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Merged
merged 4 commits into from
Mar 2, 2025
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Document NL_SINGLE_FLAG and add conda build instructions #7

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0bf8b0e
Document NL_SINGLE_FLAG
sfiligoi Mar 2, 2025
e76e95d
Fix defaults
sfiligoi Mar 2, 2025
f7e9347
Add conda build instructions
sfiligoi Mar 2, 2025
896970e
Rebuild html files
sfiligoi Mar 2, 2025
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4 changes: 2 additions & 2 deletions docs/.buildinfo
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# Sphinx build info version 1
# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 42f11e50cbc4f08b64c4600c66d325f5
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 2e9c92f25ca4f7071953c982cc4cb35f
tags: 645f666f9bcd5a90fca523b33c5a78b7
22 changes: 12 additions & 10 deletions docs/README.html
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<!DOCTYPE html>
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<meta charset="utf-8" /><meta name="viewport" content="width=device-width, initial-scale=1" />

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33 changes: 20 additions & 13 deletions docs/build.html
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<!DOCTYPE html>
<html class="writer-html5" lang="en" data-content_root="./">
<head>
<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>Build on your laptop &mdash; GACODE</title>
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Expand Down Expand Up @@ -109,6 +111,7 @@ <h2>First step<a class="headerlink" href="#first-step" title="Link to this headi
<ul class="simple">
<li><p><a class="reference internal" href="build/pre_osx.html"><span class="doc">OSX users</span></a> (MAC M2)</p></li>
<li><p><a class="reference internal" href="build/pre_linux.html"><span class="doc">Linux users</span></a> (MINT, UBUNTU)</p></li>
<li><p><a class="reference internal" href="build/pre_conda.html"><span class="doc">Conda users, works on both OSX and Linux</span></a> (CONDA_OMPI_GNU)</p></li>
</ul>
<p>If you need more help, please raise an issue at <a class="reference external" href="https://github.com/gafusion/gacode/issues">https://github.com/gafusion/gacode/issues</a></p>
</section>
Expand All @@ -121,11 +124,11 @@ <h2>Source code<a class="headerlink" href="#source-code" title="Link to this hea
</section>
<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>
<p>In order to compile the full GACODE package on a new machine, a version of the <strong>platform files</strong> must be selected. 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>To create new platform files (say, for a new platform MINE) then copy/edit the following files:</p>
<p>If you decide to create new platform files (say, for a new platform MINE) then create the following files, starting from one of the existing ones (say, CONDA_OMPI_GNU):</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
$GACODE_ROOT/platform/env/env.MINE (if needed)
Expand All @@ -145,7 +148,7 @@ <h2>Environment variables<a class="headerlink" href="#environment-variables" tit
</section>
<section id="openblas">
<h2>OpenBLAS<a class="headerlink" href="#openblas" title="Link to this heading"></a></h2>
<p>When building with gfortran, we recommend using <a class="reference external" href="https://github.com/xianyi/OpenBLAS.git">OpenBLAS</a>. It is important to build with <strong>single-threaded</strong> settings. In the Makefile.rule file in the top-level OpenBLAS directory, set:</p>
<p>Using system provided builds is better, but when building from scrath with gfortran, we recommend using <a class="reference external" href="https://github.com/xianyi/OpenBLAS.git">OpenBLAS</a>. It is important to build with <strong>single-threaded</strong> settings. In the Makefile.rule file in the top-level OpenBLAS directory, set:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">BINARY</span><span class="o">=</span><span class="mi">64</span>
<span class="n">USE_THREAD</span><span class="o">=</span><span class="mi">0</span>
<span class="n">USE_LOCKING</span><span class="o">=</span><span class="mi">1</span>
Expand All @@ -167,6 +170,10 @@ <h2>Building<a class="headerlink" href="#building" title="Link to this heading">
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cd $GACODE_ROOT ; make
</pre></div>
</div>
<p>To build just one of the tools, go into the specific subdirectory:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ cd $GACODE_ROOT/cgyro ; make
</pre></div>
</div>
<p>To test that the build is successful, you can run regression tests:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ neo -r
$ tglf -r
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143 changes: 143 additions & 0 deletions docs/build/pre_conda.html
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<section id="conda-setup">
<h1>Conda setup<a class="headerlink" href="#conda-setup" title="Link to this heading"></a></h1>
<p>The conda setup can be used as a regular user (no sudo privileges needed), and works on both OSX and Linux.</p>
<p>If you do not have an existing conda setup yet, download and install Miniconda from <a class="reference external" href="https://www.anaconda.com/download/">https://www.anaconda.com/download/</a></p>
<p>Once inside the conda setup, create the conda gacode environment.</p>
<p>On Linux:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ conda create -n gacode -c conda-forge gfortran binutils make python fftw openmpi netcdf4 libopenblas=*=*openmp*
</pre></div>
</div>
<p>On OSX:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ conda create -n gacode -c conda-forge gfortran make python fftw openmpi netcdf4
</pre></div>
</div>
<p>Since many conda environment can co-exist on a single machine, activate the gacode one when using the GACODE tools:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span>$ conda activate gacode
</pre></div>
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