An Arbor recipe is a description of a model. The recipe is queried during the model building phase to provide information about cells in the model, such as:
- the number of cells in the model;
- the type of a cell;
- a description of a cell, e.g. with soma, synapses, detectors, stimuli;
- the number of spike targets;
- the number of spike sources;
- the number of gap junction sites;
- incoming network connections from other cells terminating on a cell;
- gap junction connections on a cell.
The interface and design of Arbor recipes was motivated by the following aims:
- Building a simulation from a recipe description must be possible in a distributed system efficiently with minimal communication.
- To minimise the amount of memory used in model building, to make it possible to build and run simulations in one run.
Recipe descriptions are cell-oriented, in order that the building phase can be efficiently distributed and that the model can be built independently of any runtime execution environment.
During model building, the recipe is queried first by a load balancer, then later when building the low-level cell groups and communication network. The cell-centered recipe interface, whereby cell and network properties are specified “per-cell”, facilitates this.
The steps of building a simulation from a recipe are:
1. Load balancing
First, the cells are partitioned over MPI ranks, and each rank parses
the cells assigned to it to build a cost model.
The ranks then coordinate to redistribute cells over MPI ranks so that
each rank has a balanced workload. Finally, each rank groups its local
cell_group s that balance the work over threads (and
GPU accelerators if available).
2. Model building
The model building phase takes the cells assigned to the local rank, and builds the local cell groups and the part of the communication network by querying the recipe for more information about the cells assigned to it.
General Best Practices¶
Think of the cells
When formulating a model, think cell-first, and try to formulate the model and the associated workflow from a cell-centered perspective. If this isn’t possible, please contact the developers, because we would like to develop tools that help make this simpler.
A recipe does not have to contain a complete description of the model in memory. Precompute as little as possible, and use lazy evaluation to generate information only when requested. This has multiple benefits, including:
- thread safety;
- minimising the memory footprint of the recipe.
Arbor is designed to give reproducible results when the same model is run on a
different number of MPI ranks or threads, or on different hardware (e.g. GPUs).
This only holds when a recipe provides a reproducible model description, which
can be a challenge when a description uses random numbers, e.g. to pick incoming
connections to a cell from a random subset of a cell population.
To get a reproducible model, use the cell gid (or a hash based on the gid)
to seed random number generators, including those for
The description of multi-compartment cells also includes the specification of ion channel and synapse dynamics. In the recipe, these specifications are called mechanisms. Implementations of mechanisms are either hand-coded or a translator (modcc) is used to compile a subset of NEURON’s mechanism specification language NMODL.
- Common examples are the passive/ leaky integrate-and-fire model, the Hodgkin-Huxley mechanism, the (double-) exponential synapse model, or the Natrium current model for an axon.