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Steve Plimpton
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@ -1769,15 +1769,17 @@ computation. These thread timings are taking from the first MPI rank
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only and and thus, as the breakdown for MPI tasks can change from MPI
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rank to MPI rank, this breakdown can be very different for individual
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ranks. Here is an example output for this section:</p>
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<p>Thread timings breakdown (MPI rank 0):
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Total threaded time 0.6846 / 90.6%
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Section | min time | avg time | max time <a href="#id37"><span class="problematic" id="id38">|%varavg|</span></a> %total
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—————————————————————
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Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
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Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
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Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
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Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
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Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55</p>
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<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>
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<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>
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<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>
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<span class="o">---------------------------------------------------------------</span>
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<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>
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<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>
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<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>
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<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>
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<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>
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</pre></div>
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</div>
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<p>The third section lists the number of owned atoms (Nlocal), ghost atoms
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(Nghost), and pair-wise neighbors stored per processor. The max and min
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values give the spread of these values across processors with a 10-bin
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@ -1978,15 +1978,17 @@ only and and thus, as the breakdown for MPI tasks can change from MPI
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rank to MPI rank, this breakdown can be very different for individual
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ranks. Here is an example output for this section:
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Thread timings breakdown (MPI rank 0):
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Total threaded time 0.6846 / 90.6%
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
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Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
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Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
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Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
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Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55
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.. parsed-literal::
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Thread timings breakdown (MPI rank 0):
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Total threaded time 0.6846 / 90.6%
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
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Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
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Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89
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Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70
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Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55
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The third section lists the number of owned atoms (Nlocal), ghost atoms
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(Nghost), and pair-wise neighbors stored per processor. The max and min
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@ -196,18 +196,18 @@ described by the following piece of python code:
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for j1 in range(0,twojmax+1):
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if(diagonal==2):
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print j1/2,j1/2,j1/2
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print j1/2.,j1/2.,j1/2.
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elif(diagonal==1):
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for j in range(0,min(twojmax,2*j1)+1,2):
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print j1/2,j1/2,j/2
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print j1/2.,j1/2.,j/2.
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elif(diagonal==0):
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for j2 in range(0,j1+1):
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for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
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print j1/2,j2/2,j/2
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print j1/2.,j2/2.,j/2.
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elif(diagonal==3):
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for j2 in range(0,j1+1):
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for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
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if (j>=j1): print j1/2,j2/2,j/2
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if (j>=j1): print j1/2.,j2/2.,j/2.
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Compute *snad/atom* evaluates a per-atom array. The columns are
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arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each
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@ -278,18 +278,18 @@ each column depend on the values of <em>twojmax</em> and <em>diagonal</em>, as
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described by the following piece of python code:</p>
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<div class="highlight-default"><div class="highlight"><pre><span></span><span class="k">for</span> <span class="n">j1</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">twojmax</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
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<span class="k">if</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">2</span><span class="p">):</span>
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<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mi">2</span>
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<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span>
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<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">1</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="mi">2</span><span class="o">*</span><span class="n">j1</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
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<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mi">2</span>
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<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
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<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">0</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
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<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mi">2</span>
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<span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
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<span class="k">elif</span><span class="p">(</span><span class="n">diagonal</span><span class="o">==</span><span class="mi">3</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">j2</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="mi">0</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="mi">1</span><span class="p">):</span>
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<span class="k">for</span> <span class="n">j</span> <span class="ow">in</span> <span class="nb">range</span><span class="p">(</span><span class="n">j1</span><span class="o">-</span><span class="n">j2</span><span class="p">,</span><span class="nb">min</span><span class="p">(</span><span class="n">twojmax</span><span class="p">,</span><span class="n">j1</span><span class="o">+</span><span class="n">j2</span><span class="p">)</span><span class="o">+</span><span class="mi">1</span><span class="p">,</span><span class="mi">2</span><span class="p">):</span>
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<span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">>=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mi">2</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mi">2</span>
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<span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">>=</span><span class="n">j1</span><span class="p">):</span> <span class="nb">print</span> <span class="n">j1</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j2</span><span class="o">/</span><span class="mf">2.</span><span class="p">,</span><span class="n">j</span><span class="o">/</span><span class="mf">2.</span>
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</pre></div>
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</div>
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<p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are
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