Re: [Pytables-users] Runtime warning and import error after installation

[Antonio V. <ant...@ti...>]

Hi Serena Rhie,


Il giorno 20/ago/2012, alle ore 08:40, PyTables Org <pyt...@go...> ha scritto:

> Forwarding bounced message.
> ~Josh
> 
>> From: Arang Rhie <ar...@gm...>
>> Date: August 20, 2012 3:59:06 AM GMT+01:00
>> To: pyt...@li...
>> Subject: Runtime warning and import error after installation
>> 
>> Hi,
>> 
>> I'm new to PyTable, and now getting really frustrating with the installation process.
>> 1. What is the HDF5 runtime?
>>     I've installed HDF5 following the instruction given by HDF5.
>>     What file is PyTable looking for? And how can I set the path to it?
>>     I've installed HDF5 under /usr/local/hdf5 and set the environment variable $HDF5_DIR on /usr/local/hdf5.

this is very strange. Can you please check it again and, in case, file a new issue on [1]


>>     But still setup.py is not recognizing it without the --hdf5=/usr/local/hdf5 option.
>>     Moreover,  I don't understand the 'shared library' of HDF5. does that mean to install hdf5-1.8.9-linux-x86_64-shared.tar.gz from HDF5?
>>     I've untar the ~shared.tar.gz under /usr/local/hdf5-shared and set the $LD_LIBRARY_PATH as /usr/local/hdf5-shared.

If you maintained the layout of the official tar ball then probably you should set LD_LIBRARY_PATH to point to /usr/local/hdf5-shared/lib (please note the ending "/lib").
 
>>    What else do I need to do in addition?
>> 2. I've configured LZO with --enable-shared option, and followed the instruction (make, make check, make test, make install).
>>    I've completed without any error, and the shared libraries where set under /usr/local/lib.
>>    Do I need to explicitly set other variables for running setup.py?
>> 

No, it should be OK.

If the /usr/local/lib/liblzo2.so actually exists the setup script should not complain about a missing runtime.
Can you please check and let us know.

>> 
>> 
>> [root@gmi-student tables-2.4.0]# python setup.py install --hdf5=/usr/local/hdf5
>> * Found numpy 1.6.2 package installed.
>> * Found numexpr 2.0.1 package installed.
>> * Found Cython 0.16 package installed.
>> * Found HDF5 headers at ``/usr/local/hdf5/include``, library at ``/usr/local/hdf5/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 ``/usr/local/include``, library at ``/usr/local/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/lib64``.
>> running install
>> running build
>> running build_py
>> running build_ext
>> running build_scripts
>> running install_lib
>> running install_scripts
>> changing mode of /usr/bin/ptdump to 755
>> changing mode of /usr/bin/ptrepack to 755
>> changing mode of /usr/bin/nctoh5 to 755
>> running install_egg_info
>> Removing /usr/lib64/python2.7/site-packages/tables-2.4.0-py2.7.egg-info
>> Writing /usr/lib64/python2.7/site-packages/tables-2.4.0-py2.7.egg-info
>> [root@gmi-student tables-2.4.0]# python
>> Python 2.7 (r27:82500, Sep 16 2010, 18:02:00) 
>> [GCC 4.5.1 20100907 (Red Hat 4.5.1-3)] on linux2
>> Type "help", "copyright", "credits" or "license" for more information.
>> >>> import tables
>> Traceback (most recent call last):
>>   File "<stdin>", line 1, in <module>
>>   File "tables/__init__.py", line 30, in <module>
>>     from tables.utilsExtension import getPyTablesVersion, getHDF5Version
>> ImportError: libhdf5.so.7: cannot open shared object file: No such file or directory
>> 
>> Serena Rhie


best regards

[1] https://github.com/PyTables/PyTables/issues

--
Antonio Valentino