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<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<blockquote class="epigraph">
<div><p>Make things as simple as possible, but not any simpler.</p>
<p class="attribution">—Albert Einstein</p>
</div></blockquote>
<p>The Python Distutils are used to build and install PyTables, so it is fairly
simple to get the application up and running. If you want to install the
package from sources you can go on reading to the next section.</p>
<p>However, if you are running Windows and want to install precompiled binaries,
you can jump straight to <a class="reference internal" href="#binaryinstallationdescr"><em>Binary installation (Windows)</em></a>. In addition, binary
packages are available for many different Linux distributions, MacOSX and
other Unices. Just check the package repository for your preferred operating
system.</p>
<div class="section" id="installation-from-source">
<h2>Installation from source<a class="headerlink" href="#installation-from-source" title="Permalink to this headline">¶</a></h2>
<p>These instructions are for both Unix/MacOS X and Windows systems. If you are
using Windows, it is assumed that you have a recent version of MS Visual C++
compiler installed.
A GCC compiler is assumed for Unix, but other compilers should work as well.</p>
<p>Extensions in PyTables have been developed in Cython (see
<a class="reference internal" href="bibliography.html#cython"><em>[CYTHON]</em></a>) and the C language. You can rebuild everything from
scratch if you have Cython installed, but this is not necessary, as the Cython
compiled source is included in the source distribution.</p>
<p>To compile PyTables you will need a recent version of Python, the HDF5 (C
flavor) library from <a class="reference external" href="http://www.hdfgroup.org">http://www.hdfgroup.org</a>, and the NumPy (see
<a class="reference internal" href="bibliography.html#numpy"><em>[NUMPY]</em></a>) and Numexpr (see <a class="reference internal" href="bibliography.html#numexpr"><em>[NUMEXPR]</em></a>)
packages.</p>
<div class="section" id="prerequisites">
<h3>Prerequisites<a class="headerlink" href="#prerequisites" title="Permalink to this headline">¶</a></h3>
<p>First, make sure that you have</p>
<ul class="simple">
<li><a class="reference external" href="http://www.python.org">Python</a> >= 2.6 including Python 3.x</li>
<li><a class="reference external" href="http://www.hdfgroup.org/HDF5">HDF5</a> >= 1.8.4,</li>
<li><a class="reference external" href="http://www.numpy.org">NumPy</a> >= 1.4.1,</li>
<li><a class="reference external" href="http://code.google.com/p/numexpr">Numexpr</a> >= 2.0 and</li>
<li><a class="reference external" href="http://www.cython.org">Cython</a> >= 0.13</li>
<li><a class="reference external" href="http://code.google.com/p/argparse">argparse</a> (only Python 2.6, it it used by the <strong class="program">pt2to3</strong> utility)</li>
</ul>
<p>installed (for testing purposes, we are using <a class="reference external" href="http://www.hdfgroup.org/HDF5">HDF5</a> 1.8.9, <a class="reference external" href="http://www.numpy.org">NumPy</a> 1.7.1
and <a class="reference external" href="http://code.google.com/p/numexpr">Numexpr</a> 2.1 currently). If you don’t, fetch and install them before
proceeding.</p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Currently PyTables does not use <a class="reference external" href="https://pypi.python.org/pypi/setuptools">setuptools</a> by default so do not expect
that the setup.py script automatically install all packages PyTables
depends on.</p>
</div>
<p>Compile and install these packages (but see <a class="reference internal" href="#prerequisitesbininst"><em>Windows prerequisites</em></a> for
instructions on how to install precompiled binaries if you are not willing to
compile the prerequisites on Windows systems).</p>
<p>For compression (and possibly improved performance), you will need to install
the Zlib (see <a class="reference internal" href="bibliography.html#zlib"><em>[ZLIB]</em></a>), which is also required by HDF5 as well.
You may also optionally install the excellent LZO compression library (see
<a class="reference internal" href="bibliography.html#lzo"><em>[LZO]</em></a> and <a class="reference internal" href="optimization.html#compressionissues"><em>Compression issues</em></a>). The high-performance bzip2
compression library can also be used with PyTables (see
<a class="reference internal" href="bibliography.html#bzip2"><em>[BZIP2]</em></a>).
The Blosc (see <a class="reference internal" href="bibliography.html#blosc"><em>[BLOSC]</em></a>) compression library is embedded in
PyTables, so you don’t need to install it separately.</p>
<p><strong>Unix</strong></p>
<blockquote>
<div><p>setup.py will detect HDF5, LZO, or bzip2 libraries and include files under
<tt class="file docutils literal"><span class="pre">/usr</span></tt> or <tt class="file docutils literal"><span class="pre">/usr/local</span></tt>; this will cover most manual
installations as well as installations from packages.
If setup.py can not find libhdf5, libhdf5 (or liblzo, or libbz2 that you
may wish to use) or if you have several versions of a library installed
and want to use a particular one, then you can set the path to the
resource in the environment, by setting the values of the
<span class="target" id="index-0"></span><tt class="xref std std-envvar docutils literal"><span class="pre">HDF5_DIR</span></tt>, <span class="target" id="index-1"></span><tt class="xref std std-envvar docutils literal"><span class="pre">LZO_DIR</span></tt>, or <span class="target" id="index-2"></span><tt class="xref std std-envvar docutils literal"><span class="pre">BZIP2_DIR</span></tt> environment
variables to the path to the particular resource. You may also specify the
locations of the resource root directories on the setup.py command line.
For example:</p>
<div class="highlight-python"><pre>--hdf5=/stuff/hdf5-1.8.9
--lzo=/stuff/lzo-2.02
--bzip2=/stuff/bzip2-1.0.5</pre>
</div>
<p>If your HDF5 library was built as a shared library not in the runtime load
path, then you can specify the additional linker flags needed to find the
shared library on the command line as well. For example:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="o">--</span><span class="n">lflags</span><span class="o">=</span><span class="s">"-Xlinker -rpath -Xlinker /stuff/hdf5-1.8.9/lib"</span>
</pre></div>
</div>
<p>You may also want to try setting the <span class="target" id="index-3"></span><tt class="xref std std-envvar docutils literal"><span class="pre">LD_LIBRARY_PATH</span></tt>
environment variable to point to the directory where the shared libraries
can be found. Check your compiler and linker documentation as well as the
Python Distutils documentation for the correct syntax or environment
variable names.
It is also possible to link with specific libraries by setting the
<span class="target" id="index-4"></span><tt class="xref std std-envvar docutils literal"><span class="pre">LIBS</span></tt> environment variable:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">LIBS</span><span class="o">=</span><span class="s">"hdf5-1.8.9 nsl"</span>
</pre></div>
</div>
<p>Finally, you can give additional flags to your compiler by passing them to
the <em class="xref std std-option">--cflags</em> flag:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="o">--</span><span class="n">cflags</span><span class="o">=</span><span class="s">"-w -O3 -msse2"</span>
</pre></div>
</div>
<p>In the above case, a gcc compiler is used and you instructed it to
suppress all the warnings and set the level 3 of optimization.
Finally, if you are running Linux in 32-bit mode, and you know that your
CPU has support for SSE2 vector instructions, you may want to pass the
<em class="xref std std-option">-msse2</em> flag that will accelerate Blosc operation.</p>
<div class="admonition hint">
<p class="first admonition-title">Hint</p>
<p>some GNU/Linux distributions provide a packaged version of the HDF5
libraries with MPI support. In this case you may need to specify
the path of the MPH headers as additional include directory.</p>
<p>On Ubuntu 12.04 the following command has been reported to work:</p>
<div class="last highlight-python"><pre>$ C_INCLUDE_PATH=/usr/lib/openmpi/include pip install --upgrade tables</pre>
</div>
</div>
</div></blockquote>
<p><strong>Windows</strong></p>
<blockquote>
<div><p>You can get ready-to-use Windows binaries and other development files for
most of the following libraries from the GnuWin32 project (see
<a class="reference internal" href="bibliography.html#gnuwin32"><em>[GNUWIN32]</em></a>). In case you cannot find the LZO binaries
in the GnuWin32 repository, you can find them at
<a class="reference external" href="http://sourceforge.net/projects/pytables/files/lzo-win">http://sourceforge.net/projects/pytables/files/lzo-win</a>.
Once you have installed the prerequisites, setup.py needs to know where
the necessary library <em>stub</em> (.lib) and <em>header</em> (.h) files are installed.
You can set the path to the include and dll directories for the HDF5
(mandatory) and LZO or BZIP2 (optional) libraries in the environment, by
setting the values of the <span class="target" id="index-5"></span><tt class="xref std std-envvar docutils literal"><span class="pre">HDF5_DIR</span></tt>, <span class="target" id="index-6"></span><tt class="xref std std-envvar docutils literal"><span class="pre">LZO_DIR</span></tt>, or
<span class="target" id="index-7"></span><tt class="xref std std-envvar docutils literal"><span class="pre">BZIP2_DIR</span></tt> environment variables to the path to the particular
resource. For example:</p>
<div class="highlight-python"><pre>set HDF5_DIR=c:\\stuff\\hdf5-1.8.5-32bit-VS2008-IVF101\\release
set LZO_DIR=c:\\Program Files (x86)\\GnuWin32
set BZIP2_DIR=c:\\Program Files (x86)\\GnuWin32</pre>
</div>
<p>You may also specify the locations of the resource root directories on the
setup.py command line.
For example:</p>
<div class="highlight-python"><pre>--hdf5=c:\\stuff\\hdf5-1.8.5-32bit-VS2008-IVF101\\release
--lzo=c:\\Program Files (x86)\\GnuWin32
--bzip2=c:\\Program Files (x86)\\GnuWin32</pre>
</div>
</div></blockquote>
<p><strong>Development version (Unix)</strong></p>
<blockquote>
<div><p>Installation of the development version is very similar to installation
from a source package (described above). There are two main differences:</p>
<ol class="arabic">
<li><p class="first">sources have to be downloaded from the <a class="reference external" href="https://github.com/PyTables/PyTables">PyTables source repository</a>
hosted on <a class="reference external" href="https://github.com">GitHub</a>. Git (see <a class="reference internal" href="bibliography.html#git"><em>[GIT]</em></a>) is used as VCS.
The following command create a local copy of latest development version
sources:</p>
<div class="highlight-python"><pre>$ git clone https://github.com/PyTables/PyTables.git</pre>
</div>
</li>
<li><p class="first">sources in the git repository do not include pre-built documentation
and pre-generated C code of Cython extension modules. To be able to
generate them, both Cython (see <a class="reference internal" href="bibliography.html#cython"><em>[CYTHON]</em></a>) and
sphinx >= 1.0.7 (see <a class="reference internal" href="bibliography.html#sphinx"><em>[SPHINX]</em></a>) are mandatory
prerequisites.</p>
</li>
</ol>
</div></blockquote>
</div>
<div class="section" id="pytables-package-installation">
<h3>PyTables package installation<a class="headerlink" href="#pytables-package-installation" title="Permalink to this headline">¶</a></h3>
<p>Once you have installed the HDF5 library and the NumPy and Numexpr packages,
you can proceed with the PyTables package itself.</p>
<ol class="arabic">
<li><p class="first">Run this command from the main PyTables distribution directory, including
any extra command line arguments as discussed above:</p>
<div class="highlight-python"><pre>$ python setup.py build</pre>
</div>
</li>
<li><p class="first">To run the test suite, execute any of these commands.</p>
<dl class="docutils">
<dt><strong>Unix</strong></dt>
<dd><p class="first">In the sh shell and its variants:</p>
<div class="highlight-python"><pre>$ cd build/lib.linux-x86_64-2.7
$ env PYTHONPATH=. python tables/tests/test_all.py</pre>
</div>
<p>or, if you prefer:</p>
<div class="highlight-python"><pre>$ cd build/lib.linux-x86_64-2.7
$ env PYTHONPATH=. python -c "import tables; tables.test()"</pre>
</div>
<div class="last admonition note">
<p class="first admonition-title">Note</p>
<p>the syntax used above overrides original contents of the
<span class="target" id="index-8"></span><tt class="xref std std-envvar docutils literal"><span class="pre">PYTHONPATH</span></tt> environment variable.
If this is not the desired behaviour and the user just wants to add
some path before existing ones, then the safest syntax to use is
the following:</p>
<div class="highlight-python"><pre>$ env PYTHONPATH=.${PYTHONPATH:+:$PYTHONPATH} python tables/tests/test_all.py</pre>
</div>
<p class="last">Please refer to your <strong class="program">sh</strong> documentation for details.</p>
</div>
</dd>
</dl>
<p><strong>Windows</strong></p>
<blockquote>
<div><p>Open the command prompt (cmd.exe or command.com) and type:</p>
<div class="highlight-python"><pre>> cd build\\lib.linux-x86_64-2.7
> set PYTHONPATH=.;%PYTHONPATH%
> python tables\\tests\\test_all.py</pre>
</div>
<p>or:</p>
<div class="highlight-python"><pre>> cd build\\lib.linux-x86_64-2.7
> set PYTHONPATH=.;%PYTHONPATH%
> python -c "import tables; tables.test()"</pre>
</div>
</div></blockquote>
<p>Both commands do the same thing, but the latter still works on an already
installed PyTables (so, there is no need to set the <span class="target" id="index-9"></span><tt class="xref std std-envvar docutils literal"><span class="pre">PYTHONPATH</span></tt>
variable for this case).
However, before installation, the former is recommended because it is
more flexible, as you can see below.
If you would like to see verbose output from the tests simply add the
<em class="xref std std-option">-v</em> flag and/or the word verbose to the first of the command lines
above. You can also run only the tests in a particular test module.
For example, to execute just the test_types test suite, you only have to
specify it:</p>
<div class="highlight-python"><pre># change to backslashes for win
$ python tables/tests/test_types.py -v</pre>
</div>
<p>You have other options to pass to the <tt class="file docutils literal"><span class="pre">test_all.py</span></tt> driver:</p>
<div class="highlight-python"><pre># change to backslashes for win
$ python tables/tests/test_all.py --heavy</pre>
</div>
<p>The command above runs every test in the test unit. Beware, it can take a
lot of time, CPU and memory resources to complete:</p>
<div class="highlight-python"><pre># change to backslashes for win
$ python tables/tests/test_all.py --print-versions</pre>
</div>
<p>The command above shows the versions for all the packages that PyTables
relies on. Please be sure to include this when reporting bugs:</p>
<div class="highlight-python"><pre># only under Linux 2.6.x
$ python tables/tests/test_all.py --show-memory</pre>
</div>
<p>The command above prints out the evolution of the memory consumption after
each test module completion. It’s useful for locating memory leaks in
PyTables (or packages behind it). Only valid for Linux 2.6.x kernels.
And last, but not least, in case a test fails, please run the failing test
module again and enable the verbose output:</p>
<div class="highlight-python"><pre>$ python tables/tests/test_<module>.py -v verbose</pre>
</div>
<p>and, very important, obtain your PyTables version information by using the
<em class="xref std std-option">--print-versions</em> flag (see above) and send back both outputs to
developers so that we may continue improving PyTables.
If you run into problems because Python can not load the HDF5 library or
other shared libraries.</p>
<p><strong>Unix</strong></p>
<blockquote>
<div><p>Try setting the LD_LIBRARY_PATH or equivalent environment variable to
point to the directory where the missing libraries can be found.</p>
</div></blockquote>
<p><strong>Windows</strong></p>
<blockquote>
<div><p>Put the DLL libraries (hdf5dll.dll and, optionally, lzo1.dll and
bzip2.dll) in a directory listed in your <span class="target" id="index-10"></span><tt class="xref std std-envvar docutils literal"><span class="pre">PATH</span></tt> environment
variable. The setup.py installation program will print out a warning to
that effect if the libraries can not be found.</p>
</div></blockquote>
</li>
<li><p class="first">To install the entire PyTables Python package, change back to the root
distribution directory and run the following command (make sure you have
sufficient permissions to write to the directories where the PyTables files
will be installed):</p>
<div class="highlight-python"><pre>$ python setup.py install</pre>
</div>
<p>Of course, you will need super-user privileges if you want to install
PyTables on a system-protected area. You can select, though, a different
place to install the package using the <em class="xref std std-option">--prefix</em> flag:</p>
<div class="highlight-python"><pre>$ python setup.py install --prefix="/home/myuser/mystuff"</pre>
</div>
<p>Have in mind, however, that if you use the <em class="xref std std-option">--prefix</em> flag to
install in a non-standard place, you should properly setup your
<span class="target" id="index-11"></span><tt class="xref std std-envvar docutils literal"><span class="pre">PYTHONPATH</span></tt> environment variable, so that the Python interpreter
would be able to find your new PyTables installation.
You have more installation options available in the Distutils package.
Issue a:</p>
<div class="highlight-python"><pre>$ python setup.py install --help</pre>
</div>
<p>for more information on that subject.</p>
</li>
</ol>
<p>That’s it! Now you can skip to the next chapter to learn how to use PyTables.</p>
</div>
</div>
<div class="section" id="binary-installation-windows">
<span id="binaryinstallationdescr"></span><h2>Binary installation (Windows)<a class="headerlink" href="#binary-installation-windows" title="Permalink to this headline">¶</a></h2>
<p>This section is intended for installing precompiled binaries on Windows
platforms. You may also find it useful for instructions on how to install
<em>binary prerequisites</em> even if you want to compile PyTables itself on Windows.</p>
<div class="section" id="windows-prerequisites">
<span id="prerequisitesbininst"></span><h3>Windows prerequisites<a class="headerlink" href="#windows-prerequisites" title="Permalink to this headline">¶</a></h3>
<p>First, make sure that you have Python 2.6, NumPy 1.4.1 and Numexpr 2.0 or
higher installed (PyTables binaries have been built using NumPy 1.7 and
Numexpr 2.1). The binaries already include DLLs for HDF5 (1.8.4, 1.8.9),
zlib1 (1.2.3), szlib (2.0, uncompression support only) and bzip2 (1.0.5) for
Windows (2.8.0).
The LZO DLL can’t be included because of license issues (but read below for
directives to install it if you want so).</p>
<p>To enable compression with the optional LZO library (see the
<a class="reference internal" href="optimization.html#compressionissues"><em>Compression issues</em></a> for hints about how it may be used to improve
performance), fetch and install the LZO from
<a class="reference external" href="http://sourceforge.net/projects/pytables/files/lzo-win">http://sourceforge.net/projects/pytables/files/lzo-win</a> (choose v1.x for
Windows 32-bit and v2.x for Windows 64-bit).
Normally, you will only need to fetch that package and copy the included
lzo1.dll/lzo2.dll file in a directory in the PATH environment variable
(for example C:\WINDOWS\SYSTEM) or
python_installation_path\Lib\site-packages\tables (the last directory may
not exist yet, so if you want to install the DLL there, you should do so
<em>after</em> installing the PyTables package), so that it can be found by the
PyTables extensions.</p>
<p>Please note that PyTables has internal machinery for dealing with uninstalled
optional compression libraries, so, you don’t need to install the LZO dynamic
library if you don’t want to.</p>
</div>
<div class="section" id="id1">
<h3>PyTables package installation<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<p>Download the tables-<version>.win32-py<version>.exe file and execute it.</p>
<p>Binary packahes can be found e.g. at the <a class="reference external" href="http://www.lfd.uci.edu/~gohlke/pythonlibs/#pytables">Unofficial Windows Binaries for
Python Extension Packages</a>
page.</p>
<p>You can (and <em>you should</em>) test your installation by running the next
commands:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="kn">import</span> <span class="nn">tables</span>
<span class="gp">>>> </span><span class="n">tables</span><span class="o">.</span><span class="n">test</span><span class="p">()</span>
</pre></div>
</div>
<p>on your favorite python shell. If all the tests pass (possibly with a few
warnings, related to the potential unavailability of LZO lib) you already have
a working, well-tested copy of PyTables installed! If any test fails, please
copy the output of the error messages as well as the output of:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="gp">>>> </span><span class="n">tables</span><span class="o">.</span><span class="n">print_versions</span><span class="p">()</span>
</pre></div>
</div>
<p>and mail them to the developers so that the problem can be fixed in future
releases.</p>
<p>You can proceed now to the next chapter to see how to use PyTables.</p>
</div>
</div>
</div>
</div>
</div>
</div>
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<img class="logo" src="../_static/logo-pytables-small.png" alt="Logo"/>
</a></p>
<h3><a href="../index.html">Table Of Contents</a></h3>
<ul>
<li><a class="reference internal" href="#">Installation</a><ul>
<li><a class="reference internal" href="#installation-from-source">Installation from source</a><ul>
<li><a class="reference internal" href="#prerequisites">Prerequisites</a></li>
<li><a class="reference internal" href="#pytables-package-installation">PyTables package installation</a></li>
</ul>
</li>
<li><a class="reference internal" href="#binary-installation-windows">Binary installation (Windows)</a><ul>
<li><a class="reference internal" href="#windows-prerequisites">Windows prerequisites</a></li>
<li><a class="reference internal" href="#id1">PyTables package installation</a></li>
</ul>
</li>
</ul>
</li>
</ul>
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