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@ -1739,40 +1739,91 @@ timesteps. When the run concludes, LAMMPS prints the final
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thermodynamic state and a total run time for the simulation. It then
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appends statistics about the CPU time and storage requirements for the
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simulation. An example set of statistics is shown here:</p>
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<div class="highlight-python"><div class="highlight"><pre>Loop time of 49.002 on 2 procs for 2004 atoms
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<div class="highlight-python"><div class="highlight"><pre>Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
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97.0% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>Pair time (%) = 35.0495 (71.5267)
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Bond time (%) = 0.092046 (0.187841)
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Kspce time (%) = 6.42073 (13.103)
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Neigh time (%) = 2.73485 (5.5811)
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Comm time (%) = 1.50291 (3.06703)
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Outpt time (%) = 0.013799 (0.0281601)
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Other time (%) = 2.13669 (4.36041)
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<div class="highlight-python"><div class="highlight"><pre>MPI task timings breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60
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Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21
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Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97
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Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12
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Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74
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Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02
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Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08
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Other | | 0.007178 | | | 0.26
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>Nlocal: 1002 ave, 1015 max, 989 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8720 ave, 8724 max, 8716 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 354141 ave, 361422 max, 346860 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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<div class="highlight-python"><div class="highlight"><pre>Nlocal: 501 ave 508 max 490 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 6586.25 ave 6628 max 6548 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 177007 ave 180562 max 170212 min
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Histogram: 1 0 0 0 0 0 0 1 1 1
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</pre></div>
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</div>
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<div class="highlight-python"><div class="highlight"><pre>Total # of neighbors = 708282
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Ave neighs/atom = 353.434
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<div class="highlight-python"><div class="highlight"><pre>Total # of neighbors = 708028
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Ave neighs/atom = 353.307
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Ave special neighs/atom = 2.34032
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Number of reneighborings = 42
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Dangerous reneighborings = 2
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Neighbor list builds = 26
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Dangerous builds = 0
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</pre></div>
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</div>
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<p>The first section gives the breakdown of the CPU run time (in seconds)
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into major categories. The second section lists the number of owned
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atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored
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per processor. The max and min values give the spread of these values
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across processors with a 10-bin histogram showing the distribution.
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The total number of histogram counts is equal to the number of
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processors.</p>
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<p>The first section provides a global loop timing summary. The loop time
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is the total wall time for the section. The second line provides the
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CPU utilzation per MPI task; it should be close to 100% times the number
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of OpenMP threads (or 1). Lower numbers correspond to delays due to
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file i/o or unsufficient thread utilization. The <em>Performance</em> line is
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provided for convenience to help predicting the number of loop
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continuations required and for comparing performance with other similar
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MD codes.</p>
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<p>The second section gives the breakdown of the CPU run time (in seconds)
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into major categories:</p>
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<ul class="simple">
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<li><em>Pair</em> stands for all non-bonded force computation</li>
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<li><em>Bond</em> stands for bonded interactions: bonds, angles, dihedrals, impropers</li>
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<li><em>Kspace</em> stands for reciprocal space interactions: Ewald, PPPM, MSM</li>
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<li><em>Neigh</em> stands for neighbor list construction</li>
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<li><em>Comm</em> stands for communicating atoms and their properties</li>
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<li><em>Output</em> stands for writing dumps and thermo output</li>
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<li><em>Modify</em> stands for fixes and computes called by them</li>
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<li><em>Other</em> is the remaining time</li>
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</ul>
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<p>For each category, there is a breakdown of the least, average and most
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amount of wall time a processor spent on this section. Also you have the
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variation from the average time. Together these numbers allow to gauge
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the amount of load imbalance in this segment of the calculation. Ideally
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the difference between minimum, maximum and average is small and thus
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the variation from the average close to zero. The final column shows
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the percentage of the total loop time is spent in this section.</p>
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<p>When using the <code class="xref doc docutils literal"><span class="pre">timers</span> <span class="pre">full</span></code> setting, and additional column
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is present that also prints the CPU utilization in percent. In addition,
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when using <em>timers full</em> and the <a class="reference internal" href="package.html"><em>package omp</em></a> command are
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active, a similar timing summary of time spent in threaded regions to
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monitor thread utilization and load balance is provided. A new enrty is
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the <em>Reduce</em> section, which lists the time spend in reducing the per-thread
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data elements to the storage for non-threaded computation. These thread
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timings are taking from the first MPI rank only and and thus, as the
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breakdown for MPI tasks can change from MPI rank to MPI rank, this
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breakdown can be very different for individual ranks. Here is an example
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output for this optional output 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="#id17"><span class="problematic" id="id18">|%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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<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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histogram showing the distribution. The total number of histogram counts
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is equal to the number of processors.</p>
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<p>The last section gives aggregate statistics for pair-wise neighbors
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and special neighbors that LAMMPS keeps track of (see the
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<a class="reference internal" href="special_bonds.html"><em>special_bonds</em></a> command). The number of times
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@ -1789,21 +1840,24 @@ takes place.</p>
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<a class="reference internal" href="minimize.html"><em>minimize</em></a> command, additional information is printed,
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e.g.</p>
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<div class="highlight-python"><div class="highlight"><pre>Minimization stats:
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E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
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Gradient 2-norm init/final= 1920.78 20.9992
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Gradient inf-norm init/final= 304.283 9.61216
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Iterations = 36
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Force evaluations = 177
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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-6372.3765206 -8328.46998942 -8328.46998942
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Force two-norm initial, final = 1059.36 5.36874
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Force max component initial, final = 58.6026 1.46872
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Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
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Iterations, force evaluations = 701 1516
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</pre></div>
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</div>
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<p>The first line lists the initial and final energy, as well as the
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energy on the next-to-last iteration. The next 2 lines give a measure
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of the gradient of the energy (force on all atoms). The 2-norm is the
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“length” of this force vector; the inf-norm is the largest component.
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The last 2 lines are statistics on how many iterations and
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force-evaluations the minimizer required. Multiple force evaluations
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are typically done at each iteration to perform a 1d line minimization
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in the search direction.</p>
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<p>The first line prints the criterion that determined the minimization
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to be completed. The third line lists the initial and final energy,
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as well as the energy on the next-to-last iteration. The next 2 lines
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give a measure of the gradient of the energy (force on all atoms).
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The 2-norm is the “length” of this force vector; the inf-norm is the
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largest component. Then some information about the line search and
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statistics on how many iterations and force-evaluations the minimizer
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required. Multiple force evaluations are typically done at each
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iteration to perform a 1d line minimization in the search direction.</p>
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<p>If a <a class="reference internal" href="kspace_style.html"><em>kspace_style</em></a> long-range Coulombics solve was
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performed during the run (PPPM, Ewald), then additional information is
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printed, e.g.</p>
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|
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@ -1745,36 +1745,92 @@ thermodynamic state and a total run time for the simulation. It then
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appends statistics about the CPU time and storage requirements for the
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simulation. An example set of statistics is shown here:
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Loop time of 49.002 on 2 procs for 2004 atoms :pre
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Loop time of 2.81192 on 4 procs for 300 steps with 2004 atoms
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97.0% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 18.436 ns/day 1.302 hours/ns 106.689 timesteps/s :pre
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Pair time (%) = 35.0495 (71.5267)
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Bond time (%) = 0.092046 (0.187841)
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Kspce time (%) = 6.42073 (13.103)
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Neigh time (%) = 2.73485 (5.5811)
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Comm time (%) = 1.50291 (3.06703)
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Outpt time (%) = 0.013799 (0.0281601)
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Other time (%) = 2.13669 (4.36041) :pre
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MPI task timings breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 1.9808 | 2.0134 | 2.0318 | 1.4 | 71.60
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Bond | 0.0021894 | 0.0060319 | 0.010058 | 4.7 | 0.21
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Kspace | 0.3207 | 0.3366 | 0.36616 | 3.1 | 11.97
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Neigh | 0.28411 | 0.28464 | 0.28516 | 0.1 | 10.12
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Comm | 0.075732 | 0.077018 | 0.07883 | 0.4 | 2.74
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Output | 0.00030518 | 0.00042665 | 0.00078821 | 1.0 | 0.02
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Modify | 0.086606 | 0.086631 | 0.086668 | 0.0 | 3.08
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Other | | 0.007178 | | | 0.26 :pre
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Nlocal: 1002 ave, 1015 max, 989 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8720 ave, 8724 max, 8716 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 354141 ave, 361422 max, 346860 min
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Histogram: 1 0 0 0 0 0 0 0 0 1 :pre
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Nlocal: 501 ave 508 max 490 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Nghost: 6586.25 ave 6628 max 6548 min
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Histogram: 1 0 1 0 0 0 1 0 0 1
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Neighs: 177007 ave 180562 max 170212 min
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Histogram: 1 0 0 0 0 0 0 1 1 1 :pre
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Total # of neighbors = 708282
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Ave neighs/atom = 353.434
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Total # of neighbors = 708028
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Ave neighs/atom = 353.307
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Ave special neighs/atom = 2.34032
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Number of reneighborings = 42
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Dangerous reneighborings = 2 :pre
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Neighbor list builds = 26
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Dangerous builds = 0 :pre
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The first section gives the breakdown of the CPU run time (in seconds)
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into major categories. The second section lists the number of owned
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atoms (Nlocal), ghost atoms (Nghost), and pair-wise neighbors stored
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per processor. The max and min values give the spread of these values
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across processors with a 10-bin histogram showing the distribution.
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The total number of histogram counts is equal to the number of
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processors.
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The first section provides a global loop timing summary. The loop time
|
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is the total wall time for the section. The second line provides the
|
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CPU utilzation per MPI task; it should be close to 100% times the number
|
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of OpenMP threads (or 1). Lower numbers correspond to delays due to
|
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file i/o or unsufficient thread utilization. The {Performance} line is
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provided for convenience to help predicting the number of loop
|
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continuations required and for comparing performance with other similar
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MD codes.
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The second section gives the breakdown of the CPU run time (in seconds)
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into major categories:
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{Pair} stands for all non-bonded force computation
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{Bond} stands for bonded interactions: bonds, angles, dihedrals, impropers
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{Kspace} stands for reciprocal space interactions: Ewald, PPPM, MSM
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{Neigh} stands for neighbor list construction
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{Comm} stands for communicating atoms and their properties
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{Output} stands for writing dumps and thermo output
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{Modify} stands for fixes and computes called by them
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{Other} is the remaining time :ul
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For each category, there is a breakdown of the least, average and most
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amount of wall time a processor spent on this section. Also you have the
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variation from the average time. Together these numbers allow to gauge
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the amount of load imbalance in this segment of the calculation. Ideally
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the difference between minimum, maximum and average is small and thus
|
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the variation from the average close to zero. The final column shows
|
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the percentage of the total loop time is spent in this section.
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|
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When using the "timers full"_timers.html setting, and additional column
|
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is present that also prints the CPU utilization in percent. In addition,
|
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when using {timers full} and the "package omp"_package.html command are
|
||||
active, a similar timing summary of time spent in threaded regions to
|
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monitor thread utilization and load balance is provided. A new enrty is
|
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the {Reduce} section, which lists the time spend in reducing the per-thread
|
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data elements to the storage for non-threaded computation. These thread
|
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timings are taking from the first MPI rank only and and thus, as the
|
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breakdown for MPI tasks can change from MPI rank to MPI rank, this
|
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breakdown can be very different for individual ranks. Here is an example
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output for this optional output 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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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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histogram showing the distribution. The total number of histogram counts
|
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is equal to the number of processors.
|
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|
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The last section gives aggregate statistics for pair-wise neighbors
|
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and special neighbors that LAMMPS keeps track of (see the
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|
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@ -1794,20 +1850,23 @@ If an energy minimization was performed via the
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e.g.
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Minimization stats:
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E initial, next-to-last, final = -0.895962 -2.94193 -2.94342
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Gradient 2-norm init/final= 1920.78 20.9992
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Gradient inf-norm init/final= 304.283 9.61216
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Iterations = 36
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Force evaluations = 177 :pre
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Stopping criterion = linesearch alpha is zero
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Energy initial, next-to-last, final =
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-6372.3765206 -8328.46998942 -8328.46998942
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Force two-norm initial, final = 1059.36 5.36874
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Force max component initial, final = 58.6026 1.46872
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Final line search alpha, max atom move = 2.7842e-10 4.0892e-10
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Iterations, force evaluations = 701 1516 :pre
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|
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The first line lists the initial and final energy, as well as the
|
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energy on the next-to-last iteration. The next 2 lines give a measure
|
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of the gradient of the energy (force on all atoms). The 2-norm is the
|
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"length" of this force vector; the inf-norm is the largest component.
|
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The last 2 lines are statistics on how many iterations and
|
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force-evaluations the minimizer required. Multiple force evaluations
|
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are typically done at each iteration to perform a 1d line minimization
|
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in the search direction.
|
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The first line prints the criterion that determined the minimization
|
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to be completed. The third line lists the initial and final energy,
|
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as well as the energy on the next-to-last iteration. The next 2 lines
|
||||
give a measure of the gradient of the energy (force on all atoms).
|
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The 2-norm is the "length" of this force vector; the inf-norm is the
|
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largest component. Then some information about the line search and
|
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statistics on how many iterations and force-evaluations the minimizer
|
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required. Multiple force evaluations are typically done at each
|
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iteration to perform a 1d line minimization in the search direction.
|
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|
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If a "kspace_style"_kspace_style.html long-range Coulombics solve was
|
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performed during the run (PPPM, Ewald), then additional information is
|
||||
|
|
|
|||
File diff suppressed because one or more lines are too long
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