[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)

7 files changed, 134 insertions, 35 deletions

diff --git a/release_docs/RELEASE.txt b/release_docs/RELEASE.txt
index 6d5f50c..da49eb0 100644
--- a/release_docs/RELEASE.txt
+++ b/release_docs/RELEASE.txt
@@ -106,6 +106,9 @@ Library
     * Fixed bug where a preempted chunk in the chunk data could still be
       used by an internal pointer and cause an assertion failure or core
       dump. QAK - 2/13/02
+    * Fixed bug where non-zero fill-value was not being read correctly from
+      certain chunked datasets when using an "all" or contiguous hyperslab
+      selection.  QAK - 2/14/02
 
 Configuration
 -------------
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;
diff --git a/test/tmisc.c b/test/tmisc.c
index b5682c5..6980fc3 100644
--- a/test/tmisc.c
+++ b/test/tmisc.c
@@ -41,6 +41,16 @@ typedef struct {
       char *string;
 } misc2_struct;
 
+/* Definitions for misc. test #3 */
+#define MISC3_FILE              "tmisc3.h5"
+#define MISC3_RANK              2
+#define MISC3_DIM1              6
+#define MISC3_DIM2              6
+#define MISC3_CHUNK_DIM1        2
+#define MISC3_CHUNK_DIM2        2
+#define MISC3_FILL_VALUE        2
+#define MISC3_DSET_NAME         "/chunked"
+
 /****************************************************************
 **
 **  test_misc1(): test unlinking a dataset from a group and immediately
@@ -252,7 +262,7 @@ static void test_misc2_read_attribute(const char *filename, const char *att_name
     free(data_check.string);
 
     ret = H5Aclose(att);
-    CHECK(ret, FAIL, "HAclose");
+    CHECK(ret, FAIL, "H5Aclose");
 
     ret = H5Tclose(type);
     CHECK(ret, FAIL, "H5Tclose");
@@ -285,6 +295,73 @@ test_misc2(void)
 
 /****************************************************************
 **
+**  test_misc3(): Test reading from chunked dataset with non-zero
+**      fill value
+**
+****************************************************************/
+static void
+test_misc3(void)
+{
+    hid_t file, dataspace, dataset, dcpl;
+    int rank=MISC3_RANK;
+    hsize_t dims[MISC3_RANK]={MISC3_DIM1,MISC3_DIM2};
+    hsize_t chunk_dims[MISC3_RANK]={MISC3_CHUNK_DIM1,MISC3_CHUNK_DIM2};
+    int fill=MISC3_FILL_VALUE;
+    int read_buf[MISC3_DIM1][MISC3_DIM2];
+    int i,j;
+    herr_t ret;
+
+    /* Output message about test being performed */
+    MESSAGE(5, ("Testing reading from chunked dataset with non-zero fill-value\n"));
+
+    file = H5Fcreate(MISC3_FILE, H5F_ACC_TRUNC, H5P_DEFAULT, H5P_DEFAULT);
+    CHECK(file, FAIL, "H5Fcreate");
+
+    /* Create a simple dataspace */
+    dataspace = H5Screate_simple(rank,dims,NULL);
+    CHECK(dataspace, FAIL, "H5Screate_simple");
+
+    /* Create a dataset creation property list */
+    dcpl = H5Pcreate(H5P_DATASET_CREATE);
+    CHECK(dcpl, FAIL, "H5Pcreate"); 
+
+    /* Set the chunk information */
+    ret = H5Pset_chunk(dcpl,rank,chunk_dims);
+    CHECK(dcpl, FAIL, "H5Pset_chunk"); 
+
+    /* Set the fill-value information */
+    ret = H5Pset_fill_value(dcpl,H5T_NATIVE_INT,&fill);
+    CHECK(dcpl, FAIL, "H5Pset_fill_value"); 
+
+    /* Create the dataset */
+    dataset = H5Dcreate(file, MISC3_DSET_NAME, H5T_NATIVE_INT, dataspace, dcpl);
+    CHECK(dataset, FAIL, "H5Dcreate");
+
+    /* Read from the dataset (should be fill-values) */
+    ret = H5Dread(dataset, H5T_NATIVE_INT, H5S_ALL, H5S_ALL, H5P_DEFAULT, &read_buf);
+    CHECK(ret, FAIL, "H5Dread");
+
+    for(i=0; i<MISC3_DIM1; i++)
+        for(j=0; j<MISC3_DIM2; j++)
+            VERIFY(read_buf[i][j],fill,"H5Dread");
+
+    /* Release resources */
+    ret = H5Pclose(dcpl);
+    CHECK(ret, FAIL, "H5Pclose");
+
+    ret = H5Sclose(dataspace);
+    CHECK(ret, FAIL, "H5Sclose");
+
+    ret = H5Dclose(dataset);
+    CHECK(ret, FAIL, "H5Dclose");
+
+    ret = H5Fclose(file);
+    CHECK(ret, FAIL, "H5Fclose");
+} /* end test_misc3() */
+
+
+/****************************************************************
+**
 **  test_misc(): Main misc. test routine.
 ** 
 ****************************************************************/
@@ -296,6 +373,7 @@ test_misc(void)
 
     test_misc1();       /* Test unlinking a dataset & immediately re-using name */
     test_misc2();       /* Test storing a VL-derived datatype in two different files */
+    test_misc3();       /* Test reading from chunked dataset with non-zero fill value */
 
 } /* test_misc() */
 
@@ -320,4 +398,5 @@ cleanup_misc(void)
     remove(MISC1_FILE);
     remove(MISC2_FILE_1);
     remove(MISC2_FILE_2);
+    remove(MISC3_FILE);
 }