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
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?
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