Investigate nwb files which can crash IP
Closed this issue · 2 comments
t-b commented
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 commented
@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.