Commit bb721db8 authored by Axel Kohlmeyer's avatar Axel Kohlmeyer
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Merge branch 'integration' into fix-flow-gauss

parents 1c13b30a ef69bf86

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doc/html/Manual.html

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@@ -135,7 +135,7 @@ 
  <H1></H1><div class="section" id="lammps-documentation">

<h1>LAMMPS Documentation</h1>

<div class="section" id="aug-2016-version">

<h2>20 Aug 2016 version</h2>

<h2>23 Aug 2016 version</h2>

</div>

<div class="section" id="version-info">

<h2>Version info:</h2>

doc/html/Section_commands.html

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@@ -778,12 +778,12 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p> 
<a class="reference internal" href="Section_start.html#start-3"><span class="std std-ref">LAMMPS is built with the appropriate package</span></a>.</p>

<table border="1" class="docutils">

<colgroup>

<col width="23%" />

<col width="14%" />

<col width="22%" />

<col width="15%" />

<col width="15%" />

<col width="15%" />

<col width="20%" />

<col width="13%" />

</colgroup>

<tbody valign="top">

<tr class="row-odd"><td><a class="reference internal" href="fix_adapt_fep.html"><span class="doc">adapt/fep</span></a></td>
@@ -798,56 +798,63 @@ USER-INTEL, k = KOKKOS, o = USER-OMP, t = OPT.</p> 
<td><a class="reference internal" href="fix_eos_cv.html"><span class="doc">eos/cv</span></a></td>

<td><a class="reference internal" href="fix_eos_table.html"><span class="doc">eos/table</span></a></td>

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</tr>

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<tr class="row-even"><td><a class="reference internal" href="fix_lb_momentum.html"><span class="doc">lb/momentum</span></a></td>

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<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

<td>&nbsp;</td>

</tr>

</tbody>

</table>

doc/html/Section_start.html

+11 −9
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@@ -1769,15 +1769,17 @@ computation. These thread timings are taking from the first MPI rank 
only and and thus, as the breakdown for MPI tasks can change from MPI

rank to MPI rank, this breakdown can be very different for individual

ranks. Here is an example output for this section:</p>

<p>Thread timings breakdown (MPI rank 0):

Total threaded time 0.6846 / 90.6%

Section |  min time  |  avg time  |  max time  <a href="#id37"><span class="problematic" id="id38">|%varavg|</span></a> %total

&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;

Pair    | 0.5127     | 0.5147     | 0.5167     |   0.3 | 75.18

Bond    | 0.0043139  | 0.0046779  | 0.0050418  |   0.5 |  0.68

Kspace  | 0.070572   | 0.074541   | 0.07851    |   1.5 | 10.89

Neigh   | 0.084778   | 0.086969   | 0.089161   |   0.7 | 12.70

Reduce  | 0.0036485  | 0.003737   | 0.0038254  |   0.1 |  0.55</p>

<div class="highlight-default"><div class="highlight"><pre><span></span><span class="n">Thread</span> <span class="n">timings</span> <span class="n">breakdown</span> <span class="p">(</span><span class="n">MPI</span> <span class="n">rank</span> <span class="mi">0</span><span class="p">):</span>

<span class="n">Total</span> <span class="n">threaded</span> <span class="n">time</span> <span class="mf">0.6846</span> <span class="o">/</span> <span class="mf">90.6</span><span class="o">%</span>

<span class="n">Section</span> <span class="o">|</span>  <span class="nb">min</span> <span class="n">time</span>  <span class="o">|</span>  <span class="n">avg</span> <span class="n">time</span>  <span class="o">|</span>  <span class="nb">max</span> <span class="n">time</span>  <span class="o">|%</span><span class="n">varavg</span><span class="o">|</span> <span class="o">%</span><span class="n">total</span>

<span class="o">---------------------------------------------------------------</span>

<span class="n">Pair</span>    <span class="o">|</span> <span class="mf">0.5127</span>     <span class="o">|</span> <span class="mf">0.5147</span>     <span class="o">|</span> <span class="mf">0.5167</span>     <span class="o">|</span>   <span class="mf">0.3</span> <span class="o">|</span> <span class="mf">75.18</span>

<span class="n">Bond</span>    <span class="o">|</span> <span class="mf">0.0043139</span>  <span class="o">|</span> <span class="mf">0.0046779</span>  <span class="o">|</span> <span class="mf">0.0050418</span>  <span class="o">|</span>   <span class="mf">0.5</span> <span class="o">|</span>  <span class="mf">0.68</span>

<span class="n">Kspace</span>  <span class="o">|</span> <span class="mf">0.070572</span>   <span class="o">|</span> <span class="mf">0.074541</span>   <span class="o">|</span> <span class="mf">0.07851</span>    <span class="o">|</span>   <span class="mf">1.5</span> <span class="o">|</span> <span class="mf">10.89</span>

<span class="n">Neigh</span>   <span class="o">|</span> <span class="mf">0.084778</span>   <span class="o">|</span> <span class="mf">0.086969</span>   <span class="o">|</span> <span class="mf">0.089161</span>   <span class="o">|</span>   <span class="mf">0.7</span> <span class="o">|</span> <span class="mf">12.70</span>

<span class="n">Reduce</span>  <span class="o">|</span> <span class="mf">0.0036485</span>  <span class="o">|</span> <span class="mf">0.003737</span>   <span class="o">|</span> <span class="mf">0.0038254</span>  <span class="o">|</span>   <span class="mf">0.1</span> <span class="o">|</span>  <span class="mf">0.55</span>

</pre></div>

</div>

<p>The third section lists the number of owned atoms (Nlocal), ghost atoms

(Nghost), and pair-wise neighbors stored per processor.  The max and min

values give the spread of these values across processors with a 10-bin

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