[svn-r6942] Purpose:

    Performance improment

Description:
    Speed up chunked dataset I/O.  This breaks down into several areas:
        - Compute chunk selections in the file by using hyperslab operations
            instead of iterating over each element in the selection.
        - If the file and memory selections are the same shape, use the file
            chunk selections to compute the memory chunk selections.

    This required several additional dataspace, dataspace selection and
        hyperslab routines.

Platforms tested:
    h5committestted (although Fortran tests failed for some reason)

1 files changed, 175 insertions, 1 deletions

diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 5551412..6c3d42d 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -92,6 +92,50 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
+    H5S_select_offset
+ PURPOSE
+    Set the selection offset for a datapace
+ USAGE
+    herr_t H5S_select_offset(space, offset)
+        H5S_t *space;	        IN/OUT: Dataspace object to set selection offset
+        const hssize_t *offset; IN: Offset to position the selection at
+ RETURNS
+    Non-negative on success/Negative on failure
+ DESCRIPTION
+    Sets the selection offset for the dataspace
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+    Only works for simple dataspaces currently
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5S_select_offset(H5S_t *space, const hssize_t *offset)
+{
+    herr_t ret_value=SUCCEED;     /* return value */
+
+    FUNC_ENTER_NOAPI(H5S_select_offset, FAIL);
+
+    /* Check args */
+    assert(space);
+    assert(offset);
+
+    /* Allocate space for new offset */
+    if(space->select.offset==NULL) {
+        if (NULL==(space->select.offset = H5FL_ARR_MALLOC(hssize_t,space->extent.u.simple.rank)))
+            HGOTO_ERROR (H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed");
+    }
+
+    /* Copy the offset over */
+    HDmemcpy(space->select.offset,offset,sizeof(hssize_t)*space->extent.u.simple.rank);
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+}   /* H5S_select_offset() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
     H5S_select_copy
  PURPOSE
     Copy a selection from one dataspace to another
@@ -173,6 +217,41 @@ done:
 }   /* H5S_select_copy() */
 
 
+/*-------------------------------------------------------------------------
+ * Function:	H5S_select_release
+ *
+ * Purpose:	Releases all memory associated with a dataspace selection.
+ *
+ * Return:	Non-negative on success/Negative on failure
+ *
+ * Programmer:	Quincey Koziol
+ *		Friday, May 30, 2003
+ *
+ * Modifications:
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5S_select_release(H5S_t *ds)
+{
+    herr_t ret_value=SUCCEED;   /* Return value */
+
+    FUNC_ENTER_NOAPI(H5S_select_release, FAIL);
+
+    assert(ds);
+
+    /* If there was a previous offset for the selection, release it */
+    if(ds->select.offset!=NULL)
+        ds->select.offset=H5FL_ARR_FREE(hssize_t,ds->select.offset);
+
+    /* Call the selection type's release function */
+    (*ds->select.release)(ds);
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+}   /* end H5S_select_release() */
+
+
 /*--------------------------------------------------------------------------
  NAME
     H5Sget_select_npoints
@@ -423,7 +502,7 @@ H5Sget_select_bounds(hid_t spaceid, hsize_t *start, hsize_t *end)
     if (NULL == (space=H5I_object_verify(spaceid, H5I_DATASPACE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a data space");
 
-    ret_value = (*space->select.bounds)(space,start,end);
+    ret_value = H5S_get_select_bounds(space,start,end);
 
 done:
     FUNC_LEAVE_API(ret_value);
@@ -432,6 +511,52 @@ done:
 
 /*--------------------------------------------------------------------------
  NAME
+    H5S_get_select_bounds
+ PURPOSE
+    Gets the bounding box containing the selection.
+ USAGE
+    herr_t H5S_get_select_bounds(space, start, end)
+        H5S_t *space;           IN: Dataspace ID of selection to query
+        hsize_t *start;         OUT: Starting coordinate of bounding box
+        hsize_t *end;           OUT: Opposite coordinate of bounding box
+ RETURNS
+    Non-negative on success, negative on failure
+ DESCRIPTION
+    Retrieves the bounding box containing the current selection and places
+    it into the user's buffers.  The start and end buffers must be large
+    enough to hold the dataspace rank number of coordinates.  The bounding box
+    exactly contains the selection, ie. if a 2-D element selection is currently
+    defined with the following points: (4,5), (6,8) (10,7), the bounding box
+    with be (4, 5), (10, 8).  Calling this function on a "none" selection
+    returns fail.
+        The bounding box calculations _does_ include the current offset of the
+    selection within the dataspace extent.
+ GLOBAL VARIABLES
+ COMMENTS, BUGS, ASSUMPTIONS
+ EXAMPLES
+ REVISION LOG
+--------------------------------------------------------------------------*/
+herr_t
+H5S_get_select_bounds(const H5S_t *space, hsize_t *start, hsize_t *end)
+{
+    herr_t ret_value;        /* return value */
+
+    FUNC_ENTER_NOAPI(H5S_get_select_bounds, FAIL);
+
+    /* Check args */
+    assert(space);
+    assert(start);
+    assert(end);
+
+    ret_value = (*space->select.bounds)(space,start,end);
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value);
+}   /* H5S_get_select_bounds() */
+
+
+/*--------------------------------------------------------------------------
+ NAME
     H5S_select_iter_init
  PURPOSE
     Initializes iteration information for a selection.
@@ -1578,6 +1703,12 @@ H5S_select_read(H5F_t *f, const H5O_layout_t *layout, H5P_genplist_t *dc_plist,
             curr_mem_seq=0;
         } /* end if */
 
+#ifdef QAK
+HDfprintf(stderr,"%s: curr_file_seq=%Zu, file_nseq=%Zu\n",FUNC,curr_file_seq,file_nseq);
+HDfprintf(stderr,"%s: curr_mem_seq=%Zu, mem_nseq=%Zu\n",FUNC,curr_mem_seq,mem_nseq);
+HDfprintf(stderr,"%s: file_off[%Zu]=%Hu, file_len[%Zu]=%Zu\n",FUNC,curr_file_seq,file_off[curr_file_seq],curr_file_seq,file_len[curr_file_seq]);
+HDfprintf(stderr,"%s: mem_off[%Zu]=%Hu, mem_len[%Zu]=%Zu\n",FUNC,curr_mem_seq,mem_off[curr_mem_seq],curr_mem_seq,mem_len[curr_mem_seq]);
+#endif /* QAK */
         /* Read file sequences into current memory sequence */
         if ((tmp_file_len=H5F_seq_readvv(f, dxpl_id, layout, dc_plist, store,
                 file_nseq, &curr_file_seq, file_len, file_off,
@@ -1654,6 +1785,15 @@ H5S_select_write(H5F_t *f, H5O_layout_t *layout, H5P_genplist_t *dc_plist,
     herr_t ret_value=SUCCEED;   /* Return value */
 
     FUNC_ENTER_NOAPI(H5S_select_write, FAIL);
+#ifdef QAK
+{
+    int mpi_rank;
+    double time;
+    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+    time = MPI_Wtime();
+    HDfprintf(stderr,"%s: rank=%d - Entering, time=%f\n",FUNC,mpi_rank,time);
+}
+#endif /* QAK */
 
     /* Check args */
     assert(f);
@@ -1721,6 +1861,31 @@ H5S_select_write(H5F_t *f, H5O_layout_t *layout, H5P_genplist_t *dc_plist,
             curr_mem_seq=0;
         } /* end if */
 
+#ifdef QAK
+{
+    int mpi_rank;
+    double time;
+    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+    time = MPI_Wtime();
+    HDfprintf(stderr,"%s: rank=%d - time=%f\n",FUNC,mpi_rank,time);
+    HDfprintf(stderr,"%s: rank=%d - curr_file_seq=%Zu, file_nseq=%Zu\n",FUNC,mpi_rank,curr_file_seq,file_nseq);
+    HDfprintf(stderr,"%s: rank=%d - curr_mem_seq=%Zu, mem_nseq=%Zu\n",FUNC,mpi_rank,curr_mem_seq,mem_nseq);
+    HDfprintf(stderr,"%s: rank=%d - file_off[%Zu]=%Hu, file_len[%Zu]=%Zu\n",FUNC,mpi_rank,curr_file_seq,file_off[curr_file_seq],curr_file_seq,file_len[curr_file_seq]);
+    HDfprintf(stderr,"%s: rank=%d - mem_off[%Zu]=%Hu, mem_len[%Zu]=%Zu\n",FUNC,mpi_rank,curr_mem_seq,mem_off[curr_mem_seq],curr_mem_seq,mem_len[curr_mem_seq]);
+}
+#endif /* QAK */
+#ifdef QAK
+{
+    unsigned u;
+
+HDfprintf(stderr,"%s: curr_file_seq=%Zu, file_nseq=%Zu\n",FUNC,curr_file_seq,file_nseq);
+HDfprintf(stderr,"%s: curr_mem_seq=%Zu, mem_nseq=%Zu\n",FUNC,curr_mem_seq,mem_nseq);
+for(u=curr_file_seq; u<file_nseq; u++)
+    HDfprintf(stderr,"%s: file_off[%u]=%Hu, file_len[%u]=%Zu\n",FUNC,u,file_off[u],u,file_len[u]);
+for(u=curr_mem_seq; u<mem_nseq; u++)
+    HDfprintf(stderr,"%s: mem_off[%u]=%Hu, mem_len[%u]=%Zu\n",FUNC,u,mem_off[u],u,mem_len[u]);
+}
+#endif /* QAK */
         /* Write memory sequences into file sequences */
         if ((tmp_file_len=H5F_seq_writevv(f, dxpl_id, layout, dc_plist, store,
                 file_nseq, &curr_file_seq, file_len, file_off,
@@ -1754,6 +1919,15 @@ done:
         H5FL_ARR_FREE(size_t,mem_len);
     if(mem_off!=NULL)
         H5FL_ARR_FREE(hsize_t,mem_off);
+#ifdef QAK
+{
+    int mpi_rank;
+    double time;
+    MPI_Comm_rank(MPI_COMM_WORLD,&mpi_rank);
+    time = MPI_Wtime();
+    HDfprintf(stderr,"%s: rank=%d - Leaving, time=%f\n",FUNC,mpi_rank,time);
+}
+#endif /* QAK */
     FUNC_LEAVE_NOAPI(ret_value);
 } /* end H5S_select_write() */