[svn-r19272] Description:

    Close out various resource leaks and usages of uninitialized memory that
were flagged by valgrind.  [There's still some more valgrind warnings, but
it's better now... :-/ ]

    Also clean up warnings and code formatting.

Tested on:
    Mac OS X/32 10.6.4 (amazon) w/debug & valgrind
    (h5committest forthcoming)

17 files changed, 139 insertions, 164 deletions

diff --git a/src/H5A.c b/src/H5A.c
index 852e058..722af25 100644
--- a/src/H5A.c
+++ b/src/H5A.c
@@ -2424,18 +2424,19 @@ H5A_close(H5A_t *attr)
         HGOTO_ERROR(H5E_ATTR, H5E_CANTRELEASE, FAIL, "can't release object header info")
 
     /* Reference count can be 0.  It only happens when H5A_create fails. */
-    if(1 >= attr->shared->nrefs) {
+    if(attr->shared->nrefs <= 1) {
         /* Free dynamicly allocated items */
         if(H5A_free(attr) < 0)
             HGOTO_ERROR(H5E_ATTR, H5E_CANTRELEASE, FAIL, "can't release attribute info")
 
         /* Destroy shared attribute struct */
         attr->shared = H5FL_FREE(H5A_shared_t, attr->shared);
-    } else if(attr->shared->nrefs > 1) {
+    } /* end if */
+    else {
         /* There are other references to the shared part of the attribute.
          * Only decrement the reference count. */
         --attr->shared->nrefs;
-    }
+    } /* end else */
 
     /* Free group hierarchy path */
     if(H5G_name_free(&(attr->path)) < 0)
diff --git a/src/H5Aint.c b/src/H5Aint.c
index ba30506..101d604 100644
--- a/src/H5Aint.c
+++ b/src/H5Aint.c
@@ -1149,8 +1149,8 @@ H5A_dense_copy_file_cb(const H5A_t *attr_src, void *_udata)
     HDassert(udata->file);
     HDassert(udata->cpy_info);
 
-    if ( NULL == (attr_dst=H5A_attr_copy_file(attr_src, udata->file,
-        udata->recompute_size, udata->cpy_info,  udata->dxpl_id)))
+    if(NULL == (attr_dst = H5A_attr_copy_file(attr_src, udata->file,
+            udata->recompute_size, udata->cpy_info,  udata->dxpl_id)))
         HGOTO_ERROR(H5E_ATTR, H5E_CANTCOPY, H5_ITER_ERROR, "can't copy attribute")
 
     /* Reset shared location information */
@@ -1168,10 +1168,8 @@ H5A_dense_copy_file_cb(const H5A_t *attr_src, void *_udata)
     H5_END_TAG(H5_ITER_ERROR);
 
 done:
-    if(attr_dst) {
-        (void)H5A_free(attr_dst);
-        attr_dst = H5FL_FREE(H5A_t, attr_dst);
-    } /* end if */
+    if(attr_dst && H5A_close(attr_dst) < 0)
+        HDONE_ERROR(H5E_ATTR, H5E_CLOSEERROR, FAIL, "can't close destination attribute")
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5A_dense_copy_file_cb() */
diff --git a/src/H5Dfill.c b/src/H5Dfill.c
index 467ce4b..f6e07f2 100644
--- a/src/H5Dfill.c
+++ b/src/H5Dfill.c
@@ -585,7 +585,7 @@ H5D_fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts, hid_t dxpl_id)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
 
     /* Replicate the fill value into the cached buffer */
-    H5V_array_fill(fb_info->fill_buf, fb_info->fill_buf, fb_info->mem_elmt_size, nelmts);
+    H5V_array_fill((void *)((unsigned char *)fb_info->fill_buf + fb_info->mem_elmt_size), fb_info->fill_buf, fb_info->mem_elmt_size, nelmts);
 
     /* Reset the entire background buffer, if necessary */
     if(H5T_path_bkg(fb_info->mem_to_dset_tpath))
@@ -606,12 +606,14 @@ H5D_fill_refill_vl(H5D_fill_buf_info_t *fb_info, size_t nelmts, hid_t dxpl_id)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTCONVERT, FAIL, "data type conversion failed")
 
 done:
-    if (buf) {
+    if(buf) {
         /* Free dynamically allocated VL elements in fill buffer */
-        if (fb_info->fill->type)
-            H5T_vlen_reclaim_elmt(buf, fb_info->fill->type, dxpl_id);
+        if(fb_info->fill->type)
+            if(H5T_vlen_reclaim_elmt(buf, fb_info->fill->type, dxpl_id) < 0)
+                HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't reclaim vlen element")
         else
-            H5T_vlen_reclaim_elmt(buf, fb_info->mem_type, dxpl_id);
+            if(H5T_vlen_reclaim_elmt(buf, fb_info->mem_type, dxpl_id) < 0)
+                HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "can't reclaim vlen element")
 
         /* Free temporary fill buffer */
         if(fb_info->fill_free_func)
diff --git a/src/H5F.c b/src/H5F.c
index c1d04e0..f1a4b0c 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -1197,12 +1197,18 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
 	tent_flags = flags;
 
     if(NULL == (lf = H5FD_open(name, tent_flags, fapl_id, HADDR_UNDEF))) {
-	if(tent_flags == flags)
-	    HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file")
+	if(tent_flags == flags) {
+            time_t mytime = HDtime(NULL);
+
+	    HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: time = %s, name = '%s', tent_flags = %x", HDctime(&mytime), name, tent_flags)
+        } /* end if */
         H5E_clear_stack(NULL);
 	tent_flags = flags;
-	if(NULL == (lf = H5FD_open(name, tent_flags, fapl_id, HADDR_UNDEF)))
-	    HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file")
+	if(NULL == (lf = H5FD_open(name, tent_flags, fapl_id, HADDR_UNDEF))) {
+            time_t mytime = HDtime(NULL);
+
+	    HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: time = %s, name = '%s', tent_flags = %x", HDctime(&mytime), name, tent_flags)
+        } /* end if */
     } /* end if */
 
     /* Is the file already open? */
diff --git a/src/H5FDsec2.c b/src/H5FDsec2.c
index 7e54063..d9fa4d9 100644
--- a/src/H5FDsec2.c
+++ b/src/H5FDsec2.c
@@ -356,9 +356,8 @@ H5FD_sec2_open(const char *name, unsigned flags, hid_t fapl_id, haddr_t maxaddr)
     /* Open the file */
     if((fd = HDopen(name, o_flags, 0666)) < 0) {
         int myerrno = errno;
-        time_t mytime = HDtime(NULL);
 
-        HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: time = %s, name = '%s', errno = %d, error message = '%s', flags = %x, o_flags = %x", HDctime(&mytime), name, myerrno, HDstrerror(myerrno), flags, (unsigned)o_flags);
+        HGOTO_ERROR(H5E_FILE, H5E_CANTOPENFILE, NULL, "unable to open file: name = '%s', errno = %d, error message = '%s', flags = %x, o_flags = %x", name, myerrno, HDstrerror(myerrno), flags, (unsigned)o_flags);
     } /* end if */
     if(HDfstat(fd, &sb) < 0)
         HSYS_GOTO_ERROR(H5E_FILE, H5E_BADFILE, NULL, "unable to fstat file")
@@ -822,9 +821,9 @@ H5FD_sec2_write(H5FD_t *_file, H5FD_mem_t UNUSED type, hid_t UNUSED dxpl_id, had
     if(!H5F_addr_defined(addr))
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "addr undefined, addr = %llu", (unsigned long long)addr)
     if(REGION_OVERFLOW(addr, size))
-        HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu", (unsigned long long)addr)
+        HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu, size = %llu", (unsigned long long)addr, (unsigned long long)size)
     if((addr + size) > file->eoa)
-        HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu", (unsigned long long)addr)
+        HGOTO_ERROR(H5E_ARGS, H5E_OVERFLOW, FAIL, "addr overflow, addr = %llu, size = %llu, eoa = %llu", (unsigned long long)addr, (unsigned long long)size, (unsigned long long)file->eoa)
 
     /* Seek to the correct location */
     if((addr != file->pos || OP_WRITE != file->op) &&
diff --git a/src/H5Faccum.c b/src/H5Faccum.c
index c170671..975a6e8 100644
--- a/src/H5Faccum.c
+++ b/src/H5Faccum.c
@@ -648,6 +648,9 @@ HDmemset(f->shared->accum.buf + clear_size, 0, (f->shared->accum.alloc_size - cl
 
                 /* Note the new buffer size */
                 f->shared->accum.alloc_size = new_size;
+#ifdef H5_CLEAR_MEMORY
+HDmemset(f->shared->accum.buf + size, 0, (f->shared->accum.alloc_size - size));
+#endif /* H5_CLEAR_MEMORY */
             } /* end if */
 
             /* Update the metadata accumulator information */
diff --git a/src/H5Gent.c b/src/H5Gent.c
index 69037d4..a2e6159 100644
--- a/src/H5Gent.c
+++ b/src/H5Gent.c
@@ -248,8 +248,8 @@ H5G_ent_encode(const H5F_t *f, uint8_t **pp, const H5G_entry_t *ent)
     } /* end else */
 
     /* fill with zero */
-    while(*pp < p_ret)
-        *(*pp)++ = 0;
+    if(*pp < p_ret)
+        HDmemset(*pp, 0, (p_ret - *pp));
     *pp = p_ret;
 
 done:
diff --git a/src/H5HFtiny.c b/src/H5HFtiny.c
index ce91bd1..f11b6c0 100644
--- a/src/H5HFtiny.c
+++ b/src/H5HFtiny.c
@@ -178,6 +178,9 @@ HDfprintf(stderr, "%s: obj_size = %Zu\n", FUNC, obj_size);
         *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 - (1 + hdr->tiny_len_extended + obj_size)));
+#endif /* H5_CLEAR_MEMORY */
 
     /* Update statistics about heap */
     hdr->tiny_size += obj_size;
diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c
index 8e55503..7a10765 100644
--- a/src/H5Ocopy.c
+++ b/src/H5Ocopy.c
@@ -575,7 +575,15 @@ H5O_copy_header_real(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
     addr_new = oh_dst->chunk[0].addr;
 
     /* Create memory image for the new chunk */
-    if(NULL == (oh_dst->chunk[0].image = H5FL_BLK_MALLOC(chunk_image, (size_t)dst_oh_size)))
+    /* Note: we use calloc() instead of malloc() here because older versions of
+     *  some messages don't initialize "unused" bytes and because we want to
+     *  write out the same version of the object header and older versions of
+     *  object headers aligned messages.  In both those situations, it's
+     *  complex and error-prone to determine all the proper ways/places to
+     *  clear to zero bytes, so we just set the buffer to zero's here.
+     *  (QAK - 2010/08/17)
+     */
+    if(NULL == (oh_dst->chunk[0].image = H5FL_BLK_CALLOC(chunk_image, (size_t)dst_oh_size)))
         HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, FAIL, "memory allocation failed")
 
     /* Set dest. chunk information */
diff --git a/src/H5Odtype.c b/src/H5Odtype.c
index fec695e..51694a3 100644
--- a/src/H5Odtype.c
+++ b/src/H5Odtype.c
@@ -1272,7 +1272,7 @@ H5O_dtype_size(const H5F_t *f, const void *_mesg)
                     /* (starting with version 3 of the datatype message, use the minimum # of bytes required) */
                     if(dt->shared->version >= H5O_DTYPE_VERSION_3)
                         ret_value += offset_nbytes; 	/*member offset*/
-                    if(dt->shared->version >= H5O_DTYPE_VERSION_2)
+                    else if(dt->shared->version == H5O_DTYPE_VERSION_2)
                         ret_value += 4; 	/*member offset*/
                     else
                         ret_value += 4 +	/*member offset*/
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index 67dbf4d..e413598 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -584,6 +584,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
     H5D_copy_file_ud_t *udata = (H5D_copy_file_ud_t *)_udata;   /* Dataset copying user data */
     H5O_layout_t       *layout_src = (H5O_layout_t *) mesg_src;
     H5O_layout_t       *layout_dst = NULL;
+    hbool_t             copied = FALSE;                         /* Whether the data was copied */
     void               *ret_value;                              /* Return value */
 
     FUNC_ENTER_NOAPI_NOINIT(H5O_layout_copy_file)
@@ -607,6 +608,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
                 /* copy compact raw data */
                 if(H5D_compact_copy(file_src, &layout_src->storage.u.compact, file_dst, &layout_dst->storage.u.compact, udata->src_dtype, cpy_info, dxpl_id) < 0)
                     HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy chunked storage")
+                copied = TRUE;
 	    } /* end if */
             break;
 
@@ -615,7 +617,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
              * layout message less than version 3 because versions 1 & 2 would
              * truncate the dimension sizes to 32-bits of information. - QAK 5/26/04
              */
-            if(layout_src->version < 3)
+            if(layout_src->version < H5O_LAYOUT_VERSION_3)
                 layout_dst->storage.u.contig.size = H5S_extent_nelem(udata->src_space_extent) *
                                         H5T_get_size(udata->src_dtype);
 
@@ -623,6 +625,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
                 /* copy contiguous raw data */
                 if(H5D_contig_copy(file_src, &layout_src->storage.u.contig, file_dst, &layout_dst->storage.u.contig, udata->src_dtype, cpy_info, dxpl_id) < 0)
                     HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy contiguous storage")
+                copied = TRUE;
             } /* end if */
             break;
 
@@ -631,6 +634,7 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
                 /* Create chunked layout */
                 if(H5D_chunk_copy(file_src, &layout_src->storage.u.chunk, &layout_src->u.chunk, file_dst, &layout_dst->storage.u.chunk, udata->src_space_extent, udata->src_dtype, udata->common.src_pline, cpy_info, dxpl_id) < 0)
                     HGOTO_ERROR(H5E_OHDR, H5E_CANTCOPY, NULL, "unable to copy chunked storage")
+                copied = TRUE;
             } /* end if */
             break;
 
@@ -638,8 +642,9 @@ H5O_layout_copy_file(H5F_t *file_src, void *mesg_src, H5F_t *file_dst,
             HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "Invalid layout class")
     } /* end switch */
 
-    /* Freed by copy routine */
-    udata->src_dtype = NULL;
+    /* Check if copy routine was invoked (which frees the source datatype) */
+    if(copied)
+        udata->src_dtype = NULL;
 
     /* Set return value */
     ret_value = layout_dst;
diff --git a/src/H5SM.c b/src/H5SM.c
index 8af4d57..a971fb0 100755
--- a/src/H5SM.c
+++ b/src/H5SM.c
@@ -1742,7 +1742,7 @@ H5SM_delete_from_index(H5F_t *f, hid_t dxpl_id, H5O_t *open_oh,
         /* If this returns failure, it means that the message wasn't found.
          * If it succeeds, a copy of the modified message will be returned.
          */
-        if(H5B2_modify(bt2, dxpl_id, &key, H5SM_decr_ref, &message) <0)
+        if(H5B2_modify(bt2, dxpl_id, &key, H5SM_decr_ref, &message) < 0)
 	    HGOTO_ERROR(H5E_SOHM, H5E_NOTFOUND, FAIL, "message not in index")
 
         /* Point to the message */
diff --git a/src/H5SMcache.c b/src/H5SMcache.c
index 4a9338b..1511fd0 100644
--- a/src/H5SMcache.c
+++ b/src/H5SMcache.c
@@ -605,7 +605,7 @@ H5SM_list_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr, H5SM_lis
                 if(H5SM_message_encode(p, &(list->messages[x]), &ctx) < 0)
                     HGOTO_ERROR(H5E_SOHM, H5E_CANTFLUSH, FAIL, "unable to write shared message to disk")
 
-                p+=H5SM_SOHM_ENTRY_SIZE(f);
+                p += H5SM_SOHM_ENTRY_SIZE(f);
                 ++mesgs_written;
             } /* end if */
         } /* end for */
@@ -614,6 +614,9 @@ H5SM_list_flush(H5F_t *f, hid_t dxpl_id, hbool_t destroy, haddr_t addr, H5SM_lis
         /* Compute checksum on buffer */
         computed_chksum = H5_checksum_metadata(buf, (size_t)(p - buf), 0);
         UINT32ENCODE(p, computed_chksum);
+#ifdef H5_CLEAR_MEMORY
+HDmemset(p, 0, (list->header->list_size - (p - buf)));
+#endif /* H5_CLEAR_MEMORY */
 
         /* Write the list to disk */
         HDassert((size_t)(p - buf) <= list->header->list_size);
diff --git a/src/H5SMmessage.c b/src/H5SMmessage.c
index 32ded03..0d41a09 100644
--- a/src/H5SMmessage.c
+++ b/src/H5SMmessage.c
@@ -309,7 +309,7 @@ H5SM_message_encode(uint8_t *raw, const void *_nrecord, void *_ctx)
         *raw++ = 0;     /* reserved (possible flags byte) */
         *raw++ = (uint8_t)message->msg_type_id;
         UINT16ENCODE(raw, message->u.mesg_loc.index);
-        H5F_addr_encode_len(ctx->sizeof_addr, &raw, message->u.mesg_loc.oh_addr);
+        H5F_addr_encode_len((size_t)ctx->sizeof_addr, &raw, message->u.mesg_loc.oh_addr);
     } /* end else */
 
     FUNC_LEAVE_NOAPI(SUCCEED)
@@ -350,7 +350,7 @@ H5SM_message_decode(const uint8_t *raw, void *_nrecord, void *_ctx)
         raw++;          /* reserved */
         message->msg_type_id = *raw++;
         UINT16DECODE(raw, message->u.mesg_loc.index);
-        H5F_addr_decode_len(ctx->sizeof_addr, &raw, &message->u.mesg_loc.oh_addr);
+        H5F_addr_decode_len((size_t)ctx->sizeof_addr, &raw, &message->u.mesg_loc.oh_addr);
     } /* end else */
 
     FUNC_LEAVE_NOAPI(SUCCEED)
diff --git a/src/H5Tvlen.c b/src/H5Tvlen.c
index 95f4086..f1b1f00 100644
--- a/src/H5Tvlen.c
+++ b/src/H5Tvlen.c
@@ -100,8 +100,6 @@ H5T_init_vlen_interface(void)
  * Programmer:	Quincey Koziol
  *              Thursday, May 20, 1999
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 hid_t
@@ -144,8 +142,6 @@ done:
  * Programmer:	Quincey Koziol
  *              Tuesday, November 20, 2001
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 H5T_t *
@@ -315,11 +311,6 @@ done:
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of an hvl_t that is not aligned
- *      properly in _vl.
- *
  *-------------------------------------------------------------------------
  */
 static ssize_t
@@ -357,11 +348,6 @@ H5T_vlen_seq_mem_getlen(const void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, June 12, 2004
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of an hvl_t that is not aligned
- *      properly in _vl.
- *
  *-------------------------------------------------------------------------
  */
 static void *
@@ -399,11 +385,6 @@ H5T_vlen_seq_mem_getptr(void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of an hvl_t that is not aligned
- *      properly in _vl.
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -442,11 +423,6 @@ H5T_vlen_seq_mem_isnull(const H5F_t UNUSED *f, void *_vl)
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of an hvl_t that is not aligned
- *      properly in _vl.
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -489,8 +465,6 @@ H5T_vlen_seq_mem_read(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void *bu
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -548,8 +522,6 @@ done:
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -584,11 +556,6 @@ H5T_vlen_seq_mem_setnull(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of a char * that is not aligned
- *      properly in _vl.
- *
  *-------------------------------------------------------------------------
  */
 static ssize_t
@@ -624,12 +591,6 @@ H5T_vlen_str_mem_getlen(const void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, June 12, 2004
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of a char * that is not aligned
- *      properly in _vl.
- *      Added assertion on _vl.
- *
  *-------------------------------------------------------------------------
  */
 static void *
@@ -665,11 +626,6 @@ H5T_vlen_str_mem_getptr(void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of a char * that is not aligned
- *      properly in _vl.
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -702,11 +658,6 @@ H5T_vlen_str_mem_isnull(const H5F_t UNUSED *f, void *_vl)
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:   Neil Fortner
- *      Friday, August 22, 2008
- *      Changed function to be tolerant of a char * that is not aligned
- *      properly in _vl.
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -748,8 +699,6 @@ H5T_vlen_str_mem_read(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void *bu
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -797,8 +746,6 @@ done:
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -826,8 +773,6 @@ H5T_vlen_str_mem_setnull(H5F_t UNUSED *f, hid_t UNUSED dxpl_id, void *_vl, void
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 static ssize_t
@@ -857,8 +802,6 @@ H5T_vlen_disk_getlen(const void *_vl)
  * Programmer:	Quincey Koziol
  *		Saturday, June 12, 2004
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -884,8 +827,6 @@ H5T_vlen_disk_getptr(void UNUSED *vl)
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 static htri_t
@@ -919,8 +860,6 @@ H5T_vlen_disk_isnull(const H5F_t *f, void *_vl)
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
@@ -967,29 +906,24 @@ done:
  * Programmer:	Quincey Koziol
  *		Wednesday, June 2, 1999
  *
- * Modifications:
- *
- *		Raymond Lu
- *		Thursday, June 26, 2002
- *		Free heap objects storing old data.
- *
  *-------------------------------------------------------------------------
  */
 /* ARGSUSED */
 static herr_t
-H5T_vlen_disk_write(H5F_t *f, hid_t dxpl_id, const H5T_vlen_alloc_info_t UNUSED *vl_alloc_info, void *_vl, void *buf, void *_bg, size_t seq_len, size_t base_size)
+H5T_vlen_disk_write(H5F_t *f, hid_t dxpl_id, const H5T_vlen_alloc_info_t UNUSED *vl_alloc_info,
+    void *_vl, void *buf, void *_bg, size_t seq_len, size_t base_size)
 {
-    uint8_t *vl=(uint8_t *)_vl; /*Pointer to the user's hvl_t information*/
-    uint8_t *bg=(uint8_t *)_bg; /*Pointer to the old data hvl_t          */
+    uint8_t *vl = (uint8_t *)_vl; /*Pointer to the user's hvl_t information*/
+    uint8_t *bg = (uint8_t *)_bg; /*Pointer to the old data hvl_t          */
     H5HG_t hobjid;              /* New VL sequence's heap ID */
     size_t len;                 /* Size of new sequence on disk (in bytes) */
-    herr_t      ret_value=SUCCEED;       /* Return value */
+    herr_t ret_value = SUCCEED; /* Return value */
 
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_disk_write)
 
     /* check parameters */
     HDassert(vl);
-    HDassert(seq_len==0 || buf);
+    HDassert(seq_len == 0 || buf);
     HDassert(f);
 
     /* Free heap object for old data.  */
@@ -1004,9 +938,9 @@ H5T_vlen_disk_write(H5F_t *f, hid_t dxpl_id, const H5T_vlen_alloc_info_t UNUSED
         INT32DECODE(bg, bg_hobjid.idx);
 
         /* Free heap object for old data */
-        if(bg_hobjid.addr>0) {
+        if(bg_hobjid.addr > 0) {
             /* Free heap object */
-            if(H5HG_remove(f, dxpl_id, &bg_hobjid)<0)
+            if(H5HG_remove(f, dxpl_id, &bg_hobjid) < 0)
                 HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "Unable to remove heap object")
         } /* end if */
     } /* end if */
@@ -1015,13 +949,13 @@ H5T_vlen_disk_write(H5F_t *f, hid_t dxpl_id, const H5T_vlen_alloc_info_t UNUSED
     UINT32ENCODE(vl, seq_len);
 
     /* Write the VL information to disk (allocates space also) */
-    len=(seq_len*base_size);
-    if(H5HG_insert(f,dxpl_id,len,buf,&hobjid)<0)
+    len = (seq_len*base_size);
+    if(H5HG_insert(f, dxpl_id, len, buf, &hobjid) < 0)
         HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "Unable to write VL information")
 
     /* Encode the heap information */
-    H5F_addr_encode(f,&vl,hobjid.addr);
-    INT32ENCODE(vl,hobjid.idx);
+    H5F_addr_encode(f, &vl, hobjid.addr);
+    INT32ENCODE(vl, hobjid.idx);
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
@@ -1038,17 +972,15 @@ done:
  * Programmer:	Quincey Koziol
  *		Saturday, November 8, 2003
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 static herr_t
 H5T_vlen_disk_setnull(H5F_t *f, hid_t dxpl_id, void *_vl, void *_bg)
 {
-    uint8_t *vl=(uint8_t *)_vl; /*Pointer to the user's hvl_t information*/
-    uint8_t *bg=(uint8_t *)_bg; /*Pointer to the old data hvl_t          */
-    uint32_t seq_len=0;         /* Sequence length */
-    herr_t      ret_value=SUCCEED;       /* Return value */
+    uint8_t *vl = (uint8_t *)_vl; /*Pointer to the user's hvl_t information*/
+    uint8_t *bg = (uint8_t *)_bg; /*Pointer to the old data hvl_t          */
+    uint32_t seq_len = 0;         /* Sequence length */
+    herr_t ret_value = SUCCEED;   /* Return value */
 
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_disk_setnull)
 
@@ -1057,7 +989,7 @@ H5T_vlen_disk_setnull(H5F_t *f, hid_t dxpl_id, void *_vl, void *_bg)
     HDassert(vl);
 
     /* Free heap object for old data.  */
-    if(bg!=NULL) {
+    if(bg != NULL) {
         H5HG_t bg_hobjid;       /* "Background" VL info sequence's ID info */
 
         /* Skip the length of the sequence and heap object ID from background data. */
@@ -1068,9 +1000,9 @@ H5T_vlen_disk_setnull(H5F_t *f, hid_t dxpl_id, void *_vl, void *_bg)
         INT32DECODE(bg, bg_hobjid.idx);
 
         /* Free heap object for old data */
-        if(bg_hobjid.addr>0) {
+        if(bg_hobjid.addr > 0) {
             /* Free heap object */
-            if(H5HG_remove(f, dxpl_id, &bg_hobjid)<0)
+            if(H5HG_remove(f, dxpl_id, &bg_hobjid) < 0)
                 HGOTO_ERROR(H5E_DATATYPE, H5E_WRITEERROR, FAIL, "Unable to remove heap object")
          } /* end if */
     } /* end if */
@@ -1079,8 +1011,8 @@ H5T_vlen_disk_setnull(H5F_t *f, hid_t dxpl_id, void *_vl, void *_bg)
     UINT32ENCODE(vl, seq_len);
 
     /* Encode the "nil" heap pointer information */
-    H5F_addr_encode(f,&vl,(haddr_t)0);
-    INT32ENCODE(vl,0);
+    H5F_addr_encode(f, &vl, (haddr_t)0);
+    INT32ENCODE(vl, 0);
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
@@ -1111,8 +1043,8 @@ done:
 static herr_t
 H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, void *free_info)
 {
-    unsigned i;     /* local index variable */
-    herr_t ret_value = SUCCEED;
+    unsigned u;                     /* Local index variable */
+    herr_t ret_value = SUCCEED;     /* Return value */
 
     FUNC_ENTER_NOAPI_NOINIT(H5T_vlen_reclaim_recurse)
 
@@ -1127,9 +1059,9 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi
                 void *off;     /* offset of field */
 
                 /* Calculate the offset member and recurse on it */
-                for(i=0; i<dt->shared->u.array.nelem; i++) {
-                    off=((uint8_t *)elem)+i*(dt->shared->parent->shared->size);
-                    if(H5T_vlen_reclaim_recurse(off,dt->shared->parent,free_func,free_info)<0)
+                for(u = 0; u < dt->shared->u.array.nelem; u++) {
+                    off = ((uint8_t *)elem) + u * (dt->shared->parent->shared->size);
+                    if(H5T_vlen_reclaim_recurse(off, dt->shared->parent, free_func, free_info) < 0)
                         HGOTO_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "Unable to free array element")
                 } /* end for */
             } /* end if */
@@ -1137,14 +1069,14 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi
 
         case H5T_COMPOUND:
             /* Check each field and recurse on VL, compound, enum or array ones */
-            for (i=0; i<dt->shared->u.compnd.nmembs; i++) {
+            for(u = 0; u < dt->shared->u.compnd.nmembs; u++) {
                 /* Recurse if it's VL, compound, enum or array */
-                if(H5T_IS_COMPLEX(dt->shared->u.compnd.memb[i].type->shared->type)) {
+                if(H5T_IS_COMPLEX(dt->shared->u.compnd.memb[u].type->shared->type)) {
                     void *off;     /* offset of field */
 
                     /* Calculate the offset member and recurse on it */
-                    off=((uint8_t *)elem)+dt->shared->u.compnd.memb[i].offset;
-                    if(H5T_vlen_reclaim_recurse(off,dt->shared->u.compnd.memb[i].type,free_func,free_info)<0)
+                    off = ((uint8_t *)elem) + dt->shared->u.compnd.memb[u].offset;
+                    if(H5T_vlen_reclaim_recurse(off, dt->shared->u.compnd.memb[u].type, free_func, free_info) < 0)
                         HGOTO_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "Unable to free compound field")
                 } /* end if */
             } /* end for */
@@ -1152,8 +1084,8 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi
 
         case H5T_VLEN:
             /* Recurse on the VL information if it's VL, compound, enum or array, then free VL sequence */
-            if(dt->shared->u.vlen.type==H5T_VLEN_SEQUENCE) {
-                hvl_t *vl=(hvl_t *)elem;    /* Temp. ptr to the vl info */
+            if(dt->shared->u.vlen.type == H5T_VLEN_SEQUENCE) {
+                hvl_t *vl = (hvl_t *)elem;    /* Temp. ptr to the vl info */
 
                 /* Check if there is anything actually in this sequence */
                 if(vl->len!=0) {
@@ -1162,24 +1094,24 @@ H5T_vlen_reclaim_recurse(void *elem, const H5T_t *dt, H5MM_free_t free_func, voi
                         void *off;     /* offset of field */
 
                         /* Calculate the offset of each array element and recurse on it */
-                        while(vl->len>0) {
-                            off=((uint8_t *)vl->p)+(vl->len-1)*dt->shared->parent->shared->size;
-                            if(H5T_vlen_reclaim_recurse(off,dt->shared->parent,free_func,free_info)<0)
+                        while(vl->len > 0) {
+                            off = ((uint8_t *)vl->p) + (vl->len - 1) * dt->shared->parent->shared->size;
+                            if(H5T_vlen_reclaim_recurse(off, dt->shared->parent, free_func, free_info) < 0)
                                 HGOTO_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "Unable to free VL element")
                             vl->len--;
                         } /* end while */
                     } /* end if */
 
                     /* Free the VL sequence */
-                    if(free_func!=NULL)
-                        (*free_func)(vl->p,free_info);
+                    if(free_func != NULL)
+                        (*free_func)(vl->p, free_info);
                     else
                         H5MM_xfree(vl->p);
                 } /* end if */
-            } else if(dt->shared->u.vlen.type==H5T_VLEN_STRING) {
+            } else if(dt->shared->u.vlen.type == H5T_VLEN_STRING) {
                 /* Free the VL string */
-                if(free_func!=NULL)
-                    (*free_func)(*(char **)elem,free_info);
+                if(free_func != NULL)
+                    (*free_func)(*(char **)elem, free_info);
                 else
                     H5MM_xfree(*(char **)elem);
             } else {
@@ -1226,7 +1158,7 @@ H5T_vlen_reclaim(void *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t
 {
     H5T_vlen_alloc_info_t *vl_alloc_info = (H5T_vlen_alloc_info_t *)op_data; /* VL allocation info from iterator */
     H5T_t	*dt;
-    herr_t ret_value;
+    herr_t ret_value = SUCCEED;     /* Return value */
 
     FUNC_ENTER_NOAPI(H5T_vlen_reclaim, FAIL)
 
@@ -1235,11 +1167,12 @@ H5T_vlen_reclaim(void *elem, hid_t type_id, unsigned UNUSED ndim, const hsize_t
     HDassert(H5I_DATATYPE == H5I_get_type(type_id));
 
     /* Check args */
-    if (NULL==(dt=H5I_object_verify(type_id,H5I_DATATYPE)))
+    if(NULL == (dt = H5I_object_verify(type_id, H5I_DATATYPE)))
         HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a datatype")
 
     /* Pull the free function and free info pointer out of the op_data and call the recurse datatype free function */
-    ret_value=H5T_vlen_reclaim_recurse(elem,dt,vl_alloc_info->free_func,vl_alloc_info->free_info);
+    if(H5T_vlen_reclaim_recurse(elem, dt, vl_alloc_info->free_func, vl_alloc_info->free_info) < 0)
+        HGOTO_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "can't reclaim vlen elements")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
@@ -1289,13 +1222,13 @@ H5T_vlen_get_alloc_info(hid_t dxpl_id, H5T_vlen_alloc_info_t **vl_alloc_info)
             HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not a dataset transfer property list")
 
         /* Get the allocation functions & information */
-        if (H5P_get(plist,H5D_XFER_VLEN_ALLOC_NAME,&(*vl_alloc_info)->alloc_func)<0)
+        if (H5P_get(plist,H5D_XFER_VLEN_ALLOC_NAME,&(*vl_alloc_info)->alloc_func) < 0)
             HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value")
-        if (H5P_get(plist,H5D_XFER_VLEN_ALLOC_INFO_NAME,&(*vl_alloc_info)->alloc_info)<0)
+        if (H5P_get(plist,H5D_XFER_VLEN_ALLOC_INFO_NAME,&(*vl_alloc_info)->alloc_info) < 0)
             HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value")
-        if (H5P_get(plist,H5D_XFER_VLEN_FREE_NAME,&(*vl_alloc_info)->free_func)<0)
+        if (H5P_get(plist,H5D_XFER_VLEN_FREE_NAME,&(*vl_alloc_info)->free_func) < 0)
             HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value")
-        if (H5P_get(plist,H5D_XFER_VLEN_FREE_INFO_NAME,&(*vl_alloc_info)->free_info)<0)
+        if (H5P_get(plist,H5D_XFER_VLEN_FREE_INFO_NAME,&(*vl_alloc_info)->free_info) < 0)
             HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "unable to get value")
     } /* end else */
 
@@ -1318,8 +1251,6 @@ done:
  * Programmer:	Mike McGreevy
  *              May 11, 2010
  *
- * Modifications:
- *
  *-------------------------------------------------------------------------
  */
 herr_t
@@ -1335,12 +1266,14 @@ H5T_vlen_reclaim_elmt(void *elem, H5T_t *dt, hid_t dxpl_id)
     FUNC_ENTER_NOAPI(H5T_vlen_reclaim_elmt, FAIL)
 
     /* Get VL allocation info */
-    if (H5T_vlen_get_alloc_info(dxpl_id, &vl_alloc_info) < 0)
+    if(H5T_vlen_get_alloc_info(dxpl_id, &vl_alloc_info) < 0)
         HGOTO_ERROR(H5E_DATATYPE, H5E_CANTGET, FAIL, "unable to retrieve VL allocation info")
 
     /* Recurse on buffer to free dynamic fields */
-    ret_value = H5T_vlen_reclaim_recurse(elem,dt,vl_alloc_info->free_func,vl_alloc_info->free_info);
+    if(H5T_vlen_reclaim_recurse(elem, dt, vl_alloc_info->free_func, vl_alloc_info->free_info) < 0)
+        HGOTO_ERROR(H5E_DATATYPE, H5E_CANTFREE, FAIL, "can't reclaim vlen elements")
 
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* H5T_vlen_reclaim_elmt */
+
diff --git a/src/H5Zdeflate.c b/src/H5Zdeflate.c
index 63e7b9a..598aa97 100644
--- a/src/H5Zdeflate.c
+++ b/src/H5Zdeflate.c
@@ -101,9 +101,9 @@ H5Z_filter_deflate (unsigned flags, size_t cd_nelmts,
 
         /* Set the uncompression parameters */
 	HDmemset(&z_strm, 0, sizeof(z_strm));
-	z_strm.next_in = *buf;
+	z_strm.next_in = (Bytef *)*buf;
         H5_ASSIGN_OVERFLOW(z_strm.avail_in,nbytes,size_t,unsigned);
-	z_strm.next_out = outbuf;
+	z_strm.next_out = (Bytef *)outbuf;
         H5_ASSIGN_OVERFLOW(z_strm.avail_out,nalloc,size_t,unsigned);
 
         /* Initialize the uncompression routines */
@@ -155,7 +155,7 @@ H5Z_filter_deflate (unsigned flags, size_t cd_nelmts,
 
         /* Finish uncompressing the stream */
 	(void)inflateEnd(&z_strm);
-    }
+    } /* end if */
     else {
 	/*
 	 * Output; compress but fail if the result would be larger than the
@@ -172,19 +172,20 @@ H5Z_filter_deflate (unsigned flags, size_t cd_nelmts,
         H5_ASSIGN_OVERFLOW(aggression,cd_values[0],unsigned,int);
 
         /* Allocate output (compressed) buffer */
-	if (NULL==(z_dst=outbuf=H5MM_malloc(z_dst_nbytes)))
+	if(NULL == (outbuf = H5MM_malloc(z_dst_nbytes)))
 	    HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, 0, "unable to allocate deflate destination buffer")
+        z_dst = (Bytef *)outbuf;
 
         /* Perform compression from the source to the destination buffer */
-	status = compress2 (z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
+	status = compress2(z_dst, &z_dst_nbytes, z_src, z_src_nbytes, aggression);
 
         /* Check for various zlib errors */
-	if (Z_BUF_ERROR==status)
+	if(Z_BUF_ERROR == status)
 	    HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "overflow")
-	else if (Z_MEM_ERROR==status)
-	    HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, 0, "deflate memory error")
-	else if (Z_OK!=status)
-	    HGOTO_ERROR (H5E_PLINE, H5E_CANTINIT, 0, "other deflate error")
+	else if(Z_MEM_ERROR == status)
+	    HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "deflate memory error")
+	else if(Z_OK != status)
+	    HGOTO_ERROR(H5E_PLINE, H5E_CANTINIT, 0, "other deflate error")
         /* Successfully uncompressed the buffer */
         else {
             /* Free the input buffer */
@@ -195,8 +196,8 @@ H5Z_filter_deflate (unsigned flags, size_t cd_nelmts,
 	    outbuf = NULL;
 	    *buf_size = nbytes;
 	    ret_value = z_dst_nbytes;
-	}
-    }
+	} /* end else */
+    } /* end else */
 
 done:
     if(outbuf)
diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c
index 4bfc8b1..eb3c6e6 100644
--- a/src/H5Zscaleoffset.c
+++ b/src/H5Zscaleoffset.c
@@ -806,6 +806,11 @@ 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)
 	HGOTO_ERROR(H5E_PLINE, H5E_CANTGET, FAIL, "can't get scaleoffset parameters")
@@ -1182,6 +1187,14 @@ 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) {
             HDmemcpy(outbuf + buf_offset, *buf, nbytes);