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<div class="section" id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this headline">¶</a></h1>
<p>Unfortunatly, installing pebl is not a one-stop process although it should take
no longer than a few minutes. If you experience any problems, please contact me
at <a class="reference external" href="mailto:abhikshah%40gmail.com">abhikshah<span>@</span>gmail<span>.</span>com</a>.</p>
<p>Pebl is known to run on Linux and Mac OSX and should also run on Windows and
any platform that supports Python 2.5 and numpy. Pebl depends on the following
packages:</p>
<blockquote>
<div><ul class="simple">
<li>Numpy: tested with version 1.0.4 but should work with other recent versions</li>
<li>Pydot: tested with version 1.0.2</li>
<li>Matplotlib (optional): tested with version 0.91.2 but should work with other
recent versions</li>
<li>Graphviz (optional): any recent version of dot and neato</li>
<li>IPython1 (optional): curently, require r2815 from svn trunk</li>
<li>boto (optional): any recent version</li>
</ul>
</div></blockquote>
<div class="section" id="install-python-2-5">
<h2>Install Python 2.5<a class="headerlink" href="#install-python-2-5" title="Permalink to this headline">¶</a></h2>
<p>Check what version of Python you have with:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="n">python</span> <span class="o">--</span><span class="n">version</span>
</pre></div>
</div>
<p>You can download Python 2.5 from <a class="reference external" href="http://python.org/download">http://python.org/download</a></p>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">Pebl requires Python 2.5 or greater and will not run under earlier versions.</p>
</div>
</div>
<div class="section" id="install-easy-install">
<h2>Install easy_install<a class="headerlink" href="#install-easy-install" title="Permalink to this headline">¶</a></h2>
<p>easy_install lets you install python packages and their requirements in one
easy step. Unfortunately, easy_install is not distributed with python and needs
to be installed separately.</p>
<ol class="arabic simple">
<li>Download ez_setup.py from <a class="reference external" href="http://peak.telecommunity.com/dist/ez_setup.py">http://peak.telecommunity.com/dist/ez_setup.py</a></li>
<li>Run <strong class="command">python ez_setup.py</strong> to install easy_install</li>
</ol>
<p>Run <strong class="command">easy_install –help</strong> to make sure that it is in your path. On
unix-type systems, it is usually installed in /usr/bin/ and on Windows in
C:\Python2.5\Scripts\</p>
</div>
<div class="section" id="install-numpy">
<h2>Install Numpy<a class="headerlink" href="#install-numpy" title="Permalink to this headline">¶</a></h2>
<p>Numpy can be tricky to install because it require C and Fortran compilers and
several libraries. You can try installing it from source using easy_install:</p>
<div class="highlight-python"><pre>easy_install numpy</pre>
</div>
<p>If that doesn’t work or if you’d rather install using a binary package, consult
<a class="reference external" href="http://www.scipy.org/Download">http://www.scipy.org/Download</a>.</p>
</div>
<div class="section" id="install-pebl">
<h2>Install Pebl<a class="headerlink" href="#install-pebl" title="Permalink to this headline">¶</a></h2>
<p>You can now install (or upgrade) pebl and it’s required dependencies using
easy_install:</p>
<div class="highlight-python"><pre>easy_install pebl</pre>
</div>
<div class="admonition note">
<p class="first admonition-title">Note</p>
<p class="last">The current version of Pebl is 1.0.1</p>
</div>
<p>If you have downloaded the source code for Pebl (or installing pebl from svn),
you can run <strong class="command">sudo python setup.py install</strong> from pebl’s root directory
instead.</p>
</div>
<div class="section" id="testing-pebl-installation">
<h2>Testing Pebl Installation<a class="headerlink" href="#testing-pebl-installation" title="Permalink to this headline">¶</a></h2>
<p>To test pebl installation, you can run the automated unit tests by first install nose:</p>
<div class="highlight-python"><pre>easy_install nose</pre>
</div>
<p>and then running nose from the command line, in any directory:</p>
<div class="highlight-python"><pre>nosetests -v pebl.test</pre>
</div>
<p>If you haven’t installed all the optional dependencies, certain tests will fail
but the name of the tests should make it clear whether it’s a normal feature or
an optional one.</p>
</div>
<div class="section" id="installing-optional-dependencies">
<h2>Installing optional dependencies<a class="headerlink" href="#installing-optional-dependencies" title="Permalink to this headline">¶</a></h2>
<p>Certain features of pebl require additional dependencies. You only need to
install these if you need the optional features. Without the optional features,
you can load data, learn networks and output networks in dot format, although
not as an image. If installing pebl on a cluster, the optional features are
only necessary on the controller or the machine used interactively by the
user.</p>
<div class="section" id="for-creating-html-reports-of-pebl-results">
<h3>For creating HTML reports of Pebl results<a class="headerlink" href="#for-creating-html-reports-of-pebl-results" title="Permalink to this headline">¶</a></h3>
<p>Pebl uses Graphviz to visualize networks and matplotlib for plotting. If using
Pebl on a cluster, these don’t need to be installed on the worker nodes.</p>
<ol class="arabic simple">
<li>Install Graphviz from <a class="reference external" href="http://www.graphviz.org/Download.php">http://www.graphviz.org/Download.php</a></li>
<li>Install matplotlib from <a class="reference external" href="http://matplotlib.sourceforge.net/installing.html">http://matplotlib.sourceforge.net/installing.html</a></li>
</ol>
<p>Finally, install simplejson using easy_install:</p>
<div class="highlight-python"><pre>easy_install simplejson</pre>
</div>
<p>simplejson sometimes fails to install on Windows. In that case, you can use a
binary package:</p>
<div class="highlight-python"><pre>easy_install http://pebl-project.googlecode.com/files/simplejson-1.7.3-py2.5-win32.egg</pre>
</div>
<p>To test the html-report feature, run:</p>
<div class="highlight-python"><pre>nosetests -v pebl.test.test_result:TestHtmlReport</pre>
</div>
</div>
<div class="section" id="for-the-xgrid-task-controller">
<h3>For the XGrid Task Controller<a class="headerlink" href="#for-the-xgrid-task-controller" title="Permalink to this headline">¶</a></h3>
<p>Apple XGrid is a grid solution for Apple computers that lets desktops and
dedicated servers be used in a computational grid.</p>
<p>The Xgrid task controller only runs on platforms where XGrid is available
(currently, only Mac OSX). Pebl uses the PyXG package to access the XGrid
controller:</p>
<div class="highlight-python"><pre>easy_install PyXg</pre>
</div>
<p>To test the XGrid feature, find the location where pebl was installed by
easy_install and navigate to the src/pebl/test.manual directory. There, create
a file called xgridconfig.txt and include the relevant configuration
parameters. The file should look like:</p>
<div class="highlight-python"><div class="highlight"><pre><span class="p">[</span><span class="n">xgrid</span><span class="p">]</span>
<span class="n">controller</span> <span class="o">=</span> <span class="n">your</span><span class="o">.</span><span class="n">controller</span><span class="o">.</span><span class="n">com</span>
<span class="n">password</span> <span class="o">=</span> <span class="n">yourpassword</span>
<span class="n">grid</span> <span class="o">=</span> <span class="n">gridnumber</span>
<span class="n">pollinterval</span> <span class="o">=</span> <span class="mi">30</span>
</pre></div>
</div>
<p>Then, execute the test_xgrid.py test:</p>
<div class="highlight-python"><pre>python test_xgrid.py xgridconfig.txt</pre>
</div>
<p>Pebl will create and run 10 short learners over the XGrid. It will print some
information about submitting and retrieving data from the Xgrid controller and
finally print a list of machines where the tasks ran.</p>
</div>
<div class="section" id="for-the-ipython1-task-controller">
<h3>For the IPython1 Task Controller<a class="headerlink" href="#for-the-ipython1-task-controller" title="Permalink to this headline">¶</a></h3>
<p>IPython1 is the next version of the popular IPython shell that also includes an
interactive, clustering solution. Pebl can use IPython1 to execute learners in
parallel.</p>
<p>You will need to install both IPython and IPython1. IPython1 is in active
development and pebl requires a specific version. Once, IPython1 is oficially
released, we will use that package:</p>
<div class="highlight-python"><pre>easy_install ipython
svn co -r 2815 http://ipython.scipy.org/svn/ipython/ipython1/trunk ipython1-2815
cd ipython1-2815
sudo python setup.py install</pre>
</div>
<p>To test the IPython1 feature, make sure that IPython1’s ipcluster is in the
path and run:</p>
<div class="highlight-python"><pre>nosetests -v pebl.test.test_taskcontroller:TestIPython1TC</pre>
</div>
<p>The test will create three local IPython1 engines and run tasks on them. The
test cannot, unfortunately, terminate the engines and that needs to be done
manually. Simply run ‘ps’ and terminate the appropriate processes.</p>
</div>
<div class="section" id="for-the-ec2-task-controller">
<h3>For the EC2 Task Controller<a class="headerlink" href="#for-the-ec2-task-controller" title="Permalink to this headline">¶</a></h3>
<p>Amazon EC2 is an on-demand cloud computing solution from Amazon. It allows
users to rent computing power on an as-needed basis. Pebl can reserve, create,
use and terminate EC2 instances automatically. More information available at
<a class="reference external" href="http://aws.amazon.com/ec2/">http://aws.amazon.com/ec2/</a></p>
<p>Before you can use Amazon’s EC2 platform, you need to register with Amazon and
create the required authentication credentials. Consult the <a class="reference external" href="http://docs.amazonwebservices.com/AWSEC2/2008-02-01/GettingStartedGuide/">Getting Started
Guide</a> at
Amazon for further information.</p>
<p>Pebl uses the boto package to interact with EC2:</p>
<div class="highlight-python"><pre>easy_install boto</pre>
</div>
<p>Also see the instructions above for installing dependencies for the IPython1
Task Controller (which is required by the EC2 Task Controller).</p>
<p>To test the EC2 feature, find the location where pebl was installed by
easy_install and navigate to the src/pebl/test.manual directory. There, create
a file called ec2config.txt and include the relevant configuration
parameters. The file should look like:</p>
<div class="highlight-python"><pre>[EC2]
access_key = YOUR_AMAZON_ACCESSKEY
secret_access_key = YOUR_AMAZON_SECRET_ACCESS_KEY
ami = ami-66a3470f # or any AMI with pebl, IPython1 and svn installed
key_name = keyname-to-use
credential = ~/foo/private-key-to-use</pre>
</div>
<p>Then, execute the test_ec2.py test:</p>
<div class="highlight-python"><pre>python test_ec2.py ec2config.txt</pre>
</div>
<p>Pebl will reserve and use 3 EC2 instances, upgrade the version of pebl
installed, run 10 shorts tasks on them and terminate the instances when
finished. If all works sucessfully, Pebl will print the hostnames of the
machines used.</p>
</div>
<div class="section" id="for-developing-pebl">
<h3>For developing Pebl<a class="headerlink" href="#for-developing-pebl" title="Permalink to this headline">¶</a></h3>
<p>Pebl developers will also need nose for testing and sphinx for generating html
documentation:</p>
<div class="highlight-python"><pre>easy_install nose
easy_install sphinx</pre>
</div>
</div>
</div>
</div>
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<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="#install-python-2-5">Install Python 2.5</a></li>
<li><a class="reference internal" href="#install-easy-install">Install easy_install</a></li>
<li><a class="reference internal" href="#install-numpy">Install Numpy</a></li>
<li><a class="reference internal" href="#install-pebl">Install Pebl</a></li>
<li><a class="reference internal" href="#testing-pebl-installation">Testing Pebl Installation</a></li>
<li><a class="reference internal" href="#installing-optional-dependencies">Installing optional dependencies</a><ul>
<li><a class="reference internal" href="#for-creating-html-reports-of-pebl-results">For creating HTML reports of Pebl results</a></li>
<li><a class="reference internal" href="#for-the-xgrid-task-controller">For the XGrid Task Controller</a></li>
<li><a class="reference internal" href="#for-the-ipython1-task-controller">For the IPython1 Task Controller</a></li>
<li><a class="reference internal" href="#for-the-ec2-task-controller">For the EC2 Task Controller</a></li>
<li><a class="reference internal" href="#for-developing-pebl">For developing Pebl</a></li>
</ul>
</li>
</ul>
</li>
</ul>
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