From recipe to simulation¶
To build a simulation the following concepts are needed:
arbor.recipethat describes the cells and connections in the model;
arbor.contextused to execute the simulation.
The workflow to build a simulation is to first generate an
arbor.domain_decomposition based on the
arbor.context describing the distribution of the model
over the local and distributed hardware resources (see Domain decomposition). Then, the simulation is build using this
import arbor # Get a communication context (with 4 threads, no GPU) context = arbor.context(threads=4, gpu_id=None) # Initialise a recipe of user defined type my_recipe with 100 cells. n_cells = 100 recipe = my_recipe(n_cells) # Get a description of the partition of the model over the cores. decomp = arbor.partition_load_balance(recipe, context) # Instantiate the simulation. sim = arbor.simulation(recipe, decomp, context) # Run the simulation for 2000 ms with time stepping of 0.025 ms tSim = 2000 dt = 0.025 sim.run(tSim, dt)
- class arbor.simulation¶
The executable form of a model. A simulation is constructed from a recipe, and then used to update and monitor the model state.
Simulations take the following inputs:
The constructor takes
arbor.recipethat describes the model;
arbor.domain_decompositionthat describes how the cells in the model are assigned to hardware resources;
arbor.contextwhich is used to execute the simulation.
Simulations provide an interface for executing and interacting with the model:
Specify what data (spikes, probe results) to record.
Advance the model state by running the simulation up to some time point.
Retrieve recorded data.
Reset simulator state back to initial conditions.
- simulation(recipe, domain_decomposition, context)¶
Updating Model State:
Reset the state of the simulation to its initial state. Clears recorded spikes and sample data.
- run(tfinal, dt)¶
Run the simulation from current simulation time to
tfinal, with maximum time step size
tfinal – The final simulation time [ms].
dt – The time step size [ms].
- set_binning_policy(policy, bin_interval)¶
Set the binning
policyfor event delivery, and the binning time interval
bin_intervalif applicable [ms].
policy – The binning policy of type
bin_interval – The binning time interval [ms].
Recording spike data:
Disable or enable recorder of rank-local or global spikes, as determined by the
policy – Recording policy of type
Return a NumPy structured array of spikes recorded during the course of a simulation. Each spike is represented as a NumPy structured datatype with signature
('source', [('gid', '<u4'), ('index', '<u4')]), ('time', '<f8').
The spikes are sorted in ascending order of spike time, and spikes with the same time are sorted accourding to source gid then index.
- sample(probe_id, schedule, policy)¶
Set up a sampling schedule for the probes associated with the supplied probe_id of type
cell_member. The schedule is any schedule object, as might be used with an event generator — see Recipes for details. The policy is of type
sampling_policy. It can be omitted, in which case the sampling will accord with the
The method returns a handle which can be used in turn to retrieve the sampled data from the simulator or to remove the corresponding sampling process.
Retrieve probe metadata for the probes associated with the given probe_id of type
cell_member. The result will be a list, with one entry per probe; the specifics of each metadata entry will depend upon the kind of probe in question.
Disable the sampling process referenced by the argument
handleand remove any associated recorded data.
Disable all sampling processes and remove any associated recorded data.
Retrieve a list of sample data associated with the given
handle. There will be one entry in the list per probe associated with the probe id used when the sampling was set up. For example, if a probe was placed on a locset describing three positions, the returned list will contain three elements.
An empty list will be returned if no output was recorded for the cell. For simulations that are distributed using MPI, handles associated with non-local cells will return an empty list. It is the responsibility of the caller to gather results over the ranks.
Each entry is a pair
metais the probe metadata as would be returned by
samplescontains the recorded values.
The format of the recorded values will depend upon the specifics of the probe, though generally it will be a NumPy array, with the first column corresponding to sample time and subsequent columns holding the value or values that were sampled from that probe at that time.
- class arbor.binning¶
Enumeration for event time binning policy.
No binning policy.
Round time down to multiple of binning interval.
Round times down to previous event if within binning interval.
- class arbor.spike_recording¶
Enumeration for spike recording policy.
Disable spike recording.
Record all generated spikes from cells on this MPI rank.
Record all generated spikes from cells on all MPI ranks.
- class arbor.sampling_policy¶
Enumeration for determining sampling policy.
Sampling times may not be exactly as requested in the sampling schedule, but the process of sampling is guaranteed not to disturb the simulation progress or results.
Interrupt the progress of the simulation as required to retrieve probe samples at exactly those times requested by the sampling schedule.
By default, spikes are not recorded. Recording is enabled with the
simulation.record() method, which takes a single argument instructing
the simulation object to record no spikes, all locally generated spikes, or all
spikes generated by any MPI rank.
Spikes recorded during a simulation are returned as a NumPy structured datatype with two fields,
source field itself is a structured datatype with two fields,
index, identifying the spike detector that generated the spike.
The spikes returned by
simulation.record() are sorted in ascending order of spike time.
Spikes that have the same spike time are sorted in ascending order of gid and local index of the
import arbor # Instantiate the simulation. sim = arbor.simulation(recipe, decomp, context) # Direct the simulation to record all spikes, which will record all spikes # across multiple MPI ranks in distrubuted simulation. # To only record spikes from the local MPI rank, use arbor.spike_recording.local sim.record(arbor.spike_recording.all) # Run the simulation for 2000 ms with time stepping of 0.025 ms tSim = 2000 dt = 0.025 sim.run(tSim, dt) # Print the spikes and according spike time for s in sim.spikes(): print(s)
>>> ((0,0), 2.15168) >>> ((1,0), 14.5235) >>> ((2,0), 26.9051) >>> ((3,0), 39.4083) >>> ((4,0), 51.9081) >>> ((5,0), 64.2902) >>> ((6,0), 76.7706) >>> ((7,0), 89.1529) >>> ((8,0), 101.641) >>> ((9,0), 114.125)
A measurement that can be performed on a cell. Each cell kind will have its own sorts of probe; Cable cells (
arbor.cable_probe) allow the monitoring of membrane voltage, total membrane current, mechanism state, and a number of other quantities, measured either over the whole cell, or at specific sites (see Cable cell probing and sampling).
Probes are described by probe addresses, and the collection of probe addresses for a given cell is provided by the
recipeobject. One address may correspond to more than one probe: as an example, a request for membrane voltage on a cable cell at sites specified by a location expression will generate one probe for each site in that location expression.
- probe id¶
A designator for one or more probes as specified by a recipe. The probe id is a
cell_memberreferring to a specific cell by gid, and the index into the list of probe addresses returned by the recipe for that gid.
Each probe has associated metadata describing, for example, the location on a cell where the measurement is being taken, or other such identifying information. Metadata for the probes associated with a probe id can be retrieved from the simulation object, and is also provided along with any recorded samples.
A sampler is something that receives probe data. It amounts to setting a particular probe to a particular measuring schedule, and then having a handle with which to access the recorded probe data later on.
A record of data corresponding to the value at a specific probe at a specific time.
An object representing a series of monotonically increasing points in time, used for determining sample times (see Recipes).
There are three parts to the process of recording cell data over a simulation.
Describing what to measure.
The recipe object must provide a method
recipe.get_probes()that returns a list of probe addresses for the cell with a given
gid. The kth element of the list corresponds to the probe id
Each probe address is an opaque object describing what to measure and where, and each cell kind will have its own set of functions for generating valid address specifications. Possible cable cell probes are described in the cable cell documentation: Cable cell probing and sampling.
Instructing the simulator to record data.
Recording is set up with the method
simulation.sample()as described above. It returns a handle that is used to retrieve the recorded data after simulation.
Retrieve recorded data.
simulation.samples()takes a handle and returns the recorded data as a list, with one entry for each probe associated with the probe id that was used in step 2 above. Each entry will be a tuple
metais the metadata associated with the probe, and
datacontains all the data sampled on that probe over the course of the simulation.
The contents of
datawill depend upon the specifics of the probe, but note:
The object type and structure of
datais fully determined by the metadata.
All currently implemented probes return data that is a NumPy array, with one row per sample, first column being sample time, and the remaining columns containing the corresponding data.
import arbor # [... define recipe, decomposition, context ... ] # Initialize simulation: sim = arbor.simulation(recipe, decomp, context) # Sample probe id (0, 0) (first probe id on cell 0) every 0.1 ms with exact sample timing: handle = sim.sample((0, 0), arbor.regular_schedule(0.1), arbor.sampling_policy.exact) # Run simulation and retrieve sample data from the first probe associated with the handle. sim.run(tfinal=3, dt=0.1) data, meta = sim.samples(handle) print(data)
>>> [[ 0. -50. ] >>> [ 0.1 -55.14412111] >>> [ 0.2 -59.17057625] >>> [ 0.3 -62.58417912] >>> [ 0.4 -65.47040168] >>> [ 0.5 -67.80222861] >>> [ 0.6 -15.18191623] >>> [ 0.7 27.21110919] >>> [ 0.8 48.74665099] >>> [ 0.9 48.3515727 ] >>> [ 1. 41.08435987] >>> [ 1.1 33.53571111] >>> [ 1.2 26.55165892] >>> [ 1.3 20.16421752] >>> [ 1.4 14.37227532] >>> [ 1.5 9.16209063] >>> [ 1.6 4.50159342] >>> [ 1.7 0.34809083] >>> [ 1.8 -3.3436289 ] >>> [ 1.9 -6.61665687] >>> [ 2. -9.51020525] >>> [ 2.1 -12.05947812] >>> [ 2.2 -14.29623969] >>> [ 2.3 -16.24953688] >>> [ 2.4 -17.94631322] >>> [ 2.5 -19.41182385] >>> [ 2.6 -52.19519009] >>> [ 2.7 -62.53349949] >>> [ 2.8 -69.22068995] >>> [ 2.9 -73.41691825]]