Source code for pde.solvers.explicit_mpi

"""
Defines an explicit solver using multiprocessing via MPI

.. codeauthor:: David Zwicker <david.zwicker@ds.mpg.de> 
"""

from __future__ import annotations

from typing import Callable, Literal

import numpy as np
from numba.extending import register_jitable

from ..fields.base import FieldBase
from ..grids._mesh import GridMesh
from ..pdes.base import PDEBase
from ..tools import mpi
from ..tools.math import OnlineStatistics
from ..tools.typing import BackendType
from .explicit import ExplicitSolver


[docs] class ExplicitMPISolver(ExplicitSolver): """various explicit PDE solve using MPI Warning: This solver can only be used if MPI is properly installed. In particular, python scripts then need to be started using :code:`mpirun` or :code:`mpiexec`. Please refer to the documentation of your MPI distribution for details. The main idea of the solver is to take the full initial state in the main node (ID 0) and split the grid into roughly equal subgrids. The main node then distributes these subfields to all other nodes and each node creates the right hand side of the PDE for itself (and independently). Each node then advances the PDE independently, ensuring proper coupling to neighboring nodes via special boundary conditions, which exchange field values between sub grids. This is implemented by the :meth:`get_boundary_conditions` method of the sub grids, which takes the boundary conditions for the full grid and creates conditions suitable for the specific sub grid on the given node. The trackers (and thus all input and output) are only handled on the main node. Warning: The function providing the right hand side of the PDE needs to support MPI. This is automatically the case for local evaluations (which only use the field value at the current position), for the differential operators provided by :mod:`pde`, and integration of fields. Similarly, `modify_after_step` can only be used to do local modifications since the field data supplied to the function is local to each MPI node. Example: A minimal example using the MPI solver is .. code-block:: python from pde import DiffusionPDE, ScalarField, UnitGrid grid = UnitGrid([64, 64]) state = ScalarField.random_uniform(grid, 0.2, 0.3) eq = DiffusionPDE(diffusivity=0.1) result = eq.solve(state, t_range=10, dt=0.1, method="explicit_mpi") if result is not None: # restrict the output to the main node result.plot() Saving this script as `multiprocessing.py`, a parallel simulation is started by .. code-block:: bash mpiexec -n 2 python3 multiprocessing.py Here, the number `2` determines the number of cores that will be used. Note that macOS might require an additional hint on how to connect the processes even when they are run on the same machine (e.g., your workstation). It might help to run :code:`mpiexec -n 2 -host localhost python3 multiprocessing.py` in this case """ name = "explicit_mpi" def __init__( self, pde: PDEBase, scheme: Literal["euler", "runge-kutta", "rk", "rk45"] = "euler", decomposition: int | list[int] = -1, *, backend: BackendType = "auto", adaptive: bool = False, tolerance: float = 1e-4, ): """ Args: pde (:class:`~pde.pdes.base.PDEBase`): The instance describing the pde that needs to be solved scheme (str): Defines the explicit scheme to use. Supported values are 'euler' and 'runge-kutta' (or 'rk' for short). decomposition (list of ints): Number of subdivision in each direction. Should be a list of length `grid.num_axes` specifying the number of nodes along this axis. If one value is `-1`, its value will be determined from the number of available nodes. The default value decomposed the first axis using all available nodes. backend (str): Determines how the function is created. Accepted values are 'numpy` and 'numba'. Alternatively, 'auto' lets the code decide for the most optimal backend. adaptive (bool): When enabled, the time step is adjusted during the simulation using the error tolerance set with `tolerance`. tolerance (float): The error tolerance used in adaptive time stepping. This is used in adaptive time stepping to choose a time step which is small enough so the truncation error of a single step is below `tolerance`. """ super().__init__( pde, scheme=scheme, backend=backend, adaptive=adaptive, tolerance=tolerance ) self.decomposition = decomposition def _make_error_synchronizer(self) -> Callable[[float], float]: """return helper function that synchronizes errors between multiple processes""" if mpi.parallel_run: # in a parallel run, we need to return the maximal error from ..tools.mpi import mpi_allreduce @register_jitable def synchronize_errors(error: float) -> float: """return maximal error accross all cores""" return mpi_allreduce(error, "MAX") # type: ignore return synchronize_errors # type: ignore else: return super()._make_error_synchronizer()
[docs] def make_stepper( self, state: FieldBase, dt=None ) -> Callable[[FieldBase, float, float], float]: """return a stepper function using an explicit scheme Args: state (:class:`~pde.fields.base.FieldBase`): An example for the state from which the grid and other information can be extracted dt (float): Time step of the explicit stepping. If `None`, this solver specifies 1e-3 as a default value. Returns: Function that can be called to advance the `state` from time `t_start` to time `t_end`. The function call signature is `(state: numpy.ndarray, t_start: float, t_end: float)` """ if not mpi.parallel_run: self._logger.warning( "Using `ExplicitMPISolver` without a proper multiprocessing run. " "Scripts need to be started with `mpiexec` to profit from multiple cores" ) if dt is None: # support `None` as a default value, so the controller can signal that # the solver should use a default time step dt = 1e-3 if not self.adaptive: self._logger.warning( "Explicit stepper with a fixed time step did not receive any " f"initial value for `dt`. Using dt={dt}, but specifying a value or " "enabling adaptive stepping is advisable." ) self.info["dt"] = dt self.info["dt_adaptive"] = self.adaptive self.info["steps"] = 0 self.info["stochastic"] = self.pde.is_sde self.info["state_modifications"] = 0.0 self.info["use_mpi"] = True self.info["scheme"] = self.scheme # decompose the state into multiple cells self.mesh = GridMesh.from_grid(state.grid, self.decomposition) sub_state = self.mesh.extract_subfield(state) self.info["grid_decomposition"] = self.mesh.shape if self.adaptive: # create stepper with adaptive steps self.info["dt_statistics"] = OnlineStatistics() adaptive_stepper = self._make_adaptive_stepper(sub_state) def wrapped_stepper( state: FieldBase, t_start: float, t_end: float ) -> float: """advance `state` from `t_start` to `t_end` using adaptive steps""" nonlocal dt # `dt` stores value for the next call # distribute the end time and the field to all nodes t_end = self.mesh.broadcast(t_end) substate_data = self.mesh.split_field_data_mpi(state.data) # evolve the sub state t_last, dt, steps, modifications = adaptive_stepper( substate_data, t_start, t_end, dt, self.info["dt_statistics"] ) # check whether dt is the same for all processes dt_list = self.mesh.allgather(dt) if not np.isclose(min(dt_list), max(dt_list)): # abort simulations in all nodes when they went out of sync raise RuntimeError(f"Processes went out of sync: dt={dt_list}") # collect the data from all nodes modification_list = self.mesh.gather(modifications) self.mesh.combine_field_data_mpi(substate_data, out=state.data) if mpi.is_main: self.info["steps"] += steps self.info["state_modifications"] += sum(modification_list) # type: ignore return t_last else: # create stepper with fixed steps fixed_stepper = self._make_fixed_stepper(sub_state, dt) def wrapped_stepper( state: FieldBase, t_start: float, t_end: float ) -> float: """advance `state` from `t_start` to `t_end` using fixed steps""" # calculate number of steps (which is at least 1) steps = max(1, int(np.ceil((t_end - t_start) / dt))) # distribute the number of steps and the field to all nodes steps = self.mesh.broadcast(steps) substate_data = self.mesh.split_field_data_mpi(state.data) # evolve the sub state t_last, modifications = fixed_stepper(substate_data, t_start, steps) # check whether t_last is the same for all processes t_list = self.mesh.gather(t_last) if t_list is not None and not np.isclose(min(t_list), max(t_list)): raise RuntimeError(f"Processes went out of sync: t_last={t_list}") # collect the data from all nodes modification_list = self.mesh.gather(modifications) self.mesh.combine_field_data_mpi(substate_data, out=state.data) # store information in the main node if mpi.is_main: self.info["steps"] += steps self.info["state_modifications"] += sum(modification_list) # type: ignore return t_last return wrapped_stepper