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
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