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@ -1753,36 +1753,91 @@ 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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</P>
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<PRE>Loop time of 49.002 on 2 procs for 2004 atoms
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<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>
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<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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<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>
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<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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<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>
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<PRE>Total # of neighbors = 708282
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Ave neighs/atom = 353.434
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<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>
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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.
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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 <I>Performance</I> 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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</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:
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</P>
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<UL><LI><I>Pair</I> stands for all non-bonded force computation
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<LI><I>Bond</I> stands for bonded interactions: bonds, angles, dihedrals, impropers
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<LI><I>Kspace</I> stands for reciprocal space interactions: Ewald, PPPM, MSM
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<LI><I>Neigh</I> stands for neighbor list construction
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<LI><I>Comm</I> stands for communicating atoms and their properties
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<LI><I>Output</I> stands for writing dumps and thermo output
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<LI><I>Modify</I> stands for fixes and computes called by them
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<LI><I>Other</I> is the remaining time
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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.
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</P>
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<P>When using the <A HREF = "timers.html">timers full</A> 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 <I>timers full</I> and the <A HREF = "package.html">package omp</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 <I>Reduce</I> 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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</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 |%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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</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.
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</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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@ -1802,20 +1857,23 @@ takes place.
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e.g.
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</P>
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<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>
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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.
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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.
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</P>
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<P>If a <A HREF = "kspace_style.html">kspace_style</A> long-range Coulombics solve was
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performed during the run (PPPM, Ewald), then additional information is
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|
|
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|
@ -2069,18 +2069,22 @@
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<dt><a href="thermo.html#index-0">thermo</a>
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</dt>
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|
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</dl></td>
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<td style="width: 33%" valign="top"><dl>
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<dt><a href="thermo_modify.html#index-0">thermo_modify</a>
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</dt>
|
||||
|
||||
</dl></td>
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||||
<td style="width: 33%" valign="top"><dl>
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|
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<dt><a href="thermo_style.html#index-0">thermo_style</a>
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</dt>
|
||||
|
||||
|
||||
<dt><a href="timers.html#index-0">timestep</a>, <a href="timestep.html#index-0">[1]</a>
|
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<dt><a href="timer.html#index-0">timer</a>
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</dt>
|
||||
|
||||
|
||||
<dt><a href="timestep.html#index-0">timestep</a>
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</dt>
|
||||
|
||||
</dl></td>
|
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|
|
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|
|
@ -1,77 +1,263 @@
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<HTML>
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||||
<CENTER><A HREF = "http://lammps.sandia.gov">LAMMPS WWW Site</A> - <A HREF = "Manual.html">LAMMPS Documentation</A> - <A HREF = "Section_commands.html#comm">LAMMPS Commands</A>
|
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</CENTER>
|
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<!DOCTYPE html>
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<!--[if IE 8]><html class="no-js lt-ie9" lang="en" > <![endif]-->
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<title>timestep command — LAMMPS 15 May 2015 version documentation</title>
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<link rel="top" title="LAMMPS 15 May 2015 version documentation" href="index.html"/>
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<script src="_static/js/modernizr.min.js"></script>
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</head>
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<body class="wy-body-for-nav" role="document">
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<div class="wy-grid-for-nav">
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<a href="Manual.html" class="icon icon-home"> LAMMPS
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</a>
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<div class="wy-menu wy-menu-vertical" data-spy="affix" role="navigation" aria-label="main navigation">
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<ul>
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<li class="toctree-l1"><a class="reference internal" href="Section_intro.html">1. Introduction</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_start.html">2. Getting Started</a></li>
|
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<li class="toctree-l1"><a class="reference internal" href="Section_commands.html">3. Commands</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_packages.html">4. Packages</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_accelerate.html">5. Accelerating LAMMPS performance</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_howto.html">6. How-to discussions</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_example.html">7. Example problems</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_perf.html">8. Performance & scalability</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_tools.html">9. Additional tools</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_modify.html">10. Modifying & extending LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_python.html">11. Python interface to LAMMPS</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_errors.html">12. Errors</a></li>
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<li class="toctree-l1"><a class="reference internal" href="Section_history.html">13. Future and history</a></li>
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</ul>
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</div>
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</nav>
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<section data-toggle="wy-nav-shift" class="wy-nav-content-wrap">
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<nav class="wy-nav-top" role="navigation" aria-label="top navigation">
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<i data-toggle="wy-nav-top" class="fa fa-bars"></i>
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<a href="Manual.html">LAMMPS</a>
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</nav>
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|
||||
<HR>
|
||||
|
||||
<H3>timestep command
|
||||
</H3>
|
||||
<P><B>Syntax:</B>
|
||||
</P>
|
||||
<PRE>timers args
|
||||
</PRE>
|
||||
<LI><I>args</I> = one or more of <I>off</I> or <I>loop</I> or <I>normal</I> or <I>full</I> or <I>sync</I> or <I>nosync</I>
|
||||
|
||||
<PRE> <I>off</I> = do not collect and print timing information
|
||||
<I>loop</I> = collect only the total time for the simulation loop
|
||||
<I>normal</I> = collect timer information broken down in sections (default)
|
||||
<I>full</I> = like <I>normal</I> but also include CPU and thread utilzation
|
||||
<I>sync</I> = explicitly synchronize MPI tasks between sections
|
||||
<I>nosync</I> = do not synchronize MPI tasks when collecting timer info (default)
|
||||
</PRE>
|
||||
<P><B>Examples:</B>
|
||||
</P>
|
||||
<PRE>timers full sync
|
||||
timers loop
|
||||
</PRE>
|
||||
<P><B>Description:</B>
|
||||
</P>
|
||||
<P>Select to which level of detail LAMMPS is performing internal profiling.
|
||||
</P>
|
||||
<P>During regular runs LAMMPS will collect information about how much time is
|
||||
|
||||
<div class="wy-nav-content">
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<div class="rst-content">
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<div role="navigation" aria-label="breadcrumbs navigation">
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<ul class="wy-breadcrumbs">
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<li><a href="Manual.html">Docs</a> »</li>
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|
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<li>timestep command</li>
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<li class="wy-breadcrumbs-aside">
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|
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|
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<a href="http://lammps.sandia.gov">Website</a>
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<a href="Section_commands.html#comm">Commands</a>
|
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|
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</li>
|
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</ul>
|
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<hr/>
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|
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</div>
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<div role="main" class="document" itemscope="itemscope" itemtype="http://schema.org/Article">
|
||||
<div itemprop="articleBody">
|
||||
|
||||
<div class="section" id="timestep-command">
|
||||
<span id="index-0"></span><h1>timestep command<a class="headerlink" href="#timestep-command" title="Permalink to this headline">¶</a></h1>
|
||||
<div class="section" id="syntax">
|
||||
<h2>Syntax<a class="headerlink" href="#syntax" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>timers args
|
||||
</pre></div>
|
||||
</div>
|
||||
<ul class="simple">
|
||||
<li><em>args</em> = one or more of <em>off</em> or <em>loop</em> or <em>normal</em> or <em>full</em> or <em>sync</em> or <em>nosync</em></li>
|
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</ul>
|
||||
<pre class="literal-block">
|
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<em>off</em> = do not collect and print timing information
|
||||
<em>loop</em> = collect only the total time for the simulation loop
|
||||
<em>normal</em> = collect timer information broken down in sections (default)
|
||||
<em>full</em> = like <em>normal</em> but also include CPU and thread utilzation
|
||||
<em>sync</em> = explicitly synchronize MPI tasks between sections
|
||||
<em>nosync</em> = do not synchronize MPI tasks when collecting timer info (default)
|
||||
</pre>
|
||||
</div>
|
||||
<div class="section" id="examples">
|
||||
<h2>Examples<a class="headerlink" href="#examples" title="Permalink to this headline">¶</a></h2>
|
||||
<div class="highlight-python"><div class="highlight"><pre>timers full sync
|
||||
timers loop
|
||||
</pre></div>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="description">
|
||||
<h2>Description<a class="headerlink" href="#description" title="Permalink to this headline">¶</a></h2>
|
||||
<p>Select to which level of detail LAMMPS is performing internal profiling.</p>
|
||||
<p>During regular runs LAMMPS will collect information about how much time is
|
||||
spent in different sections of the code and thus can provide valuable
|
||||
information for determining performance and load imbalance problems. This
|
||||
can be done at different levels of detail and accuracy. For more
|
||||
information about the timing output, please have a look at the <A HREF = "Section_start.html#start_8">discussion
|
||||
of screen output</A>.
|
||||
</P>
|
||||
<P>The <I>off</I> setting will turn all time measurements off. The <I>loop</I> setting
|
||||
can be done at different levels of detail and accuracy. For more
|
||||
information about the timing output, please have a look at the <a class="reference internal" href="Section_start.html#start-8"><span>discussion of screen output</span></a>.</p>
|
||||
<p>The <em>off</em> setting will turn all time measurements off. The <em>loop</em> setting
|
||||
will only measure the total time of run loop and not collect any detailed
|
||||
per section information. With the <I>normal</I> setting, timing information for
|
||||
per section information. With the <em>normal</em> setting, timing information for
|
||||
individual sections of the code are collected and also information about
|
||||
load imbalances inside those sections presented. The <I>full</I> setting adds
|
||||
load imbalances inside those sections presented. The <em>full</em> setting adds
|
||||
information about CPU utilization and thread utilization, when multi-threading
|
||||
is enabled.
|
||||
</P>
|
||||
<P>With the <I>sync</I> setting, all MPI tasks are synchronized at each timer call
|
||||
is enabled.</p>
|
||||
<p>With the <em>sync</em> setting, all MPI tasks are synchronized at each timer call
|
||||
and thus allowing to study load imbalance more accuractly, but this usually
|
||||
has some performance impact. Using the <I>nosync</I> setting this can be turned
|
||||
off (which is the default).
|
||||
</P>
|
||||
<P>Multiple keywords can be provided and for keywords that are mutually
|
||||
exclusive, the last one in that group is taking effect.
|
||||
</P>
|
||||
<P>IMPORTANT NOTE: Using the <I>full</I> and <I>sync</I> options provides the most
|
||||
has some performance impact. Using the <em>nosync</em> setting this can be turned
|
||||
off (which is the default).</p>
|
||||
<p>Multiple keywords can be provided and for keywords that are mutually
|
||||
exclusive, the last one in that group is taking effect.</p>
|
||||
<div class="admonition warning">
|
||||
<p class="first admonition-title">Warning</p>
|
||||
<p class="last">Using the <em>full</em> and <em>sync</em> options provides the most
|
||||
detailed and accurate timing information, but also can have a significant
|
||||
negative performance impact due to the overhead of the many required system
|
||||
calls. It is thus recommended to use these settings only when making tests
|
||||
to identify the performance. For calculations with few atoms or a very
|
||||
large number of performance, even using the <I>normal</I> setting can have
|
||||
large number of performance, even using the <em>normal</em> setting can have
|
||||
a measurable performance impact. It is recommended in those cases to use
|
||||
the <I>loop</I> or <I>off</I> setting.
|
||||
</P>
|
||||
<P><B>Restrictions:</B> none
|
||||
</P>
|
||||
<P><B>Related commands:</B>
|
||||
<A HREF = "run.html">run post no</A>, <A HREF = "kspace_modify.html">kspace_modify fftbench</A>
|
||||
</P>
|
||||
<P><B>Default:</B>
|
||||
</P>
|
||||
<P>timers normal nosync
|
||||
</P>
|
||||
</HTML>
|
||||
the <em>loop</em> or <em>off</em> setting.</p>
|
||||
</div>
|
||||
</div>
|
||||
<div class="section" id="restrictions">
|
||||
<h2>Restrictions<a class="headerlink" href="#restrictions" title="Permalink to this headline">¶</a></h2>
|
||||
<blockquote>
|
||||
<div>none</div></blockquote>
|
||||
</div>
|
||||
<div class="section" id="related-commands">
|
||||
<h2>Related commands<a class="headerlink" href="#related-commands" title="Permalink to this headline">¶</a></h2>
|
||||
<p><a class="reference internal" href="run.html"><em>run post no</em></a>, <a class="reference internal" href="kspace_modify.html"><em>kspace_modify fftbench</em></a></p>
|
||||
</div>
|
||||
<div class="section" id="default">
|
||||
<h2>Default<a class="headerlink" href="#default" title="Permalink to this headline">¶</a></h2>
|
||||
<p>timers normal nosync</p>
|
||||
</div>
|
||||
</div>
|
||||
|
||||
|
||||
</div>
|
||||
</div>
|
||||
<footer>
|
||||
|
||||
|
||||
<hr/>
|
||||
|
||||
<div role="contentinfo">
|
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<p>
|
||||
© Copyright .
|
||||
</p>
|
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||||
|
||||
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|
||||
|
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|
||||
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|
||||
|
||||
</section>
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||||
|
||||
</div>
|
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|
||||
|
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|
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|
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|
||||
<script type="text/javascript">
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