size, H5S_sel_iter_t *
 
     /* Check args */
     assert (space && H5S_SEL_ALL==space->select.type);
-    assert (sel_iter);
+    assert (iter);
 
     /* Initialize the number of elements to iterate over */
-    sel_iter->all.elmt_left=H5S_get_simple_extent_npoints(space);
+    iter->elmt_left=H5S_get_simple_extent_npoints(space);
 
     /* Start at the upper left location */
-    sel_iter->all.offset=0;
+    iter->u.all.offset=0;
+
+    /* Initialize methods for selection iterator */
+    iter->iter_coords=H5S_all_iter_coords;
+    iter->iter_nelmts=H5S_all_iter_nelmts;
+    iter->iter_next=H5S_all_iter_next;
+    iter->iter_release=H5S_all_iter_release;
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
@@ -70,6 +76,41 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:	H5S_all_iter_coords
+ *
+ * Purpose:	Retrieve the current coordinates of iterator for current
+ *              selection
+ *
+ * Return:	non-negative on success, negative on failure
+ *
+ * Programmer:	Quincey Koziol
+ *              Tuesday, April 22, 2003
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_all_iter_coords (const H5S_sel_iter_t *iter, hssize_t *coords)
+{
+    herr_t ret_value=SUCCEED;        /* Return value */
+
+    FUNC_ENTER_NOAPI(H5S_all_iter_coords, FAIL);
+
+    /* Check args */
+    assert (iter);
+    assert (coords);
+
+    /* Calculate the coordinates for the current iterator offset */
+    if(H5V_array_calc(iter->u.all.offset,iter->rank,iter->dims,coords)<0)
+        HGOTO_ERROR(H5E_DATASPACE, H5E_CANTGET, FAIL, "can't retrieve coordinates");
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+}   /* H5S_all_iter_coords() */
+
+
+/*-------------------------------------------------------------------------
  * Function:	H5S_all_iter_nelmts
  *
  * Purpose:	Return number of elements left to process in iterator
@@ -84,17 +125,17 @@ done:
  *-------------------------------------------------------------------------
  */
 hsize_t
-H5S_all_iter_nelmts (const H5S_sel_iter_t *sel_iter)
+H5S_all_iter_nelmts (const H5S_sel_iter_t *iter)
 {
     hsize_t ret_value;   /* Return value */
 
     FUNC_ENTER_NOAPI(H5S_all_iter_nelmts, 0);
 
     /* Check args */
-    assert (sel_iter);
+    assert (iter);
 
     /* Set return value */
-    ret_value=sel_iter->all.elmt_left;
+    ret_value=iter->elmt_left;
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
@@ -103,12 +144,49 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
+    H5S_all_iter_next
+ PURPOSE
+    Increment selection iterator
+ USAGE
+    herr_t H5S_all_iter_next(iter, nelem)
+        H5S_sel_iter_t *iter;       IN: Pointer to selection iterator
+        size_t nelem;               IN: Number of elements to advance by
+ RETURNS
+    Non-negative on success/Negative on failure
+ DESCRIPTION
+    Advance selection iterator to the NELEM'th next element in the selection.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5S_all_iter_next(H5S_sel_iter_t *iter, size_t nelem)
+{
+    herr_t ret_value=SUCCEED;   /* Return value */
+
+    FUNC_ENTER_NOAPI(H5S_all_iter_next, FAIL);
+
+    /* Check args */
+    assert (iter);
+    assert (nelem>0);
+
+    /* Increment the iterator */
+    iter->u.all.offset+=nelem;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+}   /* H5S_all_iter_next() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
     H5S_all_iter_release
  PURPOSE
     Release "all" selection iterator information for a dataspace
  USAGE
-    herr_t H5S_all_iter_release(sel_iter)
-        H5S_sel_iter_t *sel_iter;       IN: Pointer to selection iterator
+    herr_t H5S_all_iter_release(iter)
+        H5S_sel_iter_t *iter;       IN: Pointer to selection iterator
  RETURNS
     Non-negative on success/Negative on failure
  DESCRIPTION
@@ -119,14 +197,14 @@ done:
  REVISION LOG
 --------------------------------------------------------------------------*/
 herr_t
-H5S_all_iter_release (H5S_sel_iter_t UNUSED * sel_iter)
+H5S_all_iter_release (H5S_sel_iter_t UNUSED * iter)
 {
     herr_t ret_value=SUCCEED;   /* Return value */
 
     FUNC_ENTER_NOAPI(H5S_all_iter_release, FAIL);
 
     /* Check args */
-    assert (sel_iter);
+    assert (iter);
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
@@ -542,9 +620,6 @@ H5S_select_all (H5S_t *space, unsigned rel_prev)
     space->select.get_seq_list=H5S_all_get_seq_list;
     space->select.get_npoints=H5S_all_npoints;
     space->select.release=H5S_all_release;
-    space->select.iter_init=H5S_all_iter_init;
-    space->select.iter_nelmts=H5S_all_iter_nelmts;
-    space->select.iter_release=H5S_all_iter_release;
     space->select.is_valid=H5S_all_is_valid;
     space->select.serial_size=H5S_all_serial_size;
     space->select.serialize=H5S_all_serialize;
@@ -552,6 +627,7 @@ H5S_select_all (H5S_t *space, unsigned rel_prev)
     space->select.is_contiguous=H5S_all_is_contiguous;
     space->select.is_single=H5S_all_is_single;
     space->select.is_regular=H5S_all_is_regular;
+    space->select.iter_init=H5S_all_iter_init;
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);
@@ -650,13 +726,13 @@ H5S_all_get_seq_list(const H5S_t UNUSED *space, unsigned UNUSED flags, H5S_sel_i
     assert(len);
 
     /* Calculate the number of bytes left in the selection */
-    bytes_left=iter->all.elmt_left*elem_size;
+    bytes_left=iter->elmt_left*elem_size;
 
     /* "round" off the maxbytes allowed to a multiple of the element size */
     maxbytes=(maxbytes/elem_size)*elem_size;
 
     /* Compute the offset in the dataset */
-    off[0]=iter->all.offset*elem_size;
+    off[0]=iter->u.all.offset*elem_size;
     H5_CHECK_OVERFLOW(bytes_left,hsize_t,size_t);
     len[0]=MIN(maxbytes,(size_t)bytes_left);
 
@@ -668,8 +744,8 @@ H5S_all_get_seq_list(const H5S_t UNUSED *space, unsigned UNUSED flags, H5S_sel_i
 
     /* Update the iterator */
     elem_used=len[0]/elem_size;
-    iter->all.elmt_left-=elem_used;
-    iter->all.offset+=elem_used;
+    iter->elmt_left-=elem_used;
+    iter->u.all.offset+=elem_used;
 
 done:
     FUNC_LEAVE_NOAPI(ret_value);