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<h1>Activity 10: Parallelization and multi-processing in MsSpec</h1>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#matrix-inversion-parallelization">Matrix inversion parallelization</a></li>
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<li class="toc-h2 nav-item toc-entry"><a class="reference internal nav-link" href="#process-based-parallelism">Process-based parallelism</a></li>
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<section class="tex2jax_ignore mathjax_ignore" id="activity-10-parallelization-and-multi-processing-in-msspec">
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<h1>Activity 10: Parallelization and multi-processing in MsSpec<a class="headerlink" href="#activity-10-parallelization-and-multi-processing-in-msspec" title="Link to this heading">#</a></h1>
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<p>As you can see from the previous examples, a complete simulation may require several multiple scattering calculations, for instance to calculate the total intensity of a substrate or to optimize the geometry of a system. As the calculations are often time consuming, it can be useful to distribute these tasks over several processors to make the most of hardware resources.
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Although MsSpec is not fully parallelized, the code does offer a number of features, which we will explore here.</p>
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<section id="matrix-inversion-parallelization">
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<h2>Matrix inversion parallelization<a class="headerlink" href="#matrix-inversion-parallelization" title="Link to this heading">#</a></h2>
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<p>When available during installation, MsSpec will link with the system lapack library. It will be used to invert the matrix in the <code class="docutils literal notranslate"><span class="pre">inversion</span></code> option of the MsSpec <code class="docutils literal notranslate"><span class="pre">calculator</span></code>. To allow MsSpec to use this shared memory parallelism, you need to set the number of cores to be used in the <code class="docutils literal notranslate"><span class="pre">OMP_NUM_THREADS</span></code> environment variable.</p>
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<p>You can set this variable just for the execution of your script. For example:</p>
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<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$<span class="w"> </span><span class="nv">OMP_NUM_THREADS</span><span class="o">=</span><span class="m">12</span><span class="w"> </span>python<span class="w"> </span>my_script.py
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</pre></div>
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<p>will use 12 cores for inverting the matrix in your script.</p>
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<p>It is also possible to set environment variable inside your python script.</p>
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<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="kn">import</span><span class="w"> </span><span class="nn">os</span>
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<span class="n">os</span><span class="o">.</span><span class="n">environ</span><span class="p">[</span><span class="s1">'OMP_NUM_THREADS'</span><span class="p">]</span> <span class="o">=</span> <span class="mi">12</span>
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</pre></div>
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<p>It may be useful for technical reasons or to use different number of cores in some parts of your script.</p>
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</section>
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<section id="process-based-parallelism">
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<h2>Process-based parallelism<a class="headerlink" href="#process-based-parallelism" title="Link to this heading">#</a></h2>
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<p>Another kind of parallelization used in MsSpec is multiprocessing. Quite often, you need to run different <em>independent</em> calculations. MsSpec provides a simple <em>looper</em> that can be useful for multiprocessing. Let’s demonstrate it with the previous example CO/Fe(001).</p>
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<p><a class="reference download internal" download="" href="../_downloads/cd5e8362249e8155dffd698f9d924327/COFe_mp.py"><span class="xref download myst">This script</span></a> is the multiprocessed version of the previous one. You can see that the previous nested for loops are now replaced by some declarative content (lines 63-67) and the definition of a <code class="docutils literal notranslate"><span class="pre">process</span></code> function (whose name
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can be changed).</p>
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<p>With the <code class="docutils literal notranslate"><span class="pre">msspec.looper</span></code> package, the user define <code class="docutils literal notranslate"><span class="pre">Sweep</span></code> objects that are parameters of the calculation or of the cluster. The <code class="docutils literal notranslate"><span class="pre">process</span></code> function must accept as many arguments as parameters to sweep (+ the <code class="docutils literal notranslate"><span class="pre">**kwargs</span></code>).</p>
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<p>A <code class="docutils literal notranslate"><span class="pre">Looper</span></code> object is created (line 76) and the <code class="docutils literal notranslate"><span class="pre">process</span></code> function is set to its <code class="docutils literal notranslate"><span class="pre">pipeline</span></code> attribute (line 77). When MsSpec will run the <code class="docutils literal notranslate"><span class="pre">looper</span></code>, it will combine all parameters values to unique individual sets and MsSpec will distribute the calculations over the number of processors specified in the <code class="docutils literal notranslate"><span class="pre">ncpu</span></code> option.</p>
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<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="linenos">63</span><span class="c1"># 1) Multiprocess calculations </span>
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<span class="linenos">64</span><span class="n">theta</span> <span class="o">=</span> <span class="n">Sweep</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="s1">'theta'</span><span class="p">,</span> <span class="n">comments</span><span class="o">=</span><span class="s2">"The molecule tilt angle"</span><span class="p">,</span>
|
||
<span class="linenos">65</span> <span class="n">start</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span> <span class="n">stop</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span> <span class="n">step</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">unit</span><span class="o">=</span><span class="s1">'degree'</span><span class="p">)</span>
|
||
<span class="linenos">66</span><span class="n">phi</span> <span class="o">=</span> <span class="n">Sweep</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="s1">'phi'</span><span class="p">,</span> <span class="n">comments</span><span class="o">=</span><span class="s2">"The molecule azimuthal angle"</span><span class="p">,</span>
|
||
<span class="linenos">67</span> <span class="n">values</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">45</span><span class="p">],</span> <span class="n">unit</span><span class="o">=</span><span class="s1">'degree'</span><span class="p">)</span>
|
||
<span class="linenos">68</span>
|
||
<span class="linenos">69</span><span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
|
||
<span class="linenos">70</span> <span class="n">cluster</span> <span class="o">=</span> <span class="n">create_cluster</span><span class="p">(</span><span class="n">theta</span><span class="o">=</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="o">=</span><span class="n">phi</span><span class="p">,</span> <span class="n">height</span><span class="o">=</span><span class="mf">0.6</span><span class="p">,</span> <span class="n">bond_length</span><span class="o">=</span><span class="mf">1.157</span><span class="p">)</span>
|
||
<span class="linenos">71</span> <span class="n">i</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'sweep_index'</span><span class="p">)</span>
|
||
<span class="linenos">72</span> <span class="n">data</span> <span class="o">=</span> <span class="n">compute_polar_scan</span><span class="p">(</span><span class="n">cluster</span><span class="p">,</span> <span class="n">folder</span><span class="o">=</span><span class="sa">f</span><span class="s1">'calc_</span><span class="si">{</span><span class="n">i</span><span class="si">:</span><span class="s1">d</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
|
||
<span class="linenos">73</span> <span class="n">dset</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
|
||
<span class="linenos">74</span> <span class="k">return</span> <span class="n">dset</span><span class="o">.</span><span class="n">theta</span><span class="p">,</span> <span class="n">dset</span><span class="o">.</span><span class="n">cross_section</span>
|
||
<span class="linenos">75</span>
|
||
<span class="linenos">76</span><span class="n">looper</span> <span class="o">=</span> <span class="n">Looper</span><span class="p">()</span>
|
||
<span class="linenos">77</span><span class="n">looper</span><span class="o">.</span><span class="n">pipeline</span> <span class="o">=</span> <span class="n">process</span>
|
||
<span class="linenos">78</span><span class="n">df</span> <span class="o">=</span> <span class="n">looper</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="p">,</span> <span class="n">ncpu</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>
|
||
<span class="linenos">79</span>
|
||
<span class="linenos">80</span><span class="c1"># Black magic to convert the pandas dataframe object 'df' to the </span>
|
||
<span class="linenos">81</span><span class="c1"># parameters dict and the resulst list (will be easier in a future</span>
|
||
<span class="linenos">82</span><span class="c1"># version ;-) ).</span>
|
||
<span class="linenos">83</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">to_dict</span><span class="p">(</span><span class="s1">'list'</span><span class="p">)</span>
|
||
<span class="linenos">84</span><span class="n">results</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">parameters</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">'output'</span><span class="p">),</span> <span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="mi">2</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
|
||
</pre></div>
|
||
</div>
|
||
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|
||
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|
||
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|
||
<i class="fa-solid fa-circle-question"></i> Quiz</label><div class="sd-tab-content docutils">
|
||
<p>In the paper discussed in <a class="reference internal" href="../Activity09/Activity09_light.html#rfactor"><span class="std std-ref">Activity 9: Comparing simulation and experiment with R-factors</span></a>, experimental values of the anisotropy suggest an adsorption height between 0.2 and 0.6 Å. Modify the script to add another sweep for variying the adsorption height of the CO molecule.</p>
|
||
</div>
|
||
</div>
|
||
<div class="dropdown admonition">
|
||
<p class="admonition-title"><em>Solution…</em></p>
|
||
<div class="highlight-default notranslate"><div class="highlight"><pre><span></span><span class="linenos">63</span><span class="c1"># 1) Multiprocess calculations </span>
|
||
<span class="linenos">64</span><span class="n">theta</span> <span class="o">=</span> <span class="n">Sweep</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="s1">'theta'</span><span class="p">,</span> <span class="n">comments</span><span class="o">=</span><span class="s2">"The molecule tilt angle"</span><span class="p">,</span>
|
||
<span class="linenos">65</span> <span class="n">start</span><span class="o">=</span><span class="mi">50</span><span class="p">,</span> <span class="n">stop</span><span class="o">=</span><span class="mi">60</span><span class="p">,</span> <span class="n">step</span><span class="o">=</span><span class="mi">1</span><span class="p">,</span> <span class="n">unit</span><span class="o">=</span><span class="s1">'degree'</span><span class="p">)</span>
|
||
<span class="linenos">66</span><span class="n">phi</span> <span class="o">=</span> <span class="n">Sweep</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="s1">'phi'</span><span class="p">,</span> <span class="n">comments</span><span class="o">=</span><span class="s2">"The molecule azimuthal angle"</span><span class="p">,</span>
|
||
<span class="linenos">67</span> <span class="n">values</span><span class="o">=</span><span class="p">[</span><span class="mi">0</span><span class="p">,</span><span class="mi">45</span><span class="p">],</span> <span class="n">unit</span><span class="o">=</span><span class="s1">'degree'</span><span class="p">)</span>
|
||
<span class="hll"><span class="linenos">68</span><span class="n">height</span> <span class="o">=</span> <span class="n">Sweep</span><span class="p">(</span><span class="n">key</span><span class="o">=</span><span class="s1">'height'</span><span class="p">,</span> <span class="n">comments</span><span class="o">=</span><span class="s2">"The molecule adsorption height"</span><span class="p">,</span>
|
||
</span><span class="hll"><span class="linenos">69</span> <span class="n">start</span><span class="o">=</span><span class="mf">0.2</span><span class="p">,</span> <span class="n">stop</span><span class="o">=</span><span class="mf">0.6</span><span class="p">,</span> <span class="n">num</span><span class="o">=</span><span class="mi">3</span><span class="p">,</span> <span class="n">unit</span><span class="o">=</span><span class="s1">'angström'</span><span class="p">)</span>
|
||
</span><span class="linenos">70</span>
|
||
<span class="hll"><span class="linenos">71</span><span class="k">def</span><span class="w"> </span><span class="nf">process</span><span class="p">(</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="p">,</span> <span class="n">height</span><span class="p">,</span> <span class="o">**</span><span class="n">kwargs</span><span class="p">):</span>
|
||
</span><span class="hll"><span class="linenos">72</span> <span class="n">cluster</span> <span class="o">=</span> <span class="n">create_cluster</span><span class="p">(</span><span class="n">theta</span><span class="o">=</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="o">=</span><span class="n">phi</span><span class="p">,</span> <span class="n">height</span><span class="o">=</span><span class="n">height</span><span class="p">,</span> <span class="n">bond_length</span><span class="o">=</span><span class="mf">1.157</span><span class="p">)</span>
|
||
</span><span class="linenos">73</span> <span class="n">i</span> <span class="o">=</span> <span class="n">kwargs</span><span class="o">.</span><span class="n">get</span><span class="p">(</span><span class="s1">'sweep_index'</span><span class="p">)</span>
|
||
<span class="linenos">74</span> <span class="n">data</span> <span class="o">=</span> <span class="n">compute_polar_scan</span><span class="p">(</span><span class="n">cluster</span><span class="p">,</span> <span class="n">folder</span><span class="o">=</span><span class="sa">f</span><span class="s1">'calc_</span><span class="si">{</span><span class="n">i</span><span class="si">:</span><span class="s1">d</span><span class="si">}</span><span class="s1">'</span><span class="p">)</span>
|
||
<span class="linenos">75</span> <span class="n">dset</span> <span class="o">=</span> <span class="n">data</span><span class="p">[</span><span class="o">-</span><span class="mi">1</span><span class="p">]</span>
|
||
<span class="linenos">76</span> <span class="k">return</span> <span class="n">dset</span><span class="o">.</span><span class="n">theta</span><span class="p">,</span> <span class="n">dset</span><span class="o">.</span><span class="n">cross_section</span>
|
||
<span class="linenos">77</span>
|
||
<span class="linenos">78</span><span class="n">looper</span> <span class="o">=</span> <span class="n">Looper</span><span class="p">()</span>
|
||
<span class="linenos">79</span><span class="n">looper</span><span class="o">.</span><span class="n">pipeline</span> <span class="o">=</span> <span class="n">process</span>
|
||
<span class="hll"><span class="linenos">80</span><span class="n">df</span> <span class="o">=</span> <span class="n">looper</span><span class="o">.</span><span class="n">run</span><span class="p">(</span><span class="n">theta</span><span class="p">,</span> <span class="n">phi</span><span class="p">,</span> <span class="n">height</span><span class="p">,</span> <span class="n">ncpu</span><span class="o">=</span><span class="mi">4</span><span class="p">)</span>
|
||
</span><span class="linenos">81</span>
|
||
<span class="linenos">82</span><span class="c1"># Black magic to convert the pandas dataframe object 'df' to the </span>
|
||
<span class="linenos">83</span><span class="c1"># parameters dict and the resulst list (will be easier in a future</span>
|
||
<span class="linenos">84</span><span class="c1"># version ;-) ).</span>
|
||
<span class="linenos">85</span><span class="n">parameters</span> <span class="o">=</span> <span class="n">df</span><span class="o">.</span><span class="n">to_dict</span><span class="p">(</span><span class="s1">'list'</span><span class="p">)</span>
|
||
<span class="linenos">86</span><span class="n">results</span> <span class="o">=</span> <span class="n">np</span><span class="o">.</span><span class="n">reshape</span><span class="p">(</span><span class="n">parameters</span><span class="o">.</span><span class="n">pop</span><span class="p">(</span><span class="s1">'output'</span><span class="p">),</span> <span class="p">(</span><span class="n">df</span><span class="o">.</span><span class="n">shape</span><span class="p">[</span><span class="mi">0</span><span class="p">]</span><span class="o">*</span><span class="mi">2</span><span class="p">,</span><span class="o">-</span><span class="mi">1</span><span class="p">))</span>
|
||
</pre></div>
|
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|
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