[svn-r4965] Purpose:

    Bug Fix
Description:
    If a non-zero fill-value is used for a chunked dataset, any non-existent
    chunked read with an "all" selection (or a contiguous hyperslab selection)
    will return zero for those instead of the user's fill-value.
Solution:
    Fixed I/O code to pass down fill-value to "optimized" I/O routines, so it
    will be available to fill the user's buffer with.
Platforms tested:
    FreeBSD 4.5 (sleipnir)

5 files changed, 51 insertions, 34 deletions

diff --git a/src/H5D.c b/src/H5D.c
index bb4ba39..ca017c3 100644
--- a/src/H5D.c
+++ b/src/H5D.c
@@ -2238,11 +2238,13 @@ printf("%s: check 1.1, \n",FUNC);
 #endif
         if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get pipeline");
+        if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value");
         if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list");
         status = (sconv->read)(dataset->ent.file, &(dataset->layout), &pline, 
-                               &efl, H5T_get_size(dataset->type), file_space, 
-                               mem_space, dxpl_id, buf/*out*/, &must_convert);
+                       &fill, &efl, H5T_get_size(dataset->type), file_space, 
+                       mem_space, dxpl_id, buf/*out*/, &must_convert);
 
         /* Supports only no conversion, type or space, for now. */
         if (status<0)
@@ -2725,11 +2727,14 @@ H5D_write(H5D_t *dataset, const H5T_t *mem_type, const H5S_t *mem_space,
 #endif
         if(H5P_get(dc_plist, H5D_CRT_DATA_PIPELINE_NAME, &pline) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get pipeline");
+        if(H5P_get(dc_plist, H5D_CRT_FILL_VALUE_NAME, &fill) < 0)
+            HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't retrieve fill value");
         if(H5P_get(dc_plist, H5D_CRT_EXT_FILE_LIST_NAME, &efl) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't get external file list");
         status = (sconv->write)(dataset->ent.file, &(dataset->layout), &pline, 
-                                &efl, H5T_get_size(dataset->type), file_space,
-                                mem_space, dxpl_id, buf/*out*/, &must_convert);
+                        &fill, &efl, H5T_get_size(dataset->type), file_space,
+                        mem_space, dxpl_id, buf/*out*/, &must_convert);
+
         /* Supports only no conversion, type or space, for now. */
         if (status<0)
 	    HGOTO_ERROR(H5E_DATASET, H5E_WRITEERROR, FAIL, "optimized write failed");
diff --git a/src/H5Sall.c b/src/H5Sall.c
index fed5d18..76fe0d6 100644
--- a/src/H5Sall.c
+++ b/src/H5Sall.c
@@ -393,6 +393,7 @@ H5S_all_mscat (const void *tconv_buf, size_t elmt_size,
  */
 herr_t
 H5S_all_read(H5F_t *f, const H5O_layout_t *layout, const H5O_pline_t *pline,
+             const struct H5O_fill_t *fill,
 	     const H5O_efl_t *efl, size_t elmt_size, const H5S_t *file_space,
 	     const H5S_t *mem_space, hid_t dxpl_id, void *_buf/*out*/,
 	     hbool_t *must_convert/*out*/)
@@ -623,7 +624,7 @@ for (u=0; u<=mem_space->extent.u.simple.rank; u++)
     printf("file_offset[%u]=%lu\n",u,(unsigned long)file_offset[u]);
 #endif /* QAK */
     /* Read data from the file */
-    if (H5F_arr_read(f, dxpl_id, layout, pline, NULL, efl, size,
+    if (H5F_arr_read(f, dxpl_id, layout, pline, fill, efl, size,
 		     size, mem_offset, file_offset, buf/*out*/)<0) {
         HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL,
 		      "unable to read data from the file");
@@ -661,10 +662,12 @@ done:
  */
 herr_t
 H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
-	      const H5O_pline_t *pline, const H5O_efl_t *efl,
-	      size_t elmt_size, const H5S_t *file_space,
-	      const H5S_t *mem_space, hid_t dxpl_id, const void *_buf,
-	      hbool_t *must_convert/*out*/)
+	     const H5O_pline_t *pline,
+             const struct H5O_fill_t *fill,
+             const H5O_efl_t *efl,
+	     size_t elmt_size, const H5S_t *file_space,
+	     const H5S_t *mem_space, hid_t dxpl_id, const void *_buf,
+	     hbool_t *must_convert/*out*/)
 {
     H5S_hyper_span_t *file_span=NULL,*mem_span=NULL;     /* Hyperslab span node */
     const char *buf=(const char*)_buf;  /* Get pointer to buffer */
@@ -880,7 +883,7 @@ H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
     } /* end if */
 
     /* Write data to the file */
-    if (H5F_arr_write(f, dxpl_id, layout, pline, NULL, efl, size,
+    if (H5F_arr_write(f, dxpl_id, layout, pline, fill, efl, size,
 		      size, mem_offset, file_offset, buf)<0) {
         HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL,
 		      "unable to write data to the file");
diff --git a/src/H5Smpio.c b/src/H5Smpio.c
index e6cc074..ab15ad6 100644
--- a/src/H5Smpio.c
+++ b/src/H5Smpio.c
@@ -551,6 +551,7 @@ H5S_mpio_space_type( const H5S_t *space, const size_t elmt_size,
 herr_t
 H5S_mpio_spaces_xfer(H5F_t *f, const struct H5O_layout_t *layout,
                      const struct H5O_pline_t UNUSED *pline,
+                     const struct H5O_fill_t UNUSED *fill,
                      const struct H5O_efl_t UNUSED *efl, size_t elmt_size,
                      const H5S_t *file_space, const H5S_t *mem_space,
 		     hid_t dxpl_id, void *buf /*out*/,
@@ -720,6 +721,7 @@ done:
 herr_t
 H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout,
                      const struct H5O_pline_t *pline,
+                     const struct H5O_fill_t *fill,
                      const struct H5O_efl_t *efl, size_t elmt_size,
                      const H5S_t *file_space, const H5S_t *mem_space,
                      hid_t dxpl_id, void *buf/*out*/,
@@ -729,7 +731,7 @@ H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout,
 
     FUNC_ENTER (H5S_mpio_spaces_read, FAIL);
 
-    ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
+    ret_value = H5S_mpio_spaces_xfer(f, layout, pline, fill, efl, elmt_size,
 				     file_space, mem_space, dxpl_id,
 				     buf, must_convert/*out*/, 0/*read*/);
 
@@ -755,17 +757,18 @@ H5S_mpio_spaces_read(H5F_t *f, const struct H5O_layout_t *layout,
  */
 herr_t
 H5S_mpio_spaces_write(H5F_t *f, const struct H5O_layout_t *layout,
-		      const struct H5O_pline_t *pline,
-		      const struct H5O_efl_t *efl, size_t elmt_size,
-		      const H5S_t *file_space, const H5S_t *mem_space,
-		      hid_t dxpl_id, const void *buf,
-		      hbool_t *must_convert/*out*/)
+		     const struct H5O_pline_t *pline,
+                     const struct H5O_fill_t *fill,
+		     const struct H5O_efl_t *efl, size_t elmt_size,
+		     const H5S_t *file_space, const H5S_t *mem_space,
+		     hid_t dxpl_id, const void *buf,
+		     hbool_t *must_convert/*out*/)
 {
     herr_t ret_value = FAIL;
 
     FUNC_ENTER (H5S_mpio_spaces_write, FAIL);
 
-    ret_value = H5S_mpio_spaces_xfer(f, layout, pline, efl, elmt_size,
+    ret_value = H5S_mpio_spaces_xfer(f, layout, pline, fill, efl, elmt_size,
 				     file_space, mem_space, dxpl_id,
 				     (void*)buf, must_convert/*out*/,
 				     1/*write*/);
diff --git a/src/H5Spkg.h b/src/H5Spkg.h
index 9e44930..7e3da29 100644
--- a/src/H5Spkg.h
+++ b/src/H5Spkg.h
@@ -146,16 +146,18 @@ __DLL__ herr_t H5S_all_select_deserialize(H5S_t *space, const uint8_t *buf);
 __DLL__ herr_t H5S_all_bounds(H5S_t *space, hsize_t *start, hsize_t *end);
 __DLL__ herr_t H5S_all_read(H5F_t *f, const struct H5O_layout_t *layout,
 			    const struct H5O_pline_t *pline,
+                            const struct H5O_fill_t *fill,
 			    const struct H5O_efl_t *efl, size_t elmt_size,
 			    const H5S_t *file_space, const H5S_t *mem_space,
 			    hid_t dxpl_id, void *buf/*out*/,
 			    hbool_t *must_convert/*out*/);
 __DLL__ herr_t H5S_all_write(H5F_t *f, const struct H5O_layout_t *layout,
-			     const struct H5O_pline_t *pline,
-			     const struct H5O_efl_t *efl, size_t elmt_size,
-			     const H5S_t *file_space, const H5S_t *mem_space,
-			     hid_t dxpl_id, const void *buf,
-			     hbool_t *must_convert/*out*/);
+			    const struct H5O_pline_t *pline,
+                            const struct H5O_fill_t *fill,
+			    const struct H5O_efl_t *efl, size_t elmt_size,
+			    const H5S_t *file_space, const H5S_t *mem_space,
+			    hid_t dxpl_id, const void *buf,
+			    hbool_t *must_convert/*out*/);
 __DLL__ herr_t H5S_all_select_iterate(void *buf, hid_t type_id, H5S_t *space,
 				      H5D_operator_t op, void *operator_data);
 
diff --git a/src/H5Sprivate.h b/src/H5Sprivate.h
index 42986d7..e024502 100644
--- a/src/H5Sprivate.h
+++ b/src/H5Sprivate.h
@@ -142,6 +142,7 @@ typedef struct H5S_conv_t {
     /* Read from file to application w/o intermediate scratch buffer */
     herr_t (*read)(H5F_t *f, const struct H5O_layout_t *layout,
 		   const struct H5O_pline_t *pline,
+                   const struct H5O_fill_t *fill,
 		   const struct H5O_efl_t *efl, size_t elmt_size,
 		   const H5S_t *file_space, const H5S_t *mem_space,
 		   hid_t dxpl_id, void *buf/*out*/,
@@ -150,11 +151,12 @@ typedef struct H5S_conv_t {
 
     /* Write directly from app buffer to file */
     herr_t (*write)(H5F_t *f, const struct H5O_layout_t *layout,
-		    const struct H5O_pline_t *pline,
-		    const struct H5O_efl_t *efl, size_t elmt_size,
-		    const H5S_t *file_space, const H5S_t *mem_space,
-		    hid_t dxpl_id, const void *buf,
-		    hbool_t *must_convert/*out*/);
+		   const struct H5O_pline_t *pline,
+                   const struct H5O_fill_t *fill,
+		   const struct H5O_efl_t *efl, size_t elmt_size,
+		   const H5S_t *file_space, const H5S_t *mem_space,
+		   hid_t dxpl_id, const void *buf,
+		   hbool_t *must_convert/*out*/);
     
 #ifdef H5S_DEBUG
     struct {
@@ -227,6 +229,7 @@ __DLL__ herr_t H5S_sel_iter_release(const H5S_t *space,
 __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
 				    const struct H5O_layout_t *layout,
 				    const struct H5O_pline_t *pline,
+                                    const struct H5O_fill_t *fill,
 				    const struct H5O_efl_t *efl,
 				    size_t elmt_size, const H5S_t *file_space,
 				    const H5S_t *mem_space, hid_t dxpl_id,
@@ -235,13 +238,14 @@ __DLL__ herr_t H5S_mpio_spaces_read(H5F_t *f,
 
 /* MPI-IO function to write directly from app buffer to file rky980813 */
 __DLL__ herr_t H5S_mpio_spaces_write(H5F_t *f,
-				     const struct H5O_layout_t *layout,
-				     const struct H5O_pline_t *pline,
-				     const struct H5O_efl_t *efl,
-				     size_t elmt_size, const H5S_t *file_space,
-				     const H5S_t *mem_space, hid_t dxpl_id,
-				     const void *buf,
-				     hbool_t *must_convert /*out*/ );
+				    const struct H5O_layout_t *layout,
+				    const struct H5O_pline_t *pline,
+                                    const struct H5O_fill_t *fill,
+				    const struct H5O_efl_t *efl,
+				    size_t elmt_size, const H5S_t *file_space,
+				    const H5S_t *mem_space, hid_t dxpl_id,
+				    const void *buf,
+				    hbool_t *must_convert /*out*/ );
 #ifndef _H5S_IN_H5S_C
 /* Global var whose value comes from environment variable */
 __DLLVAR__ hbool_t		H5_mpi_opt_types_g;