Investigate nwb files which can crash IP

[t-b]

Created by crashing the computer.

FTP: issue-2231

$ h5ls --enable-error-stack -v -r 2024_08_14_123155.nwb
Opened "2024_08_14_123155.nwb" with sec2 driver.
/                        Group
    Attribute: .specloc scalar
        Type:      object reference
    Attribute: namespace scalar
        Type:      4-byte null-padded UTF-8 string
    Attribute: neurodata_type scalar
        Type:      7-byte null-padded UTF-8 string
    Attribute: nwb_version scalar
        Type:      5-byte null-padded UTF-8 string
    Attribute: object_id scalar
        Type:      36-byte null-padded UTF-8 string
    Location:  1:48
    Links:     1
    Modified:  2024-08-14 21:31:56 Mitteleuropõische Sommerzeit
/acquisition             Group
    Location:  1:11895
    Links:     1
    Modified:  2024-08-14 21:31:56 Mitteleuropõische Sommerzeit
HDF5-DIAG: Error detected in HDF5 (1.14.4-3) thread 0:
  #000: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5L.c line 1928 in H5Lvisit_by_name2(): link visitation failed
    major: Links
    minor: Iteration failed
  #001: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5VLcallback.c line 5517 in H5VL_link_specific(): unable to execute link specific callback
    major: Virtual Object Layer
    minor: Can't operate on object
  #002: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5VLcallback.c line 5483 in H5VL__link_specific(): unable to execute link specific callback
    major: Virtual Object Layer
    minor: Can't operate on object
  #003: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5VLnative_link.c line 375 in H5VL__native_link_specific(): link visitation failed
    major: Links
    minor: Iteration failed
  #004: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gint.c line 1178 in H5G_visit(): can't visit links
    major: Symbol table
    minor: Iteration failed
  #005: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gobj.c line 649 in H5G__obj_iterate(): can't iterate over dense links
    major: Symbol table
    minor: Iteration failed
  #006: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gdense.c line 967 in H5G__dense_iterate(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #007: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Glink.c line 523 in H5G__link_iterate_table(): iteration operator failed
    major: Symbol table
    minor: Can't move to next iterator location
  #008: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gobj.c line 649 in H5G__obj_iterate(): can't iterate over dense links
    major: Symbol table
    minor: Iteration failed
  #009: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gdense.c line 963 in H5G__dense_iterate(): error building table of links
    major: Symbol table
    minor: Can't get value
  #010: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gdense.c line 775 in H5G__dense_build_table(): error iterating over links
    major: Symbol table
    minor: Can't move to next iterator location
  #011: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gdense.c line 954 in H5G__dense_iterate(): link iteration failed
    major: Symbol table
    minor: Iteration failed
  #012: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5B2.c line 405 in H5B2_iterate(): node iteration failed
    major: B-Tree node
    minor: Unable to list node
  #013: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5B2int.c line 1674 in H5B2__iterate_node(): node iteration failed
    major: B-Tree node
    minor: Unable to list node
  #014: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5B2int.c line 1679 in H5B2__iterate_node(): iterator function failed
    major: B-Tree node
    minor: Unable to list node
  #015: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gdense.c line 851 in H5G__dense_iterate_bt2_cb(): heap op callback failed
    major: Symbol table
    minor: Can't operate on object
  #016: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5HF.c line 656 in H5HF_op(): can't operate on object from fractal heap
    major: Heap
    minor: Can't operate on object
  #017: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5HFman.c line 507 in H5HF__man_op(): unable to operate on heap object
    major: Heap
    minor: Can't operate on object
  #018: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5HFman.c line 403 in H5HF__man_op_real(): application's callback failed
    major: Heap
    minor: Can't operate on object
  #019: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Gdense.c line 815 in H5G__dense_iterate_fh_cb(): can't decode link
    major: Symbol table
    minor: Unable to decode value
  #020: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Omessage.c line 1635 in H5O_msg_decode(): unable to decode message
    major: Object header
    minor: Unable to decode value
  #021: D:\a\hdf5\hdf5\hdf5-1.14.4-3\src\H5Olink.c line 122 in H5O__link_decode(): bad version number for message
    major: Object header
    minor: Unable to load metadata into cache
H5tools-DIAG: Error detected in HDF5:tools (1.14.4) thread 0:
  #000: D:\a\hdf5\hdf5\hdf5-1.14.4-3\tools\lib\h5trav.c line 1050 in h5trav_visit(): traverse failed
    major: Failure in tools library
    minor: error in function
  #001: D:\a\hdf5\hdf5\hdf5-1.14.4-3\tools\lib\h5trav.c line 283 in traverse(): H5Lvisit_by_name failed
    major: Failure in tools library
    minor: error in function

[t-b]

@timjarsky The usual tools don't help in recovering as the file is really broken. Now it's either hex-editor time or we give it lost.

[timjarsky]

Thanks for checking @t-b