From recipe to simulation¶
To build a simulation the following concepts are needed:
The workflow to build a simulation is to first generate a
arb::domain_decomposition that describes the distribution of the model
over the local and distributed hardware resources (see Domain Decomposition),
then build the simulation.
#include <arbor/context.hpp> #include <arbor/domain_decomposition.hpp> #include <arbor/simulation.hpp> // Get a communication context arb::context context = make_context(); // Make a recipe of user defined type my_recipe. my_recipe recipe; // Get a description of the partition the model over the cores // (and gpu if available) on node. arb::domain_decomposition decomp = arb::partition_load_balance(recipe, context); // Instantiate the simulation. arb::simulation sim(recipe, decomp, context);
The executable form of a model. A simulation is constructed from a recipe, and then used to update and monitor model state.
Simulations take the following inputs:
The constructor takes:
Experimental inputs that can change between model runs, such as external spike trains.
Simulations provide an interface for executing and interacting with the model:
- Advance model state from one time to another and reset model state to its original state before simulation was started.
- I/O interface for sampling simulation state during execution (e.g. compartment voltage and current) and spike output.
spike_export_function= std::function<void(const std::vector<spike>&)>¶
inject_events(const pse_vector &events)¶
Add events directly to targets. Must be called before calling
run(), and must contain events that are to be delivered at or after the current simulation time.
Updating Model State:
Reset the state of the simulation to its initial state.
run(time_type tfinal, time_type dt)¶
set_binning_policy(binning_kind policy, time_type bin_interval)¶
Set event binning policy on all our groups.
add_sampler(cell_member_predicate probe_ids, schedule sched, sampler_function f, sampling_policy policy = sampling_policy::lax)¶
Note: sampler functions may be invoked from a different thread than that which called
(see the Sampling API documentation.)
Remove a sampler. (see the Sampling API documentation.)
The total number of spikes generated since either construction or the last call to
Register a callback that will periodically be passed a vector with all of the spikes generated over all domains (the global spike vector) since the last call. Will be called on the MPI rank/domain with id 0.
Register a callback that will periodically be passed a vector with all of the spikes generated on the local domain (the local spike vector) since the last call. Will be called on each MPI rank/domain with a copy of the local spikes.