[svn-r11231] Purpose:

bug fix for collective chunk IO, phase 1
Optimization hasn't been done yet, the collective chunk IO bug should be fixed.
Description:
In chunking storage, memory space and file space will be remapped, So to check
whether file space and memory space are regular in order to use optimized MPI derived
datatype for collective call one has to check per-chunk wise instead of per hyperslab wise.
Even a regular memory space will be stored in span-tree and will be irregular before chunk IO.

Solution:
1. Check file space and memory space per chunk wise instead of per hyperslab wise.
2. For collective IO mode, number of chunks covered by hyperslab may be different. Since we are
handing per chunk per IO, for the extra chunk IO for some(not all) processors, collective mode will
cause program hanged. So for the extra chunk Io mode independent IO has to be used.
3. On some platforms, Complex MPI derived datatype is not working, so we have to use independent IO for collective IO mode if the selection is irregular. However, when the selection is regular, we do want to use collective IO since that will improve performance. Special cares have to be added for this case.


Platforms tested:
copper(AIX 5.1) Linux(heping mpich 1.2.6), Teragrid machine, Cobalt(altix), modi4

Misc. update:

1 files changed, 101 insertions, 185 deletions

diff --git a/src/H5Smpio.c b/src/H5Smpio.c
index 5ccf842..a9b90ee 100644
--- a/src/H5Smpio.c
+++ b/src/H5Smpio.c
@@ -462,190 +462,7 @@ done:
     FUNC_LEAVE_NOAPI(ret_value);
 }
 
-
-/*-------------------------------------------------------------------------
- * Function:	H5S_mpio_space_type
- *
- * Purpose:	Translate an HDF5 dataspace selection into an MPI type.
- *		Currently handle only hyperslab and "all" selections.
- *
- * Return:	non-negative on success, negative on failure.
- *
- * Outputs:	*new_type	  the MPI type corresponding to the selection
- *		*count		  how many objects of the new_type in selection
- *				  (useful if this is the buffer type for xfer)
- *		*extra_offset     Number of bytes of offset within dataset
- *		*is_derived_type  0 if MPI primitive type, 1 if derived
- *
- * Programmer:	rky 980813
- *
- * Modifications:
- *
- *      Quincey Koziol, June 18, 2002
- *      Added 'extra_offset' parameter
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5S_mpio_space_type( const H5S_t *space, size_t elmt_size,
-		     /* out: */
-		     MPI_Datatype *new_type,
-		     size_t *count,
-		     hsize_t *extra_offset,
-		     hbool_t *is_derived_type )
-{
-    herr_t	ret_value = SUCCEED;
-
-    FUNC_ENTER_NOAPI_NOINIT(H5S_mpio_space_type);
-
-    /* Check args */
-    assert (space);
-
-    /* Creat MPI type based on the kind of selection */
-    switch (H5S_GET_EXTENT_TYPE(space)) {
-        case H5S_NULL:
-        case H5S_SCALAR:
-        case H5S_SIMPLE:
-            switch(H5S_GET_SELECT_TYPE(space)) {
-                case H5S_SEL_NONE:
-                    if ( H5S_mpio_none_type( space, elmt_size,
-                        /* out: */ new_type, count, extra_offset, is_derived_type ) <0)
-                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
-                    break;
-
-                case H5S_SEL_ALL:
-                    if ( H5S_mpio_all_type( space, elmt_size,
-                        /* out: */ new_type, count, extra_offset, is_derived_type ) <0)
-                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
-                    break;
-
-                case H5S_SEL_POINTS:
-                    /* not yet implemented */
-                    ret_value = FAIL;
-                    break;
-
-                case H5S_SEL_HYPERSLABS:
-                    if(H5S_mpio_hyper_type( space, elmt_size,
-                            /* out: */ new_type, count, extra_offset, is_derived_type )<0)
-                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
-                    break;
-
-                default:
-                    assert("unknown selection type" && 0);
-                    break;
-            } /* end switch */
-            break;
-
-        case H5S_COMPLEX:
-            /* not yet implemented */
-            HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "complex data spaces are not supported yet");
-
-        default:
-            assert("unknown data space type" && 0);
-            break;
-    }
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value);
-}
-
-
-
-/*-------------------------------------------------------------------------
- * Function:	H5S_mpio_space_span_type
- *
- * Purpose:	Translate an HDF5 dataspace selection into a general
-                MPI derived datatype, the selection is implemented with 
-		span-tree.
- *             
- *		Currently handle only hyperslab and "all" selections.
- *
- * Return:	non-negative on success, negative on failure.
- *
- * Outputs:	*new_type	  the MPI type corresponding to the selection
- *		*count		  how many objects of the new_type in selection
- *				  (useful if this is the buffer type for xfer)
- *		*extra_offset     Number of bytes of offset within dataset
- *		*is_derived_type  0 if MPI primitive type, 1 if derived
- *
- * Programmer:	KY
- *
- * Modifications:
- *
- *      Quincey Koziol, June 18, 2002
- *      Added 'extra_offset' parameter
- *
- *-------------------------------------------------------------------------
- */
-herr_t
-H5S_mpio_space_span_type( const H5S_t *space, 
-			  size_t elmt_size,/* out: */
-			  MPI_Datatype *new_type,
-			  size_t *count,
-			  hsize_t *extra_offset,
-			  hbool_t *is_derived_type )
-{
-    herr_t	ret_value = SUCCEED;
-
-    FUNC_ENTER_NOAPI_NOINIT(H5S_mpio_space_span_type);
-
-    /* Check args */
-    assert (space);
-
-    /* Creat MPI type based on the kind of selection */
-    switch (H5S_GET_EXTENT_TYPE(space)) {
-        case H5S_NULL:
-        case H5S_SCALAR:
-        case H5S_SIMPLE:
-            switch(H5S_GET_SELECT_TYPE(space)) {
-                case H5S_SEL_NONE:
-                    if ( H5S_mpio_none_type( space, elmt_size,
-                        /* out: */ new_type, count, extra_offset, is_derived_type ) <0)
-                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
-                    break;
-
-                case H5S_SEL_ALL:
-                    if ( H5S_mpio_all_type( space, elmt_size,
-                        /* out: */ new_type, count, extra_offset, is_derived_type ) <0)
-                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
-                    break;
-
-                case H5S_SEL_POINTS:
-                    /* not yet implemented */
-                    ret_value = FAIL;
-                    break;
-
-                case H5S_SEL_HYPERSLABS:
-                    if(H5S_mpio_span_hyper_type( space, elmt_size,
-                            /* out: */ new_type, count, extra_offset, is_derived_type )<0)
-                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
-                    break;
-
-                default:
-                    assert("unknown selection type" && 0);
-                    break;
-            } /* end switch */
-            break;
-
-        case H5S_COMPLEX:
-            /* not yet implemented */
-            HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "complex data spaces are not supported yet");
-
-        default:
-            assert("unknown data space type" && 0);
-            break;
-    }
-
-done:
-    FUNC_LEAVE_NOAPI(ret_value);
-}
-
 
-/* The following codes have been used by Kent to test
-   general collective derived datatype functionality. 
-   It should NOT be called by other routines except with
-   macro #ifdef KENT #endif
-   Nov. 11th, 2004 */
 
 
 
@@ -682,20 +499,24 @@ H5S_mpio_span_hyper_type( const           H5S_t *space,
   herr_t                ret_value = SUCCEED;
   MPI_Aint              extent,lb;
 
+  
   FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5S_mpio_span_hyper_type);
 
   /* Check args */
     assert (space);
  
  /* assert(sizeof(MPI_Aint) >= sizeof(elmt_size)); not sure the reason*/
-    
+
+
     rank = space->extent.rank;
 
     /*    size = HDcalloc((size_t)rank,sizeof(hsize_t));  */ 
     if (0==elmt_size)
         goto empty;
     size = space->extent.size;
-
+    if(size == 0) 
+        goto empty;
+ 
     odown = space->select.sel_info.hslab->span_lst;
     if(odown == NULL) 
       goto empty;
@@ -904,4 +725,99 @@ static herr_t H5S_obtain_datatype(const hsize_t size[],
   FUNC_LEAVE_NOAPI(ret_value);
 }
 
+
+
+/*-------------------------------------------------------------------------
+ * Function:	H5S_mpio_space_type
+ *
+ * Purpose:	Translate an HDF5 dataspace selection into an MPI type.
+ *		Currently handle only hyperslab and "all" selections.
+ *
+ * Return:	non-negative on success, negative on failure.
+ *
+ * Outputs:	*new_type	  the MPI type corresponding to the selection
+ *		*count		  how many objects of the new_type in selection
+ *				  (useful if this is the buffer type for xfer)
+ *		*extra_offset     Number of bytes of offset within dataset
+ *		*is_derived_type  0 if MPI primitive type, 1 if derived
+ *
+ * Programmer:	rky 980813
+ *
+ * Modifications:
+ *
+ *      Quincey Koziol, June 18, 2002
+ *      Added 'extra_offset' parameter
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_mpio_space_type( const H5S_t *space, size_t elmt_size,
+		     /* out: */
+		     MPI_Datatype *new_type,
+		     size_t *count,
+		     hsize_t *extra_offset,
+		     hbool_t *is_derived_type )
+{
+    herr_t	ret_value = SUCCEED;
+
+    FUNC_ENTER_NOAPI_NOINIT(H5S_mpio_space_type);
+
+    /* Check args */
+    assert (space);
+
+    /* Creat MPI type based on the kind of selection */
+    switch (H5S_GET_EXTENT_TYPE(space)) {
+        case H5S_NULL:
+        case H5S_SCALAR:
+        case H5S_SIMPLE:
+            switch(H5S_GET_SELECT_TYPE(space)) {
+                case H5S_SEL_NONE:
+                    if ( H5S_mpio_none_type( space, elmt_size,
+                        /* out: */ new_type, count, extra_offset, is_derived_type ) <0)
+                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
+                    break;
+
+                case H5S_SEL_ALL:
+                    if ( H5S_mpio_all_type( space, elmt_size,
+                        /* out: */ new_type, count, extra_offset, is_derived_type ) <0)
+                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
+                    break;
+
+                case H5S_SEL_POINTS:
+                    /* not yet implemented */
+                    ret_value = FAIL;
+                    break;
+
+                case H5S_SEL_HYPERSLABS:
+		  if((H5S_SELECT_IS_REGULAR(space) == TRUE)) {
+		    if(H5S_mpio_hyper_type( space, elmt_size,
+                            /* out: */ new_type, count, extra_offset, is_derived_type )<0)
+                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
+		    }
+		     else {
+		       if(H5S_mpio_span_hyper_type( space, elmt_size,
+                            /* out: */ new_type, count, extra_offset, is_derived_type )<0)
+                        HGOTO_ERROR(H5E_DATASPACE, H5E_BADTYPE, FAIL,"couldn't convert \"all\" selection to MPI type");
+		     }
+                    break;
+
+                default:
+                    assert("unknown selection type" && 0);
+                    break;
+            } /* end switch */
+            break;
+
+        case H5S_COMPLEX:
+            /* not yet implemented */
+            HGOTO_ERROR(H5E_DATASPACE, H5E_UNSUPPORTED, FAIL, "complex data spaces are not supported yet");
+
+        default:
+            assert("unknown data space type" && 0);
+            break;
+    }
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+}
+
 #endif  /* H5_HAVE_PARALLEL */