Extract a subroutine that closes chunk indices,

H5D__chunk_index_close(), and call it in H5D__chunk_read() after reading
a chunked dataset.  In this way, indices based on extensible arrays and
v2 B-trees do not leave pinned/tagged entries in the metadata cache that
we cannot evict/refresh when we load changes from the shadow file.

Make some changes to the v1 B-tree code that set the pointer to the
closed B-tree to NULL and, further, tolerate a NULL pointer where
previously that was impossible.

1 files changed, 48 insertions, 12 deletions

diff --git a/src/H5Dchunk.c b/src/H5Dchunk.c
index 903c15c..556f61b 100644
--- a/src/H5Dchunk.c
+++ b/src/H5Dchunk.c
@@ -266,6 +266,8 @@ static herr_t H5D__chunk_flush(H5D_t *dset);
 static herr_t H5D__chunk_io_term(const H5D_chunk_map_t *fm);
 static herr_t H5D__chunk_dest(H5D_t *dset);
 
+static herr_t H5D__chunk_index_close(H5D_t *);
+
 /* Chunk query operation callbacks */
 static int H5D__get_num_chunks_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
 static int H5D__get_chunk_info_cb(const H5D_chunk_rec_t *chunk_rec, void *_udata);
@@ -2625,6 +2627,10 @@ H5D__chunk_read(H5D_io_info_t *io_info, const H5D_type_info_t *type_info,
         chunk_node = H5D_CHUNK_GET_NEXT_NODE(fm, chunk_node);
     } /* end while */
 
+    if(H5D__chunk_index_close(io_info->dset) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL,
+            "unable to close chunk index")
+
 done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* H5D__chunk_read() */
@@ -2882,6 +2888,35 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5D__chunk_io_term() */
 
+/* Close the given dataset's chunk index.
+ *
+ * A useful side-effect of closing the chunk index is the release
+ * pinned/tagged metadata cache entries connected with the index.
+ */
+static herr_t
+H5D__chunk_index_close(H5D_t *dset)
+{
+    H5D_chk_idx_info_t idx_info;
+    H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk);
+    herr_t      ret_value = SUCCEED;       /* Return value */
+
+    FUNC_ENTER_STATIC
+
+    H5D_CHUNK_STORAGE_INDEX_CHK(sc);
+
+    /* Compose chunked index info struct */
+    idx_info.f = dset->oloc.file;
+    idx_info.pline = &dset->shared->dcpl_cache.pline;
+    idx_info.layout = &dset->shared->layout.u.chunk;
+    idx_info.storage = sc;
+
+    /* Free any index structures */
+    if(sc->ops->dest && (sc->ops->dest)(&idx_info) < 0)
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+}
 
 /*-------------------------------------------------------------------------
  * Function:    H5D__chunk_dest
@@ -2899,18 +2934,15 @@ done:
 static herr_t
 H5D__chunk_dest(H5D_t *dset)
 {
-    H5D_chk_idx_info_t idx_info;        /* Chunked index info */
     H5D_rdcc_t    *rdcc = &(dset->shared->cache.chunk);   /* Dataset's chunk cache */
     H5D_rdcc_ent_t    *ent = NULL, *next = NULL;      /* Pointer to current & next cache entries */
     int        nerrors = 0;            /* Accumulated count of errors */
-    H5O_storage_chunk_t *sc = &(dset->shared->layout.storage.u.chunk);
     herr_t      ret_value = SUCCEED;       /* Return value */
 
     FUNC_ENTER_STATIC_TAG(dset->oloc.addr)
 
     /* Sanity checks */
     HDassert(dset);
-    H5D_CHUNK_STORAGE_INDEX_CHK(sc);
 
     /* Flush all the cached chunks */
     for(ent = rdcc->head; ent; ent = next) {
@@ -2928,15 +2960,19 @@ H5D__chunk_dest(H5D_t *dset)
         rdcc->slot = H5FL_SEQ_FREE(H5D_rdcc_ent_ptr_t, rdcc->slot);
     HDmemset(rdcc, 0, sizeof(H5D_rdcc_t));
 
-    /* Compose chunked index info struct */
-    idx_info.f = dset->oloc.file;
-    idx_info.pline = &dset->shared->dcpl_cache.pline;
-    idx_info.layout = &dset->shared->layout.u.chunk;
-    idx_info.storage = sc;
-
-    /* Free any index structures */
-    if(sc->ops->dest && (sc->ops->dest)(&idx_info) < 0)
-        HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL, "unable to release chunk index info")
+    /* Stopgap fix for VFD SWMR: close the chunk index so that
+     * pinned/tagged entries in the metadata cache (MDC) are released.
+     *
+     * Extensible chunked datasets use extensible arrays or btrees as
+     * chunk indices.  Open chunk indices leave pinned/tagged entries
+     * in the MDC, and VFD SWMR cannot (yet) evict or refresh those
+     * entries.  After we write refresh routines for those entries, this
+     * stopgap fix can go away.
+     */
+    if (H5D__chunk_index_close(dset) < 0) {
+        HGOTO_ERROR(H5E_DATASET, H5E_CANTFREE, FAIL,
+            "unable to close chunk index")
+    }
 
 done:
     FUNC_LEAVE_NOAPI_TAG(ret_value)