setup

setup(**keyValueArgs)

The setup function is used to configure ANNarchy simulations.

It takes various optional arguments. The most useful ones are:

  • dt: simulation step size in milliseconds (default: 1.0).
  • paradigm: parallel framework for code generation. Accepted values: “openmp” or “cuda” (default: “openmp”).
  • method: default method to numerize ODEs. Default is the explicit forward Euler method (‘explicit’).
  • precision: default floating precision for variables in ANNarchy. Accepted values: “float” or “double” (default: “double”)
  • structural_plasticity: allows synapses to be dynamically added/removed during the simulation (default: False).
  • seed: the seed (integer) to be used in the random number generators (default = None is equivalent to time(NULL)).
  • num_threads: number of treads used by openMP (overrides the environment variable OMP_NUM_THREADS when set, default = None).

Flags related to the optimization of the simulation kernels are:

  • sparse_matrix_format: the default matrix format for projections in ANNarchy (by default: List-In-List for CPUs and Compressed Sparse Row). Note that this affects only the C++ data structures.
  • sparse_matrix_storage_order: encodes whether the row in a connectivity matrix encodes pre-synaptic neurons (post_to_pre, default) or post-synaptic neurons (pre_to_post). Note that affects only the C++ data structures.
  • only_int_idx_type: if set to True (default) only signed integers are used to store pre-/post-synaptic ranks which was default until 4.7.If set to False, the index type used in a single projection is selected based on the size of the corresponding populations.
  • visible_cores: allows a fine-grained control which cores are useable for the created threads (default = [] for no limitation). It can be used to limit created openMP threads to a physical socket.

The following parameters are mainly for debugging and profiling, and should be ignored by most users:

  • verbose: shows details about compilation process on console (by default False). Additional some information of the network construction will be shown.
  • suppress_warnings: if True, warnings (e. g. from the mathematical parser) are suppressed.
  • show_time: if True, initialization times are shown. Attention: verbose should be set to True additionally.
  • disable_shared_library_time_offset: by default False. If set to True, the shared library generated by ANNarchy will not be extended by time offset.

Note:

This function should be used before any other functions of ANNarchy (including importing a network definition), right after import ANNarchy:

import ANNarchy as ann
ann.setup(dt=1.0, method='midpoint', num_threads=2)