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<div class="section" id="installing-pytables-when-you-re-not-root">
<h1>Installing PyTables when you’re not root<a class="headerlink" href="#installing-pytables-when-you-re-not-root" title="Permalink to this headline">¶</a></h1>
<p>By <a class="reference external" href="http://www.tibed.net">Koen van de Sande</a>.</p>
<div class="admonition warning">
<p class="first admonition-title">Warning</p>
<p class="last">contents of this recipe recipe may be outdated.</p>
</div>
<p>This guide describes how to install PyTables and its dependencies on Linux or
other *nix systems when your user account is not root.
Installing the <a class="reference external" href="http://www.hdfgroup.org/HDF5">HDF5</a> <a class="footnote-reference" href="#id1" id="id2">[1]</a> shared libraries and Python extensions NumArray and
NumPy requires some non-trivial steps to work.
We describe all steps needed.
They only assumption is that you have Python 2.3 or higher and a C/C++ compiler
(gcc) installed.</p>
<div class="section" id="installing-hdf5">
<h2>Installing HDF5<a class="headerlink" href="#installing-hdf5" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">First go to or make a temporary folder where we can download and compile
software.
We’ll assume you’re in this temporary folder in the rest of this section.</p>
</li>
<li><p class="first">Download <cite>hdf5-1.6.5.tar.gz</cite> from <a class="reference external" href="ftp://ftp.hdfgroup.org/HDF5/current16/src/">ftp://ftp.hdfgroup.org/HDF5/current16/src/</a>:</p>
<div class="highlight-python"><pre>wget ftp://ftp.hdfgroup.org/HDF5/current16/src/hdf5-1.6.5.tar.gz</pre>
</div>
</li>
<li><p class="first">Extract the archive to the current folder:</p>
<div class="highlight-python"><pre>tar xzvf hdf5-1.6.5.tar.gz</pre>
</div>
</li>
<li><p class="first">Go to the extracted HDF5 folder:</p>
<div class="highlight-python"><pre>cd hdf5-1.6.5</pre>
</div>
</li>
<li><p class="first">Run the configure script:</p>
<div class="highlight-python"><pre>./configure</pre>
</div>
</li>
<li><p class="first">Run make:</p>
<div class="highlight-python"><pre>make install</pre>
</div>
</li>
<li><p class="first">We’ve now compiled <a class="reference external" href="http://www.hdfgroup.org/HDF5">HDF5</a> <a class="footnote-reference" href="#id1" id="id3">[1]</a> into the <cite>hdf5</cite> folder inside the source tree.
We’ll need to move this to its final location.
For this guide, we’ll make a <cite>software</cite> folder inside your home directory
to store installed libraries:</p>
<div class="highlight-python"><pre>mkdir ~/software</pre>
</div>
</li>
<li><p class="first">Move the files to the right location:</p>
<div class="highlight-python"><pre>mv hdf5 ~/software/</pre>
</div>
</li>
</ul>
</div>
<div class="section" id="installing-numarray">
<h2>Installing NumArray<a class="headerlink" href="#installing-numarray" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">From the <a class="reference external" href="http://sourceforge.net/projects/numpy/files">NumArray SourceForge page</a> download
NumArray 1.5.2 to our temporary folder.</p>
</li>
<li><p class="first">Extract the archive:</p>
<div class="highlight-python"><pre>tar xzvf numarray-1.5.2.tar.gz</pre>
</div>
</li>
<li><p class="first">Go to the NumArray folder:</p>
<div class="highlight-python"><pre>cd numarray-1.5.2</pre>
</div>
</li>
<li><p class="first">Build and install the Python module into our software folder (it will
actually end up in <cite>~/software/lib/python</cite>:</p>
<div class="highlight-python"><pre>python setup.py install --home=~/software</pre>
</div>
<p>We will also need to copy the header files of NumArray so PyTables can use
them later on for compilation.
Skipping this step will lead to compilation errors for PyTables.</p>
</li>
<li><p class="first">Go into the header file folder:</p>
<div class="highlight-python"><pre>cd include</pre>
</div>
</li>
<li><p class="first">Copy the header files. We’ll put them together with the <a class="reference external" href="http://www.hdfgroup.org/HDF5">HDF5</a> <a class="footnote-reference" href="#id1" id="id4">[1]</a> header files:</p>
<div class="highlight-python"><pre>cp -r numarray ~/software/hdf5/include/</pre>
</div>
</li>
</ul>
</div>
<div class="section" id="installing-numpy-optional">
<h2>Installing NumPy (optional)<a class="headerlink" href="#installing-numpy-optional" title="Permalink to this headline">¶</a></h2>
<p>It is not required to install NumPy; PyTables will work with just NumArray
installed.
However, I do recommend that you install NumPy as well, because PyTables
can optionally use it.</p>
<ul>
<li><p class="first">From the <a class="reference external" href="http://sourceforge.net/projects/numpy/files">NumPy SourceForge page</a> download
NumPy 1.0 (at time of writing) to our temporary folder.</p>
</li>
<li><p class="first">Extract the archive:</p>
<div class="highlight-python"><pre>tar xzvf numpy-1.0.tar.gz</pre>
</div>
</li>
<li><p class="first">Go to the NumPy folder:</p>
<div class="highlight-python"><pre>cd numpy-1.0</pre>
</div>
</li>
<li><p class="first">Build and install the Python module into our software folder:</p>
<div class="highlight-python"><pre>python setup.py install --home=~/software</pre>
</div>
</li>
</ul>
</div>
<div class="section" id="python-wrapper-script">
<h2>Python wrapper script<a class="headerlink" href="#python-wrapper-script" title="Permalink to this headline">¶</a></h2>
<p>We’ve installed all dependencies of PyTables.
We need to create a wrapper script for Python to let PyTables actually find
all these dependencies.
Had we installed them as root, they’d be trivial to find, but now we need to
help a bit.</p>
<ul>
<li><p class="first">Create a script with the following contents (I’ve called this script <cite>p</cite> on
my machine):</p>
<div class="highlight-python"><pre>#!/bin/bash
export PYTHONPATH=~/software/lib/python
export HDF5_DIR=~/software/hdf5
export LD_LIBRARY_PATH=~/software/lib/python/tables:~/software/hdf5/lib
python $*</pre>
</div>
</li>
<li><p class="first">Make the script executable:</p>
<div class="highlight-python"><pre>chmod 755 p</pre>
</div>
</li>
<li><p class="first">Place the script somewhere on your path (for example, inside a folder
called <cite>bin</cite> inside your home dir, which is normally added to the path
automatically).
If you do not add this script to your path, you’ll have to replace <cite>p</cite> in
scripts below by the full path (and name of) your script, e.g.
<cite>~/pytablespython.sh</cite> if you called it <cite>pytablespython.sh</cite> and put it in
your home dir.</p>
</li>
<li><p class="first">Test your Python wrapper script:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">p</span>
</pre></div>
</div>
</li>
<li><p class="first">It should now start Python. And you should be able to import <cite>numarray</cite>
(and optionally <cite>numpy</cite>) without errors:</p>
<div class="highlight-python"><pre>Python 2.3.4 (#1, Feb 2 2005, 12:11:53)
[GCC 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numarray
>>> import numpy
>>></pre>
</div>
</li>
</ul>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">you could do this differently by defining these environment settings
somewhere in your startup scripts, but this wrapper script approach is
cleaner.</p>
</div>
</div>
<div class="section" id="installing-pytables">
<h2>Installing PyTables<a class="headerlink" href="#installing-pytables" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">From the <a class="reference external" href="http://sourceforge.net/projects/pytables/files">SourceForge page</a>
download PyTables 1.3.3 (at time of writing) to our temporary folder.</p>
</li>
<li><p class="first">Extract the archive:</p>
<div class="highlight-python"><pre>tar xzvf pytables-1.3.3.tar.gz</pre>
</div>
</li>
<li><p class="first">Go to the PyTables folder:</p>
<div class="highlight-python"><pre>cd pytables-1.3.3</pre>
</div>
</li>
<li><p class="first">Install PyTables using our wrapper script:</p>
<div class="highlight-python"><pre>p setup.py install --home=~/software</pre>
</div>
</li>
<li><p class="first">If you get the following error then you are not using the wrapper script
properly!</p>
<div class="highlight-python"><pre>.. ERROR:: Can't find a local numarray Python installation.
Please, read carefully the ``README`` file and remember that
PyTables needs the numarray package to compile and run.}}}</pre>
</div>
</li>
</ul>
</div>
<div class="section" id="running-python-with-pytables-support">
<h2>Running Python with PyTables support<a class="headerlink" href="#running-python-with-pytables-support" title="Permalink to this headline">¶</a></h2>
<ul>
<li><p class="first">Use your Python wrapper script to start Python:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">p</span>
</pre></div>
</div>
</li>
<li><p class="first">You can now import <cite>tables</cite> without errors:</p>
<div class="highlight-python"><pre>Python 2.3.4 (#1, Feb 2 2005, 12:11:53)
[GCC 3.4.2 20041017 (Red Hat 3.4.2-6.fc3)] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import tables
>>> tables.__version__
'1.3.3'
>>></pre>
</div>
</li>
</ul>
</div>
<div class="section" id="concluding-remarks">
<h2>Concluding remarks<a class="headerlink" href="#concluding-remarks" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li>It is safe to remove the temporary folder we have used in this guide,
there are no dependencies on it.</li>
<li>This guide was written for and tested with HDF5 1.6.5, PyTables 1.3.3 and
NumArray 1.5.2.</li>
</ul>
<p>Enjoy working with PyTables!</p>
<p><em>Koen</em></p>
<hr class="docutils" />
<table class="docutils footnote" frame="void" id="id1" rules="none">
<colgroup><col class="label" /><col /></colgroup>
<tbody valign="top">
<tr><td class="label">[1]</td><td><em>(<a class="fn-backref" href="#id2">1</a>, <a class="fn-backref" href="#id3">2</a>, <a class="fn-backref" href="#id4">3</a>)</em> <a class="reference external" href="http://www.hdfgroup.org/HDF5">http://www.hdfgroup.org/HDF5</a></td></tr>
</tbody>
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<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Installing PyTables when you’re not root</a><ul>
<li><a class="reference internal" href="#installing-hdf5">Installing HDF5</a></li>
<li><a class="reference internal" href="#installing-numarray">Installing NumArray</a></li>
<li><a class="reference internal" href="#installing-numpy-optional">Installing NumPy (optional)</a></li>
<li><a class="reference internal" href="#python-wrapper-script">Python wrapper script</a></li>
<li><a class="reference internal" href="#installing-pytables">Installing PyTables</a></li>
<li><a class="reference internal" href="#running-python-with-pytables-support">Running Python with PyTables support</a></li>
<li><a class="reference internal" href="#concluding-remarks">Concluding remarks</a></li>
</ul>
</li>
</ul>
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