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<section id="running-lammps-and-python-in-serial">
<h1><span class="section-number">2.3.1. </span>Running LAMMPS and Python in serial<a class="headerlink" href="#running-lammps-and-python-in-serial" title="Link to this heading"></a></h1>
<p>To run a LAMMPS in serial, type these lines into Python
interactively from the <code class="docutils literal notranslate"><span class="pre">bench</span></code> directory:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">lammps</span><span class="w"> </span><span class="kn">import</span> <span class="n">lammps</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">&quot;in.lj&quot;</span><span class="p">)</span>
</pre></div>
</div>
<p>Or put the same lines in the file <code class="docutils literal notranslate"><span class="pre">test.py</span></code> and run it as</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python3<span class="w"> </span>test.py
</pre></div>
</div>
<p>Either way, you should see the results of running the <code class="docutils literal notranslate"><span class="pre">in.lj</span></code> benchmark
on a single processor appear on the screen, the same as if you had
typed something like:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>lmp_serial<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.lj
</pre></div>
</div>
</section>
<section id="running-lammps-and-python-in-parallel-with-mpi">
<h1><span class="section-number">2.3.2. </span>Running LAMMPS and Python in parallel with MPI<a class="headerlink" href="#running-lammps-and-python-in-parallel-with-mpi" title="Link to this heading"></a></h1>
<p>To run LAMMPS in parallel, assuming you have installed the
<a class="reference external" href="https://mpi4py.readthedocs.io">mpi4py</a> package as discussed
<a class="reference internal" href="Python_install.html#python-install-mpi4py"><span class="std std-ref">Extending Python to run in parallel</span></a>, create a <code class="docutils literal notranslate"><span class="pre">test.py</span></code> file containing these lines:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">mpi4py</span><span class="w"> </span><span class="kn">import</span> <span class="n">MPI</span>
<span class="kn">from</span><span class="w"> </span><span class="nn">lammps</span><span class="w"> </span><span class="kn">import</span> <span class="n">lammps</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">&quot;in.lj&quot;</span><span class="p">)</span>
<span class="n">me</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_rank</span><span class="p">()</span>
<span class="n">nprocs</span> <span class="o">=</span> <span class="n">MPI</span><span class="o">.</span><span class="n">COMM_WORLD</span><span class="o">.</span><span class="n">Get_size</span><span class="p">()</span>
<span class="nb">print</span><span class="p">(</span><span class="s2">&quot;Proc </span><span class="si">%d</span><span class="s2"> out of </span><span class="si">%d</span><span class="s2"> procs has&quot;</span> <span class="o">%</span> <span class="p">(</span><span class="n">me</span><span class="p">,</span><span class="n">nprocs</span><span class="p">),</span><span class="n">lmp</span><span class="p">)</span>
<span class="n">MPI</span><span class="o">.</span><span class="n">Finalize</span><span class="p">()</span>
</pre></div>
</div>
<p>You can run the script in parallel as:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mpirun<span class="w"> </span>-np<span class="w"> </span><span class="m">4</span><span class="w"> </span>python3<span class="w"> </span>test.py
</pre></div>
</div>
<p>and you should see the same output as if you had typed</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>mpirun<span class="w"> </span>-np<span class="w"> </span><span class="m">4</span><span class="w"> </span>lmp_mpi<span class="w"> </span>-in<span class="w"> </span><span class="k">in</span>.lj
</pre></div>
</div>
<p>Note that without the mpi4py specific lines from <code class="docutils literal notranslate"><span class="pre">test.py</span></code></p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">from</span><span class="w"> </span><span class="nn">lammps</span><span class="w"> </span><span class="kn">import</span> <span class="n">lammps</span>
<span class="n">lmp</span> <span class="o">=</span> <span class="n">lammps</span><span class="p">()</span>
<span class="n">lmp</span><span class="o">.</span><span class="n">file</span><span class="p">(</span><span class="s2">&quot;in.lj&quot;</span><span class="p">)</span>
</pre></div>
</div>
<p>running the script with <code class="docutils literal notranslate"><span class="pre">mpirun</span></code> on <span class="math notranslate nohighlight">\(P\)</span> processors would lead to
<span class="math notranslate nohighlight">\(P\)</span> independent simulations to run parallel, each with a single
processor. Therefore, if you use the mpi4py lines and you see multiple LAMMPS
single processor outputs, mpi4py is not working correctly.</p>
<p>Also note that once you import the mpi4py module, mpi4py initializes MPI
for you, and you can use MPI calls directly in your Python script, as
described in the mpi4py documentation. The last line of your Python
script should be <code class="docutils literal notranslate"><span class="pre">MPI.finalize()</span></code>, to ensure MPI is shut down
correctly.</p>
</section>
<section id="running-python-scripts">
<h1><span class="section-number">2.3.3. </span>Running Python scripts<a class="headerlink" href="#running-python-scripts" title="Link to this heading"></a></h1>
<p>Note that any Python script (not just for LAMMPS) can be invoked in
one of several ways:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>python<span class="w"> </span>script.py
python<span class="w"> </span>-i<span class="w"> </span>script.py
./script.py
</pre></div>
</div>
<p>The last command requires that the first line of the script be
something like this:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/usr/bin/python</span>
</pre></div>
</div>
<p>or</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/usr/bin/env python</span>
</pre></div>
</div>
<p>where the path in the first case needs to point to where you have Python
installed (the second option is workaround for when this may change),
and that you have made the script file executable:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>chmod<span class="w"> </span>+x<span class="w"> </span>script.py
</pre></div>
</div>
<p>Without the <code class="docutils literal notranslate"><span class="pre">-i</span></code> flag, Python will exit when the script finishes.
With the <code class="docutils literal notranslate"><span class="pre">-i</span></code> flag, you will be left in the Python interpreter when
the script finishes, so you can type subsequent commands. As mentioned
above, you can only run Python interactively when running Python on a
single processor, not in parallel.</p>
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