Hi again,
On 19 October 2010 17:48, Francesc Alted <fal...@pytables.org> wrote:
> Hmm, that's strange that you get these errors in some machines and not
> in others. But, by looking at the failures, I don't think they are
> grave at all. One is related with the NetCDF3 interface, so if you are
> not using it, then you should not worry about it. And the other problem
> is related with old flavors in PyTables 1.x series, so if you don't need
> complete backward compatibility with existing PyTables 1.x datafiles
> then you are safe again.
I'm not using Pytables' NetCDF3 interface. However, I am using
ScientificPythons NetCDF routine to read NetCDF, and pytables to write
HDF. I thought the two should be independent, but:
- I use pytables to open a HDF5-file for writing
- I use Scientific.IO.NetCDF.NetCDFFile (a completely different
package?) to open a NetCDF file for reading
- I close the NetCDF file for reading
- the pytables HDF5-file becomes corrupted or so.
How is it possible that the NetCDF file, from a different library,
influences the HDF5 file object at all?
How can I proceed in debugging this?
If I close the pytables file before the netcdf file, all is fine.
Changing the order of opening the files has no influence.
The code:
#!/usr/bin/python
import tables
import Scientific.IO.NetCDF
h5 = tables.openFile('/tmp/foobar.h5', 'w')
netc = Scientific.IO.NetCDF.NetCDFFile('/tmp/testfile.nc', 'r')
netc.close()
h5.close()
The output:
$ python pytable_crash.py
Traceback (most recent call last):
File "pytable_crash.py", line 9, in <module>
h5.close() # fails
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/file.py",
line 2127, in close
self.root._f_close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/group.py",
line 982, in _f_close
self._g_close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/group.py",
line 949, in _g_close
self._g_closeGroup()
File "hdf5Extension.pyx", line 699, in
tables.hdf5Extension.Group._g_closeGroup (tables/hdf5Extension.c:6028)
tables.exceptions.HDF5ExtError: Problems closing the Group /
Closing remaining open files: /tmp/foobar.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
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/file.py",
line 2323, in close_open_files
fileh.close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/file.py",
line 2127, in close
self.root._f_close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/group.py",
line 982, in _f_close
self._g_close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/group.py",
line 949, in _g_close
self._g_closeGroup()
File "hdf5Extension.pyx", line 699, in
tables.hdf5Extension.Group._g_closeGroup (tables/hdf5Extension.c:6028)
HDF5ExtError: Problems closing the Group /
Error in sys.exitfunc:
Traceback (most recent call last):
File "/usr/lib/python2.6/atexit.py", line 24, in _run_exitfuncs
func(*targs, **kargs)
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/file.py",
line 2323, in close_open_files
fileh.close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/file.py",
line 2127, in close
self.root._f_close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/group.py",
line 982, in _f_close
self._g_close()
File
"/storage4/home/gerrit/.local/lib/python2.6/site-packages/tables/group.py",
line 949, in _g_close
self._g_closeGroup()
File "hdf5Extension.pyx", line 699, in
tables.hdf5Extension.Group._g_closeGroup (tables/hdf5Extension.c:6028)
tables.exceptions.HDF5ExtError: Problems closing the Group /
I have tested this on several systems. At work, with ubuntu 10.04 or
10.10, it fails. At home, with ubuntu 10.04, it succeeds. The software
is really the same.
> At any rate, I'd say that you should report the problem to Ubuntu, yes.
Actually, I get the same error if I compile from source. So I don't
know if this is ubuntu-related. It succeeds on other installations of
ubuntu.
regards,
Gerrit.
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