[Yet another bounce. I'll never give up asking people to write to the
list from a subscribed address ;-)]
A Thursday 23 October 2008, escriguéreu:
> Hi,
>
> I'm getting errors in h5ls listings with most files using pytables
> 2.0.4, hdf5 1.8.1, numpy 1.1.1, and python 2.5.2. This includes the
> provided pytables examples. An example is below. Any ideas as to the
> cause?
>
> Thanks,
>
> Frank Lind
>
>
>
> > h5ls -e objecttree.h5/group1
> HDF5-DIAG: Error detected in HDF5 (1.8.1) thread 0:
> #000: H5O.c line 242 in H5Oopen(): unable to open object
> major: Symbol table
> minor: Can't open object
> #001: H5O.c line 1283 in H5O_open_name(): object not found
> major: Symbol table
> minor: Object not found
> #002: H5Gloc.c line 468 in H5G_loc_find(): can't find object
> major: Symbol table
> minor: Object not found
> #003: H5Gtraverse.c line 861 in H5G_traverse(): internal path
> traversal failed
> major: Symbol table
> minor: Object not found
> #004: H5Gtraverse.c line 691 in H5G_traverse_real(): traversal
> operator failed
> major: Symbol table
> minor: Callback failed
> #005: H5Gloc.c line 423 in H5G_loc_find_cb(): object doesn't exist
> major: Symbol table
> minor: Object not found
> #006: H5Gobj.c line 1105 in H5G_obj_lookup(): can't locate object
> major: Symbol table
> minor: Object not found
> #007: H5Gstab.c line 857 in H5G_stab_lookup(): not found
> major: Symbol table
> minor: Object not found
> #008: H5Gnode.c line 971 in H5G_node_found(): not found
> major: Symbol table
> minor: Object not found
> array2 Dataset *ERROR*
> HDF5-DIAG: Error detected in HDF5 (1.8.1) thread 0:
> #000: H5O.c line 242 in H5Oopen(): unable to open object
> major: Symbol table
> minor: Can't open object
> #001: H5O.c line 1283 in H5O_open_name(): object not found
> major: Symbol table
> minor: Object not found
> #002: H5Gloc.c line 468 in H5G_loc_find(): can't find object
> major: Symbol table
> minor: Object not found
> #003: H5Gtraverse.c line 861 in H5G_traverse(): internal path
> traversal failed
> major: Symbol table
> minor: Object not found
> #004: H5Gtraverse.c line 691 in H5G_traverse_real(): traversal
> operator failed
> major: Symbol table
> minor: Callback failed
> #005: H5Gloc.c line 423 in H5G_loc_find_cb(): object doesn't exist
> major: Symbol table
> minor: Object not found
> #006: H5Gobj.c line 1105 in H5G_obj_lookup(): can't locate object
> major: Symbol table
> minor: Object not found
> #007: H5Gstab.c line 857 in H5G_stab_lookup(): not found
> major: Symbol table
> minor: Object not found
> table1 Dataset *ERROR*
Yeah. I can reproduce that here. However, using h5ls from 1.6.x series
seems to work well (even with files created with PyTables linked
against HDF5 1.8.x series):
~/computacio.nobackup/hdf5-1.6.7/hdf5/bin/h5ls -e objecttree.h5/group1
array2 Dataset {4}
table1 Dataset {10/Inf}
Mmmh, I don't know what's happening here. I'll report this to the HDF5
people and report back my findings.
Thanks for noticing that,
--
Francesc Alted
Freelance Developer & Consultant
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