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Quarto GHA Workflow Runner committed Jul 25, 2024
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2 changes: 1 addition & 1 deletion .nojekyll
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15 changes: 8 additions & 7 deletions chapters/introduction.html
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Expand Up @@ -254,7 +254,7 @@ <h1 class="title"><span class="chapter-number">1</span>&nbsp; <span class="chapt

<section id="introduction" class="level2" data-number="1.1">
<h2 data-number="1.1" class="anchored" data-anchor-id="introduction"><span class="header-section-number">1.1</span> Introduction</h2>
<p>The FRB-CESAB server <strong>Rossinante</strong> is dedicated to <em>medium</em> performance scientific computing (see <a href="#tbl-hardware" class="quarto-xref">Table&nbsp;<span>1.1</span></a> for hardware specification). It runs under the GNU/Linux distribution <strong>Debian 12</strong> (Bookworm).</p>
<p>The FRB-CESAB server <strong>Rossinante</strong> is dedicated to scientific computing (see <a href="#tbl-hardware" class="quarto-xref">Table&nbsp;<span>1.1</span></a> for hardware specification). It runs under the GNU/Linux distribution <strong>Debian 12</strong> (Bookworm).</p>
<p><strong>When do you want to use Rossinante?</strong></p>
<ul>
<li>You need to analyse large datasets (RAM operations) and/or,</li>
Expand Down Expand Up @@ -331,11 +331,11 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="storage"><span class="hea
<p>You have access to four personal directories:</p>
<ul>
<li><code>/home/you/</code></li>
<li><code>/media/sancho/you</code> (external drive)</li>
<li><code>/media/seagate/you</code> (external drive)</li>
<li><code>/media/cervantes/you</code> (external drive)</li>
<li><code>/media/sancho/you/</code> (external drive)</li>
<li><code>/media/seagate/you/</code> (external drive)</li>
<li><code>/media/cervantes/you/</code> (external drive)</li>
</ul>
<p>You can create, edit and remove any files/directories you want inside these directories.</p>
<p>You can create, edit, rename and remove any files/directories you want inside these directories.</p>
<div class="callout callout-style-default callout-important callout-titled">
<div class="callout-header d-flex align-content-center">
<div class="callout-icon-container">
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</div>
</div>
<div class="callout-body-container callout-body">
<p>Rossinante is <strong>not a storage server</strong>. The 30 TB of storage are shared among all users. You can store large datasets to run yours analyses, but once you’re done, please remove these files.</p>
<p>Rossinante is <strong>not a storage server</strong>. The 30 TB storage are shared among all users. You can store large datasets to run yours analyses, but once you’re done, please remove these files.</p>
<p><strong>There is no backup system!</strong> You are responsible for your data.</p>
</div>
</div>
Expand All @@ -371,14 +371,15 @@ <h2 data-number="1.4" class="anchored" data-anchor-id="useful-utilities"><span c
<li><a href="https://ffmpeg.org/"><code>FFmpeg</code></a> – Transcoding multimedia files</li>
<li><a href="https://imagemagick.org"><code>ImageMagick</code></a> – Image manipulation program</li>
<li><a href="https://poppler.freedesktop.org/"><code>Poppler</code></a> – PDF utility library</li>
<li><a href="https://exiftool.org/"><code>ExifTool</code></a> - File metadata utility</li>
<li><a href="https://exiftool.org/"><code>ExifTool</code></a> File metadata utility</li>
<li><a href="https://gdal.org/"><code>GDAL</code></a>, <a href="https://trac.osgeo.org/geos"><code>GEOS</code></a>, <a href="https://proj.org/"><code>PROJ</code></a> – Spatial libraries</li>
<li><a href="https://htop.dev/"><code>htop</code></a> – CPU, RAM, and processes monitoring tool</li>
<li><a href="https://github.com/bcicen/ctop"><code>ctop</code></a> – Docker containers monitoring tool</li>
<li><a href="https://www.nano-editor.org/"><code>nano</code></a>, <a href="https://www.vim.org/"><code>Vim</code></a> and <a href="https://neovim.io/"><code>Neovim</code></a> – CLI text editors</li>
<li><a href="https://www.gnu.org/software/screen/"><code>screen</code></a> and <a href="https://github.com/tmux/tmux/wiki"><code>tmux</code></a> – Terminal multiplexers</li>
<li><a href="http://mama.indstate.edu/users/ice/tree/"><code>tree</code></a> – Recursive directory listing program</li>
<li><a href="https://curl.se/"><code>curl</code></a> and <a href="https://www.gnu.org/software/wget/manual/wget.html"><code>wget</code></a> – Download managers</li>
<li><a href="https://rsync.samba.org/"><code>rsync</code></a> – Incremental file transfer</li>
<li><a href="https://linuxize.com/post/how-to-zip-files-and-directories-in-linux/"><code>zip</code></a> and <a href="https://linuxize.com/post/how-to-unzip-files-in-linux/"><code>unzip</code></a> – ZIP files managers</li>
<li><a href="https://www.zsh.org/"><code>zsh</code></a> – Unix shell (alternative to Bash)</li>
<li><a href="https://github.com/jesseduffield/lazygit"><code>lazygit</code></a> – CLI interface for git</li>
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Expand Up @@ -325,14 +325,15 @@ <h1 class="title"><span class="chapter-number">2</span>&nbsp; <span class="chapt
</tr>
</tbody>
</table>
<p><strong>N.B.</strong> You have to replace these values by the ones provided by the administrator.</p>
<section id="ssh-connection" class="level2 page-columns page-full" data-number="2.1">
<h2 data-number="2.1" class="anchored" data-anchor-id="ssh-connection"><span class="header-section-number">2.1</span> SSH connection</h2>
<p>To open an SSH connection, you need to launch a terminal (all modern terminals include an SSH client<a href="#fn1" class="footnote-ref" id="fnref1" role="doc-noteref"><sup>1</sup></a>):</p>
<div class="no-row-height column-margin column-container"><div id="fn1"><p><sup>1</sup>&nbsp;On Windows, you don’t need anymore to install Putty.</p></div></div><ul>
<div class="no-row-height column-margin column-container"><div id="fn1"><p><sup>1</sup>&nbsp;On Windows, you don’t need to install Putty anymore.</p></div></div><ul>
<li>On Unix-based OS (macOS and GNU/Linux), open the app called <em>Terminal</em></li>
<li>On Windows, open the <a href="https://www.atlassian.com/git/tutorials/git-bash">Git Bash</a> app<a href="#fn2" class="footnote-ref" id="fnref2" role="doc-noteref"><sup>2</sup></a> (installed by default with the <a href="https://git-scm.com/">git</a> software)</li>
</ul>
<div class="no-row-height column-margin column-container"><div id="fn2"><p><sup>2</sup>&nbsp;Don’t use PowerShell or RStudio terminal. They can be unstable. Git Bash allows you to use GNU/Linux commands on Windows.</p></div></div><div class="sourceCode" id="cb1"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1"></a><span class="co"># SSH connection to Rossinante ----</span></span>
<div class="no-row-height column-margin column-container"><div id="fn2"><p><sup>2</sup>&nbsp;Don’t use PowerShell or RStudio terminal. Git Bash allows you to use GNU/Linux commands on Windows.</p></div></div><div class="sourceCode" id="cb1"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb1-1"><a href="#cb1-1"></a><span class="co"># SSH connection to Rossinante ----</span></span>
<span id="cb1-2"><a href="#cb1-2"></a><span class="fu">ssh</span> <span class="at">-p</span> 22 [email protected]</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>When you first connect to Rossinante (and to any remote server), you will be asked if you trust this server:</p>
<pre><code>The authenticity of host '[92.168.45.3]:22' can't be established.
Expand Down Expand Up @@ -360,7 +361,7 @@ <h2 data-number="2.2" class="anchored" data-anchor-id="ssh-config-file"><span cl
<span id="cb5-4"><a href="#cb5-4"></a><span class="co"># Check if the folder .ssh/ exists ----</span></span>
<span id="cb5-5"><a href="#cb5-5"></a><span class="fu">ls</span> <span class="at">-al</span></span>
<span id="cb5-6"><a href="#cb5-6"></a></span>
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># Create a new hidden folder (if required) ----</span></span>
<span id="cb5-7"><a href="#cb5-7"></a><span class="co"># Create a new hidden folder (if not already existing) ----</span></span>
<span id="cb5-8"><a href="#cb5-8"></a><span class="fu">mkdir</span> <span class="at">-p</span> ~/.ssh</span>
<span id="cb5-9"><a href="#cb5-9"></a></span>
<span id="cb5-10"><a href="#cb5-10"></a><span class="co"># Change folder permissions ----</span></span>
Expand Down Expand Up @@ -445,23 +446,23 @@ <h2 data-number="2.4" class="anchored" data-anchor-id="git-credentials"><span cl
<section id="github-ssh-keys" class="level2" data-number="2.5">
<h2 data-number="2.5" class="anchored" data-anchor-id="github-ssh-keys"><span class="header-section-number">2.5</span> GitHub SSH keys</h2>
<p>If you want to communicate with GitHub through the SSH protocol (recommended) you need to generate a new SSH keys pair (different from the one used to connect to Rossinante).</p>
<p>Let’s create a new SSH keys pair using the cryptosystem <code>RSA</code> and a key size of <code>4096</code> bits. But this time, this SSH keys pair will be generated <strong>on Rossinante</strong>.</p>
<p>Let’s create a new SSH keys pair using the cryptosystem <code>ed25519</code>. But this time, this SSH keys pair will be generated <strong>on Rossinante</strong>.</p>
<div class="sourceCode" id="cb17"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb17-1"><a href="#cb17-1"></a><span class="co"># Create a new SSH key pair (on Rossinante) ----</span></span>
<span id="cb17-2"><a href="#cb17-2"></a><span class="fu">ssh-keygen</span> <span class="at">-f</span> ~/.ssh/id_rsa <span class="at">-t</span> rsa <span class="at">-b</span> 4096 <span class="at">-C</span> <span class="st">"[email protected]"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb17-2"><a href="#cb17-2"></a><span class="fu">ssh-keygen</span> <span class="at">-f</span> ~/.ssh/id_ed25519 <span class="at">-t</span> ed25519 <span class="at">-C</span> <span class="st">"[email protected]"</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>This new SSH keys pair has been stored in <code>~/.ssh/</code>.</p>
<div class="sourceCode" id="cb18"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb18-1"><a href="#cb18-1"></a><span class="co"># Content of the ~/.ssh folder ----</span></span>
<span id="cb18-2"><a href="#cb18-2"></a><span class="fu">ls</span> ~/.ssh</span>
<span id="cb18-3"><a href="#cb18-3"></a><span class="co">## authorized_keys id_rsa id_rsa.pub</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb18-3"><a href="#cb18-3"></a><span class="co">## authorized_keys id_ed25519 id_ed25519.pub</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Let’s restrict the access to the private key.</p>
<div class="sourceCode" id="cb19"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb19-1"><a href="#cb19-1"></a><span class="co"># Change private key permissions ----</span></span>
<span id="cb19-2"><a href="#cb19-2"></a><span class="co"># (only jdoe can only read this file)</span></span>
<span id="cb19-3"><a href="#cb19-3"></a><span class="fu">chmod</span> 400 ~/.ssh/id_rsa</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb19-3"><a href="#cb19-3"></a><span class="fu">chmod</span> 400 ~/.ssh/id_ed25519</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Now we need to store the public key on GitHub server. Visit <a href="https://github.com/settings/keys">https://github.com/settings/keys</a> and click on <strong>New SSH key</strong>.</p>
<p>On Rossinante, print the <strong>public</strong> SSH key:</p>
<div class="sourceCode" id="cb20"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb20-1"><a href="#cb20-1"></a><span class="co"># Print the public SSH key ----</span></span>
<span id="cb20-2"><a href="#cb20-2"></a><span class="fu">cat</span> ~/.ssh/id_rsa.pub</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<span id="cb20-2"><a href="#cb20-2"></a><span class="fu">cat</span> ~/.ssh/id_ed25519.pub</span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
<p>Copy the content of the public key and go back to GitHub. Give a title to your new SSH key (for example <em>Rossinante key</em>) and paste your public SSH key. Click on <strong>Add SSH key</strong>.</p>
<p>Congratulation! You can know communicate with GitHub using the SSH protocol from Rossinante. Let’s test the SSH connection between Rossinante and GitHub:</p>
<p><strong>Congratulations!</strong> You can know communicate with GitHub using the SSH protocol from Rossinante. Let’s test the SSH connection between Rossinante and GitHub:</p>
<div class="sourceCode" id="cb21"><pre class="sourceCode numberSource bash number-lines code-with-copy"><code class="sourceCode bash"><span id="cb21-1"><a href="#cb21-1"></a><span class="co"># Test SSH connection between Rossinante and GitHub ----</span></span>
<span id="cb21-2"><a href="#cb21-2"></a><span class="fu">ssh</span> <span class="at">-T</span> [email protected]</span>
<span id="cb21-3"><a href="#cb21-3"></a><span class="co">## Hi janedoe! You've successfully authenticated!, but GitHub does not provide shell access.</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
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6 changes: 3 additions & 3 deletions index.html
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<meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">

<meta name="author" content="Nicolas Casajus">
<meta name="dcterms.date" content="2024-07-24">
<meta name="dcterms.date" content="2024-07-25">
<meta name="description" content="A user guide to learn how to use the FRB-CESAB server">

<title>Rossinante Book</title>
Expand Down Expand Up @@ -264,7 +264,7 @@ <h1 class="title">Rossinante Book</h1>
<div>
<div class="quarto-title-meta-heading">Published</div>
<div class="quarto-title-meta-contents">
<p class="date">July 24, 2024</p>
<p class="date">July 25, 2024</p>
</div>
</div>

Expand All @@ -284,7 +284,7 @@ <h1 class="title">Rossinante Book</h1>
</div>
<section id="welcome" class="level1 unnumbered">
<h1 class="unnumbered">Welcome</h1>
<p>The purpose of this book is to show how to use the FRB-CESAB server <strong>Rossinante</strong>, dedicated to <em>medium</em> performance scientific computing.</p>
<p>The purpose of this book is to show how to use the FRB-CESAB server <strong>Rossinante</strong>, dedicated to scientific computing.</p>

<div class="hidden quarto-markdown-envelope-contents" data-render-id="footer-right-https://github.com/frbcesab/rossinante">
<p>Code source &nbsp;<i class="bi bi-github" role="img"></i></p>
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