Hi Jim, On Feb 13, 2015, at 9:44 AM, Rowe, Jim <[email protected]<mailto:[email protected]>> 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 _______________________________________________ Hdf-forum is for HDF software users discussion. 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_______________________________________________ Hdf-forum is for HDF software users discussion. [email protected] http://lists.hdfgroup.org/mailman/listinfo/hdf-forum_lists.hdfgroup.org Twitter: https://twitter.com/hdf5
