After I reinstalled everything, it finally works for me. The key is to set
LD_LIBRARY_PATH to find the shared HDF5 library. I still think that the
install procedure is not as clean as I'd expect. For example, I still need to
set HDF5_DIR even it is under /usr/local and instruction says it'd look there
as a standard place. I also changed from /usr/local/hdf5 to /usr/local/HDF5,
not sure if that made the difference or not. I'm still getting test failures
on Numeric stuff, but that's probably because I'm using obsolete Numeric
libraries. Thanks everybody for your help.
Jianfu
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Pan, Jianfu (GSFC-610.2)[ADNET]
Sent: Sat 5/10/2008 6:12 PM
To: Ivan Vilata i Balaguer; pytables-users@lists.sourceforge.net
Subject: Re: [Pytables-users] pytables install problem
That makes a lot of sense, and that's why it's a warning not fatal error.
However, I cannot get the runtime library (libhdf5.so.5?) when running my
program even I set the LD path environments. I even copied libhdf5.so.5 to
/usr/local/lib and still no success. I think I'm going to rebuild pytables,
thinking it probably got some unusual path when I first built it. Thanks for
the help!
Jianfu
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Ivan Vilata i Balaguer
Sent: Sat 5/10/2008 5:33 PM
To: pytables-users@lists.sourceforge.net
Subject: Re: [Pytables-users] pytables install problem
Pan, Jianfu (GSFC-610.2)[ADNET] (el 2008-05-10 a les 15:42:46 -0500) va dir::
> I'm jumping into the pytables/HDF5 world, but I'm having problem
> installing it. I have HDF5 installed in /usr/local/hdf5, which
> contains three subdirectories: bin, include and lib. When I tried to
> install pytables (with HDF5_DIR set), I got the following message:
> * 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.
> I think it's looking for libhdf5.so.5 which is in /usr/local/hdf5/lib.
> I don't understand why HDF5_DIR didn't take care of it. Any help will
> be greatly appreciated.
The setup script only looks for dynamic (runtime) libraries in the
default locations under Unix-like systems. They aren't really needed
during compilation, so the warning is just an indication that you *may*
have problems when *running* a program using PyTables.
The way to avoid runtime problems depends on your system. For instance,
under GNU/linux you should set the LD_RUN_PATH environment variable to
include ``/usr/local/hdf5/lib``. In fact, if you set it *before*
building, the path gets harcoded into the generated libraries so you no
longer need the variable.
So, regardless of the warning message, are you actually having problems
*running* your PyTables-based application?
Cheers,
::
Ivan Vilata i Balaguer >qo< http://www.carabos.com/
Cárabos Coop. V. V V Enjoy Data
""
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