Domain decomposition

An Arbor simulation requires a Recipes, a (hardware) context, and a domain decomposition. The Recipe contains the neuroscientific model, the hardware context describes the computational resources you are going to execute the simulation on, and the domain decomposition describes how Arbor will use the hardware. Since the context and domain decomposition may seem closely related at first, it might be instructive to see how recipes are used by Arbor:

Cell descriptions
gid 1
type lif_cell_0
gid 37
type cable_cell_A
Connection sites
Label dictionary
Cell kinds
gid 1
type arbor.lif_cell
gid 37
type arbor.cable_cell
Simulator: requests cell description of gid=37
Recipe: type=cable_cell_A.
Simulator: requests cell kind of gid=37
Recipe: kind=arbor.cable_cell.
Simulator: look up cell group implementation for kind arbor.cable_cell.
Domain decomposition: cable_cell_group_gpu
Simulator: cable_cell_group_gpu construct cable_cell_A object.
cable_cell_group_gpu: Construction complete.
Simulator: cable_cell_group_gpu simulate for t .. t + dt
12 threads
Domain decomposition
An illustration of the cell-specific portion of the recipe, and how it is used during the lifetime of the simulation: the simulation object will, depending on its configuration, query the recipe for the neuroscientific components it describes. This demonstration also show why the recipe separates cell descriptions from cell types. The latter is, as you might expect, shorthand, and is used in the allocation of the cell to a particular cell group. A cell group implementation is a handler for a certain kind of cell, and Arbor comes with these for all it's included cell kinds. However, users can develop their own specialized cell group implementations. More on that in the internal developer documentation.

A domain decomposition describes the distribution of the model over the available computational resources. The description partitions the cells in the model as follows:

  • group the cells into cell groups of the same kind of cell;

  • assign each cell group to either a CPU core or GPU on a specific MPI rank.

The number of cells in each cell group depends on different factors, including the type of the cell, and whether the cell group will run on a CPU core or the GPU. The domain decomposition is solely responsible for describing the distribution of cells across cell groups and domains.

The domain decomposition can be built manually by the modeler, or an automatic load balancer can be used.

We define some terms as used in the context of connectivity


Tuple of (source, target, weight, delay) describing an axon/synapse connection as travelling time (delay) and attenuation (weight) between two sites source = (gid, threshold_detector) and target = (gid, synapse) where threshold_detector and synapse are string labels.


List of same-kinded cells that share some information. Must not be split across domains.


Produced by a load_balancer, a list of all cell_groups located on the same hardware. A communicator deals with the full set of cells of one domain.


List of domains; distributed across MPI processes.

Load balancers

A load balancer generates the domain decomposition using the model recipe and a description of the available computational resources on which the model will run described by an execution context. Currently Arbor provides one automatic load balancer and a method for manually listing out the cells per MPI task. More approaches might be added over time.