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<section id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Link to this heading">#</a></h1>
<p>To install <code class="docutils literal notranslate"><span class="pre">madupite</span></code>, first clone the repository from GitHub:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">madupite</span><span class="o">/</span><span class="n">madupite</span><span class="o">.</span><span class="n">git</span>
</pre></div>
</div>
<section id="dependencies">
<h2>Dependencies<a class="headerlink" href="#dependencies" title="Link to this heading">#</a></h2>
<p>You need to make sure that the dependencies are available. A convenient way of installing them is via the conda environment file, which you can find in the repo. Make sure you have an updated version of conda installed, then run the following commands:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">cd</span> <span class="n">madupite</span>
<span class="n">conda</span> <span class="n">env</span> <span class="n">create</span> <span class="o">-</span><span class="n">f</span> <span class="n">environment</span><span class="o">.</span><span class="n">yml</span>
<span class="n">conda</span> <span class="n">activate</span> <span class="n">madupiteenv</span>
</pre></div>
</div>
<p>Users who want to use their own PETSc or MPI version should make sure that cmake can find them.</p>
</section>
<section id="python-package">
<h2>Python package<a class="headerlink" href="#python-package" title="Link to this heading">#</a></h2>
<p>After installing the necessary dependencies you can install <code class="docutils literal notranslate"><span class="pre">madupite</span></code> for Python via pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">.</span>
</pre></div>
</div>
<p>Make sure to run your executables with <code class="docutils literal notranslate"><span class="pre">mpirun</span></code> if you want to run them exploiting parallel-computing. <code class="docutils literal notranslate"><span class="pre"><number_of_ranks></span></code> could be the number of cores on your machine. If you want to check whether your installation was successful, you can run the following command:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">n</span> <span class="o"><</span><span class="n">number_of_ranks</span><span class="o">></span> <span class="n">python</span> <span class="n">examples</span><span class="o">/</span><span class="n">install</span><span class="o">/</span><span class="n">main</span><span class="o">.</span><span class="n">py</span>
</pre></div>
</div>
</section>
<section id="c">
<h2>C++<a class="headerlink" href="#c" title="Link to this heading">#</a></h2>
<p>For advanced users who want to use the software from C++, they should make sure to have a working PETSc installation. From there, you can proceed to build the project using CMake as follows:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="n">build</span>
<span class="n">cd</span> <span class="n">build</span>
<span class="n">cmake</span> <span class="o">..</span>
<span class="n">make</span>
</pre></div>
</div>
<p>Make sure to run your executables with <code class="docutils literal notranslate"><span class="pre">mpirun</span></code>. <code class="docutils literal notranslate"><span class="pre"><number_of_ranks></span></code> could be the number of cores on your machine:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mpirun</span> <span class="o">-</span><span class="n">n</span> <span class="o"><</span><span class="n">number_of_ranks</span><span class="o">></span> <span class="o">./</span><span class="n">build</span><span class="o">/</span><span class="n">main</span>
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>As of now, only the Python API is documented. However, C++ users can refer to the examples provided in the <code class="docutils literal notranslate"><span class="pre">examples</span></code> folder for guidance.</p>
</div>
</section>
<section id="euler-eth-zurich-cluster">
<h2>Euler (ETH Zurich Cluster)<a class="headerlink" href="#euler-eth-zurich-cluster" title="Link to this heading">#</a></h2>
<p><strong>Python Version:</strong></p>
<p>To install the Python package on the Euler cluster, access a login node and clone the repository</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">git</span> <span class="n">clone</span> <span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">github</span><span class="o">.</span><span class="n">com</span><span class="o">/</span><span class="n">madupite</span><span class="o">/</span><span class="n">madupite</span><span class="o">.</span><span class="n">git</span>
</pre></div>
</div>
<p>Load the necessary software modules:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">source</span> <span class="o">./</span><span class="n">examples</span><span class="o">/</span><span class="n">euler</span><span class="o">/</span><span class="n">euler</span><span class="o">-</span><span class="n">load</span><span class="o">-</span><span class="n">modules</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
<p>Then, install the Python package using pip:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">pip</span> <span class="n">install</span> <span class="o">.</span>
</pre></div>
</div>
<p><strong>Jupyter Notebook:</strong></p>
<p>If you want to use <code class="docutils literal notranslate"><span class="pre">madupite</span></code> with <cite>JupyterHub on Euler</cite> you need to install the python package as shown above. After that, copy the module load script to Jupyter.</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="o">-</span><span class="n">p</span> <span class="o">~/.</span><span class="n">config</span><span class="o">/</span><span class="n">euler</span><span class="o">/</span><span class="n">jupyterhub</span><span class="o">/</span><span class="n">jupyterlabrc</span>
<span class="n">cp</span> <span class="o">~/</span><span class="n">madupite</span><span class="o">/</span><span class="n">examples</span><span class="o">/</span><span class="n">euler</span><span class="o">/</span><span class="n">euler</span><span class="o">-</span><span class="n">load</span><span class="o">-</span><span class="n">modules</span><span class="o">.</span><span class="n">sh</span> <span class="o">~/.</span><span class="n">config</span><span class="o">/</span><span class="n">euler</span><span class="o">/</span><span class="n">jupyterhub</span><span class="o">/</span><span class="n">jupyterlabrc</span>
</pre></div>
</div>
<p>Now, you can leave the login node and go to <a class="reference external" href="https://jupyter.euler.hpc.ethz.ch/">JupyterHub on Euler</a>.</p>
<p><strong>C++ Version:</strong></p>
<p>To build the C++ project on the Euler cluster, load the necessary software modules:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">source</span> <span class="o">./</span><span class="n">examples</span><span class="o">/</span><span class="n">euler</span><span class="o">/</span><span class="n">euler</span><span class="o">-</span><span class="n">load</span><span class="o">-</span><span class="n">modules</span><span class="o">.</span><span class="n">sh</span>
</pre></div>
</div>
<p>Then, follow the same steps as for the general C++ installation:</p>
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="n">mkdir</span> <span class="n">build</span>
<span class="n">cd</span> <span class="n">build</span>
<span class="n">cmake</span> <span class="o">..</span>
<span class="n">make</span>
</pre></div>
</div>
<p>The repository contains an example launch file <cite>examples/euler/euler-launch.sh</cite> to run the executables on the Euler cluster.</p>
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