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<p><span class="math notranslate nohighlight">\(\renewcommand{\AA}{\text{Å}}\)</span></p>
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<section id="screen-and-logfile-output">
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<h1><span class="section-number">4.3. </span>Screen and logfile output<a class="headerlink" href="#screen-and-logfile-output" title="Link to this heading"></a></h1>
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<p>As LAMMPS reads an input script, it prints information to both the
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screen and a log file about significant actions it takes to setup a
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simulation. When the simulation is ready to begin, LAMMPS performs
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various initializations, and prints info about the run it is about to
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perform, including the amount of memory (in MBytes per processor) that
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the simulation requires. It also prints details of the initial
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thermodynamic state of the system. During the run itself,
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thermodynamic information is printed periodically, every few
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timesteps. When the run concludes, LAMMPS prints the final
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thermodynamic state and a total run time for the simulation. It also
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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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<pre class="literal-block">Loop time of 0.942801 on 4 procs for 300 steps with 2004 atoms
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Performance: 54.985 ns/day, 0.436 hours/ns, 318.201 timesteps/s, 637.674 katom-step/s
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195.2% CPU use with 2 MPI tasks x 2 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.61419 | 0.62872 | 0.64325 | 1.8 | 66.69
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Bond | 0.0028608 | 0.0028899 | 0.002919 | 0.1 | 0.31
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Kspace | 0.12652 | 0.14048 | 0.15444 | 3.7 | 14.90
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Neigh | 0.10242 | 0.10242 | 0.10242 | 0.0 | 10.86
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Comm | 0.026753 | 0.027593 | 0.028434 | 0.5 | 2.93
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Output | 0.00018341 | 0.00030942 | 0.00043542 | 0.0 | 0.03
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Modify | 0.039117 | 0.039348 | 0.039579 | 0.1 | 4.17
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Other | | 0.001041 | | | 0.11
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Nlocal: 1002 ave 1006 max 998 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Nghost: 8670.5 ave 8691 max 8650 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Neighs: 354010 ave 357257 max 350763 min
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Histogram: 1 0 0 0 0 0 0 0 0 1
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Total # of neighbors = 708020
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Ave neighs/atom = 353.30339
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Ave special neighs/atom = 2.3403194
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Neighbor list builds = 26
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Dangerous builds = 0</pre>
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<hr class="docutils" />
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<p>The first section provides a global loop timing summary. The <em>loop time</em>
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is the total wall-clock time for the MD steps of the simulation run,
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excluding the time for initialization and setup (i.e. the parts that may
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be skipped with <a class="reference internal" href="run.html"><span class="doc">run N pre no</span></a>). The <em>Performance</em> line is
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provided for convenience to help predict how long it will take to run a
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desired physical simulation and to have numbers useful for performance
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comparison between different simulation settings or system sizes. The
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<em>CPU use</em> line provides the CPU utilization per MPI task; it should be
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close to 100% times the number of OpenMP threads (or 1 if not using
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OpenMP). Lower numbers correspond to delays due to file I/O or
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insufficient thread utilization from parts of the code that have not
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been multi-threaded.</p>
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<hr class="docutils" />
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<p>The <em>MPI task</em> section gives the breakdown of the CPU run time (in
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seconds) into major categories:</p>
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<ul class="simple">
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<li><p><em>Pair</em> = non-bonded force computations</p></li>
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<li><p><em>Bond</em> = bonded interactions: bonds, angles, dihedrals, impropers</p></li>
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<li><p><em>Kspace</em> = long-range interactions: Ewald, PPPM, MSM</p></li>
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<li><p><em>Neigh</em> = neighbor list construction</p></li>
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<li><p><em>Comm</em> = inter-processor communication of atoms and their properties</p></li>
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<li><p><em>Output</em> = output of thermodynamic info and dump files</p></li>
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<li><p><em>Modify</em> = fixes and computes invoked by fixes</p></li>
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<li><p><em>Other</em> = all the remaining time</p></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 any processor spent on this category of
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computation. The “%varavg” is the percentage by which the max or min
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varies from the average. This is an indication of load imbalance. A
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percentage close to 0 is perfect load balance. A large percentage is
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imbalance. The final “%total” column is the percentage of the total
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loop time is spent in this category.</p>
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<p>When using the <a class="reference internal" href="timer.html"><span class="doc">timer full</span></a> setting, an additional column
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is added that also prints the CPU utilization in percent. In addition,
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when using <em>timer full</em> and the <a class="reference internal" href="package.html"><span class="doc">package omp</span></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 <em>Thread
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timings</em> section is also added, which lists the time spent in reducing
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the per-thread data elements to the storage for non-threaded
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computation. These thread timings are measured for the first MPI rank
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only and thus, because the breakdown for MPI tasks can change from
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MPI rank to MPI rank, this breakdown can be very different for
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individual ranks. Here is an example output for this section:</p>
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<pre class="literal-block">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</pre>
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<hr class="docutils" />
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<p>The third section above lists the number of owned atoms (Nlocal),
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ghost atoms (Nghost), and pairwise neighbors stored per processor.
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The max and min values give the spread of these values across
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processors with a 10-bin histogram showing the distribution. The total
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number of histogram counts is equal to the number of processors.</p>
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<hr class="docutils" />
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<p>The last section gives aggregate statistics (across all processors)
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for pairwise neighbors and special neighbors that LAMMPS keeps track
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of (see the <a class="reference internal" href="special_bonds.html"><span class="doc">special_bonds</span></a> command). The number
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of times neighbor lists were rebuilt is tallied, as is the number of
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potentially <em>dangerous</em> rebuilds. If atom movement triggered neighbor
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list rebuilding (see the <a class="reference internal" href="neigh_modify.html"><span class="doc">neigh_modify</span></a> command),
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then dangerous reneighborings are those that were triggered on the
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first timestep atom movement was checked for. If this count is
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non-zero you may wish to reduce the delay factor to ensure no force
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interactions are missed by atoms moving beyond the neighbor skin
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distance before a rebuild takes place.</p>
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<hr class="docutils" />
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<p>If an energy minimization was performed via the
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<a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> command, additional information is printed,
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e.g.</p>
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<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>Minimization stats:
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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 prints the criterion that determined minimization was
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converged. The next line lists the initial and final energy, as well
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as the energy on the next-to-last iteration. The next 2 lines give a
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measure of the gradient of the energy (force on all atoms). The
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2-norm is the “length” of this 3N-component force vector; the largest
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component (x, y, or z) of force (infinity-norm) is also given. Then
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information is provided about the line search and statistics on how
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many iterations and force-evaluations the minimizer required.
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Multiple force evaluations are typically done at each iteration to
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perform a 1d line minimization in the search direction. See the
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<a class="reference internal" href="minimize.html"><span class="doc">minimize</span></a> page for more details.</p>
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<hr class="docutils" />
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<p>If a <a class="reference internal" href="kspace_style.html"><span class="doc">kspace_style</span></a> long-range Coulombics solver
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that performs FFTs was used during the run (PPPM, Ewald), then
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additional information is printed, e.g.</p>
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<div class="highlight-none notranslate"><div class="highlight"><pre><span></span>FFT time (% of Kspce) = 0.200313 (8.34477)
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FFT Gflps 3d 1d-only = 2.31074 9.19989
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</pre></div>
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</div>
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<p>The first line is the time spent doing 3d FFTs (several per timestep)
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and the fraction it represents of the total KSpace time (listed
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above). Each 3d FFT requires computation (3 sets of 1d FFTs) and
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communication (transposes). The total flops performed is 5Nlog_2(N),
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where N is the number of points in the 3d grid. The FFTs are timed
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with and without the communication and a Gflop rate is computed. The
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3d rate is with communication; the 1d rate is without (just the 1d
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FFTs). Thus you can estimate what fraction of your FFT time was spent
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in communication, roughly 75% in the example above.</p>
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