📝 session content updated as per Google Docs

global-disease-modelling · Dec 17, 2024 · 6e4270a · 6e4270a
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diff --git a/_quarto.yml b/_quarto.yml
@@ -23,6 +23,7 @@ website:
           - session-1.qmd
           - session-2.qmd
           - session-3.qmd
+          - session-hackathon.qmd
       - section: "Resources"
         contents:
           - unix-shell.qmd

diff --git a/docs/acknowledgements.html b/docs/acknowledgements.html
@@ -149,6 +149,12 @@ <h1 class="quarto-secondary-nav-title">Acknowledgements</h1>
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/best-practice-programming.html b/docs/best-practice-programming.html
@@ -150,6 +150,12 @@ <h1 class="quarto-secondary-nav-title">Best practices for programming</h1>
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/code-of-conduct.html b/docs/code-of-conduct.html
@@ -150,6 +150,12 @@ <h1 class="quarto-secondary-nav-title">Code of Conduct</h1>
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/collaborative-git.html b/docs/collaborative-git.html
@@ -150,6 +150,12 @@ <h1 class="quarto-secondary-nav-title">Collaborative Git</h1>
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/index.html b/docs/index.html
@@ -149,6 +149,12 @@ <h1 class="quarto-secondary-nav-title">Global Disease Modelling 2025 Workshop</h
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/pawsey.html b/docs/pawsey.html
@@ -184,6 +184,12 @@ <h1 class="quarto-secondary-nav-title">Pawsey</h1>
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>

diff --git a/docs/search.json b/docs/search.json
diff --git a/docs/session-1.html b/docs/session-1.html
@@ -150,6 +150,12 @@ <h1 class="quarto-secondary-nav-title">Session 1</h1>
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -222,12 +228,9 @@ <h1 class="quarto-secondary-nav-title">Session 1</h1>
     <h2 id="toc-title">On this page</h2>
 
   <ul>
-  <li><a href="#logging-in" id="toc-logging-in" class="nav-link active" data-scroll-target="#logging-in">Logging in</a></li>
-  <li><a href="#looking-around" id="toc-looking-around" class="nav-link" data-scroll-target="#looking-around">Looking around</a></li>
-  <li><a href="#file-transfers" id="toc-file-transfers" class="nav-link" data-scroll-target="#file-transfers">File transfers</a></li>
-  <li><a href="#schedulers" id="toc-schedulers" class="nav-link" data-scroll-target="#schedulers">Schedulers</a></li>
-  <li><a href="#git" id="toc-git" class="nav-link" data-scroll-target="#git">Git</a></li>
-  <li><a href="#chitra-notes-to-self" id="toc-chitra-notes-to-self" class="nav-link" data-scroll-target="#chitra-notes-to-self">Chitra notes to self</a></li>
+  <li><a href="#unix-shell" id="toc-unix-shell" class="nav-link active" data-scroll-target="#unix-shell"><span class="header-section-number">0.1</span> Unix shell</a></li>
+  <li><a href="#logging-in-ssh" id="toc-logging-in-ssh" class="nav-link" data-scroll-target="#logging-in-ssh"><span class="header-section-number">0.2</span> Logging in (SSH)</a></li>
+  <li><a href="#git" id="toc-git" class="nav-link" data-scroll-target="#git"><span class="header-section-number">0.3</span> Git</a></li>
   </ul>
 </nav>
     </div>
@@ -237,7 +240,7 @@ <h2 id="toc-title">On this page</h2>
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title d-none d-lg-block">Session 1</h1>
-<p class="subtitle lead">Starting up Pawsey and Git</p>
+<p class="subtitle lead">Fundamentals of Unix and Git</p>
 </div>
 
 
@@ -254,8 +257,12 @@ <h1 class="title d-none d-lg-block">Session 1</h1>
 </header>
 
 
-<section id="logging-in" class="level3">
-<h3 class="anchored" data-anchor-id="logging-in">Logging in</h3>
+<section id="unix-shell" class="level3" data-number="0.1">
+<h3 data-number="0.1" class="anchored" data-anchor-id="unix-shell"><span class="header-section-number">0.1</span> Unix shell</h3>
+<p>Find Pawsey’s intro to Bash <a href="https://pawsey-internships.github.io/more_with_bash/unix_and_shells/">here</a>.</p>
+</section>
+<section id="logging-in-ssh" class="level3" data-number="0.2">
+<h3 data-number="0.2" class="anchored" data-anchor-id="logging-in-ssh"><span class="header-section-number">0.2</span> Logging in (SSH)</h3>
 <div class="callout callout-style-default callout-note no-icon callout-titled" title="Objectives">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -291,9 +298,8 @@ <h3 class="anchored" data-anchor-id="logging-in">Logging in</h3>
 <p>Why do you think we use the shell, or the command line, when interacting with Pawsey? Why not use a graphical user interface (GUI)?</p>
 </div>
 </div>
-</section>
-<section id="looking-around" class="level3">
-<h3 class="anchored" data-anchor-id="looking-around">Looking around</h3>
+<section id="looking-around" class="level4" data-number="0.2.1">
+<h4 data-number="0.2.1" class="anchored" data-anchor-id="looking-around"><span class="header-section-number">0.2.1</span> Looking around</h4>
 <div class="callout callout-style-default callout-note no-icon callout-titled" title="Objectives">
 <div class="callout-header d-flex align-content-center">
 <div class="callout-icon-container">
@@ -336,114 +342,10 @@ <h3 class="anchored" data-anchor-id="looking-around">Looking around</h3>
 <li>Remove the program <code>secret-program.sh</code> and the folder <code>old-data</code>.</li>
 </ol>
 </section>
-<section id="file-transfers" class="level3">
-<h3 class="anchored" data-anchor-id="file-transfers">File transfers</h3>
-<div class="callout callout-style-default callout-note no-icon callout-titled" title="Objectives">
-<div class="callout-header d-flex align-content-center">
-<div class="callout-icon-container">
-<i class="callout-icon no-icon"></i>
-</div>
-<div class="callout-title-container flex-fill">
-Objectives
-</div>
-</div>
-<div class="callout-body-container callout-body">
-<ul>
-<li>Use SCP and SFTP for file transfers</li>
-<li>Use the command line for basic file operations</li>
-<li>Use the text editor Vim</li>
-</ul>
-</div>
-</div>
-<ol type="1">
-<li>Log in to an SFTP session. Transfer the folder <code>secret-files</code> within your <code>scratch</code> directory to your local PC.</li>
-</ol>
-<div class="callout callout-style-default callout-important callout-titled" title="Warning">
-<div class="callout-header d-flex align-content-center">
-<div class="callout-icon-container">
-<i class="callout-icon"></i>
-</div>
-<div class="callout-title-container flex-fill">
-Warning
-</div>
-</div>
-<div class="callout-body-container callout-body">
-<p>It’s tempting to use your PC’s GUI, but please use the command line for the next steps in this exercise!</p>
-</div>
-</div>
-<ol start="2" type="1">
-<li>Open a new terminal window for your local PC. Navigate to the <code>secret-files</code> directory on your local PC and open the file <code>unmodified-secret-scenario.xml</code> using Vim.</li>
-<li>There are some values in that file that needs to be substituted; they look like: <code>@parameter@</code>. Find these and change them.</li>
-<li>When you’re done changing all the values, rename the file to <code>secret-scenario.xml</code> using the command <code>mv</code>.</li>
-<li>Using SCP, transfer the file <code>secret-scenario.xml</code> to the <code>secret-files</code> folder within your <code>scratch</code> directory on Pawsey.</li>
-</ol>
-<div class="callout callout-style-default callout-warning callout-titled" title="Discussion">
-<div class="callout-header d-flex align-content-center">
-<div class="callout-icon-container">
-<i class="callout-icon"></i>
-</div>
-<div class="callout-title-container flex-fill">
-Discussion
-</div>
-</div>
-<div class="callout-body-container callout-body">
-<p>When do you think you would use SCP, SFTP, and Rsync? Which method do you think is quicker? And when would you use GUIs?</p>
-</div>
-</div>
-</section>
-<section id="schedulers" class="level3">
-<h3 class="anchored" data-anchor-id="schedulers">Schedulers</h3>
-<div class="callout callout-style-default callout-note no-icon callout-titled" title="Objectives">
-<div class="callout-header d-flex align-content-center">
-<div class="callout-icon-container">
-<i class="callout-icon no-icon"></i>
-</div>
-<div class="callout-title-container flex-fill">
-Objectives
-</div>
-</div>
-<div class="callout-body-container callout-body">
-<ul>
-<li>Understand the Pawsey filesystem vs architecture (nodes and scheduler).</li>
-<li>Understand where jobs are executed.</li>
-</ul>
-</div>
-</div>
-<p>#TODO</p>
-<div class="callout callout-style-default callout-warning callout-titled" title="Discussion">
-<div class="callout-header d-flex align-content-center">
-<div class="callout-icon-container">
-<i class="callout-icon"></i>
-</div>
-<div class="callout-title-container flex-fill">
-Discussion
-</div>
-</div>
-<div class="callout-body-container callout-body">
-<p>Where do you think this job was executed?</p>
-</div>
-</div>
 </section>
-<section id="git" class="level3">
-<h3 class="anchored" data-anchor-id="git">Git</h3>
-<ol type="1">
-<li>Clone the secret-exercises repository to your scratch directory.</li>
-</ol>
-<p>#TODO</p>
-</section>
-<section id="chitra-notes-to-self" class="level3">
-<h3 class="anchored" data-anchor-id="chitra-notes-to-self">Chitra notes to self</h3>
-<ul>
-<li>Set up an SSH key for Git</li>
-<li>Set up an SSH key for Pawsey</li>
-<li>Navigate on Pawsey using the command line interface</li>
-<li>Clone a git repository onto Pawsey</li>
-<li>Transfer files between your local PC and Pawsey</li>
-<li>Commit and push changes</li>
-<li>Taster: run one job on Pawsey</li>
-</ul>
-<p>Ideas for directions:</p>
-<p>Clone the <code>2025-workshop-exercise</code> repository. This is one of our pipelines. You have to transfer sensitive files from your local device onto Pawsey, to then run the pipeline.</p>
+<section id="git" class="level3" data-number="0.3">
+<h3 data-number="0.3" class="anchored" data-anchor-id="git"><span class="header-section-number">0.3</span> Git</h3>
+<p>Find Pawsey’s intro to version control <a href="https://pawsey-internships.github.io/version-control/">here</a>.</p>
 
 
 </section>

diff --git a/docs/session-2.html b/docs/session-2.html
@@ -150,6 +150,12 @@ <h1 class="quarto-secondary-nav-title">Session 2</h1>
   <a href="./session-3.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text">Session 3</span></a>
   </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./session-hackathon.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text">Hackathon session</span></a>
+  </div>
 </li>
       </ul>
   </li>
@@ -217,16 +223,25 @@ <h1 class="quarto-secondary-nav-title">Session 2</h1>
 </nav>
 <div id="quarto-sidebar-glass" class="quarto-sidebar-collapse-item" data-bs-toggle="collapse" data-bs-target=".quarto-sidebar-collapse-item"></div>
 <!-- margin-sidebar -->
-    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar zindex-bottom">
-
+    <div id="quarto-margin-sidebar" class="sidebar margin-sidebar">
+        <nav id="TOC" role="doc-toc" class="toc-active">
+    <h2 id="toc-title">On this page</h2>
+
+  <ul>
+  <li><a href="#high-level-overview-of-hpc" id="toc-high-level-overview-of-hpc" class="nav-link active" data-scroll-target="#high-level-overview-of-hpc"><span class="header-section-number">0.1</span> High-level overview of HPC</a></li>
+  <li><a href="#file-transfers-more-ssh" id="toc-file-transfers-more-ssh" class="nav-link" data-scroll-target="#file-transfers-more-ssh"><span class="header-section-number">0.2</span> File transfers (more SSH)</a></li>
+  <li><a href="#software-on-hpc" id="toc-software-on-hpc" class="nav-link" data-scroll-target="#software-on-hpc"><span class="header-section-number">0.3</span> Software on HPC</a></li>
+  <li><a href="#job-scheduling-slurm" id="toc-job-scheduling-slurm" class="nav-link" data-scroll-target="#job-scheduling-slurm"><span class="header-section-number">0.4</span> Job scheduling (Slurm)</a></li>
+  </ul>
+</nav>
     </div>
 <!-- main -->
 <main class="content" id="quarto-document-content">
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
 <h1 class="title d-none d-lg-block">Session 2</h1>
-<p class="subtitle lead">Running an analysis on Pawsey</p>
+<p class="subtitle lead">Familiarising ourselves with HPCs</p>
 </div>
 
 
@@ -243,26 +258,72 @@ <h1 class="title d-none d-lg-block">Session 2</h1>
 </header>
 
 
-<p>Topics to be covered in this session:</p>
-<ul>
-<li>Submit jobs on Pawsey
-<ul>
-<li>Conceptually explain Slurm</li>
-<li>The difference between <code>sbatch</code>, <code>srun</code> and <code>salloc</code></li>
-</ul></li>
-<li>Using Git on Pawsey</li>
-<li>Git: create a pull request for your changes</li>
-<li>Debugging on Pawsey (Vim, file transfers)</li>
-<li>? Attempt writing parallelisation code on Pawsey
+<section id="high-level-overview-of-hpc" class="level3" data-number="0.1">
+<h3 data-number="0.1" class="anchored" data-anchor-id="high-level-overview-of-hpc"><span class="header-section-number">0.1</span> High-level overview of HPC</h3>
+</section>
+<section id="file-transfers-more-ssh" class="level3" data-number="0.2">
+<h3 data-number="0.2" class="anchored" data-anchor-id="file-transfers-more-ssh"><span class="header-section-number">0.2</span> File transfers (more SSH)</h3>
+<div class="callout callout-style-default callout-note no-icon callout-titled" title="Objectives">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon no-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Objectives
+</div>
+</div>
+<div class="callout-body-container callout-body">
 <ul>
-<li>instead of using job arrays, which is the current preferred approach</li>
-<li>GNU parallel</li>
-</ul></li>
-<li>? Attempt modularisation of individual project codes (ask participants to break up their code and find a better way of organising their code)</li>
-<li>? Interactive RStudio sessions on Pawsey</li>
+<li>Use SCP and SFTP for file transfers</li>
+<li>Use the command line for basic file operations</li>
+<li>Use the text editor Vim</li>
 </ul>
+</div>
+</div>
+<ol type="1">
+<li>Log in to an SFTP session. Transfer the folder <code>secret-files</code> within your <code>scratch</code> directory to your local PC.</li>
+</ol>
+<div class="callout callout-style-default callout-important callout-titled" title="Warning">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Warning
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>It’s tempting to use your PC’s GUI, but please use the command line for the next steps in this exercise!</p>
+</div>
+</div>
+<ol start="2" type="1">
+<li>Open a new terminal window for your local PC. Navigate to the <code>secret-files</code> directory on your local PC and open the file <code>unmodified-secret-scenario.xml</code> using Vim.</li>
+<li>There are some values in that file that needs to be substituted; they look like: <code>@parameter@</code>. Find these and change them.</li>
+<li>When you’re done changing all the values, rename the file to <code>secret-scenario.xml</code> using the command <code>mv</code>.</li>
+<li>Using SCP, transfer the file <code>secret-scenario.xml</code> to the <code>secret-files</code> folder within your <code>scratch</code> directory on Pawsey.</li>
+</ol>
+<div class="callout callout-style-default callout-warning callout-titled" title="Discussion">
+<div class="callout-header d-flex align-content-center">
+<div class="callout-icon-container">
+<i class="callout-icon"></i>
+</div>
+<div class="callout-title-container flex-fill">
+Discussion
+</div>
+</div>
+<div class="callout-body-container callout-body">
+<p>When do you think you would use SCP, SFTP, and Rsync? Which method do you think is quicker? And when would you use GUIs?</p>
+</div>
+</div>
+</section>
+<section id="software-on-hpc" class="level3" data-number="0.3">
+<h3 data-number="0.3" class="anchored" data-anchor-id="software-on-hpc"><span class="header-section-number">0.3</span> Software on HPC</h3>
+</section>
+<section id="job-scheduling-slurm" class="level3" data-number="0.4">
+<h3 data-number="0.4" class="anchored" data-anchor-id="job-scheduling-slurm"><span class="header-section-number">0.4</span> Job scheduling (Slurm)</h3>
 
 
+</section>
 
 </main> <!-- /main -->
 <script id="quarto-html-after-body" type="application/javascript">