[svn-r29016] Merge of r28936, 28949, 28960-29009 from trunk.

Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
           autotools serial w/ Fortran and C++
           autotools parallel (MPICH 3.1.4) w/ Fortran
           CMake serial (3.3.2, via cmakehdf5)

22 files changed, 165 insertions, 202 deletions

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 0fbd32b..ca71fca 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -868,11 +868,11 @@ set_target_properties (${HDF5_LIB_TARGET} PROPERTIES
     INTERFACE_INCLUDE_DIRECTORIES "$<INSTALL_INTERFACE:$<INSTALL_PREFIX>/include>"
 )
 
-option (HDF5_ENABLE_DEBUG_APIS "Turn on debugging in all packages" OFF)
+option (HDF5_ENABLE_DEBUG_APIS "Turn on extra debug output in all packages" OFF)
 if (HDF5_ENABLE_DEBUG_APIS)
   set_target_properties (${HDF5_LIB_TARGET} PROPERTIES
       COMPILE_DEFINITIONS
-          "H5Z_DEBUG;H5VM_DEBUG;H5T_DEBUG;H5S_DEBUG;H5P_DEBUG;H5O_DEBUG;H5MM_DEBUG;H5MF_DEBUG;H5I_DEBUG;H5HL_DEBUG;H5HG_DEBUG;H5G_DEBUG;H5F_DEBUG;H5E_DEBUG;H5D_DEBUG;H5B_DEBUG;H5AC_DEBUG"
+          "H5Z_DEBUG;H5T_DEBUG;H5ST_DEBUG;H5S_DEBUG;H5O_DEBUG;H5I_DEBUG;H5HL_DEBUG;H5F_DEBUG;H5D_DEBUG;H5B2_DEBUG;H5B_DEBUG;H5AC_DEBUG"
   )
 endif (HDF5_ENABLE_DEBUG_APIS)
 set (install_targets ${HDF5_LIB_TARGET})
diff --git a/src/H5.c b/src/H5.c
index a522398..4de5731 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -552,30 +552,29 @@ done:
 
 
 /*-------------------------------------------------------------------------
- * Function:	H5_debug_mask
+ * Function:    H5_debug_mask
  *
- * Purpose:	Set runtime debugging flags according to the string S.  The
- *		string should contain file numbers and package names
- *		separated by other characters. A file number applies to all
- *		following package names up to the next file number. The
- *		initial file number is `2' (the standard error stream). Each
- *		package name can be preceded by a `+' or `-' to add or remove
- *		the package from the debugging list (`+' is the default). The
- *		special name `all' means all packages.
+ * Purpose:     Set runtime debugging flags according to the string S.  The
+ *              string should contain file numbers and package names
+ *              separated by other characters. A file number applies to all
+ *              following package names up to the next file number. The
+ *              initial file number is `2' (the standard error stream). Each
+ *              package name can be preceded by a `+' or `-' to add or remove
+ *              the package from the debugging list (`+' is the default). The
+ *              special name `all' means all packages.
  *
- *		The name `trace' indicates that API tracing is to be turned
- *		on or off.
+ *              The name `trace' indicates that API tracing is to be turned
+ *              on or off.
  *
- * Return:	void
+ *              The name 'ttop' indicates that only top-level API calls
+ *              should be shown. This also turns on tracing as if the
+ *              'trace' word was shown.
  *
- * Programmer:	Robb Matzke
+ * Return:      void
+ *
+ * Programmer:  Robb Matzke
  *              Wednesday, August 19, 1998
  *
- * Modifications:
- *              Robb Matzke, 2002-08-08
- *              Accepts the `ttop' word. If enabled then show only the
- *              top level API calls, otherwise show all API calls.  Also
- *              turns on tracing as if the `trace' word was present.
  *-------------------------------------------------------------------------
  */
 static void
@@ -587,55 +586,57 @@ H5_debug_mask(const char *s)
     hbool_t	clear;
 
     while (s && *s) {
-	if (HDisalpha(*s) || '-'==*s || '+'==*s) {
-	    /* Enable or Disable debugging? */
-	    if ('-'==*s) {
-		clear = TRUE;
-		s++;
-	    } else if ('+'==*s) {
-		clear = FALSE;
-		s++;
-	    } else {
-		clear = FALSE;
-	    }
-
-	    /* Get the name */
-	    for (i=0; HDisalpha(*s); i++, s++)
-		if (i<sizeof pkg_name)
+
+        if (HDisalpha(*s) || '-'==*s || '+'==*s) {
+
+            /* Enable or Disable debugging? */
+            if ('-'==*s) {
+                clear = TRUE;
+                s++;
+            } else if ('+'==*s) {
+                clear = FALSE;
+                s++;
+            } else {
+                clear = FALSE;
+            } /* end if */
+
+            /* Get the name */
+            for (i=0; HDisalpha(*s); i++, s++)
+                if (i<sizeof pkg_name)
                     pkg_name[i] = *s;
-	    pkg_name[MIN(sizeof(pkg_name)-1, i)] = '\0';
+            pkg_name[MIN(sizeof(pkg_name)-1, i)] = '\0';
 
-	    /* Trace, all, or one? */
-	    if (!HDstrcmp(pkg_name, "trace")) {
-		H5_debug_g.trace = clear ? NULL : stream;
+            /* Trace, all, or one? */
+            if (!HDstrcmp(pkg_name, "trace")) {
+                H5_debug_g.trace = clear ? NULL : stream;
             } else if (!HDstrcmp(pkg_name, "ttop")) {
                 H5_debug_g.trace = stream;
                 H5_debug_g.ttop = (hbool_t)!clear;
             } else if (!HDstrcmp(pkg_name, "ttimes")) {
                 H5_debug_g.trace = stream;
                 H5_debug_g.ttimes = (hbool_t)!clear;
-	    } else if (!HDstrcmp(pkg_name, "all")) {
-		for (i=0; i<(size_t)H5_NPKGS; i++)
-		    H5_debug_g.pkg[i].stream = clear ? NULL : stream;
-	    } else {
-		for (i=0; i<(size_t)H5_NPKGS; i++) {
-		    if (!HDstrcmp(H5_debug_g.pkg[i].name, pkg_name)) {
-			H5_debug_g.pkg[i].stream = clear ? NULL : stream;
-			break;
-		    }
-		}
-		if (i>=(size_t)H5_NPKGS)
-		    fprintf(stderr, "HDF5_DEBUG: ignored %s\n", pkg_name);
-	    }
-
-	} else if (HDisdigit(*s)) {
-	    int fd = (int)HDstrtol(s, &rest, 0);
-	    H5_debug_open_stream_t *open_stream;
-
-	    if((stream = HDfdopen(fd, "w")) != NULL) {
-	        (void)HDsetvbuf(stream, NULL, _IOLBF, (size_t)0);
-
-	        if(NULL == (open_stream = (H5_debug_open_stream_t *)H5MM_malloc(sizeof(H5_debug_open_stream_t)))) {
+            } else if (!HDstrcmp(pkg_name, "all")) {
+                for (i=0; i<(size_t)H5_NPKGS; i++)
+                    H5_debug_g.pkg[i].stream = clear ? NULL : stream;
+            } else {
+                for (i=0; i<(size_t)H5_NPKGS; i++) {
+                    if (!HDstrcmp(H5_debug_g.pkg[i].name, pkg_name)) {
+                        H5_debug_g.pkg[i].stream = clear ? NULL : stream;
+                        break;
+		            } /* end if */
+                } /* end for */
+                if (i>=(size_t)H5_NPKGS)
+                    fprintf(stderr, "HDF5_DEBUG: ignored %s\n", pkg_name);
+            } /* end if-else */
+
+        } else if (HDisdigit(*s)) {
+            int fd = (int)HDstrtol(s, &rest, 0);
+            H5_debug_open_stream_t *open_stream;
+
+            if((stream = HDfdopen(fd, "w")) != NULL) {
+                (void)HDsetvbuf(stream, NULL, _IOLBF, (size_t)0);
+
+                if(NULL == (open_stream = (H5_debug_open_stream_t *)H5MM_malloc(sizeof(H5_debug_open_stream_t)))) {
                     (void)HDfclose(stream);
                     return;
                 } /* end if */
@@ -644,11 +645,15 @@ H5_debug_mask(const char *s)
                 open_stream->next = H5_debug_g.open_stream;
                 H5_debug_g.open_stream = open_stream;
             } /* end if */
-	    s = rest;
-	} else {
-	    s++;
-	}
-    }
+
+            s = rest;
+        } else {
+            s++;
+        } /* end if-else */
+    } /* end while */
+
+    return;
+
 } /* end H5_debug_mask() */
 
 #ifdef H5_HAVE_PARALLEL
diff --git a/src/H5B.c b/src/H5B.c
index 3b34c4d..9182d25 100644
--- a/src/H5B.c
+++ b/src/H5B.c
@@ -1734,14 +1734,13 @@ H5B_shared_new(const H5F_t *f, const H5B_class_t *type, size_t sizeof_rkey)
 	    (shared->two_k + 1) * shared->sizeof_rkey);	/*keys		*/
     HDassert(shared->sizeof_rnode);
 
-    /* Allocate shared buffers */
+    /* Allocate and clear shared buffers */
     if(NULL == (shared->page = H5FL_BLK_MALLOC(page, shared->sizeof_rnode)))
-	HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree page")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(shared->page, 0, shared->sizeof_rnode);
-#endif /* H5_CLEAR_MEMORY */
+        HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree page")
+    HDmemset(shared->page, 0, shared->sizeof_rnode);
+
     if(NULL == (shared->nkey = H5FL_SEQ_MALLOC(size_t, (size_t)(shared->two_k + 1))))
-	HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree native keys")
+        HGOTO_ERROR(H5E_BTREE, H5E_CANTALLOC, NULL, "memory allocation failed for B-tree native keys")
 
     /* Initialize the offsets into the native key buffer */
     for(u = 0; u < (shared->two_k + 1); u++)
diff --git a/src/H5B2cache.c b/src/H5B2cache.c
index 2c40761..928a7ee 100644
--- a/src/H5B2cache.c
+++ b/src/H5B2cache.c
@@ -890,10 +890,8 @@ H5B2__cache_int_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED le
     /* Sanity check */
     HDassert((size_t)(image - (uint8_t *)_image) <= len);
 
-#ifdef H5_CLEAR_MEMORY
     /* Clear rest of internal node */
     HDmemset(image, 0, len - (size_t)(image - (uint8_t *)_image));
-#endif /* H5_CLEAR_MEMORY */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
@@ -1300,10 +1298,8 @@ H5B2__cache_leaf_serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED l
     /* Sanity check */
     HDassert((size_t)(image - (uint8_t *)_image) <= len);
 
-#ifdef H5_CLEAR_MEMORY
     /* Clear rest of leaf node */
     HDmemset(image, 0, len - (size_t)(image - (uint8_t *)_image));
-#endif /* H5_CLEAR_MEMORY */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5B2hdr.c b/src/H5B2hdr.c
index 0676f30..578eeb9 100644
--- a/src/H5B2hdr.c
+++ b/src/H5B2hdr.c
@@ -153,9 +153,7 @@ H5B2__hdr_init(H5B2_hdr_t *hdr, const H5B2_create_t *cparam, void *ctx_udata,
     /* Allocate "page" for node I/O */
     if(NULL == (hdr->page = H5FL_BLK_MALLOC(node_page, hdr->node_size)))
         HGOTO_ERROR(H5E_BTREE, H5E_NOSPACE, FAIL, "memory allocation failed")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(hdr->page, 0, hdr->node_size);
-#endif /* H5_CLEAR_MEMORY */
+    HDmemset(hdr->page, 0, hdr->node_size);
 
     /* Allocate array of node info structs */
     if(NULL == (hdr->node_info = H5FL_SEQ_MALLOC(H5B2_node_info_t, (size_t)(hdr->depth + 1))))
diff --git a/src/H5B2int.c b/src/H5B2int.c
index a9c9ecc..aefb189 100644
--- a/src/H5B2int.c
+++ b/src/H5B2int.c
@@ -2962,17 +2962,15 @@ H5B2__create_leaf(H5B2_hdr_t *hdr, hid_t dxpl_id, void *parent, H5B2_node_ptr_t
 
     /* Increment ref. count on B-tree header */
     if(H5B2__hdr_incr(hdr) < 0)
-	HGOTO_ERROR(H5E_BTREE, H5E_CANTINC, FAIL, "can't increment ref. count on B-tree header")
+        HGOTO_ERROR(H5E_BTREE, H5E_CANTINC, FAIL, "can't increment ref. count on B-tree header")
 
     /* Share B-tree header information */
     leaf->hdr = hdr;
 
     /* Allocate space for the native keys in memory */
     if(NULL == (leaf->leaf_native = (uint8_t *)H5FL_FAC_MALLOC(hdr->node_info[0].nat_rec_fac)))
-	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree leaf native keys")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(leaf->leaf_native, 0, hdr->cls->nrec_size * hdr->node_info[0].max_nrec);
-#endif /* H5_CLEAR_MEMORY */
+        HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree leaf native keys")
+    HDmemset(leaf->leaf_native, 0, hdr->cls->nrec_size * hdr->node_info[0].max_nrec);
 
     /* Set number of records */
     leaf->nrec = 0;
@@ -2986,15 +2984,15 @@ HDmemset(leaf->leaf_native, 0, hdr->cls->nrec_size * hdr->node_info[0].max_nrec)
 
     /* Allocate space on disk for the leaf */
     if(HADDR_UNDEF == (node_ptr->addr = H5MF_alloc(hdr->f, H5FD_MEM_BTREE, dxpl_id, (hsize_t)hdr->node_size)))
-	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "file allocation failed for B-tree leaf node")
+        HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "file allocation failed for B-tree leaf node")
 
     /* Cache the new B-tree node */
     if(H5AC_insert_entry(hdr->f, dxpl_id, H5AC_BT2_LEAF, node_ptr->addr, leaf, H5AC__NO_FLAGS_SET) < 0)
-	HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "can't add B-tree leaf to cache")
+        HGOTO_ERROR(H5E_BTREE, H5E_CANTINIT, FAIL, "can't add B-tree leaf to cache")
 
 done:
     if(ret_value < 0) {
-	if(leaf)
+        if(leaf)
             if(H5B2__leaf_free(leaf) < 0)
                 HDONE_ERROR(H5E_BTREE, H5E_CANTFREE, FAIL, "unable to release v2 B-tree leaf node")
     } /* end if */
@@ -3092,16 +3090,12 @@ H5B2__create_internal(H5B2_hdr_t *hdr, hid_t dxpl_id, void *parent,
     /* Allocate space for the native keys in memory */
     if(NULL == (internal->int_native = (uint8_t *)H5FL_FAC_MALLOC(hdr->node_info[depth].nat_rec_fac)))
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree internal native keys")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(internal->int_native, 0, hdr->cls->nrec_size * hdr->node_info[depth].max_nrec);
-#endif /* H5_CLEAR_MEMORY */
+    HDmemset(internal->int_native, 0, hdr->cls->nrec_size * hdr->node_info[depth].max_nrec);
 
     /* Allocate space for the node pointers in memory */
     if(NULL == (internal->node_ptrs = (H5B2_node_ptr_t *)H5FL_FAC_MALLOC(hdr->node_info[depth].node_ptr_fac)))
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed for B-tree internal node pointers")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(internal->node_ptrs, 0, sizeof(H5B2_node_ptr_t) * (hdr->node_info[depth].max_nrec + 1));
-#endif /* H5_CLEAR_MEMORY */
+    HDmemset(internal->node_ptrs, 0, sizeof(H5B2_node_ptr_t) * (hdr->node_info[depth].max_nrec + 1));
 
     /* Set number of records & depth of the node */
     internal->nrec = 0;
diff --git a/src/H5Bcache.c b/src/H5Bcache.c
index 73136b4..2036257 100644
--- a/src/H5Bcache.c
+++ b/src/H5Bcache.c
@@ -353,10 +353,8 @@ H5B__serialize(const H5F_t *f, void *_image, size_t H5_ATTR_UNUSED len,
     /* Sanity check */
     HDassert((size_t)(image - (uint8_t *)_image) <= len);
 
-#ifdef H5_CLEAR_MEMORY
     /* Clear rest of node */
     HDmemset(image, 0, len - (size_t)(image - (uint8_t *)_image));
-#endif /* H5_CLEAR_MEMORY */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5Dcontig.c b/src/H5Dcontig.c
index 6276af1..dfa18fb 100644
--- a/src/H5Dcontig.c
+++ b/src/H5Dcontig.c
@@ -1027,10 +1027,9 @@ H5D__contig_writevv_sieve_cb(hsize_t dst_off, hsize_t src_off, size_t len,
             if(NULL == (dset_contig->sieve_buf = H5FL_BLK_CALLOC(sieve_buf, dset_contig->sieve_buf_size)))
                 HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "memory allocation failed")
 
-#ifdef H5_CLEAR_MEMORY
-if(dset_contig->sieve_size > len)
-    HDmemset(dset_contig->sieve_buf + len, 0, (dset_contig->sieve_size - len));
-#endif /* H5_CLEAR_MEMORY */
+            /* Clear memory */
+            if(dset_contig->sieve_size > len)
+                HDmemset(dset_contig->sieve_buf + len, 0, (dset_contig->sieve_size - len));
 
             /* Determine the new sieve buffer size & location */
             dset_contig->sieve_loc = addr;
diff --git a/src/H5FDcore.c b/src/H5FDcore.c
index f4aa240..778baa0 100644
--- a/src/H5FDcore.c
+++ b/src/H5FDcore.c
@@ -1295,9 +1295,7 @@ H5FD__core_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN
                 HGOTO_ERROR(H5E_FILE, H5E_CANTALLOC, FAIL, "unable to allocate memory block of %llu bytes", (unsigned long long)new_eof)
         } /* end else */
 
-#ifdef H5_CLEAR_MEMORY
         HDmemset(x + file->eof, 0, (size_t)(new_eof - file->eof));
-#endif /* H5_CLEAR_MEMORY */
         file->mem = x;
 
         file->eof = new_eof;
@@ -1469,10 +1467,8 @@ H5FD__core_truncate(H5FD_t *_file, hid_t H5_ATTR_UNUSED dxpl_id, hbool_t closing
                     HGOTO_ERROR(H5E_FILE, H5E_CANTALLOC, FAIL, "unable to allocate memory block")
             } /* end else */
 
-#ifdef H5_CLEAR_MEMORY
             if(file->eof < new_eof)
                 HDmemset(x + file->eof, 0, (size_t)(new_eof - file->eof));
-#endif /* H5_CLEAR_MEMORY */
             file->mem = x;
 
             /* Update backing store, if using it and if closing */
diff --git a/src/H5Faccum.c b/src/H5Faccum.c
index d8cd614..ef7c827 100644
--- a/src/H5Faccum.c
+++ b/src/H5Faccum.c
@@ -164,9 +164,9 @@ H5F__accum_read(const H5F_io_info_t *fio_info, H5FD_mem_t type, haddr_t addr,
 
                     /* Note the new buffer size */
                     accum->alloc_size = new_alloc_size;
-#ifdef H5_CLEAR_MEMORY
-    HDmemset(accum->buf + accum->size, 0, (accum->alloc_size - accum->size));
-#endif /* H5_CLEAR_MEMORY */
+
+                    /* Clear the memory */
+                    HDmemset(accum->buf + accum->size, 0, (accum->alloc_size - accum->size));
                 } /* end if */
 
                 /* Read the part before the metadata accumulator */
@@ -395,9 +395,9 @@ H5F__accum_adjust(H5F_meta_accum_t *accum, const H5F_io_info_t *fio_info,
             /* Update accumulator info */
             accum->buf = new_buf;
             accum->alloc_size = new_size;
-#ifdef H5_CLEAR_MEMORY
-HDmemset(accum->buf + accum->size, 0, (accum->alloc_size - (accum->size + size)));
-#endif /* H5_CLEAR_MEMORY */
+
+            /* Clear the memory */
+            HDmemset(accum->buf + accum->size, 0, (accum->alloc_size - (accum->size + size)));
         } /* end if */
     } /* end if */
 
@@ -628,9 +628,9 @@ H5F__accum_write(const H5F_io_info_t *fio_info, H5FD_mem_t type, haddr_t addr,
 
                             /* Note the new buffer size */
                             accum->alloc_size = new_alloc_size;
-#ifdef H5_CLEAR_MEMORY
-HDmemset(accum->buf + size, 0, (accum->alloc_size - size));
-#endif /* H5_CLEAR_MEMORY */
+
+                            /* Clear the memory */
+                            HDmemset(accum->buf + size, 0, (accum->alloc_size - size));
                         } /* end if */
 
                         /* Copy the new metadata to the buffer */
@@ -661,6 +661,7 @@ HDmemset(accum->buf + size, 0, (accum->alloc_size - size));
                     /* Check if we need to resize the buffer */
                     if(size > accum->alloc_size) {
                         size_t new_size;        /* New size of accumulator */
+                        size_t clear_size;      /* Size of memory that needs clearing */
 
                         /* Adjust the buffer size to be a power of 2 that is large enough to hold data */
                         new_size = (size_t)1 << (1 + H5VM_log2_gen((uint64_t)(size - 1)));
@@ -671,12 +672,10 @@ HDmemset(accum->buf + size, 0, (accum->alloc_size - size));
 
                         /* Note the new buffer size */
                         accum->alloc_size = new_size;
-#ifdef H5_CLEAR_MEMORY
-{
-size_t clear_size = MAX(accum->size, size);
-HDmemset(accum->buf + clear_size, 0, (accum->alloc_size - clear_size));
-}
-#endif /* H5_CLEAR_MEMORY */
+
+                        /* Clear the memory */
+                        clear_size = MAX(accum->size, size);
+                        HDmemset(accum->buf + clear_size, 0, (accum->alloc_size - clear_size));
                     } /* end if */
                     else {
                         /* Check if we should shrink the accumulator buffer */
@@ -721,9 +720,9 @@ HDmemset(accum->buf + clear_size, 0, (accum->alloc_size - clear_size));
 
                     /* Note the new buffer size */
                     accum->alloc_size = new_size;
-#ifdef H5_CLEAR_MEMORY
-HDmemset(accum->buf + size, 0, (accum->alloc_size - size));
-#endif /* H5_CLEAR_MEMORY */
+
+                    /* Clear the memory */
+                    HDmemset(accum->buf + size, 0, (accum->alloc_size - size));
                 } /* end if */
 
                 /* Update the metadata accumulator information */
diff --git a/src/H5Gcache.c b/src/H5Gcache.c
index a4f9530..ed1c4a3 100644
--- a/src/H5Gcache.c
+++ b/src/H5Gcache.c
@@ -328,10 +328,8 @@ H5G__cache_node_serialize(const H5F_t *f, void *_image, size_t len,
     if(H5G__ent_encode_vec(f, &image, sym->entry, sym->nsyms) < 0)
         HGOTO_ERROR(H5E_SYM, H5E_CANTENCODE, FAIL, "can't serialize")
 
-#ifdef H5_CLEAR_MEMORY
     /* Clear rest of symbol table node */
     HDmemset(image, 0, len - (size_t)(image - (uint8_t *)_image));
-#endif /* H5_CLEAR_MEMORY */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5Gprivate.h b/src/H5Gprivate.h
index 1ab5522..2ef99fd 100644
--- a/src/H5Gprivate.h
+++ b/src/H5Gprivate.h
@@ -37,13 +37,6 @@
 #include "H5RSprivate.h"        /* Reference-counted strings            */
 
 /*
- * Define this to enable debugging.
- */
-#ifdef NDEBUG
-#  undef H5G_DEBUG
-#endif
-
-/*
  * The disk size for a symbol table entry...
  */
 #define H5G_SIZEOF_SCRATCH      16
diff --git a/src/H5HFdblock.c b/src/H5HFdblock.c
index 73db840..1272ab0 100644
--- a/src/H5HFdblock.c
+++ b/src/H5HFdblock.c
@@ -146,9 +146,7 @@ H5HF_man_dblock_create(hid_t dxpl_id, H5HF_hdr_t *hdr, H5HF_indirect_t *par_iblo
 /* XXX: Change to using free-list factories */
     if((dblock->blk = H5FL_BLK_MALLOC(direct_block, dblock->size)) == NULL)
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(dblock->blk, 0, dblock->size);
-#endif /* H5_CLEAR_MEMORY */
+    HDmemset(dblock->blk, 0, dblock->size);
 
     dblock->write_buf = NULL;
     dblock->write_size = 0;
diff --git a/src/H5HFtiny.c b/src/H5HFtiny.c
index bdfe30d..711ceb9 100644
--- a/src/H5HFtiny.c
+++ b/src/H5HFtiny.c
@@ -177,10 +177,9 @@ HDfprintf(stderr, "%s: obj_size = %Zu\n", FUNC, obj_size);
                 ((enc_obj_size & H5HF_TINY_MASK_EXT_1) >> 8));
         *id++ = enc_obj_size & H5HF_TINY_MASK_EXT_2;
     } /* end else */
+
     HDmemcpy(id, obj, obj_size);
-#ifdef H5_CLEAR_MEMORY
-HDmemset(id + obj_size, 0, (hdr->id_len - ((size_t)1 + (size_t)hdr->tiny_len_extended + obj_size)));
-#endif /* H5_CLEAR_MEMORY */
+    HDmemset(id + obj_size, 0, (hdr->id_len - ((size_t)1 + (size_t)hdr->tiny_len_extended + obj_size)));
 
     /* Update statistics about heap */
     hdr->tiny_size += obj_size;
diff --git a/src/H5HG.c b/src/H5HG.c
index 41c5007..f95b607 100644
--- a/src/H5HG.c
+++ b/src/H5HG.c
@@ -154,22 +154,20 @@ H5HG_create(H5F_t *f, hid_t dxpl_id, size_t size)
     /* Create it */
     H5_CHECK_OVERFLOW(size, size_t, hsize_t);
     if(HADDR_UNDEF == (addr = H5MF_alloc(f, H5FD_MEM_GHEAP, dxpl_id, (hsize_t)size)))
-	HGOTO_ERROR(H5E_HEAP, H5E_CANTINIT, HADDR_UNDEF, "unable to allocate file space for global heap")
+        HGOTO_ERROR(H5E_HEAP, H5E_CANTINIT, HADDR_UNDEF, "unable to allocate file space for global heap")
     if(NULL == (heap = H5FL_MALLOC(H5HG_heap_t)))
-	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed")
+        HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed")
     heap->addr = addr;
     heap->size = size;
     heap->shared = H5F_SHARED(f);
 
     if(NULL == (heap->chunk = H5FL_BLK_MALLOC(gheap_chunk, size)))
-	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(heap->chunk, 0, size);
-#endif /* H5_CLEAR_MEMORY */
+        HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed")
+    HDmemset(heap->chunk, 0, size);
     heap->nalloc = H5HG_NOBJS(f, size);
     heap->nused = 1; /* account for index 0, which is used for the free object */
     if(NULL == (heap->obj = H5FL_SEQ_MALLOC(H5HG_obj_t, heap->nalloc)))
-	HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed")
+        HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, HADDR_UNDEF, "memory allocation failed")
 
     /* Initialize the header */
     HDmemcpy(heap->chunk, H5HG_MAGIC, (size_t)H5_SIZEOF_MAGIC);
@@ -452,9 +450,7 @@ H5HG_extend(H5F_t *f, hid_t dxpl_id, haddr_t addr, size_t need)
     /* Re-allocate the heap information in memory */
     if(NULL == (new_chunk = H5FL_BLK_REALLOC(gheap_chunk, heap->chunk, (heap->size + need))))
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "new heap allocation failed")
-#ifdef H5_CLEAR_MEMORY
-HDmemset(new_chunk + heap->size, 0, need);
-#endif /* H5_CLEAR_MEMORY */
+    HDmemset(new_chunk + heap->size, 0, need);
 
     /* Adjust the size of the heap */
     old_size = heap->size;
diff --git a/src/H5HLcache.c b/src/H5HLcache.c
index 678da7f..d0dde89 100644
--- a/src/H5HLcache.c
+++ b/src/H5HLcache.c
@@ -630,10 +630,8 @@ H5HL__cache_prefix_serialize(const H5F_t *f, void *_image, size_t len,
         /* Sanity check */
         HDassert((size_t)(image - (uint8_t *)_image) <= len);
 
-#ifdef H5_CLEAR_MEMORY
         /* Clear rest of local heap */
         HDmemset(image, 0, len - (size_t)(image - (uint8_t *)_image));
-#endif /* H5_CLEAR_MEMORY */
     } /* end else */
 
     FUNC_LEAVE_NOAPI(SUCCEED)
diff --git a/src/H5MFprivate.h b/src/H5MFprivate.h
index bb07f4e..22ed308 100644
--- a/src/H5MFprivate.h
+++ b/src/H5MFprivate.h
@@ -21,8 +21,6 @@
  *
  * Purpose:             Private header file for file memory management.
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 #ifndef _H5MFprivate_H
@@ -36,13 +34,6 @@
 /* Library Private Macros */
 /**************************/
 
-/*
- * Feature: Define H5MF_DEBUG on the compiler command line if you want to
- *	    see diagnostics from this layer.
- */
-#ifdef NDEBUG
-#  undef H5MF_DEBUG
-#endif
 
 /****************************/
 /* Library Private Typedefs */
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index 03a4668..44872ba 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -2517,8 +2517,8 @@ done:
  *
  *              If the length of the filename, which determines the
  *              required value of size, is unknown, a preliminary call to
- *              H5Pget_virtual_filename with the last two parameters set
- *              to NULL can be made.  The return value of this call will
+ *              H5Pget_virtual_filename with 'name' set to NULL and 'size'
+ *              set to zero can be made. The return value of this call will
  *              be the size in bytes of the filename.  That value, plus 1
  *              for a NULL terminator, is then assigned to size for a
  *              second H5Pget_virtual_filename call, which will retrieve
@@ -2578,14 +2578,14 @@ done:
  *              additional characters, if any, are not returned to the
  *              user application.
  *
- *              If the length of the filename, which determines the
+ *              If the length of the dataset name, which determines the
  *              required value of size, is unknown, a preliminary call to
- *              H5Pget_virtual_dsetname with the last two parameters set
- *              to NULL can be made.  The return value of this call will
- *              be the size in bytes of the filename.  That value, plus 1
+ *              H5Pget_virtual_dsetname with 'name' set to NULL and 'size'
+ *              set to zero can be made.  The return value of this call will
+ *              be the size in bytes of the dataset name.  That value, plus 1
  *              for a NULL terminator, is then assigned to size for a
  *              second H5Pget_virtual_dsetname call, which will retrieve
- *              the actual filename. 
+ *              the actual dataset name. 
  *
  * Return:      Returns the length of the name if successful, otherwise
  *              returns a negative value.
diff --git a/src/H5SMcache.c b/src/H5SMcache.c
index 7b94743..ff2b09f 100644
--- a/src/H5SMcache.c
+++ b/src/H5SMcache.c
@@ -769,9 +769,8 @@ H5SM__cache_list_serialize(const H5F_t *f, void *_image, size_t len,
     /* sanity check */
     HDassert((size_t)(image - (uint8_t *)_image) <= list->header->list_size);
 
-#ifdef H5_CLEAR_MEMORY
+    /* Clear memory */
     HDmemset(image, 0, (list->header->list_size - (size_t)(image - (uint8_t *)_image)));
-#endif /* H5_CLEAR_MEMORY */
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
diff --git a/src/H5STprivate.h b/src/H5STprivate.h
index 892f04a..9b49b07 100644
--- a/src/H5STprivate.h
+++ b/src/H5STprivate.h
@@ -58,7 +58,9 @@ H5_DLL H5ST_ptr_t H5ST_findfirst(H5ST_tree_t *p);
 H5_DLL H5ST_ptr_t H5ST_findnext(H5ST_ptr_t p);
 H5_DLL void *H5ST_remove(H5ST_tree_t *root, const char *s);
 H5_DLL herr_t H5ST_delete(H5ST_tree_t *root, H5ST_ptr_t p);
-H5_DLL herr_t H5ST_dump(H5ST_ptr_t p);
+#ifdef H5ST_DEBUG
+H5_DLL herr_t H5ST_dump(H5ST_tree_t *tree);
+#endif /* H5ST_DEBUG */
 
 #endif /* _H5STprivate_H */
 
diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c
index 0dc12a3..14ca9db 100644
--- a/src/H5Zscaleoffset.c
+++ b/src/H5Zscaleoffset.c
@@ -883,10 +883,8 @@ H5Z_set_local_scaleoffset(hid_t dcpl_id, hid_t type_id, hid_t space_id)
     if(NULL == (type = (H5T_t *)H5I_object_verify(type_id, H5I_DATATYPE)))
 	HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
 
-#ifdef H5_CLEAR_MEMORY
     /* Initialize the parameters to a known state */
     HDmemset(cd_values, 0, sizeof(cd_values));
-#endif /* H5_CLEAR_MEMORY */
 
     /* Get the filter's current parameters */
     if(H5P_get_filter_by_id(dcpl_plist, H5Z_FILTER_SCALEOFFSET, &flags, &cd_nelmts, cd_values, (size_t)0, NULL, NULL) < 0)
@@ -1266,13 +1264,11 @@ H5Z_filter_scaleoffset(unsigned flags, size_t cd_nelmts, const unsigned cd_value
         for(i = 0; i < sizeof(unsigned long long); i++)
             ((unsigned char *)outbuf)[5+i] = (unsigned char)((minval & ((unsigned long long)0xff << i*8)) >> i*8);
 
-#ifdef H5_CLEAR_MEMORY
         /* Zero out remaining, unused bytes */
         /* (Looks like an error in the original determination of how many
          *      bytes would be needed for parameters. - QAK, 2010/08/19)
          */
         HDmemset(outbuf + 13, 0, (size_t)8);
-#endif /* H5_CLEAR_MEMORY */
 
         /* special case: minbits equal to full precision */
         if(minbits == p.size * 8) {
diff --git a/src/libhdf5.settings.in b/src/libhdf5.settings.in
index 90224c1..3bb2936 100644
--- a/src/libhdf5.settings.in
+++ b/src/libhdf5.settings.in
@@ -3,40 +3,47 @@
 
 General Information:
 -------------------
-		   HDF5 Version: @H5_VERSION@
-		  Configured on: @CONFIG_DATE@
-		  Configured by: @CONFIG_USER@
-		 Configure mode: @CONFIG_MODE@
-		    Host system: @host_cpu@-@host_vendor@-@host_os@
-	      Uname information: @UNAME_INFO@
-		       Byte sex: @BYTESEX@
-		      Libraries: @STATIC_SHARED@
-	     Installation point: @prefix@
+                   HDF5 Version: @H5_VERSION@
+                  Configured on: @CONFIG_DATE@
+                  Configured by: @CONFIG_USER@
+                    Host system: @host_cpu@-@host_vendor@-@host_os@
+              Uname information: @UNAME_INFO@
+                       Byte sex: @BYTESEX@
+             Installation point: @prefix@
 
 Compiling Options:
 ------------------
-               Compilation Mode: @CONFIG_MODE@
-                     C Compiler: @CC_VERSION@
-                         CFLAGS: @CFLAGS@
-                      H5_CFLAGS: @H5_CFLAGS@
-                      AM_CFLAGS: @AM_CFLAGS@
-                       CPPFLAGS: @CPPFLAGS@
-                    H5_CPPFLAGS: @H5_CPPFLAGS@
-                    AM_CPPFLAGS: @AM_CPPFLAGS@
-               Shared C Library: @enable_shared@
-               Static C Library: @enable_static@
+                     Build Mode: @BUILD_MODE@
+              Debugging Symbols: @SYMBOLS@
+                        Asserts: @ASSERTS@
+                      Profiling: @PROFILING@
+             Optimization Level: @OPTIMIZATION@
+
+Linking Options:
+----------------
+                      Libraries: @STATIC_SHARED@
   Statically Linked Executables: @LT_STATIC_EXEC@
                         LDFLAGS: @LDFLAGS@
                      H5_LDFLAGS: @H5_LDFLAGS@
                      AM_LDFLAGS: @AM_LDFLAGS@
- 	 	Extra libraries: @LIBS@
- 		       Archiver: @AR@
- 		 	 Ranlib: @RANLIB@
- 	      Debugged Packages: @DEBUG_PKG@
-		    API Tracing: @TRACE_API@
+                Extra libraries: @LIBS@
+                       Archiver: @AR@
+                         Ranlib: @RANLIB@
 
 Languages:
 ----------
+                              C: yes
+                     C Compiler: @CC_VERSION@
+                       CPPFLAGS: @CPPFLAGS@
+                    H5_CPPFLAGS: @H5_CPPFLAGS@
+                    AM_CPPFLAGS: @AM_CPPFLAGS@
+                        C Flags: @CFLAGS@
+                     H5 C Flags: @H5_CFLAGS@
+                     AM C Flags: @AM_CFLAGS@
+               Shared C Library: @enable_shared@
+               Static C Library: @enable_static@
+
+
                         Fortran: @HDF_FORTRAN@
 @BUILD_FORTRAN_CONDITIONAL_TRUE@               Fortran Compiler: @FC_VERSION@
 @BUILD_FORTRAN_CONDITIONAL_TRUE@                  Fortran Flags: @FCFLAGS@
@@ -56,17 +63,19 @@ Languages:
 Features:
 ---------
                   Parallel HDF5: @PARALLEL@
-             High Level library: @HDF5_HL@
+             High-level library: @HDF5_HL@
                    Threadsafety: @THREADSAFE@
-            Default API Mapping: @DEFAULT_API_VERSION@
- With Deprecated Public Symbols: @DEPRECATED_SYMBOLS@
+            Default API mapping: @DEFAULT_API_VERSION@
+ With deprecated public symbols: @DEPRECATED_SYMBOLS@
          I/O filters (external): @EXTERNAL_FILTERS@
                             MPE: @MPE@
                      Direct VFD: @DIRECT_VFD@
                         dmalloc: @HAVE_DMALLOC@
-Clear file buffers before write: @CLEARFILEBUF@
+ Packages w/ extra debug output: @INTERNAL_DEBUG_OUTPUT@
+                    API tracing: @TRACE_API@
            Using memory checker: @USINGMEMCHECKER@
 Memory allocation sanity checks: @MEMORYALLOCSANITYCHECK@
-         Function Stack Tracing: @CODESTACK@
-      Strict File Format Checks: @STRICT_FORMAT_CHECKS@
-   Optimization Instrumentation: @INSTRUMENT@
+            Metadata trace file: @METADATATRACEFILE@
+         Function stack tracing: @CODESTACK@
+      Strict file format checks: @STRICT_FORMAT_CHECKS@
+   Optimization instrumentation: @INSTRUMENT_LIBRARY@