trying push again

gafusion · Jan 16, 2024 · 9f764f1 · 9f764f1
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diff --git a/docs/build.html b/docs/build.html
@@ -7,7 +7,7 @@
   <title>Build from sources &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="_static/documentation_options.js?v=5929fcd5"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js?v=9ee86694"></script>
+        <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />
@@ -54,7 +54,9 @@
 <li class="toctree-l1"><a class="reference internal" href="setup.html">Environment setup</a></li>
 <li class="toctree-l1 current"><a class="current reference internal" href="#">Build from sources</a><ul>
 <li class="toctree-l2"><a class="reference internal" href="#prerequisites">Prerequisites</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#concept-of-platform-files">Concept of platform files</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#environment-variables">Environment variables</a></li>
+<li class="toctree-l2"><a class="reference internal" href="#openblas">OpenBLAS</a></li>
 <li class="toctree-l2"><a class="reference internal" href="#building">Building</a></li>
 </ul>
 </li>
@@ -110,37 +112,43 @@ <h2>Prerequisites<a class="headerlink" href="#prerequisites" title="Link to this
 </pre></div>
 </div>
 </section>
-<section id="environment-variables">
-<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Link to this heading"></a></h2>
-<p>First, you need to locate a suitable platform, or make your own platform files.  After cloning the repository, you can query the existing platforms using:</p>
+<section id="concept-of-platform-files">
+<h2>Concept of platform files<a class="headerlink" href="#concept-of-platform-files" title="Link to this heading"></a></h2>
+<p>In order to compile the full GACODE package on a new machine, <strong>platform files</strong> must be created. You can use existing ones or create your own.  After cloning the repository, you can query the existing platforms using:</p>
 <div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ ./gacode/shared/bin/gacode_platforms
 </pre></div>
 </div>
-<p>In order to compile the full GACODE package on a new machine, <strong>platform files</strong> must be created.  Let’s imagine you have a new laptop, and you want this platform to be known as MY_PC.  In this case you’ll need these lines in your shell RC file:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export GACODE_PLATFORM=MY_PC
-export GACODE_ROOT=$HOME/gacode
-. $GACODE_ROOT/shared/bin/gacode_setup
-</pre></div>
-</div>
-<p>Then you must create the following files:</p>
-<ol class="arabic">
-<li><p>Machine-specific compilation options:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$GACODE_ROOT/platform/build/make.inc.MY_PC
+<p>To create new platform files (say, for a new platform MINE) then copy/edit the following files:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$GACODE_ROOT/platform/build/make.inc.MINE
+$GACODE_ROOT/platform/exec/exec.MINE
+$GACODE_ROOT/platform/env/env.MINE (if needed)
 </pre></div>
 </div>
-</li>
-<li><p>Parallel execution command syntax:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$GACODE_ROOT/platform/exec/exec.MY_PC
+<p>Numerous templates for each of these files can be found in the specific folders, and most often there will be an existing machine files that is almost exactly what you need</p>
+</section>
+<section id="environment-variables">
+<h2>Environment variables<a class="headerlink" href="#environment-variables" title="Link to this heading"></a></h2>
+<p>To use your new platform files, enter the following lines in your shell RC file:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>export GACODE_PLATFORM=MINE
+export GACODE_ROOT=$HOME/gacode
+. $GACODE_ROOT/shared/bin/gacode_setup
+. $GACODE_ROOT/platform/env/env.MINE (if needed)
 </pre></div>
 </div>
-</li>
-<li><p>Any module load commands (optional) go here:</p>
-<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$GACODE_ROOT/platform/env/env.MY_PC
+</section>
+<section id="openblas">
+<h2>OpenBLAS<a class="headerlink" href="#openblas" title="Link to this heading"></a></h2>
+<p>When building with gfortran, we recommend using <a class="reference external" href="https://github.com/xianyi/OpenBLAS.git">OpenBLAS</a>. It is important to build with <strong>single-threaded</strong> settings. In the Makefile.rule file in the top-level OpenBLAS directory, set:</p>
+<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">FC</span><span class="o">=</span><span class="n">gfortran</span>
+<span class="n">BINARY</span><span class="o">=</span><span class="mi">64</span>
+<span class="n">USE_THREAD</span><span class="o">=</span><span class="mi">0</span>
+<span class="n">NUM_THREADS</span><span class="o">=</span><span class="mi">1</span>
+<span class="n">NO_SHARED</span><span class="o">=</span><span class="mi">1</span>
+<span class="n">NO_CBLAS</span><span class="o">=</span><span class="mi">1</span>
+<span class="n">NO_LAPACKE</span><span class="o">=</span><span class="mi">1</span>
 </pre></div>
 </div>
-</li>
-</ol>
-<p>Numerous templates for each of these files can be found in the specific folders, and most often there will be an existing machine files that is almost exactly what you need.  So, the strategy is to copy a similar machine file to your new one, and tweak as required.</p>
+<p>You can find an example of linking to OpenBLAS in platform/build/make.inc.MINT.</p>
 </section>
 <section id="building">
 <h2>Building<a class="headerlink" href="#building" title="Link to this heading"></a></h2>

diff --git a/docs/cgyro.html b/docs/cgyro.html
@@ -7,7 +7,7 @@
   <title>CGYRO &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="_static/documentation_options.js?v=5929fcd5"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js?v=9ee86694"></script>
+        <script src="_static/contentui.js"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />

diff --git a/docs/cgyro/FAQ.html b/docs/cgyro/FAQ.html
@@ -7,7 +7,7 @@
   <title>FAQ &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />

diff --git a/docs/cgyro/cgyro_cori.html b/docs/cgyro/cgyro_cori.html
@@ -7,7 +7,7 @@
   <title>Running CGYRO on NERSC Cori &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 

diff --git a/docs/cgyro/cgyro_list.html b/docs/cgyro/cgyro_list.html
@@ -7,7 +7,7 @@
   <title>Alphabetical list for input.cgyro &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />

diff --git a/docs/cgyro/cgyro_table.html b/docs/cgyro/cgyro_table.html
@@ -7,7 +7,7 @@
   <title>Tabular list for input.cgyro &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />

diff --git a/docs/cgyro/cgyro_titan.html b/docs/cgyro/cgyro_titan.html
@@ -7,7 +7,7 @@
   <title>Running CGYRO on OLCF Titan (deprecated) &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 

diff --git a/docs/cgyro/outputs.html b/docs/cgyro/outputs.html
@@ -7,7 +7,7 @@
   <title>CGYRO output files &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />

diff --git a/docs/cgyro/running_cases.html b/docs/cgyro/running_cases.html
@@ -7,7 +7,7 @@
   <title>Running Cases &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" /> 

diff --git a/docs/download.html b/docs/download.html
@@ -7,7 +7,7 @@
   <title>Download and user agreement &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="_static/documentation_options.js?v=5929fcd5"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js?v=9ee86694"></script>
+        <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />

diff --git a/docs/genindex.html b/docs/genindex.html
@@ -6,7 +6,7 @@
   <title>Index &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="_static/favicon.ico"/>
@@ -19,7 +19,7 @@
         <script src="_static/documentation_options.js?v=5929fcd5"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js?v=9ee86694"></script>
+        <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="#" />
     <link rel="search" title="Search" href="search.html" /> 

diff --git a/docs/geometry.html b/docs/geometry.html
@@ -7,7 +7,7 @@
   <title>FLUX-SURFACE GEOMETRY &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="_static/documentation_options.js?v=5929fcd5"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js?v=9ee86694"></script>
+        <script src="_static/contentui.js"></script>
         <script async="async" src="https://cdn.jsdelivr.net/npm/mathjax@3/es5/tex-mml-chtml.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />

diff --git a/docs/gyro.html b/docs/gyro.html
@@ -7,7 +7,7 @@
   <title>GYRO &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="_static/documentation_options.js?v=5929fcd5"></script>
         <script src="_static/doctools.js?v=888ff710"></script>
         <script src="_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="_static/contentui.js?v=9ee86694"></script>
+        <script src="_static/contentui.js"></script>
     <script src="_static/js/theme.js"></script>
     <link rel="index" title="Index" href="genindex.html" />
     <link rel="search" title="Search" href="search.html" />

diff --git a/docs/gyro/gyro_gallery.html b/docs/gyro/gyro_gallery.html
@@ -7,7 +7,7 @@
   <title>Gallery of classic GYRO images (circa 2003) &mdash; GACODE</title>
       <link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=fa44fd50" />
       <link rel="stylesheet" type="text/css" href="../_static/css/theme.css?v=19f00094" />
-      <link rel="stylesheet" type="text/css" href="../_static/contentui.css?v=4cf5b151" />
+      <link rel="stylesheet" type="text/css" href="../_static/contentui.css" />
 
 
     <link rel="shortcut icon" href="../_static/favicon.ico"/>
@@ -20,7 +20,7 @@
         <script src="../_static/documentation_options.js?v=5929fcd5"></script>
         <script src="../_static/doctools.js?v=888ff710"></script>
         <script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
-        <script src="../_static/contentui.js?v=9ee86694"></script>
+        <script src="../_static/contentui.js"></script>
     <script src="../_static/js/theme.js"></script>
     <link rel="index" title="Index" href="../genindex.html" />
     <link rel="search" title="Search" href="../search.html" />