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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="general-tips">
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<h1><span class="section-number">7.3. </span>General tips<a class="headerlink" href="#general-tips" title="Link to this heading"></a></h1>
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>this page is still a work in progress</p>
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</div>
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<p>Here is a list of general ideas for improving simulation performance.
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Most of them are only applicable to certain models and certain
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bottlenecks in the current performance, so let the timing data you
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generate be your guide. It is hard, if not impossible, to predict how
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much difference these options will make, since it is a function of
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problem size, number of processors used, and your machine. There is
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no substitute for identifying performance bottlenecks, and trying out
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various options.</p>
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<ul class="simple">
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<li><p>rRESPA</p></li>
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<li><p>Two-FFT PPPM</p></li>
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<li><p>Staggered PPPM</p></li>
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<li><p>single vs double PPPM</p></li>
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<li><p>partial charge PPPM</p></li>
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<li><p>verlet/split run style</p></li>
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<li><p>processor command for proc layout and numa layout</p></li>
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<li><p>load-balancing: balance and fix balance</p></li>
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</ul>
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<p>Two-FFT PPPM, also called <em>analytic differentiation</em> or <em>ad</em> PPPM,
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uses 2 FFTs instead of the 4 FFTs used by the default <em>ik
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differentiation</em> PPPM. However, 2-FFT PPPM also requires a slightly
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larger mesh size to achieve the same accuracy as 4-FFT PPPM. For
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problems where the FFT cost is the performance bottleneck (typically
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large problems running on many processors), 2-FFT PPPM may be faster
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than 4-FFT PPPM.</p>
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<p>Staggered PPPM performs calculations using two different meshes, one
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shifted slightly with respect to the other. This can reduce force
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aliasing errors and increase the accuracy of the method, but also
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doubles the amount of work required. For high relative accuracy, using
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staggered PPPM allows one to half the mesh size in each dimension as
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compared to regular PPPM, which can give around a 4x speedup in the
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kspace time. However, for low relative accuracy, using staggered PPPM
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gives little benefit and can be up to 2x slower in the kspace
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time. For example, the rhodopsin benchmark was run on a single
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processor, and results for kspace time vs. relative accuracy for the
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different methods are shown in the figure below. For this system,
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staggered PPPM (using ik differentiation) becomes useful when using a
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relative accuracy of slightly greater than 1e-5 and above.</p>
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<img alt="_images/rhodo_staggered.jpg" class="align-center" src="_images/rhodo_staggered.jpg" />
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<div class="admonition note">
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<p class="admonition-title">Note</p>
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<p>Using staggered PPPM may not give the same increase in accuracy
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of energy and pressure as it does in forces, so some caution must be
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used if energy and/or pressure are quantities of interest, such as
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when using a barostat.</p>
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