PyTables cannot find the HDF5 shared library

Hi,
   I am trying to install PyTables 2.4.0. I have OS X 10.7.5 and Python
2.7. I have installed the following Python libraries: numexpr-1.4.2,
Cython-0.18 and numpy 1.5.1. For HDF5, I initially downloaded hdf5-1.8.7
from the following location:

http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.7/obtain5187.html

and made HDF5_DIR point to where I downloaded and unzipped hdf5-1.8.7, and
added $HDF5_DIR/lib to LD_LIBRARY_PATH.

    However, when I try to install PyTables by the following command

    easy_install --prefix=~/local tables-2.4.0

    I get the following message:

    Found HDF5 headers at
``/Users/bibudhlahiri/hdf5/hdf5-1.8.7-mac-intel-static/include``, library
at ``/Users/bibudhlahiri/hdf5/hdf5-1.8.7-mac-intel-static/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.

   which leads to additional problems when I try to run some Python
programs that are supposed to read some HDF5 files.

  Could you please point out where the error is, and what I can do?

Thanks
      Bibudh

···

--
Bibudh Lahiri
Data Scientist, Case Commons LLC
841 Broadway, New York, NY 10003
http://knowthynumbers.blogspot.com/

Bibudh, you've downloaded the static rather than the dynamic build. You
probably want

http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.7/bin/mac-intel/hdf5-1.8.
7-mac-intel-shared.tar.gz

or

http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.7/bin/mac-intel-x86_64/hd
f5-1.8.7-mac-intel-x86_64-shared.tar.gz

(notice the 'shared' in the name)

G.

···

From: Hdf-forum [mailto:hdf-forum-bounces@hdfgroup.org] On Behalf Of Bibudh
Lahiri
Sent: Wednesday, April 10, 2013 7:52 PM
To: hdf-forum@hdfgroup.org
Subject: [Hdf-forum] PyTables cannot find the HDF5 shared library

Hi,

   I am trying to install PyTables 2.4.0. I have OS X 10.7.5 and Python 2.7.
I have installed the following Python libraries: numexpr-1.4.2, Cython-0.18
and numpy 1.5.1. For HDF5, I initially downloaded hdf5-1.8.7 from the
following location:

http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.7/obtain5187.html

and made HDF5_DIR point to where I downloaded and unzipped hdf5-1.8.7, and
added $HDF5_DIR/lib to LD_LIBRARY_PATH.

    However, when I try to install PyTables by the following command

    easy_install --prefix=~/local tables-2.4.0

    I get the following message:

    Found HDF5 headers at
``/Users/bibudhlahiri/hdf5/hdf5-1.8.7-mac-intel-static/include``, library at
``/Users/bibudhlahiri/hdf5/hdf5-1.8.7-mac-intel-static/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.

   which leads to additional problems when I try to run some Python programs
that are supposed to read some HDF5 files.

  Could you please point out where the error is, and what I can do?

Thanks

      Bibudh

--

Bibudh Lahiri
Data Scientist, Case Commons LLC
841 Broadway, New York, NY 10003
http://knowthynumbers.blogspot.com/