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<?xml version="1.0" encoding="utf-8"?>
<feed xmlns="http://www.w3.org/2005/Atom"><title>Code für Forschung</title><link href="http://dschien.github.io/" rel="alternate"></link><link href="/atom.xml" rel="self"></link><id>http://dschien.github.io/</id><updated>2014-06-16T13:00:00+01:00</updated><entry><title>STS Agent Based Model Building</title><link href="http://dschien.github.io/blog/2014/06/16/sts-agents/" rel="alternate"></link><updated>2014-06-16T13:00:00+01:00</updated><author><name>Daniel Schien</name></author><id>tag:dschien.github.io,2014-06-16:blog/2014/06/16/sts-agents/</id><summary type="html">
<p>Step by step instructions to follow during the Agent Based Modelling day in the socio-technical systems unit
at the University of Bristol.
</p>
<h2 id="table-of-contents">Table of Contents</h2>
<div class="toc">
<ul>
<li><a href="#table-of-contents">Table of Contents</a></li>
<li><a href="#preparation">Preparation</a><ul>
<li><a href="#repast-simphony">Repast Simphony</a></li>
<li><a href="#virtual-machine">Virtual Machine</a><ul>
<li><a href="#starting-the-vm">Starting the VM</a></li>
</ul>
</li>
<li><a href="#direct-install">Direct Install</a><ul>
<li><a href="#installing-plugins">Installing Plugins</a></li>
</ul>
</li>
<li><a href="#sources-from-github">Sources from Github</a><ul>
<li><a href="#changing-to-a-specific-commit">Changing to a specific commit</a></li>
<li><a href="#changing-branch-in-eclipe">Changing Branch in Eclipe</a></li>
</ul>
</li>
</ul>
</li>
<li><a href="#building-the-model">Building the Model</a><ul>
<li><a href="#relogo-basic-concepts">Relogo Basic Concepts</a><ul>
<li><a href="#terms">Terms</a></li>
</ul>
</li>
<li><a href="#development-cycle">Development Cycle</a></li>
<li><a href="#relogo-gui">Relogo GUI</a><ul>
<li><a href="#sequence-diagram">Sequence Diagram</a></li>
</ul>
</li>
<li><a href="#phase-1-project-foundations">Phase 1 - Project Foundations</a><ul>
<li><a href="#creating-a-new-project">Creating a new project</a></li>
<li><a href="#creating-a-new-worker-turtle">Creating a new worker turtle</a></li>
<li><a href="#worker-turtle-complete">Worker Turtle Complete</a></li>
<li><a href="#preparing-userobserver">Preparing UserObserver</a></li>
<li><a href="#userobserver-complete">UserObserver Complete</a></li>
<li><a href="#create-numworkers-variable-in-userglobalsandpanelfactory">Create numWorkers Variable in UserGlobalsAndPanelFactory</a></li>
<li><a href="#complete-userglobalsandpanelfactory">Complete UserGlobalsAndPanelFactory</a></li>
<li><a href="#create-job-class">Create Job Class</a></li>
<li><a href="#start-test-run">Start Test Run</a></li>
<li><a href="#github-commit">Github commit</a></li>
</ul>
</li>
<li><a href="#phase-2-working-on-jobs">Phase 2 - Working on Jobs</a><ul>
<li><a href="#add-properties-to-class-job">Add properties to class Job</a></li>
<li><a href="#make-worker-work-on-jobs">Make Worker work on Jobs</a></li>
<li><a href="#worker-turtle-complete_1">Worker Turtle complete</a></li>
<li><a href="#control-number-of-jobs">Control number of Jobs</a></li>
<li><a href="#make-observer-manage-job-pool">Make Observer manage Job Pool</a></li>
<li><a href="#userobserver-complete_1">UserObserver Complete</a></li>
<li><a href="#github-commit_1">Github commit</a></li>
<li><a href="#run-the-project">Run the project</a></li>
</ul>
</li>
<li><a href="#phase-3-adding-monitoring">Phase 3 - Adding Monitoring</a><ul>
<li><a href="#add-a-method-for-open-and-done-job-size">Add a method for open and done job size</a></li>
<li><a href="#add-new-data-sinks-for-open-and-closed-jobs">Add new Data Sinks for open and closed Jobs</a></li>
<li><a href="#add-a-file-sink">Add a File Sink</a></li>
<li><a href="#add-new-chart">Add new Chart</a></li>
<li><a href="#run">Run</a></li>
<li><a href="#automatically-stop-the-simulation-on-jobs-complete">Automatically stop the simulation on Jobs complete</a></li>
<li><a href="#userobserver-complete_2">UserObserver complete</a></li>
<li><a href="#run_1">Run</a></li>
<li><a href="#github-commit_2">Github commit</a></li>
</ul>
</li>
<li><a href="#phase-4-normalising">Phase 4 - Normalising</a><ul>
<li><a href="#refactoring">Refactoring</a></li>
<li><a href="#initial-jobs-by-requirements-normaly-distributed-using-libraries">Initial Jobs by requirements, normaly distributed - using libraries</a></li>
<li><a href="#calculating-the-job-requirements-upper-limit-in-userobserver">Calculating the Job Requirements upper limit in UserObserver</a></li>
<li><a href="#creating-jobs-with-requirement-levels-in-userobserver">Creating Jobs with Requirement Levels in UserObserver</a></li>
<li><a href="#userobserver-complete_3">UserObserver complete</a></li>
<li><a href="#run_2">Run</a></li>
<li><a href="#github-commit_3">Github commit</a></li>
</ul>
</li>
<li><a href="#reflection">Reflection</a></li>
</ul>
</li>
<li><a href="#real-jobs">Real Jobs</a></li>
</ul>
</div>
<h1 id="preparation">Preparation</h1>
<p>We'are using repast simphony as modelling environment.
There are two options to install this on your computer:
- A) download the distribution as a binary (Windows/OSX) or install as a plugin to Eclipse.
- B) download a VirtualBox virtual machine pre-configured</p>
<p>Option B) requires you to download a 4GB archive but it guarantees, that you can run all code examples.
Option A) requires that you download the code examples separately </p>
<h2 id="repast-simphony">Repast Simphony</h2>
<h2 id="virtual-machine">Virtual Machine</h2>
<p>You must have Oracle VirtualBox installed on your computer.
- <a href="https://www.dropbox.com/sh/a69w6cm104o1dpz/AACAs_tCvXgrEyce5-724SiLa">VM Download link</a>
- <a href="https://www.virtualbox.org/wiki/Downloads">Oracle VirtualBox</a>
- You also need the virtual box extensions from the VirtualBox download page.</p>
<h3 id="starting-the-vm">Starting the VM</h3>
<p>Once you downloaded the VM it should be a matter of double clicking the <code>ABM.vbox</code> file to bring focus
to the VirtualBox settings window.</p>
<p>You'll need to amend the location of the hard disk image file in the settings dialog.
Choose the SATA controller "Add Harddisk" &gt; Choose existing and choose the <code>abm_vm.vdi</code> file.</p>
<p><img alt="vm storage settings" src="http://dschien.github.io/images/201406/virtualbox_settings.png" style="width: 606px; height: auto; max-width: 100%;"/></p>
<p>You can find additional instructions in this <a href="/4t6gk7zve0b5hqa/ABM.mp4">video</a>
<video controls="" height="None" poster="None" preload="none" width="None"><source src="https://dl.dropboxusercontent.com/s/4t6gk7zve0b5hqa/ABM.mp4" type='video/mp4; codecs="avc1.42E01E, mp4a.40.2"'></source></video></p>
<h2 id="direct-install">Direct Install</h2>
<ul>
<li>Download for Win/Mac/Linux from <a href="http://repast.sourceforge.net/download.php">here</a></li>
<li>For Linux you need Eclipse from <a href="http://www.eclipse.org/downloads/">here</a></li>
</ul>
<p>Plus you need to install <strong>all</strong> of the following plugins:</p>
<ul>
<li>Repast from this update site (http://mirror.anl.gov/repastsimphony)</li>
</ul>
<p>From the default Kepler update site (is preconfigured):</p>
<ul>
<li>GMF Tooling 3.1.0</li>
<li>GMF Tooling Runtime Extensions 3.1.0</li>
</ul>
<p>From the Groovy Update Site: http://dist.springsource.org/release/GRECLIPSE/e4.3/</p>
<ul>
<li>Extra Groovy Compilers</li>
<li>Groovy-Eclipse</li>
</ul>
<h3 id="installing-plugins">Installing Plugins</h3>
<p>Go to <em>Help</em>&gt; <em>Install New Software</em>
<img alt="eclipse update" src="http://dschien.github.io/images/201406/eclipse_update.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<ul>
<li>click "Add"</li>
<li>Paste in the url to your plugin as above and a name after your liking (I use the url as a name)</li>
<li>Wait until the plugin index has finished loading</li>
<li>Pick your plugins</li>
<li>Accept licenses if necessary</li>
<li>Repeat as necessary</li>
</ul>
<h2 id="sources-from-github">Sources from Github</h2>
<ul>
<li>You can use the command line or the GUI for Windows/ MacOS</li>
<li>
<p>Checkout by commit tag with command line or GUI</p>
</li>
<li>
<p>the repository is available <a href="https://github.com/dschien/NormalJobs">https://github.com/dschien/NormalJobs</a></p>
</li>
<li>The command to clone is: <code>git clone https://github.com/dschien/NormalJobs.git</code></li>
</ul>
<h3 id="changing-to-a-specific-commit">Changing to a specific commit</h3>
<ul>
<li>In the GUI there are buttons to do it</li>
<li>On the command line do</li>
<li><code>git log</code> to find a tag</li>
<li><code>git checkout &lt;tag&gt;</code></li>
</ul>
<h3 id="changing-branch-in-eclipe">Changing Branch in Eclipe</h3>
<ul>
<li>Right click project &gt; Team &gt; Show History</li>
</ul>
<p><img alt="eclipse update" src="http://dschien.github.io/images/201406/history.png" style="width: 514px; height: auto; max-width: 100%;"/></p>
<ul>
<li>Right click on specific version &gt; Checkout</li>
<li>If there are local changes (for example files in srg-gen) these need to be either stashed, or deleted</li>
</ul>
<h1 id="building-the-model">Building the Model</h1>
<p>The goal is to develop an alternative modeling exploration to reproduce the results from
"Early estimation of project performance: The application of a system dynamics rework model"</p>
<p>In particular we're interested in reproduce the project performance measurements.
<img alt="work done" src="http://dschien.github.io/images/201406/project-performance.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<h2 id="relogo-basic-concepts">Relogo Basic Concepts</h2>
<ul>
<li>ReLogo is based on Eclipse IDE</li>
<li>creates Repast Simphony models with <strong>turtles, links, patches, and observers</strong>. </li>
<li>Using the Logo domain specific language based on the Groovy (Groovy: A dynamic language for the Java platform) dynamic language. </li>
<li>ReLogo freely interoperates with Groovy and Java and run as a regular Repast Simphony model</li>
</ul>
<h3 id="terms">Terms</h3>
<table>
<thead>
<tr>
<th>Agent Terminology</th>
<th>Relogo Equivalent</th>
</tr>
</thead>
<tbody>
<tr>
<td>Agent</td>
<td>Turtle</td>
</tr>
<tr>
<td>Environment</td>
<td>Observer</td>
</tr>
</tbody>
</table>
<h2 id="development-cycle">Development Cycle</h2>
<ol>
<li>Code your Agents, Environment and Observer</li>
<li>Run the simulation inside the Relogo GUI </li>
<li>Log output to files or interface to other tools for analysis</li>
</ol>
<h2 id="relogo-gui">Relogo GUI</h2>
<ul>
<li>visualisation of simulation space</li>
<li>display of simulation results in charts and tables</li>
<li>define connectors to external analysis applications</li>
<li>set simulation parameters for simulation run
<img alt="work done" src="http://dschien.github.io/images/201406/relogo_gui.png" style="width: 600px; height: auto; max-width: 100%;"/></li>
</ul>
<h3 id="sequence-diagram">Sequence Diagram</h3>
<!-- contents of sd for https://www.websequencediagrams.com/
title Job Progress
note right of Worker: create new instances
Observer->Worker: initialisation
Observer->Job: initialisation
Observer->OpenJobPool: initialisation
Observer->DoneJobPool: initialisation
loop each time step
note right of Worker: executed in each time step
alt worker has no Job
Observer->OpenJobPool: get next job
Observer->Worker: assignJob
else worker has finished Job
Observer->Worker: removeJob
Observer->DoneJobPool: move Job to done Jobs
else worker needs more time
Worker->Job: increment done level
end
end
-->
<p><img alt="sequence diagram" src="http://dschien.github.io/images/201406/sd.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<h2 id="phase-1-project-foundations">Phase 1 - Project Foundations</h2>
<ol>
<li>We'll create a new project of type 'Relogo'</li>
<li>Add turtles representing Agents</li>
<li>Add a UserObserver representing the environment</li>
<li>Add a <code>setup</code> method to initialise the simulation and a <code>step</code> method to define the actions taking place in each time step </li>
</ol>
<h3 id="creating-a-new-project">Creating a new project</h3>
<ol>
<li>Select the Relogo perspective</li>
<li>Right click on workspace</li>
<li>Select New &gt; ReLogo Project</li>
<li>Title "NormalJobs"</li>
</ol>
<h3 id="creating-a-new-worker-turtle">Creating a new worker turtle</h3>
<ol>
<li>Right click src/normaljobs.relogo</li>
<li>Select New&gt; Turtle</li>
<li>Title "Worker"</li>
<li>Define new method </li>
</ol>
<div class="highlight"><pre><span class="kt">def</span> <span class="nf">step</span><span class="o">(){}</span>
</pre></div>
<h3 id="worker-turtle-complete">Worker Turtle Complete</h3>
<div class="highlight"><pre><span class="n">package</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">relogo</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">.</span><span class="o">*</span><span class="p">;</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">.</span><span class="o">*</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Plural</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Stop</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Go</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Setup</span><span class="p">;</span>
<span class="n">import</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">ReLogoTurtle</span><span class="p">;</span>
<span class="n">class</span> <span class="n">Worker</span> <span class="n">extends</span> <span class="n">ReLogoTurtle</span> <span class="p">{</span>
<span class="n">def</span> <span class="n">step</span><span class="p">(){</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<h3 id="preparing-userobserver">Preparing UserObserver</h3>
<ol>
<li>Open src/normaljobs.relogo/UserObserver</li>
<li>Remove comments around <code>step</code> and <code>go</code> methods</li>
<li>Rename <code>createTurtles</code> to <code>createWorkers</code></li>
<li>Replace constant number with variable <code>numWorkers</code></li>
<li>Rename target of go method to <code>workers</code></li>
<li>Delete body of <code>ask</code> closure</li>
</ol>
<h3 id="userobserver-complete">UserObserver Complete</h3>
<div class="highlight"><pre><span class="n">package</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">relogo</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">.</span><span class="o">*</span><span class="p">;</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">.</span><span class="o">*</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Stop</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Go</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Setup</span><span class="p">;</span>
<span class="n">import</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">ReLogoObserver</span><span class="p">;</span>
<span class="n">class</span> <span class="n">UserObserver</span> <span class="n">extends</span> <span class="n">ReLogoObserver</span><span class="p">{</span>
<span class="err">@</span><span class="n">Setup</span>
<span class="n">def</span> <span class="n">setup</span><span class="p">(){</span>
<span class="n">clearAll</span><span class="p">()</span>
<span class="n">createWorkers</span><span class="p">(</span><span class="n">numWorkers</span><span class="p">){</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="err">@</span><span class="n">Go</span>
<span class="n">def</span> <span class="n">go</span><span class="p">(){</span>
<span class="n">ask</span><span class="p">(</span><span class="n">workers</span><span class="p">()){</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<h3 id="create-numworkers-variable-in-userglobalsandpanelfactory">Create <code>numWorkers</code> Variable in <code>UserGlobalsAndPanelFactory</code></h3>
<ol>
<li>Add new slider to change the number of workers
<code>addSliderWL ("numWorkers", "Number of Workers", 1 , 1 , 1000 , 11)</code></li>
<li>Delete others</li>
</ol>
<h3 id="complete-userglobalsandpanelfactory">Complete UserGlobalsAndPanelFactory</h3>
<div class="highlight"><pre><span class="n">package</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">relogo</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">factories</span><span class="p">.</span><span class="n">AbstractReLogoGlobalsAndPanelFactory</span>
<span class="n">public</span> <span class="n">class</span> <span class="n">UserGlobalsAndPanelFactory</span> <span class="n">extends</span> <span class="n">AbstractReLogoGlobalsAndPanelFactory</span><span class="p">{</span>
<span class="n">public</span> <span class="kt">void</span> <span class="n">addGlobalsAndPanelComponents</span><span class="p">(){</span>
<span class="n">addSliderWL</span> <span class="p">(</span><span class="s">"numWorkers"</span><span class="p">,</span> <span class="s">"Number of Workers"</span><span class="p">,</span> <span class="mi">1</span> <span class="p">,</span> <span class="mi">1</span> <span class="p">,</span> <span class="mi">1000</span> <span class="p">,</span> <span class="mi">11</span><span class="p">)</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<h3 id="create-job-class">Create Job Class</h3>
<p>We'll need to track the completion level for each Job. We encapsulate this in a new object type.
1. Create a new class
2. Name 'Job'</p>
<h3 id="start-test-run">Start Test Run</h3>
<ol>
<li>Click Play &gt; NormalJobs Model</li>
<li>In the Relogo GUI Click the power-on button to initialise</li>
<li>Click play</li>
<li>Click Stop</li>
</ol>
<h3 id="github-commit">Github commit</h3>
<p>You can get the github sources via commit <a href="https://github.com/dschien/NormalJobs/commit/c9fca9d84b652a524ca1b2c478df288eb7b8a8bf">c9fca9d84b652a524ca1b2c478df288eb7b8a8bf</a> </p>
<h2 id="phase-2-working-on-jobs">Phase 2 - Working on Jobs</h2>
<ul>
<li>Creating new jobs in job pools</li>
<li>Workers adds to completion</li>
<li>Observer maintains job pools</li>
</ul>
<h3 id="add-properties-to-class-job">Add properties to class <code>Job</code></h3>
<ol>
<li>Add a property <code>double numRequirements</code> </li>
<li>Add a property <code>double completionLevel = 0</code> to track the level of completeness of this job</li>
</ol>
<h3 id="make-worker-work-on-jobs">Make Worker work on Jobs</h3>
<ol>
<li>
<p>In turtle <code>Worker</code> create class property <code>Job job</code> and a property <code>double increment = 1</code></p>
</li>
<li>
<p>in <code>step</code> method, if has job and the complemetionlevel is smaller than requirements then increment completion level by 1</p>
</li>
<li>add method <code>isJobDone</code> return <code>true</code> if job complete, <code>false</code> otherwise</li>
</ol>
<h3 id="worker-turtle-complete_1">Worker Turtle complete</h3>
<div class="highlight"><pre><span class="n">package</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">relogo</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">.</span><span class="o">*</span><span class="p">;</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">.</span><span class="o">*</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Plural</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Stop</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Go</span><span class="p">;</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Setup</span><span class="p">;</span>
<span class="n">import</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">ReLogoTurtle</span><span class="p">;</span>
<span class="cm">/**</span>
<span class="cm"> * Worker Agent</span>
<span class="cm"> * @author schien</span>
<span class="cm"> *</span>
<span class="cm"> */</span>
<span class="n">class</span> <span class="n">Worker</span> <span class="n">extends</span> <span class="n">ReLogoTurtle</span> <span class="p">{</span>
<span class="n">Job</span> <span class="n">job</span> <span class="o">=</span> <span class="n">null</span>
<span class="kt">double</span> <span class="n">increment</span> <span class="o">=</span> <span class="mi">1</span>
<span class="cm">/**</span>
<span class="cm"> * Increment completion level by increment if completion level less than requirements</span>
<span class="cm"> * @return</span>
<span class="cm"> */</span>
<span class="n">def</span> <span class="n">step</span><span class="p">(){</span>
<span class="k">if</span> <span class="p">(</span><span class="n">this</span><span class="p">.</span><span class="n">job</span> <span class="o">&amp;&amp;</span> <span class="n">this</span><span class="p">.</span><span class="n">job</span><span class="p">.</span><span class="n">completionLevel</span> <span class="o">&lt;</span> <span class="n">this</span><span class="p">.</span><span class="n">job</span><span class="p">.</span><span class="n">requirements</span><span class="p">){</span>
<span class="n">this</span><span class="p">.</span><span class="n">job</span><span class="p">.</span><span class="n">completionLevel</span> <span class="o">+=</span> <span class="n">increment</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="cm">/**</span>
<span class="cm"> * Check if job done.</span>
<span class="cm"> * @return true if done, false otherwise</span>
<span class="cm"> */</span>
<span class="n">def</span> <span class="n">isJobDone</span><span class="p">(){</span>
<span class="k">if</span> <span class="p">(</span><span class="n">this</span><span class="p">.</span><span class="n">job</span> <span class="o">&amp;&amp;</span> <span class="n">this</span><span class="p">.</span><span class="n">job</span><span class="p">.</span><span class="n">completionLevel</span> <span class="o">&gt;=</span> <span class="n">this</span><span class="p">.</span><span class="n">job</span><span class="p">.</span><span class="n">requirements</span><span class="p">){</span>
<span class="k">return</span> <span class="nb">true</span>
<span class="p">}</span>
<span class="k">return</span> <span class="nb">false</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<h3 id="control-number-of-jobs">Control number of Jobs</h3>
<ol>
<li>Create a new variable <code>numJobs</code> in <code>UserGlobalsAndPanelFactory</code> to control the number of Jobs</li>
</ol>
<h3 id="make-observer-manage-job-pool">Make Observer manage Job Pool</h3>
<ol>
<li>Create two new members <code>openJobs</code> and <code>doneJobs</code> both of type Queue</li>
<li>In the setup method create jobs with a requirement level of 100</li>
<li>you can use a for loop as you know from java or a range expression such as<code>(0..&lt;numJobs).each{}</code></li>
<li>adding to a queue can be done with the <code>add</code> method from the java <a href="http://docs.oracle.com/javase/7/docs/api/java/util/Collection.html">Collections API</a></li>
<li>or you can use the Groovy <code>&lt;&lt;</code> operator as in <code>this.openJobs &lt;&lt; new Job(requirements:100)</code>
3.. In the go method, </li>
<li>iterate over each worker, implement as a closure to the ask method
<code>Groovy
ask(workers()){ worker -&gt;
// do something with the worker
}</code></li>
<li>check if a worker has a job, </li>
<li>if it doesn't -&gt; assign a job,</li>
<li>let him work on it</li>
<li>if it does have a job -&gt; check if the job is complete</li>
<li>if it is complete -&gt; take the job away, add it to the <code>doneJob</code> pool</li>
</ol>
<h3 id="userobserver-complete_1">UserObserver Complete</h3>
<div class="highlight"><pre><span class="n">package</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">relogo</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">.</span><span class="o">*</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">.</span><span class="o">*</span>
<span class="n">import</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">ReLogoObserver</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">engine</span><span class="p">.</span><span class="n">environment</span><span class="p">.</span><span class="n">RunEnvironment</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Stop</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Go</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Setup</span>
<span class="n">class</span> <span class="n">UserObserver</span> <span class="n">extends</span> <span class="n">ReLogoObserver</span><span class="p">{</span>
<span class="n">def</span> <span class="n">openJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="n">def</span> <span class="n">doneJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="err">@</span><span class="n">Setup</span>
<span class="n">def</span> <span class="n">setup</span><span class="p">(){</span>
<span class="n">clearAll</span><span class="p">()</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="p">(</span><span class="mf">0.</span><span class="p">.</span><span class="o">&lt;</span><span class="n">numJobs</span><span class="p">).</span><span class="n">each</span><span class="p">{</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span> <span class="o">&lt;&lt;</span> <span class="n">new</span> <span class="n">Job</span><span class="p">(</span><span class="n">requirements</span><span class="o">:</span><span class="mi">100</span><span class="p">)</span>
<span class="p">}</span>
<span class="n">createWorkers</span><span class="p">(</span><span class="n">numWorkers</span><span class="p">){</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="err">@</span><span class="n">Go</span>
<span class="n">def</span> <span class="n">go</span><span class="p">(){</span>
<span class="n">ask</span><span class="p">(</span><span class="n">workers</span><span class="p">()){</span> <span class="n">worker</span> <span class="o">-&gt;</span>
<span class="k">if</span> <span class="p">(</span><span class="o">!</span><span class="n">worker</span><span class="p">.</span><span class="n">job</span><span class="p">)</span> <span class="p">{</span>
<span class="k">if</span> <span class="p">(</span><span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">){</span>
<span class="n">worker</span><span class="p">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">poll</span><span class="p">()</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="c1">// let the worker work on it</span>
<span class="n">worker</span><span class="p">.</span><span class="n">step</span><span class="p">()</span>
<span class="k">if</span> <span class="p">(</span><span class="n">worker</span><span class="p">.</span><span class="n">isJobDone</span><span class="p">()){</span>
<span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span> <span class="o">&lt;&lt;</span> <span class="n">worker</span><span class="p">.</span><span class="n">job</span>
<span class="n">worker</span><span class="p">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">null</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<h3 id="github-commit_1">Github commit</h3>
<p>You can get the github sources via commit <a href="https://github.com/dschien/NormalJobs/commit/051e412de17cf1bf6fe94199f4380ae0bb51c3e8">051e412de17cf1bf6fe94199f4380ae0bb51c3e8</a></p>
<h3 id="run-the-project">Run the project</h3>
<p>What do you see?
What do would like to see?</p>
<h2 id="phase-3-adding-monitoring">Phase 3 - Adding Monitoring</h2>
<p>We'll add monitors, so that we can track how our workers are completing jobs
We'll also add logging of output to file to plot in excel
And we'll plot output in a chart</p>
<h3 id="add-a-method-for-open-and-done-job-size">Add a method for open and done job size</h3>
<p>Repast Relogo allows us to create data sinks that track the change of variables over time.
These require to access the number of open and done jobs in our queues. Relogo requires that
they are accessible via methods.
1. Create new methods <code>getNumDoneJobs</code> and <code>getNumOpenJobs</code> and return the size of the queues</p>
<div class="highlight"><pre><span class="n">def</span> <span class="nf">getNumDoneJobs</span><span class="p">(){</span>
<span class="k">return</span> <span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span><span class="p">.</span><span class="n">size</span><span class="p">()</span>
<span class="p">}</span>
</pre></div>
<h3 id="add-new-data-sinks-for-open-and-closed-jobs">Add new Data Sinks for open and closed Jobs</h3>
<ol>
<li>Start the Relogo GUI</li>
<li>Right-click the Data Sinks Node, title 'Jobs'</li>
<li>Select an aggregate Source, keep tick count in 'standard' set tab</li>
<li>In the tab "Method data sources" select agent type "UserObserver" and method 'getNumOpenJobs', set 'Open Jobs' as the name</li>
<li>Repeat for done jobs</li>
<li>Click the Disk symbol to save these settings
It should look as in the image below
<img alt="linear Jobs" src="http://dschien.github.io/images/201406/datasink.png" style="width: 600px; height: auto; max-width: 100%;"/></li>
</ol>
<h3 id="add-a-file-sink">Add a File Sink</h3>
<ol>
<li>On Node 'Text Sink' add a new file sink</li>
<li>Select all variables from the data source jobs, including ticks</li>
<li>Set a file name
<img alt="linear Jobs" src="http://dschien.github.io/images/201406/filesink.png" style="width: 600px; height: auto; max-width: 100%;"/></li>
</ol>
<h3 id="add-new-chart">Add new Chart</h3>
<ol>
<li>Right-click the Charts Node, title 'Jobs', type Time Series</li>
<li>Select the 'Jobs' Data source you just created</li>
<li>Pick both series</li>
<li>Set a title, and y-axis lable</li>
<li>Save settings</li>
</ol>
<h3 id="run">Run</h3>
<ul>
<li>What do you see? -&gt; the graph is pretty much unreadable</li>
<li>Repeat with the maximum number of jobs</li>
<li>In eclipse, select the project folder and click 'Refresh'</li>
<li>A file jobs.{date} should appear, open it with Excel, if you please</li>
</ul>
<p><img alt="linear Jobs" src="http://dschien.github.io/images/201406/chart-linear.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<h3 id="automatically-stop-the-simulation-on-jobs-complete">Automatically stop the simulation on Jobs complete</h3>
<ol>
<li>Add a new local variable <code>idleWorkers</code> to the UserObserver</li>
<li>In the branch for empty queue and idle workers, increment the <code>idleWorkers</code> variabel</li>
<li>At the end of the <code>go</code> method, test if the <code>numWorkers == idleWorkers</code>, in that case run <code>RunEnvironment.getInstance().endRun();</code></li>
<li>Select "Source" &gt; Organize Imports to declare the class RunEnvironment </li>
</ol>
<h3 id="userobserver-complete_2">UserObserver complete</h3>
<div class="highlight"><pre><span class="n">package</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">relogo</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">.</span><span class="o">*</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">.</span><span class="o">*</span>
<span class="n">import</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">ReLogoObserver</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">engine</span><span class="p">.</span><span class="n">environment</span><span class="p">.</span><span class="n">RunEnvironment</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Stop</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Go</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Setup</span>
<span class="n">class</span> <span class="n">UserObserver</span> <span class="n">extends</span> <span class="n">ReLogoObserver</span><span class="p">{</span>
<span class="n">def</span> <span class="n">openJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="n">def</span> <span class="n">doneJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="err">@</span><span class="n">Setup</span>
<span class="n">def</span> <span class="n">setup</span><span class="p">(){</span>
<span class="n">clearAll</span><span class="p">()</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="p">(</span><span class="mf">0.</span><span class="p">.</span><span class="o">&lt;</span><span class="n">numJobs</span><span class="p">).</span><span class="n">each</span><span class="p">{</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span> <span class="o">&lt;&lt;</span> <span class="n">new</span> <span class="n">Job</span><span class="p">(</span><span class="n">requirements</span><span class="o">:</span><span class="mi">100</span><span class="p">)</span>
<span class="p">}</span>
<span class="n">createWorkers</span><span class="p">(</span><span class="n">numWorkers</span><span class="p">){</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="err">@</span><span class="n">Go</span>
<span class="n">def</span> <span class="n">go</span><span class="p">(){</span>
<span class="kt">int</span> <span class="n">idleWorkers</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">ask</span><span class="p">(</span><span class="n">workers</span><span class="p">()){</span> <span class="n">worker</span> <span class="o">-&gt;</span>
<span class="k">if</span> <span class="p">(</span><span class="o">!</span><span class="n">worker</span><span class="p">.</span><span class="n">job</span><span class="p">)</span> <span class="p">{</span>
<span class="k">if</span> <span class="p">(</span><span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">){</span>
<span class="n">worker</span><span class="p">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">poll</span><span class="p">()</span>
<span class="p">}</span> <span class="k">else</span> <span class="p">{</span>
<span class="c1">// all jobs done</span>
<span class="n">idleWorkers</span> <span class="o">++</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="c1">// let the worker work on it</span>
<span class="n">worker</span><span class="p">.</span><span class="n">step</span><span class="p">()</span>
<span class="k">if</span> <span class="p">(</span><span class="n">worker</span><span class="p">.</span><span class="n">isJobDone</span><span class="p">()){</span>
<span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span> <span class="o">&lt;&lt;</span> <span class="n">worker</span><span class="p">.</span><span class="n">job</span>
<span class="n">worker</span><span class="p">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">null</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="c1">// we've completed our work</span>
<span class="k">if</span> <span class="p">(</span><span class="n">idleWorkers</span> <span class="o">==</span> <span class="n">numWorkers</span><span class="p">){</span>
<span class="n">RunEnvironment</span><span class="p">.</span><span class="n">getInstance</span><span class="p">().</span><span class="n">endRun</span><span class="p">();</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="n">def</span> <span class="n">getNumOpenJobs</span><span class="p">(){</span>
<span class="k">return</span> <span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">size</span><span class="p">()</span>
<span class="p">}</span>
<span class="n">def</span> <span class="n">getNumDoneJobs</span><span class="p">(){</span>
<span class="k">return</span> <span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span><span class="p">.</span><span class="n">size</span><span class="p">()</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<h3 id="run_1">Run</h3>
<p>We should now see something like this
<img alt="linear Jobs" src="http://dschien.github.io/images/201406/linear-jobs.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<h3 id="github-commit_2">Github commit</h3>
<p>You can get the github sources via commit <a href="https://github.com/dschien/NormalJobs/commit/66cef351683115a3790e070d49b8e042bf88cd83">66cef351683115a3790e070d49b8e042bf88cd83</a></p>
<h2 id="phase-4-normalising">Phase 4 - Normalising</h2>
<p>Our model is completely linear. We'd like to simulate an s-shaped curve for the work done.
Because we'd like to be as quick as possible, we plan to achieve this by distributing work in our open work pool as a normal distribution
horizontally reflected.
<img alt="sigma" src="http://dschien.github.io/images/201406/sigma.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<p>We can do calculate requirements relative to some min requirement level we pick.
<img alt="increment" src="http://dschien.github.io/images/201406/increment.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<p>Idea: We'll assign requirements to a job in proportion to the probability of the normal distribution.</p>
<h3 id="refactoring">Refactoring</h3>
<p>Our jobs will have varying number of requirements. It makes sense to control the later, as the number of jobs is a function of the
number of requirements.
- In <code>UserGlobalsAndPanelFactory</code> change the variable <code>numJobs</code> number of jobs to <code>numRequirements</code>
- also increase the value boundary to 10000
- add a new slider <code>numberSteps</code> and <code>workIncrement</code></p>
<h3 id="initial-jobs-by-requirements-normaly-distributed-using-libraries">Initial Jobs by requirements, normaly distributed - using libraries</h3>
<ul>
<li>We need an implementation of the error function to calculate the CDF of the normal distribution</li>
<li>Usually we don't want to implement each method we need, so we use existing libs</li>
<li>We use norm function from the Apache stats lib</li>
<li>download the <a href="http://commons.apache.org/proper/commons-math/download_math.cgi">binary</a></li>
<li>extract, copy the <code>commons-math3-3.3.jar</code> to the <code>lib</code> folder in your eclipse project</li>
<li>go to the java perspective, browse the <code>lib</code> folder, right click the jar file &gt; Build Path &gt; 'Add to Build Path'</li>
<li>Return to the Relogo perspective</li>
</ul>
<h3 id="calculating-the-job-requirements-upper-limit-in-userobserver">Calculating the Job Requirements upper limit in <code>UserObserver</code></h3>
<ul>
<li>create two new variables for mean and standard deviation <code>def mu = 0 and def sigma = 1</code></li>
<li>Create a new instance of NormalDistribution <code>NormalDistribution norm = new NormalDistribution(mu, sigma)</code></li>
</ul>
<div class="highlight"><pre><span class="kt">double</span> <span class="n">minLevel</span> <span class="o">=</span> <span class="n">workIncrement</span> <span class="o">*</span> <span class="mi">2</span> <span class="c1">// job effort at least double the min work increment (at least 2 steps per job)</span>
<span class="kt">double</span> <span class="n">freeRequirements</span> <span class="o">=</span> <span class="p">(</span> <span class="n">numRequirements</span> <span class="o">-</span> <span class="n">minLevel</span><span class="o">*</span> <span class="n">numberSteps</span> <span class="o">*</span> <span class="n">numWorkers</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="n">freeRequirements</span> <span class="o">&lt;</span> <span class="n">numRequirements</span> <span class="o">*</span> <span class="mf">0.1</span><span class="p">){</span>
<span class="n">println</span> <span class="s">"Number of Requirements that can vary is less than 10% of total - you won't see much variation"</span>
<span class="p">}</span>
<span class="c1">// the maximum number of requirements per job batch</span>
<span class="kt">double</span> <span class="n">h</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">def</span> <span class="n">upperBound</span> <span class="o">=</span> <span class="mi">3</span> <span class="o">*</span> <span class="n">sigma</span> <span class="c1">// ~99% of all req covered</span>
</pre></div>
<ol>
<li>We add some minimum requirements, so that the min is not zero</li>
<li>The upperBound is our upper sampling limit -&gt; thus ~99% of all samples will be in this interval. </li>
</ol>
<h3 id="creating-jobs-with-requirement-levels-in-userobserver">Creating Jobs with Requirement Levels in <code>UserObserver</code></h3>
<div class="highlight"><pre><span class="p">(</span><span class="mf">0.</span><span class="p">.</span><span class="o">&lt;</span><span class="n">numberSteps</span><span class="p">).</span><span class="n">each</span><span class="p">{</span> <span class="n">i</span> <span class="o">-&gt;</span>
<span class="n">def</span> <span class="n">x_i</span> <span class="o">=</span> <span class="n">i</span> <span class="o">*</span> <span class="n">upperBound</span><span class="o">/</span><span class="n">numberSteps</span>
<span class="n">def</span> <span class="n">x_j</span> <span class="o">=</span> <span class="p">(</span><span class="n">i</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="n">upperBound</span><span class="o">/</span><span class="n">numberSteps</span>
<span class="n">def</span> <span class="n">_p</span> <span class="o">=</span> <span class="n">norm</span><span class="p">.</span><span class="n">probability</span><span class="p">(</span><span class="n">x_i</span><span class="p">,</span> <span class="n">x_j</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="n">h</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">){</span>
<span class="n">h</span> <span class="o">=</span> <span class="n">_p</span> <span class="o">*</span> <span class="n">freeRequirements</span> <span class="o">+</span> <span class="n">minLevel</span> <span class="o">*</span> <span class="n">numWorkers</span>
<span class="p">}</span>
<span class="n">def</span> <span class="n">p</span> <span class="o">=</span> <span class="n">_p</span> <span class="o">*</span> <span class="n">freeRequirements</span> <span class="c1">// normalise to total number of reqs</span>
<span class="c1">// our actual num of requirements = limit - pdf</span>
<span class="n">def</span> <span class="n">r</span> <span class="o">=</span> <span class="n">h</span> <span class="o">-</span> <span class="n">p</span>
<span class="c1">// get requirements per workers relative to number of workers</span>
<span class="n">def</span> <span class="n">job_requirements</span> <span class="o">=</span> <span class="n">r</span>
<span class="c1">// create job in batches with this level of requirement</span>
<span class="p">(</span><span class="mf">0.</span><span class="p">.</span><span class="o">&lt;</span><span class="n">numWorkers</span><span class="p">).</span><span class="n">each</span><span class="p">{</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">addFirst</span><span class="p">(</span><span class="n">new</span> <span class="n">Job</span><span class="p">(</span><span class="n">requirements</span><span class="o">:</span><span class="n">job_requirements</span><span class="p">))</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">addLast</span><span class="p">(</span> <span class="n">new</span> <span class="n">Job</span><span class="p">(</span><span class="n">requirements</span><span class="o">:</span><span class="n">job_requirements</span><span class="p">))</span>
<span class="p">}</span>
<span class="n">assignedRequirements</span><span class="o">+=</span> <span class="mi">2</span><span class="o">*</span><span class="n">r</span>
<span class="p">}</span>
</pre></div>
<ul>
<li>We want each worker to have roughly the same amount of requirements to deal with </li>
<li>
<p>We use the apache CDF function to calculate our requirements levels</p>
</li>
<li>
<p>Now we'll work from the mean to the outside, create jobs and add those to head and tail of our queue
<img alt="work done" src="http://dschien.github.io/images/201406/increment.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
</li>
<li>
<p>We add a new job, symetrically to front and end end of the queue</p>
</li>
<li>
<p>In the worker creation closure add </p>
</li>
</ul>
<div class="highlight"><pre><span class="n">it</span> <span class="o">-&gt;</span>
<span class="n">it</span><span class="p">.</span><span class="n">increment</span> <span class="o">=</span> <span class="n">this</span><span class="p">.</span><span class="n">workIncrement</span>
</pre></div>
<h3 id="userobserver-complete_3"><code>UserObserver</code> complete</h3>
<div class="highlight"><pre><span class="n">package</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">relogo</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Utility</span><span class="p">.</span><span class="o">*</span>
<span class="n">import</span> <span class="k">static</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">UtilityG</span><span class="p">.</span><span class="o">*</span>
<span class="n">import</span> <span class="n">normaljobs</span><span class="p">.</span><span class="n">ReLogoObserver</span>
<span class="n">import</span> <span class="n">org</span><span class="p">.</span><span class="n">apache</span><span class="p">.</span><span class="n">commons</span><span class="p">.</span><span class="n">math3</span><span class="p">.</span><span class="n">distribution</span><span class="p">.</span><span class="n">NormalDistribution</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">engine</span><span class="p">.</span><span class="n">environment</span><span class="p">.</span><span class="n">RunEnvironment</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">Stop</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Go</span>
<span class="n">import</span> <span class="n">repast</span><span class="p">.</span><span class="n">simphony</span><span class="p">.</span><span class="n">relogo</span><span class="p">.</span><span class="n">schedule</span><span class="p">.</span><span class="n">Setup</span>
<span class="n">class</span> <span class="n">UserObserver</span> <span class="n">extends</span> <span class="n">ReLogoObserver</span><span class="p">{</span>
<span class="n">LinkedList</span> <span class="n">openJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">LinkedList</span>
<span class="n">Queue</span> <span class="n">doneJobs</span> <span class="o">=</span> <span class="p">[]</span> <span class="n">as</span> <span class="n">Queue</span>
<span class="err">@</span><span class="n">Setup</span>
<span class="n">def</span> <span class="n">setup</span><span class="p">(){</span>
<span class="n">clearAll</span><span class="p">()</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">clear</span><span class="p">();</span>
<span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span><span class="p">.</span><span class="n">clear</span><span class="p">();</span>
<span class="c1">// initialise jobs</span>
<span class="n">def</span> <span class="n">mu</span> <span class="o">=</span> <span class="mi">0</span>
<span class="c1">// def mu = numRequirements/ 2</span>
<span class="n">def</span> <span class="n">sigma</span> <span class="o">=</span> <span class="mi">1</span>
<span class="n">NormalDistribution</span> <span class="n">norm</span> <span class="o">=</span> <span class="n">new</span> <span class="n">NormalDistribution</span><span class="p">(</span><span class="n">mu</span><span class="p">,</span> <span class="n">sigma</span><span class="p">)</span>
<span class="n">def</span> <span class="n">assignedRequirements</span> <span class="o">=</span> <span class="mi">0</span>
<span class="kt">double</span> <span class="n">minLevel</span> <span class="o">=</span> <span class="n">workIncrement</span> <span class="o">*</span> <span class="mi">2</span> <span class="c1">// job effort at least double the min work increment (at least 2 steps per job)</span>
<span class="kt">double</span> <span class="n">freeRequirements</span> <span class="o">=</span> <span class="p">(</span> <span class="n">numRequirements</span> <span class="o">-</span> <span class="n">minLevel</span><span class="o">*</span> <span class="n">numberSteps</span> <span class="o">*</span> <span class="n">numWorkers</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="n">freeRequirements</span> <span class="o">&lt;</span> <span class="n">numRequirements</span> <span class="o">*</span> <span class="mf">0.1</span><span class="p">){</span>
<span class="n">println</span> <span class="s">"Number of Requirements that can vary is less than 10% of total - you won't see much variation"</span>
<span class="p">}</span>
<span class="c1">// the maximum number of requirements per job batch</span>
<span class="kt">double</span> <span class="n">h</span> <span class="o">=</span> <span class="o">-</span><span class="mi">1</span>
<span class="n">def</span> <span class="n">upperBound</span> <span class="o">=</span> <span class="mi">3</span> <span class="o">*</span> <span class="n">sigma</span> <span class="c1">// ~99% of all req covered</span>
<span class="p">(</span><span class="mf">0.</span><span class="p">.</span><span class="o">&lt;</span><span class="n">numberSteps</span><span class="p">).</span><span class="n">each</span><span class="p">{</span> <span class="n">i</span> <span class="o">-&gt;</span>
<span class="n">def</span> <span class="n">x_i</span> <span class="o">=</span> <span class="p">(</span><span class="n">i</span><span class="o">*</span><span class="mi">2</span><span class="o">-</span><span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1</span><span class="o">/</span><span class="mi">2</span> <span class="o">*</span> <span class="n">upperBound</span><span class="o">/</span><span class="n">numberSteps</span>
<span class="n">def</span> <span class="n">x_j</span> <span class="o">=</span> <span class="p">(</span><span class="n">i</span><span class="o">*</span><span class="mi">2</span><span class="o">+</span><span class="mi">1</span><span class="p">)</span> <span class="o">*</span> <span class="mi">1</span><span class="o">/</span><span class="mi">2</span><span class="o">*</span> <span class="n">upperBound</span><span class="o">/</span><span class="n">numberSteps</span>
<span class="n">def</span> <span class="n">_p</span> <span class="o">=</span> <span class="n">norm</span><span class="p">.</span><span class="n">probability</span><span class="p">(</span><span class="n">x_i</span><span class="p">,</span> <span class="n">x_j</span><span class="p">)</span>
<span class="k">if</span> <span class="p">(</span><span class="n">h</span> <span class="o">==</span> <span class="o">-</span><span class="mi">1</span><span class="p">){</span>
<span class="n">h</span> <span class="o">=</span> <span class="n">_p</span> <span class="o">*</span> <span class="n">freeRequirements</span> <span class="o">+</span> <span class="n">minLevel</span> <span class="o">*</span> <span class="n">numWorkers</span>
<span class="p">}</span>
<span class="n">def</span> <span class="n">p</span> <span class="o">=</span> <span class="n">_p</span> <span class="o">*</span> <span class="n">freeRequirements</span> <span class="c1">// normalise to total number of reqs</span>
<span class="c1">// our actual num of requirements = limit - pdf</span>
<span class="n">def</span> <span class="n">r</span> <span class="o">=</span> <span class="n">h</span> <span class="o">-</span> <span class="n">p</span>
<span class="c1">// get requirements per workers relative to number of workers</span>
<span class="n">def</span> <span class="n">job_requirements</span> <span class="o">=</span> <span class="n">r</span>
<span class="c1">// create job in batches with this level of requirement</span>
<span class="p">(</span><span class="mf">0.</span><span class="p">.</span><span class="o">&lt;</span><span class="n">numWorkers</span><span class="p">).</span><span class="n">each</span><span class="p">{</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">addFirst</span><span class="p">(</span><span class="n">new</span> <span class="n">Job</span><span class="p">(</span><span class="n">requirements</span><span class="o">:</span><span class="n">job_requirements</span><span class="p">))</span>
<span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">addLast</span><span class="p">(</span> <span class="n">new</span> <span class="n">Job</span><span class="p">(</span><span class="n">requirements</span><span class="o">:</span><span class="n">job_requirements</span><span class="p">))</span>
<span class="p">}</span>
<span class="n">assignedRequirements</span><span class="o">+=</span> <span class="mi">2</span><span class="o">*</span><span class="n">r</span>
<span class="p">}</span>
<span class="n">createWorkers</span><span class="p">(</span><span class="n">numWorkers</span><span class="p">){</span> <span class="n">it</span> <span class="o">-&gt;</span>
<span class="n">it</span><span class="p">.</span><span class="n">increment</span> <span class="o">=</span> <span class="n">this</span><span class="p">.</span><span class="n">workIncrement</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="err">@</span><span class="n">Go</span>
<span class="n">def</span> <span class="n">go</span><span class="p">(){</span>
<span class="kt">int</span> <span class="n">idleWorkers</span> <span class="o">=</span> <span class="mi">0</span>
<span class="n">ask</span><span class="p">(</span><span class="n">workers</span><span class="p">()){</span> <span class="n">worker</span> <span class="o">-&gt;</span>
<span class="k">if</span> <span class="p">(</span><span class="o">!</span><span class="n">worker</span><span class="p">.</span><span class="n">job</span><span class="p">)</span> <span class="p">{</span>
<span class="k">if</span> <span class="p">(</span><span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">){</span>
<span class="n">worker</span><span class="p">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">poll</span><span class="p">()</span>
<span class="p">}</span> <span class="k">else</span> <span class="p">{</span>
<span class="c1">// all jobs done</span>
<span class="n">idleWorkers</span> <span class="o">++</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="c1">// let the worker work on it</span>
<span class="n">worker</span><span class="p">.</span><span class="n">step</span><span class="p">()</span>
<span class="k">if</span> <span class="p">(</span><span class="n">worker</span><span class="p">.</span><span class="n">isJobDone</span><span class="p">()){</span>
<span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span> <span class="o">&lt;&lt;</span> <span class="n">worker</span><span class="p">.</span><span class="n">job</span>
<span class="n">worker</span><span class="p">.</span><span class="n">job</span> <span class="o">=</span> <span class="n">null</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="c1">// we've completed our work</span>
<span class="k">if</span> <span class="p">(</span><span class="n">idleWorkers</span> <span class="o">==</span> <span class="n">numWorkers</span><span class="p">){</span>
<span class="n">RunEnvironment</span><span class="p">.</span><span class="n">getInstance</span><span class="p">().</span><span class="n">endRun</span><span class="p">();</span>
<span class="p">}</span>
<span class="p">}</span>
<span class="n">def</span> <span class="n">getNumOpenJobs</span><span class="p">(){</span>
<span class="k">return</span> <span class="n">this</span><span class="p">.</span><span class="n">openJobs</span><span class="p">.</span><span class="n">size</span><span class="p">()</span>
<span class="p">}</span>
<span class="n">def</span> <span class="n">getNumDoneJobs</span><span class="p">(){</span>
<span class="k">return</span> <span class="n">this</span><span class="p">.</span><span class="n">doneJobs</span><span class="p">.</span><span class="n">size</span><span class="p">()</span>
<span class="p">}</span>
<span class="p">}</span>
</pre></div>
<h3 id="run_2">Run</h3>
<p>This is what we'd like to see
<img alt="sigma" src="http://dschien.github.io/images/201406/sigmoid_results.png" style="width: 600px; height: auto; max-width: 100%;"/></p>
<h3 id="github-commit_3">Github commit</h3>
<p>You can get the github sources via commit <a href="https://github.com/dschien/NormalJobs/commit/8e06d5b689098746b6f3380ff36cba0826e21ac0">8e06d5b689098746b6f3380ff36cba0826e21ac0</a> </p>
<h2 id="reflection">Reflection</h2>
<ul>
<li>Obviously, this goes against the whole purpose of Agent Based Modelling:
One of the main principles of Agent Based Modelling is that we're constructing our system such that macro-level
phenomena <em>emerge</em> from micro-level rules and agent behaviour</li>
<li>In the above example we have plugged in the macro-level distribution of requirements</li>
<li>Thus, there isn't much we can learn from this</li>
</ul>
<h1 id="real-jobs">Real Jobs</h1>
<ul>
<li>We now construct a model that is more realistic by implementing learning</li>
<li>The source is at <a href="https://github.com/dschien/RealJobs">https://github.com/dschien/RealJobs</a></li>
<li>The basic model is identical to the normal jobs model above</li>
<li>The Observer is responsible for mainting open and done job pools</li>
<li>Our workers are toiling away on jobs given by the Observer</li>
<li>The difference is that our workers now learn and solve more requirements with each additional time step
<img alt="learn" src="http://dschien.github.io/images/201406/learn.png" style="width: 2200px; height: auto; max-width: 100%;"/></li>
</ul></summary></entry><entry><title>Testing Pelican</title><link href="http://dschien.github.io/blog/2014/06/16/testing-pelican/" rel="alternate"></link><updated>2014-06-16T13:00:00+01:00</updated><author><name>Daniel Schien</name></author><id>tag:dschien.github.io,2014-06-16:blog/2014/06/16/testing-pelican/</id><summary type="html">
<p>You have to start somewhere
</p>
<h1 id="i-test-pelican">I test pelican</h1>
<p>This is my first post</p>
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