[svn-r12700] Alert:

    File format is not stable, don't keep files produced!

Description:
    First stage of checkins modifying the format of groups to support creation
order.  Implement "dense" storage for links in groups.

    Try to clarify some of the symbols for the H5L API.

    Add the H5Pset_latest_format() flag for FAPLs, to choose to use the newest
file format options (including "dense" link storage in groups)

    Add the H5Pset_track_creation_order() flag for GCPLs, to enable creation
order tracking in groups (although no index on creation order yet).

    Remove --enable-group-revision configure flag, as file format issues are
now handled in a backwardly/forwardly compatible way.

    Clean up lots of compiler warnings and other minor formatting issues.

Tested on:
    FreeBSD/32 4.11 (sleipnir) w/threadsafe
    Linux/32 2.4 (heping) w/FORTRAN & C++
    Linux/64 2.4 (mir) w/enable-v1.6 compa
    Mac OSX/32 10.4.8 (amazon)
    AIX 5.3 (copper) w/parallel & FORTRAN

1 files changed, 73 insertions, 100 deletions

diff --git a/src/H5O.c b/src/H5O.c
index d049777..6657a79 100644
--- a/src/H5O.c
+++ b/src/H5O.c
@@ -111,19 +111,11 @@ typedef struct H5O_addr_map_t {
 const H5O_msg_class_t *const H5O_msg_class_g[] = {
     H5O_MSG_NULL,		/*0x0000 Null				*/
     H5O_MSG_SDSPACE,		/*0x0001 Simple Dimensionality		*/
-#ifdef H5_GROUP_REVISION
     H5O_MSG_LINFO,		/*0x0002 Link information		*/
-#else /* H5_GROUP_REVISION */
-    NULL,
-#endif /* H5_GROUP_REVISION */
     H5O_MSG_DTYPE,		/*0x0003 Data Type			*/
     H5O_MSG_FILL,       	/*0x0004 Old data storage -- fill value */
     H5O_MSG_FILL_NEW,		/*0x0005 New Data storage -- fill value */
-#ifdef H5_GROUP_REVISION
     H5O_MSG_LINK,		/*0x0006 Link 				*/
-#else /* H5_GROUP_REVISION */
-    NULL,
-#endif /* H5_GROUP_REVISION */
     H5O_MSG_EFL,		/*0x0007 Data storage -- external data files */
     H5O_MSG_LAYOUT,		/*0x0008 Data Layout			*/
 #ifdef H5O_ENABLE_BOGUS
@@ -131,11 +123,7 @@ const H5O_msg_class_t *const H5O_msg_class_g[] = {
 #else /* H5O_ENABLE_BOGUS */
     NULL,			/*0x0009 "Bogus"			*/
 #endif /* H5O_ENABLE_BOGUS */
-#ifdef H5_GROUP_REVISION
     H5O_MSG_GINFO,		/*0x000A Group Information		*/
-#else /* H5_GROUP_REVISION */
-    NULL,
-#endif /* H5_GROUP_REVISION */
     H5O_MSG_PLINE,		/*0x000B Data storage -- filter pipeline */
     H5O_MSG_ATTR,		/*0x000C Attribute list			*/
     H5O_MSG_NAME,		/*0x000D Object name			*/
@@ -458,7 +446,7 @@ H5Oincr_refcount(hid_t object_id)
     herr_t      ret_value = SUCCEED;
 
     FUNC_ENTER_API(H5Oincr_refcount, FAIL)
-    H5TRACE1("Is","i",object_id);
+    H5TRACE1("e","i",object_id);
 
     /* Get the object's oloc so we can adjust its link count */
     if((oloc = H5O_get_oloc(object_id)) == NULL)
@@ -499,7 +487,7 @@ H5Odecr_refcount(hid_t object_id)
     herr_t      ret_value = SUCCEED;
 
     FUNC_ENTER_API(H5Odecr_refcount, FAIL)
-    H5TRACE1("Is","i",object_id);
+    H5TRACE1("e","i",object_id);
 
     /* Get the object's oloc so we can adjust its link count */
     if((oloc = H5O_get_oloc(object_id)) == NULL)
@@ -896,22 +884,22 @@ done:
 herr_t
 H5O_reset(unsigned type_id, void *native)
 {
-    const H5O_msg_class_t *type;            /* Actual H5O class type for the ID */
-    herr_t      ret_value;              /* Return value */
+    const H5O_msg_class_t *type;        /* Actual H5O class type for the ID */
+    herr_t ret_value = SUCCEED;         /* Return value */
 
-    FUNC_ENTER_NOAPI(H5O_reset,FAIL);
+    FUNC_ENTER_NOAPI(H5O_reset, FAIL)
 
     /* check args */
-    assert(type_id < NELMTS(H5O_msg_class_g));
-    type=H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
-    assert(type);
+    HDassert(type_id < NELMTS(H5O_msg_class_g));
+    type = H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
+    HDassert(type);
 
     /* Call the "real" reset routine */
-    if((ret_value=H5O_reset_real(type, native)) < 0)
-	HGOTO_ERROR(H5E_OHDR, H5E_READERROR, FAIL, "unable to reset object header");
+    if(H5O_reset_real(type, native) < 0)
+	HGOTO_ERROR(H5E_OHDR, H5E_CANTRESET, FAIL, "unable to reset object header")
 
 done:
-    FUNC_LEAVE_NOAPI(ret_value);
+    FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5O_reset() */
 
 
@@ -933,24 +921,23 @@ done:
 static herr_t
 H5O_reset_real(const H5O_msg_class_t *type, void *native)
 {
-    herr_t      ret_value=SUCCEED;       /* Return value */
+    herr_t      ret_value = SUCCEED;       /* Return value */
 
-    FUNC_ENTER_NOAPI_NOINIT(H5O_reset_real);
+    FUNC_ENTER_NOAPI_NOINIT(H5O_reset_real)
 
     /* check args */
-    assert(type);
+    HDassert(type);
 
-    if (native) {
-	if (type->reset) {
-	    if ((type->reset) (native) < 0)
-		HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "reset method failed");
-	} else {
+    if(native) {
+	if(type->reset) {
+	    if((type->reset)(native) < 0)
+		HGOTO_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "reset method failed")
+	} else
 	    HDmemset(native, 0, type->native_size);
-	}
-    }
+    } /* end if */
 
 done:
-    FUNC_LEAVE_NOAPI(ret_value);
+    FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5O_reset_real() */
 
 
@@ -972,7 +959,7 @@ done:
  *-------------------------------------------------------------------------
  */
 void *
-H5O_free (unsigned type_id, void *mesg)
+H5O_free(unsigned type_id, void *mesg)
 {
     const H5O_msg_class_t *type;            /* Actual H5O class type for the ID */
     void * ret_value;                   /* Return value */
@@ -2011,11 +1998,11 @@ H5O_new_mesg(H5F_t *f, H5O_t *oh, unsigned *flags, const H5O_msg_class_t *orig_t
     } /* end else */
 
     /* Compute the size needed to store the message on disk */
-    if ((size = ((*new_type)->raw_size) (f, *new_mesg)) >=H5O_MAX_SIZE)
-        HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, UFAIL, "object header message is too large");
+    if((size = ((*new_type)->raw_size)(f, *new_mesg)) >=H5O_MAX_SIZE)
+        HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, UFAIL, "object header message is too large")
 
     /* Allocate space in the object headed for the message */
-    if ((ret_value = H5O_alloc(f, dxpl_id, oh, orig_type, size, oh_flags_ptr)) == UFAIL)
+    if((ret_value = H5O_alloc(f, dxpl_id, oh, orig_type, size, oh_flags_ptr)) == UFAIL)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, UFAIL, "unable to allocate space for message");
 
     /* Increment any links in message */
@@ -2124,18 +2111,18 @@ H5O_touch_oh(H5F_t *f,
 #endif /* H5_HAVE_GETTIMEOFDAY */
 
     /* Create a new message */
-    if (idx==oh->nmesgs) {
-	if (!force)
+    if(idx == oh->nmesgs) {
+	if(!force)
             HGOTO_DONE(SUCCEED); /*nothing to do*/
 	size = (H5O_MSG_MTIME_NEW->raw_size)(f, &now);
 
-	if ((idx=H5O_alloc(f, dxpl_id, oh, H5O_MSG_MTIME_NEW, size, oh_flags_ptr))==UFAIL)
+	if((idx = H5O_alloc(f, dxpl_id, oh, H5O_MSG_MTIME_NEW, size, oh_flags_ptr)) == UFAIL)
 	    HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to allocate space for modification time message");
-    }
+    } /* end if */
 
     /* Update the native part */
-    if (NULL==oh->mesg[idx].native) {
-	if (NULL==(oh->mesg[idx].native = H5FL_MALLOC(time_t)))
+    if(NULL==oh->mesg[idx].native) {
+	if(NULL==(oh->mesg[idx].native = H5FL_MALLOC(time_t)))
 	    HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "memory allocation failed for modification time message");
     }
     *((time_t*)(oh->mesg[idx].native)) = now;
@@ -3324,13 +3311,11 @@ H5O_alloc_new_chunk(H5F_t *f,
                    (found_attr < 0 ||
                     oh->mesg[u].raw_size < oh->mesg[found_attr].raw_size))
                 found_attr = u;
-#ifdef H5_GROUP_REVISION
 	} else if(H5O_LINK_ID == msg_id) {
             if(oh->mesg[u].raw_size >= cont_size &&
                    (found_link < 0 ||
                     oh->mesg[u].raw_size < oh->mesg[found_link].raw_size))
                 found_link = u;
-#endif /* H5_GROUP_REVISION */
 	} else {
             if(oh->mesg[u].raw_size >= cont_size &&
                    (found_other < 0 ||
@@ -3671,18 +3656,18 @@ H5O_raw_size(unsigned type_id, const H5F_t *f, const void *mesg)
     const H5O_msg_class_t *type;            /* Actual H5O class type for the ID */
     size_t      ret_value;       /* Return value */
 
-    FUNC_ENTER_NOAPI(H5O_raw_size,0)
+    FUNC_ENTER_NOAPI(H5O_raw_size, 0)
 
     /* Check args */
     HDassert(type_id < NELMTS(H5O_msg_class_g));
-    type=H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
+    type = H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
     HDassert(type);
     HDassert(type->raw_size);
     HDassert(f);
     HDassert(mesg);
 
     /* Compute the raw data size for the mesg */
-    if ((ret_value = (type->raw_size)(f, mesg))==0)
+    if((ret_value = (type->raw_size)(f, mesg)) == 0)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTCOUNT, 0, "unable to determine size of message")
 
 done:
@@ -3705,16 +3690,16 @@ done:
  *-------------------------------------------------------------------------
  */
 size_t
-H5O_mesg_size(unsigned type_id, const H5F_t *f, const void *mesg)
+H5O_mesg_size(unsigned type_id, const H5F_t *f, const void *mesg, size_t extra_raw)
 {
     const H5O_msg_class_t *type;            /* Actual H5O class type for the ID */
     size_t      ret_value;       /* Return value */
 
-    FUNC_ENTER_NOAPI(H5O_mesg_size,0)
+    FUNC_ENTER_NOAPI(H5O_mesg_size, 0)
 
     /* Check args */
     HDassert(type_id < NELMTS(H5O_msg_class_g));
-    type=H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
+    type = H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
     HDassert(type);
     HDassert(type->raw_size);
     HDassert(f);
@@ -3724,6 +3709,9 @@ H5O_mesg_size(unsigned type_id, const H5F_t *f, const void *mesg)
     if((ret_value = (type->raw_size)(f, mesg)) == 0)
         HGOTO_ERROR(H5E_OHDR, H5E_CANTCOUNT, 0, "unable to determine size of message")
 
+    /* Add in "extra" raw space */
+    ret_value += extra_raw;
+
     /* Adjust size for alignment, if necessary */
     ret_value = H5O_ALIGN(ret_value);
 
@@ -3999,37 +3987,38 @@ done:
  *		slu@ncsa.uiuc.edu
  *		July 13, 2004
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 herr_t
-H5O_encode(H5F_t *f, unsigned char *buf, void *obj, unsigned type_id)
+H5O_encode(H5F_t *f, unsigned char *buf, const void *obj, unsigned type_id)
 {
-    const H5O_msg_class_t   *type;            /* Actual H5O class type for the ID */
-    herr_t 	        ret_value = SUCCEED;        /* Return value */
+    const H5O_msg_class_t   *type;      /* Actual H5O class type for the ID */
+    herr_t      ret_value = SUCCEED;    /* Return value */
 
-    FUNC_ENTER_NOAPI(H5O_encode,FAIL);
+    FUNC_ENTER_NOAPI(H5O_encode,FAIL)
 
     /* check args */
-    assert(type_id < NELMTS(H5O_msg_class_g));
-    type=H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
-    assert(type);
+    HDassert(type_id < NELMTS(H5O_msg_class_g));
+    type = H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
+    HDassert(type);
 
     /* Encode */
-    if ((type->encode)(f, buf, obj) < 0)
-        HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to encode message");
+    if((type->encode)(f, buf, obj) < 0)
+        HGOTO_ERROR (H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to encode message")
 
 done:
-    FUNC_LEAVE_NOAPI(ret_value);
-}
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5O_encode() */
 
 
 /*-------------------------------------------------------------------------
  * Function:	H5O_decode
  *
- * Purpose:	Decode a binary object(data type and data space only)
- *              description and return a new object handle.
+ * Purpose:	Decode a binary object description and return a new
+ *              object handle.
+ *
+ * Note:	This routine is not guaranteed to work with all possible
+ *              header messages, use with care.
  *
  * Return:	Success:        Pointer to object(data type or space)
  *
@@ -4039,30 +4028,28 @@ done:
  *		slu@ncsa.uiuc.edu
  *		July 14, 2004
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
-void*
-H5O_decode(H5F_t *f, const unsigned char *buf, unsigned type_id)
+void *
+H5O_decode(H5F_t *f, hid_t dxpl_id, const unsigned char *buf, unsigned type_id)
 {
-    const H5O_msg_class_t   *type;            /* Actual H5O class type for the ID */
-    void 	        *ret_value=NULL;       /* Return value */
+    const H5O_msg_class_t   *type;      /* Actual H5O class type for the ID */
+    void *ret_value;                    /* Return value */
 
-    FUNC_ENTER_NOAPI(H5O_decode,NULL);
+    FUNC_ENTER_NOAPI(H5O_decode, NULL)
 
     /* check args */
-    assert(type_id < NELMTS(H5O_msg_class_g));
-    type=H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
-    assert(type);
+    HDassert(type_id < NELMTS(H5O_msg_class_g));
+    type = H5O_msg_class_g[type_id];    /* map the type ID to the actual type object */
+    HDassert(type);
 
     /* decode */
-    if((ret_value = (type->decode)(f, 0, buf))==NULL)
-        HGOTO_ERROR(H5E_OHDR, H5E_CANTDECODE, NULL, "unable to decode message");
+    if((ret_value = (type->decode)(f, dxpl_id, buf)) == NULL)
+        HGOTO_ERROR (H5E_OHDR, H5E_CANTDECODE, NULL, "unable to decode message")
 
 done:
-    FUNC_LEAVE_NOAPI(ret_value);
-}
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5O_decode() */
 
 
 /*-------------------------------------------------------------------------
@@ -4431,7 +4418,6 @@ H5O_loc_copy(H5O_loc_t *dst, const H5O_loc_t *src, H5_copy_depth_t depth)
          */
         if(src->holding_file)
             dst->file->nopen_objs++;
-        ;
     } else if(depth == H5_COPY_SHALLOW) {
         /* Discarding 'const' qualifier OK - QAK */
         H5O_loc_reset((H5O_loc_t *)src);
@@ -4772,13 +4758,8 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
                     HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, FAIL, "unable to copy object header message")
              } /* end else */
 
-            /*
-             * Encode the message.  If the message is shared then we
-             * encode a Shared Object message instead of the object
-             * which is being shared.
-             */
-            if((copy_type->encode)(oloc_dst->file, mesg_dst->raw, mesg_dst->native) < 0)
-                HGOTO_ERROR(H5E_OHDR, H5E_CANTENCODE, FAIL, "unable to encode object header message")
+            /* Mark the message in the destination as dirty, so it'll get encoded when the object header is flushed */
+            mesg_dst->dirty = TRUE;
         } /* end if (mesg_src->type->copy_file) */
     } /* end of mesgno loop */
 
@@ -4820,22 +4801,14 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
 
         HDassert(copy_type);
         if(copy_type->post_copy_file && mesg_src->native) {
-            hbool_t modified = FALSE;
-
-            /* Get destination message */
+            /* Sanity check destination message */
             HDassert(mesg_dst->type == mesg_src->type);
-
-            /* Make certain the destination's native info is available */
-            LOAD_NATIVE(oloc_dst->file, dxpl_id, mesg_dst, FAIL)
+            HDassert(mesg_dst->native);
 
             /* Perform "post copy" operation on messge */
             if((copy_type->post_copy_file)(oloc_src, mesg_src->native, oloc_dst,
-                    mesg_dst->native, &modified, dxpl_id, cpy_info) < 0)
+                    mesg_dst->native, dxpl_id, cpy_info) < 0)
                 HGOTO_ERROR(H5E_OHDR, H5E_CANTINIT, FAIL, "unable to perform 'post copy' operation on message")
-
-            /* Mark message and header as dirty if the destination message was modified */
-            if(modified)
-                mesg_dst->dirty = TRUE;
         } /* end if */
     } /* end for */