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[lammps.git] / doc / src / balance.txt

"LAMMPS WWW Site"_lws - "LAMMPS Documentation"_ld - "LAMMPS Commands"_lc :c

:link(lws,http://lammps.sandia.gov)
:link(ld,Manual.html)
:link(lc,Section_commands.html#comm)

:line

balance command :h3

[Syntax:]

balance thresh style args ... keyword args ... :pre

thresh = imbalance threshhold that must be exceeded to perform a re-balance :ulb,l
one style/arg pair can be used (or multiple for {x},{y},{z}) :l
style = {x} or {y} or {z} or {shift} or {rcb} :l
  {x} args = {uniform} or Px-1 numbers between 0 and 1
    {uniform} = evenly spaced cuts between processors in x dimension
    numbers = Px-1 ascending values between 0 and 1, Px - # of processors in x dimension
    {x} can be specified together with {y} or {z}
  {y} args = {uniform} or Py-1 numbers between 0 and 1
    {uniform} = evenly spaced cuts between processors in y dimension
    numbers = Py-1 ascending values between 0 and 1, Py - # of processors in y dimension
    {y} can be specified together with {x} or {z}
  {z} args = {uniform} or Pz-1 numbers between 0 and 1
    {uniform} = evenly spaced cuts between processors in z dimension
    numbers = Pz-1 ascending values between 0 and 1, Pz - # of processors in z dimension
    {z} can be specified together with {x} or {y}
  {shift} args = dimstr Niter stopthresh
    dimstr = sequence of letters containing "x" or "y" or "z", each not more than once
    Niter = # of times to iterate within each dimension of dimstr sequence
    stopthresh = stop balancing when this imbalance threshhold is reached
  {rcb} args = none :pre
zero or more keyword/arg pairs may be appended :l
keyword = {weight} or {out} :l
  {weight} style args = use weighted particle counts for the balancing
    {style} = {group} or {neigh} or {time} or {var} or {store}
      {group} args = Ngroup group1 weight1 group2 weight2 ...
        Ngroup = number of groups with assigned weights
        group1, group2, ... = group IDs
        weight1, weight2, ...   = corresponding weight factors
      {neigh} factor = compute weight based on number of neighbors
        factor = scaling factor (> 0)
      {time} factor = compute weight based on time spend computing
        factor = scaling factor (> 0)
      {var} name = take weight from atom-style variable
        name = name of the atom-style variable
      {store} name = store weight in custom atom property defined by "fix property/atom"_fix_property_atom.html command
        name = atom property name (without d_ prefix)
  {out} arg = filename
    filename = write each processor's sub-domain to a file :pre
:ule

[Examples:]

balance 0.9 x uniform y 0.4 0.5 0.6
balance 1.2 shift xz 5 1.1
balance 1.0 shift xz 5 1.1
balance 1.1 rcb
balance 1.0 shift x 10 1.1 weight group 2 fast 0.5 slow 2.0
balance 1.0 shift x 10 1.1 weight time 0.8 weight neigh 0.5 weight store balance
balance 1.0 shift x 20 1.0 out tmp.balance :pre

[Description:]

This command adjusts the size and shape of processor sub-domains
within the simulation box, to attempt to balance the number of atoms
or particles and thus indirectly the computational cost (load) more
evenly across processors.  The load balancing is "static" in the sense
that this command performs the balancing once, before or between
simulations.  The processor sub-domains will then remain static during
the subsequent run.  To perform "dynamic" balancing, see the "fix
balance"_fix_balance.html command, which can adjust processor
sub-domain sizes and shapes on-the-fly during a "run"_run.html.

Load-balancing is typically most useful if the particles in the
simulation box have a spatially-varying density distribution or when
the computational cost varies signficantly between different
particles.  E.g. a model of a vapor/liquid interface, or a solid with
an irregular-shaped geometry containing void regions, or "hybrid pair
style simulations"_pair_hybrid.html which combine pair styles with
different computational cost.  In these cases, the LAMMPS default of
dividing the simulation box volume into a regular-spaced grid of 3d
bricks, with one equal-volume sub-domain per procesor, may assign
numbers of particles per processor in a way that the computational
effort varies significantly.  This can lead to poor performance when
the simulation is run in parallel.

The balancing can be performed with or without per-particle weighting.
With no weighting, the balancing attempts to assign an equal number of
particles to each processor.  With weighting, the balancing attempts
to assign an equal aggregate computational weight to each processor,
which typically inducces a diffrent number of atoms assigned to each
processor.  Details on the various weighting options and examples for
how they can be used are "given below"_#weighted_balance.

Note that the "processors"_processors.html command allows some control
over how the box volume is split across processors.  Specifically, for
a Px by Py by Pz grid of processors, it allows choice of Px, Py, and
Pz, subject to the constraint that Px * Py * Pz = P, the total number
of processors.  This is sufficient to achieve good load-balance for
some problems on some processor counts.  However, all the processor
sub-domains will still have the same shape and same volume.

The requested load-balancing operation is only performed if the
current "imbalance factor" in particles owned by each processor
exceeds the specified {thresh} parameter.  The imbalance factor is
defined as the maximum number of particles (or weight) owned by any
processor, divided by the average number of particles (or weight) per
processor.  Thus an imbalance factor of 1.0 is perfect balance.

As an example, for 10000 particles running on 10 processors, if the
most heavily loaded processor has 1200 particles, then the factor is
1.2, meaning there is a 20% imbalance.  Note that a re-balance can be
forced even if the current balance is perfect (1.0) be specifying a
{thresh} < 1.0.

NOTE: Balancing is performed even if the imbalance factor does not
exceed the {thresh} parameter if a "grid" style is specified when the
current partitioning is "tiled".  The meaning of "grid" vs "tiled" is
explained below.  This is to allow forcing of the partitioning to
"grid" so that the "comm_style brick"_comm_style.html command can then
be used to replace a current "comm_style tiled"_comm_style.html
setting.

When the balance command completes, it prints statistics about the
result, including the change in the imbalance factor and the change in
the maximum number of particles on any processor.  For "grid" methods
(defined below) that create a logical 3d grid of processors, the
positions of all cutting planes in each of the 3 dimensions (as
fractions of the box length) are also printed.

NOTE: This command attempts to minimize the imbalance factor, as
defined above.  But depending on the method a perfect balance (1.0)
may not be achieved.  For example, "grid" methods (defined below) that
create a logical 3d grid cannot achieve perfect balance for many
irregular distributions of particles.  Likewise, if a portion of the
system is a perfect lattice, e.g. the initial system is generated by
the "create_atoms"_create_atoms.html command, then "grid" methods may
be unable to achieve exact balance.  This is because entire lattice
planes will be owned or not owned by a single processor.

NOTE: The imbalance factor is also an estimate of the maximum speed-up
you can hope to achieve by running a perfectly balanced simulation
versus an imbalanced one.  In the example above, the 10000 particle
simulation could run up to 20% faster if it were perfectly balanced,
versus when imbalanced.  However, computational cost is not strictly
proportional to particle count, and changing the relative size and
shape of processor sub-domains may lead to additional computational
and communication overheads, e.g. in the PPPM solver used via the
"kspace_style"_kspace_style.html command.  Thus you should benchmark
the run times of a simulation before and after balancing.

:line

The method used to perform a load balance is specified by one of the
listed styles (or more in the case of {x},{y},{z}), which are
described in detail below.  There are 2 kinds of styles.

The {x}, {y}, {z}, and {shift} styles are "grid" methods which produce
a logical 3d grid of processors.  They operate by changing the cutting
planes (or lines) between processors in 3d (or 2d), to adjust the
volume (area in 2d) assigned to each processor, as in the following 2d
diagram where processor sub-domains are shown and particles are
colored by the processor that owns them.  The leftmost diagram is the
default partitioning of the simulation box across processors (one
sub-box for each of 16 processors); the middle diagram is after a
"grid" method has been applied.

:image(JPG/balance_uniform_small.jpg,JPG/balance_uniform.jpg),image(JPG/balance_nonuniform_small.jpg,JPG/balance_nonuniform.jpg),image(JPG/balance_rcb_small.jpg,JPG/balance_rcb.jpg)
:c

The {rcb} style is a "tiling" method which does not produce a logical
3d grid of processors.  Rather it tiles the simulation domain with
rectangular sub-boxes of varying size and shape in an irregular
fashion so as to have equal numbers of particles (or weight) in each
sub-box, as in the rightmost diagram above.

The "grid" methods can be used with either of the
"comm_style"_comm_style.html command options, {brick} or {tiled}.  The
"tiling" methods can only be used with "comm_style
tiled"_comm_style.html.  Note that it can be useful to use a "grid"
method with "comm_style tiled"_comm_style.html to return the domain
partitioning to a logical 3d grid of processors so that "comm_style
brick" can afterwords be specified for subsequent "run"_run.html
commands.

When a "grid" method is specified, the current domain partitioning can
be either a logical 3d grid or a tiled partitioning.  In the former
case, the current logical 3d grid is used as a starting point and
changes are made to improve the imbalance factor.  In the latter case,
the tiled partitioning is discarded and a logical 3d grid is created
with uniform spacing in all dimensions.  This becomes the starting
point for the balancing operation.

When a "tiling" method is specified, the current domain partitioning
("grid" or "tiled") is ignored, and a new partitioning is computed
from scratch.

:line

The {x}, {y}, and {z} styles invoke a "grid" method for balancing, as
described above.  Note that any or all of these 3 styles can be
specified together, one after the other, but they cannot be used with
any other style.  This style adjusts the position of cutting planes
between processor sub-domains in specific dimensions.  Only the
specified dimensions are altered.

The {uniform} argument spaces the planes evenly, as in the left
diagrams above.  The {numeric} argument requires listing Ps-1 numbers
that specify the position of the cutting planes.  This requires
knowing Ps = Px or Py or Pz = the number of processors assigned by
LAMMPS to the relevant dimension.  This assignment is made (and the
Px, Py, Pz values printed out) when the simulation box is created by
the "create_box" or "read_data" or "read_restart" command and is
influenced by the settings of the "processors"_processors.html
command.

Each of the numeric values must be between 0 and 1, and they must be
listed in ascending order.  They represent the fractional position of
the cutting place.  The left (or lower) edge of the box is 0.0, and
the right (or upper) edge is 1.0.  Neither of these values is
specified.  Only the interior Ps-1 positions are specified.  Thus is
there are 2 procesors in the x dimension, you specify a single value
such as 0.75, which would make the left processor's sub-domain 3x
larger than the right processor's sub-domain.

:line

The {shift} style invokes a "grid" method for balancing, as
described above.  It changes the positions of cutting planes between
processors in an iterative fashion, seeking to reduce the imbalance
factor, similar to how the "fix balance shift"_fix_balance.html
command operates.

The {dimstr} argument is a string of characters, each of which must be
an "x" or "y" or "z".  Eacn character can appear zero or one time,
since there is no advantage to balancing on a dimension more than
once.  You should normally only list dimensions where you expect there
to be a density variation in the particles.

Balancing proceeds by adjusting the cutting planes in each of the
dimensions listed in {dimstr}, one dimension at a time.  For a single
dimension, the balancing operation (described below) is iterated on up
to {Niter} times.  After each dimension finishes, the imbalance factor
is re-computed, and the balancing operation halts if the {stopthresh}
criterion is met.

A rebalance operation in a single dimension is performed using a
recursive multisectioning algorithm, where the position of each
cutting plane (line in 2d) in the dimension is adjusted independently.
This is similar to a recursive bisectioning for a single value, except
that the bounds used for each bisectioning take advantage of
information from neighboring cuts if possible.  At each iteration, the
count of particles on either side of each plane is tallied.  If the
counts do not match the target value for the plane, the position of
the cut is adjusted to be halfway between a low and high bound.  The
low and high bounds are adjusted on each iteration, using new count
information, so that they become closer together over time.  Thus as
the recursion progresses, the count of particles on either side of the
plane gets closer to the target value.

Once the rebalancing is complete and final processor sub-domains
assigned, particles are migrated to their new owning processor, and
the balance procedure ends.

NOTE: At each rebalance operation, the bisectioning for each cutting
plane (line in 2d) typcially starts with low and high bounds separated
by the extent of a processor's sub-domain in one dimension.  The size
of this bracketing region shrinks by 1/2 every iteration.  Thus if
{Niter} is specified as 10, the cutting plane will typically be
positioned to 1 part in 1000 accuracy (relative to the perfect target
position).  For {Niter} = 20, it will be accurate to 1 part in a
million.  Thus there is no need ot set {Niter} to a large value.
LAMMPS will check if the threshold accuracy is reached (in a
dimension) is less iterations than {Niter} and exit early.  However,
{Niter} should also not be set too small, since it will take roughly
the same number of iterations to converge even if the cutting plane is
initially close to the target value.

:line

The {rcb} style invokes a "tiled" method for balancing, as described
above.  It performs a recursive coordinate bisectioning (RCB) of the
simulation domain. The basic idea is as follows.

The simulation domain is cut into 2 boxes by an axis-aligned cut in
the longest dimension, leaving one new box on either side of the cut.
All the processors are also partitioned into 2 groups, half assigned
to the box on the lower side of the cut, and half to the box on the
upper side.  (If the processor count is odd, one side gets an extra
processor.)  The cut is positioned so that the number of particles in
the lower box is exactly the number that the processors assigned to
that box should own for load balance to be perfect.  This also makes
load balance for the upper box perfect.  The positioning is done
iteratively, by a bisectioning method.  Note that counting particles
on either side of the cut requires communication between all
processors at each iteration.

That is the procedure for the first cut.  Subsequent cuts are made
recursively, in exactly the same manner.  The subset of processors
assigned to each box make a new cut in the longest dimension of that
box, splitting the box, the subset of processsors, and the particles
in the box in two.  The recursion continues until every processor is
assigned a sub-box of the entire simulation domain, and owns the
particles in that sub-box.

:line

This sub-section describes how to perform weighted load balancing
using the {weight} keyword. :link(weighted_balance)

By default, all particles have a weight of 1.0, which means each
particle is assumed to require the same amount of computation during a
timestep.  There are, however, scenarios where this is not a good
assumption.  Measuring the computational cost for each particle
accurately would be impractical and slow down the computation.
Instead the {weight} keyword implements several ways to influence the
per-particle weights empirically by properties readily available or
using the user's knowledge of the system.  Note that the absolute
value of the weights are not important; only their relative ratios
affect which particle is assigned to which processor.  A particle with
a weight of 2.5 is assumed to require 5x more computational than a
particle with a weight of 0.5.  For all the options below the weight
assigned to a particle must be a positive value; an error will be be
generated if a weight is <= 0.0.

Below is a list of possible weight options with a short description of
their usage and some example scenarios where they might be applicable.
It is possible to apply multiple weight flags and the weightings they
induce will be combined through multiplication.  Most of the time,
however, it is sufficient to use just one method.

The {group} weight style assigns weight factors to specified
"groups"_group.html of particles.  The {group} style keyword is
followed by the number of groups, then pairs of group IDs and the
corresponding weight factor.  If a particle belongs to none of the
specified groups, its weight is not changed.  If it belongs to
multiple groups, its weight is the product of the weight factors.

This weight style is useful in combination with pair style
"hybrid"_pair_hybrid.html, e.g. when combining a more costly manybody
potential with a fast pair-wise potential.  It is also useful when
using "run_style respa"_run_style.html where some portions of the
system have many bonded interactions and others none.  It assumes that
the computational cost for each group remains constant over time.
This is a purely empirical weighting, so a series test runs to tune
the assigned weight factors for optimal performance is recommended.

The {neigh} weight style assigns the same weight to each particle
owned by a processor based on the total count of neighbors in the
neighbor list owned by that processor.  The motivation is that more
neighbors means a higher computational cost.  The style does not use
neighbors per atom to assign a unique weight to each atom, because
that value can vary depending on how the neighbor list is built.

The {factor} setting is applied as an overall scale factor to the
{neigh} weights which allows adjustment of their impact on the
balancing operation.  The specified {factor} value must be positive.
A value > 1.0 will increase the weights so that the ratio of max
weight to min weight increases by {factor}.  A value < 1.0 will
decrease the weights so that the ratio of max weight to min weight
decreases by {factor}.  In both cases the intermediate weight values
increase/decrease proportionally as well.  A value = 1.0 has no effect
on the {neigh} weights.  As a rule of thumb, we have found a {factor}
of about 0.8 often results in the best performance, since the number
of neighbors is likely to overestimate the ideal weight.

This weight style is useful for systems where there are different
cutoffs used for different pairs of interations, or the density
fluctuates, or a large number of particles are in the vicinity of a
wall, or a combination of these effects.  If a simulation uses
multiple neighbor lists, this weight style will use the first suitable
neighbor list it finds.  It will not request or compute a new list.  A
warning will be issued if there is no suitable neighbor list available
or if it is not current, e.g. if the balance command is used before a
"run"_run.html or "minimize"_minimize.html command is used, in which
case the neighbor list may not yet have been built.  In this case no
weights are computed.  Inserting a "run 0 post no"_run.html command
before issuing the {balance} command, may be a workaround for this
case, as it will induce the neighbor list to be built.

The {time} weight style uses "timer data"_timer.html to estimate
weights.  It assigns the same weight to each particle owned by a
processor based on the total computational time spent by that
processor.  See details below on what time window is used.  It uses
the same timing information as is used for the "MPI task timing
breakdown"_Section_start.html#start_8, namely, for sections {Pair},
{Bond}, {Kspace}, and {Neigh}.  The time spent in those portions of
the timestep are measured for each MPI rank, summed, then divided by
the number of particles owned by that processor.  I.e. the weight is
an effective CPU time/particle averaged over the particles on that
processor.

The {factor} setting is applied as an overall scale factor to the
{time} weights which allows adjustment of their impact on the
balancing operation.  The specified {factor} value must be positive.
A value > 1.0 will increase the weights so that the ratio of max
weight to min weight increases by {factor}.  A value < 1.0 will
decrease the weights so that the ratio of max weight to min weight
decreases by {factor}.  In both cases the intermediate weight values
increase/decrease proportionally as well.  A value = 1.0 has no effect
on the {time} weights.  As a rule of thumb, effective values to use
are typicall between 0.5 and 1.2.  Note that the timer quantities
mentioned above can be affected by communication which occurs in the
middle of the operations, e.g. pair styles with intermediate exchange
of data witin the force computation, and likewise for KSpace solves.

When using the {time} weight style with the {balance} command, the
timing data is taken from the preceding run command, i.e. the timings
are for the entire previous run.  For the {fix balance} command the
timing data is for only the timesteps since the last balancing
operation was performed.  If timing information for the required
sections is not available, e.g. at the beginning of a run, or when the
"timer"_timer.html command is set to either {loop} or {off}, a warning
is issued.  In this case no weights are computed.

NOTE: The {time} weight style is the most generic option, and should
be tried first, unless the {group} style is easily applicable.
However, since the computed cost function is averaged over all
particles on a processor, the weights may not be highly accurate.
This style can also be effective as a secondary weight in combination
with either {group} or {neigh} to offset some of inaccuracies in
either of those heuristics.

The {var} weight style assigns per-particle weights by evaluating an
"atom-style variable"_variable.html specified by {name}.  This is
provided as a more flexible alternative to the {group} weight style,
allowing definition of a more complex heuristics based on information
(global and per atom) available inside of LAMMPS.  For example,
atom-style variables can reference the position of a particle, its
velocity, the volume of its Voronoi cell, etc.

The {store} weight style does not compute a weight factor.  Instead it
stores the current accumulated weights in a custom per-atom property
specified by {name}.  This must be a property defined as {d_name} via
the "fix property/atom"_fix_property_atom.html command.  Note that
these custom per-atom properties can be output in a "dump"_dump.html
file, so this is a way to examine, debug, or visualize the
per-particle weights computed during the load-balancing operation.

:line

The {out} keyword writes a text file to the specified {filename} with
the results of the balancing operation.  The file contains the bounds
of the sub-domain for each processor after the balancing operation
completes.  The format of the file is compatible with the
"Pizza.py"_pizza {mdump} tool which has support for manipulating and
visualizing mesh files.  An example is shown here for a balancing by 4
processors for a 2d problem:

ITEM: TIMESTEP
0
ITEM: NUMBER OF NODES
16
ITEM: BOX BOUNDS
0 10
0 10
0 10
ITEM: NODES
1 1 0 0 0
2 1 5 0 0
3 1 5 5 0
4 1 0 5 0
5 1 5 0 0
6 1 10 0 0
7 1 10 5 0
8 1 5 5 0
9 1 0 5 0
10 1 5 5 0
11 1 5 10 0
12 1 10 5 0
13 1 5 5 0
14 1 10 5 0
15 1 10 10 0
16 1 5 10 0
ITEM: TIMESTEP
0
ITEM: NUMBER OF SQUARES
4
ITEM: SQUARES
1 1 1 2 3 4
2 1 5 6 7 8
3 1 9 10 11 12
4 1 13 14 15 16 :pre

The coordinates of all the vertices are listed in the NODES section, 5
per processor.  Note that the 4 sub-domains share vertices, so there
will be duplicate nodes in the list.

The "SQUARES" section lists the node IDs of the 4 vertices in a
rectangle for each processor (1 to 4).

For a 3d problem, the syntax is similar with 8 vertices listed for
each processor, instead of 4, and "SQUARES" replaced by "CUBES".

:line

[Restrictions:]

For 2d simulations, the {z} style cannot be used.  Nor can a "z"
appear in {dimstr} for the {shift} style.

[Related commands:]

"group"_group.html, "processors"_processors.html,
"fix balance"_fix_balance.html

[Default:] none