[svn-r28912] Merge of r28908 from revise_chunks.

Tested on: 64-bit Ubuntu 15.10 (Linux 4.2.0 x86_64) gcc 5.2.1
           autotools serial w/ C++ and Fortran

11 files changed, 163 insertions, 9 deletions

diff --git a/src/H5B2.c b/src/H5B2.c
index b1371d9..bdc79bd 100644
--- a/src/H5B2.c
+++ b/src/H5B2.c
@@ -1538,3 +1538,35 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5B2_depend() */
 
+/*-------------------------------------------------------------------------
+ * Function:    H5B2_patch_file
+ *
+ * Purpose:     Patch the top-level file pointer contained in bt2
+ *              to point to idx_info->f if they are different.  
+ *		This is possible because the file pointer in bt2 can be
+ *		closed out if bt2 remains open.
+ *
+ * Return:      SUCCEED
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5B2_patch_file(H5B2_t *bt2, H5F_t *f)
+{
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+#ifdef QAK
+HDfprintf(stderr, "%s: Called\n", FUNC);
+#endif /* QAK */
+
+    /*
+     * Check arguments.
+     */
+    HDassert(bt2);
+    HDassert(f);
+
+    if(bt2->f != f || bt2->hdr->f != f)
+        bt2->f = bt2->hdr->f = f;
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* H5B2_patch_file() */
diff --git a/src/H5B2private.h b/src/H5B2private.h
index cc60c9b..dbc5d47 100644
--- a/src/H5B2private.h
+++ b/src/H5B2private.h
@@ -159,6 +159,7 @@ H5_DLL htri_t H5B2_support(H5B2_t *bt2, hid_t dxpl_id, void *udata,
 H5_DLL herr_t H5B2_unsupport(H5B2_t *bt2, hid_t dxpl_id, void *udata,
     H5AC_info_t *child);
 H5_DLL herr_t H5B2_depend(H5AC_info_t *parent_entry, H5B2_t *bt2);
+H5_DLL herr_t H5B2_patch_file(H5B2_t *fa, H5F_t *f);
 
 /* Statistics routines */
 H5_DLL herr_t H5B2_stat_info(H5B2_t *bt2, H5B2_stat_t *info);
diff --git a/src/H5Dbtree2.c b/src/H5Dbtree2.c
index f286db2..8d005fd 100644
--- a/src/H5Dbtree2.c
+++ b/src/H5Dbtree2.c
@@ -1014,10 +1014,12 @@ H5D__bt2_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata,
     HDassert(H5F_addr_defined(udata->chunk_block.offset));
 
     /* Check if the v2 B-tree is open yet */
-    if(NULL == idx_info->storage->u.btree2.bt2)
+    if(NULL == idx_info->storage->u.btree2.bt2) {
 	/* Open existing v2 B-tree */
         if(H5D__bt2_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+    } else  /* Patch the top level file pointer contained in bt2 if needed */
+	H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f);
 
     /* Set convenience pointer to v2 B-tree structure */
     bt2 = idx_info->storage->u.btree2.bt2;
@@ -1114,10 +1116,12 @@ H5D__bt2_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata)
     HDassert(udata);
 
     /* Check if the v2 B-tree is open yet */
-    if(NULL == idx_info->storage->u.btree2.bt2)
+    if(NULL == idx_info->storage->u.btree2.bt2) {
 	/* Open existing v2 B-tree */
         if(H5D__bt2_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+    } else  /* Patch the top level file pointer contained in bt2 if needed */
+	H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f);
 
     /* Set convenience pointer to v2 B-tree structure */
     bt2 = idx_info->storage->u.btree2.bt2;
@@ -1233,10 +1237,12 @@ H5D__bt2_idx_iterate(const H5D_chk_idx_info_t *idx_info,
     HDassert(chunk_udata);
 
     /* Check if the v2 B-tree is open yet */
-    if(NULL == idx_info->storage->u.btree2.bt2)
+    if(NULL == idx_info->storage->u.btree2.bt2) {
 	/* Open existing v2 B-tree */
         if(H5D__bt2_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open v2 B-tree")
+    } else  /* Patch the top level file pointer contained in bt2 if needed */
+	H5B2_patch_file(idx_info->storage->u.btree2.bt2, idx_info->f);
 
     /* Set convenience pointer to v2 B-tree structure */
     bt2 = idx_info->storage->u.btree2.bt2;
diff --git a/src/H5Dearray.c b/src/H5Dearray.c
index 84c26bf..3896172 100644
--- a/src/H5Dearray.c
+++ b/src/H5Dearray.c
@@ -1038,10 +1038,12 @@ H5D__earray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata
     HDassert(udata);
 
     /* Check if the extensible array is open yet */
-    if(NULL == idx_info->storage->u.earray.ea)
+    if(NULL == idx_info->storage->u.earray.ea) {
         /* Open the extensible array in file */
         if(H5D__earray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+     } else  /* Patch the top level file pointer contained in ea if needed */
+        H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f);
 
     /* Set convenience pointer to extensible array structure */
     ea = idx_info->storage->u.earray.ea;
@@ -1107,10 +1109,12 @@ H5D__earray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *uda
     HDassert(udata);
 
     /* Check if the extensible array is open yet */
-    if(NULL == idx_info->storage->u.earray.ea)
+    if(NULL == idx_info->storage->u.earray.ea) {
         /* Open the extensible array in file */
         if(H5D__earray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+     } else  /* Patch the top level file pointer contained in ea if needed */
+        H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f);
 
     /* Set convenience pointer to extensible array structure */
     ea = idx_info->storage->u.earray.ea;
@@ -1309,10 +1313,12 @@ H5D__earray_idx_iterate(const H5D_chk_idx_info_t *idx_info,
     HDassert(chunk_udata);
 
     /* Check if the extensible array is open yet */
-    if(NULL == idx_info->storage->u.earray.ea)
+    if(NULL == idx_info->storage->u.earray.ea) {
         /* Open the extensible array in file */
         if(H5D__earray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open extensible array")
+     } else  /* Patch the top level file pointer contained in ea if needed */
+        H5EA_patch_file(idx_info->storage->u.earray.ea, idx_info->f);
 
     /* Set convenience pointer to extensible array structure */
     ea = idx_info->storage->u.earray.ea;
diff --git a/src/H5Dfarray.c b/src/H5Dfarray.c
index 2958a66..e5541c7 100644
--- a/src/H5Dfarray.c
+++ b/src/H5Dfarray.c
@@ -989,10 +989,12 @@ H5D__farray_idx_insert(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *udata
     HDassert(udata);
 
     /* Check if the fixed array is open yet */
-    if(NULL == idx_info->storage->u.farray.fa)
+    if(NULL == idx_info->storage->u.farray.fa) {
         /* Open the fixed array in file */
         if(H5D__farray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+    } else  /* Patch the top level file pointer contained in fa if needed */
+	H5FA_patch_file(idx_info->storage->u.farray.fa, idx_info->f);
 
     /* Set convenience pointer to fixed array structure */
     fa = idx_info->storage->u.farray.fa;
@@ -1058,10 +1060,12 @@ H5D__farray_idx_get_addr(const H5D_chk_idx_info_t *idx_info, H5D_chunk_ud_t *uda
     HDassert(udata);
 
     /* Check if the fixed array is open yet */
-    if(NULL == idx_info->storage->u.farray.fa)
+    if(NULL == idx_info->storage->u.farray.fa) {
         /* Open the fixed array in file */
         if(H5D__farray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+    } else  /* Patch the top level file pointer contained in fa if needed */
+	H5FA_patch_file(idx_info->storage->u.farray.fa, idx_info->f);
 
     /* Set convenience pointer to fixed array structure */
     fa = idx_info->storage->u.farray.fa;
@@ -1196,10 +1200,12 @@ H5D__farray_idx_iterate(const H5D_chk_idx_info_t *idx_info,
     HDassert(chunk_udata);
 
     /* Check if the fixed array is open yet */
-    if(NULL == idx_info->storage->u.farray.fa)
+    if(NULL == idx_info->storage->u.farray.fa) {
         /* Open the fixed array in file */
         if(H5D__farray_idx_open(idx_info) < 0)
             HGOTO_ERROR(H5E_DATASET, H5E_CANTOPENOBJ, FAIL, "can't open fixed array")
+    } else  /* Patch the top level file pointer contained in fa if needed */
+	H5FA_patch_file(idx_info->storage->u.farray.fa, idx_info->f);
 
     /* Set convenience pointer to fixed array structure */
     fa = idx_info->storage->u.farray.fa;
diff --git a/src/H5Dio.c b/src/H5Dio.c
index c0aa83e..ac5c82b 100644
--- a/src/H5Dio.c
+++ b/src/H5Dio.c
@@ -412,6 +412,9 @@ H5D__read(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
     if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
 
+    /* Patch the top level file pointer for dt->shared->u.vlen.f if needed */
+    H5T_patch_vlen_file(dataset->shared->type, dataset->oloc.file);
+
     /* Set up datatype info for operation */
     if(H5D__typeinfo_init(dataset, dxpl_cache, dxpl_id, mem_type_id, FALSE, &type_info) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info")
@@ -632,6 +635,9 @@ H5D__write(H5D_t *dataset, hid_t mem_type_id, const H5S_t *mem_space,
     if(H5D__get_dxpl_cache(dxpl_id, &dxpl_cache) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTGET, FAIL, "can't fill dxpl cache")
 
+    /* Patch the top level file pointer for dt->shared->u.vlen.f if needed */
+    H5T_patch_vlen_file(dataset->shared->type, dataset->oloc.file);
+
     /* Set up datatype info for operation */
     if(H5D__typeinfo_init(dataset, dxpl_cache, dxpl_id, mem_type_id, TRUE, &type_info) < 0)
         HGOTO_ERROR(H5E_DATASET, H5E_CANTINIT, FAIL, "unable to set up type info")
diff --git a/src/H5EA.c b/src/H5EA.c
index bf18239..6648bcf 100644
--- a/src/H5EA.c
+++ b/src/H5EA.c
@@ -1115,3 +1115,36 @@ CATCH
         elmt = H5FL_BLK_FREE(ea_native_elmt, elmt);
 
 END_FUNC(PRIV)  /* end H5EA_iterate() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5EA_patch_file
+ *
+ * Purpose:     Patch the top-level file pointer contained in ea
+ *              to point to idx_info->f if they are different.
+ *              This is possible because the file pointer in ea can be
+ *              closed out if ea remains open.
+ *
+ * Return:      SUCCEED
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PRIV, NOERR,
+herr_t, SUCCEED, -,
+H5EA_patch_file(H5EA_t *ea, H5F_t *f))
+
+    /* Local variables */
+
+#ifdef H5EA_DEBUG
+HDfprintf(stderr, "%s: Called\n", FUNC);
+#endif /* H5EA_DEBUG */
+
+    /*
+     * Check arguments.
+     */
+    HDassert(ea);
+    HDassert(f);
+
+    if(ea->f != f || ea->hdr->f != f)
+        ea->f = ea->hdr->f = f;
+
+END_FUNC(PRIV)  /* end H5EA_patch_file() */
diff --git a/src/H5EAprivate.h b/src/H5EAprivate.h
index c00e118..78bcca8 100644
--- a/src/H5EAprivate.h
+++ b/src/H5EAprivate.h
@@ -146,6 +146,7 @@ H5_DLL herr_t H5EA_depend(H5AC_info_t *parent_entry, H5EA_t *ea);
 H5_DLL herr_t H5EA_iterate(H5EA_t *fa, hid_t dxpl_id, H5EA_operator_t op, void *udata);
 H5_DLL herr_t H5EA_close(H5EA_t *ea, hid_t dxpl_id);
 H5_DLL herr_t H5EA_delete(H5F_t *f, hid_t dxpl_id, haddr_t ea_addr, void *ctx_udata);
+H5_DLL herr_t H5EA_patch_file(H5EA_t *fa, H5F_t *f);
 
 /* Statistics routines */
 H5_DLL herr_t H5EA_get_stats(const H5EA_t *ea, H5EA_stat_t *stats);
diff --git a/src/H5FA.c b/src/H5FA.c
index a1b4fbc..70a4b56 100644
--- a/src/H5FA.c
+++ b/src/H5FA.c
@@ -850,3 +850,36 @@ HDfprintf(stderr, "%s: Called\n", FUNC);
 CATCH
 
 END_FUNC(PRIV)  /* end H5FA_undepend() */
+
+/*-------------------------------------------------------------------------
+ * Function:    H5FA_patch_file
+ *
+ * Purpose:     Patch the top-level file pointer contained in fa
+ *              to point to idx_info->f if they are different.
+ *              This is possible because the file pointer in fa can be
+ *              closed out if fa remains open.
+ *
+ * Return:      SUCCEED
+ *
+ *-------------------------------------------------------------------------
+ */
+BEGIN_FUNC(PRIV, NOERR,
+herr_t, SUCCEED, -,
+H5FA_patch_file(H5FA_t *fa, H5F_t *f))
+
+    /* Local variables */
+
+#ifdef H5FA_DEBUG
+HDfprintf(stderr, "%s: Called\n", FUNC);
+#endif /* H5FA_DEBUG */
+
+    /*
+     * Check arguments.
+     */
+    HDassert(fa);
+    HDassert(f);
+
+    if(fa->f != f || fa->hdr->f != f)
+        fa->f = fa->hdr->f = f;
+
+END_FUNC(PRIV)  /* end H5FA_patch_file() */
diff --git a/src/H5FAprivate.h b/src/H5FAprivate.h
index b7c141a..2ce9cbb 100644
--- a/src/H5FAprivate.h
+++ b/src/H5FAprivate.h
@@ -131,6 +131,7 @@ H5_DLL herr_t H5FA_depend(H5AC_info_t *parent_entry, H5FA_t *fa);
 H5_DLL herr_t H5FA_iterate(H5FA_t *fa, hid_t dxpl_id, H5FA_operator_t op, void *udata);
 H5_DLL herr_t H5FA_close(H5FA_t *fa, hid_t dxpl_id);
 H5_DLL herr_t H5FA_delete(H5F_t *f, hid_t dxpl_id, haddr_t fa_addr, void *ctx_udata);
+H5_DLL herr_t H5FA_patch_file(H5FA_t *fa, H5F_t *f);
 
 /* Statistics routines */
 H5_DLL herr_t H5FA_get_stats(const H5FA_t *ea, H5FA_stat_t *stats);
diff --git a/src/H5T.c b/src/H5T.c
index 030f5a7..6514a35 100644
--- a/src/H5T.c
+++ b/src/H5T.c
@@ -5466,6 +5466,35 @@ done:
 
 
 /*-------------------------------------------------------------------------
+ * Function:    H5T_patch_vlen_file
+ *
+ * Purpose:     Patch the top-level file pointer contained in (dt->shared->u.vlen.f)
+ *              to point to f.  This is possible because
+ *              the top-level file pointer can be closed out from under
+ *              dt while dt is contained in the shared file's cache.
+ *
+ * Return:      SUCCEED
+ *
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5T_patch_vlen_file(H5T_t *dt, H5F_t *f)
+{
+    FUNC_ENTER_NOAPI_NOINIT_NOERR
+
+    /* Sanity check */
+    HDassert(dt);
+    HDassert(dt->shared);
+    HDassert(f);
+
+    if((dt->shared->type == H5T_VLEN) && dt->shared->u.vlen.f != f)
+        dt->shared->u.vlen.f = f;
+
+    FUNC_LEAVE_NOAPI(SUCCEED)
+} /* end H5T_patch_vlen_file() */
+
+
+/*-------------------------------------------------------------------------
  * Function:    H5Tflush
  *
  * Purpose:     Flushes all buffers associated with a named datatype to disk.