Hi, I have now started using pytables ignoring the test errors, but you may be interested in the message below, from my sysop
---------- Forwarded message ---------- From: Oliver Lemke <oliver.le...@ltu.se> Date: 20 October 2010 10:31 Subject: Re: [Pytables-users] tables.test() fails on ubuntu when installing from package python-tables To: Gerrit Holl <gerrit.h...@ltu.se> I've switched from the system HDF5 library to my own local installation of the latest HDF5 version (1.8.4-patch1 -> 1.8.5-patch1). Still get the error but also some debug output from the HDF5 library complaining about invalid arguments and inappropriate types. see HDF5-DIAG messages below. Maybe the pytables guys are interested in those messages. /oliver >>> tables.test() -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= PyTables version: 2.2.1.dev HDF5 version: 1.8.5-patch1 NumPy version: 1.5.1rc1 Numexpr version: 1.5.dev245 (not using Intel's VML/MKL) Zlib version: 1.2.3.4 (in Python interpreter) Blosc version: 1.1.1 ($Date:: 2010-10-01 #$) Cython version: 0.13 Python version: 2.6.6 (r266:84292, Sep 15 2010, 16:22:56) [GCC 4.4.5] Platform: linux2-x86_64 Byte-ordering: little Detected cores: 8 -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= Performing only a light (yet comprehensive) subset of the test suite. If you want a more complete test, try passing the --heavy flag to this script (or set the 'heavy' parameter in case you are using tables.test() call). The whole suite will take more than 2 minutes to complete on a relatively modern CPU and around 80 MB of main memory. -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-= /storage4/home/olemke/python/lib/python/tables/filters.py:264: FiltersWarning: compression library ``bzip2`` is not available; using ``zlib`` instead % (complib, default_complib), FiltersWarning ) /storage4/home/olemke/python/lib/python/tables/filters.py:264: FiltersWarning: compression library ``lzo`` is not available; using ``zlib`` instead % (complib, default_complib), FiltersWarning ) .............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5D.c line 377 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5D.c line 377 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5D.c line 377 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5D.c line 377 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5T.c line 1721 in H5Tclose(): not a datatype major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5D.c line 377 in H5Dclose(): not a dataset major: Invalid arguments to routine minor: Inappropriate type HDF5-DIAG: Error detected in HDF5 (1.8.5-patch1) thread 0: #000: H5G.c line 711 in H5Gclose(): not a group major: Invalid arguments to routine minor: Inappropriate type E.... ====================================================================== ERROR: None (tables.netcdf3.tests.test_netcdf3.NetCDFFileTestCase2) ---------------------------------------------------------------------- Traceback (most recent call last): File "/storage4/home/olemke/python/lib/python/tables/tests/common.py", line 248, in newmethod return oldmethod(self, *args, **kwargs) File "/storage4/home/olemke/python/lib/python/tables/netcdf3/tests/test_netcdf3.py", line 165, in test_h5tonc f.close() File "/storage4/home/olemke/python/lib/python/tables/netcdf3/__init__.py", line 301, in close self._NetCDF_h5file.close() File "/storage4/home/olemke/python/lib/python/tables/file.py", line 2127, in close self.root._f_close() File "/storage4/home/olemke/python/lib/python/tables/group.py", line 982, in _f_close self._g_close() File "/storage4/home/olemke/python/lib/python/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 / ---------------------------------------------------------------------- Ran 2946 tests in 36.945s FAILED (errors=1) >>> -- Exploring space at 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