dealing with corrupt file

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Hello, I have a file that seems to be corrupt. Trying to read data sets and even delete the group containing an apparently corrupt items fails-often "H5O_load(): bad object header version number" is the innermost error.
Are there any repair tools as such for HDF5 files? The output for "H5Repack" on the corrupt file is below.

HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 10024:
  #000: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 657 in H5Oget_info_by_name(): object not found
    major: Symbol table
    minor: Object not found
  #001: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 747 in H5G_loc_info(): can't find object
    major: Symbol table
    minor: Object not found
  #002: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #004: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 702 in H5G_loc_info_cb(): can't get object info
    major: Symbol table
    minor: Can't get value
  #005: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 2791 in H5O_get_info(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #006: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 1684 in H5O_protect(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #007: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5AC.c line 1320 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #008: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 3574 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #009: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 7954 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #010: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Ocache.c line 275 in H5O_load(): bad object header version number
    major: Object header
    minor: Wrong version number
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 10024:
  #000: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5L.c line 1379 in H5Lvisit_by_name(): link visitation failed
    major: Symbol table
    minor: Iteration failed
  #001: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gint.c line 1175 in H5G_visit(): can't visit links
    major: Symbol table
    minor: Iteration failed
  #002: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
    major: Symbol table
    minor: Iteration failed
  #003: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #004: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1298 in H5B_iterate(): B-tree iteration failed
    major: B-Tree node
    minor: Iteration failed
  #005: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1221 in H5B_iterate_helper(): iterator function failed
    major: B-Tree node
    minor: Unable to list node
  #006: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #007: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
    major: Symbol table
    minor: Iteration failed
  #008: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #009: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1298 in H5B_iterate(): B-tree iteration failed
    major: B-Tree node
    minor: Iteration failed
  #010: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1221 in H5B_iterate_helper(): iterator function failed
    major: B-Tree node
    minor: Unable to list node
  #011: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #012: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
    major: Symbol table
    minor: Iteration failed
  #013: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #014: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1298 in H5B_iterate(): B-tree iteration failed
    major: B-Tree node
    minor: Iteration failed
  #015: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1179 in H5B_iterate_helper(): unable to list B-tree node
    major: B-Tree node
    minor: Unable to list node
  #016: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1179 in H5B_iterate_helper(): unable to list B-tree node
    major: B-Tree node
    minor: Unable to list node
  #017: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1221 in H5B_iterate_helper(): iterator function failed
    major: B-Tree node
    minor: Unable to list node
  #018: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #019: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 657 in H5Oget_info_by_name(): object not found
    major: Symbol table
    minor: Object not found
  #020: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 747 in H5G_loc_info(): can't find object
    major: Symbol table
    minor: Object not found
  #021: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #022: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #023: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 702 in H5G_loc_info_cb(): can't get object info
    major: Symbol table
    minor: Can't get value
  #024: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 2791 in H5O_get_info(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #025: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 1684 in H5O_protect(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #026: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5AC.c line 1320 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #027: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 3574 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #028: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 7954 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #029: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Ocache.c line 275 in H5O_load(): bad object header version number
    major: Object header
    minor: Wrong version number

2

Hi Jim,

···

On Feb 13, 2015, at 9:44 AM, Rowe, Jim <J.Rowe@questintegrity.com<mailto:J.Rowe@questintegrity.com>> wrote:

Hello, I have a file that seems to be corrupt. Trying to read data sets and even delete the group containing an apparently corrupt items fails—often “H5O_load(): bad object header version number” is the innermost error.
Are there any repair tools as such for HDF5 files? The output for “H5Repack” on the corrupt file is below.

Unfortunately there is no such tool is available at this point. The error stack indicates that the library cannot iterate over a group (root group?). You may try to run h5check
http://www.hdfgroup.org/products/hdf5_tools/h5check.html to get more information about the corrupted object.

Elena
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Elena Pourmal The HDF Group http://hdfgroup.org
1800 So. Oak St., Suite 203, Champaign IL 61820
217.531.6112
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 10024:
  #000: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 657 in H5Oget_info_by_name(): object not found
    major: Symbol table
    minor: Object not found
  #001: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 747 in H5G_loc_info(): can't find object
    major: Symbol table
    minor: Object not found
  #002: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #003: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #004: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 702 in H5G_loc_info_cb(): can't get object info
    major: Symbol table
    minor: Can't get value
  #005: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 2791 in H5O_get_info(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #006: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 1684 in H5O_protect(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #007: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5AC.c line 1320 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #008: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 3574 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #009: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 7954 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #010: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Ocache.c line 275 in H5O_load(): bad object header version number
    major: Object header
    minor: Wrong version number
HDF5-DIAG: Error detected in HDF5 (1.8.14) thread 10024:
  #000: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5L.c line 1379 in H5Lvisit_by_name(): link visitation failed
    major: Symbol table
    minor: Iteration failed
  #001: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gint.c line 1175 in H5G_visit(): can't visit links
    major: Symbol table
    minor: Iteration failed
  #002: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
    major: Symbol table
    minor: Iteration failed
  #003: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #004: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1298 in H5B_iterate(): B-tree iteration failed
    major: B-Tree node
    minor: Iteration failed
  #005: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1221 in H5B_iterate_helper(): iterator function failed
    major: B-Tree node
    minor: Unable to list node
  #006: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #007: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
    major: Symbol table
    minor: Iteration failed
  #008: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #009: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1298 in H5B_iterate(): B-tree iteration failed
    major: B-Tree node
    minor: Iteration failed
  #010: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1221 in H5B_iterate_helper(): iterator function failed
    major: B-Tree node
    minor: Unable to list node
  #011: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #012: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gobj.c line 708 in H5G__obj_iterate(): can't iterate over symbol table
    major: Symbol table
    minor: Iteration failed
  #013: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gstab.c line 566 in H5G__stab_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #014: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1298 in H5B_iterate(): B-tree iteration failed
    major: B-Tree node
    minor: Iteration failed
  #015: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1179 in H5B_iterate_helper(): unable to list B-tree node
    major: B-Tree node
    minor: Unable to list node
  #016: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1179 in H5B_iterate_helper(): unable to list B-tree node
    major: B-Tree node
    minor: Unable to list node
  #017: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5B.c line 1221 in H5B_iterate_helper(): iterator function failed
    major: B-Tree node
    minor: Unable to list node
  #018: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gnode.c line 1039 in H5G__node_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #019: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 657 in H5Oget_info_by_name(): object not found
    major: Symbol table
    minor: Object not found
  #020: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 747 in H5G_loc_info(): can't find object
    major: Symbol table
    minor: Object not found
  #021: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 861 in H5G_traverse(): internal path traversal failed
    major: Symbol table
    minor: Object not found
  #022: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gtraverse.c line 641 in H5G_traverse_real(): traversal operator failed
    major: Symbol table
    minor: Callback failed
  #023: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Gloc.c line 702 in H5G_loc_info_cb(): can't get object info
    major: Symbol table
    minor: Can't get value
  #024: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 2791 in H5O_get_info(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #025: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5O.c line 1684 in H5O_protect(): unable to load object header
    major: Object header
    minor: Unable to protect metadata
  #026: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5AC.c line 1320 in H5AC_protect(): H5C_protect() failed.
    major: Object cache
    minor: Unable to protect metadata
  #027: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 3574 in H5C_protect(): can't load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #028: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5C.c line 7954 in H5C_load_entry(): unable to load entry
    major: Object cache
    minor: Unable to load metadata into cache
  #029: C:\Documents\Code\Hdf5\hdf5-1.8.14\src\H5Ocache.c line 275 in H5O_load(): bad object header version number
    major: Object header
    minor: Wrong version number

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