Merge pull request #931 in HDFFV/hdf5 from ~VCHOI/my_hdf5_fork:develop to develop

* commit 'f08b8fa10e7bac5ae26e3b06f938d38ebb3f28e1':
  Enhancement to the tool h5clear (HDFFV-10360)
  Fix for HDFFV-10209 VDS SWMR test failure Free the object header when there are chksum retries.

10 files changed, 273 insertions, 45 deletions

diff --git a/src/H5F.c b/src/H5F.c
index 8e5f65a..2cd65cb 100644
--- a/src/H5F.c
+++ b/src/H5F.c
@@ -845,8 +845,6 @@ herr_t
 H5Fget_filesize(hid_t file_id, hsize_t *size)
 {
     H5F_t       *file;                  /* File object for file ID */
-    haddr_t     eof;                    /* End of file address */
-    haddr_t     eoa;                    /* End of allocation address */
     haddr_t     max_eof_eoa;            /* Maximum of the EOA & EOF */
     haddr_t     base_addr;              /* Base address for the file */
     herr_t      ret_value = SUCCEED;    /* Return value */
@@ -859,11 +857,9 @@ H5Fget_filesize(hid_t file_id, hsize_t *size)
         HGOTO_ERROR(H5E_ARGS, H5E_BADVALUE, FAIL, "not a file ID")
 
     /* Go get the actual file size */
-    eof = H5FD_get_eof(file->shared->lf, H5FD_MEM_DEFAULT);
-    eoa = H5FD_get_eoa(file->shared->lf, H5FD_MEM_DEFAULT);
-    max_eof_eoa = MAX(eof, eoa);
-    if(HADDR_UNDEF == max_eof_eoa)
-        HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "file get eof/eoa requests failed")
+    if(H5F__get_max_eof_eoa(file, &max_eof_eoa) < 0)
+        HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "file can't get max eof/eoa ")
+
     base_addr = H5FD_get_base_addr(file->shared->lf);
 
     if(size)
@@ -1949,3 +1945,87 @@ done:
     FUNC_LEAVE_API(ret_value)
 } /* H5Fget_mdc_image_info() */
 
+
+/*-------------------------------------------------------------------------
+ * Function:    H5Fget_eoa
+ *
+ * Purpose:     Returns the address of the first byte after the last
+ *              allocated memory in the file.
+ *              (See H5FDget_eoa() in H5FD.c)
+ *
+ * Return:      Success:    First byte after allocated memory.
+ *              Failure:    HADDR_UNDEF
+ *
+ * Return:      Non-negative on success/Negative on errors
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Fget_eoa(hid_t file_id, haddr_t *eoa)
+{
+    H5F_t *file;                    /* File object for file ID */
+    haddr_t rel_eoa;                /* Relative address of EOA */
+    herr_t ret_value = SUCCEED;     /* Return value */
+
+    FUNC_ENTER_API(FAIL)
+    H5TRACE2("e", "i*a", file_id, eoa);
+
+    /* Check args */
+    if(NULL == (file = (H5F_t *)H5I_object_verify(file_id, H5I_FILE)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "hid_t identifier is not a file ID")
+
+    /* This public routine will work only for drivers with this feature enabled.*/
+    /* We might introduce a new feature flag in the future */
+    if(!H5F_HAS_FEATURE(file, H5FD_FEAT_SUPPORTS_SWMR_IO))
+        HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, FAIL, "must use a SWMR-compatible VFD for this public routine")
+
+    /* The real work */
+    if(HADDR_UNDEF == (rel_eoa = H5FD_get_eoa(file->shared->lf, H5FD_MEM_DEFAULT)))
+        HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "get_eoa request failed")
+
+    /* (Note compensating for base address subtraction in internal routine) */
+    if(eoa)
+        *eoa = rel_eoa + H5FD_get_base_addr(file->shared->lf);
+done:
+    FUNC_LEAVE_API(ret_value)
+} /* H5Fget_eoa() */
+
+
+/*-------------------------------------------------------------------------
+ * Function:    H5Fincrement_filesize
+ *
+ * Purpose:     Set the EOA for the file to the maximum of (EOA, EOF) + increment
+ *
+ * Return:      Non-negative on success/Negative on errors
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5Fincrement_filesize(hid_t file_id, hsize_t increment)
+{
+    H5F_t *file;                /* File object for file ID */
+    haddr_t max_eof_eoa;        /* Maximum of the relative EOA & EOF */
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_API(FAIL)
+    H5TRACE2("e", "ih", file_id, increment);
+
+    /* Check args */
+    if(NULL == (file = (H5F_t *)H5I_object_verify(file_id, H5I_FILE)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "hid_t identifier is not a file ID")
+
+    /* This public routine will work only for drivers with this feature enabled.*/
+    /* We might introduce a new feature flag in the future */
+    if(!H5F_HAS_FEATURE(file, H5FD_FEAT_SUPPORTS_SWMR_IO))
+        HGOTO_ERROR(H5E_FILE, H5E_BADVALUE, FAIL, "must use a SWMR-compatible VFD for this public routine")
+
+    /* Get the maximum of EOA and EOF */
+    if(H5F__get_max_eof_eoa(file, &max_eof_eoa) < 0)
+        HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "file can't get max eof/eoa ")
+
+    /* Set EOA to the maximum value + increment */
+    /* H5FD_set_eoa() will add base_addr to max_eof_eoa */
+    if(H5FD_set_eoa(file->shared->lf, H5FD_MEM_DEFAULT, max_eof_eoa + increment) < 0)
+        HGOTO_ERROR(H5E_FILE, H5E_CANTSET, FAIL, "driver set_eoa request failed")
+
+done:
+    FUNC_LEAVE_API(ret_value)
+} /* H5Fincrement_filesize() */
diff --git a/src/H5Fint.c b/src/H5Fint.c
index cc5931a..24844a4 100644
--- a/src/H5Fint.c
+++ b/src/H5Fint.c
@@ -124,7 +124,6 @@ H5F_get_access_plist(H5F_t *f, hbool_t app_ref)
     H5FD_driver_prop_t driver_prop;         /* Property for driver ID & info */
     hbool_t driver_prop_copied = FALSE;     /* Whether the driver property has been set up */
     unsigned   efc_size = 0;
-    hbool_t    latest_format = FALSE;       /* Always use the latest format? */
     hid_t      ret_value = SUCCEED;         /* Return value */
 
     FUNC_ENTER_NOAPI(FAIL)
@@ -820,7 +819,6 @@ H5F_new(H5F_file_t *shared, unsigned flags, hid_t fcpl_id, hid_t fapl_id, H5FD_t
     else {
         H5P_genplist_t *plist;          /* Property list */
         unsigned efc_size;              /* External file cache size */
-        hbool_t latest_format;          /* Always use the latest format?    */
         size_t u;                       /* Local index variable */
 
         HDassert(lf != NULL);
@@ -1602,7 +1600,7 @@ H5F_open(const char *name, unsigned flags, hid_t fcpl_id, hid_t fapl_id,
     } /* end if */
     else if (1 == shared->nrefs) {
         /* Read the superblock if it hasn't been read before. */
-        if(H5F__super_read(file, meta_dxpl_id, raw_dxpl_id, TRUE) < 0)
+        if(H5F__super_read(file, meta_dxpl_id, raw_dxpl_id, fapl_id, TRUE) < 0)
             HGOTO_ERROR(H5E_FILE, H5E_READERROR, NULL, "unable to read superblock")
 
         /* Create the page buffer before initializing the superblock */
@@ -2921,6 +2919,43 @@ done:
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5F__set_paged_aggr() */
 
+/*-------------------------------------------------------------------------
+ * Function: H5F__get_max_eof_eoa
+ *
+ * Purpose:  Determine the maximum of (EOA, EOF) for the file
+ *
+ * Return:   Non-negative on success/Negative on failure
+ *-------------------------------------------------------------------------
+ */
+herr_t
+H5F__get_max_eof_eoa(const H5F_t *f, haddr_t *max_eof_eoa)
+{
+    haddr_t eof;                /* Relative address for EOF */
+    haddr_t eoa;                /* Relative address for EOA */
+    haddr_t tmp_max;
+    herr_t ret_value = SUCCEED; /* Return value */
+
+    FUNC_ENTER_PACKAGE
+
+    /* Sanity checks */
+    HDassert(f);
+    HDassert(f->shared);
+
+    /* Get the relative EOA and EOF */
+    eoa = H5FD_get_eoa(f->shared->lf, H5FD_MEM_DEFAULT);
+    eof = H5FD_get_eof(f->shared->lf, H5FD_MEM_DEFAULT);
+
+    /* Determine the maximum */
+    tmp_max = MAX(eof, eoa);
+    if(HADDR_UNDEF == tmp_max)
+        HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "file get eof/eoa requests failed")
+
+    *max_eof_eoa = tmp_max;
+
+done:
+    FUNC_LEAVE_NOAPI(ret_value)
+} /* end H5F__get_max_eof_eoa() */
+
 #ifdef H5_HAVE_PARALLEL
 
 /*-------------------------------------------------------------------------
diff --git a/src/H5Fpkg.h b/src/H5Fpkg.h
index c9aba56..a4c1a24 100644
--- a/src/H5Fpkg.h
+++ b/src/H5Fpkg.h
@@ -412,7 +412,7 @@ H5_DLL herr_t H5F_mount_count_ids(H5F_t *f, unsigned *nopen_files, unsigned *nop
 
 /* Superblock related routines */
 H5_DLL herr_t H5F__super_init(H5F_t *f, hid_t dxpl_id);
-H5_DLL herr_t H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id,
+H5_DLL herr_t H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hid_t fapl_id,
     hbool_t initial_read);
 H5_DLL herr_t H5F__super_size(H5F_t *f, hid_t dxpl_id, hsize_t *super_size, hsize_t *super_ext_size);
 H5_DLL herr_t H5F__super_free(H5F_super_t *sblock);
@@ -457,6 +457,7 @@ H5_DLL htri_t H5F_try_extend(H5F_t *f, hid_t dxpl_id, H5FD_mem_t type,
 H5_DLL herr_t H5F__set_eoa(const H5F_t *f, H5F_mem_t type, haddr_t addr);
 H5_DLL herr_t H5F__set_base_addr(const H5F_t *f, haddr_t addr);
 H5_DLL herr_t H5F__set_paged_aggr(const H5F_t *f, hbool_t paged);
+H5_DLL herr_t H5F__get_max_eof_eoa(const H5F_t *f, haddr_t *max_eof_eoa);
 
 /* Functions that flush or evict */
 H5_DLL herr_t H5F__evict_cache_entries(H5F_t *f, hid_t dxpl_id);
diff --git a/src/H5Fprivate.h b/src/H5Fprivate.h
index 856e618..28ebbd2 100644
--- a/src/H5Fprivate.h
+++ b/src/H5Fprivate.h
@@ -492,6 +492,10 @@ typedef struct H5F_t H5F_t;
 #define H5F_ACS_EFC_SIZE_NAME                   "efc_size"      /* Size of external file cache */
 #define H5F_ACS_FILE_IMAGE_INFO_NAME            "file_image_info" /* struct containing initial file image and callback info */
 #define H5F_ACS_CLEAR_STATUS_FLAGS_NAME         "clear_status_flags" /* Whether to clear superblock status_flags (private property only used by h5clear) */
+#define H5F_ACS_NULL_FSM_ADDR_NAME              "null_fsm_addr"   /* Nullify addresses of free-space managers */
+                                                                  /* Private property used only by h5clear */
+#define H5F_ACS_SKIP_EOF_CHECK_NAME             "skip_eof_check"  /* Skip EOF check */
+                                                                  /* Private property used only by h5clear */
 #define H5F_ACS_USE_MDC_LOGGING_NAME            "use_mdc_logging" /* Whether to use metadata cache logging */
 #define H5F_ACS_MDC_LOG_LOCATION_NAME           "mdc_log_location" /* Name of metadata cache log location */
 #define H5F_ACS_START_MDC_LOG_ON_ACCESS_NAME    "start_mdc_log_on_access" /* Whether logging starts on file create/open */
diff --git a/src/H5Fpublic.h b/src/H5Fpublic.h
index d333fa7..73c59f5 100644
--- a/src/H5Fpublic.h
+++ b/src/H5Fpublic.h
@@ -241,6 +241,8 @@ H5_DLL herr_t H5Fmount(hid_t loc, const char *name, hid_t child, hid_t plist);
 H5_DLL herr_t H5Funmount(hid_t loc, const char *name);
 H5_DLL hssize_t H5Fget_freespace(hid_t file_id);
 H5_DLL herr_t H5Fget_filesize(hid_t file_id, hsize_t *size);
+H5_DLL herr_t H5Fget_eoa(hid_t file_id, haddr_t *eoa);
+H5_DLL herr_t H5Fincrement_filesize(hid_t file_id, hsize_t increment);
 H5_DLL ssize_t H5Fget_file_image(hid_t file_id, void * buf_ptr, size_t buf_len);
 H5_DLL herr_t H5Fget_mdc_config(hid_t file_id,
 				H5AC_cache_config_t * config_ptr);
diff --git a/src/H5Fsuper.c b/src/H5Fsuper.c
index 4250ff0..3db9b2f 100644
--- a/src/H5Fsuper.c
+++ b/src/H5Fsuper.c
@@ -324,7 +324,7 @@ done:
  *-------------------------------------------------------------------------
  */
 herr_t
-H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial_read)
+H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hid_t fapl_id, hbool_t initial_read)
 {
     H5P_genplist_t     *dxpl = NULL;        /* DXPL object */
     H5AC_ring_t         ring, orig_ring = H5AC_RING_INV;
@@ -337,7 +337,8 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
     haddr_t             eof;                /* End of file address */
     unsigned            rw_flags;           /* Read/write permissions for file */
     hbool_t             skip_eof_check = FALSE; /* Whether to skip checking the EOF value */
-    herr_t              ret_value = SUCCEED; /* Return value */
+    H5P_genplist_t      *a_plist;               /* File access property list */
+    herr_t              ret_value = SUCCEED;    /* Return value */
 #ifdef H5_HAVE_PARALLEL
     int                 mpi_rank = 0, mpi_size = 1;
     int                 mpi_result;
@@ -595,6 +596,20 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
      * as the file can appear truncated if only part of it has been
      * been flushed to disk by the SWMR writer process.
      */
+    /* The EOF check is also skipped when the private property 
+     * H5F_ACS_SKIP_EOF_CHECK_NAME exists in the fapl.  
+     * This property is enabled by the tool h5clear with these
+     * two options: (1) --filesize (2) --increment
+     */
+
+    /* Check if this private property exists in fapl */
+    if(NULL == (a_plist = (H5P_genplist_t *)H5I_object(fapl_id)))
+        HGOTO_ERROR(H5E_ARGS, H5E_BADTYPE, FAIL, "not file access property list")
+    if(H5P_exist_plist(a_plist, H5F_ACS_SKIP_EOF_CHECK_NAME) > 0) {
+        if(H5P_get(a_plist, H5F_ACS_SKIP_EOF_CHECK_NAME, &skip_eof_check) < 0)
+            HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get clearance for persisting fsm addr")
+    }
+
     if(H5F_INTENT(f) & H5F_ACC_SWMR_READ) {
         /* 
          * When the file is opened for SWMR read access, skip the check if:
@@ -757,6 +772,7 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
         if(status) {
             H5O_fsinfo_t fsinfo;   /* File space info message from superblock extension */
             uint8_t flags;          /* Message flags */
+            hbool_t null_fsm_addr = FALSE;  /* Whether to drop free-space to the floor */
 
             /* Get message flags */
             if(H5O_msg_get_flags(&ext_loc, H5O_FSINFO_ID, meta_dxpl_id, &flags) < 0)
@@ -765,6 +781,13 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
             /* If message is NOT marked "unknown"--set up file space info  */
             if(!(flags & H5O_MSG_FLAG_WAS_UNKNOWN)) {
 
+                /* The tool h5clear uses this property to tell the library
+                   to drop free-space to the floor */
+                if(H5P_exist_plist(a_plist, H5F_ACS_NULL_FSM_ADDR_NAME) > 0) {
+                    if(H5P_get(a_plist, H5F_ACS_NULL_FSM_ADDR_NAME, &null_fsm_addr) < 0)
+                        HGOTO_ERROR(H5E_PLIST, H5E_CANTGET, FAIL, "can't get clearance for persisting fsm addr")
+                }
+
                 /* Retrieve the 'file space info' structure */
                 if(NULL == H5O_msg_read(&ext_loc, H5O_FSINFO_ID, &fsinfo, meta_dxpl_id))
                     HGOTO_ERROR(H5E_FILE, H5E_CANTGET, FAIL, "unable to get free-space manager info message")
@@ -808,13 +831,30 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
                 if(f->shared->eoa_pre_fsm_fsalloc != fsinfo.eoa_pre_fsm_fsalloc)
                     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.
+               /* f->shared->eoa_pre_fsm_fsalloc must always be HADDR_UNDEF
+                * in the absence of persistant 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.
+                 *  #1 and #2 are enabled when the tool h5clear --increment
+                 *  option is used.
                  */
-                HDassert((!f->shared->fs_persist) || (f->shared->eoa_pre_fsm_fsalloc != HADDR_UNDEF));
-                HDassert(!f->shared->first_alloc_dealloc);
+                if(!skip_eof_check && !null_fsm_addr) {
+                     HDassert((!f->shared->fs_persist) || (f->shared->eoa_pre_fsm_fsalloc != HADDR_UNDEF));
+                     HDassert(!f->shared->first_alloc_dealloc);
+                }
 
-                if((f->shared->eoa_pre_fsm_fsalloc != HADDR_UNDEF) &&
+                /* As "eoa_pre_fsm_fsalloc" may be undefined for a crashed file
+                 * with persistant 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
+                 * close via H5MF_settle_meta_data_fsm() and H5MF_settle_raw_data_fsm().
+                 */
+                if((f->shared->eoa_pre_fsm_fsalloc != HADDR_UNDEF || null_fsm_addr) &&
                    (H5F_INTENT(f) & H5F_ACC_RDWR))
                     f->shared->first_alloc_dealloc = TRUE;
 
@@ -822,7 +862,20 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
                 for(u = 1; u < NELMTS(f->shared->fs_addr); u++)
                     f->shared->fs_addr[u] = fsinfo.fs_addr[u - 1];
 
-                if(fsinfo.mapped && (rw_flags & H5AC__READ_ONLY_FLAG) == 0) {
+                /* If the following two conditions are true:
+                 *      (1) file is persisting free-space 
+                 *      (2) dropping free-space to the floor (null_fsm_addr)
+                 * nullify the addresses of the FSMs 
+                 */
+                if(f->shared->fs_persist && null_fsm_addr) {
+                    for(u = 0; u < NELMTS(fsinfo.fs_addr); u++)
+                        f->shared->fs_addr[u] = fsinfo.fs_addr[u] = HADDR_UNDEF;
+                } 
+
+                /* For fsinfo.mapped: remove the FSINFO message from the superblock extension
+                   and write a new message to the extension */
+                /* For null_fsm_addr: just update FSINFO message in the superblock extension */
+                if(((fsinfo.mapped || null_fsm_addr) && (rw_flags & H5AC__READ_ONLY_FLAG) == 0)) {
 
                     /* Do the same kluge until we know for sure.  VC */
 #if 1 /* bug fix test code -- tidy this up if all goes well */ /* JRM */
@@ -836,11 +889,16 @@ H5F__super_read(H5F_t *f, hid_t meta_dxpl_id, hid_t raw_dxpl_id, hbool_t initial
                      f->shared->sblock = sblock;
 #endif /* JRM */
 
-                    if(H5F_super_ext_remove_msg(f, meta_dxpl_id, H5O_FSINFO_ID) < 0)
-                        HGOTO_ERROR(H5E_FILE, H5E_CANTDELETE, FAIL,  "error in removing message from superblock extension")
+                    if(null_fsm_addr) {
+                        if(H5F_super_ext_write_msg(f, meta_dxpl_id, H5O_FSINFO_ID, &fsinfo, FALSE, H5O_MSG_FLAG_MARK_IF_UNKNOWN) < 0)
+                            HGOTO_ERROR(H5E_FILE, H5E_WRITEERROR, FAIL, "error in writing fsinfo message to superblock extension")
+                    } else {
+                        if(H5F_super_ext_remove_msg(f, meta_dxpl_id, H5O_FSINFO_ID) < 0)
+                            HGOTO_ERROR(H5E_FILE, H5E_CANTDELETE, FAIL,  "error in removing message from superblock extension")
 
-                    if(H5F_super_ext_write_msg(f, meta_dxpl_id, H5O_FSINFO_ID, &fsinfo, TRUE, H5O_MSG_FLAG_MARK_IF_UNKNOWN) < 0)
-                        HGOTO_ERROR(H5E_FILE, H5E_WRITEERROR, FAIL, "error in writing fsinfo message to superblock extension")
+                        if(H5F_super_ext_write_msg(f, meta_dxpl_id, H5O_FSINFO_ID, &fsinfo, TRUE, H5O_MSG_FLAG_MARK_IF_UNKNOWN) < 0)
+                            HGOTO_ERROR(H5E_FILE, H5E_WRITEERROR, FAIL, "error in writing fsinfo message to superblock extension")
+                    }
 #if 1 /* bug fix test code -- tidy this up if all goes well */ /* JRM */
                     f->shared->sblock = NULL;
 #endif /* JRM */
@@ -1637,13 +1695,13 @@ H5F_super_ext_write_msg(H5F_t *f, hid_t dxpl_id, unsigned id, void *mesg,
 
     /* Open/create the superblock extension object header */
     if(H5F_addr_defined(f->shared->sblock->ext_addr)) {
-	if(H5F_super_ext_open(f, f->shared->sblock->ext_addr, &ext_loc) < 0)
-	    HGOTO_ERROR(H5E_FILE, H5E_CANTOPENOBJ, FAIL, "unable to open file's superblock extension")
+        if(H5F_super_ext_open(f, f->shared->sblock->ext_addr, &ext_loc) < 0)
+            HGOTO_ERROR(H5E_FILE, H5E_CANTOPENOBJ, FAIL, "unable to open file's superblock extension")
     } /* end if */
     else {
         HDassert(may_create);
-	if(H5F_super_ext_create(f, dxpl_id, &ext_loc) < 0)
-	    HGOTO_ERROR(H5E_FILE, H5E_CANTCREATE, FAIL, "unable to create file's superblock extension")
+        if(H5F_super_ext_create(f, dxpl_id, &ext_loc) < 0)
+            HGOTO_ERROR(H5E_FILE, H5E_CANTCREATE, FAIL, "unable to create file's superblock extension")
         ext_created = TRUE;
     } /* end else */
     HDassert(H5F_addr_defined(ext_loc.addr));
@@ -1651,24 +1709,24 @@ H5F_super_ext_write_msg(H5F_t *f, hid_t dxpl_id, unsigned id, void *mesg,
 
     /* Check if message with ID does not exist in the object header */
     if((status = H5O_msg_exists(&ext_loc, id, dxpl_id)) < 0)
-	HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to check object header for message or message exists")
+        HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to check object header for message or message exists")
 
     /* Check for creating vs. writing */
     if(may_create) {
-	if(status)
-	    HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "Message should not exist")
+        if(status)
+            HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "Message should not exist")
 
-	/* Create the message with ID in the superblock extension */
-	if(H5O_msg_create(&ext_loc, id, (mesg_flags | H5O_MSG_FLAG_DONTSHARE), H5O_UPDATE_TIME, mesg, dxpl_id) < 0)
-	    HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to create the message in object header")
+        /* Create the message with ID in the superblock extension */
+        if(H5O_msg_create(&ext_loc, id, (mesg_flags | H5O_MSG_FLAG_DONTSHARE), H5O_UPDATE_TIME, mesg, dxpl_id) < 0)
+            HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to create the message in object header")
     } /* end if */
     else {
-	if(!status)
-	    HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "Message should exist")
+        if(!status)
+            HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "Message should exist")
 
-	/* Update the message with ID in the superblock extension */
-	if(H5O_msg_write(&ext_loc, id, (mesg_flags | H5O_MSG_FLAG_DONTSHARE), H5O_UPDATE_TIME, mesg, dxpl_id) < 0)
-	    HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to write the message in object header")
+        /* Update the message with ID in the superblock extension */
+        if(H5O_msg_write(&ext_loc, id, (mesg_flags | H5O_MSG_FLAG_DONTSHARE), H5O_UPDATE_TIME, mesg, dxpl_id) < 0)
+            HGOTO_ERROR(H5E_OHDR, H5E_CANTGET, FAIL, "unable to write the message in object header")
     } /* end else */
 
 done:
diff --git a/src/H5Ocache.c b/src/H5Ocache.c
index 94049ef..2260e12 100644
--- a/src/H5Ocache.c
+++ b/src/H5Ocache.c
@@ -262,12 +262,23 @@ H5O__cache_verify_chksum(const void *_image, size_t len, void *_udata)
         uint32_t stored_chksum;     /* Stored metadata checksum value */
         uint32_t computed_chksum;   /* Computed metadata checksum value */
 
-	/* Get stored and computed checksums */
-	H5F_get_checksums(image, len, &stored_chksum, &computed_chksum);
-
-	if(stored_chksum != computed_chksum)
-	    ret_value = FALSE;
+        /* Get stored and computed checksums */
+        H5F_get_checksums(image, len, &stored_chksum, &computed_chksum);
+
+        if(stored_chksum != computed_chksum) {
+            /* These fields are not deserialized yet in H5O__prefix_deserialize() */
+            HDassert(udata->oh->chunk == NULL);
+            HDassert(udata->oh->mesg == NULL);
+            HDassert(udata->oh->proxy == NULL);
+
+            /* Indicate that udata->oh is to be freed later
+               in H5O__prefix_deserialize() */
+            udata->free_oh = TRUE;
+            ret_value = FALSE;
+        } /* end if */
     } /* end if */
+    else
+        HDassert(!(udata->common.file_intent & H5F_ACC_SWMR_WRITE));
 
     FUNC_LEAVE_NOAPI(ret_value)
 } /* end H5O__cache_verify_chksum() */
@@ -1263,8 +1274,22 @@ H5O__prefix_deserialize(const uint8_t *_image, H5O_cache_ud_t *udata)
     /* Verify object header prefix length */
     HDassert((size_t)(image - _image) == (size_t)(H5O_SIZEOF_HDR(oh) - H5O_SIZEOF_CHKSUM_OH(oh)));
 
-    /* Save the object header for later use in 'deserialize' callback */
-    udata->oh = oh;
+    /* If udata->oh is to be freed (see H5O__cache_verify_chksum), 
+       save the pointer to udata->oh and free it later after setting
+       udata->oh with the new object header */
+    if(udata->free_oh) {
+        H5O_t *saved_oh = udata->oh;
+        HDassert(udata->oh); 
+
+        /* Save the object header for later use in 'deserialize' callback */
+        udata->oh = oh;
+        if(H5O__free(saved_oh) < 0)
+            HGOTO_ERROR(H5E_OHDR, H5E_CANTRELEASE, FAIL, "can't destroy object header")
+        udata->free_oh = FALSE;
+    } else 
+        /* Save the object header for later use in 'deserialize' callback */
+        udata->oh = oh;
+
     oh = NULL;
 
 done:
diff --git a/src/H5Oint.c b/src/H5Oint.c
index 08eb28d..2351779 100644
--- a/src/H5Oint.c
+++ b/src/H5Oint.c
@@ -875,6 +875,7 @@ H5O_protect(const H5O_loc_t *loc, hid_t dxpl_id, unsigned prot_flags,
     udata.v1_pfx_nmesgs = 0;
     udata.chunk0_size = 0;
     udata.oh = NULL;
+    udata.free_oh = FALSE;
     udata.common.f = loc->file;
     udata.common.dxpl_id = dxpl_id;
     udata.common.file_intent = file_intent;
diff --git a/src/H5Opkg.h b/src/H5Opkg.h
index e970406..9392fa8 100644
--- a/src/H5Opkg.h
+++ b/src/H5Opkg.h
@@ -379,6 +379,7 @@ typedef struct H5O_cache_ud_t {
     unsigned v1_pfx_nmesgs;             /* Number of messages from v1 prefix header */
     size_t chunk0_size;                 /* Size of serialized first chunk    */
     H5O_t *oh;                          /* Partially deserialized object header, for later use */
+    hbool_t free_oh;                    /* Whether to free the object header or not */
     H5O_common_cache_ud_t common;       /* Common object header cache callback info */
 } H5O_cache_ud_t;
 
diff --git a/src/H5Pfapl.c b/src/H5Pfapl.c
index 148c247..eded286 100644
--- a/src/H5Pfapl.c
+++ b/src/H5Pfapl.c
@@ -193,6 +193,14 @@
 /* Definition for status_flags in the superblock */
 #define H5F_ACS_CLEAR_STATUS_FLAGS_SIZE         sizeof(hbool_t)
 #define H5F_ACS_CLEAR_STATUS_FLAGS_DEF          FALSE
+
+/* Definition for dropping free-space to the floor when reading in the superblock */
+#define H5F_ACS_NULL_FSM_ADDR_SIZE          sizeof(hbool_t)
+#define H5F_ACS_NULL_FSM_ADDR_DEF           FALSE
+/* Definition for skipping EOF check when reading in the superblock */
+#define H5F_ACS_SKIP_EOF_CHECK_SIZE         sizeof(hbool_t)
+#define H5F_ACS_SKIP_EOF_CHECK_DEF          FALSE
+
 /* Definition for 'use metadata cache logging' flag */
 #define H5F_ACS_USE_MDC_LOGGING_SIZE            sizeof(hbool_t)
 #define H5F_ACS_USE_MDC_LOGGING_DEF             FALSE
@@ -374,6 +382,9 @@ static const size_t H5F_def_core_write_tracking_page_size_g = H5F_ACS_CORE_WRITE
 static const unsigned H5F_def_metadata_read_attempts_g = H5F_ACS_METADATA_READ_ATTEMPTS_DEF;  /* Default setting for the # of metadata read attempts */
 static const H5F_object_flush_t H5F_def_object_flush_cb_g = H5F_ACS_OBJECT_FLUSH_CB_DEF;      /* Default setting for object flush callback */
 static const hbool_t H5F_def_clear_status_flags_g = H5F_ACS_CLEAR_STATUS_FLAGS_DEF;           /* Default to clear the superblock status_flags */
+static const hbool_t H5F_def_skip_eof_check_g = H5F_ACS_SKIP_EOF_CHECK_DEF;    /* Default setting for skipping EOF check */
+static const hbool_t H5F_def_null_fsm_addr_g = H5F_ACS_NULL_FSM_ADDR_DEF;      /* Default setting for dropping free-space to the floor */
+
 static const hbool_t H5F_def_use_mdc_logging_g = H5F_ACS_USE_MDC_LOGGING_DEF;                 /* Default metadata cache logging flag */
 static const char *H5F_def_mdc_log_location_g = H5F_ACS_MDC_LOG_LOCATION_DEF;                 /* Default mdc log location */
 static const hbool_t H5F_def_start_mdc_log_on_access_g = H5F_ACS_START_MDC_LOG_ON_ACCESS_DEF; /* Default mdc log start on access flag */
@@ -565,6 +576,16 @@ H5P__facc_reg_prop(H5P_genclass_t *pclass)
             NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
         HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
 
+    /* Register the private property of whether to skip EOF check. It's used by h5clear only. */
+    if(H5P_register_real(pclass, H5F_ACS_SKIP_EOF_CHECK_NAME, H5F_ACS_SKIP_EOF_CHECK_SIZE, &H5F_def_skip_eof_check_g,
+            NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
+    /* Register the private property of whether to drop free-space to the floor. It's used by h5clear only. */
+    if(H5P_register_real(pclass, H5F_ACS_NULL_FSM_ADDR_NAME, H5F_ACS_NULL_FSM_ADDR_SIZE, &H5F_def_null_fsm_addr_g,
+            NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL) < 0)
+        HGOTO_ERROR(H5E_PLIST, H5E_CANTINSERT, FAIL, "can't insert property into class")
+
     /* Register the metadata cache logging flag. */
     if(H5P_register_real(pclass, H5F_ACS_USE_MDC_LOGGING_NAME, H5F_ACS_USE_MDC_LOGGING_SIZE, &H5F_def_use_mdc_logging_g,
             NULL, NULL, NULL, H5F_ACS_USE_MDC_LOGGING_ENC, H5F_ACS_USE_MDC_LOGGING_DEC, NULL, NULL, NULL, NULL) < 0)