Add slides

slides/.gitignore

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slides/index.html

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+slides.html

slides/run.sh

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+#!/bin/sh
+#pandoc -t beamer slides.md --slide-level=2 -o slides.pdf -V theme:metropolis --toc --toc-depth 1 "$@"
+pandoc -t revealjs -s --dpi 120 slides.md --css=style.css --slide-level=2 -o slides.html -V theme=white -V height=800 "$@" 
+echo "Syncing $PWD"
+rsync -Paz "$PWD/" -e 'ssh -p 2222' root@slides.todevnull.com:/data/html/ 
+echo 'Done'

slides/run_watch.sh

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+#!/bin/sh
+echo 'slides.md' | entr ./run.sh
+

slides/slides.html

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+<!DOCTYPE html>
+<html>
+<head>
+  <meta charset="utf-8">
+  <meta name="generator" content="pandoc">
+  <meta name="author" content="J. Fernando Sánchez (jf.sanchez@upm)">
+  <meta name="dcterms.date" content="2018-01-01">
+  <title>Docker for research</title>
+  <meta name="apple-mobile-web-app-capable" content="yes">
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+  <!--[if lt IE 9]>
+  <script src="reveal.js/lib/js/html5shiv.js"></script>
+  <![endif]-->
+</head>
+<body>
+  <div class="reveal">
+    <div class="slides">
+
+<section id="title-slide">
+  <h1 class="title">Docker for research</h1>
+  <p class="subtitle">… and data analysis</p>
+  <p class="author">J. Fernando Sánchez (<a href="mailto:jf.sanchez@upm">jf.sanchez@upm</a>)</p>
+  <p class="date">2018</p>
+</section>
+
+<section><section id="intro" class="title-slide slide level1 white" data-background="img/intro.jpg"><h1>Intro</h1></section><section id="before-we-begin" class="slide level2">
+<h2>Before we begin</h2>
+<p>Code available at:</p>
+<p><a href="https://github.com/balkian/lab-in-a-box" class="uri">https://github.com/balkian/lab-in-a-box</a></p>
+<p>Live demos at:</p>
+<p><strong><a href="https://github.todevnull.com" class="uri">https://github.todevnull.com</a></strong></p>
+<p><a href="https://lab.todevnull.com" class="uri">https://lab.todevnull.com</a></p>
+<p><a href="https://hub.todevnull.com" class="uri">https://hub.todevnull.com</a></p>
+<p>Feel free to log in, but try not to break them for now 😉</p>
+</section><section id="my-name-is-fernando-and" class="slide level2">
+<h2>My name is Fernando and…</h2>
+<p><img data-src="img/im-a-researcher.jpg" /></p>
+</section><section id="at-grupo-de-sistemas-inteligentes" class="slide level2">
+<h2>At Grupo de Sistemas Inteligentes</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<p><img data-src="img/gsi.png" /></p>
+</div><div class="column" style="width:50%;">
+<ul>
+<li>Machine Learning and Big Data</li>
+<li>NLP and Sentiment Analysis</li>
+<li>Social Network Analysis</li>
+<li>Agents and Simulation</li>
+<li>Linked Data and Semantic Technologies</li>
+</ul>
+</div>
+</div>
+<p><a href="http://www.gsi.dit.upm.es" class="uri">http://www.gsi.dit.upm.es</a></p>
+</section><section id="and-i-docker" class="slide level2">
+<h2>And I ❤ Docker</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<p><img data-src="img/docker.jpg" /></p>
+</div><div class="column" style="width:50%;">
+<ul>
+<li>Docker+research for 3+ years</li>
+<li>Advocate for ~2 years</li>
+<li>Internal infrastructure: ansible, k8s and docker</li>
+<li>Teach (with) it</li>
+</ul>
+</div>
+</div>
+</section><section id="about-this-talk" class="slide level2">
+<h2>About this talk</h2>
+<p>Takeaway: <strong><em>you can set up a multi-user data analysis environment with isolation in minutes</em></strong></p>
+<p>Plus: using docker to perform and share experiments is even easier</p>
+<p>Related Meetups:</p>
+<p><a href="https://www.meetup.com/Docker-Madrid/events/240357800/">Big Data and Machine Learning with Docker</a></p>
+<p><a href="https://www.meetup.com/Docker-Madrid/events/237067604/">Using Docker in Machine Learning Projects</a></p>
+</section></section>
+<section><section id="for-researchers" class="title-slide slide level1 white" data-background="img/research.jpg" style="color:white"><h1>For researchers</h1></section><section id="experiment-publish-repeat" class="slide level2">
+<h2>Experiment, publish, repeat</h2>
+<p><img data-src="img/peerreview.jpg" /></p>
+</section><section id="reproducibility" class="slide level2">
+<h2>Reproducibility</h2>
+<figure>
+<img data-src="img/goodluck.png" alt="@ianholmes" /><figcaption><a href="https://twitter.com/ianholmes/status/288689712636493824">@ianholmes</a></figcaption>
+</figure>
+</section><section id="obstacles" class="slide level2">
+<h2>Obstacles</h2>
+<div class="columns">
+<div class="column" style="width:50%;">
+<ul>
+<li><strong>Missing data</strong></li>
+<li>Bleeding edge tools and libraries</li>
+<li>Throwaway software
+<ul>
+<li>Hacky</li>
+<li>Little to no documentation</li>
+</ul></li>
+<li>Multiple languages</li>
+</ul>
+</div><div class="column" style="width:50%;">
+<figure>
+<img data-src="img/will_it_work.png" alt="https://xkcd.com/1742/" style="height:80.0%" /><figcaption><a href="https://xkcd.com/1742/" class="uri">https://xkcd.com/1742/</a></figcaption>
+</figure>
+</div>
+</div>
+</section><section id="obstacles-1" class="slide level2">
+<h2>Obstacles</h2>
+<p><img data-src="img/noidea-pc.png" /></p>
+</section><section id="is-it-a-problem" class="slide level2">
+<h2>Is it a problem?</h2>
+<figure>
+<img data-src="img/reproducibility.jpg" alt="https://www.nature.com/" style="height:80.0%" /><figcaption><a href="https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970">https://www.nature.com/</a></figcaption>
+</figure>
+</section><section id="jupyter-notebooks" class="slide level2">
+<h2>Jupyter notebooks</h2>
+<p><img data-src="img/jupyter-screenshot.png" /></p>
+</section><section id="jupyter-architecture" class="slide level2">
+<h2>Jupyter architecture</h2>
+<figure>
+<img data-src="img/jupyter-architecture.png" alt="http://jupyter.readthedocs.io" /><figcaption><a href="http://jupyter.readthedocs.io" class="uri">http://jupyter.readthedocs.io</a></figcaption>
+</figure>
+</section><section id="docker-to-the-rescue" class="slide level2">
+<h2>Docker to the rescue</h2>
+<figure>
+<img data-src="img/dockerrescue.png" alt="towardsdatascience.com" /><figcaption><a href="https://towardsdatascience.com/how-docker-can-help-you-become-a-more-effective-data-scientist-7fc048ef91d5">towardsdatascience.com</a></figcaption>
+</figure>
+</section><section id="jupyterdocker-stacks" class="slide level2">
+<h2>Jupyter/docker-stacks</h2>
+<p><img data-src="img/dockerstacks.png" style="height:50.0%" /></p>
+</section><section id="reproducible-environment" class="slide level2">
+<h2>Reproducible environment</h2>
+<div class="sourceCode" id="cb1"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb1-1" data-line-number="1"><span class="ex">docker</span> run --rm -p 8888:8888 \</a>
+<a class="sourceLine" id="cb1-2" data-line-number="2">    -v <span class="va">$(</span><span class="ex">WDIR</span><span class="va">)</span>/:/home/jovyan/work/ \</a>
+<a class="sourceLine" id="cb1-3" data-line-number="3">    jupyter/scipy-notebook</a></code></pre></div>
+</section><section id="and-friendly-too" class="slide level2">
+<h2>And friendly, too</h2>
+<div class="sourceCode" id="cb2"><pre class="sourceCode yaml"><code class="sourceCode yaml"><a class="sourceLine" id="cb2-1" data-line-number="1"><span class="fu">version:</span><span class="at"> </span><span class="st">&#39;2&#39;</span></a>
+<a class="sourceLine" id="cb2-2" data-line-number="2"><span class="fu">services:</span></a>
+<a class="sourceLine" id="cb2-3" data-line-number="3">  <span class="fu">jupyter:</span></a>
+<a class="sourceLine" id="cb2-4" data-line-number="4">    <span class="fu">image:</span><span class="at"> jupyter/scipy-notebook</span></a>
+<a class="sourceLine" id="cb2-5" data-line-number="5">    <span class="fu">volumes:</span></a>
+<a class="sourceLine" id="cb2-6" data-line-number="6">    <span class="kw">-</span> <span class="st">&quot;./.nbconfig:/home/jovyan/.jupyter/nbconfig&quot;</span></a>
+<a class="sourceLine" id="cb2-7" data-line-number="7">    <span class="kw">-</span> <span class="st">&quot;./work:/home/jovyan/work/&quot;</span></a>
+<a class="sourceLine" id="cb2-8" data-line-number="8">    <span class="fu">ports:</span></a>
+<a class="sourceLine" id="cb2-9" data-line-number="9">    <span class="kw">-</span> <span class="st">&quot;8888:8888&quot;&quot;</span></a></code></pre></div>
+<div class="sourceCode" id="cb3"><pre class="sourceCode bash"><code class="sourceCode bash"><a class="sourceLine" id="cb3-1" data-line-number="1"><span class="ex">docker-compose</span> up</a></code></pre></div>
+</section><section id="related-projects" class="slide level2">
+<h2>Related projects</h2>
+<ul>
+<li>Using docker images to share trained systems</li>
+</ul>
+<figure>
+<img data-src="img/gym.png" alt="https://gym.openai.com" height="500" /><figcaption><a href="https://gym.openai.com" class="uri">https://gym.openai.com</a></figcaption>
+</figure>
+</section></section>
+<section><section id="for-small-groups" class="title-slide slide level1 white" data-background="img/group.jpeg"><h1>For small groups</h1></section><section id="requirements" class="slide level2">
+<h2>Requirements</h2>
+<ul>
+<li>Shared environments</li>
+<li>Resource sharing</li>
+<li>Easy configuration</li>
+<li>Versioning</li>
+<li>Backups</li>
+</ul>
+<p>And <strong>little to no overhead</strong></p>
+</section><section id="isolation" class="slide level2">
+<h2>Isolation</h2>
+<p><img data-src="img/noidea.jpg" /></p>
+</section><section id="jupyterhub" class="slide level2">
+<h2>Jupyterhub</h2>
+<div class="columns">
+<div class="column" style="width:60%;">
+<figure>
+<img data-src="img/jhub-parts.png" alt="http://jupyterhub.readthedocs.io/" height="500" /><figcaption><a href="http://jupyterhub.readthedocs.io/" class="uri">http://jupyterhub.readthedocs.io/</a></figcaption>
+</figure>
+</div><div class="column" style="width:40%;">
+<h4 id="authenticators">Authenticators</h4>
+<ul>
+<li>Local</li>
+<li>OAuth</li>
+<li>LDAP</li>
+<li>JWT</li>
+</ul>
+<h4 id="spawners">Spawners</h4>
+<ul>
+<li>Local</li>
+<li>Docker</li>
+<li>Kubernetes</li>
+<li>Marathon</li>
+</ul>
+</div>
+</div>
+</section><section id="more-infrastructure" class="slide level2">
+<h2>More infrastructure</h2>
+<p><img data-src="img/docker-gitlab.jpg" class="noborder" height="250" /> <img data-src="img/nextcloud.jpg" class="noborder" height="250" /></p>
+<p><img data-src="img/sharelatex.jpg" class="noborder" height="250" /></p>
+</section></section>
+<section><section id="demo" class="title-slide slide level1" data-background="img/party.jpg"><h1>Demo</h1></section><section id="its-demo-time" class="slide level2">
+<h2>It’s demo time</h2>
+<p><img data-src="img/demogods.jpg" style="height:80.0%" /></p>
+<p><a href="https://github.todevnull.com" class="uri">https://github.todevnull.com</a> <a href="https://github.com/balkian/lab-in-a-box" class="uri">https://github.com/balkian/lab-in-a-box</a></p>
+</section></section>
+<section><section id="other-tools" class="title-slide slide level1"><h1>Other tools</h1></section><section id="zeppelin" class="slide level2">
+<h2>Zeppelin</h2>
+<ul>
+<li>Alternative to Jupyter</li>
+</ul>
+<figure>
+<img data-src="img/zeppelin.png" alt="https://zeppelin.apache.org/" /><figcaption><a href="https://zeppelin.apache.org/" class="uri">https://zeppelin.apache.org/</a></figcaption>
+</figure>
+</section><section id="cocalc" class="slide level2">
+<h2>CoCalc</h2>
+<ul>
+<li>Alternative to Jupyter</li>
+</ul>
+<figure>
+<img data-src="img/cocalc.png" alt="https://cocalc.org/" height="500" /><figcaption><a href="https://cocalc.org/" class="uri">https://cocalc.org/</a></figcaption>
+</figure>
+</section><section id="docker-nvidia" class="slide level2">
+<h2>Docker-Nvidia</h2>
+<ul>
+<li>CUDA for docker</li>
+</ul>
+<figure>
+<img data-src="img/dockernvidia.png" alt="https://github.com/NVIDIA/nvidia-docker" /><figcaption><a href="https://github.com/NVIDIA/nvidia-docker" class="uri">https://github.com/NVIDIA/nvidia-docker</a></figcaption>
+</figure>
+</section><section id="jupyter-binder" class="slide level2">
+<h2>Jupyter Binder</h2>
+<ul>
+<li>Custom Jupyter from git repositories</li>
+</ul>
+<figure>
+<img data-src="img/binder.png" alt="https://mybinder.org/" height="500" /><figcaption><a href="https://mybinder.org/" class="uri">https://mybinder.org/</a></figcaption>
+</figure>
+</section><section id="knowledge-repo" class="slide level2">
+<h2>Knowledge-Repo</h2>
+<figure>
+<img data-src="img/knowledgerepo.png" alt="http://knowledge-repo.readthedocs.io/" /><figcaption><a href="http://knowledge-repo.readthedocs.io/" class="uri">http://knowledge-repo.readthedocs.io/</a></figcaption>
+</figure>
+</section></section>
+<section><section id="conclusions" class="title-slide slide level1"><h1>Conclusions</h1></section><section id="lessons-learned" class="slide level2">
+<h2>Lessons learned</h2>
+<ul>
+<li>Docker + Docker-compose
+<ul>
+<li>Reproducible environments (partially)</li>
+<li>Reduced tooling / experience</li>
+<li>Ephemeral containers force you to automate/document installation</li>
+</ul></li>
+<li>Jupyterhub
+<ul>
+<li>Shared environments</li>
+<li>Web interface (zero knowledge)</li>
+</ul></li>
+</ul>
+</section><section id="whats-missing" class="slide level2">
+<h2>What’s missing?</h2>
+<ul>
+<li>Roles and permissions</li>
+<li><p>Backups</p></li>
+<li>Ideas:
+<ul>
+<li>Kubernetes?</li>
+<li>OpenShift?</li>
+</ul></li>
+</ul>
+</section><section id="thanks-for-listening" class="slide level2">
+<h2>Thanks for listening!</h2>
+<p><a href="https://github.com/balkian/lab-in-a-box" class="uri">https://github.com/balkian/lab-in-a-box</a></p>
+<p><a href="mailto:jf.sanchez@upm.es">jf.sanchez@upm.es</a></p>
+</section></section>
+    </div>
+  </div>
+
+  <script src="reveal.js/lib/js/head.min.js"></script>
+  <script src="reveal.js/js/reveal.js"></script>
+
+  <script>
+
+      // Full list of configuration options available at:
+      // https://github.com/hakimel/reveal.js#configuration
+      Reveal.initialize({
+        // Push each slide change to the browser history
+        history: true,
+        height: 800,
+
+        // Optional reveal.js plugins
+        dependencies: [
+          { src: 'reveal.js/lib/js/classList.js', condition: function() { return !document.body.classList; } },
+          { src: 'reveal.js/plugin/zoom-js/zoom.js', async: true },
+          { src: 'reveal.js/plugin/notes/notes.js', async: true }
+        ]
+      });
+    </script>
+    </body>
+</html>

slides/slides.md

@@ -0,0 +1,306 @@
+---
+title: Docker for research
+subtitle: ... and data analysis
+author: J. Fernando Sánchez (<jf.sanchez@upm>)
+tags: [Docker, CI, research]
+date: 2018
+abstract: Talk about docker for research and data analysis
+
+---
+
+# Intro  { .white data-background="img/intro.jpg"}
+
+## Before we begin
+
+Code available at:
+
+<https://github.com/balkian/lab-in-a-box>
+
+Live demos at: 
+
+**<https://github.todevnull.com>**
+
+<https://lab.todevnull.com>
+
+<https://hub.todevnull.com>
+
+
+Feel free to log in, but try not to break them for now 😉
+
+
+## My name is Fernando and...
+
+
+![](img/im-a-researcher.jpg)
+
+
+
+## At Grupo de Sistemas Inteligentes
+
+
+:::::::::::::: {.columns}
+::: {.column width="50%"}
+![](img/gsi.png)
+:::
+::: {.column width="50%"}
+- Machine Learning and Big Data
+- NLP and Sentiment Analysis
+- Social Network Analysis
+- Agents and Simulation
+- Linked Data and Semantic Technologies
+:::
+:::::::::::::::
+
+<http://www.gsi.dit.upm.es>
+
+## And I ❤ Docker
+
+
+:::::::::::::: {.columns}
+::: {.column width="50%"}
+![](img/docker.jpg)
+
+:::
+::: {.column width="50%"}
+* Docker+research for 3+ years
+* Advocate for ~2 years
+* Internal infrastructure: ansible, k8s and docker
+* Teach (with) it
+:::
+
+::::::::::::::
+
+## About this talk 
+
+Takeaway: ***you can set up a multi-user data analysis environment with isolation in minutes***
+
+Plus: using docker to perform and share experiments is even easier
+
+Related Meetups:
+
+[Big Data and Machine Learning with Docker](https://www.meetup.com/Docker-Madrid/events/240357800/)
+
+[Using Docker in Machine Learning Projects](https://www.meetup.com/Docker-Madrid/events/237067604/)
+
+# For researchers {.white data-background="img/research.jpg" style="color:white"}
+
+<!-- ## Research is about data -->
+
+<!-- ![The scientific method](img/scientificmethod.png){.noborder height="500px"} -->
+
+
+## Experiment, publish, repeat
+
+
+![](img/peerreview.jpg)
+
+
+## Reproducibility
+
+
+![[\@ianholmes](https://twitter.com/ianholmes/status/288689712636493824)](img/goodluck.png)
+
+## Obstacles
+
+:::::::::::::: {.columns}
+::: {.column width="50%"}
+
+* **Missing data** 
+* Bleeding edge tools and libraries
+* Throwaway software
+   * Hacky
+   * Little to no documentation
+* Multiple languages
+
+:::
+::: {.column width="50%"}
+![<https://xkcd.com/1742/>](img/will_it_work.png){ height=80% }
+:::
+
+::::::::::::::
+
+
+## Obstacles
+
+![](img/noidea-pc.png)
+
+## Is it a problem?
+
+![[https://www.nature.com/](https://www.nature.com/news/1-500-scientists-lift-the-lid-on-reproducibility-1.19970)](img/reproducibility.jpg){ height=80% }
+
+
+## Jupyter notebooks
+
+![](img/jupyter-screenshot.png)
+
+## Jupyter architecture
+
+![<http://jupyter.readthedocs.io>](img/jupyter-architecture.png)
+
+
+## Docker to the rescue
+
+![[towardsdatascience.com](https://towardsdatascience.com/how-docker-can-help-you-become-a-more-effective-data-scientist-7fc048ef91d5)](img/dockerrescue.png)
+
+
+## Jupyter/docker-stacks 
+
+![](img/dockerstacks.png){ height=50% }
+
+## Reproducible environment
+
+```bash
+docker run --rm -p 8888:8888 \
+    -v $(WDIR)/:/home/jovyan/work/ \
+    jupyter/scipy-notebook
+```
+
+## And friendly, too
+
+
+```yaml
+version: '2'
+services:
+  jupyter:
+    image: jupyter/scipy-notebook
+    volumes:
+    - "./.nbconfig:/home/jovyan/.jupyter/nbconfig"
+    - "./work:/home/jovyan/work/"
+    ports:
+    - "8888:8888""
+```
+
+```bash
+docker-compose up
+```
+
+## Related projects 
+
+* Using docker images to share trained systems
+
+![<https://gym.openai.com>](img/gym.png){ height=500px }
+
+# For small groups { .white data-background="img/group.jpeg" }
+
+
+## Requirements
+
+* Shared environments
+* Resource sharing
+* Easy configuration
+* Versioning
+* Backups
+
+And **little to no overhead**
+
+
+## Isolation
+
+![](img/noidea.jpg)
+
+## Jupyterhub
+
+
+:::::::::::::: {.columns}
+::: {.column width="60%"}
+
+![<http://jupyterhub.readthedocs.io/>](img/jhub-parts.png){ height=500px }
+
+:::
+::: {.column width="40%"}
+
+#### Authenticators
+
+* Local
+* OAuth
+* LDAP
+* JWT
+
+#### Spawners
+
+* Local
+* Docker
+* Kubernetes
+* Marathon
+
+:::
+:::::::::::::::
+
+## More infrastructure
+
+![](img/docker-gitlab.jpg){.noborder height="250px"}
+![](img/nextcloud.jpg){.noborder height="250px"}
+
+![](img/sharelatex.jpg){.noborder height="250px"}
+
+# Demo  { data-background="img/party.jpg"}
+
+## It's demo time
+
+
+![](img/demogods.jpg){ height=80% }
+
+<https://github.todevnull.com>
+<https://github.com/balkian/lab-in-a-box>
+
+# Other tools
+
+## Zeppelin
+
+* Alternative to Jupyter
+
+![<https://zeppelin.apache.org/>](img/zeppelin.png)
+
+## CoCalc
+
+* Alternative to Jupyter
+
+![<https://cocalc.org/>](img/cocalc.png){ height=500px }
+
+
+## Docker-Nvidia
+
+* CUDA for docker
+
+![<https://github.com/NVIDIA/nvidia-docker>](img/dockernvidia.png)
+
+## Jupyter Binder
+
+* Custom Jupyter from git repositories
+
+![<https://mybinder.org/>](img/binder.png){ height=500px }
+
+
+## Knowledge-Repo
+
+![<http://knowledge-repo.readthedocs.io/>](img/knowledgerepo.png)
+
+
+
+# Conclusions
+
+## Lessons learned
+
+* Docker + Docker-compose
+  * Reproducible environments (partially)
+  * Reduced tooling / experience
+  * Ephemeral containers force you to automate/document installation
+* Jupyterhub
+  * Shared environments
+  * Web interface (zero knowledge)
+  
+## What's missing?
+
+* Roles and permissions
+* Backups
+
+* Ideas:
+  * Kubernetes?
+  * OpenShift?
+
+##  Thanks for listening!
+
+<https://github.com/balkian/lab-in-a-box>
+
+<jf.sanchez@upm.es>
+

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