Hello DEMOLISHOR!
A Thursday 07 May 2009, DEMOLISHOR! the Demolishor escrigué:
> Hello all,
> I recently tried to install PyTables and got a segfault when I
> tried to run `tables.test()'
>
>
>
> [cra...@fsul1 ~]$ python
> Python 2.6.2 (r262:71600, May 7 2009, 14:58:49)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)] on linux2
> Type "help", "copyright", "credits" or "license" for more
> information.
>
> >>> import tables
> >>> tables.test()
>
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>=-=-=-= PyTables version: 2.1.1
> HDF5 version: 1.8.3
> NumPy version: 1.3.0
> Zlib version: 1.2.3
> LZO version: 2.03 (Apr 30 2008)
> BZIP2 version: 1.0.3 (15-Feb-2005)
> Python version: 2.6.2 (r262:71600, May 7 2009, 14:58:49)
> [GCC 4.1.2 20080704 (Red Hat 4.1.2-44)]
> Platform: linux2-i686
> Byte-ordering: little
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>=-=-=-= 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.
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>=-=-=-= Skipping Numeric test suite.
> Skipping numarray test suite.
> -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
>=-=-=-=
> .....................................................................
>......................................................................
>......................................................................
>......................................................................
>......................................................................
>..................................................Segmentation fault
Mmh, I've just tried HDF5 1.8.3 and had errors too:
EHDF5-DIAG: Error detected in HDF5 (1.8.3) thread 0:
#000: H5Dio.c line 174 in H5Dread(): can't read data
major: Dataset
minor: Read failed
#001: H5Dio.c line 404 in H5D_read(): can't read data
major: Dataset
minor: Read failed
#002: H5Dchunk.c line 1548 in H5D_chunk_read(): unable to read raw
data chunk
major: Low-level I/O
minor: Read failed
#003: H5Dchunk.c line 2561 in H5D_chunk_lock(): data pipeline read
failed
major: Data filters
minor: Filter operation failed
#004: H5Z.c line 1006 in H5Z_pipeline(): required filter is not
registered
major: Data filters
minor: Read failed
I'm afraid that the LZO compressor is not correctly detected (they have
probably changed the way to register filters). I'll report this as
soon as possible. Meanwhile, please try HDF5 1.8.2 instead.
> I am building this on a machine on which I do not have root
> privileges, so I built HDF5 and LZO from source and installed them
> with `--prefix=$HOME' . The output of `setup.py build_ext
> --hdf5=$HOME --lzo=$HOME' was as follows:
>
>
> [cra...@fsul1 tables-2.1.1]$ echo $LD_LIBRARY_PATH
> /home/craigb/lib:/local/scratch/root/lib
> [cra...@fsul1 tables-2.1.1]$ python setup.py build --hdf5=$HOME
> --lzo=$HOME * Found numpy 1.3.0 package installed.
> * Found HDF5 headers at ``/home/craigb/include``, library at
> ``/home/craigb/lib``.
> .. WARNING:: Could not find the HDF5 runtime.
> The HDF5 shared library was *not* found in the default library
> paths. In case of runtime problems, please remember to install it.
> * Found LZO 2 headers at ``/home/craigb/include``, library at
> ``/home/craigb/lib``.
> .. WARNING:: Could not find the LZO 2 runtime.
> The LZO 2 shared library was *not* found in the default library
> paths. In case of runtime problems, please remember to install it.
> * Skipping detection of LZO 1 since LZO 2 has already been found.
> * Found bzip2 headers at ``/usr/include``, library at ``/usr/lib``.
> running build
> running build_py
> running build_ext
> running build_scripts
> [cra...@fsul1 tables-2.1.1]$
>
>
> I don't understand the `WARNING's about not finding dynamic
> libraries--they exist at `/home/craigb/lib' and they are included in
> $LD_LIBRARY_PATH variable, as you can see. Plus, I just ran all of
> the checks in the hdf5 build directory and there were no failures.
> What did I do wrong?
Nothing :) It's just that setup.py is not intelligent enough to look
into the $LD_LIBRARY_PATH variable. This check is more for people that
are not used to put libraries in uncommon places. So don't be scared.
Cheers,
--
Francesc Alted
"One would expect people to feel threatened by the 'giant
brains or machines that think'. In fact, the frightening
computer becomes less frightening if it is used only to
simulate a familiar noncomputer."
-- Edsger W. Dykstra
"On the cruelty of really teaching computer science"
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