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-rw-r--r--src/H5.c4
-rw-r--r--src/H5AC.c6
-rw-r--r--src/H5ACmpio.c8
-rw-r--r--src/H5ACpkg.h2
-rw-r--r--src/H5ACpublic.h6
-rw-r--r--src/H5Aint.c4
-rw-r--r--src/H5Apkg.h2
-rw-r--r--src/H5B.c2
-rw-r--r--src/H5B2internal.c2
-rw-r--r--src/H5Bprivate.h2
-rw-r--r--src/H5C.c24
-rw-r--r--src/H5Cimage.c4
-rw-r--r--src/H5Cmpio.c2
-rw-r--r--src/H5Cpkg.h18
-rw-r--r--src/H5Cprivate.h24
-rw-r--r--src/H5Dbtree.c22
-rw-r--r--src/H5Dbtree2.c2
-rw-r--r--src/H5Dchunk.c47
-rw-r--r--src/H5Dint.c40
-rw-r--r--src/H5Dmpio.c153
-rw-r--r--src/H5Dvirtual.c4
-rw-r--r--src/H5Edeprec.c10
-rw-r--r--src/H5FDdirect.c6
-rw-r--r--src/H5FDfamily.c2
-rw-r--r--src/H5FDmpio.c4
-rw-r--r--src/H5FDmulti.c2
-rw-r--r--src/H5FL.c6
-rw-r--r--src/H5FS.c8
-rw-r--r--src/H5FScache.c6
-rw-r--r--src/H5FSsection.c14
-rw-r--r--src/H5Fpkg.h2
-rw-r--r--src/H5Fprivate.h2
-rw-r--r--src/H5Fsuper.c6
-rw-r--r--src/H5Gname.c2
-rw-r--r--src/H5Gobj.c2
-rw-r--r--src/H5HFcache.c34
-rw-r--r--src/H5HFdtable.c4
-rw-r--r--src/H5HFhdr.c4
-rw-r--r--src/H5HFspace.c2
-rw-r--r--src/H5HFtiny.c2
-rw-r--r--src/H5HGcache.c4
-rw-r--r--src/H5MF.c22
-rw-r--r--src/H5MFaggr.c2
-rw-r--r--src/H5O.c2
-rw-r--r--src/H5Oattr.c2
-rw-r--r--src/H5Oattribute.c2
-rw-r--r--src/H5Ocache.c30
-rw-r--r--src/H5Ocache_image.c2
-rw-r--r--src/H5Ocopy.c2
-rw-r--r--src/H5Ofill.c28
-rw-r--r--src/H5Olayout.c4
-rw-r--r--src/H5Omessage.c6
-rw-r--r--src/H5Oshared.c2
-rw-r--r--src/H5P.c4
-rw-r--r--src/H5Pdcpl.c4
-rw-r--r--src/H5Pdeprec.c4
-rw-r--r--src/H5Pdxpl.c2
-rw-r--r--src/H5Pfapl.c20
-rw-r--r--src/H5Pfcpl.c8
-rw-r--r--src/H5Pint.c34
-rw-r--r--src/H5Ppkg.h10
-rw-r--r--src/H5Ppublic.h2
-rw-r--r--src/H5SMpkg.h2
-rw-r--r--src/H5Sall.c2
-rw-r--r--src/H5Shyper.c26
-rw-r--r--src/H5Smpio.c7
-rw-r--r--src/H5Snone.c2
-rw-r--r--src/H5Spoint.c2
-rw-r--r--src/H5Sselect.c6
-rw-r--r--src/H5T.c2
-rw-r--r--src/H5Tcommit.c2
-rw-r--r--src/H5Tconv.c10
-rw-r--r--src/H5Toffset.c16
-rw-r--r--src/H5Tpkg.h2
-rw-r--r--src/H5Tprivate.h2
-rw-r--r--src/H5Znbit.c4
-rw-r--r--src/H5Zpublic.h2
-rw-r--r--src/H5Zscaleoffset.c4
-rw-r--r--src/H5Ztrans.c8
-rw-r--r--src/H5detect.c28
-rw-r--r--src/H5private.h4
-rw-r--r--src/H5public.h4
-rw-r--r--src/H5system.c10
83 files changed, 481 insertions, 356 deletions
diff --git a/src/H5.c b/src/H5.c
index 552330d..1b13fea 100644
--- a/src/H5.c
+++ b/src/H5.c
@@ -470,7 +470,7 @@ H5dont_atexit(void)
* library, which are supposed to free any unused memory they have
* allocated.
*
- * These should probably be registered dynamicly in a linked list of
+ * These should probably be registered dynamically in a linked list of
* functions to call, but there aren't that many right now, so we
* hard-wire them...
*
@@ -785,7 +785,7 @@ H5check_version(unsigned majnum, unsigned minnum, unsigned relnum)
HDfprintf (stderr, "%s", H5libhdf5_settings);
break;
default:
- /* 2 or higer: continue silently */
+ /* 2 or higher: continue silently */
break;
} /* end switch */
diff --git a/src/H5AC.c b/src/H5AC.c
index 5eccf9e..989ee10 100644
--- a/src/H5AC.c
+++ b/src/H5AC.c
@@ -318,7 +318,7 @@ H5AC_create(const H5F_t *f, H5AC_cache_config_t *config_ptr, H5AC_cache_image_co
HGOTO_ERROR(H5E_VFL, H5E_CANTGET, FAIL, "can't get mpi size")
if(NULL == (aux_ptr = H5FL_CALLOC(H5AC_aux_t)))
- HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "Can't allocate H5AC auxilary structure")
+ HGOTO_ERROR(H5E_CACHE, H5E_CANTALLOC, FAIL, "Can't allocate H5AC auxiliary structure")
aux_ptr->magic = H5AC__H5AC_AUX_T_MAGIC;
aux_ptr->mpi_comm = mpi_comm;
@@ -432,7 +432,7 @@ H5AC_create(const H5F_t *f, H5AC_cache_config_t *config_ptr, H5AC_cache_image_co
done:
#ifdef H5_HAVE_PARALLEL
- /* if there is a failure, try to tidy up the auxilary structure */
+ /* if there is a failure, try to tidy up the auxiliary structure */
if(ret_value < 0) {
if(aux_ptr != NULL) {
if(aux_ptr->d_slist_ptr != NULL)
@@ -1878,7 +1878,7 @@ done:
* from the cache, clear it, and free it without writing it to
* disk.
*
- * This verion of the function is a complete re-write to
+ * This version of the function is a complete re-write to
* use the new metadata cache. While there isn't all that
* much difference between the old and new Purpose sections,
* the original version is given below.
diff --git a/src/H5ACmpio.c b/src/H5ACmpio.c
index 7671abc..b60b933 100644
--- a/src/H5ACmpio.c
+++ b/src/H5ACmpio.c
@@ -933,7 +933,7 @@ done:
*
* Purpose: Update the dirty_bytes count for a newly inserted entry.
*
- * If mpi_rank isnt 0, this simply means adding the size
+ * If mpi_rank isn't 0, this simply means adding the size
* of the entry to the dirty_bytes count.
*
* If mpi_rank is 0, we must also add the entry to the
@@ -1332,7 +1332,7 @@ done:
* clean.
*
* This function is the main routine for handling this
- * notification proceedure. It must be called
+ * notification procedure. It must be called
* simultaniously on all processes that have the relevant
* file open. To this end, it is called only during a
* sync point, with a barrier prior to the call.
@@ -1340,7 +1340,7 @@ done:
* Note that any metadata entry writes by process 0 will
* occur after the barrier and just before this call.
*
- * Typicaly, calls to this function will be triggered in
+ * Typically, calls to this function will be triggered in
* one of two ways:
*
* 1) Dirty byte creation exceeds some user specified value.
@@ -2128,7 +2128,7 @@ HDfprintf(stdout, "%d:H5AC_propagate...:%u: (u/uu/i/iu/r/ru) = %zu/%u/%zu/%u/%zu
/* clear collective access flag on half of the entries in the
cache and mark them as independent in case they need to be
- evicted later. All ranks are guranteed to mark the same entries
+ evicted later. All ranks are guaranteed to mark the same entries
since we don't modify the order of the collectively accessed
entries except through collective access. */
if(H5C_clear_coll_entries(cache_ptr, TRUE) < 0)
diff --git a/src/H5ACpkg.h b/src/H5ACpkg.h
index 409d914..9bf84bf 100644
--- a/src/H5ACpkg.h
+++ b/src/H5ACpkg.h
@@ -189,7 +189,7 @@ H5FL_EXTERN(H5AC_aux_t);
* is permitted to write to file.
*
* dirty_bytes_threshold: Integer field containing the dirty bytes
- * generation threashold. Whenever dirty byte creation
+ * generation threshold. Whenever dirty byte creation
* exceeds this value, the metadata cache on process 0
* broadcasts a list of the entries it has flushed since
* the last broadcast (or since the beginning of execution)
diff --git a/src/H5ACpublic.h b/src/H5ACpublic.h
index 654a877..a48aa69 100644
--- a/src/H5ACpublic.h
+++ b/src/H5ACpublic.h
@@ -39,7 +39,7 @@ extern "C" {
* structure H5AC_cache_config_t
*
* H5AC_cache_config_t is a public structure intended for use in public APIs.
- * At least in its initial incarnation, it is basicaly a copy of struct
+ * At least in its initial incarnation, it is basically a copy of struct
* H5C_auto_size_ctl_t, minus the report_fcn field, and plus the
* dirty_bytes_threshold field.
*
@@ -212,7 +212,7 @@ extern "C" {
*
* flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated
* type whose value indicates whether and by which algorithm we should
- * make flash increases in the size of the cache to accomodate insertion
+ * make flash increases in the size of the cache to accommodate insertion
* of large entries and large increases in the size of a single entry.
*
* The addition of the flash increment mode was occasioned by performance
@@ -379,7 +379,7 @@ extern "C" {
* synchronize updates between caches. (See above for outline and
* motivation.)
*
- * This value MUST be consistant across all processes accessing the
+ * This value MUST be consistent across all processes accessing the
* file. This field is ignored unless HDF5 has been compiled for
* parallel.
*
diff --git a/src/H5Aint.c b/src/H5Aint.c
index e666e8c..55560c7 100644
--- a/src/H5Aint.c
+++ b/src/H5Aint.c
@@ -1152,7 +1152,7 @@ H5A__free(H5A_t *attr)
HDassert(attr);
- /* Free dynamicly allocated items */
+ /* Free dynamically allocated items */
if(attr->shared->name) {
H5MM_xfree(attr->shared->name);
attr->shared->name = NULL;
@@ -1235,7 +1235,7 @@ H5A__close(H5A_t *attr)
/* Reference count can be 0. It only happens when H5A__create fails. */
if(attr->shared->nrefs <= 1) {
- /* Free dynamicly allocated items */
+ /* Free dynamically allocated items */
if(H5A__free(attr) < 0)
HGOTO_ERROR(H5E_ATTR, H5E_CANTRELEASE, FAIL, "can't release attribute info")
diff --git a/src/H5Apkg.h b/src/H5Apkg.h
index 3315cc1..af16b55 100644
--- a/src/H5Apkg.h
+++ b/src/H5Apkg.h
@@ -86,7 +86,7 @@ typedef struct H5A_shared_t {
void *data; /* Attribute data (on a temporary basis) */
size_t data_size; /* Size of data on disk */
H5O_msg_crt_idx_t crt_idx; /* Attribute's creation index in the object header */
- unsigned nrefs; /* Ref count for times this object is refered */
+ unsigned nrefs; /* Ref count for times this object is referred */
} H5A_shared_t;
/* Define the main attribute structure */
diff --git a/src/H5B.c b/src/H5B.c
index 1f19d7b..53d5529 100644
--- a/src/H5B.c
+++ b/src/H5B.c
@@ -769,7 +769,7 @@ H5B__insert_child(H5B_t *bt, unsigned *bt_flags, unsigned idx,
* the specified type.
*
* On return, if LT_KEY_CHANGED is non-zero, then LT_KEY is
- * the new native left key. Similarily for RT_KEY_CHANGED
+ * the new native left key. Similarly for RT_KEY_CHANGED
* and RT_KEY.
*
* If the node splits, then MD_KEY contains the key that
diff --git a/src/H5B2internal.c b/src/H5B2internal.c
index 95ed769..7f6b80a 100644
--- a/src/H5B2internal.c
+++ b/src/H5B2internal.c
@@ -1192,7 +1192,7 @@ H5B2__remove_internal_by_idx(H5B2_hdr_t *hdr, hbool_t *depth_decreased,
if(swap_loc)
idx = 0;
else {
- /* Count from the orginal index value again */
+ /* Count from the original index value again */
n = orig_n;
/* Reset "found" flag - the record may have shifted during the
diff --git a/src/H5Bprivate.h b/src/H5Bprivate.h
index 270b4e6..e203b87 100644
--- a/src/H5Bprivate.h
+++ b/src/H5Bprivate.h
@@ -122,7 +122,7 @@ typedef struct H5B_class_t {
H5B_ins_t (*insert)(H5F_t*, haddr_t, void*, hbool_t*, void*, void*,
void*, hbool_t*, haddr_t*);
- /* min insert uses min leaf, not new(), similarily for max insert */
+ /* min insert uses min leaf, not new(), similarly for max insert */
hbool_t follow_min;
hbool_t follow_max;
diff --git a/src/H5C.c b/src/H5C.c
index 729b267..c4d4eed 100644
--- a/src/H5C.c
+++ b/src/H5C.c
@@ -793,8 +793,8 @@ H5C_prep_for_file_close(H5F_t *f)
* close, and since the close warning is issued after all
* non FSM related space allocations and just before the
* first sync point on close, this call will leave the caches
- * in a consistant state across the processes if they were
- * consistant before.
+ * in a consistent state across the processes if they were
+ * consistent before.
*
* 2) Since the FSM settle routines are only invoked once during
* file close, invoking them now will prevent their invocation
@@ -2255,7 +2255,7 @@ H5C_protect(H5F_t * f,
if(entry_ptr != NULL) {
if(entry_ptr->ring != ring)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, NULL, "ring type mismatch occured for cache entry")
+ HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, NULL, "ring type mismatch occurred for cache entry")
HDassert(entry_ptr->magic == H5C__H5C_CACHE_ENTRY_T_MAGIC);
@@ -3095,7 +3095,7 @@ H5C_unprotect(H5F_t *f, haddr_t addr, void *thing, unsigned flags)
*
* All this is a bit awkward, but until the metadata cache entries
* are contiguous, with only one dirty flag, we have to let the supplied
- * functions deal with the reseting the is_dirty flag.
+ * functions deal with the resetting the is_dirty flag.
*/
if(entry_ptr->clear_on_unprotect) {
/* Sanity check */
@@ -5029,7 +5029,7 @@ H5C__flash_increase_cache_size(H5C_t * cache_ptr,
if ( (cache_ptr->resize_ctl).rpt_fcn != NULL ) {
/* get the hit rate for the reporting function. Should still
- * be good as we havent reset the hit rate statistics.
+ * be good as we haven't reset the hit rate statistics.
*/
if(H5C_get_cache_hit_rate(cache_ptr, &hit_rate) != SUCCEED)
HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "Can't get hit rate")
@@ -5272,7 +5272,7 @@ H5C_flush_invalidate_ring(H5F_t * f, H5C_ring_t ring, unsigned flags)
cooked_flags = flags & H5C__FLUSH_CLEAR_ONLY_FLAG;
evict_flags = flags & H5C__EVICT_ALLOW_LAST_PINS_FLAG;
- /* The flush proceedure here is a bit strange.
+ /* The flush procedure here is a bit strange.
*
* In the outer while loop we make at least one pass through the
* cache, and then repeat until either all the pinned entries in
@@ -5421,7 +5421,7 @@ H5C_flush_invalidate_ring(H5F_t * f, H5C_ring_t ring, unsigned flags)
*
* While this optimization used to be easy, with the possibility
* of new entries being added to the slist in the midst of the
- * flush, we must keep the slist in cannonical form at all
+ * flush, we must keep the slist in canonical form at all
* times.
*/
if(((!entry_ptr->flush_me_last) ||
@@ -6280,7 +6280,7 @@ H5C__flush_single_entry(H5F_t *f, H5C_cache_entry_t *entry_ptr, unsigned flags)
entry_addr = entry_ptr->addr;
/* Internal cache data structures should now be up to date, and
- * consistant with the status of the entry.
+ * consistent with the status of the entry.
*
* Now discard the entry if appropriate.
*/
@@ -6301,10 +6301,10 @@ H5C__flush_single_entry(H5F_t *f, H5C_cache_entry_t *entry_ptr, unsigned flags)
entry_ptr->image_ptr = H5MM_xfree(entry_ptr->image_ptr);
/* If the entry is not a prefetched entry, verify that the flush
- * dependency parents addresses array has been transfered.
+ * dependency parents addresses array has been transferred.
*
* If the entry is prefetched, the free_isr routine will dispose of
- * the flush dependency parents adresses array if necessary.
+ * the flush dependency parents addresses array if necessary.
*/
if(!entry_ptr->prefetched) {
HDassert(0 == entry_ptr->fd_parent_count);
@@ -8587,7 +8587,7 @@ H5C__generate_image(H5F_t *f, H5C_t *cache_ptr, H5C_cache_entry_t *entry_ptr)
* tests will be necessary.
*/
if(cache_ptr->aux_ptr != NULL)
- HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "resize/move in serialize occured in parallel case")
+ HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "resize/move in serialize occurred in parallel case")
#endif
/* If required, resize the buffer and update the entry and the cache
@@ -8787,7 +8787,7 @@ H5C_remove_entry(void *_entry)
cache->entry_watched_for_removal = NULL;
/* Internal cache data structures should now be up to date, and
- * consistant with the status of the entry.
+ * consistent with the status of the entry.
*
* Now clean up internal cache fields if appropriate.
*/
diff --git a/src/H5Cimage.c b/src/H5Cimage.c
index 51de5c4..26b6506 100644
--- a/src/H5Cimage.c
+++ b/src/H5Cimage.c
@@ -1494,7 +1494,7 @@ H5C__prep_image_for_file_close(H5F_t *f, hbool_t *image_generated)
* if the underlying file alignment is greater than 1.
*
* Clean this up eventually by extending the size of the cache
- * image block to the next alignement boundary, and then setting
+ * image block to the next alignment boundary, and then setting
* the image_data_len to the actual size of the cache_image.
*
* On the off chance that there is some other way to get a
@@ -1554,7 +1554,7 @@ H5C__prep_image_for_file_close(H5F_t *f, hbool_t *image_generated)
* metadata cache image superblock extension message, set
* cache_ptr->image_ctl.generate_image to FALSE. This will
* allow the file close to continue normally without the
- * unecessary generation of the metadata cache image.
+ * unnecessary generation of the metadata cache image.
*/
if(cache_ptr->num_entries_in_image > 0) {
if(H5C__prep_for_file_close__setup_image_entries_array(cache_ptr) < 0)
diff --git a/src/H5Cmpio.c b/src/H5Cmpio.c
index e342d69..ecaed62 100644
--- a/src/H5Cmpio.c
+++ b/src/H5Cmpio.c
@@ -380,7 +380,7 @@ H5C_apply_candidate_list(H5F_t * f,
* Note that we are doing things in this round about manner so as
* to preserve the order of the LRU list to the best of our ability.
* If we don't do this, my experiments indicate that we will have a
- * noticably poorer hit ratio as a result.
+ * noticeably poorer hit ratio as a result.
*/
if(H5C__flush_candidate_entries(f, entries_to_flush, entries_to_clear) < 0)
HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "flush candidates failed")
diff --git a/src/H5Cpkg.h b/src/H5Cpkg.h
index c5dc8f3..98d7a01 100644
--- a/src/H5Cpkg.h
+++ b/src/H5Cpkg.h
@@ -58,7 +58,7 @@
* We maintain doubly linked lists of instances of H5C_cache_entry_t for a
* variety of reasons -- protected list, LRU list, and the clean and dirty
* LRU lists at present. The following macros support linking and unlinking
- * of instances of H5C_cache_entry_t by both their regular and auxilary next
+ * of instances of H5C_cache_entry_t by both their regular and auxiliary next
* and previous pointers.
*
* The size and length fields are also maintained.
@@ -2006,7 +2006,7 @@ if ( ( (cache_ptr)->index_size != \
* a bit more performance out of the cache.
*
* At least for the first cut, I am leaving the comments and
- * white space in the macro. If they cause dificulties with
+ * white space in the macro. If they cause difficulties with
* the pre-processor, I'll have to remove them.
*
* JRM - 7/28/04
@@ -2117,7 +2117,7 @@ if ( ( (cache_ptr)->index_size != \
* a bit more performance out of the cache.
*
* At least for the first cut, I am leaving the comments and
- * white space in the macro. If they cause dificulties with
+ * white space in the macro. If they cause difficulties with
* pre-processor, I'll have to remove them.
*
* JRM - 7/28/04
@@ -2375,7 +2375,7 @@ if ( ( (cache_ptr)->index_size != \
* a bit more performance out of the cache.
*
* At least for the first cut, I am leaving the comments and
- * white space in the macro. If they cause dificulties with
+ * white space in the macro. If they cause difficulties with
* pre-processor, I'll have to remove them.
*
* JRM - 7/28/04
@@ -2513,7 +2513,7 @@ if ( ( (cache_ptr)->index_size != \
* a bit more performance out of the cache.
*
* At least for the first cut, I am leaving the comments and
- * white space in the macro. If they cause dificulties with
+ * white space in the macro. If they cause difficulties with
* pre-processor, I'll have to remove them.
*
* JRM - 7/28/04
@@ -3057,7 +3057,7 @@ if ( ( (cache_ptr)->index_size != \
* squeeze a bit more performance out of the cache.
*
* At least for the first cut, I am leaving the comments and
- * white space in the macro. If they cause dificulties with
+ * white space in the macro. If they cause difficulties with
* pre-processor, I'll have to remove them.
*
* JRM - 7/28/04
@@ -3892,7 +3892,7 @@ typedef struct H5C_tag_info_t {
* 2) A pinned entry can be accessed or modified at any time.
* This places an additional burden on the associated pre-serialize
* and serialize callbacks, which must ensure the the entry is in
- * a consistant state before creating an image of it.
+ * a consistent state before creating an image of it.
*
* 3) A pinned entry can be marked as dirty (and possibly
* change size) while it is unprotected.
@@ -4604,7 +4604,7 @@ typedef struct H5C_tag_info_t {
* improper behavior if the next entry in the list is the target of one on
* these operations.
*
- * The following fields are use to count such occurances. They are used
+ * The following fields are use to count such occurrences. They are used
* both in tests (to verify that the scan has been restarted), and to
* obtain estimates of how frequently these restarts occur.
*
@@ -4624,7 +4624,7 @@ typedef struct H5C_tag_info_t {
* than the target entry as the result of call(s) to the
* pre_serialize or serialize callbacks.
*
- * Note that at present, this condition can only be triggerd
+ * Note that at present, this condition can only be triggered
* by a call to H5C_serialize_single_entry().
*
* The remaining stats are collected only when both H5C_COLLECT_CACHE_STATS
diff --git a/src/H5Cprivate.h b/src/H5Cprivate.h
index 522b3cf..38a86ee 100644
--- a/src/H5Cprivate.h
+++ b/src/H5Cprivate.h
@@ -87,7 +87,7 @@
#define H5C__MIN_MAX_CACHE_SIZE ((size_t)(1024))
/* Default max cache size and min clean size are give here to make
- * them generally accessable.
+ * them generally accessible.
*/
#define H5C__DEFAULT_MAX_CACHE_SIZE ((size_t)(4 * 1024 * 1024))
#define H5C__DEFAULT_MIN_CLEAN_SIZE ((size_t)(2 * 1024 * 1024))
@@ -901,7 +901,7 @@ typedef struct H5C_class_t {
H5C_get_fsf_size_t fsf_size;
} H5C_class_t;
-/* Type defintions of callback functions used by the cache as a whole */
+/* Type definitions of callback functions used by the cache as a whole */
typedef herr_t (*H5C_write_permitted_func_t)(const H5F_t *f,
hbool_t *write_permitted_ptr);
typedef herr_t (*H5C_log_flush_func_t)(H5C_t *cache_ptr, haddr_t addr,
@@ -925,7 +925,7 @@ typedef herr_t (*H5C_log_flush_func_t)(H5C_t *cache_ptr, haddr_t addr,
* flush dependency -- with the implied setup and takedown overhead and
* added complexity. Further, the flush ordering between rings need only
* be enforced on flush operations, and thus the use of flush dependencies
- * instead would apply unecessary constraints on flushes under normal
+ * instead would apply unnecessary constraints on flushes under normal
* operating circumstances.
*
* As of this writing, all metadata entries pretaining to data sets and
@@ -1092,7 +1092,7 @@ typedef int H5C_ring_t;
* 2) A pinned entry can be accessed or modified at any time.
* This places an extra burden on the pre-serialize and
* serialize callbacks, which must ensure that a pinned
- * entry is consistant and ready to write to disk before
+ * entry is consistent and ready to write to disk before
* generating an image.
*
* 3) A pinned entry can be marked as dirty (and possibly
@@ -1152,7 +1152,7 @@ typedef int H5C_ring_t;
* flush_immediately: Boolean flag used only in Phdf5 -- and then only
* for H5AC_METADATA_WRITE_STRATEGY__DISTRIBUTED.
*
- * When a destributed metadata write is triggered at a
+ * When a distributed metadata write is triggered at a
* sync point, this field is used to mark entries that
* must be flushed before leaving the sync point. At all
* other times, this field should be set to FALSE.
@@ -1430,7 +1430,7 @@ typedef int H5C_ring_t;
* The flush dependency height of any entry involved in a
* flush dependency relationship is defined to be the
* longest flush dependency path from that entry to an entry
- * with no flush depenency children.
+ * with no flush dependency children.
*
* Since the image_fd_height is used to order entries in the
* cache image so that fd parents preceed fd children, for
@@ -1468,8 +1468,8 @@ typedef int H5C_ring_t;
*
* Further, if the prefetched entry is a flush dependency parent,
* all its flush dependency children (which must also be
- * prefetched entries), must be tranfered to the new cache
- * entry returned by the deserailization callback.
+ * prefetched entries), must be transferred to the new cache
+ * entry returned by the deserialization callback.
*
* Finally, if the prefetched entry is a flush dependency child,
* this flush dependency must be destroyed prior to the
@@ -1737,7 +1737,7 @@ typedef struct H5C_cache_entry_t {
* The flush dependency height of any entry involved in a
* flush dependency relationship is defined to be the
* longest flush dependency path from that entry to an entry
- * with no flush depenency children.
+ * with no flush dependency children.
*
* Since the image_fd_height is used to order entries in the
* cache image so that fd parents preceed fd children, for
@@ -1946,7 +1946,7 @@ typedef struct H5C_image_entry_t {
*
* flash_incr_mode: Instance of the H5C_cache_flash_incr_mode enumerated
* type whose value indicates whether and by what algorithm we should
- * make flash increases in the size of the cache to accomodate insertion
+ * make flash increases in the size of the cache to accommodate insertion
* of large entries and large increases in the size of a single entry.
*
* The addition of the flash increment mode was occasioned by performance
@@ -2182,9 +2182,9 @@ typedef struct H5C_auto_size_ctl_t {
* current value, any value in excess of 255 will be the functional
* equivalent of H5AC__CACHE_IMAGE__ENTRY_AGEOUT__NONE.
*
- * flags: Unsigned integer containing flags controling which aspects of the
+ * flags: Unsigned integer containing flags controlling which aspects of the
* cache image functinality is actually executed. The primary impetus
- * behind this field is to allow developement of tests for partial
+ * behind this field is to allow development of tests for partial
* implementations that will require little if any modification to run
* with the full implementation. In normal operation, all flags should
* be set.
diff --git a/src/H5Dbtree.c b/src/H5Dbtree.c
index c23f089..8abfe27 100644
--- a/src/H5Dbtree.c
+++ b/src/H5Dbtree.c
@@ -666,12 +666,13 @@ done:
static herr_t
H5D__btree_decode_key(const H5B_shared_t *shared, const uint8_t *raw, void *_key)
{
- const H5O_layout_chunk_t *layout; /* Chunk layout description */
- H5D_btree_key_t *key = (H5D_btree_key_t *) _key; /* Pointer to decoded key */
- hsize_t tmp_offset; /* Temporary coordinate offset, from file */
- unsigned u; /* Local index variable */
+ const H5O_layout_chunk_t *layout; /* Chunk layout description */
+ H5D_btree_key_t *key = (H5D_btree_key_t *) _key; /* Pointer to decoded key */
+ hsize_t tmp_offset; /* Temporary coordinate offset, from file */
+ unsigned u; /* Local index variable */
+ herr_t ret_value = SUCCEED; /* Return value */
- FUNC_ENTER_STATIC_NOERR
+ FUNC_ENTER_STATIC
/* check args */
HDassert(shared);
@@ -684,16 +685,21 @@ H5D__btree_decode_key(const H5B_shared_t *shared, const uint8_t *raw, void *_key
/* decode */
UINT32DECODE(raw, key->nbytes);
UINT32DECODE(raw, key->filter_mask);
- for(u = 0; u < layout->ndims; u++) {
+ for(u = 0; u < layout->ndims; u++)
+ {
+ if (layout->dim[u] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u)
+
/* Retrieve coordinate offset */
- UINT64DECODE(raw, tmp_offset);
+ UINT64DECODE(raw, tmp_offset);
HDassert(0 == (tmp_offset % layout->dim[u]));
/* Convert to a scaled offset */
key->scaled[u] = tmp_offset / layout->dim[u];
} /* end for */
- FUNC_LEAVE_NOAPI(SUCCEED)
+done:
+ FUNC_LEAVE_NOAPI(ret_value)
} /* end H5D__btree_decode_key() */
diff --git a/src/H5Dbtree2.c b/src/H5Dbtree2.c
index f9074be..d60e79e 100644
--- a/src/H5Dbtree2.c
+++ b/src/H5Dbtree2.c
@@ -378,7 +378,7 @@ H5D__bt2_unfilt_encode(uint8_t *raw, const void *_record, void *_ctx)
{
H5D_bt2_ctx_t *ctx = (H5D_bt2_ctx_t *)_ctx; /* Callback context structure */
const H5D_chunk_rec_t *record = (const H5D_chunk_rec_t *)_record; /* The native record */
- unsigned u; /* Local index varible */
+ unsigned u; /* Local index variable */
FUNC_ENTER_STATIC_NOERR
diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 7216c49..4906f3c 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -695,7 +695,7 @@ H5D__chunk_set_info_real(H5O_layout_chunk_t *layout, unsigned ndims,
/* Compute the # of chunks in dataset dimensions */
for(u = 0, layout->nchunks = 1, layout->max_nchunks = 1; u < ndims; u++) {
- /* Round up to the next integer # of chunks, to accomodate partial chunks */
+ /* Round up to the next integer # of chunks, to accommodate partial chunks */
layout->chunks[u] = ((curr_dims[u] + layout->dim[u]) - 1) / layout->dim[u];
if(H5S_UNLIMITED == max_dims[u])
layout->max_chunks[u] = H5S_UNLIMITED;
@@ -947,6 +947,8 @@ H5D__chunk_init(H5F_t *f, const H5D_t *dset, hid_t dapl_id)
hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */
/* Initial scaled dimension sizes */
+ if(dset->shared->layout.u.chunk.dim[u] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", u)
rdcc->scaled_dims[u] = dset->shared->curr_dims[u] / dset->shared->layout.u.chunk.dim[u];
if( !(scaled_power2up = H5VM_power2up(rdcc->scaled_dims[u])) )
@@ -2933,8 +2935,41 @@ H5D__chunk_lookup(const H5D_t *dset, const hsize_t *scaled,
H5F_set_coll_md_read(idx_info.f, temp_cmr);
#endif /* H5_HAVE_PARALLEL */
- /* Cache the information retrieved */
- H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata);
+ /*
+ * Cache the information retrieved.
+ *
+ * Note that if we are writing to the dataset in parallel and filters
+ * are involved, we skip caching this information as it is highly likely
+ * that the chunk information will be invalidated as a result of the
+ * filter operation (e.g. the chunk gets re-allocated to a different
+ * address in the file and/or gets re-allocated with a different size).
+ * If we were to cache this information, subsequent reads/writes would
+ * retrieve the invalid information and cause a variety of issues.
+ *
+ * It has been verified that in the serial library, when writing to chunks
+ * with the real chunk cache disabled and with filters involved, the
+ * functions within this file are correctly called in such a manner that
+ * this single chunk cache is always updated correctly. Therefore, this
+ * check is not needed for the serial library.
+ *
+ * This is an ugly and potentially frail check, but the
+ * H5D__chunk_cinfo_cache_reset() function is not currently available
+ * to functions outside of this file, so outside functions can not
+ * invalidate this single chunk cache. Even if the function were available,
+ * this check prevents us from doing the work of going through and caching
+ * each chunk in the write operation, when we're only going to invalidate
+ * the cache at the end of a parallel write anyway.
+ *
+ * - JTH (7/13/2018)
+ */
+#ifdef H5_HAVE_PARALLEL
+ if ( !( (H5F_HAS_FEATURE(idx_info.f, H5FD_FEAT_HAS_MPI))
+ && (H5F_INTENT(dset->oloc.file) & H5F_ACC_RDWR)
+ && dset->shared->dcpl_cache.pline.nused
+ )
+ )
+#endif
+ H5D__chunk_cinfo_cache_update(&dset->shared->cache.chunk.last, udata);
} /* end if */
} /* end else */
@@ -3016,7 +3051,7 @@ H5D__chunk_flush_entry(const H5D_t *dset, H5D_rdcc_ent_t *ent, hbool_t reset)
} /* end if */
else {
/*
- * If we are reseting and something goes wrong after this
+ * If we are resetting and something goes wrong after this
* point then it's too late to recover because we may have
* destroyed the original data by calling H5Z_pipeline().
* The only safe option is to continue with the reset
@@ -4449,7 +4484,7 @@ H5D__chunk_update_old_edge_chunks(H5D_t *dset, hsize_t old_dim[])
/* Start off with this dimension marked as not needing to be modified */
new_full_dim[op_dim] = FALSE;
- /* Calulate offset of first previously incomplete chunk in this
+ /* Calculate offset of first previously incomplete chunk in this
* dimension */
old_edge_chunk_sc[op_dim] = (old_dim[op_dim] / chunk_dim[op_dim]);
@@ -4970,7 +5005,7 @@ H5D__chunk_prune_by_extent(H5D_t *dset, const hsize_t *old_dim)
HGOTO_DONE(SUCCEED)
} /* end if */
- /* Round up to the next integer # of chunks, to accomodate partial chunks */
+ /* Round up to the next integer # of chunks, to accommodate partial chunks */
/* Use current dims because the indices have already been updated! -NAF */
/* (also compute the number of elements per chunk) */
/* (also copy the chunk dimensions into 'hsize_t' array for creating dataspace) */
diff --git a/src/H5Dint.c b/src/H5Dint.c
index b9d9cce..e8874a2 100644
--- a/src/H5Dint.c
+++ b/src/H5Dint.c
@@ -604,7 +604,7 @@ H5D__cache_dataspace_info(const H5D_t *dset)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't cache dataspace dimensions")
dset->shared->ndims = (unsigned)sndims;
- /* Compute the inital 'power2up' values */
+ /* Compute the initial 'power2up' values */
for(u = 0; u < dset->shared->ndims; u++) {
hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */
@@ -782,7 +782,7 @@ H5D__update_oh_info(H5F_t *file, H5D_t *dset, hid_t dapl_id)
H5O_fill_t old_fill_prop; /* Copy of fill value property, for writing as "old" fill value */
/* Shallow copy the fill value property */
- /* (we only want to make certain that the shared component isnt' modified) */
+ /* (we only want to make certain that the shared component isn't modified) */
HDmemcpy(&old_fill_prop, fill_prop, sizeof(old_fill_prop));
/* Reset shared component info */
@@ -2580,10 +2580,11 @@ done:
herr_t
H5D__set_extent(H5D_t *dset, const hsize_t *size)
{
- hsize_t curr_dims[H5S_MAX_RANK]; /* Current dimension sizes */
- htri_t changed; /* Whether the dataspace changed size */
- size_t u, v; /* Local index variable */
- herr_t ret_value = SUCCEED; /* Return value */
+ hsize_t curr_dims[H5S_MAX_RANK]; /* Current dimension sizes */
+ htri_t changed; /* Whether the dataspace changed size */
+ size_t u, v; /* Local index variable */
+ unsigned dim_idx; /* Dimension index */
+ herr_t ret_value = SUCCEED; /* Return value */
FUNC_ENTER_PACKAGE_VOL_TAG(dset->oloc.addr)
@@ -2620,11 +2621,11 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size)
hbool_t update_chunks = FALSE; /* Flag to indicate chunk cache update is needed */
/* Determine if we are shrinking and/or expanding any dimensions */
- for(u = 0; u < (size_t)dset->shared->ndims; u++) {
+ for(dim_idx = 0; dim_idx < dset->shared->ndims; dim_idx++) {
/* Check for various status changes */
- if(size[u] < curr_dims[u])
+ if(size[dim_idx] < curr_dims[dim_idx])
shrink = TRUE;
- if(size[u] > curr_dims[u])
+ if(size[dim_idx] > curr_dims[dim_idx])
expand = TRUE;
/* Chunked storage specific checks */
@@ -2632,30 +2633,33 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size)
hsize_t scaled; /* Scaled value */
/* Compute the scaled dimension size value */
- scaled = size[u] / dset->shared->layout.u.chunk.dim[u];
+ if(dset->shared->layout.u.chunk.dim[dim_idx] == 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_BADVALUE, FAIL, "chunk size must be > 0, dim = %u ", dim_idx)
+
+ scaled = size[dim_idx] / dset->shared->layout.u.chunk.dim[dim_idx];
/* Check if scaled dimension size changed */
- if(scaled != dset->shared->cache.chunk.scaled_dims[u]) {
+ if(scaled != dset->shared->cache.chunk.scaled_dims[dim_idx]) {
hsize_t scaled_power2up; /* Scaled value, rounded to next power of 2 */
/* Update the scaled dimension size value for the current dimension */
- dset->shared->cache.chunk.scaled_dims[u] = scaled;
+ dset->shared->cache.chunk.scaled_dims[dim_idx] = scaled;
/* Check if algorithm for computing hash values will change */
if((scaled > dset->shared->cache.chunk.nslots &&
- dset->shared->cache.chunk.scaled_dims[u] <= dset->shared->cache.chunk.nslots)
+ dset->shared->cache.chunk.scaled_dims[dim_idx] <= dset->shared->cache.chunk.nslots)
|| (scaled <= dset->shared->cache.chunk.nslots &&
- dset->shared->cache.chunk.scaled_dims[u] > dset->shared->cache.chunk.nslots))
+ dset->shared->cache.chunk.scaled_dims[dim_idx] > dset->shared->cache.chunk.nslots))
update_chunks = TRUE;
if(!(scaled_power2up = H5VM_power2up(scaled)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "unable to get the next power of 2")
/* Check if the number of bits required to encode the scaled size value changed */
- if(dset->shared->cache.chunk.scaled_power2up[u] != scaled_power2up) {
+ if(dset->shared->cache.chunk.scaled_power2up[dim_idx] != scaled_power2up) {
/* Update the 'power2up' & 'encode_bits' values for the current dimension */
- dset->shared->cache.chunk.scaled_power2up[u] = scaled_power2up;
- dset->shared->cache.chunk.scaled_encode_bits[u] = H5VM_log2_gen(scaled_power2up);
+ dset->shared->cache.chunk.scaled_power2up[dim_idx] = scaled_power2up;
+ dset->shared->cache.chunk.scaled_encode_bits[dim_idx] = H5VM_log2_gen(scaled_power2up);
/* Indicate that the cached chunk indices need to be updated */
update_chunks = TRUE;
@@ -2664,7 +2668,7 @@ H5D__set_extent(H5D_t *dset, const hsize_t *size)
} /* end if */
/* Update the cached copy of the dataset's dimensions */
- dset->shared->curr_dims[u] = size[u];
+ dset->shared->curr_dims[dim_idx] = size[dim_idx];
} /* end for */
/*-------------------------------------------------------------------------
diff --git a/src/H5Dmpio.c b/src/H5Dmpio.c
index 107b751..d721ae6 100644
--- a/src/H5Dmpio.c
+++ b/src/H5Dmpio.c
@@ -234,7 +234,7 @@ static herr_t H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info
H5D_filtered_collective_io_info_t *local_chunk_array, size_t *local_chunk_array_num_entries);
static herr_t H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries,
size_t array_entry_size, void **gathered_array, size_t *gathered_array_num_entries,
- int nprocs, hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *));
+ hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *));
static herr_t H5D__mpio_filtered_collective_write_type(
H5D_filtered_collective_io_info_t *chunk_list, size_t num_entries,
MPI_Datatype *new_mem_type, hbool_t *mem_type_derived,
@@ -418,19 +418,16 @@ done:
* Function: H5D__mpio_array_gatherv
*
* Purpose: Given an array, specified in local_array, by each processor
- * calling this function, gathers each array into a single
+ * calling this function, collects each array into a single
* array which is then either gathered to the processor
* specified by root, when allgather is false, or is
* distributed back to all processors when allgather is true.
*
- * The size of each entry and number of entries in the array
- * contributed by an individual processor should be specified
- * in array_entry_size and local_array_num_entries,
+ * The number of entries in the array contributed by an
+ * individual processor and the size of each entry should be
+ * specified in local_array_num_entries and array_entry_size,
* respectively.
*
- * The number of processors participating in the gather
- * operation should be specified for nprocs.
- *
* The MPI communicator to use should be specified for comm.
*
* If the sort_func argument is supplied, the array is sorted
@@ -448,14 +445,13 @@ done:
static herr_t
H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries,
size_t array_entry_size, void **_gathered_array, size_t *_gathered_array_num_entries,
- int nprocs, hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *))
+ hbool_t allgather, int root, MPI_Comm comm, int (*sort_func)(const void *, const void *))
{
size_t gathered_array_num_entries = 0; /* The size of the newly-constructed array */
- size_t i;
void *gathered_array = NULL; /* The newly-constructed array returned to the caller */
- int *receive_counts_array = NULL; /* Array containing number of entries each process is contributing */
- int *displacements_array = NULL; /* Array of displacements where each process places its data in the final array */
- int mpi_code;
+ int *receive_counts_array = NULL; /* Array containing number of entries each processor is contributing */
+ int *displacements_array = NULL; /* Array of displacements where each processor places its data in the final array */
+ int mpi_code, mpi_rank, mpi_size;
int sendcount;
herr_t ret_value = SUCCEED;
@@ -464,34 +460,62 @@ H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries,
HDassert(_gathered_array);
HDassert(_gathered_array_num_entries);
- /* Determine the size of the end result array */
+ MPI_Comm_size(comm, &mpi_size);
+ MPI_Comm_rank(comm, &mpi_rank);
+
+ /*
+ * Determine the size of the end result array by collecting the number
+ * of entries contributed by each processor into a single total.
+ */
if (MPI_SUCCESS != (mpi_code = MPI_Allreduce(&local_array_num_entries, &gathered_array_num_entries, 1, MPI_INT, MPI_SUM, comm)))
HMPI_GOTO_ERROR(FAIL, "MPI_Allreduce failed", mpi_code)
- /* If 0 entries resulted from the collective operation, no one is writing anything */
+ /* If 0 entries resulted from the collective operation, no processor is contributing anything and there is nothing to do */
if (gathered_array_num_entries > 0) {
- if (NULL == (gathered_array = H5MM_malloc(gathered_array_num_entries * array_entry_size)))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate gathered array")
+ /*
+ * If gathering to all processors, all processors need to allocate space for the resulting array, as well as
+ * the receive counts and displacements arrays for the collective MPI_Allgatherv call. Otherwise, only the
+ * root processor needs to allocate the space for an MPI_Gatherv call.
+ */
+ if (allgather || (mpi_rank == root)) {
+ if (NULL == (gathered_array = H5MM_malloc(gathered_array_num_entries * array_entry_size)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate gathered array")
- if (NULL == (receive_counts_array = (int *) H5MM_malloc((size_t) nprocs * sizeof(int))))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive counts array")
+ if (NULL == (receive_counts_array = (int *) H5MM_malloc((size_t) mpi_size * sizeof(int))))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive counts array")
- if (NULL == (displacements_array = (int *) H5MM_malloc((size_t) nprocs * sizeof(int))))
- HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive displacements array")
+ if (NULL == (displacements_array = (int *) H5MM_malloc((size_t) mpi_size * sizeof(int))))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate receive displacements array")
+ } /* end if */
- /* Inform each process of how many entries each other process is contributing to the resulting array */
- if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, comm)))
- HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code)
+ /*
+ * If gathering to all processors, inform each processor of how many entries each other processor is
+ * contributing to the resulting array by collecting the counts into each processor's "receive counts"
+ * array. Otherwise, inform only the root processor of how many entries each other processor is contributing.
+ */
+ if (allgather) {
+ if (MPI_SUCCESS != (mpi_code = MPI_Allgather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Allgather failed", mpi_code)
+ } /* end if */
+ else {
+ if (MPI_SUCCESS != (mpi_code = MPI_Gather(&local_array_num_entries, 1, MPI_INT, receive_counts_array, 1, MPI_INT, root, comm)))
+ HMPI_GOTO_ERROR(FAIL, "MPI_Gather failed", mpi_code)
+ } /* end else */
- /* Multiply each receive count by the size of the array entry, since the data is sent as bytes */
- for (i = 0; i < (size_t) nprocs; i++)
- H5_CHECKED_ASSIGN(receive_counts_array[i], int, (size_t) receive_counts_array[i] * array_entry_size, size_t);
+ if (allgather || (mpi_rank == root)) {
+ size_t i;
- /* Set receive buffer offsets for MPI_Allgatherv */
- displacements_array[0] = 0;
- for (i = 1; i < (size_t) nprocs; i++)
- displacements_array[i] = displacements_array[i - 1] + receive_counts_array[i - 1];
+ /* Multiply each receive count by the size of the array entry, since the data is sent as bytes. */
+ for (i = 0; i < (size_t) mpi_size; i++)
+ H5_CHECKED_ASSIGN(receive_counts_array[i], int, (size_t) receive_counts_array[i] * array_entry_size, size_t);
+ /* Set receive buffer offsets for the collective MPI_Allgatherv/MPI_Gatherv call. */
+ displacements_array[0] = 0;
+ for (i = 1; i < (size_t) mpi_size; i++)
+ displacements_array[i] = displacements_array[i - 1] + receive_counts_array[i - 1];
+ } /* end if */
+
+ /* As the data is sent as bytes, calculate the true sendcount for the data. */
H5_CHECKED_ASSIGN(sendcount, int, local_array_num_entries * array_entry_size, size_t);
if (allgather) {
@@ -502,10 +526,11 @@ H5D__mpio_array_gatherv(void *local_array, size_t local_array_num_entries,
else {
if (MPI_SUCCESS != (mpi_code = MPI_Gatherv(local_array, sendcount, MPI_BYTE,
gathered_array, receive_counts_array, displacements_array, MPI_BYTE, root, comm)))
- HMPI_GOTO_ERROR(FAIL, "MPI_Allgatherv failed", mpi_code)
+ HMPI_GOTO_ERROR(FAIL, "MPI_Gatherv failed", mpi_code)
} /* end else */
- if (sort_func) HDqsort(gathered_array, gathered_array_num_entries, array_entry_size, sort_func);
+ if (sort_func && (allgather || (mpi_rank == root)))
+ HDqsort(gathered_array, gathered_array_num_entries, array_entry_size, sort_func);
} /* end if */
*_gathered_array = gathered_array;
@@ -706,7 +731,7 @@ H5D__chunk_collective_io(H5D_io_info_t *io_info, const H5D_type_info_t *type_inf
io_option = H5D_MULTI_CHUNK_IO;
/* via default path. branch by num threshold */
else {
- unsigned one_link_chunk_io_threshold; /* Threshhold to use single collective I/O for all chunks */
+ unsigned one_link_chunk_io_threshold; /* Threshold to use single collective I/O for all chunks */
int mpi_size; /* Number of processes in MPI job */
if(H5D__mpio_get_sum_chunk(io_info, fm, &sum_chunk) < 0)
@@ -1295,8 +1320,7 @@ H5D__link_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_in
* of the chunks in the file.
*/
if (H5D__mpio_array_gatherv(chunk_list, chunk_list_num_entries, sizeof(H5D_filtered_collective_io_info_t),
- (void **) &collective_chunk_list, &collective_chunk_list_num_entries, mpi_size,
- true, 0, io_info->comm, NULL) < 0)
+ (void **) &collective_chunk_list, &collective_chunk_list_num_entries, true, 0, io_info->comm, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes")
/* Collectively re-allocate the modified chunks (from each process) in the file */
@@ -1768,8 +1792,7 @@ H5D__multi_chunk_filtered_collective_io(H5D_io_info_t *io_info, const H5D_type_i
* of the chunks in the file
*/
if (H5D__mpio_array_gatherv(&chunk_list[i], have_chunk_to_process ? 1 : 0, sizeof(H5D_filtered_collective_io_info_t),
- (void **) &collective_chunk_list, &collective_chunk_list_num_entries, mpi_size,
- true, 0, io_info->comm, NULL) < 0)
+ (void **) &collective_chunk_list, &collective_chunk_list_num_entries, true, 0, io_info->comm, NULL) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather new chunk sizes")
/* Participate in the collective re-allocation of all chunks modified
@@ -2655,8 +2678,8 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty
* call, the gathered list will initially be sorted in increasing order of chunk offset in the file.
*/
if (H5D__mpio_array_gatherv(local_chunk_array, *local_chunk_array_num_entries, sizeof(H5D_filtered_collective_io_info_t),
- (void **) &shared_chunks_info_array, &shared_chunks_info_array_num_entries, mpi_size,
- false, 0, io_info->comm, H5D__cmp_filtered_collective_io_info_entry) < 0)
+ (void **) &shared_chunks_info_array, &shared_chunks_info_array_num_entries, false, 0,
+ io_info->comm, H5D__cmp_filtered_collective_io_info_entry) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTGATHER, FAIL, "couldn't gather array")
/* Rank 0 redistributes any shared chunks to new owners as necessary */
@@ -2765,7 +2788,7 @@ H5D__chunk_redistribute_shared_chunks(const H5D_io_info_t *io_info, const H5D_ty
if (H5S_encode(chunk_info->fspace, &mod_data_p, &mod_data_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTENCODE, FAIL, "unable to encode dataspace")
- /* Intialize iterator for memory selection */
+ /* Initialize iterator for memory selection */
if (H5S_select_iter_init(mem_iter, chunk_info->mspace, type_info->src_type_size) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init = TRUE;
@@ -2981,7 +3004,7 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
{
H5D_chunk_info_t *chunk_info = NULL;
H5S_sel_iter_t *mem_iter = NULL; /* Memory iterator for H5D__scatter_mem/H5D__gather_mem */
- unsigned char *mod_data = NULL; /* Chunk modification data sent by a process to a chunk's owner */
+ H5S_sel_iter_t *file_iter = NULL;
H5Z_EDC_t err_detect; /* Error detection info */
H5Z_cb_t filter_cb; /* I/O filter callback function */
unsigned filter_mask = 0;
@@ -2989,11 +3012,13 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
hssize_t extent_npoints;
hsize_t true_chunk_size;
hbool_t mem_iter_init = FALSE;
+ hbool_t file_iter_init = FALSE;
size_t buf_size;
size_t i;
H5S_t *dataspace = NULL; /* Other process' dataspace for the chunk */
- void *tmp_gath_buf = NULL; /* Temporary gather buffer for owner of the chunk to gather into from
- application write buffer before scattering out to the chunk data buffer */
+ void *tmp_gath_buf = NULL; /* Temporary gather buffer to gather into from application buffer
+ before scattering out to the chunk data buffer (when writing data),
+ or vice versa (when reading data) */
int mpi_code;
herr_t ret_value = SUCCEED;
@@ -3073,9 +3098,6 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
mem_iter_init = TRUE;
- if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
-
/* If this is a read operation, scatter the read chunk data to the user's buffer.
*
* If this is a write operation, update the chunk data buffer with the modifications
@@ -3084,16 +3106,39 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
*/
switch (io_info->op_type) {
case H5D_IO_OP_READ:
- if (H5D__scatter_mem(chunk_entry->buf, chunk_info->mspace, mem_iter, (size_t)iter_nelmts, io_info->u.rbuf) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer")
+ if (NULL == (file_iter = (H5S_sel_iter_t *) H5MM_malloc(sizeof(H5S_sel_iter_t))))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate file iterator")
+
+ if (H5S_select_iter_init(file_iter, chunk_info->fspace, type_info->src_type_size) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to initialize memory selection information")
+ file_iter_init = TRUE;
+
+ if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->fspace)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
+
+ if (NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size)))
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer")
+
+ if (!H5D__gather_mem(chunk_entry->buf, chunk_info->fspace, file_iter, (size_t) iter_nelmts, tmp_gath_buf))
+ HGOTO_ERROR(H5E_IO, H5E_READERROR, FAIL, "couldn't gather from chunk buffer")
+
+ if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
+
+ if (H5D__scatter_mem(tmp_gath_buf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, io_info->u.rbuf) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to read buffer")
+
break;
case H5D_IO_OP_WRITE:
+ if ((iter_nelmts = H5S_GET_SELECT_NPOINTS(chunk_info->mspace)) < 0)
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTCOUNT, FAIL, "dataspace is invalid")
+
if (NULL == (tmp_gath_buf = H5MM_malloc((hsize_t) iter_nelmts * type_info->src_type_size)))
HGOTO_ERROR(H5E_DATASET, H5E_CANTALLOC, FAIL, "couldn't allocate temporary gather buffer")
/* Gather modification data from the application write buffer into a temporary buffer */
- if(!H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t)iter_nelmts, tmp_gath_buf))
+ if(!H5D__gather_mem(io_info->u.wbuf, chunk_info->mspace, mem_iter, (size_t) iter_nelmts, tmp_gath_buf))
HGOTO_ERROR(H5E_IO, H5E_WRITEERROR, FAIL, "couldn't gather from write buffer")
if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
@@ -3111,7 +3156,7 @@ H5D__filtered_collective_chunk_entry_io(H5D_filtered_collective_io_info_t *chunk
/* Scatter the owner's modification data into the chunk data buffer according to
* the file space.
*/
- if(H5D__scatter_mem(tmp_gath_buf, chunk_info->fspace, mem_iter, (size_t)iter_nelmts, chunk_entry->buf) < 0)
+ if(H5D__scatter_mem(tmp_gath_buf, chunk_info->fspace, mem_iter, (size_t) iter_nelmts, chunk_entry->buf) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_READERROR, FAIL, "couldn't scatter to chunk data buffer")
if (H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
@@ -3177,10 +3222,12 @@ done:
H5MM_free(chunk_entry->async_info.receive_buffer_array);
if (chunk_entry->async_info.receive_requests_array)
H5MM_free(chunk_entry->async_info.receive_requests_array);
- if (mod_data)
- H5MM_free(mod_data);
if (tmp_gath_buf)
H5MM_free(tmp_gath_buf);
+ if (file_iter_init && H5S_SELECT_ITER_RELEASE(file_iter) < 0)
+ HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
+ if (file_iter)
+ H5MM_free(file_iter);
if (mem_iter_init && H5S_SELECT_ITER_RELEASE(mem_iter) < 0)
HDONE_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "couldn't release selection iterator")
if (mem_iter)
diff --git a/src/H5Dvirtual.c b/src/H5Dvirtual.c
index c7c0775..7f1ac86 100644
--- a/src/H5Dvirtual.c
+++ b/src/H5Dvirtual.c
@@ -796,7 +796,7 @@ H5D__virtual_copy(H5F_t *f_dst, H5O_layout_t *layout_dst)
if(f_dst == f_src) {
/* Increase reference count on global heap object */
if((heap_rc = H5HG_link(f_dst, (H5HG_t *)&(layout_dst->u.virt.serial_list_hobjid), 1)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap refence count")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap reference count")
} /* end if */
else
#endif /* NOT_YET */
@@ -847,7 +847,7 @@ H5D__virtual_delete(H5F_t *f, H5O_storage_t *storage)
#ifdef NOT_YET
/* Unlink the global heap block */
if((heap_rc = H5HG_link(f, (H5HG_t *)&(storage->u.virt.serial_list_hobjid), -1)) < 0)
- HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap refence count")
+ HGOTO_ERROR(H5E_DATASET, H5E_CANTMODIFY, FAIL, "unable to adjust global heap reference count")
if(heap_rc == 0)
#endif /* NOT_YET */
/* Delete the global heap block */
diff --git a/src/H5Edeprec.c b/src/H5Edeprec.c
index 9ff9f1f..fc3eb9c 100644
--- a/src/H5Edeprec.c
+++ b/src/H5Edeprec.c
@@ -227,7 +227,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Eclear1
*
- * Purpose: This function is for backward compatbility.
+ * Purpose: This function is for backward compatibility.
* Clears the error stack for the specified error stack.
*
* Return: Non-negative on success/Negative on failure
@@ -258,7 +258,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Eprint1
*
- * Purpose: This function is for backward compatbility.
+ * Purpose: This function is for backward compatibility.
* Prints the error stack in some default way. This is just a
* convenience function for H5Ewalk() with a function that
* prints error messages. Users are encouraged to write there
@@ -296,7 +296,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Ewalk1
*
- * Purpose: This function is for backward compatbility.
+ * Purpose: This function is for backward compatibility.
* Walks the error stack for the current thread and calls some
* function for each error along the way.
*
@@ -335,7 +335,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Eget_auto1
*
- * Purpose: This function is for backward compatbility.
+ * Purpose: This function is for backward compatibility.
* Returns the current settings for the automatic error stack
* traversal function and its data for specific error stack.
* Either (or both) arguments may be null in which case the
@@ -386,7 +386,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Eset_auto1
*
- * Purpose: This function is for backward compatbility.
+ * Purpose: This function is for backward compatibility.
* Turns on or off automatic printing of errors for certain
* error stack. When turned on (non-null FUNC pointer) any
* API function which returns an error indication will first
diff --git a/src/H5FDdirect.c b/src/H5FDdirect.c
index 811ea8e..906ec28 100644
--- a/src/H5FDdirect.c
+++ b/src/H5FDdirect.c
@@ -951,7 +951,7 @@ H5FD_direct_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_UN
do {
/* Read the aligned data in file first. Not able to handle interrupted
* system calls and partial results like sec2 driver does because the
- * data may no longer be aligned. It's expecially true when the data in
+ * data may no longer be aligned. It's especially true when the data in
* file is smaller than ALLOC_SIZE. */
HDmemset(copy_buf, 0, alloc_size);
@@ -1138,9 +1138,9 @@ H5FD_direct_write(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type, hid_t H5_ATTR_U
/*
* Read the aligned data first if the aligned region doesn't fall
- * entirely in the range to be writen. Not able to handle interrupted
+ * entirely in the range to be written. Not able to handle interrupted
* system calls and partial results like sec2 driver does because the
- * data may no longer be aligned. It's expecially true when the data in
+ * data may no longer be aligned. It's especially true when the data in
* file is smaller than ALLOC_SIZE. Only read the entire section if
* both ends are misaligned, otherwise only read the block on the
* misaligned end.
diff --git a/src/H5FDfamily.c b/src/H5FDfamily.c
index 3c1c7bb..e52a71a 100644
--- a/src/H5FDfamily.c
+++ b/src/H5FDfamily.c
@@ -548,7 +548,7 @@ H5FD_family_sb_encode(H5FD_t *_file, char *name/*out*/, unsigned char *buf/*out*
/*-------------------------------------------------------------------------
* Function: H5FD_family_sb_decode
*
- * Purpose: This function has 2 seperate purpose. One is to decodes the
+ * Purpose: This function has 2 separate purpose. One is to decodes the
* superblock information for this driver. The NAME argument is
* the eight-character (plus null termination) name stored in i
* the file. The FILE argument is updated according to the
diff --git a/src/H5FDmpio.c b/src/H5FDmpio.c
index ee3277d..87f8b6a 100644
--- a/src/H5FDmpio.c
+++ b/src/H5FDmpio.c
@@ -1462,7 +1462,7 @@ H5FD_mpio_read(H5FD_t *_file, H5FD_mem_t H5_ATTR_UNUSED type,
/* Only look for MPI views for raw data transfers */
if(type == H5FD_MEM_DRAW) {
- H5FD_mpio_xfer_t xfer_mode; /* I/O tranfer mode */
+ H5FD_mpio_xfer_t xfer_mode; /* I/O transfer mode */
/* Get the transfer mode from the API context */
if(H5CX_get_io_xfer_mode(&xfer_mode) < 0)
@@ -1717,7 +1717,7 @@ H5FD_mpio_write(H5FD_t *_file, H5FD_mem_t type, hid_t H5_ATTR_UNUSED dxpl_id,
#endif
int size_i;
hbool_t use_view_this_time = FALSE;
- H5FD_mpio_xfer_t xfer_mode; /* I/O tranfer mode */
+ H5FD_mpio_xfer_t xfer_mode; /* I/O transfer mode */
herr_t ret_value = SUCCEED;
FUNC_ENTER_NOAPI_NOINIT
diff --git a/src/H5FDmulti.c b/src/H5FDmulti.c
index 8ae23d2..aa1b118 100644
--- a/src/H5FDmulti.c
+++ b/src/H5FDmulti.c
@@ -263,7 +263,7 @@ H5FD_multi_term(void)
/*-------------------------------------------------------------------------
* Function: H5Pset_fapl_split
*
- * Purpose: Compatability function. Makes the multi driver act like the
+ * Purpose: Compatibility function. Makes the multi driver act like the
* old split driver which stored meta data in one file and raw
* data in another file.
*
diff --git a/src/H5FL.c b/src/H5FL.c
index 0e67414..89a580a 100644
--- a/src/H5FL.c
+++ b/src/H5FL.c
@@ -18,7 +18,7 @@
* Purpose: Manage priority queues of free-lists (of blocks of bytes).
* These are used in various places in the library which allocate and
* free differently blocks of bytes repeatedly. Usually the same size
- * of block is allocated and freed repeatly in a loop, while writing out
+ * of block is allocated and freed repeatedly in a loop, while writing out
* chunked data for example, but the blocks may also be of different sizes
* from different datasets and an attempt is made to optimize access to
* the proper free list of blocks by using these priority queues to
@@ -499,7 +499,7 @@ H5FL_reg_calloc(H5FL_reg_head_t *head H5FL_TRACK_PARAMS)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Clear to zeros */
- /* (Accomodate tracking information, if present) */
+ /* (Accommodate tracking information, if present) */
HDmemset(ret_value,0,head->size - H5FL_TRACK_SIZE);
done:
@@ -2220,7 +2220,7 @@ H5FL_fac_calloc(H5FL_fac_head_t *head H5FL_TRACK_PARAMS)
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed")
/* Clear to zeros */
- /* (Accomodate tracking information, if present) */
+ /* (Accommodate tracking information, if present) */
HDmemset(ret_value,0,head->size - H5FL_TRACK_SIZE);
done:
diff --git a/src/H5FS.c b/src/H5FS.c
index e1a760f..113c8ae 100644
--- a/src/H5FS.c
+++ b/src/H5FS.c
@@ -135,7 +135,7 @@ HDfprintf(stderr, "%s: Creating free space manager, nclasses = %Zu\n", FUNC, ncl
fspace->alignment = alignment;
fspace->align_thres = threshold;
- /* Check if the free space tracker is supposed to be persistant */
+ /* Check if the free space tracker is supposed to be persistent */
if(fs_addr) {
/* Allocate space for the free space header */
if(HADDR_UNDEF == (fspace->addr = H5MF_alloc(f, H5FD_MEM_FSPACE_HDR, (hsize_t)fspace->hdr_size)))
@@ -423,7 +423,7 @@ HDfprintf(stderr, "%s: fspace->tot_sect_count = %Hu, fspace->serial_sect_count =
HDfprintf(stderr, "%s: fspace->alloc_sect_size = %Hu, fspace->sect_size = %Hu\n", FUNC, fspace->alloc_sect_size, fspace->sect_size);
#endif /* H5FS_DEBUG */
/* If there are sections to serialize, update them */
- /* (if the free space manager is persistant) */
+ /* (if the free space manager is persistent) */
if(fspace->serial_sect_count > 0 && H5F_addr_defined(fspace->addr)) {
#ifdef H5FS_DEBUG
HDfprintf(stderr, "%s: Real sections to store in file\n", FUNC);
@@ -794,7 +794,7 @@ HDfprintf(stderr, "%s: Marking free space header as dirty\n", FUNC);
/* Sanity check */
HDassert(fspace);
- /* Check if the free space manager is persistant */
+ /* Check if the free space manager is persistent */
if(H5F_addr_defined(fspace->addr))
/* Mark header as dirty in cache */
if(H5AC_mark_entry_dirty(fspace) < 0)
@@ -883,7 +883,7 @@ H5FS_alloc_sect(H5F_t *f, H5FS_t *fspace)
HGOTO_ERROR(H5E_FSPACE, H5E_CANTINIT, FAIL, "can't add free space sections to cache")
/* Since space has been allocated for the section info and the sinfo
- * has been inserted into the cache, relinquish owership (i.e. float)
+ * has been inserted into the cache, relinquish ownership (i.e. float)
* the section info.
*/
fspace->sinfo = NULL;
diff --git a/src/H5FScache.c b/src/H5FScache.c
index 875a383..fa04ba1 100644
--- a/src/H5FScache.c
+++ b/src/H5FScache.c
@@ -457,7 +457,7 @@ H5FS__cache_hdr_pre_serialize(H5F_t *f, void *_thing,
* H5F_addr_defined(fspace->addr)
*
* will both be TRUE. If this contition does not hold, then
- * either the free space info is not persistant
+ * either the free space info is not persistent
* (!H5F_addr_defined(fspace->addr)???) or the section info
* contains no free space data that must be written to file
* ( fspace->serial_sect_count == 0 ).
@@ -487,7 +487,7 @@ H5FS__cache_hdr_pre_serialize(H5F_t *f, void *_thing,
*
* Case 1) If either fspace->serial_sect_count == 0 or
* ! H5F_addr_defined(fspace->addr) do nothing as either
- * the free space manager data is not persistant, or the
+ * the free space manager data is not persistent, or the
* section info is empty.
*
* Otherwise, allocate space for the section info in real
@@ -1454,7 +1454,7 @@ H5FS__sinfo_serialize_sect_cb(void *_item, void H5_ATTR_UNUSED *key, void *_udat
/* Call 'serialize' callback for this section */
if(sect_cls->serialize) {
if((*sect_cls->serialize)(sect_cls, sect, *udata->image) < 0)
- HGOTO_ERROR(H5E_FSPACE, H5E_CANTSERIALIZE, FAIL, "can't syncronize section")
+ HGOTO_ERROR(H5E_FSPACE, H5E_CANTSERIALIZE, FAIL, "can't synchronize section")
/* Update offset in serialization buffer */
(*udata->image) += sect_cls->serial_size;
diff --git a/src/H5FSsection.c b/src/H5FSsection.c
index 11cd722..a58347f 100644
--- a/src/H5FSsection.c
+++ b/src/H5FSsection.c
@@ -2432,7 +2432,7 @@ done:
* returns to 1) above.
*
* Similarly, if it allocates space for its own header, it
- * can go into an infinte loop as it:
+ * can go into an infinite loop as it:
*
* 1) allocates space for the header
*
@@ -2479,7 +2479,7 @@ done:
* enabled when the free space managers are read. To allow
* for this, we must ensure that space allocated for the
* free space manager header and section info is either larger
- * than a page, or resides completely withing a page.
+ * than a page, or resides completely within a page.
*
* Do this by allocating space for the free space header and
* section info starting at page boundaries, and extending
@@ -2532,7 +2532,7 @@ H5FS_vfd_alloc_hdr_and_section_info_if_needed(H5F_t *f, H5FS_t *fspace,
HDassert(fspace->sect_addr == HADDR_UNDEF);
HDassert(fspace->alloc_sect_size == 0);
- /* persistant free space managers must be enabled */
+ /* persistent free space managers must be enabled */
HDassert(f->shared->fs_persist);
/* At present, all free space strategies enable the free space managers.
@@ -2576,7 +2576,7 @@ H5FS_vfd_alloc_hdr_and_section_info_if_needed(H5F_t *f, H5FS_t *fspace,
f, hdr_alloc_size, &eoa_frag_addr, &eoa_frag_size)))
HGOTO_ERROR(H5E_FSPACE, H5E_CANTALLOC, FAIL, "can't allocate file space for hdr")
- /* if the file alignement is 1, there should be no
+ /* if the file alignment is 1, there should be no
* eoa fragment. Otherwise, drop any fragment on the floor.
*/
HDassert((eoa_frag_size == 0) || (f->shared->alignment != 1));
@@ -2616,7 +2616,7 @@ H5FS_vfd_alloc_hdr_and_section_info_if_needed(H5F_t *f, H5FS_t *fspace,
f, sinfo_alloc_size, &eoa_frag_addr, &eoa_frag_size)))
HGOTO_ERROR(H5E_FSPACE, H5E_CANTALLOC, FAIL, "can't allocate file space")
- /* if the file alignement is 1, there should be no
+ /* if the file alignment is 1, there should be no
* eoa fragment. Otherwise, drop the fragment on the floor.
*/
HDassert((eoa_frag_size == 0) || (f->shared->alignment != 1));
@@ -2637,7 +2637,7 @@ H5FS_vfd_alloc_hdr_and_section_info_if_needed(H5F_t *f, H5FS_t *fspace,
* On reflection, no.
*
* On a regular file close, any eviction will not change the
- * the contents of the free space manger(s), as all entries
+ * the contents of the free space manager(s), as all entries
* should have correct file space allocated by the time this
* function is called.
*
@@ -2658,7 +2658,7 @@ H5FS_vfd_alloc_hdr_and_section_info_if_needed(H5F_t *f, H5FS_t *fspace,
HGOTO_ERROR(H5E_FSPACE, H5E_CANTMARKDIRTY, FAIL, "unable to mark free space header as dirty")
/* since space has been allocated for the section info and the sinfo
- * has been inserted into the cache, relinquish owership (i.e. float)
+ * has been inserted into the cache, relinquish ownership (i.e. float)
* the section info.
*/
fspace->sinfo = NULL;
diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
index f815005..2ab41de 100644
--- a/src/H5Fpkg.h
+++ b/src/H5Fpkg.h
@@ -321,7 +321,7 @@ struct H5F_file_t {
haddr_t fs_addr[H5F_MEM_PAGE_NTYPES]; /* Address of free space manager info for each type */
H5FS_t *fs_man[H5F_MEM_PAGE_NTYPES]; /* Free space manager for each file space type */
hbool_t first_alloc_dealloc; /* TRUE iff free space managers */
- /* are persistant and have not */
+ /* are persistent and have not */
/* been used accessed for either */
/* allocation or deallocation */
/* since file open. */
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index f06d4d0..979ba7d 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -557,7 +557,7 @@ typedef struct H5F_t H5F_t;
#define H5F_FILE_SPACE_PAGE_SIZE_DEF 4096
/* For paged aggregation: minimum value for file space page size */
#define H5F_FILE_SPACE_PAGE_SIZE_MIN 512
-/* For paged aggregation: maxiumum value for file space page size: 1 gigabyte */
+/* For paged aggregation: maximum value for file space page size: 1 gigabyte */
#define H5F_FILE_SPACE_PAGE_SIZE_MAX 1024*1024*1024
/* For paged aggregation: drop free-space with size <= this threshold for small meta section */
diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c
index 97a6d6f..9339b3d 100644
--- a/src/H5Fsuper.c
+++ b/src/H5Fsuper.c
@@ -823,13 +823,13 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read)
f->shared->eoa_pre_fsm_fsalloc = fsinfo.eoa_pre_fsm_fsalloc;
/* f->shared->eoa_pre_fsm_fsalloc must always be HADDR_UNDEF
- * in the absence of persistant free space managers.
+ * in the absence of persistent free space managers.
*/
/* If the following two conditions are true:
* (1) skipping EOF check (skip_eof_check)
* (2) dropping free-space to the floor (null_fsm_addr)
* skip the asserts as "eoa_pre_fsm_fsalloc" may be undefined
- * for a crashed file with persistant free space managers.
+ * for a crashed file with persistent free space managers.
* #1 and #2 are enabled when the tool h5clear --increment
* option is used.
*/
@@ -839,7 +839,7 @@ H5F__super_read(H5F_t *f, H5P_genplist_t *fa_plist, hbool_t initial_read)
} /* end if */
/* As "eoa_pre_fsm_fsalloc" may be undefined for a crashed file
- * with persistant free space managers, therefore, set
+ * with persistent free space managers, therefore, set
* "first_alloc_dealloc" when the condition
* "dropping free-space to the floor is true.
* This will ensure that no action is done to settle things on file
diff --git a/src/H5Gname.c b/src/H5Gname.c
index 1ca06b9..c1156ca 100644
--- a/src/H5Gname.c
+++ b/src/H5Gname.c
@@ -1058,7 +1058,7 @@ done:
* Function: H5G_name_replace
*
* Purpose: Search the list of open IDs and replace names according to a
- * particular operation. The operation occured on the
+ * particular operation. The operation occurred on the
* SRC_FILE/SRC_FULL_PATH_R object. The new name (if there is
* one) is NEW_NAME_R. Additional entry location information
* (currently only needed for the 'move' operation) is passed in
diff --git a/src/H5Gobj.c b/src/H5Gobj.c
index af0e72c..e93896c 100644
--- a/src/H5Gobj.c
+++ b/src/H5Gobj.c
@@ -222,7 +222,7 @@ H5G__obj_create_real(H5F_t *f, const H5O_ginfo_t *ginfo,
size_t pline_size = 0; /* Size of the pipeline message */
size_t link_size; /* Size of a link message */
- /* Calculate message size infomation, for creating group's object header */
+ /* Calculate message size information, for creating group's object header */
linfo_size = H5O_msg_size_f(f, gcpl_id, H5O_LINFO_ID, linfo, (size_t)0);
HDassert(linfo_size);
diff --git a/src/H5HFcache.c b/src/H5HFcache.c
index 84d5c5f..0c5d3aa 100644
--- a/src/H5HFcache.c
+++ b/src/H5HFcache.c
@@ -702,12 +702,12 @@ H5HF__cache_hdr_pre_serialize(H5F_t *f, void *_thing, haddr_t addr, size_t len,
*
* Do this with a call to H5HF__cache_verify_hdr_descendants_clean().
*
- * Note that decendants need not be clean if the pre_serialize call
+ * Note that descendants need not be clean if the pre_serialize call
* is made during a cache serialization instead of an entry or cache
* flush.
*
* Note also that with the recent change in the definition of flush
- * dependency, not all decendants need be clean -- only direct flush
+ * dependency, not all descendants need be clean -- only direct flush
* dependency children.
*
* Finally, observe that the H5HF__cache_verify_hdr_descendants_clean()
@@ -2643,11 +2643,11 @@ H5HF__cache_dblock_fsf_size(const void *_thing, hsize_t *fsf_size)
*
* The implementation of flush dependencies has been changed.
* Prior to this change, a flush dependency parent could be
- * flushed if and only if all its flush dependency decendants
+ * flushed if and only if all its flush dependency descendants
* were clean. In the new definition, a flush dependency
* parent can be flushed if all its immediate flush dependency
* children are clean, regardless of any other dirty
- * decendants.
+ * descendants.
*
* Further, metadata cache entries are now allowed to have
* multiple flush dependency parents.
@@ -2815,7 +2815,7 @@ H5HF__cache_verify_hdr_descendants_clean(H5F_t *f, H5HF_hdr_t *hdr,
H5_BEGIN_TAG(hdr->heap_addr)
if(NULL == (root_iblock = (H5HF_indirect_t *)H5AC_protect(f, H5AC_FHEAP_IBLOCK, root_iblock_addr, NULL, H5AC__READ_ONLY_FLAG)))
- HGOTO_ERROR_TAG(H5E_HEAP, H5E_CANTPROTECT, FAIL, "H5AC_protect() faild.")
+ HGOTO_ERROR_TAG(H5E_HEAP, H5E_CANTPROTECT, FAIL, "H5AC_protect() failed.")
H5_END_TAG
@@ -2889,7 +2889,7 @@ H5HF__cache_verify_hdr_descendants_clean(H5F_t *f, H5HF_hdr_t *hdr,
H5_BEGIN_TAG(hdr->heap_addr)
if(NULL == (iblock = (H5HF_indirect_t *)H5AC_protect(f, H5AC_FHEAP_IBLOCK, root_iblock_addr, NULL, H5AC__READ_ONLY_FLAG)))
- HGOTO_ERROR_TAG(H5E_HEAP, H5E_CANTPROTECT, FAIL, "H5AC_protect() faild.")
+ HGOTO_ERROR_TAG(H5E_HEAP, H5E_CANTPROTECT, FAIL, "H5AC_protect() failed.")
H5_END_TAG
@@ -2912,7 +2912,7 @@ H5HF__cache_verify_hdr_descendants_clean(H5F_t *f, H5HF_hdr_t *hdr,
if(unprotect_root_iblock) {
HDassert(root_iblock);
if(H5AC_unprotect(f, H5AC_FHEAP_IBLOCK, root_iblock_addr, root_iblock, H5AC__NO_FLAGS_SET) < 0)
- HGOTO_ERROR(H5E_HEAP, H5E_CANTUNPROTECT, FAIL, "H5AC_unprotect() faild.")
+ HGOTO_ERROR(H5E_HEAP, H5E_CANTUNPROTECT, FAIL, "H5AC_unprotect() failed.")
} /* end if */
} /* end else */
} /* end if */
@@ -2982,7 +2982,7 @@ done:
* Function: H5HF__cache_verify_iblock_descendants_clean
*
* Purpose: Sanity checking routine that verifies that all indirect
- * and direct blocks that are decendents of the supplied
+ * and direct blocks that are descendants of the supplied
* instance of H5HF_indirect_t are clean. Set *clean
* to TRUE if this is the case, and to FALSE otherwise.
*
@@ -3009,11 +3009,11 @@ done:
*
* The implementation of flush dependencies has been changed.
* Prior to this change, a flush dependency parent could be
- * flushed if and only if all its flush dependency decendants
+ * flushed if and only if all its flush dependency descendants
* were clean. In the new definition, a flush dependency
* parent can be flushed if all its immediate flush dependency
* children are clean, regardless of any other dirty
- * decendants.
+ * descendants.
*
* Further, metadata cache entries are now allowed to have
* multiple flush dependency parents.
@@ -3126,11 +3126,11 @@ done:
*
* The implementation of flush dependencies has been changed.
* Prior to this change, a flush dependency parent could be
- * flushed if and only if all its flush dependency decendants
+ * flushed if and only if all its flush dependency descendants
* were clean. In the new definition, a flush dependency
* parent can be flushed if all its immediate flush dependency
* children are clean, regardless of any other dirty
- * decendants.
+ * descendants.
*
* Further, metadata cache entries are now allowed to have
* multiple flush dependency parents.
@@ -3290,11 +3290,11 @@ done:
*
* The implementation of flush dependencies has been changed.
* Prior to this change, a flush dependency parent could be
- * flushed if and only if all its flush dependency decendants
+ * flushed if and only if all its flush dependency descendants
* were clean. In the new definition, a flush dependency
* parent can be flushed if all its immediate flush dependency
* children are clean, regardless of any other dirty
- * decendants.
+ * descendants.
*
* Further, metadata cache entries are now allowed to have
* multiple flush dependency parents.
@@ -3468,7 +3468,7 @@ H5HF__cache_verify_descendant_iblocks_clean(H5F_t *f, haddr_t fd_parent_addr,
H5_BEGIN_TAG(iblock->hdr->heap_addr)
if(NULL == (child_iblock = (H5HF_indirect_t *) H5AC_protect(f, H5AC_FHEAP_IBLOCK, child_iblock_addr, NULL, H5AC__READ_ONLY_FLAG)))
- HGOTO_ERROR_TAG(H5E_HEAP, H5E_CANTPROTECT, FAIL, "H5AC_protect() faild.")
+ HGOTO_ERROR_TAG(H5E_HEAP, H5E_CANTPROTECT, FAIL, "H5AC_protect() failed.")
H5_END_TAG
@@ -3480,7 +3480,7 @@ H5HF__cache_verify_descendant_iblocks_clean(H5F_t *f, haddr_t fd_parent_addr,
/* pointer to the entry. This is very slimy -- */
/* come up with a better solution. */
if(H5AC_get_entry_ptr_from_addr(f, child_iblock_addr, (void **)(&child_iblock)) < 0)
- HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "H5AC_get_entry_ptr_from_addr() faild.")
+ HGOTO_ERROR(H5E_HEAP, H5E_CANTGET, FAIL, "H5AC_get_entry_ptr_from_addr() failed.")
HDassert(child_iblock);
} /* end else */
} /* end if */
@@ -3519,7 +3519,7 @@ H5HF__cache_verify_descendant_iblocks_clean(H5F_t *f, haddr_t fd_parent_addr,
/* if we protected the child iblock, unprotect it now */
if(unprotect_child_iblock) {
if(H5AC_unprotect(f, H5AC_FHEAP_IBLOCK, child_iblock_addr, child_iblock, H5AC__NO_FLAGS_SET) < 0)
- HGOTO_ERROR(H5E_HEAP, H5E_CANTUNPROTECT, FAIL, "H5AC_unprotect() faild.")
+ HGOTO_ERROR(H5E_HEAP, H5E_CANTUNPROTECT, FAIL, "H5AC_unprotect() failed.")
} /* end if */
} /* end if */
} /* end if */
diff --git a/src/H5HFdtable.c b/src/H5HFdtable.c
index 563e8c5..6e9429a 100644
--- a/src/H5HFdtable.c
+++ b/src/H5HFdtable.c
@@ -338,7 +338,7 @@ HDfprintf(stderr, "%s: end_row = %u, end_col = %u, end_entry = %u\n", "H5HF_sect
/* Check for multi-row span */
if(start_row != end_row) {
- /* Accomodate partial starting row */
+ /* Accommodate partial starting row */
if(start_col > 0) {
acc_span_size = dtable->row_block_size[start_row] *
(dtable->cparam.width - start_col);
@@ -352,7 +352,7 @@ HDfprintf(stderr, "%s: end_row = %u, end_col = %u, end_entry = %u\n", "H5HF_sect
start_row++;
} /* end while */
- /* Accomodate partial ending row */
+ /* Accommodate partial ending row */
acc_span_size += dtable->row_block_size[start_row] *
(end_col + 1);
} /* end if */
diff --git a/src/H5HFhdr.c b/src/H5HFhdr.c
index b1b8574..8166d88 100644
--- a/src/H5HFhdr.c
+++ b/src/H5HFhdr.c
@@ -46,13 +46,13 @@
/* Limit on the size of the max. direct block size */
/* (This is limited to 32-bits currently, because I think it's unlikely to
* need to be larger, the 32-bit limit for H5VM_log2_of2(n), and
- * some offsets/sizes are encoded with a maxiumum of 32-bits - QAK)
+ * some offsets/sizes are encoded with a maximum of 32-bits - QAK)
*/
#define H5HF_MAX_DIRECT_SIZE_LIMIT ((hsize_t)2 * 1024 * 1024 * 1024)
/* Limit on the width of the doubling table */
/* (This is limited to 16-bits currently, because I think it's unlikely to
- * need to be larger, and its encoded with a maxiumum of 16-bits - QAK)
+ * need to be larger, and its encoded with a maximum of 16-bits - QAK)
*/
#define H5HF_WIDTH_LIMIT (64 * 1024)
#endif /* NDEBUG */
diff --git a/src/H5HFspace.c b/src/H5HFspace.c
index 5d659a6..5260ae2 100644
--- a/src/H5HFspace.c
+++ b/src/H5HFspace.c
@@ -311,7 +311,7 @@ H5HF__space_revert_root(const H5HF_hdr_t *hdr)
/* Only need to scan the sections if the free space has been initialized */
if(hdr->fspace)
- /* Iterate over all sections, reseting the parent pointers in 'single' sections */
+ /* Iterate over all sections, resetting the parent pointers in 'single' sections */
if(H5FS_sect_iterate(hdr->f, hdr->fspace, H5HF_space_revert_root_cb, NULL) < 0)
HGOTO_ERROR(H5E_FSPACE, H5E_BADITER, FAIL, "can't iterate over sections to reset parent pointers")
diff --git a/src/H5HFtiny.c b/src/H5HFtiny.c
index 79462e9..5cf1c08 100644
--- a/src/H5HFtiny.c
+++ b/src/H5HFtiny.c
@@ -109,7 +109,7 @@ H5HF_tiny_init(H5HF_hdr_t *hdr)
/* Check if tiny objects need an extra byte for their length */
/* (account for boundary condition when length of an object would need an
* extra byte, but using that byte means that the extra length byte is
- * unneccessary)
+ * unnecessary)
*/
if((hdr->id_len - 1) <= H5HF_TINY_LEN_SHORT) {
hdr->tiny_max_len = hdr->id_len - 1;
diff --git a/src/H5HGcache.c b/src/H5HGcache.c
index 50b2669..3a770ae 100644
--- a/src/H5HGcache.c
+++ b/src/H5HGcache.c
@@ -300,7 +300,7 @@ H5HG__cache_heap_deserialize(const void *_image, size_t len, void *_udata,
image += heap->obj[0].size;
} /* end if */
else {
- size_t need;
+ size_t need = 0;
unsigned idx;
uint8_t *begin = image;
@@ -420,7 +420,7 @@ H5HG__cache_heap_image_len(const void *_thing, size_t *image_len)
*
* Purpose: Given an appropriately sized buffer and an instance of
* H5HG_heap_t, serialize the global heap for writing to file,
- * and copy the serialized verion into the buffer.
+ * and copy the serialized version into the buffer.
*
*
* Return: Success: SUCCEED
diff --git a/src/H5MF.c b/src/H5MF.c
index 6358aff..65b27db 100644
--- a/src/H5MF.c
+++ b/src/H5MF.c
@@ -1692,7 +1692,7 @@ HDfprintf(stderr, "%s: Entering\n", FUNC);
} /* end if */
/* Set the ring type in the API context. In most cases, we will
- * need H5AC_RING_RDFSM, so initialy set the ring in
+ * need H5AC_RING_RDFSM, so initially set the ring in
* the context to that value. We will alter this later if needed.
*/
H5AC_set_ring(H5AC_RING_RDFSM, &orig_ring);
@@ -1788,7 +1788,7 @@ HDfprintf(stderr, "%s: Entering\n", FUNC);
HDassert(f->shared->sblock);
/* Set the ring type in the API context. In most cases, we will
- * need H5AC_RING_RDFSM, so initialy set the ring in
+ * need H5AC_RING_RDFSM, so initially set the ring in
* the context to that value. We will alter this later if needed.
*/
H5AC_set_ring(H5AC_RING_RDFSM, &orig_ring);
@@ -1956,7 +1956,7 @@ HDfprintf(stderr, "%s: Entering\n", FUNC);
HDassert(f->shared->sblock->super_vers >= HDF5_SUPERBLOCK_VERSION_2);
/* Set the ring type in the API context. In most cases, we will
- * need H5AC_RING_RDFSM, so initialy set the ring in
+ * need H5AC_RING_RDFSM, so initially set the ring in
* the context to that value. We will alter this later if needed.
*/
H5AC_set_ring(H5AC_RING_RDFSM, &orig_ring);
@@ -2244,7 +2244,7 @@ H5MF_get_freespace(H5F_t *f, hsize_t *tot_space, hsize_t *meta_size)
HDassert(f->shared->lf);
/* Set the ring type in the API context. In most cases, we will
- * need H5AC_RING_RDFSM, so initialy set the ring in
+ * need H5AC_RING_RDFSM, so initially set the ring in
* the context to that value. We will alter this later if needed.
*/
H5AC_set_ring(H5AC_RING_RDFSM, &orig_ring);
@@ -2419,7 +2419,7 @@ H5MF_get_free_sections(H5F_t *f, H5FD_mem_t type, size_t nsects, H5F_sect_info_t
sect_udata.sect_idx = 0;
/* Set the ring type in the API context. In most cases, we will
- * need H5AC_RING_RDFSM, so initialy set the ring in
+ * need H5AC_RING_RDFSM, so initially set the ring in
* the context to that value. We will alter this later if needed.
*/
H5AC_set_ring(H5AC_RING_RDFSM, &orig_ring);
@@ -2712,7 +2712,7 @@ H5MF_settle_raw_data_fsm(H5F_t *f, hbool_t *fsm_settled)
HGOTO_ERROR(H5E_RESOURCE, H5E_CANTFREE, FAIL, "can't free aggregators")
/* Set the ring type in the DXPL. In most cases, we will
- * need H5AC_RING_MDFSM first, so initialy set the ring in
+ * need H5AC_RING_MDFSM first, so initially set the ring in
* the DXPL to that value. We will alter this later if
* needed.
*/
@@ -2829,7 +2829,7 @@ H5MF_settle_raw_data_fsm(H5F_t *f, hbool_t *fsm_settled)
* extension messages will choke if the target message is
* unexpectedly either absent or present.
*
- * Update: This is probably unecessary, as I gather that the
+ * Update: This is probably unnecessary, as I gather that the
* file space manager info message is guaranteed to exist.
* Leave it in for now, but consider removing it.
*/
@@ -3083,7 +3083,7 @@ done:
* of these free space manager(s) only to have the allocation
* result in the free space manager being empty and thus
* obliging us to free the space again. Thus there is the
- * potential for an infinte loop if we want to avoid saving
+ * potential for an infinite loop if we want to avoid saving
* empty free space managers.
*
* Similarly, it is possible that we could allocate space
@@ -3280,7 +3280,7 @@ H5MF_settle_meta_data_fsm(H5F_t *f, hbool_t *fsm_settled)
* extension message.
*
* As of this writing, we are solving this problem by
- * simply not supporting persistant FSMs with the split
+ * simply not supporting persistent FSMs with the split
* and multi file drivers.
*
* Current plans are to do away with the multi file
@@ -3296,7 +3296,7 @@ H5MF_settle_meta_data_fsm(H5F_t *f, hbool_t *fsm_settled)
/* ******************* PROBLEM: ********************
*
- * If the file has an alignement other than 1, and if
+ * If the file has an alignment other than 1, and if
* the EOA is not a multiple of this alignment, allocating space
* for the section via the VFD info has the potential of generating
* a fragment that will be added to the free space manager. This
@@ -3433,7 +3433,7 @@ H5MF__fsm_type_is_self_referential(H5F_t *f, H5F_mem_page_t fsm_type)
/* In principle, fsm_type should always be less than
* H5F_MEM_PAGE_LARGE_SUPER whenever paged aggregation
* is not enabled. However, since there is code that does
- * not observe this prinicple, force the result to FALSE if
+ * not observe this principle, force the result to FALSE if
* fsm_type is greater than or equal to H5F_MEM_PAGE_LARGE_SUPER.
*/
if(fsm_type >= H5F_MEM_PAGE_LARGE_SUPER)
diff --git a/src/H5MFaggr.c b/src/H5MFaggr.c
index 5ab1834..3db7f73 100644
--- a/src/H5MFaggr.c
+++ b/src/H5MFaggr.c
@@ -407,7 +407,7 @@ H5MF__aggr_try_extend(H5F_t *f, H5F_blk_aggr_t *aggr,
if(f->shared->feature_flags & aggr->feature_flag) {
/*
* If the block being tested adjoins the beginning of the aggregator
- * block, check if the aggregator can accomodate the extension.
+ * block, check if the aggregator can accommodate the extension.
*/
if(H5F_addr_eq(blk_end, aggr->addr)) {
haddr_t eoa; /* EOA for the file */
diff --git a/src/H5O.c b/src/H5O.c
index c5db814..9b832f1 100644
--- a/src/H5O.c
+++ b/src/H5O.c
@@ -946,7 +946,7 @@ done:
* Function: H5Odisable_mdc_flushes
*
* Purpose: To "cork" an object:
- * --keep dirty entries assoicated with the object in the metadata cache
+ * --keep dirty entries associated with the object in the metadata cache
*
* Return: Success: Non-negative
* Failure: Negative
diff --git a/src/H5Oattr.c b/src/H5Oattr.c
index f2c31d7..a62a3a3 100644
--- a/src/H5Oattr.c
+++ b/src/H5Oattr.c
@@ -249,7 +249,7 @@ done:
if(NULL == ret_value)
if(attr) {
if(attr->shared) {
- /* Free any dynamicly allocated items */
+ /* Free any dynamically allocated items */
if(H5A__free(attr) < 0)
HDONE_ERROR(H5E_ATTR, H5E_CANTRELEASE, NULL, "can't release attribute info")
diff --git a/src/H5Oattribute.c b/src/H5Oattribute.c
index 9d125e8..e8a8433 100644
--- a/src/H5Oattribute.c
+++ b/src/H5Oattribute.c
@@ -1093,7 +1093,7 @@ H5O_attr_rename_mod_cb(H5O_t *oh, H5O_mesg_t *mesg/*in,out*/,
mesg->native = NULL;
/* Delete old attribute */
- /* (doesn't decrement the link count on shared components becuase
+ /* (doesn't decrement the link count on shared components because
* the "native" pointer has been reset)
*/
if(H5O_release_mesg(udata->f, oh, mesg, FALSE) < 0)
diff --git a/src/H5Ocache.c b/src/H5Ocache.c
index 3607839..59e1705 100644
--- a/src/H5Ocache.c
+++ b/src/H5Ocache.c
@@ -1430,9 +1430,10 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
/* Check for combining two adjacent 'null' messages */
if((udata->file_intent & H5F_ACC_RDWR) &&
- H5O_NULL_ID == id && oh->nmesgs > 0 &&
- H5O_NULL_ID == oh->mesg[oh->nmesgs - 1].type->id &&
- oh->mesg[oh->nmesgs - 1].chunkno == chunkno) {
+ H5O_NULL_ID == id && oh->nmesgs > 0 &&
+ H5O_NULL_ID == oh->mesg[oh->nmesgs - 1].type->id &&
+ oh->mesg[oh->nmesgs - 1].chunkno == chunkno) {
+
size_t mesgno; /* Current message to operate on */
/* Combine adjacent null messages */
@@ -1467,13 +1468,13 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
/* Point unknown messages at 'unknown' message class */
/* (Usually from future versions of the library) */
- if(id >= H5O_UNKNOWN_ID ||
+ if(id >= H5O_UNKNOWN_ID ||
#ifdef H5O_ENABLE_BOGUS
- id == H5O_BOGUS_VALID_ID ||
+ id == H5O_BOGUS_VALID_ID ||
#endif
- NULL == H5O_msg_class_g[id]) {
+ NULL == H5O_msg_class_g[id]) {
- H5O_unknown_t *unknown; /* Pointer to "unknown" message info */
+ H5O_unknown_t *unknown; /* Pointer to "unknown" message info */
/* Allocate "unknown" message info */
if(NULL == (unknown = H5FL_MALLOC(H5O_unknown_t)))
@@ -1490,9 +1491,9 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
/* Check for "fail if unknown" message flags */
if(((udata->file_intent & H5F_ACC_RDWR) &&
- (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE))
- || (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS))
- HGOTO_ERROR(H5E_OHDR, H5E_BADMESG, FAIL, "unknown message with 'fail if unknown' flag found")
+ (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_AND_OPEN_FOR_WRITE))
+ || (flags & H5O_MSG_FLAG_FAIL_IF_UNKNOWN_ALWAYS))
+ HGOTO_ERROR(H5E_OHDR, H5E_BADMESG, FAIL, "unknown message with 'fail if unknown' flag found")
/* Check for "mark if unknown" message flag, etc. */
else if((flags & H5O_MSG_FLAG_MARK_IF_UNKNOWN) &&
!(flags & H5O_MSG_FLAG_WAS_UNKNOWN) &&
@@ -1543,7 +1544,8 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
H5O_refcount_t *refcount;
/* Decode ref. count message */
- HDassert(oh->version > H5O_VERSION_1);
+ if(oh->version <= H5O_VERSION_1)
+ HGOTO_ERROR(H5E_OHDR, H5E_VERSION, FAIL, "object header version does not support reference count message")
refcount = (H5O_refcount_t *)(H5O_MSG_REFCOUNT->decode)(udata->f, NULL, 0, &ioflags, mesg->raw_size, mesg->raw);
/* Save 'native' form of ref. count message */
@@ -1551,6 +1553,8 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
/* Set object header values */
oh->has_refcount_msg = TRUE;
+ if(!refcount)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTSET, FAIL, "can't decode refcount")
oh->nlink = *refcount;
} /* end if */
/* Check if message is a link message */
@@ -1614,6 +1618,10 @@ H5O__chunk_deserialize(H5O_t *oh, haddr_t addr, size_t len, const uint8_t *image
} /* end if */
done:
+ if(ret_value < 0 && udata->cont_msg_info->msgs) {
+ udata->cont_msg_info->msgs = (H5O_chunk_t *)H5FL_SEQ_FREE(H5O_cont_t, udata->cont_msg_info->msgs);
+ udata->cont_msg_info->alloc_nmsgs = 0;
+ }
FUNC_LEAVE_NOAPI(ret_value)
} /* H5O__chunk_deserialize() */
diff --git a/src/H5Ocache_image.c b/src/H5Ocache_image.c
index ad64297..591ac4a 100644
--- a/src/H5Ocache_image.c
+++ b/src/H5Ocache_image.c
@@ -313,7 +313,7 @@ H5O__mdci_delete(H5F_t *f, H5O_t *open_oh, void *_mesg)
* space allocations / deallocations prior to the free of the
* cache image. Verify this to the extent possible.
*
- * If the hack to work around the persistant self referential
+ * If the hack to work around the persistent self referential
* free space manager issue is NOT in use, just call H5MF_xfree()
* to release the cache iamge. In principle, we should be able
* to just reduce the EOA to the base address of the cache
diff --git a/src/H5Ocopy.c b/src/H5Ocopy.c
index e6865f1..2e628f4 100644
--- a/src/H5Ocopy.c
+++ b/src/H5Ocopy.c
@@ -1106,7 +1106,7 @@ H5O__copy_header(const H5O_loc_t *oloc_src, H5O_loc_t *oloc_dst /*out */,
HDassert(H5F_addr_defined(oloc_src->addr));
HDassert(oloc_dst->file);
- /* Intialize copy info before errors can be thrown */
+ /* Initialize copy info before errors can be thrown */
HDmemset(&cpy_info, 0, sizeof(H5O_copy_t));
/* Get the copy property list */
diff --git a/src/H5Ofill.c b/src/H5Ofill.c
index 932241f..8a6004d 100644
--- a/src/H5Ofill.c
+++ b/src/H5Ofill.c
@@ -194,7 +194,7 @@ H5FL_BLK_EXTERN(type_conv);
static void *
H5O_fill_new_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
unsigned H5_ATTR_UNUSED mesg_flags, unsigned H5_ATTR_UNUSED *ioflags,
- size_t H5_ATTR_UNUSED p_size, const uint8_t *p)
+ size_t p_size, const uint8_t *p)
{
H5O_fill_t *fill = NULL;
void *ret_value = NULL; /* Return value */
@@ -228,6 +228,8 @@ H5O_fill_new_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
INT32DECODE(p, fill->size);
if(fill->size > 0) {
H5_CHECK_OVERFLOW(fill->size, ssize_t, size_t);
+ if((size_t)fill->size > p_size)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "destination buffer too small")
if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value")
HDmemcpy(fill->buf, p, (size_t)fill->size);
@@ -307,11 +309,13 @@ done:
*-------------------------------------------------------------------------
*/
static void *
-H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
+H5O_fill_old_decode(H5F_t *f, H5O_t *open_oh,
unsigned H5_ATTR_UNUSED mesg_flags, unsigned H5_ATTR_UNUSED *ioflags,
- size_t H5_ATTR_UNUSED p_size, const uint8_t *p)
+ size_t p_size, const uint8_t *p)
{
H5O_fill_t *fill = NULL; /* Decoded fill value message */
+ htri_t exists = FALSE;
+ H5T_t *dt = NULL;
void *ret_value = NULL; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -332,6 +336,21 @@ H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
/* Only decode the fill value itself if there is one */
if(fill->size > 0) {
+ H5_CHECK_OVERFLOW(fill->size, ssize_t, size_t);
+ if((size_t)fill->size > p_size)
+ HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "destination buffer too small")
+
+ /* Get the datatype message */
+ if((exists = H5O_msg_exists_oh(open_oh, H5O_DTYPE_ID)) < 0)
+ HGOTO_ERROR(H5E_SYM, H5E_NOTFOUND, NULL, "unable to read object header")
+ if(exists) {
+ if((dt = H5O_msg_read_oh(f, open_oh, H5O_DTYPE_ID, NULL)) < 0)
+ HGOTO_ERROR(H5E_SYM, H5E_CANTGET, NULL, "can't read DTYPE message")
+ /* Verify size */
+ if(fill->size != H5T_GET_SIZE(dt))
+ HGOTO_ERROR(H5E_SYM, H5E_CANTGET, NULL, "inconsistent fill value size")
+ }
+
if(NULL == (fill->buf = H5MM_malloc((size_t)fill->size)))
HGOTO_ERROR(H5E_RESOURCE, H5E_NOSPACE, NULL, "memory allocation failed for fill value")
HDmemcpy(fill->buf, p, (size_t)fill->size);
@@ -344,6 +363,9 @@ H5O_fill_old_decode(H5F_t H5_ATTR_UNUSED *f, H5O_t H5_ATTR_UNUSED *open_oh,
ret_value = (void*)fill;
done:
+ if(dt)
+ H5O_msg_free(H5O_DTYPE_ID, dt);
+
if(!ret_value && fill) {
if(fill->buf)
H5MM_xfree(fill->buf);
diff --git a/src/H5Olayout.c b/src/H5Olayout.c
index d8f05f0..5f16837 100644
--- a/src/H5Olayout.c
+++ b/src/H5Olayout.c
@@ -125,8 +125,8 @@ H5O__layout_decode(H5F_t *f, H5O_t H5_ATTR_UNUSED *open_oh,
/* Dimensionality */
ndims = *p++;
- if(ndims > H5O_LAYOUT_NDIMS)
- HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is too large")
+ if(!ndims || ndims > H5O_LAYOUT_NDIMS)
+ HGOTO_ERROR(H5E_OHDR, H5E_CANTLOAD, NULL, "dimensionality is out of range")
/* Layout class */
mesg->type = (H5D_layout_t)*p++;
diff --git a/src/H5Omessage.c b/src/H5Omessage.c
index 930be9b..e156dcd 100644
--- a/src/H5Omessage.c
+++ b/src/H5Omessage.c
@@ -239,7 +239,7 @@ done:
* Purpose: Modifies an existing message or creates a new message.
*
* The UPDATE_FLAGS argument are flags that allow the caller
- * to skip updating the modification time or reseting the message
+ * to skip updating the modification time or resetting the message
* data. This is useful when several calls to H5O_msg_write will be
* made in a sequence.
*
@@ -296,7 +296,7 @@ done:
* Purpose: Modifies an existing message or creates a new message.
*
* The UPDATE_FLAGS argument are flags that allow the caller
- * to skip updating the modification time or reseting the message
+ * to skip updating the modification time or resetting the message
* data. This is useful when several calls to H5O_msg_write will be
* made in a sequence.
*
@@ -343,7 +343,7 @@ done:
* Purpose: Modifies an existing message or creates a new message.
*
* The UPDATE_FLAGS argument are flags that allow the caller
- * to skip updating the modification time or reseting the message
+ * to skip updating the modification time or resetting the message
* data. This is useful when several calls to H5O_msg_write will be
* made in a sequence.
*
diff --git a/src/H5Oshared.c b/src/H5Oshared.c
index 047f90e..328ba4b 100644
--- a/src/H5Oshared.c
+++ b/src/H5Oshared.c
@@ -640,7 +640,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5O__shared_post_copy_file
*
- * Purpose: Delate a shared message and replace with a new one.
+ * Purpose: Delete a shared message and replace with a new one.
* The function is needed at cases such as coping a shared reg_ref attribute.
* When a shared reg_ref attribute is copied from one file to
* another, the values in file need to be replaced. The only way
diff --git a/src/H5P.c b/src/H5P.c
index f163e9e..733af42 100644
--- a/src/H5P.c
+++ b/src/H5P.c
@@ -399,7 +399,7 @@ done:
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The 'set' callback function may be useful to range check the value being
- set for the property or may perform some tranformation/translation of the
+ set for the property or may perform some transformation/translation of the
value set. The 'get' callback would then [probably] reverse the
transformation, etc. A single 'get' or 'set' callback could handle
multiple properties by performing different actions based on the property
@@ -581,7 +581,7 @@ done:
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The 'set' callback function may be useful to range check the value being
- set for the property or may perform some tranformation/translation of the
+ set for the property or may perform some transformation/translation of the
value set. The 'get' callback would then [probably] reverse the
transformation, etc. A single 'get' or 'set' callback could handle
multiple properties by performing different actions based on the property
diff --git a/src/H5Pdcpl.c b/src/H5Pdcpl.c
index d69b063..cb13ff3 100644
--- a/src/H5Pdcpl.c
+++ b/src/H5Pdcpl.c
@@ -1332,7 +1332,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5P__dcrt_ext_file_list_get
*
- * Purpose: Copies an external file lsit property when it's retrieved from a property list
+ * Purpose: Copies an external file list property when it's retrieved from a property list
*
* Return: Success: Non-negative
* Failure: Negative
@@ -2245,7 +2245,7 @@ H5Pset_virtual(hid_t dcpl_id, hid_t vspace_id, const char *src_file_name,
done:
/* Set VDS layout information in property list */
- /* (Even on faliure, so there's not a mangled layout struct in the list) */
+ /* (Even on failure, so there's not a mangled layout struct in the list) */
if(retrieved_layout) {
if(H5P_poke(plist, H5D_CRT_LAYOUT_NAME, &virtual_layout) < 0) {
HDONE_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set layout")
diff --git a/src/H5Pdeprec.c b/src/H5Pdeprec.c
index 7f96333..226d206 100644
--- a/src/H5Pdeprec.c
+++ b/src/H5Pdeprec.c
@@ -202,7 +202,7 @@
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The 'set' callback function may be useful to range check the value being
- set for the property or may perform some tranformation/translation of the
+ set for the property or may perform some transformation/translation of the
value set. The 'get' callback would then [probably] reverse the
transformation, etc. A single 'get' or 'set' callback could handle
multiple properties by performing different actions based on the property
@@ -383,7 +383,7 @@ done:
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The 'set' callback function may be useful to range check the value being
- set for the property or may perform some tranformation/translation of the
+ set for the property or may perform some transformation/translation of the
value set. The 'get' callback would then [probably] reverse the
transformation, etc. A single 'get' or 'set' callback could handle
multiple properties by performing different actions based on the property
diff --git a/src/H5Pdxpl.c b/src/H5Pdxpl.c
index b56c137..e6eed32 100644
--- a/src/H5Pdxpl.c
+++ b/src/H5Pdxpl.c
@@ -1035,7 +1035,7 @@ done:
* for the type conversion buffer and background buffer and
* optionally supply pointers to application-allocated buffers.
* If the buffer size is smaller than the entire amount of data
- * being transfered between application and file, and a type
+ * being transferred between application and file, and a type
* conversion buffer or background buffer is required then
* strip mining will be used.
*
diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c
index eded286..7ba9c11 100644
--- a/src/H5Pfapl.c
+++ b/src/H5Pfapl.c
@@ -396,7 +396,7 @@ static const hbool_t H5F_def_coll_md_write_flag_g = H5F_ACS_COLL_MD_WRITE_FLAG_D
static const H5AC_cache_image_config_t H5F_def_mdc_initCacheImageCfg_g = H5F_ACS_META_CACHE_INIT_IMAGE_CONFIG_DEF; /* Default metadata cache image settings */
static const size_t H5F_def_page_buf_size_g = H5F_ACS_PAGE_BUFFER_SIZE_DEF; /* Default page buffer size */
static const unsigned H5F_def_page_buf_min_meta_perc_g = H5F_ACS_PAGE_BUFFER_MIN_META_PERC_DEF; /* Default page buffer minimum metadata size */
-static const unsigned H5F_def_page_buf_min_raw_perc_g = H5F_ACS_PAGE_BUFFER_MIN_RAW_PERC_DEF; /* Default page buffer minumum raw data size */
+static const unsigned H5F_def_page_buf_min_raw_perc_g = H5F_ACS_PAGE_BUFFER_MIN_RAW_PERC_DEF; /* Default page buffer mininum raw data size */
/*-------------------------------------------------------------------------
@@ -1713,7 +1713,7 @@ H5Pget_mdc_image_config(hid_t plist_id, H5AC_cache_image_config_t *config_ptr)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Unknown image config version.")
/* If we ever support multiple versions of H5AC_cache_config_t, we
- * will have to get the cannonical version here, and then translate
+ * will have to get the canonical version here, and then translate
* to the version of the structure supplied.
*/
@@ -1808,7 +1808,7 @@ H5Pget_mdc_config(hid_t plist_id, H5AC_cache_config_t *config_ptr)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "Unknown config version.")
/* If we ever support multiple versions of H5AC_cache_config_t, we
- * will have to get the cannonical version here, and then translate
+ * will have to get the canonical version here, and then translate
* to the version of the structure supplied.
*/
@@ -2322,7 +2322,7 @@ done:
* necessary to represent features used.
* (This is the "make certain to take advantage of <new feature>
* in the file format" use case (maybe <new feature> is smaller
- * or scales better than an ealier version, which would otherwise
+ * or scales better than an earlier version, which would otherwise
* be used))
*
* LOW = H5F_FORMAT_1_2_0, HIGH = H5F_FORMAT_1_6_0 => creates objects
@@ -2549,7 +2549,7 @@ H5Pset_file_image(hid_t fapl_id, void *buf_ptr, size_t buf_len)
/* validate parameters */
if(!(((buf_ptr == NULL) && (buf_len == 0)) || ((buf_ptr != NULL) && (buf_len > 0))))
- HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "inconsistant buf_ptr and buf_len")
+ HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "inconsistent buf_ptr and buf_len")
/* Get the plist structure */
if(NULL == (fapl = H5P_object_verify(fapl_id, H5P_FILE_ACCESS)))
@@ -2652,7 +2652,7 @@ H5Pget_file_image(hid_t fapl_id, void **buf_ptr_ptr, size_t *buf_len_ptr)
if(H5P_peek(fapl, H5F_ACS_FILE_IMAGE_INFO_NAME, &image_info) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get file image info")
- /* verify file image field consistancy */
+ /* verify file image field consistency */
HDassert(((image_info.buffer != NULL) && (image_info.size > 0)) ||
((image_info.buffer == NULL) && (image_info.size == 0)));
@@ -2728,7 +2728,7 @@ H5Pset_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callback
if(H5P_peek(fapl, H5F_ACS_FILE_IMAGE_INFO_NAME, &info) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get old file image info")
- /* verify file image field consistancy */
+ /* verify file image field consistency */
HDassert(((info.buffer != NULL) && (info.size > 0)) ||
((info.buffer == NULL) && (info.size == 0)));
@@ -2804,7 +2804,7 @@ H5Pget_file_image_callbacks(hid_t fapl_id, H5FD_file_image_callbacks_t *callback
if(H5P_peek(fapl, H5F_ACS_FILE_IMAGE_INFO_NAME, &info) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get file image info")
- /* verify file image field consistancy */
+ /* verify file image field consistency */
HDassert(((info.buffer != NULL) && (info.size > 0)) ||
((info.buffer == NULL) && (info.size == 0)));
@@ -2858,7 +2858,7 @@ H5P__file_image_info_copy(void *value)
info = (H5FD_file_image_info_t *)value;
- /* verify file image field consistancy */
+ /* verify file image field consistency */
HDassert(((info->buffer != NULL) && (info->size > 0)) ||
((info->buffer == NULL) && (info->size == 0)));
@@ -2932,7 +2932,7 @@ H5P__file_image_info_free(void *value)
info = (H5FD_file_image_info_t *)value;
- /* Verify file image field consistancy */
+ /* Verify file image field consistency */
HDassert(((info->buffer != NULL) && (info->size > 0)) ||
((info->buffer == NULL) && (info->size == 0)));
diff --git a/src/H5Pfcpl.c b/src/H5Pfcpl.c
index 6b0d2c0..f90dae5 100644
--- a/src/H5Pfcpl.c
+++ b/src/H5Pfcpl.c
@@ -545,7 +545,7 @@ H5Pset_sym_k(hid_t plist_id, unsigned ik, unsigned lk)
HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "istore IK value exceeds maximum B-tree entries");
if(H5P_get(plist, H5F_CRT_BTREE_RANK_NAME, btree_k) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get rank for btree interanl nodes");
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get rank for btree internal nodes");
btree_k[H5B_SNODE_ID] = ik;
if(H5P_set(plist, H5F_CRT_BTREE_RANK_NAME, btree_k) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set rank for btree nodes");
@@ -650,10 +650,10 @@ H5Pset_istore_k(hid_t plist_id, unsigned ik)
/* Set value */
if(H5P_get(plist, H5F_CRT_BTREE_RANK_NAME, btree_k) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get rank for btree interanl nodes");
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get rank for btree internal nodes");
btree_k[H5B_CHUNK_ID] = ik;
if(H5P_set(plist, H5F_CRT_BTREE_RANK_NAME, btree_k) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set rank for btree interanl nodes");
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTSET, FAIL, "can't set rank for btree internal nodes");
done:
FUNC_LEAVE_API(ret_value)
@@ -698,7 +698,7 @@ H5Pget_istore_k(hid_t plist_id, unsigned *ik /*out */ )
/* Get value */
if(ik) {
if(H5P_get(plist, H5F_CRT_BTREE_RANK_NAME, btree_k) < 0)
- HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get rank for btree interanl nodes");
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get rank for btree internal nodes");
*ik = btree_k[H5B_CHUNK_ID];
} /* end if */
diff --git a/src/H5Pint.c b/src/H5Pint.c
index 0e78463..6a0cc14 100644
--- a/src/H5Pint.c
+++ b/src/H5Pint.c
@@ -1398,7 +1398,7 @@ H5P_free_del_name_cb(void *item, void H5_ATTR_UNUSED *key, void H5_ATTR_UNUSED *
NAME
H5P_access_class
PURPOSE
- Internal routine to increment or decrement list & class dependancies on a
+ Internal routine to increment or decrement list & class dependencies on a
property list class
USAGE
herr_t H5P_access_class(pclass,mod)
@@ -1407,7 +1407,7 @@ H5P_free_del_name_cb(void *item, void H5_ATTR_UNUSED *key, void H5_ATTR_UNUSED *
RETURNS
Returns non-negative on success, negative on failure.
DESCRIPTION
- Increment/Decrement the class or list dependancies for a given class.
+ Increment/Decrement the class or list dependencies for a given class.
This routine is the final arbiter on decisions about actually releasing a
class in memory, such action is only taken when the reference counts for
both dependent classes & lists reach zero.
@@ -1425,19 +1425,19 @@ H5P_access_class(H5P_genclass_t *pclass, H5P_class_mod_t mod)
HDassert(mod > H5P_MOD_ERR && mod < H5P_MOD_MAX);
switch(mod) {
- case H5P_MOD_INC_CLS: /* Increment the dependant class count*/
+ case H5P_MOD_INC_CLS: /* Increment the dependent class count*/
pclass->classes++;
break;
- case H5P_MOD_DEC_CLS: /* Decrement the dependant class count*/
+ case H5P_MOD_DEC_CLS: /* Decrement the dependent class count*/
pclass->classes--;
break;
- case H5P_MOD_INC_LST: /* Increment the dependant list count*/
+ case H5P_MOD_INC_LST: /* Increment the dependent list count*/
pclass->plists++;
break;
- case H5P_MOD_DEC_LST: /* Decrement the dependant list count*/
+ case H5P_MOD_DEC_LST: /* Decrement the dependent list count*/
pclass->plists--;
break;
@@ -1586,12 +1586,12 @@ H5P_create_class(H5P_genclass_t *par_class, const char *name, H5P_plist_type_t t
/* Allocate room for the class */
if(NULL == (pclass = H5FL_CALLOC(H5P_genclass_t)))
- HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, NULL, "propery list class allocation failed")
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, NULL, "property list class allocation failed")
/* Set class state */
pclass->parent = par_class;
if(NULL == (pclass->name = H5MM_xstrdup(name)))
- HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, NULL, "propery list class name allocation failed")
+ HGOTO_ERROR(H5E_PLIST, H5E_CANTALLOC, NULL, "property list class name allocation failed")
pclass->type = type;
pclass->nprops = 0; /* Classes are created without properties initially */
pclass->plists = 0; /* No properties lists of this class yet */
@@ -2026,7 +2026,7 @@ done:
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The 'set' callback function may be useful to range check the value being
- set for the property or may perform some tranformation/translation of the
+ set for the property or may perform some transformation/translation of the
value set. The 'get' callback would then [probably] reverse the
transformation, etc. A single 'get' or 'set' callback could handle
multiple properties by performing different actions based on the property
@@ -2258,7 +2258,7 @@ done:
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The 'set' callback function may be useful to range check the value being
- set for the property or may perform some tranformation/translation of the
+ set for the property or may perform some transformation/translation of the
value set. The 'get' callback would then [probably] reverse the
transformation, etc. A single 'get' or 'set' callback could handle
multiple properties by performing different actions based on the property
@@ -2499,7 +2499,7 @@ done:
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The 'set' callback function may be useful to range check the value being
- set for the property or may perform some tranformation/translation of the
+ set for the property or may perform some transformation/translation of the
value set. The 'get' callback would then [probably] reverse the
transformation, etc. A single 'get' or 'set' callback could handle
multiple properties by performing different actions based on the property
@@ -2636,7 +2636,7 @@ H5P__do_prop(H5P_genplist_t *plist, const char *name, H5P_do_plist_op_t plist_op
/* Find property in changed list */
if(NULL != (prop = (H5P_genprop_t *)H5SL_search(plist->props, name))) {
- /* Call the 'found in propery list' callback */
+ /* Call the 'found in property list' callback */
if((*plist_op)(plist, name, prop, udata) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTOPERATE, FAIL, "can't operate on property")
} /* end if */
@@ -4020,7 +4020,7 @@ H5P_iterate_plist(const H5P_genplist_t *plist, hbool_t iter_all_prop, int *idx,
/* Check for iterating over all properties, or just non-default ones */
if(iter_all_prop) {
- /* Walk up the class hiearchy */
+ /* Walk up the class hierarchy */
tclass = plist->pclass;
while(tclass != NULL) {
/* Iterate over properties in property list class */
@@ -4737,7 +4737,7 @@ H5P_copy_prop_pclass(hid_t dst_id, hid_t src_id, const char *name)
/* Sanity check */
HDassert(name);
- /* Get propery list classes */
+ /* Get property list classes */
if(NULL == (src_pclass = (H5P_genclass_t *)H5I_object(src_id)))
HGOTO_ERROR(H5E_PLIST, H5E_NOTFOUND, FAIL, "source property class object doesn't exist")
if(NULL == (dst_pclass = (H5P_genclass_t *)H5I_object(dst_id)))
@@ -4854,8 +4854,8 @@ done:
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
The property list class 'close' callback routine is not called from
- here, it must have been check for and called properly prior to this routine
- being called
+ here, it must have been checked for and called properly prior to this routine
+ being called.
EXAMPLES
REVISION LOG
--------------------------------------------------------------------------*/
@@ -4981,7 +4981,7 @@ H5P_close(void *_plist)
tclass=tclass->parent;
} /* end while */
- /* Decrement class's dependant property list value! */
+ /* Decrement class's dependent property list value! */
if(H5P_access_class(plist->pclass,H5P_MOD_DEC_LST) < 0)
HGOTO_ERROR(H5E_PLIST, H5E_CANTINIT, FAIL, "Can't decrement class ref count")
diff --git a/src/H5Ppkg.h b/src/H5Ppkg.h
index 13463ae..60b2363 100644
--- a/src/H5Ppkg.h
+++ b/src/H5Ppkg.h
@@ -51,10 +51,10 @@ typedef enum {
/* Define enum for modifications to class */
typedef enum {
H5P_MOD_ERR=(-1), /* Indicate an error */
- H5P_MOD_INC_CLS, /* Increment the dependant class count*/
- H5P_MOD_DEC_CLS, /* Decrement the dependant class count*/
- H5P_MOD_INC_LST, /* Increment the dependant list count*/
- H5P_MOD_DEC_LST, /* Decrement the dependant list count*/
+ H5P_MOD_INC_CLS, /* Increment the dependent class count*/
+ H5P_MOD_DEC_CLS, /* Decrement the dependent class count*/
+ H5P_MOD_INC_LST, /* Increment the dependent list count*/
+ H5P_MOD_DEC_LST, /* Decrement the dependent list count*/
H5P_MOD_INC_REF, /* Increment the ID reference count*/
H5P_MOD_DEC_REF, /* Decrement the ID reference count*/
H5P_MOD_MAX /* Upper limit on class modifications */
@@ -89,7 +89,7 @@ struct H5P_genclass_t {
size_t nprops; /* Number of properties in class */
unsigned plists; /* Number of property lists that have been created since the last modification to the class */
unsigned classes; /* Number of classes that have been derived since the last modification to the class */
- unsigned ref_count; /* Number of oustanding ID's open on this class object */
+ unsigned ref_count; /* Number of outstanding ID's open on this class object */
hbool_t deleted; /* Whether this class has been deleted and is waiting for dependent classes & proplists to close */
unsigned revision; /* Revision number of a particular class (global) */
H5SL_t *props; /* Skip list containing properties */
diff --git a/src/H5Ppublic.h b/src/H5Ppublic.h
index a2c0418..58f3d18 100644
--- a/src/H5Ppublic.h
+++ b/src/H5Ppublic.h
@@ -139,7 +139,7 @@ typedef enum H5D_mpio_actual_chunk_opt_mode_t {
typedef enum H5D_mpio_actual_io_mode_t {
/* The following four values are conveniently defined as a bit field so that
- * we can switch from the default to indpendent or collective and then to
+ * we can switch from the default to independent or collective and then to
* mixed without having to check the original value.
*
* NO_COLLECTIVE means that either collective I/O wasn't requested or that
diff --git a/src/H5SMpkg.h b/src/H5SMpkg.h
index a9a4fd9..bb458a7 100644
--- a/src/H5SMpkg.h
+++ b/src/H5SMpkg.h
@@ -96,7 +96,7 @@
#define H5SM_B2_SPLIT_PERCENT 100
#define H5SM_B2_MERGE_PERCENT 40
-#define H5SM_LIST_VERSION 0 /* Verion of Shared Object Header Message List Indexes */
+#define H5SM_LIST_VERSION 0 /* Version of Shared Object Header Message List Indexes */
/****************************/
/* Package Typedefs */
diff --git a/src/H5Sall.c b/src/H5Sall.c
index 11dd8e1..28395b1 100644
--- a/src/H5Sall.c
+++ b/src/H5Sall.c
@@ -432,7 +432,7 @@ H5S__all_copy(H5S_t *dst, const H5S_t H5_ATTR_UNUSED *src, hbool_t H5_ATTR_UNUSE
TRUE if the selection fits within the extent, FALSE if it does not and
Negative on an error.
DESCRIPTION
- Determines if the current selection at the current offet fits within the
+ Determines if the current selection at the current offset fits within the
extent for the dataspace. Offset is irrelevant for this type of selection.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
diff --git a/src/H5Shyper.c b/src/H5Shyper.c
index 47eb573..7a6d1be 100644
--- a/src/H5Shyper.c
+++ b/src/H5Shyper.c
@@ -853,7 +853,7 @@ H5S__hyper_iter_next(H5S_sel_iter_t *iter, size_t nelem)
/* Check if we are finished with the spans in the tree */
if(curr_dim >= 0) {
- /* Walk back down the iterator positions, reseting them */
+ /* Walk back down the iterator positions, resetting them */
while(curr_dim < fast_dim) {
HDassert(curr_span);
HDassert(curr_span->down);
@@ -1037,7 +1037,7 @@ H5S__hyper_iter_next_block(H5S_sel_iter_t *iter)
/* Check if we are finished with the spans in the tree */
if(curr_dim >= 0) {
- /* Walk back down the iterator positions, reseting them */
+ /* Walk back down the iterator positions, resetting them */
while(curr_dim < fast_dim) {
HDassert(curr_span);
HDassert(curr_span->down);
@@ -1704,7 +1704,7 @@ done:
RETURNS
TRUE if the selection fits within the extent, FALSE if it does not
DESCRIPTION
- Determines if the current selection at the current offet fits within the
+ Determines if the current selection at the current offset fits within the
extent for the dataspace.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
@@ -1762,7 +1762,7 @@ done:
TRUE if the selection fits within the extent, FALSE if it does not and
Negative on an error.
DESCRIPTION
- Determines if the current selection at the current offet fits within the
+ Determines if the current selection at the current offset fits within the
extent for the dataspace.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
@@ -2052,7 +2052,7 @@ H5S__hyper_serialize_helper(const H5S_hyper_span_info_t *spans,
HDassert(rank < H5O_LAYOUT_NDIMS);
HDassert(p && pp);
- /* Walk through the list of spans, recursing or outputing them */
+ /* Walk through the list of spans, recursing or outputting them */
curr = spans->head;
while(curr != NULL) {
/* Recurse if this node has down spans */
@@ -2458,7 +2458,7 @@ H5S__hyper_span_blocklist(const H5S_hyper_span_info_t *spans, hsize_t start[],
HDassert(numblocks && *numblocks > 0);
HDassert(buf && *buf);
- /* Walk through the list of spans, recursing or outputing them */
+ /* Walk through the list of spans, recursing or outputting them */
curr = spans->head;
while(curr != NULL && *numblocks > 0) {
/* Recurse if this node has down spans */
@@ -3509,7 +3509,7 @@ done:
NAME
H5S__hyper_add_span_element_helper
PURPOSE
- Add a single elment to a span tree
+ Add a single element to a span tree
USAGE
herr_t H5S_hyper_add_span_element_helper(prev_span, span_tree, rank, coords)
H5S_hyper_span_info_t *span_tree; IN/OUT: Pointer to span tree to append to
@@ -3713,7 +3713,7 @@ done:
NAME
H5S_hyper_add_span_element
PURPOSE
- Add a single elment to a span tree
+ Add a single element to a span tree
USAGE
herr_t H5S_hyper_add_span_element(space, span_tree, rank, coords)
H5S_t *space; IN/OUT: Pointer to dataspace to add coordinate to
@@ -5903,7 +5903,8 @@ H5S__hyper_make_spans(unsigned rank, const hsize_t *start, const hsize_t *stride
last_span = NULL;
/* Generate all the span segments for this dimension */
- for(u = 0, stride_iter = 0; u < count[i]; u++, stride_iter += stride[i]) {
+ for(u = 0, stride_iter = 0; u < count[i]; u++, stride_iter += stride[i])
+ {
H5S_hyper_span_t *span; /* New hyperslab span */
/* Allocate a span node */
@@ -5945,7 +5946,8 @@ H5S__hyper_make_spans(unsigned rank, const hsize_t *start, const hsize_t *stride
} /* end for */
/* Indicate that there is a pointer to this tree */
- down->count = 1;
+ if(down)
+ down->count = 1;
/* Success! Return the head of the list in the slowest changing dimension */
ret_value = down;
@@ -8101,7 +8103,7 @@ H5S__hyper_get_seq_list_gen(const H5S_t *space, H5S_sel_iter_t *iter,
/* Check if we have more spans in the tree */
if(curr_dim >= 0) {
- /* Walk back down the iterator positions, reseting them */
+ /* Walk back down the iterator positions, resetting them */
while((unsigned)curr_dim < fast_dim) {
HDassert(curr_span);
HDassert(curr_span->down);
@@ -8280,7 +8282,7 @@ H5S__hyper_get_seq_list_gen(const H5S_t *space, H5S_sel_iter_t *iter,
break;
} /* end if */
else {
- /* Walk back down the iterator positions, reseting them */
+ /* Walk back down the iterator positions, resetting them */
while((unsigned)curr_dim < fast_dim) {
HDassert(curr_span);
HDassert(curr_span->down);
diff --git a/src/H5Smpio.c b/src/H5Smpio.c
index 5c65119..db81ffc 100644
--- a/src/H5Smpio.c
+++ b/src/H5Smpio.c
@@ -909,10 +909,9 @@ H5S_mpio_hyper_type(const H5S_t *space, size_t elmt_size,
else
inner_type = outer_type;
} /* end for */
-/***************************
-* End of loop, walking
-* thru dimensions.
-***************************/
+/******************************************
+* End of loop, walking through dimensions.
+*******************************************/
/* At this point inner_type is actually the outermost type, even for 0-trip loop */
*new_type = inner_type;
diff --git a/src/H5Snone.c b/src/H5Snone.c
index 19d0b5f..a46a71a 100644
--- a/src/H5Snone.c
+++ b/src/H5Snone.c
@@ -408,7 +408,7 @@ H5S_none_copy(H5S_t *dst, const H5S_t H5_ATTR_UNUSED *src, hbool_t H5_ATTR_UNUSE
TRUE if the selection fits within the extent, FALSE if it does not and
Negative on an error.
DESCRIPTION
- Determines if the current selection at the current offet fits within the
+ Determines if the current selection at the current offset fits within the
extent for the dataspace. Offset is irrelevant for this type of selection.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
diff --git a/src/H5Spoint.c b/src/H5Spoint.c
index 442bb2a..fb8e311 100644
--- a/src/H5Spoint.c
+++ b/src/H5Spoint.c
@@ -676,7 +676,7 @@ done:
TRUE if the selection fits within the extent, FALSE if it does not and
Negative on an error.
DESCRIPTION
- Determines if the current selection at the current offet fits within the
+ Determines if the current selection at the current offset fits within the
extent for the dataspace.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
diff --git a/src/H5Sselect.c b/src/H5Sselect.c
index 4462295..ec74523 100644
--- a/src/H5Sselect.c
+++ b/src/H5Sselect.c
@@ -160,7 +160,7 @@ H5S_select_release(H5S_t *ds)
HDassert(ds);
/* Call the selection type's release function */
- if((ret_value = (*ds->select.type->release)(ds)) < 0)
+ if((ds->select.type) && ((ret_value = (*ds->select.type->release)(ds)) < 0))
HGOTO_ERROR(H5E_DATASPACE, H5E_CANTRELEASE, FAIL, "unable to release selection")
done:
@@ -361,7 +361,7 @@ H5S_get_select_npoints(const H5S_t *space)
TRUE if the selection fits within the extent, FALSE if it does not and
Negative on an error.
DESCRIPTION
- Determines if the current selection at the current offet fits within the
+ Determines if the current selection at the current offset fits within the
extent for the dataspace.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
@@ -403,7 +403,7 @@ done:
TRUE if the selection fits within the extent, FALSE if it does not and
Negative on an error.
DESCRIPTION
- Determines if the current selection at the current offet fits within the
+ Determines if the current selection at the current offset fits within the
extent for the dataspace.
GLOBAL VARIABLES
COMMENTS, BUGS, ASSUMPTIONS
diff --git a/src/H5T.c b/src/H5T.c
index c220890..fa97506 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -309,7 +309,7 @@ static H5T_path_t *H5T__path_find_real(const H5T_t *src, const H5T_t *dst,
/* Library Private Variables */
/*****************************/
-/* The native endianess of the platform */
+/* The native endianness of the platform */
H5T_order_t H5T_native_order_g = H5T_ORDER_ERROR;
diff --git a/src/H5Tcommit.c b/src/H5Tcommit.c
index 4e4a551..1719f8f 100644
--- a/src/H5Tcommit.c
+++ b/src/H5Tcommit.c
@@ -385,7 +385,7 @@ H5T__commit(H5F_t *file, H5T_t *type, hid_t tcpl_id)
if(H5T_set_version(file, type) < 0)
HGOTO_ERROR(H5E_DATASET, H5E_CANTSET, FAIL, "can't set version of datatype")
- /* Calculate message size infomation, for creating object header */
+ /* Calculate message size information, for creating object header */
dtype_size = H5O_msg_size_f(file, tcpl_id, H5O_DTYPE_ID, type, (size_t)0);
HDassert(dtype_size);
diff --git a/src/H5Tconv.c b/src/H5Tconv.c
index f3af9e1..803a6da 100644
--- a/src/H5Tconv.c
+++ b/src/H5Tconv.c
@@ -109,7 +109,7 @@
* least as large as the destination. Overflows can occur when
* the destination is narrower than the source.
*
- * xF: Integers to float-point(float or double) values where the desination
+ * xF: Integers to float-point(float or double) values where the destination
* is at least as wide as the source. This case cannot generate
* overflows.
*
@@ -2102,7 +2102,7 @@ H5T__conv_struct_subset(const H5T_cdata_t *cdata)
*
* For each element do
* For I=1..NELMTS do
- * If sizeof detination type <= sizeof source type then
+ * If sizeof destination type <= sizeof source type then
* Convert member to destination type;
* Move member as far left as possible;
*
@@ -2314,7 +2314,7 @@ done:
* function. The algorithm is basically:
*
* For each member of the struct
- * If sizeof detination type <= sizeof source type then
+ * If sizeof destination type <= sizeof source type then
* Convert member to destination type for all elements
* Move memb to BKG buffer for all elements
* Else
@@ -2421,7 +2421,7 @@ H5T__conv_struct_opt(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata,
offset -= src_memb->size;
if(dst_memb->size > src->shared->size-offset) {
cdata->priv = H5T_conv_struct_free(priv);
- HGOTO_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, FAIL, "convertion is unsupported by this function")
+ HGOTO_ERROR(H5E_DATATYPE, H5E_UNSUPPORTED, FAIL, "conversion is unsupported by this function")
} /* end if */
} /* end if */
} /* end for */
@@ -4250,7 +4250,7 @@ H5T__conv_f_f(hid_t src_id, hid_t dst_id, H5T_cdata_t *cdata, size_t nelmts,
/*
* The exponent is too small to fit in the exponent field,
* but by shifting the mantissa to the right we can
- * accomodate that value. The mantissa of course is no
+ * accommodate that value. The mantissa of course is no
* longer normalized.
*/
mrsh += (size_t)(1 - expo);
diff --git a/src/H5Toffset.c b/src/H5Toffset.c
index 668e730..c0e94fc 100644
--- a/src/H5Toffset.c
+++ b/src/H5Toffset.c
@@ -33,12 +33,12 @@ static herr_t H5T_set_offset(const H5T_t *dt, size_t offset);
* Function: H5Tget_offset
*
* Purpose: Retrieves the bit offset of the first significant bit. The
- * signficant bits of an atomic datum can be offset from the
+ * significant bits of an atomic datum can be offset from the
* beginning of the memory for that datum by an amount of
* padding. The `offset' property specifies the number of bits
* of padding that appear to the "right of" the value. That is,
* if we have a 32-bit datum with 16-bits of precision having
- * the value 0x1122 then it will be layed out in memory as (from
+ * the value 0x1122 then it will be laid out in memory as (from
* small byte address toward larger byte addresses):
*
* Big Big Little Little
@@ -84,12 +84,12 @@ done:
* Function: H5T_get_offset
*
* Purpose: Retrieves the bit offset of the first significant bit. The
- * signficant bits of an atomic datum can be offset from the
+ * significant bits of an atomic datum can be offset from the
* beginning of the memory for that datum by an amount of
* padding. The `offset' property specifies the number of bits
* of padding that appear to the "right of" the value. That is,
* if we have a 32-bit datum with 16-bits of precision having
- * the value 0x1122 then it will be layed out in memory as (from
+ * the value 0x1122 then it will be laid out in memory as (from
* small byte address toward larger byte addresses):
*
* Big Big Little Little
@@ -134,12 +134,12 @@ done:
* Function: H5Tset_offset
*
* Purpose: Sets the bit offset of the first significant bit. The
- * signficant bits of an atomic datum can be offset from the
+ * significant bits of an atomic datum can be offset from the
* beginning of the memory for that datum by an amount of
* padding. The `offset' property specifies the number of bits
* of padding that appear to the "right of" the value. That is,
* if we have a 32-bit datum with 16-bits of precision having
- * the value 0x1122 then it will be layed out in memory as (from
+ * the value 0x1122 then it will be laid out in memory as (from
* small byte address toward larger byte addresses):
*
* Big Big Little Little
@@ -203,12 +203,12 @@ done:
* Function: H5T_set_offset
*
* Purpose: Sets the bit offset of the first significant bit. The
- * signficant bits of an atomic datum can be offset from the
+ * significant bits of an atomic datum can be offset from the
* beginning of the memory for that datum by an amount of
* padding. The `offset' property specifies the number of bits
* of padding that appear to the "right of" the value. That is,
* if we have a 32-bit datum with 16-bits of precision having
- * the value 0x1122 then it will be layed out in memory as (from
+ * the value 0x1122 then it will be laid out in memory as (from
* small byte address toward larger byte addresses):
*
* Big Big Little Little
diff --git a/src/H5Tpkg.h b/src/H5Tpkg.h
index 96132b0..e1b996c 100644
--- a/src/H5Tpkg.h
+++ b/src/H5Tpkg.h
@@ -295,7 +295,7 @@ typedef enum H5T_state_t {
H5T_STATE_OPEN /*named constant, open object header */
} H5T_state_t;
- /* This struct is shared between all occurances of an open named type */
+ /* This struct is shared between all occurrences of an open named type */
typedef struct H5T_shared_t {
hsize_t fo_count; /* number of references to this file object */
H5T_state_t state; /*current state of the type */
diff --git a/src/H5Tprivate.h b/src/H5Tprivate.h
index 8051b6d..89cdcfd 100644
--- a/src/H5Tprivate.h
+++ b/src/H5Tprivate.h
@@ -100,7 +100,7 @@ typedef struct H5T_subset_info_t {
/* Forward declarations for prototype arguments */
struct H5O_t;
-/* The native endianess of the platform */
+/* The native endianness of the platform */
H5_DLLVAR H5T_order_t H5T_native_order_g;
/* Private functions */
diff --git a/src/H5Znbit.c b/src/H5Znbit.c
index c0afc38..fe0041c 100644
--- a/src/H5Znbit.c
+++ b/src/H5Znbit.c
@@ -558,7 +558,7 @@ H5Z_set_parms_array(const H5T_t *type, unsigned *cd_values_index,
H5T_t *dtype_base = NULL; /* Array datatype's base datatype */
H5T_class_t dtype_base_class; /* Array datatype's base datatype's class */
size_t dtype_size; /* Array datatype's size (in bytes) */
- htri_t is_vlstring; /* flag indicating if datatype is varible-length string */
+ htri_t is_vlstring; /* flag indicating if datatype is variable-length string */
herr_t ret_value=SUCCEED; /* Return value */
FUNC_ENTER_NOAPI_NOINIT
@@ -667,7 +667,7 @@ H5Z_set_parms_compound(const H5T_t *type, unsigned *cd_values_index,
size_t dtype_member_offset; /* Compound datatype's current member datatype's offset (in bytes) */
size_t dtype_next_member_offset;/* Compound datatype's next member datatype's offset (in bytes) */
size_t dtype_size; /* Compound datatype's size (in bytes) */
- htri_t is_vlstring; /* flag indicating if datatype is varible-length string */
+ htri_t is_vlstring; /* flag indicating if datatype is variable-length string */
unsigned u; /* Local index variable */
herr_t ret_value = SUCCEED; /* Return value */
diff --git a/src/H5Zpublic.h b/src/H5Zpublic.h
index fcb2d37..0df05f0 100644
--- a/src/H5Zpublic.h
+++ b/src/H5Zpublic.h
@@ -50,7 +50,7 @@ typedef int H5Z_filter_t;
* unlimited amount, but currently each
* filter uses a bit in a 32-bit field,
* so the format would have to be
- * changed to accomodate that)
+ * changed to accommodate that)
*/
/* Flags for filter definition (stored) */
diff --git a/src/H5Zscaleoffset.c b/src/H5Zscaleoffset.c
index d139696..cdf31a4 100644
--- a/src/H5Zscaleoffset.c
+++ b/src/H5Zscaleoffset.c
@@ -988,7 +988,7 @@ H5Z_set_local_scaleoffset(hid_t dcpl_id, hid_t type_id, hid_t space_id)
if(status == H5D_FILL_VALUE_UNDEFINED)
cd_values[H5Z_SCALEOFFSET_PARM_FILAVAIL] = H5Z_SCALEOFFSET_FILL_UNDEFINED;
else {
- int need_convert = FALSE; /* Flag indicating convertion of byte order */
+ int need_convert = FALSE; /* Flag indicating conversion of byte order */
cd_values[H5Z_SCALEOFFSET_PARM_FILAVAIL] = H5Z_SCALEOFFSET_FILL_DEFINED;
@@ -1047,7 +1047,7 @@ H5Z_filter_scaleoffset(unsigned flags, size_t cd_nelmts, const unsigned cd_value
uint32_t minbits = 0; /* minimum number of bits to store values */
unsigned long long minval= 0; /* minimum value of input buffer */
enum H5Z_scaleoffset_t type; /* memory type corresponding to dataset datatype */
- int need_convert = FALSE; /* flag indicating convertion of byte order */
+ int need_convert = FALSE; /* flag indicating conversion of byte order */
unsigned char *outbuf = NULL; /* pointer to new output buffer */
unsigned buf_offset = 21; /* buffer offset because of parameters stored in file */
unsigned i; /* index */
diff --git a/src/H5Ztrans.c b/src/H5Ztrans.c
index d4b59a6..67646a0 100644
--- a/src/H5Ztrans.c
+++ b/src/H5Ztrans.c
@@ -329,7 +329,7 @@ static void H5Z_print(H5Z_node *tree, FILE *stream);
}
/* The difference of this macro from H5Z_XFORM_DO_OP3 is that it handles the operations when the left operand is empty, like -x or +x.
- * The reason that it's seperated from H5Z_XFORM_DO_OP3 is because compilers don't accept operations like *x or /x. So in H5Z_do_op,
+ * The reason that it's separated from H5Z_XFORM_DO_OP3 is because compilers don't accept operations like *x or /x. So in H5Z_do_op,
* these two macros are called in different ways. (SLU 2012/3/20)
*/
#define H5Z_XFORM_DO_OP6(OP) \
@@ -967,7 +967,7 @@ done:
/*-------------------------------------------------------------------------
* Function: H5Z_new_node
- * Purpose: Create and initilize a new H5Z_node structure.
+ * Purpose: Create and initialize a new H5Z_node structure.
* Return: Success: Valid H5Z_node ptr
* NULLure: NULL
* Programmer: Bill Wendling
@@ -999,7 +999,7 @@ done:
* Purpose: If the transform is trivial, this function applies it.
* Otherwise, it calls H5Z_xform_eval_full to do the full
* transform.
- * Return: SUCCEED if transform applied succesfully, FAIL otherwise
+ * Return: SUCCEED if transform applied successfully, FAIL otherwise
* Programmer: Leon Arber
* 5/1/04
* Modifications:
@@ -1485,7 +1485,7 @@ H5Z_xform_reduce_tree(H5Z_node* tree)
* Purpose: If the root of the tree passed in points to a simple
* arithmetic operation and the left and right subtrees are both
* integer or floating point values, this function does that
- * operation, free the left and rigt subtrees, and replaces
+ * operation, free the left and right subtrees, and replaces
* the root with the result of the operation.
* Return: None.
* Programmer: Leon Arber
diff --git a/src/H5detect.c b/src/H5detect.c
index 1c5554e..2d33a3d 100644
--- a/src/H5detect.c
+++ b/src/H5detect.c
@@ -43,7 +43,7 @@ static const char *FileHeader = "\n\
* system or configure has detected those Unix
* features which aren't available. We're not
* running on a Vax or other machine with mixed
- * endianess.
+ * endianness.
*
* Modifications:
*
@@ -55,13 +55,13 @@ static const char *FileHeader = "\n\
#include "H5Rpublic.h"
#if defined(__has_attribute)
-#if __has_attribute(no_sanitize)
-#define HDF_NO_UBSAN __attribute__((no_sanitize("undefined")))
+# if __has_attribute(no_sanitize_address)
+# define HDF_NO_UBSAN __attribute__((no_sanitize_address))
+# else
+# define HDF_NO_UBSAN
+# endif
#else
-#define HDF_NO_UBSAN
-#endif
-#else
-#define HDF_NO_UBSAN
+# define HDF_NO_UBSAN
#endif
#define MAXDETECT 64
@@ -695,7 +695,7 @@ H5T__init_native(void)\n\
FUNC_ENTER_PACKAGE\n");
for(i = 0; i < nd; i++) {
- /* The native endianess of this machine */
+ /* The native endianness of this machine */
/* The INFO.perm now contains `-1' for bytes that aren't used and
* are always zero. This happens on the Cray for `short' where
* sizeof(short) is 8, but only the low-order 4 bytes are ever used.
@@ -1079,8 +1079,8 @@ fix_order(int n, int last, int *perm, const char **mesg)
} else {
/*
* Bi-endian machines like VAX.
- * (NOTE: This is not an actual determination of the VAX-endianess.
- * It could have some other endianess and fall into this
+ * (NOTE: This is not an actual determination of the VAX-endianness.
+ * It could have some other endianness and fall into this
* case - JKM & QAK)
*/
HDassert(0 == n % 2);
@@ -1111,7 +1111,7 @@ fix_order(int n, int last, int *perm, const char **mesg)
*
* This function assumes that the exponent occupies higher
* order bits than the mantissa and that the most significant
- * bit of the mantissa is next to the least signficant bit
+ * bit of the mantissa is next to the least significant bit
* of the exponent.
*
*
@@ -1271,7 +1271,7 @@ mark. Bits of integer types are printed as\n\
If the most significant bit of the normalized\n\
mantissa (always a `1' except for `0.0') is\n\
not stored then an `implicit=yes' appears\n\
-under the field description. In thie case,\n\
+under the field description. In this case,\n\
the radix point is still assumed to be\n\
before the first `M' but after the implicit\n\
bit.\n";
@@ -1675,11 +1675,13 @@ detect_alignments(void)
*/
static int verify_signal_handlers(int signum, void (*handler)(int))
{
-#if defined(__has_feature)
+#if defined(__has_feature) /* Clang */
#if __has_feature(address_sanitizer) || __has_feature(thread_sanitizer)
/* Under the address and thread sanitizers, don't raise any signals. */
return 0;
#endif
+#elif defined(__SANITIZE_ADDRESS__) || defined(__SANITIZE_THREAD__) /* GCC */
+ return 0;
#endif
void (*save_handler)(int) = HDsignal(signum, handler);
volatile int i, val;
diff --git a/src/H5private.h b/src/H5private.h
index 6334f39..8974e46 100644
--- a/src/H5private.h
+++ b/src/H5private.h
@@ -116,7 +116,7 @@
#endif
/*
- * flock() in sys/file.h is used for the implemention of file locking.
+ * flock() in sys/file.h is used for the implementation of file locking.
*/
#if defined(H5_HAVE_FLOCK) && defined(H5_HAVE_SYS_FILE_H)
# include <sys/file.h>
@@ -132,7 +132,7 @@
/*
* Unix ioctls. These are used by h5ls (and perhaps others) to determine a
- * resonable output width.
+ * reasonable output width.
*/
#ifdef H5_HAVE_SYS_IOCTL_H
# include <sys/ioctl.h>
diff --git a/src/H5public.h b/src/H5public.h
index 9157366..a4c80cd 100644
--- a/src/H5public.h
+++ b/src/H5public.h
@@ -115,7 +115,7 @@ extern "C" {
/*
* Status return values. Failed integer functions in HDF5 result almost
* always in a negative value (unsigned failing functions sometimes return
- * zero for failure) while successfull return is non-negative (often zero).
+ * zero for failure) while successful return is non-negative (often zero).
* The negative failure value is most commonly -1, but don't bet on it. The
* proper way to detect failure is something like:
*
@@ -298,7 +298,7 @@ typedef enum {
} H5_iter_order_t;
/* Iteration callback values */
-/* (Actually, any postive value will cause the iterator to stop and pass back
+/* (Actually, any positive value will cause the iterator to stop and pass back
* that positive value to the function that called the iterator)
*/
#define H5_ITER_ERROR (-1)
diff --git a/src/H5system.c b/src/H5system.c
index 719b7e0..186d8fa 100644
--- a/src/H5system.c
+++ b/src/H5system.c
@@ -294,13 +294,13 @@ HDfprintf(FILE *stream, const char *fmt, ...)
unsigned short x = (unsigned short)va_arg(ap, unsigned int);
n = fprintf(stream, format_templ, x);
} else if(!*modifier) {
- unsigned int x = va_arg(ap, unsigned int); /*lint !e732 Loss of sign not really occuring */
+ unsigned int x = va_arg(ap, unsigned int); /*lint !e732 Loss of sign not really occurring */
n = fprintf(stream, format_templ, x);
} else if(!HDstrcmp(modifier, "l")) {
- unsigned long x = va_arg(ap, unsigned long); /*lint !e732 Loss of sign not really occuring */
+ unsigned long x = va_arg(ap, unsigned long); /*lint !e732 Loss of sign not really occurring */
n = fprintf(stream, format_templ, x);
} else {
- uint64_t x = va_arg(ap, uint64_t); /*lint !e732 Loss of sign not really occuring */
+ uint64_t x = va_arg(ap, uint64_t); /*lint !e732 Loss of sign not really occurring */
n = fprintf(stream, format_templ, x);
}
break;
@@ -333,7 +333,7 @@ HDfprintf(FILE *stream, const char *fmt, ...)
case 'a':
{
- haddr_t x = va_arg(ap, haddr_t); /*lint !e732 Loss of sign not really occuring */
+ haddr_t x = va_arg(ap, haddr_t); /*lint !e732 Loss of sign not really occurring */
if(H5F_addr_defined(x)) {
len = 0;
@@ -387,7 +387,7 @@ HDfprintf(FILE *stream, const char *fmt, ...)
case 's':
case 'p':
{
- char *x = va_arg(ap, char*); /*lint !e64 Type mismatch not really occuring */
+ char *x = va_arg(ap, char*); /*lint !e64 Type mismatch not really occurring */
n = fprintf(stream, format_templ, x);
}
break;