Re: [Pytables-users] Wondering if data can be recovered

[Francesc A. <fa...@py...>]

A Saturday 26 July 2008, Anand Patil escrigué:
> Hi all,
> I seem to have lost a long-running simulation... it was writing out
> to an hdf5 archive, and when I try to open the archive after the
> simulation is over I get the following and several nodes are missing
> from
> Africa.S.db.group0:
>
>
> In [2]: Africa.S.db._group
>
> HDF5-DIAG: Error detected in HDF5 (1.8.0) thread 0:
>   #000: H5Gdeprec.c line 777 in H5Giterate(): group iteration failed
>     major: Symbol table
>     minor: Iteration failed
>   #001: H5G.c line 1657 in H5G_iterate(): error iterating over links
>     major: Symbol table
>     minor: Iteration failed
>   #002: H5Gobj.c line 681 in H5G_obj_iterate(): can't iterate over
> symbol table
>     major: Symbol table
>     minor: Iteration failed
>   #003: H5Gstab.c line 522 in H5G_stab_iterate(): iteration operator
> failed major: Symbol table
>     minor: Can't move to next iterator location
>   #004: H5B.c line 1218 in H5B_iterate(): iterator function failed
>     major: B-Tree node
>     minor: Unable to list node
>   #005: H5Gnode.c line 1425 in H5G_node_iterate(): unable to load
> symbol table node
>     major: Symbol table
>     minor: Unable to load metadata into cache
>   #006: H5AC.c line 1970 in H5AC_protect(): H5C_protect() failed.
>     major: Object cache
>     minor: Unable to protect metadata
>   #007: H5C.c line 5928 in H5C_protect(): can't load entry
>     major: Object cache
>     minor: Unable to load metadata into cache
>   #008: H5C.c line 10567 in H5C_load_entry(): unable to load entry
>     major: Object cache
>     minor: Unable to load metadata into cache
>   #009: H5Gnode.c line 384 in H5G_node_load(): unable to read symbol
> table node
>     major: Symbol table
>     minor: Read failed
>   #010: H5F.c line 2974 in H5F_block_read(): file read failed
>     major: Low-level I/O
>     minor: Read failed
>   #011: H5FD.c line 2046 in H5FD_read(): driver read request failed
>     major: Virtual File Layer
>     minor: Read failed
>   #012: H5FDsec2.c line 725 in H5FD_sec2_read(): addr overflow
>     major: Invalid arguments to routine
>     minor: Address overflowed
>
> Out[2]:
> /chain0 (Group) 'Chain #0'
>   children := ['__state__' (VLArray), 'group0' (Group)]
>
> Is there any way I can fix this?

Hmm, I'm guessing that this happened after a crash of your program, 
right?.  As fas as I know, there is not a way to recover from a corrupt 
HDF5.

Your best bet when running large simulations is to provide a checkpoint 
and recovery functionality to your simulation software, so that you can 
restart the computations from the last sane HDF5 file saved before the 
crash.

HTH,

-- 
Francesc Alted
Freelance developer
Tel +34-964-282-249