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  <div class="section" id="configuration-parameters-reference">
<h1>Configuration Parameters Reference<a class="headerlink" href="#configuration-parameters-reference" title="Permalink to this headline"></a></h1>
<p>Here are the configuration parameters supported by pebl. These can set in a
configuration file or via the config.set() function.</p>
<div class="section" id="data">
<h2>data<a class="headerlink" href="#data" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-data.discretize">
<tt class="descname">data.discretize</tt><a class="headerlink" href="#confparam-data.discretize" title="Permalink to this definition"></a></dt>
<dd><p>Number of bins used to discretize data. Specify 0 to indicate that data should not be discretized.
default=0</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-data.filename">
<tt class="descname">data.filename</tt><a class="headerlink" href="#confparam-data.filename" title="Permalink to this definition"></a></dt>
<dd><p>File to read data from.
default=None</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-data.text">
<tt class="descname">data.text</tt><a class="headerlink" href="#confparam-data.text" title="Permalink to this definition"></a></dt>
<dd><p>The text of a dataset included in config file.
default=</p>
</dd></dl>

</div>
<div class="section" id="learner">
<h2>learner<a class="headerlink" href="#learner" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-learner.numtasks">
<tt class="descname">learner.numtasks</tt><a class="headerlink" href="#confparam-learner.numtasks" title="Permalink to this definition"></a></dt>
<dd><p>Number of learner tasks to run.
default=1</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-learner.type">
<tt class="descname">learner.type</tt><a class="headerlink" href="#confparam-learner.type" title="Permalink to this definition"></a></dt>
<dd><blockquote>
<div>Type of learner to use.</div></blockquote>
<dl class="docutils">
<dt>The following learners are included with pebl:</dt>
<dd><ul class="first simple">
<li>greedy.GreedyLearner</li>
<li>simanneal.SimulatedAnnealingLearner</li>
<li>exhaustive.ListLearner</li>
</ul>
<p class="last">default=greedy.GreedyLearner</p>
</dd>
</dl>
</dd></dl>

</div>
<div class="section" id="greedy">
<h2>greedy<a class="headerlink" href="#greedy" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-greedy.max_iterations">
<tt class="descname">greedy.max_iterations</tt><a class="headerlink" href="#confparam-greedy.max_iterations" title="Permalink to this definition"></a></dt>
<dd><p>Maximum number of iterations to run.
default=1000</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-greedy.max_time">
<tt class="descname">greedy.max_time</tt><a class="headerlink" href="#confparam-greedy.max_time" title="Permalink to this definition"></a></dt>
<dd><p>Maximum learner runtime in seconds.
default=0</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-greedy.max_unimproved_iterations">
<tt class="descname">greedy.max_unimproved_iterations</tt><a class="headerlink" href="#confparam-greedy.max_unimproved_iterations" title="Permalink to this definition"></a></dt>
<dd><p>Maximum number of iterations without score improvement before a restart.
default=500</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-greedy.seed">
<tt class="descname">greedy.seed</tt><a class="headerlink" href="#confparam-greedy.seed" title="Permalink to this definition"></a></dt>
<dd><p>Starting network for a greedy search.
default=</p>
</dd></dl>

</div>
<div class="section" id="simanneal">
<h2>simanneal<a class="headerlink" href="#simanneal" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-simanneal.delta_temp">
<tt class="descname">simanneal.delta_temp</tt><a class="headerlink" href="#confparam-simanneal.delta_temp" title="Permalink to this definition"></a></dt>
<dd><p>Change in temp between steps.
default=0.5</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-simanneal.max_iters_at_temp">
<tt class="descname">simanneal.max_iters_at_temp</tt><a class="headerlink" href="#confparam-simanneal.max_iters_at_temp" title="Permalink to this definition"></a></dt>
<dd><p>Max iterations at any temperature.
default=100</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-simanneal.seed">
<tt class="descname">simanneal.seed</tt><a class="headerlink" href="#confparam-simanneal.seed" title="Permalink to this definition"></a></dt>
<dd><p>Starting network for a greedy search.
default=</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-simanneal.start_temp">
<tt class="descname">simanneal.start_temp</tt><a class="headerlink" href="#confparam-simanneal.start_temp" title="Permalink to this definition"></a></dt>
<dd><p>Starting temperature for a run.
default=100.0</p>
</dd></dl>

</div>
<div class="section" id="listlearner">
<h2>listlearner<a class="headerlink" href="#listlearner" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-listlearner.networks">
<tt class="descname">listlearner.networks</tt><a class="headerlink" href="#confparam-listlearner.networks" title="Permalink to this definition"></a></dt>
<dd><p>List of networks to score.
default=</p>
</dd></dl>

</div>
<div class="section" id="localscore-cache">
<h2>localscore_cache<a class="headerlink" href="#localscore-cache" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-localscore_cache.maxsize">
<tt class="descname">localscore_cache.maxsize</tt><a class="headerlink" href="#confparam-localscore_cache.maxsize" title="Permalink to this definition"></a></dt>
<dd><p>Max number of localscores to cache. Default=-1 means unlimited size.
default=-1</p>
</dd></dl>

</div>
<div class="section" id="result">
<h2>result<a class="headerlink" href="#result" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-result.filename">
<tt class="descname">result.filename</tt><a class="headerlink" href="#confparam-result.filename" title="Permalink to this definition"></a></dt>
<dd><p>The name of the result output file
default=result.pebl</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-result.format">
<tt class="descname">result.format</tt><a class="headerlink" href="#confparam-result.format" title="Permalink to this definition"></a></dt>
<dd><p>The format for the pebl result file (pickle or html).
default=pickle</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-result.size">
<tt class="descname">result.size</tt><a class="headerlink" href="#confparam-result.size" title="Permalink to this definition"></a></dt>
<dd><p>Number of top-scoring networks to save. Specify 0 to indicate that all scored networks should be saved.
default=1000</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-gibbs.burnin">
<tt class="descname">gibbs.burnin</tt><a class="headerlink" href="#confparam-gibbs.burnin" title="Permalink to this definition"></a></dt>
<dd><p>Burn-in period for the gibbs sampler (specified as a multiple of the number of missing values)
default=10</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-gibbs.max_iterations">
<tt class="descname">gibbs.max_iterations</tt><a class="headerlink" href="#confparam-gibbs.max_iterations" title="Permalink to this definition"></a></dt>
<dd><p>Stopping criteria for the gibbs sampler.</p>
<blockquote>
<div><p>The number of Gibb&#8217;s sampler iterations to run. Should be a valid
python expression using the variable n (number of missing values).
Examples:</p>
<blockquote>
<div><ul class="simple">
<li>n**2  (for n-squared iterations)</li>
<li>100   (for 100 iterations)</li>
</ul>
</div></blockquote>
</div></blockquote>
<p>default=n**2</p>
</dd></dl>

</div>
<div class="section" id="taskcontroller">
<h2>taskcontroller<a class="headerlink" href="#taskcontroller" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-taskcontroller.type">
<tt class="descname">taskcontroller.type</tt><a class="headerlink" href="#confparam-taskcontroller.type" title="Permalink to this definition"></a></dt>
<dd><p>The task controller to use.
default=serial</p>
</dd></dl>

</div>
<div class="section" id="multiprocess">
<h2>multiprocess<a class="headerlink" href="#multiprocess" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-multiprocess.poolsize">
<tt class="descname">multiprocess.poolsize</tt><a class="headerlink" href="#confparam-multiprocess.poolsize" title="Permalink to this definition"></a></dt>
<dd><p>Number of processes to run concurrently (0 means no limit)
default=0</p>
</dd></dl>

</div>
<div class="section" id="xgrid">
<h2>xgrid<a class="headerlink" href="#xgrid" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-xgrid.controller">
<tt class="descname">xgrid.controller</tt><a class="headerlink" href="#confparam-xgrid.controller" title="Permalink to this definition"></a></dt>
<dd><p>Hostname or IP of the Xgrid controller.
default=</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-xgrid.grid">
<tt class="descname">xgrid.grid</tt><a class="headerlink" href="#confparam-xgrid.grid" title="Permalink to this definition"></a></dt>
<dd><p>Id of the grid to use at the Xgrid controller.
default=0</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-xgrid.password">
<tt class="descname">xgrid.password</tt><a class="headerlink" href="#confparam-xgrid.password" title="Permalink to this definition"></a></dt>
<dd><p>Password for the Xgrid controller.
default=</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-xgrid.peblpath">
<tt class="descname">xgrid.peblpath</tt><a class="headerlink" href="#confparam-xgrid.peblpath" title="Permalink to this definition"></a></dt>
<dd><p>Full path to the pebl script on Xgrid agents
default=pebl</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-xgrid.pollinterval">
<tt class="descname">xgrid.pollinterval</tt><a class="headerlink" href="#confparam-xgrid.pollinterval" title="Permalink to this definition"></a></dt>
<dd><p>Time (in secs) to wait between polling the Xgrid controller.
default=60.0</p>
</dd></dl>

</div>
<div class="section" id="ipython1">
<h2>ipython1<a class="headerlink" href="#ipython1" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-ipython1.controller">
<tt class="descname">ipython1.controller</tt><a class="headerlink" href="#confparam-ipython1.controller" title="Permalink to this definition"></a></dt>
<dd><p>IPython1 TaskController (default is 127.0.0.1:10113)
default=127.0.0.1:10113</p>
</dd></dl>

</div>
<div class="section" id="ec2">
<h2>ec2<a class="headerlink" href="#ec2" title="Permalink to this headline"></a></h2>
<dl class="confparam">
<dt id="confparam-ec2.config">
<tt class="descname">ec2.config</tt><a class="headerlink" href="#confparam-ec2.config" title="Permalink to this definition"></a></dt>
<dd><p>EC2 config file. This is kept seperate from pebl config because it contains
authentication keys, etc.
default=</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-ec2.max_count">
<tt class="descname">ec2.max_count</tt><a class="headerlink" href="#confparam-ec2.max_count" title="Permalink to this definition"></a></dt>
<dd><p>Maximum number of EC2 instances to create (default=0 means the same number as ec2.min_count).
default=0</p>
</dd></dl>

<dl class="confparam">
<dt id="confparam-ec2.min_count">
<tt class="descname">ec2.min_count</tt><a class="headerlink" href="#confparam-ec2.min_count" title="Permalink to this definition"></a></dt>
<dd><p>Minimum number of EC2 instances to create (default=1).
default=1</p>
</dd></dl>

</div>
</div>


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  <h3><a href="index.html">Table Of Contents</a></h3>
  <ul>
<li><a class="reference internal" href="#">Configuration Parameters Reference</a><ul>
<li><a class="reference internal" href="#data">data</a></li>
<li><a class="reference internal" href="#learner">learner</a></li>
<li><a class="reference internal" href="#greedy">greedy</a></li>
<li><a class="reference internal" href="#simanneal">simanneal</a></li>
<li><a class="reference internal" href="#listlearner">listlearner</a></li>
<li><a class="reference internal" href="#localscore-cache">localscore_cache</a></li>
<li><a class="reference internal" href="#result">result</a></li>
<li><a class="reference internal" href="#taskcontroller">taskcontroller</a></li>
<li><a class="reference internal" href="#multiprocess">multiprocess</a></li>
<li><a class="reference internal" href="#xgrid">xgrid</a></li>
<li><a class="reference internal" href="#ipython1">ipython1</a></li>
<li><a class="reference internal" href="#ec2">ec2</a></li>
</ul>
</li>
</ul>

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