deploy: 10eb3d1

_sources/cluster.rst.txt

@@ -1,8 +1,8 @@
-Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)
-===============================================================================
+Running in Jupyter Notebook on a HPC platform
+=============================================
 
 .. note::
-   This example is based on CSD3 for people associated with the University of Cambridge but the workflow can mostly be applied to other clusters as well.
+   This example is based on CSD3 for people associated with the University of Cambridge but the workflow can be applied to other HPC clusters.
 
 This guide provides step-by-step instructions on how to set up a virtual environment for Jupyter Notebook on an HPC system, run Jupyter Notebook on both login and compute nodes, install the ``detectree2`` package, and run it on a GPU compute node.
 

cluster.html

@@ -6,7 +6,7 @@
   <meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />
 
   <meta name="viewport" content="width=device-width, initial-scale=1.0" />
-  <title>4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3) &mdash; detectree2 1.0.8 documentation</title>
+  <title>4. Running in Jupyter Notebook on a HPC platform &mdash; detectree2 1.0.8 documentation</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=80d5e7a1" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=e59714d7" />
 
@@ -48,7 +48,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1 current"><a class="current reference internal" href="#">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a><ul>
+<li class="toctree-l1 current"><a class="current reference internal" href="#">4. Running in Jupyter Notebook on a HPC platform</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#setting-up-a-virtual-environment-for-jupyter-notebook">4.1. Setting Up a Virtual Environment for Jupyter Notebook</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#running-jupyter-notebook-on-the-login-node-cpu-only">4.2. Running Jupyter Notebook on the Login Node (CPU Only)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#running-jupyter-notebook-on-a-compute-node-cpu-or-gpu">4.3. Running Jupyter Notebook on a Compute Node (CPU or GPU)</a></li>
@@ -74,7 +74,7 @@
           <div role="navigation" aria-label="Page navigation">
   <ul class="wy-breadcrumbs">
       <li><a href="index.html" class="icon icon-home" aria-label="Home"></a></li>
-      <li class="breadcrumb-item active"><span class="section-number">4. </span>Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</li>
+      <li class="breadcrumb-item active"><span class="section-number">4. </span>Running in Jupyter Notebook on a HPC platform</li>
       <li class="wy-breadcrumbs-aside">
             <a href="_sources/cluster.rst.txt" rel="nofollow"> View page source</a>
       </li>
@@ -84,17 +84,17 @@
           <div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
            <div itemprop="articleBody">
 
-  <section id="running-jupyter-notebook-and-installing-detectree2-on-a-hpc-platform-like-csd3">
-<h1><a class="toc-backref" href="#id1" role="doc-backlink"><span class="section-number">4. </span>Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a><a class="headerlink" href="#running-jupyter-notebook-and-installing-detectree2-on-a-hpc-platform-like-csd3" title="Link to this heading"></a></h1>
+  <section id="running-in-jupyter-notebook-on-a-hpc-platform">
+<h1><a class="toc-backref" href="#id1" role="doc-backlink"><span class="section-number">4. </span>Running in Jupyter Notebook on a HPC platform</a><a class="headerlink" href="#running-in-jupyter-notebook-on-a-hpc-platform" title="Link to this heading"></a></h1>
 <div class="admonition note">
 <p class="admonition-title">Note</p>
-<p>This example is based on CSD3 for people associated with the University of Cambridge but the workflow can mostly be applied to other clusters as well.</p>
+<p>This example is based on CSD3 for people associated with the University of Cambridge but the workflow can be applied to other HPC clusters.</p>
 </div>
 <p>This guide provides step-by-step instructions on how to set up a virtual environment for Jupyter Notebook on an HPC system, run Jupyter Notebook on both login and compute nodes, install the <code class="docutils literal notranslate"><span class="pre">detectree2</span></code> package, and run it on a GPU compute node.</p>
 <nav class="contents" id="contents">
 <p class="topic-title">Contents</p>
 <ul class="simple">
-<li><p><a class="reference internal" href="#running-jupyter-notebook-and-installing-detectree2-on-a-hpc-platform-like-csd3" id="id1">Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></p>
+<li><p><a class="reference internal" href="#running-in-jupyter-notebook-on-a-hpc-platform" id="id1">Running in Jupyter Notebook on a HPC platform</a></p>
 <ul>
 <li><p><a class="reference internal" href="#setting-up-a-virtual-environment-for-jupyter-notebook" id="id2">Setting Up a Virtual Environment for Jupyter Notebook</a></p></li>
 <li><p><a class="reference internal" href="#running-jupyter-notebook-on-the-login-node-cpu-only" id="id3">Running Jupyter Notebook on the Login Node (CPU Only)</a></p></li>

contributing.html

@@ -21,7 +21,7 @@
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
     <link rel="next" title="6. Git/Github" href="using-git.html" />
-    <link rel="prev" title="4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)" href="cluster.html" /> 
+    <link rel="prev" title="4. Running in Jupyter Notebook on a HPC platform" href="cluster.html" /> 
 </head>
 
 <body class="wy-body-for-nav"> 
@@ -48,7 +48,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">5. Contributing guide</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#contributing-to-detectree2">5.1. Contributing to Detectree2</a><ul>
 <li class="toctree-l3"><a class="reference internal" href="#code-of-conduct">5.1.1. Code of Conduct</a></li>
@@ -655,7 +655,7 @@ <h2><a class="toc-backref" href="#id50" role="doc-backlink"><span class="section
            </div>
           </div>
           <footer><div class="rst-footer-buttons" role="navigation" aria-label="Footer">
-        <a href="cluster.html" class="btn btn-neutral float-left" title="4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
+        <a href="cluster.html" class="btn btn-neutral float-left" title="4. Running in Jupyter Notebook on a HPC platform" accesskey="p" rel="prev"><span class="fa fa-arrow-circle-left" aria-hidden="true"></span> Previous</a>
         <a href="using-git.html" class="btn btn-neutral float-right" title="6. Git/Github" accesskey="n" rel="next">Next <span class="fa fa-arrow-circle-right" aria-hidden="true"></span></a>
     </div>
 

detectree2.data_loading.html

@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

detectree2.html

@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

detectree2.models.html

@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

detectree2.preprocessing.html

@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

detectree2.tests.html

@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

genindex.html

@@ -45,7 +45,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

index.html

@@ -49,7 +49,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>
@@ -122,7 +122,7 @@ <h2>Citation<a class="headerlink" href="#citation" title="Link to this heading">
 <li class="toctree-l2"><a class="reference internal" href="tutorial_multi.html#landscape-predictions">3.3. Landscape predictions</a></li>
 </ul>
 </li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a><ul>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="cluster.html#setting-up-a-virtual-environment-for-jupyter-notebook">4.1. Setting Up a Virtual Environment for Jupyter Notebook</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cluster.html#running-jupyter-notebook-on-the-login-node-cpu-only">4.2. Running Jupyter Notebook on the Login Node (CPU Only)</a></li>
 <li class="toctree-l2"><a class="reference internal" href="cluster.html#running-jupyter-notebook-on-a-compute-node-cpu-or-gpu">4.3. Running Jupyter Notebook on a Compute Node (CPU or GPU)</a></li>

installation.html

@@ -58,7 +58,7 @@
 </li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

modules.html

@@ -46,7 +46,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

py-modindex.html

@@ -48,7 +48,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

search.html

@@ -48,7 +48,7 @@
 <li class="toctree-l1"><a class="reference internal" href="installation.html">1. Installation</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial.html">2. Tutorial</a></li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>

tutorial.html

@@ -60,7 +60,7 @@
 </ul>
 </li>
 <li class="toctree-l1"><a class="reference internal" href="tutorial_multi.html">3. Tutorial (multiclass)</a></li>
-<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running Jupyter Notebook and Installing Detectree2 on a HPC platform (like CSD3)</a></li>
+<li class="toctree-l1"><a class="reference internal" href="cluster.html">4. Running in Jupyter Notebook on a HPC platform</a></li>
 <li class="toctree-l1"><a class="reference internal" href="contributing.html">5. Contributing guide</a></li>
 <li class="toctree-l1"><a class="reference internal" href="using-git.html">6. Git/Github</a></li>
 </ul>