I'm running PyTables 2.1.2 which HDF5 version 1.8.4. As I've mentioned
earlier I have some code that has multiple file handles to a single
file, one for writing, others for reading. I'm trying to refactor my
code to avoid this, but I've stumbled across this bug.
In [1]: import tables
In [2]: fyle = tables.openFile("foo.h5")
In [3]: fyle2 = tables.openFile("foo.h5",mode="a")
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5F.c line 1512 in H5Fopen(): unable to open file
major: File accessability
minor: Unable to open file
#001: H5F.c line 1241 in H5F_open(): file is already open for read-only
major: File accessability
minor: Unable to open file
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5F.c line 2477 in H5Fget_mdc_config(): not a file ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5F.c line 2530 in H5Fset_mdc_config(): not a file ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5Gdeprec.c line 293 in H5Gopen1(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 241 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5Adeprec.c line 208 in H5Aopen_name(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 241 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5G.c line 694 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5Gdeprec.c line 293 in H5Gopen1(): not a location
major: Invalid arguments to routine
minor: Inappropriate type
#001: H5Gloc.c line 241 in H5G_loc(): invalid object ID
major: Invalid arguments to routine
minor: Bad value
---------------------------------------------------------------------------
HDF5ExtError Traceback (most recent call last)
/scrap/afoglia/uni/<ipython console> in <module>()
/usr/local/lib/python2.6/dist-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/file.pyc
in openFile(filename, mode, title, rootUEP, filters, nodeCacheSize,
**kwargs)
228
229 # Finally, create the File instance, and return it
--> 230 return File(filename, mode, title, rootUEP, filters, **kwargs)
231
232
/usr/local/lib/python2.6/dist-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/file.pyc
in __init__(self, filename, mode, title, rootUEP, filters, **kwargs)
518
519 # Get the root group from this file
--> 520 self.root = root = self.__getRootGroup(rootUEP, title,
filters)
521 # Complete the creation of the root node
522 # (see the explanation in ``RootGroup.__init__()``.
/usr/local/lib/python2.6/dist-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/file.pyc
in __getRootGroup(self, rootUEP, title, filters)
563 # Create new attributes for the root Group instance and
564 # create the object tree
--> 565 return RootGroup(self, rootUEP, title=title, new=new,
filters=filters)
566
567
/usr/local/lib/python2.6/dist-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/group.pyc
in __init__(self, ptFile, name, title, new, filters)
1133 self._g_new(ptFile, name, init=True)
1134 # Open the node and get its object ID.
-> 1135 self._v_objectID = self._g_open()
1136
1137 # Set disk attributes and read children names.
/usr/local/lib/python2.6/dist-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/hdf5Extension.so
in tables.hdf5Extension.Group._g_open()
HDF5ExtError: Can't open the group: '/'.
In [4]: tables.file._open_files.keys()
Segmentation fault (core dumped)
If instead of tables.file._open_files.keys(), I simply do a Ctrl-D, I
get the following errors:
Closing remaining open files: Global/ASAAsset/1/Captured-2002.h5... done
Global/ASAAsset/1/Captured-2002.h5... Error in atexit._run_exitfuncs:
Traceback (most recent call last):
File "/usr/lib/python2.6/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File
"/usr/local/lib/python2.6/dist-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/file.py",
line 2175, in close_open_files
fileh.close()
File
"/usr/local/lib/python2.6/dist-packages/tables-2.1.2-py2.6-linux-x86_64.egg/tables/file.py",
line 1985, in close
self.root._f_close()
AttributeError: 'File' object has no attribute 'root'
Error in sys.exitfunc:
HDF5-DIAG: Error detected in HDF5 (1.8.4) thread 0:
#000: H5G.c line 694 in H5Gclose(): not a group
major: Invalid arguments to routine
minor: Inappropriate type
Exception tables.exceptions.HDF5ExtError: HDF5ExtError('Problems closing
the Group /',) in ignored
[And then a barebones traceback from IPython ending with
"AttributeError: 'File' object has no attribute 'root'"]
I understand what I'm doing is not well accepted, but PyTables should be
robust enough to handle it in a stable manner. (I don't even understand
the "Can't open the group: '/'" error as the file obviously has one.)
--
Anthony Foglia
Princeton Consultants
(609) 987-8787 x233
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