hoomd.tune

Overview

CustomTuner

Tuner wrapper for hoomd.custom.Action objects.

LoadBalancer

Adjusts the boundaries of the domain decomposition.

ManualTuneDefinition

Class for defining y = f(x) relationships for tuning x for a set y target.

ParticleSorter

Order particles in memory to improve performance.

ScaleSolver

Solves equations of f(x) = y using a ratio of the current y with the target.

SecantSolver

Solves equations of f(x) = y using the secant method.

SolverStep

Abstract base class for “solving” stepwise equations of f(x) = y.

Details

class hoomd.tune.ManualTuneDefinition(get_y, target, get_x, set_x, domain=None)

Class for defining y = f(x) relationships for tuning x for a set y target.

This class is made to be used with SolverStep subclasses. Here y represents a dependent variable of x. In general, x and y should be of type float, but specific SolverStep subclasses may accept other types.

A special case for the return type of y is None. If the value is currently inaccessible or would be invalid, a ManualTuneDefinition object can return a y of None to indicate this. SolverStep objects will handle this automatically. Since we check for None internally in SolverStep objects, a ManualTuneDefinition object’s y property should be consistant when called multiple times within a timestep.

Parameters
  • get_y (callable) – A callable that gets the current value for y.

  • target (any) – The target y value to approach.

  • get_x (callable) – A callable that gets the current value for x.

  • set_x (callable) – A callable that sets the current value for x.

  • domain (tuple [any, any], optional) – A tuple pair of the minimum and maximum accepted values of x, defaults to None. When, the domain is None then any value of x is accepted. Either the minimum or maximum can be set to None as well which means there is no maximum or minimum. The domain is used to wrap values within the specified domain when setting x.

Note

Placing domain restrictions on x can lead to the target y value being impossible to converge to. This will lead to the SolverStep object passed this tunable to never finish solving regardless if all other ManualTuneDefinition objects are converged.

clamp_into_domain(value)

Return the closest value within the domain.

Parameters

value (any) – A value of the same type as x.

Returns

The value clamps within the domains of x. Clamping here refers to returning the value or minimum or maximum of the domain if value is outside the domain.

property domain

A tuple pair of the minimum and maximum accepted values of x.

When, the domain is None then any value of x is accepted. Either the minimum or maximum can be set to None as well which means there is no maximum or minimum. The domain is used to wrap values within the specified domain when setting x.

Type

tuple[any, any]

in_domain(value)

Check whether a value is in the domain.

Parameters

value (any) – A value that can be compared to the minimum and maximum of the domain.

Returns

Whether the value is in the domain of x.

Return type

bool

property max_x

Maximum allowed x value.

property min_x

Minimum allowed y value.

property target

The targetted y value, can be set.

property x

The dependent variable.

Can be set. When set the setting value is clamped within the provided domain. See clamp_into_domain for further explanation.

property y

The independent variable, and is unsettable.

class hoomd.tune.CustomTuner(action, trigger=1)

Tuner wrapper for hoomd.custom.Action objects.

For usage see hoomd.custom.CustomOperation.

class hoomd.tune.LoadBalancer(trigger, x=True, y=True, z=True, tolerance=1.02, max_iterations=1)

Adjusts the boundaries of the domain decomposition.

Parameters
  • trigger (hoomd.trigger.Trigger) – Select the timesteps on which to perform load balancing.

  • x (bool) – Balance the x direction when True.

  • y (bool) – Balance the y direction when True.

  • z (bool) – Balance the z direction when True.

  • tolerance (float) – Load imbalance tolerance.

  • max_iterations (int) – Maximum number of iterations to attempt in a single step.

LoadBalancer adjusts the boundaries of the MPI domains to distribute the particle load close to evenly between them. The load imbalance is defined as the number of particles owned by a rank divided by the average number of particles per rank if the particles had a uniform distribution:

\[I = \frac{N_i}{N / P}\]

where \(N_i\) is the number of particles on rank \(i\), \(N\) is the total number of particles, and \(P\) is the number of ranks.

In order to adjust the load imbalance, LoadBalancer scales by the inverse of the imbalance factor. To reduce oscillations and communication overhead, it does not move a domain more than 5% of its current size in a single rebalancing step, and not more than half the distance to its neighbors.

Simulations with interfaces (so that there is a particle density gradient) or clustering should benefit from load balancing. The potential speedup is roughly \(I-1.0\), so that if the largest imbalance is 1.4, then the user can expect a roughly 40% speedup in the simulation. This is of course an estimate that assumes that all algorithms are roughly linear in \(N\), all GPUs are fully occupied, and the simulation is limited by the speed of the slowest processor. It also assumes that all particles roughly equal. If you have a simulation where, for example, some particles have significantly more pair force neighbors than others, this estimate of the load imbalance may not produce the optimal results.

A load balancing adjustment is only performed when the maximum load imbalance exceeds a tolerance. The ideal load balance is 1.0, so setting tolerance less than 1.0 will force an adjustment every update. The load balancer can attempt multiple iterations of balancing on each update, and up to maxiter attempts can be made. The optimal values of update and maxiter will depend on your simulation.

Load balancing can be performed independently and sequentially for each dimension of the simulation box. A small performance increase may be obtained by disabling load balancing along dimensions that are known to be homogeneous. For example, if there is a planar vapor-liquid interface normal to the \(z\) axis, then it may be advantageous to disable balancing along \(x\) and \(y\).

In systems that are well-behaved, there is minimal overhead of balancing with a small update. However, if the system is not capable of being balanced (for example, due to the density distribution or minimum domain size), having a small update and high maxiter may lead to a large performance loss. In such systems, it is currently best to either balance infrequently or to balance once in a short test run and then set the decomposition statically in a separate initialization.

Balancing is ignored if there is no domain decomposition available (MPI is not built or is running on a single rank).

trigger

Select the timesteps on which to perform load balancing.

Type

hoomd.trigger.Trigger

x

Balance the x direction when True.

Type

bool

y

Balance the y direction when True.

Type

bool

z

Balance the z direction when True.

Type

bool

tolerance

Load imbalance tolerance.

Type

float

max_iterations

Maximum number of iterations to attempt in a single step.

Type

int

class hoomd.tune.ParticleSorter(trigger=200, grid=None)

Order particles in memory to improve performance.

Parameters
  • trigger (hoomd.trigger.Trigger) – Select the timesteps on which to sort. Defaults to a hoomd.trigger.Periodic(200) trigger.

  • grid (int) – Resolution of the grid to use when sorting. The default value of None sets grid=4096 in 2D simulations and grid=256 in 3D simulations.

ParticleSorter improves simulation performance by sorting the particles in memory along a space-filling curve. This takes particles that are close in space and places them close in memory, leading to a higher rate of cache hits when computing pair potentials.

Note

New Operations instances include a ParticleSorter constructed with default parameters.

trigger

Select the timesteps on which to sort.

Type

hoomd.trigger.Trigger

grid

Set the resolution of the space-filling curve. grid rounds up to the nearest power of 2 when set. Larger values of grid provide more accurate space-filling curves, but consume more memory (grid**D * 4 bytes, where D is the dimensionality of the system).

Type

int

class hoomd.tune.ScaleSolver(max_scale=2.0, gamma=2.0, correlation='positive', tol=1e-05)

Solves equations of f(x) = y using a ratio of the current y with the target.

Parameters
  • max_scale (float, optional) – The maximum amount to scale the current x value with, defaults to 2.0.

  • gamma (float, optional) – nonnegative real number used to dampen or increase the rate of change in x. gamma is added to the numerator and denominator of the y / target ratio. Larger values of gamma lead to smaller changes while a gamma of 0 leads to scaling x by exactly the y / target ratio.

  • correlation (str, optional) – Defines whether the relationship between x and y is of a positive or negative correlation, defaults to ‘positive’. This determines which direction to scale x in for a given y.

  • tol (float, optional) – The absolute tolerance for convergence of y, defaults to 1e-5.

Note

This solver is only usable when quantities are strictly positive.

solve_one(tunable)

Takes in a tunable object and attempts to solve x for a specified y.

Parameters

tunable (hoomd.tune.ManualTuneDefinition) – A tunable object that represents a relationship of f(x) = y.

Returns

Whether or not the tunable converged to the target.

Return type

bool

class hoomd.tune.SecantSolver(gamma=0.9, tol=1e-05)

Solves equations of f(x) = y using the secant method.

Parameters
  • gamma (float, optional) – real number between 0 and 1 used to dampen the rate of change in x. gamma scales the corrections to x each iteration. Larger values of gamma lead to larger changes while a gamma of 0 leads to no change in x at all.

  • tol (float, optional) – The absolute tolerance for convergence of y, defaults to 1e-5.

Note

Tempering the solver with a smaller than 1 gamma value is crucial for numeric stability. If instability is found, then lowering gamma accordingly should help.

solve_one(tunable)

Takes in a tunable object and attempts to solve x for a specified y.

Parameters

tunable (hoomd.tune.ManualTuneDefinition) – A tunable object that represents a relationship of f(x) = y.

Returns

Whether or not the tunable converged to the target.

Return type

bool

class hoomd.tune.SolverStep

Abstract base class for “solving” stepwise equations of f(x) = y.

Requires a single method SolverStep.solve_one that steps forward one iteration in solving the given variable relationship. Users can use subclasses of this with hoomd.tune.ManualTuneDefinition to tune attributes with a functional relation.

Note

A SolverStep object requires manual iteration to converge. This is to support the use case of measuring quantities that require running the simulation for some amount of time after one iteration before remeasuring the dependent variable (i.e. the y). SolverStep object can be used in hoomd.custom.Action subclasses for user defined tuners and updaters.

solve(tunables)

Iterates towards a solution for a list of tunables.

If a y for one of the tunables is None then we skip that tunable. Skipping implies that the quantity is not tuned and solve will return False.

Parameters

tunables (list[hoomd.tune.ManualTuneDefinition]) – A list of tunable objects that represent a relationship f(x) = y.

Returns

Returns whether or not all tunables were considered tuned by the object.

Return type

bool

abstract solve_one(tunable)

Takes in a tunable object and attempts to solve x for a specified y.

Parameters

tunable (hoomd.tune.ManualTuneDefinition) – A tunable object that represents a relationship of f(x) = y.

Returns

Whether or not the tunable converged to the target.

Return type

bool