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<!doctype html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0, maximum-scale=1.0, user-scalable=no">
<title>Parallel-Macro</title>
<link rel="stylesheet" href="dist/reset.css">
<link rel="stylesheet" href="dist/reveal.css">
<link rel="stylesheet" href="dist/theme/simple.css" id="theme">
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<link rel="stylesheet" href="plugin/highlight/monokai.css" id="highlight-theme">
</head>
<body>
<div class="reveal">
<div class="slides">
<section>
<h2> Bridging Fiji and OpenMPI for Easy-to-Use Parallel Processing of Images </h2>
<img src="images/bridge.png" class="r-stretch">
</section>
<section>
<h2> Outline </h2>
<ul>
<li> Gain access to remote HPC </li>
<li> Installation and configuration of the plugin </li>
<li> Upload, run and download macros remotely </li>
<li> Monitoring progress, output and error reporting </li>
<li> Parallelization of a Macro script </li>
<li> How to use the progress reporting functions </li>
<li> Demonstration of a real parallel macro </li>
<br/>
<li> Advanced parallelization of processing on large images by use of MPI-aware Ops </li>
</ul>
</section>
<section>
<h2> Workshop structure </h2>
<ul>
<li> Each part of the workshop is hands-on. </li>
<li> The participants are expected to first attempt to work through the practical worksheets. </li>
<li> Follow the link in the presentation to open the worksheet. </li>
<li> The worksheets will then be presented and explained by the presenter. </li>
</ul>
</section>
<section>
<section>
<h2> Gain access to remote HPC </h2>
</section>
<section>
<h3> Gain access to remote HPC </h3>
<ul>
<li> <a href="https://scs.it4i.cz/training">Get training credentials</a> </li>
<img src="images/cluster.png" class="r-strech">
</ul>
</section>
</section>
<section>
<section>
<h2> Installation and configuration of the plugin </h2>
</section>
<section>
<h3> Installation and configuration of the plugin </h3>
<ul>
<li> Installation: </li>
<ul>
<li>
<a href="https://github.com/MKrumnikl/Ij1MPIWrapper/wiki/How-to-install-HPC-Workflow-Manager-client">How to install HPC Workflow Manager client</a>
</li>
</ul>
</ul>
</section>
<section>
<h3> Installation and configuration of the plugin </h3>
<ul>
<li> Configuration: </li>
<ul>
<li> <a href="https://github.com/MKrumnikl/Ij1MPIWrapper/wiki/How-to-set-up-the-paradigm-for-Parallel-Macro">How to set up the paradigm for Parallel Macro</a> </li>
</ul>
</ul>
<img src="images/paradigm.png" class="r-stretch">
</section>
</section>
<section>
<section>
<h2> Upload, run and download macros remotely </h2>
</section>
<section>
<h3> Upload, run and download macros remotely </h3>
<ul>
<li> <a href="https://github.com/MKrumnikl/Ij1MPIWrapper/wiki/Using-HPC-Workflow-Manager-to-start-a-new-Macro-job">Using HPC Workflow Manager to start a new Macro job</a> </li>
</ul>
<img src="images/clusterSide.png" class="r-stretch">
</section>
</section>
<section>
<section>
<h2> Monitoring progress, output and error reporting </h2>
</section>
<section>
<h3> Monitoring progress, output and error reporting </h3>
<ul>
<li> <a href="https://github.com/MKrumnikl/Ij1MPIWrapper/wiki/Monitoring-progress%2C-output-and-error-reporting">Monitoring progress, output and error reporting</a> </li> </li>
</ul>
<img src="images/progress.png" class="r-stretch">
</section>
</section>
<section>
<section>
<h2> Parallelization of a Macro script </h2>
</section>
<section>
<h3> Parallelization of a Macro script </h3>
<ul>
<li> <a href="https://github.com/MKrumnikl/Ij1MPIWrapper/wiki/How-to-write-a-parallel-Macro">How to write a parallel Macro</a> </li>
</ul>
<img src="images/editor.png" class="r-stretch">
</section>
</section>
<section>
<section>
<h2>How to use the progress reporting functions</h2>
</section>
<section>
<h3>How to use the progress reporting functions</h3>
<ul>
<li>
<a href="https://github.com/MKrumnikl/Ij1MPIWrapper/wiki/How-to-use-the-progress-reporting-functions">How to use the progress reporting functions</a>
</li>
</ul>
</section>
</section>
<section>
<section>
<h2> Demonstration of a real parallel macro </h2>
</section>
<section>
<h3> Demonstration of a real parallel macro </h3>
<ul>
<li> <a href="https://github.com/MKrumnikl/Ij1MPIWrapper/wiki/Demonstration-of-a-real-parallel-macro">Demonstration of a real parallel macro</a> </li>
</ul>
</section>
</section>
<section>
<section>
<h2> Advanced parallelization of processing on large images by use of MPI-aware Ops </h2>
</section>
<section>
<h3> Advanced parallelization of processing on large images by use of MPI-aware Ops </h3>
<ul>
<li>
<a href="http://linedu.cs.vsb.cz/~trn0038/prez/">OpenMPI-enabled Fiji with scijava-parallel-mpi</a>
</li>
</ul>
</section>
</section>
<section>
<section>
<h2> Discussion </h2>
</section>
<section data-background-image="images/qna.png">
<h3> Discussion </h3>
<ul>
<li> Recap </li>
<ul>
<li> Gain access to remote HPC </li>
<li> Installation and configuration of the plugin </li>
<li> Upload, run and download macros remotely </li>
<li> Monitoring progress, output and error reporting </li>
<li> Parallelization of a Macro script </li>
<li> How to use the progress reporting functions </li>
<li> Demonstration of a real parallel macro </li>
<br/>
<li> Advanced parallelization of processing on large images by use of MPI-aware Ops </li>
</ul>
</ul>
<p>Thank you!</p>
</section>
</section>
<section>
<h3>Advanced Remote Fiji Installation</h3>
<li>
<a href="https://github.com/MKrumnikl/Ij1MPIWrapper/blob/master/README.md">How to install Parallel Macro on a remote cluster.</a>
</li>
</section>
</div>
</div>
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</body>
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