[svn-r16764] To fix a bug in extensible arrays as chunk index:

When the dataset is closed in H5D_close(), the pointer
to the extensible array struct in the layout message
is copied via H5D_flush_real() before H5D_chunk_dest().
This causes an abort from "Assertion `ea->hdr' failed"
later when the dataset is re-opened and read.
The bug was fixed by adding a flag to the reset function 
for indexed storage to set/not set the address of the indexed
array. H5O_layout_copy() calls H5D_chunk_idx_reset() to reset
only the pointer of the array struct for the chunked index storage.

7 files changed, 50 insertions, 14 deletions

diff --git a/src/H5Dbtree.c b/src/H5Dbtree.c
index 7db99d0..fe0349c 100644
--- a/src/H5Dbtree.c
+++ b/src/H5Dbtree.c
@@ -153,7 +153,7 @@ static herr_t H5D_btree_idx_copy_shutdown(H5O_layout_t *layout_src,
     H5O_layout_t *layout_dst, hid_t dxpl_id);
 static herr_t H5D_btree_idx_size(const H5D_chk_idx_info_t *idx_info,
     hsize_t *size);
-static herr_t H5D_btree_idx_reset(H5O_layout_t *layout);
+static herr_t H5D_btree_idx_reset(H5O_layout_t *layout, hbool_t reset_addr);
 static herr_t H5D_btree_idx_dump(const H5D_chk_idx_info_t *idx_info,
     FILE *stream);
 static herr_t H5D_btree_idx_dest(const H5D_chk_idx_info_t *idx_info);
@@ -1347,17 +1347,22 @@ done:
  * Programmer:	Quincey Koziol
  *              Thursday, January 15, 2009
  *
+ * Modifications:
+ *	Vailin Choi; April 2009
+ *	Reset address of the chunked storage index if RESET_ADDR is set
+ *
  *-------------------------------------------------------------------------
  */
 static herr_t
-H5D_btree_idx_reset(H5O_layout_t *layout)
+H5D_btree_idx_reset(H5O_layout_t *layout, hbool_t reset_addr)
 {
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_btree_idx_reset)
 
     HDassert(layout);
 
     /* Reset index info */
-    layout->u.chunk.u.btree.addr = HADDR_UNDEF;
+    if(reset_addr)
+	layout->u.chunk.u.btree.addr = HADDR_UNDEF;
     layout->u.chunk.u.btree.shared = NULL;
 
     FUNC_LEAVE_NOAPI(SUCCEED)
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 5e45886..a88df43 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -281,6 +281,10 @@ H5FL_DEFINE_STATIC(H5D_chunk_prune_stack_t);
  * Programmer:	Quincey Koziol
  *              Thursday, May 22, 2008
  *
+ * Modifications:
+ *	Vailin Choi; April 2009
+ * 	Reset address and pointer of the array struct for the chunked storage index
+ *
  *-------------------------------------------------------------------------
  */
 static herr_t
@@ -344,8 +348,8 @@ H5D_chunk_new(H5F_t *f, hid_t dapl_id, hid_t dxpl_id, H5D_t *dset,
     /* Retain computed chunk size */
     H5_ASSIGN_OVERFLOW(dset->shared->layout.u.chunk.size, chunk_size, uint64_t, uint32_t);
 
-    /* Reset index address */
-    if(H5D_chunk_idx_reset(&dset->shared->layout) < 0)
+    /* Reset address and pointer of the array struct for the chunked storage index */
+    if(H5D_chunk_idx_reset(&dset->shared->layout, TRUE) < 0)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to reset chunked storage index")
 
     /* Initialize the chunk cache for the dataset */
@@ -1919,11 +1923,15 @@ done:
  *
  * Programmer:	Quincey Koziol
  *              Thursday, January 15, 2009
+ * 
+ * Modifications:
+ *	Vailin Choi; April 2009
+ *	Pass along RESET_ADDR: whether to reset the address of chunked storage index
  *
  *-------------------------------------------------------------------------
  */
 herr_t
-H5D_chunk_idx_reset(H5O_layout_t *layout)
+H5D_chunk_idx_reset(H5O_layout_t *layout, hbool_t reset_addr)
 {
     herr_t ret_value = SUCCEED;         /* Return value */
 
@@ -1938,7 +1946,7 @@ H5D_chunk_idx_reset(H5O_layout_t *layout)
                 H5D_COPS_BTREE == layout->u.chunk.ops));
 
     /* Reset index structures */
-    if((layout->u.chunk.ops->reset)(layout) < 0)
+    if((layout->u.chunk.ops->reset)(layout, reset_addr) < 0)
 	HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to reset chunk index info")
 
 done:
diff --git a/src/H5Dearray.c b/src/H5Dearray.c
index 35cdad6..7ae62e4 100644
--- a/src/H5Dearray.c
+++ b/src/H5Dearray.c
@@ -131,7 +131,7 @@ static herr_t H5D_earray_idx_copy_shutdown(H5O_layout_t *layout_src,
     H5O_layout_t *layout_dst, hid_t dxpl_id);
 static herr_t H5D_earray_idx_size(const H5D_chk_idx_info_t *idx_info,
     hsize_t *size);
-static herr_t H5D_earray_idx_reset(H5O_layout_t *layout);
+static herr_t H5D_earray_idx_reset(H5O_layout_t *layout, hbool_t reset_addr);
 static herr_t H5D_earray_idx_dump(const H5D_chk_idx_info_t *idx_info,
     FILE *stream);
 static herr_t H5D_earray_idx_dest(const H5D_chk_idx_info_t *idx_info);
@@ -1409,17 +1409,22 @@ done:
  * Programmer:	Quincey Koziol
  *              Saturday, January 31, 2009
  *
+ * Modifications:
+ *      Vailin Choi; April 2009
+ *      Reset address of the chunked storage index if RESET_ADDR is set
+ *
  *-------------------------------------------------------------------------
  */
 static herr_t
-H5D_earray_idx_reset(H5O_layout_t *layout)
+H5D_earray_idx_reset(H5O_layout_t *layout, hbool_t reset_addr)
 {
     FUNC_ENTER_NOAPI_NOINIT_NOFUNC(H5D_earray_idx_reset)
 
     HDassert(layout);
 
     /* Reset index info */
-    layout->u.chunk.u.earray.addr = HADDR_UNDEF;
+    if(reset_addr)
+	layout->u.chunk.u.earray.addr = HADDR_UNDEF;
     layout->u.chunk.u.earray.ea = NULL;
 
     FUNC_LEAVE_NOAPI(SUCCEED)
diff --git a/src/H5Dpkg.h b/src/H5Dpkg.h
index 4122326..b936dba 100644
--- a/src/H5Dpkg.h
+++ b/src/H5Dpkg.h
@@ -281,7 +281,7 @@ typedef herr_t (*H5D_chunk_copy_shutdown_func_t)(H5O_layout_t *layout_src,
     H5O_layout_t *layout_dst, hid_t dxpl_id);
 typedef herr_t (*H5D_chunk_size_func_t)(const H5D_chk_idx_info_t *idx_info,
     hsize_t *idx_size);
-typedef herr_t (*H5D_chunk_reset_func_t)(H5O_layout_t *layout);
+typedef herr_t (*H5D_chunk_reset_func_t)(H5O_layout_t *layout, hbool_t reset_addr);
 typedef herr_t (*H5D_chunk_dump_func_t)(const H5D_chk_idx_info_t *idx_info,
     FILE *stream);
 typedef herr_t (*H5D_chunk_dest_func_t)(const H5D_chk_idx_info_t *idx_info);
diff --git a/src/H5Dprivate.h b/src/H5Dprivate.h
index 7327d0d..ad9c795 100644
--- a/src/H5Dprivate.h
+++ b/src/H5Dprivate.h
@@ -166,7 +166,7 @@ H5_DLL herr_t H5D_contig_delete(H5F_t *f, hid_t dxpl_id,
     const H5O_layout_t *layout);
 
 /* Functions that operate on chunked storage */
-H5_DLL herr_t H5D_chunk_idx_reset(H5O_layout_t *layout);
+H5_DLL herr_t H5D_chunk_idx_reset(H5O_layout_t *layout, hbool_t reset_addr);
 H5_DLL herr_t H5D_chunk_delete(H5F_t *f, hid_t dxpl_id, H5O_t *oh,
     H5O_layout_t *layout);
 
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index b92a8bb..c79f328 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -447,6 +447,10 @@ done:
  * Programmer:  Robb Matzke
  *              Wednesday, October  8, 1997
  *
+ * Modifications:
+ *      Vailin Choi; April 2009
+ *      Reset the pointer of the chunked storage index but not the address
+ *
  *-------------------------------------------------------------------------
  */
 static void *
@@ -474,8 +478,13 @@ H5O_layout_copy(const void *_mesg, void *_dest)
 
         /* Copy over the raw data */
         HDmemcpy(dest->u.compact.buf, mesg->u.compact.buf, dest->u.compact.size);
+
     } /* end if */
 
+    /* Reset the pointer of the chunked storage index but not the address */
+    if(dest->type == H5D_CHUNKED && dest->u.chunk.ops)
+	H5D_chunk_idx_reset(dest, FALSE);
+
     /* Set return value */
     ret_value = dest;
 
@@ -654,6 +663,10 @@ done:
  * Programmer:  Peter Cao
  *              July 23, 2005
  *
+ * Modifications:
+ *      Vailin Choi; April 2009
+ *      Reset address and pointer of the array struct for the chunked storage index
+ *
  *-------------------------------------------------------------------------
  */
 static void *
@@ -713,7 +726,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
         case H5D_CHUNKED:
             if(H5D_chunk_is_space_alloc(layout_src)) {
                 /* Layout is not created in the destination file, reset index address */
-                if(H5D_chunk_idx_reset(layout_dst) < 0)
+                if(H5D_chunk_idx_reset(layout_dst, TRUE) < 0)
                     HGOTO_ERROR(H5E_IO, H5E_CANTINIT, NULL, "unable to reset chunked storage index in dest")
 
                 /* Create chunked layout */
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index dcd120e..b2bd71d 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -223,6 +223,10 @@ done:
  * Programmer:     Raymond Lu
  *                 Tuesday, October 2, 2001
  *
+ * Modifications:
+ *      Vailin Choi; April 2009
+ *      Reset address and pointer of the array struct for the chunked storage index
+ *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -280,7 +284,8 @@ H5P_dcrt_copy(hid_t dst_plist_id, hid_t src_plist_id, void UNUSED *copy_data)
 
             /* Reset index info, if the chunk ops are set */
             if(dst_layout.u.chunk.ops)
-                if(H5D_chunk_idx_reset(&dst_layout) < 0)
+		/* Reset address and pointer of the array struct for the chunked storage index */
+                if(H5D_chunk_idx_reset(&dst_layout, TRUE) < 0)
                     HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "unable to reset chunked storage index in dest")
 
             /* Reset chunk index ops */