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Steve Plimpton
2016-08-23 16:28:36 -06:00
parent 268fdab71b
commit e27196e91c
4 changed files with 30 additions and 26 deletions
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20
doc/html/Section_start.html
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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 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 rank to MPI rank, this breakdown can be very different for individual
ranks. Here is an example output for this section:</p> ranks. Here is an example output for this section:</p>
<p>Thread timings breakdown (MPI rank 0): <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>
Total threaded time 0.6846 / 90.6% <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>
Section | min time | avg time | max time <a href="#id37"><span class="problematic" id="id38">|%varavg|</span></a> %total <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>
&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212;&#8212; <span class="o">---------------------------------------------------------------</span>
Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18 <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>
Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68 <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>
Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89 <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>
Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70 <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>
Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55</p> <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 <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 (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 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
rank to MPI rank, this breakdown can be very different for individual rank to MPI rank, this breakdown can be very different for individual
ranks. Here is an example output for this section: ranks. Here is an example output for this section:
Thread timings breakdown (MPI rank 0): .. parsed-literal::
Total threaded time 0.6846 / 90.6%
Section | min time | avg time | max time |%varavg| %total Thread timings breakdown (MPI rank 0):
--------------------------------------------------------------- Total threaded time 0.6846 / 90.6%
Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18 Section | min time | avg time | max time |%varavg| %total
Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68 ---------------------------------------------------------------
Kspace | 0.070572 | 0.074541 | 0.07851 | 1.5 | 10.89 Pair | 0.5127 | 0.5147 | 0.5167 | 0.3 | 75.18
Neigh | 0.084778 | 0.086969 | 0.089161 | 0.7 | 12.70 Bond | 0.0043139 | 0.0046779 | 0.0050418 | 0.5 | 0.68
Reduce | 0.0036485 | 0.003737 | 0.0038254 | 0.1 | 0.55 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
The third section lists the number of owned atoms (Nlocal), ghost atoms The third section lists the number of owned atoms (Nlocal), ghost atoms
(Nghost), and pair-wise neighbors stored per processor. The max and min (Nghost), and pair-wise neighbors stored per processor. The max and min

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doc/html/_sources/compute_sna_atom.txt
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@ -196,18 +196,18 @@ described by the following piece of python code:
for j1 in range(0,twojmax+1): for j1 in range(0,twojmax+1):
if(diagonal==2): if(diagonal==2):
print j1/2,j1/2,j1/2 print j1/2.,j1/2.,j1/2.
elif(diagonal==1): elif(diagonal==1):
for j in range(0,min(twojmax,2*j1)+1,2): for j in range(0,min(twojmax,2*j1)+1,2):
print j1/2,j1/2,j/2 print j1/2.,j1/2.,j/2.
elif(diagonal==0): elif(diagonal==0):
for j2 in range(0,j1+1): for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2): for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
print j1/2,j2/2,j/2 print j1/2.,j2/2.,j/2.
elif(diagonal==3): elif(diagonal==3):
for j2 in range(0,j1+1): for j2 in range(0,j1+1):
for j in range(j1-j2,min(twojmax,j1+j2)+1,2): for j in range(j1-j2,min(twojmax,j1+j2)+1,2):
if (j>=j1): print j1/2,j2/2,j/2 if (j>=j1): print j1/2.,j2/2.,j/2.
Compute *snad/atom* evaluates a per-atom array. The columns are Compute *snad/atom* evaluates a per-atom array. The columns are
arranged into *ntypes* blocks, listed in order of atom type *I*\ . Each 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
described by the following piece of python code:</p> described by the following piece of python code:</p>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<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> <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>
<span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">&gt;=</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> <span class="k">if</span> <span class="p">(</span><span class="n">j</span><span class="o">&gt;=</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>
</pre></div> </pre></div>
</div> </div>
<p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are <p>Compute <em>snad/atom</em> evaluates a per-atom array. The columns are