Sync develop branch changes since 2/16 to hdf5_1_14 branch (#4058)

* Remove oneapi return value warning. (#4028)

* Replaced last sprintf with snprintf (#4007)

* Replaced last sprintf with snprintf

To have the size of the buffer, it was required to change a function signature, and change all users of it.

In most cases, determining the buffer size wasn't  trivial and so SIZE_MAX is passed. But at least this improves the infrastructure. Someone can later figure out the correct sizes.

* Test vlen sequence IO in API tests (#4027)

* Check argument for CMake REGEX FCMangle.h. (#4029)

* Replace deprecated Fortran 'include mpif.h' with 'USE mpi' (#4031)

With MPI 4.1 the use of the mpif.h include file has been deprecated. Codes
should transition to USE mpi or USE mpi_f08.

Signed-off-by: Christoph Niethammer <niethammer@hlrs.de>

* Fix H5F_get_access_plist to copy file locking settings (#4030)

H5F_get_access_plist previously did not copy over the file locking settings
from a file into the new File Access Property List that it creates. This would
make it difficult to match the file locking settings between an external file
and its parent file.

* Fix missing NOT from if check in HL folder (#4036)

* Fix the datatype passed to H5*exists_async APIs in tests. (#4033)

Add a new testing function to verify C_BOOL values.

* Add deb and rpm binaries to snapshots (#4035)

* Update and Add general INSTALL (#4016)

* Improve performance of flushing single objects (#4017)

Improve performance of flushing a single object, and remove metadata
cache flush markers

* Fix memory leak in H5LTopen_file_image when H5LT_FILE_IMAGE_DONT_COPY flag is used (#4021)

When the H5LT_FILE_IMAGE_DONT_COPY flag is passed to H5LTopen_file_image, the internally-allocated
udata structure gets leaked as the core file driver doesn't have a way to determine when or if it
needs to call the 'udata_free' callback. This has been fixed by freeing the udata structure when
the 'image_free' callback gets made during file close, where the file is holding the last reference
to the udata structure.

* Fix allocating too much memory in dset API test (#4041)

* Don't try to load general-19 warnings file for icc (#4042)

The Autools Classic Intel compiler configuration attempts to load a file
named `general-19` from the intel-warnings/classic directory, which does
not exist.

This removes the attempted load of the file.

* Remove unused AIX cross-compile cache overrides (#4043)

The ibm-aix Autotools config file had some unmaintained and unnecessary
Autoconf cache overrides. These have been removed.

* Consolidate Autotools linux files (#4044)

There are many architecture-specific linux files in the config
directory, all of which simply redirect to linux-gnulibc1.

This change renames linux-gnulibc1 to linux-gnu and deletes the more
specific files.

* Remove check for gettimeofday + tz in CMake (#4045)

This is not used in the library

* Remove limitations on preset generators (#4051)

* Fix issue with FAPL file locking setting inheriting test (#4053)

Fixes an issue where the HDF5_USE_FILE_LOCKING environment variable being
set can interfere with the file locking setting that the test expects to
be returned.

* Bump the github-actions group with 2 updates (#4054)

Bumps the github-actions group with 2 updates: [actions/download-artifact](https://github.com/actions/download-artifact) and [github/codeql-action](https://github.com/github/codeql-action).

* Fix VOL-compatibility issues in External Link API test  (#4039)

Fix link API tests with incorrect filename

* Add upddated cmake tools from source location (#4040)

* Add options to allow tools type selection and naming (#4046)

* Improve error messages when tools attempt to use non-enabled S3 and HDFS VFDs. (#4047)

* Correct several 1.15/1.15.0 references to 1.14/1.14.4.

* Ignore HDF5Examples/CMakeUserPresets.json

1 files changed, 30 insertions, 49 deletions

diff --git a/src/H5C.c b/src/H5C.c
index eb6e49e..1713e83 100644
--- a/src/H5C.c
+++ b/src/H5C.c
@@ -493,7 +493,7 @@ H5C_dest(H5F_t *f)
 #endif /* H5AC_DUMP_IMAGE_STATS_ON_CLOSE */
 
     /* Enable the slist, as it is needed in the flush */
-    if (H5C_set_slist_enabled(f->shared->cache, true, false) < 0)
+    if (H5C_set_slist_enabled(f->shared->cache, true, true) < 0)
         HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "set slist enabled failed");
 
     /* Flush and invalidate all cache entries */
@@ -567,7 +567,7 @@ H5C_evict(H5F_t *f)
     assert(f);
 
     /* Enable the slist, as it is needed in the flush */
-    if (H5C_set_slist_enabled(f->shared->cache, true, false) < 0)
+    if (H5C_set_slist_enabled(f->shared->cache, true, true) < 0)
         HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "set slist enabled failed");
 
     /* Flush and invalidate all cache entries except the pinned entries */
@@ -575,7 +575,7 @@ H5C_evict(H5F_t *f)
         HGOTO_ERROR(H5E_CACHE, H5E_CANTFLUSH, FAIL, "unable to evict entries in the cache");
 
     /* Disable the slist */
-    if (H5C_set_slist_enabled(f->shared->cache, false, true) < 0)
+    if (H5C_set_slist_enabled(f->shared->cache, false, false) < 0)
         HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "set slist disabled failed");
 
 done:
@@ -1042,41 +1042,32 @@ done:
  *
  *              1) Verifies that the slist is empty.
  *
- *              2) Scans the index list, and inserts all dirty entries
- *                 into the slist.
+ *              2) If the populate_slist parameter is true, scans the
+ *                 index list, and inserts all dirty entries into the
+ *                 slist.
  *
  *              3) Sets cache_ptr->slist_enabled = true.
  *
- *              Note that the clear_slist parameter is ignored if
- *              the slist_enabed parameter is true.
- *
  *
  *              If the slist_enabled_parameter is false, the function
- *              shuts down the slist.
- *
- *              Normally the slist will be empty at this point, however
- *              that need not be the case if H5C_flush_cache() has been
- *              called with the H5C__FLUSH_MARKED_ENTRIES_FLAG.
- *
- *              Thus shutdown proceeds as follows:
+ *              shuts down the slist:
  *
  *              1) Test to see if the slist is empty.  If it is, proceed
  *                 to step 3.
  *
- *              2) Test to see if the clear_slist parameter is true.
- *
- *                 If it is, remove all entries from the slist.
- *
- *                 If it isn't, throw an error.
+ *              2) Remove all entries from the slist.
  *
  *              3) set cache_ptr->slist_enabled = false.
  *
+ *              Note that the populate_slist parameter is ignored if
+ *              the slist_enabed parameter is false.
+ *
  * Return:      SUCCEED on success, and FAIL on failure.
  *
  *-------------------------------------------------------------------------
  */
 herr_t
-H5C_set_slist_enabled(H5C_t *cache_ptr, bool slist_enabled, bool clear_slist)
+H5C_set_slist_enabled(H5C_t *cache_ptr, bool slist_enabled, bool populate_slist)
 {
     H5C_cache_entry_t *entry_ptr;
     herr_t             ret_value = SUCCEED; /* Return value */
@@ -1097,40 +1088,30 @@ H5C_set_slist_enabled(H5C_t *cache_ptr, bool slist_enabled, bool clear_slist)
          */
         cache_ptr->slist_enabled = true;
 
-        /* scan the index list and insert all dirty entries in the slist */
-        entry_ptr = cache_ptr->il_head;
-        while (entry_ptr != NULL) {
-            if (entry_ptr->is_dirty)
-                H5C__INSERT_ENTRY_IN_SLIST(cache_ptr, entry_ptr, FAIL);
-            entry_ptr = entry_ptr->il_next;
-        }
+        if (populate_slist) {
+            /* scan the index list and insert all dirty entries in the slist */
+            entry_ptr = cache_ptr->il_head;
+            while (entry_ptr != NULL) {
+                if (entry_ptr->is_dirty)
+                    H5C__INSERT_ENTRY_IN_SLIST(cache_ptr, entry_ptr, FAIL);
+                entry_ptr = entry_ptr->il_next;
+            }
 
-        /* we don't maintain a dirty index len, so we can't do a cross
-         * check against it.  Note that there is no point in cross checking
-         * against the dirty LRU size, as the dirty LRU may not be maintained,
-         * and in any case, there is no requirement that all dirty entries
-         * will reside on the dirty LRU.
-         */
-        assert(cache_ptr->dirty_index_size == cache_ptr->slist_size);
+            /* we don't maintain a dirty index len, so we can't do a cross
+             * check against it.  Note that there is no point in cross checking
+             * against the dirty LRU size, as the dirty LRU may not be maintained,
+             * and in any case, there is no requirement that all dirty entries
+             * will reside on the dirty LRU.
+             */
+            assert(cache_ptr->dirty_index_size == cache_ptr->slist_size);
+        }
     }
     else { /* take down the skip list */
         if (!cache_ptr->slist_enabled)
             HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "slist already disabled?");
 
-        if ((cache_ptr->slist_len != 0) || (cache_ptr->slist_size != 0)) {
-            if (clear_slist) {
-                H5SL_node_t *node_ptr;
-
-                node_ptr = H5SL_first(cache_ptr->slist_ptr);
-                while (node_ptr != NULL) {
-                    entry_ptr = (H5C_cache_entry_t *)H5SL_item(node_ptr);
-                    H5C__REMOVE_ENTRY_FROM_SLIST(cache_ptr, entry_ptr, false, FAIL);
-                    node_ptr = H5SL_first(cache_ptr->slist_ptr);
-                }
-            }
-            else
-                HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "slist not empty?");
-        }
+        if ((cache_ptr->slist_len != 0) || (cache_ptr->slist_size != 0))
+            HGOTO_ERROR(H5E_CACHE, H5E_SYSTEM, FAIL, "slist not empty?");
 
         cache_ptr->slist_enabled = false;