Hi,
I can't create a table, which (I think) I could before updating my hdf5
and pytables versions (both self compiled).
The attached code is a minimal example that on my machine (Linux)
results in the error message below.
Any ideas about what is wrong?
All the best, Gabriel
Error output:
=============
gabr...@gabriel-desktop:~$ python problem.py
1.8.2
2.1
HDF5-DIAG: Error detected in HDF5 (1.8.2) thread 0:
#000: H5Ddeprec.c line 170 in H5Dcreate1(): unable to create dataset
major: Dataset
minor: Unable to initialize object
#001: H5Dint.c line 429 in H5D_create_named(): unable to create and
link to dataset
major: Dataset
minor: Unable to initialize object
#002: H5L.c line 1633 in H5L_link_object(): unable to create new link
to object
major: Links
minor: Unable to initialize object
#003: H5L.c line 1856 in H5L_create_real(): can't insert link
major: Symbol table
minor: Unable to insert object
#004: H5Gtraverse.c line 877 in H5G_traverse(): internal path
traversal failed
major: Symbol table
minor: Object not found
#005: H5Gtraverse.c line 703 in H5G_traverse_real(): traversal
operator failed
major: Symbol table
minor: Callback failed
#006: H5L.c line 1679 in H5L_link_cb(): unable to create object
major: Object header
minor: Unable to initialize object
#007: H5O.c line 2531 in H5O_obj_create(): unable to open object
major: Object header
minor: Can't open object
#008: H5Doh.c line 278 in H5O_dset_create(): unable to create dataset
major: Dataset
minor: Unable to initialize object
#009: H5Dint.c line 1139 in H5D_create(): can't update the metadata
cache
major: Dataset
minor: Unable to initialize object
#010: H5Dint.c line 846 in H5D_update_oh_info(): unable to update new
fill value header message
major: Dataset
minor: Unable to initialize object
#011: H5Omessage.c line 188 in H5O_msg_append_oh(): unable to create
new message in header
major: Attribute
minor: Unable to insert object
#012: H5Omessage.c line 228 in H5O_msg_append_real(): unable to create
new message
major: Object header
minor: No space available for allocation
#013: H5Omessage.c line 1936 in H5O_msg_alloc(): unable to allocate
space for message
major: Object header
minor: Unable to initialize object
#014: H5Oalloc.c line 972 in H5O_alloc(): object header message is too
large
major: Object header
minor: Unable to initialize object
Traceback (most recent call last):
File "problem.py", line 11, in <module>
testfile.createTable(where=testfile.root, name='test',
description=TestTable)
File "/usr/lib/python2.5/site-packages/tables/file.py", line 714, in
createTable
chunkshape=chunkshape, byteorder=byteorder)
File "/usr/lib/python2.5/site-packages/tables/table.py", line 569, in
__init__
byteorder, _log)
File "/usr/lib/python2.5/site-packages/tables/leaf.py", line 290, in
__init__
super(Leaf, self).__init__(parentNode, name, _log)
File "/usr/lib/python2.5/site-packages/tables/node.py", line 296, in
__init__
self._v_objectID = self._g_create()
File "/usr/lib/python2.5/site-packages/tables/table.py", line 761, in
_g_create
self._v_new_title, self.filters.complib or '', obversion )
File "tableExtension.pyx", line 214, in
tables.tableExtension.Table._createTable
tables.exceptions.HDF5ExtError: Problems creating the table
Closing remaining open files: test.h5... done
gabr...@gabriel-desktop:~$
import tables
import numpy
print tables.getHDF5Version() # in my case 1.8.2
print tables.getPyTablesVersion() # in my case 2.1
class TestTable(tables.IsDescription):
signal = tables.Col.from_dtype(numpy.dtype((numpy.float32, (32, 3891))))
testfile = tables.openFile('test.h5','w')
testfile.createTable(where=testfile.root, name='test', description=TestTable)
testfile.close()------------------------------------------------------------------------------
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